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Langan LM, Lovin LM, Taylor RB, Scarlett KR, Kevin Chambliss C, Chatterjee S, Scott JT, Brooks BW. Proteome changes in larval zebrafish (Danio rerio) and fathead minnow (Pimephales promelas) exposed to (±) anatoxin-a. ENVIRONMENT INTERNATIONAL 2024; 185:108514. [PMID: 38394915 DOI: 10.1016/j.envint.2024.108514] [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: 12/15/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
Anatoxin-a and its analogues are potent neurotoxins produced by several genera of cyanobacteria. Due in part to its high toxicity and potential presence in drinking water, these toxins pose threats to public health, companion animals and the environment. It primarily exerts toxicity as a cholinergic agonist, with high affinity at neuromuscular junctions, but molecular mechanisms by which it elicits toxicological responses are not fully understood. To advance understanding of this cyanobacteria, proteomic characterization (DIA shotgun proteomics) of two common fish models (zebrafish and fathead minnow) was performed following (±) anatoxin-a exposure. Specifically, proteome changes were identified and quantified in larval fish exposed for 96 h (0.01-3 mg/L (±) anatoxin-a and caffeine (a methodological positive control) with environmentally relevant treatment levels examined based on environmental exposure distributions of surface water data. Proteomic concentration - response relationships revealed 48 and 29 proteins with concentration - response relationships curves for zebrafish and fathead minnow, respectively. In contrast, the highest number of differentially expressed proteins (DEPs) varied between zebrafish (n = 145) and fathead minnow (n = 300), with only fatheads displaying DEPs at all treatment levels. For both species, genes associated with reproduction were significantly downregulated, with pathways analysis that broadly clustered genes into groups associated with DNA repair mechanisms. Importantly, significant differences in proteome response between the species was also observed, consistent with prior observations of differences in response using both behavioral assays and gene expression, adding further support to model specific differences in organismal sensitivity and/or response. When DEPs were read across from humans to zebrafish, disease ontology enrichment identified diseases associated with cognition and muscle weakness consistent with the prior literature. Our observations highlight limited knowledge of how (±) anatoxin-a, a commonly used synthetic racemate surrogate, elicits responses at a molecular level and advances its toxicological understanding.
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Affiliation(s)
- Laura M Langan
- Department of Environmental Science, Baylor University, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA; Department of Environmental Health Sciences, University of South Carolina, Columbia, SC 29208, USA.
| | - Lea M Lovin
- Department of Environmental Science, Baylor University, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA; Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Raegyn B Taylor
- Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA; Department of Chemistry, Baylor University, Waco, TX 76798, USA
| | - Kendall R Scarlett
- Department of Environmental Science, Baylor University, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA
| | - C Kevin Chambliss
- Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA; Department of Chemistry, Baylor University, Waco, TX 76798, USA
| | - Saurabh Chatterjee
- Department of Medicine, Department of Environmental and Occupational Health, University of California Irvine, Irvine, CA 92617, USA
| | - J Thad Scott
- Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA; Department of Biology, Baylor University, Waco, TX 76798, USA
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA.
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2
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Pinto A, Botelho MJ, Churro C, Asselman J, Pereira P, Pereira JL. A review on aquatic toxins - Do we really know it all regarding the environmental risk posed by phytoplankton neurotoxins? JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118769. [PMID: 37597370 DOI: 10.1016/j.jenvman.2023.118769] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/24/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023]
Abstract
Aquatic toxins are potent natural toxins produced by certain cyanobacteria and marine algae species during harmful cyanobacterial and algal blooms (CyanoHABs and HABs, respectively). These harmful bloom events and the toxins produced during these events are a human and environmental health concern worldwide, with occurrence, frequency and severity of CyanoHABs and HABs being predicted to keep increasing due to ongoing climate change scenarios. These contexts, as well as human health consequences of some toxins produced during bloom events have been thoroughly reviewed before. Conversely, the wider picture that includes the non-human biota in the assessment of noxious effects of toxins is much less covered in the literature and barely covered by review works. Despite direct human exposure to aquatic toxins and related deleterious effects being responsible for the majority of the public attention to the blooms' problematic, it constitutes a very limited fraction of the real environmental risk posed by these toxins. The disruption of ecological and trophic interactions caused by these toxins in the aquatic biota building on deleterious effects they may induce in different species is paramount as a modulator of the overall magnitude of the environmental risk potentially involved, thus necessarily constraining the quality and efficiency of the management strategies that should be placed. In this way, this review aims at updating and consolidating current knowledge regarding the adverse effects of aquatic toxins, attempting to going beyond their main toxicity pathways in human and related models' health, i.e., also focusing on ecologically relevant model organisms. For conciseness and considering the severity in terms of documented human health risks as a reference, we restricted the detailed revision work to neurotoxic cyanotoxins and marine toxins. This comprehensive revision of the systemic effects of aquatic neurotoxins provides a broad overview of the exposure and the hazard that these compounds pose to human and environmental health. Regulatory approaches they are given worldwide, as well as (eco)toxicity data available were hence thoroughly reviewed. Critical research gaps were identified particularly regarding (i) the toxic effects other than those typical of the recognized disease/disorder each toxin causes following acute exposure in humans and also in other biota; and (ii) alternative detection tools capable of being early-warning signals for aquatic toxins occurrence and therefore provide better human and environmental safety insurance. Future directions on aquatic toxins research are discussed in face of the existent knowledge, with particular emphasis on the much-needed development and implementation of effective alternative (eco)toxicological biomarkers for these toxins. The wide-spanning approach followed herein will hopefully stimulate future research more broadly addressing the environmental hazardous potential of aquatic toxins.
