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Escobar-Sierra C, Cañedo-Argüelles M, Vinyoles D, Lampert KP. Unraveling the molecular mechanisms of fish physiological response to freshwater salinization: A comparative multi-tissue transcriptomic study in a river polluted by potash mining. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124400. [PMID: 38906407 DOI: 10.1016/j.envpol.2024.124400] [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: 03/15/2024] [Revised: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
Freshwater salinization is an escalating global environmental issue that threatens freshwater biodiversity, including fish populations. This study aims to uncover the molecular basis of salinity physiological responses in a non-native minnow species (Phoxinus septimaniae x P. dragarum) exposed to saline effluents from potash mines in the Llobregat River, Barcelona, Spain. Employing high-throughput mRNA sequencing and differential gene expression analyses, brain, gills, and liver tissues collected from fish at two stations (upstream and downstream of saline effluent discharge) were examined. Salinization markedly influenced global gene expression profiles, with the brain exhibiting the most differentially expressed genes, emphasizing its unique sensitivity to salinity fluctuations. Pathway analyses revealed the expected enrichment of ion transport and osmoregulation pathways across all tissues. Furthermore, tissue-specific pathways associated with stress, reproduction, growth, immune responses, methylation, and neurological development were identified in the context of salinization. Rigorous validation of RNA-seq data through quantitative PCR (qPCR) underscored the robustness and consistency of our findings across platforms. This investigation unveils intricate molecular mechanisms steering salinity physiological response in non-native minnows confronting diverse environmental stressors. This comprehensive analysis sheds light on the underlying genetic and physiological mechanisms governing fish physiological response in salinity-stressed environments, offering essential knowledge for the conservation and management of freshwater ecosystems facing salinization.
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Affiliation(s)
- Camilo Escobar-Sierra
- Institute of Zoology, Universität zu Köln Mathematisch-Naturwissenschaftliche Fakultät, Zülpicher Str. 47b, Köln, NRW, 50674, Germany.
| | - Miguel Cañedo-Argüelles
- FEHM-Lab, Institute of Environmental Assessment and Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Dolors Vinyoles
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Avda. Diagonal 643, Barcelona, 08028, Catalonia, Spain
| | - Kathrin P Lampert
- Institute of Zoology, Universität zu Köln Mathematisch-Naturwissenschaftliche Fakultät, Zülpicher Str. 47b, Köln, NRW, 50674, Germany
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2
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Harter TS, Smith EA, Salmerón C, Thies AB, Delgado B, Wilson RW, Tresguerres M. Soluble adenylyl cyclase is an acid-base sensor in rainbow trout red blood cells that regulates intracellular pH and haemoglobin-oxygen binding. Acta Physiol (Oxf) 2024:e14205. [PMID: 39031444 DOI: 10.1111/apha.14205] [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: 02/12/2024] [Revised: 06/12/2024] [Accepted: 07/04/2024] [Indexed: 07/22/2024]
Abstract
AIM To identify the physiological role of the acid-base sensing enzyme, soluble adenylyl cyclase (sAC), in red blood cells (RBC) of the model teleost fish, rainbow trout. METHODS We used: (i) super-resolution microscopy to determine the subcellular location of sAC protein; (ii) live-cell imaging of RBC intracellular pH (pHi) with specific sAC inhibition (KH7 or LRE1) to determine its role in cellular acid-base regulation; (iii) spectrophotometric measurements of haemoglobin-oxygen (Hb-O2) binding in steady-state conditions; and (iv) during simulated arterial-venous transit, to determine the role of sAC in systemic O2 transport. RESULTS Distinct pools of sAC protein were detected in the RBC cytoplasm, at the plasma membrane and within the nucleus. Inhibition of sAC decreased the setpoint for RBC pHi regulation by ~0.25 pH units compared to controls, and slowed the rates of RBC pHi recovery after an acid-base disturbance. RBC pHi recovery was entirely through the anion exchanger (AE) that was in part regulated by HCO3 --dependent sAC signaling. Inhibition of sAC decreased Hb-O2 affinity during a respiratory acidosis compared to controls and reduced the cooperativity of O2 binding. During in vitro simulations of arterial-venous transit, sAC inhibition decreased the amount of O2 that is unloaded by ~11%. CONCLUSION sAC represents a novel acid-base sensor in the RBCs of rainbow trout, where it participates in the modulation of RBC pHi and blood O2 transport though the regulation of AE activity. If substantiated in other species, these findings may have broad implications for our understanding of cardiovascular physiology in vertebrates.
