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  • Molecular Diversity Preservation International  (56,267)
  • American Chemical Society (ACS)  (36,729)
  • Frontiers Media
  • 2020-2022
  • 2015-2019  (108,850)
  • 1945-1949
  • 2017  (62,044)
  • 2016  (46,806)
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  • 2015-2019  (108,850)
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  • 1
    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 Frontiers in Microbiology 8 (2017): 882, doi:10.3389/fmicb.2017.00882.
    Description: Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 μm and 〉2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.
    Description: This research is funded by the Gordon and Betty Moore Foundation (GBMF 2293 and 2928), the U.S. National Science Foundation (OCE-0934095, OCE-0424602, DEB-1256724), and the São Paulo Research Foundation (FAPESP 12/51187-0).
    Keywords: Amazon River ; Tropical Atlantic Ocean ; River plume ; Microbial diversity ; Freshwater bacteria ; Marine bacteria ; Diatom-diazotroph assemblage ; Columbia River
    Repository Name: Woods Hole Open Access Server
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  • 2
    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 Frontiers in Microbiology 8 (2017): 1496, doi:10.3389/fmicb.2017.01496.
    Description: Synechococcus are ubiquitous and cosmopolitan cyanobacteria that play important roles in global productivity and biogeochemical cycles. This study investigated the fine scale microdiversity, seasonal patterns, and spatial distributions of Synechococcus in estuarine waters of Little Sippewissett salt marsh (LSM) on Cape Cod, MA. The proportion of Synechococcus reads was higher in the summer than winter, and higher in coastal waters than within the estuary. Variations in the V4–V6 region of the bacterial 16S rRNA gene revealed 12 unique Synechococcus oligotypes. Two distinct communities emerged in early and late summer, each comprising a different set of statistically co-occurring Synechococcus oligotypes from different clades. The early summer community included clades I and IV, which correlated with lower temperature and higher dissolved oxygen levels. The late summer community included clades CB5, I, IV, and VI, which correlated with higher temperatures and higher salinity levels. Four rare oligotypes occurred in the late summer community, and their relative abundances more strongly correlated with high salinity than did other co-occurring oligotypes. The analysis revealed that multiple, closely related oligotypes comprised certain abundant clades (e.g., clade 1 in the early summer and clade CB5 in the late summer), but the correlations between these oligotypes varied from pair to pair, suggesting they had slightly different niches despite being closely related at the clade level. Lack of tidal water exchange between sampling stations gave rise to a unique oligotype not abundant at other locations in the estuary, suggesting physical isolation plays a role in generating additional microdiversity within the community. Together, these results contribute to our understanding of the environmental and ecological factors that influence patterns of Synechococcus microbial community composition over space and time in salt marsh estuarine waters.
    Description: This work was supported through a subcontract from the Woods Hole Center for Oceans and Human Health, from the National Institutes of Health and the National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724), a National Research Council Research Associateship Award and L'Oreal USA Fellowship (JH), an Alfred P. Sloan Research Fellowship in Ocean Sciences and the Clare Boothe Luce Program (KM), NASA Astrobiology Institute Cooperative Agreement NNA04CC04A (MS), the Alfred P. Sloan Foundation's ICoMM field project, and the W. M. Keck Foundation.
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  • 3
    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 Frontiers in Marine Science 4 (2017): 337, doi:10.3389/fmars.2017.00337.
    Description: The fishery for American lobster is currently the highest-valued commercial fishery in the United States, worth over US$620 million in dockside value in 2015. During a marine heat wave in 2012, the fishery was disrupted by the early warming of spring ocean temperatures and subsequent influx of lobster landings. This situation resulted in a price collapse, as the supply chain was not prepared for the early and abundant landings of lobsters. Motivated by this series of events, we have developed a forecast of when the Maine (USA) lobster fishery will shift into its high volume summer landings period. The forecast uses a regression approach to relate spring ocean temperatures derived from four NERACOOS buoys along the coast of Maine to the start day of the high landings period of the fishery. Tested against conditions in past years, the forecast is able to predict the start day to within 1 week of the actual start, and the forecast can be issued 3–4 months prior to the onset of the high-landings period, providing valuable lead-time for the fishery and its associated supply chain to prepare for the upcoming season. Forecast results are conveyed in a probabilistic manner and are updated weekly over a 6-week forecasting period so that users can assess the certainty and consistency of the forecast and factor the uncertainty into their use of the information in a given year. By focusing on the timing of events, this type of seasonal forecast provides climate-relevant information to users at time scales that are meaningful for operational decisions. As climate change alters seasonal phenology and reduces the reliability of past experience as a guide for future expectations, this type of forecast can enable fishing industry participants to better adjust to and prepare for operating in the context of climate change.
    Description: This forecast was initiated with support from NSF Coastal SEES (OCE 1325484) and was developed with funds from NASA EPSCoR through Maine Space Grant Consortium (EP-15-03).
    Keywords: Seasonal forecast ; Temperature ; Fishery landings ; Lobster fishery ; Climate variability
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  • 4
    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 Frontiers in Microbiology 7 (2016): 1731, doi: 10.3389/fmicb.2016.01731.
    Description: The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.
    Description: CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR.
    Keywords: 16S rRNA gene ; Ecological succession ; Antarctica ; Bacterial production ; Bacterial community composition ; Polaribacter ; Pelagibacter ubique (SAR11) ; Rhodobacteraceae
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  • 5
    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 Frontiers in Microbiology 8 (2017): 264, doi:10.3389/fmicb.2017.00264.
    Description: The occurrence of bacteria in the food processing environments plays a key role in food contamination and development of spoilage. Species of the genus Pseudomonas are recognized as major food spoilers and the capability to actually determine spoilage can be species- as well as strain-dependent. In order to improve the taxonomic resolution of 16S rRNA gene amplicons, in this study we used oligotyping to investigate the diversity of Pseudomonas populations in meat and dairy processing environments. Sequences of the V1–V3 regions from previous studies were used, including environmental swabs and food samples from both meat and dairy processing plants. We showed that the most frequently found oligotypes belonged to Pseudomonas fragi and P. fluorescens, that the most abundant oligotypes co-occurred, and were shared between the meat and dairy datasets. All the oligotypes occurring in foods were also identified in the environmental samples of the corresponding plants, highlighting the important role of the environment as a source of strains for food contamination. Oligotypes of the same species showed different levels depending on food processing and type of sample, suggesting that different strains of the same species can have different adaptation efficiency, leading to resilient bacterial associations.
    Keywords: Pseudomonas fragi ; Food contamination ; Food processing environment ; Oligotyping ; 16S rRNA gene sequencing
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  • 6
    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 Frontiers in Marine Science 4 (2017): 109, doi:10.3389/fmars.2017.00109.
    Description: Assessment of underwater noise is of particular interest given the increase in noise-generating human activities and the potential negative effects on marine mammals which depend on sound for many vital processes. The Azores archipelago is an important migratory and feeding habitat for blue (Balaenoptera musculus), fin (Balaenoptera physalus) and sei whales (Balaenoptera borealis) en route to summering grounds in northern Atlantic waters. High levels of low frequency noise in this area could displace whales or interfere with foraging behavior, impacting energy intake during a critical stage of their annual cycle. In this study, bottom-mounted Ecological Acoustic Recorders were deployed at three Azorean seamounts (Condor, Açores, and Gigante) to measure temporal variations in background noise levels and ship noise in the 18–1,000 Hz frequency band, used by baleen whales to emit and receive sounds. Monthly average noise levels ranged from 90.3 dB re 1 μPa (Açores seamount) to 103.1 dB re 1 μPa (Condor seamount) and local ship noise was present up to 13% of the recording time in Condor. At this location, average contribution of local boat noise to background noise levels is almost 10 dB higher than wind contribution, which might temporally affect detection ranges for baleen whale calls and difficult communication at long ranges. Given the low time percentatge with noise levels above 120 dB re 1 μPa found here (3.3% at Condor), we woud expect limited behavioral responses to ships from baleen whales. Sound pressure levels measured in the Azores are lower than those reported for the Mediterranean basin and the Strait of Gibraltar. However, the currently unknown effects of baleen whale vocalization masking and the increasing presence of boats at the monitored sites underline the need for continuous monitoring to understand any long-term impacts on whales.
    Description: Fundação para a Ciência e a Tecnologia (FCT) and Fundo Regional da Ciência e Tecnologia (FRCT), through research projects TRACE (PTDC/MAR/74071/2006), MAPCET (M2.1.2/F/012/2011), and FCT Exploratory project (IF/00943/2013/CP1199/CT0001), supported by funds from FEDER, the Competitiveness Factors Operational (COMPETE), QREN, POPH, European Social Fund, Portuguese Ministry for Science and Education, and Proconvergencia Açores/EU Program. We also acknowledge funds provided by FCT to MARE, through the strategic project UID/MAR/04292/2013, that also supported fees for this open access publication. MR is supported by a DRCT doctoral grant (M3.1.a/F/028/2015), IC was supported by a FCT doctoral grant (SFRH/BD/41192/2007) and MAS is supported by an FCT-Investigator contract (IF/00943/2013).
    Keywords: Underwater noise ; Ship noise ; Baleen whales ; MSFD ; Open ocean environment
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  • 7
    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 Frontiers in Microbiology 8 (2017): 682, doi:10.3389/fmicb.2017.00682.
    Description: The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
    Description: The study was supported by a Discovery Outstanding Researcher Award (DP120103498) and an Australian Laureate Fellowship (FL150100038) from the Australian Research Council.
