Project | Data Management Plan |
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A phylogenetic and functional understanding of microbial sulfur cycling in oxygen minimum zones | DMP_Stewart_OCE-1151698.pdf (71.50 KB), DMP_Stewart_OCE-1151698_Rvsd.pdf (71.63 KB) |
Principal Investigator: Frank J. Stewart (Georgia Tech Research Corporation)
Nature Geoscience~2013~6~Stewart FJ~~688~~~~Commentary: Where the genes flow~~~~~~~
The ISME Journal~2014~8~Ganesh S, Parris DJ, DeLong EF, Stewart FJ~10.1038/ismej.2013.144~187~~~~Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone.~~~~~~~
Frontiers in Microbiology~2014~5~Parris DJ, Ganesh S, Edgcomb VP, DeLong EF, Stewart FJ~10.3389/fmicb.2014.00543~~~~~Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile~~~~~~~
Nature Geoscience~2013~6~Stewart FJ~10.1038/ngeo1939~688~~~~Commentary: Where the genes flow~~~~~~~
Methods in Enzymology~2013~531~Stewart FJ~10.1016/B978-0-12-407863-5.00010-1~187~~~~Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton~~~~~~~
FEMS Microbiology Ecology~2015~~Duret MT, Paciadaki MG, Stewart FJ, Sarode N, Christaki U, Monchy S, Edgcomb VP~10.1093/femsec/fiv037~~~~~Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone~~~~~~2015-12-02 13:22:29.990~
The ISME Journal~2015~~Ganesh S, Bristow LA, Larsen M, Sarode N, Thamdrup B, Stewart FJ~10.1038/ismej.2015.44~~~~~Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone~~~~~~2015-12-02 13:22:29.996~
Frontiers in Microbiology~2015~~Glass JB, Kretz CB, Ganesh S, Ranjan P, Seston SL, Buck KN, Landing WM, Morton PL, Moffett JW, Giovannoni SJ, Vergin KL, Beszteri B, Stewart FJ.~10.3389/fmicb.2015.00998~~~~~Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones.~~~~~~2015-12-02 13:22:30.0~
Limnology and Oceanography~2015~~Bristow LA, Sarode N, Cartee J, Thamdrup B, Stewart FJ~10.1002/lno.10130~~~~~Metagenomics and biogeochemical analysis of nitrite accumulation in the Gulf of Mexico hypoxic zone~~~~~~2015-12-02 13:22:30.10~
Frontiers in Microbiology~2015~~Padilla C, Ganesh S, Gantt S, Huhman A, Parris DJ, Sarode N, Stewart FJ~10.3389/fmicb.2015.00547~~~~~Standard filtration practices may significantly distort planktonic microbial diversity estimates~~~~~~2015-12-02 13:22:30.13~
The ISME Journal~2014~~Ganesh S, Parris DJ, DeLong EF, Stewart FJ~10.1038/ismej.2013.144~~~~~Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone~~~~~~2015-12-02 13:22:30.16~
Frontiers in Microbiology~2014~~Parris DJ, Ganesh S, Edgcomb VP, DeLong EF, Stewart FJ~10.3389/fmicb.2014.00543~~~~~Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile~~~~~~2015-12-02 13:22:30.20~
Nature Geoscience~2013~~Stewart FJ~10.1038/ngeo1939~~~~~Where the genes flow~~~~~~2015-12-02 13:22:30.23~
Methods in Enzymology~2013~~Stewart FJ~10.1016/B978-0-12-407863-5.00010-1~~~~~Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton~~~~~~2015-12-02 13:22:30.26~
Marine Chemistry~2016~178~Beckler JS, Kiiazis N, Rabouille C, Stewart FJ, Taillefert M~10.1016/j.marchem.2015.12.003~22~~~~Importance of microbial iron reduction in deep sediments of river-dominated continental margins~~~~~~2017-01-30 12:13:01.360~
Limnology & Oceanography~2015~60~Bristow LA, Sarode N, Cartee J, Thamdrup B, Stewart FJ.~10.1002/lno.10130~1733~~~~Metagenomics and biogeochemical analysis of nitrite accumulation in the Gulf of Mexico hypoxic zone.~~~~~~2017-01-30 12:13:01.486~
