Progress 01/01/24 to 12/31/24
Outputs
Target Audience:During the 2024 reporting period, the project primarily reached (1) academic and scientific researchers in the fields of environmental chemistry and watershed science, and (2) natural resource managers and agency collaborators working in the Upper Klamath Basin. 1. Academic and scientific research community: In 2024, project efforts were focused on data analysis and interpretation of the chemical fingerprinting dataset generated during the 2023 field season. The results were prepared for presentation at a national scientific meeting, targeting researchers working at the intersection of chemical monitoring, non-target analysis, and watershed management. The audience was selected to ensure that the methods and results reached peers who are actively developing or applying similar approaches. These interactions helped refine our interpretation, validate methodology, and establish future collaborations. Results were presented at the SETAC (Society of Environmental Toxicology and Chemistry) North America meeting, which served as the primary outreach venue for academic dissemination during this period. 2. Regional resource managers and agency collaborators: Preliminary results were also shared informally with staff from the U.S. Geological Survey (USGS) Klamath Falls office and the Klamath Irrigation District (KID), who were involved in the 2023 fieldwork and remained interested in the outcomes. These partners represent key stakeholders who manage surface water and irrigation infrastructure in the Upper Klamath Basin. Communication with this audience focused on early interpretation of chemical patterns and potential implications for identifying dominant sources contributing to water quality issues in the lake. These interactions helped maintain continuity with past collaborators and supported ongoing integration of science into local decision-making. Changes/Problems:During the 2024 reporting period, the project underwent a strategic shift in approach under Objective 3. Based on findings from the 2023-2024 data analysis, we determined that dissolved organic chemical fingerprints are not suitable for tracing terrestrial phosphorus sources due to high variability and rapid transformation in surface waters. This conclusion was supported by separate research within the lab group, which showed that microbial activity significantly alters organic chemical composition during transport. As a result, the project has transitioned from a dissolved organic chemical source-tracking approach to a sediment-based fingerprinting approach focused on elemental composition. Sediment is expected to provide a more stable and time-integrated indicator of source origin. A new graduate student was hired in late 2024 to lead this phase of the project, and sediment sampling and elemental analysis are planned for the next reporting period. This change in scope was submitted to and formally approved by the agency. No major problems, delays, or additional changes are expected. What opportunities for training and professional development has the project provided?During the 2024 reporting period, the project supported professional development opportunities for two graduate students. Daphne Guo, an M.S. student in Biological and Ecological Engineering, completed data analysis, defended her thesis, and presented findings from the project at the 2024 SETAC North America meeting. Conference participation provided experience in scientific communication, peer networking, and exposure to other research in the field of non-targeted chemical analysis and watershed science. Daphne also participated in internal and external discussions to interpret multivariate data outputs and refine her results for publication and presentation. In addition, a new graduate student (Corey De la Cruz) was recruited and onboarded in late 2024 to begin work on the next phase of the project, focused on sediment fingerprinting. The student received training in project background, chemical forensics concepts, and standard lab practices related to solid-phase extraction and sample preparation. Planning and logistical coordination for 2025 fieldwork began during this period, giving the student early exposure to field study design and collaboration with agency partners. These activities contributed to building technical skills, scientific literacy, and professional engagement for both graduate researchers. How have the results been disseminated to communities of interest?Daphne Guo presented results from the 2023 field season and 2024 data analysis at the Society of Environmental Toxicology and Chemistry (SETAC) North America annual meeting. Her presentation focused on the use of non-negative matrix factorization (NMF) to identify dominant chemical patterns across the Upper Klamath Basin and discussed the limitations of non-targeted organic chemical fingerprints for source tracking. This venue provided an opportunity to share findings with a national audience of scientists working on chemical monitoring, environmental forensics, and water quality. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, the project will begin the sediment fingerprinting phase to advance Objective 3: tracing the terrestrial origins of chemical loadings into Upper Klamath Lake (UKL). We will collect sediment samples from known source areas across the Upper Klamath Basin, including eroded agricultural fields, canal and drainage outflows, tributary beds and banks, and relatively undisturbed reference sites. These source sediments will be compared to depositional sediments from within Upper Klamath Lake. All sediment samples will be analyzed for elemental composition rather than organic compounds, with the goal of identifying geochemical markers that differentiate source types. In addition to laboratory analysis, we will apply existing machine learning classification tools to develop a predictive model capable of assigning unknown UKL sediment samples to their most likely source category. This approach builds on our prior experience with supervised classification techniques and will be used to evaluate whether elemental fingerprints provide a reliable, spatially explicit tool for sediment source tracking. Sampling protocols and site selection will be finalized in consultation with regional stakeholders and land managers. This next phase is intended to address the limitations identified in the prior year's work with dissolved organic chemical data, which were found to be too dynamic for tracing terrestrial phosphorus sources.
