Literature DB >> 26598941

Microbial diversity--exploration of natural ecosystems and microbiomes.

Sean M Gibbons1, Jack A Gilbert2.   

Abstract

Microorganisms are the pillars of life on Earth. Over billions of years, they have evolved into every conceivable niche on the planet. Microbes reshaped the oceans and atmosphere and gave rise to conditions conducive to multicellular organisms. Only in the past decade have we started to peer deeply into the microbial cosmos, and what we have found is amazing. Microbial ecosystems behave, in many ways, like large-scale ecosystems, although there are important exceptions. We review recent advances in our understanding of how microbial diversity is distributed across environments, how microbes influence the ecosystems in which they live, and how these nano-machines might be harnessed to advance our understanding of the natural world.
Copyright © 2015 Elsevier Ltd. All rights reserved.

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Year:  2015        PMID: 26598941      PMCID: PMC4852739          DOI: 10.1016/j.gde.2015.10.003

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  58 in total

Review 1.  The bacterial species challenge: making sense of genetic and ecological diversity.

Authors:  Christophe Fraser; Eric J Alm; Martin F Polz; Brian G Spratt; William P Hanage
Journal:  Science       Date:  2009-02-06       Impact factor: 47.728

Review 2.  Going back to the roots: the microbial ecology of the rhizosphere.

Authors:  Laurent Philippot; Jos M Raaijmakers; Philippe Lemanceau; Wim H van der Putten
Journal:  Nat Rev Microbiol       Date:  2013-09-23       Impact factor: 60.633

3.  Resource partitioning and sympatric differentiation among closely related bacterioplankton.

Authors:  Dana E Hunt; Lawrence A David; Dirk Gevers; Sarah P Preheim; Eric J Alm; Martin F Polz
Journal:  Science       Date:  2008-05-23       Impact factor: 47.728

Review 4.  The generation and maintenance of diversity in microbial communities.

Authors:  Noah Fierer; Jay T Lennon
Journal:  Am J Bot       Date:  2011-02-17       Impact factor: 3.844

Review 5.  Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis.

Authors:  J A Eisen
Journal:  Genome Res       Date:  1998-03       Impact factor: 9.043

6.  Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment.

Authors:  Hasan Celiker; Jeff Gore
Journal:  Nat Commun       Date:  2014-08-08       Impact factor: 14.919

7.  Coexistence of evolving bacteria stabilized by a shared Black Queen function.

Authors:  J Jeffrey Morris; Spiridon E Papoulis; Richard E Lenski
Journal:  Evolution       Date:  2014-08-01       Impact factor: 3.694

8.  Methane dynamics regulated by microbial community response to permafrost thaw.

Authors:  Carmody K McCalley; Ben J Woodcroft; Suzanne B Hodgkins; Richard A Wehr; Eun-Hae Kim; Rhiannon Mondav; Patrick M Crill; Jeffrey P Chanton; Virginia I Rich; Gene W Tyson; Scott R Saleska
Journal:  Nature       Date:  2014-10-23       Impact factor: 49.962

9.  Oligotyping analysis of the human oral microbiome.

Authors:  A Murat Eren; Gary G Borisy; Susan M Huse; Jessica L Mark Welch
Journal:  Proc Natl Acad Sci U S A       Date:  2014-06-25       Impact factor: 11.205

10.  The Earth Microbiome project: successes and aspirations.

Authors:  Jack A Gilbert; Janet K Jansson; Rob Knight
Journal:  BMC Biol       Date:  2014-08-22       Impact factor: 7.431

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  25 in total

1.  Metabolic Trade-Offs Promote Diversity in a Model Ecosystem.

Authors:  Anna Posfai; Thibaud Taillefumier; Ned S Wingreen
Journal:  Phys Rev Lett       Date:  2017-01-12       Impact factor: 9.161

2.  Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota.

Authors:  Fanshu Xiao; Yuhe Yu; Jinjin Li; Philippe Juneau; Qingyun Yan
Journal:  Curr Microbiol       Date:  2018-05-25       Impact factor: 2.188

Review 3.  Endophytic Penicillium species and their agricultural, biotechnological, and pharmaceutical applications.

Authors:  Rufin Marie Kouipou Toghueo; Fabrice Fekam Boyom
Journal:  3 Biotech       Date:  2020-02-08       Impact factor: 2.406

4.  Impacts of Invasive Australian Acacias on Soil Bacterial Community Composition, Microbial Enzymatic Activities, and Nutrient Availability in Fynbos Soils.

Authors:  Jan-Hendrik Keet; Allan G Ellis; Cang Hui; Ana Novoa; Johannes J Le Roux
Journal:  Microb Ecol       Date:  2021-01-29       Impact factor: 4.552

5.  BLANKA: an Algorithm for Blank Subtraction in Mass Spectrometry of Complex Biological Samples.

Authors:  Jessica L Cleary; Gordon T Luu; Emily C Pierce; Rachel J Dutton; Laura M Sanchez
Journal:  J Am Soc Mass Spectrom       Date:  2019-04-16       Impact factor: 3.109

6.  Searching for principles of microbial physiology.

Authors:  Frank J Bruggeman; Robert Planqué; Douwe Molenaar; Bas Teusink
Journal:  FEMS Microbiol Rev       Date:  2020-11-24       Impact factor: 16.408

7.  Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes.

Authors:  Yuanchen Zhang; Erik K Kastman; Jeffrey S Guasto; Benjamin E Wolfe
Journal:  Nat Commun       Date:  2018-01-23       Impact factor: 14.919

8.  Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers.

Authors:  Jason T Payne; Justin J Millar; Colin R Jackson; Clifford A Ochs
Journal:  PLoS One       Date:  2017-03-28       Impact factor: 3.240

9.  Multiple Streptomyces species with distinct secondary metabolomes have identical 16S rRNA gene sequences.

Authors:  Sanjay Antony-Babu; Didier Stien; Véronique Eparvier; Delphine Parrot; Sophie Tomasi; Marcelino T Suzuki
Journal:  Sci Rep       Date:  2017-09-11       Impact factor: 4.379

10.  Abundance estimation and differential testing on strain level in metagenomics data.

Authors:  Martina Fischer; Benjamin Strauch; Bernhard Y Renard
Journal:  Bioinformatics       Date:  2017-07-15       Impact factor: 6.937

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