1
|
Koll R, Theilen J, Hauten E, Woodhouse JN, Thiel R, Möllmann C, Fabrizius A. Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173656. [PMID: 38830414 DOI: 10.1016/j.scitotenv.2024.173656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.
Collapse
Affiliation(s)
- Raphael Koll
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany.
| | - Jesse Theilen
- University of Hamburg, Department of Biology, Biodiversity Research, Germany
| | - Elena Hauten
- University of Hamburg, Institute of Marine Ecosystem and Fishery Science, Marine ecosystem dynamics, Germany
| | - Jason Nicholas Woodhouse
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Microbial and phytoplankton Ecology, Germany
| | - Ralf Thiel
- Leibniz Institute for the Analysis of Biodiversity Change (LIB) - Hamburg site, Centre for Taxonomy & Morphology, Zoological Museum, Germany; University of Hamburg, Department of Biology, Biodiversity Research, Germany
| | - Christian Möllmann
- University of Hamburg, Institute of Marine Ecosystem and Fishery Science, Marine ecosystem dynamics, Germany
| | - Andrej Fabrizius
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany
| |
Collapse
|
2
|
Hechler RM, Yates MC, Chain FJJ, Cristescu ME. Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms? Mol Ecol 2023. [PMID: 37792902 DOI: 10.1111/mec.17152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 08/10/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
To safeguard biodiversity in a changing climate, taxonomic information about species turnover and insights into the health of organisms are required. Environmental DNA approaches are increasingly used for species identification, but cannot provide functional insights. Transcriptomic methods reveal the physiological states of macroorganisms, but are currently species-specific and require tissue sampling or animal sacrifice, making community-wide assessments challenging. Here, we test whether broad functional information (expression level of the transcribed genes) can be harnessed from environmental RNA (eRNA), which includes extra-organismal RNA from macroorganisms along with whole microorganisms. We exposed Daphnia pulex as well as phytoplankton prey and microorganism colonizers to control (20°C) and heat stress (28°C) conditions for 7 days. We sequenced eRNA from tank water (after complete removal of Daphnia) as well as RNA from Daphnia tissue, enabling comparisons of extra-organismal and organismal RNA-based gene expression profiles. Both RNA types detected similar heat stress responses of Daphnia. Using eRNA, we identified 32 Daphnia genes to be differentially expressed following heat stress. Of these, 17 were also differentially expressed and exhibited similar levels of relative expression in organismal RNA. In addition to the extra-organismal Daphnia response, eRNA detected community-wide heat stress responses consisting of distinct functional profiles and 121 differentially expressed genes across eight taxa. Our study demonstrates that environmental transcriptomics based on extra-organismal eRNA can noninvasively reveal gene expression responses of macroorganisms following environmental changes, with broad potential implications for the biomonitoring of health across the trophic chain.
Collapse
Affiliation(s)
- Robert M Hechler
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Matthew C Yates
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | | |
Collapse
|
3
|
Wang Y, Bass AL, Hinch SG, Li S, Di Cicco E, Kaukinen KH, Ferguson H, Ming TJ, Patterson DA, Miller KM. Infectious agents and their physiological correlates in early marine Chinook salmon ( Oncorhynchus tshawytscha). CONSERVATION PHYSIOLOGY 2023; 11:coad031. [PMID: 37701371 PMCID: PMC10494280 DOI: 10.1093/conphys/coad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/27/2023] [Accepted: 04/24/2023] [Indexed: 09/14/2023]
Abstract
The early marine life of Pacific salmon is believed to be a critical period limiting population-level survival. Recent evidence suggests that some infectious agents are associated with survival but linkages with underlying physiological mechanisms are lacking. While challenge studies can demonstrate cause and effect relationships between infection and pathological change or mortality, in some cases pathological change may only manifest in the presence of environmental stressors; thus, it is important to gain context from field observations. Herein, we examined physiological correlates with infectious agent loads in Chinook salmon during their first ocean year. We measured physiology at the molecular (gene expression), metabolic (plasma chemistry) and cellular (histopathology) levels. Of 46 assayed infectious agents, 27 were detected, including viruses, bacteria and parasites. This exploratory study identified. a strong molecular response to viral disease and pathological change consistent with jaundice/anemia associated with Piscine orthoreovirus,strong molecular signals of gill inflammation and immune response associated with gill agents `Candidatus Branchiomonas cysticola' and Parvicapsula pseudobranchicola,a general downregulation of gill immune response associated with Parvicapsula minibicornis complementary to that of P. pseudobranchicola.Importantly, our study provides the first evidence that the molecular activation of viral disease response and the lesions observed during the development of the PRV-related disease jaundice/anemia in farmed Chinook salmon are also observed in wild juvenile Chinook salmon.
Collapse
Affiliation(s)
- Yuwei Wang
- Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Arthur L Bass
- Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC, V9T 6N7, Canada
| | - Scott G Hinch
- Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC, V9T 6N7, Canada
| | - Emiliano Di Cicco
- Pacific Salmon Foundation, 1682 W 7th Ave, Vancouver, BC, V6J 4S6, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC, V9T 6N7, Canada
| | - Hugh Ferguson
- School of Veterinary Medicine, St. George’s University, University Centre Grenada, W. Indies, Grenada
| | - Tobi J Ming
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC, V9T 6N7, Canada
| | - David A Patterson
- Fisheries and Oceans Canada, School of Resource and Environmental Mangement, Simon Fraser University, Science Branch, 643A Science Rd, Burnaby, BC, V5A 1S6, Canada
| | - Kristina M Miller
- Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC, V9T 6N7, Canada
| |
Collapse
|
4
|
Bass AL, Bateman AW, Kaukinen KH, Li S, Ming T, Patterson DA, Hinch SG, Miller KM. The spatial distribution of infectious agents in wild Pacific salmon along the British Columbia coast. Sci Rep 2023; 13:5473. [PMID: 37016008 PMCID: PMC10071257 DOI: 10.1038/s41598-023-32583-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 03/29/2023] [Indexed: 04/06/2023] Open
Abstract
Although infectious agents can act as strong population regulators, knowledge of their spatial distributions in wild Pacific salmon is limited, especially in the marine environment. Characterizing pathogen distributions during early marine residence, a period considered a survival bottleneck for Pacific salmon, may reveal where salmon populations are exposed to potentially detrimental pathogens. Using high-throughput qPCR, we determined the prevalence of 56 infectious agents in 5719 Chinook, 2032 Coho and 4062 Sockeye salmon, sampled between 2008 and 2018, in their first year of marine residence along coastal Western Canada. We identified high prevalence clusters, which often shifted geographically with season, for most of the 41 detected agents. A high density of infection clusters was found in the Salish Sea along the east coast of Vancouver Island, an important migration route and residence area for many salmon populations, some experiencing chronically poor marine survival. Maps for each infectious agent taxa showing clusters across all host species are provided. Our novel documentation of salmon pathogen distributions in the marine environment contributes to the ecological knowledge regarding some lesser known pathogens, identifies salmon populations potentially impacted by specific pathogens, and pinpoints priority locations for future research and remediation.
Collapse
Affiliation(s)
- Arthur L Bass
- Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T 1Z4, Canada.
| | - Andrew W Bateman
- Pacific Salmon Foundation, Vancouver, V6J 4S6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 1A1, Canada
| | - Karia H Kaukinen
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, V9T 6N7, Canada
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, V9T 6N7, Canada
| | - Tobi Ming
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, V9T 6N7, Canada
| | - David A Patterson
- Fisheries and Oceans Canada, Science Branch, Pacific Region, School of Resource and Environmental Management, Simon Fraser University, Burnaby, V5A 1S6, Canada
| | - Scott G Hinch
- Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Kristina M Miller
- Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T 1Z4, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, V9T 6N7, Canada
| |
Collapse
|
5
|
Bowen L, Manlove K, Roug A, Waters S, LaHue N, Wolff P. Using transcriptomics to predict and visualize disease status in bighorn sheep ( Ovis canadensis). CONSERVATION PHYSIOLOGY 2022; 10:coac046. [PMID: 35795016 PMCID: PMC9252122 DOI: 10.1093/conphys/coac046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/18/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Increasing risk of pathogen spillover coupled with overall declines in wildlife population abundance in the Anthropocene make infectious disease a relevant concern for species conservation worldwide. While emerging molecular tools could improve our diagnostic capabilities and give insight into mechanisms underlying wildlife disease risk, they have rarely been applied in practice. Here, employing a previously reported gene transcription panel of common immune markers to track physiological changes, we present a detailed analysis over the course of both acute and chronic infection in one wildlife species where disease plays a critical role in conservation, bighorn sheep (Ovis canadensis). Differential gene transcription patterns distinguished between infection statuses over the course of acute infection and differential correlation (DC) analyses identified clear changes in gene co-transcription patterns over the early stages of infection, with transcription of four genes-TGFb, AHR, IL1b and MX1-continuing to increase even as transcription of other immune-associated genes waned. In a separate analysis, we considered the capacity of the same gene transcription panel to aid in differentiating between chronically infected animals and animals in other disease states outside of acute disease events (an immediate priority for wildlife management in this system). We found that this transcription panel was capable of accurately identifying chronically infected animals in the test dataset, though additional data will be required to determine how far this ability extends. Taken together, our results showcase the successful proof of concept and breadth of potential utilities that gene transcription might provide to wildlife disease management, from direct insight into mechanisms associated with differential disease response to improved diagnostic capacity in the field.
Collapse
Affiliation(s)
| | - Kezia Manlove
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT, 84322, USA
| | - Annette Roug
- Centre for Veterinary Wildlife Studies, Faculty of Veterinary Medicine, University of Pretoria, Onderstepoort, 0110, South Africa
| | - Shannon Waters
- U.S. Geological Survey, Western Ecological Research Center, Davis, CA, 95616, USA
| | - Nate LaHue
- Nevada Department of Wildlife, Reno, NV, 89512, USA
| | | |
Collapse
|
6
|
Thorstensen MJ, Vandervelde CA, Bugg WS, Michaleski S, Vo L, Mackey TE, Lawrence MJ, Jeffries KM. Non-Lethal Sampling Supports Integrative Movement Research in Freshwater Fish. Front Genet 2022; 13:795355. [PMID: 35547248 PMCID: PMC9081360 DOI: 10.3389/fgene.2022.795355] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Freshwater ecosystems and fishes are enormous resources for human uses and biodiversity worldwide. However, anthropogenic climate change and factors such as dams and environmental contaminants threaten these freshwater systems. One way that researchers can address conservation issues in freshwater fishes is via integrative non-lethal movement research. We review different methods for studying movement, such as with acoustic telemetry. Methods for connecting movement and physiology are then reviewed, by using non-lethal tissue biopsies to assay environmental contaminants, isotope composition, protein metabolism, and gene expression. Methods for connecting movement and genetics are reviewed as well, such as by using population genetics or quantitative genetics and genome-wide association studies. We present further considerations for collecting molecular data, the ethical foundations of non-lethal sampling, integrative approaches to research, and management decisions. Ultimately, we argue that non-lethal sampling is effective for conducting integrative, movement-oriented research in freshwater fishes. This research has the potential for addressing critical issues in freshwater systems in the future.
