1
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Onukwufor JO, Somo DA, Richards JG, Wood CM. Osmo-respiratory compromise in the mosshead sculpin (Clinocottus globiceps): effects of temperature, hypoxia, and re-oxygenation on rates of diffusive water flux and oxygen uptake. FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:853-866. [PMID: 37526893 DOI: 10.1007/s10695-023-01226-0] [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: 04/19/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
In nature, mosshead sculpins (Clinocottus globiceps) are challenged by fluctuations in temperature and oxygen levels in their environment. However, it is unclear how mosshead sculpins modulate the permeability of their branchial epithelia to water and O2 in response to temperature or hypoxia stress. Acute decrease in temperature from 13 to 6 oC reduced diffusive water flux rate by 22% and ṀO2 by 51%, whereas acute increase in temperature from 13 to 25 oC increased diffusive water flux rate by 217% and ṀO2 by 140%, yielding overall Q10 values of 2.08 and 2.47 respectively. Acute reductions in oxygen tension from >95% to 20% or 10% air saturation did not impact diffusive water flux rates, however, ṀO2 was reduced significantly by 36% and 65% respectively. During 1-h or 3-h recovery periods diffusive water flux rates were depressed while ṀO2 exhibited overshoots beyond the normoxic control level. Many responses differed from those seen in our parallel earlier study on the tidepool sculpin, a cottid with similar hypoxia tolerance but much smaller gill area that occupies a similar environment. Overall, our data suggest that during temperature stress, diffusive water flux rates and ṀO2 follow the traditional osmo-respiratory compromise pattern, but during hypoxia and re-oxygenation stress, diffusive water flux rates are decoupled from ṀO2.
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Affiliation(s)
- John O Onukwufor
- Department of Zoology, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
| | - Derek A Somo
- Department of Zoology, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jeffrey G Richards
- Department of Zoology, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Chris M Wood
- Department of Zoology, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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2
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Li J, Yang Z, Yan J, Zhang K, Ning X, Wang T, Ji J, Zhang G, Yin S, Zhao C. Multi-omics analysis revealed the brain dysfunction induced by energy metabolism in Pelteobagrus vachelli under hypoxia stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 254:114749. [PMID: 36907096 DOI: 10.1016/j.ecoenv.2023.114749] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/21/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
Hypoxia in water environment has become increasingly frequent and serious due to global warming and environmental pollution. Revealing the molecular mechanism of fish hypoxia adaptation will help to develop markers of environmental pollution caused by hypoxia. Here, we used a multi-omics method to identify the hypoxia-associated mRNA, miRNA, protein, and metabolite involved in various biological processes in Pelteobagrus vachelli brain. The results showed that hypoxia stress caused brain dysfunction by inhibiting energy metabolism. Specifically, the biological processes involved in energy synthesis and energy consumption are inhibited in P. vachelli brain under hypoxia, such as oxidative phosphorylation, carbohydrate metabolism and protein metabolism. Brain dysfunction is mainly manifested as blood-brain barrier injury accompanied by neurodegenerative diseases and autoimmune diseases. In addition, compared with previous studies, we found that P. vachelli has tissue specificity in response to hypoxia stress and the muscle suffers more damage than the brain. This is the first report to the integrated analysis of the transcriptome, miRNAome, proteome, and metabolome in fish brain. Our findings could provide insights into the molecular mechanisms of hypoxia, and the approach could also be applied to other fish species. DATA AVAILABILITY: The raw data of transcriptome has been uploaded to NCBI database (ID: SUB7714154 and SUB7765255). The raw data of proteome has been uploaded to ProteomeXchange database (PXD020425). The raw data of metabolome has been uploaded to Metabolight (ID: MTBLS1888).
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Affiliation(s)
- Jie Li
- College of Marine Science and Engineering, College of Life Science, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, China
| | - Zhiru Yang
- College of Marine Science and Engineering, College of Life Science, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Jie Yan
- College of Marine Science and Engineering, College of Life Science, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, China
| | - Kai Zhang
- College of Marine Science and Engineering, College of Life Science, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, China
| | - Xianhui Ning
- College of Marine Science and Engineering, College of Life Science, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, China
| | - Tao Wang
- College of Marine Science and Engineering, College of Life Science, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, China
| | - Jie Ji
- College of Marine Science and Engineering, College of Life Science, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, China
| | - Guosong Zhang
- Key Laboratory for Physiology Biochemistry and Application, Heze University, Heze 274015, China
| | - Shaowu Yin
- College of Marine Science and Engineering, College of Life Science, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, China.
| | - Cheng Zhao
- College of Marine Science and Engineering, College of Life Science, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, China.
