Diversity and predicted functional roles of cultivable bacteria in vermicompost: bioprospecting for potential inoculum.

Vermicompost (VC) harbours diverse microbes, including plant growth-promoting microorganisms (PGPM) that are beneficial for sustainable crop production. Hence, this study aimed to analyse bacterial diversity of VC samples as a first high-throughput screening step towards subsequent targeted isolation of potential bacterial inoculum candidates. To achieve this, bacterial communities in VC collected from five production farms were enriched in nutrient-rich media before high-throughput sequence (HTS) analysis of the partial 16S rRNA gene. HTS analysis revealed 572 amplicon sequence variants (ASVs) in all enriched VC samples. Firmicutes, Proteobacteria, Planctomycetes and Bacteroidetes were the most dominant phyla, while Lysinibacillus, Escherichia-Shigella, Bacillus, Pseudomonas, Clostridium sensu stricto 1, Morganella, Vibrio and Aeromonas were the predominant genera across the enriched VC. The presence of Clostridium sensu stricto 1, Escherichia-Shigella and Vibrio genera, which are potentially pathogenic species, suggests the need to improve vermicomposting efficiency and safety. Predicted functional profiling of the bacterial communities using PICRUSt2 showed abundance profiles of nitrogenases, phosphatases and sulfatases. In addition, the potential to produce siderophore, indole acetic acids (IAA) and phytohormone regulator 1-aminocyclopropane-1-carboxylate (ACC) were predicted. Lysinibacillus, Bacillus, Paenibacillus and Pseudomonas were major bacterial communities with potential plant growth-promoting traits and could serve as resources in bacterial inoculum production. The findings in this study provide insight into the community composition, abundance and the potential functional capability of cultivable bacterial species of enriched VC. This study also points to VC as a suitable source of potentially beneficial bacterial candidates for inoculum production.

Insights into the Microbiological Safety of Vermicompost and Vermicompost Tea Produced by South African Smallholder Farmers.

Feedstock used in the production of vermicompost (VC) and vermicompost tea (VCT) may harbour various pathogenic bacteria responsible for a number of animal and human diseases worldwide. The identification and characterisation of such pathogenic organisms is necessary for assessing the safety of these products. In the present study, our goal was to determine the presence of possible pathogens in VC and VCT and, if present, to determine the antimicrobial susceptibility profiles of the organisms. VC and VCT samples were collected from five different farms in the Winterveldt, South Africa. Only one out of 60 VC and VCT samples was found to contain a potentially pathogenic organism. The use of phenotypic procedures aided the final identification of the isolate, which was confirmed to be Salmonella enterica serovar Typhimurium. This isolate tested positive for species specific invA genes. Antibiotic testing using the agar diffusion technique showed that the Salmonella isolate was resistant to only kanamycin. The Salmonella counts that were observed in this study were lower than the generally accepted infective doses of these bacteria. In the light of these findings, it was concluded that VC and VCT produced by the farmers involved presented a low risk in terms of the safety of the products.