Mining the microbiome of Lake Afdera to gain insights into microbial diversity and biosynthetic potential

Ermias Sissay Balcha; Michael C Macey; Mesfin Tafesse Gemeda; Barbara Cavalazzi; Adugna Abdi Woldesemayat

doi:10.1093/femsmc/xtae008

Mining the microbiome of Lake Afdera to gain insights into microbial diversity and biosynthetic potential

FEMS Microbes. 2024 Mar 7:5:xtae008. doi: 10.1093/femsmc/xtae008. eCollection 2024.

Authors

Ermias Sissay Balcha^{1

2}, Michael C Macey³, Mesfin Tafesse Gemeda², Barbara Cavalazzi^{4

5}, Adugna Abdi Woldesemayat²

Affiliations

¹ School of Medical Laboratory Science, College of Health Sciences, Hawassa University, 16417, Hawassa, Ethiopia.
² Biotechnology and Bioprocess Center of Excellence, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, 16417, Addis Ababa, Ethiopia.
³ Astrobiology OU, School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, MK7 6AA, United Kingdom.
⁴ Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy.
⁵ Department of Geology, University of Johannesburg, Johannesburg, South Africa.

Abstract

Microorganisms inhabiting hypersaline environments have received significant attention due to their ability to thrive under poly-extreme conditions, including high salinity, elevated temperatures and heavy metal stress. They are believed to possess biosynthetic gene clusters (BGCs) that encode secondary metabolites as survival strategy and offer potential biotechnological applications. In this study, we mined BGCs in shotgun metagenomic sequences generated from Lake Afdera, a hypersaline lake in the Afar Depression, Ethiopia. The microbiome of Lake Afdera is predominantly bacterial, with Acinetobacter (18.6%) and Pseudomonas (11.8%) being ubiquitously detected. A total of 94 distinct BGCs were identified in the metagenomic data. These BGCs are found to encode secondary metabolites with two main categories of functions: (i) potential pharmaceutical applications (nonribosomal peptide synthase NRPs, polyketide synthase, others) and (ii) miscellaneous roles conferring adaptation to extreme environment (bacteriocins, ectoine, others). Notably, NRPs (20.6%) and bacteriocins (10.6%) were the most abundant. Furthermore, our metagenomic analysis predicted gene clusters that enable microbes to defend against a wide range of toxic metals, oxidative stress and osmotic stress. These findings suggest that Lake Afdera is a rich biological reservoir, with the predicted BGCs playing critical role in the survival and adaptation of extremophiles.

Keywords: Lake Afdera; biosynthetic gene clusters; metagenomics; microbiome; secondary metabolites; shotgun sequencing.