Impacts
What was accomplished under these goals?
3) Trace the terrestrial origins of chemical loadings into Upper Klamath Lake. In 2024, efforts under this objective focused on analyzing the non-targeted chemical data collected during the 2023 field season to evaluate whether organic chemical fingerprints could be used to trace phosphorus source areas within the Upper Klamath Lake (UKL) sub-basin. Daphne Guo, an M.S. student in Biological and Ecological Engineering, completed her thesis based on this dataset and successfully defended in December 2024. Her work used non-negative matrix factorization (NMF) and other multivariate tools to examine spatial and temporal patterns in chemical composition across surface waters in the basin. Her results identified three major chemical factors, one of which (NMF1) was dominant across the majority of samples regardless of land use or sample location. The widespread presence of this factor--across canals, rivers, springs, and lake sites--suggested that the organic chemical profile in surface waters is shaped by region-wide processes rather than discrete, local sources. A second factor (NMF2) appeared more seasonally driven, with stronger expression during spring runoff events. A third, more sporadic factor (NMF3) was observed near developed areas and road crossings but was not consistent enough to use for source attribution. Overall, Daphne's work concluded that non-targeted organic chemical profiles reflect broader ecosystem functions and chemical cycling dynamics but do not provide a reliable means of tracing landscape-specific phosphorus sources. Separate research conducted by another student within the lab, working on a different dataset, identified that microbial processing in surface waters significantly alters the composition of dissolved organic chemicals over short timescales. These findings helped explain the patterns observed in Daphne's work and confirmed that organic molecules are not stable enough for use in source tracking applications aimed at identifying terrestrial phosphorus inputs. As a result of these combined findings, the project has shifted its approach under Objective 3. A new graduate student was hired in late 2024 to develop a sediment fingerprinting framework that focuses on more stable chemical and elemental markers. Sediment sampling is planned for the next reporting period and will support efforts to identify terrestrial sources of phosphorus and other nutrient loadings to UKL.
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Progress 01/01/23 to 12/31/23
Outputs
Target Audience:The primary target audiences reached during this reporting period included (1) water managers and technical staff within the Klamath Basin, (2) students and educators at Chiloquin High School, and (3) agency collaborators and scientific partners involved in regional monitoring programs. These audiences were engaged through regular field coordination, mentorship, and collaboration during the 2023 field season. 1. Water Managers and Staff in the Klamath Basin: Project personnel coordinated directly with the Klamath Irrigation District (KID) to plan sampling routes and access canal locations throughout the irrigation season. Early in the project, we met with KID staff to present our proposed work and identify shared objectives. We maintained contact with KID staff throughout the summer, particularly for logistics and sample access. This audience was targeted due to their role in managing irrigation infrastructure and interest in understanding how canal systems contribute to regional water quality. 2. Chiloquin High School Students and Educators: Two students from Chiloquin High School were hired on stipend to assist with water sample processing from April through October. Samples were delivered to the high school every two weeks, where students helped with vacuum filtration and labeling under supervision. Their chemistry teacher, Aaron Martin, provided lab space and partnered with the graduate student to integrate water quality sampling and chemical concepts into classroom instruction. This audience was targeted to provide exposure to environmental chemistry and research practices in a rural school setting. The collaboration also supported development of a small ecotoxicology teaching module based on project methods. 3. Agency Collaborators and Scientific Partners: Fieldwork on Upper Klamath Lake was coordinated closely with the USGS Klamath Falls office, who were conducting regular sampling for harmful algal blooms and nutrients. Our team worked from the USGS boat during lake sampling days, reducing sample volumes to 60 mL (from the originally planned 1000 mL) to accommodate onboard storage constraints. This adjustment improved sample handling and processing efficiency. We maintained biweekly contact with USGS field personnel from April to October, exchanging updates and coordinating efforts. These collaborators were engaged to ensure complementary data collection and build alignment with ongoing monitoring work in the basin. These audiences were reached primarily through in-person collaboration during fieldwork, with biweekly sampling efforts between April and October. All three groups played an active role in shaping the success of the sampling campaign and contributed to ongoing conversations about chemical forensics, water quality monitoring, and educational outreach in the Upper Klamath Basin. