Progress 11/15/20 to 11/14/24
Outputs
Target Audience:Our project was intended for the following target audiences: Lummi Natural Resources.The mission of the Lummi Natural Resources Department is to enhance, manage and protect the natural resources into perpetuity for the benefit of the Lummi people in accordance with the policies and procedures of the Lummi Nation. Like all federally recognized tribes in the state of Washington, the Lummi Tribe, together with the state government, co-manages local fisheries resources. Longfin Smelt are a historically important subsistence food for the Lummi people, yet little is known about the natural history and current status of the species. Heavily committed with responsibilitiesto manage and restore stocks of salmon, shellfish and crab, combat invasive species, adjudicatedisputed demands for Nooksack River waterand advocate for treaty rights, Lummi Natural Resources has the desire--but neither the staff nor the budget--to study Longfin Smelt. Information provided by this project has helpedto fillknowledgegaps and complements the efforts of the Lummi Tribe to manage the resources upon which their community members depend. Local governments.Longfin Smelt find habitat in aquatic environments that touchWhatcom, Skagit and Island Counties, as well as the munincipalities of Bellingham and Ferndale. These local governments have regulatory responsibility forurban development, road construction, wastewater treatment, agriculture, flood control, industries, restoration projects and other activitiesthat can directly influenceLongfin Smelt. While aknowledging potential impacts, local governments are unable to more accurately depict howLongfin Smelt may be affected by endeavors over which they hold jurisdiction. Findings from this research project can help to better inform local governments on where critical habitats for Longfin Smelt are located, how to attenuate some of the adverse impacts of human activities on smelt, and how to create or enhance Longfin Smelt habitat. State government.The Washington Department of Fish and Wildlife is the state agency tasked with preserving, protecting and perpetuating the state's fish, wildlife and ecosystems. Forage fish are essential to the function and productivity of the state's marine ecosystems. Longfin Smelt are the 5th most important forage fish in Washington State waters (in order of importance, the others are Pacific Herring, Pacific Sand Lance, surf smelt and Northern Anchovy). Information from theis project will help the Department of Fish and Wildlife to devise regulations to ensure that Longfin Smelt are sustainably managed. The research community.Using environmental DNA to monitor fish populations is an emerging science. Knowledge created by this project contributes to our understanding of Longfin Smelt, an under-studied species, andadds to the growing body of information on the possibilities and limitations of using environmental DNA to study fish. Changes/Problems:1) We changed our spatial sampling approach. In the first years of the project, we relied on fixed sampling points along the Nooksack River that were revisited several times during the Longfin Smelt spawning season. We continued to usethose sampling stations, but alsosampledthrought the delta and along the entire length of the river where wedetected smelt. The motivation for this was to locate and characterize Longfin Smelt spawning habitat. 2) We changed our temporal sampling approach. In the first years of the project, we sampled once at each sampling station after nightfall. This approach continued to evolve until the 2024 spawning run, when we sampled continuously along the length of the river during a 24-hour period. 3) To relate Longfin Smelt eDNA concentrations to fish abundance, we simultaneously collected eDNA samples and captured smelt with a dip net while monitoring flow rate. Our ultimate goal is to leverage eDNA data to produce an estimate of the size of the spawning population. 4) In addition to the molecular techniques that were developed during the initial phase of this grant, we usedother approaches to detect spawning, such as placing artificial spawning substrates. This wasnecessary because molecular techniques do not distinguish between life stages and are not sufficient to confirm spawning. 5) In line with the previous point, we supplementedour molecular techniques with other methods of inquiry, such as using otoliths and scales to age spawning fish, and stomach analyses of smelt in spawning condition. Supplementing our molecular methods providedadditional information on smelt biology that eDNA cannot provide. 