Fuhrman Jed A.

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Jed A.

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Global distribution and diversity of marine Verrucomicrobia

2011-12-08 , Freitas, Sara , Hatosy, Stephen , Fuhrman, Jed A. , Huse, Susan M. , Mark Welch, David B. , Sogin, Mitchell L. , Martiny, Adam C.

Verrucomicrobia is a bacterial phylum that is commonly detected in soil but little is known about the distribution and diversity of this phylum in the marine environment. To address this, we analyzed the marine microbial community composition in 506 samples from the International Census of Marine Microbes as well as eleven coastal samples taken from the California Current. These samples from both the water column and sediments covered a wide range of environmental conditions. Verrucomicrobia were present in 98% of the analyzed samples and thus appeared nearly ubiquitous in the ocean. Based on the occurrence of amplified 16S rRNA sequences, Verrucomicrobia constituted on average 2% of the water column and 1.4% of the sediment bacterial communities. The diversity of Verrucomicrobia displayed a biogeography at multiple taxonomic levels and thus, specific lineages appeared to have clear habitat preference. We found that Subdivision 1 and 4 generally dominated marine bacterial communities, whereas Subdivision 2 was confined to low salinity waters. Within the subdivisions, Verrucomicrobia community composition were significantly different in the water column compared to sediment as well as within the water column along gradients of salinity, temperature, nitrate, depth, and overall water column depth. Although we still know little about the ecophysiology of Verrucomicrobia lineages, the ubiquity of this phylum suggests that it may be important for the biogeochemical cycle of carbon in the ocean.

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Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

2011-01-04 , Yilmaz, Pelin , Kottmann, Renzo , Field, Dawn , Knight, Rob , Cole, James R. , Amaral-Zettler, Linda A. , Gilbert, Jack A. , Karsch-Mizrachi, Ilene , Johnston, Anjanette , Cochrane, Guy R. , Vaughan, Robert , Hunter, Christopher , Park, Joonhong , Morrison, Norman , Rocca-Serra, Philippe , Sterk, Peter , Arumugam, Manimozhiyan , Bailey, Mark , Baumgartner, Laura , Birren, Bruce W. , Blaser, Martin J. , Bonazzi, Vivien , Booth, Tim , Bork, Peer , Bushman, Frederic D. , Buttigieg, Pier Luigi , Chain, Patrick S. G. , Charlson, Emily , Costello, Elizabeth K. , Huot-Creasy, Heather , Dawyndt, Peter , DeSantis, Todd , Fierer, Noah , Fuhrman, Jed A. , Gallery, Rachel E. , Gevers, Dirk , Gibbs, Richard A. , San Gil, Inigo , Gonzalez, Antonio , Gordon, Jeffrey I. , Guralnick, Robert P. , Hankeln, Wolfgang , Highlander, Sarah , Hugenholtz, Philip , Jansson, Janet K. , Kau, Andrew L. , Kelley, Scott T. , Kennedy, Jerry , Knights, Dan , Koren, Omry , Kuczynski, Justin , Kyrpides, Nikos C. , Larsen, Robert , Lauber, Christian L. , Legg, Teresa , Ley, Ruth E. , Lozupone, Catherine A. , Ludwig, Wolfgang , Lyons, Donna , Maguire, Eamonn , Methe, Barbara A. , Meyer, Folker , Muegge, Brian , Nakielny, Sara , Nelson, Karen E. , Nemergut, Diana , Neufeld, Josh D. , Newbold, Lindsay K. , Oliver, Anna E. , Pace, Norman R. , Palanisamy, Giriprakash , Peplies, Jorg , Petrosino, Joseph , Proctor, Lita , Pruesse, Elmar , Quast, Christian , Raes, Jeroen , Ratnasingham, Sujeevan , Ravel, Jacques , Relman, David A. , Assunta-Sansone, Susanna , Schloss, Patrick D. , Schriml, Lynn M. , Sinha, Rohini , Smith, Michelle I. , Sodergren, Erica , Spor, Ayme , Stombaugh, Jesse , Tiedje, James M. , Ward, Doyle V. , Weinstock, George M. , Wendel, Doug , White, Owen , Whiteley, Andrew , Wilke, Andreas , Wortman, Jennifer R. , Yatsunenko, Tanya , Glockner, Frank Oliver

Here we present a standard developed by the Genomic Standards Consortium (GSC) to describe marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The “environmental packages” apply to any sequence whose origin is known and can therefore be used in combination with MIMARKS or other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we establish the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.