Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera Soda Pans, Zimbabwe

Abstract

The use of metagenomics has substantially improved our understanding of the taxonomy, phylogeny and ecology of extreme environment microbiomes. Advances in bioinformatics now permit the reconstruction of almost intact microbial genomes, called metagenome-assembled genomes (MAGs), from metagenomic sequence data, allowing for more precise cell-level taxonomic, phylogenetic and functional profiling of uncultured extremophiles. Here, we report on the recovery and characterisation of metagenome-assembled genomes from the Buhera soda pans located in eastern Zimbabwe. This ecosystem has not been studied despite its unique geochemistry and potential as a habitat for unique microorganisms. Metagenomic DNA from the soda pan was sequenced using the DNA Nanoball Sequencing (DNBSEQR) technique. Sequence analysis, done on the Knowledgebase (KBase) platform, involved quality assessment, read assembly, contig binning, and MAG extraction. The MAGs were subjected to taxonomic placement, phylogenetic profiling and functional annotation in order to establish their possible ecological roles in the soda pan ecosystem. A total of 16 bacterial MAGs of medium to high quality were recovered, all distributed among five phyla dominated by Proteobacteria and Firmicutes. Of the ten MAGs that were taxonomically classified up to genus level, five of them belonged to the halophilic/ haloalkaliphilic genera Alkalibacterium, Vibrio, Thioalkalivibrio, Cecembia and Nitrincola. Functional profiling revealed the use of diverse carbohydrate-metabolising pathways among the MAGs, with glycolysis and the pentose phosphate pathways appearing to be key pathways in this ecosystem. Several MAGs harboured both sulphur/ sulphate reduction and respiratory pathways, suggesting a possible mechanism of energy generation through sulphur/ suphate respiration. In conclusion, this study revealed a highly taxonomically and functionally diverse microbial community in the soda pans, dominated by halophilic and haloalkaliphilic bacteria.