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  • 1
    Publication Date: 2017-01-05
    Description: Author Posting. © Inter-Research, 2008. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Diseases of Aquatic Organisms 81 (2008): 219-229, doi:10.3354/dao01948.
    Description: Quahog Parasite Unknown (QPX) is the cause of mass mortality events of hard clams Mercenaria mercenaria from Virginia, USA, to New Brunswick, Canada. Aquaculture areas in Massachusetts, USA, have been particularly hard hit. The parasite has been shown to be a directly infective organism, but it is unclear whether it could exist or persist outside of its clam host. We used molecular methods to examine water, sediment, seaweeds, seagrass and various invertebrates for the presence of QPX. Sites in Virginia and Massachusetts were selected based upon the incidence of QPX-induced clam die-offs, and they were monitored seasonally. QPX was detectable in almost all of our different sample types from Massachusetts, indicating that the parasite was widely distributed in the environment. Significantly more samples from Massachusetts were positive than from Virginia, and there was a seasonal pattern to the types of samples positive from Massachusetts. The data suggest that, although it may be difficult to completely eradicate QPX from the environment, it may be possible to keep the incidence of disease under control through good plot husbandry and the removal of infected and dying clams.
    Description: This work is the result of research sponsored by NOAA National Sea Grant College Program Office, Department of Commerce, under Grant No. NA16RG2273, Woods Hole Oceanographic Institution Sea Grant Project No. R/B-168.
    Keywords: Quahog Parasite Unknown ; QPX ; Environmental detection ; Remediation
    Repository Name: Woods Hole Open Access Server
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  • 2
    Publication Date: 2017-11-16
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biogeosciences 14 (2017): 4637-4662, doi:10.5194/bg-14-4637-2017.
    Description: The stoichiometry of biological components and their influence on dissolved distributions have long been of interest in the study of the oceans. Cobalt has the smallest oceanic inventory of inorganic micronutrients and hence is particularly vulnerable to influence by internal oceanic processes including euphotic zone uptake, remineralization, and scavenging. Here we observe not only large variations in dCo : P stoichiometry but also the acceleration of those dCo : P ratios in the upper water column in response to several environmental processes. The ecological stoichiometry of total dissolved cobalt (dCo) was examined using data from a US North Atlantic GEOTRACES transect and from a zonal South Atlantic GEOTRACES-compliant transect (GA03/3_e and GAc01) by Redfieldian analysis of its statistical relationships with the macronutrient phosphate. Trends in the dissolved cobalt to phosphate (dCo : P) stoichiometric relationships were evident in the basin-scale vertical structure of cobalt, with positive dCo : P slopes in the euphotic zone and negative slopes found in the ocean interior and in coastal environments. The euphotic positive slopes were often found to accelerate towards the surface and this was interpreted as being due to the combined influence of depleted phosphate, phosphorus-sparing (conserving) mechanisms, increased alkaline phosphatase metalloenzyme production (a zinc or perhaps cobalt enzyme), and biochemical substitution of Co for depleted Zn. Consistent with this, dissolved Zn (dZn) was found to be drawn down to only 2-fold more than dCo, despite being more than 18-fold more abundant in the ocean interior. Particulate cobalt concentrations increased in abundance from the base of the euphotic zone to become  ∼  10 % of the overall cobalt inventory in the upper euphotic zone with high stoichiometric values of  ∼  400 µmol Co mol−1 P. Metaproteomic results from the Bermuda Atlantic Time-series Study (BATS) station found cyanobacterial isoforms of the alkaline phosphatase enzyme to be prevalent in the upper water column, as well as a sulfolipid biosynthesis protein indicative of P sparing. The negative dCo : P relationships in the ocean interior became increasingly vertical with depth, and were consistent with the sum of scavenging and remineralization processes (as shown by their dCo : P vector sums). Attenuation of the remineralization with depth resulted in the increasingly vertical dCo : P relationships. Analysis of particulate Co with particulate Mn and particulate phosphate also showed positive linear relationships below the euphotic zone, consistent with the presence and increased relative influence of Mn oxide particles involved in scavenging. Visualization of dCo : P slopes across an ocean section revealed hotspots of scavenging and remineralization, such as at the hydrothermal vents and below the oxygen minimum zone (OMZ) region, respectively, while that of an estimate of Co* illustrated stoichiometrically depleted values in the mesopelagic and deep ocean due to scavenging. This study provides insights into the coupling between the dissolved and particulate phase that ultimately creates Redfield stoichiometric ratios, demonstrating that the coupling is not an instantaneous process and is influenced by the element inventory and rate of exchange between phases. Cobalt's small water column inventory and the influence of external factors on its biotic stoichiometry can erode its limited inertia and result in an acceleration of the dissolved stoichiometry towards that of the particulate phase in the upper euphotic zone. As human use of cobalt grows exponentially with widespread adoption of lithium ion batteries, there is a potential to affect the limited biogeochemical inertia of cobalt and its resultant ecology in the oceanic euphotic zone.
