Niche adaptations of the vibrionaceae, from the coastal ocean to the laboratory

Abstract

Microorganisms play a significant role in biogeochemical cycling, thus their dynamics in the environment influence the biosphere. Yet how do features of the environment - such as abiotic conditions, resources, and predators - influence their activity and abundance, i.e. what constitutes their ecological niche? This study examines this question for members of a diverse marine heterotrophic family of bacteria, the Vibrionaceae. In chapter 2, I review the current knowledge of the environmental conditions and habitats in which Vibrionaceae populations are found. Through a meta-analysis of Vibrio abundance and bulk environmental variables, I show that temperature and salinity are strong correlates of Vibrio, but the patterns vary among species. By contrast, other commonly measured abiotic variables, like nitrogen and phosphate, are only weak correlates. Studies furthermore show that Vibrio engage in a diversity of lifestyles, from free-living to attached, in a wide range of habitats, though the patterns have largely not been characterized at a genetic or molecular scale. These observations motivate a finer-scale investigation of the microbial niche. In chapter 3, I explore how a single Vibrio strain is adapted to growth on different ecologically relevant resources, using nutrients extracted from habitat models - the copepod Apocyclops royi, and the brown alga Fucus vesiculosus - as well as the algal constituent, alginate. By selecting a transposon-mutant collection for growth on these resources, I find that Apocyclops is a replete resource, whereas Fucus is intermediate to Apocyclops and alginate in its anabolic requirements; that catabolic pathways have redundancy, which anabolic ones lack, that appears to mask fitness effects; and more generally, that these habitats contain complex resources that buffer fitness costs relative to growth on single carbohydrate resources. In appendix A, I determine how environmental phage isolates recognize the Vibrio strain: by its extracellular polysaccharide capsule. Losing the capsule enables the strain to resist infection from these bacteriophage; however, it suffers the tradeoff of becoming susceptible to others. By integrating environmental observations and genetic methods, this thesis provides an intimate view of the life of a marine microorganism.