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  • American Chemical Society  (381,811)
  • Public Library of Science  (118,249)
  • Blackwell Publishing Ltd
  • 2015-2019  (366,389)
  • 2000-2004  (147,868)
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  • 1
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    Reef-fidelity and migration of tiger sharks, Galeocerdo cuvier, across the Coral Sea (2015)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e83249, doi:10.1371/journal.pone.0083249.
    Description: Knowledge of the habitat use and migration patterns of large sharks is important for assessing the effectiveness of large predator Marine Protected Areas (MPAs), vulnerability to fisheries and environmental influences, and management of shark–human interactions. Here we compare movement, reef-fidelity, and ocean migration for tiger sharks, Galeocerdo cuvier, across the Coral Sea, with an emphasis on New Caledonia. Thirty-three tiger sharks (1.54 to 3.9 m total length) were tagged with passive acoustic transmitters and their localised movements monitored on receiver arrays in New Caledonia, the Chesterfield and Lord Howe Islands in the Coral Sea, and the east coast of Queensland, Australia. Satellite tags were also used to determine habitat use and movements among habitats across the Coral Sea. Sub-adults and one male adult tiger shark displayed year-round residency in the Chesterfields with two females tagged in the Chesterfields and detected on the Great Barrier Reef, Australia, after 591 and 842 days respectively. In coastal barrier reefs, tiger sharks were transient at acoustic arrays and each individual demonstrated a unique pattern of occurrence. From 2009 to 2013, fourteen sharks with satellite and acoustic tags undertook wide-ranging movements up to 1114 km across the Coral Sea with eight detected back on acoustic arrays up to 405 days after being tagged. Tiger sharks dove 1136 m and utilised three-dimensional activity spaces averaged at 2360 km3. The Chesterfield Islands appear to be important habitat for sub-adults and adult male tiger sharks. Management strategies need to consider the wide-ranging movements of large (sub-adult and adult) male and female tiger sharks at the individual level, whereas fidelity to specific coastal reefs may be consistent across groups of individuals. Coastal barrier reef MPAs, however, only afford brief protection for large tiger sharks, therefore determining the importance of other oceanic Coral Sea reefs should be a priority for future research.
    Description: Funding was provided by the the Agence Francaise de Développement (http://www.afd.fr), French Pacific Fund, the CRISP program (www.crisponline.info) and QLD Fisheries.
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  • 2
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    Chemical composition and potential environmental impacts of water-soluble polar crude oil components inferred from ESI FT-ICR MS (2015)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0136376, doi:10.1371/journal.pone.0136376.
    Description: Polar petroleum components enter marine environments through oil spills and natural seepages each year. Lately, they are receiving increased attention due to their potential toxicity to marine organisms and persistence in the environment. We conducted a laboratory experiment and employed state-of-the-art Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) to characterize the polar petroleum components within two operationally-defined seawater fractions: the water-soluble fraction (WSF), which includes only water-soluble molecules, and the water-accommodated fraction (WAF), which includes WSF and microscopic oil droplets. Our results show that compounds with higher heteroatom (N, S, O) to carbon ratios (NSO:C) than the parent oil were selectively partitioned into seawater in both fractions, reflecting the influence of polarity on aqueous solubility. WAF and WSF were compositionally distinct, with unique distributions of compounds across a range of hydrophobicity. These compositional differences will likely result in disparate impacts on environmental health and organismal toxicity, and thus highlight the need to distinguish between these often-interchangeable terminologies in toxicology studies. We use an empirical model to estimate hydrophobicity character for individual molecules within these complex mixtures and provide an estimate of the potential environmental impacts of different crude oil components.
    Description: This study is funded by the Gulf of Mexico Research Initiative (GOMRI) Project # 161684 to Dr. Elizabeth B. Kujawinski.
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  • 3
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    An unexpected diversity of photoreceptor classes in the longfin squid, Doryteuthis pealeii (2015)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0135381, doi:10.1371/journal.pone.0135381.
    Description: Cephalopods are famous for their ability to change color and pattern rapidly for signaling and camouflage. They have keen eyes and remarkable vision, made possible by photoreceptors in their retinas. External to the eyes, photoreceptors also exist in parolfactory vesicles and some light organs, where they function using a rhodopsin protein that is identical to that expressed in the retina. Furthermore, dermal chromatophore organs contain rhodopsin and other components of phototransduction (including retinochrome, a photoisomerase first found in the retina), suggesting that they are photoreceptive. In this study, we used a modified whole-mount immunohistochemical technique to explore rhodopsin and retinochrome expression in a number of tissues and organs in the longfin squid, Doryteuthis pealeii. We found that fin central muscles, hair cells (epithelial primary sensory neurons), arm axial ganglia, and sucker peduncle nerves all express rhodopsin and retinochrome proteins. Our findings indicate that these animals possess an unexpected diversity of extraocular photoreceptors and suggest that extraocular photoreception using visual opsins and visual phototransduction machinery is far more widespread throughout cephalopod tissues than previously recognized.
    Description: This research was supported by the Office of Naval Research Basic Research Challenge grant number N00014-10-0989 to TWC and RTH and a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship BB/L024667/1 to TJW. The authors gratefully acknowledge support from the Air Force Office of Scientific Research via grants numbered FA9550-09-0346 to RTH. and FA9550-12-1-0321 to TWC.
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  • 4
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    Analysis of lung microbiota in bronchoalveolar lavage, protected brush and sputum samples from subjects with mild-to-moderate cystic fibrosis Lung Disease (2016)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0149998, doi:10.1371/journal.pone.0149998.
    Description: Individuals with cystic fibrosis (CF) often acquire chronic lung infections that lead to irreversible damage. We sought to examine regional variation in the microbial communities in the lungs of individuals with mild-to-moderate CF lung disease, to examine the relationship between the local microbiota and local damage, and to determine the relationships between microbiota in samples taken directly from the lung and the microbiota in spontaneously expectorated sputum. In this initial study, nine stable, adult CF patients with an FEV1〉50% underwent regional sampling of different lobes of the right lung by bronchoalveolar lavage (BAL) and protected brush (PB) sampling of mucus plugs. Sputum samples were obtained from six of the nine subjects immediately prior to the procedure. Microbial community analysis was performed on DNA extracted from these samples and the extent of damage in each lobe was quantified from a recent CT scan. The extent of damage observed in regions of the right lung did not correlate with specific microbial genera, levels of community diversity or composition, or bacterial genome copies per ml of BAL fluid. In all subjects, BAL fluid from different regions of the lung contained similar microbial communities. In eight out of nine subjects, PB samples from different regions of the lung were also similar in microbial community composition, and were similar to microbial communities in BAL fluid from the same lobe. Microbial communities in PB samples were more diverse than those in BAL samples, suggesting enrichment of some taxa in mucus plugs. To our knowledge, this study is the first to examine the microbiota in different regions of the CF lung in clinically stable individuals with mild-to-moderate CF-related lung disease.
    Description: Support from the Cystic Fibrosis Foundation Research Development Program (STANTO07R0) as a pilot grant to DAH and AA. Research reported in this publication was also supported by grants from the National Institutes of Health to DAH (R01 AI091702 to DAH) and the American Asthma Foundation Scholars Award and CFFT-ASHARE15A0 and R01HL122372 to AA and R01 HL074175 (BAS). The Dartmouth Lung Biology Center and CF Translational Research Core was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P30GM106394 and by the CFF RDP (CFRDP STANTO11R0).
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  • 5
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    Abundance and distribution of sperm whales in the Canary Islands : can sperm whales in the archipelago sustain the current level of ship-strike mortalities? (2016)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0150660, doi:10.1371/journal.pone.0150660.
    Description: Sperm whales are present in the Canary Islands year-round, suggesting that the archipelago is an important area for this species in the North Atlantic. However, the area experiences one of the highest reported rates of sperm whale ship-strike in the world. Here we investigate if the number of sperm whales found in the archipelago can sustain the current rate of ship-strike mortality. The results of this study may also have implications for offshore areas where concentrations of sperm whales may coincide with high densities of ship traffic, but where ship-strikes may be undocumented. The absolute abundance of sperm whales in an area of 52933 km2, covering the territorial waters of the Canary Islands, was estimated from 2668 km of acoustic line-transect survey using Distance sampling analysis. Data on sperm whale diving and acoustic behaviour, obtained from bio-logging, were used to calculate g(0) = 0.92, this is less than one because of occasional extended periods when whales do not echolocate. This resulted in an absolute abundance estimate of 224 sperm whales (95% log-normal CI 120–418) within the survey area. The recruitment capability of this number of whales, some 2.5 whales per year, is likely to be exceeded by the current ship-strike mortality rate. Furthermore, we found areas of higher whale density within the archipelago, many coincident with those previously described, suggesting that these are important habitats for females and immature animals inhabiting the archipelago. Some of these areas are crossed by active shipping lanes increasing the risk of ship-strikes. Given the philopatry in female sperm whales, replacement of impacted whales might be limited. Therefore, the application of mitigation measures to reduce the ship-strike mortality rate seems essential for the conservation of sperm whales in the Canary Islands.
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  • 6
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    LOBSTAHS : an adduct-based lipidomics strategy for discovery and identification of oxidative stress biomarkers (2016)
    American Chemical Society
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    Publication Date: 2022-05-26
    Description: © The American Chemical Society, 2016. This is an open access article published under an ACS AuthorChoice License. The definitive version was published in Analytical Chemistry 88 (2016): 7154–7162, doi:10.1021/acs.analchem.6b01260.
    Description: Discovery and identification of molecular biomarkers in large LC/MS data sets requires significant automation without loss of accuracy in the compound screening and annotation process. Here, we describe a lipidomics workflow and open-source software package for high-throughput annotation and putative identification of lipid, oxidized lipid, and oxylipin biomarkers in high-mass-accuracy HPLC-MS data. Lipid and oxylipin biomarker screening through adduct hierarchy sequences, or LOBSTAHS, uses orthogonal screening criteria based on adduct ion formation patterns and other properties to identify thousands of compounds while providing the user with a confidence score for each assignment. Assignments are made from one of two customizable databases; the default databases contain 14 068 unique entries. To demonstrate the software’s functionality, we screened more than 340 000 mass spectral features from an experiment in which hydrogen peroxide was used to induce oxidative stress in the marine diatom Phaeodactylum tricornutum. LOBSTAHS putatively identified 1969 unique parent compounds in 21 869 features that survived the multistage screening process. While P. tricornutum maintained more than 92% of its core lipidome under oxidative stress, patterns in biomarker distribution and abundance indicated remodeling was both subtle and pervasive. Treatment with 150 μM H2O2 promoted statistically significant carbon-chain elongation across lipid classes, with the strongest elongation accompanying oxidation in moieties of monogalactosyldiacylglycerol, a lipid typically localized to the chloroplast. Oxidative stress also induced a pronounced reallocation of lipidome peak area to triacylglycerols. LOBSTAHS can be used with environmental or experimental data from a variety of systems and is freely available at https://github.com/vanmooylipidomics/LOBSTAHS.
    Description: This research was supported by the Gordon and Betty Moore Foundation through Grant GBMF3301 to B.A.S.V.M. This research was also funded in part by a grant to B.A.S.V.M. from the Simons Foundation and is a contribution of the Simons Collaboration on Ocean Processes and Ecology (SCOPE). J.R.C. acknowledges support from a U.S. Environmental Protection Agency (EPA) STAR Graduate Fellowship (Fellowship Assistance Agreement No. FP-91744301-0).
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  • 7
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    Cisplatin resistant spheroids model clinically relevant survival mechanisms in ovarian tumors (2016)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0151089, doi: 10.1371/journal.pone.0151089 .
    Description: The majority of ovarian tumors eventually recur in a drug resistant form. Using cisplatin sensitive and resistant cell lines assembled into 3D spheroids we profiled gene expression and identified candidate mechanisms and biological pathways associated with cisplatin resistance. OVCAR-8 human ovarian carcinoma cells were exposed to sub-lethal concentrations of cisplatin to create a matched cisplatin-resistant cell line, OVCAR-8R. Genome-wide gene expression profiling of sensitive and resistant ovarian cancer spheroids identified 3,331 significantly differentially expressed probesets coding for 3,139 distinct protein-coding genes (Fc 〉2, FDR 〈 0.05) (S2 Table). Despite significant expression changes in some transporters including MDR1, cisplatin resistance was not associated with differences in intracellular cisplatin concentration. Cisplatin resistant cells were significantly enriched for a mesenchymal gene expression signature. OVCAR-8R resistance derived gene sets were significantly more biased to patients with shorter survival. From the most differentially expressed genes, we derived a 17-gene expression signature that identifies ovarian cancer patients with shorter overall survival in three independent datasets. We propose that the use of cisplatin resistant cell lines in 3D spheroid models is a viable approach to gain insight into resistance mechanisms relevant to ovarian tumors in patients. Our data support the emerging concept that ovarian cancers can acquire drug resistance through an epithelial-to-mesenchymal transition.
    Description: This work was funded by the NIH NCRR supplement grant P41 RR001395-27S1 (J.W.H.), NSF DBI-1005378 “REU Site: Biological Discovery in Woods Hole”, faculty startup funds from the Office of Research at Oklahoma State University (W.C.), and the Mary Kay Foundation (A.S.B.).
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  • 8
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    Multi-method assessment of whale shark (Rhincodon typus) residency, distribution, and dispersal behavior at an aggregation site in the Red Sea (2019)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cochran, J. E. M., Braun, C. D., Cagua, E. F., Campbell, M. F., Hardenstine, R. S., Kattan, A., Priest, M. A., Sinclair-Taylor, T. H., Skomal, G. B., Sultan, S., Sun, L., Thorrold, S. R., & Berumen, M. L. Multi-method assessment of whale shark (Rhincodon typus) residency, distribution, and dispersal behavior at an aggregation site in the Red Sea. Plos One, 14(9), (2019): e0222285, doi:10.1371/journal.pone.0222285.
    Description: Whale sharks (Rhincodon typus) are typically dispersed throughout their circumtropical range, but the species is also known to aggregate in specific coastal areas. Accurate site descriptions associated with these aggregations are essential for the conservation of R. typus, an Endangered species. Although aggregations have become valuable hubs for research, most site descriptions rely heavily on sightings data. In the present study, visual census, passive acoustic monitoring, and long range satellite telemetry were combined to track the movements of R. typus from Shib Habil, a reef-associated aggregation site in the Red Sea. An array of 63 receiver stations was used to record the presence of 84 acoustically tagged sharks (35 females, 37 males, 12 undetermined) from April 2010 to May 2016. Over the same period, identification photos were taken for 76 of these tagged individuals and 38 were fitted with satellite transmitters. In total of 37,461 acoustic detections, 210 visual encounters, and 33 satellite tracks were analyzed to describe the sharks’ movement ecology. The results demonstrate that the aggregation is seasonal, mostly concentrated on the exposed side of Shib Habil, and seems to attract sharks of both sexes in roughly equal numbers. The combined methodologies also tracked 15 interannual homing-migrations, demonstrating that many sharks leave the area before returning in later years. When compared to acoustic studies from other aggregations, these results demonstrate that R. typus exhibits diverse, site-specific ecologies across its range. Sightings-independent data from acoustic telemetry and other sources are an effective means of validating more common visual surveys.
    Description: Financial support was provided in part by KAUST baseline research funds (to MLB), KAUST award nos. USA00002 and KSA 00011 (to SRT), and the U.S. National Science Foundation (OCE 0825148 to SRT and GBS).
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  • 9
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    Ocean Dumping of Containerized DDT Waste Was a Sloppy Process (2019)
    American Chemical Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Chemical Society, 2019. This article is posted here by permission of American Chemical Society for personal use, not for redistribution. The definitive version was published in Kivenson, V., Lemkau, K. L., Pizarro, O., Yoerger, D. R., Kaiser, C., Nelson, R. K., Carmichael, C., Paul, B. G., Reddy, C. M., & Valentine, D. L. (2019). Ocean Dumping of Containerized DDT Waste Was a Sloppy Process. Environmental Science and Technology (2019), doi:10.1021/acs.est.8b05859.
    Description: Industrial-scale dumping of organic waste to the deep ocean was once common practice, leaving a legacy of chemical pollution for which a paucity of information exists. Using a nested approach with autonomous and remotely operated underwater vehicles, a dumpsite offshore California was surveyed and sampled. Discarded waste containers littered the site and structured the suboxic benthic environment. Dichlorodiphenyltrichloroethane (DDT) was reportedly dumped in the area, and sediment analysis revealed substantial variability in concentrations of p,p-DDT and its analogs, with a peak concentration of 257 μg g–1, ∼40 times greater than the highest level of surface sediment contamination at the nearby DDT Superfund site. The occurrence of a conspicuous hydrocarbon mixture suggests that multiple petroleum distillates, potentially used in DDT manufacture, contributed to the waste stream. Application of a two end-member mixing model with DDTs and polychlorinated biphenyls enabled source differentiation between shelf discharge versus containerized waste. Ocean dumping was found to be the major source of DDT to more than 3000 km2 of the region’s deep seafloor. These results reveal that ocean dumping of containerized DDT waste was inherently sloppy, with the contents readily breaching containment and leading to regional scale contamination of the deep benthos.
    Description: This material is based upon work supported by the National Science Foundation Graduate Research Fellowship for V.K. under Grant No. 1650114. Expeditions AT-18-11 and AT-26-06 were funded by the NSF (OCE-0961725 and OCE-1046144). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. We thank the captain and crew of the RV Atlantis, the pilots and crew of the ROV Jason, the crew of the AUV Sentry, the scientific party of the AT-18-11 and AT-26-06 expeditions, Justin Tran for assistance with the preparation of multibeam data, M. Indira Venkatesan for a helpful discussion of the NOAA datasets, and Nathan Dodder for advice on the procedure for compound identification.
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  • 10
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    Multiplexed spectral imaging of 120 different fluorescent labels (2016)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This article is distributed under the terms of the Creative Commons public domain dedication. The definitive version was published in PLoS One 11 (2016): e0158495, doi:10.1371/journal.pone.0158495.
    Description: The number of fluorescent labels that can unambiguously be distinguished in a single image when acquired through band pass filters is severely limited by the spectral overlap of available fluorophores. The recent development of spectral microscopy and the application of linear unmixing algorithms to spectrally recorded image data have allowed simultaneous imaging of fluorophores with highly overlapping spectra. However, the number of distinguishable fluorophores is still limited by the unavoidable decrease in signal to noise ratio when fluorescence signals are fractionated over multiple wavelength bins. Here we present a spectral image analysis algorithm to greatly expand the number of distinguishable objects labeled with binary combinations of fluorophores. Our algorithm utilizes a priori knowledge about labeled specimens and imposes a binary label constraint on the unmixing solution. We have applied our labeling and analysis strategy to identify microbes labeled by fluorescence in situ hybridization and here demonstrate the ability to distinguish 120 differently labeled microbes in a single image.
    Description: This work was supported by Grant 2007-3- 13 from the Alfred P. Sloan Foundation (to GGB), National Institutes of Health Grant 1RC1-DE020630 from the National Institute of Dental and Craniofacial Research (NIDCR) (to GGB) and by National Institutes of Health Fellowship 1F31-DE019576 from NIDCR (to AMV).
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  • 11
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    Influence of acidic pH on hydrogen and acetate production by an electrosynthetic microbiome (2015)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e109935, doi:10.1371/journal.pone.0109935.
    Description: Production of hydrogen and organic compounds by an electrosynthetic microbiome using electrodes and carbon dioxide as sole electron donor and carbon source, respectively, was examined after exposure to acidic pH (~5). Hydrogen production by biocathodes poised at −600 mV vs. SHE increased〉100-fold and acetate production ceased at acidic pH, but ~5–15 mM (catholyte volume)/day acetate and〉1,000 mM/day hydrogen were attained at pH ~6.5 following repeated exposure to acidic pH. Cyclic voltammetry revealed a 250 mV decrease in hydrogen overpotential and a maximum current density of 12.2 mA/cm2 at −765 mV (0.065 mA/cm2 sterile control at −800 mV) by the Acetobacterium-dominated community. Supplying −800 mV to the microbiome after repeated exposure to acidic pH resulted in up to 2.6 kg/m3/day hydrogen (≈2.6 gallons gasoline equivalent), 0.7 kg/m3/day formate, and 3.1 kg/m3/day acetate ( = 4.7 kg CO2 captured).
