Listeria monocytogenes contamination continues to pose challenges for the food industry and there is demand for effective methods of food preservation and protection that can also be considered clean label. A promising source of antilisterial compounds may be sourced from bacteria that produce novel byproducts. Ribosomally synthesized and post-translationally modified...
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2.4 The ecology of dairy processing
The black-footed ferret is a meso-predator within the Great Plains region of North America. Before the 1900s, black-footed ferret populations were self-sustaining in large ecological patches throughout the geographical range of the Great Plains. During the 1900s, various factors such as the systematic extermination of prairie dogs (the primary food...
Food waste (FW), brewery waste (BW), and fats, oils, and greases (FOG), are prevalent waste streams in municipalities across the country, particularly in the Pacific Northwest (PNW). Anaerobic digestion (AD), the microbial-mediated transformation of organic waste into methane-rich biogas, offers a sustainable, energy-generating, waste management solution for these wastes. Anaerobic...
Kombucha is a fermented sweet tea beverage of Asian origin which has become popular in the West due to its distinct flavor and possible health benefits. Kombucha is fermented by inoculating sweet tea with yeast and bacteria until a pellicle, referred to as a SCOBY (symbiotic culture of bacteria and...
The Northern Rubber Boa (Charina bottae) is a small, secretive boa native to the Pacific Northwest. Despite this being possibly the highest latitude boas and one of only two boas native to the continental U.S., it has received surprisingly little attention. Most of the research on the natural history of...
Two ecologically important lamprey species found in the endorheic Goose Lake Basin face conservation threats; however, relatively little is known about their habitat needs or spatial distribution. Lamprey and their habitat are often found to be patchy; to evaluate these relationships for the lamprey in this basin, I utilized a...
Tooth decay in the form of dental caries and cavities is estimated to be among the most common health conditions globally, with treatment of these oral diseases resulting in a massive, world-wide economic burden. The cause of this demineralization of teeth is rooted in the action of complex microbial biofilms...
Through a desk-top analysis, this research shows that South African women have gained and utilize specialized skills, behaviors, and adaptations through their daily activities which are useful when applied to water resource management. Further, South African women are shown to build and draw on social capital as a way to...
The Goose Lake Basin, situated on the border of Oregon and California, USA, faces significant challenges from drought, wildfire, and other environmental stressors. This region hosts numerous endemic fish species such as the Goose Lake redband trout (Oncorhynchus mykiss newberri), Goose Lake lamprey (Entosphenus sp.), Goose Lake tui chub (Siphateles...
Managed honey bees (Apis mellifera) play a vital role in pollinating cultivated crops worldwide. Honey bee colony declines reported in the past two decades have been associated with stressors such as pests and diseases, pesticide exposure, and poor nutrition. In the wake of these colony declines, beekeepers have strived to...
Microplastics (MPs) are plastic particles less than 5 mm in diameter. These contaminants are increasingly found in the environment due to increased plastic production, use, and improper disposal. Detecting and measuring these contaminants in the environment has proven difficult, requiring the use of fate and transport models to assess MP...
Daikon, mizuna, mizspoona, and komatsuna are novel Asian vegetables for which a market exists in Oregon, especially in the organic sector. However, these crops are currently not grown widely in the area, despite the favorable growing environment of Oregon’s Willamette Valley. Little is known about the appropriate application level of...
Septoria canker remains the most important disease of poplars in intensively managed forest plantations. Genetic resistance has long been considered the best way to manage for this disease. Transgenic resistance mediated by RNA silencing against pathogens and pests (HIGS: host-induced gene silencing) has shown promise in other pathosystems but has...
Streptococcus pneumoniae and Influenza A Virus both primarily infect the upper respiratory tract, with more severe disease occurring during coinfection than would be caused by either pathogen independently. Until recently, characterization of the interactions between these two pathogens has occurred exclusively in the context of a host or using host-derived...