The ISME Journal~2015~9~Ganesh S, Bristow LA, Larsen M, Sarode N, Thamdrup B, Stewart FJ.~10.1038/ismej.2015.44~2682~~~~Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone.~~~~~~2017-01-30 12:13:01.493~
The ISME Journal~2014~8~Ganesh S, Parris DJ, DeLong EF, Stewart FJ.~10.1038/ismej.2013.144~187~~~~Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone~~~~~~2017-01-30 12:13:01.506~
Frontiers in Microbiology~2015~6~Glass JB, Kretz CB, Ganesh S, Ranjan P, Seston SL, Buck KN, Landing WM, Morton PL, Moffett JW, Giovannoni SJ, Vergin KL, Beszteri B, Stewart FJ.~10.3389/fmicb.2015.00998~998~~~~Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones.~~~~~~2017-01-30 12:13:01.520~
Limnology & Oceanography Methods~2016~14~Larsen M, Lehner P, Borisov SM, Klimant I, Fischer J, Stewart FJ, Canfield DE, Glud RN~10.1002/lom3.10126~784~~~~In situ quantification of ultra-low O2 concentrations in oxygen minimum zones.~~~~~~2017-01-30 12:13:01.533~
Frontiers in Microbiology~2015~6~Padilla C, Ganesh S, Gantt S, Huhman A, Parris DJ, Sarode N, Stewart FJ~10.3389/fmicb.2015.00547~547~~~~Standard filtration practices may significantly distort planktonic microbial diversity estimates.~~~~~~2017-01-30 12:13:01.546~
Frontiers in Marine Science~2017~~Padilla CC, Bertagnolli AD, Bristow LA, Sarode N, Glass JB, Thamdrup B, Stewart FJ~doi: 10.3389/fmars.2017.00023~~~~~Metagenomic binning identifies a transcriptionally active Gammaproteobacterium linking methanotrophy to partial denitrification in an anoxic oxygen minimum zone~~~~~~2017-01-30 12:13:01.556~
The ISME Journal~2016~10~Padilla CC, Bristow LA, Sarode N, Garcia-Robledo E, Gómez Ramírez E, Benson CR, Bourbonnais A, Altabet MA, Girguis PR, Thamdrup B, Stewart FJ~10.1038/ismej.2015.262~2067~~~~NC10 bacteria in marine oxygen minimum zones~~~~~~2017-01-30 12:13:01.563~
Frontiers in Microbiology~2014~5~Parris DJ, Ganesh S, Edgcomb VP, DeLong EF, Stewart FJ~10.3389/fmicb.2014.00543~543~~~~Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile~~~~~~2017-01-30 12:13:01.573~
Frontiers in Microbiology~2016~7~Seston SL, Beinart R, Sarode N, Shockey AC, Ranjan P, Ganesh S, Girguis PR, Stewart FJ.~doi.org/10.3389/fmicb.2016.01074~1074~~~~Metatranscriptional response of chemoautotrophic Ifremeria nautilei endosymbionts to differing sulfur regimes.~~~~~~2017-01-30 12:13:01.580~
Methods in Enzymology~2013~531~Stewart FJ~10.1016/B978-0-12-407863-5.00010-1~187~~~~Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton.~~~~~~2017-01-30 12:13:01.586~
Nature~2016~536~Tsementzi D, Wu J, Deutsch S, Nath N, Rodriguez-R LM, Burns AS, Ranjan P, Sarode N, Malmstrom RR, Padilla CC, Stone BK, Bristow LA, Larsen M, Glass JB, Thamdrup B, Woyke T, Konstantinidis KT, Stewart FJ.~10.1038/nature19068~179~~~~SAR11 bacteria linked to ocean anoxia and nitrogen loss~~~~~~2017-01-30 12:13:01.626~
Marine Chemistry~2016~~Beckler JS, Kiiazis N, Rabouille C, Stewart FJ, Taillefert M~10.1016/j.marchem.2015.12.003~~~~~Importance of microbial iron reduction in deep sediments of river-dominated continental margins.~~~~~~2018-02-13 15:17:19.356~
Environmental Microbiology~2017~~Bertagnolli AD, Padilla CC, Glass JB, Thamdrup B, Stewart FJ~10.1111/1462-2920.13879~~~~~Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column~~~~~~2018-02-13 15:17:19.390~
The ISME Journal~2015~~Ganesh S, Bristow LA, Larsen M, Sarode N, Thamdrup B, Stewart FJ~10.1038/ismej.2015.44~~~~~Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone~~~~~~2018-02-13 15:17:19.406~