5) Finally, we adopted methods ofspatial analysis to identify habitat preferences of Longfin Smelt. What opportunities for training and professional development has the project provided?1) Through this project, Native lab staff and student interns received excellent training and professional development opportunities in the collection, processing and analysis of environmental DNA samples. A total of 15Native students have had important roles with the Longfin Smelt project. Indeed, the majority of the field and laboratory work connected to this project wasconducted by Native student interns and lab technicians. This experience will translate directly to similar projects conducted elsewhere, and generally to work in any Life Sciences laboratory. As eDNA becomes more widely adopted as a tool to study fish populations, some of the Native students and technicians who have worked on the Longfin Smelt project may find opportunities to assist other tribes establish their own environmental genetics programs. 2) The Nooksack Longfin Smelt project PI has also received ample hands-on professional development opportunities in field and lab molecular techniques. During the final six months of this project, our co-PI Dr. Andrés Lopez began to teach the people associated with the Longfin Smelt project techniques of metabarcoding, which is another rapidly developing method used to analyze environmental DNA. In the future we will use metabarcoding tounlock a wealth of information from ourextensive archive of eDNA samples. 3) Through this project, Salish Sea Research Center student interns and technicians have had the opportunity to attend conferences and make professional connections that will help them to develop careers in the life sciences. Our interns have become adept at designing and presenting scientific posters, and can do so now with confidence. 4) One of our Native student interns was invited by the Deputy Secretary of Agriculture to represent tribal perspectives at the 2024 G7 summit in Borgo Egnazia, Italy. How have the results been disseminated to communities of interest?1) Many of our Native students and staff are members of the Lummi Nation. By sharing findings from this project with friends, family members and through social media, they actively disseminate new findings about Longfin Smelt to the Native Community. 2) During the Longfin Smelt spawning run, we often engaged with Lummi community members who were fishing for smelt. They shared their knowledge about hooligans, and we shared ours. These informal riverbank meetings were rich learning opportunities for all involved. 3) Meetings with the managers at Lummi Natural Resources are the primary way in which project findings were relayed to the agency most directly involved with the management and recovery of the Nooksack River Longfin Smelt population. 4) Scientific findings from this project were shared with the research community through oral presentations and posters at conferences. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
G1. A sensitive and robust genetic assay for Longfin Smelt was developed in year one of this project. Using this assay, more than 2300 environmental samples have been tested for the presence of Longfin Smelt. The assay is incredibly sensistive: it iscapable of detecting less than one fragment of Longfin Smelt DNA in oneliter of water. To put this into perspective, this concentration is 10 million times more dilute than one part in a trillion! If Longfin Smelt are present in a body of water, this assay will likely detect their presence. G2. Indigenous students were intimately involved in all aspects of this project. The majority of the field and lab work--eDNA sample collection, eDNA extraction from field samples, and qPCR analysis of eDNA extracts--was conducted by Indigenous students and technicians. Through the Longfin Smelt project, emerging Native scientistsare receiving extensive hands-on opportunities for training in environmental genetics. After their work with this project, these scholarsare certainly well-trained to engage in other research projects that use environmental DNA, work for Tribal, state or other entities that use eDNA as a tool, or enter graduate-level academic programs. G3. The PI has related and will continue torelate findings from the Longfin Smelt project to managers at Lummi Natural Resources. Although Longfin Smelt are a beloved subsistence resource for the Lummi Community, Lummi Natural Resources does not have the capacity to study nor monitor the species. Information from this project on the natural history of Longfin Smelt in the Nooksack River is helping the managers at Lummi Natural Resources to guide the recovery of this unique species. Our data show that relatively small numbers of Longfin Smelt ascend the Nooksack River as far upstream as the city