Abstract
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.
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Acknowledgements
The authors are grateful to the Agricultural Research Council for providing the platform to execute the research project. The Centre for High-Performance Computing (CHPC), South Africa, is acknowledged for providing computational resources for this study (Project number CBBI1183)
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This study was supported by the National Research Foundation (Thutuka grant unique number 84168 and Competitive Support for Rated Researchers- grant number -) 116251).
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Supplementary file1 Rarefaction curve for sequence reads from all data sets normalised to an even depth of 44000 sequences indicates sufficient subsampling was achieved to capture the diversity in all data sets. VC1–5 denote enriched VC samples from farms 1–5 (JPG 124 KB)
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Raimi, A.R., Atanda, A.C., Ezeokoli, O.T. et al. Diversity and predicted functional roles of cultivable bacteria in vermicompost: bioprospecting for potential inoculum. Arch Microbiol 204, 261 (2022). https://doi.org/10.1007/s00203-022-02864-3
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DOI: https://doi.org/10.1007/s00203-022-02864-3