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?he project provided training and professional development opportunities primarily through graduate student involvement in all aspects of fieldwork and early-stage data processing. Daphne Guo, an M.S. student in Biological and Ecological Engineering, led field sampling from April to October 2023, coordinating biweekly trips in collaboration with the USGS and managing logistics with the Klamath Irrigation District. She developed and implemented field protocols, including modifications to sample volumes and mobile solid-phase extraction (SPE) techniques to accommodate remote sampling conditions. In addition to field training, Daphne gained experience with lab workflows, QA/QC practices, and early-stage data management in preparation for non-targeted mass spectrometry analysis. She was involved in optimizing extraction and instrument methods for the newly acquired high-resolution mass spectrometer (Sciex ZenoTOF 7600+), including coordination with OSU core facility staff and external collaborators. Daphne also developed mentorship skills by supervising two high school students from Chiloquin High School, who assisted with sample processing throughout the summer. This included biweekly visits to the school, where students helped with filtration and labeling under her guidance. She also worked with their chemistry teacher to integrate water quality sampling into an ecotoxicology module for classroom use. Together, these activities supported the professional development of a graduate researcher in fieldwork design, interagency coordination, laboratory methods, mentoring, and scientific communication. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we plan to analyze the chemical data collected in 2023 to identify diagnostic chemical fingerprints associated with different source types and landscape gradients within the Upper Klamath Lake sub-basin. This will involve processing the high-resolution mass spectrometry data, applying multivariate and machine learning techniques, and interpreting chemical patterns in the context of watershed processes. Preliminary findings will be shared with collaborators and prepared for presentation at a scientific conference, likely the Society of Environmental Toxicology and Chemistry (SETAC) North America meeting in 2024. Additional sampling or follow-up analyses may be conducted as needed to support interpretation of results.
Impacts
What was accomplished under these goals?
The accomplishments for the 2023 reporting period are listed below: 1 & 2) Generate diagnostic chemical fingerprints that are indicative of specific sources and various landscape gradients within the Upper Klamath Lake sub-basin. The primary focus of the 2023 reporting period was completion of a full field sampling season and setup of laboratory instrumentation to support chemical fingerprinting work. From April to October, water samples were collected every two weeks at eight locations on Upper Klamath Lake (UKL) in coordination with USGS field staff. In addition, single or repeated grab samples were collected from major tributaries (Wood, Williamson, and Sprague Rivers), springs, winter floodwaters from agricultural fields, and the Wood River Wetland. Within the Klamath Irrigation District (KID), six canal sites were sampled six times between June and October. An additional ten canal locations were sampled once in August to capture chemical gradients along the irrigation system. Samples were also collected from the Klamath River and the Lost River to allow for comparison between natural and managed waterways. All water samples were processed using solid-phase extraction (SPE) for non-targeted chemical analysis. Due to logistical constraints during field operations, sample volumes were reduced from 1000 mL to 60 mL. This adjustment improved filtration times and reduced handling error while maintaining analytical quality. Approximately 180 unique water samples were processed and archived. A high-resolution mass spectrometry instrument (Sciex ZenoTOF 7600+), housed at Oregon State University, was brought online and optimized for non-targeted environmental chemical analysis. Instrument methods were finalized, including column selection and MS acquisition settings, and data collection was initiated by the end of the reporting period. 3) Trace the terrestrial origins of chemical loadings into Upper Klamath Lake. No work was conducted on Objective 3 during this reporting period. Planning and coordination with collaborators to support this objective are ongoing and will be implemented in the next phase of the project.
