Disentangling the impact of three contrasting crop management practices on soil microbial communities – Importance of rare bacterial community members. The effects of agricultural management on soil microbial communities

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 contrasting crop management practices on microbial abundance and prokaryotic diversity, we analysed soils 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 diversity 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.

农业活动对土壤微生物群落具有显著调控作用，但目前仍未明确不同农田管理措施如何驱动其多样性与群落组成。为厘清不同作物管理模式对微生物丰度及原核生物多样性的影响机制，本研究分析了一项为期60年的长期农田定位试验的土壤样品，该试验设置了植物残体移出（RE）与残体归还（RR）两种对比处理。本研究在2.5年周期内追踪了玉米-冬小麦-大麦的轮作序列，并额外设置一项间作处理：在小麦种植季间作豌豆一次。基于土壤提取的总DNA，本研究通过结构域特异性qPCR分析了细菌、古菌与真菌的丰度，并通过16S rRNA基因扩增子测序解析了原核生物群落的多样性与组成。长期残体归还处理显著提升了细菌与真菌的丰度，但对古菌丰度无显著影响；且该效应仅在春季可被检测到，因冬季微生物丰度处于稳定状态。当区分群落中的稀有类群与优势类群时，残体归还对细菌多样性的长期效应更为显著，且稀有类群对该处理的响应灵敏度更高。与之相反，轮作序列对两类细菌类群的影响并无显著差异。间作带来的作物多样性短期提升效应在碳元素耗竭的RE处理土壤中更为显著，而在碳损失得到补偿的RR处理土壤中则不明显，这表明作物残体归还提升了土壤微生物群落的环境抗逆性。最后，本研究证实，被认为属于贫营养型与协同型细菌的稀有类群，其群落内部的网络结构相较于优势类群（被认为属于富营养型与竞争型）更为紧密。因此，本研究结果强调，在评估农业管理措施对土壤微生物组的长期影响时，需充分考虑稀有微生物群落类群的响应特征。