Metagenomic Analysis Revealed the Changes in Antibiotic Resistance Genes and Heavy Metal Resistance Genes in Phosphate Tailings Compost

Abstract

Phosphate tailings are usually rich in phosphorus and some other mineral nutrients, which is very suitable for composting. In this study, 60 days of composting using phosphate tailings, chicken manure, and straw resulted in a significant decrease in total nitrogen (TN) content from 1.75 ± 0.12 g/kg to 0.98 ± 0.23 g/kg (p < 0.01), with a nitrogen retention of 56%, an increase in water-soluble phosphorus (Ws-P) from 3.24 ± 0.14 mg/kg to 7.21 ± 0.09 mg/kg, and an increase in immediate potassium (AK) from 0.56 ± 0.21 mg/kg to 1.90 ± 0.11 mg/kg (p < 0.05). Metagenomic sequencing showed little changes in the diversity and abundance of microbial communities before and after composting, but changes in species composition and the abundance of archaea, bacteria, and fungi resulted in differences in community structure before and after composting. Composting contributed to a lower gene abundance of ARGs and MRGs. The addition of phosphate tailings combined the functions of chemical regulation and nutrient enrichment, and its synergistic effect significantly optimized the nutrient cycling in the composting system.

Keywords: antibiotic resistome gene; compost; metal resistome gene; microbial community; phosphate tailings.

Figure 1

Bray–Curtis PCoA analysis based on differences in community structure at the microbial genus level before and after composting. (a) Archaea; (b) bacteria; (c) fungi. (A: before composting; B: after composting).

Figure 2

Changes in relative abundance of archaea, bacteria, and fungi at the phylum level prior to and subsequent to composting. (A: before composting; B: after composting).

Figure 3

Changes in relative abundance of microbial metabolic pathways before and after composting; (a) changes in relative abundance of the KEGG secondary metabolic pathway in the composting system; (b) contribution of different species to metabolic pathways; (c) Fisher’s exact test for KEGG secondary metabolic pathways. (A: before composting; B: after composting. *, p < 0.05; **, p < 0.01; ***, p < 0.001).

Figure 4

Changes in abundance of microbial functional genes at different composting stages. (a) Lignin and cellulose degradation genes; (b) phosphorus solubilization functional genes. (A: before composting; B: after composting).

Figure 5

Changes in abundance of resistance genes at different composting stages. (a) Heavy metal resistance genes; (b) antibiotic resistance genes. (A: before composting; B: after composting).

Figure 6

Correlation between resistance gene abundance and microbial abundance. (a) Correlation between heavy metal resistance genes and microorganisms; (b) correlation between antibiotic resistance genes and microorganisms. (*, p < 0.05; **, p < 0.01; ***, p < 0.001).