Phenotypic and genomic stability in a halophilic model organism

Abstract

Although microbial adaptation to new environments has been studied extensively in laboratory evolution experiments, less is understood about how natural strains adapt to new, constant laboratory conditions after transitioning to become model organisms. In this dissertation, I took a cross-sectional approach to query the osmotolerance repertoire of a decades-old model halophilic archaeon compared with recently isolated conspecific natural isolates. Using growth rate reaction norms and whole genome sequencing, I found that fitness is highly variable across gradients in total salinity and ion composition for both laboratory and natural strains. Although we expected divergent reaction norms and genome sequences to support evidence of specialization in the model organism, both the model and natural isolates shared similar growth patterns across conditions and shared >95% sequence similarity. In the following chapters, I characterize the hypersaline environment in the Great Salt Lake, quantify osmotolerance phenotypes across three gradients in salinity, and I explore gene expression signatures across an ion composition gradient in H. salinarum NRC-1. I close by comparing fitness profiles and genome sequences of the model and natural strains, and I address the unexpected similarity among strains, even after eliminating contamination as an explanation. Ultimately, despite at least 50 years of evolutionary opportunity between the lab and natural isolates, we find that osmotolerance phenotypes and nucleotide sequence is largely maintained in the laboratory, and that a decades-old model organism remains a relevant study organism for microbial-environmental response.