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3
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Xiang JX, Saha M, Zhong KL, Zhang QS, Zhang D, Jueterbock A, Krueger-Hadfield SA, Wang GG, Weinberger F, Hu ZM. Genome-scale signatures of adaptive gene expression changes in an invasive seaweed Gracilaria vermiculophylla. Mol Ecol 2023; 32:613-627. [PMID: 36355347 DOI: 10.1111/mec.16776] [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: 08/05/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022]
Abstract
Invasive species can successfully and rapidly colonize new niches and expand ranges via founder effects and enhanced tolerance towards environmental stresses. However, the underpinning molecular mechanisms (i.e., gene expression changes) facilitating rapid adaptation to harsh environments are still poorly understood. The red seaweed Gracilaria vermiculophylla, which is native to the northwest Pacific but invaded North American and European coastal habitats over the last 100 years, provides an excellent model to examine whether enhanced tolerance at the level of gene expression contributed to its invasion success. We collected G. vermiculophylla from its native range in Japan and from two non-native regions along the Delmarva Peninsula (Eastern United States) and in Germany. Thalli were reared in a common garden for 4 months at which time we performed comparative transcriptome (mRNA) and microRNA (miRNA) sequencing. MRNA-expression profiling identified 59 genes that were differently expressed between native and non-native thalli. Of these genes, most were involved in metabolic pathways, including photosynthesis, abiotic stress, and biosynthesis of products and hormones in all four non-native sites. MiRNA-based target-gene correlation analysis in native/non-native pairs revealed that some target genes are positively or negatively regulated via epigenetic mechanisms. Importantly, these genes are mostly associated with metabolism and defence capability (e.g., metal transporter Nramp5, senescence-associated protein, cell wall-associated hydrolase, ycf68 protein and cytochrome P450-like TBP). Thus, our gene expression results indicate that resource reallocation to metabolic processes is most likely a predominant mechanism contributing to the range-wide persistence and adaptation of G. vermiculophylla in the invaded range. This study, therefore, provides molecular insight into the speed and nature of invasion-mediated rapid adaption.
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Affiliation(s)
| | - Mahasweta Saha
- Marine Ecology Division, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
- Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Plymouth, UK
| | - Kai-Le Zhong
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | - Di Zhang
- Ocean School, YanTai University, Yantai, China
| | - Alexander Jueterbock
- Algal and Microbial Biotechnology Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Gao-Ge Wang
- Institute of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Florian Weinberger
- Marine Ecology Division, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
| | - Zi-Min Hu
- Ocean School, YanTai University, Yantai, China
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4
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Ekwudo MN, Malek MC, Anderson CE, Yampolsky LY. The interplay between prior selection, mild intermittent exposure, and acute severe exposure in phenotypic and transcriptional response to hypoxia. Ecol Evol 2022; 12:e9319. [PMID: 36248677 PMCID: PMC9548574 DOI: 10.1002/ece3.9319] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Here we report the lifespan effects of chronic, mild, intermittent hypoxia, and short-term survival in acute severe hypoxia in four clones of Daphnia magna originating from either permanent or intermittent habitats. We test the hypothesis that acclimation to chronic mild intermittent hypoxia can extend lifespan through activation of antioxidant and stress-tolerance pathways and increase survival in acute severe hypoxia through activation of oxygen transport and storage proteins and adjustment to carbohydrate metabolism. Unexpectedly, we show that chronic hypoxia extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to acute hypoxia. Exposure to chronic hypoxia did not protect against acute hypoxia; to the contrary, Daphnia from the chronic hypoxia treatment had lower acute hypoxia tolerance than normoxic controls. Few transcripts changed their abundance in response to the chronic hypoxia treatment in any of the clones. After 12 h of acute hypoxia treatment, the transcriptional response was more pronounced, with numerous protein-coding genes with functionality in oxygen transport, mitochondrial and respiratory metabolism, and gluconeogenesis, showing upregulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to acute hypoxia than those from permanent habitats, contrary to predictions, there were no significant hypoxia-by-habitat of origin or chronic-by-acute treatment interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through upregulation of cuticular proteins and neurotrophins, respectively.
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Affiliation(s)
- Millicent N. Ekwudo
- Department of Biological SciencesEast Tennessee State UniversityJohnson CityTennesseeUSA
- Ann Romney Center for Neurologic Diseases, Brigham and Women's HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Morad C. Malek
- Department of Biological SciencesEast Tennessee State UniversityJohnson CityTennesseeUSA
| | - Cora E. Anderson
- Department of Biological SciencesEast Tennessee State UniversityJohnson CityTennesseeUSA
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
| | - Lev Y. Yampolsky
- Department of Biological SciencesEast Tennessee State UniversityJohnson CityTennesseeUSA
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5
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Blewett TA, Binning SA, Weinrauch AM, Ivy CM, Rossi GS, Borowiec BG, Lau GY, Overduin SL, Aragao I, Norin T. Physiological and behavioural strategies of aquatic animals living in fluctuating environments. J Exp Biol 2022; 225:275292. [PMID: 35511083 DOI: 10.1242/jeb.242503] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Shallow or near-shore environments, such as ponds, estuaries and intertidal zones, are among the most physiologically challenging of all aquatic settings. Animals inhabiting these environments experience conditions that fluctuate markedly over relatively short temporal and spatial scales. Living in these habitats requires the ability to tolerate the physiological disturbances incurred by these environmental fluctuations. This tolerance is achieved through a suite of physiological and behavioural responses that allow animals to maintain homeostasis, including the ability to dynamically modulate their physiology through reversible phenotypic plasticity. However, maintaining the plasticity to adjust to some stresses in a dynamic environment may trade off with the capacity to deal with other stressors. This paper will explore studies on select fishes and invertebrates exposed to fluctuations in dissolved oxygen, salinity and pH. We assess the physiological mechanisms these species employ to achieve homeostasis, with a focus on the plasticity of their responses, and consider the resulting physiological trade-offs in function. Finally, we discuss additional factors that may influence organismal responses to fluctuating environments, such as the presence of multiple stressors, including parasites. We echo recent calls from experimental biologists to consider physiological responses to life in naturally fluctuating environments, not only because they are interesting in their own right but also because they can reveal mechanisms that may be crucial for living with increasing environmental instability as a consequence of climate change.