Humans have always been fascinated with whales; from prominent features in mythology, to stories of terrifying monsters on the high seas, to globalized utility, to symbolic wildness and radical environmentalism, to figures and statistics, how have human relationships with whales been understood throughout time? Because humans have a need to...
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...
Deep mixing events in the ocean’s surface layer act as physical drivers of carbon export by detraining dissolved and particulate organic matter, including surface phytoplankton communities, to depth. Once removed from the sunlit surface ocean environment, phytoplankton accumulation rates are dependent on the relative contributions of loss processes, such as...
Coral reefs, found in tropical regions, are renowned for their rich biodiversity and their contributions to ecological, cultural, and economic aspects worldwide. The success of coral reefs hinges on the symbiotic partnership between corals and their dinoflagellate algae, from the family Symbiodiniaceae. The algae reside within the coral host’s gastrodermal...
Since the decline of salmonid populations in the Pacific Northwest, supplementation programs have become frequently implemented by hatcheries as a way to protect and conserve wild stock. However, hatchery-reared fish have lower fitness than wild fish which is likely due to adaptation to the hatchery environment, i.e., domestication selection. Fish...
Early seral forests regenerating from stand-replacing disturbances provide unique habitat for many species in productive, temperate forest landscapes and contribute to supporting biodiversity. Population declines in some species associated with early seral forests have prompted concerns about the conservation of these habitats, particularly the characteristic structural and compositional complexity associated...
Honey bees are vital for our food production and ecosystem due to their critical pollination services. The beekeepers in the United States and worldwide have reported significant colony losses for over fifteen years. Several stressors are implicated in these colony declines, including parasites, diseases, poor nutrition, and pesticide exposure. There...
There has been much discussion in the conservation and policy realms of COVID-19 as a zoonotic disease, or a disease transmitted from wildlife to humans. However, wildlife consumption in China is not only a potential source of disease but also a practice embedded in complex beliefs about health. This paper...
Continental shelf sediments are sinks for dissolved oxygen and sources of many major and minor nutrients required for oceanic surface primary production, resulting in a strong coupling between benthic and pelagic biogeochemical cycling. However, the influence and spatiotemporal variability of benthic remineralization on bottom-water chemistry and the supply of nutrients...
Oregon's estuaries are important ecosystems for scientific study. Consequently, knowledge of what research has been conducted helps us identify benchmarks and plan new projects. A comprehensive bibliography of published research, technical reports, local documents, and data sets is one means of recording this knowledge. For these reasons, the Guin Library...
Oregon's estuaries are important ecosystems for scientific study. Consequently, knowledge of what research has been conducted helps us identify benchmarks and plan new projects. A comprehensive bibliography of published research, technical reports, local documents, and data sets is one means of recording this knowledge. For these reasons, the Guin Library...
Oregon's estuaries are important ecosystems for scientific study. Consequently, knowledge of what research has been conducted helps us identify benchmarks and plan new projects. A comprehensive bibliography of published research, technical reports, local documents, and data sets is one means of recording this knowledge. For these reasons, the Guin Library...
Oregon's estuaries are important ecosystems for scientific study. Consequently, knowledge of what research has been conducted helps us identify benchmarks and plan new projects. A comprehensive bibliography of published research, technical reports, local documents, and data sets is one means of recording this knowledge. For these reasons, the Guin Library...
Oregon's estuaries are important ecosystems for scientific study. Consequently, knowledge of what research has been conducted helps us identify benchmarks and plan new projects. A comprehensive bibliography of published research, technical reports, local documents, and data sets is one means of recording this knowledge. For these reasons, the Guin Library...
Oregon's estuaries are important ecosystems for scientific study. Consequently, knowledge of what research has been conducted helps us identify benchmarks and plan new projects. A comprehensive bibliography of published research, technical reports, local documents, and data sets is one means of recording this knowledge. For these reasons, the Guin Library...
Oregon's estuaries are important ecosystems for scientific study. Consequently, knowledge of what research has been conducted helps us identify benchmarks and plan new projects. A comprehensive bibliography of published research, technical reports, local documents, and data sets is one means of recording this knowledge. For these reasons, the Guin Library...