    Description: This research was supported by a grant from the Department of Energy, Advanced Projects Research Agency – Energy (DE-AR0000089). CWM was supported with a Director's Postdoctoral Fellowship from Argonne National Laboratory.
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  • 12
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    Searching for the oldest baobab of Madagascar : radiocarbon investigation of large Adansonia rubrostipa trees (2015)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0121170, doi:10.1371/journal.pone.0121170.
    Description: We extended our research on the architecture, growth and age of trees belonging to the genus Adansonia, by starting to investigate large individuals of the most widespread Malagasy species. Our research also intends to identify the oldest baobabs of Madagascar. Here we present results of the radiocarbon investigation of the two most representative Adansonia rubrostipa (fony baobab) specimens, which are located in south-western Madagascar, in the Tsimanampetsotse National Park. We found that the fony baobab called “Grandmother” consists of 3 perfectly fused stems of different ages. The radiocarbon date of the oldest sample was found to be 1136 ± 16 BP. We estimated that the oldest part of this tree, which is mainly hollow, has an age close to 1,600 yr. This value is comparable to the age of the oldest Adansonia digitata (African baobab) specimens. By its age, the Grandmother is a major candidate for the oldest baobab of Madagascar. The second investigated specimen, called the “polygamous baobab”, consists of 6 partially fused stems of different ages. According to dating results, this fony baobab is 1,000 yr old. This research is the first investigation of the structure and age of Malagasy baobabs.
    Description: The research was fully funded by the Romanian Ministry of National Education CNCS-UEFISCDI under grant PN-II-ID-PCE-2013-76 (URL: http://uefiscdi.gov.ro/).
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  • 13
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    Methanol production by a broad phylogenetic array of marine phytoplankton (2016)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0150820, doi:10.1371/journal.pone.0150820.
    Description: Methanol is a major volatile organic compound on Earth and serves as an important carbon and energy substrate for abundant methylotrophic microbes. Previous geochemical surveys coupled with predictive models suggest that the marine contributions are exceedingly large, rivaling terrestrial sources. Although well studied in terrestrial ecosystems, methanol sources are poorly understood in the marine environment and warrant further investigation. To this end, we adapted a Purge and Trap Gas Chromatography/Mass Spectrometry (P&T-GC/MS) method which allowed reliable measurements of methanol in seawater and marine phytoplankton cultures with a method detection limit of 120 nanomolar. All phytoplankton tested (cyanobacteria: Synechococcus spp. 8102 and 8103, Trichodesmium erythraeum, and Prochlorococcus marinus), and Eukarya (heterokont diatom: Phaeodactylum tricornutum, coccolithophore: Emiliania huxleyi, cryptophyte: Rhodomonas salina, and non-diatom heterokont: Nannochloropsis oculata) produced methanol, ranging from 0.8–13.7 micromolar in culture and methanol per total cellular carbon were measured in the ranges of 0.09–0.3%. Phytoplankton culture time-course measurements displayed a punctuated production pattern with maxima near early stationary phase. Stabile isotope labeled bicarbonate incorporation experiments confirmed that methanol was produced from phytoplankton biomass. Overall, our findings suggest that phytoplankton are a major source of methanol in the upper water column of the world’s oceans.
    Description: This project was solely supported by a grant to TJM from the National Science Foundation (Award# CHE-OCE 1131415).
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  • 14
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    Interspecific hybridization in pilot whales and asymmetric genetic introgression in northern Globicephala melas under the scenario of global warming (2016)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0160080, doi: 10.1371/journal.pone.0160080 .
    Description: Pilot whales are two cetacean species (Globicephala melas and G. macrorhynchus) whose distributions are correlated with water temperature and partially overlap in some areas like the North Atlantic Ocean. In the context of global warming, distribution range shifts are expected to occur in species affected by temperature. Consequently, a northward displacement of the tropical pilot whale G. macrorynchus is expected, eventually leading to increased secondary contact areas and opportunities for interspecific hybridization. Here, we describe genetic evidences of recurrent hybridization between pilot whales in northeast Atlantic Ocean. Based on mitochondrial DNA sequences and microsatellite loci, asymmetric introgression of G. macrorhynchus genes into G. melas was observed. For the latter species, a significant correlation was found between historical population growth rate estimates and paleotemperature oscillations. Introgressive hybridization, current temperature increases and lower genetic variation in G. melas suggest that this species could be at risk in its northern range. Under increasing environmental and human-mediated stressors in the North Atlantic Ocean, it seems recommendable to develop a conservation program for G. melas.
    Description: LM had a PCTI Grant from the Asturias Regional Government, referenced BP 10-004. MAS was supported by a 2013 FCT Investigator contract through POPH, QREN European Social Fund and the Portuguese Ministry for Science and Education. This study was also supported by a grant from the Principality of Asturias (reference: GRUPIN-2014-093).
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    Using a Bayesian network to understand the importance of coastal storms and undeveloped landscapes for the creation and maintenance of early successional habitat (2019)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zeigler, S. L., Gutierrez, B. T., Sturdivant, E. J., Catlin, D. H., Fraser, J. D., Hecht, A., Karpanty, S. M., Plant, N. G., & Thieler, E. R. Using a Bayesian network to understand the importance of coastal storms and undeveloped landscapes for the creation and maintenance of early successional habitat. Plos One, 14(7), (2019): e0209986, doi:10.1371/journal.pone.0209986.
    Description: Coastal storms have consequences for human lives and infrastructure but also create important early successional habitats for myriad species. For example, storm-induced overwash creates nesting habitat for shorebirds like piping plovers (Charadrius melodus). We examined how piping plover habitat extent and location changed on barrier islands in New York, New Jersey, and Virginia after Hurricane Sandy made landfall following the 2012 breeding season. We modeled nesting habitat using a nest presence/absence dataset that included characterizations of coastal morphology and vegetation. Using a Bayesian network, we predicted nesting habitat for each study site for the years 2010/2011, 2012, and 2014/2015 based on remotely sensed spatial datasets (e.g., lidar, orthophotos). We found that Hurricane Sandy increased piping plover habitat by 9 to 300% at 4 of 5 study sites but that one site saw a decrease in habitat by 27%. The amount, location, and longevity of new habitat appeared to be influenced by the level of human development at each site. At three of the five sites, the amount of habitat created and the time new habitat persisted were inversely related to the amount of development. Furthermore, the proportion of new habitat created in high-quality overwash was inversely related to the level of development on study areas, from 17% of all new habitat in overwash at one of the most densely developed sites to 80% of all new habitat at an undeveloped site. We also show that piping plovers exploited new habitat after the storm, with 14–57% of all nests located in newly created habitat in the 2013 breeding season. Our results quantify the importance of storms in creating and maintaining coastal habitats for beach-nesting species like piping plovers, and these results suggest a negative correlation between human development and beneficial ecological impacts of these natural disturbances.
    Description: Funding for this work was provided through a U.S. Geological Survey Mendenhall Post-Doctoral Fellowship awarded to S. Zeigler, with funding for this fellowship made through a grant to E.R. Thieler from the North Atlantic Landscape Conservation Cooperative. Funders did not play a role in study design, data collection or analysis, decision to publish, or preparation of the manuscript.
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    Occurrence and sources of radium in groundwater associated with oil fields in the southern San Joaquin Valley, California (2019)
    American Chemical Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Chemical Society, 2019. This is an open access article published under an ACS AuthorChoice License. The definitive version was published in Environmental Science and Technology 53(16), (2019): 9398-9406, doi:10.1021/acs.est.9b02395.
    Description: Geochemical data from 40 water wells were used to examine the occurrence and sources of radium (Ra) in groundwater associated with three oil fields in California (Fruitvale, Lost Hills, South Belridge). 226Ra+228Ra activities (range = 0.010–0.51 Bq/L) exceeded the 0.185 Bq/L drinking-water standard in 18% of the wells (not drinking-water wells). Radium activities were correlated with TDS concentrations (p 〈 0.001, ρ = 0.90, range = 145–15,900 mg/L), Mn + Fe concentrations (p 〈 0.001, ρ = 0.82, range = 〈0.005–18.5 mg/L), and pH (p 〈 0.001, ρ = −0.67, range = 6.2–9.2), indicating Ra in groundwater was influenced by salinity, redox, and pH. Ra-rich groundwater was mixed with up to 45% oil-field water at some locations, primarily infiltrating through unlined disposal ponds, based on Cl, Li, noble-gas, and other data. Yet 228Ra/226Ra ratios in pond-impacted groundwater (median = 3.1) differed from those in oil-field water (median = 0.51). PHREEQC mixing calculations and spatial geochemical variations suggest that the Ra in the oil-field water was removed by coprecipitation with secondary barite and adsorption on Mn–Fe precipitates in the near-pond environment. The saline, organic-rich oil-field water subsequently mobilized Ra from downgradient aquifer sediments via Ra-desorption and Mn/Fe-reduction processes. This study demonstrates that infiltration of oil-field water may leach Ra into groundwater by changing salinity and redox conditions in the subsurface rather than by mixing with a high-Ra source.
    Description: This article was improved by the reviews of John Izbicki and anonymous reviewers for the journal. This work was funded by the California State Water Resources Control Board’s Regional Groundwater Monitoring in Areas of Oil and Gas Production Program and the USGS Cooperative Water Program. A.V., A.J.K., and Z.W were supported by USDA-NIFA grant (#2017-68007-26308). Any use of trade, firm, or product names is for description purposes only and does not imply endorsement by the U.S. Government.
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    Differential cellular responses associated with oxidative stress and cell fate decision under nitrate and phosphate limitations in Thalassiosira pseudonana : comparative proteomics (2017)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 12 (2017): e0184849, doi:10.1371/journal.pone.0184849.
    Description: Diatoms are important components of marine ecosystems and contribute greatly to the world's primary production. Despite their important roles in ecosystems, the molecular basis of how diatoms cope with oxidative stress caused by nutrient fluctuations remains largely unknown. Here, an isobaric tags for relative and absolute quantitation (iTRAQ) proteomic method was coupled with a series of physiological and biochemical techniques to explore oxidative stress- and cell fate decision-related cellular and metabolic responses of the diatom Thalassiosira pseudonana to nitrate (N) and inorganic phosphate (P) stresses. A total of 1151 proteins were detected; 122 and 56 were significantly differentially expressed from control under N- and P-limited conditions, respectively. In N-limited cells, responsive proteins were related to reactive oxygen species (ROS) accumulation, oxidative stress responses and cell death, corresponding to a significant decrease in photosynthetic efficiency, marked intracellular ROS accumulation, and caspase-mediated programmed cell death activation. None of these responses were identified in P-limited cells; however, a significant up-regulation of alkaline phosphatase proteins was observed, which could be the major contributor for P-limited cells to cope with ambient P deficiency. These findings demonstrate that fundamentally different metabolic responses and cellular regulations are employed by the diatom in response to different nutrient stresses and to keep the cells viable.
    Description: This study was funded by the National Natural Science Foundation of China (41576138, 41076080, 41576138) to Dr. Jun-Rong Liang; the Woods Hole Center for Oceans and Human Health, National Science Foundation (OCE-1314642) to Dr. DonaldM Anderson; the National Institute of Environmental Health Sciences (1-P01-ES021923- 01) to Dr. DonaldM Anderson; and the ERC Advanced Award Diatomite and ANR project DiaDomOil to Dr. Chris Bowler.
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    Positive feedbacks enhance macroalgal resilience on degraded coral reefs (2017)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 11 (2016): e0155049, doi:10.1371/journal.pone.0155049.
    Description: Many reefs have shifted from coral and fish dominated habitats to less productive macroalgal dominated habitats, and current research is investigating means of reversing this phase shift. In the tropical Pacific, overfished reefs with inadequate herbivory can become dominated by the brown alga Sargassum polycystum. This alga suppresses recruitment and survival of corals and fishes, thus limiting the potential for reef recovery. Here we investigate the mechanisms that reinforce S. polycystum dominance and show that in addition to negatively affecting other species, this species acts in a self-reinforcing manner, positively promoting survival and growth of conspecifics. We found that survival and growth of both recruit-sized and mature S. polycystum fronds were higher within Sargassum beds than outside the beds and these results were found in both protected and fished reefs. Much of this benefit resulted from reduced herbivory within the Sargassum beds, but adult fronds also grew ~50% more within the beds even when herbivory did not appear to be occurring, suggesting some physiological advantage despite the intraspecific crowding. Thus via positive feedbacks, S. polycystum enhances its own growth and resistance to herbivores, facilitating its dominance (perhaps also expansion) and thus its resilience on degraded reefs. This may be a key feedback mechanism suppressing the recovery of coral communities in reefs dominated by macroalgal beds.
    Description: Financial support came to MEH from the National Science Foundation (OCE 0929119), the National Institutes of Health (2 U19 TW007401-10), and the Teasley Endowment to the Georgia Institute of Technology.
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    Preservation of three-dimensional spatial structure in the gut microbiome (2017)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0188257, doi:10.1371/journal.pone.0188257.
    Description: Preservation of three-dimensional structure in the gut is necessary in order to analyze the spatial organization of the gut microbiota and gut luminal contents. In this study, we evaluated preparation methods for mouse gut with the goal of preserving micron-scale spatial structure while performing fluorescence imaging assays. Our evaluation of embedding methods showed that commonly used media such as Tissue-Tek Optimal Cutting Temperature (OCT) compound, paraffin, and polyester waxes resulted in redistribution of luminal contents. By contrast, a hydrophilic methacrylate resin, Technovit H8100, preserved three-dimensional organization. Our mouse intestinal preparation protocol optimized using the Technovit H8100 embedding method was compatible with microbial fluorescence in situ hybridization (FISH) and other labeling techniques, including immunostaining and staining with both wheat germ agglutinin (WGA) and 4', 6-diamidino-2-phenylindole (DAPI). Mucus could be visualized whether the sample was fixed with paraformaldehyde (PFA) or with Carnoy’s fixative. The protocol optimized in this study enabled simultaneous visualization of micron-scale spatial patterns formed by microbial cells in the mouse intestines along with biogeographical landmarks such as host-derived mucus and food particles.
    Description: Funding provided by National Science Foundation (www.nsf.gov) grant 1650141 to J.L.M.W. and National Institutes of Health National Institute of Dental and Craniofacial Research (www.nidcr.nih.gov) grant DE022586 to G.G.B.
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    Indoles induce metamorphosis in a broad diversity of jellyfish, but not in a crown jelly (Coronatae) (2018)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0188601, doi:10.1371/journal.pone.0188601.
    Description: Many animals go through one or more metamorphoses during their lives, however, the molecular underpinnings of metamorphosis across diverse species are not well understood. Medusozoa (Cnidaria) is a clade of animals with complex life cycles, these life cycles can include a polyp stage that metamorphoses into a medusa (jellyfish). Medusae are produced through a variety of different developmental mechanisms—in some species polyps bud medusae (Hydrozoa), in others medusae are formed through polyp fission (Scyphozoa), while in others medusae are formed through direct transformation of the polyp (Cubozoa). To better understand the molecular mechanisms that may coordinate these different forms of metamorphosis, we tested two compounds first identified to induce metamorphosis in the moon jellyfish Aurelia aurita (indomethacin and 5-methoxy-2-methylindole) on a broad diversity of medusozoan polyps. We discovered that indole-containing compounds trigger metamorphosis across a broad diversity of species. All tested discomedusan polyps metamorphosed in the presence of both compounds, including species representatives of several major lineages within the clade (Pelagiidae, Cyaneidae, both clades of Rhizostomeae). In a cubozoan, low levels of 5-methoxy-2-methylindole reliably induced complete and healthy metamorphosis. In contrast, neither compound induced medusa metamorphosis in a coronate scyphozoan, or medusa production in either hydrozoan tested. Our results support the hypothesis that metamorphosis is mediated by a conserved induction pathway within discomedusan scyphozoans, and possibly cubozoans. However, failure of these compounds to induce metamorphosis in a coronate suggests this induction mechanism may have been lost in this clade, or is convergent between Scyphozoa and Cubozoa.
    Description: National Science Foundation Graduate Research Fellowship (DGE - 1058262; https://www.nsfgrfp.org/general_resources/about) to RRH. Evo-Devo-Eco Network (IOS # 0955517; http://edenrcn.com/) Research Exchange Funds, awarded to RRH. National Science Foundation Rhode Island Established Program to Stimulate Competitive Graduate Research Fellowship to RRH (DEB-1256695; http://web.uri.edu/rinsfepscor/grad-fellowships/). Brown University Ecology and Evolutionary Biology Dissertation Development Grant from the Bushnell Research and Education Fund awarded to RRH.
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    Linking deep convection and phytoplankton blooms in the northern Labrador Sea in a changing climate (2018)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 13 (2018): e0191509, doi:10.1371/journal.pone.0191509.
    Description: Wintertime convective mixing plays a pivotal role in the sub-polar North Atlantic spring phytoplankton blooms by favoring phytoplankton survival in the competition between light-dependent production and losses due to grazing and gravitational settling. We use satellite and ocean reanalyses to show that the area-averaged maximum winter mixed layer depth is positively correlated with April chlorophyll concentration in the northern Labrador Sea. A simple theoretical framework is developed to understand the relative roles of winter/spring convection and gravitational sedimentation in spring blooms in this region. Combining climate model simulations that project a weakening of wintertime Labrador Sea convection from Arctic sea ice melt with our framework suggests a potentially significant reduction in the initial fall phytoplankton population that survive the winter to seed the region’s spring bloom by the end of the 21st century.
    Description: KB, LB, PJR and LRL were supported by the Office of Science (BER), U. S. Department of Energy as part of the Regional and Global Climate Modelling (RGCM) Program. SCD acknowledges support from NASA Award NNX15AE65G North Atlantic Aerosol and Marine Ecosystem Study (NAAMES).
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    Prion protein inhibits fast axonal transport through a mechanism involving casein kinase 2 (2018)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0188340, doi:10.1371/journal.pone.0188340.
    Description: Prion diseases include a number of progressive neuropathies involving conformational changes in cellular prion protein (PrPc) that may be fatal sporadic, familial or infectious. Pathological evidence indicated that neurons affected in prion diseases follow a dying-back pattern of degeneration. However, specific cellular processes affected by PrPc that explain such a pattern have not yet been identified. Results from cell biological and pharmacological experiments in isolated squid axoplasm and primary cultured neurons reveal inhibition of fast axonal transport (FAT) as a novel toxic effect elicited by PrPc. Pharmacological, biochemical and cell biological experiments further indicate this toxic effect involves casein kinase 2 (CK2) activation, providing a molecular basis for the toxic effect of PrPc on FAT. CK2 was found to phosphorylate and inhibit light chain subunits of the major motor protein conventional kinesin. Collectively, these findings suggest CK2 as a novel therapeutic target to prevent the gradual loss of neuronal connectivity that characterizes prion diseases.
    Description: This work was supported by Alzheimer Association New Investigator Research Grant to Promote Diversity NIRGD-11-206379 and Consejo Nacional de Investigaciones Científicas y Técnicas PIP 112 20150100954 CO (to GP), National Institutes of Health NS066942A and NS096642 (to GM), R01-NS023868 and R01-NS041170 (to STB).
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    Cells containing aragonite crystals mediate responses to gravity in Trichoplax adhaerens (Placozoa), an animal lacking neurons and synapses (2018)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 13 (2018): e0190905, doi:10.1371/journal.pone.0190905.
    Description: Trichoplax adhaerens has only six cell types. The function as well as the structure of crystal cells, the least numerous cell type, presented an enigma. Crystal cells are arrayed around the perimeter of the animal and each contains a birefringent crystal. Crystal cells resemble lithocytes in other animals so we looked for evidence they are gravity sensors. Confocal microscopy showed that their cup-shaped nuclei are oriented toward the edge of the animal, and that the crystal shifts downward under the influence of gravity. Some animals spontaneously lack crystal cells and these animals behaved differently upon being tilted vertically than animals with a typical number of crystal cells. EM revealed crystal cell contacts with fiber cells and epithelial cells but these contacts lacked features of synapses. EM spectroscopic analyses showed that crystals consist of the aragonite form of calcium carbonate. We thus provide behavioral evidence that Trichoplax are able to sense gravity, and that crystal cells are likely to be their gravity receptors. Moreover, because placozoans are thought to have evolved during Ediacaran or Cryogenian eras associated with aragonite seas, and their crystals are made of aragonite, they may have acquired gravity sensors during this early era.