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Affiliation(s)
- Tamzin A Blewett
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada, T6G 2E9
| | - Sandra A Binning
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada, H2V 0B3
| | - Alyssa M Weinrauch
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2
| | - Catherine M Ivy
- Department of Biology, Western University, London, ON, Canada, N6A 5B7
| | - Giulia S Rossi
- Department of Biological Science, University of Toronto, Scarborough, ON, Canada, M1C 1A4
| | - Brittney G Borowiec
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada, N2L 3C5
| | - Gigi Y Lau
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Sienna L Overduin
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada, T6G 2E9
| | - Isabel Aragao
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada, T6G 2E9
| | - Tommy Norin
- DTU Aqua: National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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6
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Li J, Zhang G, Yin D, Li Y, Zhang Y, Cheng J, Zhang K, Ji J, Wang T, Jia Y, Yin S. Integrated application of multi-omics strategies provides insights into the environmental hypoxia response in Pelteobagrus vachelli muscle. Mol Cell Proteomics 2022; 21:100196. [PMID: 35031490 PMCID: PMC8938323 DOI: 10.1016/j.mcpro.2022.100196] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 11/07/2021] [Accepted: 01/05/2022] [Indexed: 11/28/2022] Open
Abstract
Increasing pressures on aquatic ecosystems because of pollutants, nutrient enrichment, and global warming have severely depleted oxygen concentrations. This sudden and significant lack of oxygen has resulted in persistent increases in fish mortality rates. Revealing the molecular mechanism of fish hypoxia adaptation will help researchers to find markers for hypoxia induced by environmental stress. Here, we used a multiomics approach to identify several hypoxia-associated miRNAs, mRNAs, proteins, and metabolites involved in diverse biological pathways in the muscles of Pelteobagrus vachelli. Our findings revealed significant hypoxia-associated changes in muscles over 4 h of hypoxia exposure and discrete tissue-specific patterns. We have previously reported that P. vachelli livers exhibit increased anaerobic glycolysis, heme synthesis, erythropoiesis, and inhibit apoptosis when exposed to hypoxia for 4 h. However, the opposite was observed in muscles. According to our comprehensive analysis, fishes show an acute response to hypoxia, including activation of catabolic pathways to generate more energy, reduction of biosynthesis to decrease energy consumption, and shifting from aerobic to anaerobic metabolic contributions. Also, we found that hypoxia induced muscle dysfunction by impairing mitochondrial function, activating inflammasomes, and apoptosis. The hypoxia-induced mitochondrial dysfunction enhanced oxidative stress, apoptosis, and further triggered interleukin-1β production via inflammasome activation. In turn, interleukin-1β further impaired mitochondrial function or apoptosis by suppressing downstream mitochondrial biosynthesis–related proteins, thus resulting in a vicious cycle of inflammasome activation and mitochondrial dysfunction. Our findings contribute meaningful insights into the molecular mechanisms of hypoxia, and the methods and study design can be utilized across different fish species. First multiomics analysis of mRNA, miRNA, protein, and metabolite in fishes. Liver and muscle were tissue-specific induced by hypoxia. About 70 genes and 16 miRNAs related to hypoxia adaptation were detected. Hypoxia affects muscle function by mediating energy metabolism via HIF pathway.
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Affiliation(s)
- Jie Li
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Key Laboratory for Physiology Biochemistry and Application, Heze University, Heze, 274015, China
| | - Guosong Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Key Laboratory for Physiology Biochemistry and Application, Heze University, Heze, 274015, China.
| | - Danqing Yin
- School of Computer Science, University of Sydney, Sydney, 2006, Australia
| | - Yao Li
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yiran Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jinghao Cheng
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Kai Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jie Ji
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Tao Wang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yongyi Jia
- Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China
| | - Shaowu Yin
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China.
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7
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Borowiec BG, Hoffman RD, Hess CD, Galvez F, Scott GR. Interspecific variation in hypoxia tolerance and hypoxia acclimation responses in killifish from the family Fundulidae. J Exp Biol 2020; 223:jeb209692. [PMID: 31988166 PMCID: PMC7044458 DOI: 10.1242/jeb.209692] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 01/20/2020] [Indexed: 01/25/2023]
Abstract
Hypoxia is a pervasive stressor in aquatic environments, and both phenotypic plasticity and evolutionary adaptation could shape the ability to cope with hypoxia. We investigated evolved variation in hypoxia tolerance and the hypoxia acclimation response across fundulid killifishes that naturally experience different patterns of hypoxia exposure. We compared resting O2 consumption rate (ṀO2 ), and various indices of hypoxia tolerance [critical O2 tension (Pcrit), regulation index (RI), O2 tension (PO2 ) at loss of equilibrium (PLOE) and time to LOE (tLOE) at 0.6 kPa O2] in Fundulus confluentus, Fundulus diaphanus, Fundulus heteroclitus, Fundulus rathbuni, Lucania goodei and Lucania parva We examined the effects of chronic (28 days) exposure to constant hypoxia (2 kPa) or nocturnal intermittent hypoxia (12 h normoxia:12 h hypoxia) in a subset of species. Some species exhibited a two-breakpoint model in ṀO2 caused by early, modest declines in ṀO2 in moderate hypoxia. We found that hypoxia tolerance varied appreciably across species: F. confluentus was the most tolerant (lowest PLOE and Pcrit, longest tLOE), whereas F. rathbuni and F. diaphanus were the least tolerant. However, there was not a consistent pattern of interspecific variation for different indices of hypoxia tolerance, with or without taking phylogenetic relatedness into account, probably because these different indices are underlain by partially distinct mechanisms. Hypoxia acclimation generally improved hypoxia tolerance, but the magnitude of plasticity and responsiveness to different hypoxia patterns varied interspecifically. Our results therefore suggest that hypoxia tolerance is a complex trait that is best appreciated by considering multiple indices of tolerance.
