Literature DB >> 23466702

Loss in microbial diversity affects nitrogen cycling in soil.

Laurent Philippot1, Aymé Spor, Catherine Hénault, David Bru, Florian Bizouard, Christopher M Jones, Amadou Sarr, Pierre-Alain Maron.   

Abstract

Microbial communities have a central role in ecosystem processes by driving the Earth's biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial community using a dilution approach to analyze the functional consequences of diversity loss. A trait-centered approach was embraced using the denitrifiers as model guild due to their role in nitrogen cycling, a major ecosystem service. How various diversity metrics related to richness, eveness and phylogenetic diversity of the soil denitrifier community were affected by the removal experiment was assessed by 454 sequencing. As expected, the diversity metrics indicated a decrease in diversity in the 1/10(3) and 1/10(5) dilution treatments compared with the undiluted one. However, the extent of dilution and the corresponding reduction in diversity were not commensurate, as a dilution of five orders of magnitude resulted in a 75% decrease in estimated richness. This reduction in denitrifier diversity resulted in a significantly lower potential denitrification activity in soil of up to 4-5 folds. Addition of wheat residues significantly increased differences in potential denitrification between diversity levels, indicating that the resource level can influence the shape of the microbial diversity-functioning relationship. This study shows that microbial diversity loss can alter terrestrial ecosystem processes, which suggests that the importance of functional redundancy in soil microbial communities has been overstated.

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Year:  2013        PMID: 23466702      PMCID: PMC3721106          DOI: 10.1038/ismej.2013.34

Source DB:  PubMed          Journal:  ISME J        ISSN: 1751-7362            Impact factor:   10.302


  42 in total

1.  Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments.

Authors:  R B Franklin; J L Garland; C H Bolster; A L Mills
Journal:  Appl Environ Microbiol       Date:  2001-02       Impact factor: 4.792

2.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

Authors:  Alexandros Stamatakis
Journal:  Bioinformatics       Date:  2006-08-23       Impact factor: 6.937

3.  Maintenance of soil functioning following erosion of microbial diversity.

Authors:  Sophie Wertz; Valérie Degrange; James I Prosser; Franck Poly; Claire Commeaux; Thomas Freitag; Nadine Guillaumaud; Xavier Le Roux
Journal:  Environ Microbiol       Date:  2006-12       Impact factor: 5.491

4.  Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon mineralization.

Authors:  Johannes Rousk; Philip C Brookes; Erland Bååth
Journal:  Appl Environ Microbiol       Date:  2009-01-16       Impact factor: 4.792

5.  Reduction of rare soil microbes modifies plant-herbivore interactions.

Authors:  W H Gera Hol; Wietse de Boer; Aad J Termorshuizen; Katrin M Meyer; Johannes H M Schneider; Nicole M van Dam; Johannes A van Veen; Wim H van der Putten
Journal:  Ecol Lett       Date:  2010-01-11       Impact factor: 9.492

6.  Disentangling the rhizosphere effect on nitrate reducers and denitrifiers: insight into the role of root exudates.

Authors:  S Henry; S Texier; S Hallet; D Bru; C Dambreville; D Chèneby; F Bizouard; J C Germon; L Philippot
Journal:  Environ Microbiol       Date:  2008-04-03       Impact factor: 5.491

Review 7.  Consequences of changing biodiversity.

Authors:  F S Chapin; E S Zavaleta; V T Eviner; R L Naylor; P M Vitousek; H L Reynolds; D U Hooper; S Lavorel; O E Sala; S E Hobbie; M C Mack; S Díaz
Journal:  Nature       Date:  2000-05-11       Impact factor: 49.962

Review 8.  Terrestrial ecosystem responses to species gains and losses.

Authors:  David A Wardle; Richard D Bardgett; Ragan M Callaway; Wim H Van der Putten
Journal:  Science       Date:  2011-06-10       Impact factor: 47.728

9.  Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils.

Authors:  S Henry; D Bru; B Stres; S Hallet; L Philippot
Journal:  Appl Environ Microbiol       Date:  2006-08       Impact factor: 4.792

10.  HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors.

Authors:  Yuan Zhang; Yanni Sun
Journal:  BMC Bioinformatics       Date:  2011-05-24       Impact factor: 3.169

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  121 in total

1.  Litter quality versus soil microbial community controls over decomposition: a quantitative analysis.

Authors:  Cory C Cleveland; Sasha C Reed; Adrienne B Keller; Diana R Nemergut; Sean P O'Neill; Rebecca Ostertag; Peter M Vitousek
Journal:  Oecologia       Date:  2014-01       Impact factor: 3.225

2.  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

3.  Soil-borne microbiome: linking diversity to function.

Authors:  Lucas W Mendes; Siu M Tsai; Acácio A Navarrete; Mattias de Hollander; Johannes A van Veen; Eiko E Kuramae
Journal:  Microb Ecol       Date:  2015-01-14       Impact factor: 4.552

4.  Revisiting the dilution procedure used to manipulate microbial biodiversity in terrestrial systems.

Authors:  Yan Yan; Eiko E Kuramae; Peter G L Klinkhamer; Johannes A van Veen
Journal:  Appl Environ Microbiol       Date:  2015-04-17       Impact factor: 4.792

5.  Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing.

Authors:  N B Justice; A Sczesnak; T C Hazen; A P Arkin
Journal:  Appl Environ Microbiol       Date:  2017-09-29       Impact factor: 4.792

6.  Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities.

Authors:  Carl Wepking; Bethany Avera; Brian Badgley; John E Barrett; Josh Franklin; Katharine F Knowlton; Partha P Ray; Crystal Smitherman; Michael S Strickland
Journal:  Proc Biol Sci       Date:  2017-03-29       Impact factor: 5.349

7.  Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors.

Authors:  Minghong Gao; Jiwen Liu; Yanlu Qiao; Meixun Zhao; Xiao-Hua Zhang
Journal:  Microb Ecol       Date:  2016-12-06       Impact factor: 4.552

8.  The more, the merrier: heterotroph richness stimulates methanotrophic activity.

Authors:  Adrian Ho; Karen de Roy; Olivier Thas; Jan De Neve; Sven Hoefman; Peter Vandamme; Kim Heylen; Nico Boon
Journal:  ISME J       Date:  2014-05-02       Impact factor: 10.302

9.  Diversity of nitrogen cycling genes at a Midwest long-term ecological research site with different management practices.

Authors:  Zheng Li; Alison M Cupples
Journal:  Appl Microbiol Biotechnol       Date:  2021-05-04       Impact factor: 4.813

10.  Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere.

Authors:  Yan Yan; Eiko E Kuramae; Mattias de Hollander; Peter G L Klinkhamer; Johannes A van Veen
Journal:  ISME J       Date:  2016-08-02       Impact factor: 10.302

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