he ISME Journal~2014~~Ganesh S, Parris DJ, DeLong EF, Stewart FJ~10.1038/ismej.2013.144~~~~~Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone~~~~~~2018-02-13 15:17:19.413~
Frontiers in Microbiology~2014~~Parris DJ, Ganesh S, Edgcomb VP, DeLong EF, Stewart FJ~10.3389/fmicb.2014.00543~~~~~Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile~~~~~~2018-02-13 15:17:19.466~
Nature Geoscience~2013~~Stewart FJ~10.1038/ngeo1939~~~~~Where the genes flow~~~~~~2018-02-13 15:17:19.490~
Nature~2016~~Tsementzi D, Wu J, Deutsch S, Nath N, Rodriguez-R LM, Burns AS, Ranjan P, Sarode N, Malmstrom RR, Padilla CC, Stone BK, Bristow LA, Larsen M, Glass JB, Thamdrup B, Woyke T, Konstantinidis KT, Stewart FJ~10.1038/nature19068~~~~~SAR11 bacteria linked to ocean anoxia and nitrogen loss~~~~~~2018-02-13 15:17:19.496~
PeerJ~2017~~Vik DR, Roux S, Brum JR, Bolduc B, Emerson JB, Padilla CC, Stewart FJ, Sullivan MB~10.7717/peerj.3428~~~~~Putative Archaeal viruses from the mesopelagic ocean~~~~~~2018-02-13 15:17:19.500~
The ISME Journal.~2018~~Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, Bourbonnais A, Altabet MA, Woyke T, Ulloa O, Konstantinidis KK, Thamdrup B, Stewart FJ~~~~~~Genomic evidence for the use of alternative nitrogen substrates by anammox bacteria~~~~~~2019-02-10 11:39:43.223~
Nature Microbiology~2019~~Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, Könneke M, Littmann S, Mooshammer M, Niggemann J, Petrov S, Richter A, Stewart FJ, Wagner M, Kuypers MMM, Bristow LA.~~~~~~Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment~~~~~~2019-02-10 11:39:43.270~
Marine Chemistry~2016~~Beckler JS, Kiriazis N, Rabouille C, Stewart FJ, Taillefert M~~~~~~Importance of microbial iron reduction in deep sediments of river-dominated continental-margins~~~~~~2020-06-19 15:51:30.476~
Nature Reviews Microbiology~2018~~Bertagnolli AD, Stewart FJ~~~~~~Microbial niches in marine oxygen minimum zones~~~~~~2020-06-19 15:51:30.526~
Journal of Marine Research~2019~~Canfield DE, Kraft B, Löscher C, Boyle RA, Thamdrup B, Stewart FJ~~~~~~The regulation of oxygen to low concentrations in marine oxygen-minimum zones~~~~~~2020-06-19 15:51:30.580~
FEMS Microbiology Ecology~2015~~Duret MT, Pachiadaki MG, Stewart FJ, Sarode N, Christaki U, Monchy S, Edgcomb VP~~~~~~Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone~~~~~~2020-06-19 15:51:30.593~
The ISME Journal~2018~~Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, Bourbonnais A, Altabet MA, Woyke T, Ulloa O, Konstantinidis KK, Thamdrup B, Stewart FJ~~~~~~Genomic evidence for the use of alternative nitrogen substrates by anammox bacteria~~~~~~2020-06-19 15:51:30.600~
The ISME Journal~2015~~Ganesh S, Bristow LA, Larsen M, Sarode N, Thamdrup B, Stewart FJ~~~~~~Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone~~~~~~2020-06-19 15:51:30.613~
Frontiers in Microbiology~2015~~Glass JB, Kretz CB, Ganesh S, Ranjan P, Seston SL, Buck KN, Landing WL, Morton PL, Moffett JW, Giovannoni SJ, Vergin KL, Stewart FJ~~~~~~Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones~~~~~~2020-06-19 15:51:30.646~
Nature Communications~2020~~Kitzinger K, Marchant HK, Bristow LA, Herbold CW, Padilla CC, Kidane AT, Littmann S, Daims H, Pjevac P, Stewart FJ, Wagner M, Kuypers MMM~~~~~~Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean~~~~~~2020-06-19 15:51:30.660~
