Response of soil microbiota to various soil management practices in 100-year-old agriculture field and identification of potential bacterial ecological indicator

The study aimed to comprehensively investigate the structural dynamics of a soil microbial community within a 100-year agricultural field experiment. The experimental design encompasses three distinct soil management practices, namely monoculture, five–year rotation, and random rotation, each with or without the incorporation of legumes and manure. Soil microbial communities were determined by the Next-Generation Sequencing (Illumina MiSeq analysis) of both the V3 and V4 hypervariable regions of the 16S rRNA gene for bacteria and Archaea, as well as ITS1 for fungi. In all soils, dominant bacterial phyla were Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi, and dominant orders were Actinomycetales, Rhizobiales, Acidimicrobiales, and Sphingomonadales. However, dominant fungal phyla were Ascomycota, Basidiomycota, and Zygomycota, and dominant fungal orders were Pleosporales, Eurotiales, Hypocreales, or Mortierellales. Compared to fallow land, agricultural soil management affected the microbial community of the soil, reducing the ratio of oligotrophs (e.g. Acidobacteria and Armatimonadetes) to copiotrophs (Actinobacteria or Gemmatimonadetes). Moreover, agricultural soil management contributed to an increased number of plant growth-promoting bacterial groups (PGPB), antagonistic to many fungal (e.g., Fusarium spp.) and bacterial pathogens (e.g., Bukholderiales, Xanthomonadales). However, generally in the study, there were no significant differences in microbial communities between monoculture and crop rotations. Moreover, two taxa can be considered as potential indicators of “healthy soil”: the nitrifying bacteria Nitrospira spp. whose abundance was strongly dependent on nitrogen, potassium, phosphorus, organic carbon, and soil pH, and the PGP fungi of the genus Mortierellla which depended mainly on nitrogen and pH. Finally, the genus Mortierellla was generally the most abundant in agricultural soils, especially in the five–year rotation with legumes, while fallow soils did not favour these microorganisms. In conclusion, various soil management practices strongly affect the soil microbiota and thus their ability to support land productivity.