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Affiliation(s)
- Albano Pinto
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Portugal.
| | - Maria João Botelho
- IPMA, Portuguese Institute for the Sea and Atmosphere, Av. Alfredo Magalhães Ramalho 6, 1495-165, Algés, Portugal; CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Catarina Churro
- IPMA, Portuguese Institute for the Sea and Atmosphere, Av. Alfredo Magalhães Ramalho 6, 1495-165, Algés, Portugal; CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Jana Asselman
- Blue Growth Research Lab, Ghent University, Bluebridge Building, Ostend Science Park 1, 8400, Ostend, Belgium
| | - Patrícia Pereira
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Portugal
| | - Joana Luísa Pereira
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Portugal
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3
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Zhao M, Lin Z, Zheng Z, Yao D, Yang S, Zhao Y, Chen X, Aweya JJ, Zhang Y. The mechanisms and factors that induce trained immunity in arthropods and mollusks. Front Immunol 2023; 14:1241934. [PMID: 37744346 PMCID: PMC10513178 DOI: 10.3389/fimmu.2023.1241934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
Besides dividing the organism's immune system into adaptive and innate immunity, it has long been thought that only adaptive immunity can establish immune memory. However, many studies have shown that innate immunity can also build immunological memory through epigenetic reprogramming and modifications to resist pathogens' reinfection, known as trained immunity. This paper reviews the role of mitochondrial metabolism and epigenetic modifications and describes the molecular foundation in the trained immunity of arthropods and mollusks. Mitochondrial metabolism and epigenetic modifications complement each other and play a key role in trained immunity.
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Affiliation(s)
- Mingming Zhao
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Zhongyang Lin
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Zhihong Zheng
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Defu Yao
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Shen Yang
- College of Ocean Food and Biological Engineering, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, Fujian, China
| | - Yongzhen Zhao
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, China
| | - Xiuli Chen
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, China
| | - Jude Juventus Aweya
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
- College of Ocean Food and Biological Engineering, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, Fujian, China
| | - Yueling Zhang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
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4
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Wikumpriya GC, Prabhatha MWS, Lee J, Kim CH. Epigenetic Modulations for Prevention of Infectious Diseases in Shrimp Aquaculture. Genes (Basel) 2023; 14:1682. [PMID: 37761822 PMCID: PMC10531180 DOI: 10.3390/genes14091682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/19/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Aquaculture assumes a pivotal role in meeting the escalating global food demand, and shrimp farming, in particular, holds a significant role in the global economy and food security, providing a rich source of nutrients for human consumption. Nonetheless, the industry faces formidable challenges, primarily attributed to disease outbreaks and the diminishing efficacy of conventional disease management approaches, such as antibiotic usage. Consequently, there is an urgent imperative to explore alternative strategies to ensure the sustainability of the industry. In this context, the field of epigenetics emerges as a promising avenue for combating infectious diseases in shrimp aquaculture. Epigenetic modulations entail chemical alterations in DNA and proteins, orchestrating gene expression patterns without modifying the underlying DNA sequence through DNA methylation, histone modifications, and non-coding RNA molecules. Utilizing epigenetic mechanisms presents an opportunity to enhance immune gene expression and bolster disease resistance in shrimp, thereby contributing to disease management strategies and optimizing shrimp health and productivity. Additionally, the concept of epigenetic inheritability in marine animals holds immense potential for the future of the shrimp farming industry. To this end, this comprehensive review thoroughly explores the dynamics of epigenetic modulations in shrimp aquaculture, with a particular emphasis on its pivotal role in disease management. It conveys the significance of harnessing advantageous epigenetic changes to ensure the long-term viability of shrimp farming while deliberating on the potential consequences of these interventions. Overall, this appraisal highlights the promising trajectory of epigenetic applications, propelling the field toward strengthening sustainability in shrimp aquaculture.
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Affiliation(s)
| | | | | | - Chan-Hee Kim
- Division of Fisheries Life Science, Pukyong National University, Busan 48513, Republic of Korea (M.W.S.P.); (J.L.)
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5
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Sol Dourdin T, Rivière G, Cormier A, Di Poi C, Guyomard K, Rabiller M, Akcha F, Bah Sadialiou T, Le Monier P, Sussarellu R. Molecular and phenotypic effects of early exposure to an environmentally relevant pesticide mixture in the Pacific oyster, Crassostrea gigas. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 326:121472. [PMID: 36965683 DOI: 10.1016/j.envpol.2023.121472] [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: 12/27/2022] [Revised: 03/06/2023] [Accepted: 03/19/2023] [Indexed: 06/18/2023]
Abstract
Early life stages are crucial for organism development, especially for those displaying external fertilization, whose gametes and early stages face environmental stressors such as xenobiotics. The pacific oyster, Crassostrea gigas, is considered a model species in ecotoxicology because of its ecological characteristics (benthic, sessile, filter feeding). So far studies have investigated the impact of xenobiotics at embryotoxic, genotoxic and physiological endpoints, sometimes at the multigenerational scale, highlighting the role of epigenetic mechanisms in transmitting alterations induced by exposure to single xenobiotics. However, to date, little is known about the impact of environmentally-mimicking contaminants cocktails. Thus, we examined the impact of an early exposure to environmentally relevant mixture on the Pacific oyster life history. We studied transcriptomic, epigenetic and physiological alterations induced in oysters exposed to 18 pesticides and metals at environmental concentration (nominal sum concentration: 2.85 μg.L-1, measured sum concentration: 3.74 ± 0.013 μg.L-1) during embryo-larval stage (0-48 h post fertilization, hpf). No significant differences in embryo-larval abnormalities at 24 hpf were observed during larval and spat rearing; the swimming behaviour of exposed individuals was disturbed, while they were longer and heavier at specific time points, and exhibited a lower epinephrine-induced metamorphosis rate as well as a higher survival rate in the field. In addition, RNA-seq analyses of gastrula embryos revealed the differential expression of development-related genes (e.g. Hox orthologues and cell cycle regulators) between control and exposed oysters. Whole-genome DNA methylation analyses demonstrated a significant modification of DNA methylation in exposed larvae marked by a demethylation trend. Those findings suggest that early exposure to an environmentally relevant pesticide mixture induces multi-scale latent effects possibly affecting life history traits in the Pacific oyster.
