1
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deMayo JA, Ragland GJ. (Limited) Predictability of thermal adaptation in invertebrates. J Exp Biol 2025; 228:JEB249450. [PMID: 40052398 DOI: 10.1242/jeb.249450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2025]
Abstract
Evolutionary genomic approaches provide powerful tools to understand variation in and evolution of physiological processes. Untargeted genomic or transcriptomic screens can identify functionally annotated candidate genes linked to specific physiological processes, in turn suggesting evolutionary roles for these processes. Such studies often aim to inform modeling of the potential of natural populations to adapt to climate change, but these models are most accurate when evolutionary responses are repeatable, and thus predictable. Here, we synthesize the evolutionary genetic and comparative transcriptomic literature on terrestrial and marine invertebrates to assess whether evolutionary responses to temperature are repeatable within populations, across populations and across species. There is compelling evidence for repeatability, sometimes even across species. However, responses to laboratory selection and geographic variation across thermal gradients appear to be highly idiosyncratic. We also survey whether genetic/transcriptomic studies repeatedly identify candidate genes in three functional groups previously associated with the response to thermal stress: heat shock protein (Hsp) genes, proteolysis genes and immunity genes. Multiple studies across terrestrial and marine species identify candidates included in these gene sets. Yet, each of the gene sets are identified in only a minority of studies. Together, these patterns suggest that there is limited predictability of evolutionary responses to natural selection, including across studies within species. We discuss specific patterns for the candidate gene sets, implications for predictive modeling, and other potential applications of evolutionary genetics in elucidating physiology and gene function. Finally, we discuss limitations of inferences from available evolutionary genetic studies and directions for future research.
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Affiliation(s)
- James A deMayo
- Department of Integrative Biology, University of Colorado Denver, 1151 Arapahoe St, Denver, CO 80204, USA
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado Denver, 1151 Arapahoe St, Denver, CO 80204, USA
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2
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Voolstra CR, Alderdice R, Colin L, Staab S, Apprill A, Raina JB. Standardized Methods to Assess the Impacts of Thermal Stress on Coral Reef Marine Life. ANNUAL REVIEW OF MARINE SCIENCE 2025; 17:193-226. [PMID: 39116436 DOI: 10.1146/annurev-marine-032223-024511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
The Earth's oceans have absorbed more than 90% of the excess, climate change-induced atmospheric heat. The resulting rise in oceanic temperatures affects all species and can lead to the collapse of marine ecosystems, including coral reefs. Here, we review the range of methods used to measure thermal stress impacts on reef-building corals, highlighting current standardization practices and necessary refinements to fast-track discoveries and improve interstudy comparisons. We also present technological developments that will undoubtedly enhance our ability to record and analyze standardized data. Although we use corals as an example, the methods described are widely employed in marine sciences, and our recommendations therefore apply to all species and ecosystems. Enhancing collaborative data collection efforts, implementing field-wide standardized protocols, and ensuring data availability through dedicated, openly accessible databases will enable large-scale analysis and monitoring of ecosystem changes, improving our predictive capacities and informing active intervention to mitigate climate change effects on marine life.
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Affiliation(s)
| | - Rachel Alderdice
- Department of Biology, University of Konstanz, Konstanz, Germany;
| | - Luigi Colin
- Department of Biology, University of Konstanz, Konstanz, Germany;
| | - Sebastian Staab
- Department of Biology, University of Konstanz, Konstanz, Germany;
| | - Amy Apprill
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia;
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3
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Chille EE, Stephens TG, Misri D, Strand EL, Putnam HM, Bhattacharya D. Gene expression response under thermal stress in two Hawaiian corals is dominated by ploidy and genotype. Ecol Evol 2024; 14:e70037. [PMID: 39050655 PMCID: PMC11268936 DOI: 10.1002/ece3.70037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/03/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024] Open
Abstract
Transcriptome data are frequently used to investigate coral bleaching; however, the factors controlling gene expression in natural populations of these species are poorly understood. We studied two corals, Montipora capitata and Pocillopora acuta, that inhabit the sheltered Kāne'ohe Bay, Hawai'i. M. capitata colonies in the bay are outbreeding diploids, whereas P. acuta is a mixture of clonal diploids and triploids. Populations were sampled from six reefs and subjected to either control (no stress), thermal stress, pH stress, or combined pH and thermal stress treatments. RNA-seq data were generated to test two competing hypotheses: (1) gene expression is largely independent of genotype, reflecting a shared treatment-driven response (TDE) or, (2) genotype dominates gene expression, regardless of treatment (GDE). Our results strongly support the GDE model, even under severe stress. We suggest that post-transcriptional processes (e.g., control of translation, protein turnover) modify the signal from the transcriptome, and may underlie the observed differences in coral bleaching sensitivity via the downstream proteome and metabolome.
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Affiliation(s)
- Erin E. Chille
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNew JerseyUSA
| | - Timothy G. Stephens
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNew JerseyUSA
| | - Deeksha Misri
- Department of GeneticsRutgers UniversityNew BrunswickNew JerseyUSA
| | - Emma L. Strand
- Department of Biological SciencesUniversity of Rhode IslandKingstonRhode IslandUSA
- Gloucester Marine Genomics InstituteGloucesterMassachusettsUSA
| | - Hollie M. Putnam
- Department of Biological SciencesUniversity of Rhode IslandKingstonRhode IslandUSA
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4
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Strader ME, Wright RM, Pezner AK, Nuttall MF, Aichelman HE, Davies SW. Intersection of coral molecular responses to a localized mortality event and ex situ deoxygenation. Ecol Evol 2024; 14:e11275. [PMID: 38654712 PMCID: PMC11036075 DOI: 10.1002/ece3.11275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024] Open
Abstract
In July 2016, East Bank of Flower Garden Banks (FGB) National Marine Sanctuary experienced a localized mortality event (LME) of multiple invertebrate species that ultimately led to reductions in coral cover. Abiotic data taken directly after the event suggested that acute deoxygenation contributed to the mortality. Despite the large impact of this event on the coral community, there was no direct evidence that this LME was driven by acute deoxygenation, and thus we explored whether gene expression responses of corals to the LME would indicate what abiotic factors may have contributed to the LME. Gene expression of affected and unaffected corals sampled during the mortality event revealed evidence of the physiological consequences of the LME on coral hosts and their algal symbionts from two congeneric species (Orbicella franksi and Orbicella faveolata). Affected colonies of both species differentially regulated genes involved in mitochondrial regulation and oxidative stress. To further test the hypothesis that deoxygenation led to the LME, we measured coral host and algal symbiont gene expression in response to ex situ experimental deoxygenation (control = 6.9 ± 0.08 mg L-1, anoxic = 0.083 ± 0.017 mg L-1) in healthy O. faveolata colonies from the FGB. However, this deoxygenation experiment revealed divergent gene expression patterns compared to the corals sampled during the LME and was more similar to a generalized coral environmental stress response. It is therefore likely that while the LME was connected to low oxygen, it was a series of interconnected stressors that elicited the unique gene expression responses observed here. These in situ and ex situ data highlight how field responses to stressors are unique from those in controlled laboratory conditions, and that the complexities of deoxygenation events in the field likely arise from interactions between multiple environmental factors simultaneously.
