MikroNet: From Microbiomes to Microbial Networks
Soil Sciences
Microbial Ecology and Applied Microbiology
Ecology of Land Use
Organismic Interactions, Chemical Ecology and Microbiomes of Plant Systems
Final Report Abstract
The phenotypic characteristics of plants have been genetically enhanced through plant domestication. However, whether plant domestication and genetic improvement have had an impact on the rhizosphere microbial ecology is not entirely understood. Tackling these knowledge gap, we aimed to investigate root-associated microbiome structure, diversity, co-occurrence and co-evolution of seeds, root endophytes, and the rhizosphere microbiome of various wild and domesticated wheat and barley varieties. In the first phase of the study, using next-generation sequencing techniques, the impact of domestication on seed endophytes of wild and domesticated wheat and barley species was studied. We found that seed microbiome became more diverse as a consequence of cereal domestication. In contrast, more microbe-microbe interactions were observed in wild species. A strong phylogenetic congruence between seed endophytes and host plants was discovered through co-evolutionary analysis. Furthermore, domestication also altered microbiome composition; for example the human-associated bacterial genus Cutibacterium was found enriched in cultivated cereals as compared to wild cereals, where environmental Pseudomonas prevailed. After investigating the seed microbiome, a field experiment was carried out in three different experimental fields, to evaluate the effect of plant domestication on the microbial abundance, diversity, microbial network, and the assembly process of endorhiza and rhizosphere microbiome of two wild wheat species (diploid Aegilops tauschii and tetraploid T. dicoccoides) and two modern cereal crops (hexaploid Triticum aestivum and tetraploid T. durum). The microbiomes were analyzed by high-throughput sequencing of the bacterial 16S rRNA gene and fungal ITS2. First, the effect of domestication and location on the seed-transmission of microbes to endorhiza and rhizosphere was investigated. We found that higher and more diverse seed-transmitted microbiome in the endorhiza and rhizosphere of diploid A. tauschii compared to other tetraploid and hexaploid wheat species in the different locations. Second, we investigated rhizosphere and endosphere microbiome structure, abundance, and co-occurrence of microorganisms of wild and modern wheat varieties. We found strong effect of location as well as plant genotype on microbial rhizosphere colonization using differential abundance test. Co-occurrence analysis showed less cross-kingdom connectedness in the rhizosphere of modern species compared to their ancestors. In summary, based on obtained results we demonstrated that domestication of cereals impacted their seed-, root-, and rhizosphere-associated microbiome, in terms of structure, diversity, colonization patterns and microbial cross-kingdom interactions. This project provided important insights on microbe-host co-evolution during crop domestication, and shed light on the ecology of the plant holobiont from an evolutionary perspective.
Publications
- (2021) Domestication affects the composition, diversity, and co-occurrence of the cereal seed microbiota. Journal of Advanced Research 31: 75-86
Abdullaeva Y., Ambika Manirajan B., Honermeier B., Schnell S. and Cardinale M.
(See online at https://doi.org/10.1016/j.jare.2020.12.008) - (2022) Domestication impacts the wheat-associated microbiota and the rhizosphere colonization by seed- and soil-originated microbiomes, across different fields. Frontiers in Plant Science 12: 3213
Abdullaeva Y., Ratering S., Ambika Manirajan B., Rosado-Porto D., Schnell S. and Cardinale M.
(See online at https://doi.org/10.3389/fpls.2021.806915) - 2022 Domestication of cereals affected seed and rhizosphere microbiota - microbial composition and diversity analysis of modern and ancient wheat and barley varieties grown at different locations. Dissertation an der JLU Gießen
Abdullaeva Y.
(See online at https://doi.org/10.22029/jlupub-628)