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Affiliation(s)
- Thomas Sol Dourdin
- Ifremer, Unité Contamination Chimique des Ecosystèmes Marins, Nantes, France.
| | - Guillaume Rivière
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), UMR8067, Muséum National D'Histoire Naturelle (MNHN), Centre National de La Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris, CEDEX, France
| | | | - Carole Di Poi
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), France
| | | | | | - Farida Akcha
- Ifremer, Unité Contamination Chimique des Ecosystèmes Marins, Nantes, France
| | | | - Pauline Le Monier
- Ifremer, Unité Contamination Chimique des Ecosystèmes Marins, Nantes, France
| | - Rossana Sussarellu
- Ifremer, Physiologie et Toxines des Microalgues Toxiques, Nantes, France
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6
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Pham K, Ho L, D'Incal CP, De Cock A, Berghe WV, Goethals P. Epigenetic analytical approaches in ecotoxicological aquatic research. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 330:121737. [PMID: 37121302 DOI: 10.1016/j.envpol.2023.121737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/15/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Environmental epigenetics has become a key research focus in global climate change studies and environmental pollutant investigations impacting aquatic ecosystems. Specifically, triggered by environmental stress conditions, intergenerational DNA methylation changes contribute to biological adaptive responses and survival of organisms to increase their tolerance towards these conditions. To critically review epigenetic analytical approaches in ecotoxicological aquatic research, we evaluated 78 publications reported over the past five years (2016-2021) that applied these methods to investigate the responses of aquatic organisms to environmental changes and pollution. The results show that DNA methylation appears to be the most robust epigenetic regulatory mark studied in aquatic animals. As such, multiple DNA methylation analysis methods have been developed in aquatic organisms, including enzyme restriction digestion-based and methyl-specific immunoprecipitation methods, and bisulfite (in)dependent sequencing strategies. In contrast, only a handful of aquatic studies, i.e. about 15%, have been focusing on histone variants and post-translational modifications due to the lack of species-specific affinity based immunological reagents, such as specific antibodies for chromatin immunoprecipitation applications. Similarly, ncRNA regulation remains as the least popular method used in the field of environmental epigenetics. Insights into the opportunities and challenges of the DNA methylation and histone variant analysis methods as well as decreasing costs of next generation sequencing approaches suggest that large-scale epigenetic environmental studies in model and non-model organisms will soon become available in the near future. Moreover, antibody-dependent and independent methods, such as mass spectrometry-based methods, can be used as an alternative epigenetic approach to characterize global changes of chromatin histone modifications in future aquatic research. Finally, a systematic guide for DNA methylation and histone variant methods is offered for ecotoxicological aquatic researchers to select the most relevant epigenetic analytical approach in their research.
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Affiliation(s)
- Kim Pham
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium.
| | - Long Ho
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
| | - Claudio Peter D'Incal
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Andrée De Cock
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Peter Goethals
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
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7
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Tang J, Song A, Pan L, Miao J, Li Z, Zhou Y. Study of DNA methylation of hsd17β, er and reproductive endocrine disrupting effects in female Chlamys farreri under benzo[a]pyrene stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 328:121667. [PMID: 37080513 DOI: 10.1016/j.envpol.2023.121667] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Benzo[a]pyrene (B[a]P) is one kind of persistent organic pollutants (POPs) in the marine environment which has multiple toxic effects. However, epigenetic studies correlated with reproductive endocrine disruption in invertebrates have not been explored. In our study, Chlamys farreri in the mature stage were exposed to B[a]P (0, 0.4, 2 and 10 μg/L) for 5 and 10 d to explore the effects on reproductive endocrine and DNA methylation. The results proved that B[a]P stress significantly restrained the growth of mature oocytes, reduced the content of sex hormones, and affected the expression of genes related to ovarian development. Histological observation showed that the ovarian microstructure was damaged. The detection of SAM/SAH, dnmts, GNMT in the ovary showed that the level of global DNA methylation fluctuated. Significant hypermethylation of the hsd17β promoter region in the ovary was associated with a significant downregulation of its gene expression. In summary, our results suggested that exposure to B[a]P might affect DNA methylation to regulate key reproductive genes, interfere with the synthesis of sex hormones, and inhibit ovarian development. These findings provide a basis for a better understanding of how epigenetic mechanisms are involved in the response of marine invertebrates to POPs stress, opening up new avenues for incorporating environmental epigenetic approaches into marine invertebrate management and conservation plans.
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Affiliation(s)
- Jian Tang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Aimin Song
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Jingjing Miao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Zeyuan Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yueyao Zhou
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
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8
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Silliman K, Spencer LH, White SJ, Roberts SB. Epigenetic and Genetic Population Structure is Coupled in a Marine Invertebrate. Genome Biol Evol 2023; 15:evad013. [PMID: 36740242 PMCID: PMC10468963 DOI: 10.1093/gbe/evad013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 01/10/2023] [Accepted: 01/24/2023] [Indexed: 02/07/2023] Open
Abstract
Delineating the relative influence of genotype and the environment on DNA methylation is critical for characterizing the spectrum of organism fitness as driven by adaptation and phenotypic plasticity. In this study, we integrated genomic and DNA methylation data for two distinct Olympia oyster (Ostrea lurida) populations while controlling for within-generation environmental influences. In addition to providing the first characterization of genome-wide DNA methylation patterns in the oyster genus Ostrea, we identified 3,963 differentially methylated loci between populations. Our results show a clear coupling between genetic and epigenetic patterns of variation, with 27% of variation in interindividual methylation differences explained by genotype. Underlying this association are both direct genetic changes in CpGs (CpG-SNPs) and genetic variation with indirect influence on methylation (mQTLs). When comparing measures of genetic and epigenetic population divergence at specific genomic regions this relationship surprisingly breaks down, which has implications for the methods commonly used to study epigenetic and genetic coupling in marine invertebrates.