of Ferndale, WA, a distance of more than six miles against a strong current. This finding supports the views of knowledge-holders in the Lummi Tribe, who inform that in the past Longfin Smelt spawned on gravel beds near Ferndale. However, we found much higher concentrations of Longfin Smelt DNA in delta sloughs that are dense with sunken woody debris. Our projectsuggests that perhaps the majority ofLongfin Smelt spawners may be finding spawning habitat in the Nooksack delta, in addition to ascending the river several miles upstream to spawn on gravel bars.Now that thesecritical areas havebeen identified, we can focus efforts on identifying the microhabitats that Longfin Smelt are using for spawning. If spawning sites can be confirmed, the Lummi Nation can take measures to protectand enhance the smelt's spawning habitat. What do you plan to do during the next reporting period to accomplish the goals? 1) In 2023, we used eDNA to learn that Longfin Smelt may be utilizing spawning habitat in the Nooksack River Delta. Prior to this finding, we had assumed the smelt were utilizing spawning sites well upstream (5-6 miles) from the river mouth, but had been unable to locate these sites. In the fall of 2024, we placedartificial substrates at potential delta spawning sites to check for the presence of eggs. No eggs were deposited on the substrates, suggesting that smelt spawning in the delta may be placing eggs onbenthic substrates.2) If we are able to confirm spawning in the delta, we will use eDNA and spatial analysis to characterize the types of microenvironments that are used by Longfin Smelt for spawning. The result would be both a description and a map of Longfin Smelt spawning habitat in the Nooksack River. This would be a major milestone for this project. 3) With this information, managers at Lummi Natural Resources will have an improved ability to identify, protect and restore critical habitat for Longfin Smelt in the Nooksack River.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2024
Citation:
Black-Williams, J., Kinley, S., Miles, N., and J. Rombold. 2024. Distribution of Longfin Smelt in the Salish Sea. Poster presentation, 2024 Annual Meeting of the North Pacific Marine Science Organization.
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Progress 11/15/22 to 11/14/23
Outputs
Target Audience:This project uses techniques of environmental DNA (eDNA) analysis to study Longfin Smelt in the Nooksack River, WA. eDNA is DNA shed by an organism into its environment. In the case of Longfin Smelt, eDNA may originate from scales, slime, feces,urine, wounds, eggs, sperm, and deceased individuals. eDNA enables us to study Longfin Smelt without impacting the (declining) population, and to search for this cryptic species during floods or darkness when conventional methods such as seining would be too hazardous to use. The project aspires to use information gained through eDNA analysis to better understand spawning of Longfin Smelt in the Nooksack River: what environmental cuestrigger the initiation of the spawning run, how long spawning lasts, how far upstream Longfin Smelt swim to find spawning habitat, how many spawning fish enter the river, and what habitats and substrates are used for spawning. The Lummi Nation community is theprimary target audience for this information. Managers atthe Lummi Nation Natural Resources (LNR) Department will use the results of this study to better manage the population of Longfin Smelt--an important subsistence food for the Lummi people. Beyond the Lummi Community, other groups are studying Longfin Smelt, especially the state-listed population of Longfin Smelt in San Francisco Bay. Finally, the science of eDNA is still developing. This project makes valuable contributions to the community of researchers dedicated to unlocking the full potential of eDNA as a tool for research and management. Changes/Problems:1) We changed our sampling approach. In the past, we have relied on fixed sampling points along the Nooksack River that wererevisited several times during the Longfin Smelt spawning season. We are still using those sampling stations, but are now sampling throught the delta and along the entire length of the river where we have detected smelt. The motivationfor this is to locate and characterize Longfin Smelt spawning habitat. 2) In addition to the molecular techniques that were developed during the initial phase of this grant, we will use other approaches to detect spawning, such as placing artificial spawning substrates. This is necessary because molecular techniques do not distinguish between life stages and are not sufficient to confirm spawning. 