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Affiliation(s)
- Till S Harter
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Emma A Smith
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Cristina Salmerón
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Angus B Thies
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Bryan Delgado
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Rod W Wilson
- Biosciences Department, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Martin Tresguerres
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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3
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Belding LD, Thorstensen MJ, Quijada-Rodriguez AR, Bugg WS, Yoon GR, Loeppky AR, Allen GJP, Schoen AN, Earhart ML, Brandt C, Ali JL, Weihrauch D, Jeffries KM, Anderson WG. Integrated organismal responses induced by projected levels of CO 2 and temperature exposures in the early life stages of lake sturgeon. Mol Ecol 2024; 33:e17432. [PMID: 38887831 DOI: 10.1111/mec.17432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/26/2024] [Accepted: 05/31/2024] [Indexed: 06/20/2024]
Abstract
Atmospheric CO2 and temperature are rising concurrently, and may have profound impacts on the transcriptional, physiological and behavioural responses of aquatic organisms. Further, spring snowmelt may cause transient increases of pCO2 in many freshwater systems. We examined the behavioural, physiological and transcriptomic responses of an ancient fish, the lake sturgeon (Acipenser fulvescens) to projected levels of warming and pCO2 during its most vulnerable period of life, the first year. Specifically, larval fish were raised in either low (16°C) or high (22°C) temperature, and/or low (1000 μatm) or high (2500 μatm) pCO2 in a crossed experimental design over approximately 8 months. Following overwintering, lake sturgeon were exposed to a transient increase in pCO2 of 10,000 μatm, simulating a spring melt based on data in freshwater systems. Transcriptional analyses revealed potential connections to otolith formation and reduced growth in fish exposed to high pCO2 and temperature in combination. Network analyses of differential gene expression revealed different biological processes among the different treatments on the edges of transcriptional networks. Na+/K+-ATPase activity increased in fish not exposed to elevated pCO2 during development, and mRNA abundance of the β subunit was most strongly predictive of enzyme activity. Behavioural assays revealed a decrease in total activity following an acute CO2 exposure. These results demonstrate compensatory and compounding mechanisms of pCO2 and warming dependent on developmental conditions in lake sturgeon. Conserved elements of the cellular stress response across all organisms provide key information for how other freshwater organisms may respond to future climate change.
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Affiliation(s)
- Luke D Belding
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Matt J Thorstensen
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - William S Bugg
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Pacific Salmon Foundation, Vancouver, British Columbia, Canada
| | - Gwangseok R Yoon
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Alison R Loeppky
- Ecology and Environmental Impact, WSP Canada Inc., Winnipeg, Manitoba, Canada
| | - Garrett J P Allen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Alexandra N Schoen
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Biology, University of Winnipeg, Winnipeg, Manitoba, Canada
| | - Madison L Earhart
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Jennifer L Ali
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Dirk Weihrauch
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kenneth M Jeffries
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - W Gary Anderson
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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4
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Mallett MC, Thiem JD, Butler GL, Kennard MJ. A systematic review of approaches to assess fish health responses to anthropogenic threats in freshwater ecosystems. CONSERVATION PHYSIOLOGY 2024; 12:coae022. [PMID: 38706739 PMCID: PMC11069195 DOI: 10.1093/conphys/coae022] [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: 12/04/2023] [Revised: 03/04/2024] [Accepted: 04/05/2024] [Indexed: 05/07/2024]
Abstract
Anthropogenic threats such as water infrastructure, land-use changes, overexploitation of fishes and other biological resources, invasive species and climate change present formidable challenges to freshwater biodiversity. Historically, management of fish and fishery species has largely been based on studies of population- and community-level dynamics; however, the emerging field of conservation physiology promotes the assessment of individual fish health as a key management tool. Fish health is highly sensitive to environmental disturbances and is also a fundamental driver of fitness, with implications for population dynamics such as recruitment and resilience. However, the mechanistic links between particular anthropogenic disturbances and changes in fish health, or impact pathways, are diverse and complex. The diversity of ways in which fish health can be measured also presents a challenge for researchers deciding on methods to employ in studies seeking to understand the impact of these threats. In this review, we aim to provide an understanding of the pathway through which anthropogenic threats in freshwater ecosystems impact fish health and the ways in which fish health components impacted by anthropogenic threats can be assessed. We employ a quantitative systematic approach to a corpus of papers related to fish health in freshwater and utilize a framework that summarizes the impact pathway of anthropogenic threats through environmental alterations and impact mechanisms that cause a response in fish health. We found that land-use changes were the most prolific anthropogenic threat, with a range of different health metrics being suitable for assessing the impact of this threat. Almost all anthropogenic threats impacted fish health through two or more impact pathways. A robust understanding of the impact pathways of anthropogenic threats and the fish health metrics that are sensitive to these threats is crucial for fisheries managers seeking to undertake targeted management of freshwater ecosystems.
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Affiliation(s)
- Maxwell C Mallett
- Australian Rivers Institute, School of Environment and Science, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - Jason D Thiem
- New South Wales Department of Primary Industries, Narrandera Fisheries Centre, 70 Buckingbong Road, Narrandera, NSW 2700, Australia
| | - Gavin L Butler
- New South Wales Department of Primary Industries, Grafton Fisheries Centre,16 Experiment Farm Road, Trenayr, NSW 2460, Australia
| | - Mark J Kennard
- Australian Rivers Institute, School of Environment and Science, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
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5
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Morin M, Jönsson M, Wang CK, Craik DJ, Degnan SM, Degnan BM. Seasonal tissue-specific gene expression in wild crown-of-thorns starfish reveals reproductive and stress-related transcriptional systems. PLoS Biol 2024; 22:e3002620. [PMID: 38743647 PMCID: PMC11093393 DOI: 10.1371/journal.pbio.3002620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
Animals are influenced by the season, yet we know little about the changes that occur in most species throughout the year. This is particularly true in tropical marine animals that experience relatively small annual temperature and daylight changes. Like many coral reef inhabitants, the crown-of-thorns starfish (COTS), well known as a notorious consumer of corals and destroyer of coral reefs, reproduces exclusively in the summer. By comparing gene expression in 7 somatic tissues procured from wild COTS sampled on the Great Barrier Reef, we identified more than 2,000 protein-coding genes that change significantly between summer and winter. COTS genes that appear to mediate conspecific communication, including both signalling factors released into the surrounding sea water and cell surface receptors, are up-regulated in external secretory and sensory tissues in the summer, often in a sex-specific manner. Sexually dimorphic gene expression appears to be underpinned by sex- and season-specific transcription factors (TFs) and gene regulatory programs. There are over 100 TFs that are seasonally expressed, 87% of which are significantly up-regulated in the summer. Six nuclear receptors are up-regulated in all tissues in the summer, suggesting that systemic seasonal changes are hormonally controlled, as in vertebrates. Unexpectedly, there is a suite of stress-related chaperone proteins and TFs, including HIFa, ATF3, C/EBP, CREB, and NF-κB, that are uniquely and widely co-expressed in gravid females. The up-regulation of these stress proteins in the summer suggests the demands of oogenesis in this highly fecund starfish affects protein stability and turnover in somatic cells. Together, these circannual changes in gene expression provide novel insights into seasonal changes in this coral reef pest and have the potential to identify vulnerabilities for targeted biocontrol.