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Affiliation(s)
- Katherine Silliman
- South Carolina Department of Natural Resources, Marine Resources Research
Institute, Charleston, South Carolina
| | - Laura H Spencer
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
| | - Samuel J White
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
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Dang X, Lim YK, Li Y, Roberts SB, Li L, Thiyagarajan V. Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment. Mol Ecol 2023; 32:412-427. [PMID: 36314404 DOI: 10.1111/mec.16751] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/22/2022]
Abstract
For marine invertebrates with a pelagic-benthic life cycle, larval exposure to ocean acidification (OA) can affect adult performance in response to another environmental stressor. This carry-over effect has the potential to alter phenotypic traits. However, the molecular mechanisms that mediate "OA"-triggered carry-over effects have not been explored despite such information being key to improving species fitness and management strategies for aquafarming. This study integrated the genome-wide DNA methylome and transcriptome to examine epigenetic modification-mediated carry-over OA impacts on phenotypic traits of the ecologically and commercially important oyster species Crassostrea hongkongensis under field conditions. Larvae of C. hongkongensis were exposed to control pH 8.0 and low pH 7.4 conditions, mimicking near future OA scenario in their habitat, before being outplanted as post-metamorphic juveniles at two mariculture field sites with contrasting environmental stressors for 9 months. The larval carry-over OA effect was found to have persistent impacts on the growth and survival trade-off traits on the outplanted juveniles, although the beneficial or adverse effect depended on the environmental conditions at the outplanted sites. Site-specific plasticity was demonstrated with a diverse DNA methylation-associated gene expression profile, with signal transduction and the endocrine system being the most common and highly enriched functions. Highly methylated exons prevailed in the key genes related to general metabolic and endocytic responses and these genes are evolutionarily conserved in various marine invertebrates in response to OA. These results suggest that oysters with prior larval exposure history to OA had the ability to trigger rapid local adaptive responses via epigenetic modification to cope with multiple stressors in the field.
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Affiliation(s)
- Xin Dang
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Yong-Kian Lim
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.,School of Applied Science, Temasek Polytechnic, Singapore, Singapore
| | - Yang Li
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,The Joint Laboratory for Marine Ecology and Environmental Sciences (JLMEES), Institute of Oceanology, Chinese Acadamy of Sciences, Beijing, China
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.,The Joint Laboratory for Marine Ecology and Environmental Sciences (JLMEES), The Swire Institute of Marine Sciences, The University of Hong Kong, Hong Kong SAR, China
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10
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Rahman MF, Billah MM, Kline RJ, Rahman MS. Effects of elevated temperature on 8-OHdG expression in the American oyster ( Crassostrea virginica): Induction of oxidative stress biomarkers, cellular apoptosis, DNA damage and γH2AX signaling pathways. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2022; 4:100079. [PMID: 36589260 PMCID: PMC9798191 DOI: 10.1016/j.fsirep.2022.100079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/10/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Global temperature is increasing due to anthropogenic activities and the effects of elevated temperature on DNA lesions are not well documented in marine organisms. The American oyster (Crassostrea virginica, an edible and commercially important marine mollusk) is an ideal shellfish species to study oxidative DNA lesions during heat stress. In this study, we examined the effects of elevated temperatures (24, 28, and 32 °C for one-week exposure) on heat shock protein-70 (HSP70, a biomarker of heat stress), 8‑hydroxy-2'-deoxyguanosine (8-OHdG, a biomarker of pro-mutagenic DNA lesion), double-stranded DNA (dsDNA), γ-histone family member X (γH2AX, a molecular biomarker of DNA damage), caspase-3 (CAS-3, a key enzyme of apoptotic pathway) and Bcl-2-associated X (BAX, an apoptosis regulator) protein and/or mRNA expressions in the gills of American oysters. Immunohistochemical and qRT-PCR results showed that HSP70, 8-OHdG, dsDNA, and γH2AX expressions in gills were significantly increased at high temperatures (28 and 32 °C) compared with control (24°C). In situ TUNEL analysis showed that the apoptotic cells in gill tissues were increased in heat-exposed oysters. Interestingly, the enhanced apoptotic cells were associated with increased CAS-3 and BAX mRNA and/or protein expressions, along with 8-OHdG levels in gills after heat exposure. Moreover, the extrapallial (EP) fluid (i.e., extracellular body fluid) protein concentrations were lower; however, the EP glucose levels were higher in heat-exposed oysters. Taken together, these results suggest that heat shock-driven oxidative stress alters extracellular body fluid conditions and induces cellular apoptosis and DNA damage, which may lead to increased 8-OHdG levels in cells/tissues in oysters.
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Key Words
- 8-OHdG, 8‑hydroxy-2′-deoxyguanosine
- BAX, bcl-2-associate X
- BSA, bovine serum albumin
- CAS-3, caspase-3
- Caspase 3
- DSBs, double-stranded breaks
- EP, extrapallial
- Extrapallial fluid
- HSP70
- HSP70, heat shock protein 70
- Heat stress
- Marine mollusks
- PBS, Phosphate buffer saline
- SSBs, single-stranded breaks
- TUNEL, terminal deoxynucleotidyl transferase (TdT) dUTP nick-end labeling
- dsDNA breaks
- dsDNA, double-stranded DNA
- qRT-PCR, quantitative real-time polymerase chain reaction
- ssDNA, single-stranded DNA
- γ-H2AX, γ-histone family member X
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Affiliation(s)
- Md Faizur Rahman
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Mohammad Maruf Billah
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Richard J. Kline
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA,Department of Biology, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Md Saydur Rahman
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA,Department of Biology, University of Texas Rio Grande Valley, Brownsville, TX, USA,Corresponding author at: Department of Biology, University of Texas Rio Grande Valley, 1 West University Blvd., Brownsville, Texas 78520, USA.
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11
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Trigg SA, Venkataraman YR, Gavery MR, Roberts SB, Bhattacharya D, Downey-Wall A, Eirin-Lopez JM, Johnson KM, Lotterhos KE, Puritz JB, Putnam HM. Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases. Mol Ecol Resour 2021; 22:1247-1261. [PMID: 34709728 DOI: 10.1111/1755-0998.13542] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022]
Abstract
There is a growing focus on the role of DNA methylation in the ability of marine invertebrates to rapidly respond to changing environmental factors and anthropogenic impacts. However, genome-wide DNA methylation studies in nonmodel organisms are currently hampered by a limited understanding of methodological biases. Here, we compare three methods for quantifying DNA methylation at single base-pair resolution-whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and methyl-CpG binding domain bisulfite sequencing (MBDBS)-using multiple individuals from two reef-building coral species with contrasting environmental sensitivity. All methods reveal substantially greater methylation in Montipora capitata (11.4%) than the more sensitive Pocillopora acuta (2.9%). The majority of CpG methylation in both species occurs in gene bodies and flanking regions. In both species, MBDBS has the greatest capacity for detecting CpGs in coding regions at our sequencing depth, but MBDBS may be influenced by intrasample methylation heterogeneity. RRBS yields robust information for specific loci albeit without enrichment of any particular genome feature and with significantly reduced genome coverage. Relative genome size strongly influences the number and location of CpGs detected by each method when sequencing depth is limited, illuminating nuances in cross-species comparisons. As genome-wide methylation differences, supported by data across bisulfite sequencing methods, may contribute to environmental sensitivity phenotypes in critical marine invertebrate taxa, these data provide a genomic resource for investigating the functional role of DNA methylation in environmental tolerance.
