Crop rotational diversity increases disease suppressive capacity of soil microbiomes

Abstract

Abstract. Microbiomes can aid in the protection of hosts from infection and disease, but the mechanisms underpinning these functions in complex environmental systems remain unresolved. Soils contain microbiomes that influence plant performance, including their susceptibility to disease. For example, some soil microorganisms produce antimicrobial compounds that suppress the growth of plant pathogens, which can provide benefits for sustainable agricultural management. Evidence shows that crop rotations increase soil fertility and tend to promote microbial diversity, and it has been hypothesized that crop rotations can enhance disease suppressive capacity, either through the influence of plant diversity impacting soil bacterial composition or through the increased abundance of disease suppressive microorganisms. In this study, we used a long-term field experiment to test the effects of crop diversity through time (i.e., rotations) on soil microbial diversity and disease suppressive capacity. We sampled soil from seven treatments along a crop diversity gradient (from monoculture to five crop species rotation) and a spring fallow (non-crop) treatment to examine crop diversity influence on soil microbiomes including bacteria that are capable of producing antifungal compounds. Crop diversity significantly influenced bacterial community composition, where the most diverse cropping systems with cover crops and fallow differed from bacterial communities in the 1-3 crop species diversity treatments. While soil bacterial diversity was about 4% lower in the most diverse crop rotation (corn-soybean-wheat + 2 cover crops) compared to monoculture corn, crop diversity increased disease suppressive functional group prnD gene abundance in the more diverse rotation by about 9% compared to monocultures. In addition, disease suppressive potential was significantly diminished in the (non-crop) fallow treatment compared to the most diverse crop rotation treatments. The composition of the microbial community could be more important than diversity to disease suppressive function in our study. Identifying patterns in microbial diversity and ecosystem function relationships can provide insight into microbiome management, which will require manipulating soil nutrients and resources mediated through plant diversity.

Effect of Long-Term Cropping Systems on the Diversity of the Soil Bacterial Communities

“…The bacterial diversity represented by the Shannon Index H' was significantly lower in the higher crop diversity systems (CR7) compared to the lower crop diversity systems (CR1: p = 0.0478; CR3: p = 0.0263; CR5: p = 0.0208). Similar to the studies of Soman et al [38] and Peralta et al [39], the differences in the structure of communities were not widely reflected in Shannon Index H', indicating the necessity of using more indicators in order to understand differences between bacterial communities. The true richness and diversity, measured in estimated number of T-RFs, rather than Shannon Index H', might better highlight the hypothetical influence of crop rotations on bacterial communities.…”

“…The true richness and diversity, measured in estimated number of T-RFs, rather than Shannon Index H', might better highlight the hypothetical influence of crop rotations on bacterial communities. Rotation has been widely considered as one of the most promising practices for the improvement of soil microbial diversity [39][40][41]. However, according to our results, the lowest diversity was found in the bacterial community associated to the most intense rotation system studied (Norfolk-type).…”

Conditioning the soil microbiome through plant–soil feedbacks suppresses an aboveground insect pest

“…Recent studies have shown that the genetic background of the test plant can determine the root-associated microbiome and whether conspecific plant-soil feedback effects on plant growth are negative or neutral (Hu et al, 2018;Carrillo et al, 2019). This has been an oft-overlooked aspect during the breeding process (P erez-Jaramillo et al, 2016;Carrillo et al, 2019), and here we show that a certain crop or cultivar may inhibit beneficial microbial groups such as mycorrhiza.…”

“…The soil is the source of most beneficial microbes that colonize the rhizosphere (Bulgarelli et al, 2013) the thin interface of root surface with attached soilwhich are key players in plant immunity and overall plant performance. To date, soil management typically focuses on avoiding detrimental effects such as allelopathy or accumulation of pathogens and pests via crop rotation (Peralta et al, 2018). However, an exciting possibility is to manage soils to steer microbial communities to a desired beneficial state with a focus on promoting the presence and activity of beneficial microbes, instead of simply avoiding the pathogenic ones.…”

Soil biodiversity and biogeochemical function in managed ecosystems

“…As a result, the rhizosphere supports a marked proliferation and enrichment of specific microorganisms (Jones et al 2009). Beneficial microorganisms associated with plant roots can play an important role in nutrient uptake and plant growth (Gaiero et al 2013), disease suppression (Peralta et al 2018), reducing damage from pests (Elhady et al 2018), and resilience during periods of stress (Gaudin et al 2015). The advent of molecular techniques has facilitated a more comprehensive investigation of biodiversity and function at the root surface.…”