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Affiliation(s)
- Marie E. Strader
- Department of BiologyTexas A&M UniversityCollege StationTexasUSA
| | - Rachel M. Wright
- Department of Biological SciencesSouthern Methodist UniversityDallasTexasUSA
| | | | | | | | - Sarah W. Davies
- Department of BiologyBoston UniversityBostonMassachusettsUSA
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5
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Dilworth J, Million WC, Ruggeri M, Hall ER, Dungan AM, Muller EM, Kenkel CD. Synergistic response to climate stressors in coral is associated with genotypic variation in baseline expression. Proc Biol Sci 2024; 291:20232447. [PMID: 38531406 DOI: 10.1098/rspb.2023.2447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/16/2024] [Indexed: 03/28/2024] Open
Abstract
As environments are rapidly reshaped due to climate change, phenotypic plasticity plays an important role in the ability of organisms to persist and is considered an especially important acclimatization mechanism for long-lived sessile organisms such as reef-building corals. Often, this ability of a single genotype to display multiple phenotypes depending on the environment is modulated by changes in gene expression, which can vary in response to environmental changes via two mechanisms: baseline expression and expression plasticity. We used transcriptome-wide expression profiling of eleven genotypes of common-gardened Acropora cervicornis to explore genotypic variation in the expression response to thermal and acidification stress, both individually and in combination. We show that the combination of these two stressors elicits a synergistic gene expression response, and that both baseline expression and expression plasticity in response to stress show genotypic variation. Additionally, we demonstrate that frontloading of a large module of coexpressed genes is associated with greater retention of algal symbionts under combined stress. These results illustrate that variation in the gene expression response of individuals to climate change stressors can persist even when individuals have shared environmental histories, affecting their performance under future climate change scenarios.
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Affiliation(s)
| | | | - Maria Ruggeri
- University of Southern California, Los Angeles, CA, USA
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6
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Fiesinger A, Held C, Schmidt AL, Putchim L, Melzner F, Wall M. Dominance of the coral Pocillopora acuta around Phuket Island in the Andaman Sea, Thailand. Ecol Evol 2023; 13:e10724. [PMID: 38020692 PMCID: PMC10643679 DOI: 10.1002/ece3.10724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Pocillopora damicornis (Linnaeus, 1758), a species complex, consists of several genetic lineages, some of which likely represent reproductively isolated species, including the species Pocillopora acuta Lamarck, 1816. Pocillopora acuta can exhibit similar morphological characteristics as P. damicornis, thus making it difficult to identify species-level taxonomic units. To determine whether the P. damicornis-like colonies on the reefs in the Andaman Sea (previously often identified as P. damicornis) consist of different species, we sampled individual colonies at five sites along a 50 km coastal stretch at Phuket Island and four island sites towards Krabi Province, Thailand. We sequenced 210 coral samples for the mitochondrial open reading frame and identified six distinct haplotypes, all belonging to P. acuta according to the literature. Recently, P. acuta was observed to efficiently recolonize heat-damaged reefs in Thailand as well as globally, making it a potentially important coral species in future reefs. Specifically in the light of global change, this study underscores the importance of high-resolution molecular species recognition, since taxonomic units are important factors for population genetic studies, and the latter are crucial for management and conservation efforts.
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Affiliation(s)
- Anna Fiesinger
- GEOMAR Helmholtz Centre for Ocean Research KielKielGermany
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Christoph Held
- Alfred‐Wegener‐InstitutHelmholtz‐Zentrum für Polar‐ und MeeresforschungBremerhavenGermany
| | - Andrea L. Schmidt
- GEOMAR Helmholtz Centre for Ocean Research KielKielGermany
- Cooperative Institute for Marine and Atmospheric ResearchUniversity of Hawai‘i at ManoaHonoluluHonoluluUSA
| | | | - Frank Melzner
- GEOMAR Helmholtz Centre for Ocean Research KielKielGermany
| | - Marlene Wall
- GEOMAR Helmholtz Centre for Ocean Research KielKielGermany
- Alfred‐Wegener‐InstitutHelmholtz‐Zentrum für Polar‐ und MeeresforschungBremerhavenGermany
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7
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Oakley CA, Newson GI, Peng L, Davy SK. The Symbiodinium Proteome Response to Thermal and Nutrient Stresses. PLANT & CELL PHYSIOLOGY 2023; 64:433-447. [PMID: 36565060 PMCID: PMC10109209 DOI: 10.1093/pcp/pcac175] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/18/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Coral bleaching is primarily caused by high sea surface temperatures, and nutrient enrichment of reefs is associated with lower resilience to thermal stress and ecological degradation. Excess inorganic nitrogen relative to phosphate has been proposed to sensitize corals to thermal bleaching. We assessed the physiological and proteomic responses of cultures of the dinoflagellate coral symbiont Symbiodinium microadriaticum to elevated temperature under low-nutrient, high-nutrient and phosphate-limited conditions. Elevated temperature induced reductions of many chloroplast proteins, particularly the light-harvesting complexes, and simultaneously increased the abundance of many chaperone proteins. Proteomes were similar when the N:P ratio was near the Redfield ratio, regardless of absolute N and P concentrations, but were strongly affected by phosphate limitation. Very high N:P inhibited Symbiodinium cell division while increasing the abundance of chloroplast proteins. The proteome response to phosphate limitation was greater than that to elevated temperature, as measured by the number of differentially abundant proteins. Increased physiological sensitivity to high temperatures under high nutrients or imbalanced N:P ratios was not apparent; however, oxidative stress response proteins were enriched among proteins responding to thermal stress under imbalanced N:P ratios. These data provide a detailed catalog of the effects of high temperatures and nutrients on a coral symbiont proteome.
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Affiliation(s)
| | - Grace I Newson
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Lifeng Peng
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
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8
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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9
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Mayfield AB. Multi-macromolecular Extraction from Endosymbiotic Anthozoans. Methods Mol Biol 2023; 2625:17-56. [PMID: 36653630 DOI: 10.1007/978-1-0716-2966-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Obligately symbiotic associations between reef-building corals (anthozoan cnidarians) and photosynthetically active dinoflagellates of the family Symbiodiniaceae comprise the functional basis of all coral reef ecosystems. Given the existential threats of global climate change toward these thermo-sensitive entities, there is an urgent need to better understand the physiological implications of changes in the abiotic milieu of scleractinian corals and their mutualistic algal endosymbionts. Although initially slow to leverage the immense breakthroughs in molecular biotechnology that have benefited humankind, coral biologists are making up for lost time in exploiting an array of ever-advancing molecular tools for answering key questions pertaining to the survival of corals in an ever-changing world. In order to comprehensively characterize the multi-omic landscape of the coral holobiont-the cnidarian host, its intracellular dinoflagellates, and a plethora of other microbial constituents-I introduce a series of protocols herein that yield large quantities of high-quality RNA, DNA, protein, lipids, and polar metabolites from a diverse array of reef corals and endosymbiotic sea anemones. Although numerous published articles in the invertebrate zoology field feature protocols that lead to sufficiently high yield of intact host coral macromolecules, through using the approach outlined herein one may simultaneously acquire a rich, multi-compartmental biochemical pool that truly reflects the complex and dynamic nature of these animal-plant chimeras.
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10
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Pei Y, Chen S, Diao X, Wang X, Zhou H, Li Y, Li Z. Deciphering the disturbance mechanism of BaP on the symbiosis of Montipora digitata via 4D-Proteomics approach. CHEMOSPHERE 2023; 312:137223. [PMID: 36372339 DOI: 10.1016/j.chemosphere.2022.137223] [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: 05/25/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
The coral holobiont is mainly composed of coral polyps, zooxanthellae, and coral symbiotic microorganisms, which form the basis of coral reef ecosystems. In recent years, the severe degradation of coral reefs caused by climate warming and environmental pollution has aroused widespread concern. Benzo(a)pyrene (BaP) is a widely distributed pollutant in the environment. However, the underlying mechanisms of coral symbiosis destruction due to the stress of BaP are not well understood. In this study, diaPASEF proteomics and 16S rRNA amplicon pyrosequencing technology were used to reveal the effects of 50 μg/L BaP on Montipora digitate. Data analysis was performed from the perspective of the main symbionts of M. digitata (coral polyps, zooxanthellae, and coral symbiotic microorganisms). The results showed that BaP impaired cellular antioxidant capacity by disrupting the GSH/GSSG cycle, and sustained stress causes severe impairment of energy metabolism and protein degradation in coral polyps. In zooxanthellae, BaP downregulated the protein expression of SOD2 and mtHSP70, which then resulted in oxidative free radical accumulation and apoptosis. For coral symbiotic microorganisms, BaP altered the community structure of microorganisms and decreased immunity. Coral symbiotic microorganisms adapted to the stress of BaP by adjusting energy metabolism and enhancing extracellular electron transfer. BaP adversely affected the three main symbionts of M. digitata via different mechanisms. Decreased antioxidant capacity is a common cause of damages to coral polyps and zooxanthellae, whereas coral symbiotic microorganisms are able to appropriately adapt to oxidative stress. This study assessed the effects of BaP on corals from a symbiotic perspective, which is more comprehensive and reliable. At the same time, data from the study supports new directions for coral research and coral reef protection.