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Affiliation(s)
- Shelly A Trigg
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Yaamini R Venkataraman
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA.,Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Mackenzie R Gavery
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Alan Downey-Wall
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA
| | - Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, North Miami, Florida, USA
| | - Kevin M Johnson
- Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, California, USA.,California Sea Grant, University of California San Diego, La Jolla, California, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA
| | - Jonathan B Puritz
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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12
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Acute benzo[a]pyrene exposure induced oxidative stress, neurotoxicity and epigenetic change in blood clam Tegillarca granosa. Sci Rep 2021; 11:18744. [PMID: 34548601 PMCID: PMC8455545 DOI: 10.1038/s41598-021-98354-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/22/2021] [Indexed: 12/16/2022] Open
Abstract
The blood clam (Tegillarca granosa) is being developed into a model bivalve mollusc for assessing and monitoring marine pollution on the offshore seabed. However, the information on the response of blood clam to PAHs, an organic pollutant usually deposited in submarine sediment, remains limited. Herein, we employed multiple biomarkers, including histological changes, oxidative stress, neurotoxicity and global DNA methylation, to investigate the effects of 10 and 100 μg/L Bap exposure on the blood clams under laboratory conditions, as well as the potential mechanisms. Acute Bap exposure can induce significant morphological abnormalities in gills as shown through hematoxylin–eosin (H.E) staining, providing an intuitive understanding on the effects of Bap on the structural organization of the blood clams. Meanwhile, the oxidative stress was significantly elevated as manifested by the increase of antioxidants activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) and glutathione-s-transferase (GST), lipid peroxidation (LPO) level and 8-hydroxy-2′-deoxyguanosine (8-OHdG) content. The neurotoxicity was also strengthened by Bap toxicity manifested as inhibited acetylcholinesterase (AChE) and choline acetyltransferase (ChAT) activities. In addition, the global DNA methylation level was investigated, and a significant DNA hypomethylation was observed in Bap exposed the blood clam. The correlation analysis showed that the global DNA methylation was negatively correlated with antioxidants (SOD, CAT and POD) activities, but positively correlated choline enzymes (AChE and ChAT) activities. These results collectively suggested that acute Bap exposure can cause damage in gills structures in the blood clam possibly by generating oxidative stress and neurotoxicity, and the global DNA methylation was inhibited to increase the transcriptional expression level of antioxidants genes and consequently elevate antioxidants activities against Bap toxicity. These results are hoped to shed some new light on the study of ecotoxicology effect of PAHs on marine bivalves.
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13
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Chandra Rajan K, Meng Y, Yu Z, Roberts SB, Vengatesen T. Oyster biomineralization under ocean acidification: From genes to shell. GLOBAL CHANGE BIOLOGY 2021; 27:3779-3797. [PMID: 33964098 DOI: 10.1111/gcb.15675] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/02/2021] [Indexed: 05/27/2023]
Abstract
Biomineralization is one of the key processes that is notably affected in marine calcifiers such as oysters under ocean acidification (OA). Understanding molecular changes in the biomineralization process under OA and its heritability, therefore, is key to developing conservation strategies for protecting ecologically and economically important oyster species. To do this, in this study, we have explicitly chosen the tissue involved in biomineralization (mantle) of an estuarine commercial oyster species, Crassostrea hongkongensis. The primary aim of this study is to understand the influence of DNA methylation over gene expression of mantle tissue under decreased ~pH 7.4, a proxy of OA, and to extrapolate if these molecular changes can be observed in the product of biomineralization-the shell. We grew early juvenile C. hongkongensis, under decreased ~pH 7.4 and control ~pH 8.0 over 4.5 months and studied OA-induced DNA methylation and gene expression patterns along with shell properties such as microstructure, crystal orientation and hardness. The population of oysters used in this study was found to be moderately resilient to OA at the end of the experiment. The expression of key biomineralization-related genes such as carbonic anhydrase and alkaline phosphatase remained unaffected; thus, the mechanical properties of the shell (shell growth rate, hardness and crystal orientation) were also maintained without any significant difference between control and OA conditions with signs of severe dissolution. In addition, this study makes three major conclusions: (1) higher expression of Ca2+ binding/signalling-related genes in the mantle plays a key role in maintaining biomineralization under OA; (2) DNA methylation changes occur in response to OA; however, these methylation changes do not directly control gene expression; and (3) OA would be more of a 'dissolution problem' rather than a 'biomineralization problem' for resilient species that maintain calcification rate with normal shell growth and mechanical properties.
