Swine Manure Composting With Compound Microbial Inoculants: Removal of Antibiotic Resistance Genes and Their Associations With Microbial Community

Abstract

In this study, compound microbial inoculants, including three Bacillus strains and one Yeast strain, were inoculated into swine manure composting to explore the effects on antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), microbial community structure, and pathogenic bacteria. The results indicated that the abundances of the detected ARGs ranged from 3.6 × 10 3 to 1.13 × 10 8 copies/g. The ARGs with the highest abundance was sul2, and the lowest was blaCTX. Composting removes most of the ARGs and MGEs by 22.8-99.7%. These ARGs were significantly reduced during the thermophilic phase of compost. The removal rate of ARGs at the different layers of compost pile was different as follows: middle layer > upper layer > lower layer. But some ARGs proliferated significantly in the maturation phase of compost, especially the sulfonamide resistance genes. Compound microbial inoculants increased the temperature of compost, accelerated water loss, nitrogen fixation, and increased the removal rate of β-lactamase resistance genes, the transposon gene tn916 and part of tetracycline resistance genes by 3.7-23.8% in compost. Compound microbial inoculants changed the community structure and increased the Bacillus abundance in the thermophilic phase of compost. And it was helpful for removing pathogens during composting. The addition of compound microbial inoculants causes the decrease of Firmicutes and the increase of Bacteroidetes, which may be related to the removal and proliferation of ARGs.

Antibiotic Resistance: From Pig to Meat

“…Several of the enriched genes were correlated with int1, which could mean that horizontal transfer was a factor in the enrichment of those genes [82]. This suggests that the microbial compound used has an influence on the type of ARGs that could be removed or enriched [82]. According to current data, one treatment cannot be used to reduce the ARGs of all classes of antibiotics, nor can it be used to completely remove ARGs of a given class.…”

“…Ectopic fermentation systems were tested and reduced the abundance of tetracycline resistance genes and metal resistance genes in manure [81]. The use of microbial agents during composting can also reduce the number of ARGs and antibiotic residues [75,82]. A study by Liu et al reported that a combination of Phanerochaete chrysosporium, Aspergillus niger, and Bacillus licheniformis was effective in removing oxytetracycline and tetracycline residues, reducing them by 87.8% and 93.7%, respectively, and that P. chrysosporium was more effective for removing doxycycline and enrofloxacin [75].…”

“…A study by Liu et al reported that a combination of Phanerochaete chrysosporium, Aspergillus niger, and Bacillus licheniformis was effective in removing oxytetracycline and tetracycline residues, reducing them by 87.8% and 93.7%, respectively, and that P. chrysosporium was more effective for removing doxycycline and enrofloxacin [75]. A study by Li et al using a commercial microbial compound during composting found that it could reduce the abundance of ARGs in manure, however, some aminoglycoside and sulfonamide resistance genes were enriched during composting [82]. Several of the enriched genes were correlated with int1, which could mean that horizontal transfer was a factor in the enrichment of those genes [82].…”

“…A study by Li et al using a commercial microbial compound during composting found that it could reduce the abundance of ARGs in manure, however, some aminoglycoside and sulfonamide resistance genes were enriched during composting [82]. Several of the enriched genes were correlated with int1, which could mean that horizontal transfer was a factor in the enrichment of those genes [82]. This suggests that the microbial compound used has an influence on the type of ARGs that could be removed or enriched [82].…”

Dissipation Dynamics of Doxycycline and Gatifloxacin and Accumulation of Heavy Metals during Broiler Manure Aerobic Composting

“…However, their dissipation and persistence still remained unclear, especially the depletion and fate of GAT during the broiler composting process. Most of the studies were based on pig manure composting [ 20 , 21 ], and there was limited understanding of broiler manure composting. This study thus examined the accumulation of six metal elements and the fate and depletion of DOX and GAT during the composting process of broiler manure.…”