A survey of marine pelagic coastal microbial communities was conducted over a large geographic la... more A survey of marine pelagic coastal microbial communities was conducted over a large geographic latitude range, from Cape Mendocino in northern California USA to Queen Charlotte Sound in British Columbia Canada, during the spring to summer transition. DNA metabarcoding and flow cytometry were used to characterize microbial communities. Physical and chemical oceanography indicated moderate conditions during the survey with no widespread upwelling, marine heat wave, or other extreme conditions. However, four locations displayed features approaching acidified conditions: Heceta Head, Newport, Copalis Beach, and Cape Flattery. Although bacterial and archaeal communities at the Juan de Fuca canyon and northward had high similarity, those south of the Juan de Fuca canyon were well differentiated from each other. In contrast, eukaryotic microbial communities exhibited stronger geographic differentiation than bacterial and archaeal communities across the extent of the survey. Seawater parameters that were best predictors of bacterial and archaeal community structure were temperature, pH, and dissolved inorganic nutrients (nitrate, phosphate, silicate), while those that were best predictors of eukaryotic microbial community structure were salinity, dissolved oxygen, total alkalinity, and dissolved inorganic nutrients (nitrite, silicate). Although five bacterial and archaeal indicators for potentially corrosive waters were identified (Colwellia, Nitrosopumilus, Nitrosopelagicus, Sup05 cluster, Sva0996 marine group), no eukaryotic microbial indicators were found. Potentially pathogenic taxa detected in the survey included four disease-causing bacteria for mammals, finfish, and/or shellfish (Coxiella, Flavobacterium, Francisella, Tenacibaculum), sixteen genera of microalgae capable of producing biotoxins, and fifteen parasitic species. This study demonstrates the value of coordinating microbial sampling and analysis with broadscale oceanographic surveys to generate insights into community structures of these important pelagic trophic levels. KEYWORDS nearshore microbial communities, bacteria and archaea, eukaryotic phytoplankton, 16S and 18S rRNA metabarcoding, Northeastern Pacific Ocean Frontiers in Marine Science frontiersin.org 01
Marine aquaculture in the United States primarily produces bivalves (oysters, clams, mussels), cr... more Marine aquaculture in the United States primarily produces bivalves (oysters, clams, mussels), crustaceans (shrimp), and finfish (salmon), and currently accounts for 21% of domestic fisheries landings. In 2020, the Executive Order on Promoting American Seafood Competitiveness and Economic Growth (E.O. 13921) was established. Among its objectives were to improve U.S. food security, facilitate permitting of aquaculture facilities, and provide environmentally safe and sustainable seafood. Federal support for offshore aquaculture, including ongoing efforts by NOAA to identify Aquaculture Opportunity Areas (AOAs), is likely to result in significant expansion of this industry in the coming decade. This expansion is expected to include marine finfish species other than salmon, and cultivation of seaweed/macroalgae. It is likely to involve a range of entrepreneurs, from small independent operators through larger established corporations. Organism health, disease management, and biosecurity are major concerns for an industry that relies on natural resources. This document presents guidance for conducting marine aquaculture that protects the health of cultured organisms and the natural resources where an aquaculture farm is located. This review is based on peer-reviewed science, aquaculture practitioner observations, and existing regulations or policies within the United States or from nations with mature aquaculture industries. Furthermore, this review can inform and augment any national plan or policy governing marine aquaculture in federally managed waters. This document is intended to be a readable reference; considerable effort has been made to keep the text succinct, accurate, and free of highly technical terminology. It begins with a short introduction to biosecurity, followed by disease management and biosecurity across the three aquaculture sectors (finfish, shellfish, and seaweed/macroalgae). The next sections present topics specific to each of these sectors. The next section presents examples of region-specific biosecurity threats for the Gulf of Mexico and Southern California. The final section is a summary of a workshop on marine aquaculture best practices that included participants from the aquaculture industry, disease researchers and diagnosticians, and government agencies. Although technologies to monitor health and disease are constantly emerging, good husbandry and awareness of vulnerabilities to disease threats are at the heart of maintaining biosecurity. The guidance and practices described in this document consistently reach back to these fundamentals.
Disease epidemiology requires information about ecological and environmental condi- tions to iden... more Disease epidemiology requires information about ecological and environmental condi- tions to identify factors that can influence disease progression. Bacterial kidney disease (BKD) is an endemic disease among Pacific Northwest salmonids that causes significant morbidity and mortality in artificially propagated stocks, but risk factors for infection among free-living salmon are unknown. We evaluated infection by the causative agent of BKD, Renibacterium salmoninarum, in 1752 fish across 52 sampling sites monthly from May to November 2003 as a component of a broader study of neritic habitat use in Puget Sound by juvenile Chinook salmon Oncorhynchus tshawytscha. Infection intensity was ≤10 cells per slide for 77% of the fish. Correlations between the density of Chinook salmon with infection prevalence and with infection intensity were observed across multiple spatial scales. Capture location was a stronger predictor of infection than fish origin (based on coded wire tags) or genetic stock. Influential risk factors by logistic regression were temperature, densities of marked and unmarked Chinook salmon, and density of river lamprey Lampetra ayresis. Renibac- terium salmoninarum were found in gut contents and kidney of river lamprey, suggesting this species may be a transmission vector. The low infection intensity, lack of an effect of fish origin, effect of capture bay, and strong associations with Chinook salmon density are consistent with horizontal transmission of R. salmoninarum during the juvenile neritic phase, posing a potential for infectious interaction between sympatric hatchery and wild fish.
Investigating the contribution of kelp- and eelgrass-derived carbon and nitrogen to marine herbivores and carnivores in Puget Sound
In the Salish Sea Nereocystis luetkeana (bull kelp) and Zostera marina (eelgrass) are highly prod... more In the Salish Sea Nereocystis luetkeana (bull kelp) and Zostera marina (eelgrass) are highly productive and because of their three-dimensional size and structure are reported to provide shelter for a variety of valued Puget Sound species, including Species of Concern like Chinook salmon, Oncorhynchus tshawytscha, and quillback rockfish, Sebastes maliger. Less understood is the extent to which bull kelp forests and eelgrass beds are a source of energy for invertebrates and fishes. To answer this question we conducted a project in 2018 and 2019 to reconstruct the trophic linkages among kelp, seagrass, and several herbivorous and carnivorous species, including rockfish. We used stable isotopes of carbon and nitrogen to estimate the kelp- and eelgrass-derived isotope contributions to invertebrate and fish tissue. Understanding these connections, and their strengths, is necessary for effective management and recovery. In this presentation we will place our findings in the context of ongoing kelp recovery plans
In response to reported findings of infectious salmon anaemia virus (ISAV) in British Columbia (B... more In response to reported findings of infectious salmon anaemia virus (ISAV) in British Columbia (BC), Canada, in 2011, U.S. national, state and tribal fisheries managers and fish health specialists developed and implemented a collaborative ISAV surveillance plan for the Pacific Northwest region of the United States. Accordingly, over a 3‐1/2‐year period, 4,962 salmonids were sampled and successfully tested by real‐time reverse‐transcription PCR. The sample set included multiple tissues from free‐ranging Pacific salmonids from coastal regions of Alaska and Washington and farmed Atlantic salmon (Salmo salar L.) from Washington, all representing fish exposed to marine environments. The survey design targeted physiologically compromised or moribund animals more vulnerable to infection as well as species considered susceptible to ISAV. Samples were handled with a documented chain of custody and testing protocols, and criteria for interpretation of test results were defined in advance. All...