3) In line with the previous point, we are supplementing our molecular techniqueswith other methods of inquiry, such as using otoliths and scales to age spawning fish, and stomach analysesof smelt in spawning condition. Supplementing our molecular methods provides additional information that on smelt biology that eDNA cannot provide. 4) Finally, we are now usingspatial analysis to identify habitat preferences of Longfin Smelt. What opportunities for training and professional development has the project provided?1) Through this project, Native lab staff and student interns have received excellent training and professional development opportunities in the collection, processing and analysis of environmental DNA samples. Indeed, the majority of the field and laboratory work connected to this project is conducted by Native student interns and lab technicians.This experience willtranslatedirectly to similar projects conducted elesewhere, and generally towork in any Life Sciences laboratory. 2) The Nooksack Longfin Smelt project PI has also received ample hands-on professional development opportunities in field and lab molecular techniques. 3) Through this project, Salish Sea Resrearch Center student interns have had the opportunity to attend conferences and make professional connections that will help them to develop careers in the life sciences. How have the results been disseminated to communities of interest?1) Many of our Native students and staff are members of the Lummi Nation. By sharing findings from this project with friends, family members and through social media, they actively disseminate new findingsabout Longfin Smelt to the Native Community. 2) Meetings with the managers at Lummi Natural Resources are the primary way in which project findings are relayed to the agency most directly involved with the management and recovery of the Nooksack River Longfin Smelt population. 3) Scientific findings from this project have been relayed to the researchcommunity through oralpresentations and posters at conferences. What do you plan to do during the next reporting period to accomplish the goals?1) In2023, we used eDNA to learn that Longfin Smelt may be utilizingspawning habitat inthe Nooksack River Delta. Prior to this finding, we had assumed the smelt were utilizing spawning sites well upstream (5-6 miles) from the river mouth, but had been unable to locate these sites. In the fall of 2024, we plan to place artificial substrates at potential delta spawning sites to check for the presence of eggs. 2) If we are able to confirm spawning in the delta, we will use eDNA and spatial analysis to characterize the types of microenvironments that are used by Longfin Smelt for spawning. The result would be both a description and a map of Longfin Smelt spawning habitat in the Nooksack River. This would be a major milestone for this project. 3) With this information, managers at Lummi Natural Resources will have an improved abilityto identify, protect and restore critical habitat for Longfin Smelt in the Nooksack River.
Impacts
What was accomplished under these goals?
G1.Asensitive and robust genetic assay for Longfin Smelt was developed in year one of this project. Using this assay, more than 1500 environmental samples have been tested for thepresence of Longfin Smelt. G2.Indigenous students are intimately involved in all aspects of this project. The majority of the field and lab work--eDNA sample collection, eDNA extraction from field samples, and qPCR analysis of eDNA extracts--is conducted by Indigenous students. Through the Longfin Smelt project, Native students are receiving extensive hands-on opportunities for training in environmental genetics. After their work with this project, these students are certainly well-trained to do similar work elsewhere. G3.The PI continues to relate findings from the Longfin Smelt project to managers at Lummi Natural Resources. Although Longfin Smelt are a beloved subsistence resource for the Lummi Community, Lummi Natural Resources does not have the capacity to study nor monitor the species. Information from this project on the natural history of Longfin Smelt in the Nooksack River will help the managers atLummi Natural Resources to guide the recovery of this unique species.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Williams-Black, J. 2023. Learning through experience at the Salish Sea Research Center (poster).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Williams-Black, J. 2023. Supporting Indigenous students as the next generation of ocean leaders (poster).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Rombold, J. 2023. Using eDNA to detect Longfin Smelt in Bellingham Bay, WA (presentation). Proceedings of the annual meeting of the Alaska Chapter of the American Fisheries Society. Fairbanks, Alaska.