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Affiliation(s)
- Yuebin Pei
- School of Life Sciences, Hainan University, Haikou, 570228, China; State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China; One Health Institute, Hainan University, Haikou, Hainan, 570228, China
| | - Shuai Chen
- School of Life Sciences, Hainan University, Haikou, 570228, China; State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China; One Health Institute, Hainan University, Haikou, Hainan, 570228, China
| | - Xiaoping Diao
- State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China
| | - Xiaobing Wang
- School of Life Sciences, Hainan University, Haikou, 570228, China; One Health Institute, Hainan University, Haikou, Hainan, 570228, China
| | - Hailong Zhou
- School of Life Sciences, Hainan University, Haikou, 570228, China; State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China; One Health Institute, Hainan University, Haikou, Hainan, 570228, China.
| | - Yuanchao Li
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, 571126, China
| | - Zhiyong Li
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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11
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Stephens TG, Lee J, Jeong Y, Yoon HS, Putnam HM, Majerová E, Bhattacharya D. High-quality genome assembles from key Hawaiian coral species. Gigascience 2022; 11:giac098. [PMID: 36352542 PMCID: PMC9646523 DOI: 10.1093/gigascience/giac098] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/11/2022] [Accepted: 09/22/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Coral reefs house about 25% of marine biodiversity and are critical for the livelihood of many communities by providing food, tourism revenue, and protection from wave surge. These magnificent ecosystems are under existential threat from anthropogenic climate change. Whereas extensive ecological and physiological studies have addressed coral response to environmental stress, high-quality reference genome data are lacking for many of these species. The latter issue hinders efforts to understand the genetic basis of stress resistance and to design informed coral conservation strategies. RESULTS We report genome assemblies from 4 key Hawaiian coral species, Montipora capitata, Pocillopora acuta, Pocillopora meandrina, and Porites compressa. These species, or members of these genera, are distributed worldwide and therefore of broad scientific and ecological importance. For M. capitata, an initial assembly was generated from short-read Illumina and long-read PacBio data, which was then scaffolded into 14 putative chromosomes using Omni-C sequencing. For P. acuta, P. meandrina, and P. compressa, high-quality assemblies were generated using short-read Illumina and long-read PacBio data. The P. acuta assembly is from a triploid individual, making it the first reference genome of a nondiploid coral animal. CONCLUSIONS These assemblies are significant improvements over available data and provide invaluable resources for supporting multiomics studies into coral biology, not just in Hawai'i but also in other regions, where related species exist. The P. acuta assembly provides a platform for studying polyploidy in corals and its role in genome evolution and stress adaptation in these organisms.
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Affiliation(s)
- Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu, Buk-gu 41566, Korea
| | - YuJin Jeong
- Department of Oceanography, Kyungpook National University, Daegu, Buk-gu 41566, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Eva Majerová
- Hawaiʻi Institute of Marine Biology, Kāneʻohe, HI 96744, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
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12
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Yao S, Li L, Guan X, He Y, Jouaux A, Xu F, Guo X, Zhang G, Zhang L. Pooled resequencing of larvae and adults reveals genomic variations associated with Ostreid herpesvirus 1 resistance in the Pacific oyster Crassostrea gigas. Front Immunol 2022; 13:928628. [PMID: 36059443 PMCID: PMC9437489 DOI: 10.3389/fimmu.2022.928628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/29/2022] [Indexed: 11/30/2022] Open
Abstract
The Ostreid herpesvirus 1 (OsHV-1) is a lethal pathogen of the Pacific oyster (Crassostrea gigas), an important aquaculture species. To understand the genetic architecture of the defense against the pathogen, we studied genomic variations associated with herpesvirus-caused mortalities by pooled whole-genome resequencing of before and after-mortality larval samples as well as dead and surviving adults from a viral challenge. Analysis of the resequencing data identified 5,271 SNPs and 1,883 genomic regions covering 3,111 genes in larvae, and 18,692 SNPs and 28,314 regions covering 4,863 genes in adults that were significantly associated with herpesvirus-caused mortalities. Only 1,653 of the implicated genes were shared by larvae and adults, suggesting that the antiviral response or resistance in larvae and adults involves different sets of genes or differentiated members of expanded gene families. Combined analyses with previous transcriptomic data from challenge experiments revealed that transcription of many mortality-associated genes was also significantly upregulated by herpesvirus infection confirming their importance in antiviral response. Key immune response genes especially those encoding antiviral receptors such as TLRs and RLRs displayed strong association between variation in regulatory region and herpesvirus-caused mortality, suggesting they may confer resistance through transcriptional modulation. These results point to previously undescribed genetic mechanisms for disease resistance at different developmental stages and provide candidate polymorphisms and genes that are valuable for understanding antiviral immune responses and breeding for herpesvirus resistance.
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Affiliation(s)
- Shanshan Yao
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Li Li
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, College of Marine Science, Beijing, China
| | - Xudong Guan
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yan He
- Ministry of Education (MOE) Key Laboratory of Molecular Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Aude Jouaux
- UMR BOREA, “Biologie des Organismes et Ecosystèmes Aquatiques”, MNHN, UPMC, UCBN, CNRS-7208, IRD, Université de Caen Basse-Normandie, Esplanade de la Paix, Caen, France
| | - Fei Xu
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ, United States
| | - Guofan Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, College of Marine Science, Beijing, China
| | - Linlin Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, College of Marine Science, Beijing, China
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13
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Pei Y, Chen S, Zhang Y, Olga V, Li Y, Diao X, Zhou H. Coral and it's symbionts responses to the typical global marine pollutant BaP by 4D-Proteomics approach. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119440. [PMID: 35623566 DOI: 10.1016/j.envpol.2022.119440] [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: 01/07/2022] [Revised: 04/13/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
The symbiosis of corals, zooxanthellae, and microbes is the foundation of the coral reef ecosystem. In addition to global warming, marine pollutants are another important factor causing the breakdown of coral symbiosis. Benzo(a)pyrene (BaP) is a globally widespread marine environmental pollutant that poses a severe threat to marine ecosystems. However, responses of coral symbionts to global marine pollutant stress remain unclear. In this study, we selected Acropora formosa as the target coral to explore its response to 50 μg L-1 BaP stress using diaPASEF proteomics and 16s rRNA microbiome analysis. The results showed that: 1) the coral symbionts were sensitive to BaP stress; 2) the photosynthetic system of zooxanthellae was crucial for the balance of symbiotic relationships; 3) the destruction of the photosynthetic system induced a zooxanthellae hypoxic stress response; 4) corals adapted to BaP stress by promoting non-essential protein degradation and changing energy metabolism strategies; 5) symbiotic bacteria showed strong adaptability to BaP. This study not only fills the gap in understanding the response mechanism of coral symbionts under BaP stress, but also provides fundamental data for coral reef protection strategies.
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Affiliation(s)
- Yuebin Pei
- State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China; School of Life Sciences, Hainan University, Haikou, 570228, China; One Health Institute, Hainan University, Haikou, Hainan, 570228, China
| | - Shuai Chen
- State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China; School of Life Sciences, Hainan University, Haikou, 570228, China; One Health Institute, Hainan University, Haikou, Hainan, 570228, China
| | - Yuting Zhang
- State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China; School of Life Sciences, Hainan University, Haikou, 570228, China; One Health Institute, Hainan University, Haikou, Hainan, 570228, China
| | - Volovych Olga
- State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China; School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Yuanchao Li
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, 571126, China
| | - Xiaoping Diao
- State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China
| | - Hailong Zhou
- State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China; School of Life Sciences, Hainan University, Haikou, 570228, China; One Health Institute, Hainan University, Haikou, Hainan, 570228, China.
