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1. Deepening the Decade: Collaborative Action for Advancing Deep‐Ocean Science and Policy in the United Nations Decade of Ocean Science for Sustainable Development

Author

Hetherington, Elizabeth D, Anderson, Clarissa, Bastian, Liliana, Boon, Naomi, Chu, Nan‐Chin, Cruz, Ceci Rodriguez, Drennon, Hayley, Gates, Andrew, Gertz, Brandon, Goodwin, Kelly D, Halfter, Svenja, Howell, Kerry, Howes, Ella, Lopes, Vanessa, Martin, Tinah, McConnell, Terrence, Qian, Pei‐Yuan, Seabrook, Sarah, Smith, Leslie, Snyder, Glen, Stocks, Karen I, Sylvan, Rosalynn, Wright, Dawn, and Levin, Lisa A

Subjects
Earth Sciences, Oceanography, Life Below Water, Sustainable Cities and Communities
Abstract

Abstract: The current United Nations Decade of Ocean Science for Sustainable Development (2021–2030; hereafter, the Decade) offers a unique opportunity and framework to globally advance ocean science and policy. Achieving meaningful progress within the Decade requires collaboration and coordination across Decade Actions (Programs, Projects, and Centres). This coordination is particularly important for the deep ocean, which remains critically under‐sampled compared to other ecosystems. Despite the limited sampling, the deep ocean accounts for over 95% of Earth's habitable space, plays a crucial role in regulating the carbon cycle and global temperatures, and supports diverse ecosystems. To collectively advance deep‐ocean science, we gathered representatives from 20 Decade Actions that focus at least partially on the deep ocean. We identified five broad themes that aim to advance deep‐ocean science in alignment with the Decade's overarching 10 Challenges: natural capital and the blue economy, biodiversity, deep‐ocean observing, best practices in data sharing, and capacity building. Within each theme, we propose concrete objectives (termed Cohesive Asks) and milestones (Targets) for the deep‐ocean community. Developing these Cohesive Asks and Targets reflects a commitment to better coordination across deep‐ocean Decade Actions. We aim to build bridges across deep‐ocean disciplines, which encompass natural science, ocean observing, policy, and capacity development.

Published
2024

3. Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region

Author

James, Chase C, Barton, Andrew D, Allen, Lisa Zeigler, Lampe, Robert H, Rabines, Ariel, Schulberg, Anne, Zheng, Hong, Goericke, Ralf, Goodwin, Kelly D, and Allen, Andrew E

Subjects
Oceanography, Biological Sciences, Ecology, Microbiology, Earth Sciences, Microbiome, Biodiversity, Ecosystem, Microbiota, Nutrients, Plankton, Seawater
Abstract

The ecological and oceanographic processes that drive the response of pelagic ocean microbiomes to environmental changes remain poorly understood, particularly in coastal upwelling ecosystems. Here we show that seasonal and interannual variability in coastal upwelling predicts pelagic ocean microbiome diversity and community structure in the Southern California Current region. Ribosomal RNA gene sequencing, targeting prokaryotic and eukaryotic microbes, from samples collected seasonally during 2014-2020 indicate that nitracline depth is the most robust predictor of spatial microbial community structure and biodiversity in this region. Striking ecological changes occurred due to the transition from a warm anomaly during 2014-2016, characterized by intense stratification, to cooler conditions in 2017-2018, representative of more typical upwelling conditions, with photosynthetic eukaryotes, especially diatoms, changing most strongly. The regional slope of nitracline depth exerts strong control on the relative proportion of highly diverse offshore communities and low biodiversity, but highly productive nearshore communities.

Published
2022

4. Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

Author

Gold, Zachary, Curd, Emily E, Goodwin, Kelly D, Choi, Emma S, Frable, Benjamin W, Thompson, Andrew R, Walker, Harold J, Burton, Ronald S, Kacev, Dovi, Martz, Lucas D, and Barber, Paul H

Subjects
Animals, Biodiversity, DNA Barcoding, Taxonomic, DNA, Environmental, Ecosystem, Fishes, Seawater, California Current Large Marine Ecosystem, eDNA, environmental DNA, metabarcoding, MiFish primers, reference database, Biological Sciences, Evolutionary Biology
Abstract

DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus-specific validation efforts.

Published
2021

5. Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes.

