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

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 microcosms using five soils from different locations to investigate the impacts of liquid dairy manure on bacterial communities. Moreover, we used combinations of autoclaved liquid dairy 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. Bacterial amplicon sequence variants (ASVs) 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, autoclaved manure amended to soil elicited a similar response from indigenous soil microbes as did live manure, indicating that organic matter, nutrients, or other physiochemical factors associated with manure amendments are responsible for changes in indigenous soil populations.