Insights into bacterial diversity in compost: Core microbiome and prevalence of potential pathogenic bacteria

Abstract

Fertilizer-replacement programs by the ministry of agriculture and rural affairs are extraordinary actions for environment protection and sustainable agriculture in China. A national-level survey was performed to acquire consensuses of bio-physiochemical properties for composts. A total of 116 compost samples collected from 16 provinces in China were analyzed by high throughput sequencing of bacterial 16S rRNA gene amplicons. The germination index and bacterial alpha-diversity were lower in composts from poultry manure than others. This large-scale survey revealed that bacterial communities were distinct among different composts and slightly explained by pH, moisture and total nitrogen, but not by raw material or composting process. Nevertheless, 26 OTUs affiliated with Firmicutes (Cerasibacillus, Atopostipes and Bacillus) and Actinobacteria (Thermobifida, Actinomadura and Nocardiopsis) were present in most (>90%) composts and majority of these bacterial species were possibly associated with the biodegradation of organic materials. Surprisingly, 629 potential human or animal bacterial pathogens accounting an average of 1.21% of total 16S rRNA gene were detected and these bacteria were mainly affiliated with Helicobacter, Staphylococcus, Acinotobacter, Streptococcus, Mycobacterium and Enterococcus. In summary, this study provides baseline data for the diversity and abundance of core microbiome and potential pathogens in composts.

Keywords: 16S rRNA; Composting process; Microbial diversity; National-level survey; Pathogens.