Progress 09/01/20 to 08/31/23

Outputs
Target Audience:Out target audiences are partners in the salmon aquaculture industry, marine scientists in aquaculture and the decision makers at the Maine Department of Marine Resources. Changes/Problems:Covid-19 affected the laboratory, modeling and information sharing portions of the project. Getting lice for the lab was problematic since covid-19 issues began. Covid-19 in general caused a lot of project delays in our research lab and distributing computational resources and expertise towards the modeling efforts in many of the projects, including this one, was difficult. Covid-19 also made communication with stakeholders more difficult in the past several years. Delays were also caused becasue the building that housed the experimental flume at UMaine was renovated and our experiments were interupted several times and finally moved to another location off campus. Lastly, PI Cole began teaching full time a year and a half ago and it caused delay in the modeling effort - as of last year the funds were still in the budget to hire someone with this expertise and we were hopeful to get a project extension. We were unaware that the project could not be extended beyond a third year. PI Brady is still in the process of hiring a research scientist specializing in hydrodynamic modeling for his lab that will help continue work on this project beyond its end date. What opportunities for training and professional development has the project provided?Eleanor Glahn, a Masters student in UMaine School of Marine Sciences in Aquaculture, presented her dissertation and graduated in Spring 2023. This project has funded her graduate student tuition, stipend and travel for nearly three years. This project has funded an undergraduate in the UMaine School of Marine Sciences, Madeline Abell, to help in the lab and participate in marine research for several summers. This project funded travel to the international Seal Lice 2022 conference in the Faroe Islands for Master's student Eleanor Glahn and co-PI Ian Bricknell. Kelly Cole, research faculty at UMaine, was invited to be a 2022 AGU/ASLO/TOS Ocean Science Meeting session chair for a coastal buoyancy driven flow session and presented this project at the meeting. Team collaboration with the engineering firm W. L. Gore and Associates, Inc, who are interested in small scale flow around a salmon cage has been initiated and expands the industry reach of the project. Damian Brady and Kelly Cole have served on the Portland Nutrient Councill, a group focused on water quality monitoring and improvements in the Portland, ME region throughout 2020/2021 because of their expertise related to these project efforts. This project has initiated several team/stakeholder/industry meetings to discuss direction in model development and further collaboration with government and other aquaculture industry partners in Maine. How have the results been disseminated to communities of interest?Results from this project have been presented in several conferences and local seminar series: AGU/ASLO/TOS Ocean Science Meeting, Sea Lice 2022, UMaine CIE Coastal Group seminar, UMaine School of Marine Sciences dissertation presentation, Eastern Maine Community College Computer Technology Program talk/lectures. Email and zoom have been used often for science team meeting and with Cooke. Powerpoint slides and animations of the preliminary particle tracking experiments have been passed around to the group members and people of interest in industry and at UMaine. What do you plan to do during the next reporting period to accomplish the goals?There are no more reporting periods on this project, but this effort overlaps with other ongoing projects so the work will continue. We are working on several projects using the same modeling infrastructure designed for this project for other aquaculture initiatives with government and industry across the state. The next steps are to validate the biological particle tracking side of the model. Damian Brady (co-PI) has an ongoing search out for a research scientist for his lab to continue this modeling effort. Ellie Glahn is working on publishing her masters thesis. Her thesis was three chapters long and we are working to publish two of these chapters from the lab effort. She plans to continue on to a PhD program in aquacutlure.

Impacts
What was accomplished under these goals? The goal of this project is to build and implement a Decision Support System (DSS) to manage the spread of sea lice in salmon aquaculture by helping growers decide 1) when and in what order to treat existing farms for lice and 2) where to site future farms. Specific objectives of the project are to 1) expand and validate sea lice modeling infrastructure, 2) create a decision support system for farmers and 3) integrate the DSS into farmers' decision-making and assess its benefit. Our team has worked on lab and modeling efforts over the last three years towards these goals. Two hydrodynamic models have been updated and applied to this project: a localized model of Cobscook Bay and a regional model of the entire Gulf of Maine. The models are fullly-3D, unstructured grid models, with the required resolution and extensive domain to sufficiently track sea lice in the eastern Gulf of Maine. The Bay model has been run in several short term scenarios and the Gulf-scale model has been run over a spring-summer-fall season. Both of these models are ready to run future scenarios as part of a sea lice decision support system and have been expanded to support new modeling projects beyond sea-lice tracking as a result of our work. In the lab, several sea lice experiments have been run in a flume. Pilot experiments were performed exploring egg hatch and attachment in high current velocity. The strongest experimental results were achieved when PIT-tagged Atlantic salmon were challenged with a standardized dose of salmon lice at low, moderate, and high current velocities commonly experienced by salmon in net-pens in Cobscook Bay at 5, 10, and 15 cm sec-1 (0.10, 0.19, and 0.29 knots), respectively. Mean percent settlement was calculated for each velocity group, and a permutation-based ANOVA was conducted to determine if significant differences existed between groups. Percent settlement was significantly different in all three velocity groups, with optimum settlement occurring at moderate velocity, with high velocity resulting in the lowest average settlement success. The results of this study exhibit similar patterns to what has been observed in other studies and are compared to sentinel cage surveys previously conducted in Cobscook Bay (edited from E. Glahn's master's thesis, UMaine 2023). The lab experiments will be used to inform a biological model of sea lice tracking embedded in the hydrodynamic models as our efforts continue. Several particle and dye tracking scenarios have been run with the hydrodynamic models with regards to lice spread between farms, but realistic biological behavior has not been fully implemented. Overall, our team has made much progress in objectives #1 and #2; objective #2 and #3 require more long-term effort. Given the opportunity for more collaboration with farmers, we will share more of the model outputs and capabilities to apply it to problems of interest.