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Affiliation(s)
- Marie Morin
- Centre for Marine Science, School of the Environment, The University of Queensland, Brisbane, Australia
| | - Mathias Jönsson
- Centre for Marine Science, School of the Environment, The University of Queensland, Brisbane, Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Australia
| | - Sandie M. Degnan
- Centre for Marine Science, School of the Environment, The University of Queensland, Brisbane, Australia
| | - Bernard M. Degnan
- Centre for Marine Science, School of the Environment, The University of Queensland, Brisbane, Australia
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Wagner T, McLaughlin P, Faunce KE, Austin S, Smalling K. The Effects of Wastewater Reuse on Smallmouth Bass (Micropterus dolomieu) Relative Abundance in the Shenandoah River Watershed, USA. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024. [PMID: 38517104 DOI: 10.1002/etc.5849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/17/2023] [Accepted: 02/14/2024] [Indexed: 03/23/2024]
Abstract
Municipal and industrial wastewater effluent is an important source of water for lotic systems, especially during periods of low flow. The accumulated wastewater effluent flows-expressed as a percentage of total streamflow (ACCWW%)-contain chemical mixtures that pose a risk to aquatic life; fish may be particularly vulnerable when chronically exposed. Although there has been considerable focus on individual-level effects of exposure to chemical mixtures found in wastewater effluent, scaling up to population-level effects remains a challenging component needed to better understand the potential consequences of exposure in wild populations. This may be particularly important under a changing climate in which wastewater reuse could be essential to maintain river flows. We evaluated the effects of chronic exposure to wastewater effluent, as measured by ACCWW%, on the relative abundance of young-of-year (YOY), juvenile, and adult smallmouth bass (Micropterus dolomieu) populations in the Shenandoah River Watershed (USA). We found that increases in ACCWW% in the previous year and during the prespawn period were negatively correlated with the relative abundance of YOY, resulting in an average 41% predicted decrease in abundance (range = 0.5%-94% predicted decrease in abundance). This lagged effect suggests that adult fish reproductive performance may be compromised by chemical exposure during periods of high ACCWW%. No relationships between ACCWW% and juvenile or adult relative abundance were found, suggesting that negative effects of ACCWW% on YOY abundance may be offset due to compensatory mechanisms following higher ACCWW% exposure. Understanding the effects of wastewater effluent exposure at multiple levels of biological organization will help in the development of management strategies aimed at protecting aquatic life. Environ Toxicol Chem 2024;00:1-11. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Tyler Wagner
- US Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Paul McLaughlin
- Pennsylvania Cooperative Fish and Wildlife Research Unit, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kaycee E Faunce
- Virginia and West Virginia Water Science Center, US Geological Survey, Richmond, Virginia
| | - Samuel Austin
- Virginia and West Virginia Water Science Center, US Geological Survey, Richmond, Virginia
| | - Kelly Smalling
- New Jersey Water Science Center, US Geological Survey, Lawrenceville, New Jersey
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Thoral E, Dargère L, Medina-Suárez I, Clair A, Averty L, Sigaud J, Morales A, Salin K, Teulier L. Non-lethal sampling for assessment of mitochondrial function does not affect metabolic rate and swimming performance. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220483. [PMID: 38186271 PMCID: PMC10772603 DOI: 10.1098/rstb.2022.0483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/26/2023] [Indexed: 01/09/2024] Open
Abstract
A fundamental issue in the metabolic field is whether it is possible to understand underlying mechanisms that characterize individual variation. Whole-animal performance relies on mitochondrial function as it produces energy for cellular processes. However, our lack of longitudinal measures to evaluate how mitochondrial function can change within and among individuals and with environmental context makes it difficult to assess individual variation in mitochondrial traits. The aims of this study were to test the repeatability of muscle mitochondrial metabolism by performing two biopsies of red muscle, and to evaluate the effects of biopsies on whole-animal performance in goldfish Carassius auratus. Our results show that basal mitochondrial respiration and net phosphorylation efficiency are repeatable at 14-day intervals. We also show that swimming performance (optimal cost of transport and critical swimming speed) was repeatable in biopsied fish, whereas the repeatability of individual oxygen consumption (standard and maximal metabolic rates) seemed unstable over time. However, we noted that the means of individual and mitochondrial traits did not change over time in biopsied fish. This study shows that muscle biopsies allow the measurement of mitochondrial metabolism without sacrificing animals and that two muscle biopsies 14 days apart affect the intraspecific variation in fish performance without affecting average performance of individuals. This article is part of the theme issue 'The evolutionary significance of variation in metabolic rates'.
