Sea lice (Lepeophtheirus and Caligus spp) are parasitic copepods that infect the external surfaces of fish hosts. Salmon lice (L. salmonis) outbreaks are commonly reported by operations in Canada, Norway, Scotland, Ireland, and the United States and are a primary concern in aquaculture because of their fish health and economic impacts. When farmed fish mortalities and treatments are accounted for, annual losses from sea louse infestations exceed $300,000,000 (Costello 2009). Farms experiencing sea lice infections risk on-site re-infection and transmission to wild populations and other farms that are hydrographically connected. In Maine, Atlantic salmon farms are located in the northeast, with major operations in Machiasport and Cobscook Bay. The primary aim of this study was to establish the infection dynamics of sea lice in Cobscook because it is positioned at the mouth of the Bay of Fundy, where outbreaks are increasingly common but are not well described in the available literature. Sentinel cages housed Atlantic salmon juveniles for a total of 7 days every month to monitor sea lice settlement at 4 sites within Cobscook Bay: Broad Cove, Comstock Cove, Prince Cove, and Pembroke Landing. The survey revealed a pre-season (early summer) and season (autumn) peak for sea lice prevalence (percent infected fish) and abundance (lice/fish). Spatial differences in prevalence and abundance were also detected for most months of the study and Pembroke Landing became a site of interest because the observed infection trends were unique relative to the remaining coves. Copepodid and chalimus stages were not detected in the late winter or early spring in 2014 because temperatures were not supportive of egg hatching, naupliar survival, or copepodid attachment. The source of the infections observed over the course of 18 months was unclear and farm counts from the time of the study were not made available for farm to sentinel comparisons. The relationship between environmental factors and total sea lice counts were investigated using generalized linear mixed effect models (GLMMs) with a negative binomial distribution and a log link function. A mathematical model estimating body surface area of Atlantic salmon juveniles was designed and then used to generate fish morphometric data for GLMM development. Data from individual sites were initially pooled to generate a general model for the entire bay, but the significance of Pembroke Landing as an individual site prompted a need to generate site-specific GLMMs. Temperature had a positive relationship on total sea lice count at all sites, which was expected because of its biological relevance in expediting sea louse development and growth. Current velocity had a negative relationship with sea lice at Prince Cove and Pembroke Landing, likely because average velocities were within a range that limits sea lice attachment. Results from the survey and the mathematical model were linked with previous work on sea lice infection dynamics to develop scenarios that describe potential sources of infection for Cobscook Bay. These data and scenarios will be used to inform future bio-physical models and assist in developing hypotheses that can be tested once models are validated and confirmed