    Keywords: Epsilonproteobacteria ; Taxonomy ; Classification ; Genome ; Phylogenomics ; Epsilonbacteraeota ; Evolution
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  • 8
    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 Frontiers in Marine Science 4 (2017): 334, doi:10.3389/fmars.2017.00334.
    Description: Scattering structures, including deep (〉200 m) scattering layers are common in most oceans, but have not previously been properly documented in the Arctic Ocean. In this work, we combine acoustic data for distribution and abundance estimation of zooplankton and fish with biological sampling from the region west and north of Svalbard, to examine high latitude meso- and epipelagic scattering layers and their biological constituents. Our results show that typically, there was strong patchy scattering in the upper part of the epipelagic zone (〈50 m) throughout the area. It was mainly dominated by copepods, krill, and amphipods in addition to 0-group fish that were particularly abundant west of the Spitsbergen Archipelago. Off-shelf there was a distinct deep scattering layer (DSL) between 250 and 600 m containing a range of larger longer lived organisms (mesopelagic fish and macrozooplankton). In eastern Fram Strait, the DSL also included and was in fact dominated by larger fish close to the shelf/slope break that were associated with Warm Atlantic Water moving north toward the Arctic Ocean, but switched to dominance by species having weaker scattering signatures further offshore. The Weighted Mean Depths of the DSL were deeper (WMD 〉 440 m) in the Arctic habitat north of Svalbard compared to those south in the Fram Strait west of Svalbard (WMD ~400 m). The surface integrated backscatter [Nautical Area-Scattering Coefficient, NASC, sA (m2 nmi−2)] was considerably lower in the waters around Svalbard compared to the more southern regions (62–69°N). Also, the integrated DSL nautical area scattering coefficient was a factor of ~6–10 lower around Svalbard compared to the areas in the south-eastern part of the Norwegian Sea ~62°30′N. The documented patterns and structures, particularly the DSL and its constituents, will be key reference points for understanding and quantifying future changes in the pelagic ecosystem at the entrance to the Arctic Ocean.
    Description: The Research Council of Norway is thanked for the financial support through the projects “The Arctic Ocean Ecosystem”—(SI_ARCTIC, RCN 228896), the “Effects of climate change on the Calanus complex”—(ECCO, RCN 200508), “Harvesting marine cold water plankton species—abundance estimation and stock assessment”—(Harvest II, RCN 203871) as well as the Institute of Marine Research, Bergen.
    Keywords: Arctic ; Bioacoustics ; Scattering layers ; Fish ; Micronekton ; Zooplankton ; Svalbard
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  • 9
    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 Frontiers in Chemistry 4 (2016): 5, doi:10.3389/fchem.2016.00005.
    Description: Biological production and decay of the reactive oxygen species (ROS) hydrogen peroxide (H2O2) and superoxide (O−2) likely have significant effects on the cycling of trace metals and carbon in marine systems. In this study, extracellular production rates of H2O2 and O−2 were determined for five species of marine diatoms in the presence and absence of light. Production of both ROS was measured in parallel by suspending cells on filters and measuring the ROS downstream using chemiluminescence probes. In addition, the ability of these organisms to break down O−2 and H2O2 was examined by measuring recovery of O−2 and H2O2 added to the influent medium. O−2 production rates ranged from undetectable to 7.3 × 10−16 mol cell−1 h−1, while H2O2 production rates ranged from undetectable to 3.4 × 10−16 mol cell−1 h−1. Results suggest that extracellular ROS production occurs through a variety of pathways even amongst organisms of the same genus. Thalassiosira spp. produced more O−2 in light than dark, even when the organisms were killed, indicating that O−2 is produced via a passive photochemical process on the cell surface. The ratio of H2O2 to O−2 production rates was consistent with production of H2O2 solely through dismutation of O−2 for T. oceanica, while T. pseudonana made much more H2O2 than O−2. T. weissflogii only produced H2O2 when stressed or killed. P. tricornutum cells did not make cell-associated ROS, but did secrete H2O2-producing substances into the growth medium. In all organisms, recovery rates for killed cultures (94–100% H2O2; 10–80% O−2) were consistently higher than those for live cultures (65–95% H2O2; 10–50% O−2). While recovery rates for killed cultures in H2O2 indicate that nearly all H2O2 was degraded by active cell processes, O−2 decay appeared to occur via a combination of active and passive processes. Overall, this study shows that the rates and pathways for ROS production and decay vary greatly among diatom species, even between those that are closely related, and as a function of light conditions.
    Description: This research was supported by NSF grant OCE-1131734/1246174 to BV and CH.
    Keywords: Reactive oxygen species ; Superoxide ; Hydrogen peroxide ; Diatoms ; Culture
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  • 10
    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 Frontiers in Microbiology 7 (2016): 1318, doi:10.3389/fmicb.2016.01318.
    Description: Characterizing the community structure of naturally occurring microbes through marker gene amplicons has gained widespread acceptance for profiling microbial populations. The 16S ribosomal RNA (rRNA) gene provides a suitable target for most studies since (1) it meets the criteria for robust markers of evolution, e.g., both conserved and rapidly evolving regions that do not undergo horizontal gene transfer, (2) microbial ecologists have identified widely adopted primers and protocols for generating amplicons for sequencing, (3) analyses of both cultivars and environmental DNA have generated well-curated databases for taxonomic profiling, and (4) bioinformaticians and computational biologists have published comprehensive software tools for interpreting the data and generating publication-ready figures. Since the initial descriptions of high-throughput sequencing of 16S rRNA gene amplicons to survey microbial diversity, we have witnessed an explosion of association-based inferences of interactions between microbes and their environment.
    Description: AME was supported by the University of Chicago and the Marine Biological Laboratory collaboration award.
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  • 11
    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 Frontiers in Microbiology 8 (2017): 1786, doi:10.3389/fmicb.2017.01786.
    Description: Semi-labile dissolved organic matter (DOM) accumulates in surface waters of the oligotrophic ocean gyres and turns over on seasonal to annual timescales. This reservoir of DOM represents an important source of carbon, energy, and nutrients to marine microbial communities but the identity of the microorganisms and the biochemical pathways underlying the cycling of DOM remain largely uncharacterized. In this study we describe bacteria isolated from the North Pacific Subtropical Gyre (NPSG) near Hawaii that are able to degrade phosphonates associated with high molecular weight dissolved organic matter (HMWDOM), which represents a large fraction of semi-labile DOM. We amended dilution-to-extinction cultures with HMWDOM collected from NPSG surface waters and with purified HMWDOM enriched with polysaccharides bearing alkylphosphonate esters. The HMWDOM-amended cultures were enriched in Roseobacter isolates closely related to Sulfitobacter and close relatives of hydrocarbon-degrading bacteria of the Oceanospirillaceae family, many of which encoded phosphonate degradation pathways. Sulfitobacter cultures encoding C-P lyase were able to catabolize methylphosphonate and 2-hydroxyethylphosphonate, as well as the esters of these phosphonates found in native HMWDOM polysaccharides to acquire phosphorus while producing methane and ethylene, respectively. Conversely, growth of these isolates on HMWDOM polysaccharides as carbon source did not support robust increases in cell yields, suggesting that the constituent carbohydrates in HMWDOM were not readily available to these individual isolates. We postulate that the complete remineralization of HMWDOM polysaccharides requires more complex microbial inter-species interactions. The degradation of phosphonate esters and other common substitutions in marine polysaccharides may be key steps in the turnover of marine DOM.
    Description: Financial support for this work was provided by the National Science Foundation Center for Microbial Oceanography: Research and Education (award #EF0424599 to DK and ED), the National Science Foundation HOT program (OCE-1260164 to M. J. Church and DK), the Gordon and Betty Moore Foundation (grants #492.01 and #3777 to ED, #3298 to DR, and #3794 to DK), and the Simons Foundation (award ID 329108 to DK, DR, and ED). Additional support was provided by the Agouron Institute through a fellowship to OS.
    Keywords: Bacterial degradation ; Dissolved organic matter (DOM) ; Phosphonate metabolism ; C-P lyase ; Methane ; Ethylene ; Oligotrophic conditions
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  • 12
    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 Frontiers in Microbiology 7 (2016): 59, doi:10.3389/fmicb.2016.00059.
    Description: Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. However, deciphering the chemical drivers of these interspecies interactions remains challenging. Here, we report the isolation of 2-heptyl-4-quinolone (HHQ), released by Pseudoalteromonas piscicida, a marine gamma-proteobacteria previously reported to induce phytoplankton mortality through a hitherto unknown algicidal mechanism. HHQ functions as both an antibiotic and a bacterial signaling molecule in cell–cell communication in clinical infection models. Co-culture of the bloom-forming coccolithophore, Emiliania huxleyi with both live P. piscicida and cell-free filtrates caused a significant decrease in algal growth. Investigations of the P. piscicida exometabolome revealed HHQ, at nanomolar concentrations, induced mortality in three strains of E. huxleyi. Mortality of E. huxleyi in response to HHQ occurred slowly, implying static growth rather than a singular loss event (e.g., rapid cell lysis). In contrast, the marine chlorophyte, Dunaliella tertiolecta and diatom, Phaeodactylum tricornutum were unaffected by HHQ exposures. These results suggest that HHQ mediates the type of inter-domain interactions that cause shifts in phytoplankton population dynamics. These chemically mediated interactions, and other like it, ultimately influence large-scale oceanographic processes.
