Bacterial communities in chitin-amended soil as revealed by 16S rRNA gene based pyrosequencing

Abstract

Chitin and its derivatives are natural biopolymers that are often used as compounds for the control of soil-borne plant pathogens. In spite of recent advances in agricultural practices involving chitin amendments, the microbial communities in chitin-amended soils remain poorly known. The objectives of this study were (1) to investigate the bacterial diversity and abundance in an agricultural soil supplemented with chitin that turned disease-suppressive and (2) to assess the emergence of chitinolytic bacteria under conditions of raised soil pH. Amplicon pyrosequencing of soil-extracted DNA based on the 16S rRNA genes was used to characterize the structures of bacterial communities in soil, chitin-amended or not, with native versus raised pH (5.7 vs 8.7), in microcosms and the field. As a result of chitin addition, changes in the relative abundances of Actinobacteria, Proteobacteria and Bacteroidetes were observed in the field soil. A large and significant increase of the relative abundance of Oxalobacteraceae (Betaproteobacteria, Burkholderiales) was found. Within the Oxalobacteraceae, the genera Duganella and Massilia showed large increases. Moreover, responses of the Alpha- and Gammaproteobacteria appeared shortly after the alteration of the soil pH in the microcosms. A significant decrease in the abundance of Actinobacteria was observed in the chitin-amended field soil and in the microcosm at high pH. Overall, the bacterial abundance in soil tended to decrease with the addition of chitin. Two groups, Actinobacteria and Oxalobacteraceae, were found to be most responsive to the amendment. These results enhance the understanding of responses to chitin and possible interactions within bacterial communities in soil that can be correlated to soil disease suppressiveness.