PRJNA477363
Eighteen-year farming management moderately shapes the soil microbial community structure but promotes habitat-specific taxa
Soil microbes have critical influence on the productivity and sustainability of agricultural ecosystems, yet the magnitude and direction to which management practices affect the soil microbial community remains unclear. We compared the soil microbial community and putative gene abundances of N transformations via high-throughput sequencing of 16S and ITS amplicons in three common farming systems, conventional grain cropping (CON), organic grain cropping (ORG), and grain cropping-pasture rotation (ICL). A forest plantation (PF) and an abandoned agricultural field subject to natural succession (SUC) were also included to offer the baseline, scale, and strength of evaluation. Five systems did not differ in bacterial species richness or Shannon diversity, but showed moderate divergence in fungal community, with lowest fungal species richness and Shannon diversity in CON and ORG, respectively. Bacterial and fungal community structures in three cropping systems also clustered and separated from those in PF and SUC. This suggests that farming management practices as such played minor roles in shaping the soil microbial community compared to vegetation types (i.e., woody versus herbaceous plants). However, management practices substantially promoted habitat-specific taxa. Compared to CON, ORG promoted bacteria belonging to the phyla, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Gemmatimonadetes. The most dramatic alternation by ORG is on the fungal community, with Lecanoromycetes, a class of Ascomycota, accounting for ~10% of total fungal population compared to almost nil in the other four systems. Nitrogen-cycle community compositions predicted by PICRUSt also diverged between ORG (or ICL) and CON, with ORG (or ICL) drifting further away from PF and SUC than CON with. Soil pH, together with inorganic N, extractable organic C, and soil organic C:N ratio explained a significant portion of total variations in bacterial (48%) and fungal communities (39%). Plant type (woody versus herbaceous), fertilization, and source of N (synthetic versus organic) were also important to structure the soil microbial community. Management-associated taxa need to be further investigated for ecological significance.