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Abdelnour SA, Naiel MAE, Said MB, Alnajeebi AM, Nasr FA, Al-Doaiss AA, Mahasneh ZMH, Noreldin AE. Environmental epigenetics: Exploring phenotypic plasticity and transgenerational adaptation in fish. ENVIRONMENTAL RESEARCH 2024; 252:118799. [PMID: 38552831 DOI: 10.1016/j.envres.2024.118799] [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: 11/28/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
Epigenetics plays a vital role in the interaction between living organisms and their environment by regulating biological functions and phenotypic plasticity. Considering that most aquaculture activities take place in open or natural habitats that are vulnerable to environmental changes. Promising findings from recent research conducted on various aquaculture species have provided preliminary evidence suggesting a link between epigenetic mechanisms and economically valuable characteristics. Environmental stressors, including climate changes (thermal stress, hypoxia, and water salinity), anthropogenic impacts such as (pesticides, crude oil pollution, nutritional impacts, and heavy metal) and abiotic factors (infectious diseases), can directly trigger epigenetic modifications in fish. While experiments have confirmed that many epigenetic alterations caused by environmental factors have plastic responses, some can be permanently integrated into the genome through genetic integration and promoting rapid transgenerational adaptation in fish. These environmental factors might cause irregular DNA methylation patterns in genes related to many biological events leading to organs dysfunction by inducing alterations in genes related to oxidative stress or apoptosis. Moreover, these environmental issues alter DNA/histone methylation leading to decreased reproductive competence. This review emphasizes the importance of understanding the effects of environmentally relevant issues on the epigenetic regulation of phenotypic variations in fish. The goal is to expand our knowledge of how epigenetics can either facilitate or hinder species' adaptation to these adverse conditions. Furthermore, this review outlines the areas that warrant further investigation in understanding epigenetic reactions to various environmental issues.
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Affiliation(s)
- Sameh A Abdelnour
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt.
| | - Mohammed A E Naiel
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt
| | - Mourad Ben Said
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, Manouba, 2010, Tunisia; Department of Basic Sciences, Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, Manouba, 2010, Tunisia
| | - Afnan M Alnajeebi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Fahd A Nasr
- Biology Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Amin A Al-Doaiss
- Biology Department, College of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Zeinab M H Mahasneh
- Department of Animal Production, School of Agriculture, The University of Jordan, Amman, 11942, Jordan
| | - Ahmed E Noreldin
- Department of Histology and Cytology, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, Egypt
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2
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Czaja R, Pales-Espinosa E, Cerrato RM, Lwiza K, Allam B. Using meta-analysis to explore the roles of global upwelling exposure and experimental design in bivalve responses to low pH. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:165900. [PMID: 37572507 DOI: 10.1016/j.scitotenv.2023.165900] [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: 02/07/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023]
Abstract
Low pH conditions, associated with ocean acidification, represent threats to many commercially and ecologically important organisms, including bivalves. However, there are knowledge gaps regarding factors explaining observed differences in biological responses to low pH in laboratory experiments. Specific sources of local adaptation such as upwelling exposure and the role of experimental design, such as carbonate chemistry parameter changes, should be considered. Linking upwelling exposure, as an individual oceanographic phenomenon, to responses measured in laboratory experiments may further our understanding of local adaptation to global change. Here, meta-analysis is used to test the hypotheses that upwelling exposure and experimental design affect outcomes of individual, laboratory-based studies that assess bivalve metabolic (clearance and respiration rate) responses to low pH. Results show that while bivalves generally decrease metabolic activity in response to low pH, upwelling exposure and experimental design can significantly impact outcomes. Bivalves from downwelling or weak upwelling areas decrease metabolic activity in response to low pH, but bivalves from strong upwelling areas increase or do not change metabolic activity in response to low pH. Furthermore, experimental temperature, exposure time and magnitude of the change in carbonate chemistry parameters all significantly affect outcomes. These results suggest that bivalves from strong upwelling areas may be less sensitive to low pH. This furthers our understanding of local adaptation to global change by demonstrating that upwelling alone can explain up to 49 % of the variability associated with bivalve metabolic responses to low pH. Furthermore, when interpreting outcomes of individual, laboratory experiments, scientists should be aware that higher temperatures, shorter exposure times and larger changes in carbonate chemistry parameters may increase the chance of suppressed metabolic activity.
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Affiliation(s)
- Raymond Czaja
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11790-5000, United States of America.
| | - Emmanuelle Pales-Espinosa
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11790-5000, United States of America
| | - Robert M Cerrato
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11790-5000, United States of America
| | - Kamazima Lwiza
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11790-5000, United States of America
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11790-5000, United States of America.
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3
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Bogan SN, Strader ME, Hofmann GE. Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity. BMC Biol 2023; 21:149. [PMID: 37365578 DOI: 10.1186/s12915-023-01645-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Epigenetic processes are proposed to be a mechanism regulating gene expression during phenotypic plasticity. However, environmentally induced changes in DNA methylation exhibit little-to-no association with differential gene expression in metazoans at a transcriptome-wide level. It remains unexplored whether associations between environmentally induced differential methylation and expression are contingent upon other epigenomic processes such as chromatin accessibility. We quantified methylation and gene expression in larvae of the purple sea urchin Strongylocentrotus purpuratus exposed to different ecologically relevant conditions during gametogenesis (maternal conditioning) and modeled changes in gene expression and splicing resulting from maternal conditioning as functions of differential methylation, incorporating covariates for genomic features and chromatin accessibility. We detected significant interactions between differential methylation, chromatin accessibility, and genic feature type associated with differential expression and splicing. RESULTS Differential gene body methylation had significantly stronger effects on expression among genes with poorly accessible transcriptional start sites while baseline transcript abundance influenced the direction of this effect. Transcriptional responses to maternal conditioning were 4-13 × more likely when accounting for interactions between methylation and chromatin accessibility, demonstrating that the relationship between differential methylation and gene regulation is partially explained by chromatin state. CONCLUSIONS DNA methylation likely possesses multiple associations with gene regulation during transgenerational plasticity in S. purpuratus and potentially other metazoans, but its effects are dependent on chromatin accessibility and underlying genic features.
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Affiliation(s)
- Samuel N Bogan
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA.
| | - Marie E Strader
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA
- Department of Biology, Texas A&M University, College Station, USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA
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4
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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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Li C, Wang Y, Wei M, Wang X. The involvement of a novel calmodulin-like protein isoform from oyster Crassostrea gigas in transcription factor regulation provides new insight into acclimation to ocean acidification. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 257:106423. [PMID: 36822075 DOI: 10.1016/j.aquatox.2023.106423] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Marine organisms need to adapt to improve organismal fitness under ocean acidification (OA). Recent studies have shown that marine calcifiers can achieve acclimation by stimulating calcium binding/signaling pathways. Here, a CaM-like gene (CgCaLP-2) from oyster Crassostrea gigas which typically responded to long-term CO2 exposure (two months) rather than short-term exposure (one week) was characterized. The cloned cDNA was 678 bp and was shorter than the retrieved sequence from NCBI (1125 bp). The two sequences, designated as CgCaLP-2-v1 and CgCaLP-2-v2, were demonstrated to be different splice variants by the genome sequence analysis. Western blotting analysis revealed two bands of 23 kD and 43 kD in mantle and hemocytes, corresponding to predicted molecular weight of CgCaLP-2-v1 and CgCaLP-2-v2, respectively. The isoform CgCaLP-2-v1 (the 23 kD band) was highly stimulated in response to long-term CO2 exposure (42-day and 56-day treatment) in hemocytes and mantle tissue. The fluorescence signal of CgCaLP-2 in mantle and hemocytes became more intensive after long-term CO2 exposure. Besides, in hemocytes, CgCaLP-2 presented a higher localization on the nuclear membrane after long-term CO2 exposure (56 d). The target gene network of CgCaLP-2 was predicted, and a transcription factor (TF) gene annotated as Homeobox protein SIX4 (CgSIX4) showed a similar expressive trend to CgCaLP-2 during CO2 exposure. Suppression of CgCaLP-2 via RNA interference significantly reduced the mRNA expression of CgSIX4. The results suggested that CgCaLP-2 might mediate the Ca2+-CaLP-TF signal transduction pathway under long-term CO2 exposure. This study serves as an example to reveal that alternative splicing is an important mechanism for generation multiple protein isoforms and thus shape the plastic responses under CO2 exposure, providing new insight into the potential acclimation ability of marine calcifiers to future OA.