    Description: This research was support through funding from the Gordon and Betty Moore Foundation through Grant GBMF3301 to MJ and TM; NIH grant from the National Institute of Allergy and Infectious Disease (NIAID – 1R21Al119311-01) to TM and KW; the National Science Foundation (OCE – 1313747) and US National Institute of Environmental Health Science (P01-ES021921) through the Oceans and Human Health Program to BM. Additional financial support was provided to TM from the Flatley Discovery Lab.
    Keywords: Infochemicals ; Algicidal compound ; Bacteria–phytoplankton interaction ; HHQ ; Pseudoalteromonas ; Emiliania huxleyi ; IC50 ; Mortality
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  • 13
    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 Frontiers in Microbiology 8 (2017): 702, doi:10.3389/fmicb.2017.00702.
    Description: The unique geochemistry of marine shallow-water hydrothermal systems promotes the establishment of diverse microbial communities with a range of metabolic pathways. In contrast to deep-sea vents, shallow-water vents not only support chemosynthesis, but also phototrophic primary production due to the availability of light. However, comprehensive studies targeting the predominant biogeochemical processes are rare, and consequently a holistic understanding of the functioning of these ecosystems is currently lacking. To this end, we combined stable isotope probing of lipid biomarkers with an analysis of the bacterial communities to investigate if chemoautotrophy, in parallel to photoautotrophy, plays an important role in autotrophic carbon fixation and to identify the key players. The study was carried out at a marine shallow-water hydrothermal system located at 5 m water depth off Dominica Island (Lesser Antilles), characterized by up to 55°C warm hydrothermal fluids that contain high amounts of dissolved Fe2+. Analysis of the bacterial diversity revealed Anaerolineae of the Chloroflexi as the most abundant bacterial class. Furthermore, the presence of key players involved in iron cycling generally known from deep-sea hydrothermal vents (e.g., Zetaproteobacteria and Geothermobacter), supported the importance of iron-driven redox processes in this hydrothermal system. Uptake of 13C-bicarbonate into bacterial fatty acids under light and dark conditions revealed active photo- and chemoautotrophic communities, with chemoautotrophy accounting for up to 65% of the observed autotrophic carbon fixation. Relatively increased 13C-incorporation in the dark allowed the classification of aiC15:0, C15:0, and iC16:0 as potential lipid biomarkers for bacterial chemoautotrophy in this ecosystem. Highest total 13C-incorporation into fatty acids took place at the sediment surface, but chemosynthesis was found to be active down to 8 cm sediment depth. In conclusion, this study highlights the relative importance of chemoautotrophy compared to photoautotrophy in a shallow-water hydrothermal system, emphasizing chemosynthesis as a prominent process for biomass production in marine coastal environments influenced by hydrothermalism.
    Description: SS was supported by NSF grant OCE-1124272. This work was financed through the DFG Emmy Noether Grant BU 2606/1-1 to SB.
    Keywords: Chemoautotrophy ; Marine shallow-water hydrothermal systems ; Lipid biomarker ; Stable isotope probing (SIP) ; Fatty acids ; Dominica (Lesser Antilles) ; Zetaproteobacteria ; Geothermobacter
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  • 14
    Publication Date: 2017-04-04
    Description: During volcanic eruptions, measurements of the rate at which magma is erupted underpin hazard assessments. For eruptions dominated by the effusion of lava, estimates are often made using satellite data; here, in a case study at Mount Etna (Sicily), we make the first measurements based on terrestrial laser scanning (TLS), and we also include explosive products. During the study period (17–21 July 2012), regular Strombolian explosions were occurring within the Bocca Nuova crater, producing a ~50 m-high scoria cone and a small lava flow field. TLS surveys over multi-day intervals determined a mean cone growth rate (effusive and explosive products) of ~0.24 m3·s−1. Differences between 0.3-m resolution DEMs acquired at 10-minute intervals captured the evolution of a breakout lava flow lobe advancing at 0.01–0.03 m3·s−1. Partial occlusion within the crater prevented similar measurement of the main flow, but integrating TLS data with time-lapse imagery enabled lava viscosity (7.4 × 105 Pa·s) to be derived from surface velocities and, hence, a flux of 0.11 m3·s−1 to be calculated. Total dense rock equivalent magma discharge estimates are ~0.1–0.2 m3·s−1 over the measurement period and suggest that simultaneous estimates from satellite data are somewhat overestimated. Our results support the use of integrated TLS and time-lapse photography for ground-truthing space-based measurements and highlight the value of interactive image analysis when automated approaches, such as particle image velocimetry (PIV), fail.
    Description: Published
    Description: 14967 - 14987
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: open
    Keywords: lava flow; scoria cone; effusion rate; terrestrial laser scanning; time-lapse photography; Mt. Etna ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
    Publication Date: 2017-04-04
    Description: In order to improve the observation capability in one of the most active volcanic areas in the world, Mt. Etna, we developed a processing method to use the surveillance cameras for a quasi real-time mapping of syn-eruptive processes. Following an evaluation of the current performance of the Etna permanent ground NEtwork of Thermal and Visible Sensors (Etna_NETVIS), its possible implementation and optimization was investigated to determine the locations of additional observation sites to be rapidly set up during emergencies. A tool was then devised to process time series of ground-acquired images and extract a coherent multi-temporal dataset of georeferenced map. The processed datasets can be used to extract 2D features such as evolution maps of active lava flows. The tool was validated on ad-hoc test fields and then adopted to map the evolution of two recent lava flows. The achievable accuracy (about three times the original pixel size) and the short processing time makes the tool suitable for rapidly assessing lava flow evolutions, especially in the case of recurrent eruptions, such as those of the 2011–2015 Etna activity. The tool can be used both in standard monitoring activities and during emergency phases (eventually improving the present network with additional mobile stations) when it is mandatory to carry out a quasi-real-time mapping to support civil protection actions. The developed tool could be integrated in the control room of the Osservatorio Etneo, thus enabling the Etna_NETVIS for mapping purposes and not only for video surveillance.
    Description: Published
    Description: 192
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: open
    Keywords: volcano monitoring ; lava flow mapping ; surveillance camera ; hazard assessment ; geo spatial dataset ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 16
    Publication Date: 2017-04-04
    Description: The 2002-2003 Stromboli eruption triggered the failure of part of the Sciara del Fuoco slope, which generated a tsunami that struck the island and the northern coastline of Sicily. The Sciara del Fuoco is a very steep slope where all lava flows from the craters' emplacement; most lateral eruptions usually take place from fissures propagating in this sector of the volcano. The eruption went on to produce a lava field that filled the area affected by the landslide. This in turn led to further instability, renewing the threat of another slope failure and a potentially related tsunami. This work describes a new joint approach, combining surveying data and aerial image correlometry methods, to study the motion of this unstable slope. The combination has the advantage of very precise surveying measurements, which can be considered the ground truth to constrain the very-high-resolution aerial photogrammetric data, thereby obtaining highly detailed and accurate ground deformation maps. The joint use of the two methods can be very useful to obtain a more complete image of the deformation field for monitoring dangerous and/or rather inaccessible places. The proposed combined methodology improves our ability to study and assess hazardous processes associated with significant ground deformation.
    Description: This Research has been supported by the Spanish Ministry of Economy and Competitiveness research projects AYA2010-17448 and ESP2013-47780-557 C2-1-R, and the EU 7th FP MED-SUV project (contract 308665). It is a contribution to the Moncloa Campus of International Excellence
    Description: Published
    Description: 463
    Description: 1V. Storia e struttura dei sistemi vulcanici
    Description: JCR Journal
    Description: open
    Keywords: surveying ; data integration ; aerial photogrammetry ; monitoring ; flank instability ; sector collapse ; landslide ; tsunami ; volcanoes ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 17
    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 Frontiers in Microbiology 7 (2016): 564, doi:10.3389/fmicb.2016.00564.
    Description: Dental plaque is a bacterial biofilm composed of a characteristic set of organisms. Relatively little information from cultivation-independent, high-throughput analyses has been published on the temporal dynamics of the dental plaque microbiome. We used Minimum Entropy Decomposition, an information theory-based approach similar to oligotyping that provides single-nucleotide resolution, to analyze a previously published time series data set and investigate the dynamics of the plaque microbiome at various analytic and taxonomic levels. At both the genus and 97% Operational Taxonomic Unit (OTU) levels of resolution, the range of variation within each individual overlapped that of other individuals in the data set. When analyzed at the oligotype level, however, the overlap largely disappeared, showing that single-nucleotide resolution enables differentiation of individuals from one another without ambiguity. The overwhelming majority of the plaque community in all samples was made up of bacteria from a moderate number of plaque-typical genera, indicating that the overall community framework is shared among individuals. Each of these genera fluctuated in abundance around a stable mean that varied between individuals, with some genera having higher inter-individual variability than others. Thus, at the genus level, differences between individuals lay not in the identity of the major genera but in consistently differing proportions of these genera from mouth to mouth. However, at the oligotype level, we detected oligotype “fingerprints,” a highly individual-specific set of persistently abundant oligotypes fluctuating around a stable mean over time. For example, within the genus Corynebacterium, more than a dozen oligotypes were detectable in each individual, of which a different subset reached high abundance in any given person. This pattern suggests that each mouth contains a subtly different community of organisms. We also compared the Chinese plaque community characterized here to previously characterized Western plaque communities, as represented by analyses of data emerging from the Human Microbiome Project, and found no major differences between Chinese and Western supragingival plaque. In conclusion, we found the plaque microbiome to be highly individualized at the oligotype level and characterized by stability of community membership, with variability in the relative abundance of community members between individuals and over time.
    Description: Our work was supported by National Institutes of Health (NIH) National Institute of Dental and Craniofacial Research Grant DE022586 (to GGB). Additional support was provided by Harvard University's Department of Organismic and Evolutionary Biology graduate program (to DRU).
