The organic content of the Columbia River suspended particulate matter (SPM) results from the input of autochthonous (phytoplankton) and allochthonous (terrestrial vascular plants) production. The contribution of these two sources appears seasonal and responds to factors such as rainfall, runoff, river flow, light and nutrients availability. While numerous studies have...
The compositions and loadings of organic matter in soils and sediments from a diverse range of environments along the Fly River system were determined to investigate carbon transport and sequestration in this region. Soil horizons from highland sites representative of upland sources have organic carbon contents (%OC) that range from...
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, YvanAlleau 1**, David 3
Merrell 1‡ 4
Revision of GCA-D-00049 5
Submitted to Geochimica et
The compositions and loadings of organic matter in soils and sediments from a diverse range of environments along the Fly River system were determined to investigate carbon transport and sequestration in this region. Soil horizons from highland sites representative of upland sources have organic carbon contents (%OC) that range from...
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The compositions and loadings of organic matter in soils and sediments from a diverse range of environments along the Fly River system were determined to investigate carbon transport and sequestration in this region. Soil horizons from highland sites representative of upland sources have organic carbon contents (%OC) that range from...
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Soil Location, sampling and site description. Lat. Lon. Alt. Dist. River Zone, Reach
Code Type (m
The compositions and loadings of organic matter in soils and sediments from a diverse range of environments along the Fly River system were determined to investigate carbon transport and sequestration in this region. Soil horizons from highland sites representative of upland sources have organic carbon contents (%OC) that range from...
The compositions and loadings of organic matter in soils and sediments from a diverse range of environments along the Fly River system were determined to investigate carbon transport and sequestration in this region. Soil horizons from highland sites representative of upland sources have organic carbon contents (%OC) that range from...
The decomposition of marine plankton in two-chamber, seawater-filled microbial fuel cells (MFCs) has been investigated and related to resulting chemical changes, electrode potentials, current efficiencies, and microbial diversity. Six experiments were run at various discharge potentials, and a seventh served as an open-circuit control. The plankton consisted of a mixture...
Prevention of wellbore CO₂ leakage is a critical component of any successful carbon capture, utilization, and storage program. Sporosarcina pasteurii is a bacterium that has demonstrated the potential ability to seal a compromised wellbore through the enzymatic precipitation of CaCO₃. Here we investigate the growth of S. pasteurii in a...
Sporosarcina pasteurii is known to produce calcite or biocement in the presence of urea and Ca²⁺. Herein, we report the use of novel ultramicrosensors such as pH, Ca²⁺, and redox sensors, along with a scanning electrochemical microscope (SECM), to monitor a real-time, bacteria-mediated urea hydrolysis process and subsequent changes in...
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, Yvan Allau2, Circe
Verba3, Frederick Colwell2, Marta E. Torres2, Dipankar Koley1,*
1 Department of
Sporosarcina pasteurii is known to produce calcite or biocement in the presence of urea and Ca²⁺. Herein, we report the use of novel ultramicrosensors such as pH, Ca²⁺, and redox sensors, along with a scanning electrochemical microscope (SECM), to monitor a real-time, bacteria-mediated urea hydrolysis process and subsequent changes in...
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. Thurber,b Yvan Allau,b
Circe Verba,c Frederick Colwell,b Marta E. Torresb and Dipankar Koley*a
Sporosarcina pasteurii is known to produce calcite or biocement in the presence of urea and Ca²⁺. Herein, we report the use of novel ultramicrosensors such as pH, Ca²⁺, and redox sensors, along with a scanning electrochemical microscope (SECM), to monitor a real-time, bacteria-mediated urea hydrolysis process and subsequent changes in...
It has been recognized since the 1950's that radioisotopic disequilibrium between naturally occurring parent-daughter isotope pairs in seawater can provide information on the rate of processes segregating them. In the surface ocean, the U-238:Th-234 parent-daughter pair tends to display measurable disequilibrium that is attributable to the effects of scavenging on...
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...
In the last twenty years, human trafficking has gained attention in government agendas and media coverage, while anti-trafficking projects have burgeoned worldwide. Anti-trafficking efforts, however, have almost exclusively addressed the issue of sex trafficking with a focus on rescuing women, while overlooking other types of exploitation. This is noteworthy, given...
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 Lena River in central Siberia is one of the
major pathways translocating terrestrial organic matter (OM)
from its vast catchment area to the coastal zone of the Laptev
Sea and the Arctic Ocean. The permafrost soils of its far
south-stretching catchment, which store huge amounts of
OM, will most...