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Affiliation(s)
- Changmei Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yilin Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Manman Wei
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xiudan Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China; College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.
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6
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Jiang L, Liu CY, Cui G, Huang LT, Yu XL, Sun YF, Tong HY, Zhou GW, Yuan XC, Hu YS, Zhou WL, Aranda M, Qian PY, Huang H. Rapid shifts in thermal reaction norms and tolerance of brooded coral larvae following parental heat acclimation. Mol Ecol 2023; 32:1098-1116. [PMID: 36528869 DOI: 10.1111/mec.16826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/24/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Thermal priming of reef corals can enhance their heat tolerance; however, the legacy effects of heat stress during parental brooding on larval resilience remain understudied. This study investigated whether preconditioning adult coral Pocillopora damicornis to high temperatures (29°C and 32°C) could better prepare their larvae for heat stress. Results showed that heat-acclimated adults brooded larvae with reduced symbiont density and shifted thermal performance curves. Reciprocal transplant experiments demonstrated higher bleaching resistance and better photosynthetic and autotrophic performance in heat-exposed larvae from acclimated adults compared to unacclimated adults. RNA-seq revealed strong cellular stress responses in larvae from heat-acclimated adults that could have been effective in rescuing host cells from stress, as evidenced by the widespread upregulation of genes involved in cell cycle and mitosis. For symbionts, a molecular coordination between light harvesting, photoprotection and carbon fixation was detected in larvae from heat-acclimated adults, which may help optimize photosynthetic activity and yield under high temperature. Furthermore, heat acclimation led to opposing regulations of symbiont catabolic and anabolic pathways and favoured nutrient translocation to the host and thus a functional symbiosis. Notwithstanding, the improved heat tolerance was paralleled by reduced light-enhanced dark respiration, indicating metabolic depression for energy saving. Our findings suggest that adult heat acclimation can rapidly shift thermal tolerance of brooded coral larvae and provide integrated physiological and molecular evidence for this adaptive plasticity, which could increase climate resilience. However, the metabolic depression may be maladaptive for long-term organismal performance, highlighting the importance of curbing carbon emissions to better protect corals.
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Affiliation(s)
- Lei Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science and Hong Kong Branch (HKB) of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology (HKUST), Hong Kong, China
| | - Cheng-Yue Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science and Hong Kong Branch (HKB) of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology (HKUST), Hong Kong, China
| | - Guoxin Cui
- Biological and Environmental Sciences and Engineering Division, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Lin-Tao Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou, China.,CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya, China.,Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Lei Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou, China.,CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya, China.,Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - You-Fang Sun
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science and Hong Kong Branch (HKB) of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology (HKUST), Hong Kong, China
| | - Hao-Ya Tong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science and Hong Kong Branch (HKB) of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology (HKUST), Hong Kong, China
| | - Guo-Wei Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou, China.,CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya, China.,Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Xiang-Cheng Yuan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou, China.,CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya, China.,Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Yi-Si Hu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Wen-Liang Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Manuel Aranda
- Biological and Environmental Sciences and Engineering Division, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science and Hong Kong Branch (HKB) of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology (HKUST), Hong Kong, China
| | - Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya, China.,Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
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7
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Lv C, Hu Z, Wei J, Wang Y. Transgenerational effects of elevated CO 2 on rice photosynthesis and grain yield. PLANT MOLECULAR BIOLOGY 2022; 110:413-424. [PMID: 35763210 DOI: 10.1007/s11103-022-01294-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Chunhua Lv
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of Ministry of Education, Peking University, Beijing, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenghua Hu
- School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Jian Wei
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of Ministry of Education, Peking University, Beijing, China
| | - Yin Wang
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of Ministry of Education, Peking University, Beijing, China.
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8
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Deconinck A, Willett CS. Hypoxia tolerance, but not low pH tolerance, is associated with a latitudinal cline across populations of Tigriopus californicus. PLoS One 2022; 17:e0276635. [PMID: 36301968 PMCID: PMC9612455 DOI: 10.1371/journal.pone.0276635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Intertidal organisms must tolerate daily fluctuations in environmental parameters, and repeated exposure to co-occurring conditions may result in tolerance to multiple stressors correlating. The intertidal copepod Tigriopus californicus experiences diurnal variation in dissolved oxygen levels and pH as the opposing processes of photosynthesis and cellular respiration lead to coordinated highs during the day and lows at night. While environmental parameters with overlapping spatial gradients frequently result in correlated traits, less attention has been given to exploring temporally correlated stressors. We investigated whether hypoxia tolerance correlates with low pH tolerance by separately testing the hypoxia and low pH stress tolerance separately of 6 genetically differentiated populations of T. californicus. We independently checked for similarities in tolerance for each of the two stressors by latitude, sex, size, and time since collection as predictors. We found that although hypoxia tolerance correlated with latitude, low pH tolerance did not, and no predictor was significant for both stressors. We concluded that temporally coordinated exposure to low pH and low oxygen did not result in populations developing equivalent tolerance for both. Although climate change alters several environmental variables simultaneously, organisms' abilities to tolerate these changes may not be similarly coupled.
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Affiliation(s)
- Aimee Deconinck
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Christopher S. Willett
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
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9
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Leung JYS, Zhang S, Connell SD. Is Ocean Acidification Really a Threat to Marine Calcifiers? A Systematic Review and Meta-Analysis of 980+ Studies Spanning Two Decades. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107407. [PMID: 35934837 DOI: 10.1002/smll.202107407] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Ocean acidification is considered detrimental to marine calcifiers, but mounting contradictory evidence suggests a need to revisit this concept. This systematic review and meta-analysis aim to critically re-evaluate the prevailing paradigm of negative effects of ocean acidification on calcifiers. Based on 5153 observations from 985 studies, many calcifiers (e.g., echinoderms, crustaceans, and cephalopods) are found to be tolerant to near-future ocean acidification (pH ≈ 7.8 by the year 2100), but coccolithophores, calcifying algae, and corals appear to be sensitive. Calcifiers are generally more sensitive at the larval stage than adult stage. Over 70% of the observations in growth and calcification are non-negative, implying the acclimation capacity of many calcifiers to ocean acidification. This capacity can be mediated by phenotypic plasticity (e.g., physiological, mineralogical, structural, and molecular adjustments), transgenerational plasticity, increased food availability, or species interactions. The results suggest that the impacts of ocean acidification on calcifiers are less deleterious than initially thought as their adaptability has been underestimated. Therefore, in the forthcoming era of ocean acidification research, it is advocated that studying how marine organisms persist is as important as studying how they perish, and that future hypotheses and experimental designs are not constrained within the paradigm of negative effects.