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Affiliation(s)
- Kanmani Chandra Rajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Yuan Meng
- State Key Laboratory of Respiratory Disease, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ziniu Yu
- South China Sea Institute of Oceanology, Guangzhou, China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Thiyagarajan Vengatesen
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
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14
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Wong JM, Hofmann GE. Gene expression patterns of red sea urchins (Mesocentrotus franciscanus) exposed to different combinations of temperature and pCO 2 during early development. BMC Genomics 2021; 22:32. [PMID: 33413121 PMCID: PMC7792118 DOI: 10.1186/s12864-020-07327-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The red sea urchin Mesocentrotus franciscanus is an ecologically important kelp forest herbivore and an economically valuable wild fishery species. To examine how M. franciscanus responds to its environment on a molecular level, differences in gene expression patterns were observed in embryos raised under combinations of two temperatures (13 °C or 17 °C) and two pCO2 levels (475 μatm or 1050 μatm). These combinations mimic various present-day conditions measured during and between upwelling events in the highly dynamic California Current System with the exception of the 17 °C and 1050 μatm combination, which does not currently occur. However, as ocean warming and acidification continues, warmer temperatures and higher pCO2 conditions are expected to increase in frequency and to occur simultaneously. The transcriptomic responses of the embryos were assessed at two developmental stages (gastrula and prism) in light of previously described plasticity in body size and thermotolerance under these temperature and pCO2 treatments. RESULTS Although transcriptomic patterns primarily varied by developmental stage, there were pronounced differences in gene expression as a result of the treatment conditions. Temperature and pCO2 treatments led to the differential expression of genes related to the cellular stress response, transmembrane transport, metabolic processes, and the regulation of gene expression. At each developmental stage, temperature contributed significantly to the observed variance in gene expression, which was also correlated to the phenotypic attributes of the embryos. On the other hand, the transcriptomic response to pCO2 was relatively muted, particularly at the prism stage. CONCLUSIONS M. franciscanus exhibited transcriptomic plasticity under different temperatures, indicating their capacity for a molecular-level response that may facilitate red sea urchins facing ocean warming as climate change continues. In contrast, the lack of a robust transcriptomic response, in combination with observations of decreased body size, under elevated pCO2 levels suggest that this species may be negatively affected by ocean acidification. High present-day pCO2 conditions that occur due to coastal upwelling may already be influencing populations of M. franciscanus.
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Affiliation(s)
- Juliet M Wong
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
- Present address: Department of Biological Sciences, Florida International University, North Miami, FL, 33181, USA.
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
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15
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Genome-wide identification and transcriptional modulation of histone variants and modification related genes in the low pH-exposed marine rotifer Brachionus koreanus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100748. [PMID: 33032078 DOI: 10.1016/j.cbd.2020.100748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/05/2020] [Accepted: 09/18/2020] [Indexed: 11/22/2022]
Abstract
Histone modification is considered to be a major epigenetic control mechanism. These modifications (e.g. acetylation, phosphorylation, and methylation) may affect the interaction of histones with DNA and/or regulate DNA-based processes (e.g., recombination, repair, replication, and transcription) and chromatin remodeling complexes. Despite their significance in metazoan life and evolution, few studies have been conducted to identify genes undergoing epigenetic control modification in aquatic invertebrates. In this study, we identified whole core histones (70 total genes) and post-translational modification (PTM) histone genes (63 total genes) in the marine rotifer Brachionus koreanus through whole-genome analysis, and annotated them according to the human nomenclature. Notably, upon comparative analysis of cis-regulatory motif sequences, we found that B. koreanus core histone protein structures were similar to those of mammals. Furthermore, to examine the effect of parental low pH stress on the offspring's epigenetic regulation, we investigated the expression of PTM genes in two generations of B. koreanus exposed to low pH conditions. Given that the B. koreanus genome does not possess DNA methyltransferase 1 and 3 genes, we concluded that histone genes could be involved as an important epigenetic mechanism in B. koreanus. Therefore, the histone-associated genes identified in this study could be useful for ecotoxicological studies and facilitate the application of chromatin immunoprecipitation sequencing using high-throughput DNA sequencing based on the genome-wide identification of transcription factor binding sites in rotifers.
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16
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Fallet M, Luquet E, David P, Cosseau C. Epigenetic inheritance and intergenerational effects in mollusks. Gene 2019; 729:144166. [PMID: 31678264 DOI: 10.1016/j.gene.2019.144166] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 01/01/2023]
Abstract
Recent insights in evolutionary biology have shed light on epigenetic variation that interacts with genetic variation to convey heritable information. An important characteristic of epigenetic changes is that they can be produced in response to environmental cues and passed on to later generations, potentially facilitating later genetic adaptation. While our understanding of epigenetic mechanisms in vertebrates is rapidly growing, our knowledge about invertebrates remains lower, or is restricted to model organisms. Mollusks in particular, are a large group of invertebrates, with several species important for ecosystem function, human economy and health. In this review, we attempt to summarize the literature on epigenetic and intergenerational studies in mollusk species, with potential importance for adaptive evolution. Our review highlights that two molecular bearers of epigenetic information, DNA methylation and histone modifications, are key features for development in mollusk species, and both are sensitive to environmental conditions to which developing individuals are exposed. Further, although studies are still scarce, various environmental factors (e.g. predator cues, chemicals, parasites) can induce intergenerational effects on the phenotype (life-history traits, morphology, behaviour) of several mollusk taxa. More work is needed to better understand whether environmentally-induced changes in DNA methylation and histone modifications have phenotypic impacts, whether they can be inherited through generations and their role in intergenerational effects on phenotype. Such work may bring insights into the potential role of epigenetic in adaptation and evolution in mollusks.
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Affiliation(s)
- Manon Fallet
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Emilien Luquet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, F-69622 Villeurbanne, France
| | - Patrice David
- CEFE, UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, IRD, EPHE, Montpellier, France
| | - Céline Cosseau
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France.
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17
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Rodriguez‐Casariego JA, Ladd MC, Shantz AA, Lopes C, Cheema MS, Kim B, Roberts SB, Fourqurean JW, Ausio J, Burkepile DE, Eirin‐Lopez JM. Coral epigenetic responses to nutrient stress: Histone H2A.X phosphorylation dynamics and DNA methylation in the staghorn coral Acropora cervicornis. Ecol Evol 2018; 8:12193-12207. [PMID: 30598811 PMCID: PMC6303763 DOI: 10.1002/ece3.4678] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 09/28/2018] [Accepted: 10/05/2018] [Indexed: 12/19/2022] Open
Abstract
Nutrient pollution and thermal stress constitute two of the main drivers of global change in the coastal oceans. While different studies have addressed the physiological effects and ecological consequences of these stressors in corals, the role of acquired modifications in the coral epigenome during acclimatory and adaptive responses remains unknown. The present work aims to address that gap by monitoring two types of epigenetic mechanisms, namely histone modifications and DNA methylation, during a 7-week-long experiment in which staghorn coral fragments (Acropora cervicornis) were exposed to nutrient stress (nitrogen, nitrogen + phosphorus) in the presence of thermal stress. The major conclusion of this experiment can be summarized by two main results: First, coral holobiont responses to the combined effects of nutrient enrichment and thermal stress involve the post-translational phosphorylation of the histone variant H2A.X (involved in responses to DNA damage), as well as nonsignificant modifications in DNA methylation trends. Second, the reduction in H2A.X phosphorylation (and the subsequent potential impairment of DNA repair mechanisms) observed after prolonged coral exposure to nitrogen enrichment and thermal stress is consistent with the symbiont-driven phosphorus limitation previously observed in corals subject to nitrogen enrichment. The alteration of this epigenetic mechanism could help to explain the synergistic effects of nutrient imbalance and thermal stress on coral fitness (i.e., increased bleaching and mortality) while supporting the positive effect of phosphorus addition to improving coral resilience to thermal stress. Overall, this work provides new insights into the role of epigenetic mechanisms during coral responses to global change, discussing future research directions and the potential benefits for improving restoration, management and conservation of coral reef ecosystems worldwide.
