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

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 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.

Microbial Responses to the Reduction of Chemical Fertilizers in the Rhizosphere Soil of Flue-Cured Tobacco

“…Compared to conventional fertilization, the strategy of reducing nitrogen fertilization might change the relative abundance of JG30-KF-AS9 and JG30-KF-CM45 to improve the productive function of the bacterial community of the tobacco-planting soil ( Chinta et al, 2021 ; Neupane et al, 2021 ; Zhang et al, 2021 ). Meanwhile, the reduction in nitrogen fertilizer might increase the relative abundance of Streptomyces (D30F) and Elsterales (D20F), which had the potential abilities to decrease the relative abundance of pathogens and their pathogenicity ( Vurukonda et al, 2018 ; Wang et al, 2021 ; Momesso et al, 2022 ).…”

Soil Microbial Indicators within Rotations and Tillage Systems

“…Similarly, Ktedonobacterales (O) is relatively unknown but have been found to inhabit forests, gardens, and sand in low numbers, as well as extreme environments, such as volcanoes and geothermal areas [61]. However, Neupane, Bulbul, Wang, Lehman, Nafziger, and Marzano [27] detected elevated Ktedonobacterales (O) levels from a CCC rotation, although little supporting information regarding their biological significance was found. The increased RAs from the CCC rotation and chisel tillage show that these resilient microbes are adapted to the harsh and acidic conditions in this treatment.…”

“…Indicator microbes usually refer to an ASV that explains variability in a dataset [23]. Studies on indicator microbes have shown that organic matter inputs and pH alter the cycling of N and C, resulting in significant changes in soil biological properties [2,15,26,27]. Given the complexity of using metagenomics to identify indicator microbes, field studies are scarce, especially from a long-term setting.…”

“…Given the complexity of using metagenomics to identify indicator microbes, field studies are scarce, especially from a long-term setting. A few long-term studies (15-130 years) have determined indicator microbes from typical cropping systems [2,15,27], though none have analyzed crop rotation and tillage simultaneously. As these are the most common tools used by growers to improve yields, a thorough investigation of these indicator microbes is necessary.…”

Fungal Indicators of Sensitivity and Resistance to Long-Term Maize Monoculture: A Culture-Independent Approach

“…Considering the complexity of the process of selecting appropriate indicators, at the beginning they were divided into biotic and abiotic indicators of soil health. The biotic indicators may include but are not limited to total biomass, activities, functioning, community composition, and interactions of soil-inhabiting macroorganisms and microorganisms that determine the trophic or food-web complexity of soil ecosystems ( Pervaiz et al, 2020 ; Behnke et al, 2021 ; Beule and Karlovsky, 2021 ; Neupane et al, 2021 ). The abiotic indicators of soil health include but are not limited to soil aggregation, aggregate stability, organic C and organic matter contents, nutrient cycling and sequestration, the composition of soil exudates and metabolites, nutrient balance, and other essential properties such as pH and CEC ( Pervaiz et al, 2020 ; Behnke et al, 2021 ).…”