Ecology of Acidobacteria and Verrucomicrobia in the plant-soil ecosystem

PhD ceremony: Mr. U. Nunes da Rocha, 11.00 uur, Academiegebouw, Broerstraat 5, Groningen

Thesis: Ecology of Acidobacteria and Verrucomicrobia in the plant-soil ecosystem

Promotor(s): prof. J.D. van Elsas

Faculty: Mathematics and Natural Sciences

The thesis of Ulisses Nunes da Rocha shows that Acidobacteria and Verrucomicrobia are part of the dominant bacterial community in the rhizosphere. Moreover, two Holophaga spp., affiliating to the Acidobacteria, four Luteolibacter spp., four Candidatus genus Rhizospheria spp. and one Verrucomicrobium sp., affiliating with Verrucomicrobium subdivision 1 were isolated from rhizosphere samples. These previously yet-to-be cultured bacteria give new directions to the study of Acidobacterium and Verrucomicrobium ecology in plant-soil systems. These strains were phenotypically characterized, and Nunes da Rocha demonstrated that Holophaga sp. have similar, and Verrucomicrobium subdivision 1 more diverse phenotypic profiles. Real time PCR was shown by him to be an excellent tool to follow the fate of these Acidobacterium and Verrucomicrobium subdivision 1 targets in plant/soil systems. In vitro colonization assays and plant-soil microcosms gave insights in the ecology of Holophagae and Candidatus genus Rhizospheria and their relationship with plants. On the other hand, in the plant-soil microcosm experiments, Nunes da Rocha found that Luteolibacter preferred bulk over rhizosphere soil. In the field experiment, Acidobacterium subgroups 1, 3, 4 were found to prefer bulk over rhizosphere soil. The subgroup 6 of Acidobacteria was clearly rhizosphere competent, whereas the Holophaga distribution over the different rhizospheres and bulk soils indicated that this acidobacterial group occupies a specific niche in the leek rhizosphere. The success in culturing some of these strains clearly facilitated further testing and challenging of ecological theories about them in soil-plant systems.