Disentangling the impact of contrasting agricultural management practices on soil microbial communities-Importance of rare bacterial community members

Agriculture has a strong effect on soil microbial communities, but it is still unclear how different management practices drive their diversity and composition. To disentangle the effects of temporally contrasting crop man-agement practices on soil microbial abundance and prokaryotic diversity, we analysed samples from a long-term agricultural field experiment, in which plant residues were exported (RE) or returned to soil, i.e., restituted (RR), over a period of 60 years. For 2.5 years, we followed a cropping sequence of maize, winter wheat and barley, in which, as an additional treatment, wheat cultivation was diversified once with pea intercropping. Based on soil-extracted DNA, abundances of bacteria, archaea and fungi were analysed by domain-specific qPCR and the di-versity and composition of the prokaryotic community by 16S rRNA gene amplicon sequencing. The abundance of bacteria and fungi, but not for archaea, increased with the long-term restitution, but this effect was only detectable in spring due to their stabilized abundance during winter. The long-term effect of crop restitution on bacterial diversity became tangible when rare and dominant community members were differentiated, with higher sensitivity shown for the rare. In contrast, the cropping sequence equally affected members of both groups. The short-term effect of crop diversification by intercropping was much stronger in the C-depleted RE soils, than in RR soils where the C-loss was compensated, indicating that crop residue restitution increased the environmental resilience of soil microbial communities. Finally, we could confirm that rare bacterial community members, suspected to represent more oligotrophs and synergistic bacteria, formed stronger network structures to each other than the dominant, suspected to be more copiotrophic and competitive. Therefore, our results emphasize the importance to consider the response of rare microbial community members when evaluating long-term effects of agricultural management on the soil microbiome.