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Progress 11/15/21 to 11/14/22
Outputs
Target Audience:Environmental DNA (eDNA) is genetic material (DNA) released by organisms in the environment. Quantitative polymerase chain reaction (qPCR) is a molecular method that uses a fluorescent probe in a traditional PCR reaction to monitor the amplification of DNA in real time. A fluorometer detects fluorescent signal that is produced once a molecular target has been amplified, this allows us to quantify target DNA in the environment of interest. The eDNA work on the Spirinchus thaleichthys, Longfin Smelt (also known as "Tiokowe" or "Hoolies"), is important because detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species. The goal for the Hoolie eDNA project is to determine where Hoolies are spawning in the Nooksack River, WA. This work applies scientific methods for issues that are important to Native American tribes served by Northwest Indian College (NWIC). NWIC and Lummi Natural Resources are working together to improve understanding of the unique Nooksack spawning population of Hoolies. Meetings were held with NWIC, the Salish Sea Research Center (SSRC), and Lummi Natural Resources (LNR) to identify collaborative priorities and responsibilities for LNR, NWIC, and SSRC. Both the PI and the LNR Sock Assessment Manager have determined a creative way to disseminate project updates to the Lummi community. To make sure that local, tribal voices are heard regarding any approach to leveraging Hoolie data, the teams are requesting community information that they would like to share regarding Hoolies, either directly or indirectly. Both LNR and the SSRC want to preserve fishing opportunities while also collecting information to understand the population. As we look ahead to collecting this valuable information about the Hoolie, we will enact food sovereignty and governance for the Lummi Nation. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?In year 2, we were able to support two additional students in conducting hands-on genomics-related research projects at the Salish Sea Research Center. The two student interns were trained in molecular field methods (using the Smith-Root eDNA sampler to collect water samples) and molecular lab methods (extractions of eDNA samples). In year 2, additional researchers and technicians at the Salish Sea Research Center learned how to collect environmental DNA (eDNA) from marine and freshwater systems using a Smith-Root backpack sampler. SOPs for various parts of the project were developed and used for training of new staff and interns. Continued method development for field sampling, as well as SOPs for gDNA extractions have assisted in the training for two student interns as well as one senior staff member. SSRC director Dr. Misty Peacock presented for Co-I Mallon at the annual Meeting for the North Pacific Marine Science Organization (PICES). In addition,SSRC intern and NWIC BSNES senior, Sandra James presented at the 152ndAnnual American Fisheries Society Studentmeeting inSpokane, WA. The title of her posterwas"Studentperspective on a diverse partnership to find Hooligans." How have the results been disseminated to communities of interest?Results of this research have been presented to Lummi Natural Resources.We continue to partner with Lummi Natural Resources to disseminate project updates to our communities of interest. Meetings with Lummi Natural resources occur monthly leading up to and during the spawning season to collaborate on research and monitoring efforts, otherwise meetings are quarterly.In addition, we will continue to communicate our findings with Lummi Natural Resources and upon completion of this research will work with LNR to disseminate the results to the local Lummi community. What do you plan to do during the next reporting period to accomplish the goals?In the final year of this project, we will focus the majority of our efforts on continuing to support staff and student research and communicating our results to the community. We will continue our sampling effort along the Nooksack River and expand sampling if needed depending upon results from year 2. We have supported two Northwest Indian College (NWIC) students in paid internships for this project and we will continue to support these and future students in their research and capstone efforts. Results of this research will be disseminated to the greater community in a paper to be submitted to a peer-reviewed journal, which is currently in process by the PI's of the project. Community members requested TikTok or YouTube videos explaining the Hooligan study and results. We plan to use footage from previous field sampling and interviews with local fisher, Jeff Solomon to create social media content.
Impacts
What was accomplished under these goals?
