Browsing by Subject "Microbial communities"
Item Ecological, evolutionary, and behavioral determinants of gut microbiomes in Malagasy mammals(2018-09-24) Perofsky, Amanda Claire; Meyers, Lauren Ancel; Di Fiore, Anthony; Lewis, Rebecca J; Ochman, Howard; Scott, James G; Wilke, Claus OMammalian gut microbial communities govern host development, metabolism, immune function, and physiology, through interactions that range from commensal and mutualistic to pathogenic. However, we know little about the relative contributions of vertical, horizontal, and environmental transmission to gut microbiome composition, despite its importance to host health. To address this knowledge gap, I integrated field-collected data, molecular analyses, and computational and statistical approaches to examine how social networks and proximity to other host species influence bacteria transmission and gut microbiome composition in the wild mammals inhabiting Kirindy Mitea Biosphere Reserve in western Madagascar. In Chapter 1, I estimated the impacts of multilevel social structure, individual demographic traits, diet, scent-marking, and habitat overlap on gut bacteria acquisition in a wild lemur population (Verreaux’s sifaka, Propithecus verreauxi). The gut microbiomes of wild sifaka clearly reflected their social group membership, and both grooming and scent-marking behaviors promote microbial exchange and within-host diversity. In Chapter 2, I extended this work by examining how sifaka social dynamics influenced gut microbial turnover within individual animals and social groups over the course of several years. Sifaka social groups harbored distinct gut microbial communities throughout the study period, and compositional changes in the microbiota of individual animals were influenced by the gain or loss of unique social partners and dispersal between groups. In Chapter 3, I assayed the gut microbial communities of six sympatric (i.e., co-occurring) mammal populations— three lemur and three non-primate species – and assessed evolutionary, dietary, and behavioral predictors of microbiome functionality and composition. The ecological relationships among mammalian gut microbiomes mirrored their hosts’ phylogeny, with the three lemur species clustering separately from the other mammal species. The predicted functionality of lemur microbiomes differentiated according to diet, and distantly-related terrestrial mammals exhibited overlapping microbial communities, suggesting that ground dwelling facilitates the indirect horizontal transmission of gut bacteria among sympatric wild mammals. Together, these findings demonstrate that patterns of gut microbiome composition in wild mammals are scale-dependent: host phylogeny, diet, and substrate use shape microbial variation among sympatric mammal taxa, while social groupings and social contacts constrain the horizontal transmission of gut bacteria within a single host populationItem Microbial responses to CO₂ during carbon sequestration : insights into an unexplored extreme environment(2014-05) Santillan, Eugenio Felipe Unson; Bennett, Philip C. (Philip Charles), 1959-; Cardenas, Bayani; Shanahan, Timothy M; Omelon, Christopher R; Altman, Susan JWhen CO₂ is sequestered into deep saline aquifers, significant changes to the biogeochemistry of the system are inevitable and will affect native microbial populations both directly and indirectly. These communities are important as they catalyze many geochemical reactions in these reservoirs. We present evidence that the injection of CO₂ will cause a large scale disturbance to subsurface microbial populations which will ultimately affect the solution and mineral trapping of CO₂ as well as the movement of CO₂ charged water through the subsurface. Representative subsurface microorganisms including a Gram negative bacterium (G⁻), two Gram positive bacteria (G⁺), and an archaeon were tested for CO₂ survival at pressures up to 50 bar and exposure times up to 24 hours. CO₂ tolerance varied but shows effects on microbes is more complex than just decreasing pH and is not significantly dependent on cell wall structure. Imaging reveals that CO₂ disrupts the cytoplasm possibly from changes to intracellular pH. The geochemical effect of CO₂ stress is a decrease in metabolic activity such as Fe reduction and methanogenesis. Subsurface microbial populations interact with the surrounding reservoir minerals which likely influence their ability to survive under CO₂ stress. When the G⁻ organism was grown in the presence of a mineral substrate, survival depended on the mineral type. Quartz sandstone provided a good substrate for survival while kaolinite provided a poor substrate for survival. Biofilms on quartz sandstone were rich in extracellular polymeric substances (EPS) that likely act as a barrier to slow the penetration of CO₂ into the cell. The release of toxic metals from mineral dissolution at high PCO₂ enhanced cell death. To understand the long term effects of CO₂ on microbial communities, water samples were taken from CO₂ springs in the western United States and compared to unaffected springs. Community 16S rRNA sequence data suggests that CO₂ exposed environments exhibit lower microbial diversity, suggesting environmentally stressed communities. However, differences among diversity in the springs surveyed also indicates other environmental factors that affect diversity beyond CO₂. Furthermore, the isolation of a novel fermentative Lactobacillus strain from a CO₂ spring, indicates viable microbial communities can exist at high PCO₂.Item Overcoming antibiotic resistance in microbial populations : an interdisciplinary perspective(2015-08) Kaushik, Karishma Surendra; Gordon, Vernita DianeAntibiotic resistance is a major public health problem. The increase in antibiotic-resistant bacteria and decline in the approval of newer antibiotics has prompted the need for novel therapeutic approaches. In the environment and in the human body, microbes are exposed to varying spatial landscapes. Further, bacteria assemble into multicellular assemblies called biofilms, which possess intricate spatial structure. Inherent to this spatial structure, microbial communities also possess population structure, characterized by cell density, spatial organization, and different cell types. This dissertation has three main goals: i) to study the effect of microbial population structure on the survival of antibiotic resistant mutants, using P. aeruginosa, an opportunistic human pathogen as a model organism, ii) to evaluate the therapeutic potential of using bicarbonate to enhance the efficacy of aminoglycoside antibiotics, first-line agents for P. aeruginosa infections, and develop an improved method of analysis of drug interactions iii) to develop a low-cost, hands-on, educational module to characterize antimicrobial compounds using an interdisciplinary, biophysical approach.