Adding alfalfa to an annual crop rotation shifts the composition and functional responses of tomato rhizosphere microbial communities

Abstract Alfalfa (Medicago sativa L.) is widely cultivated to reduce nitrogen (N) fertilizer inputs for the subsequent crop and can improve soil nitrogen (N) availability and crop yields, widely referred to as the “rotation effect.” The soil mechanisms behind these effects may be due to changes associated with the rhizosphere microbial community of alfalfa. We hypothesized that a compositionally and functionally distinct microbial community would colonize the rhizosphere of tomato plants grown following alfalfa, compared to following maize, and that some of the microbial groups would be carried over from the alfalfa. We also hypothesized that including alfalfa in rotation would lead to greater abundance of genes associated with nitrogen cycling in the tomato rhizosphere. Amplicon sequencing targeting the 16s rDNA gene of bacteria and ITS of fungi were employed to characterize the functional and compositional diversity of the rhizosphere microbial community in two systems under tomato cultivation at the Russell Ranch Sustainable Agriculture Facility Century Experiment (Davis, CA, USA): i) maize-tomato rotation in which we sampled tomatoes (CMT); and ii) alfalfa-maize-tomato rotation in which we sampled tomatoes (AMTT) and alfalfa (AMTA). Bacterial and fungal communities were significantly different among the three systems, with AMTA showing the greatest differences from the others, consistent with the importance of plant species in recruiting specific rhizosphere microbial communities. Changes between the tomato systems were primarily due to increased abundances of bacterial groups Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes and the fungal group Glomeromycota that includes arbuscular mycorrhizal fungi. The abundance of bacterial and fungal genera, Niastella, Kribbella and Preussia was similar in AMTA and AMTT but not in CMT, which suggests a carry-over effect from alfalfa to the subsequent tomato crop rhizosphere. Groups enriched or carried over into tomato included taxa with the ability to enhance soil nutrient availability, plant growth promotion, and suppress harmful effects of pathogens. Genes encoding enzymes related to denitrification were significantly less abundant in the tomato rhizosphere following alfalfa than maize. Improving our understanding of how crop rotation influences soil microbial community composition and functions could enable the designing of crop rotations to foster the proliferation of specific beneficial microbial groups.