G1:In year 1, we developed a species-specific quantitative polymerase chainreaction (qPCR) assay to identify Longfin Smelt in eDNA samples. O1: This objective was met and reported in year 2. To summarize, aquantitative polymerase chain reaction (qPCR) Taqman assay was developed, tested, and optimized for Hoolie DNA. O2: This objective was met and reported in year 2. To summarize, in situ testing has been completed using aquantitative polymerase chain reaction (qPCR) Taqman assay that isoptimized for Hoolie DNA G2:We have increased the capacity for Indigenous students to conduct genomics-relatedresearch andteach others how to do soat the Salish Sea Research Center. O1: Northwest Indian College is offering only online courses. To meet the needs of the students that work in the Salish Sea Research Center, the PI developed an online course that includes modules written by Indigenous Geneticists. It can be found at: https://genomicstribalcommunities.opencraft.hosting/dashboard. The SSRC is utilizing these materials to teach introductory genetics material to interns that start genetics research. O2: Summer interns that were hired in 2021, continueto work in the laboratory into 2023. They arenot only conducting research but also training new employees at the SSRC how to conduct eDNA extractions from LFS samples and livers. O3: SSRC intern and NWIC BSNES senior, Sandra James presented at the 152nd Annual American Fisheries Society Student meeting in Spokane, WA. The title of her poster was "Student perspective on a diverse partnership to find Hooligans." G3: The PI and Co-I continue to reach out to the local community about the research developments. O1: The PI,Dr. Brandi Kamermans presented results at the Whatcom Marine Research Symposium February 23, 2022. This was avirtual meeting with scientists and community members from Whatcom County. A virtual meeting was held with stakeholders and Lummi Natural Resources on March 2, 2022. Interested community members heard results from Year 2. O2: In year 2, we developed an "eDNA glitter exercise" curriculum targeted for Lummi Nation School 3rd and 5th graders. In year 3, the eDNA outreach curriculum was presented by researchers at the University of Alaska Museum of the North. The curriculum tailored the eDNA glitter exercise for different age groups during the University of Alaska Fairbanks' Arctic Research Open House and the museum's Family Day (Water) event. In total, both events drew 800 children and parents alike. Researchers used glitter, filters, and small plastic animals to visually demonstrate how they detect varied species in river water. This led to interest from Elisabeth Padilla (erobins@alaska.edu, UAM's Outreach Specialist & Field Trip Coordinator) who is implementing and 'packaging' the eDNA activity(ies) to include in kits that schools and families borrow from the museum.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
James, S., Rombold, J., Peacock, M.B., "Student perspective on a diverse partnership to find Hooligans 152nd Annual American Fisheries Society Student meeting in Spokane, WA (Poster)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Kamermans, B.R., Mallon, R. Peacock, M.B. Searching for Alexandrium and Hooligans: the Salish Sea Research Center applies molecular methods to inform local communities about microalgae and forage fish at the Whatcom Marine Research Symposium, February 23, 2022 (Oral presentation; Virtual Meeting)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Mallon, R., Kamermans B.R., Peacock, M.B., L�pez, J.A., and Arnold, R.. "Searching for Longfin Smelt in the Nooksack Estuary and Bellingham Bay" Ocean Sciences Meeting, February 24- March 4, 2022 (Virtual Meeting).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Mallon, R., Kamermans, B.R., L�pez, J.A., Garrity, M., James, S. Flawd, D. Solomon, J., Peacock, M.B., Arnold, R. "The Lhaq'temish Search for An Important Forage Fish?" American Fisheries Society Meeting. August 21-25 2022 Spokane, WA
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Mallon, R., Kamermans B.R., Peacock, M.B., L�pez, J.A., and Arnold, R.. "Searching for Longfin Smelt in the Nooksack Estuary and Bellingham Bay" 2nd National Workshop on Marine Environmental DNA September 12-13, 2022 Costa Mesa, CA
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Mallon, R., Kamermans, B.R., L�pez, J.A., Garrity, M., James, S. Flawd, D. Solomon, J., Peacock, M.B., Arnold, R. "The Lhaq'temish Search for An Important Forage Fish?" North Pacific Marine Science Organization Annual Meeting (PICES). Sept 23Oct 2, 2022 Busan, Korea
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Progress 11/15/20 to 11/14/21
Outputs