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Affiliation(s)
- Jonathan Y S Leung
- Faculty of Materials and Energy, Southwest University, Chongqing, 400715, P. R. China
- Southern Seas Ecology Laboratories, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Sam Zhang
- Faculty of Materials and Energy, Southwest University, Chongqing, 400715, P. R. China
| | - Sean D Connell
- Southern Seas Ecology Laboratories, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
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10
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Strader ME, Wolak ME, Simon OM, Hofmann GE. Genetic variation underlies plastic responses to global change drivers in the purple sea urchin, Strongylocentrotus purpuratus. Proc Biol Sci 2022; 289:20221249. [PMID: 36043281 PMCID: PMC9428524 DOI: 10.1098/rspb.2022.1249] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/05/2022] [Indexed: 11/12/2022] Open
Abstract
Phenotypic plasticity and adaptive evolution enable population persistence in response to global change. However, there are few experiments that test how these processes interact within and across generations, especially in marine species with broad distributions experiencing spatially and temporally variable temperature and pCO2. We employed a quantitative genetics experiment with the purple sea urchin, Strongylocentrotus purpuratus, to decompose family-level variation in transgenerational and developmental plastic responses to ecologically relevant temperature and pCO2. Adults were conditioned to controlled non-upwelling (high temperature, low pCO2) or upwelling (low temperature, high pCO2) conditions. Embryos were reared in either the same conditions as their parents or the crossed environment, and morphological aspects of larval body size were quantified. We find evidence of family-level phenotypic plasticity in response to different developmental environments. Among developmental environments, there was substantial additive genetic variance for one body size metric when larvae developed under upwelling conditions, although this differed based on parental environment. Furthermore, cross-environment correlations indicate significant variance for genotype-by-environment interactive effects. Therefore, genetic variation for plasticity is evident in early stages of S. purpuratus, emphasizing the importance of adaptive evolution and phenotypic plasticity in organismal responses to global change.
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Affiliation(s)
- Marie E. Strader
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Matthew E. Wolak
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Olivia M. Simon
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Gretchen E. Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
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Marčeta T, Locatello L, Alban S, Hassan MSA, Azmi NNNM, Finos L, Badocco D, Marin MG. Transgenerational effects and phenotypic plasticity in sperm and larvae of the sea urchin Paracentrotus lividus under ocean acidification. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 248:106208. [PMID: 35635983 DOI: 10.1016/j.aquatox.2022.106208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 05/11/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
In marine organisms, differing degree of sensitivity to ocean acidification (OA) is expected for each life stage, and disturbance at one stage can carry over into the following stage or following generation. In this study we investigated phenotypic changes of sperm and larvae of the sea urchin Paracentrotus lividus in response to different pH conditions (8.0, 7.7, 7.4) experienced by the parents during gametogenesis. In sperm from two-months exposed males, sperm motility, velocity, ATP content, ATP consumption and respiration rate were evaluated at three pH values of the activating medium (8.0, 7.7 and 7.4). Moreover, larvae from each parental group were reared at pH 8.0 and 7.7 for 20 days and larval mortality and growth were then assessed. Sperm motility and respiration rate were not affected either by exposure of males to low pH or by the post-activation pH. Sperm velocity did not differ among post-activation pH values in all sperm groups, but it decreased slower in sperm developed under acidified conditions, suggesting the presence of positive carryover effect on sperm longevity. This positive carryover effect of exposure of males to low pH values was highlighted also for the sperm ATP content, which was higher in these groups of sperm. ATP consumption rate was affected by post-activation pH with higher values at pH 8.0 in sperm from males maintained at control condition and pH 7.7 while the energy consumption appeared to be differently modulated at different experimental conditions. A negative carry over effect of OA was observed on survival of larvae from parents acclimated at pH 7.4 and additive negative effects of both parental and larval exposure to low pH can be suggested. In all groups of larvae, decreased somatic growth was observed at low rearing pH, thus larvae from parents maintained at low pH did not show an increased capability to cope with OA.
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Affiliation(s)
- Tihana Marčeta
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova 35131, Italy; Institute of Marine Sciences (ISMAR), CNR, Venezia, Italy
| | - Lisa Locatello
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova 35131, Italy; Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Fano Marine Centre, Viale Adriatico 1/N, Fano 61032, Italy
| | - Silvia Alban
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova 35131, Italy
| | - Mohamad Sofi Abu Hassan
- Faculty of Science and Marine Environment, University of Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | | | - Livio Finos
- Department of Developmental Psychology and Socialization, University of Padova, Via Venezia 8, Padova 35131, Italy
| | - Denis Badocco
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, Padova 35131, Italy
| | - Maria Gabriella Marin
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova 35131, Italy.
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12
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13
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Chavarria-Pizarro T, Resl P, Janjic A, Werth S. Gene expression responses to thermal shifts in the endangered lichen Lobaria pulmonaria. Mol Ecol 2021; 31:839-858. [PMID: 34784096 DOI: 10.1111/mec.16281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022]
Abstract
Anthropogenic climate change has led to unprecedented shifts in temperature across many ecosystems. In a context of rapid environmental changes, acclimation is an important process as it may influence the capacity of organisms to survive under novel thermal conditions. Mechanisms of acclimation could involve upregulation of stress response genes involved in protein folding, DNA damage repair and the regulation of signal transduction genes, along with a simultaneous downregulation of genes involved in growth or the cell cycle, in order to maintain cellular functions and equilibria. We transplanted Lobaria pulmonaria lichens originating from different forests to determine the relative effects of long-term acclimation and genetic factors on the variability in expression of mycobiont and photobiont genes. We found a strong response of the mycobiont and photobiont to high temperatures, regardless of sample origin. The green-algal photobiont had an overall lower response than the mycobiont. Gene expression of both symbionts was also influenced by acclimation to transplantation sites and by genetic factors. L. pulmonaria seems to have evolved powerful molecular pathways to deal with environmental fluctuations and stress and can acclimate to new habitats by transcriptomic convergence. Although L. pulmonaria has the molecular machinery to counteract short-term thermal stress, survival of lichens such as L. pulmonaria depends mostly on their long-term positive carbon balance, which can be compromised by higher temperatures and reduced precipitation, and both these outcomes have been predicted for Central Europe in connection with global climate change.
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Affiliation(s)
| | - Philipp Resl
- Systematic Botany and Mycology, Faculty of Biology, LMU Munich, Munich, Germany.,Institute of Biology, University of Graz, Graz, Austria
| | - Aleksandar Janjic
- Anthropology and Human Genomics, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Silke Werth
- Systematic Botany and Mycology, Faculty of Biology, LMU Munich, Munich, Germany.,Institute of Biology, University of Graz, Graz, Austria
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De novo Assembly and Analysis of Tissue-Specific Transcriptomes of the Edible Red Sea Urchin Loxechinus albus Using RNA-Seq. BIOLOGY 2021; 10:biology10100995. [PMID: 34681094 PMCID: PMC8533317 DOI: 10.3390/biology10100995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023]
Abstract
Simple Summary Edible red sea urchin (Loxechinus albus) is an endemic species of echinoderm distributed along the Chilean coasts. This resource has been overexploited in recent years, depleting their natural populations. At present, there are few reported gene sequences available in public databases, restricting the molecular studies associated with aquaculture for this species. The aim of this study was to present the first annotated reference transcriptome of L. albus using NGS technologies and the differential expression transcripts analysis of the evaluated tissues. The transcriptome data obtained in this study will serve as a reference for future molecular research in the edible red sea urchin and other sea urchin species. Abstract Edible red sea urchin (Loxechinus albus) is an endemic echinoderm species of the Chilean coasts. The worldwide demand for high-quality gonads of this species has addressed the depletion of its natural populations. Studies on this sea urchin are limited, and genomic information is almost nonexistent. Hence, generate a transcriptome is crucial information that will considerably enrich molecular data and promote future findings for the L. albus aquaculture. Here, we obtained transcriptomic data of the edible red sea urchin by Illumina platform. Total RNA was extracted from gonads, intestines, and coelomocytes of juvenile urchins, and samples were sequenced using MiSeq Illumina technology. A total of 91,119,300 paired-end reads were de novo assembled, 185,239 transcripts produced, and a reference transcriptome created with 38.8% GC content and an N50 of 1769 bp. Gene ontology analysis revealed notable differences in the expression profiles between gonads, intestines, and coelomocytes, allowing the detection of transcripts associated with specific biological processes and KEGG pathways. These data were validated using 12 candidate transcripts by real-time qPCR. This dataset will provide a valuable molecular resource for L. albus and other species of sea urchins.
