Natural farming diversifies resource-utilisation patterns and increases network complexity in soil microbial community of paddy fields

Natural farming does not involve the use of pesticides or fertilisers, and its success depends heavily on the soil microbial community. In rice paddy fields, the effects of natural farming on soil microbial communities, as compared to conventional farming, remain unclear. We hypothesised that natural farming results in a high abundance and diversity of nutrient-cycling microbes in soils, as such organisms rely on nutrients from decomposition and atmospheric fixation rather than fertilisers. In the same vein, we predicted that naturally farmed soils have higher microbial species diversity and more interactions among microbial species due to the absence of chemical stresses. To test these hypotheses, soil samples were collected from natural and conventional rice paddy fields at three sites across Hokkaido, Japan, during three seasons. The samples were analysed for fungal and prokaryotic community structures using amplicon sequencing. The type of farming management used on the rice paddies (natural or conventional) significantly influenced the fungal and prokaryotic community structures, but no significant difference was observed in soil properties between management types. In agreement with our hypothesis, the diversity of saprotrophic fungi and predicted prokaryotic N- and C- metabolism genes were higher in soil samples from natural farms compared to those from conventional farms; however, the abundance of C-metabolism genes was higher in conventional farms. Further, fungal diversity and the complexity of both fungal and prokaryotic networks in soil samples from natural farms were higher than those from conventional farms. Thus, our findings suggest that natural farming may improve microbial nutrient-cycling potential, diversity, and networks in comparison to conventional farming.