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

Authors: NEUPANE, A - South Dakota State University; BULBUL, I - South Dakota State University; WANG, Z - South Dakota State University; Lehman, R - Michael; NAFZIGER, E - South Dakota State University; MARZANO, SHINYI - South Dakota State University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/16/2021
Publication Date: 4/28/2021
Citation: Neupane, A., Bulbul, I., Wang, Z., Lehman, R.M., Nafziger, E., Marzano, S. 2021. Long term crop rotation effect on subsequent soybean yield explained by soil- and root-associated microbiome and soil health indicators. Scientific Reports. 11. Article 9200. https://doi.org/10.1038/s41598-021-88784-6.
DOI: https://doi.org/10.1038/s41598-021-88784-6

Interpretive Summary: Crop rotation is an important management tactic that farmers use to manage crop production and reduce pests and diseases. Long-term crop rotations may enrich specific 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 (14 year), replicated, crop rotation treatments: continuous corn (Zea mays) (CC), corn/corn/soybean (CCS), corn/soybeans/corn (CS), soybean/corn/soybean (SCS). Following the 14-yr period, each rotation was terminated by soybean (Glycine max). Soybean yield and soil health indicators were measured, along with the bulk soil microbiome and root-associated microbiome of soybean. Soybean yields were significantly higher following CC than the other treatments at both locations. Soil protein as a soil health indicator had the highest level in CC plots among all the rotational treatments. Differential abundances of bacterial and fungal taxa were related to yield differences in a site-specific manner. Multivariate statisitical analyses associated soil health indicators with the soybean yields, but not with differentially abundant microbial taxa in the treatments. Our study is the first report demonstrating that soil and root-associated microbiome members, as well as soil health indicators, can partially explain yield differences due to crop rotation and crop sequencing.

Technical Abstract: Crop rotation is an important management tactic that farmers use to manage crop production and reduce pests and diseases. Long-term crop rotations may enrich specific 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 (14 year), replicated, crop rotation treatments: continuous corn (Zea mays) (CC), corn/corn/soybean (CCS), corn/soybeans/corn (CS), soybean/corn/soybean (SCS). Following the 14-yr period, each rotation was terminated by soybean (Glycine max). Soybean yield and soil health indicators were measured, along with the bulk soil microbiome and root-associated microbiome of soybean. Soybean yields were significantly higher following CC than the other treatments at both locations. Soil protein as a soil health indicator had the highest level in CC plots among all the rotational treatments. Differential abundances of bacterial and fungal taxa were related to yield differences in a site-specific manner. Uncultured bacterial taxa under order Ktedonobacterales in family JG30-KF-AS9 was enriched in the high yield CC plots in Monmouth, whereas Microvirga, Rhodomicrobium, and Micromonosporaceae were enriched in the low yield SCS plots. Members of the fungal phylum Ascomycota were informative in explaining the yield difference among the treatments mostly as pathogens, but Tumularia, Pyrenochaetopsis and Schizothecium were enriched in the high yield CC plots, suggesting either corn pathogens or beneficial fungal taxa for soybean. Canonical correspondence analyses associated soil health indicators with the soybean yields, but not with differentially abundant microbial taxa in the treatments. Our study is the first report demonstrating that soil and root-associated microbiome members, as well as soil health indicators, can partially explain yield differences due to crop rotation and crop sequencing.