Steen
Andrew D.
Steen
Andrew D.
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ArticleAnalytical and computational advances, opportunities, and challenges in marine organic biogeochemistry in an era of "Omics"(Frontiers Media, 2020-09-02) Steen, Andrew D. ; Kusch, Stephanie ; Abdulla, Hussain A. ; Cakić, Nevenka ; Coffinet, Sarah ; Dittmar, Thorsten ; Fulton, James M. ; Galy, Valier ; Hinrichs, Kai-Uwe ; Ingalls, Anitra ; Koch, Boris P. ; Kujawinski, Elizabeth B. ; Liu, Zhanfei ; Osterholz, Helena ; Rush, Darci ; Seidel, Michael ; Sepulveda, Julio ; Wakeham, Stuart G.Advances in sampling tools, analytical methods, and data handling capabilities have been fundamental to the growth of marine organic biogeochemistry over the past four decades. There has always been a strong feedback between analytical advances and scientific advances. However, whereas advances in analytical technology were often the driving force that made possible progress in elucidating the sources and fate of organic matter in the ocean in the first decades of marine organic biogeochemistry, today process-based scientific questions should drive analytical developments. Several paradigm shifts and challenges for the future are related to the intersection between analytical progress and scientific evolution. Untargeted “molecular headhunting” for its own sake is now being subsumed into process-driven targeted investigations that ask new questions and thus require new analytical capabilities. However, there are still major gaps in characterizing the chemical composition and biochemical behavior of macromolecules, as well as in generating reference standards for relevant types of organic matter. Field-based measurements are now routinely complemented by controlled laboratory experiments and in situ rate measurements of key biogeochemical processes. And finally, the multidisciplinary investigations that are becoming more common generate large and diverse datasets, requiring innovative computational tools to integrate often disparate data sets, including better global coverage and mapping. Here, we compile examples of developments in analytical methods that have enabled transformative scientific advances since 2004, and we project some challenges and opportunities in the near future. We believe that addressing these challenges and capitalizing on these opportunities will ensure continued progress in understanding the cycling of organic carbon in the ocean.
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DatasetDrill site locations from MPSV GREATSHIP MANISHA IODP-347 cruise in the Baltic Sea in 2013 (IODP-347 Microbial Quantification project)(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2016-11-15) Lloyd, Karen G. ; Steen, Andrew D.In 2013, Integrated Ocean Drilling Program Expedition 347 sampled six subbasins within the Baltic Sea Basin in an effort to understand the sedimentological record of climate dynamics over the last 140,000 years. These sites, including Bornholm Basin (BSB-7), Lille Belt (BSB-3), and Anholt Loch (BSB-9), were selected because they contain varved, rapidly deposited sediments that represent an archive of paleoclimatological information spanning from the last glacial cycle. This expedition was led by Dr. Bo Barker Jørgensen of Aarhus University and Dr. Thomas Andrén of Södertörn University aboard the vessel MPSV GREATSHIP MANISHA. Data included here are dates sampled, latitude and longitude, and depth of overlying water. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/641342
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DatasetQuantitative PCR data from sediment samples from MPSV GREATSHIP MANISHA IODP-347 cruise in the Baltic Sea in 2013 (IODP-347 Microbial Quantification project)(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2016-11-15) Lloyd, Karen G. ; Steen, Andrew D.These data include the quantification of specific microbial taxa within the sediments collected during Integrated Ocean Drilling Program (IODP) Expedition 347: Baltic Sea. DNA was extracted from the interior of frozen whole round cores sampled from Little Belt, Anholt Loch, Landsort Deep, and Bornholm Basin at The University of Tennessee. For a more detailed description of drill sites, access the data set, "IODP-347 drill site locations". Primers specifically targeting the 16S rRNA gene of bacteria, archaea, anaerobic methane oxidizers (ANME-1), and Miscellaneous Crenarchaeota Group (MCG; taxonomically reassigned as the Bathyarchaeota phylum of Archaea) were used to assess abundance of these microbial groups. Abundance data was generated using quantitative-PCR (qPCR) and a non-specific, intercalating DNA stain, SYBR Green. Values were compared against a standard curve to generate copies/uL. These data were collected by Alex Shumaker as part of Dr. Karen Lloyd and Dr. Andrew Steen’s project funded by the National Science Foundation entitled, "Quantifying the contribution of the deep biosphere in the marine sediment carbon cycle using deep-sea sediment cores from the Baltic Sea". For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/641358
