Exploring the microbiota of deep-rooted crops - Culture-independent characterization of the bacterial and fungal communities in association with roots down to 3 m depth

Summary

Agriculture and crop production are facing a severe amount of pressure to feed a growing population, as the human population is estimated to increase from around 7.7 billion people to 9 billion in 2050. We need to increase crop yield on the current agricultural land, as the total arable land area of the world already reached its maximum around 1990. The use of crops with roots growing down to 3 m depth could be a sustainable alternative to conventional cropping systems, as the deep roots can reach further for water and nutrients, consequently enabling farmers to use less fertilizer and reduce irrigation levels. As many soil microbes have been proven to improve plant health, development, and productivity, a profound understanding of the close two-way interaction between plant roots and microbes is essential to increase crop yield.
However, almost no information is available of the microbial communities present in subsoil in association with roots of crops, as a lot of challenges are associated with collecting root samples at these depths. This thesis offers a unique first glimpse of the belowground microbial world associated with roots, as it explores and compares the bacterial and fungal communities associated with roots of different deep-rooted crops. Culture-independent characterization and comparative studies are performed using amplicon sequencing targeting the 16S rRNA gene and ITS1 region, together with 16S rRNA and ITS1 qPCR. The functionality of the bacterial communities is further investigated by estimating the relative abundance of four genes involved in nitrogen cycling. By employing these methods, this thesis aims at describing the bacterial and fungal communities found in association with deep roots down to 3 m depth and to compare them to the communities in the topsoil rhizosphere, as well as investigating the recruitment of specific microbes by different crop species, and how the deep roots are colonized.
This study shows that the deep-root microbial communities differed from those in the topsoil, as especially the community structures were significantly different. In general, the microbial abundance and diversity decreased with depth, though we observed some variation between crop species. However, the deep root-associated communities were more abundant and less diverse than the corresponding bulk soil communities, indicating specific recruitment by the roots. This was further supported by the fact that plant species significantly influenced both bacterial and fungal diversity and community structure, both in top- and subsoils. Colonization studies on chicory revealed that the deep-root microbial communities are partly transferred down with the roots when they grow, as well as being recruited from the different soil layers down through the soil profile.
Overall, nitrogen cycling capacity was not influenced by depth, but we did observe a significant increase in genes associated with nitrogen fixation in the deep subsoil (3 m depth) after one year of plant-derived carbon had been present, indicating an increased capacity of nitrogen turnover hotspots in deep subsoil after planting with deep-rooted crops.
In conclusion, the research performed in this Ph.D. provides novel insights into the unexplored bacterial and fungal communities associated with deep-rooted crops, and how they colonize roots down to 3 m depth. Findings from this thesis can be the stepping stone for future research in both fundamental and applied science, as a lot more is to be discovered of these underground microbial communities found in associated with deep roots.Overall, nitrogen cycling capacity was not influenced by depth, but we did observe a significant increase in genes associated with nitrogen fixation in the deep subsoil (3 m depth) after one year of plant-derived carbon had been present, indicating an increased capacity of nitrogen turnover hotspots in deep subsoil after planting with deep-rooted crops.
In conclusion, the research performed in this Ph.D. provides novel insights into the unexplored bacterial and fungal communities associated with deep-rooted crops, and how they colonize roots down to 3 m depth. Findings from this thesis can be the stepping stone for future research in both fundamental and applied science, as a lot more is to be discovered of these underground microbial communities found in associated with deep roots.