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Crop rotation is an important management tactic that farmers use to manage crop production and reduce pests and diseases. Long-term crop rotations may select groups of microbes that form beneficial or pathogenic associations with the following crops, which could explain observed crop yield differences with different crop sequences. To test this hypothesis, we used two locations each with four long-term (12–14-year), replicated, rotation treatments: continuous corn (CCC), corn/corn/soybean (SCC), corn/soybean (CSC), and soybean/corn (SCS). Afterwards, soybean was planted, and yield and soil health indicators, bulk soil microbiome, and soybean root-associated microbiome were assessed. Soybean yields, as well as soil protein, and POXC as soil health indicators were higher following CCC than in the other three treatments at both locations. A bacterial taxon in family  JG30-KF-AS9  was enriched in CCC, whereas  Microvirga ,  Rhodomicrobium , and  Micromonosporaceae  were enriched in SCS. Several ascomycetes explain lowered yield as soybean pathogens in SCS. Surprisingly,  Tumularia ,  Pyrenochaetopsis  and  Schizothecium  were enriched in soybean roots after CCC, suggesting corn pathogens colonizing soybean roots as nonpathogens. Our finding of associations between soil health indicators related to microbiomes and soybean yield has wide-ranging implications, opening the possibility of manipulating microbiomes to improve crop yield potential.

Long term crop rotation effect on subsequent soybean yield explained by soil and root-associated microbiomes and soil health indicators