    Description: This research was supported by the intramural research program of the NIH, NINDS.
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    The use of mesoscale eddies by juvenile loggerhead sea turtles (Caretta caretta) in the southwestern Atlantic (2017)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This is an open access article, free of all copyright. The definitive version was published in PLoS ONE 12 (2017): e0172839, doi:10.1371/journal.pone.0172839.
    Description: Marine animals, such as turtles, seabirds and pelagic fishes, are observed to travel and congregate around eddies in the open ocean. Mesoscale eddies, large swirling ocean vortices with radius scales of approximately 50–100 km, provide environmental variability that can structure these populations. In this study, we investigate the use of mesoscale eddies by 24 individual juvenile loggerhead sea turtles (Caretta caretta) in the Brazil-Malvinas Confluence region. The influence of eddies on turtles is assessed by collocating the turtle trajectories to the tracks of mesoscale eddies identified in maps of sea level anomaly. Juvenile loggerhead sea turtles are significantly more likely to be located in the interiors of anticyclones in this region. The distribution of surface drifters in eddy interiors reveals no significant association with the interiors of cyclones or anticyclones, suggesting higher prevalence of turtles in anticyclones is a result of their behavior. In the southern portion of the Brazil-Malvinas Confluence region, turtle swimming speed is significantly slower in the interiors of anticyclones, when compared to the periphery, suggesting that these turtles are possibly feeding on prey items associated with anomalously low near-surface chlorophyll concentrations observed in those features.
    Description: A Woods Hole Postdoctoral Fellowship awarded to PG and NASA grant NNX13AE47G funded this work. CB is grateful for support from NOAA and the NSF-GRFP (Grant No. 1314109). DJM gratefully acknowledges support from NASA and NSF.
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    Hurricane Isaac brings more than oil ashore: Characteristics of beach deposits following the Deepwater Horizon spill. (2019)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lemkau, K. L., Reddy, C. M., Carmichael, C. A., Aeppli, C., Swarthout, R. F., & White, H. K. Hurricane Isaac brings more than oil ashore: Characteristics of beach deposits following the Deepwater Horizon spill. Plos One, 14(3), (2019):e0213464, doi:10.1371/journal.pone.0213464.
    Description: Prior to Hurricane Isaac making landfall along the Gulf of Mexico coast in August 2012, local and state officials were concerned that the hurricane would mobilize submerged oiled-materials from the Deepwater Horizon (DWH) spill. In this study, we investigated materials washed ashore following the hurricane to determine if it affected the chemical composition or density of oil-containing sand patties regularly found on Gulf Coast beaches. While small changes in sand patty density were observed in samples collected before and after the hurricane, these variations appear to have been driven by differences in sampling location and not linked to the passing of Hurricane Isaac. Visual and chemical analysis of sand patties confirmed that the contents was consistent with oil from the Macondo well. Petroleum hydrocarbon signatures of samples collected before and after the hurricane showed no notable changes. In the days following Hurricane Isaac, dark-colored mats were also found on the beach in Fort Morgan, AL, and community reports speculated that these mats contained oil from the DWH spill. Chemical analysis of these mat samples identified n-alkanes but no other petroleum hydrocarbons. Bulk and δ13C organic carbon analyses indicated mat samples were comprised of marshland peat and not related to the DWH spill. This research indicates that Hurricane Isaac did not result in a notable change the composition of oil delivered to beaches at the investigated field sites. This study underscores the need for improved communications with interested stakeholders regarding how to differentiate oiled from non-oiled materials. This is especially important given the high cost of removing oiled debris and the increasing likelihood of false positives as oiled-materials washing ashore from a spill become less abundant over time.
    Description: The authors wish to acknowledge support for this project from the Gulf of Mexico Research Initiative (RFP-V), the Deep-C Consortium (SA 16-30), NSF (OCE-1333148) awarded to CMR, and a Gulf Research Program Early-Career Research Fellowship to HKW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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    Significance of perylene for source allocation of terrigenous organic matter in aquatic sediments. (2019)
    American Chemical Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Chemical Society, 2019. This is an open access article published under an ACS AuthorChoice License. The definitive version was published in Environmental Science and Technology 53(14), (2019):8244-8251, doi:10.1021/acs.est.9b02344.
    Description: Perylene is a frequently abundant, and sometimes the only polycyclic aromatic hydrocarbon (PAH) in aquatic sediments, but its origin has been subject of a longstanding debate in geochemical research and pollutant forensics because its historical record differs markedly from typical anthropogenic PAHs. Here we investigate whether perylene serves as a source-specific molecular marker of fungal activity in forest soils. We use a well-characterized sedimentary record (1735 to 1999) from the anoxic-bottom waters of the Pettaquamscutt River basin, RI, USA to examine mass accumulation rates and isotope records of perylene, and compare them with total organic carbon and the anthropogenic PAH fluoranthene. We support our arguments with radiocarbon (14C) data of higher plant leaf-wax n-alkanoic acids. Isotope-mass balance calculations of perylene and n-alkanoic acids indicate that ~40 % of sedimentary organic matter is of terrestrial origin. Further, both terrestrial markers are pre-aged on millennial time-scales prior to burial in sediments and insensitive to elevated 14C concentrations following nuclear weapons testing in the mid-20th Century. Instead, changes coincide with enhanced erosional flux during urban sprawl. These findings suggest that perylene is definitely a product of soil derived fungi, and a powerful chemical tracer to study spatial and temporal connectivity between terrestrial and aquatic environments.
    Description: We thank John King, Sean Sylva, Brad Hubeny, Peter Sauer, and Jim Broda for their help in sampling; Carl Johnson and Daniel Montluçon for their incessant help with analyses; as well as Mark Yunker for critical discussion on the perils of perylene. Professor Phil Meyers and two anonymous reviewers provided comments that improved the quality of the manuscript. U.M.H. acknowledges the Swiss National Science Foundation for his postdoctoral fellowship and T.I.E. and K.A.H. acknowledges the NSF for research grants CHE-0089172 and OCE-9708478.
    Description: 2020-06-19
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    From the track to the ocean : using flow control to improve marine bio-logging tags for cetaceans (2017)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This is an open access article, free of all copyright. The definitive version was published in PLoS ONE 12 (2017): e0170962, doi:10.1371/journal.pone.0170962.
    Description: Bio-logging tags are an important tool for the study of cetaceans, but superficial tags inevitably increase hydrodynamic loading. Substantial forces can be generated by tags on fast-swimming animals, potentially affecting behavior and energetics or promoting early tag removal. Streamlined forms have been used to reduce loading, but these designs can accelerate flow over the top of the tag. This non-axisymmetric flow results in large lift forces (normal to the animal) that become the dominant force component at high speeds. In order to reduce lift and minimize total hydrodynamic loading this work presents a new tag design (Model A) that incorporates a hydrodynamic body, a channel to reduce fluid speed differences above and below the housing and wing to redirect flow to counter lift. Additionally, three derivatives of the Model A design were used to examine the contribution of individual flow control features to overall performance. Hydrodynamic loadings of four models were compared using computational fluid dynamics (CFD). The Model A design eliminated all lift force and generated up to ~30 N of downward force in simulated 6 m/s aligned flow. The simulations were validated using particle image velocimetry (PIV) to experimentally characterize the flow around the tag design. The results of these experiments confirm the trends predicted by the simulations and demonstrate the potential benefit of flow control elements for the reduction of tag induced forces on the animal.
    Description: This project was funded by the National Oceanographic Partnership Program [National Science Foundation via the Office of Naval Research N00014-11-1-0113]. C. Spencer Garborg was supported by a Grove City College Swezey Student Fellowship to Erik Anderson. Mark Johnson was funded by a Marie Curie-Sklodowska grant from the European Union.
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    Evidence of molting and the function of “rock-nosing” behavior in bowhead whales in the eastern Canadian Arctic (2017)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 12 (2017): e0186156, doi:10.1371/journal.pone.0186156.
    Description: Bowhead whales (Balaena mysticetus) have a nearly circumpolar distribution, and occasionally occupy warmer shallow coastal areas during summertime that may facilitate molting. However, relatively little is known about the occurrence of molting and associated behaviors in bowhead whales. We opportunistically observed whales in Cumberland Sound, Nunavut, Canada with skin irregularities consistent with molting during August 2014, and collected a skin sample from a biopsied whale that revealed loose epidermis and sloughing. During August 2016, we flew a small unmanned aerial system (sUAS) over whales to take video and still images to: 1) determine unique individuals; 2) estimate the proportion of the body of unique individuals that exhibited sloughing skin; 3) determine the presence or absence of superficial lines representative of rock-rubbing behavior; and 4) measure body lengths to infer age-class. The still images revealed that all individuals (n = 81 whales) were sloughing skin, and that nearly 40% of them had mottled skin over more than two-thirds of their bodies. The video images captured bowhead whales rubbing on large rocks in shallow, coastal areas—likely to facilitate molting. Molting and rock rubbing appears to be pervasive during late summer for whales in the eastern Canadian Arctic.
    Description: Fieldwork was funded by: Fisheries and Oceans Canada (Emerging Fisheries 41436-810-120-4D875), Nunavut Wildlife Research Trust Fund (project 3-13-29 Bowhead Whale Movement's and Ecology), Molson Foundation (318366), Ocean Tracking Network (NSERC NETGP 375118-08), and ArcticNet Centre of Excellence (317588) awarded to S.H. Ferguson and World Wildlife Fund Canada (Arctic Species Conservation Fund) awarded to W.R. Koski and S.M.E. Fortune. Additional field work support was provided by: U.S. Department of the Interior, Minerals Management Service (MMS; now Bureau of Ocean Energy Management), through Inter-agency Agreement No. M08PG20021 with the U.S. Department of Commerce, National Oceanic and Atmospheric Administration, as part of the MMS Alaska Environmental Studies Program awarded to M.F. Baumgartner. Personnel support was provided by: Natural Sciences and Engineering Research Council Canadian Graduate Scholarship, the W. Garfield Weston Award for Northern Research, University of British Columbia Affiliated Fellowship and Northern Scientific Training Program (Canadian Polar Commission) awarded to S.M.E. Fortune
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    Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities (2019)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Thomas, F., Morris, J. T., Wigand, C., & Sievert, S. M. Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities. Plos One, 14(4), (2019):e0215767, doi:10.1371/journal.pone.0215767.
    Description: Coastal climate adaptation strategies are needed to build salt marsh resiliency and maintain critical ecosystem services in response to impacts caused by climate change. Although resident microbial communities perform crucial biogeochemical cycles for salt marsh functioning, their response to restoration practices is still understudied. One promising restoration strategy is the placement of sand or sediment onto the marsh platform to increase marsh resiliency. A previous study examined the above- and below-ground structure, soil carbon dioxide emissions, and pore water constituents in Spartina alterniflora-vegetated natural marsh sediments and sand-amended sediments at varying inundation regimes. Here, we analyzed samples from the same experiment to test the effect of sand-amendments on the microbial communities after 5 months. Along with the previously observed changes in biogeochemistry, sand amendments drastically modified the bacterial communities, decreasing richness and diversity. The dominant sulfur-cycling bacterial community found in natural sediments was replaced by one dominated by iron oxidizers and aerobic heterotrophs, the abundance of which correlated with higher CO2-flux. In particular, the relative abundance of iron-oxidizing Zetaproteobacteria increased in the sand-amended sediments, possibly contributing to acidification by the formation of iron oxyhydroxides. Our data suggest that the bacterial community structure can equilibrate if the inundation regime is maintained within the optimal range for S. alterniflora. While long-term effects of changes in bacterial community on the growth of S. alterniflora are not clear, our results suggest that analyzing the microbial community composition could be a useful tool to monitor climate adaptation and restoration efforts.
    Description: This work was supported by NSF grants DEB-1050557 (SMS) and OCE-1637630 (JM), and WHOI Investment in Science Funds (SMS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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    Simulating gas–liquid−water partitioning and fluid properties of petroleum under pressure : implications for deep-sea blowouts (2016)
    American Chemical Society
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    Publication Date: 2022-05-26
    Description: © American Chemical Society, 2016. This article is distributed under the terms of the AuthorsChoice License. The definitive version was published in Environmental Science & Technology 50 (2016): 7397–7408, doi:10.1021/acs.est.5b04617.
    Description: With the expansion of offshore petroleum extraction, validated models are needed to simulate the behaviors of petroleum compounds released in deep (〉100 m) waters. We present a thermodynamic model of the densities, viscosities, and gas–liquid−water partitioning of petroleum mixtures with varying pressure, temperature, and composition based on the Peng–Robinson equation-of-state and the modified Henry’s law (Krychevsky−Kasarnovsky equation). The model is applied to Macondo reservoir fluid released during the Deepwater Horizon disaster, represented with 279–280 pseudocomponents, including 131–132 individual compounds. We define 〉n-C8 pseudocomponents based on comprehensive two-dimensional gas chromatography (GC × GC) measurements, which enable the modeling of aqueous partitioning for n-C8 to n-C26 fractions not quantified individually. Thermodynamic model predictions are tested against available laboratory data on petroleum liquid densities, gas/liquid volume fractions, and liquid viscosities. We find that the emitted petroleum mixture was ∼29–44% gas and ∼56–71% liquid, after cooling to local conditions near the broken Macondo riser stub (∼153 atm and 4.3 °C). High pressure conditions dramatically favor the aqueous dissolution of C1−C4 hydrocarbons and also influence the buoyancies of bubbles and droplets. Additionally, the simulated densities of emitted petroleum fluids affect previous estimates of the volumetric flow rate of dead oil from the emission source.
    Description: This research was made possible by grants from the NSF (OCE- 0960841, OCE-1043976, and EAR-0950600) and the Gulf of Mexico Research Initiative (GoMRI) to the C-IMAGE and DEEP-C consortia.
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    Evaluating coral trophic strategies using fatty acid composition and indices (2019)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Radice, V. Z., Brett, M. T., Fry, B., Fox, M. D., Hoegh-Guldberg, O., & Dove, S. G. Evaluating coral trophic strategies using fatty acid composition and indices. Plos One, 14(9), (2019): e0222327, doi:10.1371/journal.pone.0222327.
    Description: The ecological success of shallow water reef-building corals has been linked to the symbiosis between the coral host and its dinoflagellate symbionts (herein ‘symbionts’). As mixotrophs, symbiotic corals depend on nutrients 1) transferred from their photosynthetic symbionts (autotrophy) and 2) acquired by host feeding on particulate organic resources (heterotrophy). However, coral species differ in the extent to which they depend on heterotrophy for nutrition and these differences are typically poorly defined. Here, a multi-tracer fatty acid approach was used to evaluate the trophic strategies of three species of common reef-building coral (Galaxea fascicularis, Pachyseris speciosa, and Pocillopora verrucosa) whose trophic strategies had previously been identified using carbon stable isotopes. The composition and various indices of fatty acids were compared to examine the relative contribution of symbiont autotrophy and host heterotrophy in coral energy acquisition. A linear discriminant analysis (LDA) was used to estimate the contribution of polyunsaturated fatty acids (PUFA) derived from various potential sources to the coral hosts. The total fatty acid composition and fatty acid indices revealed differences between the more heterotrophic (P. verrucosa) and more autotrophic (P. speciosa) coral hosts, with the coral host G. fascicularis showing overlap with the other two species and greater variability overall. For the more heterotrophic P. verrucosa, the fatty acid indices and LDA results both indicated a greater proportion of copepod-derived fatty acids compared to the other coral species. Overall, the LDA estimated that PUFA derived from particulate resources (e.g., copepods and diatoms) comprised a greater proportion of coral host PUFA in contrast to the lower proportion of symbiont-derived PUFA. These estimates provide insight into the importance of heterotrophy in coral nutrition, especially in productive reef systems. The study supports carbon stable isotope results and demonstrates the utility of fatty acid analyses for exploring the trophic strategies of reef-building corals.
    Description: This study was made possible by funding from the XL Catlin Seaview Survey (OHG and VZR; http://catlinseaviewsurvey.com/), Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies (CE140100020; SD and OHG; https://www.coralcoe.org.au/), an ARC Laureate Fellowship (FL120100066; OHG; https://www.arc.gov.au), the University of Queensland Research Training Scholarship (VZR; https://www.uq.edu.au/), and the University of Washington Dale A. Carlson Endowed Faculty Support Fund (MTB and VZR; https://www.washington.edu/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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    Temperature-induced viral resistance in Emiliania huxleyi (Prymnesiophyceae) (2015)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e112134, doi:10.1371/journal.pone.0112134.
    Description: Annual Emiliania huxleyi blooms (along with other coccolithophorid species) play important roles in the global carbon and sulfur cycles. E. huxleyi blooms are routinely terminated by large, host-specific dsDNA viruses, (Emiliania huxleyi Viruses; EhVs), making these host-virus interactions a driving force behind their potential impact on global biogeochemical cycles. Given projected increases in sea surface temperature due to climate change, it is imperative to understand the effects of temperature on E. huxleyi’s susceptibility to viral infection and its production of climatically active dimethylated sulfur species (DSS). Here we demonstrate that a 3°C increase in temperature induces EhV-resistant phenotypes in three E. huxleyi strains and that successful virus infection impacts DSS pool sizes. We also examined cellular polar lipids, given their documented roles in regulating host-virus interactions in this system, and propose that alterations to membrane-bound surface receptors are responsible for the observed temperature-induced resistance. Our findings have potential implications for global biogeochemical cycles in a warming climate and for deciphering the particular mechanism(s) by which some E. huxleyi strains exhibit viral resistance.
    Description: This study was supported by funding from the National Science Foundation (OCE-1061883 to KDB, BVM, and OCE-1061876 to GRD) and in part by grants from The Gordon and Betty Moore Foundation (to BVM and KDB).
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    Protist community grazing on prokaryotic prey in deep ocean water masses (2015)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0124505, doi:10.1371/journal.pone.0124505.
    Description: Oceanic protist grazing at mesopelagic and bathypelagic depths, and their subsequent effects on trophic links between eukaryotes and prokaryotes, are not well constrained. Recent studies show evidence of higher than expected grazing activity by protists down to mesopelagic depths. This study provides the first exploration of protist grazing in the bathypelagic North Atlantic Deep Water (NADW). Grazing was measured throughout the water column at three stations in the South Atlantic using fluorescently-labeled prey analogues. Grazing in the deep Antarctic Intermediate water (AAIW) and NADW at all three stations removed 3.79% ± 1.72% to 31.14% ± 8.24% of the standing prokaryote stock. These results imply that protist grazing may be a significant source of labile organic carbon at certain meso- and bathypelagic depths.
    Description: Funding for the cruise was provided by the National Science Foundation (OCE-1154320) to EBK. Funding for the laboratory work was provided by contributions from the Woods Hole Oceanographic Institution Director of Research, Ocean Life Institute, and Deep Ocean Exploration Institute to VE.
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    Exploration of the canyon-incised continental margin of the northeastern United States reveals dynamic habitats and diverse communities (2015)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright. The definitive version was published in PLoS One 10 (2015): e0139904, doi: 10.1371/journal.pone.0139904.
    Description: The continental margin off the northeastern United States (NEUS) contains numerous, topographically complex features that increase habitat heterogeneity across the region. However, the majority of these rugged features have never been surveyed, particularly using direct observations. During summer 2013, 31 Remotely-Operated Vehicle (ROV) dives were conducted from 494 to 3271 m depth across a variety of seafloor features to document communities and to infer geological processes that produced such features. The ROV surveyed six broad-scale habitat features, consisting of shelf-breaching canyons, slope-sourced canyons, inter-canyon areas, open-slope/landslide-scar areas, hydrocarbon seeps, and Mytilus Seamount. Four previously unknown chemosynthetic communities dominated by Bathymodiolus mussels were documented. Seafloor methane hydrate was observed at two seep sites. Multivariate analyses indicated that depth and broad-scale habitat significantly influenced megafaunal coral (58 taxa), demersal fish (69 taxa), and decapod crustacean (34 taxa) assemblages. Species richness of fishes and crustaceans significantly declined with depth, while there was no relationship between coral richness and depth. Turnover in assemblage structure occurred on the middle to lower slope at the approximate boundaries of water masses found previously in the region. Coral species richness was also an important variable explaining variation in fish and crustacean assemblages. Coral diversity may serve as an indicator of habitat suitability and variation in available niche diversity for these taxonomic groups. Our surveys added 24 putative coral species and three fishes to the known regional fauna, including the black coral Telopathes magna, the octocoral Metallogorgia melanotrichos and the fishes Gaidropsarus argentatus, Guttigadus latifrons, and Lepidion guentheri. Marine litter was observed on 81% of the dives, with at least 12 coral colonies entangled in debris. While initial exploration revealed the NEUS region to be both geologically dynamic and biologically diverse, further research into the abiotic conditions and the biotic interactions that influence species abundance and distribution is needed.