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Affiliation(s)
- Javier A. Rodriguez‐Casariego
- Environmental Epigenetics Laboratory, Institute of Water and Environment, Department of Biological SciencesFlorida International UniversityMiamiFlorida
| | - Mark C. Ladd
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
| | - Andrew A. Shantz
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
| | - Christian Lopes
- Seagrass Laboratory, Institute of Water and Environment, Department of Biological SciencesFlorida International UniversityMiamiFlorida
| | - Manjinder S. Cheema
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Bohyun Kim
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Steven B. Roberts
- School of Aquatic and Fishery ScienceUniversity of WashingtonSeattleWashington
| | - James W. Fourqurean
- Seagrass Laboratory, Institute of Water and Environment, Department of Biological SciencesFlorida International UniversityMiamiFlorida
| | - Juan Ausio
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Deron E. Burkepile
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
| | - Jose M. Eirin‐Lopez
- Environmental Epigenetics Laboratory, Institute of Water and Environment, Department of Biological SciencesFlorida International UniversityMiamiFlorida
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18
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Chatterjee N, Gim J, Choi J. Epigenetic profiling to environmental stressors in model and non-model organisms: Ecotoxicology perspective. ENVIRONMENTAL HEALTH AND TOXICOLOGY 2018; 33:e2018015-0. [PMID: 30286591 PMCID: PMC6182246 DOI: 10.5620/eht.e2018015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/19/2018] [Indexed: 05/16/2023]
Abstract
Epigenetics, potentially heritable changes in genome function that occur without alterations to DNA sequence, is an important but understudied component of ecotoxicology studies. A wide spectrum of environmental challenge, such as temperature, stress, diet, toxic chemicals, are known to impact on epigenetic regulatory mechanisms. Although the role of epigenetic factors in certain biological processes, such as tumourigenesis, has been heavily investigated, in ecotoxicology field, epigenetics still have attracted little attention. In ecotoxicology, potential role of epigenetics in multi- and transgenerational phenomenon to environmental stressors needs to be unrevealed. Natural variation in the epigenetic profiles of species in responses to environmental stressors, nature of dose-response relationships for epigenetic effects, and how to incorporate this information into ecological risk assessment should also require attentions. In this review, we presented the available information on epigenetics in ecotoxicological context. For this, we have conducted a systemic review on epigenetic profiling in response to environmental stressors, mostly chemical exposure, in model organisms, as well as, in ecotoxicologically relevant wildlife species.
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Affiliation(s)
- Nivedita Chatterjee
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dondaemun-gu, Seoul 02504, Republic of Korea
| | - Jiwan Gim
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dondaemun-gu, Seoul 02504, Republic of Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dondaemun-gu, Seoul 02504, Republic of Korea
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19
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Li Y, Liew YJ, Cui G, Cziesielski MJ, Zahran N, Michell CT, Voolstra CR, Aranda M. DNA methylation regulates transcriptional homeostasis of algal endosymbiosis in the coral model Aiptasia. SCIENCE ADVANCES 2018; 4:eaat2142. [PMID: 30116782 PMCID: PMC6093633 DOI: 10.1126/sciadv.aat2142] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/06/2018] [Indexed: 05/02/2023]
Abstract
The symbiotic relationship between cnidarians and dinoflagellates is the cornerstone of coral reef ecosystems. Although research has focused on the molecular mechanisms underlying this symbiosis, the role of epigenetic mechanisms, that is, the study of heritable changes that do not involve changes in the DNA sequence, is unknown. To assess the role of DNA methylation in the cnidarian-dinoflagellate symbiosis, we analyzed genome-wide CpG methylation, histone associations, and transcriptomic states of symbiotic and aposymbiotic anemones in the model system Aiptasia. We found that methylated genes are marked by histone 3 lysine 36 trimethylation (H3K36me3) and show significant reduction of spurious transcription and transcriptional noise, revealing a role of DNA methylation in the maintenance of transcriptional homeostasis. Changes in DNA methylation and expression show enrichment for symbiosis-related processes, such as immunity, apoptosis, phagocytosis recognition, and phagosome formation, and reveal intricate interactions between the underlying pathways. Our results demonstrate that DNA methylation provides an epigenetic mechanism of transcriptional homeostasis that responds to symbiosis.
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20
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Beal A, Rodriguez-Casariego J, Rivera-Casas C, Suarez-Ulloa V, Eirin-Lopez JM. Environmental Epigenomics and Its Applications in Marine Organisms. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/13836_2018_28] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Leonardo S, Toldrà A, Rambla-Alegre M, Fernández-Tejedor M, Andree KB, Ferreres L, Campbell K, Elliott CT, O'Sullivan CK, Pazos Y, Diogène J, Campàs M. Self-assembled monolayer-based immunoassays for okadaic acid detection in seawater as monitoring tools. MARINE ENVIRONMENTAL RESEARCH 2018; 133:6-14. [PMID: 29174400 DOI: 10.1016/j.marenvres.2017.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 11/10/2017] [Accepted: 11/12/2017] [Indexed: 06/07/2023]
Abstract
Rapid and cost-effective methods to monitor the presence of diarrhetic shellfish poisoning (DSP) toxins in seawater samples in an easy and reliable manner are required to protect human health and avoid economic losses to shellfish industry. Immunoassays for the detection of okadaic acid (OA) and dinophysistoxin-1 and dinophysistoxin-2 are developed by immobilising OA on self-assembled monothiols or dithiols in an ordered and oriented way, providing an effective limit of detection of ∼1 ng OA equiv./mL seawater. The immunoassays are applied to the analysis of the particulate fraction of seawater samples from two Catalan harbours (NW Mediterranean) and samples collected periodically from the Galician Rias (E Atlantic), as well as a reference mussel sample. Results are in agreement with LC-MS/MS and the certified values. OA concentration in seawater correlates with Dinophysis cell abundance, with a 1-2 weeks lag. The immunoassays provide powerful high-throughput analytical methods potentially applicable as alternative monitoring tools.