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– Part 2: Lignin-derived
phenol compositions
Winterfeld, M., Goñi, M. A., Just, J., Hefter, J
Caspian terns (Hydroprogne caspia) and double-crested cormorants
(Phalacrocorax auritus) nest in large colonies on East Sand Island in the Columbia
River estuary, the largest known colonies for the two species in the world. Both
species of piscivorous colonial waterbirds have been identified as predators with a
significant impact on the...
Recent studies of estuarine sediment deposits have focused on grain size spectra as a tool to better understand depositional processes, in particular those associated with tidal inlet and basin dynamics. The key to accurate interpretation of lithostratigraphic sequences is establishing clear connections between morphodynamic changes and the resulting shifts in...
The occurrence of two wildfires separated by 31 yr in the chaparral-dominated Arroyo Seco watershed (293 km²) of California provides a unique opportunity to evaluate the effects of wildfire on suspended-sediment yield. Here, we compile discharge and suspended-sediment sampling data from before and after the fires and show that the...
Water samples along the Washington, Oregon and California coastline were collected using high resolution sampling and analyzed to determine particulate organic carbon and nitrogen concentrations. Over 28 days during August 2011, nearly 1500 samples were collected aboard the R/V Wecoma (W1108C) using a semi-automated filtration system. Additional subsurface samples were...
Three stations, at ∼80 m water depth on the Oregon shelf between 44.7°N and 43.9 N, were studied under hypoxic conditions in late spring and summer of 2009 to determine benthic oxygen consumption rates. Oxygen fluxes were derived from eddy correlation (EC) measurements made from an autonomous lander deployed for...
The hierarchical organization of aggregates in soil is responsible for the presence of inter and intra-aggregate pores. This research aimed to investigate effects of soil surface liming, considering lime rates of 0, 10 and 15 t ha(-1), on the intra-aggregate porous system of soil aggregates with equivalent diameters of 2-4...
Three stations, at similar to ~80 m water depth on the Oregon shelf between 44.7 degrees N and 43.9 N, were studied under hypoxic conditions in late spring and summer of 2009 to determine benthic oxygen consumption rates. Oxygen fluxes were derived from eddy correlation (EC) measurements made from an...
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...
The Agricultural Model Intercomparison and Improvement Project (AgMIP) is a major international effort linking the climate, crop, and economic modeling communities with cutting-edge information technology
to produce improved crop and economic models and the next generation of climate impact projections for
the agricultural sector. The goals of AgMIP are to...
Small, mountainous river systems have been increasingly studied due to their importance as sources of fluvial sediment and organic matter to the coastal ocean. Thus far, studies of small, mountainous river systems have focused on rivers with very high sediment loads. The well-studied Eel River dispersal system in northern California...
Continental margin sediments have been recognized as a major source of dissolved iron to the global ocean. The focus of this study was to build an early diagenetic model that can be used to simulate iron fluxes from continental margins and thereby identify key controlling factors. The model uses the...
Soils contain the largest pool of carbon that is actively cycling on human timescales, leading many to view soils as a natural climate solution with multiple co-benefits. The field of soil science is rapidly evolving, but without a unified understanding of soil carbon dynamics. This dissertation leverages two distinct long-term...
Most oceanographic instruments on the seafloor have no connections with the surface and therefore have to run on batteries and store data until recovery. To demonstrate a developing technology, sensors and acoustic modems were powered with energy harvested from the seafloor, and data were relayed acoustically in near–real time to...
Outcrops of old strata at the shelf edge resulting from erosive gravity‐driven flows
have been globally described on continental margins. The reexposure of old strata allows
for the reintroduction of aged organic carbon (OC), sequestered in marine sediments for
thousands of years, into the modern carbon cycle. This pool of...
Water samples from the Arctic Ocean were analyzed in order to assess the present nature of particulate organic matter and investigate the effect of climate-driven changes on the ecology of the region. 661 individual surface water samples and 216 samples from CTD casts were collected from the Bering, Chukchi, and...
Fisheries bycatch threatens populations of marine megafauna such as marine mammals, turtles, seabirds, sharks and rays, but fisheries impacts on non-target populations are often difficult to assess due to factors such as data limitation, poorly defined management objectives and lack of quantitative bycatch reduction targets. Limit reference points can be...
Swiss needle cast (SNC) is a foliage disease of Douglas-fir caused by Nothophaeocryptopus gaeumannii, an Ascomycete fungus (Mycosphaerellaceae) that causes growth reductions in Douglas-fir plantations across the Pacific Northwest. Epidemiology of the fungus is generally well known in plantation trees, but the relationship between disease expression and foliage nutrition and...