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Affiliation(s)
- Elisa Thoral
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
- Department of Biology, Section for Evolutionary Ecology, Lund University, Sölvegatan 37, Lund 223 62, Sweden
| | - Lauréliane Dargère
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
| | - Ione Medina-Suárez
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, Unidad Asociada ULPGC-CSIC, Campus de Taliarte, 35214 Telde, Gran Canaria, Canary Islands, Spain
| | - Angéline Clair
- Plateforme Animalerie Conventionnelle et Sauvage Expérimentale de la Doua (ACSED), Fédération de Recherche 3728, Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENS-Lyon, INRAE, INSA, VetAgroSup 69622, Villeurbanne, France
| | - Laetitia Averty
- Plateforme Animalerie Conventionnelle et Sauvage Expérimentale de la Doua (ACSED), Fédération de Recherche 3728, Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENS-Lyon, INRAE, INSA, VetAgroSup 69622, Villeurbanne, France
| | - Justine Sigaud
- Plateforme Animalerie Conventionnelle et Sauvage Expérimentale de la Doua (ACSED), Fédération de Recherche 3728, Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENS-Lyon, INRAE, INSA, VetAgroSup 69622, Villeurbanne, France
| | - Anne Morales
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
| | - Karine Salin
- Ifremer, CNRS, RD, Laboratory of Environmental Marine Sciences, Université de Brest, 29280 Plouzané, France
| | - Loïc Teulier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
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Ericson JA, Laroche O, Biessy L, Delorme NJ, Pochon X, Thomson-Laing J, Ragg NLC, Smith KF. Differential responses of selectively bred mussels ( Perna canaliculus) to heat stress-survival, immunology, gene expression and microbiome diversity. Front Physiol 2024; 14:1265879. [PMID: 38425477 PMCID: PMC10902150 DOI: 10.3389/fphys.2023.1265879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/15/2023] [Indexed: 03/02/2024] Open
Abstract
New Zealand's green-lipped mussel (Perna canaliculus) is an ecologically and economically important species. Marine heatwaves are increasing in frequency around NZ's coastline, and these events are correlated with increased stress and mortality of some aquaculture species. This study aimed to identify general biomarkers of heat stress in P. canaliculus and to assess whether responses differed between genetically distinct selectively bred mussels. We exposed three families of selectively bred mussels (families A, B and C) to three seawater temperature regimes in the laboratory: 1) a "control" treatment (ambient 12°C), 2) a 26°C heat challenge with a subsequent recovery period, and 3) a sustained 26°C heat challenge with no recovery. We investigated whether the survival, immune response (hemocyte concentration and viability, oxidative stress and total antioxidant capacity), hemocyte gene expression and gill microbiome differed between the families during the temperature challenges. In the sustained heat-stress treatment, family A had the highest survival rate (42% compared with 25% and 5% for families C and B, respectively). Gene expression levels significantly shifted during thermal stress and differed between families, with family A more dissimilar than families B and C. Family C had substantially more genes impacted by temperature treatment and timepoint than the other families, while family B had very little genes/pathways that responded to thermal stress. Genes related to heat shock proteins and immune responses (e.g., AIF1, CTSC, TOLL8, CASP9, FNTA, AHCY, CRYAB, PPIF) were upregulated in all families during heat stress. Microbiome species-richness differed between families before and during heat-stress, with family A having a distinctly different microbiome flora than the other families. Microbial diversity changed similarly in all families exposed to prolonged heat-stress, with species of Vibrio and Campylobacter increasing in these mussels. Our study highlights the use of non-lethal sampling of hemocytes as a diagnostic tool to explore the immune response and gene expression of selectively bred mussels, to predict their response to ocean warming. This approach can identify potential thermotolerant candidates for further selective breeding, which may increase the resilience of the mussel aquaculture industry in a warming ocean.
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Affiliation(s)
| | | | | | | | - Xavier Pochon
- Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | | | | | - Kirsty F. Smith
- Cawthron Institute, Nelson, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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9
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Thoré ESJ, Aulsebrook AE, Brand JA, Almeida RA, Brodin T, Bertram MG. Time is of the essence: The importance of considering biological rhythms in an increasingly polluted world. PLoS Biol 2024; 22:e3002478. [PMID: 38289905 PMCID: PMC10826942 DOI: 10.1371/journal.pbio.3002478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
Biological rhythms have a crucial role in shaping the biology and ecology of organisms. Light pollution is known to disrupt these rhythms, and evidence is emerging that chemical pollutants can cause similar disruption. Conversely, biological rhythms can influence the effects and toxicity of chemicals. Thus, by drawing insights from the extensive study of biological rhythms in biomedical and light pollution research, we can greatly improve our understanding of chemical pollution. This Essay advocates for the integration of biological rhythmicity into chemical pollution research to gain a more comprehensive understanding of how chemical pollutants affect wildlife and ecosystems. Despite historical barriers, recent experimental and technological advancements now facilitate the integration of biological rhythms into ecotoxicology, offering unprecedented, high-resolution data across spatiotemporal scales. Recognizing the importance of biological rhythms will be essential for understanding, predicting, and mitigating the complex ecological repercussions of chemical pollution.