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Affiliation(s)
| | - Ryan D Hoffman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Chelsea D Hess
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Fernando Galvez
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1
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8
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Collins M, Tills O, Turner LM, Clark MS, Spicer JI, Truebano M. Moderate reductions in dissolved oxygen may compromise performance in an ecologically-important estuarine invertebrate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133444. [PMID: 31362229 DOI: 10.1016/j.scitotenv.2019.07.250] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/27/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
Coastal ecosystems, including estuaries, are increasingly pressured by expanding hypoxic regions as a result of human activities such as increased release of nutrients and global warming. Hypoxia is often defined as oxygen concentrations below 2 mL O2 L-1. However, taxa vary markedly in their sensitivity to hypoxia and can be affected by a broad spectrum of low oxygen levels. To better understand how reduced oxygen availability impacts physiological and molecular processes in invertebrates, we investigated responses of an estuarine amphipod to an ecologically-relevant level of moderate hypoxia (~2.6 mL O2 L-1) or severe hypoxia (~1.3 mL O2 L-1). Moderate hypoxia elicited a reduction in aerobic scope, and widespread changes to gene expression, including upregulation of metabolic genes and stress proteins. Under severe hypoxia, a marked hyperventilatory response associated with maintenance of aerobic performance was accompanied by a muted transcriptional response. This included a return of metabolic genes to baseline levels of expression and downregulation of transcripts involved in protein synthesis, most of which indicate recourse to hypometabolism and/or physiological impairment. We conclude that adverse ecological effects may occur under moderate hypoxia through compromised individual performance and, therefore, even modest declines in future oxygen levels may pose a significant challenge to coastal ecosystems.
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Affiliation(s)
- Michael Collins
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK.
| | - Oliver Tills
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - Lucy M Turner
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - John I Spicer
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - Manuela Truebano
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
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9
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Lau GY, Arndt S, Murphy MP, Richards JG. Species- and tissue-specific differences in ROS metabolism during exposure to hypoxia and hyperoxia plus recovery in marine sculpins. ACTA ACUST UNITED AC 2019; 222:jeb.206896. [PMID: 31628206 DOI: 10.1242/jeb.206896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/12/2019] [Indexed: 12/16/2022]
Abstract
Animals that inhabit environments that fluctuate in oxygen must not only contend with disruptions to aerobic metabolism, but also the potential effects of reactive oxygen species (ROS). The goal of this study was to compare aspects of ROS metabolism in response to O2 variability (6 h hypoxia or hyperoxia, with subsequent normoxic recovery) in two species of intertidal sculpin fishes (Cottidae, Actinopterygii) that can experience O2 fluctuations in their natural environment and differ in whole-animal hypoxia tolerance. To assess ROS metabolism, we measured the ratio of glutathione to glutathione disulfide as an indicator of tissue redox environment, MitoP/MitoB ratio to assess in vivo mitochondrial ROS generation, thiobarbituric acid reactive substances (TBARS) for lipid peroxidation, and total oxidative scavenging capacity (TOSC) in the liver, brain and gill. In the brain, the more hypoxia-tolerant O ligocottus maculosus showed large increases in TBARS levels following hypoxia and hyperoxia exposure that were generally not associated with large changes in mitochondrial H2O2 In contrast, the less-tolerant S corpaenichthys marmoratus showed no significant changes in TBARS or mitochondrial H2O2 in the brain. More moderate increases were observed in the liver and gill of O. maculosus exposed to hypoxia and hyperoxia with normoxic recovery, whereas S. marmoratus had a greater response to O2 variability in these tissues compared with the brain. Our results show a species- and tissue-specific relationship between hypoxia tolerance and ROS metabolism.
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Affiliation(s)
- Gigi Y Lau
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada
| | - Sabine Arndt
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Jeffrey G Richards
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada
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10
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Yamazaki A, Nishimiya Y, Tsuda S, Togashi K, Munehara H. Freeze Tolerance in Sculpins (Pisces; Cottoidea) Inhabiting North Pacific and Arctic Oceans: Antifreeze Activity and Gene Sequences of the Antifreeze Protein. Biomolecules 2019; 9:biom9040139. [PMID: 30959891 PMCID: PMC6523315 DOI: 10.3390/biom9040139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/28/2019] [Accepted: 04/03/2019] [Indexed: 11/16/2022] Open
Abstract
Many marine species inhabiting icy seawater produce antifreeze proteins (AFPs) to prevent their body fluids from freezing. The sculpin species of the superfamily Cottoidea are widely found from the Arctic to southern hemisphere, some of which are known to express AFP. Here we clarified DNA sequence encoding type I AFP for 3 species of 2 families (Cottidae and Agonidae) belonging to Cottoidea. We also examined antifreeze activity for 3 families and 32 species of Cottoidea (Cottidae, Agonidae, and Rhamphocottidae). These fishes were collected in 2013–2015 from the Arctic Ocean, Alaska, Japan. We could identify 8 distinct DNA sequences exhibiting a high similarity to those reported for Myoxocephalus species, suggesting that Cottidae and Agonidae share the same DNA sequence encoding type I AFP. Among the 3 families, Rhamphocottidae that experience a warm current did not show antifreeze activity. The species inhabiting the Arctic Ocean and Northern Japan that often covered with ice floe showed high activity, while those inhabiting Alaska, Southern Japan with a warm current showed low/no activity. These results suggest that Cottoidea acquires type I AFP gene before dividing into Cottidae and Agonidae, and have adapted to each location with optimal antifreeze activity level.