Collapse
Affiliation(s)
- Matt J. Thorstensen
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Bowen L, Waters S, Stott JL, Duncan A, Meyerson R, Woodhouse S. Baseline Gene Expression Levels in Falkland-Malvinas Island Penguins: Towards a New Monitoring Paradigm. Life (Basel) 2022; 12:life12020258. [PMID: 35207543 PMCID: PMC8880734 DOI: 10.3390/life12020258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 11/29/2022] Open
Abstract
Health diagnostics of wildlife have historically relied on the evaluation of select serum biomarkers and the identification of a contaminant or pathogen burden within specific tissues as an indicator of a level of insult. However, these approaches fail to measure the physiological reaction of the individual to stressors, thus limiting the scope of interpretation. Gene-based health diagnostics provide an opportunity for an alternate, whole-system, or holistic assessment of health, not only in individuals or populations but potentially in ecosystems. Seabirds are among the most threatened marine taxonomic groups in the world, with ~25% of this species currently listed as threatened or considered of special concern; among seabirds, the penguins (Family Spheniscidae) are the most threatened seabird Family. We used gene expression to develop baseline physiological indices for wild penguins in the Falkland-Malvinas Islands, and captive zoo penguins. We identified the almost complete statistical separation of penguin groups (gentoo Detroit Zoo, gentoo Falkland-Malvinas Islands, rockhopper Detroit Zoo, and rockhopper Falkland-Malvinas Islands) based on gene expression profiles. Implementation of long-term longitudinal studies would allow for the assessment of temporal increases or decreases of select transcripts and would facilitate interpretation of the drivers of change.
Collapse
Affiliation(s)
- Lizabeth Bowen
- U.S. Geological Survey, Western Ecological Research Center, One Shields Avenue, Davis, CA 95616, USA;
- Correspondence: ; Tel.: +1-530-574-4353
| | - Shannon Waters
- U.S. Geological Survey, Western Ecological Research Center, One Shields Avenue, Davis, CA 95616, USA;
| | - Jeffrey L. Stott
- Department of Pathology, Microbiology and Immunology, University of California, One Shields Avenue, Davis, CA 95616, USA;
| | - Ann Duncan
- Detroit Zoo, 8450 W. 10 Mile Road, Royal Oak, MI 48067, USA;
| | | | - Sarah Woodhouse
- Henry Doorly Zoo and Aquarium, 3701 S 10th St, Omaha, NE 68107, USA;
| |
Collapse
|
8
|
Bass AL, Bateman AW, Connors BM, Staton BA, Rondeau EB, Mordecai GJ, Teffer AK, Kaukinen KH, Li S, Tabata AM, Patterson DA, Hinch SG, Miller KM. Identification of infectious agents in early marine Chinook and Coho salmon associated with cohort survival. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Recent decades have seen an increased appreciation for the role infectious diseases can play in mass mortality events across a diversity of marine taxa. At the same time many Pacific salmon populations have declined in abundance as a result of reduced marine survival. However, few studies have explicitly considered the potential role pathogens could play in these declines. Using a multi-year dataset spanning 59 pathogen taxa in Chinook and Coho salmon sampled along the British Columbia coast, we carried out an exploratory analysis to quantify evidence for associations between pathogen prevalence and cohort survival and between pathogen load and body condition. While a variety of pathogens had moderate to strong negative correlations with body condition or survival for one host species in one season, we found that Tenacibaculum maritimum and Piscine orthoreovirus had consistently negative associations with body condition in both host species and seasons and were negatively associated with survival for Chinook salmon collected in the fall and winter. Our analyses, which offer the most comprehensive examination of associations between pathogen prevalence and Pacific salmon survival to date, suggest that pathogens in Pacific salmon warrant further attention, especially those whose distribution and abundance may be influenced by anthropogenic stressors.
Collapse
Affiliation(s)
- Arthur L. Bass
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrew W. Bateman
- Pacific Salmon Foundation, Vancouver, BC V6J 4S6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Brendan M. Connors
- Institute of Ocean Sciences, Fisheries and Oceans Canada, Sidney, BC V8L 5T5, Canada
| | - Benjamin A. Staton
- Fisheries Science Department, Columbia River Inter-Tribal Fish Commission, Portland, OR 97232, USA
| | - Eric B. Rondeau
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Gideon J. Mordecai
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC V9T 6N7, Canada
| | - Amy K. Teffer
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Karia H. Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Amy M. Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - David A. Patterson
- Fisheries and Oceans Canada, School of Resource and Environmental Management, Simon Fraser University, Science Branch, Burnaby, BC V5A 1S6, Canada
| | - Scott G. Hinch
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kristina M. Miller
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| |
Collapse
|
9
|
Deeg CM, Kanzeparova AN, Somov AA, Esenkulova S, Di Cicco E, Kaukinen KH, Tabata A, Ming TJ, Li S, Mordecai G, Schulze A, Miller KM. Way out there: pathogens, health, and condition of overwintering salmon in the Gulf of Alaska. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Salmon are keystone species across the North Pacific, supporting ecosystems, commercial opportunities, and cultural identity. Nevertheless, many wild salmon stocks have experienced significant declines. Salmon restoration efforts focus on fresh and coastal waters, but little is known about the open ocean environment. Here we use high throughput RT-qPCR tools to provide the first report on the health, condition, and infection profile of coho, chum, pink, and sockeye salmon in the Gulf of Alaska during the 2019 winter. We found lower infectious agent number, diversity, and burden compared with coastal British Columbia in all species except coho, which exhibited elevated stock-specific infection profiles. We identified Loma sp. and Ichthyophonus hoferi as key pathogens, suggesting transmission in the open ocean. Reduced prey availability, potentially linked to change in ocean conditions due to an El Niño event, correlated with energetic deficits and immunosuppression in salmon. Immunosuppressed individuals showed higher relative infection burden and higher prevalence of opportunistic pathogens. We highlight the cumulative effects of infection and environmental stressors on overwintering salmon, establishing a baseline to document the impacts of a changing ocean on salmon.
Collapse
Affiliation(s)
- Christoph M. Deeg
- Department of Forest & Conservation Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Pacific Salmon Foundation, Vancouver, BC V6J 4S6, Canada
| | | | - Alexei A. Somov
- Pacific branch of VNIRO (“TINRO”), Vladivostok, Russia 690091
| | | | | | - Karia H. Kaukinen
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Amy Tabata
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Tobi J. Ming
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Gideon Mordecai
- Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Angela Schulze
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Kristina M. Miller
- Department of Forest & Conservation Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| |
Collapse
|
10
|
Akbarzadeh A, Selbie DT, Pon LB, Miller KM. Endangered Cultus Lake sockeye salmon exhibit genomic evidence of hypoxic and thermal stresses while rearing in degrading freshwater lacustrine critical habitat. CONSERVATION PHYSIOLOGY 2021; 9:coab089. [PMID: 34858597 PMCID: PMC8633632 DOI: 10.1093/conphys/coab089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/25/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Water quality degradation due to lake eutrophication and climate change contributes to the risk of extirpation for the endangered Cultus Lake sockeye salmon. Sockeye salmon juveniles experience both low-oxygen water in profundal lake habitats and elevated temperatures above the thermocline during diel vertical migrations in summer and fall when the lake is thermally stratified. We used a transcriptomic tool (Salmon Fit-Chip) to determine whether salmon were experiencing thermal and/or hypoxic stress during this period. The results showed that over one-third of the fish were responding to either hypoxic (35.5%) or thermal stress (40.9%) during periods when these environmental stressors were pronounced within the lake, but not during periods when profundal dissolved oxygen was elevated and the water column was isothermal and cool. The most consistent signs of hypoxic stress occurred during July (52.2%) and September (44.4%). A total of 25.7% of individual fish sampled during months when both stressors were occurring (July, September, October) showed signatures of both stressors. When a combination of hypoxic and thermal stress biomarkers was applied, 92% of fish showed evidence of one or both stressors; hence, for at least several months of the year, most sockeye salmon juveniles in Cultus Lake are experiencing anthropogenically environmentally induced stress. We also detected the presence of pathogenic ciliate Ichthyoptherius multifiliis in the gill tissue of juveniles, with a higher infection signal in Cultus Lake compared to juveniles from nearby Chilliwack Lake. These data provide powerful new evidence that Cultus Lake sockeye salmon, which experience relatively lower juvenile survival than Chilliwack sockeye salmon, are more compromised by stress and carry a higher level of infection of at least one pathogenic agent. Thus, we hypothesize that the cumulative or synergistic interplay between stressors and diseases, clearly documented to be occurring within Cultus Lake, are contributing to increased mortality of endangered sockeye salmon.
Collapse
Affiliation(s)
- Arash Akbarzadeh
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, British Columbia, V9T 6N7, Canada
- Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, 9th km of Minab Road, Bandar Abbas, 79161 93145, Iran
| | - Daniel T Selbie
- Fisheries and Oceans Canada, Science Branch, Pacific Region, Cultus Lake Salmon Research Laboratory, 4222 Columbia Valley Hwy, Cultus Lake, British Columbia, V2R 5B6, Canada
| | - Lucas B Pon
- Fisheries and Oceans Canada, Science Branch, Pacific Region, Cultus Lake Salmon Research Laboratory, 4222 Columbia Valley Hwy, Cultus Lake, British Columbia, V2R 5B6, Canada
| | - Kristina M Miller
- Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, 9th km of Minab Road, Bandar Abbas, 79161 93145, Iran
| |
Collapse
|
11
|
Krasnov A, Johansen LH, Karlsen C, Sveen L, Ytteborg E, Timmerhaus G, Lazado CC, Afanasyev S. Transcriptome Responses of Atlantic Salmon ( Salmo salar L.) to Viral and Bacterial Pathogens, Inflammation, and Stress. Front Immunol 2021; 12:705601. [PMID: 34621264 PMCID: PMC8490804 DOI: 10.3389/fimmu.2021.705601] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/03/2021] [Indexed: 11/15/2022] Open
Abstract
Transcriptomics provides valuable data for functional annotations of genes, the discovery of biomarkers, and quantitative assessment of responses to challenges. Meta-analysis of Nofima’s Atlantic salmon microarray database was performed for the selection of genes that have shown strong and reproducible expression changes. Using data from 127 experiments including 6440 microarrays, four transcription modules (TM) were identified with a total of 902 annotated genes: 161 virus responsive genes – VRG (activated with five viruses and poly I:C), genes that responded to three pathogenic bacteria (523 up and 33 down-regulated genes), inflammation not caused by infections – wounds, melanized foci in skeletal muscle and exposure to PAMP (180 up and 72 down-regulated genes), and stress by exercise, crowding and cortisol implants (33 genes). To assist the selection of gene markers, genes in each TM were ranked according to the scale of expression changes. In terms of functional annotations, association with diseases and stress was unknown or not reflected in public databases for a large part of genes, including several genes with the highest ranks. A set of multifunctional genes was discovered. Cholesterol 25-hydroxylase was present in all TM and 22 genes, including most differentially expressed matrix metalloproteinases 9 and 13 were assigned to three TMs. The meta-analysis has improved understanding of the defense strategies in Atlantic salmon. VRG have demonstrated equal or similar responses to RNA (SAV, IPNV, PRV, and ISAV), and DNA (gill pox) viruses, injection of bacterial DNA (plasmid) and exposure of cells to PAMP (CpG and gardiquimod) and relatively low sensitivity to inflammation and bacteria. Genes of the highest rank show preferential expression in erythrocytes. This group includes multigene families (gig and several trim families) and many paralogs. Of pathogen recognition receptors, only RNA helicases have shown strong expression changes. Most VRG (82%) are effectors with a preponderance of ubiquitin-related genes, GTPases, and genes of nucleotide metabolism. Many VRG have unknown roles. The identification of TMs makes possible quantification of responses and assessment of their interactions. Based on this, we are able to separate pathogen-specific responses from general inflammation and stress.