    Description: Funding for the ship and ROV time was provided by NOAA’s Office of Ocean Exploration and Research with support from NOAA’s Deep Sea Coral Research and Technology Program, Northeast Initiative.
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    The amyloid precursor protein of Alzheimer’s disease clusters at the organelle/microtubule interface on organelles that bind microtubules in an ATP dependent manner (2016)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0147808, doi:10.1371/journal.pone.0147808.
    Description: The amyloid precursor protein (APP) is a causal agent in the pathogenesis of Alzheimer’s disease and is a transmembrane protein that associates with membrane-limited organelles. APP has been shown to co-purify through immunoprecipitation with a kinesin light chain suggesting that APP may act as a trailer hitch linking kinesin to its intercellular cargo, however this hypothesis has been challenged. Previously, we identified an mRNA transcript that encodes a squid homolog of human APP770. The human and squid isoforms share 60% sequence identity and 76% sequence similarity within the cytoplasmic domain and share 15 of the final 19 amino acids at the C-terminus establishing this highly conserved domain as a functionally import segment of the APP molecule. Here, we study the distribution of squid APP in extruded axoplasm as well as in a well-characterized reconstituted organelle/microtubule preparation from the squid giant axon in which organelles bind microtubules and move towards the microtubule plus-ends. We find that APP associates with microtubules by confocal microscopy and co-purifies with KI-washed axoplasmic organelles by sucrose density gradient fractionation. By electron microscopy, APP clusters at a single focal point on the surfaces of organelles and localizes to the organelle/microtubule interface. In addition, the association of APP-organelles with microtubules is an ATP dependent process suggesting that the APP-organelles contain a microtubule-based motor protein. Although a direct kinesin/APP association remains controversial, the distribution of APP at the organelle/microtubule interface strongly suggests that APP-organelles have an orientation and that APP like the Alzheimer’s protein tau has a microtubule-based function.
    Description: Research reported in this publication was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103430.
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    Influence of environmental variables on Gambierdiscus spp. (Dinophyceae) growth and distribution (2016)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0153197, doi:10.1371/journal.pone.0153197.
    Description: Benthic dinoflagellates in the genus Gambierdiscus produce the ciguatoxin precursors responsible for the occurrence of ciguatera toxicity. The prevalence of ciguatera toxins in fish has been linked to the presence and distribution of toxin-producing species in coral reef ecosystems, which is largely determined by the presence of suitable benthic habitat and environmental conditions favorable for growth. Here using single factor experiments, we examined the effects of salinity, irradiance, and temperature on growth of 17 strains of Gambierdiscus representing eight species/phylotypes (G. belizeanus, G. caribaeus, G. carolinianus, G. carpenteri, G. pacificus, G. silvae, Gambierdiscus sp. type 4–5), most of which were established from either Marakei Island, Republic of Kiribati, or St. Thomas, United States Virgin Island (USVI). Comparable to prior studies, growth rates fell within the range of 0–0.48 divisions day-1. In the salinity and temperature studies, Gambierdiscus responded in a near Gaussian, non-linear manner typical for such studies, with optimal and suboptimal growth occurring in the range of salinities of 25 and 45 and 21.0 and 32.5°C. In the irradiance experiment, no mortality was observed; however, growth rates at 55μmol photons · m-2 · s-1 were lower than those at 110–400μmol photons · m-2 · s-1. At the extremes of the environmental conditions tested, growth rates were highly variable, evidenced by large coefficients of variability. However, significant differences in intraspecific growth rates were typically found only at optimal or near-optimal growth conditions. Polynomial regression analyses showed that maximum growth occurred at salinity and temperature levels of 30.1–38.5 and 23.8–29.2°C, respectively. Gambierdiscus growth patterns varied among species, and within individual species: G. belizeanus, G. caribaeus, G. carpenteri, and G. pacificus generally exhibited a wider range of tolerance to environmental conditions, which may explain their broad geographic distribution. In contrast, G. silvae and Gambierdiscus sp. types 4–5 all displayed a comparatively narrow range of tolerance to temperature, salinity, and irradiance.
    Description: This study was funded by the National Natural Science Foundation of China (41506137); Guangxi Natural Science Foundation (2015GXNSFCA139003), Centers for Disease Control and Prevention (U01 EH000421); USFDA (F223201000060C); NOAA NOS through the CiguaHAB program (Cooperative Agreement NA11NOS4780060, NA11NOS4780028); the Lana Vento Trust and VI-EPSCoR Program (NSF award # 346483 & 081441); and a System Fund from Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (2014BGERLXT01). Support was also provided by the Woods Hole Center for Oceans and Human Health through National Science Foundation (NSF) Grant OCE-1314642, National Institute of Environmental Health Sciences (NIEHS) Grant 1-P01-ES021923-014, as well as the China Scholarship Council.
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    Comparative analysis of secretome profiles of manganese(II)-oxidizing Ascomycete fungi (2016)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
    Description: Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.
    Description: This work was supported by the National Science Foundation (www.nsf.gov), grant numbers EAR-1249489 and CBET-1336496, both awarded to CMH. Personal support for CAZ was also provided by Harvard University (www.harvard.edu) and by a Ford Foundation (www.fordfoundation.org) Predoctoral Fellowship administered by the National Academies.
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    Potential impacts of offshore wind farms on North Sea stratification (2016)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0160830, doi:10.1371/journal.pone.0160830 .
    Description: Advances in offshore wind farm (OWF) technology have recently led to their construction in coastal waters that are deep enough to be seasonally stratified. As tidal currents move past the OWF foundation structures they generate a turbulent wake that will contribute to a mixing of the stratified water column. In this study we show that the mixing generated in this way may have a significant impact on the large-scale stratification of the German Bight region of the North Sea. This region is chosen as the focus of this study since the planning of OWFs is particularly widespread. Using a combination of idealised modelling and in situ measurements, we provide order-of-magnitude estimates of two important time scales that are key to understanding the impacts of OWFs: (i) a mixing time scale, describing how long a complete mixing of the stratification takes, and (ii) an advective time scale, quantifying for how long a water parcel is expected to undergo enhanced wind farm mixing. The results are especially sensitive to both the drag coefficient and type of foundation structure, as well as the evolution of the pycnocline under enhanced mixing conditions—both of which are not well known. With these limitations in mind, the results show that OWFs could impact the large-scale stratification, but only when they occupy extensive shelf regions. They are expected to have very little impact on large-scale stratification at the current capacity in the North Sea, but the impact could be significant in future large-scale development scenarios.
    Description: Funding was provided by the Helmholtz Foundation through the Polar Regions and Coasts in the Changing Earth System II (PACES II) program.
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    Predicting interactions between common dolphins and the pole-and-line tuna fishery in the Azores (2016)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 11 (2016): e0164107, doi:10.1371/journal.pone.0164107.
    Description: Common dolphins (Delphinus delphis) are responsible for the large majority of interactions with the pole-and-line tuna fishery in the Azores but the underlying drivers remain poorly understood. In this study we investigate the influence of various environmental and fisheries-related factors in promoting the interaction of common dolphins with this fishery and estimate the resultant catch losses. We analysed 15 years of fishery and cetacean interaction data (1998–2012) collected by observers placed aboard tuna fishing vessels. Dolphins interacted in less than 3% of the fishing events observed during the study period. The probability of dolphin interaction varied significantly between years with no evident trend over time. Generalized additive modeling results suggest that fishing duration, sea surface temperature and prey abundance in the region were the most important factors explaining common dolphin interaction. Dolphin interaction had no impact on the catches of albacore, skipjack and yellowfin tuna but resulted in significantly lower catches of bigeye tuna, with a predicted median annual loss of 13.5% in the number of fish captured. However, impact on bigeye catches varied considerably both by year and fishing area. Our work shows that rates of common dolphin interaction with the pole-and-line tuna fishery in the Azores are low and showed no signs of increase over the study period. Although overall economic impact was low, the interaction may lead to significant losses in some years. These findings emphasize the need for continued monitoring and for further research into the consequences and economic viability of potential mitigation measures.
    Description: This work was funded by Fundação para a Ciência e a Tecnologia (FCT) and DRCT/SRCTE, though FEDER, the Competitiveness Factors Operational (COMPETE), QREN European Social Fund, the Portuguese Ministry for Science and Education, under research projects TRACE (PTDC/MAR/74071/2006), FCT Exploratory Project (IF/00943/2013/CP1199/CT0001), and MAPCET (M2.1.2/F/012/2011). We acknowledge the support of Fundação para a Ciência e Tecnologia (FCT), through the strategic project UID/MAR/04292/2013 granted to MARE. We thank the Azorean Regional Government for funding POPA, the Ship-owners Association and the Association of the Tuna Canning Industries for their support to the program. MJC was supported by a DRCT doctoral grant (M3.1.2/F/008/2009). MAS was supported by POPH, QREN, European Social Fund and Portuguese Ministry for Science and Education, through an FCT Investigator grant (IF/00943/2013).
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    Light control of G protein signaling pathways by a novel photopigment (2018)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 13 (2018): e0205015, doi:10.1371/journal.pone.0205015.
    Description: Channelopsins and photo-regulated ion channels make it possible to use light to control electrical activity of cells. This powerful approach has lead to a veritable explosion of applications, though it is limited to changing membrane voltage of the target cells. An enormous potential could be tapped if similar opto-genetic techniques could be extended to the control of chemical signaling pathways. Photopigments from invertebrate photoreceptors are an obvious choice—as they do not bleach upon illumination -however, their functional expression has been problematic. We exploited an unusual opsin, pScop2, recently identified in ciliary photoreceptors of scallop. Phylogenetically, it is closer to vertebrate opsins, and offers the advantage of being a bi-stable photopigment. We inserted its coding sequence and a fluorescent protein reporter into plasmid vectors and demonstrated heterologous expression in various mammalian cell lines. HEK 293 cells were selected as a heterologous system for functional analysis, because wild type cells displayed the largest currents in response to the G-protein activator, GTP-γ-S. A line of HEK cells stably transfected with pScop2 was generated; after reconstitution of the photopigment with retinal, light responses were obtained in some cells, albeit of modest amplitude. In native photoreceptors pScop2 couples to Go; HEK cells express poorly this G-protein, but have a prominent Gq/PLC pathway linked to internal Ca mobilization. To enhance pScop2 competence to tap into this pathway, we swapped its third intracellular loop—important to confer specificity of interaction between 7TMDRs and G-proteins—with that of a Gq-linked opsin which we cloned from microvillar photoreceptors present in the same retina. The chimeric construct was evaluated by a Ca fluorescence assay, and was shown to mediate a robust mobilization of internal calcium in response to illumination. The results project pScop2 as a potentially powerful optogenetic tool to control signaling pathways.
    Description: This work was funded by Colciencias grant FP44842-010-2015 and Connecticut Fund for Science.
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    Petrocarbon evolution: Ramped pyrolysis/oxidation and isotopic studies of contaminated oil sediments from the Deepwater Horizon oil spill in the Gulf of Mexico. (2019)
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    Publication Date: 2022-05-25
    Description: © The Authors, 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Rogers, K. L., Bosman, S. H., Lardie-Gaylord, M., McNichol, A., Rosenheim, B. E., Montoya, J. P., & Chanton, J. P. (2019). Petrocarbon evolution: Ramped pyrolysis/oxidation and isotopic studies of contaminated oil sediments from the Deepwater Horizon oil spill in the Gulf of Mexico. PLoS One, 14(2), (2019):e0212433, doi:10.1371/journal.pone.0212433.
    Description: Hydrocarbons released during the Deepwater Horizon (DWH) oil spill weathered due to exposure to oxygen, light, and microbes. During weathering, the hydrocarbons’ reactivity and lability was altered, but it remained identifiable as “petrocarbon” due to its retention of the distinctive isotope signatures (14C and 13C) of petroleum. Relative to the initial estimates of the quantity of oil-residue deposited in Gulf sediments based on 2010–2011 data, the overall coverage and quantity of the fossil carbon on the seafloor has been attenuated. To analyze recovery of oil contaminated deep-sea sediments in the northern Gulf of Mexico we tracked the carbon isotopic composition (13C and 14C, radiocarbon) of bulk sedimentary organic carbon through time at 4 sites. Using ramped pyrolysis/oxidation, we determined the thermochemical stability of sediment organic matter at 5 sites, two of these in time series. There were clear differences between crude oil (which decomposed at a lower temperature during ramped oxidation), natural hydrocarbon seep sediment (decomposing at a higher temperature; Δ14C = -912‰) and our control site (decomposing at a moderate temperature; Δ14C = -189‰), in both the stability (ability to withstand ramped temperatures in oxic conditions) and carbon isotope signatures. We observed recovery toward our control site bulk Δ14C composition at sites further from the wellhead in ~4 years, whereas sites in closer proximity had longer recovery times. The thermographs also indicated temporal changes in the composition of contaminated sediment, with shifts towards higher temperature CO2 evolution over time at a site near the wellhead, and loss of higher temperature CO2 peaks at a more distant site.
    Description: This research was made possible by grants from The Gulf of Mexico Research Initiative through its consortiums: Ecosystem Impacts of Oil & Gas Inputs to the Gulf (ECOGIG), The Center for the Integrated Modeling and Analysis of the Gulf Ecosystem (C-Image), and Deep Sea to Coast Connectivity in the Eastern Gulf of Mexico (Deep-C) and the Resuspension, Redistribution and Deposition of DWH Recalcitrant Material (Re-Direct) project. This is ECOGIG Contribution # 521. Funding was also provided by the National Ocean Sciences Accelerator Mass Spectrometry Facility (NOSAMS) Graduate Student Internship Program (NSF OCE-1239667). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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    Microbial iron mats at the Mid-Atlantic Ridge and evidence that Zetaproteobacteria may be restricted to iron-oxidizing marine systems (2015)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0119284, doi:10.1371/journal.pone.0119284 .
    Description: Chemolithoautotrophic iron-oxidizing bacteria play an essential role in the global iron cycle. Thus far, the majority of marine iron-oxidizing bacteria have been identified as Zetaproteobacteria, a novel class within the phylum Proteobacteria. Marine iron-oxidizing microbial communities have been found associated with volcanically active seamounts, crustal spreading centers, and coastal waters. However, little is known about the presence and diversity of iron-oxidizing communities at hydrothermal systems along the slow crustal spreading center of the Mid-Atlantic Ridge. From October to November 2012, samples were collected from rust-colored mats at three well-known hydrothermal vent systems on the Mid-Atlantic Ridge (Rainbow, Trans-Atlantic Geotraverse, and Snake Pit) using the ROV Jason II. The goal of these efforts was to determine if iron-oxidizing Zetaproteobacteria were present at sites proximal to black smoker vent fields. Small, diffuse flow venting areas with high iron(II) concentrations and rust-colored microbial mats were observed at all three sites proximal to black smoker chimneys. A novel, syringe-based precision sampler was used to collect discrete microbial iron mat samples at the three sites. The presence of Zetaproteobacteria was confirmed using a combination of 16S rRNA pyrosequencing and single-cell sorting, while light micros-copy revealed a variety of iron-oxyhydroxide structures, indicating that active iron-oxidizing communities exist along the Mid-Atlantic Ridge. Sequencing analysis suggests that these iron mats contain cosmopolitan representatives of Zetaproteobacteria, but also exhibit diversity that may be uncommon at other iron-rich marine sites studied to date. A meta-analysis of publically available data encompassing a variety of aquatic habitats indicates that Zetaproteobacteria are rare if an iron source is not readily available. This work adds to the growing understanding of Zetaproteobacteria ecology and suggests that this organism is likely locally restricted to iron-rich marine environments but may exhibit wide-scale geographic distribution, further underscoring the importance of Zetaproteobacteria in global iron cycling.
    Description: This work was supported by grants from the National Science Foundation [grants OCE-0926805 (DE and JAB), OCE-1155754 (DE), and OCE-1131109 (GWL)] and the National Aeronautics and Space Administration [NNX12AG20G (GWL and DE)].
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    Microbial gene abundance and expression patterns across a river to ocean salinity gradient (2015)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0140578, doi: 10.1371/journal.pone.0140578.
    Description: Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.
    Description: This study was carried out within the context of the Science and Technology Center for Coastal Margin Observation & Prediction (CMOP) supported by the National Science Foundation, grant number OCE-0424602 to Antonio Baptista (http://www.stccmop.org).
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    Mercury-pollution induction of intracellular lipid accumulation and lysosomal compartment amplification in the benthic foraminifer Ammonia parkinsoniana (2016)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The definitive version was published in PLoS One 11 (2016): e0162401, doi:10.1371/journal.pone.0162401.
    Description: Heavy metals such as mercury (Hg) pose a significant health hazard through bioaccumulation and biomagnification. By penetrating cell membranes, heavy metal ions may lead to pathological conditions. Here we examined the responses of Ammonia parkinsoniana, a benthic foraminiferan, to different concentrations of Hg in the artificial sea water. Confocal images of untreated and treated specimens using fluorescent probes (Nile Red and Acridine Orange) provided an opportunity for visualizing the intracellular lipid accumulation and acidic compartment regulation. With increased Hg over time, we observed an increased number of lipid droplets, which may have acted as a detoxifying organelle where Hg is sequestered and biologically inactivated. Further, Hg seems to promote the proliferation of lysosomes both in terms of number and dimension that, at the highest level of Hg, resulted in cell death. We report, for the first time, the presence of Hg within the foraminiferal cell: at the basal part of pores, in the organic linings of the foramen/septa, and as cytoplasmic accumulations.
    Description: The research for this paper was partially made possible by the financial support from the PRIN 2010-2011 Ministero dell’Istruzione, dell’Università e della Ricerca (MIUR) (protocollo 2010RMTLYR) to RC. JMB acknowledges support from The Investment in Science Fund at WHOI. BG, JRE, AJ, LZ, and EMP were supported in part by the Office of Biological and Environmental Research, US Department of Energy (DOE) as part of the Mercury Science Focus Area at Oak Ridge National Laboratory, which is managed by UT-Battelle LLC for the DOE under contract DE-AC05-00OR22725.
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    Shipboard design and fabrication of custom 3D-printed soft robotic manipulators for the investigation of delicate deep-sea organisms (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLos One 13 (2018): e0200386, doi:10.1371/journal.pone.0200386.
    Description: Soft robotics is an emerging technology that has shown considerable promise in deep-sea marine biological applications. It is particularly useful in facilitating delicate interactions with fragile marine organisms. This study describes the shipboard design, 3D printing and integration of custom soft robotic manipulators for investigating and interacting with deep-sea organisms. Soft robotics manipulators were tested down to 2224m via a Remotely-Operated Vehicle (ROV) in the Phoenix Islands Protected Area (PIPA) and facilitated the study of a diverse suite of soft-bodied and fragile marine life. Instantaneous feedback from the ROV pilots and biologists allowed for rapid re-design, such as adding “fingernails”, and re-fabrication of soft manipulators at sea. These were then used to successfully grasp fragile deep-sea animals, such as goniasterids and holothurians, which have historically been difficult to collect undamaged via rigid mechanical arms and suction samplers. As scientific expeditions to remote parts of the world are costly and lengthy to plan, on-the-fly soft robot actuator printing offers a real-time solution to better understand and interact with delicate deep-sea environments, soft-bodied, brittle, and otherwise fragile organisms. This also offers a less invasive means of interacting with slow-growing deep marine organisms, some of which can be up to 18,000 years old.