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Affiliation(s)
- Eli S. J. Thoré
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- TRANSfarm—Science, Engineering, & Technology Group, KU Leuven, Lovenjoel, Belgium
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Anne E. Aulsebrook
- Department of Ornithology, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Jack A. Brand
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Rafaela A. Almeida
- Laboratory of Aquatic Ecology, Evolution, and Conservation, Department of Biology, KU Leuven, Leuven, Belgium
| | - Tomas Brodin
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Michael G. Bertram
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
- School of Biological Sciences, Monash University, Melbourne, Australia
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10
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Péron M, Simon V, Le Grand F, Soudant P, Mazurais D, Vagner M. Non-lethal sampling method for the analysis of white muscle fatty acid profiles in European sea bass (Dicentrarchus labrax). FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:1381-1390. [PMID: 37948014 DOI: 10.1007/s10695-023-01262-w] [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: 07/27/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
This study presents a novel non-lethal sampling method for assessing fatty acid (FA) composition in juvenile European sea bass (Dicentrarchus labrax) using subcutaneous white muscle biopsies. This research aimed to evaluate the suitability of the biopsy for FA analysis using two lipid extraction protocols and comparing them to a lethal routine method. The results showed that a mass of fresh tissue as low as 1.4 mg provided good quality FA chromatograms for both reserve and membrane lipids. Although the biopsy method displayed high variability in terms of FA quantity among intra-individual replicates, it showed good FA profile repeatability in both reserve and membrane lipids. The study highlights the potential of this non-lethal approach for studying FA dynamics in fish, with its application being particularly promising for ecological and experimental studies. However, careful biopsy implementation is recommended to account for potential lipid droplet and lipid distribution variability within the tissue.
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Affiliation(s)
- Mickaël Péron
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France.
| | - Victor Simon
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
| | | | - Philippe Soudant
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
| | - David Mazurais
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
| | - Marie Vagner
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
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11
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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.
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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
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12
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DePasquale SW, Howell BE, Navarroli G, Jeffries KM, Cooke SJ, Wijenayake S, Jeffrey JD, Hasler CT. Are the effects of catch-and-release angling evident in changes to mRNA abundances related to metabolism, acid-base regulation and stress in lake trout ( Salvelinus namaycush) gills? CONSERVATION PHYSIOLOGY 2023; 11:coad065. [PMID: 37637261 PMCID: PMC10452961 DOI: 10.1093/conphys/coad065] [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: 05/26/2023] [Revised: 08/02/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
Catch-and-release (C&R) angling is a conservation-oriented practice intended to reduce the impact recreational angling has on fish populations. Even though most recreationally angled fish are released, little is known about how C&R angling impacts fish at the cellular or tissue level. As the first to explore the impacts of C&R angling on mRNA abundances, our study aimed to identify how the stress of angling influenced metabolism, acid-base regulation and cellular stress in the gills of lake trout (Salvelinus namaycush). Because gills are responsible for metabolic gas exchange, are crucial sites of acid-base homeostasis and respond to stressors quickly, we hypothesized that the relative mRNA abundance of genes related to these three physiological processes would be altered after angling. We took gill samples of live lake trout at 0, 2 or 48 h after fish were angled by rod and reel, and then used quantitative PCR (qPCR) to measure the relative abundance of nine candidate mRNA transcripts. Heat shock protein 70 (hsp70) mRNA levels significantly increased over 5-fold 2 h after angling, indicating a potential activation of a cytoprotective response. However, contrary to our hypothesis, we observed no change in the relative mRNA abundance of genes related to metabolism or acid-base regulation in response to C&R angling within a 48-h period. As C&R angling can negatively impact fish populations, further use of transcript-level studies will allow us to understand the impact C&R has on specific tissues and improve our knowledge of how C&R influences overall fish health.
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Affiliation(s)
- Simon W DePasquale
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada R3B 2E9
| | - Bradley E Howell
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada R3B 2E9
| | - Giulio Navarroli
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada R3B 2E9
| | - Kenneth M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, MB, Canada R3T 2N2
| | - Steven J Cooke
- Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6
| | - Sanoji Wijenayake
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada R3B 2E9
| | - Jennifer D Jeffrey
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada R3B 2E9
| | - Caleb T Hasler
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada R3B 2E9
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13
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Thorstensen MJ, Weinrauch AM, Bugg WS, Jeffries KM, Anderson WG. Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish. Database (Oxford) 2023; 2023:baad055. [PMID: 37590163 PMCID: PMC10434735 DOI: 10.1093/database/baad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/16/2023] [Accepted: 07/23/2023] [Indexed: 08/19/2023]
Abstract
The lake sturgeon (Acipenser fulvescens) is an ancient, octoploid fish faced with conservation challenges across its range in North America, but a lack of genomic resources has hindered molecular research in the species. To support such research, we created a transcriptomic database from 13 tissues: brain, esophagus, gill, head kidney, heart, white muscle, liver, glandular stomach, muscular stomach, anterior intestine, pyloric cecum, spiral valve and rectum. The transcriptomes for each tissue were sequenced and assembled individually from a mean of 98.3 million (±38.9 million SD) reads each. In addition, an overall transcriptome was assembled and annotated with all data used for each tissue-specific transcriptome. All assembled transcriptomes and their annotations were made publicly available as a scientific resource. The non-gut transcriptomes provide important resources for many research avenues. However, we focused our analysis on messenger ribonucleic acid (mRNA) observations in the gut because the gut represents a compartmentalized organ system with compartmentalized functions, and seven of the sequenced tissues were from each of these portions. These gut-specific analyses were used to probe evidence of microbiome regulation by studying heterogeneity in microbial genes and genera identified from mRNA annotations. Gene set enrichment analyses were used to reveal the presence of photoperiod and circadian-related transcripts in the pyloric cecum, which may support periodicity in lake sturgeon digestion. Similar analyses were used to identify different types of innate immune regulation across the gut, while analyses of unique transcripts annotated to microbes revealed heterogeneous genera and genes among different gut tissues. The present results provide a scientific resource and information about the mechanisms of compartmentalized function across gut tissues in a phylogenetically ancient vertebrate. Database URL: https://figshare.com/projects/Lake_Sturgeon_Transcriptomes/133143.