Author

Thompson, Luke R, Haroon, Mohamed F, Shibl, Ahmed A, Cahill, Matt J, Ngugi, David K, Williams, Gareth J, Morton, James T, Knight, Rob, Goodwin, Kelly D, and Stingl, Ulrich

Subjects
Genetics, Life Below Water, Alphaproteobacteria, Genome, Bacterial, Indian Ocean, Metagenome, Phylogeny, Prochlorococcus, Seawater, Pelagibacter, metagenomics, metatranscriptomics, population genomics, single-cell genomics, Pelagibacter, Microbiology
Abstract

Evidence suggests many marine bacteria are cosmopolitan, with widespread but sparse strains poised to seed abundant populations under conducive growth conditions. However, studies supporting this "microbial seed bank" hypothesis have analyzed taxonomic marker genes rather than whole genomes/metagenomes, leaving open the possibility that disparate ocean regions harbor endemic gene content. The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the oceans; we therefore asked whether it harbors endemic gene content. We sequenced and assembled single-cell genomes of 21 SAR11 (subclades Ia, Ib, Id, and II) and 5 Prochlorococcus (ecotype HLII) samples from the Red Sea and combined them with globally sourced reference genomes to cluster genes into ortholog groups (OGs). Ordination of OG composition could distinguish clades, including phylogenetically cryptic Prochlorococcus ecotypes LLII and LLIII. Compared with reference genomes, 1% of Prochlorococcus and 17% of SAR11 OGs were unique to the Red Sea genomes (RS-OGs). Most (83%) RS-OGs had no annotated function, but 65% of RS-OGs were expressed in diel Red Sea metatranscriptomes, suggesting they are functional. Searching Tara Oceans metagenomes, RS-OGs were as likely to be found as non-RS-OGs; nevertheless, Red Sea and other warm samples could be distinguished from cooler samples using the relative abundances of OGs. The results suggest that the prevalence of OGs in these surface ocean bacteria is largely cosmopolitan, with differences in population metagenomes manifested by differences in relative abundance rather than complete presence/absence of OGs.IMPORTANCE Studies have shown that as we sequence seawater from a selected environment deeper and deeper, we approach finding every bacterial taxon known for the ocean as a whole. However, such studies have focused on taxonomic marker genes rather than on whole genomes, raising the possibility that the lack of endemism results from the method of investigation. We took a geographically isolated water body, the Red Sea, and sequenced single cells from it. We compared those single-cell genomes to available genomes from around the ocean and to ocean-spanning metagenomes. We showed that gene ortholog groups found in Red Sea genomes but not in other genomes are nevertheless common across global ocean metagenomes. These results suggest that Baas Becking's hypothesis "everything is everywhere, but the environment selects" also applies to gene ortholog groups. This widely dispersed functional diversity may give oceanic microbial communities the functional capacity to respond rapidly to changing conditions.

Published
2019

6. OBSERVING LIFE IN THE SEA USING ENVIRONMENTAL DNA

Author

Chavez, Francisco P., Min, Markus, Pitz, Kathleen, Truelove, Nathan, Baker, Jacoby, LaScala-Grunewald, Diana, Blum, Marguerite, Walz, Kristine, Nye, Charles, Djurhuus, Anni, Miller, Robert J., Goodwin, Kelly D., Muller-Karger, Frank E., Ruhl, Henry A., and Scholin, Christopher A.

Published
2021

8. Underway measurement of cyanobacterial microcystins using a surface plasmon resonance sensor on an autonomous underwater vehicle

Author

Ussler, William, primary, Doucette, Gregory J., additional, Preston, Christina M., additional, Weinstock, Chloe, additional, Allaf, Nadia, additional, Roman, Brent, additional, Jensen, Scott, additional, Yamahara, Kevan, additional, Lingerfelt, Louise A., additional, Mikulski, Christina M., additional, Hobson, Brett W., additional, Kieft, Brian, additional, Raanan, Ben‐Yair, additional, Zhang, Yanwu, additional, Errera, Reagan M., additional, Ruberg, Steven A., additional, Den Uyl, Paul A., additional, Goodwin, Kelly D., additional, Soelberg, Scott D., additional, Furlong, Clement E., additional, Birch, James M., additional, and Scholin, Christopher A., additional

Published
2024
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9. A communal catalogue reveals Earth’s multiscale microbial diversity

Author

Thompson, Luke R, Sanders, Jon G, McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J, Prill, Robert J, Tripathi, Anupriya, Gibbons, Sean M, Ackermann, Gail, Navas-Molina, Jose A, Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T, Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F, Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A, Lefler, Joshua, Brislawn, Colin J, Humphrey, Gregory, Owens, Sarah M, Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A, Clauset, Aaron, Stevens, Rick L, Shade, Ashley, Pollard, Katherine S, Goodwin, Kelly D, Jansson, Janet K, Gilbert, Jack A, and Knight, Rob

