Functional root ecology –microbiomes as source for plant stress protection


Background: The root microbiome is a key determinant of plant health and fitness whose composition and activity is shaped by plants and edaphic factors as well as individual microbes. The latter is of high relevance regarding the utilisation of beneficial microbes and small beneficial communities as ‘soil vaccines’ to generate plant-beneficial microbiomes. Members of the fungal order Sebacinales (e.g. Serendipita indica) mediate abiotic / biotic stress protection in a broad range of host plants (incl. all major crops). Their occurrence in different ecosystems worldwide suggests a high ecological competitiveness and relevance for ecosystem functioning.

Project: Although S. indica can adopt a saprotrophic lifestyle for survival, it depends on its living environment for propagation. We identified a thiamine auxotrophy of the fungus that can be satisfied by plant growth promoting, thiamine-producing Bacillus subtilis. The S. indica-B. subitilis co-symbiosis enhances the environmental plasticity of both microbes. While it allows S. indica to grow under unfavourable nitrogen regimes (e.g. nitrate), B. subtilis shows improved root colonisation. In addition, we observed that S. indica supports root-nodulating Sinorhizobium spp. in Medicago truncatula. We currently study the robustness of these co-symbioses in different agricultural environments by scrutinising the effect of plant, microbe-derived and edaphic factors on the stability and activity of the co-symbioses. Our clear aim is to validate the ability of each co-symbiosis to establish beneficial microbiomes in the field. Gaining further insights into community functionality and ecological sustainability requires a better understanding of metabolite-based communication patterns within minimal and complex microbiomes.

Lab tools / techniques: Microbiome analyses, microbial cultivation and plant “vaccination”, field-based validation of microbiome functions

Relevant publications:

Jiang, X., Zerfaß, C., Feng, S., Eichmann, R., Asally, M., Schäfer, P.1,2, Soyer, OS1,2. (2018) Impact of spatial organization on a novel auxotrophic interaction among soil microbes. ISME J 12:1443-1456.


Sergaki, C., Lagunas, B., Lidbury, I., Gifford, M.L., Schäfer, P. (2018) Challenges and approaches in microbiome research: from fundamental to applied. Frontiers in Plant Science 9: 1205.


Lareen A, Burton F, Schäfer P (2016) Plant root-microbe communication in shaping root microbiomes. Plant Molecular Biology 90:575-87.


Lagunas, B., Schäfer, P., Gifford, M.L. (2015) Housing helpful invaders: the evolutionary and molecular architecture underlying plant root-mutualist microbe interactions. Journal of Experimental Botany 66:2177-86.