    Description: This work is supported by NOAA OER Grant # NA17OAR0110083 “Exploration of the Seamounts of the Phoenix Islands Protected Area” to RDR, EEC, TMS and DFG and Schmidt Ocean Institute Grant: “What is the Current State of the Deep-Sea Coral Ecosystem in the Phoenix Island Protected Area?” to EEC, RDR, TMS and DFG; NSF Instrument Development for Biological Research Award # 1556164 to RJW and #1556123 to DFG; the National Academies Keck Futures Initiative of the National Academy of Sciences under award #NAKFI DBS21 to RJW and DFG; and NFS Research Fellowship awarded to KPB (#DGE1144152). It is also supported by the Wyss Institute for Biologically Inspired Engineering at Harvard University. We are grateful for the support from the National Geographic Society Innovation Challenge (Grant No.: SP 12-14) to RJW and DFG.
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    Resonance control of acoustic focusing systems through an environmental reference table and impedance spectroscopy (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 13 (2018): e0207532, doi:10.1371/journal.pone.0207532.
    Description: Acoustic standing waves can precisely focus flowing particles or cells into tightly positioned streams for interrogation or downstream separations. The efficiency of an acoustic standing wave device is dependent upon operating at a resonance frequency. Small changes in a system’s temperature and sample salinity can shift the device’s resonance condition, leading to poor focusing. Practical implementation of an acoustic standing wave system requires an automated resonance control system to adjust the standing wave frequency in response to environmental changes. Here we have developed a rigorous approach for quantifying the optimal acoustic focusing frequency at any given environmental condition. We have demonstrated our approach across a wide range of temperature and salinity conditions to provide a robust characterization of how the optimal acoustic focusing resonance frequency shifts across these conditions. To generalize these results, two microfluidic bulk acoustic standing wave systems (a steel capillary and an etched silicon wafer) were examined. Models of these temperature and salinity effects suggest that it is the speed of sound within the liquid sample that dominates the resonance frequency shift. Using these results, a simple reference table can be generated to predict the optimal resonance condition as a function of temperature and salinity. Additionally, we show that there is a local impedance minimum associated with the optimal system resonance. The integration of the environmental results for coarse frequency tuning followed by a local impedance characterization for fine frequency adjustments, yields a highly accurate method of resonance control. Such an approach works across a wide range of environmental conditions, is easy to automate, and could have a significant impact across a wide range of microfluidic acoustic standing wave systems.
    Description: This research was supported by grants from the National Institute of General Medical Sciences of the National Institutes of Health under award number R21GM107805 and the NSF under award number (OCE-1130140 and OCE-1131134) to SWG, RJO, and HMS.
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    Regenerative capacity in the lamprey spinal cord is not altered after a repeated transection (2019)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 14(1), (2019):e0204193, doi: 10.1371/journal.pone.0204193.
    Description: The resilience of regeneration in vertebrates is not very well understood. Yet understanding if tissues can regenerate after repeated insults, and identifying limitations, is important for elucidating the underlying mechanisms of tissue plasticity. This is particularly challenging in tissues, such as the nervous system, which possess a large number of terminally differentiated cells and often exhibit limited regeneration in the first place. However, unlike mammals, which exhibit very limited regeneration of spinal cord tissues, many non-mammalian vertebrates, including lampreys, bony fishes, amphibians, and reptiles, regenerate their spinal cords and functionally recover even after a complete spinal cord transection. It is well established that lampreys undergo full functional recovery of swimming behaviors after a single spinal cord transection, which is accompanied by tissue repair at the lesion site, as well as axon and synapse regeneration. Here we begin to explore the resilience of spinal cord regeneration in lampreys after a second spinal transection (re-transection). We report that by all functional and anatomical measures tested, lampreys regenerate after spinal re-transection just as robustly as after single transections. Recovery of swimming, synapse and cytoskeletal distributions, axon regeneration, and neuronal survival were nearly identical after spinal transection or re-transection. Only minor differences in tissue repair at the lesion site were observed in re-transected spinal cords. Thus, regenerative potential in the lamprey spinal cord is largely unaffected by spinal re-transection, indicating a greater persistent regenerative potential than exists in some other highly regenerative models. These findings establish a new path for uncovering pro-regenerative targets that could be deployed in non-regenerative conditions.
    Description: The authors would like to thank Dr. Cristina Roman-Vendrell and Louie Kerr, Director of the Central Microscopy Facility at the MBL, for technical support. We also thank Dr. Juan Diaz-Quiroz for helpful comments on the manuscript. EG was supported in part by an NSF REU Award (#1659604: Biological Discovery in Woods Hole at the Marine Biological Laboratory).
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    Inbreeding ratio and genetic relationships among strains of the Western clawed frog, Xenopus tropicalis (2015)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0133963, doi: 10.1371/journal.pone.0133963.
    Description: The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts.
    Description: This work was supported by grants from the Wellcome Trust (101480/Z/13/Z, http://www.wellcome.ac.uk/stellent/group​s/corporatesite/@msh_publishing_group/do​cuments/web_document/wts058331.pdf) and Biotechnology and Biological Sciences Research Council (BB/K019988/1, http://www.bbsrc.ac.uk/pa/grants/AwardDe​tails.aspx?FundingReference=BB/K019988/1) to the European Xenopus Resource Centre. This work was also supported by a Grant-in-Aid for Young Scientists (B) (No. 23710282, http://kaken.nii.ac.jp/d/p/23710282.en.h​tml) to TI from the Ministry of Education, Culture, Sports, Science and Technology, Japan and a Grant-in-Aid for Scientific Research (B) (No. 20510216, http://kaken.nii.ac.jp/d/p/24310173.en.h​tml) to MS from the Ministry of Education, Culture, Sports, Science and Technology, Japan.
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    The influence of age and gender on skin-associated microbial communities in urban and rural human populations (2015)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One (10): e0141842, doi:10.1371/journal.pone.0141842.
    Description: Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~5x greater than random.
    Description: This work was supported by a grant from Johnson & Johnson (China).
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    The good, the bad, and the tiny : a simple, mechanistic-probabilistic model of virus-nutrient colimitation in microbes (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0143299, doi:10.1371/journal.pone.0143299.
    Description: For phytoplankton and other microbes, nutrient receptors are often the passages through which viruses invade. This presents a bottom-up vs. top-down, co-limitation scenario; how do these would-be-hosts balance minimizing viral susceptibility with maximizing uptake of limiting nutrient(s)? This question has been addressed in the biological literature on evolutionary timescales for populations, but a shorter timescale, mechanistic perspective is lacking, and marine viral literature suggests the strong influence of additional factors, e.g. host size; while the literature on both nutrient uptake and host-virus interactions is expansive, their intersection, of ubiquitous relevance to marine environments, is understudied. I present a simple, mechanistic model from first principles to analyze the effect of this co-limitation scenario on individual growth, which suggests that in environments with high risk of viral invasion or spatial/temporal heterogeneity, an individual host’s growth rate may be optimized with respect to receptor coverage, producing top-down selective pressure on short timescales. The model has general applicability, is suggestive of hypotheses for empirical exploration, and can be extended to theoretical studies of more complex behaviors and systems.
    Description: This work was supported by the Massachusetts Institute of Technology Charles Vest Presidential Fellowship.
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    Tools for the microbiome : nano and beyond (2016)
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    Publication Date: 2022-05-25
    Description: © American Chemical Society, 2015. This article is posted here by permission of American Chemical Society; copying and redistribution for non-commercial research and education purposes only. The definitive version was published in ACS Nano 10 (2016): 6-37, doi:10.1021/acsnano.5b07826.
    Description: The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.
    Description: This research was supported by the Office of Naval Research Grant #N000141410051 (P.S.W., G.C.L.W., and T.Y.), the Genomic Science Program of the U.S. DOE-OBER,
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    Site-specific variation in gene expression from Symbiodinium spp. associated with offshore and inshore Porites astreoides in the lower Florida Keys is lost with bleaching and disease stress (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0173350, doi:10.1371/journal.pone.0173350.
    Description: Scleractinian coral are experiencing unprecedented rates of mortality due to increases in sea surface temperatures in response to global climate change. Some coral species however, survive high temperature events due to a reduced susceptibility to bleaching. We investigated the relationship between bleaching susceptibility and expression of five metabolically related genes of Symbiodinium spp. from the coral Porites astreoides originating from an inshore and offshore reef in the Florida Keys. The acclimatization potential of Symbiodinium spp. to changing temperature regimes was also measured via a two-year reciprocal transplant between the sites. Offshore coral fragments displayed significantly higher expression in Symbiodinium spp. genes PCNA, SCP2, G3PDH, PCP and psaE than their inshore counterparts (p〈0.05), a pattern consistent with increased bleaching susceptibility in offshore corals. Additionally, gene expression patterns in Symbiodinium spp. from site of origin were conserved throughout the two-year reciprocal transplant, indicating acclimatization did not occur within this multi-season time frame. Further, laboratory experiments were used to investigate the influence of acute high temperature (32°C for eight hours) and disease (lipopolysaccharide of Serratia marcescens) on the five metabolically related symbiont genes from the same offshore and inshore P. astreoides fragments. Gene expression did not differ between reef fragments, or as a consequence of acute exposure to heat or heat and disease, contrasting to results found in the field. Gene expression reported here indicates functional variation in populations of Symbiodinium spp. associated with P. astreoides in the Florida Keys, and is likely a result of localized adaptation. However, gene expression patterns observed in the lab imply that functional variation in zooxanthellae observed under conditions of chronic moderate stress is lost under the acute extreme conditions studied here.
    Description: Funding for this research was provided by Coastal Preservation network (KBS, BHS).
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    Characterization of trace metal content in the developing zebrafish embryo (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0179318, doi: 10.1371/journal.pone.0179318.
    Description: Trace metals are essential for health but toxic when present in excess. The maintenance of trace metals at physiologic levels reflects both import and export by cells and absorption and excretion by organs. The mechanism by which this maintenance is achieved in vertebrate organisms is incompletely understood. To explore this, we chose zebrafish as our model organism, as they are amenable to both pharmacologic and genetic manipulation and comprise an ideal system for genetic screens and toxicological studies. To characterize trace metal content in developing zebrafish, we measured levels of three trace elements, copper, zinc, and manganese, from the oocyte stage to 30 days post-fertilization using inductively coupled plasma mass spectrometry. Our results indicate that metal levels are stable until zebrafish can acquire metals from the environment and imply that the early embryo relies on maternal contribution of metals to the oocyte. We also measured metal levels in bodies and yolks of embryos reared in presence and absence of the copper chelator neocuproine. All three metals exhibited different relative abundances between yolks and bodies of embryos. While neocuproine treatment led to an expected phenotype of copper deficiency, total copper levels were unaffected, indicating that measurement of total metal levels does not equate with measurement of biologically active metal levels. Overall, our data not only can be used in the design and execution of genetic, physiologic, and toxicologic studies but also has implications for the understanding of vertebrate metal homeostasis.
    Description: This work was supported by the National Institutes of Health, R00 DK84122.
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    Photochemical oxidation of oil reduced the effectiveness of aerial dispersants applied in response to the Deepwater Horizon spill (2018)
    American Chemical Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Chemical Society, 2018. This is an open access article published under an ACS AuthorChoice License. The definitive version was published in Environmental Science and Technology Letters 5 (2018): 226–231, doi:10.1021/acs.estlett.8b00084.
    Description: Chemical dispersants are one of many tools used to mitigate the overall environmental impact of oil spills. In principle, dispersants break up floating oil into small droplets that disperse into the water column where they are subject to multiple fate and transport processes. The effectiveness of dispersants typically decreases as oil weathers in the environment. This decrease in effectiveness is often attributed to evaporation and emulsification, with the contribution of photochemical weathering assumed to be negligible. Here, we aim to test this assumption using Macondo well oil released during the Deepwater Horizon spill as a case study. Our results indicate that the effects of photochemical weathering on Deepwater Horizon oil properties and dispersant effectiveness can greatly outweigh the effects of evaporative weathering. The decrease in dispersant effectiveness after light exposure was principally driven by the decreased solubility of photo-oxidized crude oil residues in the solvent system that comprises COREXIT EC9500A. Kinetic modeling combined with geospatial analysis demonstrated that a considerable fraction of aerial applications targeting Deepwater Horizon surface oil had low dispersant effectiveness. Collectively, the results of this study challenge the paradigm that photochemical weathering has a negligible impact on the effectiveness of oil spill response and provide critical insights into the “window of opportunity” to apply chemical dispersants in response to oil spills in sunlit waters.
    Description: This work was supported, in part, by National Science Foundation Grant OCE-1333148, Gulf of Mexico Research Initiative Grants 015, SA 16-30, the DEEP-C consortium, and the Clark Family Foundation, Inc. EPA funding was provided to R.N.C. from the Oil Spill Liability Trust Fund.
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    African baobabs with false inner cavities : the radiocarbon investigation of the Lebombo Eco Trail Baobab (2015)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 10 (2015): e0117193, doi:10.1371/journal.pone.0117193.
    Description: The article reports the radiocarbon investigation results of the Lebombo Eco Trail tree, a representative African baobab from Mozambique. Several wood samples collected from the large inner cavity and from the outer part of the tree were investigated by AMS radiocarbon dating. According to dating results, the age values of all samples increase from the sampling point with the distance into the wood. For samples collected from the cavity walls, the increase of age values with the distance into the wood (up to a point of maximum age) represents a major anomaly. The only realistic explanation for this anomaly is that such inner cavities are, in fact, natural empty spaces between several fused stems disposed in a ring-shaped structure. We named them false cavities. Several important differences between normal cavities and false cavities are presented. Eventually, we dated other African baobabs with false inner cavities. We found that this new architecture enables baobabs to reach large sizes and old ages. The radiocarbon date of the oldest sample was 1425 ± 24 BP, which corresponds to a calibrated age of 1355 ± 15 yr. The dating results also show that the Lebombo baobab consists of five fused stems, with ages between 900 and 1400 years; these five stems build the complete ring. The ring and the false cavity closed 800–900 years ago. The results also indicate that the stems stopped growing toward the false cavity over the past 500 years.
    Description: The research was fully funded by the Romanian Ministry of National Education CNCS-UEFISCDI under grant PN-II-ID-PCE-2013-76.
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    An integrated assessment model for helping the United States sea scallop (Placopecten magellanicus) fishery plan ahead for ocean acidification and warming (2015)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This is an open access article, free of all copyright. The definitive version was published in PLoS One 10 (2015): e0124145, doi:10.1371/journal.pone.0124145.
    Description: Ocean acidification, the progressive change in ocean chemistry caused by uptake of atmospheric CO2, is likely to affect some marine resources negatively, including shellfish. The Atlantic sea scallop (Placopecten magellanicus) supports one of the most economically important single-species commercial fisheries in the United States. Careful management appears to be the most powerful short-term factor affecting scallop populations, but in the coming decades scallops will be increasingly influenced by global environmental changes such as ocean warming and ocean acidification. In this paper, we describe an integrated assessment model (IAM) that numerically simulates oceanographic, population dynamic, and socioeconomic relationships for the U.S. commercial sea scallop fishery. Our primary goal is to enrich resource management deliberations by offering both short- and long-term insight into the system and generating detailed policy-relevant information about the relative effects of ocean acidification, temperature rise, fishing pressure, and socioeconomic factors on the fishery using a simplified model system. Starting with relationships and data used now for sea scallop fishery management, the model adds socioeconomic decision making based on static economic theory and includes ocean biogeochemical change resulting from CO2 emissions. The model skillfully reproduces scallop population dynamics, market dynamics, and seawater carbonate chemistry since 2000. It indicates sea scallop harvests could decline substantially by 2050 under RCP 8.5 CO2 emissions and current harvest rules, assuming that ocean acidification affects P. magellanicus by decreasing recruitment and slowing growth, and that ocean warming increases growth. Future work will explore different economic and management scenarios and test how potential impacts of ocean acidification on other scallop biological parameters may influence the social-ecological system. Future empirical work on the effect of ocean acidification on sea scallops is also needed.
    Description: Cooley, Rheuban, and Doney were supported by NOAA Grant NA12NOS4780145 (www.noaa.gov) and the Center for Climate and Energy Decision Making (CEDM, NSF SES-0949710) (www.nsf.gov). Luu was supported by a WHOI Summer Student Fellowship (www.whoi.edu).
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    Destructive changes in the neuronal structure of the FVB/N mouse retina (2015)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0129719, doi: 10.1371/journal.pone.0129719.
    Description: We applied a series of selective antibodies for labeling the various cell types in the mammalian retina. These were used to identify the progressive loss of neurons in the FVB/N mouse, a model of early onset retinal degeneration produced by a mutation in the pde6b gene. The immunocytochemical studies, together with electroretinogram (ERG) recordings, enabled us to examine the time course of the degenerative changes that extended from the photoreceptors to the ganglion cells at the proximal end of the retina. Our study indicates that photoreceptors in FVB/N undergo a rapid degeneration within three postnatal weeks, and that there is a concomitant loss of retinal neurons in the inner nuclear layer. Although the loss of rods was detected at an earlier age during which time M- and S-opsin molecules were translocated to the cone nuclei; by 6 months all cones had also degenerated. Neuronal remodeling was also seen in the second-order neurons with horizontal cells sprouting processes proximally and dendritic retraction in rod-driven bipolar cells. Interestingly, the morphology of cone-driven bipolar cells were affected less by the disease process. The cellular structure of inner retinal neurons, i.e., ChAT amacrine cells, ganglion cells, and melanopsin-positive ganglion cells did not exhibit any gross changes of cell densities and appeared to be relatively unaffected by the massive photoreceptor degeneration in the distal retina. However, Muller cell processes began to express GFAP at their endfeet at p14, and it climbed progressively to the cell’s distal ends by 6 months. Our study indicates that FVB/N mouse provides a useful model with which to assess possible intervention strategies to arrest photoreceptor death in related diseases.
    Description: This study was supported by grants from the National Science Foundation (NSF, IOS-1021646, WS) and the National Eye Institute (NEI, EY 14161, WS).
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    AMS radiocarbon dating of large za baobabs (Adansonia za) of Madagascar (2016)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0146977, doi:10.1371/journal.pone.0146977 .
    Description: The article reports the radiocarbon investigation of Anzapalivoro, the largest za baobab (Adansonia za) specimen of Madagascar and of another za, namely the Big cistern baobab. Several wood samples collected from the large inner cavity and from the outer part/exterior of the tree were investigated by AMS (accelerator mass spectrometry) radiocarbon dating. For samples collected from the cavity walls, the age values increase with the distance into the wood up to a point of maximum age, after which the values decrease toward the outer part. This anomaly of age sequences indicates that the inner cavity of Anzapalivoro is a false cavity, practically an empty space between several fused stems disposed in a ring-shaped structure. The radiocarbon date of the oldest sample was 780 ± 30 bp, which corresponds to a calibrated age of around 735 yr. Dating results indicate that Anzapalivoro has a closed ring-shaped structure, which consists of 5 fused stems that close a false cavity. The oldest part of the biggest za baobab has a calculated age of 900 years. We also disclose results of the investigation of a second za baobab, the Big cistern baobab, which was hollowed out for water storage. This specimen, which consists of 4 fused stems, was found to be around 260 years old.
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    Biochemical mechanisms for geographical adaptations to novel toxin exposures in butterflyfish (2016)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The definitive version was published in PLoS One 11 (2016): e0154208, doi: 10.1371/journal.pone.0154208
    Description: Some species of butterflyfish have had preyed upon corals for millions of years, yet the mechanism of butterflyfish specialized coral feeding strategy remains poorly understood. Certain butterflyfish have the ability to feed on allelochemically rich soft corals, e.g. Sinularia maxima. Cytochrome P450 (CYP) is the predominant enzyme system responsible for the detoxification of dietary allelochemicals. CYP2-like and CYP3A-like content have been associated with butterflyfish that preferentially consumes allelochemically rich soft corals. To investigate the role of butterflyfish CYP2 and CYP3A enzymes in dietary preference, we conducted oral feeding experiments using homogenates of S. maxima and a toxin isolated from the coral in four species of butterflyfish with different feeding strategies. After oral exposure to the S. maxima toxin 5-episinulaptolide (5ESL), which is not normally encountered in the Hawaiian butterflyfish diet, an endemic specialist, Chaetodon multicinctus experienced 100% mortality compared to a generalist, Chaetodon auriga, which had significantly more (3–6 fold higher) CYP3A-like basal content and catalytic activity. The specialist, Chaetodon unimaculatus, which preferentially feed on S. maxima in Guam, but not in Hawaii, had 100% survival, a significant induction of 8–12 fold CYP3A-like content, and an increased ability (2-fold) to metabolize 5ESL over other species. Computer modeling data of CYP3A4 with 5ESL were consistent with microsomal transformation of 5ESL to a C15-16 epoxide from livers of C. unimaculatus. Epoxide formation correlated with CYP3A-like content, catalytic activity, induction, and NADPH-dependent metabolism of 5ESL. These results suggest a potentially important role for the CYP3A family in butterflyfish-coral diet selection through allelochemical detoxification.