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Progress 01/01/22 to 12/31/22
Outputs
Target Audience: The target audience reached by our efforts during this reporting period include the following: 1. Water managers, specifically from the Klamath Irrigation District. We met in person to present our proposed research, to discuss shared goals and objectives, and coordinate with staff for their assistance during field sampling. 2. Chiloquin High School: We collaborated with Aaron Martin to share a module on water quality with several of his classes. We also hired two high school students on stipend to assist with water sample processing throughout the summer (April - October). Changes/Problems:In order to collect samples on Upper Klamath Lake, we coordinate with USGS, who collect harmful algal bloom samples as well as nutrient samples. We agreed to exachange data to increase the value of both data sets. Our collaborators asked us to minimize the size of our sampling. They were unable to accomodate an ice chest for our 1000 mL samples, so we updated our sample protocol to reduce the volume. This process took additional time but was ultimately an asset. As a result, the samples were easier to filter and process, which reduced the processing time. All of this reduced handing time and thus errors associated with the processing. Preliminary results indicate that the data are high quality, which will increase our ability to answer our questions. What opportunities for training and professional development has the project provided? Training: Daphne Guo, the graduate student on this project, completed a field season from April to October in the Klamath Basin. The sampling focused on sampling in conjunction with the USGS on Upper Klamath Lake. Because of covid restrictions and because of the need to collaborate with other agencies, we developed a mobile laboratory and changed the sampling methods to facilitate analysis of smaller water volumes (e.g., 60 mL vs 1000 mL). Professional development: Daphne Guo was able to create and maintain collaborative working relationships with research personnel and management from the Klamath Falls USGS office and Klamath Irrigation District, with contact to receive samples and report on research progress roughly every 2 weeks during the sampling period (late April to early October). She also maintained a mentorship role with two Chiloquin high school students who assisted with sample processing (on stipend), and a more collegial role with their chemistry teacher (e.g. sharing of relevant lab materials, collaboration on an ecotoxicology module for students). Daphne trained two high school students at Chiloquin High School how to process the samples. Every two weeks, Daphne brough the samples to the High School where the two students met under the supervision of staff at the high school. The students helped process the samples gaining exposure to wet chemistry lab practices. Daphne also attended the national SETAC (Society of Environmental Toxicology and Chemistry) conference to establish a greater network. How have the results been disseminated to communities of interest?The samples have been collected, processed in the lab, and run on the instrument. The data are currently being processed and will be presented in 2024. What do you plan to do during the next reporting period to accomplish the goals? Generate diagnostic chemical fingerprints that are indicative of specific sources. In the 2024 calendar year, we plan to further collect and analyze samples (~10 each) to build chemical fingerprints for each of the following sources: wetlands, river sediments, and pumped winter flooding from agricultural fields. Determine whether irrigation canals provide similar ecological functions as natural flowing waters. Time and funding permitted, we may sample the same locations as in 2023 for a replicate dataset, possibly earlier in the year. Trace the terrestrial origins of chemical loadings into Upper Klamath Lake. We plan to carry out an extensive sediment sampling campaign in the spring of 2024, as soon as it is safe to travel to the Klamath Basin and collect sediment from the rivers (i.e. some weeks after spring thaw and highest flows in the rivers). Planned sampling sites include 8-10 sites each on the Wood, Williamson, and Sprague Rivers, and Recreation Creek on UKL's northwest side.
Impacts
What was accomplished under these goals?
