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. 2020 Nov 3:11:592592.
doi: 10.3389/fmicb.2020.592592. eCollection 2020.

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

Ke Li  1 , Rui Cao  1 , Shangkun Mo  1 , Rensheng Yao  2 , Zhuqing Ren  1 , Jian Wu  1
Affiliations

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

Ke Li et al. Front Microbiol. .

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 × 103 to 1.13 × 108 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.

Keywords: 16S rRNA sequencing; aerobic composting; antibiotic resistance genes; compound microbial inoculants; swine manure.

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Figures

Figure 1
Figure 1
Physicochemical changes during swine manure composting. (A) Temperature, (B) moisture, (C) pH, (D) TC, (E) TN, and (F) C/N in the two treatment conditions during the composting process. CK: the swine manure composting. AB: add 1% compound microbial agents in the swine manure composting.
Figure 2
Figure 2
Abundances of tetracycline resistance genes during swine manure composting. (A–C) refer to the upper, middle, and lower layers of compost, respectively. CK: the swine manure composting. AB: add 1% compound microbial agents in the swine manure composting. 0, 1, 2, 5, 12, and 32 are the days for composting.
Figure 3
Figure 3
Abundances of ARGs and MGEs during swine manure composting. (A–C) refer to the upper, middle, and lower layers of compost, respectively. CK: the swine manure composting. AB: add 1% compound microbial agents in the swine manure composting. 0, 1, 2, 5, 12, and 32 are the days for composting.
Figure 4
Figure 4
Structure and abundance of flora at the phylum level. CK: the swine manure composting. AB: add 1% compound microbial agents in the swine manure composting. D1 represents the mesophilic phase, D2 represents the thermophilic phase, and D32 represents the maturation phase.
Figure 5
Figure 5
Heat map of species abundance at the genus level in compost. CK: the swine manure composting. AB: add 1% compound microbial agents in the swine manure composting. D1 represents the mesophilic phase, D2 represents the thermophilic phase, and D32 represents the maturation phase.
Figure 6
Figure 6
Relative abundance changes of human pathogenic bacteria (HPB) during composting. CK: the swine manure composting. AB: add 1% compound microbial agents in the swine manure composting. D1 represents the mesophilic phase, D2 represents the thermophilic phase, and D32 represents the maturation phase.
Figure 7
Figure 7
Redundancy analysis between environmental factors and microbial community structure (phylum level). CK: the swine manure composting. AB: add 1% compound microbial agents in the swine manure composting. D1 represents the mesophilic phase, D2 represents the thermophilic phase, and D32 represents the maturation phase.
Figure 8
Figure 8
Correlation between antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial community. CK: the swine manure composting. AB: add 1% compound microbial agents in the swine manure composting. D1 represents the mesophilic phase, D2 represents the thermophilic phase, and D32 represents the maturation phase.
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