title: The rhizosphere selects for particular groups of acidobacteria and verrucomicrobia.
abstract: 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.
authors.affiliation: Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands ; Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology, Berkeley, California, United States of America.
authors.forename: Ulisses
authors.initials: U
authors.lastname: Nunes da Rocha
authors.affiliation: Laboratory for Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands.
authors.forename: Caroline M
authors.initials: CM
authors.lastname: Plugge
authors.affiliation: Laboratoire d'Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Bruxelles, Belgium.
authors.forename: Isabelle
authors.initials: I
authors.lastname: George
authors.affiliation: Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, Groningen University, Groningen, The Netherlands.
authors.forename: Jan Dirk
authors.initials: JD
authors.lastname: van Elsas
authors.affiliation: Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands.
authors.forename: Leonard Simon
authors.initials: LS
authors.lastname: van Overbeek
mesh_terms: D061271:Acidobacteria / Q000145:classification / Q000235:genetics; D044822:Biodiversity; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D012336:RNA, Ribosomal, 16S; D058441:Rhizosphere; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology; D061327:Verrucomicrobia / Q000145:classification / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S; D012987:Soil