Literature DB >> 23487761

Evidence for a persistent microbial seed bank throughout the global ocean.

Sean M Gibbons1, J Gregory Caporaso, Meg Pirrung, Dawn Field, Rob Knight, Jack A Gilbert.   

Abstract

Do bacterial taxa demonstrate clear endemism, like macroorganisms, or can one site's bacterial community recapture the total phylogenetic diversity of the world's oceans? Here we compare a deep bacterial community characterization from one site in the English Channel (L4-DeepSeq) with 356 datasets from the International Census of Marine Microbes (ICoMM) taken from around the globe (ranging from marine pelagic and sediment samples to sponge-associated environments). At the L4-DeepSeq site, increasing sequencing depth uncovers greater phylogenetic overlap with the global ICoMM data. This site contained 31.7-66.2% of operational taxonomic units identified in a given ICoMM biome. Extrapolation of this overlap suggests that 1.93 × 10(11) sequences from the L4 site would capture all ICoMM bacterial phylogenetic diversity. Current technology trends suggest this limit may be attainable within 3 y. These results strongly suggest the marine biosphere maintains a previously undetected, persistent microbial seed bank.

Mesh:

Year:  2013        PMID: 23487761      PMCID: PMC3607043          DOI: 10.1073/pnas.1217767110

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  31 in total

1.  Global dispersal of free-living microbial eukaryote species.

Authors:  Bland J Finlay
Journal:  Science       Date:  2002-05-10       Impact factor: 47.728

2.  Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

Authors:  T Z DeSantis; P Hugenholtz; N Larsen; M Rojas; E L Brodie; K Keller; T Huber; D Dalevi; P Hu; G L Andersen
Journal:  Appl Environ Microbiol       Date:  2006-07       Impact factor: 4.792

3.  Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors.

Authors:  Quansong Ruan; Debojyoti Dutta; Michael S Schwalbach; Joshua A Steele; Jed A Fuhrman; Fengzhu Sun
Journal:  Bioinformatics       Date:  2006-07-31       Impact factor: 6.937

4.  Microbial population structures in the deep marine biosphere.

Authors:  Julie A Huber; David B Mark Welch; Hilary G Morrison; Susan M Huse; Phillip R Neal; David A Butterfield; Mitchell L Sogin
Journal:  Science       Date:  2007-10-05       Impact factor: 47.728

5.  Emergent biogeography of microbial communities in a model ocean.

Authors:  Michael J Follows; Stephanie Dutkiewicz; Scott Grant; Sallie W Chisholm
Journal:  Science       Date:  2007-03-30       Impact factor: 47.728

Review 6.  Microbial seed banks: the ecological and evolutionary implications of dormancy.

Authors:  Jay T Lennon; Stuart E Jones
Journal:  Nat Rev Microbiol       Date:  2011-02       Impact factor: 60.633

7.  Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions.

Authors:  Jens Reeder; Rob Knight
Journal:  Nat Methods       Date:  2010-09       Impact factor: 28.547

8.  The Western English Channel contains a persistent microbial seed bank.

Authors:  J Gregory Caporaso; Konrad Paszkiewicz; Dawn Field; Rob Knight; Jack A Gilbert
Journal:  ISME J       Date:  2011-11-10       Impact factor: 10.302

9.  TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.

Authors:  Meg Pirrung; Ryan Kennedy; J Gregory Caporaso; Jesse Stombaugh; Doug Wendel; Rob Knight
Journal:  Bioinformatics       Date:  2011-09-08       Impact factor: 6.937

10.  Defining seasonal marine microbial community dynamics.

Authors:  Jack A Gilbert; Joshua A Steele; J Gregory Caporaso; Lars Steinbrück; Jens Reeder; Ben Temperton; Susan Huse; Alice C McHardy; Rob Knight; Ian Joint; Paul Somerfield; Jed A Fuhrman; Dawn Field
Journal:  ISME J       Date:  2011-08-18       Impact factor: 10.302

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  79 in total

1.  New approaches indicate constant viral diversity despite shifts in assemblage structure in an Australian hypersaline lake.

Authors:  Joanne B Emerson; Brian C Thomas; Karen Andrade; Karla B Heidelberg; Jillian F Banfield
Journal:  Appl Environ Microbiol       Date:  2013-08-30       Impact factor: 4.792

2.  Fungal diversity in permafrost and tallgrass prairie soils under experimental warming conditions.

Authors:  C Ryan Penton; Derek St Louis; James R Cole; Yiqi Luo; Liyou Wu; E A G Schuur; Jizhong Zhou; James M Tiedje
Journal:  Appl Environ Microbiol       Date:  2013-09-06       Impact factor: 4.792

3.  Spatial scale drives patterns in soil bacterial diversity.

Authors:  Sarah L O'Brien; Sean M Gibbons; Sarah M Owens; Jarrad Hampton-Marcell; Eric R Johnston; Julie D Jastrow; Jack A Gilbert; Folker Meyer; Dionysios A Antonopoulos
Journal:  Environ Microbiol       Date:  2016-03-21       Impact factor: 5.491

4.  The niche of an invasive marine microbe in a subtropical freshwater impoundment.

Authors:  K David Hambright; Jessica E Beyer; James D Easton; Richard M Zamor; Anne C Easton; Thayer C Hallidayschult
Journal:  ISME J       Date:  2014-06-20       Impact factor: 10.302

5.  Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes.

Authors:  Fernando Espínola; Hebe M Dionisi; Sharon Borglin; Colin J Brislawn; Janet K Jansson; Walter P Mac Cormack; JoLynn Carroll; Sara Sjöling; Mariana Lozada
Journal:  Microb Ecol       Date:  2017-07-12       Impact factor: 4.552

6.  Local-global overlap in diversity informs mechanisms of bacterial biogeography.

Authors:  Joshua A Livermore; Stuart E Jones
Journal:  ISME J       Date:  2015-04-07       Impact factor: 10.302

Review 7.  Ecology and exploration of the rare biosphere.

Authors:  Michael D J Lynch; Josh D Neufeld
Journal:  Nat Rev Microbiol       Date:  2015-03-02       Impact factor: 60.633

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

Authors:  Luke R Thompson; Mohamed F Haroon; Ahmed A Shibl; Matt J Cahill; David K Ngugi; Gareth J Williams; James T Morton; Rob Knight; Kelly D Goodwin; Ulrich Stingl
Journal:  Appl Environ Microbiol       Date:  2019-06-17       Impact factor: 4.792

9.  Identifying the core seed bank of a complex boreal bacterial metacommunity.

Authors:  Clara Ruiz-González; Juan Pablo Niño-García; Steven W Kembel; Paul A Del Giorgio
Journal:  ISME J       Date:  2017-06-06       Impact factor: 10.302

Review 10.  Ancient and modern environmental DNA.

Authors:  Mikkel Winther Pedersen; Søren Overballe-Petersen; Luca Ermini; Clio Der Sarkissian; James Haile; Micaela Hellstrom; Johan Spens; Philip Francis Thomsen; Kristine Bohmann; Enrico Cappellini; Ida Bærholm Schnell; Nathan A Wales; Christian Carøe; Paula F Campos; Astrid M Z Schmidt; M Thomas P Gilbert; Anders J Hansen; Ludovic Orlando; Eske Willerslev
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2015-01-19       Impact factor: 6.237

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