Chinook Salmon (Oncorhynchus tshawytscha) Have Multiple Interferon-gamma Genes (81.7)
The Journal of Immunology
Interferon-gamma (IFNg) is a central cytokine in modulating innate and adaptive immunity in a wid... more Interferon-gamma (IFNg) is a central cytokine in modulating innate and adaptive immunity in a wide range of vertebrates. A study of genes associated with an effective host response by Chinook salmon (Oncorhynchus tshawytscha) to a persistent Gram-positive bacterial pathogen (Renibacterium salmoninarum) suggested that an interferon-inducible signal was abrogated during early stages of exposure. Splenic DNA was amplified with IFNg primers from a related species, rainbow trout (Oncorhynchus mykiss), and multiple clones from individual fish were sequenced. Up to five genotypes per fish were found, and sequence variations included microsatellites within introns and single nucleotide polymorphisms (SNPs) within exons. Southern hybridizations supported the prediction that Chinook salmon possess at least three related IFNg loci. Multiple clones of cDNA, synthesized from RNA isolated from pronephros of fish exposed to an attenuated strain of R. salmoninarum, displayed a surprising abundance ...
Invertebrate, Microbial, and Environmental Data from Surface and Hyporheic Waters of Urban and Forested Streams of the Cedar River-Lake Washington Watershed
Abstract Sablefish ( Anoplopoma fimbria ) is a highly desired seafood product, which encourages d... more Abstract Sablefish ( Anoplopoma fimbria ) is a highly desired seafood product, which encourages development of sustainable aquaculture methods for this marine fish. Conventional marine fish-based feeds provide essential nutrients including long chain fatty acids for piscivorous species such as sablefish. Alternative terrestrial ingredients could reduce fishing pressures on pelagic species that are the source of fish meal and fish oil, and improve source sustainability. Using juvenile sablefish, we compared the effects of a standard fish-based diet to two diets that contained primarily terrestrial plant ingredients with flaxseed or corn oil replacing the added fish oil. After an 8-week trial feeding period, there were striking differences attributable to diet. Fish receiving the alternative feeds had lower weight gain and shorter length than fish receiving the fish-based feed, suggesting sablefish obtained lower nutrients from the alternative feeds. Among the histological differences, the intestinal mucosa was significantly less vacuolated and the frequency of intestinal mucous cells was reduced in alternative feed fish. The most dramatic lesions were observed in the liver, where severe bile duct hyperplasia (53%, flaxseed oil diet; 33%, corn oil diet), and hepatocellular lesions (nuclear pleomorphism/megalocytosis, regeneration, hypertrophy, clear cell foci) occurred in only alternative feed fish. The hepatic and biliary lesions indicate the alternative diets may be deficient or possibly harmful to sablefish. The bacterial community structures from corn oil fish showed much less diversity than those for the other diets, and the microbiome structures from the three diets were distinctly different from each other. The intestinal microbiome for the fish-based diet included the largest number of families (68), and these fish also had the largest number of unique bacterial families (11) compared to those for corn oil (two) or flaxseed oil (one) fish. Regardless of diet, the stomach and intestinal microbiomes differed significantly from each other, and the feed microbiome differed from all gastrointestinal communities, suggesting that feed is not a significant source of gut bacterial diversity. Similar to other teleosts, the sablefish gastrointestinal microbiome is dominated by Bacteroidetes, Firmicutes, and Proteobacteria. These results suggest that diet-induced shifts in microbiome can occur relatively quickly in sablefish, but the shifts may not be sufficiently adaptive or cannot overcome nutrient deficiencies. This multidisciplinary study demonstrates the utility of histology and microbiology in characterizing dietary effects for novel aquaculture species. Statement of relevance Physiological assessments such as gastrointestinal microbiomes and histopathology can provide a near-term evaluation of the nutritional adequacy of alternative feeds, such as plant-based lipid diets for marine carnivorous finfish. This is the first examination of the microbiome of sablefish, a marine species under development for sustainable aquaculture.
Physical attributes of nearshore waters across greater Puget Sound, with an emphasis on dissolved oxygen and pH
The pelagic zone is a major part of the Puget Sound ecosystem that is sensitive to human influenc... more The pelagic zone is a major part of the Puget Sound ecosystem that is sensitive to human influences, yet our understanding of relationships among its abiotic features, water quality, biota, and anthropogenic influences in spatial and temporal context is limited. To characterize the pelagic zone in greater detail, we conducted a multi-trophic level assessment that measured over 20 potential indicators of pelagic ecosystem health at 79 sites in six oceanographic basins of Puget Sound from April to October 2011. Among the many strong spatiotemporal patterns observed were basin and seasonal differences in temperature, salinity, and turbidity linked to freshwater influences; and inorganic nutrient concentrations. DO concentrations also followed distinct seasonal patterns within oceanographic basins. Seasonally, the monthly percentage of sites with DO concentrations below the threshold for biological stress of 5 mg L-1 increased from 0% in April to 45% in October. Spatially, DO concentrations below 5 mg L-1 were recorded at sites within all basins with the exception of the Central basin. By October, the proportion of sites with biologically stressful DO concentrations was highest among sites in Rosario (100%), Hood Canal (77%), and Whidbey (75%) basins. A persistent significant positive correlation between DO and pH was observed across Puget Sound. Both the strength (R2) and magnitude (slope) of the relationship increased with depth. This linkage was also observed in independently collected water column profiles by the Washington State Department of Ecology (WDOE) in 2011 over the same geographic extent. Furthermore, a 22-year long WDOE dataset (1990-2011) indicates that the relationship between DO and pH may be a persistent predictable feature in Puget Sound with biological implications, given that biological stress associated with low DO is likely to be accompanied by low pH stress
The influence of land use on the nearshore pelagic foodweb
In the oceanographically diverse and urbanized fjord estuary we know as greater Puget Sound, our ... more In the oceanographically diverse and urbanized fjord estuary we know as greater Puget Sound, our scientific understanding of pelagic ecology is poor, and systematic monitoring and assessment of living systems has long been neglected. Improved understanding of biological responses to our human footprint is needed to predict the response of the pelagic ecosystem to human actions. In this talk, we examine existing spatial and seasonal patterns of Puget Sound’s nearshore pelagic foodwebs measured along natural and anthropogenic gradients. We tested whether abiotic and biotic metrics were sensitive to land use activities (urbanization and agriculture) in the catchments surrounding sampling sites in nearshore pelagic waters. To address this question, we conducted a large survey effort (monthly sampling of 79 sites from April to October) in 2011 examining multiple foodweb components in nearshore surface waters of six oceanographic sub-basins of Puget Sound. We observed strong spatial and seasonal structure in a suite of abiotic variables (e.g., temperature, dissolved oxygen, pH, inorganic nutrients) and biological attributes (e.g., bacterial production, chlorophyll a concentrations, zooplankton density, catch of fish and jellyfish). Despite this large-scale variation, many metrics nevertheless exhibited associations with local measures of land use, although these associations were often subtle (\u3c 10% of the observed variation) and variable across basins. The general pattern was that abiotic and lower trophic attributes were more sensitive and fish abundance and diversity were less sensitive. These findings suggest that current management practices that assume uniform conditions across Puget Sound and that ignore the cumulative effects of land use actions are unlikely to adequately redress human impacts on pelagic ecosystems
Patterns and relationships of lower trophic levels of Puget Sound's pelagic food web
Unicellular microscopic organisms are the interface between the marine chemical domain and the pe... more Unicellular microscopic organisms are the interface between the marine chemical domain and the pelagic food web. Phytoplankton, bacteria, and archea transfer molecules to and from food webs, but can be limited by physical parameters such as insolation and temperature. A geographically extensive survey of Puget Sound in 2011 addressed patterns and relationships of the lower trophic levels of the pelagic food web. Chlorophyll a and fluorescence (primary production proxies) were positively associated with bacterial biomass and heterotrophic production, while all four of these biotic measures displayed strong inverse relationships with dissolved nutrients. These observations coupled with nitrate stable isotope results suggest microbes were effectively regulating inorganic nitrogen and phosphorous concentrations. The abundance of picophytoplankton was positively associated with cyanobacterial (Synecococcus spp.) abundance, the abundance of low nucleic acid bacterioplankton, silicic acid concentration, and pH across the six oceanographic basins surveyed, indicating coordinated fluctuations of microbial subsets and abiotic conditions. The structures of bacterial communities, which were characterized by DNA profiling, displayed convergent patterns between adjacent oceanographic basins over time, with highest similarities occurring in the fall. Hood Canal, however, was distinct from other basins in bacterial community structure and in concentration of dissolved inorganic nitrogen. Anthropogenic influences were measured by detection of human-sourced or bovine-sourced fecal indicators, which were observed most frequently at sites near urban centers or in basins with higher densities of dairy operations, respectively. These observations highlight the value of integrated measurements in evaluating lower trophic levels of pelagic food webs
Mucorales infections are increasing in frequency and are a One Health pathogen of concern. In hum... more Mucorales infections are increasing in frequency and are a One Health pathogen of concern. In humans and domestic animals, risk factors include being immunocompromised, elevated circulating serum iron, contaminated open wounds, or metabolic diseases such as ketoacidosis or uncontrolled diabetes. Mucormycosis was first identified in 2012 in Pacific Northwest marine mammals, predominantly in harbor porpoises. We performed an assessment to determine the overall qualitative risk, or risk score, of mucormycosis in harbor porpoises. Risk factors for this disease are unknown in aquatic mammals. In a separate risk factor analysis, potential risk factors such as pollutants, trace metals (e.g., iron), and co-infection with other pathogens (e.g., viruses and Brucella spp.) were examined in mucormycosis cases and noncases using a matched case-control study design, to determine the presence and strength of association of these factors with mucormycosis. Disease severity (gross and histopathology...