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Griffiths JS, Johnson KM, Sirovy KA, Yeats MS, Pan FTC, La Peyre JF, Kelly MW. Transgenerational plasticity and the capacity to adapt to low salinity in the eastern oyster, Crassostrea virginica. Proc Biol Sci 2021; 288:20203118. [PMID: 34004136 PMCID: PMC8131124 DOI: 10.1098/rspb.2020.3118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Salinity conditions in oyster breeding grounds in the Gulf of Mexico are expected to drastically change due to increased precipitation from climate change and anthropogenic changes to local hydrology. We determined the capacity of the eastern oyster, Crassostrea virginica, to adapt via standing genetic variation or acclimate through transgenerational plasticity (TGP). We outplanted oysters to either a low- or medium-salinity site in Louisiana for 2 years. We then crossed adult parents using a North Carolina II breeding design, and measured body size and survival of larvae 5 dpf raised under low or ambient salinity. We found that TGP is unlikely to significantly contribute to low-salinity tolerance since we did not observe increased growth or survival in offspring reared in low salinity when their parents were also acclimated at a low-salinity site. However, we detected genetic variation for body size, with an estimated heritability of 0.68 ± 0.25 (95% CI). This suggests there is ample genetic variation for this trait to evolve, and that evolutionary adaptation is a possible mechanism through which oysters will persist with future declines in salinity. The results of this experiment provide valuable insights into successfully breeding low-salinity tolerance in this commercially important species.
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Affiliation(s)
- Joanna S. Griffiths
- Department of Environmental Toxicology and Department of Wildlife, Fish, and Conservation Biology, University of California, 4121 Meyer Hall, Davis, CA 95616, USA
| | - Kevin M. Johnson
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Kyle A. Sirovy
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Mark S. Yeats
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Francis T. C. Pan
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jerome F. La Peyre
- Department of Veterinary Science, Louisiana State University, Baton Rouge, LA, USA
| | - Morgan W. Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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Masullo T, Biondo G, Natale MD, Tagliavia M, Bennici CD, Musco M, Ragusa MA, Costa S, Cuttitta A, Nicosia A. Gene Expression Changes after Parental Exposure to Metals in the Sea Urchin Affect Timing of Genetic Programme of Embryo Development. BIOLOGY 2021; 10:biology10020103. [PMID: 33535713 PMCID: PMC7912929 DOI: 10.3390/biology10020103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/20/2021] [Accepted: 01/30/2021] [Indexed: 12/14/2022]
Abstract
It is widely accepted that phenotypic traits can be modulated at the epigenetic level so that some conditions can affect the progeny of exposed individuals. To assess if the exposure of adult animals could result in effects on the offspring, the Mediterranean sea urchin and its well-characterized gene regulatory networks (GRNs) was chosen as a model. Adult animals were exposed to known concentrations of zinc and cadmium (both individually and in combination) for 10 days, and the resulting embryos were followed during the development. The oxidative stress occurring in parental gonads, embryo phenotypes and mortality, and the expression level of a set of selected genes, including members of the skeletogenic and endodermal GRNs, were evaluated. Increased oxidative stress at F0, high rates of developmental aberration with impaired gastrulation, in association to deregulation of genes involved in skeletogenesis (dri, hex, sm50, p16, p19, msp130), endodermal specification (foxa, hox11/13b, wnt8) and epigenetic regulation (kat2A, hdac1, ehmt2, phf8 and UBE2a) occurred either at 24 or 48 hpf. Results strongly indicate that exposure to environmental pollutants can affect not only directly challenged animals but also their progeny (at least F1), influencing optimal timing of genetic programme of embryo development, resulting in an overall impairment of developmental success.
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Affiliation(s)
- Tiziana Masullo
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
| | - Girolama Biondo
- Institute for Anthropic Impacts and Sustainability in Marine Environment-National Research Council (IAS-CNR), Detached Unit of Capo Granitola, Via del mare 3, 91021 Campobello di Mazara, Italy;
| | - Marilena Di Natale
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
- Department of Earth and Marine Science (DiSTeM), University of Palermo, Via Archirafi 20, 90123 Palermo, Italy
| | - Marcello Tagliavia
- Institute for Biomedical Research and Innovation-National Research Council-(IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy;
| | - Carmelo Daniele Bennici
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
| | - Marianna Musco
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
| | - Maria Antonietta Ragusa
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy; (M.A.R.); (S.C.)
| | - Salvatore Costa
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy; (M.A.R.); (S.C.)
| | - Angela Cuttitta
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
- Correspondence: (A.C.); (A.N.)
| | - Aldo Nicosia
- Institute for Biomedical Research and Innovation-National Research Council-(IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy;
- Correspondence: (A.C.); (A.N.)
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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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Devens HR, Davidson PL, Deaker DJ, Smith KE, Wray GA, Byrne M. Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma. Mol Ecol 2020; 29:4618-4636. [PMID: 33002253 PMCID: PMC8994206 DOI: 10.1111/mec.15664] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 09/01/2023]
Abstract
Ocean acidification (OA) from seawater uptake of rising carbon dioxide emissions impairs development in marine invertebrates, particularly in calcifying species. Plasticity in gene expression is thought to mediate many of these physiological effects, but how these responses change across life history stages remains unclear. The abbreviated lecithotrophic development of the sea urchin Heliocidaris erythrogramma provides a valuable opportunity to analyse gene expression responses across a wide range of life history stages, including the benthic, post-metamorphic juvenile. We measured the transcriptional response to OA in H. erythrogramma at three stages of the life cycle (embryo, larva, and juvenile) in a controlled breeding design. The results reveal a broad range of strikingly stage-specific impacts of OA on transcription, including changes in the number and identity of affected genes; the magnitude, sign, and variance of their expression response; and the developmental trajectory of expression. The impact of OA on transcription was notably modest in relation to gene expression changes during unperturbed development and much smaller than genetic contributions from parentage. The latter result suggests that natural populations may provide an extensive genetic reservoir of resilience to OA. Taken together, these results highlight the complexity of the molecular response to OA, its substantial life history stage specificity, and the importance of contextualizing the transcriptional response to pH stress in light of normal development and standing genetic variation to better understand the capacity for marine invertebrates to adapt to OA.
