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  • 1
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    The GEOTRACES Intermediate Data Product 2017 (2018)
    Elsevier
    In:  Chemical Geology, 493 . pp. 210-223.
    Details
    Publication Date: 2021-02-08
    Description: The GEOTRACES Intermediate Data Product 2017 (IDP2017) is the second publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2016. The IDP2017 includes data from the Atlantic, Pacific, Arctic, Southern and Indian oceans, with about twice the data volume of the previous IDP2014. For the first time, the IDP2017 contains data for a large suite of biogeochemical parameters as well as aerosol and rain data characterising atmospheric trace element and isotope (TEI) sources. The TEI data in the IDP2017 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at crossover stations. The IDP2017 consists of two parts: (1) a compilation of digital data for more than 450 TEIs as well as standard hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing an on-line atlas that includes more than 590 section plots and 130 animated 3D scenes. The digital data are provided in several formats, including ASCII, Excel spreadsheet, netCDF, and Ocean Data View collection. Users can download the full data packages or make their own custom selections with a new on-line data extraction service. In addition to the actual data values, the IDP2017 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering and for statistical analysis. Metadata about data originators, analytical methods and original publications related to the data are linked in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2017 as section plots and rotating 3D scenes. The basin-wide 3D scenes combine data from many cruises and provide quick overviews of large-scale tracer distributions. These 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of tracer plumes near ocean margins or along ridges. The IDP2017 is the result of a truly international effort involving 326 researchers from 22 countries. This publication provides the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP2017.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1016/j.chemgeo.2018.05.040
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 2
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    The GEOTRACES Intermediate Data Product 2014 (2015)
    Elsevier
    In:  Marine Chemistry, 177 . pp. 1-8.
    Details
    Publication Date: 2020-06-26
    Description: Highlights: • GEOTRACES releases its first integrated and quality controlled Intermediate Data Product 2014 (IDP2014). • The IDP2014 digital data are available at http://www.bodc.ac.uk/geotraces/data/idp2014/ in 4 different formats. • The eGEOTRACES Electronic Atlas at http://egeotraces.org/ provides 329 section plots and 90 animated 3D tracer scenes. • The new 3D scenes provide geographical and bathymetric context crucial for tracer assessment and interpretation. Abstract: The GEOTRACES Intermediate Data Product 2014 (IDP2014) is the first publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2013. It consists of two parts: (1) a compilation of digital data for more than 200 trace elements and isotopes (TEIs) as well as classical hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing a strongly inter-linked on-line atlas including more than 300 section plots and 90 animated 3D scenes. The IDP2014 covers the Atlantic, Arctic, and Indian oceans, exhibiting highest data density in the Atlantic. The TEI data in the IDP2014 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at cross-over stations. The digital data are provided in several formats, including ASCII spreadsheet, Excel spreadsheet, netCDF, and Ocean Data View collection. In addition to the actual data values the IDP2014 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering. Metadata about data originators, analytical methods and original publications related to the data are linked to the data in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2014 data providing section plots and a new kind of animated 3D scenes. The basin-wide 3D scenes allow for viewing of data from many cruises at the same time, thereby providing quick overviews of large-scale tracer distributions. In addition, the 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of observed tracer plumes, as well as for making inferences about controlling processes.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1016/j.marchem.2015.04.005
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 3
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    Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation (2017)
    ASLO (Association for the Sciences of Limnology and Oceanography)
    In:  Limnology and Oceanography, 62 (5). pp. 1984-2003.
