Browsing by Subject "Comparative Genomics"

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    Meddling with Marinobacter: Microbial Interactions with the Environment
    (2018-06) Bonis, Benjamin
    Despite inhabiting a wide variety of biomes and conditions, relatively little work has been devoted to the genus Marinobacter beyond isolation and initial characterization. The broad range of tolerances displayed by the Marinobacter suggest a metabolically diverse clade with great potential for biotechnological use and environmental study. In addition to hydrocarbon degradation and the synthesis of wax esters, many strains have been found to influence the redox state of metals and oxidize cathodes. Ubiquitously found and readily cultivated, a surfeit of genomic sequences and metadata are available for this genus, though little effort devoted to curation during deposition. Here we utilize 71 public and private Marinobacter genomes to curate the taxonomic and phylogenetic status of these strains, and use comparative genomics to assay the core and pangenome content and how it relates to the demonstrated plasticity of this genus. We find a number of strains erroneously assigned or lacking species identifiers, and offer an updated taxonomy. We also find a deeply branching clade of psychrophilic Marinobacter, suggesting a dearth in the continuity of sequence space of the genus. Due to their extensive distribution and abundance, of particular interest regarding the Marinobacter is the contribution to elemental cycling through extracellular redox chemistry. Utilizing a novel species of Marinobacter isolated from the Soudan Iron Mine in northern Minnesota, we develop a model system to better interrogate the interactions of Marinobacter with the environment. Characterization, development of a robust genetic system, and the establishment of Marinobacter subterrani strain JG233 as an Fe(II)-oxidizing bacterium additionally provides a model organism for the assessment of environment-microbe interactions. Using the techniques optimized in Marinobacter subterrani, genetic systems were developed for an additional 6 strains of Marinobacter to assess essential gene profiles across a genus using transposon mutant libraries. Comparative essential gene profiling using strains from diverse biomes of isolation provides the foundational tools to begin assessment of the effect of environment on gene content, regulation, and conditional essentiality.