Opportunities to assess odontocete health are restricted due to their limited time at the surface... more Opportunities to assess odontocete health are restricted due to their limited time at the surface, relatively quick movements and large geographic ranges. For endangered populations such as the southern resident killer whales (SKRWs) of the northeast Pacific Ocean, taking advantage of non-invasive samples such as expelled mucus and exhaled breath is appealing. Over the past 12 years, such samples were collected, providing a chance to analyse and assess their bacterial microbiomes using amplicon sequencing. Based on operational taxonomic units, microbiome communities from SRKW and transient killer whales showed little overlap between mucus, breath and seawater from SRKW habitats and six bacterial phyla were prominent in expelled mucus but not in seawater. Mollicutes and Fusobacteria were common and abundant in mucus, but not in breath or seawater, suggesting these bacterial classes may be normal constituents of the SRKW microbiome. Out of 134 bacterial families detected, 24 were uniq...
Ocean acidification and disease: How will a changing climate impact Vibrio tubiashii growth and p... more Ocean acidification and disease: How will a changing climate impact Vibrio tubiashii growth and pathogenicity to Pacific oyster larvae?
Influence of waste water treatment plants on water quality and microbiota within Penn Cove
Anthropogenic point sources, such as waste water treatment plants (WWTP) are often considered as ... more Anthropogenic point sources, such as waste water treatment plants (WWTP) are often considered as contributors to hypoxic conditions due to nutrient enrichment. Penn Cove, which is located within Whidbey basin of Puget Sound, has been designated as an impaired water body due to chronic low dissolved oxygen (DO). To determine whether the WWTP outfalls in Penn Cove might contribute to low DO, we assessed relationships among physical parameters, dissolved nutrients, and microbial features, such as bacterial community structure and heterotrophic production, both within and outside of Penn Cove. Hyperbenthic DO measurements revealed contrasting monthly patterns with low values in August and November and higher values in February and May. Concentrations of dissolved nutrients varied both temporally and by depth, but concentration patterns were similar regardless of distance from WWTP outfalls. Similarly, abundances of microbial populations, such as total baterioplankton, picophytoplankton, and coccoid cyanobacteria (Synechococcus spp) were associated with sampling month, rather than WWTP outfalls. Linkages of bacterial community structure were found among sampling locations, however the strongest relationships between community structures were seen by season and depth, rather than proximity to WWTPs. The abundances of indicators for human- or bovine-sourced fecal bacteria were positively associated with mean daily flow at the lower Skagit River during the prior month, but not by proximity to WWTP outfalls. Furthermore, total suspended particles and particles with associated bacterioplankton were both correlated with Skagit River flow (Pearson\u27s r \u3e 0.61), suggesting that Penn Cove may be strongly influenced by the Skagit River. WWTP influences on nutrient inputs, microbial abundances, and bacterial community structure appear to be minimal compared to the seasonally driven influences, such as river discharge from the nearby Skagit River
A survey of marine pelagic coastal microbial communities was conducted over a large geographic la... more A survey of marine pelagic coastal microbial communities was conducted over a large geographic latitude range, from Cape Mendocino in northern California USA to Queen Charlotte Sound in British Columbia Canada, during the spring to summer transition. DNA metabarcoding and flow cytometry were used to characterize microbial communities. Physical and chemical oceanography indicated moderate conditions during the survey with no widespread upwelling, marine heat wave, or other extreme conditions. However, four locations displayed features approaching acidified conditions: Heceta Head, Newport, Copalis Beach, and Cape Flattery. Although bacterial and archaeal communities at the Juan de Fuca canyon and northward had high similarity, those south of the Juan de Fuca canyon were well differentiated from each other. In contrast, eukaryotic microbial communities exhibited stronger geographic differentiation than bacterial and archaeal communities across the extent of the survey. Seawater parameters that were best predictors of bacterial and archaeal community structure were temperature, pH, and dissolved inorganic nutrients (nitrate, phosphate, silicate), while those that were best predictors of eukaryotic microbial community structure were salinity, dissolved oxygen, total alkalinity, and dissolved inorganic nutrients (nitrite, silicate). Although five bacterial and archaeal indicators for potentially corrosive waters were identified (Colwellia, Nitrosopumilus, Nitrosopelagicus, Sup05 cluster, Sva0996 marine group), no eukaryotic microbial indicators were found. Potentially pathogenic taxa detected in the survey included four disease-causing bacteria for mammals, finfish, and/or shellfish (Coxiella, Flavobacterium, Francisella, Tenacibaculum), sixteen genera of microalgae capable of producing biotoxins, and fifteen parasitic species. This study demonstrates the value of coordinating microbial sampling and analysis with broadscale oceanographic surveys to generate insights into community structures of these important pelagic trophic levels. KEYWORDS nearshore microbial communities, bacteria and archaea, eukaryotic phytoplankton, 16S and 18S rRNA metabarcoding, Northeastern Pacific Ocean Frontiers in Marine Science frontiersin.org 01
Marine aquaculture in the United States primarily produces bivalves (oysters, clams, mussels), cr... more Marine aquaculture in the United States primarily produces bivalves (oysters, clams, mussels), crustaceans (shrimp), and finfish (salmon), and currently accounts for 21% of domestic fisheries landings. In 2020, the Executive Order on Promoting American Seafood Competitiveness and Economic Growth (E.O. 13921) was established. Among its objectives were to improve U.S. food security, facilitate permitting of aquaculture facilities, and provide environmentally safe and sustainable seafood. Federal support for offshore aquaculture, including ongoing efforts by NOAA to identify Aquaculture Opportunity Areas (AOAs), is likely to result in significant expansion of this industry in the coming decade. This expansion is expected to include marine finfish species other than salmon, and cultivation of seaweed/macroalgae. It is likely to involve a range of entrepreneurs, from small independent operators through larger established corporations. Organism health, disease management, and biosecurity are major concerns for an industry that relies on natural resources. This document presents guidance for conducting marine aquaculture that protects the health of cultured organisms and the natural resources where an aquaculture farm is located. This review is based on peer-reviewed science, aquaculture practitioner observations, and existing regulations or policies within the United States or from nations with mature aquaculture industries. Furthermore, this review can inform and augment any national plan or policy governing marine aquaculture in federally managed waters. This document is intended to be a readable reference; considerable effort has been made to keep the text succinct, accurate, and free of highly technical terminology. It begins with a short introduction to biosecurity, followed by disease management and biosecurity across the three aquaculture sectors (finfish, shellfish, and seaweed/macroalgae). The next sections present topics specific to each of these sectors. The next section presents examples of region-specific biosecurity threats for the Gulf of Mexico and Southern California. The final section is a summary of a workshop on marine aquaculture best practices that included participants from the aquaculture industry, disease researchers and diagnosticians, and government agencies. Although technologies to monitor health and disease are constantly emerging, good husbandry and awareness of vulnerabilities to disease threats are at the heart of maintaining biosecurity. The guidance and practices described in this document consistently reach back to these fundamentals.