Collapse
Affiliation(s)
| | | | | | - Lene Sveen
- Fish Health Department, Nofima AS, Ås, Norway
| | | | | | | | - Sergey Afanasyev
- Laboratory of Neurophysiology and Behavioral Pathology, I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint-Petersburg, Russia
| |
Collapse
|
12
|
Teffer AK, Hinch SG, Miller KM, Patterson DA, Bass AL, Cooke SJ, Farrell AP, Beacham TD, Chapman JM, Juanes F. Host-pathogen-environment interactions predict survival outcomes of adult sockeye salmon (Oncorhynchus nerka) released from fisheries. Mol Ecol 2021; 31:134-160. [PMID: 34614262 DOI: 10.1111/mec.16214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 11/27/2022]
Abstract
Incorporating host-pathogen(s)-environment axes into management and conservation planning is critical to preserving species in a warming climate. However, the role pathogens play in host stress resilience remains largely unexplored in wild animal populations. We experimentally characterized how independent and cumulative stressors (fisheries handling, high water temperature) and natural infections affected the health and longevity of released wild adult sockeye salmon (Oncorhynchus nerka) in British Columbia, Canada. Returning adults were collected before and after entering the Fraser River, yielding marine- and river-collected groups, respectively (N = 185). Fish were exposed to a mild (seine) or severe (gill net) fishery treatment at collection, and then held in flow-through freshwater tanks for up to four weeks at historical (14°C) or projected migration temperatures (18°C). Using weekly nonlethal gill biopsies and high-throughput qPCR, we quantified loads of up to 46 pathogens with host stress and immune gene expression. Marine-collected fish had less severe infections than river-collected fish, a short migration distance (100 km, 5-7 days) that produced profound infection differences. At 14°C, river-collected fish survived 1-2 weeks less than marine-collected fish. All fish held at 18°C died within 4 weeks unless they experienced minimal handling. Gene expression correlated with infections in river-collected fish, while marine-collected fish were more stressor-responsive. Cumulative stressors were detrimental regardless of infections or collection location, probably due to extreme physiological disturbance. Because river-derived infections correlated with single stressor responses, river entry probably decreases stressor resilience of adult salmon by altering both physiology and pathogen burdens, which redirect host responses toward disease resistance.
Collapse
Affiliation(s)
- Amy K Teffer
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada.,Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott G Hinch
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kristina M Miller
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - David A Patterson
- Fisheries and Oceans Canada, Cooperative Resource Management Institute, School of Resource and Environmental Management, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Arthur L Bass
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Anthony P Farrell
- Department of Zoology, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Terry D Beacham
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Jacqueline M Chapman
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Francis Juanes
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| |
Collapse
|
13
|
Polinski MP, Zhang Y, Morrison PR, Marty GD, Brauner CJ, Farrell AP, Garver KA. Innate antiviral defense demonstrates high energetic efficiency in a bony fish. BMC Biol 2021; 19:138. [PMID: 34253202 PMCID: PMC8276435 DOI: 10.1186/s12915-021-01069-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/09/2021] [Indexed: 11/18/2022] Open
Abstract
Background Viruses can impose energetic demands on organisms they infect, in part by hosts mounting resistance. Recognizing that oxygen uptake reliably indicates steady-state energy consumption in all vertebrates, we comprehensively evaluated oxygen uptake and select transcriptomic messaging in sockeye salmon challenged with either a virulent rhabdovirus (IHNV) or a low-virulent reovirus (PRV). We tested three hypotheses relating to the energetic costs of viral resistance and tolerance in this vertebrate system: (1) mounting resistance incurs a metabolic cost or limitation, (2) induction of the innate antiviral interferon system compromises homeostasis, and (3) antiviral defenses are weakened by acute stress. Results IHNV infections either produced mortality within 1–4 weeks or the survivors cleared infections within 1–9 weeks. Transcription of three interferon-stimulated genes (ISGs) was strongly correlated with IHNV load but not respiratory performance. Instead, early IHNV resistance was associated with a mean 19% (95% CI = 7–31%; p = 0.003) reduction in standard metabolic rate. The stress of exhaustive exercise did not increase IHNV transcript loads, but elevated host inflammatory transcriptional signaling up to sevenfold. For PRV, sockeye tolerated high-load systemic PRV blood infections. ISG transcription was transiently induced at peak PRV loads without associated morbidity, microscopic lesions, or major changes in aerobic or anaerobic respiratory performance, but some individuals with high-load blood infections experienced a transient, minor reduction in hemoglobin concentration and increased duration of excess post-exercise oxygen consumption. Conclusions Contrary to our first hypothesis, effective resistance against life-threatening rhabdovirus infections or tolerance to high-load reovirus infections incurred minimal metabolic costs to salmon. Even robust systemic activation of the interferon system did not levy an allostatic load sufficient to compromise host homeostasis or respiratory performance, rejecting our second hypothesis that this ancient innate vertebrate antiviral defense is itself energetically expensive. Lastly, an acute stress experienced during testing did not weaken host antiviral defenses sufficiently to promote viral replication; however, a possibility for disease intensification contingent upon underlying inflammation was indicated. These data cumulatively demonstrate that fundamental innate vertebrate defense strategies against potentially life-threatening viral exposure impose limited putative costs on concurrent aerobic or energetic demands of the organism. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01069-2.
Collapse
Affiliation(s)
- Mark P Polinski
- Fisheries and Oceans Canada Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, V9T6N7, Canada.
| | - Yangfan Zhang
- Faculty of Land and Food Systems, University of British Columbia, MCML 344-2357 Main Mall, Vancouver, V6T1Z4, Canada
| | - Phillip R Morrison
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, V6T1Z4, Canada
| | - Gary D Marty
- Animal Health Centre, Ministry of Agriculture, Food and Fisheries, 1767 Angus Campbell Rd, Abbotsford, V3G2M3, Canada
| | - Colin J Brauner
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, V6T1Z4, Canada
| | - Anthony P Farrell
- Faculty of Land and Food Systems, University of British Columbia, MCML 344-2357 Main Mall, Vancouver, V6T1Z4, Canada.,Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, V6T1Z4, Canada
| | - Kyle A Garver
- Fisheries and Oceans Canada Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, V9T6N7, Canada.
| |
Collapse
|
14
|
Jeffries KM, Teffer A, Michaleski S, Bernier NJ, Heath DD, Miller KM. The use of non-lethal sampling for transcriptomics to assess the physiological status of wild fishes. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110629. [PMID: 34058376 DOI: 10.1016/j.cbpb.2021.110629] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
Fishes respond to different abiotic and biotic stressors through changes in gene expression as a part of an integrated physiological response. Transcriptomics approaches have been used to quantify gene expression patterns as a reductionist approach to understand responses to environmental stressors in animal physiology and have become more commonly used to study wild fishes. We argue that non-lethal sampling for transcriptomics should become the norm for assessing the physiological status of wild fishes, especially when there are conservation implications. Processes at the level of the transcriptome provide a "snapshot" of the cellular conditions at a given time; however, by using a non-lethal sampling protocol, researchers can connect the transcriptome profile with fitness-relevant ecological endpoints such as reproduction, movement patterns and survival. Furthermore, telemetry is a widely used approach in fisheries to understand movement patterns in the wild, and when combined with transcriptional profiling, provides arguably the most powerful use of non-lethal sampling for transcriptomics in wild fishes. In this review, we discuss the different tissues that can be successfully incorporated into non-lethal sampling strategies, which is particularly useful in the context of the emerging field of conservation transcriptomics. We briefly describe different methods for transcriptional profiling in fishes from high-throughput qPCR to whole transcriptome approaches. Further, we discuss strategies and the limitations of using transcriptomics for non-lethally studying fishes. Lastly, as 'omics' technology continues to advance, transcriptomics paired with different omics approaches to study wild fishes will provide insight into the factors that regulate phenotypic variation and the physiological responses to changing environmental conditions in the future.
Collapse
Affiliation(s)
- Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada.
| | - Amy Teffer
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, United States of America
| | - Sonya Michaleski
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Nicholas J Bernier
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Daniel D Heath
- Department of Integrative Biology, Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| |
Collapse
|
15
|
Banerjee SM, Stoll JA, Allen CD, Lynch JM, Harris HS, Kenyon L, Connon RE, Sterling EJ, Naro-Maciel E, McFadden K, Lamont MM, Benge J, Fernandez NB, Seminoff JA, Benson SR, Lewison RL, Eguchi T, Summers TM, Hapdei JR, Rice MR, Martin S, Jones TT, Dutton PH, Balazs GH, Komoroske LM. Species and population specific gene expression in blood transcriptomes of marine turtles. BMC Genomics 2021; 22:346. [PMID: 33985425 PMCID: PMC8117300 DOI: 10.1186/s12864-021-07656-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms' responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations. RESULTS We generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance. CONCLUSIONS Obtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles.
Collapse
Affiliation(s)
- Shreya M Banerjee
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Jamie Adkins Stoll
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Camryn D Allen
- Marine Turtle Biology and Assessment Program, Protected Species Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Honolulu, HI, USA.,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Jennifer M Lynch
- Chemical Sciences Division, National Institute of Standards and Technology, Hawai'i Pacific University, Waimanalo, HI, USA
| | - Heather S Harris
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Lauren Kenyon
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Richard E Connon
- Department of Anatomy, Physiology and Cell Biology, University of California, Davis, Davis, CA, USA
| | - Eleanor J Sterling
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY, USA
| | | | - Kathryn McFadden
- School of Agricultural, Forest, and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Margaret M Lamont
- United States Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - James Benge
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Nadia B Fernandez
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Jeffrey A Seminoff
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Scott R Benson
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Moss Landing, CA, 95039, USA.,Moss Landing Marine Laboratories, San Jose State University, Moss Landing, CA, 95039, USA
| | - Rebecca L Lewison
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Tomoharu Eguchi
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | | | - Jessy R Hapdei
- Jessy's Tag Services, Saipan, Commonwealth of the Northern Mariana Islands, USA
| | - Marc R Rice
- Hawai'i Preparatory Academy, Kamuela, HI, USA
| | - Summer Martin
- Marine Turtle Biology and Assessment Program, Protected Species Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Honolulu, HI, USA
| | - T Todd Jones
- Marine Turtle Biology and Assessment Program, Protected Species Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Honolulu, HI, USA
| | - Peter H Dutton
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | | | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA. .,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.
| |
Collapse
|
16
|
Furey NB, Bass AL, Miller KM, Li S, Lotto AG, Healy SJ, Drenner SM, Hinch SG. Infected juvenile salmon can experience increased predation during freshwater migration. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201522. [PMID: 33959321 PMCID: PMC8074935 DOI: 10.1098/rsos.201522] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/03/2021] [Indexed: 05/07/2023]
Abstract
Predation risk for animal migrants can be impacted by physical condition. Although size- or condition-based selection is often observed, observing infection-based predation is rare due to the difficulties in assessing infectious agents in predated samples. We examined predation of outmigrating sockeye salmon (Oncorhynchus nerka) smolts by bull trout (Salvelinus confluentus) in south-central British Columbia, Canada. We used a high-throughput quantitative polymerase chain reaction (qPCR) platform to screen for the presence of 17 infectious agents found in salmon and assess 14 host genes associated with viral responses. In one (2014) of the two years assessed (2014 and 2015), the presence of infectious haematopoietic necrosis virus (IHNv) resulted in 15-26 times greater chance of predation; in 2015 IHNv was absent among all samples, predated or not. Thus, we provide further evidence that infection can impact predation risk in migrants. Some smolts with high IHNv loads also exhibited gene expression profiles consistent with a virus-induced disease state. Nine other infectious agents were observed between the two years, none of which were associated with increased selection by bull trout. In 2014, richness of infectious agents was also associated with greater predation risk. This is a rare demonstration of predator consumption resulting in selection for prey that carry infectious agents. The mechanism by which this selection occurs is not yet determined. By culling infectious agents from migrant populations, fish predators could provide an ecological benefit to prey.
