Literature DB >> 25730701

Ecology and exploration of the rare biosphere.

Michael D J Lynch1, Josh D Neufeld1.   

Abstract

The profound influence of microorganisms on human life and global biogeochemical cycles underlines the value of studying the biogeography of microorganisms, exploring microbial genomes and expanding our understanding of most microbial species on Earth: that is, those present at low relative abundance. The detection and subsequent analysis of low-abundance microbial populations—the 'rare biosphere'—have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. We discuss the ecology of rare microbial populations, and highlight molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities.

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Year:  2015        PMID: 25730701     DOI: 10.1038/nrmicro3400

Source DB:  PubMed          Journal:  Nat Rev Microbiol        ISSN: 1740-1526            Impact factor:   60.633


  162 in total

1.  'Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say?

Authors:  Rutger de Wit; Thierry Bouvier
Journal:  Environ Microbiol       Date:  2006-04       Impact factor: 5.491

2.  Ecology. Dipping into the rare biosphere.

Authors:  Carlos Pedrós-Alió
Journal:  Science       Date:  2007-01-12       Impact factor: 47.728

3.  The seasonal structure of microbial communities in the Western English Channel.

Authors:  Jack A Gilbert; Dawn Field; Paul Swift; Lindsay Newbold; Anna Oliver; Tim Smyth; Paul J Somerfield; Sue Huse; Ian Joint
Journal:  Environ Microbiol       Date:  2009-07-31       Impact factor: 5.491

4.  The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes.

Authors:  David L Kirchman; Matthew T Cottrell; Connie Lovejoy
Journal:  Environ Microbiol       Date:  2010-02-03       Impact factor: 5.491

5.  Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads.

Authors:  Andrea K Bartram; Michael D J Lynch; Jennifer C Stearns; Gabriel Moreno-Hagelsieb; Josh D Neufeld
Journal:  Appl Environ Microbiol       Date:  2011-04-01       Impact factor: 4.792

6.  Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next-generation sequence data.

Authors:  T Frisli; T H A Haverkamp; K S Jakobsen; N Chr Stenseth; K Rudi
Journal:  J Appl Microbiol       Date:  2012-11-01       Impact factor: 3.772

7.  Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets.

Authors:  Angélique Gobet; Christopher Quince; Alban Ramette
Journal:  Nucleic Acids Res       Date:  2010-06-14       Impact factor: 16.971

8.  Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts.

Authors:  Nicole S Webster; Michael W Taylor; Faris Behnam; Sebastian Lücker; Thomas Rattei; Stephen Whalan; Matthias Horn; Michael Wagner
Journal:  Environ Microbiol       Date:  2009-09-29       Impact factor: 5.491

9.  Structure, function and diversity of the healthy human microbiome.

Authors: 
Journal:  Nature       Date:  2012-06-13       Impact factor: 49.962

10.  Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production.

Authors:  Andrew C Doxey; Daniel A Kurtz; Michael D J Lynch; Laura A Sauder; Josh D Neufeld
Journal:  ISME J       Date:  2014-08-15       Impact factor: 10.302

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  227 in total

1.  Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?

Authors:  Luciana F Santoferrara; Jean-David Grattepanche; Laura A Katz; George B McManus
Journal:  ISME J       Date:  2016-02-05       Impact factor: 10.302

2.  Characterization of bacterial diversity associated with deep sea ferromanganese nodules from the South China Sea.

Authors:  De-Chao Zhang; Yan-Xia Liu; Xin-Zheng Li
Journal:  J Microbiol       Date:  2015-08-27       Impact factor: 3.422

3.  Divergent Co-occurrence Patterns and Assembly Processes Structure the Abundant and Rare Bacterial Communities in a Salt Marsh Ecosystem.

Authors:  Shicong Du; Francisco Dini-Andreote; Nan Zhang; Chunling Liang; Zhiyuan Yao; Huajun Zhang; Demin Zhang
Journal:  Appl Environ Microbiol       Date:  2020-06-17       Impact factor: 4.792

4.  Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes.

Authors:  Erin A McKenney; Michael Maslanka; Allen Rodrigo; Anne D Yoder
Journal:  Microb Ecol       Date:  2017-11-29       Impact factor: 4.552

5.  A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology.

Authors:  Yushi Tang; Tianjiao Dai; Zhiguo Su; Kohei Hasegawa; Jinping Tian; Lujun Chen; Donghui Wen
Journal:  Microb Ecol       Date:  2019-08-19       Impact factor: 4.552

6.  Local biotic interactions drive species-specific divergence in soil bacterial communities.

Authors:  Xin-Feng Zhao; Yi-Qi Hao; Da-Yong Zhang; Quan-Guo Zhang
Journal:  ISME J       Date:  2019-07-29       Impact factor: 10.302

7.  Small-Scale Variability in Bacterial Community Structure in Different Soil Types.

Authors:  Mylène Hugoni; Naoise Nunan; Jean Thioulouse; Audrey Dubost; Danis Abrouk; Jean M F Martins; Deborah Goffner; Claire Prigent-Combaret; Geneviève Grundmann
Journal:  Microb Ecol       Date:  2021-01-14       Impact factor: 4.552

8.  Distribution, Community Composition, and Potential Metabolic Activity of Bacterioplankton in an Urbanized Mediterranean Sea Coastal Zone.

Authors:  Kumari Richa; Cecilia Balestra; Roberta Piredda; Vladimir Benes; Marco Borra; Augusto Passarelli; Francesca Margiotta; Maria Saggiomo; Elio Biffali; Remo Sanges; David J Scanlan; Raffaella Casotti
Journal:  Appl Environ Microbiol       Date:  2017-08-17       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.  Probing the evolution, ecology and physiology of marine protists using transcriptomics.

Authors:  David A Caron; Harriet Alexander; Andrew E Allen; John M Archibald; E Virginia Armbrust; Charles Bachy; Callum J Bell; Arvind Bharti; Sonya T Dyhrman; Stephanie M Guida; Karla B Heidelberg; Jonathan Z Kaye; Julia Metzner; Sarah R Smith; Alexandra Z Worden
Journal:  Nat Rev Microbiol       Date:  2016-11-21       Impact factor: 60.633

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