Dissertation Abstract
Life in the cold biosphere: The ecology of psychrophile communities, genomes, and genes
Bowman, Jeff S 2014 http://blogs.cuit.columbia.edu/jsb2233/
School of Oceanography, University of Washington (United States), 297 pp.
The prevalence of low temperature habitats on Earth makes the ecology of organisms adapted to low temperature environments (psychrophiles) an important area of research. Studies of low temperature ecosystems including the deep sea, sea ice, glacial ice, permafrost, and snow have provided a wealth of knowledge on the resilience of psychrophilic microbial ecosystems in the face of anthropogenic and natural disturbance, the history of microbial life on Earth, and the potential distribution of life in extraterrestrial environments. Taking these three knowledge areas as motivation this dissertation further explores psychrophile ecology.
Chapter 1 introduces the history of research on psychrophiles, and the current state of knowledge regarding sea ice microbial communities, an important ecosystem dominated by psychrophiles. This chapter also explores one method for making the jump from descriptive ecological studies to process-based studies that have predictive power. Chapters 2 and 3 explore the diversity of Bacteria found in two understudied psychrophile habitats; multiyear sea ice and frost flowers. In the first quantitative analysis of sea ice community composition, Chapter 2 describes the multiyear sea ice microbial community as diverse, and in agreement with previous studies, dramatically different from the seawater microbial community. Chapter 3 describes an unusual community of Bacteria in frost flowers, dominated by members of the order Rhizobiales. This metabolic plasticity of the Rhizobiales could have important implications for elemental cycling within young sea ice, particularly for nitrogen and sulfur species, an idea explored through an analysis of metabolic potential in Chapter 4. Chapter 5 describes a new method for evaluating genomic plasticity within any group of genomes, and applies this method to a comparative analysis of psychrophile and mesophile genomes, finding evidence for greater genome plasticity within psychrophile genomes. Application of a molecular clock to horizontal gene transfer events in these genomes suggests a link between cold periods in the Phanerozoic and the rate of retention of genes acquired by psychrophiles. Chapter 6 looks at how psychrophilic enzymes are optimized for low temperatures through amino acid substitutions, and introduces a model for further exploration of amino acid preferences. Experiments with this model suggest a role for serine, preferred in some psychrophile proteins, in adaptation to both low temperature and high salinity. Chapter 7 explores the potential for psychrophiles to degrade alkanes, a major component of crude oil, by the presence of genes coding for alkane hydroxylases. Several likely alkane hydroxylase genes in psychrophiles, not currently annotated as alkane hydroxylases, were identified. Analysis of the protein physical parameters coded by these genes suggests some optimization to low temperature. These findings have important implications for the in situ bioremediation of crude oil in cold environments, and for efforts to develop remediation technologies that function at low temperature.
Chapter 1 introduces the history of research on psychrophiles, and the current state of knowledge regarding sea ice microbial communities, an important ecosystem dominated by psychrophiles. This chapter also explores one method for making the jump from descriptive ecological studies to process-based studies that have predictive power. Chapters 2 and 3 explore the diversity of Bacteria found in two understudied psychrophile habitats; multiyear sea ice and frost flowers. In the first quantitative analysis of sea ice community composition, Chapter 2 describes the multiyear sea ice microbial community as diverse, and in agreement with previous studies, dramatically different from the seawater microbial community. Chapter 3 describes an unusual community of Bacteria in frost flowers, dominated by members of the order Rhizobiales. This metabolic plasticity of the Rhizobiales could have important implications for elemental cycling within young sea ice, particularly for nitrogen and sulfur species, an idea explored through an analysis of metabolic potential in Chapter 4. Chapter 5 describes a new method for evaluating genomic plasticity within any group of genomes, and applies this method to a comparative analysis of psychrophile and mesophile genomes, finding evidence for greater genome plasticity within psychrophile genomes. Application of a molecular clock to horizontal gene transfer events in these genomes suggests a link between cold periods in the Phanerozoic and the rate of retention of genes acquired by psychrophiles. Chapter 6 looks at how psychrophilic enzymes are optimized for low temperatures through amino acid substitutions, and introduces a model for further exploration of amino acid preferences. Experiments with this model suggest a role for serine, preferred in some psychrophile proteins, in adaptation to both low temperature and high salinity. Chapter 7 explores the potential for psychrophiles to degrade alkanes, a major component of crude oil, by the presence of genes coding for alkane hydroxylases. Several likely alkane hydroxylase genes in psychrophiles, not currently annotated as alkane hydroxylases, were identified. Analysis of the protein physical parameters coded by these genes suggests some optimization to low temperature. These findings have important implications for the in situ bioremediation of crude oil in cold environments, and for efforts to develop remediation technologies that function at low temperature.