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Affiliation(s)
| | | | - Dione J Deaker
- School of Life and Environmental Science, The University of Sydney, Sydney, NSW, Australia
| | - Kathryn E Smith
- The Laboratory, The Marine Biological Association, Plymouth, UK
| | - Gregory A Wray
- Department of Biology, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Maria Byrne
- School of Life and Environmental Science, The University of Sydney, Sydney, NSW, Australia
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19
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Dixon G, Matz M. Benchmarking DNA methylation assays in a reef-building coral. Mol Ecol Resour 2020; 21:464-477. [PMID: 33058551 DOI: 10.1111/1755-0998.13282] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/17/2020] [Accepted: 10/02/2020] [Indexed: 11/28/2022]
Abstract
Interrogation of chromatin modifications, such as DNA methylation, has the potential to improve forecasting and conservation of marine ecosystems. The standard method for assaying DNA methylation (whole genome bisulphite sequencing), however, is currently too costly to apply at the scales required for ecological research. Here, we evaluate different methods for measuring DNA methylation for ecological epigenetics. We compare whole genome bisulphite sequencing (WGBS) with methylated CpG binding domain sequencing (MBD-seq), and a modified version of MethylRAD we term methylation-dependent restriction site-associated DNA sequencing (mdRAD). We evaluate these three assays in measuring variation in methylation across the genome, between genotypes, and between polyp types in the reef-building coral Acropora millepora. We find that all three assays measure absolute methylation levels similarly for gene bodies (gbM), as well as exons and 1 Kb windows with a minimum Pearson correlation 0.66. Differential gbM estimates were less correlated, but still concurrent across assays. We conclude that MBD-seq and mdRAD are reliable and cost-effective alternatives to WGBS. The considerably lower sequencing effort required for mdRAD to produce comparable methylation estimates makes it particularly useful for ecological epigenetics.
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Affiliation(s)
- Groves Dixon
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Mikhail Matz
- Department of Integrative Biology, University of Texas, Austin, TX, USA
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20
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Wang X, Wang M, Wang W, Liu Z, Xu J, Jia Z, Chen H, Qiu L, Lv Z, Wang L, Song L. Transcriptional changes of Pacific oyster Crassostrea gigas reveal essential role of calcium signal pathway in response to CO 2-driven acidification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140177. [PMID: 32570066 DOI: 10.1016/j.scitotenv.2020.140177] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
There is increasing evidence that ocean acidification (OA) has a significant impact on marine organisms. However, the ability of most marine organisms to acclimate to OA and the underlying mechanisms are still not well understood. In the present study, whole transcriptome analysis was performed to compare the impacts of short- (7 days, named as short group) and long- (60 days, named as long group) term CO2 exposure (pH 7.50) on Pacific oyster Crassostrea gigas. The responses of C. gigas to short- and long-term CO2 exposure shared common mechanisms in metabolism, membrane-associated transportation and binding processes. Long-term CO2 exposure induced significant expression of genes involved in DNA or RNA binding, indicating the activated transcription after long-term CO2 exposure. Oysters in the short-term group underwent significant intracellular calcium variation and oxidative stress. In contrast, the intracellular calcium, ROS level in hemocytes and H2O2 in serum recovered to normal levels after long-term CO2 exposure, suggesting the compensation of physiological status and mutual interplay between calcium and oxidative level. The compensation was supported by the up-regulation of a series of calcium binding proteins (CBPs) and calmodulins (CaMs) related signal pathway. The results provided valuable information to understand the molecular mechanism underlying the responses of Pacific oyster to the acidified ocean and might have implications for predicting the possible effects of global climate changes on oyster aquaculture.
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Affiliation(s)
- Xiudan Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Mengqiang Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Weilin Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China
| | - Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China
| | - Jiachao Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhihao Jia
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hao Chen
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Limei Qiu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhao Lv
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Diseases Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Diseases Prevention and Control, Dalian Ocean University, Dalian 116023, China.
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Harrington AM, Clark KF, Hamlin HJ. Expected ocean warming conditions significantly alter the transcriptome of developing postlarval American lobsters (Homarus americanus): Implications for energetic trade-offs. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100716. [PMID: 32777773 DOI: 10.1016/j.cbd.2020.100716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/27/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
The American lobster (Homarus americanus) is one of the most iconic and economically valuable fishery species in the Northwestern Atlantic. Surface ocean temperatures are rapidly increasing across much of the species' range, raising concern about resiliency in the face of environmental change. Warmer temperatures accelerate rates of larval development and enhance survival to the postlarval stage, but the potential costs at the molecular level have rarely been addressed. We explored how exposure to current summer temperatures (16 °C) or temperature regimes mimicking projected moderate or extreme warming scenarios (18 °C and 22 °C, respectively) for the Gulf of Maine during development influences the postlarval lobster transcriptome. After de novo assembling the transcriptome, we identified 2542 differentially expressed (DE; adjusted p < 0.05) transcripts in postlarvae exposed to 16 °C vs. 22 °C, and 422 DE transcripts in postlarvae reared at 16 °C vs. 18 °C. Lobsters reared at 16 °C significantly over-expressed transcripts related to cuticle formation and the immune response up to 14.4- and 8.5-fold respectively, relative to those reared at both 18 °C and 22 °C. In contrast, the expression of transcripts affiliated with metabolism increased up to 7.1-fold as treatment temperature increased. These results suggest that lobsters exposed to projected warming scenarios during development experience a shift in the transcriptome that reflects a potential trade-off between maintaining immune defenses and sustaining increased physiological rates under a warming environment. This could have major implications for post-settlement survival through increased risk of mortality due to disease and/or starvation if energetic demands cannot be met.
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Affiliation(s)
- Amalia M Harrington
- School of Marine Sciences, University of Maine, 5751 Murray Hall, Orono, ME 04469, USA; Aquaculture Research Institute, University of Maine, Orono, ME 04469, USA.
| | - K Fraser Clark
- Department of Animal Sciences and Aquaculture, Faculty of Agriculture, Dalhousie University, 58 Sipu Awti, Bible Hill, NS B2N 5E3, Canada.
| | - Heather J Hamlin
- School of Marine Sciences, University of Maine, 5751 Murray Hall, Orono, ME 04469, USA; Aquaculture Research Institute, University of Maine, Orono, ME 04469, USA.
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Transcriptomes shed light on transgenerational and developmental effects of ocean warming on embryos of the sea urchin Strongylocentrotus intermedius. Sci Rep 2020; 10:7931. [PMID: 32404890 PMCID: PMC7221070 DOI: 10.1038/s41598-020-64872-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 04/21/2020] [Indexed: 11/29/2022] Open
Abstract
Ocean warming increasingly endangers the fitness of marine invertebrates. Transgenerational effects (TE) potentially mitigate the impacts of environmental stress on the embryos of marine invertebrates. The molecular mechanisms, however, remain largely unknown. Using high-throughput RNA sequencing technology, we investigated the gene expression patterns of embryos (the gastrula stage) of the sea urchin Strongylocentrotus intermedius at different developmental temperatures, whose parents were exposed to long-term (15 months) elevated temperature (A) or not (B). The temperatures at which adults were held for ~4 weeks prior to the start of the experiment (21 °C for A and 18 °C for B) were also used for the development of offspring (high: 21 °C and ambient (laboratory): 18 °C) resulting in four experimental groups (HA and HB at 21 °C, and LA and LB at 18 °C). The embryos were sampled ~24 h after fertilization. All samples were in the gastrula stage. Twelve mRNA libraries (groups HA, HB, LA, LB, 3 replicates for each group) were established for the following sequencing. Embryos whose parents were exposed to elevated temperatures or not showed 1891 significantly different DEGs (differentially expressed genes) at the ambient developmental temperature (LB vs LA, LB as control) and 2203 significantly different DEGs at the high developmental temperature (HB vs HA, HB as control), respectively. This result indicates complex molecular mechanisms of transgenerational effects of ocean warming, in which a large number of genes are involved. With the TE, we found 904 shared DEGs in both LB vs LA (LB as control) and HB vs HA (HB as control) changed in the same direction of expression (i.e., up- or down-regulated), indicating that parental exposed temperatures affect the expression of these genes in the same manner regardless of the development temperature. With developmental exposure, we found 198 shared DEGs in both HB vs LB (HB as control) and HA vs LA (HA as control) changed in the same direction of expression. Of the 198 DEGs, more genes were up-regulated at high developmental temperature. Interestingly, embryos whose parents were exposed to high temperature showed fewer differently expressed DEGs between high and low developmental temperatures than the individuals whose parents were exposed to ambient temperature. The results indicate that gene expressions are probably depressed by the transgenerational effect of ocean warming. The roles of hsp70 and hnf6 in thermal acclimation are highlighted for future studies. The present study provides new insights into the molecular mechanisms of the transgenerational and developmental effects of ocean warming on the embryos of sea urchins.