Disease epidemiology requires information about ecological and environmental condi- tions to iden... more Disease epidemiology requires information about ecological and environmental condi- tions to identify factors that can influence disease progression. Bacterial kidney disease (BKD) is an endemic disease among Pacific Northwest salmonids that causes significant morbidity and mortality in artificially propagated stocks, but risk factors for infection among free-living salmon are unknown. We evaluated infection by the causative agent of BKD, Renibacterium salmoninarum, in 1752 fish across 52 sampling sites monthly from May to November 2003 as a component of a broader study of neritic habitat use in Puget Sound by juvenile Chinook salmon Oncorhynchus tshawytscha. Infection intensity was ≤10 cells per slide for 77% of the fish. Correlations between the density of Chinook salmon with infection prevalence and with infection intensity were observed across multiple spatial scales. Capture location was a stronger predictor of infection than fish origin (based on coded wire tags) or genetic stock. Influential risk factors by logistic regression were temperature, densities of marked and unmarked Chinook salmon, and density of river lamprey Lampetra ayresis. Renibac- terium salmoninarum were found in gut contents and kidney of river lamprey, suggesting this species may be a transmission vector. The low infection intensity, lack of an effect of fish origin, effect of capture bay, and strong associations with Chinook salmon density are consistent with horizontal transmission of R. salmoninarum during the juvenile neritic phase, posing a potential for infectious interaction between sympatric hatchery and wild fish.
Investigating the contribution of kelp- and eelgrass-derived carbon and nitrogen to marine herbivores and carnivores in Puget Sound
In the Salish Sea Nereocystis luetkeana (bull kelp) and Zostera marina (eelgrass) are highly prod... more In the Salish Sea Nereocystis luetkeana (bull kelp) and Zostera marina (eelgrass) are highly productive and because of their three-dimensional size and structure are reported to provide shelter for a variety of valued Puget Sound species, including Species of Concern like Chinook salmon, Oncorhynchus tshawytscha, and quillback rockfish, Sebastes maliger. Less understood is the extent to which bull kelp forests and eelgrass beds are a source of energy for invertebrates and fishes. To answer this question we conducted a project in 2018 and 2019 to reconstruct the trophic linkages among kelp, seagrass, and several herbivorous and carnivorous species, including rockfish. We used stable isotopes of carbon and nitrogen to estimate the kelp- and eelgrass-derived isotope contributions to invertebrate and fish tissue. Understanding these connections, and their strengths, is necessary for effective management and recovery. In this presentation we will place our findings in the context of ongoing kelp recovery plans
In response to reported findings of infectious salmon anaemia virus (ISAV) in British Columbia (B... more In response to reported findings of infectious salmon anaemia virus (ISAV) in British Columbia (BC), Canada, in 2011, U.S. national, state and tribal fisheries managers and fish health specialists developed and implemented a collaborative ISAV surveillance plan for the Pacific Northwest region of the United States. Accordingly, over a 3‐1/2‐year period, 4,962 salmonids were sampled and successfully tested by real‐time reverse‐transcription PCR. The sample set included multiple tissues from free‐ranging Pacific salmonids from coastal regions of Alaska and Washington and farmed Atlantic salmon (Salmo salar L.) from Washington, all representing fish exposed to marine environments. The survey design targeted physiologically compromised or moribund animals more vulnerable to infection as well as species considered susceptible to ISAV. Samples were handled with a documented chain of custody and testing protocols, and criteria for interpretation of test results were defined in advance. All...
Chinook Salmon (Oncorhynchus tshawytscha) Have Multiple Interferon-gamma Genes (81.7)
The Journal of Immunology
Interferon-gamma (IFNg) is a central cytokine in modulating innate and adaptive immunity in a wid... more Interferon-gamma (IFNg) is a central cytokine in modulating innate and adaptive immunity in a wide range of vertebrates. A study of genes associated with an effective host response by Chinook salmon (Oncorhynchus tshawytscha) to a persistent Gram-positive bacterial pathogen (Renibacterium salmoninarum) suggested that an interferon-inducible signal was abrogated during early stages of exposure. Splenic DNA was amplified with IFNg primers from a related species, rainbow trout (Oncorhynchus mykiss), and multiple clones from individual fish were sequenced. Up to five genotypes per fish were found, and sequence variations included microsatellites within introns and single nucleotide polymorphisms (SNPs) within exons. Southern hybridizations supported the prediction that Chinook salmon possess at least three related IFNg loci. Multiple clones of cDNA, synthesized from RNA isolated from pronephros of fish exposed to an attenuated strain of R. salmoninarum, displayed a surprising abundance ...
Invertebrate, Microbial, and Environmental Data from Surface and Hyporheic Waters of Urban and Forested Streams of the Cedar River-Lake Washington Watershed
Abstract Sablefish ( Anoplopoma fimbria ) is a highly desired seafood product, which encourages d... more Abstract Sablefish ( Anoplopoma fimbria ) is a highly desired seafood product, which encourages development of sustainable aquaculture methods for this marine fish. Conventional marine fish-based feeds provide essential nutrients including long chain fatty acids for piscivorous species such as sablefish. Alternative terrestrial ingredients could reduce fishing pressures on pelagic species that are the source of fish meal and fish oil, and improve source sustainability. Using juvenile sablefish, we compared the effects of a standard fish-based diet to two diets that contained primarily terrestrial plant ingredients with flaxseed or corn oil replacing the added fish oil. After an 8-week trial feeding period, there were striking differences attributable to diet. Fish receiving the alternative feeds had lower weight gain and shorter length than fish receiving the fish-based feed, suggesting sablefish obtained lower nutrients from the alternative feeds. Among the histological differences, the intestinal mucosa was significantly less vacuolated and the frequency of intestinal mucous cells was reduced in alternative feed fish. The most dramatic lesions were observed in the liver, where severe bile duct hyperplasia (53%, flaxseed oil diet; 33%, corn oil diet), and hepatocellular lesions (nuclear pleomorphism/megalocytosis, regeneration, hypertrophy, clear cell foci) occurred in only alternative feed fish. The hepatic and biliary lesions indicate the alternative diets may be deficient or possibly harmful to sablefish. The bacterial community structures from corn oil fish showed much less diversity than those for the other diets, and the microbiome structures from the three diets were distinctly different from each other. The intestinal microbiome for the fish-based diet included the largest number of families (68), and these fish also had the largest number of unique bacterial families (11) compared to those for corn oil (two) or flaxseed oil (one) fish. Regardless of diet, the stomach and intestinal microbiomes differed significantly from each other, and the feed microbiome differed from all gastrointestinal communities, suggesting that feed is not a significant source of gut bacterial diversity. Similar to other teleosts, the sablefish gastrointestinal microbiome is dominated by Bacteroidetes, Firmicutes, and Proteobacteria. These results suggest that diet-induced shifts in microbiome can occur relatively quickly in sablefish, but the shifts may not be sufficiently adaptive or cannot overcome nutrient deficiencies. This multidisciplinary study demonstrates the utility of histology and microbiology in characterizing dietary effects for novel aquaculture species. Statement of relevance Physiological assessments such as gastrointestinal microbiomes and histopathology can provide a near-term evaluation of the nutritional adequacy of alternative feeds, such as plant-based lipid diets for marine carnivorous finfish. This is the first examination of the microbiome of sablefish, a marine species under development for sustainable aquaculture.