Over the last several decades, potato production has increased globally as it has been recognized as an important component to improving food security. However, potato production has been continuously challenged by pests. Current pest management practices rely heavily on chemical pesticides. Unfortunately, the overuse of pesticides can be harmful to...
Grapevine Trunk Diseases (GTDs) are caused by a group of fungal pathogens that attack the xylem tissue of mature grapevines worldwide. In the past 30 years, their incidence has increased, both in emerging grape-producing regions, as well as those with an extended history of viticulture. In the same time span,...
Beginning in 2020, the International Maritime Organization International Convention for the Prevention of Pollution from Ships (MARPOL) required vessels to comply with new sulfur air emission standards in Sulphur Emission Control Areas (Baltic Sea, North Sea, and off the coasts of the US and Canada) by: 1) using 0.1% sulfur...
Natural products have long been an important source of resources for humans. Many of these compounds possess unique chemical structures and potent biological properties. By targeting natural products with specific chemical properties, we can gain a better understanding of the roles these compounds play in the environment and their interactions...
Rhizopus microsporus is a globally ubiquitous opportunistic human and plant pathogen that is known to harbor endosymbiotic bacteria. Differences between populations of clinical and environmental R. microsporus isolates have yet to be assessed on a global scale. Whole-genome sequence data were used to explore fungal biology and to assess potential...
Copper and iron are essential micronutrients that are required by marine primary producers for a variety of metabolic processes. Over 99% of both copper and iron are bound within organic complexes in the marine environment, however the molecular identity of many of these complexes remains unknown. The speciation of these...
The red tree vole (Arborimus longicaudus) is an arboreal Arvicoline rodent endemic to conifer dominated forests of western Oregon and northwestern California. While commonly associated with old forests, often inhabiting stands over 80 years old, tree voles have also been found in young forests between 20 and 80 years old....
Anthropogenic induced climate change is predicted to alter distribution of existing plant populations. As plants migrate over space and time, populations often fragment and contract, affecting basic elements of population dynamics (e.g., population size, gene flow, genetic diversity, etc.). Little is known, however, how these impacts on plant species will...
In Oregon perennial and annual grass seed cropping systems conservation management practices and their impacts on soil health and soil microbial community is not well understood. There is strong motivation to employ conservation tillage and other conservation practices to curb atmospheric carbon levels and improve soil health. However, the few...
The seafood industry has a problem of underutilization of harvested and processed fish. Up to 60% of the weight of the fish is considered a byproduct that is typically made into fishmeal for livestock and aquaculture feed, a low-value and non-food grade product. Two species that make up major fisheries...
A dissertation describing the results of a series of greenhouse experiments conducted to better understand phytoremediation in stormwater bioretention systems.
Southeast Alaska is located on the traditional territory of the Lingít, Haida, and Tsimshian People. It is comprised of the largest temperate rainforest in the world, with subregions receiving over 500 cm of rain annually. Climate change is predicted to alter the region's timing, type, and magnitude of precipitation and...
In the United States, children from underserved racial/ethnic backgrounds encounter greater environmental risk both in terms of the physical environment (e.g., housing quality, access to resources like health services and jobs, and exposure to environmental toxins) and the social environment (e.g., social support, neighborhood crime, racism, and discrimination), due to...
The effects of fire on above-ground forest systems have been extensively studied. However, research on fire effects on belowground processes is lacking. While the soil microbiome is understood to be vital to conifer growth and regeneration, the complexity of soils means that research on the topic has largely been accomplished...
In the past fifty years, per- and polyfluoroalkyl substances (PFASs) have become alarming global pollutants. In 2019, the United States (U.S.) Environmental Protection Agency (EPA) ultimately classified them as emerging contaminants and established an action plan to address PFAS and protect public health through developing, identifying, monitoring, and remediating current...
