In host-associated microbiomes, the mechanisms that regulate community composition or the principles that govern dynamics remain far from clear. However, understanding how the structure of microbial communities shift as the system moves away from a healthy state is critical to assessing disease progression and to formulate any potential mitigation strategy....
The marine psychrophilic bacterium Vibrio marinus MP-4
possessed a maximum temperature and hydrostatic pressure of
20 C and 425 atm for growth. The effects of temperatures of 21 and
25 C and hydrostatic pressures of 200, 400, 500, and 1,000 atm on
protein, RNA and DNA synthesis by V. marinus...
The relationship of temperature and salinity to protein synthesis
was determined for cells of Vibrio marinus, MP-1. Protein synthesis
was measured by the incorporation of radioactive proline into
hot trichloroacetic acid precipitable material. At all salinities protein
synthesis occurred at 15°C and 20°C but not at 25°C. The critical
temperature...
Renibacterium salmoninarum produces bacterial kidney
disease (BKD) in salmonid fish. Soluble antigen(s) (SA) produced
by the bacterium was characterized by physicochemical,
functional and immunological methods. The molecular weight
determination by SDS-PAGE analysis of SA yielded 14 different
molecular weight species. Seven of these species were
prominent, 57 kd protein being...
A great deal of research has been focused on the microbiomes of terrestrial angiosperms (flowering plants), but much less research has been performed on the microbiomes of aquatic angiosperms (Turner et al. 2013). Eelgrass beds are extremely productive ecosystems that provide habitat for many marine organisms, such as fish, shellfish,...
Escherichia coli K12, UC41 (an auxotroph) and UC175 (a wild type)
were used to determine possible relationships between binding, uptake,
and respiration and minimum growth temperature.
Both E. coli strains had a minimum growth temperature of 8.0 C in
glucose minimal medium when cells were previously grown at 15 C....
The focus of this thesis is to design, characterize, and apply novel computational methods and molecular systems to interrogate heterogeneous human gut microbiome-related phenomena. In Chapter 2, I design, implement, and characterize a method for embedding co-occurrence patterns derived from massive 16s amplicon datasets. I use this method to 1....
The freshwater polychaete Manayunkia speciosa was identified as an obligate host of the salmonid parasite Ceratomyxa shasta in 1997, prompting increased research on the small benthic invertebrate. Ceratomyxa shasta infection in fish can cause mortality, and presents a disease risk for both hatchery and wild salmon and trout. Ceratomyxa shasta...
Research on natural environments, over the last decade, is replete with microbial diversity studies that used culture-independent approaches. The cloning and sequencing of the 16S rRNA genes has been the driving force in the expansion of awareness about the great diversity of previously undiscovered microorganisms. Well-known uncultured groups of microorganisms...
Some enzymes of the citric acid cycle and glycolytic pathway
in cell-free extracts of Vibrio marinus MP-1 were compared for
thermal lability. After one hour of moderate temperature exposure,
enzymes of both pathways rapidly lost catalytic activity. For all
but one enzyme, 50 percent remaining activity occurred near an
averaged...
Comparatively little work has been done on bacterial lipids.
There are profound differences between bacterial lipids in general
and lipids of the higher forms of life in such respects as the absence
of sterols, phospholipids low in nitrogen but high in inositol
and carbohydrate, the presence of large proportions of...
Four-fold partially purified glucose-6-phosphate dehydrogenase
(G-6-PDH) from the obligately psychrophilic marine bacterium
Vibrio marinus was effected by thermally induced leakage of the
enzyme, ammonium sulfate fractionation and column chromatography
on Sephadex G-200 gel.
The effects of temperature, pressure, salinity, and pH were
determined for the various degrees of enzyme purity....
Proper immune function is indispensable, as failure to mount an immune response against a pathogen can lead to serious complications or even death. T cells act by enhancing the activation of phagocytic cells as well as the activation of B cells. Their widespread influence on an immune response makes optimal...
Corals provide a diversity of ecosystem services, are among the most biologically diverse ecosystems on Earth, and directly support ~500 million people globally; however, corals are increasingly experiencing significant threats and are undergoing severe bleaching events as the result of the warming climate. Using a two-year data set surrounding a...