Physical attributes of nearshore waters across greater Puget Sound, with an emphasis on dissolved oxygen and pH
The pelagic zone is a major part of the Puget Sound ecosystem that is sensitive to human influenc... more The pelagic zone is a major part of the Puget Sound ecosystem that is sensitive to human influences, yet our understanding of relationships among its abiotic features, water quality, biota, and anthropogenic influences in spatial and temporal context is limited. To characterize the pelagic zone in greater detail, we conducted a multi-trophic level assessment that measured over 20 potential indicators of pelagic ecosystem health at 79 sites in six oceanographic basins of Puget Sound from April to October 2011. Among the many strong spatiotemporal patterns observed were basin and seasonal differences in temperature, salinity, and turbidity linked to freshwater influences; and inorganic nutrient concentrations. DO concentrations also followed distinct seasonal patterns within oceanographic basins. Seasonally, the monthly percentage of sites with DO concentrations below the threshold for biological stress of 5 mg L-1 increased from 0% in April to 45% in October. Spatially, DO concentrations below 5 mg L-1 were recorded at sites within all basins with the exception of the Central basin. By October, the proportion of sites with biologically stressful DO concentrations was highest among sites in Rosario (100%), Hood Canal (77%), and Whidbey (75%) basins. A persistent significant positive correlation between DO and pH was observed across Puget Sound. Both the strength (R2) and magnitude (slope) of the relationship increased with depth. This linkage was also observed in independently collected water column profiles by the Washington State Department of Ecology (WDOE) in 2011 over the same geographic extent. Furthermore, a 22-year long WDOE dataset (1990-2011) indicates that the relationship between DO and pH may be a persistent predictable feature in Puget Sound with biological implications, given that biological stress associated with low DO is likely to be accompanied by low pH stress
The influence of land use on the nearshore pelagic foodweb
In the oceanographically diverse and urbanized fjord estuary we know as greater Puget Sound, our ... more In the oceanographically diverse and urbanized fjord estuary we know as greater Puget Sound, our scientific understanding of pelagic ecology is poor, and systematic monitoring and assessment of living systems has long been neglected. Improved understanding of biological responses to our human footprint is needed to predict the response of the pelagic ecosystem to human actions. In this talk, we examine existing spatial and seasonal patterns of Puget Sound’s nearshore pelagic foodwebs measured along natural and anthropogenic gradients. We tested whether abiotic and biotic metrics were sensitive to land use activities (urbanization and agriculture) in the catchments surrounding sampling sites in nearshore pelagic waters. To address this question, we conducted a large survey effort (monthly sampling of 79 sites from April to October) in 2011 examining multiple foodweb components in nearshore surface waters of six oceanographic sub-basins of Puget Sound. We observed strong spatial and seasonal structure in a suite of abiotic variables (e.g., temperature, dissolved oxygen, pH, inorganic nutrients) and biological attributes (e.g., bacterial production, chlorophyll a concentrations, zooplankton density, catch of fish and jellyfish). Despite this large-scale variation, many metrics nevertheless exhibited associations with local measures of land use, although these associations were often subtle (\u3c 10% of the observed variation) and variable across basins. The general pattern was that abiotic and lower trophic attributes were more sensitive and fish abundance and diversity were less sensitive. These findings suggest that current management practices that assume uniform conditions across Puget Sound and that ignore the cumulative effects of land use actions are unlikely to adequately redress human impacts on pelagic ecosystems
Patterns and relationships of lower trophic levels of Puget Sound's pelagic food web
Unicellular microscopic organisms are the interface between the marine chemical domain and the pe... more Unicellular microscopic organisms are the interface between the marine chemical domain and the pelagic food web. Phytoplankton, bacteria, and archea transfer molecules to and from food webs, but can be limited by physical parameters such as insolation and temperature. A geographically extensive survey of Puget Sound in 2011 addressed patterns and relationships of the lower trophic levels of the pelagic food web. Chlorophyll a and fluorescence (primary production proxies) were positively associated with bacterial biomass and heterotrophic production, while all four of these biotic measures displayed strong inverse relationships with dissolved nutrients. These observations coupled with nitrate stable isotope results suggest microbes were effectively regulating inorganic nitrogen and phosphorous concentrations. The abundance of picophytoplankton was positively associated with cyanobacterial (Synecococcus spp.) abundance, the abundance of low nucleic acid bacterioplankton, silicic acid concentration, and pH across the six oceanographic basins surveyed, indicating coordinated fluctuations of microbial subsets and abiotic conditions. The structures of bacterial communities, which were characterized by DNA profiling, displayed convergent patterns between adjacent oceanographic basins over time, with highest similarities occurring in the fall. Hood Canal, however, was distinct from other basins in bacterial community structure and in concentration of dissolved inorganic nitrogen. Anthropogenic influences were measured by detection of human-sourced or bovine-sourced fecal indicators, which were observed most frequently at sites near urban centers or in basins with higher densities of dairy operations, respectively. These observations highlight the value of integrated measurements in evaluating lower trophic levels of pelagic food webs
Mucorales infections are increasing in frequency and are a One Health pathogen of concern. In hum... more Mucorales infections are increasing in frequency and are a One Health pathogen of concern. In humans and domestic animals, risk factors include being immunocompromised, elevated circulating serum iron, contaminated open wounds, or metabolic diseases such as ketoacidosis or uncontrolled diabetes. Mucormycosis was first identified in 2012 in Pacific Northwest marine mammals, predominantly in harbor porpoises. We performed an assessment to determine the overall qualitative risk, or risk score, of mucormycosis in harbor porpoises. Risk factors for this disease are unknown in aquatic mammals. In a separate risk factor analysis, potential risk factors such as pollutants, trace metals (e.g., iron), and co-infection with other pathogens (e.g., viruses and Brucella spp.) were examined in mucormycosis cases and noncases using a matched case-control study design, to determine the presence and strength of association of these factors with mucormycosis. Disease severity (gross and histopathology...
Opportunities to assess odontocete health are restricted due to their limited time at the surface... more Opportunities to assess odontocete health are restricted due to their limited time at the surface, relatively quick movements and large geographic ranges. For endangered populations such as the southern resident killer whales (SKRWs) of the northeast Pacific Ocean, taking advantage of non-invasive samples such as expelled mucus and exhaled breath is appealing. Over the past 12 years, such samples were collected, providing a chance to analyse and assess their bacterial microbiomes using amplicon sequencing. Based on operational taxonomic units, microbiome communities from SRKW and transient killer whales showed little overlap between mucus, breath and seawater from SRKW habitats and six bacterial phyla were prominent in expelled mucus but not in seawater. Mollicutes and Fusobacteria were common and abundant in mucus, but not in breath or seawater, suggesting these bacterial classes may be normal constituents of the SRKW microbiome. Out of 134 bacterial families detected, 24 were uniq...