    Description: This work received support from the following sources: Resource Allocation Program of the Agricultural Research Station for UCR to DS; Summer funding by Hilda and George Liebig Environmental Sciences Summer Fellowship and travel grant Albert March Environmental Sciences Scholarship from the University of California, Riverside; and the Chemistry and DMPK CORE of COBRE, P20GM104932 from the National Institute of General Medical Sciences (NIGMS), a component of the National Institutes of Health (NIH) supported the chemistry studies.
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    Smartphone-based distributed data collection enables rapid assessment of shorebird habitat suitability (2016)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright. The definitive version was published in PLoS ONE 11 (2016): e0164979, doi: 10.1371/journal.pone.0164979.
    Description: Understanding and managing dynamic coastal landscapes for beach-dependent species requires biological and geological data across the range of relevant environments and habitats. It is difficult to acquire such information; data often have limited focus due to resource constraints, are collected by non-specialists, or lack observational uniformity. We developed an open-source smartphone application called iPlover that addresses these difficulties in collecting biogeomorphic information at piping plover (Charadrius melodus) nest sites on coastal beaches. This paper describes iPlover development and evaluates data quality and utility following two years of collection (n = 1799 data points over 1500 km of coast between Maine and North Carolina, USA). We found strong agreement between field user and expert assessments and high model skill when data were used for habitat suitability prediction. Methods used here to develop and deploy a distributed data collection system have broad applicability to interdisciplinary environmental monitoring and modeling.
    Description: This work was supported by the North Atlantic Landscape Conservation Cooperative through the U.S. Department of the Interior Hurricane Sandy recovery program under the Disaster Relief Appropriations Act of 2013, and the U.S. Geological Survey Coastal and Marine Geology Program.
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    Strength in numbers : collaborative science for new experimental model systems (2018)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: The work is made available under the Creative Commons CCO public domain dedication.. The definitive version was published in PLoS Biology 16 (2018): e2006333, doi:10.1371/journal.pbio.2006333.
    Description: Our current understanding of biology is heavily based on a small number of genetically tractable model organisms. Most eukaryotic phyla lack such experimental models, and this limits our ability to explore the molecular mechanisms that ultimately define their biology, ecology, and diversity. In particular, marine protists suffer from a paucity of model organisms despite playing critical roles in global nutrient cycles, food webs, and climate. To address this deficit, an initiative was launched in 2015 to foster the development of ecologically and taxonomically diverse marine protist genetic models. The development of new models faces many barriers, some technical and others institutional, and this often discourages the risky, long-term effort that may be required. To lower these barriers and tackle the complexity of this effort, a highly collaborative community-based approach was taken. Herein, we describe this approach, the advances achieved, and the lessons learned by participants in this novel community-based model for research.
    Description: The research efforts, connections, and collaborations described in this paper and protocols.io (https://www.protocols.io/) were supported by the Gordon and Betty Moore Foundation’s Marine Microbiology Initiative.
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    Use of existing hydrographic infrastructure to forecast the environmental spawning conditions for Eastern Baltic cod (2018)
    Public Library of Science
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    Publication Date: 2022-04-26
    Description: The semi-enclosed nature and estuarine characteristics, together with its strongly alternating bathymetry, make the Baltic Sea prone to much stronger interannual variations in the abiotic environment, than other spawning habitats of Atlantic cod (Gadus morhua). Processes determining salinity and oxygen conditions in the basins are influenced both by long term gradual climate change, e.g. global warming, but also by short-term meteorological variations and events. Specifically one main factor influencing cod spawning conditions, the advection of highly saline and well-oxygenated water masses from the North Sea, is observed in irregular frequencies and causes strong interannual variations in stock productivity. This study investigates the possibility to use the available hydrographic process knowledge to predict the annual spawning conditions for Eastern Baltic cod in its most important spawning ground, the Bornholm Basin, only by salinity measurements from a specific location in the western Baltic. Such a prediction could serve as an environmental early warning indicator to inform stock assessment and management. Here we used a hydrodynamic model to hindcast hydrographic property fields for the last 40+ years. High and significant correlations were found for months early in the year between the 33m salinity level in the Arkona Basin and the oxygen-dependent cod spawning environment in the Bornholm Basin. Direct prediction of the Eastern Baltic cod egg survival in the Bornholm Basin based on salinity values in the Arkona Basin at the 33 m depth level is shown to be possible for eggs spawned by mid-age and young females, which currently predominate the stock structure. We recommend to routinely perform short-term predictions of the Eastern Baltic cod spawning environment, in order to generate environmental information highly relevant for stock dynamics. Our statistical approach offers the opportunity to make best use of permanently existing infrastructure in the western Baltic to timely provide scientific knowledge on the spawning conditions of Eastern Baltic cod. Furthermore it could be a tool to assist ecosystem-based fisheries management with a cost-effective implementation by including the short term predictions as a simple indicator in the annual assessments.
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    Aerobic Microbial Respiration In Oceanic Oxygen Minimum Zones (2015)
    Public Library of Science
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    Publication Date: 2022-02-18
    Description: Oxygen minimum zones are major sites of fixed nitrogen loss in the ocean. Recent studies have highlighted the importance of anaerobic ammonium oxidation, anammox, in pelagic nitrogen removal. Sources of ammonium for the anammox reaction, however, remain controversial, as heterotrophic denitrification and alternative anaerobic pathways of organic matter remineralization cannot account for the ammonium requirements of reported anammox rates. Here, we explore the significance of microaerobic respiration as a source of ammonium during organic matter degradation in the oxygen-deficient waters off Namibia and Peru. Experiments with additions of double-labelled oxygen revealed high aerobic activity in the upper OMZs, likely controlled by surface organic matter export. Consistently observed oxygen consumption in samples retrieved throughout the lower OMZs hints at efficient exploitation of vertically and laterally advected, oxygenated waters in this zone by aerobic microorganisms. In accordance, metagenomic and metatranscriptomic analyses identified genes encoding for aerobic terminal oxidases and demonstrated their expression by diverse microbial communities, even in virtually anoxic waters. Our results suggest that microaerobic respiration is a major mode of organic matter remineralization and source of ammonium (~45-100%) in the upper oxygen minimum zones, and reconcile hitherto observed mismatches between ammonium producing and consuming processes therein.
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    Hyperspectral lmaging Based Method for Rapid Detection of Microplastics in the Intestinal Tracts of Fish (2019)
    American Chemical Society
    In:  Environmental Science & Technology, 53 (9). pp. 5151-5158.
    Details
    Publication Date: 2022-01-31
    Description: Microplastics (MPs) in aquatic organisms are raising increasing concerns regarding their potential damage to ecosystems. To date, Raman and Fourier transform infrared spectroscopy techniques have been widely used for detection of MPs in aquatic organisms, which requires complex protocols of tissue digestion and MP separation and are time- and reagentconsuming. This novel approach directly separates, identifies, and characterizes MPs from the hyperspectral image (HSI) of the intestinal tract content in combination with a support vector machine classification model, instead of using the real digestion/separation protocols. The procedures of HSI acquisition ( 1 min) and data analysis (5 min) can be completed within 6 min plus the sample preparation and drying time (30 min) where necessary. This method achieved a promising efficiency (recall 〉98.80%, precision 〉96.22%) for identifying five types of MPs (particles 〉0.2 mm). Moreover, the method was also demonstrated to be effective on field fish from three marine fish species, revealing satisfying detection accuracy (particles 〉0.2 mm) comparable to Raman analysis. The present technique omits the digestion protocol (reagent free), thereby significantly reducing reagent consumption, saving time, and providing a rapid and efficient method for MP analysis.
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    Assessing SNP-markers to study population mixing and ecological adaptation in Baltic cod (2019)
    Public Library of Science
    In:  PLoS ONE, 14 (6). e0218127.
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    Publication Date: 2022-01-31
    Description: Atlantic cod (Gadus morhua) is a species of great ecological and economical importance in the Baltic Sea. Here, two genetically differentiated stocks, the western and the eastern Baltic cod, display substantial mechanical mixing, hampering our understanding of cod ecology and impeding stock assessments and management. Based on whole-genome re-sequencing data from reference samples obtained from the study area, we designed two different panels of Single Nucleotide Polymorphisms markers (SNPs), which take into account the exceptional genome architecture of cod. A minimum panel of 20 diagnostic SNPs and an extended panel (20 diagnostic and 18 biologically informative SNPs, 38 in total) were developed and validated to distinguish unambiguously between the western and the eastern Baltic cod stocks and to enable studies of local adaptation to the specific environment in the Baltic Sea, respectively. We tested both panels on cod sampled from the southern Baltic Sea (n = 603) caught in 2015 and 2016. Genotyping results showed that catches from the mixing zone in the Arkona Sea, were composed of similar proportions of individuals of the western and the eastern stock. Catches from adjacent areas to the east, the Bornholm Basin and Gdańsk Deep, were exclusively composed of eastern Baltic cod, whereas catches from adjacent western areas (Belt Sea and Öresund) were composed of western Baltic cod. Interestingly, the two Baltic cod stocks showed strong genetic differences at loci associated with life-history trait candidate genes, highlighting the species’ potential for ecological adaptation even at small geographical scales. The minimum and the extended panel of SNP markers presented in this study provide powerful tools for future applications in research and fisheries management to further illuminate the mixing dynamics of cod in the Baltic Sea and to better understand Baltic cod ecology.
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    Year-round distribution, activity patterns and habitat use of a poorly studied pelagic seabird, the fluttering shearwater Puffinus gavia (2019)
    Public Library of Science
    In:  PLoS ONE, 14 (8). e0219986.
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    Publication Date: 2022-01-31
    Description: We present the first study to examine the year-round distribution, activity patterns, and habitat use of one of New Zealand's most common seabirds, the fluttering shearwater (Puffinus gavia). Seven adults from Burgess Island, in the Hauraki Gulf, and one individual from Long Island, in the Marlborough Sounds, were successfully tracked with combined light-saltwater immersion loggers for one to three years. Our tracking data confirms that fluttering shearwaters employ different overwintering dispersal strategies, where three out of eight individuals, for at least one of the three years when they were being tracked, crossed the Tasman Sea to forage over coastal waters along eastern Tasmania and southeastern Australia. Resident birds stayed confined to waters of northern and central New Zealand year-round. Although birds frequently foraged over pelagic shelf waters, the majority of tracking locations were found over shallow waters close to the coast. All birds foraged predominantly in daylight and frequently visited the colony at night throughout the year. We found no significant inter-seasonal differences in the activity patterns, or between migratory and resident individuals. Although further studies of inter-colony variation in different age groups will be necessary, this study presents novel insights into year-round distribution, activity patterns and habitat use of the fluttering shearwater, which provide valuable baseline information for conservation as well as for further ecological studies.
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    Human Consumption of Microplastics (2019)
    American Chemical Society
    In:  Environmental Science & Technology, 53 (12). pp. 7068-7074.
    Details
    Publication Date: 2022-01-31
    Description: Microplastics are ubiquitous across ecosystems, yet the exposure risk to humans is unresolved. Focusing on the American diet, we evaluated the number of microplastic particles in commonly consumed foods in relation to their recommended daily intake. The potential for microplastic inhalation and how the source of drinking water may affect microplastic consumption were also explored. Our analysis used 402 data points from 26 studies, which represents over 3600 processed samples. Evaluating approximately 15% of Americans’ caloric intake, we estimate that annual microplastics consumption ranges from 39000 to 52000 particles depending on age and sex. These estimates increase to 74000 and 121000 when inhalation is considered. Additionally, individuals who meet their recommended water intake through only bottled sources may be ingesting an additional 90000 microplastics annually, compared to 4000 microplastics for those who consume only tap water. These estimates are subject to large amounts of variation; however, given methodological and data limitations, these values are likely underestimates.
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    On the impact of Citizen Science-derived data quality on deep learning based classification in marine images (2019)
    Public Library of Science
    In:  PLOS ONE, 14 (6). e0218086.
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    Publication Date: 2022-01-31
    Description: The evaluation of large amounts of digital image data is of growing importance for biology, including for the exploration and monitoring of marine habitats. However, only a tiny percentage of the image data collected is evaluated by marine biologists who manually interpret and annotate the image contents, which can be slow and laborious. In order to overcome the bottleneck in image annotation, two strategies are increasingly proposed: “citizen science” and “machine learning”. In this study, we investigated how the combination of citizen science, to detect objects, and machine learning, to classify megafauna, could be used to automate annotation of underwater images. For this purpose, multiple large data sets of citizen science annotations with different degrees of common errors and inaccuracies observed in citizen science data were simulated by modifying “gold standard” annotations done by an experienced marine biologist. The parameters of the simulation were determined on the basis of two citizen science experiments. It allowed us to analyze the relationship between the outcome of a citizen science study and the quality of the classifications of a deep learning megafauna classifier. The results show great potential for combining citizen science with machine learning, provided that the participants are informed precisely about the annotation protocol. Inaccuracies in the position of the annotation had the most substantial influence on the classification accuracy, whereas the size of the marking and false positive detections had a smaller influence.
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    Life histories of Antarctic incirrate octopods (Cephalopoda: Octopoda) (2019)
    Public Library of Science
    In:  PLoS ONE, 14 (7). e0219694.
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    Publication Date: 2022-01-31
    Description: As a general trend in the life history of marine organisms, species inhabiting cold waters have reduced growth rates and increased lifespans. Studies based on egg sizes and brooding times of deep-sea and polar octopods support this hypothesis, but empirical data on growth are still scarce. To test the hypothesis that octopods inhabiting cold waters (〈 3°C) live longer than temperate and warm water species, this study investigated size-at-age, maturation and growth rates in incirrate Antarctic octopods. Octopod age was estimated via the interpretation and quantification of beak growth increments, which in shallow water octopods have been validated to be formed on a daily basis. Specimens from the families Megaleledonidae (Adelieledone spp., Pareledone spp. and Megaleledone setebos) and Enteroctopodidae (Muusoctopus rigbyae) were collected on the shelf and slope regions off the Antarctic Peninsula during a cruise in 2012. Examined specimens included early juveniles to animals in advanced maturity. The total number of growth increments ranged from 192–599 in Pareledone aequipapillae (body mass [BM] 2–109 g), 182–431 in Pareledone charcoti (BM 5–124 g), 98–906 in M. setebos (BM 10–6000 g) and 207–425 in M. rigbyae (BM 24–256 g). After the cruise, eleven specimens of P. charcoti were kept alive in captivity for more than 12 months and these animals had 219–364 growth increments, suggesting that increment formation in this species takes longer than one day. The complex population structure (size, age and maturity range) of the specimens that were captured during a relatively short time, the number of beak increments quantified, and the preliminary validation observations indicate that Antarctic octopods do not deposit increments daily, and may have lifespans exceeding 3 years. These findings corroborate the general trend that cold water molluscs have a longer lifespan than their warm water relatives.
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  • 70
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    Year-round distribution, activity patterns and habitat use of a poorly studied pelagic seabird, the fluttering shearwater Puffinus gavia (2019)
    Public Library of Science
    In:  PLoS ONE, 14 (8). e0219986.
    Details
    Publication Date: 2022-01-31
    Description: We present the first study to examine the year-round distribution, activity patterns, and habitat use of one of New Zealand’s most common seabirds, the fluttering shearwater (Puffinus gavia). Seven adults from Burgess Island, in the Hauraki Gulf, and one individual from Long Island, in the Marlborough Sounds, were successfully tracked with combined light-saltwater immersion loggers for one to three years. Our tracking data confirms that fluttering shearwaters employ different overwintering dispersal strategies, where three out of eight individuals, for at least one of the three years when they were being tracked, crossed the Tasman Sea to forage over coastal waters along eastern Tasmania and southeastern Australia. Resident birds stayed confined to waters of northern and central New Zealand year-round. Although birds frequently foraged over pelagic shelf waters, the majority of tracking locations were found over shallow waters close to the coast. All birds foraged predominantly in daylight and frequently visited the colony at night throughout the year. We found no significant inter-seasonal differences in the activity patterns, or between migratory and resident individuals. Although further studies of inter-colony variation in different age groups will be necessary, this study presents novel insights into year-round distribution, activity patterns and habitat use of the fluttering shearwater, which provide valuable baseline information for conservation as well as for further ecological studies.
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  • 71
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    Rigorous Physicochemical Framework for Metal Ion Binding by Aqueous Nanoparticulate Humic Substances: Implications for Speciation Modeling by the NICA-Donnan and WHAM Codes (2019)
    American Chemical Society
    In:  Environmental Science & Technology, 53 (15). pp. 8516-8532.
    Details
    Publication Date: 2022-01-31
    Description: Latest knowledge on the reactivity of charged nanoparticulate complexants toward aqueous metal ions is discussed in mechanistic detail. We present a rigorous generic description of electrostatic and chemical contributions to metal ion binding by nanoparticulate complexants, and their dependence on particle size, particle type (i.e., reactive sites distributed within the particle body or confined to the surface), ionic strength of the aqueous medium, and the nature of the metal ion. For the example case of soft environmental particles such as fulvic and humic acids, practical strategies are delineated for determining intraparticulate metal ion speciation, and for evaluating intrinsic chemical binding affinities and heterogeneity. The results are compared with those obtained by popular codes for equilibrium speciation modeling (namely NICA-Donnan and WHAM). Physicochemical analysis of the discrepancies generated by these codes reveals the a priori hypotheses adopted therein and the inappropriateness of some of their key parameters. The significance of the characteristic time scales governing the formation and dissociation rates of metal−nanoparticle complexes in defining the relaxation properties and the complete equilibration of the metal− nanoparticulate complex dispersion is described. The dynamic features of nanoparticulate complexes are also discussed in the context of predictions of the labilities and bioavailabilities of the metal species.
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  • 72
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    Diet and stable isotope analyses reveal the feeding ecology of the orangeback squid Sthenoteuthis pteropus (Steenstrup 1855) (Mollusca, Ommastrephidae) in the eastern tropical Atlantic (2017)
    Public Library of Science
    In:  PLoS ONE, 12 (12). e0189691.
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    Publication Date: 2021-05-19
    Description: In the eastern tropical Atlantic, the orangeback flying squid Sthenoteuthis pteropus (Steenstrup 1855) (Cephalopoda, Ommastrephidae) is a dominant species of the epipelagic nekton community. This carnivore squid has a short lifespan and is one of the fastest-growing squids. In this study, we characterise the role of S. pteropus in the pelagic food web of the eastern tropical Atlantic by investigating its diet and the dynamics of its feeding habits throughout its ontogeny and migration. During three expeditions in the eastern tropical Atlantic in 2015, 129 specimens were caught by hand jigging. Stomach content analyses (via visual identification and DNA barcoding) were combined with stable isotope data (∂15N and ∂13C) of muscle tissue to describe diet, feeding habits and trophic ecology of S. pteropus. Additionally, stable isotope analyses of incremental samples along the squid’s gladius—the chitinous spiniform structure supporting the muscles and organs—were carried out to explore possible diet shifts through ontogeny and migration. Our results show that S. pteropus preys mainly on myctophid fishes (e.g. Myctophum asperum, Myctophum nitidulum, Vinciguerria spp.), but also on other teleost species, cephalopods (e.g. Enoploteuthidae, Bolitinidae, Ommastrephidae), crustaceans and possibly on gelatinous zooplankton as well. The squid shows a highly opportunistic feeding behaviour that includes cannibalism. Our study indicates that the trophic position of S. pteropus may increase by approximately one trophic level from a mantle length of 15 cm to 47 cm. The reconstructed isotope-based feeding chronologies of the gladii revealed high intra- and inter-individual variability in the squid’s trophic position and foraging area. These findings are not revealed by diet or muscle tissue stable isotope analysis. This suggests a variable and complex life history involving individual variation and migration. The role of S. pteropus in transferring energy and nutrients from lower to higher trophic levels may be underestimated and important for understanding how a changing ocean impacts food webs in the eastern Atlantic.