Oomycete and fungal pathogens threaten food, fiber, and forests around the world. With climate change, these pathogens are expected to emerge more frequently. Evolution can facilitate their emergence through mechanisms such as mutations that change or expand host range. Characterizing evolutionary mechanisms in plant pathogens will contribute to our ability...
The intricate relationship between wildlife health and the quality of their environment is well established, with technological advances increasing our understanding and aiding the unraveling of underlying mechanisms. Large herbivores require forage of sufficient quality to maintain their condition to reproduce and survive, all while warding off parasites and predators...
Ocean deoxygenation is predicted to increase in severity over the next few decades, posing a threat to marine life and fishing economies. Improved predictions of ocean deoxygenation depend on a better understanding of the biogeochemical mechanisms that underly this process. Within the realm of biogeochemical mechanisms, this project specifically investigated...
Sound is a crucial aspect of the underwater environment for fishes – various species use sound to communicate, identify predators, navigate, and many other activities needed for survival in their habitat. Disruptions and disturbances in the natural soundscape can have important impacts on all these activities and are likely to...
Following their extirpation due to the maritime fur trade, northern sea otter (Enhydra lutris kenyoni) reintroduction in the 1960s has facilitated their recolonization in southeast Alaska. Sea otters are now sympatric with wolves (Canis lupus), which are widespread in southeast Alaska, and a colonizing coyote population (Canis latrans). Recent studies...
Toxin production by cyanobacterial harmful algal blooms (cyanoHABs) in freshwater systems has lasting ecological and human impacts. Nutrients, light availability, hydrology, and microbial community composition impact the frequency and intensity of toxic cyanoHABs. Climate change will exacerbate toxic cyanoHABs, making real time and predictive monitoring a vital tool for managing...
Rhizopogon salebrosus is an abundant ectomycorrhizal fungus common throughout Western North America that forms mutualistic partnerships with Pinus species. Studied for its systematics, use in sapling nurseries, post-fire seedling establishment, and unique evolutionary history, R. salebrosus holds many secrets within its genome. This thesis aims to characterize the mating system,...
Ceratonova shasta is a myxozoan fish parasite that impacts hatchery and wild populations of salmon and trout in the Pacific Northwest. Levels of the parasite in river water can be effectively monitored through direct filtration of parasite spores from water, extraction of total "environmental DNA" (eDNA), then quantitative polymerase chain...
Marine heatwaves (“MHWs”) are discrete periods of anomalously warm ocean conditions that can lead to shifts in the distribution and abundance of marine organisms. Low-trophic level, pelagic forage species are frequently among those affected by MHWs, often resulting in considerable impacts upon their predators. In the North Atlantic Ocean, Atlantic...
Managing invasive species is vital to preserving native species and maintaining the integrity of environments and ecological roles. Rats are one of the most prolific and intrusive invasive species that have successfully cohabitated with humans over centuries as we have expanded and advanced our societies. Thus, rats have historically been...
For university students, academic misconduct policies are designed to promote learning and protect the university’s reputation. Misconduct consequences can impact students’ grades, finances, and even visa status. While elements of such policies are similar across institutions, there are uneven reporting patterns within institutions, leaving some students more vulnerable to these...
The phylum Cnidaria contains three main branches: Anthozoa (corals, sea anemones) Medusozoa (jellyfish, hydra), and Endocnidozoa. This latter branch is characterized by parasitism and contains the microscopic fish-parasites Myxozoa. Myxozoa are highly simplified, consisting of only a few cell types, however they have retained the nematocyst stinging cells and complex...
Phytophthora ramorum is the causal agent of Sudden Oak Death (SOD), which is an economically and environmentally important disease causing up to 80% mortality of tanoaks in Pacific Northwest coastal forests (LeBoldus et al., 2022). There are currently four clonal lineages in the United States and Europe, named North America...
Little is known about the fall and winter ecology of hibernating bats in western North America. Filling knowledge gaps for these populations has become more urgent with the westward spread of the white-nose syndrome, a disease that infects bats during hibernation. Due to the thermal requirements of the fungal pathogen...
