Soil bacterial and fungal community structure of a rice monoculture and rice-pasture rotation systems

Abstract

Rice monoculture has been the main rice-cropping system for several years. Rice-pasture rotation system has raised in recent years as an alternative, as this practice not only increases rice yield but also adds value through the use of implanted pastures, livestock production and diversification of the system. To evaluate the impact on soil microbial diversity, we used Illumina Mi-Seq sequencing technology and phylogenetic structure analysis to study the bacterial and fungal soil communities in these two rice-cropping systems within a rice-production region of Entre Ríos province, Argentina. We detected over 11,000 and 3000 bacterial and fungal OTUs, respectively. Among them, members of the Acidobacteria, Proteobacteria, Verrucomicrobia and Ascomycota fungi phyla were the most abundant. None of the bacterial and fungal OTU differed significantly in composition between systems. In addition, microbial community diversity did not differ between rice-cropping systems, even though we found they were phylogenetically structured by a non-random pattern, mainly, due to environmental selection. In addition, the environmental variables explaining the differences between rice-cropping systems were pH, as well as the abundance of organic and inorganic elements. The results suggest that the rice-cropping system may be one of various factors influencing these observations, with a certain degree of relevance, in conjunction with other environmental variables that are not controlled but considered in this analysis.