Subjects
Microbiology, Biological Sciences, Ecology, Human Genome, Genetics, Infection, Generic health relevance, Animals, Archaea, Bacteria, Biodiversity, Earth, Planet, Gene Dosage, Geographic Mapping, Humans, Microbiota, Plants, RNA, Ribosomal, 16S, Earth Microbiome Project Consortium, General Science & Technology
Abstract

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Published
2017

10. Using a long‐range autonomous underwater vehicle to find and sample harmful algal blooms in Lake Erie

Author

Zhang, Yanwu, primary, Kieft, Brian, additional, Hobson, Brett W., additional, Raanan, Ben‐Yair, additional, Ussler, William, additional, Preston, Christina M., additional, Errera, Reagan M., additional, Den Uyl, Paul A., additional, Woude, Andrea Vander, additional, Doucette, Gregory J., additional, Ruberg, Steven A., additional, Goodwin, Kelly D., additional, Birch, James M., additional, and Scholin, Christopher A., additional

Published
2024
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12. Critical considerations for communicating environmental DNA science

Author

Stein, Eric D., primary, Jerde, Christopher L., additional, Allan, Elizabeth Andruszkiewicz, additional, Sepulveda, Adam J., additional, Abbott, Cathryn L., additional, Baerwald, Melinda R., additional, Darling, John, additional, Goodwin, Kelly D., additional, Meyer, Rachel S., additional, Timmers, Molly A., additional, and Thielen, Peter M., additional

Published
2023
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13. Description of Toluene Inhibition of Methyl Bromide Biodegradation in Seawater and Isolation of a Marine Toluene Oxidizer That Degrades Methyl Bromide

Author

Goodwin, Kelly D, Tokarczyk, Ryszard, Stephens, F Carol, and Saltzman, Eric S

Subjects
Microbiology, Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Life Below Water, Biodegradation, Environmental, Carbon Isotopes, Culture Media, Hydrocarbons, Brominated, Methyl Chloride, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, Seawater, Sequence Analysis, DNA, Sphingomonadaceae, Toluene, Medical microbiology
Abstract

Methyl bromide (CH3Br) and methyl chloride (CH3Cl) are important precursors for destruction of stratospheric ozone, and oceanic uptake is an important component of the biogeochemical cycle of these methyl halides. In an effort to identify and characterize the organisms mediating halocarbon biodegradation, we surveyed the effect of potential cometabolic substrates on CH3Br biodegradation using a 13CH3Br incubation technique. Toluene (160 to 200 nM) clearly inhibited CH3Br and CH3Cl degradation in seawater samples from the North Atlantic, North Pacific, and Southern Oceans. Furthermore, a marine bacterium able to co-oxidize CH3Br while growing on toluene was isolated from subtropical Western Atlantic seawater. The bacterium, Oxy6, was also able to oxidize o-xylene and the xylene monooxygenase (XMO) pathway intermediate 3-methylcatechol. Patterns of substrate oxidation, lack of acetylene inhibition, and the inability of the toluene 4-monooxygenase (T4MO)-containing bacterium Pseudomonas mendocina KR1 to degrade CH3Br ruled out participation of the T4MO pathway in Oxy6. Oxy6 also oxidized a variety of toluene (TOL) pathway intermediates such as benzyl alcohol, benzylaldehyde, benzoate, and catechol, but the inability of Pseudomonas putida mt-2 to degrade CH3Br suggested that the TOL pathway might not be responsible for CH3Br biodegradation. Molecular phylogenetic analysis identified Oxy6 to be a member of the family Sphingomonadaceae related to species within the Porphyrobacter genus. Although some Sphingomonadaceae can degrade a variety of xenobiotic compounds, this appears to be the first report of CH3Br degradation for this class of organism. The widespread inhibitory effect of toluene on natural seawater samples and the metabolic capabilities of Oxy6 indicate a possible link between aromatic hydrocarbon utilization and the biogeochemical cycle of methyl halides.