    Description: This work was funded by the National Science Foundation as part of the US GEOTRACES North Atlantic Zonal Transect program under grants OCE-0928414 and OCE-1435056 (to Mak A. Saito), OCE-0928289 (to Benjamin S. Twining), OCE-0963026 (to Phoebe Lam) and support from the Gordon and Betty Moore Foundation (3782 to Mak A. Saito).
    Repository Name: Woods Hole Open Access Server
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  • 3
    Publication Date: 2016-09-23
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Chemistry 1 (2013): 25, doi:10.3389/fchem.2013.00025.
    Description: Dissolved and particulate metal concentrations are reported from three sites beneath and at the base of the McMurdo Sound seasonal sea ice in the Ross Sea of Antarctica. This dataset provided insight into Co and Mn biogeochemistry, supporting a previous hypothesis for water column mixing occurring faster than scavenging. Three observations support this: first, Mn-containing particles with Mn/Al ratios in excess of the sediment were present in the water column, implying the presence of bacterial Mn-oxidation processes. Second, dissolved and labile Co were uniform with depth beneath the sea ice after the winter season. Third, dissolved Co:PO3−4 ratios were consistent with previously observed Ross Sea stoichiometry, implying that over-winter scavenging was slow relative to mixing. Abundant dissolved Fe and Mn were consistent with a winter reserve concept, and particulate Al, Fe, Mn, and Co covaried, implying that these metals behaved similarly. Elevated particulate metals were observed in proximity to the nearby Islands, with particulate Fe/Al ratios similar to that of nearby sediment, consistent with a sediment resuspension source. Dissolved and particulate metals were elevated at the shallowest depths (particularly Fe) with elevated particulate P/Al and Fe/Al ratios in excess of sediments, demonstrating a sea ice biomass source. The sea ice biomass was extremely dense (chl a 〉9500 μg/L) and contained high abundances of particulate metals with elevated metal/Al ratios. A hypothesis for seasonal accumulation of bioactive metals at the base of the McMurdo Sound sea ice by the basal algal community is presented, analogous to a capacitor that accumulates iron during the spring and early summer. The release and transport of particulate metals accumulated at the base of the sea ice by sloughing is discussed as a potentially important mechanism in providing iron nutrition during polynya phytoplankton bloom formation and could be examined in future oceanographic expeditions.
    Description: This research was funded by NSF OPP grant 0732665, NSF-OCE grant numbers 1031271, 0928414, 0752291, 1233261, and the Gordon and Betty Moore Foundation.
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2018-09-25
    Description: © The Author(s), 2011. This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited. The definitive version was published in Frontiers in Microbiology 2 (2011): 215, doi:10.3389/fmicb.2011.00215.
    Description: Improvements in temporal and spatial sampling frequency have the potential to open new windows into the understanding of marine microbial dynamics. In recent years, efforts have been made to allow automated samplers to collect microbial biomass for DNA/RNA analyses from moored observatories and autonomous underwater vehicles. Measurements of microbial proteins are also of significant interest given their biogeochemical importance as enzymes that catalyze reactions and transporters that interface with the environment. We examined the influence of five preservatives solutions (SDS-extraction buffer, ethanol, trichloroacetic acid, B-PER, and RNAlater) on the proteome integrity of the marine cyanobacterium Synechococcus WH8102 after 4 weeks of storage at room temperature. Four approaches were used to assess degradation: total protein recovery, band integrity on an SDS detergent polyacrylamide electrophoresis (SDS-PAGE) gel, and number of protein identifications and relative abundances by 1-dimensional LC–MS/MS proteomic analyses. Total protein recoveries from the preserved samples were lower than the frozen control due to processing losses, which could be corrected for with internal standardization. The trichloroacetic acid preserved sample showed significant loss of protein band integrity on the SDS-PAGE gel. The RNAlater preserved sample showed the highest number of protein identifications (103% relative to the control; 520 ± 31 identifications in RNAlater versus 504 ± 4 in the control), equivalent to the frozen control. Relative abundances of individual proteins in the RNAlater treatment were quite similar to that of the frozen control (average ratio of 1.01 ± 0.27 for the 50 most abundant proteins), while the SDS-extraction buffer, ethanol, and B-PER all showed significant decreases in both number of identifications and relative abundances of individual proteins. Based on these findings, RNAlater was an effective proteome preservative, although further study is warranted on additional marine microbes.
