Energetics, epigenetics, and memory as acclimation strategies of marine bacteria in subzero brines

Abstract

Memory is familiar to us all. Our memories structure our beings and inform how we respond to the present. The principle that memory alters an individual's response to a given stimulus structures the work conducted in this thesis. I ask: why do bacteria respond the way they do to environmental stressors in the Arctic? I set out to enable the study of memory in subzero brines and investigate its existence in a model sea-ice bacterium. As the Arctic transforms at an unprecedented pace, understanding memory in this ecosystem is urgent. Larger fluctuations in environmental conditions will select for organisms with well-suited acclimation mechanisms. Memory appears to be precisely such a mechanism, allowing organisms capable of encoding, storing, and recalling information about past conditions to be more fit in the face of change. Despite the diversity of functions, mechanisms, and timescales in bacterial memory, its ecological role remains obscure. Two Arctic ecosystems provide complementary natural laboratories to investigate the ecological function of memory: cryopeg brines and sea ice. Cryopeg brines are volumes of hypersaline subzero liquid water isolated in permafrost for millennia and relatively stable until the Anthropocene. Sea ice is shorter-lived and fluctuates significantly more. With respect to variability and timescale, they offer a natural contrast in which to study memory.In Chapter 1, I reconstructed the environmental history of heterotrophic bacterial communities in cryopeg brines by developing a model relating cell density, enzyme kinetics, energetic requirements, and available energy. I estimated cell-specific metabolic rates to be higher than those in marine sediments despite lower temperatures, challenging expectations. This high energy cost suggests substantial investment in producing extracellular enzymes to liberate organic carbon and synthesizing protective compounds for cryoprotection and osmoprotection. These results provide context for considering memory: if these bacteria possess memory of a more variable past, does that memory remain after 40,000 years of environmental stability? What are the implications for their capacity to acclimate as permafrost thaws? Such questions motivate an investigation of memory in these and related Arctic environments. The fluctuations experienced by sea ice, especially in a changing Arctic, make it a promising environment in which to begin searching for memory. In Chapter 2, I searched for bacterial memory in Colwellia psychrerythraea strain 34H, a model sea-ice bacterium. Culturing 34H in alternating salinity conditions showed acclimation to repeated stress evidenced by changes in growth rates and lag times, phenotypic evidence suggestive of bacterial memory. I used DNA sequencing to determine whether DNA methylation might serve as an underlying mechanism. DNA methylation clearly regulated gene expression in response to osmotic stress. However, DNA methylation did not clearly emerge as the mechanism for memory in 34H, though further investigation is warranted. Chapter 3 extended this work to the environment by studying DNA methylation patterns of entire sea-ice bacterial communities in situ. Comparing the thermally variable top ice with the more stable bottom ice, I found differential methylation across temperature and salinity gradients in various community members. DNA methylation served multiple roles: immune defense through restriction-modification systems, gene regulation across environmental gradients, and novel roles in prophage-host interactions. The abundance of orphan methyltransferases suggests that much of this methylation was serving purposes beyond classical immune defense. These chapters show the different acclimation mechanisms used by bacteria in subzero brines, from energetic strategies to memory. By understanding what allows bacteria to thrive in these extreme environments on Earth, we push the boundaries for what can be considered habitable, with implications for ice-bound brines on Europa, Enceladus, and Mars. This dissertation lays foundational work for further investigations of memory's ecological role in bacterial communities facing rapid environmental change.