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Anaerobic microbes and communities in the context of soil and the equine digestive tract

Amy Sanders Biddle, University of Massachusetts Amherst


Soil and herbivore gut environments present different challenges to plant degrading bacteria in terms of nutrient availability, fluctuations in moisture, pH and temperature, and temporal constraints, however complex communities of microbes in each serve similar roles in hydrolyzing and fermenting the diverse components of plant biomass. This dissertation describes four projects with the underlying purpose to further understand the structure and functioning of anaerobic plant degrading communities. (1) A three-year microcosm experiment using enrichment and serial transfers to reduce the diversity of a complex soil community over time, tested the hypothesis that changes in community structure would be consistent across replicate samples and enabled the detection and isolation of persistent community members. (2) A second project to track the changes in bacterial community structure and function that occur during starch induced lactate acidosis in horses identified specific microbes that could be implicated in the recovery and/or resistance to these community changes. (3) Genomic data was used to compare clostridial species inhabiting the gut (belonging to the Lachnospiraceae, and Ruminococcaceae) and those that are free-living (belonging to the Clostridiaceae) to identify metabolic strategies that could enable specialization to a host associated or free-living lifestyle. (4) The genomic sequence analysis of Clostridium indolis, a member of the C. saccharolyticum species group, provided insights into the genetic potential of this poorly described taxa which will drive hypotheses regarding its metabolic and ecological activities and help to resolve distinctions between closely related taxa in this taxonomically confusing clade within the Lachnospiraceae. ^

Subject Area


Recommended Citation

Biddle, Amy Sanders, "Anaerobic microbes and communities in the context of soil and the equine digestive tract" (2014). Doctoral Dissertations Available from Proquest. AAI3615399.