    Keywords: Human microbiome ; 16S rRNA ; Community dynamics ; Oral microbiota ; Community ecology
    Repository Name: Woods Hole Open Access Server
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  • 18
    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 Frontiers in Microbiology 7 (2016): 75, doi:10.3389/fmicb.2016.00075.
    Description: The hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region.
    Description: AT acknowledges a W. Reynolds research leave from UNC, Guaymas-relevant support from the Center for Dark Energy Biosphere Investigations (C-DEBI) at the University of Southern California
    Keywords: Guaymas basin ; Hydrothermal circulation ; Hydrothermal sediment ; Beggiatoa mat ; In situ profiles ; Heatflow ; Porewater chemistry
    Repository Name: Woods Hole Open Access Server
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  • 19
    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 Frontiers in Microbiology 7 (2016): 163, doi:10.3389/fmicb.2016.00163.
    Description: Some benthic foraminiferal species are reportedly capable of nitrate storage and denitrification, however, little is known about nitrate incorporation and subsequent utilization of nitrate within their cell. In this study, we investigated where and how much 15N or 34S were assimilated into foraminiferal cells or possible endobionts after incubation with isotopically labeled nitrate and sulfate in dysoxic or anoxic conditions. After 2 weeks of incubation, foraminiferal specimens were fixed and prepared for Transmission Electron Microscopy (TEM) and correlative nanometer-scale secondary ion mass spectrometry (NanoSIMS) analyses. TEM observations revealed that there were characteristic ultrastructural features typically near the cell periphery in the youngest two or three chambers of the foraminifera exposed to anoxic conditions. These structures, which are electron dense and ~200–500 nm in diameter and co-occurred with possible endobionts, were labeled with 15N originated from 15N-labeled nitrate under anoxia and were labeled with both 15N and 34S under dysoxia. The labeling with 15N was more apparent in specimens from the dysoxic incubation, suggesting higher foraminiferal activity or increased availability of the label during exposure to oxygen depletion than to anoxia. Our results suggest that the electron dense bodies in Ammonia sp. play a significant role in nitrate incorporation and/or subsequent nitrogen assimilation during exposure to dysoxic to anoxic conditions.
    Description: This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan (Young Scientists B No. 22740340 and Scientific Research C No. 24540504 to HN), an Invitation Fellowship for Research in Japan to JB by Japan Society for the Promotion of Science (JSPS), the Robert W. Morse Chair for Excellence in Oceanography at WHOI to JB, and The Investment in Science Fund at WHOI to JB.
    Keywords: Foraminifer ; Nitrate ; NanoSIMS ; Electron dense body ; Endobionts ; Ultrastructure ; Denitrification
    Repository Name: Woods Hole Open Access Server
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  • 20
    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 Frontiers in Microbiology 7 (2016): 941, doi:10.3389/fmicb.2016.00941.
    Description: Pockmarks are crater-like depression on the seafloor associated with hydrocarbon ascent through muddy sediments in continental shelves around the world. In this study, we examine the diversity and distribution of benthic microbial communities at shallow-water pockmarks adjacent to the Middle Adriatic Ridge. We integrate microbial diversity data with characterization of local hydrocarbons concentrations and sediment geochemistry. Our results suggest these pockmarks are enriched in sedimentary hydrocarbons, and host a microbial community dominated by Bacteria, even in deeper sediment layers. Pockmark sediments showed higher prokaryotic abundance and biomass than surrounding sediments, potentially due to the increased availability of organic matter and higher concentrations of hydrocarbons linked to pockmark activity. Prokaryotic diversity analyses showed that the microbial communities of these shallow-water pockmarks are unique, and comprised phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders. Altogether, this study suggests that shallow-water pockmark habitats enhance the diversity of the benthic prokaryotic biosphere by providing specialized environmental niches.
    Description: This work was partially supported by a Postdoctoral Fellowship from the Center for Dark Energy Biosphere Investigations [C-DEBI, grant OCE-0939564] awarded to DG, by National Science Foundation grant OCE 11-24141 to CV, and European Science Foundation EuroDeep BIOFUN grant CTM2007-28739-E to EM. This article commits to EU HERMIONE [contract no. 226354] and CoCoNet [contract no. 287844] programs, and the Italian MIUR flag Ritmare within the National Research Program 2011–2013.
    Keywords: Pockmarks ; Cold seeps ; Hydrocarbons ; Prokaryotic diversity ; Bacteria ; Archaea ; Hydrocarbon degradation ; Microbial diversity
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  • 21
    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 Frontiers in Microbiology 7 (2016): 1240, doi:10.3389/fmicb.2016.01240.
    Description: Thermophilic methanogens are common autotrophs at hydrothermal vents, but their growth constraints and dependence on H2 syntrophy in situ are poorly understood. Between 2012 and 2015, methanogens and H2-producing heterotrophs were detected by growth at 80∘C and 55∘C at most diffuse (7–40∘C) hydrothermal vent sites at Axial Seamount. Microcosm incubations of diffuse hydrothermal fluids at 80∘C and 55∘C demonstrated that growth of thermophilic and hyperthermophilic methanogens is primarily limited by H2 availability. Amendment of microcosms with NH4+ generally had no effect on CH4 production. However, annual variations in abundance and CH4 production were observed in relation to the eruption cycle of the seamount. Microcosm incubations of hydrothermal fluids at 80∘C and 55∘C supplemented with tryptone and no added H2 showed CH4 production indicating the capacity in situ for methanogenic H2 syntrophy. 16S rRNA genes were found in 80∘C microcosms from H2-producing archaea and H2-consuming methanogens, but not for any bacteria. In 55∘C microcosms, sequences were found from H2-producing bacteria and H2-consuming methanogens and sulfate-reducing bacteria. A co-culture of representative organisms showed that Thermococcus paralvinellae supported the syntrophic growth of Methanocaldococcus bathoardescens at 82∘C and Methanothermococcus sp. strain BW11 at 60∘C. The results demonstrate that modeling of subseafloor methanogenesis should focus primarily on H2 availability and temperature, and that thermophilic H2 syntrophy can support methanogenesis within natural microbial assemblages and may be an important energy source for thermophilic autotrophs in marine geothermal environments.
    Description: This work was funded by the Gordon and Betty Moore Foundation grant GBMF 3297, the NASA Earth and Space Science Fellowship Program grant NNX11AP78H, the National Science Foundation grant OCE-1547004, with funding from NOAA/PMEL, contribution #4493, and JISAO under NOAA Cooperative Agreement NA15OAR4320063, contribution #2706.
    Repository Name: Woods Hole Open Access Server
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  • 22
    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 Frontiers in Marine Science 2 (2016): 118, doi:10.3389/fmars.2015.00118.
    Description: Characterization of dissolved organic matter (DOM) in terms of its composition and optical properties, with an eye toward ultimately understanding its deep ocean dynamics, is the currently active frontier in DOM research. We used UV-visible absorption spectroscopy and fluorescence excitation-emission matrix (EEM) spectroscopy to characterize DOM in the open ocean along sections of the U.S. CO2/CLIVAR Repeat Hydrography Project located in all the major ocean basins outside the Arctic. Despite large differences in fluorescence intensity between ocean basins, some variability patterns were similar throughout the global ocean, suggesting similar processes controlling the composition of the DOM. We find that commercially available single channel CDOM sensors are sensitive to the fluorescence of humic materials in the deep ocean and thermocline but not to the UVA-fluorescing and absorbing materials that characterize freshly produced CDOM in surface waters, revealing fundamental diversity in the DOM profile. In surface waters, UVA fluorescence and absorption signatures indicate the presence of freshly produced material and the process of bleaching removal, but in the upper mesopelagic and in the main thermocline these optical signatures are replaced by those of humic materials, with distribution patterns correlated to apparent oxygen utilization (AOU) and other signatures of remineralization. Empirical orthogonal function analysis (EOF) of the EEM data suggests the presence of two (unidentified) processes which convert “fresh” DOM to humic materials: one located in the surface ocean (shallower than 500 m) and one located in the main thermocline. These inferred humification processes represent less than 5% of the overall variability in oceanic humic DOM fluorescence, which appears to be dominated by terrestrial input and solar bleaching of humic materials.
    Description: This research was supported by grants from NASA (grants NAG5-13277 and NNX14AG24G) and NSF (OCE-0241614 and OCE-0648541) to NN and D. A. Siegel.
    Keywords: CDOM ; FDOM ; Humic material ; Oceanic CDOM cycling ; Fluorescence analysis
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  • 23
    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 Frontiers in Marine Science 3 (2016): 27, doi:10.3389/fmars.2016.00027.
    Description: The distributions of dissolved iron and organic iron-binding ligands were examined in water column profiles and deckboard incubation experiments in the southern California Current System (sCCS) along a transition from coastal to semi-oligotrophic waters. Analysis of the iron-binding ligand pool by competitive ligand exchange-adsorptive cathodic stripping voltammetry (CLE-ACSV) using multiple analytical windows (MAWs) revealed three classes of iron-binding ligands present throughout the water column (L1−L3), whose distributions closely matched those of dissolved iron and nitrate. Despite significant biogeochemical gradients, ligand profiles were similar between stations, with surface minima in strong ligands (L1 and L2), and relatively constant concentrations of weaker ligands (L3) down to 500 m. A phytoplankton grow-out incubation, initiated from an iron-limited water mass, showed dynamic temporal cycling of iron-binding ligands. A biological iron model was able to capture the patterns of the strong ligands in the grow-out incubation relatively well with only the microbial community as a biological source. An experiment focused on remineralization of particulate organic matter showed production of both strong and weak iron-binding ligands by the heterotrophic community, supporting a mechanism for in-situ production of both strong and weak iron-binding ligands in the subsurface water column. Photochemical experiments showed a variable influence of sunlight on the degradation of natural iron-binding ligands, providing some evidence to explain differences in surface ligand concentrations between stations. Patterns in ligand distributions between profiles and in the incubation experiments were primarily related to macronutrient concentrations, suggesting microbial remineralization processes might dominate on longer time-scales over short-term changes associated with photochemistry or phytoplankton growth.