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  • 73
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    Abundance of the iron containing biomolecule, heme b, during the progression of a spring phytoplankton bloom in a mesocosm experiment (2017)
    Public Library of Science
    In:  PLoS ONE, 12 (4). e0176268.
    Details
    Publication Date: 2021-04-23
    Description: Concentrations of heme b were determined in a mesocosm experiment situated in Gullmar Fjord off Sweden. The mesocosm experiment lasted for ca. one hundred days and was characterised by the growth of a primary nutrient replete and a secondary nutrient deplete phytoplankton bloom. Heme b varied between 40 ± 10 pmol L-1 in the prebloom period up to a maximum of 700 ± 400 pmol L-1 just prior to the time of the primary chlorophyll a maximum. Thereafter, heme b concentrations decreased again to an average of 120 ± 60 pmol L-1. When normalised to total particulate carbon, heme b was most abundant during the initiation of the nutrient replete spring bloom, when ratios reached 52 ± 24 μmol mol-1; ten times higher than values observed both pre and post the primary bloom. Concentrations of heme b correlated with those of chlorophyll a. Nevertheless, differences were observed in the relative concentrations of the two parameters, with heme b concentrations increasing relative to chlorophyll a during the growth of the primary bloom, decreasing over the period of the secondary bloom and increasing again through the latter period of the experiment. Heme b abundance was therefore influenced by nutrient concentrations and also likely by changing community composition. In half of the mesocosms, pCO2 was elevated and maintained at ca.1000 μatm, however we observed no significant differences between heme b in plus or ambient pCO2 mesocosms, either in absolute terms, or relative to total particulate carbon and chlorophyll a. The results obtained in this study contribute to our understanding of the distribution of this significant component of the biogenic iron pool, and provide an iron replete coastal water end member that aids the interpretation of the distributions of heme b in more iron deplete open ocean waters.
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  • 74
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    Enhanced transfer of organic matter to higher trophic levels caused by ocean acidification and its implications for export production: A mass balance approach (2018)
    Public Library of Science
    In:  PLoS ONE, 13 (5). e0197502.
    Details
    Publication Date: 2021-04-23
    Description: Ongoing acidification of the ocean through uptake of anthropogenic CO2 is known to affect marine biota and ecosystems with largely unknown consequences for marine food webs. Changes in food web structure have the potential to alter trophic transfer, partitioning, and biogeochemical cycling of elements in the ocean. Here we investigated the impact of realistic end-of-the-century CO2 concentrations on the development and partitioning of the carbon, nitrogen, phosphorus, and silica pools in a coastal pelagic ecosystem (Gullmar Fjord, Sweden). We covered the entire winter-to-summer plankton succession (100 days) in two sets of five pelagic mesocosms, with one set being CO2 enriched (~760 μatm pCO2) and the other one left at ambient CO2 concentrations. Elemental mass balances were calculated and we highlight important challenges and uncertainties we have faced in the closed mesocosm system. Our key observations under high CO2 were: (1) A significantly amplified transfer of carbon, nitrogen, and phosphorus from primary producers to higher trophic levels, during times of regenerated primary production. (2) A prolonged retention of all three elements in the pelagic food web that significantly reduced nitrogen and phosphorus sedimentation by about 11 and 9%, respectively. (3) A positive trend in carbon fixation (relative to nitrogen) that appeared in the particulate matter pool as well as the downward particle flux. This excess carbon counteracted a potential reduction in carbon sedimentation that could have been expected from patterns of nitrogen and phosphorus fluxes. Our findings highlight the potential for ocean acidification to alter partitioning and cycling of carbon and nutrients in the surface ocean but also show that impacts are temporarily variable and likely depending upon the structure of the plankton food web.
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  • 75
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    Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak (2017)
    Public Library of Science
    In:  PLoS ONE, 12 (4). e0175808.
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    Publication Date: 2021-04-23
    Description: The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.
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  • 76
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    Influence of Ocean Acidification on a Natural Winter-to-Summer Plankton Succession: First Insights from a Long-Term Mesocosm Study Draw Attention to Periods of Low Nutrient Concentrations (2016)
    Public Library of Science
    In:  PLoS ONE, 11 (8). e0159068.
    Details
    Publication Date: 2021-04-23
    Description: Every year, the oceans absorb about 30% of anthropogenic carbon dioxide (CO2) leading to a re-equilibration of the marine carbonate system and decreasing seawater pH. Today, there is increasing awareness that these changes–summarized by the term ocean acidification (OA)–could differentially affect the competitive ability of marine organisms, thereby provoking a restructuring of marine ecosystems and biogeochemical element cycles. In winter 2013, we deployed ten pelagic mesocosms in the Gullmar Fjord at the Swedish west coast in order to study the effect of OA on plankton ecology and biogeochemistry under close to natural conditions. Five of the ten mesocosms were left unperturbed and served as controls (~380 μatm pCO2), whereas the others were enriched with CO2-saturated water to simulate realistic end-of-the-century carbonate chemistry conditions (~760 μatm pCO2). We ran the experiment for 113 days which allowed us to study the influence of high CO2 on an entire winter-to-summer plankton succession and to investigate the potential of some plankton organisms for evolutionary adaptation to OA in their natural environment. This paper is the first in a PLOS collection and provides a detailed overview on the experimental design, important events, and the key complexities of such a “long-term mesocosm” approach. Furthermore, we analyzed whether simulated end-of-the-century carbonate chemistry conditions could lead to a significant restructuring of the plankton community in the course of the succession. At the level of detail analyzed in this overview paper we found that CO2-induced differences in plankton community composition were non-detectable during most of the succession except for a period where a phytoplankton bloom was fueled by remineralized nutrients. These results indicate: (1) Long-term studies with pelagic ecosystems are necessary to uncover OA-sensitive stages of succession. (2) Plankton communities fueled by regenerated nutrients may be more responsive to changing carbonate chemistry than those having access to high inorganic nutrient concentrations and may deserve particular attention in future studies.
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  • 77
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    Growth performance and survival of larval Atlantic herring, under the combined effects of elevated temperatures and CO2 (2018)
    Public Library of Science
    In:  PLoS ONE, 13 (1). e0191947.
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    Publication Date: 2021-03-19
    Description: In the coming decades, environmental change like warming and acidification will affect life in the ocean. While data on single stressor effects on fish are accumulating rapidly, we still know relatively little about interactive effects of multiple drivers. Of particular concern in this context are the early life stages of fish, for which direct effects of increased CO2 on growth and development have been observed. Whether these effects are further modified by elevated temperature was investigated here for the larvae of Atlantic herring (Clupea harengus), a commercially important fish species. Over a period of 32 days, larval survival, growth in size and weight, and instantaneous growth rate were assessed in a crossed experimental design of two temperatures (10°C and 12°C) with two CO2 levels (400 μatm and 900 μatm CO2) at food levels mimicking natural levels using natural prey. Elevated temperature alone led to increased swimming activity, as well as decreased survival and instantaneous growth rate (Gi). The comparatively high sensitivity to elevated temperature in this study may have been influenced by low food levels offered to the larvae. Larval size, Gi and swimming activity were not affected by CO2, indicating tolerance of this species to projected "end of the century" CO2 levels. A synergistic effect of elevated temperature and CO2 was found for larval weight, where no effect of elevated CO2 concentrations was detected in the 12°C treatment, but a negative CO2 effect was found in the 10°C treatment. Contrasting CO2 effects were found for survival between the two temperatures. Under ambient CO2 conditions survival was increased at 12°C compared to 10°C. In general, CO2 effects were minor and considered negligible compared to the effect of temperature under these mimicked natural food conditions. These findings emphasize the need to include biotic factors such as energy supply via prey availability in future studies on interactive effects of multiple stressors. © 2018 Sswat et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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    In situ observations of coral bleaching in the central Saudi Arabian Red Sea during the 2015/2016 global coral bleaching event (2018)
    Public Library of Science
    In:  PLoS ONE, 13 (4). e0195814.
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    Publication Date: 2021-02-08
    Description: Coral bleaching continues to be one of the most devastating and immediate impacts of climate change on coral reef ecosystems worldwide. In 2015, a major bleaching event was declared as the “3rd global coral bleaching event” by the United States National Oceanic and Atmospheric Administration, impacting a large number of reefs in every major ocean. The Red Sea was no exception, and we present herein in situ observations of the status of coral reefs in the central Saudi Arabian Red Sea from September 2015, following extended periods of high temperatures reaching upwards of 32.5C in our study area. We examined eleven reefs using line-intercept transects at three different depths, including all reefs that were surveyed during a previous bleaching event in 2010. Bleaching was most prevalent on inshore reefs (55.6% ± 14.6% of live coral cover exhibited bleaching) and on shallower transects (41% ± 10.2% of live corals surveyed at 5m depth) within reefs. Similar taxonomic groups (e.g., Agariciidae) were affected in 2015 and in 2010. Most interestingly, Acropora and Porites had similar bleaching rates (~30% each) and similar relative coral cover (~7% each) across all reefs in 2015. Coral genera with the highest levels of bleaching (〉60%) were also among the rarest (〈1% of coral cover) in 2015. While this bodes well for the relative retention of coral cover, it may ultimately lead to decreased species richness, often considered an important component of a healthy coral reef. The resultant long-term changes in these coral reef communities remain to be seen.
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  • 79
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    Effect of temperature on the accumulation of marine biogenic gels in the surface microlayer near the outlet of nuclear power plants and adjacent areas in the Daya Bay, China (2018)
    Public Library of Science
    In:  PLoS ONE, 13 (6). e0198735.
    Details
    Publication Date: 2021-02-08
    Description: The surface microlayer (SML) in marine systems is often characterized by an enrichment of biogenic, gel-like particles, such as the polysaccharide-containing transparent exopolymer particles (TEP) and the protein-containing Coomassie stainable particles (CSP). This study investigated the distribution of TEP and CSP, in the SML and underlying water, as well as their bio-physical controlling factors in Daya Bay, an area impacted by warm discharge from two Nuclear power plants (Npp’s) and aquaculture during a research cruise in July 2014. The SML had higher proportions of cyanobacteria and of pico-size Chl a contrast to the underlayer water, particularly at the nearest outlet station characterized by higher temperature. Diatoms, dinoflagellates and chlorophyll a were depleted in the SML. Both CSP and TEP abundance and total area were enriched in the SML relative to the underlying water, with enrichment factors (EFs) of 1.5–3.4 for CSP numbers and 1.32–3.2 for TEP numbers. Although TEP and CSP showed highest concentration in the region where high productivity and high nutrient concertation were observed, EFs of gels and of dissolved organic carbon (DOC) and dissolved acidic polysaccharide (〉 1 kDa), exhibited higher values near the outlet of the Npp’s than in the adjacent waters. The positive relation between EF’s of gels and temperature and the enrichment of cyanobacteria in the SML may be indicative of future conditions in a warmer ocean, suggesting potential effects on adjusting phytoplankton community, biogenic element cycling and air-sea exchange processes
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  • 80
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    Increased fitness of a key appendicularian zooplankton species under warmer, acidified seawater conditions (2018)
    Public Library of Science
    In:  PLoS ONE, 13 (1). e0190625.
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    Publication Date: 2021-02-08
    Description: Ocean warming and acidification (OA) may alter the fitness of species in marine pelagic ecosystems through community effects or direct physiological impacts. We used the zooplanktonic appendicularian, Oikopleura dioica, to assess temperature and pH effects at mesocosm and microcosm scales. In mesocosms, both OA and warming positively impacted O. dioica abundance over successive generations. In microcosms, the positive impact of OA, was observed to result from increased fecundity. In contrast, increased pH, observed for example during phytoplankton blooms, reduced fecundity. Oocyte fertility and juvenile development were equivalent under all pH conditions, indicating that the positive effect of lower pH on O. dioica abundance was principally due to increased egg number. This effect was influenced by food quantity and quality, supporting possible improved digestion and assimilation at lowered pH. Higher temperature resulted in more rapid growth, faster maturation and earlier reproduction. Thus, increased temperature and reduced pH had significant positive impacts on O. dioica fitness through increased fecundity and shortened generation time, suggesting that predicted future ocean conditions may favour this zooplankton species. © 2018 Bouquet et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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  • 81
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    Interannual changes in zooplankton echo subtropical and high latitude climate effects in the southern East China Sea (2018)
    Public Library of Science
    In:  PLoS ONE, 13 (5). e0197382.
    Details
    Publication Date: 2021-02-08
    Description: Climate variability plays a central role in the dynamics of marine pelagic ecosystems shaping the structure and abundance changes of plankton communities, thereby affecting energy pathways and biogeochemical fluxes in the ocean. Here we have investigated complex interactions driven a climate-hydrology-plankton system in the southern East China Sea over the period 2000 to 2012. In particular, we aimed at quantifying the influence of climate phenomena playing out in tropical (El Nino 3.4) and middle-high latitudes (East Asia Winter Monsoon, EAWM, and Pacific Decadal Oscillation, PDO) on pelagic copepods. We found that the EAWM and El Nino 3.4 showed a non-stationary and non-linear relationship with local temperature variability. In the two cases, the strength of the relationship, as indexed by the wavelet coherence analysis, decreased along with the positive phase of the PDO. Likewise, the influence of EAWM and El Nino3.4 on copepods exhibited a non-stationary link that changed along with the PDO state. Indeed, copepods and EAWM were closely related during the positive phase, while the link copepods–El Nino 3.4 was stronger during the negative phase. Our results pointed out cascading effects from climate to plankton driven by the positive phase of the PDO through its effect on temperature conditions, and likely through a larger southward transport of nutrient-rich water masses to northern Taiwan and the Taiwan Strait. We suggest a chain of mechanisms whereby the PDO shapes interannual dynamics of pelagic copepods and highlight that these results have implications for integrative management measures, as pelagic copepods plays a prominent role in food web dynamics and for harvested fish in the East China Sea. © 2018 Molinero et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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  • 82
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    Long-term exposure to acidification disrupts reproduction in a marine invertebrate (2018)
    Public Library of Science
    In:  PLoS ONE, 13 (2). e0192036.
    Details
    Publication Date: 2021-02-08
    Description: Climate change research is advancing to more complex and more comprehensive studies that include long-term experiments, multiple life-history stages, multi-population, and multi-trait approaches. We used a population of the barnacle Balanus improvisus known to be sensitive to short-term acidification to determine its potential for long-term acclimation to acidification. We reared laboratory-bred individuals (as singles or pairs), and field-collected assemblages of barnacles, at pH 8.1 and 7.5 ( 400 and 1600 ?atm pCO2 respectively) for up to 16 months. Acidification caused strong mortality and reduced growth rates. Acidification suppressed respiration rates and induced a higher feeding activity of barnacles after 6 months, but this suppression of respiration rate was absent after 15 months. Laboratory-bred barnacles developed mature gonads only when they were held in pairs, but nonetheless failed to produce fertilized embryos. Field-collected barnacles reared in the laboratory for 8 months at the same pH’s developed mature gonads, but only those in pH 8.1 produced viable embryos and larvae. Because survivors of long-term acidification were not capable of reproducing, this demonstrates that B. improvisus can only partially acclimate to long-term acidification. This represents a clear and significant bottleneck in the ontogeny of this barnacle population that may limit its potential to persist in a future ocean.
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  • 83
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    Anaerobic methane oxidation inducing carbonate precipitation at abiogenic methane seeps in the Tuscan archipelago (Italy) (2018)
    Public Library of Science
    In:  PLoS ONE, 13 (12). e0207305.
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    Publication Date: 2021-02-08
    Description: Seepage of methane (CH4) on land and in the sea may significantly affect Earth's biogeochemical cycles. However processes of CH4 generation and consumption, both abiotic and microbial, are not always clear. We provide new geochemical and isotope data to evaluate if a recently discovered CH4 seepage from the shallow seafloor close to the Island of Elba (Tuscany) and two small islands nearby are derived from abiogenic or biogenic sources and whether carbonate encrusted vents are the result of microbial or abiotic processes. Emission of gas bubbles (predominantly CH4) from unlithified sands was observed at seven spots in an area of 100 m(2) at Pomonte (Island of Elba), with a total rate of 234 ml m(-2) d(-1). The measured carbon isotope values of CH4 of around -18 parts per thousand (VPDB) in combination with the measured delta H-2 value of -120 parts per thousand (VSMOW) and the inverse correlation of delta C-13-value with carbon number of hydrocarbon gases are characteristic for sites of CH4 formation through abiogenic processes, specifically abiogenic formation of CH4 via reduction of CO2 by H-2. The H-2 for methanogenesis likely derives from ophiolitic host rock within the Ligurian accretionary prism. The lack of hydrothermal activity allows CH4 gas to become decoupled from the stagnant aqueous phase. Hence no hyperalkaline fluid is currently released at the vent sites. Within the seep area a decrease in porewater sulphate concentrations by ca. 5 mmol/l relative to seawater and a concomitant increase in sulphide and dissolved inorganic carbon (DIC) indicate substantial activity of sulphate-dependent anaerobic oxidation of methane (AOM). In absence of any other dissimilatory pathway, the delta C-13-values between -17 and -5 parts per thousand in dissolved inorganic carbon and aragonite cements suggest that the inorganic carbon is largely derived from CH4. The formation of seep carbonates is thus microbially induced via anaerobic oxidation of abiotic CH4.
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    MAIA—A machine learning assisted image annotation method for environmental monitoring and exploration (2018)
    Public Library of Science
    In:  PLoS ONE, 13 (11). e0207498.
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    Publication Date: 2021-02-08
    Description: Digital imaging has become one of the most important techniques in environmental monitoring and exploration. In the case of the marine environment, mobile platforms such as autonomous underwater vehicles (AUVs) are now equipped with high-resolution cameras to capture huge collections of images from the seabed. However, the timely evaluation of all these images presents a bottleneck problem as tens of thousands or more images can be collected during a single dive. This makes computational support for marine image analysis essential. Computer-aided analysis of environmental images (and marine images in particular) with machine learning algorithms is promising, but challenging and different to other imaging domains because training data and class labels cannot be collected as efficiently and comprehensively as in other areas. In this paper, we present Machine learning Assisted Image Annotation (MAIA), a new image annotation method for environmental monitoring and exploration that overcomes the obstacle of missing training data. The method uses a combination of autoencoder networks and Mask Region-based Convolutional Neural Network (Mask R-CNN), which allows human observers to annotate large image collections much faster than before. We evaluated the method with three marine image datasets featuring different types of background, imaging equipment and object classes. Using MAIA, we were able to annotate objects of interest with an average recall of 84.1% more than twice as fast as compared to “traditional” annotation methods, which are purely based on software-supported direct visual inspection and manual annotation. The speed gain increases proportionally with the size of a dataset. The MAIA approach represents a substantial improvement on the path to greater efficiency in the annotation of large benthic image collections.
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  • 85
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    Contrasting seasonal responses in dinitrogen fixation between shallow and deep-water colonies of the model coral Stylophora pistillata in the northern Red Sea (2018)
    Public Library of Science
    In:  PLoS ONE, 13 (6). e0199022.
    Details
    Publication Date: 2021-02-08
    Description: Tropical corals are often associated with dinitrogen (N-2)-fixing bacteria (diazotrophs), and seasonal changes in key environmental parameters, such as dissolved inorganic nitrogen (DIN) availability and seawater temperature, are known to affect N-2 fixation in coral-microbial holobionts. Despite, then, such potential for seasonal and depth-related changes in N-2 fixation in reef corals, such variation has not yet been investigated. Therefore, this study quantified seasonal (winter vs. summer) N-2 fixation rates associated with the reef-building coral Stylophora pistillata collected from depths of 5, 10 and 20 m in the northern Gulf of Aqaba (Red Sea). Findings revealed that corals from all depths exhibited the highest N-2 fixation rates during the oligotrophic summer season, when up to 11% of their photo-metabolic nitrogen demand (CPND) could be met by N-2 fixation. While N-2 fixation remained seasonally stable for deep corals (20 m), it significantly decreased for the shallow corals (5 and 10 m) during the DIN-enriched winter season, accounting for less than 2% of the corals' CPND. This contrasting seasonal response in N-2 fixation across corals of different depths could be driven by 1) release rates of coral-derived organic matter, 2) the community composition of the associated diazotrophs, and/or 3) nutrient acquisition by the Symbiodinium community.
