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

A R Raimi; A C Atanda; O T Ezeokoli; P J Jooste; E Madoroba; R A Adeleke

doi:10.1007/s00203-022-02864-3

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

Arch Microbiol. 2022 Apr 15;204(5):261. doi: 10.1007/s00203-022-02864-3.

Authors

A R Raimi^{1

2}, A C Atanda^{1

3

4}, O T Ezeokoli^{1

2}, P J Jooste³, E Madoroba^{4

5}, R A Adeleke^{6

7}

Affiliations

¹ Microbiology and Environmental Biotechnology Research Group Agricultural Research Council-Institute for Soil, Climate and Water, Pretoria, 0001, South Africa.
² Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2520, South Africa.
³ Department of Biotechnology and Food Technology, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa.
⁴ Agricultural Research Council-Onderstepoort Veterinary Research, Onderstepoort, 0110, South Africa.
⁵ Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa, 3886, South Africa.
⁶ Microbiology and Environmental Biotechnology Research Group Agricultural Research Council-Institute for Soil, Climate and Water, Pretoria, 0001, South Africa. rasheed.adeleke@nwu.ac.za.
⁷ Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2520, South Africa. rasheed.adeleke@nwu.ac.za.

PMID: 35426530
DOI: 10.1007/s00203-022-02864-3

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.

Keywords: Bacterial communities; Biofertiliser; Enzyme-coding genes; High-throughput sequencing; Plant growth-promoting bacteria; Vermicompost.

MeSH terms

Bacillus* / genetics
Bioprospecting
Paenibacillus* / genetics
Phylogeny
Plant Development
RNA, Ribosomal, 16S / genetics

Substances

RNA, Ribosomal, 16S

Grants and funding

132803/National Research Foundation