    Description: RB, KB, and MC were supported by NSF OCE #10-2667 for the CCE-LTER program. MJ was funded by NSF ANT grant 0948378 and Harbor Branch Oceanographic Institute Foundation.
    Keywords: California Current Ecosystem ; Long term ecological research ; Iron limitation ; Dissolved iron-binding ligands ; Multiple analytical windows ; Electrochemistry
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  • 24
    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 Frontiers in Earth Science 4 (2016): 77, doi:10.3389/feart.2016.00077.
    Description: Arctic deltas are dynamic and vulnerable regions that play a key role in land-ocean interactions and the global carbon cycle. Delta lakes may provide valuable historical records of the quality and quantity of fluvial fluxes, parameters that are challenging to investigate in these remote regions. Here we study lakes from across the Mackenzie Delta, Arctic Canada, that receive fluvial sediments from the Mackenzie River when spring flood water levels rise above natural levees. We compare downcore lake sediments with suspended sediments collected during the spring flood, using bulk (% organic carbon, % total nitrogen, δ13C, Δ14C) and molecular organic geochemistry (lignin, leaf waxes). High-resolution age models (137Cs, 210Pb) of downcore lake sediment records (n = 11) along with lamina counting on high-resolution radiographs show sediment deposition frequencies ranging between annually to every 15 years. Down-core geochemical variability in a representative delta lake sediment core is consistent with historical variability in spring flood hydrology (variability in peak discharge, ice jamming, peak water levels). Comparison with earlier published Mackenzie River depth profiles shows that (i) lake sediments reflect the riverine surface suspended load, and (ii) hydrodynamic sorting patterns related to spring flood characteristics are reflected in the lake sediments. Bulk and molecular geochemistry of suspended particulate matter from the spring flood peak and lake sediments are relatively similar showing a mixture of modern higher-plant derived material, older terrestrial permafrost material, and old rock-derived material. This suggests that deltaic lake sedimentary records hold great promise as recorders of past (century-scale) riverine fluxes and may prove instrumental in shedding light on past behavior of arctic rivers, as well as how they respond to a changing climate.
    Description: Funding was provided by the US National Science Foundation as part of the Arctic Great Rivers Observatory (NSF-0732522 and NSF-1107774), as well as the Netherlands Organization for Scientific Research (Rubicon #825.10.022, and Veni #863.12.004). Additional funding for the lake coring was provided from WHOI through its Ocean and Climate Change Institute.
    Keywords: Lignin ; Biomarkers ; Mackenzie River ; Carbon isotopes ; Lake sediments
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  • 25
    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 Frontiers in Marine Science 3 (2016): 22, doi:10.3389/fmars.2016.00022.
    Description: Ocean ecosystems play a critical role in the Earth's carbon cycle and the quantification of their impacts for both present conditions and for predictions into the future remains one of the greatest challenges in oceanography. The goal of the EXport Processes in the Ocean from Remote Sensing (EXPORTS) Science Plan is to develop a predictive understanding of the export and fate of global ocean net primary production (NPP) and its implications for present and future climates. The achievement of this goal requires a quantification of the mechanisms that control the export of carbon from the euphotic zone as well as its fate in the underlying “twilight zone” where some fraction of exported carbon will be sequestered in the ocean's interior on time scales of months to millennia. Here we present a measurement/synthesis/modeling framework aimed at quantifying the fates of upper ocean NPP and its impacts on the global carbon cycle based upon the EXPORTS Science Plan. The proposed approach will diagnose relationships among the ecological, biogeochemical, and physical oceanographic processes that control carbon cycling across a range of ecosystem and carbon cycling states leading to advances in satellite diagnostic and numerical prognostic models. To collect these data, a combination of ship and robotic field sampling, satellite remote sensing, and numerical modeling is proposed which enables the sampling of the many pathways of NPP export and fates. This coordinated, process-oriented approach has the potential to foster new insights on ocean carbon cycling that maximizes its societal relevance through the achievement of research goals of many international research agencies and will be a key step toward our understanding of the Earth as an integrated system.
    Description: The development of the EXPORTS Science Plan was supported by NASA Ocean Biology and Biogeochemistry program (award NNX13AC35G).
    Keywords: Satellite remote sensing ; Field campain ; Science plan ; Ocean carbon cycling ; Biological pump
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  • 26
    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 Frontiers in Microbiology 8 (2017): 2117, doi:10.3389/fmicb.2017.02117.
    Description: Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August–December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.
    Description: CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR. The Gordon and Betty Moore Foundation grant 1711 supported work by DR.
    Keywords: 16S rRNA ; Amplicon sequencing ; Community assembly ; Bacterial succession ; Mesocosms ; Collwelliaceae ; Polaribacter ; Phytoplankton exudates
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  • 27
    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 Frontiers in Marine Science 4 (2017): 332, doi:10.3389/fmars.2017.00332.
    Description: While sound scattering layers (SSLs) have been described previously from ice-covered waters in the Arctic, the existence of a viable mesopelagic community that also includes mesopelagic fishes in the Arctic has been questioned. In addition, it has been hypothesized that vertical migration would hardly exist in these areas. We wanted to check if deep scattering layers (DSLs) was found to the west and north of Svalbard (79°30′N−82°10′N) during autumn 2015, and if present; whether organisms in such DSLs undertook vertical migrations. Our null hypothesis was that there would be no evidence of diel vertical migration. Multi-frequency acoustic observations by hull mounted echo sounder (18, 38, and 120 kHz) revealed a DSL at depths ~210–510 m in areas with bottom depths exceeding ~600 m. Investigating eight geographical locations that differed with respect to time periods, light cycle and sea ice conditions, we show that the deeper layer of DSL displayed a clear ascending movement during night time and a descending movement during daytime. The high-light weighted mean depth (WMD) (343–514 m) with respect to backscattered energy was statistically deeper than the low-light WMD (179–437 m) for the locations studied. This behavior of the DSL was found to be consistent both when the sun was continuously above the horizon and after it started to set on 1 September, and both in open water and sea ice covered waters. The WMD showed an increasing trend, while the nautical area backscattering strength from the DSL showed a decreasing trend from south to north among the studied locations. Hydrographic observations revealed that the diel migration was found in the lower part of the north-flowing Atlantic Water, and was disconnected from the surface water masses above the Atlantic Water during day and night. The organisms conducting vertical migrations were studied by vertical and oblique hauls with zooplankton nets and pelagic trawls. These data suggest that these organisms were mainly various mesopelagic fishes, some few larger fishes, large zooplankton like krill and amphipods, and various gelatinous forms.
    Description: The Research Council of Norway is thanked for the financial support through the projects “The Arctic Ocean Ecosystem” — (SI_ARCTIC, RCN 228896), the “Effects of climate change on the Calanus complex”—(ECCO, RCN 200508), “Harvesting marine cold water plankton species—abundance estimation and stock assessment”—(Harvest II, RCN 203871).
    Keywords: Arctic Ocean ; Deep scattering layer ; Diel vertical migration ; Mesopelagic organisms ; Acoustics
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  • 28
    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 Frontiers in Marine Science 3 (2016): 1, doi:10.3389/fmars.2016.00001.
    Description: The coccolithophore Emiliania huxleyi forms massive blooms and plays a critical role in global elemental cycles, sequestering significant amounts of atmospheric carbon dioxide on geological time scales via production of calcium carbonate coccoliths and emitting dimethyl sulfoniopropionate (DMSP), which has the potential for increasing atmosph-eric albedo. Because grazing in pelagic systems is a major top-down force structuring microbial communities, the influence of grazers on E. huxleyi populations has been of interest to researchers. Roles of DMSP (and related metabolites) in interactions between E. huxleyi and protist grazers have been investigated, however, little is known about the release of other metabolites that may influence, or be influenced by, such grazing interactions. We used high-resolution mass spectrometry in an untargeted approach to survey the suite of low molecular weight compounds released by four different E. huxleyi strains in response to grazing by the dinoflagellate Oxyrrhis marina. Overall, a strikingly small number of metabolites were detected from E. huxleyi and O. marina cells, but these were distinctly informative to construct metabolic footprints. At most, E. huxleyi strains shared 25% of released metabolites. Furthermore, there appeared to be no unified metabolic response in E. huxleyi strains to grazing; rather, these responses were strain specific. Concentrations of several metabolites also positively correlated with grazer activities, including grazing, ingestion, and growth rates; however, no single metabolite responded uniformly across all strains of E. huxleyi tested. Regardless, grazing clearly transformed the constituents of dissolved organic matter produced by these marine microbes. This study addresses several technical challenges, and presents a platform to further study the influence of chemical cues in aquatic systems and demonstrates the impact of strain diversity and grazing on the complexity of dissolved organic matter in marine systems.
    Description: Funding for this work was provided by the Gordon and Betty Moore Foundation, Grant #3301 awarded to A Vardi, BAS. Van Mooy, K Bidle, MJ, and TM. Additional funding for this work was provided by an award from the Flatley Discovery Lab to TM.
