Influence of manure application on the soil bacterial microbiome in integrated crop-livestock farms in Maryland

Authors: PENG, MENGFEI - University Of Maryland; Millner, Patricia; PARVEEN, SALINA - University Of Maryland Eastern Shore (UMES); BISWAS, DEBABRATA - University Of Maryland

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/13/2021
Publication Date: 12/15/2021
Citation: Peng, M., Millner, P.D., Parveen, S., Biswas, D. 2021. Influence of manure application on the soil bacterial microbiome in integrated crop-livestock farms in Maryland. Microorganisms. https://doi.org/10.3390/microorganisms9122586.
DOI: https://doi.org/10.3390/microorganisms9122586

Interpretive Summary: Integrated crop-livestock farms (ICLFs) rely on animal manure products (untreated, incompletely treated, or composted) for soil health, crop fertility, and C sequestration. However, use of raw or inadequately composted animal manure has been associated with increased survival of pathogens in the manured soil and their transfer to fresh produce. Survival of enteric (manure-based) pathogens in a soil environment involves interactions between the introduced microbial communities in the soil and those in the manure amendments, and can present a food safety risk for fresh produce that is likely to be consumed without cooking. In this study of six ICLFs in Maryland, we characterized the impacts of manure amendment on the soil bacterial community, using a metagenomic, non-culture based approach, to capture the breadth of the pre- and post-amendment bacterial community shifts. Results showed that the application of on-farm manure products in ICLFs could substitute for many indigenous soil bacteria, and that manure amendment increased the various types of soil bacterial groups present, disrupting the original rich contents as well as the overall even distribution of soil bacteria. Significant genus-level shifts occurred from use of manure amendments. However, the potential risk of introducing foodborne illness pathogens such as Salmonella and Listeria remain. The findings provide risk assessors and producers unique insights on the effects of manure product amendments on soil bacterial community changes in small-scale private commercial ICLFs. This evaluation sets the stage for further in-depth investigations of the relationships among the altered soil bacterial communities resulting from manure amendment and key soil microbial functions, as related to nutrient transformations, soil carbon cycling, and quality and safety of produce from ICLFs.

Technical Abstract: As a traditional agricultural system, integrated crop-livestock farms (ICLFs) involve production of animals and crops in a shared environment. The ICLFs in the mid-Atlantic region of the United States practice sustainable manure aging or composting processes to provide an on-farm source of soil amendment for use as natural fertilizer and soil conditioner for crop production. However, crop fertilization by soil incorporation of aged manure or compost may introduce different microbes and alter the soil microbial community. The aim of this study was to characterize the influence of aged or composted manure on the soil bacterial community diversity in ICLFs. DNA extracted from soil samples from six ICLFs in Maryland collected before (pre-crop) and during the season (2020-2021), was used to analyze the soil bacterial microbiome by 16S rDNA sequencing. Results showed that both phylum- and genus-level alterations of soil bacterial communities were associated with amendment with aged or composted manure. Particularly, Proteobacteria and Actinobacteria were enriched, while Acidobacteria, Bacteroidetes, Planctomycetes, Firmicutes, and Chloroflexi were reduced after manure product application. Meanwhile, the relative abundance of Bacillus was decreased, while two zoonotic pathogens, Salmonella and Listeria, were enriched by manure amendments. Overall, animal manure amendment of soil increased the phylogenetic diversity but reduced the richness and evenness of the soil bacterial communities. Although manure composting management in ICLFs benefits agricultural sustainable production, the amendments altered the soil bacterial communities and were associated with the finding of two major zoonotic bacterial pathogens, which raises the possibility of their potential transfer to fresh horticultural produce crops that may be produced on the manured soils and then subsequently consumed without cooking.