Collapse
Affiliation(s)
- Nathan B. Furey
- Department of Biological Sciences, University of New Hampshire, Durham, NH, USA
| | - Arthur L. Bass
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | - Kristi M. Miller
- Fisheries and Oceans Canada, Molecular Genetics Section, Pacific Biological Station, Nanaimo, Canada
| | - Shaorong Li
- Fisheries and Oceans Canada, Molecular Genetics Section, Pacific Biological Station, Nanaimo, Canada
| | - Andrew G. Lotto
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | - Stephen J. Healy
- Fisheries and Oceans Canada, Science Branch, Pacific Region, 4160 Marine Dr., West Vancouver, British Columbia, Canada
| | - S. Matthew Drenner
- Stillwater Sciences, 555 W. Fifth St, 35th floor, Los Angeles, CA, USA
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Scott G. Hinch
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| |
Collapse
|
17
|
Yates MC, Derry AM, Cristescu ME. Environmental RNA: A Revolution in Ecological Resolution? Trends Ecol Evol 2021; 36:601-609. [PMID: 33757695 DOI: 10.1016/j.tree.2021.03.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022]
Abstract
Current advancements in environmental RNA (eRNA) exploit its relatively fast turnover rate relative to environmental DNA (eDNA) to assess 'metabolically active' or temporally/spatially recent community diversity. However, this focus significantly underutilizes the trove of potential ecological information encrypted in eRNA. Here, we argue for pushing beyond current species-level eDNA detection capabilities by using eRNA to detect any organisms with unique eRNA profiles, potentially including different life-history stages, sexes, or even specific phenotypes within a species. We also discuss the future of eRNA as a means of assessing the physiological status of organisms and the ecological health of populations and communities, reflecting ecosystem-level conditions. We posit that eRNA has the potential to significantly improve the resolution of organism detection, biological monitoring, and biomonitoring applications in ecology.
Collapse
Affiliation(s)
- Matthew C Yates
- Département des Sciences Biologiques, Université du Québec à Montréal, 141 Avenue Président-Kennedy, Montréal, QC, H2X 1Y4, Canada.
| | - Alison M Derry
- Département des Sciences Biologiques, Université du Québec à Montréal, 141 Avenue Président-Kennedy, Montréal, QC, H2X 1Y4, Canada
| | - Melania E Cristescu
- Department of Biology, McGill University, 1205 Dr Penfield Avenue, Montreal, QC, H3A 1B1, Canada
| |
Collapse
|
18
|
Bateman AW, Schulze AD, Kaukinen KH, Tabata A, Mordecai G, Flynn K, Bass A, Di Cicco E, Miller KM. Descriptive multi-agent epidemiology via molecular screening on Atlantic salmon farms in the northeast Pacific Ocean. Sci Rep 2021; 11:3466. [PMID: 33568681 PMCID: PMC7876018 DOI: 10.1038/s41598-020-78978-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Rapid expansion of salmon aquaculture has resulted in high-density populations that host diverse infectious agents, for which surveillance and monitoring are critical to disease management. Screening can reveal infection diversity from which disease arises, differential patterns of infection in live and dead fish that are difficult to collect in wild populations, and potential risks associated with agent transmission between wild and farmed hosts. We report results from a multi-year infectious-agent screening program of farmed salmon in British Columbia, Canada, using quantitative PCR to assess presence and load of 58 infective agents (viruses, bacteria, and eukaryotes) in 2931 Atlantic salmon (Salmo salar). Our analysis reveals temporal trends, agent correlations within hosts, and agent-associated mortality signatures. Multiple agents, most notably Tenacibaculum maritimum, were elevated in dead and dying salmon. We also report detections of agents only recently shown to infect farmed salmon in BC (Atlantic salmon calicivirus, Cutthroat trout virus-2), detection in freshwater hatcheries of two marine agents (Kudoa thyrsites and Tenacibaculum maritimum), and detection in the ocean of a freshwater agent (Flavobacterium psychrophilum). Our results provide information for farm managers, regulators, and conservationists, and enable further work to explore patterns of multi-agent infection and farm/wild transmission risk.
Collapse
Affiliation(s)
- Andrew W Bateman
- Pacific Salmon Foundation, Vancouver, Canada. .,Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.
| | - Angela D Schulze
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Karia H Kaukinen
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Amy Tabata
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Gideon Mordecai
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Kelsey Flynn
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Arthur Bass
- Pacific Salmon Foundation, Vancouver, Canada.,Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | | | - Kristina M Miller
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada.,Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| |
Collapse
|
19
|
Multigene Expression Assay for Assessment of the Immune Status of Atlantic Salmon. Genes (Basel) 2020; 11:genes11111236. [PMID: 33105610 PMCID: PMC7690445 DOI: 10.3390/genes11111236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022] Open
Abstract
We report the development of a multigene gene expression assay on the BioMark HD platform for the evaluation of immune competence (ImCom) in farmed Atlantic salmon. The first version of the assay included 92 genes selected on the basis of transcriptome analyses in 54 trials that challenged the immune system; annotations were taken into account to represent the key pathways of innate and adaptive immunity. ImCom was tested on samples collected from seven independent projects. Fish were reared from the start feeding to eight months in the sea at eight units in different parts of Norway. Several tissues were analyzed. Linear discriminant analysis (LDA) showed that no more than 10 genes were required to separate groups, and a set of 46 immune genes was sufficient for any task. The second version of the assay was tested in the gills of two groups of high-performing healthy smolts and in groups with intermediate and high mortality rates (IM and HM, respectively). A set of 645 gill samples from clinically healthy Atlantic salmon was used as a reference. The IM group showed general suppression of immunity. All HM group salmon were above the threshold by the squared deviation from the reference. This group showed marked upregulation of genes involved in acute stress and inflammation: mmp-9, mmp-13, hsp70, il-1b, lect2, and cathelicidin. Further work will clarify the boundaries of the norm and explore various cases of impaired immunity.
Collapse
|
20
|
Shea D, Bateman A, Li S, Tabata A, Schulze A, Mordecai G, Ogston L, Volpe JP, Neil Frazer L, Connors B, Miller KM, Short S, Krkošek M. Environmental DNA from multiple pathogens is elevated near active Atlantic salmon farms. Proc Biol Sci 2020; 287:20202010. [PMID: 33081614 PMCID: PMC7661312 DOI: 10.1098/rspb.2020.2010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The spread of infection from reservoir host populations is a key mechanism for disease emergence and extinction risk and is a management concern for salmon aquaculture and fisheries. Using a quantitative environmental DNA methodology, we assessed pathogen environmental DNA in relation to salmon farms in coastal British Columbia, Canada, by testing for 39 species of salmon pathogens (viral, bacterial, and eukaryotic) in 134 marine environmental samples at 58 salmon farm sites (both active and inactive) over 3 years. Environmental DNA from 22 pathogen species was detected 496 times and species varied in their occurrence among years and sites, likely reflecting variation in environmental factors, other native host species, and strength of association with domesticated Atlantic salmon. Overall, we found that the probability of detecting pathogen environmental DNA (eDNA) was 2.72 (95% CI: 1.48, 5.02) times higher at active versus inactive salmon farm sites and 1.76 (95% CI: 1.28, 2.42) times higher per standard deviation increase in domesticated Atlantic salmon eDNA concentration at a site. If the distribution of pathogen eDNA accurately reflects the distribution of viable pathogens, our findings suggest that salmon farms serve as a potential reservoir for a number of infectious agents; thereby elevating the risk of exposure for wild salmon and other fish species that share the marine environment.
Collapse
Affiliation(s)
- Dylan Shea
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Andrew Bateman
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Salmon Coast Field Station, Simoom Sound, British Columbia, Canada.,Pacific Salmon Foundation, Vancouver, British Columbia, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Angela Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Gideon Mordecai
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lindsey Ogston
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - John P Volpe
- School of Environmental Studies, University of Victoria, Victoria, British Columbia, Canada
| | - L Neil Frazer
- Department of Earth Sciences, University of Hawaii at Mānoa, Honolulu, Hawaii, Canada
| | - Brendan Connors
- Institute of Ocean Sciences, Fisheries and Oceans Canada, Sidney, British Columbia, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Steven Short
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Mississauga, British Columbia, Canada
| | - Martin Krkošek
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Salmon Coast Field Station, Simoom Sound, British Columbia, Canada
| |
Collapse
|
21
|
Bowen L, von Biela VR, McCormick SD, Regish AM, Waters SC, Durbin-Johnson B, Britton M, Settles ML, Donnelly DS, Laske SM, Carey MP, Brown RJ, Zimmerman CE. Transcriptomic response to elevated water temperatures in adult migrating Yukon River Chinook salmon ( Oncorhynchus tshawytscha). CONSERVATION PHYSIOLOGY 2020; 8:coaa084. [PMID: 34512988 PMCID: PMC7486460 DOI: 10.1093/conphys/coaa084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/01/2020] [Accepted: 08/25/2020] [Indexed: 06/01/2023]
Abstract
Chinook salmon (Oncorhynchus tshawytscha) declines are widespread and may be attributed, at least in part, to warming river temperatures. Water temperatures in the Yukon River and tributaries often exceed 18°C, a threshold commonly associated with heat stress and elevated mortality in Pacific salmon. Untangling the complex web of direct and indirect physiological effects of heat stress on salmon is difficult in a natural setting with innumerable system challenges but is necessary to increase our understanding of both lethal and sublethal impacts of heat stress on populations. The goal of this study was to characterize the cellular stress response in multiple Chinook salmon tissues after acute elevated temperature challenges. We conducted a controlled 4-hour temperature exposure (control, 18°C and 21°C) experiment on the bank of the Yukon River followed by gene expression (GE) profiling using a 3'-Tag-RNA-Seq protocol. The full transcriptome was analysed for 22 Chinook salmon in muscle, gill and liver tissue. Both the 21°C and 18°C treatments induced greater activity in genes associated with protein folding (e.g. HSP70, HSP90 mRNA) processes in all tissues. Global GE patterns indicate that transcriptomic responses to heat stress were highly tissue-specific, underscoring the importance of analyzing multiple tissues for determination of physiological effect. Primary superclusters (i.e. groupings of loosely related terms) of altered biological processes were identified in each tissue type, including regulation of DNA damage response (gill), regulation by host of viral transcription (liver) and regulation of the force of heart contraction (muscle) in the 21°C treatment. This study provides insight into mechanisms potentially affecting adult Chinook salmon as they encounter warm water during their spawning migration in the Yukon River and suggests that both basic and more specialized cellular functions may be disrupted.