    Keywords: Dissolved organic matter ; Environmental metabolomics ; Grazing ; Metabolic footprinting ; Phytoplankton
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  • 29
    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 Frontiers in Marine Science 2 (2016): 202, doi:10.3389/fmars.2016.00202.
    Description: Marine spatial planning and ecological research call for high-resolution species distribution data. However, those data are still not available for most marine large vertebrates. The dynamic nature of oceanographic processes and the wide-ranging behavior of many marine vertebrates create further difficulties, as distribution data must incorporate both the spatial and temporal dimensions. Cetaceans play an essential role in structuring and maintaining marine ecosystems and face increasing threats from human activities. The Azores holds a high diversity of cetaceans but the information about spatial and temporal patterns of distribution for this marine megafauna group in the region is still very limited. To tackle this issue, we created monthly predictive cetacean distribution maps for spring and summer months, using data collected by the Azores Fisheries Observer Programme between 2004 and 2009. We then combined the individual predictive maps to obtain species richness maps for the same period. Our results reflect a great heterogeneity in distribution among species and within species among different months. This heterogeneity reflects a contrasting influence of oceanographic processes on the distribution of cetacean species. However, some persistent areas of increased species richness could also be identified from our results. We argue that policies aimed at effectively protecting cetaceans and their habitats must include the principle of dynamic ocean management coupled with other area-based management such as marine spatial planning.
    Description: This work was supported by FEDER funds, through the Competitiveness Factors Operational Programme - COMPETE, by national funds, through FCT - Foundation for Science and Technology, under project TRACE (PTDC/ MAR/74071/2006), and by regional funds, through DRCT/SRCTE, under projects MAPCET (M2.1.2/F/012/2011) and 2020 (M2.1.2/I/026/2011). We acknowledge funds provided by FCT to MARE, through the strategic project UID/MAR/04292/2013. RP is supported by an FCT postdoctoral grant (SFRH/BPD/108007/2015); MAS is supported by Program Investigator FCT (IF/00943/2013) and MT was supported by a research fellowship under the Exploratory project (IF/00943/2013/CP1199/CT0001) that also paid the fees for this open-access publication. IF/00943/2013 and IF/00943/2013/CP1199/CT0001 are funded by FSE and MCTES, through POPH and QREN.
    Keywords: Cetacean ; Spatio-temporal distribution ; Azores ; Species distribution models (SDMs) ; Richness ; MaxEnt
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  • 30
    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 Frontiers in Physiology 7 (2016): 620, doi:10.3389/fphys.2016.00620.
    Description: Vertebrates with laterally placed eyes typically exhibit preferential eye use for ecological activities such as scanning for predators or prey. Processing visual information predominately through the left or right visual field has been associated with specialized function of the left and right brain. Lateralized vertebrates often share a general pattern of lateralized brain function at the population level, whereby the left hemisphere controls routine behaviors and the right hemisphere controls emergency responses. Recent studies have shown evidence of preferential eye use in some invertebrates, but whether the visual fields are predominately associated with specific ecological activities remains untested. We used the European common cuttlefish, Sepia officinalis, to investigate whether the visual field they use is the same, or different, during anti-predatory, and predatory behavior. To test for lateralization of anti-predatory behavior, individual cuttlefish were placed in a new environment with opaque walls, thereby obliging them to choose which eye to orient away from the opaque wall to scan for potential predators (i.e., vigilant scanning). To test for lateralization of predatory behavior, individual cuttlefish were placed in the apex of an isosceles triangular arena and presented with two shrimp in opposite vertexes, thus requiring the cuttlefish to choose between attacking a prey item to the left or to the right of them. Cuttlefish were significantly more likely to favor the left visual field to scan for potential predators and the right visual field for prey attack. Moreover, individual cuttlefish that were leftward directed for vigilant scanning were predominately rightward directed for prey attack. Lateralized individuals also showed faster decision-making when presented with prey simultaneously. Cuttlefish appear to have opposite directions of lateralization for anti-predatory and predatory behavior, suggesting that there is functional specialization of each optic lobe (i.e., brain structures implicated in visual processing). These results are discussed in relation to the role of lateralized brain function and the evolution of population level lateralization.
    Description: This work was supported by a post-doctoral study grant from the Fyssen Foundation to AS, and by a research grant “Sélavie” from the Fyssen Foundation to CJ-A. The Sholley Foundation provided partial support for the research in Woods Hole.
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  • 31
    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 Frontiers in Marine Science 3 (2016): 137, doi:10.3389/fmars.2016.00137.
    Keywords: Right whales ; Conservation ; Mortalities ; Entanglements ; Population recovery
    Repository Name: Woods Hole Open Access Server
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  • 32
    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 Frontiers in Marine Science 4 (2017): 105, doi:10.3389/fmars.2017.00105.
    Description: Little is still known of the impacts of protist grazing on bacterioplankton communities in the dark ocean. Furthermore, the accuracy of assessments of in situ microbial activities, including protist grazing, can be affected by sampling artifacts introduced during sample retrieval and downstream manipulations. Potential artifacts may be increased when working with deep-sea samples or samples from chemically unique water columns such as oxygen minimum zones (OMZs). OMZs are oxygen-depleted regions in the ocean, where oxygen concentrations can drop to 〈20 μM. These regions are typically located near eastern boundary upwelling systems and currently occur in waters occupying below about 8% of total ocean surface area, representing ~1% of the ocean's volume. OMZs have a profound impact not only on the distribution of marine Metazoa, but also on the composition and activities of microbial communities at the base of marine food webs. Here we present an overview of current knowledge of protist phagotrophy below the photic zone, emphasizing studies of oxygen-depleted waters and presenting results of the first attempt to implement new technology for conducting these incubation studies completely in situ (the Microbial Sampling- Submersible Incubation Device, MS-SID). We performed 24-h incubation experiments in the Eastern Tropical South Pacific (ETSP) OMZ. This preliminary study shows that up to 28% of bacterial biomass may be consumed by protists in waters where oxygen concentrations were down to ~4.8 μM and up to 13% at a station with nitrite accumulation where oxygen concentrations were undetectable. Results also show that shipboard measurements of grazing rates were lower than rates measured from the same water using the MS-SID, suggesting that in situ experiments help to minimize artifacts that may be introduced when conducting incubation studies using waters collected from below the photic zone, particularly from oxygen-depleted regions of the water column.
    Description: This work was funded by the Agouron Institute, grant AI-M010.16.1 WHO to OU, M. Sullivan, and VE, and the Millenium Science Initiative, grant IC 120019. Ship time was provided the Chilean National Commission for Scientific and Technological Research (CONICYT) grant AUB 150006/12806.
    Keywords: OMZ ; Phagotrophy ; In situ technology ; Incubation studies ; ETSP ; Eastern Tropical South Pacific OMZ
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  • 33
    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 Frontiers in Cellular Neuroscience 11 (2017): 388, doi:10.3389/fncel.2017.00388.
    Description: α-Synuclein is a presynaptic protein that regulates synaptic vesicle (SV) trafficking. In Parkinson’s disease (PD) and several other neurodegenerative disorders, aberrant oligomerization and aggregation of α-synuclein lead to synaptic dysfunction and neurotoxicity. Despite evidence that α-synuclein oligomers are generated within neurons under physiological conditions, and that altering the balance of monomers and oligomers contributes to disease pathogenesis, how each molecular species of α-synuclein impacts SV trafficking is currently unknown. To address this, we have taken advantage of lamprey giant reticulospinal (RS) synapses, which are accessible to acute perturbations via axonal microinjection of recombinant proteins. We previously reported that acute introduction of monomeric α-synuclein inhibited SV recycling, including effects on the clathrin pathway. Here, we report the effects of α-synuclein dimers at synapses. Similar to monomeric α-synuclein, both recombinant α-synuclein dimers that were evaluated bound to small liposomes containing anionic lipids in vitro, but with reduced efficacy. When introduced to synapses, the α-synuclein dimers also induced SV recycling defects, which included a build up of clathrin-coated pits (CCPs) with constricted necks that were still attached to the plasma membrane, a phenotype indicative of a vesicle fission defect. Interestingly, both α-synuclein dimers induced longer necks on CCPs as well as complex, branching membrane tubules, which were distinct from the CCPs induced by a dynamin inhibitor, Dynasore. In contrast, monomeric α-synuclein induced a buildup of free clathrin-coated vesicles (CCVs), indicating an inhibition of clathrin-mediated endocytosis at a later stage during the clathrin uncoating process. Taken together, these data further support the conclusion that excess α-synuclein impairs SV recycling. The data additionally reveal that monomeric and dimeric α-synuclein produce distinct effects on clathrin-mediated endocytosis, predicting different molecular mechanisms. Understanding what these mechanisms are could help to further elucidate the normal functions of this protein, as well as the mechanisms underlying PD pathologies.
    Description: This study was supported by a research grant from the National Institutes of Health (NINDS/NIA R01NS078165 to JRM), research funds from the Marine Biological Laboratory (to JRM) and a research grant from Horizon 2020 Grant no. InCure EU Joint Programme—JPND (to LB).
    Keywords: Dynamin ; Dynasore ; Endocytosis ; Lamprey ; Reticulospinal synapse
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  • 34
    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 Frontiers in Marine Science 3 (2016): 232, doi:10.3389/fmars.2016.00232.