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ArticleComplex organic matter degradation by secondary consumers in chemolithoautotrophy-based subsurface geothermal ecosystems(Public Library of Science, 2023-08-18) Paul, Raegan ; Rogers, Timothy J. ; Fullerton, Kate M. ; Selci, Matteo ; Cascone, Martina ; Stokes, Murray H. ; Steen, Andrew D. ; de Moor, J. Maarten ; Chiodi, Agostina ; Stefansson, Andri ; Halldorsson, Saemundur ; Ramirez, Carlos J. ; Jessen, Gerdhard L. ; Barry, Peter H. ; Cordone, Angelina ; Giovannelli, Donato ; Lloyd, Karen G.Microbial communities in terrestrial geothermal systems often contain chemolithoautotrophs with well-characterized distributions and metabolic capabilities. However, the extent to which organic matter produced by these chemolithoautotrophs supports heterotrophs remains largely unknown. Here we compared the abundance and activity of peptidases and carbohydrate active enzymes (CAZymes) that are predicted to be extracellular identified in metagenomic assemblies from 63 springs in the Central American and the Andean convergent margin (Argentinian backarc of the Central Volcanic Zone), as well as the plume-influenced spreading center in Iceland. All assemblies contain two orders of magnitude more peptidases than CAZymes, suggesting that the microorganisms more often use proteins for their carbon and/or nitrogen acquisition instead of complex sugars. The CAZy families in highest abundance are GH23 and CBM50, and the most abundant peptidase families are M23 and C26, all four of which degrade peptidoglycan found in bacterial cells. This implies that the heterotrophic community relies on autochthonous dead cell biomass, rather than allochthonous plant matter, for organic material. Enzymes involved in the degradation of cyanobacterial- and algal-derived compounds are in lower abundance at every site, with volcanic sites having more enzymes degrading cyanobacterial compounds and non-volcanic sites having more enzymes degrading algal compounds. Activity assays showed that many of these enzyme classes are active in these samples. High temperature sites (> 80°C) had similar extracellular carbon-degrading enzymes regardless of their province, suggesting a less well-developed population of secondary consumers at these sites, possibly connected with the limited extent of the subsurface biosphere in these high temperature sites. We conclude that in < 80°C springs, chemolithoautotrophic production supports heterotrophs capable of degrading a wide range of organic compounds that do not vary by geological province, even though the taxonomic and respiratory repertoire of chemolithoautotrophs and heterotrophs differ greatly across these regions.
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ArticleDepth-partitioning of particulate organic carbon composition in the rising and falling stages of the Amazon River(American Geophysical Union, 2024-06-25) Rosengard, Sarah Z. ; Moura, Jose Mauro S. ; Spencer, Robert G. M. ; Johnson, Carl G. ; McNichol, Ann P. ; Steen, Andrew D. ; Galy, ValierThe Amazon River mobilizes organic carbon across one of the world's largest terrestrial carbon reservoirs. Quantifying the sources of particulate organic carbon (POC) to this flux is typically challenging in large systems such as the Amazon River due to hydrodynamic sorting of sediments. Here, we analyze the composition of POC collected from multiple total suspended sediment (TSS) profiles in the mainstem at Óbidos, and surface samples from the Madeira, Solimões and Tapajós Rivers. As hypothesized, TSS and POC concentrations in the mainstem increased with depth and fit well to Rouse models for sediment sorting by grain size. Coupling these profiles with Acoustic Doppler Current Profiler discharge data, we estimate a large decrease in POC flux (from 540 to 370 kg per second) between the rising and falling stages of the Amazon River mainstem. The C/N ratio and stable and radiocarbon signatures of bulk POC are less variable within the cross-section at Óbidos and suggest that riverine POC in the Amazon River is predominantly soil-derived. However, smaller shifts in these compositional metrics with depth, including leaf wax n-alkanes and fatty acids, are consistent with the perspective that deeper and larger particles carry fresher, less degraded organic matter sources (i.e., vegetation debris) through the mainstem. Overall, our cross-sectional surveys at Óbidos highlight the importance of depth-specific sampling for estimating riverine export fluxes. At the same time, they imply that this approach to sampling is perhaps less essential with respect to characterizing the composition of POC sources exported by the river.