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Affiliation(s)
- Aya Yamazaki
- Nanae Fresh-Water Station, Field Science Center for Northern Biosphere, Hokkaido University, Nanae Town Kameda-gun 041-1105, Japan.
| | - Yoshiyuki Nishimiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan.
| | - Sakae Tsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan.
| | - Koji Togashi
- Graduate School of Environmental Sciences, Hokkaido University, Sapporo 060-0810, Japan.
| | - Hiroyuki Munehara
- Usujiri Fisheries Station, Field Science Center of Northern Biosphere, Hokkaido University, Hakodate 041-1613, Japan.
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11
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Healy TM, Schulte PM. Patterns of alternative splicing in response to cold acclimation in fish. ACTA ACUST UNITED AC 2019; 222:jeb.193516. [PMID: 30692167 DOI: 10.1242/jeb.193516] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/23/2019] [Indexed: 12/26/2022]
Abstract
Phenotypic plasticity is an important aspect of an organism's response to environmental change that often requires the modulation of gene expression. These changes in gene expression can be quantitative, as a result of increases or decreases in the amounts of specific transcripts, or qualitative, as a result of the expression of alternative transcripts from the same gene (e.g. via alternative splicing of pre-mRNAs). Although the role of quantitative changes in gene expression in phenotypic plasticity is well known, relatively few studies have examined the role of qualitative changes. Here, we use skeletal muscle RNA-seq data from Atlantic killifish (Fundulus heteroclitus), threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio) to investigate the extent of qualitative changes in gene expression in response to cold acclimation. Fewer genes demonstrated alternative splicing than differential expression as a result of cold acclimation; however, differences in splicing were detected for 426 to 866 genes depending on species, indicating that large numbers of qualitative changes in gene expression are associated with cold acclimation. Many of these alternatively spliced genes were also differentially expressed, and there was functional enrichment for involvement in muscle contraction among the genes demonstrating qualitative changes in response to cold acclimation. Additionally, there was a common group of 29 genes with cold-acclimation-mediated changes in splicing in all three species, suggesting that there may be a set of genes with expression patterns that respond qualitatively to prolonged exposure to cold temperatures across fishes.
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Affiliation(s)
- Timothy M Healy
- The University of British Columbia, Department of Zoology, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
| | - Patricia M Schulte
- The University of British Columbia, Department of Zoology, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
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12
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Mandic M, Ramon ML, Gerstein AC, Gracey AY, Richards JG. Variable gene transcription underlies phenotypic convergence of hypoxia tolerance in sculpins. BMC Evol Biol 2018; 18:163. [PMID: 30390629 PMCID: PMC6215679 DOI: 10.1186/s12862-018-1275-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 10/18/2018] [Indexed: 01/03/2023] Open
Abstract
Background The degree by which mechanisms underlying phenotypic convergence are similar among taxa depends on the number of evolutionary paths available for selection to act upon. Likelihood of convergence will be influenced by an interplay of factors such as genetic architecture, phylogenetic history and population demography. To determine if there is convergence or divergence in mechanisms underlying phenotypic similarity, we assessed whether gene transcription patterns differed among species with similar levels of hypoxia tolerance. Results Three species of marine fish from the superfamily Cottoidea (smoothhead sculpin [Artedius lateralis], sailfin sculpin [Nautichthys oculofasciatus] and Pacific staghorn sculpin [Leptocottus armatus]), all of which have previously been shown to share the same level of hypoxia tolerance, were exposed to short-(8 h) and longer-term (72 h) hypoxia and mRNA transcripts were assessed using a custom microarray. We examined hypoxia-induced transcription patterns in metabolic and protein production pathways and found that a high proportion of genes associated with these biological processes showed significant differences among the species. Specifically, the data suggest that the smoothhead sculpin, unlike the sailfin sculpin and the Pacific staghorn sculpin, relied on amino acid degradation rather than glycolysis or fatty acid oxidation to generate ATP during hypoxia exposure. There was also variation across the species in the transcription of genes involved in protein production (e.g. mRNA processing and protein translation), such that it increased in the smoothhead sculpin, decreased in the sailfin sculpin and was variable in the Pacific staghorn sculpin. Conclusions Changes in metabolic and protein production pathways are part of the key responses of fishes to exposures to environmental hypoxia. Yet, species with similar overall hypoxia tolerance exhibited different transcriptional responses in these pathways, indicating flexibility and complexity of interactions in the evolution of the mechanisms underlying the hypoxia tolerance phenotype. The variation in the hypoxia-induced transcription of genes across species with similar hypoxia tolerance suggests that similar whole-animal phenotypes can emerge from divergent evolutionary paths that may affect metabolically important functions. Electronic supplementary material The online version of this article (10.1186/s12862-018-1275-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Milica Mandic
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada. .,Bamfield Marine Sciences Centre, 100 Pachena Dr, Bamfield, BC, V0R 1B0, Canada.