There are three goals (one was altered, see Changes/Problems section) associated with this project, and the accomplishments associated with each are presented below: 1. Generate diagnostic chemical fingerprints that are indicative of specific sources. Water samples from 8 locations on Upper Klamath Lake (UKL) were taken and processed 12 times throughout the sampling period (Apr-Oct), to be analyzed for the presence of specific sources. Water from three main tributaries (Williamson River, Sprague River, Wood River), several springs, winter floodwaters from a local farm, and the Wood River Wetland were also sampled as sources of chemicals to UKL. Six locations on irrigation canals within the Klamath Irrigation District were sampled six times later in the sampling period (June - Oct) that will, while not being a true source of chemicals to UKL, provide a chemical signature for irrigation water within the region. Solid-phase extraction and mass spectrometry were performed on these water samples to obtain their non-target organic chemical composition. 2. Determine whether irrigation canals provide similar ecological functions as natural flowing waters. Twelve (12) samples along the length of the Lost River were collected and processed, along with ten (10) samples along the length of the Klamath Irrigation District canals and five (5) along part of the Klamath River below UKL. Solid-phase extraction and mass spectrometry were performed on these water samples to obtain their non-target organic chemical composition. 3. Trace the terrestrial origins of chemical loadings into Upper Klamath Lake Upon discussions with collaborators at Oregon State University and within the Klamath Basin (including the USGS), we decided to reach this goal through sediment sampling of UKL's tributaries and in other land use areas (e.g. agriculture, forest) in the basin. Samples will first be extracted for adsorbed organic content (and subsequently processed as the Jones Lab does for water samples), then analyzed using ICP-MS for its elemental make-up.
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Progress 01/01/21 to 12/31/21
Outputs
Target Audience:The target audiences reached by our efforts during this reporting period include the following: 1. Farming stakeholders (Family Farm Alliance) and water managers (Klamath Water Users Association, Klamath Irrigation District): Zoom meetings were held to introduce ourselves, present our proposed research, and present preliminary results. 2. Local farmers: Individual farmers and ranchers were contacted to identify potential properties to collect water samples during the 2022 sampling season. In September, we visited these properties during site visits. 3. Klamath Tribes: Mark Buettner, Stan Swerdloff, and Alex Gonyaw from Klamath Tribes were contacted to share preliminary results and identify potential collaborations for collecting samples and sharing data. 4. Chiloquin High School: We met with Emma Tibay, Aaron Martin, and Scott Preston at Chiloquin High School. The purpose of this conversation was to identify ways in which we could collaborate. In exchange for us to be able to use their space for a remote laboratory, we would develop laboratory curricula that would engage middle school and high school students in research. Changes/Problems:Due to Covid 19 and its impacts, the project start has been delayed and has been slow to advance. Specifically, Covid delayed the start of the PhD student working on the project. Other delays include laboratory closures and access restrictions. We've developed contingency plans and are executing those plans to make progress, but it is unknown at this point if or how Covid could impact the long-term success of the project. If long-term impacts are apparent, we will contact NIFA as soon as possible. What opportunities for training and professional development has the project provided?Training: In July 2021, Daphne Guo started as a PhD student on this project. Since then, Daphne has participated in several formal and informal training events. She has completed OSU's general laboratory safety training as well as the specific laboratory training in PI Jones' lab for collecting samples in the field, processing samples in the lab, analyzing samples at Oregon State University's mass spectrometry center, and processing the mass spectrometry data using proprietary software. She assisted other graduate in PI Jones' lab in both field work and lab work. In September, we traveled to Klamath Basin for a site visit. During this visit, we traveled to different locations as well as collected preliminary/background samples. In the field and lab, Daphne is proficient. Currently, she is being trained to process the mass spectrometry data using XCMS, which is an open source software package in R. In addition, she is working with PI Jones to become proficient in multivariate statistical tools that will be useful when analyzing the non-target chemical data. Professional development: In addition to training for doing research, she also attended two conferences: EmCon (Emerging Contaminants; September 2021) and SETAC (Society of Environmental Toxicology and Chemistry; November 2021). At SETAC, her work in PI Jones' lab was part of a poster presentation. