EMERGENCE OF MICROBIAL INTERACTIONS UNDER CHANGING ENVIRONMENTS

Microbial life forms possess diverse adaptive properties. They wield this power not only to adapt to their surroundings but also to reshape their environment actively. This dual capability, while holding the potential for both beneficial and harmful consequences, underscores the dynamic interplay of microbial communities and the environment. At an individual level microbes respond to changes by modifying their behaviors, while at a population level the cumulative adaptation of individuals often transcends individual adaptation and achieve a higher biological fitness than possible by an individual. To comprehend this intricate dance of microbial adaptation, extensive studies have been made connecting external cues to behavior across a diverse spectrum. However, recent studies show a non-homogeneous adaptive response in a (even monoclonal) population under optimal conditions. While this is thought to be linked with alternate forms of adaption, till date, two key areas are not well understood. i) Why do organisms go against inherent adaptive programs, incurring an apparent fitness cost and ii) what are the underlying mechanisms (behavioral and molecular). The doctoral thesis presented here is one of the first experimental investigations of active emergence of microbial adaptation under uniform conditions. Additionally, there is an in-depth outline of mechanistic aspects, that is currently lacking in literature. To conduct the studies, this thesis embarks on a multifaceted journey through the microcosms of microbial life, particularly bacteria and phytoplankton, the main focus being the latter. From an experimental point of view, we developed highly customizable and automated visualization setups such as ‘ocean-on-a-chip’ to visualize phenotypic traits and behavior in real time. Utilizing scientific programming and machine-learning-based image processing, we established custom pipelines for converting raw images into visualizable data through data analysis. Combining the main results, this thesis shows that adaptation in microbes is a variable itself and the underlying mechanism emerges as a combination of single cell, population scale and community scale dynamics. For example, one of the key results reveal the emergence of novel gravitactic subpopulations of phytoplankton even under uniform conditions, challenging the conventional understanding of their behavior governed solely by their internal circadian clock. Mechanistically, we have unraveled that this adaptation is facilitated by self-regulation of the local microenvironment, particularly pH, and is driven by active changes in cell morphology. This knowledge not only deepens our understanding of how phytoplankton adapt, but also sheds light on their ability to mitigate stress under fluctuating pH conditions—a concern relevant to the ongoing changes in oceanic pH due to anthropogenic activities. This study offers a quantitative mechanistic framework for understanding how microbes adapt and evolve under the current climatic and lifestyle shifts and offers the potential to uncover the secrets of microbes and harness their capabilities for the betterment of our world. While this study looks at adaptation of a single species, another key result comes from my research on nutrient starvation response of 2 strains of phytoplankton from the same specie under uniform conditions. These strains, often found to coexist in nature, shows complementary adaptation, mediated by change in swimming strategies, that overall increases the chance of survival of the species by expanding the effective nutrient search area and sunlight harnessing. This is another example of adaptation itself has evolved to being greater than the sum of individual organism, limited not just to a population but occurs collectively across an ecosystem and all the strains available in it. To further verify the nature of adaptation, I undertook another study where I crossed the species barrier and studied another form of microbe, i.e. bacteria. Using the same sets of tools and pipelines I build from my phytoplankton study, I studied bacterial colony adaptation under variable environmental parameters such as temperature. The results indicate that irrespective species, the principles of adaptation remain similar across microbial life and is the basis of my research; to build an unified understanding of adaptation across all life. To do so, I also built custom hardware and software which I will talk about in details later. These setups are flexible; they can be used to address similar questions no matter the specie we study, with lots of customizability that can be used to observe novel behavior if needed.