Limnology & Oceanography Methods~2016~~Larsen M, Lehner P, Borisov SM, Klimant I, Fischer J, Stewart FJ, Canfield DE, Glud RN~~~~~~In situ quantification of ultra-low O2 concentrations in oxygen minimum zones~~~~~~2020-06-19 15:51:30.696~
Bioinformatics Research and Applications. ISBRA 2017. Lecture Notes in Computer Science, vol 10330~2017~~Mandric I, Knyazev S, Padilla C, Stewart F, Mandoiu II, Zelikovsky A~~~~~~Metabolic analysis of metatranscriptomic data from planktonic communities~~~~~~2020-06-19 15:51:30.703~
Frontiers in Marine Science~2017~~Padilla CC, Bertagnolli AD, Bristow LA, Sarode N, Glass JB, Thamdrup B, Stewart FJ~~~~~~Metagenomic binning recovers a transcriptionally active Gammaproteobacterium linking methanotrophy to partial denitrification in an anoxic oxygen minimum zone~~~~~~2020-06-19 15:51:30.720~
The ISME Journal~2016~~Padilla CC, Bristow LA, Sarode N, Garcia-Robledo E, Gomez Ramirez E, Benson CR, Bourbonnais A, Altabet MA, Girguis PR, Thamdrup B, Stewart FJ~~~~~~NC10 bacteria in marine oxygen minimum zones~~~~~~2020-06-19 15:51:30.736~
Frontiers in Microbiology~2015~~Padilla CC, Ganesh S, Gantt S, Huhman A, Parris DJ, Sarode N, Stewart FJ~~~~~~Standard filtration practices may significantly distort planktonic microbial diversity estimates~~~~~~2020-06-19 15:51:30.750~
Frontiers in Microbiology~2014~~Parris DJ, Ganesh S, Edgcomb VP, DeLong EF, Stewart FJ~~~~~~Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile~~~~~~2020-06-19 15:51:30.763~
Frontiers in Microbiology~2016~~Seston SL, Beinart R, Sarode N, Shockey AC, Ranjan P, Ganesh S, Girguis PR, Stewart FJ~~~~~~Metatranscriptional response of chemoautotrophic Ifremeria nautilei endosymbionts to differing sulfur regimes~~~~~~2020-06-19 15:51:30.773~
Methods in Enzymology~2013~~Stewart FJ~~~~~~Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton~~~~~~2020-06-19 15:51:30.786~
Nature Geoscience~2013~~Stewart FJ~~~~~~Where the genes flow~~~~~~2020-06-19 15:51:30.813~
Nature~2016~~Tsementzi D, Wu J, Deutsch S, Nath N, Rodriguez-R LM, Burns AS, Ranjan P, Sarode N, Malmstrom RR, Padilla CC, Stone BK, Bristow LA, Larsen M, Glass JB, Thamdrup B, Woyke T, Konstantinidis KT, Stewart FJ~~~~~~SAR11 bacteria linked to ocean anoxia and nitrogen loss~~~~~~2020-06-19 15:51:30.840~
PeerJ~2017~~Vik DR, Roux S, Brum JR, Bolduc B, Emerson JB, Padilla CC, Stewart FJ, Sullivan MB~~~~~~Putative Archaeal viruses from the mesopelagic ocean~~~~~~2020-06-19 15:51:30.860~
Frontiers in Microbiology~2015~~Padilla C, Ganesh S, Gantt S, Huhman A, Parris DJ, Sarode N, Stewart FJ~10.3389/fmicb.2015.00547~~~~~Standard filtration practices may significantly distort planktonic microbial diversity estimates~~~~~~2018-02-13 15:17:19.450~
The ISME Journal~2014~~Ganesh S, Parris DJ, DeLong EF, Stewart FJ~~~~~~Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone~~~~~~2020-06-19 15:51:30.626~
Frontiers in Microbiology~2015~~Glass JB, Kretz CB, Ganesh S, Ranjan P, Seston SL, Buck KN, Landing WM, Morton PL, Moffett JW, Giovannoni SJ, Vergin KL, Beszteri B, Stewart FJ~10.3389/fmicb.2015.00998~~~~~Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones~~~~~~2018-02-13 15:17:19.426~
Bioinformatics Research and Applications. ISBRA 2017. Lecture Notes in Computer Science, vol 10330~2017~~Mandric I, Knyazev S, Padilla C, Stewart F, Mandoiu II, Zelikovsky A~10.1007/978-3-319-59575-7_41~~~~~Metabolic analysis of metatranscriptomic data from planktonic communities.~~~~~~2018-02-13 15:17:19.443~
