Effects of sustainable agricultural practices on soil microbial diversity, composition, and functions

Abstract

Soil microorganisms can provide multiple benefits to agroecosystems, which are assumed to be promoted by sustainable agricultural practices. However, the mechanisms that explain this relationship have not been clearly elucidated. Although studies have reported that sustainable agricultural practices promote microbial biomass, the broader implications for soil microbial composition and functions remain uncertain. Accordingly, we searched field experiments worldwide contrasting soil microbial communities under conventional and sustainable agricultural practices. We analysed 924 results of relative abundance of bacteria or fungi (using 16 S and ITS rRNA amplicon sequencing, respectively) at the Family taxonomic level obtained from 46 articles. We found higher soil bacterial richness and higher abundance of copiotrophic bacteria under sustainable agricultural practices. Organic fertilisation promoted the abundance of bacteria involved in C and N cycling, while conservation tillage decreased those involved in the decomposition of plant residue. While sustainable agricultural practices had a minor effect on the overall fungal structure, they led to increases in symbiotic fungi abundance (e.g., Geoglossaceae). Additionally, we observed a slight increase in arbuscular mycorrhizal fungi and a slight reduction in pathogenic fungi associated with plant disease (e.g., Botryosphaeriaceae). Higher soil microbial taxonomic diversity did not lead to increased soil multifunctionality; however, it could safeguard resilience for soil functions via the diversity insurance effect. This study establishes that sustainable agricultural practices can significantly influence microbial communities, leading to compositional and structural changes, as well as promoting relevant functions for agroecosystems. Altogether, these results highlight the importance of integrating concepts of community ecology into agricultural management practices for reaching sustainable agricultural systems.