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Affiliation(s)
- Matt J Thorstensen
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Alyssa M Weinrauch
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - William S Bugg
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - W Gary Anderson
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
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14
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Cyr A, Murillo-Cisneros DA, López JA, Furin C, O'Hara T. Comparison of Two Total Mercury Screening and Assessment Methods in Fishes: Biopsy Punch and Dried Muscle Samples. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2023; 85:119-128. [PMID: 37573269 DOI: 10.1007/s00244-023-01020-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/25/2023] [Indexed: 08/14/2023]
Abstract
Rapid and effective quantification of total mercury concentrations ([THg]) in fish muscle is an important part of ongoing monitoring to provide reliable and near real-time public health guidance. Methods for quantifying THg in fish muscle frequently require the use of large sample mass and numerous preparation steps. Wet (aka fresh weight) biopsy punch samples of fish muscle have been used to quantify THg directly, without drying and homogenization. Both methods have advantages and disadvantages. We compare the use of fresh weight biopsy punches for quantifying THg to using larger, dried homogenized samples. The [THg] determination for the two sampling methods was EPA method 7473. Three separate biopsy punch samples and a large muscle sample were taken from each fish and analyzed on a Direct Mercury Analyzer. There were no statistical differences between mean log transformed wet weight [THg] from biopsy punches and homogenized muscle across all samples or within individual species. Similarly, across the range of [THg] (7.5-612.7 ng/g ww), linear regression of [THg] from biopsy punch and homogenized muscle samples was not different from a 1:1 linear relationship. Linear regression statistics of [THg] with fish fork length produced similar results for both biopsy punch and homogenized muscle samples. However, the coefficient of variation among biopsy punch replicates for individual fish was frequently above the acceptable threshold of 15%. We recommend biopsy punches be used as an effective tool for broad-scale rapid monitoring of fish resources for Hg, while homogenized muscle samples be used for fine-scale ecological and health questions.
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Affiliation(s)
- Andrew Cyr
- Department of Veterinary Medicine, University of Alaska Fairbanks, 2141 Koyukuk Dr, Fairbanks, AK, 99775-7750, USA.
| | - Daniella A Murillo-Cisneros
- Centro de Investigaciones Biológicas Del Noroeste, S.C. Planeación Ambiental Y Conservación, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, 23096, La Paz, Baja California Sur, Mexico
| | - J Andrés López
- University of Alaska Museum of the North, University of Alaska, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 905 N Koyukuk Drive, Fairbanks, AK, 99775-7220, USA
| | - Christoff Furin
- Alaska Department of Environmental Conservation, 5251 Dr. Martin Luther King Jr. Ave., Anchorage, AK, 99507, USA
| | - Todd O'Hara
- Bilingual Laboratory of Toxicology, Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
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15
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Giareta EP, Hauser-Davis RA, Abilhoa V, Wosnick N. Carbonic anhydrase in elasmobranchs and implications of the current climate change scenario. Comp Biochem Physiol A Mol Integr Physiol 2023; 281:111435. [PMID: 37086909 DOI: 10.1016/j.cbpa.2023.111435] [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: 02/01/2023] [Revised: 04/16/2023] [Accepted: 04/17/2023] [Indexed: 04/24/2023]
Abstract
The enzyme carbonic anhydrase (CA) has well-known functions in acid-base balance, respiratory gas exchange, and osmoregulation in teleost fishes. However, studies concerning the role of CA in elasmobranchs are still scarce. Therefore, the aim of this study is to present the current status of CA studies in sharks and rays, as well as to identify gaps and emerging needs, in order to guide future studies. This review is organized according to the main roles of CA, with further considerations on climate change and CA effects indicated as paramount, as strategies in the face of climate change can be crucial for species response. The literature review revealed a reduction in publications on CA over the years. In addition, a historical research differentiation is noted, where the first assessments on the subject addressed investigations on basic CA functions, while the most recent studies present a comparative approach among species as well as interdisciplinary discussions, such as ecology and phylogeny. Considering that most elasmobranchs are threatened, future studies should prioritize non-lethal methodologies, in addition to expanding studies to climate change effects on CA.