Ocean acidification and disease: How will a changing climate impact Vibrio tubiashii growth and p... more Ocean acidification and disease: How will a changing climate impact Vibrio tubiashii growth and pathogenicity to Pacific oyster larvae?
Influence of waste water treatment plants on water quality and microbiota within Penn Cove
Anthropogenic point sources, such as waste water treatment plants (WWTP) are often considered as ... more Anthropogenic point sources, such as waste water treatment plants (WWTP) are often considered as contributors to hypoxic conditions due to nutrient enrichment. Penn Cove, which is located within Whidbey basin of Puget Sound, has been designated as an impaired water body due to chronic low dissolved oxygen (DO). To determine whether the WWTP outfalls in Penn Cove might contribute to low DO, we assessed relationships among physical parameters, dissolved nutrients, and microbial features, such as bacterial community structure and heterotrophic production, both within and outside of Penn Cove. Hyperbenthic DO measurements revealed contrasting monthly patterns with low values in August and November and higher values in February and May. Concentrations of dissolved nutrients varied both temporally and by depth, but concentration patterns were similar regardless of distance from WWTP outfalls. Similarly, abundances of microbial populations, such as total baterioplankton, picophytoplankton, and coccoid cyanobacteria (Synechococcus spp) were associated with sampling month, rather than WWTP outfalls. Linkages of bacterial community structure were found among sampling locations, however the strongest relationships between community structures were seen by season and depth, rather than proximity to WWTPs. The abundances of indicators for human- or bovine-sourced fecal bacteria were positively associated with mean daily flow at the lower Skagit River during the prior month, but not by proximity to WWTP outfalls. Furthermore, total suspended particles and particles with associated bacterioplankton were both correlated with Skagit River flow (Pearson\u27s r \u3e 0.61), suggesting that Penn Cove may be strongly influenced by the Skagit River. WWTP influences on nutrient inputs, microbial abundances, and bacterial community structure appear to be minimal compared to the seasonally driven influences, such as river discharge from the nearby Skagit River
Although the United States produced 5.4% of the global marine capture fisheries (~4 million tonne... more Although the United States produced 5.4% of the global marine capture fisheries (~4 million tonnes), it also led all other nations in seafood imports in 2020 (1). Among marine aquaculture sectors (finfish, shellfish, seaweed/macroalgae), the United States is only a significant producer of mollusks, where it ranks seventh at ~180,000 tonnes annually (1). Increasing marine aquaculture production in the United States is an approach to reducing import demand. Concurrent with increased production is a need for scientific support on health management and biosecurity to ensure production sustainability, to inform environmental consultations and appropriate site selection for aquaculture operations, and to protect both aquatic stocks and surrounding marine resources. Fortunately, there is an existing wealth of knowledge about aquaculture-based health management and biosecurity in peer-reviewed scientific literature and in current production practices and regulations. This technical memorandum contains an overview of the available science regarding health management and biosecurity throughout the marine aquaculture industry for finfish, invertebrates, and seaweed/macroalgae value chains. This report intends to provide understandable and citable information for non-specialists in marine aquaculture diseases and biosecurity, within the context of NOAA Fisheries’ mission of responsible stewardship of U.S. ocean resources and habitats, and using sound science and an ecosystem-based management approach.1 At points throughout this document, there is information specific to two regions: the Gulf of Mexico and the Southern California Bight. Within each of these regions, NOAA Fisheries previously characterized areas of interest and study areas that included potential Aquaculture Opportunity Area (AOA) options. This information was published in two marine spatial planning atlases, collectively referred to as Aquaculture Atlases (2, 3). The information included here that is specific to those two regions seeks to inform NOAA’s ongoing assessment of the study areas. This document introduces a basic conceptual model of factors affecting disease likelihood, namely host susceptibility, pathogen abundance or virulence, and environmental conditions that favor disease. Lists of pathogens and diseases of known concern for marine aquaculture, and brief descriptions of diseases with common prevention and management actions, are included in the appendices. To help understand how diseases are introduced and disseminated, pathogen transfer mechanisms are briefly described, including: • Waterborne transmission. • Physical contact between infected and susceptible individuals. • Association with organisms (including feeds) that can carry pathogens, either as reservoirs or as intermediate hosts. • Association with substrates and structures. • Active movement by pathogens from infected to other susceptible individuals. 1 https://www.fisheries.noaa.gov/about-us x
The concepts of pathogen transfer from cultured to wild individuals and from wild to cultured individuals are also presented. Because proximity of endemic aquatic species to an aquaculture facility can increase the hazard of pathogen transfer, results of an analysis of geographic overlap of endemic species of concern (federally listed as endangered or threatened, commercially important) with the AOA study areas are presented, with data tables included in the appendices. Although pathogen transmission routes are common for each aquaculture sector (i.e., finfish, shellfish, seaweed/macroalgae), requirements and practices for each sector are different. Health management and biosecurity topics specific to each sector are presented in separate sections. Because factors affect disease throughout the production cycle, these are presented sequentially (e.g., hatchery or nursery, transport, grow-out) for each sector. Modern commercial finfish aquaculture formally began in the United States in 1853 with brook trout (Salvelinus fontinalis) in Ohio, and rearing salmonids for release to supplement commercial and recreational harvests became established in the 1870s (4). Information on marine finfish aquaculture in the United States is dominated by the culture of salmonids (5), and the wealth of information on biosecurity from that sector of the industry is often applied to other marine finfish species. However, there are significant differences between salmonid and non-salmonid aquaculture practices, such as differences in early-stage feeding strategies and differences in pathogen susceptibilities. Influent water security and reliability are essential during hatchery and nursery phases, and recirculating aquaculture systems are increasingly used for these life stages due to the feasibility and economics of managing the reduced volume of influent water. The hope of disease-resistant fish stocks remains mostly unrealized at this time. Transport and grow-out practices rely increasingly on better equipment (e.g., self-contained transport boats), operational planning for both routine and emergency events, and staff biosecurity training. Because marine finfish facilities attract and aggregate wildlife, which increases the potential for pathogen or disease transmission, a discussion about the causes, effects, and mitigations is included. Potential water chemistry changes from a finfish facility, such as dissolved nutrients and benthic deposition, are briefly described. An examination of the average depths for the AOA options in the Gulf of Mexico and Southern California indicate that most are deep enough to sustain low benthic impact from a farm. The long history of molluskan aquaculture in the United States and current production scale implies that it may have more advanced procedures in place for disease management and biosecurity relative to finfish and seaweed/macroalgae. However, the open- environment nature of molluskan aquaculture makes it vulnerable to pathogen exposure, and using healthy seed is one of the best biosecurity measures. The United States does have some advanced planning, such as the Regional Shellfish Seed Biosecurity Program (RSSBP), developed to streamline animal movement through evaluations and audits of shellfish nurseries (6). Nonetheless, pathogens such as OsHV-1 (virus) and Perkinsus spp. (protozoan parasites) pose persistent threats to the industry. Hatchery and nursery operations require a secure incoming water supply, similar to the needs in finfish culture. Potential exposure to pathogens can be reduced through filtration, UV treatment (alone or following filtration), and by timing plantings and grow-out transfers for favorable temperature regimes or a lower likelihood of pathogen presence in seawater. Because invertebrates lack the adaptive immunity found in vertebrates, traditional vaccination is not possible. Currently, much xi