| | - Marina L Ramon
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Aleeza C Gerstein
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church Street, Minneapolis, MN, 55455, USA
| | - Andrew Y Gracey
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Jeffrey G Richards
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.,Bamfield Marine Sciences Centre, 100 Pachena Dr, Bamfield, BC, V0R 1B0, Canada
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13
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Turko AJ, Tatarenkov A, Currie S, Earley RL, Platek A, Taylor DS, Wright PA. Emersion behaviour underlies variation in gill morphology and aquatic respiratory function in the amphibious fish Kryptolebias marmoratus. ACTA ACUST UNITED AC 2018; 221:jeb.168039. [PMID: 29511069 DOI: 10.1242/jeb.168039] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 03/01/2018] [Indexed: 12/21/2022]
Abstract
Fishes acclimated to hypoxic environments often increase gill surface area to improve O2 uptake. In some species, surface area is increased via reduction of an interlamellar cell mass (ILCM) that fills water channels between gill lamellae. Amphibious fishes, however, may not increase gill surface area in hypoxic water because these species can, instead, leave water and breathe air. To differentiate between these possibilities, we compared wild amphibious mangrove rivulus Kryptolebias marmoratus from two habitats that varied in O2 availability - a hypoxic freshwater pool versus nearly anoxic crab burrows. Fish captured from crab burrows had less gill surface area (as ILCMs were enlarged by ∼32%), increased rates of normoxic O2 consumption and increased critical O2 tension compared with fish from the freshwater pool. Thus, wild mangrove rivulus do not respond to near-anoxic water by decreasing metabolism or increasing O2 extraction. Instead, fish from the crab burrow habitat spent three times longer out of water, which probably caused the observed changes in gill morphology and respiratory phenotype. We also tested whether critical O2 tension is influenced by genetic heterozygosity, as K. marmoratus is one of only two hermaphroditic vertebrate species that can produce both self-fertilized (inbred) or out-crossed (more heterozygous) offspring. We found no evidence for inbreeding depression, suggesting that self-fertilization does not impair respiratory function. Overall, our results demonstrate that amphibious fishes that inhabit hypoxic aquatic habitats can use a fundamentally different strategy from that used by fully aquatic water-breathing fishes, relying on escape behaviour rather than metabolic depression or increased O2 extraction ability.
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Affiliation(s)
- A J Turko
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - A Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - S Currie
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada E4L 1E2
| | - R L Earley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - A Platek
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - D S Taylor
- Brevard County Environmentally Endangered Lands Program, Melbourne, FL 32904, USA
| | - P A Wright
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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14
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Xia JH, Li HL, Li BJ, Gu XH, Lin HR. Acute hypoxia stress induced abundant differential expression genes and alternative splicing events in heart of tilapia. Gene 2017; 639:52-61. [PMID: 28986317 DOI: 10.1016/j.gene.2017.10.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/26/2017] [Accepted: 10/02/2017] [Indexed: 01/10/2023]
Abstract
Hypoxia is one of the critical environmental stressors for fish in aquatic environments. Although accumulating evidences indicate that gene expression is regulated by hypoxia stress in fish, how genes undergoing differential gene expression and/or alternative splicing (AS) in response to hypoxia stress in heart are not well understood. Using RNA-seq, we surveyed and detected 289 differential expressed genes (DEG) and 103 genes that undergo differential usage of exons and splice junctions events (DUES) in heart of a hypoxia tolerant fish, Nile tilapia, Oreochromis niloticus following 12h hypoxic treatment. The spatio-temporal expression analysis validated the significant association of differential exon usages in two randomly selected DUES genes (fam162a and ndrg2) in 5 tissues (heart, liver, brain, gill and spleen) sampled at three time points (6h, 12h, and 24h) under acute hypoxia treatment. Functional analysis significantly associated the differential expressed genes with the categories related to energy conservation, protein synthesis and immune response. Different enrichment categories were found between the DEG and DUES dataset. The Isomerase activity, Oxidoreductase activity, Glycolysis and Oxidative stress process were significantly enriched for the DEG gene dataset, but the Structural constituent of ribosome and Structural molecule activity, Ribosomal protein and RNA binding protein were significantly enriched only for the DUES genes. Our comparative transcriptomic analysis reveals abundant stress responsive genes and their differential regulation function in the heart tissues of Nile tilapia under acute hypoxia stress. Our findings will facilitate future investigation on transcriptome complexity and AS regulation during hypoxia stress in fish.