Target Audience:Environmental DNA (eDNA) is genetic material (DNA) released by organisms in the environment. Quantitative polymerase chain reaction (qPCR) is a molecular method that uses a fluorescent probe in a traditional PCR reaction to monitor the amplification of DNA in real time. A fluorometer detects fluorescent signal that is produced once a molecular target has been amplified, this allows us to quantify target DNA in the environment of interest.The eDNA work on the Spirinchus thaleichthys, Longfin Smelt (also known as "Tiokowe" or "Hoolies"), is important because detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species. The goal for the Hoolie eDNA project is to determine where Hoolies are spawning in the Nooksack River, WA. This work applies scientific methods for issues that are important to Native American tribes served by Northwest Indian College (NWIC). NWIC and Lummi Natural Resources are working together to improve understanding of the unique Nooksack spawning population of Hoolies. Meetings were held with NWIC, the Salish Sea Research Center (SSRC), and Lummi Natural Resources (LNR) to identify collaborative priorities and responsibilities for LNR, NWIC, and SSRC. Both the PI and the LNR Sock Assessment Manager have determined a creative way to disseminate project updates to the Lummi community. To make sure that local, tribal voices are heard regarding any approach to leveraging Hoolie data, the teams are requesting community information that they would like to share regarding Hoolies, either directly or indirectly. Both LNR and the SSRC want to preserve fishing opportunities while also collecting information to understand the population. As we look ahead to collecting this valuable information about the Hoolie, we will enact food sovereignty and governance for the Lummi Nation. In 2020, the SSRC captured 10-20 fish and kept them in a fish tank for preservation and outreach purposes. The fish tank was used for live webcam feed. These live feeds were available to the Lummi community members and students at local K-12 institutions. The SSRC student outreach coordinator, Thayne Yazzie, developed an "eDNA" curriculum for grades K-12. The curriculum invites students to discover how scientists that study DNA (geneticists) investigate ocean, river, and lake environments for endangered or invasive animals. The Salish Sea Research Center has a Hoolie dip-net. The dip-net was repaired by Lummi Natural Resource Technician, Jeff Solomon. The net is now available for community members to learn about Hoolie dip-netting (fishing for Hoolies). Jamielee Rose Johnson is the Workforce Development Re-Engagement Specialist/ Case Manager at Lummi Indian Business Council (LIBC) and she is going to use the repaired dip-net to teach young adults how to fish for Hoolies. Changes/Problems:Due to the global pandemic some delays have impacted dissemination of results to communities of interest, outreach at K-12 institiutions, and teaching and/or mentoring outcomes. The research center was not allowed in-person internships until September 2020. We hired two new interns October 4, 2021. No in-person outreach can be conducted and is still conducted remotely. What opportunities for training and professional development has the project provided?Two researchers at the Salish Sea Research Center learned how to collect environmental DNA (eDNA) from marine and freshwater systems using a Smith-Root backpack sampler. The Co-PI wrote a standard operating procedure for the Smith-Root sampler for the collection of DNA for the target species. A protocol was warranted because troubleshooting a turbid river required method development beyond the scope of the Smith-Root user manual. The PI determined the optimal PCR parameters for the Taqman probe that was designed for the this study. The PI wrote a standard operating procedure for the QuantStudio 6 Applied Biosystems thermocycler for quantitative polymerase chain reaction (qPCR) detection of the target species. The PI presented preliminary eDNA results at the Banse Early Career Scientist Seminar Series at University of Washinghon. The PI attended the Alaska Chapter American Fisheries 2021 Virtual Meeting. Two Northwest Indian College (NWIC) students were supported with paid internships for this project. Interns participated in sampling efforts at the marine and freshwater sampling locations. The students utilized the standard operating procedure for the Smith-Root sampler and the QuantStudio 6 Applied Biosystems thermocycler for collection of eDNA and detection using qPCR of the target species. How have the results been disseminated to communities of interest?We continue to partner wtih Lummi Natural Resources to disseminate project updates to our communities of interest. We have also developed curricula targeted for Lummi Nation School 3rd and 5th graders. To date, the project results have been presented to colleagues at the University of Alaska and the University of Washington Department of Oceanography, and NIFA support has been acknowledged. Webcam footage