Long-term effects of agricultural production systems on structure and function of the soil microbial community

Microbes are central drivers of soil processes and in-depth knowledge on how agricultural management practices effects the soil microbiome is essential in the development of sustainable food production systems. Our objective was therefore to explore the long-term effects of organic and conventional cropping systems on soil bacterial and fungal quantity, their community structures and their combined function. To do so, we sampled soil from a long-term experiment in Southeast Norway in 2014, 25 years after the experiment was established, and performed a range of microbial analyses on the samples. The experiment consists of six cropping systems with differences in crop rotations, soil tillage, and with nutrient application regimes covering inorganic fertilizers, cattle slurry (both separately and combined with inorganic fertilizers) and biogas residues from digested household biowaste. The quantity of soil microbes was assessed by extraction of microbial C and N and by analysis of soil DNA (bacterial 16S rRNA, and fungal rRNA internal transcribed spacer region). The structures of the microbial communities were determined and assessment of relatedness of bacterial and fungal communities was done by the unweighted pair group method. Estimates of richness and diversity were based on numbers of unique operational taxonomic units from DNA sequencing and the function of the microbial assembly was measured by means of enzyme assays. Our results showed that production systems including leys had higher microbial biomass and higher numbers of bacterial and fungal gene copies than did systems with cash crops only. A cropping system which appeared to be particularly unfavourable was a reference-system where stubble, roots and exudates were the single source of organic material. Production system significantly affected both bacterial and fungal community structures in the soil. Systems including leys and organic fertilization had higher enzyme activities than did systems with cash crops only. An inclusion of ley in the rotation did not, however, increase either microbial richness or microbial diversity. In fact, the otherwise suboptimal reference-system appeared to have a richness and diversity of both bacteria and fungi at levels similar to those of the other cropping systems, indicating that the microbial function is largely maintained under less favourable agricultural treatments because of the general resilience of soil microorganisms to various stresses. Neither disturbance through tillage nor the use of chemical fertilizer or chemical plant protection measures seemed as such to influence soil microbial communities. Thus, no differences between conventional and organic farming practices as such were found. We conclude that the choice of agricultural management determines the actual microbial community structure, but that biodiversity in general is almost unaffected by cropping system over many years. Adequate addition of organic material is essential to ensure a properly functioning microbial ensemble and, thus, to secure soil structure and fertility over time.