Published
2005

15. Toward a national eDNA strategy for the United States

Author

Kelly, Ryan P., primary, Lodge, David M., additional, Lee, Kai N., additional, Theroux, Susanna, additional, Sepulveda, Adam J., additional, Scholin, Christopher A., additional, Craine, Joseph M., additional, Andruszkiewicz Allan, Elizabeth, additional, Nichols, Krista M., additional, Parsons, Kim M., additional, Goodwin, Kelly D., additional, Gold, Zachary, additional, Chavez, Francisco P., additional, Noble, Rachel T., additional, Abbott, Cathryn L., additional, Baerwald, Melinda R., additional, Naaum, Amanda M., additional, Thielen, Peter M., additional, Simons, Ariel Levi, additional, Jerde, Christopher L., additional, Duda, Jeffrey J., additional, Hunter, Margaret E., additional, Hagan, John A., additional, Meyer, Rachel Sarah, additional, Steele, Joshua A., additional, Stoeckle, Mark Y., additional, Bik, Holly M., additional, Meyer, Christopher P., additional, Stein, Eric, additional, James, Karen E., additional, Thomas, Austen C., additional, Demir‐Hilton, Elif, additional, Timmers, Molly A., additional, Griffith, John F., additional, Weise, Michael J., additional, and Weisberg, Stephen B., additional

Published
2023
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16. methyl bromide loss rate constants in the north Pacific Ocean

Author

Tokarczyk, Ryszard, Goodwin, Kelly D, and Saltzman, Eric S

Subjects
Meteorology & Atmospheric Sciences
Abstract

The degration rate constant of CH 3Br in the North Pacific Ocean was measured in surface seawater between September and October 1999, using a stable isotope ( 13CH 3Br) incubation technique. Total degradation rate constants ranged from 0.02 to 0.43 d -1, decreasing in colder waters as a results of the temperature-dependence of chemical losses. Biological rate constants ranged from 0.01 to 0.20 d -1. In subtropical waters (13-20°N), biological loss rate constants were small compared to chemical loss rate constant. North of Hawaii, biological processes played an increasingly significant role in CH 3Br degradation. In subpolar waters (40-58°N), biological losses dominated the removal of methyl bromide. Comparison of the measured loss rate constants with surface water CH 3Br concentrations suggest that the CH 3Br production rate is higher in warm, low latitude waters than in cold subpolar waters at this time of year. Diel studies revealed a midday maximum in biological degration of methyl bromide.

Published
2001

18. Contributors

Author

Adebambo, Olubukola, primary, Agardy, Tundi, additional, Allen, Andrew E., additional, Altieri, Andrew H., additional, Andrade, Francisco, additional, Angiolillo, Michela, additional, Avery-Gomm, Stephanie, additional, Bai, Jiayu, additional, Baker, Joel, additional, Barboza, Luís Gabriel A., additional, Barros, Thayanne Lima, additional, Baxter, John M., additional, Bayley, Daniel T.I., additional, Bellucci, Luca G., additional, Birkeland, Charles, additional, Bond, Alex, additional, Booth, Andy M., additional, Borrelle, Stephanie, additional, Bradford, Jessica, additional, Bueno, Paula, additional, Canonico Hyde, Gabrielle, additional, Chen, Bing, additional, Cheng, Jing, additional, Cózar, Andrés, additional, Crawford, Rory, additional, Crowder, Larry B., additional, Dachs, Jordi, additional, Darbra, Rosa M., additional, David, Matej, additional, Day, Jon C., additional, Del Aguila Feijoo, Monica C., additional, Diaz, Robert J., additional, Djurhuus, Anni, additional, Dong, Zhijun, additional, Edwards, Stuart Johnston, additional, Ehler, Charles N., additional, Elhaimer, Elias, additional, Filbee-Dexter, Karen, additional, Filgueira, Ramón, additional, Fingas, Merv, additional, Foster, Greg, additional, Frazão Santos, Catarina, additional, Frias, João P.G.L., additional, Friess, Daniel A., additional, Gimenez, Barbara C.G., additional, Giuliani, Silvia, additional, Gollasch, Stephan, additional, Good, Thomas P., additional, Goodwin, Kelly D., additional, Guilhermino, Lúcia, additional, Hatfield, Jeff, additional, Heery, Eliza C., additional, Hodum, Peter, additional, Hossain, Tahazzud, additional, Jing, Liang, additional, Kershaw, Peter J., additional, Krumhansl, Kira, additional, Laffoley, Dan, additional, Lee, Shing Yip, additional, Lee, Kenneth, additional, Lively, Julie A., additional, Lohmann, Rainer, additional, Loke, Lynette H.L., additional, Major, Heather L., additional, Mallory, Mark, additional, Masura, Julie, additional, Matchinski, Ethan J., additional, McCoy, Karen D., additional, McCrow, John P., additional, Merkel, Flemming, additional, Mogg, Andrew O.M., additional, Morrison, Courtney E., additional, Muller-Karger, Frank E., additional, Orbach, Michael K., additional, Panigada, Simone, additional, Pauly, Daniel, additional, Pedersen, Morten F., additional, Picciulin, Marta, additional, Primavera, Jurgenne H., additional, Provencher, Jennifer F., additional, Puig, Martí, additional, Rako-Gospić, Nikolina, additional, Reynolds, Michelle, additional, Ritter, Fabian, additional, Rodríguez-Rodríguez, David, additional, Rogers, Alex D., additional, Romo, Jessica, additional, Sharma, Nameeta, additional, Sherley, Richard B., additional, Spatz, Dena, additional, Steeves, Laura, additional, Tam, Nora F.Y., additional, Taylor, Stephanie, additional, Todd, Peter A., additional, Van Lavieren, Hanneke, additional, Vieira, Luís R., additional, Votier, Stephen, additional, Wakefield, Jill, additional, Walker, Tony R., additional, Wang, Yafen, additional, Weitzman, Jenny, additional, Wenzel, Lauren, additional, Wernberg, Thomas, additional, Ye, Xudong, additional, Zeigler Allen, Lisa, additional, Zeller, Dirk, additional, Zhang, Baiyu, additional, Zischka, Katherine, additional, and Zomorodi, Sanam, additional