Collapse
Affiliation(s)
- Lizabeth Bowen
- U.S. Geological Survey, Western Ecological Research Center, One Shields Avenue, Davis, CA, 95616, USA
| | - Vanessa R von Biela
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Stephen D McCormick
- U.S. Geological Survey, Leetown Science Center, Conte Anadromous Fish Research Laboratory, 1 Migratory Way, Turner Falls, Massachusetts, 01376, USA
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Amy M Regish
- U.S. Geological Survey, Leetown Science Center, Conte Anadromous Fish Research Laboratory, 1 Migratory Way, Turner Falls, Massachusetts, 01376, USA
| | - Shannon C Waters
- U.S. Geological Survey, Western Ecological Research Center, One Shields Avenue, Davis, CA, 95616, USA
| | - Blythe Durbin-Johnson
- University of California, Genome Center and Bioinformatics Core Facility, One Shields Avenue, Davis, CA, 95616, USA
| | - Monica Britton
- University of California, Genome Center and Bioinformatics Core Facility, One Shields Avenue, Davis, CA, 95616, USA
| | - Matthew L Settles
- University of California, Genome Center and Bioinformatics Core Facility, One Shields Avenue, Davis, CA, 95616, USA
| | - Daniel S Donnelly
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Sarah M Laske
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Michael P Carey
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Randy J Brown
- U.S. Fish and Wildlife Service, 101 12 Avenue, Room 110, Fairbanks, AK, 99701, USA
| | - Christian E Zimmerman
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| |
Collapse
|
22
|
Gjessing MC, Krasnov A, Timmerhaus G, Brun S, Afanasyev S, Dale OB, Dahle MK. The Atlantic Salmon Gill Transcriptome Response in a Natural Outbreak of Salmon Gill Pox Virus Infection Reveals New Biomarkers of Gill Pathology and Suppression of Mucosal Defense. Front Immunol 2020; 11:2154. [PMID: 33013908 PMCID: PMC7509425 DOI: 10.3389/fimmu.2020.02154] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/07/2020] [Indexed: 12/19/2022] Open
Abstract
The salmon gill poxvirus (SGPV) is a large DNA virus that infects gill epithelial cells in Atlantic salmon and is associated with acute high mortality disease outbreaks in aquaculture. The pathological effects of SGPV infection include gill epithelial apoptosis in the acute phase of the disease and hyperplasia of gill epithelial cells in surviving fish, causing damage to the gill respiratory surface. In this study, we sampled gills from Atlantic salmon presmolts during a natural outbreak of SGPV disease (SGPVD). Samples covered the early phase of infection, the acute mortality phase, the resolving phase of the disease and control fish from the same group and facility. Mortality, the presence and level of SGPV and gill epithelial apoptosis were clearly associated. The gene expression pattern in the acute phase of SGPVD was in tune with the pathological findings and revealed novel transcript-based disease biomarkers, including pro-apoptotic and proliferative genes, along with changes in expression of ion channels and mucins. The innate antiviral response was strongly upregulated in infected gills and chemokine expression was altered. The regenerating phase did not reveal adaptive immune activity within the study period, but several immune effector genes involved in mucosal protection were downregulated into the late phase, indicating that SGPV infection could compromise mucosal defense. These data provide novel insight into the infection mechanisms and host interaction of SGPV.
Collapse
Affiliation(s)
- Mona C Gjessing
- Department of Fish Health, Norwegian Veterinary Institute, Oslo, Norway
| | - Aleksei Krasnov
- Norwegian Institute of Food, Fisheries and Aquaculture Research, Tromsø, Norway
| | - Gerrit Timmerhaus
- Norwegian Institute of Food, Fisheries and Aquaculture Research, Tromsø, Norway
| | | | - Sergey Afanasyev
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, Russia
| | - Ole Bendik Dale
- Department of Fish Health, Norwegian Veterinary Institute, Oslo, Norway
| | - Maria K Dahle
- Department of Fish Health, Norwegian Veterinary Institute, Oslo, Norway.,The Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
23
|
Identification of Hypoxia-Specific Biomarkers in Salmonids Using RNA-Sequencing and Validation Using High-Throughput qPCR. G3-GENES GENOMES GENETICS 2020; 10:3321-3336. [PMID: 32694198 PMCID: PMC7466982 DOI: 10.1534/g3.120.401487] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (Oncorhynchus tshawytscha), held in normoxia [dissolved oxygen (DO) > 8 mg L-1] and hypoxia (DO = 4‒5 mg L-1) in 10 and 18° temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; P < 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.
Collapse
|
24
|
Mordecai GJ, Di Cicco E, Günther OP, Schulze AD, Kaukinen KH, Li S, Tabata A, Ming TJ, Ferguson HW, Suttle CA, Miller KM. Discovery and surveillance of viruses from salmon in British Columbia using viral immune-response biomarkers, metatranscriptomics, and high-throughput RT-PCR. Virus Evol 2020; 7:veaa069. [PMID: 33623707 PMCID: PMC7887441 DOI: 10.1093/ve/veaa069] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The emergence of infectious agents poses a continual economic and environmental challenge to aquaculture production, yet the diversity, abundance, and epidemiology of aquatic viruses are poorly characterised. In this study, we applied salmon host transcriptional biomarkers to identify and select fish in a viral disease state, but only those that were negative for known viruses based on RT-PCR screening. These fish were selected for metatranscriptomic sequencing to discover potential viral pathogens of dead and dying farmed Atlantic (Salmo salar) and Chinook (Oncorhynchus tshawytscha) salmon in British Columbia (BC). We found that the application of the biomarker panel increased the probability of discovering viruses in aquaculture populations. We discovered two viruses that have not previously been characterised in Atlantic salmon farms in BC (Atlantic salmon calicivirus and Cutthroat trout virus-2), as well as partially sequenced three putative novel viruses. To determine the epidemiology of the newly discovered or emerging viruses, we conducted high-throughput reverse transcription polymerase chain reaction (RT-PCR) and screened over 9,000 farmed and wild salmon sampled over one decade. Atlantic salmon calicivirus and Cutthroat trout virus-2 were in more than half of the farmed Atlantic salmon we tested. Importantly we detected some of the viruses we first discovered in farmed Atlantic salmon in Chinook salmon, suggesting a broad host range. Finally, we applied in situ hybridisation to determine infection and found differing cell tropism for each virus tested. Our study demonstrates that continual discovery and surveillance of emerging viruses in these ecologically important salmon will be vital for management of both aquaculture and wild resources in the future.
Collapse
Affiliation(s)
- Gideon J Mordecai
- Department of Medicine, University of British Columbia, 2775 Laurel Street, 10th Floor Vancouver, BC Canada V5Z 1M9, Canada
- Corresponding author: E-mail:
| | - Emiliano Di Cicco
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
- Pacific Salmon Foundation, 1682 W 7th Ave, Vancouver, BC V6J 4S6, Canada
| | - Oliver P Günther
- Günther Analytics, 402-5775 Hampton Place, Vancouver, BC, V6T 2G6, Canada
| | - Angela D Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Tobi J Ming
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Hugh W Ferguson
- School of Veterinary Medicine, St George’s University, True Blue, GrenadaWest Indies
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Immunology, University of British Columbia, 1365 - 2350 Health Sciences Mall Vancouver, British Columbia Canada V6T 1Z3
- Department of Botany, University of British Columbia, 3156-6270 University Blvd. Vancouver, BC Canada V6T 1Z4, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| |
Collapse
|
25
|
Siah A, Breyta RB, Warheit KI, Gagne N, Purcell MK, Morrison D, Powell JFF, Johnson SC. Genomes reveal genetic diversity of Piscine orthoreovirus in farmed and free-ranging salmonids from Canada and USA. Virus Evol 2020; 6:veaa054. [PMID: 33381304 PMCID: PMC7751156 DOI: 10.1093/ve/veaa054] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Piscine orthoreovirus (PRV-1) is a segmented RNA virus, which is commonly found in salmonids in the Atlantic and Pacific Oceans. PRV-1 causes the heart and skeletal muscle inflammation disease in Atlantic salmon and is associated with several other disease conditions. Previous phylogenetic studies of genome segment 1 (S1) identified four main genogroups of PRV-1 (S1 genogroups I–IV). The goal of the present study was to use Bayesian phylogenetic inference to expand our understanding of the spatial, temporal, and host patterns of PRV-1 from the waters of the northeast Pacific. To that end, we determined the coding genome sequences of fourteen PRV-1 samples that were selected to improve our knowledge of genetic diversity across a broader temporal, geographic, and host range, including the first reported genome sequences from the northwest Atlantic (Eastern Canada). Nucleotide and amino acid sequences of the concatenated genomes and their individual segments revealed that established sequences from the northeast Pacific were monophyletic in all analyses. Bayesian inference phylogenetic trees of S1 sequences using BEAST and MrBayes also found that sequences from the northeast Pacific grouped separately from sequences from other areas. One PRV-1 sample (WCAN_BC17_AS_2017) from an escaped Atlantic salmon, collected in British Columbia but derived from Icelandic broodstock, grouped with other S1 sequences from Iceland. Our concatenated genome and S1 analysis demonstrated that PRV-1 from the northeast Pacific is genetically distinct but descended from PRV-1 from the North Atlantic. However, the analyses were inconclusive as to the timing and exact source of introduction into the northeast Pacific, either from eastern North America or from European waters of the North Atlantic. There was no evidence that PRV-1 was evolving differently between free-ranging Pacific Salmon and farmed Atlantic Salmon. The northeast Pacific PRV-1 sequences fall within genogroup II based on the classification of Garseth, Ekrem, and Biering (Garseth, A. H., Ekrem, T., and Biering, E. (2013) ‘Phylogenetic Evidence of Long Distance Dispersal and Transmission of Piscine Reovirus (PRV) between Farmed and Wild Atlantic Salmon’, PLoS One, 8: e82202.), which also includes North Atlantic sequences from Eastern Canada, Iceland, and Norway. The additional full-genome sequences herein strengthen our understanding of phylogeographical patterns related to the northeast Pacific, but a more balanced representation of full PRV-1 genomes from across its range, as well additional sequencing of archived samples, is still needed to better understand global relationships including potential transmission links among regions.
Collapse
Affiliation(s)
- A Siah
- British Columbia Centre for Aquatic Health Sciences, 871A Island Highway, V9W 2C2, Campbell River, BC, Canada
| | - R B Breyta
- School of Aquatic Fisheries Sciences, University of Washington, Western Fisheries Research Center, USGS, 6505 NE 65th Street Seattle, WA 98115-5016, USA
| | - K I Warheit
- Washington Department of Fish and Wildlife PO Box 43200, Olympia, WA 98504-3200, USA
| | - N Gagne
- Gulf Fisheries Center, Fisheries & Oceans, 343 Université Ave, Moncton, NB E1C 5K4, Canada
| | - M K Purcell
- Western Fisheries Research Center, U.S. Geological Survey, 56505 NE 65th Street Seattle, WA 98115-5016, USA
| | - D Morrison
- Mowi Canada West, Campbell River, BC, Canada
| | - J F F Powell
- British Columbia Centre for Aquatic Health Sciences, 871A Island Highway, V9W 2C2, Campbell River, BC, Canada
| | - S C Johnson
- Fisheries & Oceans Canada, Nanaimo, British Columbia, Canada
| |
Collapse
|
26
|
Lennox RJ, Eldøy SH, Vollset KW, Miller KM, Li S, Kaukinen KH, Isaksen TE, Davidsen JG. How pathogens affect the marine habitat use and migration of sea trout (Salmo trutta) in two Norwegian fjord systems. JOURNAL OF FISH DISEASES 2020; 43:729-746. [PMID: 32364277 DOI: 10.1111/jfd.13170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 06/11/2023]
Abstract
Wild fish are confronting changing pathogen dynamics arising from anthropogenic disturbance and climate change. Pathogens can influence animal behaviour and life histories, yet there are little such data from fish in the high north where pathogen dynamics may differ from comparatively southern regions. We aimed to compare the pathogen communities of 160 wild anadromous brown trout in two fjords in northern Norway and to determine whether pathogens influenced area use or return to spawn. Application of high-throughput qPCR detected 11 of the 46 pathogens screened for; most frequently encountered were Ichthyobodo spp., Flavobacterium psychrophilum and Candidatus Branchiomonas cysticola. The rate of returning to freshwater during the spawning season was significantly lower for the Skjerstadfjord fish. Piscichlamydia salmonis and F. psychrophilum were indicator species for the Skjerstadfjord and pathogen communities in the two fjords differed according to perMANOVA. Individual length, Fulton's condition factor and the time between first and last detection of the fish were not related to the presence of pathogens ordinated using non-metric multidimensional scaling (NMDS). However, there was evidence that pathogen load was correlated with the expression of smoltification genes, which are upregulated by salmonids in freshwater. Correspondingly, percentage of time in freshwater after release was longer for fish with greater pathogen burdens.