Publications

• Type: Conference Papers and Presentations Status: Accepted Year Published: 2022 Citation: Cole, K.L. and D.C. Brady, Tracking pathogens on the Maine coast, Ocean Sciences Meeting, March 2022. Conference abstract.
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2022 Citation: Glahn, E.R and I. Bricknell. A novel study on sea lice (Lepeophtheirus salmonis) settlement success during Atlantic salmon (Salmo salar) encounters, Sea Lice Conference International 2022, Faroe Islands. Conference abstract.
• Type: Theses/Dissertations Status: Published Year Published: 2023 Citation: Glahn, Eleanor R., "Biophysical Factors Impacting Sea Lice Settlement and Survival" (2023). University of Maine Electronic Theses and Dissertations. 3784.
• Type: Journal Articles Status: Other Year Published: 2024 Citation: Glahn, E.R., Bricknell, I., Pietrak, M., Brady, D.C., and K.L. Cole, Biophysical Factors Impacting Sea Lice Settlement and Survival: the effects of flume horizontal current velocity, in prep, to be submitted 2024 to Aquaculture.

Progress 09/01/21 to 08/31/22

Outputs
Target Audience:Our target audiences are the salmon aquaculture industry, marine scientists in aquaculture and decision makers in the Maine Department of Marine Resources. Changes/Problems:There have been some delays in both the lab and modelling efforts. COVID-19 has made it extremely difficult to obtain sea lice for our lab experiments. Additionally, our flume experiments were originally set up in a building that is being remodeled, so our lab site has moved to a new location and we have experienced some technical problems, including pump failures. The modeling effort is underway. The biological modeling component is quite complex and would benefit from more time spent on it; unfamiliar software, a new supercomputer and parallel software has caused delays as well. (Copied from our one-year extension request) What opportunities for training and professional development has the project provided?This project has funded Conference travel for Ellie Glahn (Masters student) and Ian Bricknell (co-PI) to Sea Lice 2022 in the Faroe Islands. How have the results been disseminated to communities of interest?Email and zoom have been used often for science team meeting and with Cooke. Powerpoint slides and animations of the preliminary particle tracking experiments have been passed around to the group members and people of interest in industry and at UMaine. What do you plan to do during the next reporting period to accomplish the goals?We plan to stick to our timeline as best we can and push the modeling effort forward. We will continue to spend funds towards personnel working on the project and towards the materials and supplies needed towards the lab effort.

Impacts
What was accomplished under these goals? A pilot trial was conducted at the University of Maine's Aquaculture Research Center, Orono, ME, 04469, in December 2021. The goal of the pilot trial was to evaluate the initial experimental design and determine if modifications needed to be made to the experimental methods testing settlement in different velocity currents in the flume. The modelling effort in this project is ongoing. Investigation of prior observations with sentinel cages in Cobscook Bay is part of Ellie Glahn's thesis and PI Coles effort throughout the first few years of this project. Hydrodynamic runs of the region have been performed with two different grids for the area. These runs include short several-tidal cycle runs and seasonal runs in the year of the previous sentinel cage study. The remainder of this project will be making additional hydrodynamic runs of Cobscook Bay circulation and implementing more realistic biological behaviors to particles within the modeled fields. Our masters student on the project, Ellie Glahn, has held several committee meetings to share progress and her program of study has been approved in the UMaine School of Marine Sciences with an Aquaculture concentration. She has begun passing around drafts of her thesis chapters to her committee and will be traveling to Sea Lice 2022 in the Faroe Islands to present her work on this project later this year.