Published
2019
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19. The founding charter of the Omic Biodiversity Observation Network (Omic BON)

Author

Meyer, Raïssa, Davies, Neil, Pitz, Kathleen J, Meyer, Chris, Samuel, Robyn, Anderson, Jane, Appeltans, Ward, Barker, Katharine, Chavez, Francisco P, Duffy, J Emmett, Goodwin, Kelly D, Hudson, Maui, Hunter, Margaret E, Karstensen, Johannes, Laney, Christine M, Leinen, Margaret, Mabee, Paula, Macklin, James A, Muller-Karger, Frank, Pade, Nicolas, Pearlman, Jay, Phillips, Lori, Provoost, Pieter, Santi, Ioulia, Schigel, Dmitry, Schriml, Lynn M, Soccodato, Alice, Suominen, Saara, Thibault, Katherine M, Ung, Visotheary, van de Kamp, Jodie, Wallis, Elycia, Walls, Ramona, Buttigieg, Pier Luigi, Meyer, Raïssa, Davies, Neil, Pitz, Kathleen J, Meyer, Chris, Samuel, Robyn, Anderson, Jane, Appeltans, Ward, Barker, Katharine, Chavez, Francisco P, Duffy, J Emmett, Goodwin, Kelly D, Hudson, Maui, Hunter, Margaret E, Karstensen, Johannes, Laney, Christine M, Leinen, Margaret, Mabee, Paula, Macklin, James A, Muller-Karger, Frank, Pade, Nicolas, Pearlman, Jay, Phillips, Lori, Provoost, Pieter, Santi, Ioulia, Schigel, Dmitry, Schriml, Lynn M, Soccodato, Alice, Suominen, Saara, Thibault, Katherine M, Ung, Visotheary, van de Kamp, Jodie, Wallis, Elycia, Walls, Ramona, and Buttigieg, Pier Luigi

Abstract

Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

Published
2023
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21. Toward a national eDNA strategy for the United States.

Author

Kelly, Ryan P., Lodge, David M., Lee, Kai N., Theroux, Susanna, Sepulveda, Adam J., Scholin, Christopher A., Craine, Joseph M., Andruszkiewicz Allan, Elizabeth, Nichols, Krista M., Parsons, Kim M., Goodwin, Kelly D., Gold, Zachary, Chavez, Francisco P., Noble, Rachel T., Abbott, Cathryn L., Baerwald, Melinda R., Naaum, Amanda M., Thielen, Peter M., Simons, Ariel Levi, and Jerde, Christopher L.

Published
2024
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26. The founding charter of the Omic Biodiversity Observation Network (Omic BON)

Author

Meyer, Raïssa, primary, Davies, Neil, additional, Pitz, Kathleen J, additional, Meyer, Chris, additional, Samuel, Robyn, additional, Anderson, Jane, additional, Appeltans, Ward, additional, Barker, Katharine, additional, Chavez, Francisco P, additional, Duffy, J Emmett, additional, Goodwin, Kelly D, additional, Hudson, Maui, additional, Hunter, Margaret E, additional, Karstensen, Johannes, additional, Laney, Christine M, additional, Leinen, Margaret, additional, Mabee, Paula, additional, Macklin, James A, additional, Muller-Karger, Frank, additional, Pade, Nicolas, additional, Pearlman, Jay, additional, Phillips, Lori, additional, Provoost, Pieter, additional, Santi, Ioulia, additional, Schigel, Dmitry, additional, Schriml, Lynn M, additional, Soccodato, Alice, additional, Suominen, Saara, additional, Thibault, Katherine M, additional, Ung, Visotheary, additional, van de Kamp, Jodie, additional, Wallis, Elycia, additional, Walls, Ramona, additional, and Buttigieg, Pier Luigi, additional

