Abiotic and biotic filters determine the response of soil bacterial communities to manure amendment

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

Submitted to: Applied Soil Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/22/2022
Publication Date: 12/1/2022
Citation: Schlatter, D.C., Gamble, J.D., Castle, S., Rogers, J., Wilson, M. 2022. Abiotic and biotic filters determine the response of soil bacterial communities to manure amendment. Applied Soil Ecology. 180. Article 104618. https://doi.org/10.1016/j.apsoil.2022.104618.
DOI: https://doi.org/10.1016/j.apsoil.2022.104618

Interpretive Summary: Applying manure to agricultural fields provides many soil health benefits, which are often mediated through soil microbes. However, manure application can also introduce pathogens and antibiotic resistance elements to soils. Studies were conducted to investigate how manure impacts soil bacterial communities from different soils, the mechanisms by which manures drive changes in indigenous soil communities, and how soils resist invasion by manure-borne bacteria. We found that the response of soil communities to manure depended on the location of soil origin, but that most manure-borne bacteria died off rapidly. The rapid die-off of manure-borne bacteria could be largely attributed to the soil abiotic environment and the promotion of potentially beneficial indigenous soil bacteria over time was driven by abiotic factors associated with manure. Our results suggest that the impacts of manure amendments on indigenous bacterial populations will depend on soil origin and be driven primarily by inputs of carbon and nutrients rather than interactions with manure-borne bacteria. Moreover, the rapid die-off of most manure-borne bacteria even in the absence of indigenous microbial communities indicates that the soil abiotic environment is a strong barrier to colonization by manure-borne bacteria. This work builds upon our understanding of how manure amendments impact potentially beneficial and detrimental components of soil communities. Specifically, our work suggests that there may be added value of manure amendments for growers by promoting beneficial soil bacteria, and that the soil environment provides a strong buffer against potentially pathogenic manure-borne bacteria.

Technical Abstract: Manure amendments are a common soil amendment in forage and row cropping systems used to provide plant-available nutrients, build soil organic matter, and enhance soil health. Many of the benefits of manure applications are thought to be driven via their impacts on soil microbial communities. However, manure amendments may also introduce potential undesirable microbes (pathogens, or those with antibiotic resistance elements) to soils. Despite the widespread use of manure amendments and their importance in agricultural systems, the forces governing the assembly of bacterial communities in soil in response to manure amendments are poorly characterized, limiting our ability to predict their impacts on soil communities. We constructed soil mesocosms using five soils from different locations to investigate the impacts of manure amendments on bacterial communities. Moreover, we used combinations of sterilized (autoclaved) manure and soils to determine the roles of abiotic and biotic factors in the response of indigenous soil communities to manure and the fate of manure-borne bacteria. We found that the taxa that responded to manure amendment were largely dependent on soil origin. Initial shifts in soil communities after manure amendment were driven by the introduction of manure-borne taxa. However, introduced taxa died off rapidly while some indigenous taxa increased in relative abundance over time. Introduced taxa died off even in the absence of indigenous microbiota, suggesting that the soil abiotic environment is a strong barrier to colonization by manure-borne bacteria. Finally, sterilized (autoclaved) manure amended to soil elicited a similar response from indigenous soil microbes as did unsterilized manure, suggesting that organic matter, nutrients, or other physiochemical factors associated with manure amendments are responsible for changes in indigenous soil populations.