    Description: This work was funded by the National Science Foundation Chemical and Biological Oceanography, Center for Microbial Oceanography Research and Education (C-MORE), and the Gordon and Betty Moore Foundation.
    Keywords: Proteome ; Preservation ; Autonomous sampling ; Cyanobacteria ; Alkaline phosphatase ; Proteomics ; Synechococcus WH8102
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2018-09-07
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biogeosciences 15 (2018): 4923-4942, doi:10.5194/bg-15-4923-2018.
    Description: Phaeocystis antarctica is an important phytoplankter of the Ross Sea where it dominates the early season bloom after sea ice retreat and is a major contributor to carbon export. The factors that influence Phaeocystis colony formation and the resultant Ross Sea bloom initiation have been of great scientific interest, yet there is little known about the underlying mechanisms responsible for these phenomena. Here, we present laboratory and field studies on Phaeocystis antarctica grown under multiple iron conditions using a coupled proteomic and transcriptomic approach. P. antarctica had a lower iron limitation threshold than a Ross Sea diatom Chaetoceros sp., and at increased iron nutrition (〉120pM Fe') a shift from flagellate cells to a majority of colonial cells in P. antarctica was observed, implying a role for iron as a trigger for colony formation. Proteome analysis revealed an extensive and coordinated shift in proteome structure linked to iron availability and life cycle transitions with 327 and 436 proteins measured as significantly different between low and high iron in strains 1871 and 1374, respectively. The enzymes flavodoxin and plastocyanin that can functionally replace iron metalloenzymes were observed at low iron treatments consistent with cellular iron-sparing strategies, with plastocyanin having a larger dynamic range. The numerous isoforms of the putative iron-starvation-induced protein (ISIP) group (ISIP2A and ISIP3) had abundance patterns coinciding with that of either low or high iron (and coincident flagellate or the colonial cell types in strain 1871), implying that there may be specific iron acquisition systems for each life cycle type. The proteome analysis also revealed numerous structural proteins associated with each cell type: within flagellate cells actin and tubulin from flagella and haptonema structures as well as a suite of calcium-binding proteins with EF domains were observed. In the colony-dominated samples a variety of structural proteins were observed that are also often found in multicellular organisms including spondins, lectins, fibrillins, and glycoproteins with von Willebrand domains. A large number of proteins of unknown function were identified that became abundant at either high or low iron availability. These results were compared to the first metaproteomic analysis of a Ross Sea Phaeocystis bloom to connect the mechanistic information to the in situ ecology and biogeochemistry. Proteins associated with both flagellate and colonial cells were observed in the bloom sample consistent with the need for both cell types within a growing bloom. Bacterial iron storage and B12 biosynthesis proteins were also observed consistent with chemical synergies within the colony microbiome to cope with the biogeochemical conditions. Together these responses reveal a complex, highly coordinated effort by P. antarctica to regulate its phenotype at the molecular level in response to iron and provide a window into the biology, ecology, and biogeochemistry of this group.
    Description: Support for this study was provided by an Investigator grant to Mak A. Saito from the Gordon and Betty Moore Foundation (GBMF3782), National Science Foundation grants NSF-PLR 0732665, OCE-1435056, OCE-1220484, and ANT-1643684, the WHOI Coastal Ocean Institute, and a CINAR Postdoctoral Scholar Fellowship provided to Sara J. Bender through the Woods Hole Oceanographic Institution. Support was provided to Andrew E. Allen through NSF awards ANT-0732822, ANT-1043671, and OCE-1136477 and Gordon and Betty Moore Foundation grant GBMF3828. Additional support was provided to GRD through NSF award OPP-0338097.
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  • 6
    Publication Date: 2019-03-04
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 License. The definitive version was published in mSystems 4(1), (2019): 4:e00317-18, doi:10.1128/mSystems.00317-18.