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14
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Synergistic Effect of Elevated Temperature and Light Stresses on Physiology of Pocillopora acuta from Different Environments. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Increasing levels of greenhouse gases lead to ocean warming, which affects a range of marine organisms. Corals live in a narrow temperature range and become stressed when the temperatures change. Bleaching occurs when the temperature exceeds the coral’s threshold, and can be severe when this is combined with other stressors such as light. In order to understand how temperature and light affect corals in their physiological responses and photosynthetic performance, Pocillopora acuta from Maiton Island (MT) and Panwa Cape (PW), representing different environments, were investigated. The results show that light and temperature had by regime different effects on Symbiodiniaceae photosynthesis and the coral growth rate. There was a synergistic effect of elevated temperature and light on photosynthesis, as observed in the photochemical efficiency and pigment contents, suggesting photo-damage. A higher growth rate in Panwa corals was observed in control, and while elevated temperature reduced coral growth. Elevated temperature affected the Panwa coral less, suggesting that corals from this regime might be able to recover when the temperature returns to normal. This information is important for predicting the coral responses to elevated temperature especially in the summer, as regards the possibility of coral bleaching.
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15
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Sun Y, Jiang L, Gong S, Diaz-Pulido G, Yuan X, Tong H, Huang L, Zhou G, Zhang Y, Huang H. Changes in physiological performance and protein expression in the larvae of the coral Pocillopora damicornis and their symbionts in response to elevated temperature and acidification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151251. [PMID: 34728194 DOI: 10.1016/j.scitotenv.2021.151251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Climate change causes ocean warming and acidification, which threaten coral reef ecosystems. Ocean warming and acidification cause bleaching and mortality, and decrease calcification in adult corals, leading to changes in the composition of coral communities; however, their interactive effects on coral larvae are not comprehensively understood. To examine the underlying molecular mechanisms of larval responses to elevated temperature and pCO2, we examined the physiological performance and protein expression profiles of Pocillopora damicornis at two temperatures (29 and 33 °C) and pCO2 levels (500 and 1000 μatm) for 5 d. Extensive physiological and proteomic changes were observed in coral larvae. The results indicated a significant decrease in net photosynthesis (PNET) and autotrophic capability (PNET/RD) of larvae exposed to elevated temperature but a marked increase in PNET and PNET/RD of larvae exposed to high pCO2 levels. Elevated temperature significantly reduced endosymbiont densities by 70% and photochemical efficiency, indicating that warming impaired host-symbiont symbiosis. Expression of photosynthesis-related proteins, the photosystem (PS) I reaction center subunits IV and XI as well as oxygen-evolving enhancer 1, was downregulated at higher temperatures in symbionts, whereas expression of the PS I iron‑sulfur center protein was increased under high pCO2 conditions. Furthermore, expression of phosphoribulokinase (involved in the Calvin cycle) and phosphoenolpyruvate carboxylase (related to the C4 pathway) was downregulated in symbionts under thermal stress; this finding suggests reduced carbon fixation at high temperatures. The abundance of carbonic anhydrase-associated proteins, which are predicted to exert biochemical roles in dissolved inorganic carbon transport in larvae, was reduced in coral host and symbionts at high temperatures. These results elucidate potential mechanisms underlying the responses of coral larvae exposed to elevated temperature and acidification and suggest an important role of symbionts in the response to warming and acidification.
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Affiliation(s)
- Youfang 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, Chinese Academy of Sciences, Guangzhou 510301, China; Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong 999077, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - 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, Chinese Academy of Sciences, Guangzhou 510301, China; Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong 999077, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China
| | - Sanqiang Gong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Guillermo Diaz-Pulido
- School of Environment and Science, and Australian Rivers Institute - Coast & Estuaries, Nathan Campus, Griffith University, Brisbane, Nathan Campus, Queensland 4111, Australia
| | - Xiangcheng 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, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China
| | - Haoya Tong
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong 999077, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China
| | - Lintao 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, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guowei 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, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China
| | - Yuyang Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, 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, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Sanya National Marine Ecosystem Research Station; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China.
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16
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Machine-Learning-Based Proteomic Predictive Modeling with Thermally-Challenged Caribbean Reef Corals. DIVERSITY 2022. [DOI: 10.3390/d14010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Coral health is currently diagnosed retroactively; colonies are deemed “stressed” upon succumbing to bleaching or disease. Ideally, health inferences would instead be made on a pre-death timescale that would enable, for instance, environmental mitigation that could promote coral resilience. To this end, diverse Caribbean coral (Orbicella faveolata) genotypes of varying resilience to high temperatures along the Florida Reef Tract were exposed herein to elevated temperatures in the laboratory, and a proteomic analysis was taken with a subset of 20 samples via iTRAQ labeling followed by nano-liquid chromatography + mass spectrometry; 46 host coral and 40 Symbiodiniaceae dinoflagellate proteins passed all stringent quality control criteria, and the partial proteomes of biopsies of (1) healthy controls, (2) sub-lethally stressed samples, and (3) actively bleaching corals differed significantly from one another. The proteomic data were then used to train predictive models of coral colony bleaching susceptibility, and both generalized regression and machine-learning-based neural networks were capable of accurately forecasting the bleaching susceptibility of coral samples based on their protein signatures. Successful future testing of the predictive power of these models in situ could establish the capacity to proactively monitor coral health.
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17
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Takahashi-Kariyazono S, Terai Y. Two divergent haplogroups of a sacsin-like gene in Acropora corals. Sci Rep 2021; 11:23018. [PMID: 34837037 PMCID: PMC8626496 DOI: 10.1038/s41598-021-02386-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/08/2021] [Indexed: 11/24/2022] Open
Abstract
Reef-building corals are declining due to environmental changes. Sacsin is a member of the heat shock proteins and has been reported as a candidate protein associated with the stress response in Acropora corals. Recently, high nucleotide diversity and the persistence of two divergent haplogroups of sacsin-like genes in Acropora millepora have been reported. While it was not clear when the two haplogroups have split and whether the haplogroups have persisted in only A. millepora or the other lineages in the genus Acropora. In this study, we analyzed a genomic region containing a sacsin-like gene from Acropora and Montipora species. Higher nucleotide diversity in the sacsin-like gene compared with that of surrounding regions was also observed in A. digitifera. This nucleotide diversity is derived from two divergent haplogroups of a sacsin-like gene, which are present in at least three Acropora species. The origin of these two haplogroups can be traced back before the divergence of Acropora and Montipora (119 Ma). Although the link between exceptionally high genetic variation in sacsin-like genes and functional differences in sacsin-like proteins is not clear, the divergent haplogroups may respond differently to envionmental stressors and serve in the adaptive phsiological ecology of these keystone species.
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Affiliation(s)
- Shiho Takahashi-Kariyazono
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, 240-0193, Japan.
| | - Yohey Terai
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, 240-0193, Japan.