Collapse
Affiliation(s)
- Robert J Lennox
- Laboratory for Freshwater Ecology and Inland Fisheries, NORCE Norwegian Research Centre, Bergen, Norway
| | - Sindre H Eldøy
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Knut W Vollset
- Laboratory for Freshwater Ecology and Inland Fisheries, NORCE Norwegian Research Centre, Bergen, Norway
| | - Kristi M Miller
- Pacific Biological Station, Fisheries and Oceans, The Canadian Coastguard, Nanaimo, BC, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans, The Canadian Coastguard, Nanaimo, BC, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans, The Canadian Coastguard, Nanaimo, BC, Canada
| | - Trond E Isaksen
- Laboratory for Freshwater Ecology and Inland Fisheries, NORCE Norwegian Research Centre, Bergen, Norway
| | - Jan G Davidsen
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
27
|
Chapman JM, Teffer AK, Bass AL, Hinch SG, Patterson DA, Miller KM, Cooke SJ. Handling, infectious agents and physiological condition influence survival and post-release behaviour in migratory adult coho salmon after experimental displacement. CONSERVATION PHYSIOLOGY 2020; 8:coaa033. [PMID: 32440351 PMCID: PMC7233283 DOI: 10.1093/conphys/coaa033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/24/2020] [Accepted: 03/31/2020] [Indexed: 06/11/2023]
Abstract
For Pacific salmon captured and released by fisheries, post-release behaviour and survival may be influenced by their health and condition at time of capture. We sought to characterize the interactions between infectious agent burden, fish immune and stress physiology and fisheries stressors to investigate the potential for capture-mediated pathogen-induced mortality in adult coho salmon Oncorhynchus kisutch. We used radio-telemetry paired with high-throughput qPCR of non-lethal gill biopsies for infectious agents and host biomarkers from 200 tagged fish experimentally displaced and exposed to various experimental fisheries treatments (gill net entanglement, recreational angling and recreational angling with air exposure vs. non-sampled control). We characterized relationships among post-release behaviour and survival, infectious agent presence and loads, physiological parameters and transcription profiles of stress and immune genes. All infectious agents detected were endemic and in loads consistent with previous adult Pacific salmon monitoring. Individuals exposed to fisheries treatments were less likely to reach spawning habitat compared to controls, and handling duration independent of fisheries gear had a negative effect on survival. High infectious agent burden was associated with accelerated migration initiation post-release, revealing behavioural plasticity in response to deteriorating condition in this semelparous species. Prevalence and load of infectious agents increased post-migration as well as transcription signatures reflected changes in immune and stress profiles consistent with senescence. Results from this study further our understanding of factors associated with fisheries that increase risk of post-release mortality and characterize some physiological mechanisms that underpin migratory behaviour.
Collapse
Affiliation(s)
- J M Chapman
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6 Canada
| | - A K Teffer
- Pacific Salmon Ecology Laboratory, Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada. Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - A L Bass
- Pacific Salmon Ecology Laboratory, Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada. Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - S G Hinch
- Pacific Salmon Ecology Laboratory, Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada. Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - D A Patterson
- Pacific Salmon Ecology Laboratory, Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada. Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Cooperative Resource Management Institute, School of Resource and Environmental Management, Fisheries and Oceans Canada, Burnaby, BC, Canada. Fisheries and Oceans Canada, Cooperative Resource Management Institute, School of Resource and Environmental Management, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - K M Miller
- Fisheries and Oceans Canada, Molecular Genetics Section, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - S J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6 Canada
| |
Collapse
|
28
|
Houde ALS, Günther OP, Strohm J, Ming TJ, Li S, Kaukinen KH, Patterson DA, Farrell AP, Hinch SG, Miller KM. Discovery and validation of candidate smoltification gene expression biomarkers across multiple species and ecotypes of Pacific salmonids. CONSERVATION PHYSIOLOGY 2019; 7:coz051. [PMID: 31620289 PMCID: PMC6788492 DOI: 10.1093/conphys/coz051] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 06/27/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
Early marine survival of juvenile salmon is intimately associated with their physiological condition during smoltification and ocean entry. Smoltification (parr-smolt transformation) is a developmental process that allows salmon to acquire seawater tolerance in preparation for marine living. Traditionally, this developmental process has been monitored using gill Na+/K+-ATPase (NKA) activity or plasma hormones, but gill gene expression offers the possibility of another method. Here, we describe the discovery of candidate genes from gill tissue for staging smoltification using comparisons of microarray studies with particular focus on the commonalities between anadromous Rainbow trout and Sockeye salmon datasets, as well as a literature comparison encompassing more species. A subset of 37 candidate genes mainly from the microarray analyses was used for TaqMan quantitative PCR assay design and their expression patterns were validated using gill samples from four groups, representing three species and two ecotypes: Coho salmon, Sockeye salmon, stream-type Chinook salmon and ocean-type Chinook salmon. The best smoltification biomarkers, as measured by consistent changes across these four groups, were genes involved in ion regulation, oxygen transport and immunity. Smoltification gene expression patterns (using the top 10 biomarkers) were confirmed by significant correlations with NKA activity and were associated with changes in body brightness, caudal fin darkness and caudal peduncle length. We incorporate gene expression patterns of pre-smolt, smolt and de-smolt trials from acute seawater transfers from a companion study to develop a preliminary seawater tolerance classification model for ocean-type Chinook salmon. This work demonstrates the potential of gene expression biomarkers to stage smoltification and classify juveniles as pre-smolt, smolt or de-smolt.
Collapse
Affiliation(s)
- Aimee Lee S Houde
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
| | - Oliver P Günther
- Günther Analytics, 402-5775 Hampton Place, Vancouver, British Columbia, V6T 2G6, Canada
| | - Jeffrey Strohm
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
| | - Tobi J Ming
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
| | - David A Patterson
- School of Resource and Environmental Management, Fisheries and Oceans Canada, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Anthony P Farrell
- Department of Zoology and Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Scott G Hinch
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
| |
Collapse
|
29
|
Mordecai GJ, Miller KM, Di Cicco E, Schulze AD, Kaukinen KH, Ming TJ, Li S, Tabata A, Teffer A, Patterson DA, Ferguson HW, Suttle CA. Endangered wild salmon infected by newly discovered viruses. eLife 2019; 8:e47615. [PMID: 31478480 PMCID: PMC6721791 DOI: 10.7554/elife.47615] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/16/2019] [Indexed: 12/16/2022] Open
Abstract
The collapse of iconic, keystone populations of sockeye (Oncorhynchus nerka) and Chinook (Oncorhynchus tshawytscha) salmon in the Northeast Pacific is of great concern. It is thought that infectious disease may contribute to declines, but little is known about viruses endemic to Pacific salmon. Metatranscriptomic sequencing and surveillance of dead and moribund cultured Chinook salmon revealed a novel arenavirus, reovirus and nidovirus. Sequencing revealed two different arenavirus variants which each infect wild Chinook and sockeye salmon. In situ hybridisation localised arenavirus mostly to blood cells. Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture.
Collapse
Affiliation(s)
- Gideon J Mordecai
- Department of Earth, Ocean and Atmospheric SciencesUniversity of British ColumbiaVancouverCanada
| | | | - Emiliano Di Cicco
- Pacific Biological StationFisheries and Oceans CanadaNanaimoCanada
- Pacific Salmon FoundationVancouverCanada
| | - Angela D Schulze
- Pacific Biological StationFisheries and Oceans CanadaNanaimoCanada
| | - Karia H Kaukinen
- Pacific Biological StationFisheries and Oceans CanadaNanaimoCanada
| | - Tobi J Ming
- Pacific Biological StationFisheries and Oceans CanadaNanaimoCanada
| | - Shaorong Li
- Pacific Biological StationFisheries and Oceans CanadaNanaimoCanada
| | - Amy Tabata
- Pacific Biological StationFisheries and Oceans CanadaNanaimoCanada
| | - Amy Teffer
- Department of Forest SciencesUniversity of British ColumbiaVancouverCanada
| | - David A Patterson
- Fisheries and Oceans Canada, Science Branch, Cooperative Resource Management Institute, School of Resource and Environmental ManagementSimon Fraser UniversityBurnabyCanada
| | - Hugh W Ferguson
- School of Veterinary MedicineSt. George’s UniversityTrue BlueGrenada
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric SciencesUniversity of British ColumbiaVancouverCanada
- Department of Microbiology and ImmunologyUniversity of British ColumbiaVancouverCanada
- Department of BotanyUniversity of British ColumbiaVancouverCanada
- Institute for the Oceans and FisheriesUniversity of British ColumbiaVancouverCanada
| |
Collapse
|
30
|
Teffer AK, Miller KM. A Comparison of Nonlethal and Destructive Methods for Broad-Based Infectious Agent Screening of Chinook Salmon Using High-Throughput qPCR. JOURNAL OF AQUATIC ANIMAL HEALTH 2019; 31:274-289. [PMID: 31343778 DOI: 10.1002/aah.10079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/20/2019] [Indexed: 06/10/2023]
Abstract
Molecular tools, such as high-throughput quantitative polymerase chain reaction (HT-qPCR), are useful for monitoring multiple infectious agents in wild animal populations (i.e., broad-based screening). If destructive tissue samples cannot be obtained due to experimental design requirements (e.g., bio-telemetry; holding with repeated biopsy) or the conservation status of host species, then nonlethally sampled tissues can be substituted. However, infection profiles have been found to differ between nonlethally and destructively sampled tissues. We present a comparative analysis of nonlethal (gill and blood) and destructive (pool of internal and external tissue) approaches for broad-based infectious agent screening of adult Chinook Salmon Oncorhynchus tshawytscha. Of a possible 47 agents, 16 were detected overall by nonlethal and destructive methods. Our results indicated moderate differences in infection profiles among tissues, with limitations of each tissue type dependent on the ecology of each agent. The gill was the most comprehensive screening tissue, as more infectious agents were detected overall in gill (n = 16) than in blood (n = 12) or multi-tissue pools (n = 15). The agreement in the estimated agent prevalence between tissue types ranged from poor to excellent, while overall agent community structure (the combined prevalence of all agents) showed low agreement between tissue types. Two agents occurred at 100% prevalence in all tissue types. Nine agents, including types of bacteria and gill parasites, were more prevalent in gill than in blood, while five agents, including one virus and several microparasites, were more prevalent in blood. Future studies should pair microscopy and histopathology with HT-qPCR to better characterize host health and disease development relative to molecular detection of agents across tissue types.