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  • 86
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    Beached bachelors: An extensive study on the largest recorded sperm whale Physeter macrocephalus mortality event in the North Sea (2018)
    Public Library of Science
    In:  PLoS ONE, 13 (8). e0201221.
    Details
    Publication Date: 2021-02-08
    Description: Between the 8th January and the 25th February 2016, the largest sperm whale Physeter macrocephalus mortality event ever recorded in the North Sea occurred with 30 sperm whales stranding in five countries within six weeks. All sperm whales were immature males. Groups were stratified by size, with the smaller animals stranding in the Netherlands, and the largest in England. The majority (n = 27) of the stranded animals were necropsied and/or sampled, allowing for an international and comprehensive investigation into this mortality event. The animals were in fair to good nutritional condition and, aside from the pathologies caused by stranding, did not exhibit significant evidence of disease or trauma. Infectious agents were found, including various parasite species, several bacterial and fungal pathogens and a novel alphaherpesvirus. In nine of the sperm whales a variety of marine litter was found. However, none of these findings were considered to have been the primary cause of the stranding event. Potential anthropogenic and environmental factors that may have caused the sperm whales to enter the North Sea were assessed. Once sperm whales enter the North Sea and head south, the water becomes progressively shallower (〈40 m), making this region a global hotspot for sperm whale strandings. We conclude that the reasons for sperm whales to enter the southern North Sea are the result of complex interactions of extrinsic environmental factors. As such, these large mortality events seldom have a single ultimate cause and it is only through multidisciplinary, collaborative approaches that potentially multifactorial large-scale stranding events can be effectively investigated.
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  • 87
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    Salinity reduction benefits European eel larvae: Insights at the morphological and molecular level (2018)
    Public Library of Science
    In:  PLoS ONE, 13 (6). e0198294.
    Details
    Publication Date: 2021-02-08
    Description: European eel (Anguilla anguilla) is a euryhaline species, that has adapted to cope with both, hyper- and hypo-osmotic environments. This study investigates the effect of salinity, from a morphological and molecular point of view on European eel larvae reared from 0 to 12 days post hatch (dph). Offspring reared in 36 practical salinity units (psu; control), were compared with larvae reared in six scenarios, where salinity was decreased on 0 or 3 dph and in rates of 1, 2 or 4 psu/day, towards iso-osmotic conditions. Results showed that several genes relating to osmoregulation (nkcc2α, nkcc2β, aqp1dup, aqpe), stress response (hsp70, hsp90), and thyroid metabolism (thrαA, thrαB, thrβB, dio1, dio2, dio3) were differentially expressed throughout larval development, while nkcc1α, nkcc2β, aqp3, aqp1dup, aqpe, hsp90, thrαA and dio3 showed lower expression in response to the salinity reduction. Moreover, larvae were able to keep energy metabolism related gene expression (atp6, cox1) at stable levels, irrespective of the salinity reduction. As such, when reducing salinity, an energy surplus associated to reduced osmoregulation demands and stress (lower nkcc, aqp and hsp expression), likely facilitated the observed increased survival, improved biometry and enhanced growth efficiency. Additionally, the salinity reduction decreased the amount of severe deformities such as spinal curvature and emaciation but also induced an edematous state of the larval heart, resulting in the most balanced mortality/deformity ratio when salinity was decreased on 3 dph and at 2 psu/day. However, the persistency of the pericardial edema and if or how it represents an obstacle in further larval development needs to be further clarified. In conclusion, this study clearly showed that salinity reduction regimes towards iso-osmotic conditions facilitated the European eel pre-leptocephalus development and revealed the existence of highly sensitive and regulated osmoregulation processes at such early life stage of this species.
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  • 88
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    Functional Metabolome Analysis of Penicillium roqueforti by Means of Differential Off-Line LC–NMR (2019)
    American Chemical Society
    In:  Journal of Agricultural and Food Chemistry, 67 (18). pp. 5135-5146.
    Details
    Publication Date: 2021-01-08
    Description: UPLC–TOF/MS profiling, followed by the recently reported differential off-line LC–NMR (DOLC–NMR) and quantitative 1H NMR spectroscopy (qHNMR), led to the differential qualitative analysis and accurate quantitation of l-tryptophan-induced metabolome alterations of Penicillium roqueforti, which is typically used in making blue-mold cheese. Among the 24 metabolites identified, two tetrapeptides, namely, d-Phe-l-Val-d-Val-l-Tyr and d-Phe-l-Val-d-Val-l-Phe, as well as cis-bis(methylthio)silvatin, are reported for the first time as metabolites of P. roqueforti. Antimicrobial activity tests showed strong effects of the catabolic l-tryptophan metabolites 3-hydroxyanthranilic acid, anthranilic acid, and 3-indolacetic acid against Saccharomyces cerevisiae, with IC50 values between 15.6 and 24.0 μg/mL, while roquefortine C and cis-bis(methylthio)silvatin inhibited the growth of Gram-negative Escherichia coli and Gram-positive Bacillus subtilis with IC50 values between 30.0 and 62.5 μg/mL.
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  • 89
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    Magnetite- and Iodine-Containing Nanoemulsion as a Dual Modal Contrast Agent for X-ray/Magnetic Resonance Imaging (2019)
    American Chemical Society
    In:  ACS Applied Materials & Interfaces, 11 (1). pp. 403-416.
    Details
    Publication Date: 2020-12-03
    Description: Noninvasive diagnostic by imaging combined with a contrast agent (CA) is by now the most used technique to get insight into human bodies. X-ray and magnetic resonance imaging (MRI) are widely used technologies providing complementary results. Nowadays, it seems clear that bimodal CAs could be an emerging approach to increase the patient compliance, accessing different imaging modalities with a single CA injection. Owing to versatile designs, targeting properties, and high payload capacity, nanocarriers are considered as a viable solution to reach this goal. In this study, we investigated efficient superparamagnetic iron oxide nanoparticle (SPION)-loaded iodinated nano-emulsions (NEs) as dual modal injectable CAs for X-ray imaging and MRI. The strength of this new CA lies not only in its dual modal contrasting properties and biocompatibility, but also in the simplicity of the nanoparticulate assembling: iodinated oily core was synthesized by the triiodo-benzene group grafting on vitamin E (41.7% of iodine) via esterification, and SPIONs were produced by thermal decomposition during 2, 4, and 6 h to generate SPIONs with different morphologies and magnetic properties. SPIONs with most anisotropic shape and characterized by the highest r2/r1 ratio once encapsulated into iodinated NE were used for animal experimentation. The in vivo investigation showed an excellent contrast modification because of the presence of the selected NEs, for both imaging techniques explored, that is, MRI and X-ray imaging. This work provides the description and in vivo application of a simple and efficient nanoparticulate system capable of enhancing contrast for both preclinical imaging modalities, MRI, and computed tomography.
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  • 90
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    Bioavailability and Chronic Toxicity of Metal Sulfide Minerals to Benthic Marine Invertebrates: Implications for Deep Sea Exploration, Mining and Tailings Disposal (2016)
    American Chemical Society
    In:  Environmental Science & Technology, 50 (7). pp. 4061-4070.
    Details
    Publication Date: 2020-12-02
    Description: The exploration and proposed mining of sulfide massive deposits in deep-sea environments and increased use deep-sea tailings placement (DSTP) in coastal zones has highlighted the need to better understand the fate and effects of mine-derived materials in marine environments. Metal sulfide ores contain high concentrations of metal(loid)s, of which a large portion exist in highly mineralized or sulfidised forms and are predicted to exhibit low bioavailability. In this study, sediments were spiked with a range of natural sulfide minerals (including chalcopyrite, chalcocite, galena, sphalerite) to assess the bioavailability and toxicity to benthic invertebrates (bivalve survival and amphipod survival and reproduction). The metal sulfide phases were considerably less bioavailable than metal contaminants introduced to sediment in dissolved forms, or in urban estuarine sediments contaminated with mixtures of metal(loid)s. Compared to total concentrations, the dilute-acid extractable metal(loid) (AEM) concentrations, which are intended to represent the more oxidized and labile forms, were more effective for predicting the toxicity of the sulfide mineral contaminated sediments. The study indicates that sediment quality guidelines based on AEM concentrations provide a useful tool for assessing and monitoring the risk posed by sediments impacted by mine-derived materials in marine environments.
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  • 91
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    Growth, ammonium metabolism, and photosynthetic properties of Ulva australis (Chlorophyta) under decreasing pH and ammonium enrichment (2017)
    Public Library of Science
    In:  PLoS ONE, 12 (11). e0188389.
    Details
    Publication Date: 2020-11-09
    Description: The responses of macroalgae to ocean acidification could be altered by availability of macronutrients, such as ammonium (NH4+). This study determined how the opportunistic macroalga, Ulva australis responded to simultaneous changes in decreasing pH and NH4+ enrichment. This was investigated in a week-long growth experiment across a range of predicted future pHs with ambient and enriched NH4+ treatments followed by measurements of relative growth rates (RGR), NH4+ uptake rates and pools, total chlorophyll, and tissue carbon and nitrogen content. Rapid light curves (RLCs) were used to measure the maximum relative electron transport rate (rETRmax) and maximum quantum yield of photosystem II (PSII) photochemistry (Fv/Fm). Photosynthetic capacity was derived from the RLCs and included the efficiency of light harvesting (α), slope of photoinhibition (β), and the light saturation point (Ek). The results showed that NH4+ enrichment did not modify the effects of pH on RGRs, NH4+ uptake rates and pools, total chlorophyll, rETRmax, α, β, Fv/Fm, tissue C and N, and the C:N ratio. However, Ek was differentially affected by pH under different NH4+ treatments. Ek increased with decreasing pH in the ambient NH4+ treatment, but not in the enriched NH4+ treatment. NH4+ enrichment increased RGRs, NH4+ pools, total chlorophyll, rETRmax, α, β, Fv/Fm, and tissue N, and decreased NH4+ uptake rates and the C:N ratio. Decreased pH increased total chlorophyll content, rETRmax, Fv/Fm, and tissue N content, and decreased the C:N ratio. Therefore, the results indicate that U. australis growth is increased with NH4+ enrichment and not with decreasing pH. While decreasing pH influenced the carbon and nitrogen metabolisms of U. australis, it did not result in changes in growth.
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  • 92
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    Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data (2015)
    Public Library of Science
    In:  PLoS ONE, 10 (7). e0134377.
    Details
    Publication Date: 2020-10-26
    Description: Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence data from a marine fungi culture collection. We further enriched this dataset by adding validated contextual data. Specifically, we included data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This dataset has been created with the intention to serve as a valuable reference dataset for aquatic fungi including a phylogenetic reference tree. The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.
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  • 93
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    Penicillium expansum : Consistent Production of Patulin, Chaetoglobosins, and Other Secondary Metabolites in Culture and Their Natural Occurrence in Fruit Products (2004)
    American Chemical Society
    In:  Journal of Agricultural and Food Chemistry, 52 (8). pp. 2421-2428.
    Details
    Publication Date: 2020-09-03
    Description: Penicillium expansum is known for its destructive rot and patulin production in apple juice. According to the literature, P. expansum can, among other compounds, produce citrinin, ochratoxin A, patulin, penitrem A, and rubratoxin B. In this study the qualitative production of metabolites was examined using TLC (260 isolates), HPLC (85 isolates), and MS (22 isolates). The results showed that none of the 260 isolates produced ochratoxin A, penitrem A, or rubratoxin B. However, chaetoglobosin A and communesin B were produced consistently by all 260 isolates. Patulin and roquefortine C were produced by 98% of the isolates. Expansolides A/B and citrinin were detected in 91 and 85% of the isolates, respectively. Chaetoglobosins and communesins were detected in naturally infected juices and potato pulp, whereas neither patulin nor citrinin was found. Because most P. expansum isolates produce patulin, citrinin, chaetoglobosins, communesins, roquefortine C, and expansolides A and B, foods contaminated with this fungus should ideally be examined for chaetoglobosin A as well as patulin.
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  • 94
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    Lost, but Found with Nile Red: A Novel Method for Detecting and Quantifying Small Microplastics (1 mm to 20 μm) in Environmental Samples (2017)
    American Chemical Society
    In:  Environmental Science & Technology, 51 (23). pp. 13641-13648.
    Details
    Publication Date: 2020-09-02
    Description: Marine plastic debris is a global environmental problem. Surveys have shown that 〈5 mm plastic particles, known as microplastics, are significantly more abundant in surface seawater and on shorelines than larger plastic particles are. Nevertheless, quantification of microplastics in the environment is hampered by a lack of adequate high-throughput methods for distinguishing and quantifying smaller size fractions (〈1 mm), and this has probably resulted in an underestimation of actual microplastic concentrations. Here we present a protocol that allows high-throughput detection and automated quantification of small microplastic particles (20–1000 μm) using the dye Nile red, fluorescence microscopy, and image analysis software. This protocol has proven to be highly effective in the quantification of small polyethylene, polypropylene, polystyrene, and nylon-6 particles, which frequently occur in the water column. Our preliminary results from sea surface tows show a power-law increase in small microplastics (i.e., 〈1 mm) with a decreasing particle size. Hence, our data help to resolve speculation about the “apparent” loss of this fraction from surface waters. We consider that this method presents a step change in the ability to detect small microplastics by substituting the subjectivity of human visual sorting with a sensitive and semiautomated procedure.
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  • 95
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    Guest Migration Revealed in CO2 Clathrate Hydrates (2015)
    American Chemical Society
    In:  Energy & Fuels, 29 (9). pp. 5681-5691.
    Details
    Publication Date: 2020-07-31
    Description: The shrinking-core model of the formation of gas hydrates from ice spheres with well-defined geometry gives experimental access to the gas permeation in bulk hydrates which is relevant to their use as energy storage materials, their exploitation from natural resources, as well as to their role in flow assurance. Here we report on a new approach to model CO2 clathration experiments in the temperature range from 230 to 272 K. We develop a comprehensive description of the gas permeation based on the diffusion along the network of polyhedral cages, some of them being empty. Following earlier molecular dynamics simulation results, the jump from a cage to one of its empty neighbors is assumed to proceed via a “hole-in-cage-wall” mechanism involving water vacancies in cage walls. The rate-limiting process in the investigated temperature range can be explained by the creation of water-vacancy-interstitial pairs. The gas diffusion leads to a time-dependent cage filling which decreases across the hydrate layer with the distance from the particle surface. The model allows a prediction of the time needed for a complete conversion of ice spheres into clathrate as well as the time needed for a full equilibration of the cage fillings. The findings essentially support our earlier results obtained in the framework of a purely phenomenological permeation model in terms of the overall transformation kinetics, yet it provides for the first time insight into the cage equilibration processes. The diffusion of CO2 molecules through bulk hydrate is found to be about three to four times faster in comparison with the CH4 case.
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  • 96
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    Experimental Study on Methane Production from Hydrate-Bearing Sandstone by Flue Gas Swapping (2018)
    American Chemical Society
    In:  Energy & Fuels, 32 (8). pp. 8167-8174.
    Details
    Publication Date: 2020-07-31
    Description: Methane recovery from artificial hydrate-bearing sandstones by simulated flue gas swapping was tested using a core flooding experimental setup. Seven groups of experiments were conducted to investigate the effect of hydrate saturation as well as the initial porosity and permeability of sandstones on methane production and carbon dioxide capture. The results show that the CH4 recovery efficiency and the amount of CO2 captured increase with the increase of hydrate saturation at the same initial porosity and permeability of sandstone. The highest CH4 recovery obtained is 51.6% and 99.4% of CO2 in simulated flue gas is sequestered in the hydrate phase after swapping at 9.2 MPa and 277.15 K. Hydrate saturation was 82.5% and the initial porosity and permeability of sandstone are 25.1% and 49 mD, respectively. With the increase of initial porosity and permeability of sandstone, the CH4 recovery efficiency and the amount of CO2 captured increase when other conditions (the hydrate saturation and reaction time) are similar. For investigating the CH4-flue gas swapping mechanism, a micro-differential scanning calorimetry was used to test the heat changes in the whole reaction. No noticeable endothermic or exothermic phenomenon was detected in the CH4-flue gas swapping, which indicates that CH4 hydrate would form mixed hydrates directly instead of going through a dissociation and reformation process. Based on the observed experimental results, a CH4-flue gas swapping mechanism is proposed and the reaction process is found to be essentially controlled by mass transfer.
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  • 97
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    Phase-Controlled Colloidal Syntheses of Iron Sulfide Nanocrystals via Sulfur Precursor Reactivity and Direct Pyrite Precipitation (2017)
    American Chemical Society
    In:  Chemistry of Materials, 29 (19). pp. 8521-8530.
    Details
    Publication Date: 2020-07-27
    Description: In the colloidal synthesis of iron sulfides, a series of dialkyl disulfides, alkyl thiols, and dialkyl disulfides (allyl, benzyl, tert-butyl, and phenyl) were employed as sulfur sources. Their reactivity was found to tune the phase between pyrite (FeS2), greigite (Fe3S4), and pyrrhotite (Fe7S8). DFT was used to show that sulfur-rich phases were favored when the C–S bond strength was low in the organosulfurs, yet temperature dependent studies and other observations indicated the reasons for phase selectivity were more nuanced; the different precursors decomposed through different reaction mechanisms, some involving the oleylamine solvent. The formation of pyrite from diallyl disulfide was carefully studied as it was the only precursor to yield FeS2. Raman spectroscopy indicated that FeS2 forms directly without an FeS intermediate, unlike most synthetic procedures to pyrite. Diallyl disulfide releases persulfide (S–S)2– due to the lower C–S bond strength relative to the S–S bond strength, as well as facile decomposition in the presence of amines through SN2′ mechanisms at elevated temperatures.
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  • 98
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    Aldisine alkaloids from the Philippine sponge Stylissa massa are potent inhibitors of mitogen-activated protein kinase kinase-1 (MEK-1) (2002)
    American Chemical Society
    In:  Journal of Medicinal Chemistry, 45 (2). pp. 529-532.
    Details
    Publication Date: 2020-07-23
    Description: Raf/MEK-1/MAPK cascade inhibitor activity-directed fractionation of the sponge Stylissa massa afforded eight known alkaloids:  aldisine (1), 2-bromoaldisine (2), 10Z-debromohymenialdisine (3), 10E-hymenialdisine (4), 10Z-hymenialdisine (5), hymenin (6), oroidin (7), and 4,5-dibromopyrrole-2-carbonamide (8). Both 4 and 5 showed significant enzyme inhibitory activity (IC50 3 and 6 nM, respectively). Secondary assays identified these compounds as potent MEK-1 inhibitors. Compounds 4 and 5 also inhibited the growth of human tumor LoVo cells.
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  • 99
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    Microcionamides A and B, bioactive peptides from the Philippine sponge Clathria (Thalysias) abietina (2004)
    American Chemical Society
    In:  Journal of Organic Chemistry, 69 (12). pp. 4170-4176.
    Details
    Publication Date: 2020-07-22
    Description: Microcionamides A (1) and B (2) have been isolated from the Philippine marine sponge Clathria (Thalysias) abietina. These new linear peptides are cyclized via a cystine moiety and have their C-terminus blocked by a 2-phenylethylenamine group. Their total structures, including absolute stereochemistry, were determined by a combination of spectral and chemical methods. Compound 1 was shown to slowly isomerize about the C-36/C-37 double bond when stored in DMSO. Microcionamides A (1) and B (2) exhibited significant cytotoxicity against the human breast tumor cells lines MCF-7 and SKBR-3 and displayed inhibitory activity against Mycobacterium tuberculosis H37Ra.
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  • 100
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    An iridoid glucoside from Euphrasia pectinata (2000)
    American Chemical Society
    In:  Journal of Natural Products, 63 (10). pp. 1449-1450.
    Details
    Publication Date: 2020-07-22
    Description: A new iridoid glucoside, 5β,6β-dihydroxyboschnaloside (1), was isolated from the aerial parts of Euphrasia pectinata. Five known iridoid glucosides, 6β-hydroxyboschnaloside (2), aucubin, euphroside, plantarenaloside, and geniposidic acid, and two known phenylethanoid glycosides, verbascoside (= acteoside) and leucosceptoside A, were also obtained and characterized. The structure of compound 1 was established by spectroscopic evidence.
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