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18
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Soto D, De Palmas S, Ho M, Denis V, Allen Chen C. A molecular census of early-life stage scleractinian corals in shallow and mesophotic zones. Ecol Evol 2021; 11:14573-14584. [PMID: 34765126 PMCID: PMC8571570 DOI: 10.1002/ece3.8122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/06/2022] Open
Abstract
The decline of coral reefs has fueled interest in determining whether mesophotic reefs can shield against disturbances and help replenish deteriorated shallower reefs. In this study, we characterized spatial (horizontal and vertical) and seasonal patterns of diversity in coral recruits from Dabaisha and Guiwan reefs at Ludao, Taiwan. Concrete blocks supporting terra-cotta tiles were placed at shallow (15m) and mesophotic (40m) depths, during 2016-2018. Half of the tiles were retrieved and replaced biannually over three 6-month surveys (short-term); the remainder retrieved at the end of the 18-month (long-term) survey. 451 recruits were located using fluorescent censusing and identified by DNA barcoding. Barcoding the mitochondrial cytochrome oxidase I (COI) gene resulted in 17 molecular operational taxonomic units (MOTUs). To obtain taxonomic resolution to the generic level, Pocillopora were phylotyped using the mitochondrial open reading frame (ORF), resolving eight MOTUs. Acropora, Isopora, and Montipora recruits were identified by the nuclear PaxC intron, yielding ten MOTUs. Overall, 35 MOTUs were generated and were comprised primarily of Pocillopora and, in fewer numbers, Acropora, Isopora, Pavona, Montipora, Stylophora, among others. 40% of MOTUs recruited solely within mesophotic reefs while 20% were shared by both depth zones. MOTUs recruiting across a broad depth distribution appear consistent with the hypothesis of mesophotic reefs acting as a refuge for shallow-water coral reefs. In contrast, Acropora and Isopora MOTUs were structured across depth zones representing an exception to this hypothesis. This research provides an imperative assessment of coral recruitment in understudied mesophotic reefs and imparts insight into the refuge hypothesis.
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Affiliation(s)
- Derek Soto
- Biodiversity ProgramTaiwan International Graduate ProgramAcademia Sinica and National Taiwan Normal UniversityTaipeiTaiwan
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Department of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Stéphane De Palmas
- Biodiversity ProgramTaiwan International Graduate ProgramAcademia Sinica and National Taiwan Normal UniversityTaipeiTaiwan
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Department of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Ming‐Jay Ho
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Green Island Marine Research StationAcademia SinicaLudao, Taitung CountyTaiwan
| | - Vianney Denis
- Institute of OceanographyNational Taiwan UniversityTaipeiTaiwan
| | - Chaolun Allen Chen
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Department of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
- Department of Life ScienceTung Hai UniversityTaichungTaiwan
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19
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Broad scale proteomic analysis of heat-destabilised symbiosis in the hard coral Acropora millepora. Sci Rep 2021; 11:19061. [PMID: 34561509 PMCID: PMC8463592 DOI: 10.1038/s41598-021-98548-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023] Open
Abstract
Coral reefs across the globe are threatened by warming oceans. The last few years have seen the worst mass coral bleaching events recorded, with more than one quarter of all reefs irreversibly impacted. Considering the widespread devastation, we need to increase our efforts to understanding the physiological and metabolic shifts underlying the breakdown of this important symbiotic ecosystem. Here, we investigated the proteome (PRIDE accession # PXD011668) of both host and symbionts of the reef-building coral Acropora millepora exposed to ambient (~ 28 °C) and elevated temperature (~ 32 °C for 2 days, following a five-day incremental increase) and explored associated biomolecular changes in the symbiont, with the aim of gaining new insights into the mechanisms underpinning the collapse of the coral symbiosis. We identified 1,230 unique proteins (774 host and 456 symbiont) in the control and thermally stressed corals, of which 107 significantly increased and 125 decreased in abundance under elevated temperature relative to the control. Proteins involved in oxidative stress and proteolysis constituted 29% of the host proteins that increased in abundance, with evidence of impairment to endoplasmic reticulum and cytoskeletal regulation proteins. In the symbiont, we detected a decrease in proteins responsible for photosynthesis and energy production (33% of proteins decreased in abundance), yet minimal signs of oxidative stress or proteolysis. Lipid stores increased > twofold despite reduction in photosynthesis, suggesting reduced translocation of carbon to the host. There were significant changes in proteins related to symbiotic state, including proteins linked to nitrogen metabolism in the host and the V-ATPase (-0.6 fold change) known to control symbiosome acidity. These results highlight key differences in host and symbiont proteomic adjustments under elevated temperature and identify two key proteins directly involved in bilateral nutrient exchange as potential indicators of symbiosis breakdown.
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20
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Morphological stasis masks ecologically divergent coral species on tropical reefs. Curr Biol 2021; 31:2286-2298.e8. [PMID: 33811819 DOI: 10.1016/j.cub.2021.03.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/13/2021] [Accepted: 03/09/2021] [Indexed: 01/07/2023]
Abstract
Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa) and uncover, through a comprehensive genomic and phenotypic assessment, that it comprises morphologically indistinguishable but ecologically divergent lineages. Demographic modeling based on whole-genome resequencing indicated that morphological crypsis (across micro- and macromorphological traits) was due to ancient morphological stasis rather than recent divergence. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid molecular assay revealed differentiation of their ecological distributions. Leveraging "common garden" conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate the presence of ecologically and phenotypically divergent coral species without substantial morphological differentiation and provide new leads into the potential mechanisms facilitating such divergence. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.
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21
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Ma H, Liao H, Dellisanti W, Sun Y, Chan LL, Zhang L. Characterizing the Host Coral Proteome of Platygyra carnosa Using Suspension Trapping (S-Trap). J Proteome Res 2021; 20:1783-1791. [PMID: 33630606 DOI: 10.1021/acs.jproteome.0c00812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Stony corals form the foundation of coral reefs, which are of prominent ecological and economic significance. A robust workflow for investigating the coral proteome is essential in understanding coral biology. Here we investigated different preparative workflows and characterized the proteome of Platygyra carnosa, a common stony coral of the South China Sea. We found that a combination of bead homogenization with suspension trapping (S-Trap) preparation could yield more than 2700 proteins from coral samples. Annotation using a P. carnosa transcriptome database revealed that the majority of proteins were from the coral host cells (2140, 212, and 427 proteins from host coral, dinoflagellate, and other compartments, respectively). Label-free quantification and functional annotations indicated that a high proportion were involved in protein and redox homeostasis. Furthermore, the S-Trap method achieved good reproducibility in quantitative analysis. Although yielding a low symbiont:host ratio, the method is efficient in characterizing the coral host proteomic landscape, which provides a foundation to explore the molecular basis of the responses of coral host tissues to environmental stressors.
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Affiliation(s)
- Haiying Ma
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.,State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China.,Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Herui Liao
- Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Walter Dellisanti
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.,State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China.,Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Yanni Sun
- Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Leo Lai Chan
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.,State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China.,Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong, China
| | - Liang Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
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22
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Boilard A, Dubé CE, Gruet C, Mercière A, Hernandez-Agreda A, Derome N. Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont. Microorganisms 2020; 8:microorganisms8111682. [PMID: 33138319 PMCID: PMC7692791 DOI: 10.3390/microorganisms8111682] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Coral microbiomes are critical to holobiont health and functioning, but the stability of host–microbial interactions is fragile, easily shifting from eubiosis to dysbiosis. The heat-induced breakdown of the symbiosis between the host and its dinoflagellate algae (that is, “bleaching”), is one of the most devastating outcomes for reef ecosystems. Yet, bleaching tolerance has been observed in some coral species. This review provides an overview of the holobiont’s diversity, explores coral thermal tolerance in relation to their associated microorganisms, discusses the hypothesis of adaptive dysbiosis as a mechanism of environmental adaptation, mentions potential solutions to mitigate bleaching, and suggests new research avenues. More specifically, we define coral bleaching as the succession of three holobiont stages, where the microbiota can (i) maintain essential functions for holobiont homeostasis during stress and/or (ii) act as a buffer to mitigate bleaching by favoring the recruitment of thermally tolerant Symbiodiniaceae species (adaptive dysbiosis), and where (iii) environmental stressors exceed the buffering capacity of both microbial and dinoflagellate partners leading to coral death.
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Affiliation(s)
- Aurélie Boilard
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
| | - Caroline E. Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA;
- Correspondence: (C.E.D.); (N.D.)
| | - Cécile Gruet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
| | - Alexandre Mercière
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66860 Perpignan CEDEX, France;
- Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea, French Polynesia
| | | | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada
- Correspondence: (C.E.D.); (N.D.)
