Composts of poultry litter or dairy manure differentially affect survival of enteric bacteria in fields with spinach

Abstract

Aims The aim was to determine the survival and persistence of Escherichia coli in soil amended with compost from different manure sources. Method and Results Complex interactions of abiotic and biotic factors on E. coli survival were characterized in field experiment plots receiving randomly assigned compost treatments: dairy windrow, dairy vermicompost, poultry windrow or no compost. Biomass, activity and function of indigenous microbial communities in the composts and soils were measured concurrently to determine whether mechanisms of compost were driven by biotic or abiotic properties. E. coli persisted in compost containing poultry amendments but not in composts containing dairy or no amendments. Poultry compost contained more NH4‐N and a distinct microbial community compared to dairy and no compost treatments. A laboratory experiment performed on compost extracts suggested that E. coli survived better in extracts devoid of indigenous microbes as long as bioavailable nutrients were plentiful. Conclusions Dairy‐based composts are less likely to support E. coli survival than poultry‐based composts. Significance and Impact of the Study Results aid in risk assessment of the use of different types of manure‐based compost and soil amendments in fruit and vegetable production by elucidating the roles of nutrient and microbial community composition on survival of E. coli in amended field soils.

Bacterial Community Dynamics Distinguish Poultry Compost from Dairy Compost and Non-Amended Soils Planted with Spinach

“…Soils amended with PLC contain greater abundances of Sphingobacteriales and Flavobacteriales than DMC or NoC soils. The positive correlation between PLC and Sphingobacteria in 2015 [ 16 ] was confirmed in the years 2016 and 2017. The presence of known denitrifiers and copiotrophs, such as Sphingobacteriales (e.g., Pedobacter ), indicates a high N and C availability in PLC [ 32 ].…”

“…The presence of known denitrifiers and copiotrophs, such as Sphingobacteriales (e.g., Pedobacter ), indicates a high N and C availability in PLC [ 32 ]. The increase in environmental Bacteroidetes is an indication that the conditions are more favorable to a copiotrophic community [ 16 , 33 ], which in turn is conducive to soil-borne fungal phytopathogens such as Rhizoctonia solani [ 17 ].…”

“…In the current study, the only variability in ecoenzyme activity was found at the beginning of the season, likely a reflection of the disturbance caused by tilling [ 38 ]. Carbon availability and nutrient limitations suggest that soils in this study became increasingly C- and P-limited for soil microbes as the experiment progressed [ 15 , 16 , 26 ].…”

“…DMC and PLC were obtained from commercial or research sources that regularly provide products with similar recipes and maturities ( Table 1 ) [ 16 ]. Application rates were based on preliminary experiments, industry recommendations, and product availability ( Table 2 ) [ 16 , 17 ]. DMC applications added 282, 101, and 180 kg total nitrogen ha −1 and 33, 12, and 21 kg total phosphorus ha −1 in 2015, 2016, and 2017, respectively.…”

“…Sequences were clustered into operational taxonomic units (OTUs) at the >97% sequence similarity level, with the taxonomic identity of each OTU determined using the RDP classifier with a threshold of 0.5 [ 21 ] trained against either the Greengenes database for bacterial and archaeal 16S rRNA gene sequences [ 22 ] or the UNITE database for fungal ITS sequences [ 23 ]. Detailed methods are available [ 16 ]. Raw amplicon sequence data are available in the public Figshare database (URL: and DOI:10.6084/m9.figshare.11286113).…”