Microbial-induced calcite (CaCO₃) precipitation (MICP) is a well-known natural phenomenon where microbes precipitate calcite in their environment as a result of metabolic activity. It has recently been of interest as a bioengineered technique to stabilize soils for construction applications. A known metabolic pathway to induce MICP is ureolysis, where introduced...
Investigations of 16S rRNA gene sequences hallmark modern microbiology. These sequences provide culture-independent insight into the abundance and distribution of microbiota and serve as a principle resource through which microbial community diversity is measured. Consequently, researchers rely on 16S gene sequences to test hypotheses rooted in ecology, evolution, and disease....
The in vitro effects of cortisol in regulating salmonid B cell functions were
investigated. B cells at three distinct stages of differentiation were examined for
cortisol sensitivity. B lymphocyte responses were examined 1) during the early stage
of the precursor, 2) during the intermediate stage of differentiation associated with
clonal...
This research has focussed upon both the in vitro and in vivo characterization
of the recycling pathway leading from 5'-deoxy-5'-methylthioadenosine
to methionine in fruit. In addition to contributing towards polyamine
biosynthesis and other important cellular functions, in plant tissues
these events also serve to generate the hormone ethylene. A broad...
The role of viral proteins in the pathogenesis of infectious hematopoietic necrosis
virus (IHNV) was studied at the molecular level. The expression of the viral genes at the
protein and RNA level, and their cellular localization, were characterized to further our
understanding of viral pathogenesis. The pathogenic effect of individual...
Limnology is undergoing a transition to high-throughput -omic analysis of freshwater
bacterial communities. An important first step in making the transition is to
characterize several genomes that can be used as references to guide metagenome
assembly and analysis. Here I characterize four new freshwater cyanobacterial
genomes, a pair of lake...
In this thesis, we examined the effects of the exposures to anthropogenic pollutants on the fish, primarily juvenile chinook salmon, immune system using newly and recently developed immune assays. In addition, we developed a new assay for measuring immunocompetence of fish. In the first chapter, the Alamar Blue assay was...
Little is known about the virulence factors of Renibacterium
salmoninarum, the causative agent of salmonid bacterial kidney disease.
The predominant protein produced by R. salmoninarum in broth culture or
during infection is a 57/58 kDa protein (p57) which is associated with strain
virulence. In this study monoclonal antibodies (MAbs) to...
Cell-based biosensors are function-based detectors that use the physiological response of a living cell to sense biologically stimulating agents. This emerging technology extends the application of current detection methods by reporting on the toxicity of a sample and the potential to cause disease. Previously, Betta splendens erythrophores have been described...
Freshwater systems cycle carbon along a spatial and temporal biogeochemical continuum, across which ecosystem processes contribute to transformations of organic matter (OM). Various ecological constraints impact rates OM transformation and production and consumption of the energetic end of respiration, methane. Microbiological processing and complete reduction of carbon substrates to methane...
Marine sediments are vast sources and reservoirs of methane, a potent greenhouse gas. Most of this methane is anaerobically oxidized by archaea before it can reach the overlying ocean, though the efficiency of this process often depends on methane fluxes and mechanisms of fluid transport. Anaerobic methanotrophic archaea, or ANME,...
On coral reefs, disturbances rarely occur in isolation. Global stressors such as increasing seawater temperature often coincide with local stressors like nutrient pollution. In the face of increasing anthropogenic stress, corals can function as environmental sentinels, although little is known about how multiple stressors interact to disrupt their associated bacterial...
Biotic and abiotic processes at continent-ocean interfaces cycle a disproportionate mass of carbon and nutrients relative to their global surface area, and microbial activity is a principal determinant of organic and inorganic matter flux in these transition zones. Most studies using modern high-throughput ‘omics techniques to link microorganisms with costal...
The combined activities of diverse heterotrophic marine microorganisms significantly shape global biogeochemical cycles, but models of these activities are currently limited to aggregate microbial community processes, and it remains unclear how community structure and the functional roles of specific microbial taxa should be integrated into these models. Therefore, understanding the...