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Affiliation(s)
- Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Hong Lian Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Xiao Hui Gu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
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15
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Yeh A, Marcinek DJ, Meador JP, Gallagher EP. Effect of contaminants of emerging concern on liver mitochondrial function in Chinook salmon. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 190:21-31. [PMID: 28668760 PMCID: PMC5590637 DOI: 10.1016/j.aquatox.2017.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/09/2017] [Accepted: 06/14/2017] [Indexed: 05/05/2023]
Abstract
We previously reported the bioaccumulation of contaminants of emerging concern (CECs), including pharmaceuticals and personal care products (PPCPs) and perfluorinated compounds, in field-collected juvenile Chinook salmon from urban estuaries of Puget Sound, WA (Meador et al., 2016). Although the toxicological impacts of CECs on salmon are poorly understood, several of the detected contaminants disrupt mitochondrial function in other species. Here, we sought to determine whether environmental exposures to CECs are associated with hepatic mitochondrial dysfunction in juvenile Chinook. Fish were exposed in the laboratory to a dietary mixture of 16 analytes representative of the predominant CECs detected in our field study. Liver mitochondrial content was reduced in fish exposed to CECs, which occurred concomitantly with a 24-32% reduction in expression of peroxisome proliferator-activated receptor (PPAR) Y coactivator-1a (pgc-1α), a positive transcriptional regulator of mitochondrial biogenesis. The laboratory exposures also caused a 40-70% elevation of state 4 respiration per unit mitochondria, which drove a 29-38% reduction of efficiency of oxidative phosphorylation relative to controls. The mixture-induced elevation of respiration was associated with increased oxidative injury as evidenced by increased mitochondrial protein carbonyls, elevated expression of glutathione (GSH) peroxidase 4 (gpx4), a mitochondrial-associated GSH peroxidase that protects against lipid peroxidation, and reduction of mitochondrial GSH. Juvenile Chinook sampled in a WWTP effluent-impacted estuary with demonstrated releases of CECs showed similar trends toward reduced liver mitochondrial content and elevated respiratory activity per mitochondria (including state 3 and uncoupled respiration). However, respiratory control ratios were greater in fish from the contaminated site relative to fish from a minimally-polluted reference site, which may have been due to differences in the timing of exposure to CECs under laboratory and field conditions. Our results indicate that exposure to CECs can affect both mitochondrial quality and content, and support the analysis of mitochondrial function as an indicator of the sublethal effects of CECs in wild fish.
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Affiliation(s)
- Andrew Yeh
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98105-6099, United States
| | - David J Marcinek
- Department of Radiology, Pathology, and Bioengineering University of Washington Medical School, Seattle, WA 98195, United States
| | - James P Meador
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. East, Seattle, WA 98112, United States
| | - Evan P Gallagher
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98105-6099, United States.
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16
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Horn RL, Ramaraj T, Devitt NP, Schilkey FD, Cowley DE. De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis. Mol Ecol Resour 2016; 17:161-171. [PMID: 27292122 DOI: 10.1111/1755-0998.12555] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 06/05/2016] [Accepted: 06/07/2016] [Indexed: 01/16/2023]
Abstract
Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory-controlled setting and in two different water types, a native and a non-native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.
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Affiliation(s)
- Rebekah L Horn
- Biology Department, Trent University, 1600 West Bank Drive, Peterborough, ON, Canada, K9J 7B8
| | - Thiruvarangan Ramaraj
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Nicholas P Devitt
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Faye D Schilkey
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - David E Cowley
- Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Box 30003, MSC 4901, Las Cruces, NM, 88003, USA
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17
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Gallo ND, Levin LA. Fish Ecology and Evolution in the World's Oxygen Minimum Zones and Implications of Ocean Deoxygenation. ADVANCES IN MARINE BIOLOGY 2016; 74:117-198. [PMID: 27573051 DOI: 10.1016/bs.amb.2016.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Oxygen minimum zones (OMZs) and oxygen limited zones (OLZs) are important oceanographic features in the Pacific, Atlantic, and Indian Ocean, and are characterized by hypoxic conditions that are physiologically challenging for demersal fish. Thickness, depth of the upper boundary, minimum oxygen levels, local temperatures, and diurnal, seasonal, and interannual oxycline variability differ regionally, with the thickest and shallowest OMZs occurring in the subtropics and tropics. Although most fish are not hypoxia-tolerant, at least 77 demersal fish species from 16 orders have evolved physiological, behavioural, and morphological adaptations that allow them to live under the severely hypoxic, hypercapnic, and at times sulphidic conditions found in OMZs. Tolerance to OMZ conditions has evolved multiple times in multiple groups with no single fish family or genus exploiting all OMZs globally. Severely hypoxic conditions in OMZs lead to decreased demersal fish diversity, but fish density trends are variable and dependent on region-specific thresholds. Some OMZ-adapted fish species are more hypoxia-tolerant than most megafaunal invertebrates and are present even when most invertebrates are excluded. Expansions and contractions of OMZs in the past have affected fish evolution and diversity. Current patterns of ocean warming are leading to ocean deoxygenation, causing the expansion and shoaling of OMZs, which is expected to decrease demersal fish diversity and alter trophic pathways on affected margins. Habitat compression is expected for hypoxia-intolerant species, causing increased susceptibility to overfishing for fisheries species. Demersal fisheries are likely to be negatively impacted overall by the expansion of OMZs in a warming world.