Published
2022
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27. Lake Erie field trials to advance autonomous monitoring of cyanobacterial harmful algal blooms

Author

Den Uyl, Paul A., primary, Thompson, Luke R., additional, Errera, Reagan M., additional, Birch, James M., additional, Preston, Christina M., additional, Ussler, William, additional, Yancey, Colleen E., additional, Chaganti, Subba Rao, additional, Ruberg, Steven A., additional, Doucette, Gregory J., additional, Dick, Gregory J., additional, Scholin, Christopher A., additional, and Goodwin, Kelly D., additional

Published
2022
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29. Multi-laboratory evaluations of the performance of Catellicoccus marimammalium PCR assays developed to target gull fecal sources

Author

Sinigalliano, Christopher D., Ervin, Jared S., Van De Werfhorst, Laurie C., Badgley, Brian D., Ballesté, Elisenda, Bartkowiak, Jakob, Boehm, Alexandria B., Byappanahalli, Muruleedhara, Goodwin, Kelly D., Gourmelon, Michèle, Griffith, John, Holden, Patricia A., Jay, Jenny, Layton, Blythe, Lee, Cheonghoon, Lee, Jiyoung, Meijer, Wim G., Noble, Rachel, Raith, Meredith, Ryu, Hodon, Sadowsky, Michael J., Schriewer, Alexander, Wang, Dan, Wanless, David, Whitman, Richard, Wuertz, Stefan, and Santo Domingo, Jorge W.

Published
2013
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30. Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods

Author

Ebentier, Darcy L., Hanley, Kaitlyn T., Cao, Yiping, Badgley, Brian D., Boehm, Alexandria B., Ervin, Jared S., Goodwin, Kelly D., Gourmelon, Michèle, Griffith, John F., Holden, Patricia A., Kelty, Catherine A., Lozach, Solen, McGee, Charles, Peed, Lindsay A., Raith, Meredith, Ryu, Hodon, Sadowsky, Michael J., Scott, Elizabeth A., Domingo, Jorge Santo, Schriewer, Alexander, Sinigalliano, Christopher D., Shanks, Orin C., Van De Werfhorst, Laurie C., Wang, Dan, Wuertz, Stefan, and Jay, Jennifer A.

Published
2013
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31. Performance evaluation of canine-associated Bacteroidales assays in a multi-laboratory comparison study

Author

Schriewer, Alexander, Goodwin, Kelly D., Sinigalliano, Christopher D., Cox, Annie M., Wanless, David, Bartkowiak, Jakob, Ebentier, Darcy L., Hanley, Kaitlyn T., Ervin, Jared, Deering, Louise A., Shanks, Orin C., Peed, Lindsay A., Meijer, Wim G., Griffith, John F., SantoDomingo, Jorge, Jay, Jennifer A., Holden, Patricia A., and Wuertz, Stefan

Published
2013
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36. Expanding the temporal and spatial scales of environmental DNA research with autonomous sampling

Author

Truelove, Nathan K., primary, Patin, Nastassia V., additional, Min, Markus, additional, Pitz, Kathleen J., additional, Preston, Chris M., additional, Yamahara, Kevan M., additional, Zhang, Yanwu, additional, Raanan, Ben Y., additional, Kieft, Brian, additional, Hobson, Brett, additional, Thompson, Luke R., additional, Goodwin, Kelly D., additional, and Chavez, Francisco P., additional

Published
2022
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37. Metagenomic and Metatranscriptomic Insights into Population Diversity of Microcystis Blooms: Spatial and Temporal Dynamics of mcy Genotypes, Including a Partial Operon That Can Be Abundant and Expressed

Author

Yancey, Colleen E., primary, Smith, Derek J., additional, Den Uyl, Paul A., additional, Mohamed, Osama G., additional, Yu, Fengan, additional, Ruberg, Steven A., additional, Chaffin, Justin D., additional, Goodwin, Kelly D., additional, Tripathi, Ashootosh, additional, Sherman, David H., additional, and Dick, Gregory J., additional

Published
2022
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44. Consumption of tropospheric levels of methyl bromide by C(sub 1) compound-utilizing bacteria and comparison to saturation kinetics

Author

Goodwin, Kelly D., Varner, Ruth K., Crill, Patrick M., and Oremland, Ronald S.