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?1. Generate diagnostic chemical fingerprints that are indicative of specific sources. Sampling locations for specific sources will be finalized during January-March 2022. Sampling season will begin in earnest in April and end in September. Our sampling and processing protocols are fully developed as are our chemical fingerprinting workflow methods. Therefore, we expect no problems in this portion of the project. While we have proficiency processing the mass spectrometry data, these steps rely on proprietary software, which makes the data essentially irreproducible. Currently, the PhD student is gaining experience with XCMS to solve this issue. XCMS is an open-source platform that was developed to process mass spectrometry data. We expect to be proficient with this platform by September. Therefore, we anticipate sample collection and processing, mass spectrometry analysis, mass spectrometry data processing, and chemical fingerprinting to occur without delays. Therefore, we anticipate to complete objective 1 by the end of 2022. 2. Generate diagnostic chemical fingerprints that are indicative of landscape sources. Based on preliminary data, the chemical composition of watersheds is more closely related to the microbial composition of the sample compared to the land use of the watershed. Currently, we are using other datasets generated by Pacific Northwest National Laboratory to inform our sampling. Multiple datasets have been collected (aquatic samples) or are in the process of being collected (soil samples) from different watersheds. These data will help us determine which media is better for quantifying the chemical gradients present in a water sample that are derived from the surrounding landscape. Only after this analysis will we start collecting watershed samples within the Klamath Basin. This work is currently ongoing. These challenges are considered small and are not expected to change any of the outcomes associated with the project. 3. Trace the terrestrial-origins of chemical loadings into Upper Klamath Lake. Starting summer 2022, we will begin collecting water samples within Upper Klamath Lake and Agency Lake. These samples will be collected concurrently with source specific samples. Therefore, the data will be available concurrent with the source samples (objective 1). By the end of 2022, we expect to screen lake samples for the presence of each of our source specific samples. This will be completed by the end of 2022.
Impacts
What was accomplished under these goals?
There are three goals associated with this project, and the accomplishments associated with each are presented below. 1. Generate diagnostic chemical fingerprints that are indicative of specific sources. To date, we have finalized our fingerprinting workflow using support vector classification with the linear kernel. This workflow was developed using algorithms provided by scikit-learn and are programmed in python. This script works well when the chemical compositions of the different sources are linearly separable; however, this assumption may not always hold. Therefore, we've developed analogous workflows that utilize other machine learning classifiers including random forest, extra trees, decision trees, gradient boosting, logistic regression. The support vector classification script will be posted onto GitHub for the masses in January. The other classification tools are nearly finalized and will be posted to GitHub by March. In addition to the workflow programming, other progress was made on objective 1. In September, we travelled to the Klamath region for a site visit. We visited multiple field sites that could be used for sampling. This trip focused on sites at various points in the irrigation distribution system including the system inlet and outlet and multiple fields in between. These sites will be sampled in April-September 2022 to develop the chemical fingerprints. 2. Generate diagnostic chemical fingerprints that are indicative of landscape sources. We've collected data from a previous study conducted by PI Jones. In this study, water samples were collected from four different watersheds from five different locations. Our goal was to determine which landscape features were responsible for driving patterns within the chemical composition. To our surprise, the chemical composition was more related to the microbial community composition instead of the landscape composition. This could be due to many factors. Specifically, it is possible that the mass range that we are using within the mass spectrometer (100-1000 m/z) is more representative of microbial metabolites instead of organic matter derived from the landscape. Alternatively, it is possible that the C18 SPE cartridges that we used to collect the data bias the chemical space towards microbial metabolites instead of landscape organic matter. Finally, it is possible that aquatic samples are in appropriate for sufficiently extracting chemicals from the landscape. For example, during the summer dry season, base flows are supported by groundwater instead of surface runoff. Therefore, the carbon that was detected is potentially more likely to be autochthonous instead of allochthonous. Moving forward, we will consider sampling soils to evaluate the chemical composition of the landscape instead of collecting water samples. 3. Trace the terrestrial-origins of chemical loadings into Upper Klamath Lake. During our September site visit, we met with Stan Swerdloff, Mark Buettner, and Alex Gonyaw, who work for the Klamath Tribes fisheries division. As part of ongoing research, these scientists are responsible for helping to preserve the native sucker fish populations within the region. Part of their sampling regime is to collect samples from Upper Klamath Lake and Agency Lake. They collect biweekly samples on the lakes and have volunteered to collect samples on our behalf during 2022 sampling season. This is advantageous because it will save our time and we will have the opportunity to share water quality data with the Klamath Tribes.
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