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Affiliation(s)
| | - Rachel Ann Hauser-Davis
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Vinícius Abilhoa
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Paraná, Curitiba, Brazil
| | - Natascha Wosnick
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Paraná, Curitiba, Brazil
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16
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Müller MF, Banks SC, Crewe TL, Campbell HA. The rise of animal biotelemetry and genetics research data integration. Ecol Evol 2023; 13:e9885. [PMID: 36937069 PMCID: PMC10019913 DOI: 10.1002/ece3.9885] [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: 10/11/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
The advancement and availability of innovative animal biotelemetry and genomic technologies are improving our understanding of how the movements of individuals influence gene flow within and between populations and ultimately drive evolutionary and ecological processes. There is a growing body of work that is integrating what were once disparate fields of biology, and here, we reviewed the published literature up until January 2023 (139 papers) to better understand the drivers of this research and how it is improving our knowledge of animal biology. The review showed that the predominant drivers for this research were as follows: (1) understanding how individual-based movements affect animal populations, (2) analyzing the relationship between genetic relatedness and social structuring, and (3) studying how the landscape affects the flow of genes, and how this is impacted by environmental change. However, there was a divergence between taxa as to the most prevalent research aim and the methodologies applied. We also found that after 2010 there was an increase in studies that integrated the two data types using innovative statistical techniques instead of analyzing the data independently using traditional statistics from the respective fields. This new approach greatly improved our understanding of the link between the individual, the population, and the environment and is being used to better conserve and manage species. We discuss the challenges and limitations, as well as the potential for growth and diversification of this research approach. The paper provides a guide for researchers who wish to consider applying these disparate disciplines and advance the field.
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Affiliation(s)
- Mara F. Müller
- Research Institute for the Environment and LivelihoodsFaculty of Science and Technology, Charles Darwin UniversityNorthern TerritoryDarwinAustralia
| | - Sam C. Banks
- Research Institute for the Environment and LivelihoodsFaculty of Science and Technology, Charles Darwin UniversityNorthern TerritoryDarwinAustralia
| | - Tara L. Crewe
- Department of Natural Resources and RenewablesGovernment of Nova ScotiaKentvilleNova ScotiaCanada
| | - Hamish A. Campbell
- Research Institute for the Environment and LivelihoodsFaculty of Science and Technology, Charles Darwin UniversityNorthern TerritoryDarwinAustralia
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17
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Chiari Y, Howard L, Moreno N, Relyea S, Dunnigan J, Boyer MC, Kardos M, Glaberman S, Luikart G. Influence of RNA-Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation. Mol Ecol Resour 2023; 23:803-817. [PMID: 36704853 DOI: 10.1111/1755-0998.13757] [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: 01/19/2021] [Revised: 12/14/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023]
Abstract
RNA sequencing (RNA-Seq) is popular for measuring gene expression in non-model organisms, including wild populations. While RNA-Seq can detect gene expression variation among wild-caught individuals and yield important insights into biological function, sampling methods can also affect gene expression estimates. We examined the influence of multiple technical variables on estimated gene expression in a non-model fish, the westslope cutthroat trout (Oncorhynchus clarkii lewisi), using two RNA-Seq library types: 3' RNA-Seq (QuantSeq) and whole mRNA-Seq (NEB). We evaluated effects of dip netting versus electrofishing, and of harvesting tissue immediately versus 5 min after euthanasia on estimated gene expression in blood, gill, and muscle. We found no significant differences in gene expression between sampling methods or tissue collection times with either library type. When library types were compared using the same blood samples, 58% of genes detected by both NEB and QuantSeq showed significantly different expression between library types, and NEB detected 31% more genes than QuantSeq. Although the two library types recovered different numbers of genes and expression levels, results with NEB and QuantSeq were consistent in that neither library type showed differences in gene expression between sampling methods and tissue harvesting times. Our study suggests that researchers can safely rely on different fish sampling strategies in the field. In addition, while QuantSeq is more cost effective, NEB detects more expressed genes. Therefore, when it is crucial to detect as many genes as possible (especially low expressed genes), when alternative splicing is of interest, or when working with an organism lacking good genomic resources, whole mRNA-Seq is more powerful.