Subjects
Biodegradation -- Research, Methanobacteriaceae -- Research, Biological sciences
Abstract

Methylotrophs and methanotrophs such as strain IMB-1 and Leisingeria methylohalidivorans strain MB2(super T) can oxidize methyl bromide at tropospheric concentrations of 12 parts per trillion by volume. Methyl bromide is a fumigant that contributes to ozone depletion.

Published
2001

46. Foreword

Author

Miller, Laurence G. and Goodwin, Kelly D.

Published
2002

48. Marine bacterial degradation of brominated methanes

Author

Goodwin, Kelly D., Lidstrom, Mary E., and Oremland, Ronald S.

Subjects
Marine bacteria -- Research, Methane -- Research, Environmental issues, Science and technology
Abstract

Bacteria found in seawater is not able to completely degrade brominated methanes, which are produced by sources such as marine algae. The bacteria is able to degrade dibromomethane, but it is not as successful in degrading bromoform. However, this degradation of dibromomethane is inhibited by the presence of nitrifiers and methanotrophs.

Published
1997

49. AORA - Atlantic Ocean Research Alliance - Marine Microbiome Roadmap

Author

Bolhuis, H., Buttigieg, Pier Luigi, Goodwin, Kelly D., Groben, R., Iudicone, D., Lacoursière-Roussel, A., Pesant, Stéphane, Robinson, Shaun, Björnsson, S., Erlendsson, L.S., Rae, M., Bolhuis, H., Buttigieg, Pier Luigi, Goodwin, Kelly D., Groben, R., Iudicone, D., Lacoursière-Roussel, A., Pesant, Stéphane, Robinson, Shaun, Björnsson, S., Erlendsson, L.S., and Rae, M.

Published
2020

50. A communal catalogue reveals Earth’s multiscale microbial diversity

Author

Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jirˇí, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, Zhao, Hongxia, University of California [San Diego] (UC San Diego), University of California, University of Southern Mississippi (USM), NOAA Atlantic Oceanographic and Meteorological Laboratory (AOML), National Oceanic and Atmospheric Administration (NOAA), Southwest Fisheries Science Center (SWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), University of California [San Francisco] (UCSF), Indiana University [Bloomington], Indiana University System, IBM Almaden Research Center [San Jose], IBM, Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], University of California-University of California, Massachusetts Institute of Technology (MIT), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Harvard University [Cambridge], The Pathogen and Microbiome Institute, Northern Arizona University [Flagstaff], Pacific Northwest National Laboratory (PNNL), Argonne National Laboratory [Lemont] (ANL), University of Illinois [Chicago] (UIC), University of Illinois System, University of Colorado [Boulder], University of Southern California (USC), University of Chicago, Michigan State University [East Lansing], Michigan State University System, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Tieleman lab, Biological Sciences, Department of Food and Nutrition, Arctic Microbial Ecology, Thompson, Luke R., Sanders, Jon G., Mcdonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Xu, Zhenjiang Zech, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Song, Se Jin, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, Mckenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Agosto Rivera, Jose L., Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jiří, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, Jolynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chri, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Ander, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lanede Graaf, Kelly, Laroche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., Maccormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., Mcdonald, James E., Mcguire, Krista L., Mcmahon, Katherine D., Mcminds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Luca, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Mile, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguinorlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Taş, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., Van Der Lelie, Daniel, Van Treuren, William, Van Zwieten, Luka, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia

Subjects
MARINE BACTERIAL, 0301 basic medicine, Earth, Planet, Gene Dosage, Biodiversity, MESH: Plants, Geographic Mapping, OPERON COPY NUMBER, MESH: Gene Dosage, purl.org/becyt/ford/1 [https], RNA, Ribosomal, 16S, EARTH MICROBIOME PROJECT, MESH: Animals, MESH: Geographic Mapping, MESH: Earth, Planet, GENE-EXPRESSION, media_common, GLOBAL PATTERNS, Multidisciplinary, Ecology, Microbiota, Bacteriologie, GUT MICROBIOTA, 1184 Genetics, developmental biology, physiology, ARCHAEAL, Bacteriology, Host Pathogen Interaction & Diagnostics, Plants, MESH: RNA, Ribosomal, 16S, Food Quality and Design, MESH: Archaea, CIENCIAS NATURALES Y EXACTAS, MESH: Ecology, Rare biosphere, Otras Ciencias Biológicas, Ecology (disciplines), media_common.quotation_subject, CONSISTENT, 030106 microbiology, Context (language use), [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Article, MESH: Biodiversity, Ciencias Biológicas, 03 medical and health sciences, Microbial ecology, Animals, Humans, Life Science, MESH: Microbiota, Microbiome, purl.org/becyt/ford/1.6 [https], VLAG, Host Pathogen Interaction & Diagnostics, BACTERIAL DIVERSITY, MESH: Humans, SEQUENCES, Bacteria, Bacteriology, NESTEDNESS, 15. Life on land, RARE BIOSPHERE, Archaea, Data science, Host Pathogen Interactie & Diagnostiek, EVOLUTION, ONTOLOGY, AMPLICON SEQUENCING, MESH: Bacteria, 030104 developmental biology, Earth Microbiome Project, Bacteriologie, Host Pathogen Interactie & Diagnostiek, NESTEDNESS ANALYSIS, COMMUNITIES, MICROBIAL DIVERSITY, Diversity (politics)
Abstract

