The Rhizosphere Selects for Particular Groups of Acidobacteria and Verrucomicrobia

Nunes da Rocha, Ulisses; Plugge, Caroline M.; George, Isabelle; van Elsas, Jan Dirk; van Overbeek, Leonard Simon

doi:10.1371/journal.pone.0082443

The Rhizosphere Selects for Particular Groups of Acidobacteria and Verrucomicrobia

Journal Article · Fri Dec 13 04:00:00 EST 2013 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0082443· OSTI ID:1627665

Nunes da Rocha, Ulisses ^[1]; Plugge, Caroline M. ^[2]; George, Isabelle ^[3]; van Elsas, Jan Dirk ^[4]; van Overbeek, Leonard Simon ^[2]

Wageningen University (Netherlands); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); DOE/OSTI
Wageningen University (Netherlands)
Université Libre de Bruxelles (Belgium)
Groningen University (Netherlands)

There is a lack in our current understanding on the putative interactions of species of the phyla of Acidobacteria and Verrucomicrobia with plants. Moreover, progress in this area is seriously hampered by the recalcitrance of members of these phyla to grow as pure cultures. The purpose of this study was to investigate whether particular members of Acidobacteria and Verrucomicrobia are avid colonizers of the rhizosphere. Based on previous work, rhizosphere competence was demonstrated for the Verrucomicrobia subdivision 1 groups of Luteolibacter and Candidatus genus Rhizospheria and it was hypothesized that the rhizosphere is a common habitat for Acidobacteria subdivision 8 (class Holophagae). We assessed the population densities of Bacteria, Verrucomicrobia subdivision 1 groups Luteolibacter and Candidatus genus Rhizospheria and Acidobacteria subdivisions 1, 3, 4, 6 and Holophagae in bulk soil and in the rhizospheres of grass, potato and leek in the same field at different points in time using real-time quantitative PCR. Primers of all seven verrucomicrobial, acidobacterial and holophagal PCR systems were based on 16S rRNA gene sequences of cultivable representatives of the different groups. Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres. In particular, the Holophaga 16S rRNA gene number were more abundant in the leek rhizosphere than in bulk soil and the rhizospheres of grass and potato. Attraction to, and colonization of, leek roots by Holophagae strain CHC25 was further shown in an experimental microcosm set-up. In the light of this remarkable capacity, we propose to coin strain CHC25 Candidatus Porrumbacterium oxyphilus (class Holophagae, Phylum Acidobacteria), the first cultured representative with rhizosphere competence.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); Netherlands Genomic Initiative (NGI): Dutch Ministry of Agriculture

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1627665

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 12 Vol. 8; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Genomic and Physiological Characterization of the Verrucomicrobia Isolate Diplosphaera colitermitum gen. nov., sp. nov., Reveals Microaerophily and Nitrogen Fixation Genes Wertz, John T.; Kim, Eunji; Breznak, John A. Applied and Environmental Microbiology, Vol. 78, Issue 5 https://doi.org/10.1128/AEM.06466-11	journal	December 2011
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Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes Janssen, P. H. Applied and Environmental Microbiology, Vol. 72, Issue 3 https://doi.org/10.1128/AEM.72.3.1719-1728.2006	journal	March 2006
Effect of pH on Isolation and Distribution of Members of Subdivision 1 of the Phylum Acidobacteria Occurring in Soil Sait, Michelle; Davis, Kathryn E. R.; Janssen, Peter H. Applied and Environmental Microbiology, Vol. 72, Issue 3 https://doi.org/10.1128/AEM.72.3.1852-1857.2006	journal	March 2006
Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity Hugenholtz, Philip; Goebel, Brett M.; Pace, Norman R. Journal of Bacteriology, Vol. 180, Issue 18 https://doi.org/10.1128/JB.180.18.4765-4774.1998	journal	September 1998

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Soil microbial community composition in tallgrass prairie restorations converge with remnants across a 27‐year chronosequence Barber, Nicholas A.; Chantos‐Davidson, Karley M.; Amel Peralta, Rene Environmental Microbiology, Vol. 19, Issue 8 https://doi.org/10.1111/1462-2920.13785	journal	July 2017
The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes Hardoim, Pablo R.; van Overbeek, Leonard S.; Berg, Gabriele Microbiology and Molecular Biology Reviews, Vol. 79, Issue 3 https://doi.org/10.1128/mmbr.00050-14	journal	July 2015

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