Abiotic and biotic drivers of soil fungal communities in response to dairy manure amendment

Authors: Schlatter, Daniel; Gamble, Joshua; CASTLE, SARAH - Sustainable Conservation; ROGERS, JULIA - University Of Minnesota; WILSON, MELISSA - University Of Minnesota

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2023
Publication Date: 5/22/2023
Citation: Schlatter, D.C., Gamble, J.D., Castle, S.C., Rogers, J., Wilson, M. 2023. Abiotic and biotic drivers of soil fungal communities in response to dairy manure amendment. Applied and Environmental Microbiology. 89(6). Article e01931-22. https://doi.org/10.1128/aem.01931-22.
DOI: https://doi.org/10.1128/aem.01931-22

Interpretive Summary: Dairy manure application to agricultural fields is a valuable means to enhance the fertility and productivity of soil. In contrast to synthetic fertilizers, manure often contributes soil health benefits by supporting soil microbial communities. Soil fungi are essential components of soil microbial communities, where they drive decomposition and organic matter processing, contribute to soil structure, and act as plant mutualists, pathogens, and symbionts. Studies were conducted to investigate how dairy manure influences fungal communities in different soils, whether shifts in indigenous fungal communities are due to biotic or abiotic factors, and how manure-borne fungi persist in soils. Soil origin was the most important determinant of soil fungal communities amended with dairy manure, and manure-amended communities did not show a strong initial response to manure. Rather, fungal communities diverged from non-amended communities over 60 days of incubation. Moreover, soil fungal communities amended with autoclaved manure exhibited similar dynamics as those amended with live manure. A small number of manure-borne fungi were identified, and the majority died off rapidly in both live and autoclaved soils. Results suggest that manure promotes the growth of specific indigenous fungal taxa in soils, and that these taxa are highly variable among soils from different locations. Moreover, these dynamics appear to be driven by inputs of organic matter, rather than introduction of manure-borne fungi. Manure-borne fungi belonged to anaerobic phyla, and are likely inhabitants of the animal rumen that do not persist in soil. In total, this work builds on our knowledge of how manure inputs drive changes in soil fungal communities and the fate of manure-borne fungi.

Technical Abstract: Modern agriculture often relies on large inputs of synthetic fertilizers to maximize crop yield potential, yet their intensive use has led to land degradation, substantial nutrient losses, and impaired soil health. Alternatively, manure amendments have been used for thousands of years to support productive soils, where they provide plant available nutrients, build organic carbon, and enhance soil health. Beneficial impacts of manure amendments are driven in part via their effects on soil microbial communities. However, we lack a clear understanding of how consistently manure impacts fungal communities, the mechanisms via which manure impacts soil fungi, and the fate of manure-borne fungi in soils. To fill these knowledge gaps, we assembled soil microcosms using five soils representative of dairy producing regions and used high throughput DNA sequencing of fungal ITS2 marker genes to investigate how manure amendments impact fungal communities over a 60 day incubation. Further, we used autoclaving treatments of soils and manure to determine if observed changes in soil fungal communities were due to abiotic or biotic properties, and if indigenous soil communities constrained colonization of manure-borne fungi. We found that soil fungal communities consistently diverged from non-amended communities over time, often in concert with a reduction in diversity. However, there was little overlap in fungal taxa promoted or depressed by manure amendments among different soils. Fungal communities responded to live and autoclaved manure in a similar manner, suggesting that abiotic forces, such as carbon and nutrient inputs with manure, are primarily responsible for the observed dynamics. Finally, manure-borne fungi, which largely belonged to anaerobic phylum associated with rumen environments, declined quickly in both live and sterile soil, indicating that the soil environment is unsuitable for their survival. In total, this work suggests that soil fungi are highly responsive to manure inputs, but that unique communities will assemble in different soils.