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Affiliation(s)
- Sandra Leonardo
- IRTA, Ctra. Poble Nou, Km. 5.5, 43540 Sant Carles de la Ràpita, Spain
| | - Anna Toldrà
- IRTA, Ctra. Poble Nou, Km. 5.5, 43540 Sant Carles de la Ràpita, Spain
| | | | | | - Karl B Andree
- IRTA, Ctra. Poble Nou, Km. 5.5, 43540 Sant Carles de la Ràpita, Spain
| | - Laura Ferreres
- IRTA, Ctra. Poble Nou, Km. 5.5, 43540 Sant Carles de la Ràpita, Spain
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - Christopher T Elliott
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans, 26, 43007 Tarragona, Spain; Institució Catalana de Recerca i Estudis Avançats, Pg. Lluís Companys, 23, 08010 Barcelona, Spain
| | - Yolanda Pazos
- INTECMAR, Peirao de Vilaxoán, s/n, 36611 Vilagarcía de Arousa, Spain
| | - Jorge Diogène
- IRTA, Ctra. Poble Nou, Km. 5.5, 43540 Sant Carles de la Ràpita, Spain
| | - Mònica Campàs
- IRTA, Ctra. Poble Nou, Km. 5.5, 43540 Sant Carles de la Ràpita, Spain.
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22
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Gavery MR, Roberts SB. Epigenetic considerations in aquaculture. PeerJ 2017; 5:e4147. [PMID: 29230373 PMCID: PMC5723431 DOI: 10.7717/peerj.4147] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/17/2017] [Indexed: 12/14/2022] Open
Abstract
Epigenetics has attracted considerable attention with respect to its potential value in many areas of agricultural production, particularly under conditions where the environment can be manipulated or natural variation exists. Here we introduce key concepts and definitions of epigenetic mechanisms, including DNA methylation, histone modifications and non-coding RNA, review the current understanding of epigenetics in both fish and shellfish, and propose key areas of aquaculture where epigenetics could be applied. The first key area is environmental manipulation, where the intention is to induce an ‘epigenetic memory’ either within or between generations to produce a desired phenotype. The second key area is epigenetic selection, which, alone or combined with genetic selection, may increase the reliability of producing animals with desired phenotypes. Based on aspects of life history and husbandry practices in aquaculture species, the application of epigenetic knowledge could significantly affect the productivity and sustainability of aquaculture practices. Conversely, clarifying the role of epigenetic mechanisms in aquaculture species may upend traditional assumptions about selection practices. Ultimately, there are still many unanswered questions regarding how epigenetic mechanisms might be leveraged in aquaculture.
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Affiliation(s)
- Mackenzie R Gavery
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA, USA
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Rivera-Casas C, Gonzalez-Romero R, Garduño RA, Cheema MS, Ausio J, Eirin-Lopez JM. Molecular and Biochemical Methods Useful for the Epigenetic Characterization of Chromatin-Associated Proteins in Bivalve Molluscs. Front Physiol 2017; 8:490. [PMID: 28848447 PMCID: PMC5550673 DOI: 10.3389/fphys.2017.00490] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/26/2017] [Indexed: 12/11/2022] Open
Abstract
Bivalve molluscs constitute a ubiquitous taxonomic group playing key functions in virtually all ecosystems, and encompassing critical commercial relevance. Along with a sessile and filter-feeding lifestyle in most cases, these characteristics make bivalves model sentinel organisms routinely used for environmental monitoring studies in aquatic habitats. The study of epigenetic mechanisms linking environmental exposure and specific physiological responses (i.e., environmental epigenetics) stands out as a very innovative monitoring strategy, given the role of epigenetic modifications in acclimatization and adaptation. Furthermore, the heritable nature of many of those modifications constitutes a very promising avenue to explore the applicability of epigenetic conditioning and selection in management and restoration strategies. Chromatin provides a framework for the study of environmental epigenetic responses. Unfortunately, chromatin and epigenetic information are very limited in most non-traditional model organisms and even completely lacking in most environmentally and ecologically relevant organisms. The present work aims to provide a comprehensive and reproducible experimental workflow for the study of bivalve chromatin. First, a series of guidelines for the molecular isolation of genes encoding chromatin-associated proteins is provided, including information on primers suitable for conventional PCR, Rapid Amplification of cDNA Ends (RACE), genome walking and quantitative PCR (qPCR) experiments. This section is followed by the description of methods specifically developed for the analysis of histone and SNBP proteins in different bivalve tissues, including protein extraction, purification, separation and immunodetection. Lastly, information about available antibodies, their specificity and performance is also provided. The tools and protocols described here complement current epigenetic analyses (usually limited to DNA methylation) by incorporating the study of structural elements modulating chromatin dynamics.
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Affiliation(s)
- Ciro Rivera-Casas
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International UniversityNorth Miami, FL, United States
| | - Rodrigo Gonzalez-Romero
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International UniversityNorth Miami, FL, United States
| | - Rafael A Garduño
- Department of Microbiology and Immunology, Dalhousie UniversityHalifax, NS, Canada
| | - Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of VictoriaVictoria, BC, Canada
| | - Juan Ausio
- Department of Biochemistry and Microbiology, University of VictoriaVictoria, BC, Canada
| | - Jose M Eirin-Lopez
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International UniversityNorth Miami, FL, United States
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