A µBUG’S LIFE: STUDIES OF MICROBIAL PHENOTYPIC ADAPTATIONS AND INTERACTIONS IN VARIED HOSTS AND ENVIRONMENTS

Microbes (such as bacteria and archaea) have colonized essentially all environments on Earth, from soil and plants to the human body, they play pivotal roles in biogeochemical cycling, host health, and ecosystem structuring. These communities are constantly subjected to environmental shifts, nutrient fluctuations, and host-derived factors that drive dynamic changes in their metabolic activity and community structure. Understanding microbial phenotypic adaptations, how microbes transition between dormant and active states, interact with hosts, and adapt to environmental variability, is essential for understanding the complexity of host-microbe associations and predicting how these interactions influence host health and ecosystem stability.

This thesis, through three independent studies, investigates microbial phenotypic adaptations and interactions response to variability in the environment, host or inter-species dynamics. First, a novel cultivation-dependent approach, BONCAT-Live, was developed to selectively isolate metabolically active microbes from complex environments by combining bioorthogonal non-canonical amino acid tagging (BONCAT) with optimized parallel cultivation. This approach was successfully validated in three dynamic ecosystems- thawing Arctic subsurface, and with more rapidly changing host-dependent dynamic environments such as Populus rhizosphere and human oral microbiome. In the second study, I investigated plant-microbe dynamics to assess how is root-microbiome is assembled in different soil-origins and how resilient or dynamic these communities are with respect to changes in the host and soil. Lastly, in the third study, I characterized a specific host-epibiont interaction between Desulfomicrobium and SR1, in a first ever observed interaction of an SR1 member with a deltaproteobacterium. This study resulted in successful cultivation of SR1 with its host. Together, this work demonstrates cultivation-dependent and independent approaches in studying microbial responses to variability in host and environments.