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity. Fil: Thompson, Luke R.. University of California at San Diego; Estados Unidos. University of Southern Mississippi; Estados Unidos. National Oceanic and Atmospheric Administration; Estados Unidos Fil: Sanders, Jon G.. University of California at San Diego; Estados Unidos Fil: McDonald, Daniel. University of California at San Diego; Estados Unidos Fil: Amir, Amnon. University of California at San Diego; Estados Unidos Fil: Ladau, Joshua. University of California San Francisco; Estados Unidos Fil: Locey, Kenneth J.. Indiana University; Estados Unidos Fil: Prill, Robert J.. IBM Almaden Research Center; Estados Unidos Fil: Tripathi, Anupriya. University of California at San Diego; Estados Unidos Fil: Gibbons, Sean M.. Massachusetts Institute of Technology; Estados Unidos Fil: Ackermann, Gail. University of California San Diego; Estados Unidos Fil: Navas Molina, Jose A.. University of California at San Diego; Estados Unidos Fil: Janssen, Stefan. University of California at San Diego; Estados Unidos Fil: Kopylova, Evguenia. University of California at San Diego; Estados Unidos Fil: Vázquez Baeza, Yoshiki. University of California at San Diego; Estados Unidos Fil: González, Antonio. University of California at San Diego; Estados Unidos Fil: Morton, James T.. University of California at San Diego; Estados Unidos Fil: Mirarab, Siavash. University of California at San Diego; Estados Unidos Fil: Xu, Zhenjiang Zech. University of California at San Diego; Estados Unidos Fil: Jiang, Lingjing. University of California at San Diego; Estados Unidos Fil: Haroon, Mohamed F.. Harvard University; Estados Unidos Fil: Kanbar, Jad. University of California at San Diego; Estados Unidos Fil: Zhu, Qiyun. University of California at San Diego; Estados Unidos Fil: Song, Se Jin. University of California at San Diego; Estados Unidos Fil: Kosciolek, Tomasz. University of California at San Diego; Estados Unidos Fil: Bokulich, Nicholas A.. Northern Arizona University; Estados Unidos Fil: Lefler, Joshua. University of California at San Diego; Estados Unidos Fil: Brislawn, Colin J.. Earth and Biological Sciences Directorate; Estados Unidos Fil: Humphrey, Gregory. University of California at San Diego; Estados Unidos Fil: Owens, Sarah M.. Argonne National Laboratory; Estados Unidos Fil: Hampton Marcell, Jarrad. Argonne National Laboratory; Estados Unidos. University of Illinois at Chicago; Estados Unidos Fil: Berg Lyons, Donna. University of Colorado; Estados Unidos Fil: McKenzie, Valerie. University of Colorado; Estados Unidos Fil: Fierer, Noah. University of Colorado; Estados Unidos Fil: Fuhrman, Jed A.. University of Colorado; Estados Unidos Fil: Clauset, Aaron. University of Colorado; Estados Unidos Fil: Stevens, Rick L.. Argonne National Laboratory; Estados Unidos. University of Chicago; Estados Unidos Fil: Shade, Ashley. Michigan State University; Estados Unidos Fil: Pollard, Katherine S.. The Gladstone Institutes; Estados Unidos. University of California San Francisco; Estados Unidos Fil: Goodwin, Kelly D.. National Oceanic and Atmospheric Administration; Estados Unidos Fil: Jansson, Janet K.. Earth and Biological Sciences Directorate; Estados Unidos Fil: Gilbert, Jack A.. Argonne National Laboratory; Estados Unidos. University of Chicago; Estados Unidos Fil: Knight, Rob. University of California San Diego; Estados Unidos Fil: Dionisi, Hebe Monica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; Argentina Fil: Lozada, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; Argentina Fil: Mac Cormack, Walter Patricio. Universidad de Buenos Aires; Argentina. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina

Published
2017
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