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Johnson KM, Kelly MW. Population epigenetic divergence exceeds genetic divergence in the Eastern oyster Crassostrea virginica in the Northern Gulf of Mexico. Evol Appl 2020; 13:945-959. [PMID: 32431745 PMCID: PMC7232765 DOI: 10.1111/eva.12912] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/23/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022] Open
Abstract
Populations may respond to environmental heterogeneity via evolutionary divergence or phenotypic plasticity. While evolutionary divergence occurs through DNA sequence differences among populations, plastic divergence among populations may be generated by changes in the epigenome. Here, we present the results of a genome-wide comparison of DNA methylation patterns and genetic structure among four populations of Eastern oyster (Crassostrea virginica) in the northern Gulf of Mexico. We used a combination of restriction site-associated DNA sequencing (RADseq) and reduced representation bisulfite sequencing (RRBS) to explore population structure, gene-wide averages of F ST, and DNA methylation differences between oysters inhabiting four estuaries with unique salinity profiles. This approach identified significant population structure despite a moderately low F ST (0.02) across the freshwater boundary of the Mississippi river, a finding that may reflect recent efforts to restore oyster stock populations. Divergence between populations in CpG methylation was greater than for divergence in F ST, likely reflecting environmental effects on DNA methylation patterns. Assessment of CpG methylation patterns across all populations identified that only 26% of methylated DNA was intergenic; and, only 17% of all differentially methylated regions (DMRs) were within these same regions. DMRs within gene bodies between sites were associated with genes known to be involved in DNA damage repair, ion transport, and reproductive timing. Finally, when assessing the correlation between genomic variation and DNA methylation between these populations, we observed population-specific DNA methylation profiles that were not directly associated with single nucleotide polymorphisms or broader gene-body mean F ST trends. Our results suggest that C. virginica may use DNA methylation to generate environmentally responsive plastic phenotypes and that there is more divergence in methylation than divergence in allele frequencies.
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Affiliation(s)
- Kevin M. Johnson
- Department of Biological SciencesLouisiana State UniversityBaton RougeLAUSA
| | - Morgan W. Kelly
- Department of Biological SciencesLouisiana State UniversityBaton RougeLAUSA
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Lee YH, Jeong CB, Wang M, Hagiwara A, Lee JS. Transgenerational acclimation to changes in ocean acidification in marine invertebrates. MARINE POLLUTION BULLETIN 2020; 153:111006. [PMID: 32275552 DOI: 10.1016/j.marpolbul.2020.111006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 06/11/2023]
Abstract
The rapid pace of increasing oceanic acidity poses a major threat to the fitness of the marine ecosystem, as well as the buffering capacity of the oceans. Disruption in chemical equilibrium in the ocean leads to decreased carbonate ion precipitation, resulting in calcium carbonate saturation. If these trends continue, calcifying invertebrates will experience difficultly maintaining their calcium carbonate exoskeleton and shells. Because malfunction of exoskeleton formation by calcifiers in response to ocean acidification (OA) will have non-canonical biological cascading results in the marine ecosystem, many studies have investigated the direct and indirect consequences of OA on ecosystem- and physiology-related traits of marine invertebrates. Considering that evolutionary adaptation to OA depends on the duration of OA effects, long-term exposure to OA stress over multi-generations may result in adaptive mechanisms that increase the potential fitness of marine invertebrates in response to OA. Transgenerational studies have the potential to elucidate the roles of acclimation, carryover effects, and evolutionary adaptation within and over generations in response to OA. In particular, understanding mechanisms of transgenerational responses (e.g., antioxidant responses, metabolic changes, epigenetic reprogramming) to changes in OA will enhance our understanding of marine invertebrate in response to rapid climate change.
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Affiliation(s)
- Young Hwan Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea; Department of Marine Science, College of Nature Science, Incheon National University, Incheon 22012, South Korea
| | - Minghua Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment & Ecology, Xiamen University, Xiamen 36110, China; Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
| | - Atsushi Hagiwara
- Institute of Integrated Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan; Organization for Marine Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Johnson KM, Hofmann GE. Combined stress of ocean acidification and warming influence survival and drives differential gene expression patterns in the Antarctic pteropod, Limacina helicina antarctica. CONSERVATION PHYSIOLOGY 2020; 8:coaa013. [PMID: 32257214 PMCID: PMC7098371 DOI: 10.1093/conphys/coaa013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 01/12/2020] [Accepted: 02/02/2020] [Indexed: 06/11/2023]
Abstract
The ecologically important thecosome pteropods in the Limacina spp. complex have recently been the focus of studies examining the impacts global change factors - e.g., ocean acidification (OA) and ocean warming (OW) - on their performance and physiology. This focus is driven by conservation concerns where the health of pteropod populations is threatened by the high susceptibility of their shells to dissolution in low aragonite saturation states associated with OA and how coupling of these stressors may push pteropods past the limits of physiological plasticity. In this manipulation experiment, we describe changes in the transcriptome of the Antarctic pteropod, Limacina helicina antarctica, to these combined stressors. The conditions used in the laboratory treatments met or exceeded those projected for the Southern Ocean by the year 2100. We made two general observations regarding the outcome of the data: (1) Temperature was more influential than pH in terms of changing patterns of gene expression, and (2) these Antarctic pteropods appeared to have a significant degree of transcriptomic plasticity to respond to acute abiotic stress in the laboratory. In general, differential gene expression was observed amongst the treatments; here, for example, transcripts associated with maintaining protein structure and cell proliferation were up-regulated. To disentangle the effects of OA and OW, we used a weighted gene co-expression network analysis to explore patterns of change in the transcriptome. This approach identified gene networks associated with OW that were enriched for transcripts proposed to be involved in increasing membrane fluidity at warmer temperatures. Together these data provide evidence that L.h.antarctica has a limited capacity to acclimate to the combined conditions of OA and OW used in this study. This reduced scope of acclimation argues for continued study of how adaptation to polar aquatic environments may limit the plasticity of present-day populations in responding to future environmental change.
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Affiliation(s)
- Kevin M Johnson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9620 USA
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Strader ME, Wong JM, Hofmann GE. Ocean acidification promotes broad transcriptomic responses in marine metazoans: a literature survey. Front Zool 2020; 17:7. [PMID: 32095155 PMCID: PMC7027112 DOI: 10.1186/s12983-020-0350-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/06/2020] [Indexed: 01/16/2023] Open
Abstract
For nearly a decade, the metazoan-focused research community has explored the impacts of ocean acidification (OA) on marine animals, noting that changes in ocean chemistry can impact calcification, metabolism, acid-base regulation, stress response and behavior in organisms that hold high ecological and economic value. Because OA interacts with several key physiological processes in marine organisms, transcriptomics has become a widely-used method to characterize whole organism responses on a molecular level as well as inform mechanisms that explain changes in phenotypes observed in response to OA. In the past decade, there has been a notable rise in studies that examine transcriptomic responses to OA in marine metazoans, and here we attempt to summarize key findings across these studies. We find that organisms vary dramatically in their transcriptomic responses to pH although common patterns are often observed, including shifts in acid-base ion regulation, metabolic processes, calcification and stress response mechanisms. We also see a rise in transcriptomic studies examining organismal response to OA in a multi-stressor context, often reporting synergistic effects of OA and temperature. In addition, there is an increase in studies that use transcriptomics to examine the evolutionary potential of organisms to adapt to OA conditions in the future through population and transgenerational experiments. Overall, the literature reveals complex organismal responses to OA, in which some organisms will face more dramatic consequences than others. This will have wide-reaching impacts on ocean communities and ecosystems as a whole.
