Performing Department
(N/A)
Non Technical Summary
The high capacity of Illumina NextSeq 2000 would be an asset to researchers within UMCES, IMET and greater Baltimore region. With regard to the Appalachian Laboratory Molecular Ecology Unit, ongoing projects funded through US Department of Defense, Maryland DNR and US Geological Survey would benefit greatly from the availability of such a machine at the collaborating IMET BASLab facility.Our efforts will target technology transfer/technical assistance to address industry constraints/barriers and will expand our salmon RAS website (ras-n.org) and other technology-sharing methods to inform end-users. Other extension efforts will also include community engagement with public stakeholders, regarding emerging and established commercial RAS facilities nationwide. Our goal will be to work with local communities to foster sustainable practices, increase food security and provide transparency on how industry utilizes technologies to address common concerns in aquaculture.
Animal Health Component
30%
Research Effort Categories
Basic
50%
Applied
30%
Developmental
20%
Goals / Objectives
The DNA/RNA sequencing capability of IMET's BASLab, a multiuser facilityfor molecular sequence analysis will be upgraded through the acquisition of an IlluminaNextSeq 2000 Sequencing System, providing small whole-genome sequencing, whole exomesequencing and RNA-Seq analysis of Atlantic Salmon as well as high-throughput inference ofdietary niche breadth to environmental DNA (eDNA) surveys. These are capabilities notcurrently available in the BASLab. This acquisition will support research needs of the (SAS)2Sustainable Aquaculture Systems Serving Atlantic Salmon grant, a coordinated, nationalpublic-private consortium of experts funded by USDA NIFA that was awarded in September,2022. The overarching vision of this effort is to facilitate the growth of environmentallysustainable and economically feasible Atlantic salmon production in the US towards providingfood security and reducing the current trade 3.4 B deficit associated with salmon imports Theoverarching goal of (SAS)2 is to build capacity and establish a holistic hub of knowledge thatwill integrate past, current and future research as well as outreach, education and extension topromote the successful growth, stability and economic feasibility of the Atlantic salmon RASsector and, more broadly, sustainable US aquaculture. The specific research objectives thisinstrumentation would target are the genomic sequences of the bacteria producing off-flavorcompounds, the microbial community associated with removal of dissolved and solid waste,and the microbiome and host response of Atlantic Salmon when fed RAS specific feeds. Theenhanced sequencing capabilities that the Nextseq would provide will empower researchers atUMCES involved with oyster aquaculture genome-assisted breeding, Callinectes and Portunisspp crab aquaculture, and future assembly and genotyping efforts for emerging aquaculturespecies in and around the Mid Atlantic region.
Project Methods
Metagenome assemblies will be performed with MetaSPAdes (version 3.15.1, 02/2021), gene finding using MetaMark and functional annotation using several databases including KEGGas previously described by our group. Mixed effect models will be applied to identify associations between the composition, function of the microbiomes, diets, health outcomes, and water conditions. RNAseq analysis will be performed using DESeq2 and other commonly used tools .Project Timeline: Upon receipt of the award, the order for the Illumina NextSeq 2000 Sequencing System will be placed, delivery scheduled and installation completed. The hope is this will occur in the late Fall of 2024.Instrument Location: IMET, Room 3001, 701 East Pratt Street, Baltimore, MD. The instrument to be acquired will be physically located in the IMET BASLab (Room 3001), the primary location of which includes 1,000 square meters of laboratory space that is purposely designed for molecular analysis and instrumentation. The BASLab has additional space availability of ca. 1,200 sq.ft for a total of 2,200 sq. ft. indicating the commitment of IMET towards this capability. This facility includes enhanced cooling capabilities and appropriate utilities including clean power and adequate back-up generating capacity and adjacent clean rooms (3) for sample preparation. All of the faculty members who would use the facilities have offices or laboratories in very close proximity to the BASLab. The existence and availability of other instrumentations are outlined in the Facilities & Other Resources and Equipment documents.