    Details
    Publication Date: 2020-02-06
    Description: Thaumarchaea are among the most abundant microbial groups in the ocean, but controls on their abundance and the distribution and metabolic potential of different subpopulations are poorly constrained. Here, two ecotypes of ammonia-oxidizing thaumarchaea were quantified using ammonia monooxygenase (amoA) genes across the equatorial Pacific Ocean. The shallow, or water column “A” (WCA), ecotype was the most abundant ecotype at the depths of maximum nitrification rates, and its abundance correlated with other biogeochemical indicators of remineralization such as NO3 : Si and total Hg. Metagenomes contained thaumarchaeal genes encoding for the catalytic subunit of the urease enzyme (ureC) at all depths, suggesting that members of both WCA and the deep, water column “B” (WCB) ecotypes may contain ureC. Coupled urea hydrolysis-ammonia oxidation rates were similar to ammonia oxidation rates alone, suggesting that urea could be an important source of ammonia for mesopelagic ammonia oxidizers. Potential inducement of metal limitation of both ammonia oxidation and urea hydrolysis was demonstrated via additions of a strong metal chelator. The water column inventory of WCA was correlated with the depth-integrated abundance of WCB, with both likely controlled by the flux of sinking particulate organic matter, providing strong evidence of vertical connectivity between the ecotypes. Further, depth-integrated amoA gene abundance and nitrification rates were correlated with particulate organic nitrogen flux measured by contemporaneously deployed sediment traps. Together, the results refine our understanding of the controls on thaumarchaeal distributions in the ocean, and provide new insights on the relationship between material flux and microbial communities in the mesopelagic.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1002/lno.10547
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 4
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    The GEOTRACES Intermediate Data Product 2017 (2018)
    In:  EPIC3Chemical Geology, 493, pp. 210-223, ISSN: 00092541
    Details
    Publication Date: 2018-08-13
    Description: The GEOTRACES Intermediate Data Product 2017 (IDP2017) is the second publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2016. The IDP2017 includes data from the Atlantic, Pacific, Arctic, Southern and Indian oceans, with about twice the data volume of the previous IDP2014. For the first time, the IDP2017 contains data for a large suite of biogeochemical parameters as well as aerosol and rain data characterising atmospheric trace element and isotope (TEI) sources. The TEI data in the IDP2017 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at crossover stations. The IDP2017 consists of two parts: (1) a compilation of digital data for more than 450 TEIs as well as standard hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing an on-line atlas that includes more than 590 section plots and 130 animated 3D scenes. The digital data are provided in several formats, including ASCII, Excel spreadsheet, netCDF, and Ocean Data View collection. Users can download the full data packages or make their own custom selections with a new on-line data extraction service. In addition to the actual data values, the IDP2017 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering and for statistical analysis. Metadata about data originators, analytical methods and original publications related to the data are linked in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2017 as section plots and rotating 3D scenes. The basin-wide 3D scenes combine data from many cruises and provide quick overviews of large-scale tracer distributions. These 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of tracer plumes near ocean margins or along ridges. The IDP2017 is the result of a truly international effort involving 326 researchers from 25 countries. This publication provides the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP2017. This article is part of a special issue entitled: Conway GEOTRACES - edited by Tim M. Conway, Tristan Horner, Yves Plancherel, and Aridane G. González.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
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  • 5
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    The GEOTRACES Intermediate Data Product 2014 (2015)
    In:  EPIC3Marine Chemistry, 177, pp. 1-8, ISSN: 03044203
    Details
    Publication Date: 2018-03-26
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 6
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    The {GEOTRACES} Intermediate Data Product 2014 (2015)
    In:  EPIC3Marine Chemistry, 177, P, pp. 1 - 8
    Details
    Publication Date: 2016-02-29
    Description: Abstract The {GEOTRACES} Intermediate Data Product 2014 (IDP2014) is the first publicly available data product of the international {GEOTRACES} programme, and contains data measured and quality controlled before the end of 2013. It consists of two parts: (1) a compilation of digital data for more than 200 trace elements and isotopes (TEIs) as well as classical hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing a strongly inter-linked on-line atlas including more than 300 section plots and 90 animated 3D scenes. The {IDP2014} covers the Atlantic, Arctic, and Indian oceans, exhibiting highest data density in the Atlantic. The {TEI} data in the {IDP2014} are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at cross-over stations. The digital data are provided in several formats, including {ASCII} spreadsheet, Excel spreadsheet, netCDF, and Ocean Data View collection. In addition to the actual data values the {IDP2014} also contains data quality flags and 1-� data error values where available. Quality flags and error values are useful for data filtering. Metadata about data originators, analytical methods and original publications related to the data are linked to the data in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the {IDP2014} data providing section plots and a new kind of animated 3D scenes. The basin-wide 3D scenes allow for viewing of data from many cruises at the same time, thereby providing quick overviews of large-scale tracer distributions. In addition, the 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of observed tracer plumes, as well as for making inferences about controlling processes.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
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  • 7
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    Irreversibly increased nitrogen fixation in Trichodesmium experimentally adapted to elevated carbon dioxide (2015)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-25
    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].
