Exploring environmental adaptations and habitat preferences in three microbial lineages using comparative (meta)genomic approaches

Abstract

The utilization of -omics based approaches (metagenomics, genomics, transcriptomics, proteomics, and metabolomics) in the field of microbiology has greatly advanced our understanding of the microbial world. The utilization of such approaches, either on pure cultures, or directly on environmental samples has provided novel insights into the role of microorganisms in earth biogeochemical cycles, microbial evolutionary dynamics, and their potential biotechnological applications. In the field of microbial pathogenesis, informatics-based methods have helped in uncovering several venues of pathogenesis including pathogens strain-specific characteristics, virulence genes, antimicrobial resistance, and understanding the landscape of various diseases.

Here, I present my 3 research projects based on exploiting various -omics based approaches to understand the ecology, evolution, and pathogenic determinants of various groups of cultured, and yet- uncultured microorganisms. In chapter I, I implemented genome-resolved metagenomics to elucidate the ecological roles, metabolic capabilities, and physiological preferences of a novel yet-uncultured microbial phylum recovered from enrichments of tertiary oil reservoir. I showed that this lineage is a slow-growing member of rare biosphere and an aminolytic halothermophilic organism. We proposed creating a new candidate phylum "Mcinerneybacteriota" to accommodate this organism. This work has been published in the journal “Systematic and Applied Microbiology”. In chapter II, I analyzed multiple genome-resolved metagenomes of uncultured Group 18 Acidobacteria to understand their biogeochemical roles and elucidate the key evolutionary innovations that enable Acidobacteria to thrive in soil ecosystems. I demonstrated that soil-dwelling genera were characterized by larger genomes, higher CRISPR loci, expanded CAZyme machinery, possession of a C1 metabolism, and a sole dependence on aerobic respiration, whereas nonsoil genomes encoded a more versatile respiratory capacity and potential for utilizing the Wood-Ljungdahl (WL) pathway as an electron sink. This work is published in the journal “Applied and Environmental Microbiology”. Lastly, my third project (Chapter III) is about utilizing genomics and transcriptomics for an intracellular pathogen, Coxiella burnetii, to understand the changes in its genes crucial for intracellular success during long-term culturing in an axenic media. Here, I showed the expression changes and mutations in multiple genes that are known or most likely predicted to be crucial to their normal intracellular growth lifestyle or pathogenesis.