Influence of Manure Application on the Soil Bacterial Microbiome in Integrated Crop-Livestock Farms in Maryland

Abstract

As a traditional agricultural system, integrated crop-livestock farms (ICLFs) involve the 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 application on the diversity of soil bacterial community in ICLFs. Soil samples from six ICLFs in Maryland were collected before (pre-crop) and during the season (2020–2021) and used to analyze soil bacterial microbiome by 16S rDNA sequencing. Results showed that both phylum- and genus-level alterations of soil bacterial communities were associated with amendment of 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.

The quality of organic amendments affects soil microbiome and nitrogen-cycling bacteria in an organic farming system

“…Organic N fertilizers increased Proteobacteria and Bacteroidetes, but decreased Acidobacteria, Chloroflexi, and Gemmatimonadetes. Similar changes in the relative abundances of these phyla have been identified through on-farm surveys of manure or compost treated soils (48).…”

Divergence in the soil and rhizosphere microbial communities of monoculture and silvopastoral traditional C. dodecandra agroforestry systems in Yucatan, Mexico

“…This was to be expected, because of nutrient sources, such as sheep excrement and grass remnants, which are rich in organic carbon, organic matter, carbonates and nitrogen (Wan et al, 2021). Moreover, several studies have shown that cover crops improve C, N and P cycling by retaining moisture, and by increasing soil microbiota diversity (Kim et al, 2020); and animal manures can promote differential growth of prokaryotic microorganisms thus increasing soil fertility (Gómez‐Tenorio et al, 2021; Peng et al, 2021; Wan et al, 2021). In contrast, in the Monoc the main source of organic matter is the leaf litter of C. dodecandra trees.…”

“…A possible explanation is that the higher richness, evenness and Shannon diversity in Silvo, causes the abundance of all orders to be relatively low. Another unexpected result was the low abundance of Enterobacteriales in the Silvo samples (0%–0.28%), because sheep excrement contains around 40% of this bacterial order (Shabana et al, 2021), and usually prokaryotic communities in the soil are enriched in it when manure is applied (Peng et al, 2021). It may be that these soils have characteristics that somehow inhibit the proliferation of this order, since similar results were obtained in a previous analysis of Yucatan soils (Estrada‐Medina et al, 2016).…”

“…Kim et al, 2020). Besides, sheep excrement can increase the abundance of some prokaryotic OTUs (Gómez-Tenorio et al, 2021) and after decomposition, it can increase diversity as well, as has been shown for different manure amendments when applied to soil (Peng et al, 2021).…”

Effects of Organic Fertilizer with Different Degrees of Maturity on Bacteria in Saline–Alkali Soil

“…Applying organic fertilizer is an important measure of soil improvement and soil fertility enhancement. Organic fertilizer can effectively change the species and quantity of soil microorganisms and thereby affect the structure and spatial distribution of the soil bacterial community [5][6][7][8]. Soil bacterial diversity and community structure can sensitively reflect soil quality, soil fertility, and soil health [9,10].…”