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

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