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Affiliation(s)
- Marie E Strader
- 1Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106 USA.,2Department of Biological Sciences, Auburn University, Auburn, AL 36849 USA
| | - Juliet M Wong
- 1Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106 USA.,3Present address: Department of Biological Sciences, Florida International University, North Miami, FL 33181 USA
| | - Gretchen E Hofmann
- 1Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106 USA
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Melzner F, Mark FC, Seibel BA, Tomanek L. Ocean Acidification and Coastal Marine Invertebrates: Tracking CO 2 Effects from Seawater to the Cell. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:499-523. [PMID: 31451083 DOI: 10.1146/annurev-marine-010419-010658] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the last few decades, numerous studies have investigated the impacts of simulated ocean acidification on marine species and communities, particularly those inhabiting dynamic coastal systems. Despite these research efforts, there are many gaps in our understanding, particularly with respect to physiological mechanisms that lead to pathologies. In this review, we trace how carbonate system disturbances propagate from the coastal environment into marine invertebrates and highlight mechanistic links between these disturbances and organism function. We also point toward several processes related to basic invertebrate biology that are severely understudied and prevent an accurate understanding of how carbonate system dynamics influence organismic homeostasis and fitness-related traits. We recommend that significant research effort be directed to studying cellular phenotypes of invertebrates acclimated or adapted to elevated seawater pCO2 using biochemical and physiological methods.
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Affiliation(s)
- Frank Melzner
- Marine Ecology Research Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany;
| | - Felix C Mark
- Department of Integrative Ecophysiology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany;
| | - Brad A Seibel
- College of Marine Science, University of South Florida, St. Petersburg, Florida 33701, USA;
| | - Lars Tomanek
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California 93407, USA;
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Byrne M, Foo SA, Ross PM, Putnam HM. Limitations of cross- and multigenerational plasticity for marine invertebrates faced with global climate change. GLOBAL CHANGE BIOLOGY 2020; 26:80-102. [PMID: 31670444 DOI: 10.1111/gcb.14882] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/12/2019] [Indexed: 05/18/2023]
Abstract
Although cross generation (CGP) and multigenerational (MGP) plasticity have been identified as mechanisms of acclimation to global change, the weight of evidence indicates that parental conditioning over generations is not a panacea to rescue stress sensitivity in offspring. For many species, there were no benefits of parental conditioning. Even when improved performance was observed, this waned over time within a generation or across generations and fitness declined. CGP and MGP studies identified resilient species with stress tolerant genotypes in wild populations and selected family lines. Several bivalves possess favourable stress tolerance and phenotypically plastic traits potentially associated with genetic adaptation to life in habitats where they routinely experience temperature and/or acidification stress. These traits will be important to help 'climate proof' shellfish ventures. Species that are naturally stress tolerant and those that naturally experience a broad range of environmental conditions are good candidates to provide insights into the physiological and molecular mechanisms involved in CGP and MGP. It is challenging to conduct ecologically relevant global change experiments over the long times commensurate with the pace of changing climate. As a result, many studies present stressors in a shock-type exposure at rates much faster than projected scenarios. With more gradual stressor introduction over longer experimental durations and in context with conditions species are currently acclimatized and/or adapted to, the outcomes for sensitive species might differ. We highlight the importance to understand primordial germ cell development and the timing of gametogenesis with respect to stressor exposure. Although multigenerational exposure to global change stressors currently appears limited as a universal tool to rescue species in the face of changing climate, natural proxies of future conditions (upwelling zones, CO2 vents, naturally warm habitats) show that phenotypic adjustment and/or beneficial genetic selection is possible for some species, indicating complex plasticity-adaptation interactions.
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Affiliation(s)
- Maria Byrne
- School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Shawna A Foo
- Center for Global Discovery and Conservation Science, Arizona State University, Tempe, AZ, USA
| | - Pauline M Ross
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
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Abstract
Echinoderms and especially echinoids have a rich history as model systems for the study of oogenesis, fertilization, and early embryogenesis. The ease of collecting and maintaining adults, as well as in obtaining gametes and culturing large quantities of synchronous embryos, is complemented by the ability to do biochemistry, reverse genetics, embryo manipulations and study gene regulatory networks. The diversity of species and developmental modes as well as unparalleled transparency in early developmental stages also makes echinoderms an excellent system in which to study evolutionary aspects of developmental biology. This chapter provides a practical guide to experimental methods for procuring adults and gametes, achieving synchronous in vitro fertilization, and culturing embryos through early larval stages for several echinoderm species representing four classes (Echinoidea, Asteroidea, Ophiuroidea, and Holothuroidea). We provide specific examples of protocols for obtaining adults and gametes and for culturing embryos of a selected number of species for experimental analysis of their development. The species were chosen to provide breadth across the phylum Echinodermata, as well as to provide practical guidelines for handling some of the more commonly studied species. For each species, we highlight specific advantages, and special note is made of key issues to consider when handling adults, collecting gametes, or setting and maintaining embryo cultures. Finally, information regarding interspecific crosses is provided.
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Griffiths JS, Pan TCF, Kelly MW. Differential responses to ocean acidification between populations of Balanophyllia elegans corals from high and low upwelling environments. Mol Ecol 2019; 28:2715-2730. [PMID: 30770604 DOI: 10.1111/mec.15050] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/22/2022]
Abstract
Ocean acidification (OA), the global decrease in surface water pH from absorption of anthropogenic CO2 , may put many marine taxa at risk. However, populations that experience extreme localized conditions, and are adapted to these conditions predicted in the global ocean in 2,100, may be more tolerant to future OA. By identifying locally adapted populations, researchers can examine the mechanisms used to cope with decreasing pH. One oceanographic process that influences pH is wind-driven upwelling. Here we compare two Californian populations of the coral Balanophyllia elegans from distinct upwelling regimes, and test their physiological and transcriptomic responses to experimental seawater acidification. We measured respiration rates, protein and lipid content, and gene expression in corals from both populations exposed to pH levels of 7.8 and 7.4 for 29 days. Corals from the population that experiences lower pH due to high upwelling maintained the same respiration rate throughout the exposure. In contrast, corals from the low upwelling site had reduced respiration rates, protein content and lipid-class content at low pH exposure, suggesting they have depleted their energy reserves. Using RNA-Seq, we found that corals from the high upwelling site upregulated genes involved in calcium ion binding and ion transport, most likely related to pH homeostasis and calcification. In contrast, corals from the low upwelling site downregulated stress response genes at low pH exposure. Divergent population responses to low pH observed in B. elegans highlight the importance of multi-population studies for predicting a species' response to future OA.