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Affiliation(s)
- Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, Virginia, USA
| | - Leif Howard
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Science, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
| | - Nickolas Moreno
- Department of Biology, George Mason University, Fairfax, Virginia, USA
| | - Scott Relyea
- Sekokini Springs Hatchery, Montana Fish Wildlife and Parks, Bozeman, Montana, USA
| | - James Dunnigan
- Sekokini Springs Hatchery, Montana Fish Wildlife and Parks, Bozeman, Montana, USA
| | | | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Scott Glaberman
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Science, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
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18
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Lennox RJ, Dahlmo LS, Ford AT, Sortland LK, Vogel EF, Vollset KW. Predation research with electronic tagging. WILDLIFE BIOLOGY 2022. [DOI: 10.1002/wlb3.01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Robert J. Lennox
- Norwegian Inst. for Nature Research Trondheim Norway
- NORCE Norwegian Research Centre, Laboratory for Freshwater Ecology and Inland Fisheries Bergen Norway
| | - Lotte S. Dahlmo
- NORCE Norwegian Research Centre, Laboratory for Freshwater Ecology and Inland Fisheries Bergen Norway
- Dept of Biological Sciences, Univ. of Bergen Bergen Norway
| | - Adam T. Ford
- Univ. of British Columbia Okanagan Kelowna BC Canada
| | - Lene K. Sortland
- NORCE Norwegian Research Centre, Laboratory for Freshwater Ecology and Inland Fisheries Bergen Norway
- Dept of Biological Sciences, Univ. of Bergen Bergen Norway
| | - Emma F. Vogel
- UiT − The Arctic Univ. of Norway, Faculty of Biosciences, Fisheries and Economics Tromsø Norway
| | - Knut Wiik Vollset
- NORCE Norwegian Research Centre, Laboratory for Freshwater Ecology and Inland Fisheries Bergen Norway
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19
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Quéméneur JB, Danion M, Cabon J, Collet S, Zambonino-Infante JL, Salin K. The relationships between growth rate and mitochondrial metabolism varies over time. Sci Rep 2022; 12:16066. [PMID: 36167968 PMCID: PMC9515119 DOI: 10.1038/s41598-022-20428-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial metabolism varies significantly between individuals of the same species and can influence animal performance, such as growth. However, growth rate is usually determined before the mitochondrial assay. The hypothesis that natural variation in mitochondrial metabolic traits is linked to differences in both previous and upcoming growth remains untested. Using biopsies to collect tissue in a non-lethal manner, we tested this hypothesis in a fish model (Dicentrarchus labrax) by monitoring individual growth rate, measuring mitochondrial metabolic traits in the red muscle, and monitoring the growth of the same individuals after the mitochondrial assay. Individual variation in growth rate was consistent before and after the mitochondrial assay; however, the mitochondrial traits that explained growth variation differed between the growth rates determined before and after the mitochondrial assay. While past growth was correlated with the activity of the cytochrome c oxidase, a measure of mitochondrial density, future growth was linked to mitochondrial proton leak respiration. This is the first report of temporal shift in the relationship between growth rate and mitochondrial metabolic traits, suggesting an among-individual variation in temporal changes in mitochondrial traits. Our results emphasize the need to evaluate whether mitochondrial metabolic traits of individuals can change over time.
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Affiliation(s)
- Jean-Baptiste Quéméneur
- Ifremer, Laboratory of Environmental Marine Sciences, University Brest, CNRS, IRD, 29280, Plouzané, France
| | - Morgane Danion
- Anses, Ploufragan-Plouzané Niort Laboratory, VIMEP Unit, Technopôle Brest-Iroise, 29280, Plouzané, France
| | - Joëlle Cabon
- Anses, Ploufragan-Plouzané Niort Laboratory, VIMEP Unit, Technopôle Brest-Iroise, 29280, Plouzané, France
| | - Sophie Collet
- Ifremer, Laboratory of Environmental Marine Sciences, University Brest, CNRS, IRD, 29280, Plouzané, France
| | | | - Karine Salin
- Ifremer, Laboratory of Environmental Marine Sciences, University Brest, CNRS, IRD, 29280, Plouzané, France.
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20
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Thorstensen MJ, Turko AJ, Heath DD, Jeffries KM, Pitcher TE. Acute thermal stress elicits interactions between gene expression and alternative splicing in a fish of conservation concern. J Exp Biol 2022; 225:275812. [DOI: 10.1242/jeb.244162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/27/2022] [Indexed: 11/20/2022]
Abstract
Transcriptomic research provides a mechanistic understanding of an organism's response to environmental challenges such as increasing temperatures, which can provide key insights into the threats posed by thermal challenges associated with urbanization and climate change. Differential gene expression and alternative splicing are two elements of the transcriptomic stress response that may work in tandem, but relatively few studies have investigated these interactions in fishes of conservation concern. We studied the imperilled redside dace (Clinostomus elongatus) as thermal stress is hypothesised to be an important cause of population declines. We tested the hypothesis that gene expression-splicing interactions contribute to the thermal stress response. Wild fish exposed to acute thermal stress were compared with both handling controls and fish sampled directly from a river. Liver tissue was sampled to study the transcriptomic stress response. With a gene set enrichment analysis, we found that thermally stressed fish showed a transcriptional response related to transcription regulation and responses to unfolded proteins, and alternatively spliced genes related to gene expression regulation and metabolism. One splicing factor, prpf38b, was upregulated in the thermally stressed group compared to the other treatments. This splicing factor may have a role in the Jun/AP-1 cellular stress response, a pathway with wide-ranging and context-dependent effects. Given large gene interaction networks and the context-dependent nature of transcriptional responses, our results highlight the importance of understanding interactions between gene expression and splicing for understanding transcriptomic responses to thermal stress. Our results also reveal transcriptional pathways that can inform conservation breeding, translocation, and reintroduction programs for redside dace and other imperilled species by identifying appropriate source populations.
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Affiliation(s)
- Matt J. Thorstensen
- 1 Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Andy J. Turko
- 2 Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; Department of Psychology, Neuroscience, and Behaviour, McMaster University, Hamilton, ON L8S 4L8, Canada
- 3 Department of Integrative Biology & Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Daniel D. Heath
- 3 Department of Integrative Biology & Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Ken M. Jeffries
- 1 Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Trevor E. Pitcher
- 3 Department of Integrative Biology & Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
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21
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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.
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Affiliation(s)
- Matt J. Thorstensen
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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22
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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.
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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
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