Publications

Progress 09/01/20 to 08/31/21

Outputs
Target Audience:There were two industry groups and one academic group that our project reached. 1) Cooke Aquaculture via our scheduled project industry meeting. 2) W. L. Gore and Associates, Inc, an engineering consulting firm modeling compound dispersion around salmon farms in Cobscook Bay, currently designing an effort to work in parallel with our modeling project. 3) UMaine Civil and Environmental Engineering Coastal Research Group via research discussion and presentations. Changes/Problems:1) Egg hatch experimental issues have led the team to move towards the lice attachment trials, delaying the egg hatch effort. We want to optimize the remaining fish and lice we have in the laboratory on these highly anticipated experiments. 2) The UMaine Aquaculture Research Center facility availability in is in question for future laboratory experiments. We have other options for location but there will be a fee and cost of commute that we will have to rearrange the budget for. 3) The new supercomputer at UMaine is evolving and requires much troubleshooting, slowing down the modeling effort. We are making progress and these issues should be resolved in the spring. 4) Covid restrictions continue to interfere with in-person team meetings and meeting with the industry advisory committee. We have utilized Zoom but hopefully we will have more in-person interaction in the spring. 5) Covid has limited the ability to collect sea lice from industry partners due to restrictions put in place to separate international crews and visitors. This has severely limited the number of lice collected and is a major reason we have chosen to focus on the attachment studies rather than the egg trials. What opportunities for training and professional development has the project provided?1) We have hired Eleanor Glahn, a Masters student in UMaine School of Marine Sciences in Aquaculture that has developed a program of study and proposal for the laboratory effort. She has begun her classes and research effort and communicates with the team/committee regularly. 2) Kelly Cole was invited to be a 2022 AGU/ASLO/TOS Ocean Science Meeting session chair for a coastal buoyancy driven flow session and has submitted an abstract related to this project. 3) Team collaboration with the engineering firm W. L. Gore and Associates, Inc, who are interested in small scale flow around a salmon cage, has been initiated and expands the industry reach of the project. 4) Damian Brady and Kelly Cole have served on the Portland Nutrient Councill, a group focused on water quality monitoring and improvements in the Portland, ME region throughout 2020/2021 because of their expertise related to these project efforts. How have the results been disseminated to communities of interest?Email and Zoom have been used often for science team meetings and interaction with Cooke. Powerpoint slides and animations of the preliminary particle tracking experiments have been passed around to the group members and people of interest in industry and at UMaine. What do you plan to do during the next reporting period to accomplish the goals?We will stick to our proposed timeline the best we can. More communication between the modeling and laboratory efforts has begun between Kelly Cole and Eleanor Glahn that has proved helpful in tuning both efforts. We have been discussing the parameters from literature and potential lab experiments to incorporate into the bio model. The meeting will continue in the spring and hopefully be more technical as the bio modeling effort begins. We will schedule a meeting with the industry advisory committee sometime in the spring as well to communicate results and get feedback.

Impacts
What was accomplished under these goals? We have begun work expanding and validating sea lice modeling infrastructure and communicated some of these experiments to Cooke Aquaculture farmers. We have run the realistic hydrodynamic models of Cobscook Bay and Downeast Maine and designed and run several preliminary particle tracking experiments (without behaviors at this point) based on farmers' hypotheses. An Industry Advisory Committee was created with scientists and Cooke representatives and these experiments were shared and feedback and guidance was given on future experiments and information transfer between the groups. Further, Cooke has shared several years of data for model validation that we have been looking through. These interactions initiated the development of the DSS. The first laboratory trials on egg hatch success were completed, but due to high, abnormal mortality related to tank environmental conditions (water temperature) we are skeptical of the results. Given some complications with the tank environmental controls we will proceed with the lice attachment trials in the spring in a different setup/facility.

Publications

• Type: Conference Papers and Presentations Status: Submitted Year Published: 2021 Citation: Cole, Kelly, AGU/TOS/ASLO Ocean Science Meeting abstract, 'Using ocean numerical modeling tools for decision making in aquaculture on the Maine coast', Honolulu, HI, Feb 2022, abstract submitted Sept 2021. Two of the largest threats to aquaculture on the Maine coast are pathogenic bacteria and marine ectoparasites. In this work, tools for decision support in industry and government are developed from hydrodynamic and biological models that track the spread of these species throughout the marine environment from estuaries to coasts. Two high resolution Finite Volume Coastal Ocean (FVCOM) models of the Maine Downeast coast and Cobscook Bay are employed, along with particle tracking and passive tracer releases, to assess how processes in the physical environment, such as wind, fresh water and tides disperse and accrete pathogens throughout the region. Two issues are addressed: 1) Better understanding of connectivity and sea lice dispersal between salmon farms during treatments and 2) updating shellfish growing area boundaries based on concentration and residence time of pathogenic fecal coliform bacteria/Vibrio species. New information on circulation and hydrography and potential transport of pathogens is provided to the Maine Department of Marine Resources and aquaculturists make strategic management decisions.