Understanding the principles and mechanisms underpinning microbial dynamics in changing environments

Abstract

Environmental variation is an inherent characteristic of natural systems. It can influence different ecological (e.g., demography, phenotypic diversity) and evolutionary (e.g., genetic diversity, rate of adaptation) processes and dynamics in microbial organisms. Ultimately, through this influence, environmental variation modulates microbial intra- and inter-specific diversity, shaping ecological interactions at different biological scales (from strain-strain to microbial communities and associated hosts). Under this context, this thesis aims to assess and elucidate the general principles and mechanisms underpinning microbial dynamics in changing environments, using various biological systems (e.g., Escherichia coli or host-associated microbial communities). At the populational level, this study found that microbial patterns and responses to environmental variation (i.e., nutrient source and availability; novel and challenging environmental conditions), are determined by their ability for rapid phenotypic adjustments. These characteristics vary among microbes (i.e., fitness differences driven by intra-specific differences in tolerances and physiological plasticity), as a consequence of functional constraints derived from genetic (e.g., genome size, ribosomal production) and environmental interactions. At the community level, this study found that microbial communities associated with animal hosts inhabiting extreme environments exhibit temporal stability despite the marked physiological stress experienced by the hosts. This suggests the microbial communities are resilient to the external (habitat) and internal (host) environmental (i.e., temperature changes). In addition, this study assessed ecological and evolutionary mechanisms influencing microbial communities associated with diverse animal hosts in highly fluctuating environments. Findings revealed that variation in the microbial community structure is primarily explained by their host taxonomic identity (species or subclass level), evolutionary history, and host ecology (intertidal vertical position and geographical location). Overall, this thesis utilized various approaches and biological systems that encompass broad subjects to offer a deeper understanding of how microbial organisms and their interaction with other entities (microbes or multicellular hosts) respond to temporally dynamic natural environments.