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Gene Expression and Photophysiological Changes in Pocillopora acuta Coral Holobiont Following Heat Stress and Recovery. Microorganisms 2020; 8:microorganisms8081227. [PMID: 32806647 PMCID: PMC7463449 DOI: 10.3390/microorganisms8081227] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 12/25/2022] Open
Abstract
The ability of corals to withstand changes in their surroundings is a critical survival mechanism for coping with environmental stress. While many studies have examined responses of the coral holobiont to stressful conditions, its capacity to reverse responses and recover when the stressor is removed is not well-understood. In this study, we investigated among-colony responses of Pocillopora acuta from two sites with differing distance to the mainland (Kusu (closer to the mainland) and Raffles Lighthouse (further from the mainland)) to heat stress through differential expression analysis of target genes and quantification of photophysiological metrics. We then examined how these attributes were regulated after the stressor was removed to assess the recovery potential of P. acuta. The fragments that were subjected to heat stress (2 °C above ambient levels) generally exhibited significant reduction in their endosymbiont densities, but the extent of recovery following stress removal varied depending on natal site and colony. There were minimal changes in chl a concentration and maximum quantum yield (Fv/Fm, the proportion of variable fluorescence (Fv) to maximum fluorescence (Fm)) in heat-stressed corals, suggesting that the algal endosymbionts’ Photosystem II was not severely compromised. Significant changes in gene expression levels of selected genes of interest (GOI) were observed following heat exposure and stress removal among sites and colonies, including Actin, calcium/calmodulin-dependent protein kinase type IV (Camk4), kinesin-like protein (KIF9), and small heat shock protein 16.1 (Hsp16.1). The most responsive GOIs were Actin, a major component of the cytoskeleton, and the adaptive immune-related Camk4 which both showed significant reduction following heat exposure and subsequent upregulation during the recovery phase. Our findings clearly demonstrate specific responses of P. acuta in both photophysiological attributes and gene expression levels, suggesting differential capacity of P. acuta corals to tolerate heat stress depending on the colony, so that certain colonies may be more resilient than others.
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Fuller ZL, Mocellin VJL, Morris LA, Cantin N, Shepherd J, Sarre L, Peng J, Liao Y, Pickrell J, Andolfatto P, Matz M, Bay LK, Przeworski M. Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science 2020; 369:369/6501/eaba4674. [PMID: 32675347 DOI: 10.1126/science.aba4674] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
Although reef-building corals are declining worldwide, responses to bleaching vary within and across species and are partly heritable. Toward predicting bleaching response from genomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora We obtained whole-genome sequences for 237 phenotyped samples collected at 12 reefs along the Great Barrier Reef, among which we inferred little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin We conducted a genome-wide association study of visual bleaching score for 213 samples, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for genomics-based approaches in conservation strategies.
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Affiliation(s)
- Zachary L Fuller
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| | | | - Luke A Morris
- Australian Institute of Marine Science, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Neal Cantin
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Jihanne Shepherd
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Luke Sarre
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Julie Peng
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Yi Liao
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | | | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Mikhail Matz
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, QLD, Australia.
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY, USA. .,Department of Systems Biology, Columbia University, New York, NY, USA.,Program for Mathematical Genomics, Columbia University, New York, NY, USA
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25
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Mayfield AB. Proteomic Signatures of Corals from Thermodynamic Reefs. Microorganisms 2020; 8:microorganisms8081171. [PMID: 32752238 PMCID: PMC7465421 DOI: 10.3390/microorganisms8081171] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/30/2022] Open
Abstract
Unlike most parts of the world, coral reefs of Taiwan’s deep south have generally been spared from climate change-induced degradation. This has been linked to the oceanographically unique nature of Nanwan Bay, where intense upwelling occurs. Specifically, large-amplitude internal waves cause shifts in temperature of 6–9 °C over the course of several hours, and the resident corals not only thrive under such conditions, but they have also been shown to withstand multi-month laboratory incubations at experimentally elevated temperatures. To gain insight into the sub-cellular basis of acclimation to upwelling, proteins isolated from reef corals (Seriatopora hystrix) featured in laboratory-based reciprocal transplant studies in which corals from upwelling and non-upwelling control reefs (<20 km away) were exposed to stable or variable temperature regimes were analyzed via label-based proteomics (iTRAQ). Corals exposed to their “native” temperature conditions for seven days (1) demonstrated highest growth rates and (2) were most distinct from one another with respect to their protein signatures. The latter observation was driven by the fact that two Symbiodiniaceae lipid trafficking proteins, sec1a and sec34, were marginally up-regulated in corals exposed to their native temperature conditions. Alongside the marked degree of proteomic “site fidelity” documented, this dataset sheds light on the molecular mechanisms underlying acclimatization to thermodynamically extreme conditions in situ.
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Affiliation(s)
- Anderson B. Mayfield
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, 4301 Rickenbacker Causeway, Miami, FL 33149, USA; or ; Tel.: +1-337-501-1976
- Cooperative Institutes for Marine and Atmospheric Studies, University of Miami, 4300 Rickenbacker Causeway, Miami, FL 33149, USA
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26
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Reynolds DA, Yoo MJ, Dixson DL, Ross C. Exposure to the Florida red tide dinoflagellate, Karenia brevis, and its associated brevetoxins induces ecophysiological and proteomic alterations in Porites astreoides. PLoS One 2020; 15:e0228414. [PMID: 32032360 PMCID: PMC7006924 DOI: 10.1371/journal.pone.0228414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/14/2020] [Indexed: 01/27/2023] Open
Abstract
As reef-building corals are increasingly being exposed to persistent threats that operate on both regional and global scales, there is a pressing need to better understand the complex processes that diminish coral populations. This study investigated the impacts of the Florida red tide dinoflagellate Karenia brevis and associated brevetoxins on selected facets of coral biology using Porites astreoides as a model system. When provided with choice assays, P. astreoides larvae were shown to actively avoid seawater containing red tide (5×105 cells L-1–7.6×106 cells L-1) or purified brevetoxins (0.018 μg mL-1 brevetoxin-2 and 0.0018 μg mL-1 brevetoxin-3). However, forced exposure to similar treatments induced time-dependent physiological and behavioral changes that were captured by PAM fluorometry and settlement and survival assays, respectively. Adult fragments of P. astreoides exposed to red tide or associated brevetoxins displayed signs of proteomic alterations that were characterized by the use of an iTRAQ-based quantitative proteomic analysis. The novel use of this technique with P. astreoides demonstrated that protein regulation was highly contingent upon biological versus chemical treatment (i.e. live K. brevis vs. solely brevetoxin exposure) and that several broad pathways associated with cell stress were affected including redox homeostasis, protein folding, energy metabolism and reactive oxygen species production. The results herein provide new insight into the ecology, behavior and sublethal stress of reef-building corals in response to K. brevis exposure and underscore the importance of recognizing the potential of red tide to act as a regional stressor to these important foundation species.
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Affiliation(s)
- David A. Reynolds
- Department of Biology, University of North Florida, Jacksonville, Florida, United States of America
| | - Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, New York, United States of America
| | - Danielle L. Dixson
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, United States of America
| | - Cliff Ross
- Department of Biology, University of North Florida, Jacksonville, Florida, United States of America
- * E-mail:
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27
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Jiang J, Lu Y. Metabolite profiling of Breviolum minutum in response to acidification. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 213:105215. [PMID: 31200330 DOI: 10.1016/j.aquatox.2019.05.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Coral reefs are in significant decline globally due to climate change and environmental pollution. The ocean is becoming more acidic due to rising atmospheric pCO2, and ocean acidification is considered a major threat to coral reefs. However, little is known about the exact mechanism by which acidification impacts coral symbiosis. As an important component of the symbiotic association, to explore the responses of symbionts could greatly enhance our understanding of this issue. The present work aimed to identify metabolomic changes of Breviolum minutum in acidification (low pH) condition, and investigate the underlying mechanisms responsible. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was applied to determine metabolite profiles after exposure to ambient and acidic conditions. We analysed the resulting metabolite data, and acidification appeared to have little effect on photosynthetic parameters, but it inhibited growth. Marked alterations in metabolite pools were observed in response to acidification that may be important in acclimation to climate change. Acidification may affect the biosynthesis of amino acids and proteins, and thereby inhibit the growth of B. minutum. Metabolites identified using this approach provide targets for future analyses aimed at understanding the responses of Symbiodiniaceae to environmental disturbance.