Vineyards in Oregon’s Willamette Valley are predominately planted to perennial grass cover in the alleyways of vineyards. This grass cover is grown to increase worker and equipment traction, as well as reduce erosion and manage vine vegetative vigor. However, with increasing frequencies of drought and warming temperatures, the use of...
Natural products (a.k.a. secondary metabolites) are produced by living organisms that are not essential for their growth, development, or reproduction, but may play a role in their survival or adaptability in nature. Many secondary metabolites isolated from plants and microbes have found use as molecular probes, drug leads, or medicine...
As coral reefs continue to experience decline from human-related stressors, the countless species that depend upon them for food and shelter are likely to follow, constituting a loss of one of the most biodiverse ecosystems on the planet. Though laboratory studies of corals remain difficult, promising model organisms may hold...
Grasslands in the Pacific Northwest are characterized by seasonally wet, acidic soils that mainly support cool season grasses and a limited number of legume species. A major limitation to efficient animal production in grass-dominant pastures is the decline in the herbage growth rate and nutritional quality of forage from late...
The objective of this study is to evaluate the potential of removing organic carbon and inorganic nitrogen contaminants, and metals from the leachate prior to any land application. New guidelines are needed to ensure the environment and our health is not put at risk. The cost of installation, operation and...
The body of work aims to contribute to the area of Quantitative analysis in Environmental Sciences, and is focused on the microbiome. The underlying theme for the dissertation is methods and workflow. The unique bioinformatics workflow used for the analysis of genomic data was used to answer distinct and pressing...
Background/Purpose: US public health, criminal justice, and many other social and scientific processes are affected by the quality of data obtained about death. Yet, little research has focused on how death investigations are conducted. The overall goal of this research was to examine the process by which information was obtained...
Common bean (Phaseolus vulgaris L.) comes in a huge assortment of fresh and dried varieties, including snap beans, kidney beans, and pinto beans. Together, these and other market classes provide a third of the daily dietary protein in some cultures, particularly in Africa, Asia, and developing nations in the Americas....
Null networks are a type of random graph that is favored for the analysis of a wide variety of real-world networks, including gene-regulatory networks, food webs, and species co-occurrence matrices. As a hypothesis-generating tool, null networks are invaluable because they can reveal network motifs and unusual large-scale properties of networks...
Following European-American colonization of North America and associated landscape changes, barred owls (Strix varia) underwent a dramatic expansion of their historical range. The barred owl expanded across the previously tree-less Great Plains that had limited their distribution, and into the forests along the west coast. In these western forests they...
Micro-plankton are a crucial component of pelagic food webs, responding rapidly to environmental changes, and providing a first step in the acquisition and transfer of nutrients to life in the ocean. In addition to the uptake of carbon, phytoplankton provide essential fatty acids (FAs) that can limit the growth of...
Black stain root disease (BSRD) is a vascular wilt disease of conifers caused by three varieties of the native, insect-vectored fungal pathogen, Leptographium wageneri (L. wageneri var. wageneri, L. wageneri var. ponderosum, and L. wageneri var. pseudotsugae). Although morphological, physiological, and ecological characteristics differ among the three varieties of L....
Understanding how spatial variation in climate correlates with phenotypic variation among individuals may offer insights about local adaptation, population performance, and species’ response to climate change. Desert bighorn sheep (Ovis canadensis nelsoni) in the Mojave Desert of southern California experience a broad range of temperature and aridity, inhabiting mountain ranges...
Based on current trends both pesticide and plastic production are expected to continue to rise in the coming decade. A growing global population coupled with the effects of climate change are the main drivers of increased pesticide use. Throughout this dissertation pesticides refer to herbicides, fungicides, and insecticides. Plastic production...
Buddleja davidii (butterfly bush) is a highly adaptable landscape plant known for pollinator attraction. Unfortunately, it is also regarded as an invasive plant in highly disturbed environments across the globe. It is an invasive species in Oregon, officially classified as a class B noxious weed in 2004. Currently the state...