Collapse
Affiliation(s)
- Amy K Teffer
- Department of Biology, University of Victoria, Post Office Box 1700, Station CSC, Victoria, British Columbia, V8W 2Y2, Canada
| | - Kristina M Miller
- Fisheries and Oceans Canada, Molecular Genetics Section, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, British Columbia, V9T 6N7, Canada
| |
Collapse
|
31
|
Houde ALS, Akbarzadeh A, Günther OP, Li S, Patterson DA, Farrell AP, Hinch SG, Miller KM. Salmonid gene expression biomarkers indicative of physiological responses to changes in salinity and temperature, but not dissolved oxygen. J Exp Biol 2019; 222:jeb198036. [PMID: 31209112 PMCID: PMC6633282 DOI: 10.1242/jeb.198036] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 06/06/2019] [Indexed: 12/27/2022]
Abstract
An organism's ability to respond effectively to environmental change is critical to its survival. Yet, life stage and overall condition can dictate tolerance thresholds to heightened environmental stressors, such that stress may not be equally felt across individuals and at all times. Also, the transcriptional responses induced by environmental changes can reflect both generalized responses as well as others that are highly specific to the type of change being experienced. Thus, if transcriptional biomarkers specific to a stressor, even under multi-stressor conditions, can be identified, the biomarkers could then be applied in natural environments to determine when and where an individual experiences such a stressor. Here, we experimentally challenged juvenile Chinook salmon (Oncorhynchus tshawytscha) to validate candidate gill gene expression biomarkers. A sophisticated experimental design manipulated salinity (freshwater, brackish water and seawater), temperature (10, 14 and 18°C) and dissolved oxygen (normoxia and hypoxia) in all 18 possible combinations for 6 days using separate trials for three smolt statuses (pre-smolt, smolt and de-smolt). In addition, changes in juvenile behaviour, plasma variables, gill Na+/K+-ATPase activity, body size, body morphology and skin pigmentation supplemented the gene expression responses. We identified biomarkers specific to salinity and temperature that transcended the multiple stressors, smolt status and mortality (live, dead and moribund). Similar biomarkers for dissolved oxygen were not identified. This work demonstrates the unique power of gene expression biomarkers to identify a specific stressor even under multi-stressor conditions, and we discuss our next steps for hypoxia biomarkers using an RNA-seq study.
Collapse
Affiliation(s)
- Aimee Lee S Houde
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada, V9T 6N7
| | - Arash Akbarzadeh
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada, V9T 6N7
- Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, PO Box 3995, Bandar Abbas, Iran
| | - Oliver P Günther
- Günther Analytics, 402-5775 Hampton Place, Vancouver, BC, Canada, V6T 2G6
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada, V9T 6N7
| | - David A Patterson
- School of Resource and Environmental Management, Fisheries and Oceans Canada, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Anthony P Farrell
- Department of Zoology and Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Scott G Hinch
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada, V9T 6N7
| |
Collapse
|
32
|
Kibenge MJT, Wang Y, Gayeski N, Morton A, Beardslee K, McMillan B, Kibenge FSB. Piscine orthoreovirus sequences in escaped farmed Atlantic salmon in Washington and British Columbia. Virol J 2019; 16:41. [PMID: 30940162 PMCID: PMC6444584 DOI: 10.1186/s12985-019-1148-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 03/19/2019] [Indexed: 01/10/2023] Open
Abstract
Background Piscine orthoreovirus (PRV) is an emergent virus in salmon aquaculture belonging to the family Reoviridae. PRV is associated with a growing list of pathological conditions including heart and skeletal inflammation (HSMI) of farmed Atlantic salmon. Despite widespread PRV infection in commercially farmed Atlantic salmon, information on PRV prevalence and on the genetic sequence variation of PRV in Atlantic salmon on the north Pacific Coast is limited. Methods Feral Atlantic salmon caught in Washington State and British Columbia following a large containment failure at a farm in northern Puget Sound were sampled. Fish tissues were tested for PRV by RT-qPCR assay for segment L1 and conventional RT-PCR for PRV segment S1. The PCR products were sequenced and their relationship to PRV strains in GenBank was determined using phylogenetic analysis and nucleotide and amino acid homology comparisons. Results Following the escape of 253,000 Atlantic salmon from a salmon farm in Washington State, USA, 72/73 tissue samples from 27 Atlantic salmon captured shortly after the escape tested PRV-positive. We estimate PRV-prevalence in the source farm population at 95% or greater. The PRV found in the fish was identified as PRV sub-genotype Ia and very similar to PRV from farmed Atlantic salmon in Iceland. This correlates with the source of the fish in the farm. Eggs of infected fish were positive for PRV indicating the possibility of vertical transfer and spread with fish egg transports. Conclusions PRV prevalence was close to 100% in farmed Atlantic salmon that were caught in Washington State and British Columbia following a large containment failure at a farm in northern Puget Sound. The PRV strains present in the escaped Atlantic salmon were very similar to the PRV strain reported in farmed Atlantic salmon from the source hatchery in Iceland that was used to stock commercial aquaculture sites in Washington State. This study emphasizes the need to screen Atlantic salmon broodstock for PRV, particularly where used to supply eggs to the global Atlantic salmon farming industry thereby improving our understanding of PRV epidemiology. Electronic supplementary material The online version of this article (10.1186/s12985-019-1148-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Molly J T Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, P.E.I C1A 4P3, Canada
| | - Yingwei Wang
- School of Mathematical and Computational Sciences, University of Prince Edward Island, 550 University Ave, Charlottetown, P.E.I C1A 4P3, Canada
| | - Nick Gayeski
- Wild Fish Conservancy, PO Box 402, 15629 Main St. NE, Duvall, WA, 98019, USA
| | - Alexandra Morton
- Raincoast Research Society, Box 399, Sointula, BC, V0N 3E0, Canada
| | - Kurt Beardslee
- Wild Fish Conservancy, PO Box 402, 15629 Main St. NE, Duvall, WA, 98019, USA
| | - Bill McMillan
- Wild Fish Conservancy, PO Box 402, 15629 Main St. NE, Duvall, WA, 98019, USA
| | - Frederick S B Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, P.E.I C1A 4P3, Canada.
| |
Collapse
|
33
|
Thakur KK, Vanderstichel R, Kaukinen K, Nekouei O, Laurin E, Miller KM. Infectious agent detections in archived Sockeye salmon (Oncorhynchus nerka) samples from British Columbia, Canada (1985-94). JOURNAL OF FISH DISEASES 2019; 42:533-547. [PMID: 30742305 DOI: 10.1111/jfd.12951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 05/06/2023]
Abstract
In response to concerns that novel infectious agents were introduced through the movement of eggs as Atlantic salmon aquaculture developed in British Columbia (BC), Canada, we estimated the prevalence of infectious agents in archived return-migrating Sockeye salmon, from before and during aquaculture expansion in BC (1985-94). Of 45 infectious agents assessed through molecular assays in 652 samples, 23 (7 bacterial, 2 viral and 14 parasitic) were detected in liver tissue from six regions in BC. Prevalence ranged from 0.005 to 0.83 and varied significantly by region and year. Agent diversity ranged from 0 to 12 per fish (median 4), with the lowest diversity observed in fish from the Trans-Boundary and Central Coast regions. Agents known to be endemic in Sockeye salmon in BC, including Flavobacterium psychrophilum, Infectious haematopoietic necrosis virus, Ceratonova shasta and Parvicapsula minibicornis, were commonly observed. Others, such as Kudoa thyrsites and Piscirikettsia salmonis, were also detected. Surprisingly, infectious agents described only recently in BC salmon, Ca. Branchiomonas cysticola, Parvicapsula pseudobranchicola and Paranucleospora theridion, were also detected, indicating their potential presence prior to the expansion of the aquaculture industry. In general, our data suggest that agent distributions may not have substantially changed because of the salmon aquaculture industry.
Collapse
Affiliation(s)
- Krishna K Thakur
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Raphaël Vanderstichel
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Karia Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Omid Nekouei
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Emilie Laurin
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| |
Collapse
|
34
|
Kibenge FS. Emerging viruses in aquaculture. Curr Opin Virol 2019; 34:97-103. [PMID: 30711892 DOI: 10.1016/j.coviro.2018.12.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/23/2018] [Accepted: 12/28/2018] [Indexed: 11/25/2022]
Abstract
Aquaculture remains the world's fastest-growing sector producing food of animal origin. Unlike in terrestrial animal agriculture, in aquaculture both farmed and wild aquatic animals in the same water column experience the same virus challenges. Additionally, the burgeoning international aquaculture expansion and expanding global trade in live aquatic animals and their products have been accompanied by long distance geographical redistribution of aquatic animal species and their viruses. The outcome is a continuous emergence of viral diseases in aquaculture, which may be driven by virus factors, animal host factors, environmental factors, and/or anthropogenic factors. Examples of emerging viruses in aquaculture include viral haemorrhagic septicaemia virus, infectious haematopoietic necrosis virus, infectious salmon anaemia virus, piscine orthoreovirus, Tilapia lake virus, Covert mortality nodavirus, Shrimp hemocyte iridescent virus, and Abalone herpesvirus.
Collapse
Affiliation(s)
- Frederick Sb Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P E I C1A 4P3, Canada.
| |
Collapse
|
35
|
Piscine Orthoreovirus 3 Is Not the Causative Pathogen of Proliferative Darkening Syndrome (PDS) of Brown Trout ( Salmo trutta fario). Viruses 2019; 11:v11020112. [PMID: 30696111 PMCID: PMC6410266 DOI: 10.3390/v11020112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 01/18/2019] [Accepted: 01/25/2019] [Indexed: 12/17/2022] Open
Abstract
The proliferative darkening syndrome (PDS) is a lethal disease of brown trout (Salmo trutta fario) which occurs in several alpine Bavarian limestone rivers. Because mortality can reach 100%, PDS is a serious threat for affected fish populations. Recently, Kuehn and colleagues reported that a high throughput RNA sequencing approach identified a piscine orthoreovirus (PRV) as a causative agent of PDS. We investigated samples from PDS-affected fish obtained from two exposure experiments performed at the river Iller in 2008 and 2009. Using a RT-qPCR and a well-established next-generation RNA sequencing pipeline for pathogen detection, PRV-specific RNA was not detectable in PDS fish from 2009. In contrast, PRV RNA was readily detectable in several organs from diseased fish in 2008. However, similar virus loads were detectable in the control fish which were not exposed to Iller water and did not show any signs of the disease. Therefore, we conclude that PRV is not the causative agent of PDS of brown trout in the rhithral region of alpine Bavarian limestone rivers. The abovementioned study by Kuehn used only samples from the exposure experiment from 2008 and detected a subclinical PRV bystander infection. Work is ongoing to identify the causative agent of PDS.
Collapse
|
36
|
Twardek WM, Chapman JM, Miller KM, Beere MC, Li S, Kaukinen KH, Danylchuk AJ, Cooke SJ. Evidence of a hydraulically challenging reach serving as a barrier for the upstream migration of infection-burdened adult steelhead. CONSERVATION PHYSIOLOGY 2019; 7:coz023. [PMID: 31191906 PMCID: PMC6553125 DOI: 10.1093/conphys/coz023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 04/15/2019] [Accepted: 04/30/2019] [Indexed: 05/04/2023]
Abstract
Anadromous fishes such as steelhead trout, Oncorhynchus mykiss, are exposed to a suite of infectious agents and migratory challenges during their freshwater migrations. We assessed infectious agent load and richness and immune system gene expression in gill tissue of Bulkley River (British Columbia, CA) steelhead captured at and upstream of a migratory barrier to evaluate whether infectious burdens impacted migration success. We further considered the potential influences of water temperature, sex and fish size on host infectious agents and transcription profiles. There were eight infectious agents detected in steelhead gill tissue, with high prevalence of the bacteria Candidatus Branchiomonas cysticola (80%) and Flavobacterium psychrophilum (95%) and the microparasite Sphaerothecum destruens (53%). Fish sampled at the falls had significantly greater relative loads of Ca. B. cysticola and F. psychrophilum, higher infectious agent richness and differential gene expression compared to fish captured upstream. Flavobacterium psychrophilum was only associated with immune gene expression (particularly humoral immunity) of fish sampled at the falls, while water temperature was positively correlated with genes involved in the complement system, metabolic stress and oxidative stress for fish captured upstream. This work highlights interesting differences in agent-host interactions across fisheries and suggests that hydraulic barriers may reduce the passage of fish with the heaviest infectious agent burdens, emphasizing the selective role of areas of difficult passage. Further, this work expands our knowledge of infectious agent prevalence in wild salmonids and provides insight into the relationships between infectious agents and host physiology.