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 8
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    Dynamic mercury methylation and demethylation in oligotrophic marine water (2018)
    Copernicus Publications on behalf of the European Geosciences Union
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biogeosciences 15 (2018): 6451-6460, doi:10.5194/bg-15-6451-2018.
    Description: Mercury bioaccumulation in open-ocean food webs depends on the net rate of inorganic mercury conversion to monomethylmercury in the water column. We measured significant methylation rates across large gradients in oxygen utilization in the oligotrophic central Pacific Ocean. Overall, methylation rates over 24h incubation periods were comparable to those previously published from Arctic and Mediterranean waters despite differences in productivity between these marine environments. In contrast to previous studies that have attributed Hg methylation to heterotrophic bacteria, we measured higher methylation rates in filtered water compared to unfiltered water. Furthermore, we observed enhanced demethylation of newly produced methylated mercury in incubations of unfiltered water relative to filtered water. The addition of station-specific bulk filtered particulate matter, a source of inorganic mercury substrate and other possibly influential compounds, did not stimulate sustained methylation, although transient enhancement of methylation occurred within 8h of addition. The addition of dissolved inorganic cobalt also produced dramatic, if transient, increases in mercury methylation. Our results suggest important roles for noncellular or extracellular methylation mechanisms and demethylation in determining methylated mercury concentrations in marine oligotrophic waters. Methylation and demethylation occur dynamically in the open-ocean water column, even in regions with low accumulation of methylated mercury.
    Description: This work was funded by the National Science Foundation in a Chemical Oceanography Program Grant (OCE-1031271) awarded to Carl H. Lamborg and Mak A. Saito and a graduate student fellowship to Kathleen M. Munson.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 9
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    Needles in the blue sea : sub-species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome (2015)
    Details
    Publication Date: 2022-05-25
    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
    Type: Preprint
    Format: application/pdf
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  • 10
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    Divergent responses of Atlantic coastal and oceanic Synechococcus to iron limitation (2015)
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 112 (2015): 9944-9949, doi:10.1073/pnas.1509448112.
    Description: Marine Synechococcus are some of the most diverse and ubiquitous phytoplankton, and iron (Fe) is an essential micronutrient that limits productivity in many parts of the ocean. To investigate how coastal and oceanic Atlantic Synechococcus strains acclimate to Fe availability, we compared the growth, photophysiology, and quantitative proteomics of two Synechococcus strains from different Fe regimes. Synechococcus strain WH8102, from a region in the southern Sargasso Sea that receives substantial dust deposition, showed impaired growth and photophysiology as Fe declined, yet utilized few acclimation responses. Coastal WH8020, from the dynamic, seasonally variable New England shelf, displayed a multi-tiered, hierarchical cascade of acclimation responses with different Fe thresholds. The multi-tiered response included changes in Fe acquisition, storage, and photosynthetic proteins, substitution of flavodoxin for ferredoxin, and modified photophysiology, all while maintaining remarkably stable growth rates over a range of Fe concentrations. Modulation of two distinct ferric uptake regulator (Fur) proteins that coincided with the multi-tiered proteome response was found, implying the coastal strain has different regulatory threshold responses to low Fe availability. Low nitrogen (N) and phosphorus (P) availability in the open ocean may favor the loss of Fe response genes when Fe availability is consistent over time, whereas these genes are retained in dynamic environments where Fe availability fluctuates and N and P are more abundant.
    Description: This work was supported by a National Science Foundation Postdoctoral Research Fellowship in Biology to K.R.M.M. (NSF 1103575), National Science Foundation Oceanography grants OCE-1220484, OCE-0928414, OCE-1233261, OCE- 1155566, OCE-1131387, and OCE-0926092, as well as Gordon and Betty Moore Foundation grants 3782 and 3934.
    Keywords: Iron adaptation ; Synechococcus ; Photosynthesis ; Quantitative proteomics
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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