    Description: Two-component sensory (TCS) systems link microbial physiology to the environment and thus may play key roles in biogeochemical cycles. In this study, we surveyed the TCS systems of 328 diverse marine bacterial species. We identified lifestyle traits such as copiotrophy and diazotrophy that are associated with larger numbers of TCS system genes within the genome. We compared marine bacterial species with 1,152 reference bacterial species from a variety of habitats and found evidence of extra response regulators in marine genomes. Examining the location of TCS genes along the circular bacterial genome, we also found that marine bacteria have a large number of “orphan” genes, as well as many hybrid histidine kinases. The prevalence of “extra” response regulators, orphan genes, and hybrid TCS systems suggests that marine bacteria break with traditional understanding of how TCS systems operate. These trends suggest prevalent regulatory networking, which may allow coordinated physiological responses to multiple environmental signals and may represent a specific adaptation to the marine environment. We examine phylogenetic and lifestyle traits that influence the number and structure of two-component systems in the genome, finding, for example, that a lack of two-component systems is a hallmark of oligotrophy. Finally, in an effort to demonstrate the importance of TCS systems to marine biogeochemistry, we examined the distribution of Prochlorococcus/Synechococcus response regulator PMT9312_0717 in metaproteomes of the tropical South Pacific. We found that this protein’s abundance is related to phosphate concentrations, consistent with a putative role in phosphate regulation.
    Description: We thank Joe Jennings at Oregon State University and Chris Dupont at the J. Craig Venter Institute for providing nutrient and metagenomic analyses, respectively, for the KM1128 METZYME research expedition. We also thank our anonymous reviewers for their thoughtful comments. This material is based on work supported by a National Science Foundation Graduate Research Fellowship under grant number 1122274 (N. A. Held). It was also supported by the Gordon and Betty Moore Foundation (grant number 3782 [M. Saito]) and by the National Science Foundation (grant numbers OCE-1657766, EarthCube 1639714, OCE-1658030, and OCE-1260233).
    Keywords: biogeochemistry ; cell signaling ; gene regulation ; marine microbiology ; proteomics ; regulatory network ; two-component system
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  • 7
    Publication Date: 2017-01-04
    Description: Author Posting. © Inter-Research, 2006. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Diseases of Aquatic Organisms 70 (2006): 115-122, doi:10.3354/dao070115.
    Description: Quahog Parasite Unknown (QPX) is a significant cause of hard clam Mercenaria mercenaria mortality along the northeast coast of the United States. It infects both wild and cultured clams, often annually in plots that are heavily farmed. Subclinically infected clams can be identified by histological examination of the mantle tissue, but there is currently no method available to monitor the presence of QPX in the environment. Here, we report on a polymerase chain reaction (PCR)-based method that will facilitate the detection of QPX in natural samples and seed clams. With our method, between 10 and 100 QPX cells can be detected in 1 l of water, 1 g of sediment and 100 mg of clam tissue. Denaturing gradient gel electrophoresis (DGGE) is used to establish whether the PCR products are the same as those in the control QPX culture. We used the method to screen 100 seed clams of 15 mm, and found that 10 to 12% of the clams were positive for the presence of the QPX organism. This method represents a reliable and sensitive procedure for screening both environmental samples and potentially contaminated small clams.
    Description: Quahog Parasite Unknown (QPX) is a significant cause of hard clam Mercenaria mercenaria mortality along the northeast coast of the United States. It infects both wild and cultured clams, often annually in plots that are heavily farmed. Subclinically infected clams can be identified by histological examination of the mantle tissue, but there is currently no method available to monitor the presence of QPX in the environment. Here, we report on a polymerase chain reaction (PCR)-based method that will facilitate the detection of QPX in natural samples and seed clams. With our method, between 10 and 100 QPX cells can be detected in 1 l of water, 1 g of sediment and 100 mg of clam tissue. Denaturing gradient gel electrophoresis (DGGE) is used to establish whether the PCR products are the same as those in the control QPX culture. We used the method to screen 100 seed clams of 15 mm, and found that 10 to 12% of the clams were positive for the presence of the QPX organism. This method represents a reliable and sensitive procedure for screening both environmental samples and potentially contaminated small clams.
    Keywords: Quahog Parasite Unknown ; Detection limit ; Seed clams ; SSU rDNA
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2016-06-11
    Description: Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Proteomics 15 (2015): 3521-3531, doi:10.1002/pmic.201400630.