of invertebrate health management relies on stress reduction through environmental optimization, including good seawater quality, density management, temperature management, and minimizing handling. Breeding for disease resistance is possible in shellfish, and genomic sequencing is likely to identify gene targets for selection. Although commercial-scale seaweed/macroalgae aquaculture has been established in Asia since the 1950s, it is a relatively young industry in the United States and Europe, where the cultivated species are different from those reared in Asia. Knowledge of diseases for seaweed/macroalgae cultured in the United States and Europe is not as well developed as for finfish and invertebrates. Seaweed/macroalgae naturally carry other organisms, including other algal species, on their surfaces, and preventing introduction of non-native species is a biosecurity concern for broodstock and seedling selection and before outplanting. Unfavorable environmental conditions, such as temperature shocks, appear to be primary initiating factors for disease development. A genetic approach to identifying specific pathogens of seaweed/macroalgae is increasingly feasible with the expansion of molecular tools to characterize and identify beneficial and harmful microorganisms. The effects of future climate change on aquaculture may be anticipated from observations of changes in natural settings and from controlled experiments. For the AOA areas of interest of the Gulf of Mexico and Southern California, International Panel on Climate Change Coupled Model Intercomparison Project 6 (IPCC CMIP6) models project that average sea surface temperatures will rise between 0.6°C and 0.8°C, that surface pH will decrease 0.1 units, and that dissolved oxygen and salinities will decline (7). Cultured species unable to move from unfavorable environmental conditions will experience higher physiological stress and changes in their associated beneficial microbial communities (their “microbiomes”), potentially increasing susceptibility to infection and disease. Temperature fluxes, such as marine heat waves, are expected to be a major driver to vulnerability to disease, because adjustment and adaptations can be more metabolically demanding. Changes in temperature and pH can independently and synergistically alter ocean chemistry, such as dissolved oxygen, dissolved nutrients, and bioavailable carbonate for calcification. Lower pH can reduce immune responsiveness in shellfish and finfish, and early life stages are especially vulnerable to negative effects. Climate changes are already altering the distribution of fisheries species, changing the endemic species composition and the potential for disease transmission near aquaculture facilities. There will also be impacts on indigenous pathogens, which can change their geographic distribution or ability to cause disease. For example, certain ectoparasites can tolerate a wider range of seawater pH than the hosts, possibly resulting in more severe infestations. In the two AOAs of interest, increased hypoxia (Gulf of Mexico) and o...
Background: and wild organisms are major concerns. This document summarizes guidance and
best pr... more Background: and wild organisms are major concerns. This document summarizes guidance and best practices for disease management and biosecurity for marine aquaculture in the United States, including a report from a July 2022 workshop on best practices for disease management in marine aquaculture. This review relied upon peer-reviewed science, the observations and experience of aquaculture practitioners, and current regulations and policies, both domestic and international. Specifically, this document provides information supporting NOAA Fisheries’ assessments of Aquaculture Opportunity Areas in the Gulf of Mexico and Southern California. Key Points: Biosecurity includes plans and actions to prevent the introduction and spread of diseases within a culture facility. • A biosecurity plan for an aquaculture facility is a critical tool for preventing and managing disease. It requires good knowledge of the cultured organisms and the facility’s operations to accurately identify hazards and actions to prevent and mitigate those hazards. • There are common features for disease management and biosecurity for shellfish, finfish, and seaweed/macroalgae. These include appropriate stock selection, incoming water quality and security, quarantine, disinfection and decontamination, health and pathogen surveillance, and environmental monitoring. • Each aquaculture sector (shellfish, finfish, and seaweed/macroalgae) has biosecurity needs specific to the type of cultured organism. • The Aquaculture Opportunity Areas of the Gulf of Mexico and Southern California have region-specific issues that can affect biosecurity, including hurricanes, petroleum pollution, harmful algal blooms, wildfires, and pesticides.
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of domestic fisheries landings. In 2020, the Executive Order on Promoting American Seafood Competitiveness and Economic Growth (E.O. 13921) was established. Among its objectives were to improve U.S. food security, facilitate permitting of aquaculture facilities, and provide environmentally safe and sustainable seafood. Federal support for offshore aquaculture, including ongoing efforts by NOAA to identify Aquaculture Opportunity Areas (AOAs), is likely to result in significant expansion of this industry in the coming decade. This expansion is expected to include marine finfish species other than salmon, and cultivation of seaweed/macroalgae. It is likely to involve a range of entrepreneurs, from small independent operators through larger established corporations.
Organism health, disease management, and biosecurity are major concerns for an industry that relies on natural resources. This document presents guidance for conducting marine aquaculture that protects the health of cultured organisms and the natural resources where an aquaculture farm is located. This review is based on peer-reviewed science, aquaculture practitioner observations, and existing regulations or policies within the United States or from nations with mature aquaculture industries. Furthermore, this review can inform and augment any national plan or policy governing marine aquaculture in federally managed waters.
This document is intended to be a readable reference; considerable effort has been made to keep the text succinct, accurate, and free of highly technical terminology. It begins with a short introduction to biosecurity, followed by disease management and biosecurity across the three aquaculture sectors (finfish, shellfish, and seaweed/macroalgae). The next sections present topics specific to each of these sectors. The next section presents examples of region-specific biosecurity threats for the Gulf of Mexico and Southern California. The final section is a summary of a workshop on marine aquaculture best practices that included participants from the aquaculture industry, disease researchers and diagnosticians, and government agencies.
Although technologies to monitor health and disease are constantly emerging, good husbandry and awareness of vulnerabilities to disease threats are at the heart of maintaining biosecurity. The guidance and practices described in this document consistently reach back to these fundamentals.
of domestic fisheries landings. In 2020, the Executive Order on Promoting American Seafood Competitiveness and Economic Growth (E.O. 13921) was established. Among its objectives were to improve U.S. food security, facilitate permitting of aquaculture facilities, and provide environmentally safe and sustainable seafood. Federal support for offshore aquaculture, including ongoing efforts by NOAA to identify Aquaculture Opportunity Areas (AOAs), is likely to result in significant expansion of this industry in the coming decade. This expansion is expected to include marine finfish species other than salmon, and cultivation of seaweed/macroalgae. It is likely to involve a range of entrepreneurs, from small independent operators through larger established corporations.
Organism health, disease management, and biosecurity are major concerns for an industry that relies on natural resources. This document presents guidance for conducting marine aquaculture that protects the health of cultured organisms and the natural resources where an aquaculture farm is located. This review is based on peer-reviewed science, aquaculture practitioner observations, and existing regulations or policies within the United States or from nations with mature aquaculture industries. Furthermore, this review can inform and augment any national plan or policy governing marine aquaculture in federally managed waters.
This document is intended to be a readable reference; considerable effort has been made to keep the text succinct, accurate, and free of highly technical terminology. It begins with a short introduction to biosecurity, followed by disease management and biosecurity across the three aquaculture sectors (finfish, shellfish, and seaweed/macroalgae). The next sections present topics specific to each of these sectors. The next section presents examples of region-specific biosecurity threats for the Gulf of Mexico and Southern California. The final section is a summary of a workshop on marine aquaculture best practices that included participants from the aquaculture industry, disease researchers and diagnosticians, and government agencies.
Although technologies to monitor health and disease are constantly emerging, good husbandry and awareness of vulnerabilities to disease threats are at the heart of maintaining biosecurity. The guidance and practices described in this document consistently reach back to these fundamentals.
At points throughout this document, there is information specific to two regions: the Gulf of Mexico and the Southern California Bight. Within each of these regions, NOAA Fisheries previously characterized areas of interest and study areas that included potential Aquaculture Opportunity Area (AOA) options. This information was published in two marine spatial planning atlases, collectively referred to as Aquaculture Atlases (2, 3). The information included here that is specific to those two regions seeks to inform NOAA’s ongoing assessment of the study areas.