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Affiliation(s)
- Jiaoyun Jiang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou 570228, Hainan, China; College of Life Sciences, Guangxi Normal University, Guilin 541004, Guangxi, China.
| | - Yandu Lu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou 570228, Hainan, China.
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28
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Evans JS. The Biomineralization Proteome: Protein Complexity for a Complex Bioceramic Assembly Process. Proteomics 2019; 19:e1900036. [DOI: 10.1002/pmic.201900036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/04/2019] [Indexed: 12/20/2022]
Affiliation(s)
- John Spencer Evans
- Laboratory for Chemical PhysicsDepartment of Skeletal and Craniofacial BiologyNew York University College of Dentistry New York NY 10010 USA
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29
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Hernández-Elizárraga VH, Olguín-López N, Hernández-Matehuala R, Ocharán-Mercado A, Cruz-Hernández A, Guevara-González RG, Caballero-Pérez J, Ibarra-Alvarado C, Sánchez-Rodríguez J, Rojas-Molina A. Comparative Analysis of the Soluble Proteome and the Cytolytic Activity of Unbleached and Bleached Millepora complanata ("Fire Coral") from the Mexican Caribbean. Mar Drugs 2019; 17:E393. [PMID: 31277227 PMCID: PMC6669453 DOI: 10.3390/md17070393] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 01/24/2023] Open
Abstract
Coral bleaching caused by global warming has resulted in massive damage to coral reefs worldwide. Studies addressing the consequences of elevated temperature have focused on organisms of the class Anthozoa, and up to now, there is little information regarding the mechanisms by which reef forming Hydrozoans face thermal stress. In this study, we carried out a comparative analysis of the soluble proteome and the cytolytic activity of unbleached and bleached Millepora complanata ("fire coral") that inhabited reef colonies exposed to the 2015-2016 El Niño-Southern Oscillation in the Mexican Caribbean. A differential proteomic response involving proteins implicated in key cellular processes, such as glycolysis, DNA repair, stress response, calcium homeostasis, exocytosis, and cytoskeleton organization was found in bleached hydrocorals. Four of the proteins, whose levels increased in bleached specimens, displayed sequence similarity to a phospholipase A2, an astacin-like metalloprotease, and two pore forming toxins. However, a protein, which displayed sequence similarity to a calcium-independent phospholipase A2, showed lower levels in bleached cnidarians. Accordingly, the hemolytic effect of the soluble proteome of bleached hydrocorals was significantly higher, whereas the phospholipase A2 activity was significantly reduced. Our results suggest that bleached M. complanata is capable of increasing its toxins production in order to balance the lack of nutrients supplied by its symbionts.
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Affiliation(s)
- Víctor Hugo Hernández-Elizárraga
- Posgrado en Ciencias Químico Biológicas, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, C.P. 76010 Querétaro, Querétaro, México
| | - Norma Olguín-López
- Posgrado en Ciencias Químico Biológicas, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, C.P. 76010 Querétaro, Querétaro, México
| | - Rosalina Hernández-Matehuala
- Posgrado en Ciencias Químico Biológicas, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, C.P. 76010 Querétaro, Querétaro, México
| | - Andrea Ocharán-Mercado
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, C.P. 76010 Querétaro, Querétaro, México
| | - Andrés Cruz-Hernández
- Laboratorio de Biología Molecular. Escuela de Agronomía, Universidad de La Salle Bajío, Av. Universidad 15 602, Colonia Lomas del Campestre, C.P. 37150 León, Guanajuato, México
| | - Ramón Gerardo Guevara-González
- C.A Ingeniería de Biosistemas, Facultad de Ingeniería-Campus Amazcala, Universidad Autónoma de Querétaro, Carr. Chichimequillas-Amazcala Km. 1, S/N, C.P. 76265 Amazcala, El Marqués, Querétaro, México
| | - Juan Caballero-Pérez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, C.P. 76010 Querétaro, Querétaro, México
| | - César Ibarra-Alvarado
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, C.P. 76010 Querétaro, Querétaro, México
| | - Judith Sánchez-Rodríguez
- Unidad Académica de Sistemas Arrecifales Puerto Morelos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Prolongación Niños Héroes S/N, Puerto Morelos, C.P. 77580 Quintana Roo, México
| | - Alejandra Rojas-Molina
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, C.P. 76010 Querétaro, Querétaro, México.
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30
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Ricci CA, Kamal AHM, Chakrabarty JK, Fuess LE, Mann WT, Jinks LR, Brinkhuis V, Chowdhury SM, Mydlarz LD. Proteomic Investigation of a Diseased Gorgonian Coral Indicates Disruption of Essential Cell Function and Investment in Inflammatory and Other Immune Processes. Integr Comp Biol 2019; 59:830-844. [DOI: 10.1093/icb/icz107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Abstract
As scleractinian coral cover declines in the face of increased frequency in disease outbreaks, future reefs may become dominated by octocorals. Understanding octocoral disease responses and consequences is therefore necessary if we are to gain insight into the future of ecosystem services provided by coral reefs. In Florida, populations of the octocoral Eunicea calyculata infected with Eunicea black disease (EBD) were observed in the field in the fall of 2011. This disease was recognized by a stark, black pigmentation caused by heavy melanization. Histological preparations of E. calyculata infected with EBD demonstrated granular amoebocyte (GA) mobilization, melanin granules in much of the GA population, and the presence of fungal hyphae penetrating coral tissue. Previous transcriptomic analysis also identified immune trade-offs evidenced by increased immune investment at the expense of growth. Our investigation utilized proteogenomic techniques to reveal decreased investment in general cell signaling while increasing energy production for immune responses. Inflammation was also prominent in diseased E. calyculata and sheds light on factors driving the extreme phenotype observed with EBD. With disease outbreaks continuing to increase in frequency, our results highlight new targets within the cnidarian immune system and provide a framework for understanding transcriptomics in the context of an organismal disease phenotype and its protein expression.
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Affiliation(s)
- Contessa A Ricci
- Department of Biology, University of Texas at Arlington, Arlington, 501 S Nedderman Dr., TX 76010, USA
| | - Abu Hena Mostafa Kamal
- Department of Chemistry and Biochemistry, University of Texas at Arlington, 700 Planetarium Pl, Arlington, TX 76010, USA
| | - Jayanta Kishor Chakrabarty
- Department of Chemistry and Biochemistry, University of Texas at Arlington, 700 Planetarium Pl, Arlington, TX 76010, USA
| | - Lauren E Fuess
- Department of Ecology and Evolutionary Biology University of Connecticut, Storrs, CT 06269, USA
| | - Whitney T Mann
- Department of Biology, University of Texas at Arlington, Arlington, 501 S Nedderman Dr., TX 76010, USA
| | - Lea R Jinks
- Department of Biology, University of Texas at Arlington, Arlington, 501 S Nedderman Dr., TX 76010, USA
| | - Vanessa Brinkhuis
- Washington State Department of Ecology—Central Regional Office, 1250 Alder Street, Union Gap, WA 98903, USA
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, 700 Planetarium Pl, Arlington, TX 76010, USA
| | - Laura D Mydlarz
- Department of Biology, University of Texas at Arlington, Arlington, 501 S Nedderman Dr., TX 76010, USA
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Abstract
Herein we propose an ambitious confrontation of the current coral reef crisis through the establishment of a "Coral Hospital." In an analogous manner to a human hospital, "sick" corals will first be diagnosed either in situ or in the hospital's diagnostic "clinic" such that the root cause of illness can be discerned (e.g., disease, high temperatures, or pollutant stress). Then, corals will be "treated" (when necessary) and allowed to "convalesce" in precisely controlled coral husbandry facilities. Upon "rehabilitation," the recovered corals will be returned to their home reef (if this reef was not found to have degraded), or, alternatively, to a site featuring oceanographic conditions favoring a high level of health, as determined by husbandry experiments performed in other hospital "wards." When possible, diagnostic data from the sick corals (i.e., the underlying cause of sickness) will be used to guide environmental remediation schemes aimed at promoting coral resilience in the ocean. If the home reef improves to an appreciable extent during the time the corals are "hospitalized," these corals could be replanted there upon rehabilitation. Regardless of the site of outplanting, recuperated corals will be monitored over time to validate the "quality of care" in the hospital. In the event that the home reefs suffer to such an extent that environmental mitigation is no longer possible, coral gametes will be collected and cryopreserved such that they may be fertilized, reared in officinarum, and later reseeded once/if global marine conditions again permit coral survival.