    Description: The reactive oxygen species (ROS) superoxide has been implicated in both beneficial and detrimental processes in coral biology, ranging from pathogenic disease resistance to coral bleaching. Despite the critical role of ROS in coral health, there is a distinct lack of ROS measurements and thus an incomplete understanding of underpinning ROS sources and production mechanisms within coral systems. Here, we quantified in situ extracellular superoxide concentrations at the surfaces of aquaria-hosted Porites astreoides during a diel cycle. High concentrations of superoxide (~10's of nM) were present at coral surfaces, and these levels did not change significantly as a function of time of day. These results indicate that the coral holobiont produces extracellular superoxide in the dark, independent of photosynthesis. As a short-lived anion at physiological pH, superoxide has a limited ability to cross intact biological membranes. Further, removing surface mucus layers from the P. astreoides colonies did not impact external superoxide concentrations. We therefore attribute external superoxide derived from the coral holobiont under these conditions to the activity of the coral host epithelium, rather than mucus-derived epibionts or internal sources such as endosymbionts (e.g., Symbiodinium). However, endosymbionts likely contribute to internal ROS levels via extracellular superoxide production. Indeed, common coral symbionts, including multiple strains of Symbiodinium (clades A to D) and the bacterium Endozoicomonas montiporae LMG 24815, produced extracellular superoxide in the dark and at low light levels. Further, representative P. astreoides symbionts, Symbiodinium CCMP2456 (clade A) and E. montiporae, produced similar concentrations of superoxide alone and in combination with each other, in the dark and low light, and regardless of time of day. Overall, these results indicate that healthy, non-stressed P. astreoides and representative symbionts produce superoxide externally, which is decoupled from photosynthetic activity and circadian control. Corals may therefore produce extracellular superoxide constitutively, highlighting an unclear yet potentially beneficial role for superoxide in coral physiology and health.
    Description: This work was supported by a Postdoctoral Fellowship from the Ford Foundation (JD), the National Science Foundation under grants OCE 1225801 (JD) and OCE 1233612 (AA), the Ocean and Climate Change Institute of the Woods Hole Oceanographic Institution (CH), a BIOS Grant in aid award (SM), the Sidney Stern Memorial Trust (CH and AA), as well as an anonymous donor.
    Keywords: Coral ; Superoxide ; Reactive oxygen species ; Photosynthesis ; Symbiodinium ; Stress
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  • 35
    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 Frontiers in Marine Science 3 (2016): 243, doi:10.3389/fmars.2016.00243.
    Description: Organic ligands form strong complexes with many trace elements in seawater. Various metals can compete for the same ligand chelation sites, and the final speciation of bound metals is determined by relative binding affinities, concentrations of binding sites, uncomplexed metal concentrations, and association/dissociation kinetics. Different ligands have a wide range of metal affinities and specificities. However, the chemical composition of these ligands in the marine environment remains poorly constrained, which has hindered progress in modeling marine metal speciation. In this study, we detected and characterized natural ligands that bind copper (Cu) and nickel (Ni) in the eastern South Pacific Ocean with liquid chromatography tandem inductively coupled plasma mass spectrometry (LC-ICPMS), and high-resolution electrospray ionization mass spectrometry (ESIMS). Dissolved Cu, Ni, and ligand concentrations were highest near the coast. Chromatographically unresolved polar compounds dominated ligands isolated near the coast by solid phase extraction. Offshore, metal and ligand concentrations decreased, but several new ligands appeared. One major ligand was detected that bound both Cu2+ and Ni2+. Based on accurate mass and fragmentation measurements, this compound has a molecular formula of [C20H21N4O8S2+M]+ (M = metal isotope) and contains several azole-like metal binding groups. Additional lipophilic Ni complexes were also present only in oligotrophic waters, with masses of 649, 698, and 712 m/z (corresponding to the 58Ni metal complex). Molecular formulae of [C32H54N3O6S2Ni]+ and [C33H56N3O6S2Ni]+ were determined for two of these compounds. Addition of Cu and Ni to the samples also revealed the presence of additional compounds that can bind both Ni and Cu. Although these specific compounds represent a small fraction of the total dissolved Cu and Ni pool, they highlight the compositional diversity and spatial heterogeneity of marine Ni and Cu ligands, as well as variability in the extent to which different metals in the same environment compete for ligand binding.
    Description: Support was provided by the National Science Foundation (NSF) program in Chemical Oceanography (OCE-1356747, OCE-1233261, OCE-1233733, OCE-1233502, and OCE-1237034), the NSF Science and Technology Center for Microbial Oceanography Research and Education (C-MORE; DBI-0424599), the Gordon and Betty Moore Foundation (#3298 and 3934), and the Simons Foundation (#329108, DR).
    Keywords: Copper ; Nickel ; Marine ligands ; Metal competition ; GEOTRACES ; Eastern Pacific
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  • 36
    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 Frontiers in Microbiology 7 (2016): 2017, doi:10.3389/fmicb.2016.02017.
    Description: Ciliates from the genus Mesodinium are globally distributed in marine and freshwater ecosystems and may possess either heterotrophic or mixotrophic nutritional modes. Members of the Mesodinium major/rubrum species complex photosynthesize by sequestering and maintaining organelles from cryptophyte prey, and under certain conditions form periodic or recurrent blooms (= red tides). Here, we present an analysis of the genetic diversity of Mesodinium and cryptophyte populations from 10 environmental samples (eight globally dispersed habitats including five Mesodinium blooms), using group-specific primers for Mesodinium partial 18S, ITS, and partial 28S rRNA genes as well as cryptophyte large subunit RuBisCO genes (rbcL). In addition, 22 new cryptophyte and four new M. rubrum cultures were used to extract DNA and sequence rbcL and 18S-ITS-28S genes, respectively, in order to provide a stronger phylogenetic context for our environmental sequences. Bloom samples were analyzed from coastal Brazil, Chile, two Northeastern locations in the United States, and the Pribilof Islands within the Bering Sea. Additionally, samples were also analyzed from the Baltic and Barents Seas and coastal California under non-bloom conditions. Most blooms were dominated by a single Mesodinium genotype, with coastal Brazil and Chile blooms composed of M. major and the Eastern USA blooms dominated by M. rubrum variant B. Sequences from all four blooms were dominated by Teleaulax amphioxeia-like cryptophytes. Non-bloom communities revealed more diverse assemblages of Mesodinium spp., including heterotrophic species and the mixotrophic Mesodinium chamaeleon. Similarly, cryptophyte diversity was also higher in non-bloom samples. Our results confirm that Mesodinium blooms may be caused by M. major, as well as multiple variants of M. rubrum, and further implicate T. amphioxeia as the key cryptophyte species linked to these phenomena in temperate and subtropical regions.
    Description: MJ thanks the funding support of the National Science Foundations Grants NSF-OCE 1031718 and NSF-IOS 1326228.
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  • 37
    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 Frontiers in Marine Science 4 (2017): 338, doi:10.3389/fmars.2017.00338.
    Description: The Santa Maria di Leuca (SML) cold-water coral province (northern Ionian Sea) has the largest occurrence of a living white coral community currently known in the Mediterranean Sea. Madrepora oculata and Lophelia pertusa, identified as marking sensitive habitats of relevance by the General Fisheries Commission for the Mediterranean, have been observed heterogeneously distributed on the summits of several mounds. This particularly patchy and uneven distribution in addition to their importance for regional biodiversity highlights the need to better understand their environmental preferences and predict their distribution. Bathymetric data (40 m resolution) was used to derive seafloor characteristics. A fine scale index quantifying the landscape elevation (Bathymetric Position Index at 120 m resolution) was used to select all the elevated features considered as candidate morphologies for potential coral mounds. Statistics on 22 known coral topped mounds were computed. Two statistical methods were then used to identify other potential coral mounds based on predictive variables. The first method, the Geomorphometric proxies method, consists in computing basic statistics of terrain variables, using them for a step-by-step classification in a quantitative approach to select a subset of candidate morphologies. The second method consists in using a predictive Habitat Suitability Model (Maxent model). The Geomorphometric proxies method identified 736 potential coral mounds while the Maxent method predicted 1,252 potential coral mounds. A subset of 517 potential coral mounds was common to both methods. The analysis of the contribution of each variable with the Maxent method showed that the variable “Vector Ruggedness Measure” at a resolution of 5 pixels (200 m) contributed to 53% of the final Maxent model, followed by the “Terrain Texture” index (31%) at a resolution of 11 pixels (440 m). The common potential coral mounds are mainly located in an area characterized by a mass transport deposit, also called the mounds area because of the roughness of the seafloor, in accordance with the high proportional contribution of the noticeable first roughness index to the Maxent model. The results highlight the importance of the global conservation of the entire Province, with white coral probably widespread over the entire 600 km2 SML area.
    Description: The Habitat Suitability model study was part of a post-doctoral grant funded by the “Agence de l'Eau Rhône Méditerranée & Corse” under Convention Number 2015 0348, Ifremer and ISMAR Bologna. We are grateful to all the participants and the P.I. of the Aplabes 2004; Aplabes 2005, HERMES M70-1, MEDECO 2007 (http://dx.doi.org/10.17600/7030090) and magic CoralFISH 2010 cruises. The authors also benefited from EU FP7 project CoralFish (Grant agreement number: 213144—http://www.eu-fp7-coralfish.net), the Flag Project Ritmare (Ricerca Italiana per il Mare), funded by the Italian Ministry of Universities and Research (MIUR) and the ESF COCARDE Network. FM was funded through a Ph. D. fellowship in Earth Sciences at the University of Milano-Bicocca.
    Keywords: Predictive habitat mapping ; Maxent ; Cold-water coral ; Ecological proxies ; Santa Maria di Leuca ; Mediterranean Sea
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  • 38
    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 Frontiers in Microbiology 7 (2016): 1074, doi:10.3389/fmicb.2016.01074.