Limnology & Oceanography~2015~~Bristow LA, Sarode N, Cartee J, Caro-Quintero A, Thamdrup B, Stewart FJ~~~~~~Biogeochemical and metagenomic analysis of nitrite accumulation in the Gulf of Mexico hypoxic zone~~~~~~2020-06-19 15:51:30.553~
Frontiers in Microbiology~2016~~Seston SL, Beinart R, Sarode N, Shockey AC, Ranjan P, Ganesh S, Girguis PR, Stewart FJ~10.3389/fmicb.2016.01074~~~~~Metatranscriptional response of chemoautotrophic Ifremeria nautilei endosymbionts to differing sulfur regimes~~~~~~2018-02-13 15:17:19.470~
Limnology & Oceanography~2015~~Bristow LA, Sarode N, Cartee J, Thamdrup B, Stewart FJ~10.1002/lno.10130~~~~~Metagenomics and biogeochemical analysis of nitrite accumulation in the Gulf of Mexico hypoxic zone~~~~~~2018-02-13 15:17:19.396~
Proceedings of the National Academy of Sciences of the USA~2017~~Garcia-Robledo E, Padilla CC, Aldunate M, Paulmier A, Gregori G, Stewart FJ, Ulloa O, Revsbech NP~10.1073/pnas.1619844114~~~~~Cryptic oxygen cycling in anoxic oxygen minimum zones~~~~~~2018-02-13 15:17:19.423~
Proceedings of the National Academy of Sciences of the USA~2017~~Garcia-Robledo E, Padilla CC, Aldunate M, Paulmier A, Gregori G, Stewart FJ, Ulloa O, Revsbech NP~~~~~~Cryptic oxygen cycling in anoxic marine zones~~~~~~2020-06-19 15:51:30.636~
Limnology & Oceanography Methods~2016~~Larsen M, Lehner P, Borisov SM, Klimant I, Fischer J, Stewart FJ, Canfield DE, Glud RN~10.1002/lom3.10126~~~~~In situ quantification of ultra-low O2 concentrations in oxygen minimum zones~~~~~~2018-02-13 15:17:19.436~
Nature Reviews Microbiology~2018~16~Bertagnolli AD, Stewart FJ~~~~~~Microbial niches in marine oxygen minimum zones.~~~~~~2019-02-10 11:39:43.273~
Applied and Environmental Microbiology~2018~~Burns AS, Padilla CC, Pratte ZA, Gilde K, Regensburger M, Hall E, Dove ADM, Stewart FJ~~~~~~Broad phylogenetic diversity associated with nitrogen loss through sulfur oxidation in a large public marine aquarium~~~~~~2020-06-19 15:51:30.566~
The ISME Journal~2016~~Padilla CC, Bristow LA, Sarode N, Garcia-Robledo E, Go?mez Rami?rez E, Benson CR, Bourbonnais A, Altabet MA, Girguis PR, Thamdrup B, Stewart FJ~10.1038/ismej.2015.262~~~~~NC10 bacteria in marine oxygen minimum zones~~~~~~2018-02-13 15:17:19.463~
Limnology & Oceanography~2019~~Thamdrup B, Steinsdóttir HGR, Bertagnolli AD, Patin NV, Padilla CC, García-Robledo E, Bristow LA, Stewart FJ~~~~~~Anaerobic methane oxidation is an important sink for methane in the ocean’s largest oxygen minimum zone~~~~~~2020-06-19 15:51:30.826~
Environmental Microbiology~2017~~Bertagnolli AD, Padilla CC, Glass JB, Thamdrup B, Stewart FJ~~~~~~Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column~~~~~~2020-06-19 15:51:30.513~
Nature Microbiology~2019~~Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, Könneke M, Littmann S, Mooshammer M, Niggemann J, Petrov S, Richter A, Stewart FJ, Wagner M, Kuypers MMM, Bristow LA~~~~~~Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment~~~~~~2020-06-19 15:51:30.683~
Frontiers in Marine Science~2017~~Padilla CC, Bertagnolli AD, Bristow LA, Sarode N, Glass JB, Thamdrup B, Stewart FJ~10.3389/fmars.2017.00023~~~~~Metagenomic binning identifies a transcriptionally active Gammaproteobacterium linking methanotrophy to partial denitrification in an anoxic oxygen minimum zone~~~~~~2018-02-13 15:17:19.453~
Methods in Enzymology~2013~~Stewart FJ~10.1016/B978-0-12-407863-5.00010-1~~~~~Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton~~~~~~2018-02-13 15:17:19.486~