Fungal community shifts in soils with varied cover crop treatments and edaphic properties

Abstract

Cover cropping is proposed to enhance soil microbial diversity and activity, with cover crop type affecting microbial groups in different ways. We compared fungal community compositions of bulk soils differing by cover crop treatment, season, and edaphic properties in the third year of an organic, conventionally tilled rotation of corn-soybean-wheat planted with winter cover crops. We used Illumina amplicon sequencing fungal assemblages to evaluate effects of nine treatments, each replicated four times, consisting of six single winter cover crop species, a three-species mixture, a six-species mixture, and fallow. Alpha-diversity of fungal communities was not affected by cover crop species identity, function, or diversity. Sampling season influenced community composition as well as genus-level abundances of arbuscular mycorrhizal (AM) fungi. Cover crop mixtures, specifically the three-species mixture, had distinct AM fungal community compositions, while cereal rye and forage radish monocultures had unique Core OTU compositions. Soil texture, pH, permanganate oxidizable carbon, and chemical properties including Cu, and P were important variables in models of fungal OTU distributions across groupings. These results showed how fungal composition and potential functions were shaped by cover crop treatment as well as soil heterogeneity.Microbial diversity is an important aspect of soil health, as soil microbial communities mediate many biogeochemical processes and are sensitive to disturbances that can lead to long-lasting ecosystem effects 1 . Greater richness and evenness in the representation of bacteria and fungi in soils can help mitigate plant responses to environmental stressors 2 . With the advent of high-throughput DNA sequencing technologies that allow for more detailed genetic information, we can determine if and how microbial compositions shift in response to disturbance and edaphic differences and, to some degree, what those changes may mean for ecosystem processes.Cover cropping is the practice of growing ground-covering crops during the intervals between successive cash crops. Cover cropping imparts numerous benefits to soil, including the addition of organic carbon (C) from roots, root exudates, and aboveground residues and the improvement of soil structure and tilth 3-5 . Ecosystem services provided by cover crops include protection from soil erosion, enhanced soil water-holding capacity, reduced weed colonization and growth, plant resilience to pathogens and increased crop yield 5,6 . Legume cover crops provide biologically fixed nitrogen (N), while grasses take up excess soil inorganic N and improve N retention. A complete suite of ecosystem services is not deliverable by any one cover crop species. Thus, planting mixtures of cover crops has been proposed as a means to provide varied combinations of ecosystem services based on the functional traits of individual cover crop species 5,7-10 .Cover crops may alter microbial community diversity and function by varying the types and composition of exuded C...

Microbial Community Dynamics of Soybean (Glycine max) Is Affected by Cropping Sequence

“…At the phylum level, there was no significant difference in relative fungal abundance based on crop sequence. In addition to our study, the Mortierellomycetes , Sordariomycetes , and Tremellomycetes have all been reported as the dominant fungal classes in other crop rotation studies ( Maarastawi et al, 2018 ; Cloutier et al, 2020 ). For example, the Mortierellomycetes has been identified as a soybean-associated taxon and reported to increase in continuous soybean fields ( Hu et al, 2018 , 2019 ).…”

“…We showed that crop sequence did not significantly alter fungal community diversity and richness structure at all time-points. In a study that investigated fungal community composition in soils with varied cover crop treatments using a 3-year vegetable-cover crop rotation, it was reported that fungal community diversity was not affected by the identity, function, and diversity of cover crop species ( Cloutier et al, 2020 ). In addition, it has been reported that rotation of different vegetables can have different effects on the diversity and richness of fungi in a continuous cropping matrix where rotation of celery improved the richness and diversity of fungi while beans and cabbage reduced the richness and diversity of fungi ( Lyu et al, 2020 ).…”

Plant Microbiota Beyond Farming Practices: A Review

“…Indeed, mixing cover crops seems to favor more abundant and specialized microbiomes (Finney et al, 2017). Overall, although the α-diversity of soil microbial communities is not impacted, specific microbial guilds seem to be recruited when catch crops are implemented in crop rotation (Cloutier et al, 2020;Kim et al, 2020). Cloutier et al (2020) identified significant changes in soil fungal microbiome with more abundant and distinct arbuscular mycorrhizal fungal communities under cover crop mixtures.…”

Western Corn Rootworm, Plant and Microbe Interactions: A Review and Prospects for New Management Tools

“…Winter cover crops increase soil health by reducing erosion, limiting nutrient loss, and increasing microbial abundance and diversity [ 163 , 164 ]. Different species of cover crop can refine AMF and other microbial communities in distinct ways [ 165 , 166 , 167 , 168 ], and the legacy effects of cover crops can increase AMF colonization of cash crop roots [ 158 , 167 ]). Winter cover crops can also increase predator populations and correlate to reductions in root damage and WCR larvae [ 169 ].…”