Collapse
Affiliation(s)
- W M Twardek
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, Colonel By Dr., Ottawa, ON, Canada
- Corresponding author: Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, 1125 Colonel By Dr., Ottawa, ON, K1S 5B6, Canada. Tel: +613 986 3786.
| | - J M Chapman
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, Colonel By Dr., Ottawa, ON, Canada
| | - K M Miller
- Fisheries and Oceans Canada, Pacific Biological Station, Hammond Bay Rd, Nanaimo, BC, Canada
| | - M C Beere
- British Columbia Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Fisheries Branch, Alfred Ave, Smithers, BC, Canada
| | - S Li
- Fisheries and Oceans Canada, Pacific Biological Station, Hammond Bay Rd, Nanaimo, BC, Canada
| | - K H Kaukinen
- Fisheries and Oceans Canada, Pacific Biological Station, Hammond Bay Rd, Nanaimo, BC, Canada
| | - A J Danylchuk
- Department of Environmental Conservation, University of Massachusetts Amherst, Holdsworth Way, Amherst, MA, USA
| | - S J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, Colonel By Dr., Ottawa, ON, Canada
| |
Collapse
|
37
|
Akbarzadeh A, Günther OP, Houde AL, Li S, Ming TJ, Jeffries KM, Hinch SG, Miller KM. Developing specific molecular biomarkers for thermal stress in salmonids. BMC Genomics 2018; 19:749. [PMID: 30326831 PMCID: PMC6192343 DOI: 10.1186/s12864-018-5108-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/21/2018] [Indexed: 12/12/2022] Open
Abstract
Background Pacific salmon (Oncorhynchus spp.) serve as good biological indicators of the breadth of climate warming effects on fish because their anadromous life cycle exposes them to environmental challenges in both marine and freshwater environments. Our study sought to mine the extensive functional genomic studies in fishes to identify robust thermally-responsive biomarkers that could monitor molecular physiological signatures of chronic thermal stress in fish using non-lethal sampling of gill tissue. Results Candidate thermal stress biomarkers for gill tissue were identified using comparisons among microarray datasets produced in the Molecular Genetics Laboratory, Pacific Biological Station, Nanaimo, BC, six external, published microarray studies on chronic and acute temperature stress in salmon, and a comparison of significant genes across published studies in multiple fishes using deep literature mining. Eighty-two microarray features related to 39 unique gene IDs were selected as candidate chronic thermal stress biomarkers. Most of these genes were identified both in the meta-analysis of salmon microarray data and in the literature mining for thermal stress markers in salmonids and other fishes. Quantitative reverse transcription PCR (qRT-PCR) assays for 32 unique genes with good efficiencies across salmon species were developed, and their activity in response to thermally challenged sockeye salmon (O. nerka) and Chinook salmon (O. tshawytscha) (cool, 13–14 °C and warm temperatures 18–19 °C) over 5–7 days was assessed. Eight genes, including two transcripts of each SERPINH1 and HSP90AA1, FKBP10, MAP3K14, SFRS2, and EEF2 showed strong and robust chronic temperature stress response consistently in the discovery analysis and both sockeye and Chinook salmon validation studies. Conclusions The results of both discovery analysis and gene expression showed that a panel of genes involved in chaperoning and protein rescue, oxidative stress, and protein biosynthesis were differentially activated in gill tissue of Pacific salmon in response to elevated temperatures. While individually, some of these biomarkers may also respond to other stressors or biological processes, when expressed in concert, we argue that a biomarker panel comprised of some or all of these genes could provide a reliable means to specifically detect thermal stress in field-caught salmon. Electronic supplementary material The online version of this article (10.1186/s12864-018-5108-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Arash Akbarzadeh
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada. .,Department of Fisheries, Faculty of Marine Science and technology, University of Hormozgan, P.O. Box: 3995, Bandar Abbas, Iran.
| | | | - Aimee Lee Houde
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - Tobi J Ming
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - Kenneth M Jeffries
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Scott G Hinch
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T1Z4, Canada
| | - Kristina M Miller
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| |
Collapse
|
38
|
Di Cicco E, Ferguson HW, Kaukinen KH, Schulze AD, Li S, Tabata A, Günther OP, Mordecai G, Suttle CA, Miller KM. The same strain of Piscine orthoreovirus (PRV-1) is involved in the development of different, but related, diseases in Atlantic and Pacific Salmon in British Columbia. Facets (Ott) 2018. [DOI: 10.1139/facets-2018-0008] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Piscine orthoreovirus Strain PRV-1 is the causative agent of heart and skeletal muscle inflammation (HSMI) in Atlantic salmon ( Salmo salar Linnaeus, 1758). Given its high prevalence in net pen salmon, debate has arisen on whether PRV poses a risk to migratory salmon, especially in British Columbia (BC) where commercially important wild Pacific salmon are in decline. Various strains of PRV have been associated with diseases in Pacific salmon, including erythrocytic inclusion body syndrome (EIBS), HSMI-like disease, and jaundice/anemia in Japan, Norway, Chile and Canada. We examined the developmental pathway of HSMI and jaundice/anemia associated with PRV-1 in farmed Atlantic and chinook ( Oncorhynchus tshawytscha (Walbaum, 1792)) salmon in BC, respectively. In situ hybridization localized PRV-1 within developing lesions in both diseases. The two diseases showed dissimilar pathological pathways, with inflammatory lesions in heart and skeletal muscle in Atlantic salmon and degenerative-necrotic lesions in kidney and liver in chinook salmon, plausibly explained by differences in PRV load tolerance in red blood cells. Viral genome sequencing revealed no consistent differences in PRV-1 variants intimately involved in the development of both diseases suggesting that migratory chinook salmon may be at more than a minimal risk of disease from exposure to the high levels of PRV occurring in salmon farms.
Collapse
Affiliation(s)
- Emiliano Di Cicco
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
- Pacific Salmon Foundation, Vancouver, BC V6J 4S6, Canada
| | - Hugh W. Ferguson
- School of Veterinary Medicine, St. George’s University, True Blue, Grenada, West Indies
| | - Karia H. Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | - Angela D. Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | | | - Gideon Mordecai
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Microbiology and Immunology, Department of Botany, Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kristina M. Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| |
Collapse
|
39
|
Thakur KK, Vanderstichel R, Li S, Laurin E, Tucker S, Neville C, Tabata A, Miller KM. A comparison of infectious agents between hatchery-enhanced and wild out-migrating juvenile chinook salmon (Oncorhynchus tshawytscha) from Cowichan River, British Columbia. Facets (Ott) 2018. [DOI: 10.1139/facets-2017-0113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Infectious diseases are likely contributing to large-scale declines in chinook salmon stocks in the Pacific Northwest, but the specific agents and diseases involved, and the prevalences in migratory salmon, are mostly unknown. We applied a high-throughput microfluidics platform to screen for 45 infectious agents in 556 out-migrating juvenile chinook salmon, collected from freshwater (FW) and saltwater (SW) locations in the Cowichan River system on Vancouver Island, Canada, during 2014. Nineteen agents (5 bacterial, 2 viral, and 12 parasitic) were detected, with prevalences ranging from 0.2% to 57.6%. Co-infections between Candidatus Branchiomonas cysticola Toenshoff, Kvellestad, Mitchell, Steinum, Falk, Colquhoun & Horn, 2012, Paranucleospora theridion Nylund, Nylund, Watanabe, Arnesen & Kalrsbakk, 2010, and gill chlamydia, all associated with gill disease, were observed in SW samples. We detected agents known to cause large-scale mortalities in Pacific salmon ( Ceratonova shasta (Noble, 1950), Parvicapsula minibicornis Kent, Whitaker & Dawe, 1977), and agents only recently reported in Pacific salmon in BC ( Ca. B. cysticola, P. theridion, Facilispora margolisi Jones, Prosperi-Porta & Kim, 2012 and Parvicapsula pseudobranchicola Karlsbakk, Saether, Hostlund, Fjellsoy & Nylund, 2002). Wild and hatchery fish were most divergent in agent profiles in FW, with higher agent diversity in wild fish. Differences in prevalence largely dissipated once they converged in the marine environment, although hatchery fish may be infected by a greater diversity of agents sooner after ocean entry by virtue of their more rapid migration from nearshore to offshore environments.
Collapse
Affiliation(s)
- Krishna K. Thakur
- Department of Health Management, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Raphaël Vanderstichel
- Department of Health Management, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | - Emilie Laurin
- Department of Health Management, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Strahan Tucker
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | - Chrys Neville
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | - Kristina M. Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
- Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| |
Collapse
|
40
|
Connon RE, Jeffries KM, Komoroske LM, Todgham AE, Fangue NA. The utility of transcriptomics in fish conservation. ACTA ACUST UNITED AC 2018; 221:221/2/jeb148833. [PMID: 29378879 DOI: 10.1242/jeb.148833] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers.
Collapse
Affiliation(s)
- Richard E Connon
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba, Canada R3T 2N2
| | - Lisa M Komoroske
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA 92037, USA.,Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Anne E Todgham
- Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Nann A Fangue
- Wildlife, Fish & Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| |
Collapse
|
41
|
Morton A, Routledge R, Hrushowy S, Kibenge M, Kibenge F. The effect of exposure to farmed salmon on piscine orthoreovirus infection and fitness in wild Pacific salmon in British Columbia, Canada. PLoS One 2017; 12:e0188793. [PMID: 29236731 PMCID: PMC5728458 DOI: 10.1371/journal.pone.0188793] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/13/2017] [Indexed: 12/29/2022] Open
Abstract
The disease Heart and Skeletal Muscle Inflammation (HSMI) is causing substantial economic losses to the Norwegian salmon farming industry where the causative agent, piscine orthoreovirus (PRV), is reportedly spreading from farmed to wild Atlantic salmon (Salmo salar) with as yet undetermined impacts. To assess if PRV infection is epidemiologically linked between wild and farmed salmon in the eastern Pacific, wild Pacific salmon (Oncorhynchus sp.) from regions designated as high or low exposure to salmon farms and farmed Atlantic salmon reared in British Columbia (BC) were tested for PRV. The proportion of PRV infection in wild fish was related to exposure to salmon farms (p = 0.0097). PRV was detected in: 95% of farmed Atlantic salmon, 37-45% of wild salmon from regions highly exposed to salmon farms and 5% of wild salmon from the regions furthest from salmon farms. The proportion of PRV infection was also significantly lower (p = 0.0008) where wild salmon had been challenged by an arduous return migration into high-elevation spawning habitat. Inter-annual PRV infection declined in both wild and farmed salmon from 2012-2013 (p ≤ 0.002). These results suggest that PRV transfer is occurring from farmed Atlantic salmon to wild Pacific salmon, that infection in farmed salmon may be influencing infection rates in wild salmon, and that this may pose a risk of reduced fitness in wild salmon impacting their survival and reproduction.
Collapse
Affiliation(s)
- Alexandra Morton
- Raincoast Research Society, Sointula, British Columbia, Canada
- * E-mail:
| | - Richard Routledge
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Stacey Hrushowy
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Molly Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Frederick Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| |
Collapse
|