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.
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Claims 7
Claim · model-written summary
Luteolibacter preferred one or more plant rhizospheres.
- Taxon
- grass, potato and leeke1
- Interactor
- LuteolibacterLuteolibactere0other
- Outcome
- preferences for one or more rhizospherese0
Verbatim
e0“Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres”
e1“rhizospheres of grass, potato and leek”
Claim · model-written summary
Candidatus genus Rhizospheria preferred one or more plant rhizospheres.
Verbatim
e0“Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres”
e1“rhizospheres of grass, potato and leek”
Claim · model-written summary
Subdivision 6 acidobacteria preferred one or more plant rhizospheres.
Verbatim
e0“Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres”
e1“rhizospheres of grass, potato and leek”
Claim · model-written summary
Holophaga preferred one or more plant rhizospheres.
HolophagaOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres”
e1“rhizospheres of grass, potato and leek”
Claim · model-written summary
Holophaga 16S rRNA genes were more abundant in the leek rhizosphere than in bulk soil or the grass and potato rhizospheres.
- Taxon
- leek
Allium ampeloprasume0 - Outcome
- Holophaga 16S rRNA gene numbere0
- Direction
- more abundante0
- Comparator
- bulk soil and the rhizospheres of grass and potatoe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the Holophaga 16S rRNA gene number were more abundant in the leek rhizosphere than in bulk soil and the rhizospheres of grass and potato”
Claim · model-written summary
Holophagae strain CHC25 was attracted to and colonized leek roots in a microcosm.
- Taxon
- leekAllium ampeloprasume0
- Interactor
- Holophagae strain CHC25Holophagaee0other
- Outcome
- Attraction to, and colonization of, leek rootse0
- Setting
- experimental microcosm set-upe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Attraction to, and colonization of, leek roots by Holophagae strain CHC25 was further shown in an experimental microcosm set-up”
Claim · model-written summary
The authors propose the name Candidatus Porrumbacterium oxyphilus for strain CHC25.
- Taxon
- leekAllium ampeloprasume1
- Interactor
- Candidatus Porrumbacterium oxyphiluse0other
- Outcome
- first cultured representative with rhizosphere competencee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we propose to coin strain CHC25 Candidatus Porrumbacterium oxyphilus (class Holophagae, Phylum Acidobacteria), the first cultured representative with rhizosphere competence”
e1“leek roots by Holophagae strain CHC25”