Previous projects in the Gulf of Lion have investigated the path of terrigenous material
in the Rhone deltaic system, the continental shelf and the nearby canyon heads. This
study focuses on the slope region of the Gulf of Lion to further describe particulate
exchanges with ocean’s interior through submarine canyons....
Forest soils contain a substantial portion of global terrestrial carbon stores. Forest management can influence the soil carbon pool and how soil organic matter functions. The long-term productivity of forests is an ongoing goal where land managers utilize biomass and timber. A site-specific understanding of intensively managed forests can ensure...
Rotating disc electrodes (RDEs) exploit the induced flushing of a radially spun electrode to increase the overall rate of analyte flux to an electrode sensing surface and its resulting signal current (i). Here initial efforts to evaluate a rotating platinum (Pt) microelectrode for efficacy as a rapid in situ dissolved...
In ponderosa pine (Pinus ponderosa) forests of the western United States, prescribed fires are used to reduce fuel loads and restore historical fire regimes. The season in which prescribed burns are performed and the interval between burns can have complex consequences for the ecosystem, including soil carbon cycling through the...
We investigated the export of particulate organic matter (POM) to the ocean by two contrasting small, mountainous rivers, the Umpqua and Eel Rivers, by collecting suspended sediment samples over a range of discharges and analyzing them for a variety of constituents, including organic carbon, nitrogen, biomarkers with distinct biochemical sources,...
Polylactic acid (PLA), a renewable material, is used widely in a variety of commercial and specialty applications. However, certain limitations such as high temperature stability and brittleness limit its applicability. This problem is addressed by reinforcing PLA with a variety of materials but the process gives rise to different issues...
Shallow subsurface flow and surface runoff are spatially and temporally variable in forested environments. The location and timing of this runoff depends on both site characteristics (e.g., vegetation, soil texture, geology, and topography) and on time-varying conditions (e.g., soil water content, precipitation type, duration, magnitude, and intensity). Forest management activities...
As part of the International Polar Year research program, we conducted a survey of surface marine sediments from box cores along a section extending from the Bering Sea to Davis Strait via the Canadian Archipelago. We used bulk elemental and isotopic compositions, together with biomarkers and principal components analysis, to...
In this thesis, we develop a simulator for estimating the energy consumed in executing tasks on a mobile device - the Palm Pilot. We measured the energy consumed by each instruction of the device's assembly language and incorporated these measurements into a public domain emulator for the Palm Pilot. This...
Thorough understanding of the mechanisms controlling the temperature structure in the surface mixed layer of the ocean and, in particular, accurate values of sea surface temperature are critical for properly parameterizing air-sea heat exchange and quantifying the amount of heat redistributed below the surface. It is however difficult to obtain...
Sediment cores were retrieved from a landslide-dammed lake, recording events back to the 5th century AD in a forested, mountainous catchment. These cores provide an opportunity to compare the impacts of known recent perturbations, including floods and timber harvesting with those of the early period of the core, flood, fire,...
Small mountainous watersheds are disproportionate sources of land-derived particulate organic matter (POM) to long-term sinks like lake bottoms and the ocean. As such, these ecosystems are an essential component of the global carbon cycle. The burial of POM in lacustrine and marine sediments contributes to the drawdown of atmospheric CO2...
Tannins are a diverse group of plant-produced, polyphenolic compounds with metal-chelating and antimicrobial properties that are prevalent in many soils. Using transcriptomics, we determined that tannic acid, a form of hydrolysable tannin, broadly affects the expression of genes involved in iron and zinc homeostases, sulfur metabolism, biofilm formation, motility, and...
In intensively managed forest plantations in the northern Oregon Coast Range, herbicides are often applied during site preparation and early stand regeneration to reduce competition for resources for planted conifer seedlings. In addition to reducing competition for crop trees, herbicide applications may affect soil processes including decomposition and nutrient cycling,...
Mutation testing is one of the effective approaches measuring test adequacy of test suites. It is widely used in both academia and industry. Unfortunately, the adoption and practical use of mutation testing for Python 2.x programs face three obstacles. First, limited useful mutation operators. Existing mutation testing tools support very...
I compare the seasonal abundance variation, population dynamics, fecundity, egg hatching mechanism and success, and apostome ciliate parasites of the euphausiids Euphausia pac?fica and Thysanoessa spinfera from the Oregon coast, USA. Community structure and nearshore distributions were examined from bi-weekly oceanographic surveys (1970-1972). This region has a strong cross-shelf change...