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Affiliation(s)
- N D Gallo
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States.
| | - L A Levin
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
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18
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Komoroske LM, Connon RE, Jeffries KM, Fangue NA. Linking transcriptional responses to organismal tolerance reveals mechanisms of thermal sensitivity in a mesothermal endangered fish. Mol Ecol 2015; 24:4960-81. [DOI: 10.1111/mec.13373] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 08/27/2015] [Accepted: 09/01/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Lisa M. Komoroske
- National Research Council under contract to Southwest Fisheries Science Center; National Marine Fisheries Service; National Oceanic and Atmospheric Administration; 8901 La Jolla Shores Drive La Jolla CA 92037 USA
- Wildlife, Fish & Conservation Biology; University of California; One Shields Avenue Davis CA 95616 USA
- Anatomy, Physiology & Cell Biology; School of Veterinary Medicine; University of California; One Shields Avenue Davis CA 95616 USA
| | - Richard E. Connon
- Anatomy, Physiology & Cell Biology; School of Veterinary Medicine; University of California; One Shields Avenue Davis CA 95616 USA
| | - Ken M. Jeffries
- Wildlife, Fish & Conservation Biology; University of California; One Shields Avenue Davis CA 95616 USA
- Anatomy, Physiology & Cell Biology; School of Veterinary Medicine; University of California; One Shields Avenue Davis CA 95616 USA
| | - Nann A. Fangue
- Wildlife, Fish & Conservation Biology; University of California; One Shields Avenue Davis CA 95616 USA
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19
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Tiedke J, Borner J, Beeck H, Kwiatkowski M, Schmidt H, Thiel R, Fabrizius A, Burmester T. Evaluating the Hypoxia Response of Ruffe and Flounder Gills by a Combined Proteome and Transcriptome Approach. PLoS One 2015; 10:e0135911. [PMID: 26273839 PMCID: PMC4537130 DOI: 10.1371/journal.pone.0135911] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/29/2015] [Indexed: 11/24/2022] Open
Abstract
Hypoxia has gained ecological importance during the last decades, and it is the most dramatically increasing environmental factor in coastal areas and estuaries. The gills of fish are the prime target of hypoxia and other stresses. Here we have studied the impact of the exposure to hypoxia (1.5 mg O2/l for 48 h) on the protein expression of the gills of two estuarine fish species, the ruffe (Gymnocephalus cernua) and the European flounder (Platichthys flesus). First, we obtained the transcriptomes of mixed tissues (gills, heart and brain) from both species by Illumina next-generation sequencing. Then, the gill proteomes were investigated using two-dimensional gel electrophoresis and mass spectrometry. Quantification of the normalized proteome maps resulted in a total of 148 spots in the ruffe, of which 28 (18.8%) were significantly regulated (> 1.5-fold). In the flounder, 121 spots were found, of which 27 (22.3%) proteins were significantly regulated. The transcriptomes were used for the identification of these proteins, which was successful for 15 proteins of the ruffe and 14 of the flounder. The ruffe transcriptome dataset comprised 87,169,850 reads, resulting in an assembly of 72,108 contigs (N50 = 1,828 bp). 20,860 contigs (26.93%) had blastx hits with E < 1e-5 in the human sequences in the RefSeq database, representing 14,771 unique accession numbers. The flounder transcriptome with 78,943,030 reads assembled into 49,241 contigs (N50 = 2,106 bp). 20,127 contigs (40.87%) had a hit with human proteins, corresponding to 14,455 unique accession numbers. The regulation of selected genes was confirmed by quantitative real-time RT-PCR. Most of the regulated proteins that were identified by this approach function in the energy metabolism, while others are involved in the immune response, cell signalling and the cytoskeleton.
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Affiliation(s)
- Jessica Tiedke
- Institute of Zoology, University of Hamburg, Hamburg, Germany
| | - Janus Borner
- Institute of Zoology, University of Hamburg, Hamburg, Germany
| | - Hendrik Beeck
- Institute of Zoology, University of Hamburg, Hamburg, Germany
| | - Marcel Kwiatkowski
- Department of Clinical Chemistry, University Medical Centre Hamburg-Eppendorf, Campus Forschung, Hamburg, Germany
| | - Hanno Schmidt
- Institute of Molecular Genetics, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Ralf Thiel
- Zoological Museum, Centre of Natural History, University of Hamburg, Hamburg, Germany
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20
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Lockwood BL, Connor KM, Gracey AY. The environmentally tuned transcriptomes of Mytilus mussels. J Exp Biol 2015; 218:1822-33. [DOI: 10.1242/jeb.118190] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
ABSTRACT
Transcriptomics is a powerful tool for elucidating the molecular mechanisms that underlie the ability of organisms to survive and thrive in dynamic and changing environments. Here, we review the major contributions in this field, and we focus on studies of mussels in the genus Mytilus, which are well-established models for the study of ecological physiology in fluctuating environments. Our review is organized into four main sections. First, we illustrate how the abiotic forces of the intertidal environment drive the rhythmic coupling of gene expression to diel and tidal cycles in Mytilus californianus. Second, we discuss the challenges and pitfalls of conducting transcriptomic studies in field-acclimatized animals. Third, we examine the link between transcriptomic responses to environmental stress and biogeographic distributions in blue mussels, Mytilus trossulus and Mytilus galloprovincialis. Fourth, we present a comparison of transcriptomic datasets and identify 175 genes that share common responses to heat stress across Mytilus species. Taken together, these studies demonstrate that transcriptomics can provide an informative snapshot of the physiological state of an organism within an environmental context. In a comparative framework, transcriptomics can reveal how natural selection has shaped patterns of transcriptional regulation that may ultimately influence biogeography.
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Affiliation(s)
- Brent L. Lockwood
- Department of Biology, University of Vermont, 120 Marsh Life Science, 109 Carrigan Drive, Burlington, VT 05405, USA
| | - Kwasi M. Connor
- Marine Environmental Biology, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA 90089, USA
| | - Andrew Y. Gracey
- Marine Environmental Biology, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA 90089, USA
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