Effects of cropping systems on plant-associated microbial communities of faba bean and wheat

Beneficial plant-associated microorganisms are widely acknowledged as key promoter in plant growth and health. Although playing crucial roles in ecosystem functioning and in a sustainable agriculture, our knowledge on the effects of agricultural practices on the plant microbiome is still limited. The main focus of this thesis was to understand which factors shape microbial community composition and diversity in response to different cropping systems, namely monoculture and intercropping, in winter wheat (Triticum aestivum L.) and winter faba bean (Vicia faba L.) using next generation-sequencing. In the second Chapter, we investigated the influence of cropping systems (monoculture, row and mixed intercropping) on bacterial and fungal community composition and interactions in soil and endosphere under greenhouse conditions. We detected significant differences in microbial diversity and richness between mixed and row intercropping as well as between mixed intercropping and monoculture. In addition, microbial communities differed between the crop species wheat and faba bean as well as between plant compartment. This resulted in different response of these communities towards cropping systems. We further recorded changes in microbial interactions. The number of negative inter-domain correlations between fungi and bacteria decreased in bulk and rhizosphere soil in intercropping regimes compared to monocultures. However, the observed differences were plant species-dependent. These results indicate that intra- and interspecific competition between plants had different effects on the plant species and thus on their associated microbial communities. In the following chapters, we investigated the effect of cropping systems and water deficit on plant physiological parameters (Chapter 3) as well as on the active (RNA-based) fungal and bacterial communities in different plant compartments (Chapter 4, 5). For this purpose, wheat and two genotypes of faba bean were grown in monoculture and in row intercropping with (water-deficit treatments) and without water stress (control treatments) under greenhouse conditions. Plant material and rhizosphere soil of all treatments were collected at three time points with different water availability (beginning, during and after water deficit stress). Plant physiological parameters such as gas exchange, relative water content of leaves, plant biomass production and water use efficiency (WUE) were studied. As a result, we observed that plants exhibited a clear genotype x cropping system effect towards water deficit. For example, water deficit reduced overall biomass and WUE of faba bean for the one genotype in monoculture and for the other genotype grown in intercropping. Furthermore, investigations on the plant microbiome showed that in the rhizosphere bacterial IV and fungal communities were altered by water deficit; however, these alterations in the communities were pronounced differently towards water deficit. Fungal community composition responded stronger towards water deficit, and changes of fungal alpha-diversity were dependent on faba bean genotype. Response of bacterial community composition towards water deficit was dependent on crop species and genotype, whereas bacterial alpha-diversity was not affected by water deficit. In contrast, leaf bacterial diversity and richness significantly decreased under water deficit specific for one faba bean genotype. This was mainly related to significant changes of plant physiological parameters, such as sugar concentration and chlorophyll content in leaves. Furthermore, cropping system alone was only a minor factor determining the active plant microbiome. Obtained results highlight that there are complex interactions between plants, associated microorganisms and their environment that influence agricultural productivity. In the sixth Chapter, we evaluated the impact of cropping systems and Metarhizium brunneum Cb15-III seed application on bacterial and fungal community composition and diversity in soil as well as in the endosphere after five and seven weeks of plant growing. For this purpose, faba bean and wheat were grown in monoculture and in row intercropping under greenhouse conditions. We found that plant compartment, crop species and sampling time altered the influence of fungal inoculation and cropping system on microbial communities in rhizosphere and endosphere. Seed application of M. brunneum changed the fungal community composition in the rhizosphere soil only, whereas bacterial community composition in both the rhizosphere and the leaf endosphere were affected. In addition, microbial diversity and richness showed harvest date- and kingdom-specific responses towards M. brunneum application. A significantly lower fungal diversity and richness was observed in the leaf endosphere and rhizosphere soil of inoculated wheat compared to control plants after seven weeks of growth. Cropping system alone but also in combination with seed application exhibited significantly higher microbial diversity and richness in intercropped wheat compared to wheat in monoculture. However, this was only observed for fungi in the root endosphere and for bacteria in the rhizosphere. Alterations in microbial communities towards cropping system and application were partly explained by changes in total organic carbon and nitrogen in the rhizosphere soil as well as in the plant. The present findings improve our understanding of how the combination of cropping system and application of an entomopathogenic fungus affects microbial communities and plant productivity which might gain further importance for biological control strategies in the future. As the plant endosphere is a great reservoir of beneficial microorganisms, we further V investigated the draft genomes of three endophytic bacteria, namely Bacillus mycoides (Strain GM5LP; Chapter 7), Pseudomonas putida (Strain GM4FR; Chapter 8) and Paenibacillus amylolyticus (Strain GM1FR; Chapter 9) isolated from Lolium perenne or Festuca rubra L. We identified several genes, which might be important for plant-growth promotion and biocontrol options. Further research is needed to validate these findings. In conclusion, plant-associated microbial communities including bacteria and fungi in soil and endosphere are influenced by cropping system as well as fungal inoculation and water deficit. In particular, we observed that bacteria and fungi responded differently towards agricultural practices and environmental changes. However, effects were strongly shaped by plant related traits such as compartment or crop species. Fundamental knowledge of plant-associated microorganisms and their responses towards agricultural practices are important to successfully implement a sustainable agriculture.