Pseudomonas aeruginosa is a ubiquitous environmental microbe, opportunistic pathogen, and a highly social organism. P. aeruginosa utilizes a wide array of cooperative behaviors to adapt to the environmental conditions around it. These behaviors include quorum sensing (QS), a form a cell-to-cell signaling that coordinates the expression of secreted products in...
Hydraulic conductivity of hemp stems under water-stress conditions was investigated. When plants face with water-stress conditions, embolies (cavitation) are triggered in xylem channels and water transport from the root to the leaves is affected. The relation between percentage loss of water transfer ability within the xylem channels can be described...
Xanthomonas hortorum pv. carotae (Xhc) is an epiphytic, plant pathogenic bacterium that causes the disease bacterial blight of carrot (Daucus carota subsp. sativus). Infection with Xhc can result in blighting of leaves and umbels and reduce quality and yield of carrot seed crops. Carrot production in the United States approaches...
The field of toxicology is challenged with a vast number of environmental chemicals and mixtures to which humans and ecosystems are exposed with limited toxicity data available. Chemical hazard assessment traditionally utilizes mammalian models and can be both cost- and time-limiting and may pose ethical concerns. To rapidly tackle this...
This dissertation investigates the microbial diversity and factors influencing the assembly of microbial communities in kombucha production, using a combination of 1H Nuclear Magnetic Resonance Spectroscopy, 16S and ITS rRNA metabarcoding, and traditional culture-based microbiological methods. It also explores the diversity of kombucha starter cultures through shotgun sequencing and metabarcoding...
Consistent with its charge under Oregon House Bill 3543, the Oregon Climate Change Research Institute (OCCRI) conducts a biennial assessment of the state of climate change science, including biological, physical, and social science, as it relates to Oregon and the likely effects of climate change on Oregon. This sixth Oregon...
Bibliographia Bopyridarum is prepared and maintained by John Markham, Arch Cape, Oregon, USA. Any reports of errors or omissions are greatly appreciated. Please contact Dr. Markham with suggestions: jmarkham@seasurf.net This file is updated annually.
Molecular phylogenetic and chemical analyses, and morphological characterization of collections of North American Paraisaria specimens support the description of two new species and two new combinations for known species. P. cascadensis sp. nov. is a pathogen of Cyphoderris (Orthoptera) from the Pacific Northwest USA and P. pseudoheteropoda sp. nov. is...
Post-Consumer Recycled (PCR) resin grades have been successfully incorporated into plastic ink supply cartridges, with 80% of cartridge products containing 45% to 70% recycled polyethylene terephthalate (rPET). With this tremendously successful experience, incorporation of recycled polypropylene (rPP) into Injection Stretch Blow Molding (ISBM) bottles has been attempted to increase sustainability...
Juvenile Chinook Salmon (Oncorhynchus tshawytscha) leave the natal reach at different times and move downstream at different rates which can increase their productivity by allowing them to utilize habitats on different temporal scales and spreading risk of localized stochastic events. This life history diversity can also allow fish to adapt...
Fungi and Actinobacteria are essential actors in global biogeochemical cycles of carbon and nutrients, and have both been recently appreciated for their roles in marine ecosystems. However, the diversity and distribution of these ubiquitous, but low-abundance microbes in deep-sea habitats remains poorly understood, particularly in chemosynthetic habitats such as methane...
Sea otters act as valuable indicators of ecosystem health and consume prey items that contain anthropogenic microparticles, including microplastics. Microplastic ingestion can exert a wide range of deleterious effects depending on the organism and plastic type. We investigated the ingestion of microparticles by wild sea otters (Enhydra lutris) in Alaska...
Here the diversity and phylogeny of the genus, Sthereus Motschulsky, 1845, and its nearest associates in the large subfamily Molytinae are explored through molecular and morphological characters. Sanger sequencing of five genes determined that Sthereus is not monophyletic. Instead, the one species in the genus Gastrotaphrus Buchanan 1936, G. barberi...