Extended abstract written by Laura Häkkinen, Helsinki University
Although we know from natural systems that plants shape soil microbial communities, our understanding of plant-soil microbial interactions in agroecosystems is limited. Agricultural plant communities, consisting of cultivated crops and associated weeds, differ from their natural counterparts by being typically less diverse and part of the agricultural management practices.
To assess how soil microbial communities are affected by crop type, plant diversity, and agricultural management we studied 73 fields in South-Finland. Seven crop types — pasture, ley, oat, rye, faba bean, oilseed, and cabbage — as well as a long-term environmental fallow as a plant-diverse reference were included. The fields were either conventionally or organically farmed to determine the effect of production method. Other farming practices, such as tillage, nitrogen fertilization rate, fertilization type, pesticide use, and crop rotation diversity, were similarly analysed for their impacts. Soil bacterial and fungal communities were analysed with DNA sequencing of the 16S and ITS 2 regions, and microbial functional groups were assigned based on database analyses.
We found that crop type significantly impacted the bacterial and fungal community composition, cabbage and fallow having the most distinct microbial communities. In addition, plant diversity measured as species richness, and in the case of fungi also the plant coverage, further shaped microbial communities. Our results thus showed that plant community is a strong driver of agricultural soil microbiomes.
Although microbial diversity varied between the crop types, soil chemical properties explained most of the differences. We were surprised to find that fallow with the highest plant diversity did not have the highest microbial diversity. At least in natural systems, the above ground plant diversity and below ground soil diversities are typically positively linked. Instead, we found soil carbon-to-nitrogen-ratio and pH to be the strongest drivers of bacterial and fungal diversity, respectively.
Microbial groups relevant to nutrient availability varied between the crop types and were positively associated with plant diversity. Fallow had the highest proportions of genes involved in nitrogen fixation and inorganic phosphorus solubilization as well as the highest proportion of arbuscular mycorrhizal fungi (AMF), which form mycorrhizal associations with plants benefitting their water and nutrient uptake. The AMF varied significantly also between the other crop types being higher in perennial crop types (pasture and ley) as well as oat, and lower in cabbage belonging to the Brassicaceae plants, which are known to not form AMF symbiosis.
However, the other Brassicaceae crop type, oilseed, showed higher AMF proportions, likely due to being part of a more diverse crop rotation system compared to cabbage. As AMF also positively correlated with plant diversity, it seems that increasing plant diversity or crop cycle diversity are both ways to support agricultural soil AMF communities. As nitrogen availability-increasing nitrogen fixing and plant -available phosphate producing inorganic phosphorous solubilizing bacteria did not vary between other crop types apart from fallow, but were positively associated with plant diversity, these beneficial functions could similarly be enhanced by plant diversification.
Organic production increased the proportions of AMF and the genes involved in nitrogen fixation relative to conventional production. This may be partially explained by plant diversity and organic fertilization effects; however, the statistical model indicated that the production method was a better predictor for these microbial groups compared to any other farming practice.
Interestingly the overall microbial diversity was a poor indicator of the genes involved in beneficial soil functions. Fallow with the relatively low microbial diversities was associated with enhanced genomic potential for beneficial soil functions. Our results demonstrate the importance of including bacterial and fungal functional groups in the study of agricultural soil microbiomes.