    Description: Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at hydrothermal vents. These environments are distinguished by high physico-chemical variability, yet we know little about how these symbioses respond to environmental fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent snail Ifremeria nautilei respond to changes in sulfur geochemistry. Via shipboard high-pressure incubations, we subjected snails to 105 μM hydrogen sulfide (LS), 350 μM hydrogen sulfide (HS), 300 μM thiosulfate (TS) and seawater without any added inorganic electron donor (ND). While transcript levels of sulfur oxidation genes were largely consistent across treatments, HS and TS treatments stimulated genes for denitrification, nitrogen assimilation, and CO2 fixation, coincident with previously reported enhanced rates of inorganic carbon incorporation and sulfur oxidation in these treatments. Transcripts for genes mediating oxidative damage were enriched in the ND and LS treatments, potentially due to a reduction in O2 scavenging when electron donors were scarce. Oxidative TCA cycle gene transcripts were also more abundant in ND and LS treatments, suggesting that I. nautilei symbionts may be mixotrophic when inorganic electron donors are limiting. These data reveal the extent to which I. nautilei symbionts respond to changes in sulfur concentration and species, and, interpreted alongside coupled biochemical metabolic rates, identify gene targets whose expression patterns may be predictive of holobiont physiology in environmental samples.
    Description: This work was supported by National Science Foundation Grants OCE-0732369 (to PG), DGE-1144152 (to RB), and (1151698 to FS) and the Alfred P. Sloan Foundation (grant RC944 to FS).
    Keywords: Ifremeria nautilei ; Chemoautotroph ; Endosymbiont ; Methanotrophic bacteria ; Sulfur oxidizers ; Metatranscriptomics ; Deep sea vents
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  • 39
    Publication Date: 2016-07-12
    Description: Chemical Reviews DOI: 10.1021/acs.chemrev.6b00082
    Print ISSN: 0009-2665
    Electronic ISSN: 1520-6890
    Topics: Chemistry and Pharmacology
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  • 40
    Publication Date: 2016-07-10
    Description: Environmental Science & Technology DOI: 10.1021/acs.est.6b01283
    Print ISSN: 0013-936X
    Electronic ISSN: 1520-5851
    Topics: Chemistry and Pharmacology , Energy, Environment Protection, Nuclear Power Engineering
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  • 41
    Publication Date: 2016-07-10
    Description: Environmental Science & Technology DOI: 10.1021/acs.est.6b02784
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    Electronic ISSN: 1520-5851
    Topics: Chemistry and Pharmacology , Energy, Environment Protection, Nuclear Power Engineering
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  • 42
    Publication Date: 2016-07-12
    Description: Organic Letters DOI: 10.1021/acs.orglett.6b01518
    Print ISSN: 1523-7060
    Electronic ISSN: 1523-7052
    Topics: Chemistry and Pharmacology
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  • 43
    Publication Date: 2016-07-12
    Description: Organic Letters DOI: 10.1021/acs.orglett.6b01501
    Print ISSN: 1523-7060
    Electronic ISSN: 1523-7052
    Topics: Chemistry and Pharmacology
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  • 44
    Publication Date: 2016-07-13
    Description: ACS Sustainable Chemistry & Engineering DOI: 10.1021/acssuschemeng.6b00700
    Electronic ISSN: 2168-0485
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
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  • 45
    Publication Date: 2016-07-13
    Description: ACS Sustainable Chemistry & Engineering DOI: 10.1021/acssuschemeng.6b00316
    Electronic ISSN: 2168-0485
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
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  • 46
    Publication Date: 2016-07-13
    Description: ACS Sustainable Chemistry & Engineering DOI: 10.1021/acssuschemeng.6b00753
    Electronic ISSN: 2168-0485
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
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  • 47
    Publication Date: 2016-07-13
    Description: Analytical Chemistry DOI: 10.1021/acs.analchem.6b00946
    Print ISSN: 0003-2700
    Electronic ISSN: 1520-6882
    Topics: Chemistry and Pharmacology
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  • 48
    Publication Date: 2016-07-11
    Description: Journal of the American Chemical Society DOI: 10.1021/jacs.6b04345
    Print ISSN: 0002-7863
    Electronic ISSN: 1520-5126
    Topics: Chemistry and Pharmacology
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  • 49
    Publication Date: 2016-07-12
    Description: ACS Sustainable Chemistry & Engineering DOI: 10.1021/acssuschemeng.6b00173
    Electronic ISSN: 2168-0485
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
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  • 50
    Publication Date: 2016-07-12
    Description: Analytical Chemistry DOI: 10.1021/acs.analchem.6b02124
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    Electronic ISSN: 1520-6882
    Topics: Chemistry and Pharmacology
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  • 51
    Publication Date: 2016-07-12
    Description: Analytical Chemistry DOI: 10.1021/acs.analchem.6b01292
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    Electronic ISSN: 1520-6882
    Topics: Chemistry and Pharmacology
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  • 52
    Publication Date: 2016-07-13
    Description: Journal of Chemical & Engineering Data DOI: 10.1021/acs.jced.5b00914
    Print ISSN: 0021-9568
    Electronic ISSN: 1520-5134
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
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  • 53
    Publication Date: 2016-07-13
    Description: Journal of Chemical Information and Modeling DOI: 10.1021/acs.jcim.6b00109
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  • 54
    Publication Date: 2016-07-13
    Description: Journal of Chemical & Engineering Data DOI: 10.1021/acs.jced.6b00295
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  • 55
    Publication Date: 2016-07-13
    Description: Crystal Growth & Design DOI: 10.1021/acs.cgd.6b00420
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    Description: Crystal Growth & Design DOI: 10.1021/acs.cgd.6b00655
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    Publication Date: 2016-07-13
    Description: The Journal of Organic Chemistry DOI: 10.1021/acs.joc.6b01111
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    Publication Date: 2016-07-13
    Description: The Journal of Organic Chemistry DOI: 10.1021/acs.joc.6b00979
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    Publication Date: 2016-07-13
    Description: Journal of the American Chemical Society DOI: 10.1021/jacs.6b05430
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    Description: Journal of the American Chemical Society DOI: 10.1021/jacs.6b05271
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    Description: Journal of the American Chemical Society DOI: 10.1021/jacs.6b03995
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    Description: Journal of the American Chemical Society DOI: 10.1021/jacs.6b04454
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    Description: Journal of the American Chemical Society DOI: 10.1021/jacs.6b05227
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    Description: Journal of the American Chemical Society DOI: 10.1021/jacs.6b06137
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    Description: Langmuir DOI: 10.1021/acs.langmuir.6b01688
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    Publication Date: 2016-07-14
    Description: Biochemistry DOI: 10.1021/acs.biochem.6b00401
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    Description: Analytical Chemistry DOI: 10.1021/acs.analchem.6b01857
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    Description: Analytical Chemistry DOI: 10.1021/acs.analchem.6b01314
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    Description: Analytical Chemistry DOI: 10.1021/acs.analchem.6b00926
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    Description: Analytical Chemistry DOI: 10.1021/acs.analchem.6b02032
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    Publication Date: 2016-07-14
    Description: ACS Sustainable Chemistry & Engineering DOI: 10.1021/acssuschemeng.6b00894
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    Description: Analytical Chemistry DOI: 10.1021/acs.analchem.6b01250
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    Publication Date: 2016-07-14
    Description: Crystal Growth & Design DOI: 10.1021/acs.cgd.6b00791
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    Publication Date: 2016-07-14
    Description: Organic Letters DOI: 10.1021/acs.orglett.6b01559
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    Description: Organic Letters DOI: 10.1021/acs.orglett.6b01795
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    Description: Journal of Chemical Information and Modeling DOI: 10.1021/acs.jcim.5b00753
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    Description: Organic Letters DOI: 10.1021/acs.orglett.6b01796
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    Publication Date: 2016-07-15
    Description: Analytical Chemistry DOI: 10.1021/acs.analchem.6b01682
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    Description: Organic Letters DOI: 10.1021/acs.orglett.6b01743
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    Description: Journal of Chemical & Engineering Data DOI: 10.1021/acs.jced.6b00532
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    Description: Journal of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.6b00681
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    Publication Date: 2016-07-15
    Description: The Journal of Organic Chemistry DOI: 10.1021/acs.joc.6b00965
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    Publication Date: 2016-07-15
    Description: The Journal of Organic Chemistry DOI: 10.1021/acs.joc.6b01060
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    Publication Date: 2016-07-15
    Description: The Journal of Organic Chemistry DOI: 10.1021/acs.joc.6b01210
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    Description: The Journal of Organic Chemistry DOI: 10.1021/acs.joc.6b00992
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    Description: The Journal of Organic Chemistry DOI: 10.1021/acs.joc.6b00996
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    Publication Date: 2016-07-15
    Description: The Journal of Organic Chemistry DOI: 10.1021/acs.joc.6b00651
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    Description: The Journal of Physical Chemistry B DOI: 10.1021/acs.jpcb.6b05271
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    Publication Date: 2016-07-15
    Description: The Journal of Organic Chemistry DOI: 10.1021/acs.joc.6b00816
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    Description: The Journal of Organic Chemistry DOI: 10.1021/acs.joc.6b00858
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    Description: The Journal of Physical Chemistry B DOI: 10.1021/acs.jpcb.6b05697
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    Description: The Journal of Physical Chemistry B DOI: 10.1021/acs.jpcb.6b05342
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    Description: The Journal of Physical Chemistry B DOI: 10.1021/acs.jpcb.6b04796
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