This document introduces a basic conceptual model of factors affecting disease likelihood, namely host susceptibility, pathogen abundance or virulence, and environmental conditions that favor disease. Lists of pathogens and diseases of known concern for marine aquaculture, and brief descriptions of diseases with common prevention and management actions, are included in the appendices. To help understand how diseases are introduced and disseminated, pathogen transfer mechanisms are briefly described, including:
• Waterborne transmission.
• Physical contact between infected and susceptible individuals.
• Association with organisms (including feeds) that can carry pathogens, either as
reservoirs or as intermediate hosts.
• Association with substrates and structures.
• Active movement by pathogens from infected to other susceptible individuals.
1 https://www.fisheries.noaa.gov/about-us
x
The concepts of pathogen transfer from cultured to wild individuals and from wild to cultured individuals are also presented. Because proximity of endemic aquatic species to an aquaculture facility can increase the hazard of pathogen transfer, results of an analysis of geographic overlap of endemic species of concern (federally listed as endangered or threatened, commercially important) with the AOA study areas are presented, with data tables included in the appendices.
Although pathogen transmission routes are common for each aquaculture sector (i.e., finfish, shellfish, seaweed/macroalgae), requirements and practices for each sector are different. Health management and biosecurity topics specific to each sector are presented in separate sections. Because factors affect disease throughout the production cycle, these are presented sequentially (e.g., hatchery or nursery, transport, grow-out) for each sector.
Modern commercial finfish aquaculture formally began in the United States in 1853 with brook trout (Salvelinus fontinalis) in Ohio, and rearing salmonids for release to supplement commercial and recreational harvests became established in the 1870s (4). Information on marine finfish aquaculture in the United States is dominated by the culture of salmonids (5), and the wealth of information on biosecurity from that sector of the industry is often applied to other marine finfish species. However, there are significant differences between salmonid and non-salmonid aquaculture practices, such as differences in early-stage feeding strategies and differences in pathogen susceptibilities. Influent water security and reliability are essential during hatchery and nursery phases, and recirculating aquaculture systems are increasingly used for these life stages due to the feasibility and economics of managing the reduced volume of influent water. The hope of disease-resistant fish stocks remains mostly unrealized at this time. Transport and grow-out practices rely increasingly on better equipment (e.g., self-contained transport boats), operational planning for both routine and emergency events, and staff biosecurity training. Because marine finfish facilities attract and aggregate wildlife, which increases the potential for pathogen or disease transmission, a discussion about
the causes, effects, and mitigations is included. Potential water chemistry changes from a finfish facility, such as dissolved nutrients and benthic deposition, are briefly described. An examination of the average depths for the AOA options in the Gulf of Mexico and Southern California indicate that most are deep enough to sustain low benthic impact from a farm.
The long history of molluskan aquaculture in the United States and current production scale implies that it may have more advanced procedures in place for disease management and biosecurity relative to finfish and seaweed/macroalgae. However, the open- environment nature of molluskan aquaculture makes it vulnerable to pathogen exposure, and using healthy seed is one of the best biosecurity measures. The United States does have some advanced planning, such as the Regional Shellfish Seed Biosecurity Program (RSSBP), developed to streamline animal movement through evaluations and audits of shellfish nurseries (6). Nonetheless, pathogens such as OsHV-1 (virus) and Perkinsus spp. (protozoan parasites) pose persistent threats to the industry. Hatchery and nursery operations require a secure incoming water supply, similar to the needs in finfish culture. Potential exposure to pathogens can be reduced through filtration, UV treatment (alone or following filtration), and by timing plantings and grow-out transfers for favorable temperature regimes or a lower likelihood of pathogen presence in seawater. Because invertebrates lack the adaptive immunity found in vertebrates, traditional vaccination is not possible. Currently, much
xi
of invertebrate health management relies on stress reduction through environmental optimization, including good seawater quality, density management, temperature management, and minimizing handling. Breeding for disease resistance is possible in shellfish, and genomic sequencing is likely to identify gene targets for selection.
Although commercial-scale seaweed/macroalgae aquaculture has been established in Asia since the 1950s, it is a relatively young industry in the United States and Europe, where
the cultivated species are different from those reared in Asia. Knowledge of diseases for seaweed/macroalgae cultured in the United States and Europe is not as well developed
as for finfish and invertebrates. Seaweed/macroalgae naturally carry other organisms, including other algal species, on their surfaces, and preventing introduction of non-native species is a biosecurity concern for broodstock and seedling selection and before outplanting. Unfavorable environmental conditions, such as temperature shocks, appear to be primary initiating factors for disease development. A genetic approach to identifying specific pathogens of seaweed/macroalgae is increasingly feasible with the expansion of molecular tools to characterize and identify beneficial and harmful microorganisms.
The effects of future climate change on aquaculture may be anticipated from observations of changes in natural settings and from controlled experiments. For the AOA areas of interest of the Gulf of Mexico and Southern California, International Panel on Climate Change Coupled Model Intercomparison Project 6 (IPCC CMIP6) models project that average sea surface temperatures will rise between 0.6°C and 0.8°C, that surface pH will decrease 0.1 units,
and that dissolved oxygen and salinities will decline (7). Cultured species unable to move from unfavorable environmental conditions will experience higher physiological stress
and changes in their associated beneficial microbial communities (their “microbiomes”), potentially increasing susceptibility to infection and disease. Temperature fluxes, such as marine heat waves, are expected to be a major driver to vulnerability to disease, because adjustment and adaptations can be more metabolically demanding. Changes in temperature and pH can independently and synergistically alter ocean chemistry, such as dissolved oxygen, dissolved nutrients, and bioavailable carbonate for calcification. Lower pH can reduce immune responsiveness in shellfish and finfish, and early life stages are especially vulnerable to negative effects. Climate changes are already altering the distribution of fisheries species, changing the endemic species composition and the potential for disease transmission near aquaculture facilities. There will also be impacts on indigenous pathogens, which can change their geographic distribution or ability to cause disease. For example, certain ectoparasites can tolerate a wider range of seawater pH than the hosts, possibly resulting in more severe infestations. In the two AOAs of interest, increased hypoxia (Gulf of Mexico) and o...
best practices for disease management and biosecurity for marine aquaculture in the United States, including a report from a July 2022 workshop on best practices for disease management in marine aquaculture. This review relied upon peer-reviewed science, the observations and experience of aquaculture practitioners, and current regulations and policies, both domestic and international. Specifically, this document provides information supporting NOAA Fisheries’ assessments of Aquaculture Opportunity Areas in the Gulf of Mexico and Southern California.
Key Points:
Biosecurity includes plans and actions to prevent the introduction and spread of diseases within a culture facility.
• A biosecurity plan for an aquaculture facility is a critical tool for preventing and managing disease. It requires good knowledge of the cultured organisms and the facility’s operations to accurately identify hazards and actions to prevent and mitigate those hazards.
• There are common features for disease management and biosecurity for shellfish, finfish, and seaweed/macroalgae. These include appropriate stock selection, incoming water quality and security, quarantine, disinfection and decontamination, health and pathogen surveillance, and environmental monitoring.
• Each aquaculture sector (shellfish, finfish, and seaweed/macroalgae) has biosecurity needs specific to the type of cultured organism.
• The Aquaculture Opportunity Areas of the Gulf of Mexico and Southern California have region-specific issues that can affect biosecurity, including hurricanes, petroleum pollution, harmful algal blooms, wildfires, and pesticides.