Larkin, Patrick D.Reese, Brandi KielMullis, Megan2022-04-152022-04-152021-12https://hdl.handle.net/1969.6/90444Microbes play fundamental roles in ecosystem function through mediating biogeochemical cycles, yet we know very little about how microbes interact and what drives community diversity. They form complex communities and engage in a wide variety of biotic interactions. Fundamentally, microorganisms can utilize one or more biosynthetic pathways for survival: 1) outcompete their neighbor(s) by adapting their metabolism to the available resources; 2) work with their neighbor by forming a mutualistic cooperation; and/or 3) remove their competition through inhibition or lysis. My dissertation aims to address microorganism survival mechanisms in the subsurface in a variety of locales. My research chapters incorporate various methods including culture-dependent and -independent techniques that aim to answer what the microbial community diversity is, if any microorganisms are metabolically active, and how microorganisms are surviving within those environments. Many continental and marine subsurface environments were examined for functional genes in microbial communities, with specific focus on sediments collected from Mariana Forearc mud volcanoes and the western flank of the Mid-Atlantic Ridge. The first survival mechanism was identified in cultivated isolates from western flank sediment of the Mid-Atlantic Ridge in which microbial populations could utilize many resources including oxygen, nitrogen, sulfur, and carbon. The second survival mechanism was identified in the Mariana Forearc mud volcanoes where microbial communities were potentially coupling denitrification and anaerobic methane oxidation. The final survival mechanism was identified across many continental and marine subsurface environments using data derived from the Deep Carbon Observatory’s Census of Deep Life and across Bacteria and Archaea, including Methanobacteria, Actinobacterota, Desulfobulbia, Gammaproteobacteria, and Planctomycetes. Many of the genes identified for the third survival mechanism were similar to antimicrobial genes that are used medicinally. Microbial communities in the subsurface environments experience a wide array of environmental conditions even extreme and utilize various resources for metabolism as well as use specific mechanisms that confer a competitive advantage.324 pagesen-USThis material is made available for use in research, teaching, and private study, pursuant to U.S. Copyright law. The user assumes full responsibility for any use of the materials, including but not limited to, infringement of copyright and publication rights of reproduced materials. Any materials used should be fully credited with its source. All rights are reserved and retained regardless of current or future development or laws that may apply to fair use standards. Permission for publication of this material, in part or in full, must be secured with the author and/or publisher.antimicrobialInternational Ocean Discovery Programmarine subsurface biospheremetagenomemetatranscriptomemolecular geomicrobiologyText