    Description: Proteomics has great potential for studies of marine microbial biogeochemistry, yet high microbial diversity in many locales presents us with unique challenges. We addressed this challenge with a targeted metaproteomics workflow for NtcA and P-II, two nitrogen regulatory proteins, and demonstrated its application for cyanobacterial taxa within microbial samples from the Central Pacific Ocean. Using METATRYP, an open-source Python toolkit, we examined the number of shared (redundant) tryptic peptides in representative marine microbes, with the number of tryptic peptides shared between different species typically being 1% or less. The related cyanobacteria Prochlorococcus and Synechococcus shared an average of 4.8+1.9% of their tryptic peptides, while shared intraspecies peptides were higher, 13+15% shared peptides between 12 Prochlorococcus genomes. An NtcA peptide was found to target multiple cyanobacteria species, whereas a P-II peptide showed specificity to the high-light Prochlorococcus ecotype. Distributions of NtcA and P-II in the Central Pacific Ocean were similar except at the Equator likely due to differential nitrogen stress responses between Prochlorococcus and Synechococcus. The number of unique tryptic peptides coded for within three combined oceanic microbial metagenomes was estimated to be ~4x107, 1000-fold larger than an individual microbial proteome and 27-fold larger than the human proteome, yet still 20 orders of magnitude lower than the peptide diversity possible in all protein space, implying that peptide mapping algorithms should be able to withstand the added level of complexity in metaproteomic samples.
    Description: This research was funded by the Gordon and Betty Moore Foundation and the US National Science Foundation under grant numbers 3782, 3934, OCE-1260233, OCE-1233261, OCE-1220484, OCE-1333212 and OCE-1155566, and the Center for Microbial Oceanography Research and Education (C-MORE).
    Description: 2016-06-11
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2016-09-23
    Description: This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 6 (2015): 8155, doi:10.1038/ncomms9155.
    Description: Nitrogen fixation rates of the globally distributed, biogeochemically important marine cyanobacterium Trichodesmium increase under high carbon dioxide (CO2) levels in short-term studies due to physiological plasticity. However, its long-term adaptive responses to ongoing anthropogenic CO2 increases are unknown. Here we show that experimental evolution under extended selection at projected future elevated CO2 levels results in irreversible, large increases in nitrogen fixation and growth rates, even after being moved back to lower present day CO2 levels for hundreds of generations. This represents an unprecedented microbial evolutionary response, as reproductive fitness increases acquired in the selection environment are maintained after returning to the ancestral environment. Constitutive rate increases are accompanied by irreversible shifts in diel nitrogen fixation patterns, and increased activity of a potentially regulatory DNA methyltransferase enzyme. High CO2-selected cell lines also exhibit increased phosphorus-limited growth rates, suggesting a potential advantage for this keystone organism in a more nutrient-limited, acidified future ocean.
    Description: Grant support was provided by U.S. National Science Foundation OCE 1260490 and OCE 1143760 to D.A.H., E.A.W., and F.-X.F, and OCE 1260233, OCE OA 1220484, and G.B. Moore Foundation 3782 and 3934 to M.A.S.© The Author(s), [year].
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  • 10
    Publication Date: 2017-01-04
    Description: Author Posting. © American Society for Microbiology, 2003. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 69 (2003): 5492-5502, doi:10.1128/AEM.69.9.5492-5502.2003.
    Description: A method was developed for the rapid detection and enumeration of Aureococcus anophagefferens, the cause of harmful algal blooms called "brown tides" in estuaries of the Mid-Atlantic United States. The method employs a monoclonal antibody (MAb) and a colorimetric, enzyme-linked immunosorbent assay format. The MAb obtained exhibits high reactivity with A. anophagefferens and very low cross-reactivities with a phylogenetically diverse array of other protists and bacteria. Standard curves are constructed for each 96-well microtiter plate by using known amounts of a preserved culture of A. anophagefferens. This approach allows estimation of the abundance of the alga in natural samples. The MAb method was compared to an existing method that employs polyclonal antibodies and epifluorescence microscopy and to direct microscopic counts of A. anophagefferens in samples with high abundances of the alga. The MAb method provided increased quantitative accuracy and greatly reduced sample processing time. A spatial survey of several Long Island estuaries in May 2000 using this new approach documented a range of abundances of A. anophagefferens in these bays spanning nearly 3 orders of magnitude.
    Description: This work was supported by a grant from The Seaver Institute.
    Keywords: Aureococcus anophagefferens ; Harmful algal blooms (HAB) ; Monoclonal antibody (MAb)
    Repository Name: Woods Hole Open Access Server
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