The effect of crop rotation between wetland rice and upland maize on the microbial communities associated with roots

Microorganisms colonize plant roots for mutual benefits. Colonization is initiated by the soil microbial community but is also affected by soil conditions and plant type. Rice typically grows under wetland conditions that are anoxic, thus being supportive for an anaerobic methanogenic microbial community. Maize, however, grows under upland conditions that are oxic, thus being supportive for an aerobic microbial community. Crop rotation between wetland rice and upland maize is not uncommon, but the effect of this management on microbial colonization of plant roots is largely unknown and was the aim of our study. We used the roots of rice and maize from a two-year study in the Philippines, where on the same soil wetland rice was cultivated either in both wet and dry season or was rotated with upland maize in the dry season. The microbial colonization of the root ecto- and endorhizosphere was assessed by using quantitative PCR and illumina sequencing of the bacterial and archaeal 16S rRNA genes. The data showed that maize roots had completely different microbial community structures than the rice roots from continuous wetland cultivation, while rice roots from crop rotation were in-between. These effects of management were seen for each of the different bacterial phyla. For example, among the most abundant operational taxonomic units (OTUs) Firmicutes, Deltaproteobacteria and the methanogenic Methanocella spp. were less abundant while Alphaproteobacteria and the methanogenic Methanobacterium spp. were more abundant on maize than on rice roots. Our study showed that root colonization by Archaea and Bacteria was strongly affected by crop rotation between wetland rice and upland maize.