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Affiliation(s)
- Joanna S Griffiths
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Tien-Chien Francis Pan
- Department of Biological Sciences, University of Southern California, Los Angeles, California
| | - Morgan W Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
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Fox RJ, Donelson JM, Schunter C, Ravasi T, Gaitán-Espitia JD. Beyond buying time: the role of plasticity in phenotypic adaptation to rapid environmental change. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180174. [PMID: 30966962 PMCID: PMC6365870 DOI: 10.1098/rstb.2018.0174] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2018] [Indexed: 12/18/2022] Open
Abstract
How populations and species respond to modified environmental conditions is critical to their persistence both now and into the future, particularly given the increasing pace of environmental change. The process of adaptation to novel environmental conditions can occur via two mechanisms: (1) the expression of phenotypic plasticity (the ability of one genotype to express varying phenotypes when exposed to different environmental conditions), and (2) evolution via selection for particular phenotypes, resulting in the modification of genetic variation in the population. Plasticity, because it acts at the level of the individual, is often hailed as a rapid-response mechanism that will enable organisms to adapt and survive in our rapidly changing world. But plasticity can also retard adaptation by shifting the distribution of phenotypes in the population, shielding it from natural selection. In addition to which, not all plastic responses are adaptive-now well-documented in cases of ecological traps. In this theme issue, we aim to present a considered view of plasticity and the role it could play in facilitating or hindering adaption to environmental change. This introduction provides a re-examination of our current understanding of the role of phenotypic plasticity in adaptation and sets the theme issue's contributions in their broader context. Four key themes emerge: the need to measure plasticity across both space and time; the importance of the past in predicting the future; the importance of the link between plasticity and sexual selection; and the need to understand more about the nature of selection on plasticity itself. We conclude by advocating the need for cross-disciplinary collaborations to settle the question of whether plasticity will promote or retard species' rates of adaptation to ever-more stressful environmental conditions. This article is part of the theme issue 'The role of plasticity in phenotypic adaptation to rapid environmental change'.
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Affiliation(s)
- Rebecca J. Fox
- Division of Ecology and Evolution, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Jennifer M. Donelson
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4810, Australia
| | - Celia Schunter
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Juan D. Gaitán-Espitia
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
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Di Natale M, Bennici C, Biondo G, Masullo T, Monastero C, Tagliavia M, Torri M, Costa S, Ragusa MA, Cuttitta A, Nicosia A. Aberrant gene expression profiles in Mediterranean sea urchin reproductive tissues after metal exposures. CHEMOSPHERE 2019; 216:48-58. [PMID: 30359916 DOI: 10.1016/j.chemosphere.2018.10.137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/12/2018] [Accepted: 10/18/2018] [Indexed: 06/08/2023]
Abstract
Marine organisms are simultaneously exposed to numerous pollutants, among which metals probably represent the most abundant in marine environments. In order to evaluate the effects of metal exposure at molecular level in reproductive tissues, we profiled the sea urchin transcriptional response after non-lethal exposures using pathway-focused mRNA expression analyses. Herein, we show that exposures to relatively high concentrations of both essential and toxic metals hugely affected the gonadic expression of several genes involved in stress-response, detoxification, transcriptional and post-transcriptional regulation, without significant changes in gonadosomatic indices. Even though treatments did not result in reproductive tissues visible alterations, metal exposures negatively affected the main mechanisms of stress-response, detoxification and survival of adult P. lividus. Additionally, transcriptional changes observed in P. lividus gonads may cause altered gametogenesis and maintenance of heritable aberrant epigenetic effects. This study leads to the conclusion that exposures to metals, as usually occurs in polluted coastal areas, may affect sea urchin gametogenesis, thus supporting the hypothesis that parental exposure to environmental stressors affects the phenotype of the offspring.
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Affiliation(s)
- Marilena Di Natale
- National Research Council-Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino (IAS-CNR), Laboratory of Molecular Ecology and Biotechnology, Detached Unit of Capo Granitola, Via del mare, 91021, Torretta Granitola (TP), Sicily, Italy.
| | - Carmelo Bennici
- National Research Council-Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino (IAS-CNR), Laboratory of Molecular Ecology and Biotechnology, Detached Unit of Capo Granitola, Via del mare, 91021, Torretta Granitola (TP), Sicily, Italy.
| | - Girolama Biondo
- National Research Council-Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino (IAS-CNR), Laboratory of Molecular Ecology and Biotechnology, Detached Unit of Capo Granitola, Via del mare, 91021, Torretta Granitola (TP), Sicily, Italy.
| | - Tiziana Masullo
- National Research Council-Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino (IAS-CNR), Laboratory of Molecular Ecology and Biotechnology, Detached Unit of Capo Granitola, Via del mare, 91021, Torretta Granitola (TP), Sicily, Italy.
| | - Calogera Monastero
- National Research Council-Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino (IAS-CNR), Laboratory of Molecular Ecology and Biotechnology, Detached Unit of Capo Granitola, Via del mare, 91021, Torretta Granitola (TP), Sicily, Italy.
| | - Marcello Tagliavia
- National Research Council-Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino (IAS-CNR), Laboratory of Molecular Ecology and Biotechnology, Detached Unit of Capo Granitola, Via del mare, 91021, Torretta Granitola (TP), Sicily, Italy.
| | - Marco Torri
- National Research Council-Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino (IAS-CNR), Laboratory of Molecular Ecology and Biotechnology, Detached Unit of Capo Granitola, Via del mare, 91021, Torretta Granitola (TP), Sicily, Italy.
| | - Salvatore Costa
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Ed. 16, 90128, Palermo, Sicily, Italy.
| | - Maria Antonietta Ragusa
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Ed. 16, 90128, Palermo, Sicily, Italy.
| | - Angela Cuttitta
- National Research Council-Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino (IAS-CNR), Laboratory of Molecular Ecology and Biotechnology, Detached Unit of Capo Granitola, Via del mare, 91021, Torretta Granitola (TP), Sicily, Italy.
| | - Aldo Nicosia
- National Research Council-Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino (IAS-CNR), Laboratory of Molecular Ecology and Biotechnology, Detached Unit of Capo Granitola, Via del mare, 91021, Torretta Granitola (TP), Sicily, Italy.
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Clark MS, Suckling CC, Cavallo A, Mackenzie CL, Thorne MAS, Davies AJ, Peck LS. Molecular mechanisms underpinning transgenerational plasticity in the green sea urchin Psammechinus miliaris. Sci Rep 2019; 9:952. [PMID: 30700813 PMCID: PMC6353892 DOI: 10.1038/s41598-018-37255-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 11/30/2018] [Indexed: 01/01/2023] Open
Abstract
The pre-conditioning of adult marine invertebrates to altered conditions, such as low pH, can significantly impact offspring outcomes, a process which is often referred to as transgenerational plasticity (TGP). This study describes for the first time, the gene expression profiles associated with TGP in the green sea urchin Psammechinus miliaris and evaluates the transcriptional contribution to larval resilience. RNA-Seq was used to determine how the expression profiles of larvae spawned into low pH from pre-acclimated adults differed to those of larvae produced from adults cultured under ambient pH. The main findings demonstrated that adult conditioning to low pH critically pre-loads the embryonic transcriptional pool with antioxidants to prepare the larvae for the “new” conditions. In addition, the classic cellular stress response, measured via the production of heat shock proteins (the heat shock response (HSR)), was separately evaluated. None of the early stage larvae either spawned in low pH (produced from both ambient and pre-acclimated adults) or subjected to a separate heat shock experiment were able to activate the full HSR as measured in adults, but the capacity to mount an HSR increased as development proceeded. This compromised ability clearly contributes to the vulnerability of early stage larvae to acute environmental challenge.
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Affiliation(s)
- Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - Coleen C Suckling
- School of Ocean Sciences, Bangor University, Askew Street, Menai Bridge, Anglesey, LL59 5AB, UK.,Fisheries, Animal and Veterinary Sciences, University of Rhode Island, 4 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Alessandro Cavallo
- School of Biological and Marine Sciences, Plymouth University, Drake Circus, Plymouth, PL4 8AA, UK
| | - Clara L Mackenzie
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Michael A S Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Andrew J Davies
- School of Ocean Sciences, Bangor University, Askew Street, Menai Bridge, Anglesey, LL59 5AB, UK.,Biological Sciences, University of Rhode Island, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
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