of the Hooligan was made available to the Lummi community and students at K-12 serving institutions. An article was written for the Encyclopedia of Puget Sound, "Once Hearty Hooligans declining in the Salish Sea." The writer, Eric Wagner, interviewed Co-PI, Rachael Mallon, while sampling for the Hoolies in November 2020. The article was also featured in Whatcom Watch Online (A community forum on government, environmental issues and media). A request for information about the Hoolie was published in the Lummi Newsletter asking people for their input and to make sure that local, tribal voices are heard regarding any approach to leveraging the data. What do you plan to do during the next reporting period to accomplish the goals?A quantitative polymerase chain reaction (qPCR) Taqman assay was developed, tested, and optimized for Hoolie DNA. The assay consistently and sensitively detects Hoolies. In the next year, we will test the assay specificty against closely related Night Smelt. We will increase sampling effort along the Nooksack River. We will begin sampling 3 weeks earlier and end 3 weeks past previous sampling time periods along the Nooksack. Efforts in 2018-2020 were for only 3-5 days. The sampling will now be for 7 weeks. We have broadened the sampling efforts to include marine settings in Bellingham and Lummi Bay. The marine sampling effort will continue in the next year. We will continue to train student interns in genomics related summer projects. We have supported two Northwest Indian College (NWIC) students in paid internships for this project. Two students will be using data collected during the year to work towards student capstone projects. This includes the student interns collecting environmental DNA (eDNA) using the Simth-Root eDNA sampler in freshwater and marine settings. This will also include the students extracting DNA from Hooligan hearts and conducting PCR and qPCR with DNA extracts.
Impacts
What was accomplished under these goals?
A quantitative polymerase chain reaction (qPCR) Taqman assay was designed, tested and optimized. The assay consistently and sensitively detects Spirinchus thaleichthys (common name is Longfin Smelt; also known as "Tiokowe" or "Hoolies"). The qPCR Taqman probe and primer set was designed by the PI, Dr. Brandi Kamermans, and subawardee, Dr. Andres Lopez. The PI, Dr. Brandi Kamermans, wrote a standard operarting procedure for developing primers and probes for Hoolies. Briefly, previously published Spirinchus thaleichthys cytb protein data was collected using the NCBI database. The bioinformatics software, Geneious, was used to align the Spirinchus thaleichthys sequences. A consensus sequences was generated using a region that was 156 base pairs in length. Foward and reverse primers and a Taqman probe were designed based on a region of the sequence that was similar among samples. The forward and reverse primers and Taqman probe were ordered from Integrated DNA Techonologies. Then, once received, in situ testing commenced. The Taqman assay was tested against samples with known Hoolie DNA present. These were samples that were collected in November 2018, 2019, 2020, and 2021 during the annual spawing run in the Nooksack River, WA. Sites where Hoolies are known to be absent were also collected and provided negative results. A qPCR positive control was developed. The control is a double-stranded 156 basepair length strand of DNA, called a gBlock Gene Fragment (Integrated DNA Technologies; Coralville, Iowa, United States). The gBlock was designed and synthesized for Spirinchus thaleichthys using aligned Spirinchus thaleichthys sequences. A consensus sequences was generated using a region that was 156 base pairs in length. Together these tests confirmed that the Taqman assay is consistently and sensitively detecting Hoolies in the Nooksack River samples. We have increased the capacity for Indigenous students to conduct genomics-related research projects at the Salish Sea Research Center. The Salish Sea Research Center hired two Indigenous students to conduct Hoolie eDNA research projects. The two student interns were trained to use the Smith-Root eDNA sampler to collect water samples. Interns were also trained to conduct qPCR with the Taqman probe and primers. Outreach curriculum was developed on the importance of eDNA for the study of endangered species. The STEM coordinator developed amodule on the importance of eDNA for the detection of Longfin Smelt for the Lummi People and K-12 students.
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Banse Early Career Scientist Seminar Series at School of Oceanography at the University of Washington (Seattle)
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Once hearty 'hooligans' declining in the Salish Sea
https://www.eopugetsound.org/magazine/IS/longfin-smelt
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