Bacterial endophytes of rice – their diversity, characteristics and perspectives

PhD ceremony: Mr. P.R. Hardoim, 11.00 uur, Aula Academiegebouw, Broerstraat 5, Groningen

Dissertation: Bacterial endophytes of rice – their diversity, characteristics and perspectives

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

Faculty: Mathematics and Natural Sciences

With their capacity to synthesize a vast range of photoassimilates, plants attract a diverse number of heterotrophic organisms, including bacteria. Specialized bacteria capable to colonize the internal plant tissues are denoted endophytes. Their ecological role is largely unknown. In his studies, Pablo Rodrigo Hardoim aimed to characterize the bacterial communities that inhabit rice roots and to identify deterministic factors influencing the ecology of bacterial endophytes. He demonstrated that host genotype has major influence on the composition of the bacterial community, whereas relatively few endophytes were found across cultivars. This suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities.

Inside rice roots, Gammaproteobacteria appeared to be the most dominant class, with Enterobacter being the most commonly isolated genus. Selected Enterobacter strains revealed several plant growth-promoting capacities as well as plant adaptation traits, of which none were common to all of them, suggesting that more than just one single factor might contribute to host adaptation.

Under controlled conditions, rice seeds were an important source of bacterial endophytes, which allow the colonization of the internal plant tissues, the rhizosphere and the surrounding soil. This suggested that under natural conditions seed-borne endophytes might also be released by the plant. Metagenome analysis of the bacterial endophytic microbiome revealed the overrepresentation of several genes involved in niche adaptation and host-microbe interactions, while only a limited number of genes potentially involved in beneficial traits were detected. In summary, the studies of Hardoim suggest that the plant endosphere is an exexclusive microhabitat requiring numerous bacterial adaptations.