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Affiliation(s)
- Anderson B Mayfield
- 1Taiwan Coral Research Center, National Museum of Marine Biology and Aquarium, Checheng, Taiwan
| | - Sujune Tsai
- 2Department of Post-Modern Agriculture, Ming-Dao University, Beidou, Taiwan
| | - Chiahsin Lin
- 1Taiwan Coral Research Center, National Museum of Marine Biology and Aquarium, Checheng, Taiwan.,3Graduate Institute of Marine Biology, National Dong-Hwa University, Checheng, Taiwan
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32
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Olguín-López N, Hérnandez-Elizárraga VH, Hernández-Matehuala R, Cruz-Hernández A, Guevara-González R, Caballero-Pérez J, Ibarra-Alvarado C, Rojas-Molina A. Impact of El Niño-Southern Oscillation 2015-2016 on the soluble proteomic profile and cytolytic activity of Millepora alcicornis ("fire coral") from the Mexican Caribbean. PeerJ 2019; 7:e6593. [PMID: 30918755 PMCID: PMC6428038 DOI: 10.7717/peerj.6593] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/09/2019] [Indexed: 12/24/2022] Open
Abstract
Reef-forming cnidarians are extremely susceptible to the “bleaching” phenomenon caused by global warming. The effect of elevated seawater temperature has been extensively studied on Anthozoans; however, to date the impact of thermal stress on the expression of genes and proteins in Hydrozoan species has not been investigated. The present study aimed to determine the differential proteomic profile of Millepora alcicornis, which inhabits the Mexican Caribbean, in response to the El Niño-Southern Oscillation 2015–2016. Additionally, the cytolytic activity of the soluble proteomes obtained from normal and bleached M. alcicornis was assessed. Bleached specimens showed decreased symbiont’s density and chlorophyll a and c2 levels. After bleaching, we observed a differential expression of 17 key proteins, tentatively identified as related to exocytosis, calcium homeostasis, cytoskeletal organization, and potential toxins, including a metalloprotease, a phospholipase A2 (PLA2), and an actitoxin. Although, some of the differentially expressed proteins included potential toxins, the hemolytic, PLA2, and proteolytic activities elicited by the soluble proteomes from bleached and normal specimens were not significantly different. The present study provides heretofore-unknown evidence that thermal stress produces a differential expression of proteins involved in essential cellular processes of Hydrozoan species. Even though our results showed an over-expression of some potential toxin-related proteins, the cytolytic effect (as assessed by hemolytic, PLA2, and caseinolytic activities) was not increased in bleached M. alcicornis, which suggests that the cytolysis is mainly produced by toxins whose expression was not affected by temperature stress. These findings allow hypothesizing that this hydrocoral is able to prey heterotrophically when suffering from moderate bleaching, giving it a better chance to withstand the effects of high temperature.
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Affiliation(s)
- Norma Olguín-López
- Posgrado en Ciencias Químico Biológicas-Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, Querétaro, Mexico.,Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, Querétaro, Mexico
| | - Víctor Hugo Hérnandez-Elizárraga
- Posgrado en Ciencias Químico Biológicas-Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, Querétaro, Mexico.,Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, Querétaro, Mexico
| | - Rosalina Hernández-Matehuala
- Posgrado en Ciencias Químico Biológicas-Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, Querétaro, Mexico.,Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, Querétaro, Mexico
| | - Andrés Cruz-Hernández
- Laboratorio de Biología Molecular-Escuela de Agronomía, Universidad De la Salle Bajío, León, Guanajuato, México
| | - Ramón Guevara-González
- C.A Ingeniería de Biosistemas-Facultad de Ingeniería-Campus Amazcala, Universidad Autónoma de Querétaro, Querétaro, Querétaro, Mexico
| | - Juan Caballero-Pérez
- Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, Querétaro, Mexico
| | - César Ibarra-Alvarado
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, Querétaro, Mexico
| | - Alejandra Rojas-Molina
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, Querétaro, Mexico
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Détrée C, Haddad I, Demey-Thomas E, Vinh J, Lallier FH, Tanguy A, Mary J. Global host molecular perturbations upon in situ loss of bacterial endosymbionts in the deep-sea mussel Bathymodiolus azoricus assessed using proteomics and transcriptomics. BMC Genomics 2019; 20:109. [PMID: 30727955 PMCID: PMC6364412 DOI: 10.1186/s12864-019-5456-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/16/2019] [Indexed: 01/16/2023] Open
Abstract
Background Colonization of deep-sea hydrothermal vents by most invertebrates was made efficient through their adaptation to a symbiotic lifestyle with chemosynthetic bacteria, the primary producers in these ecosystems. Anatomical adaptations such as the establishment of specialized cells or organs have been evidenced in numerous deep-sea invertebrates. However, very few studies detailed global inter-dependencies between host and symbionts in these ecosystems. In this study, we proposed to describe, using a proteo-transcriptomic approach, the effects of symbionts loss on the deep-sea mussel Bathymodiolus azoricus’ molecular biology. We induced an in situ depletion of symbionts and compared the proteo-transcriptome of the gills of mussels in three conditions: symbiotic mussels (natural population), symbiont-depleted mussels and aposymbiotic mussels. Results Global proteomic and transcriptomic results evidenced a global disruption of host machinery in aposymbiotic organisms. We observed that the total number of proteins identified decreased from 1118 in symbiotic mussels to 790 in partially depleted mussels and 761 in aposymbiotic mussels. Using microarrays we identified 4300 transcripts differentially expressed between symbiont-depleted and symbiotic mussels. Among these transcripts, 799 were found differentially expressed in aposymbiotic mussels and almost twice as many in symbiont-depleted mussels as compared to symbiotic mussels. Regarding apoptotic and immune system processes – known to be largely involved in symbiotic interactions – an overall up-regulation of associated proteins and transcripts was observed in symbiont-depleted mussels. Conclusion Overall, our study showed a global impairment of host machinery and an activation of both the immune and apoptotic system following symbiont-depletion. One of the main assumptions is the involvement of symbiotic bacteria in the inhibition and regulation of immune and apoptotic systems. As such, symbiotic bacteria may increase their lifespan in gill cells while managing the defense of the holobiont against putative pathogens.
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Affiliation(s)
- Camille Détrée
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile.,Sorbonne Université, CNRS, Lab. Adaptation et Diversité en Milieu Marin, Team ABICE, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Iman Haddad
- ESPCI ParisTech, CNRS, USR 3149, Spectrométrie de Masse Biologique et Protéomique, 75231, Paris Cedex 05, France
| | - Emmanuelle Demey-Thomas
- ESPCI ParisTech, CNRS, USR 3149, Spectrométrie de Masse Biologique et Protéomique, 75231, Paris Cedex 05, France
| | - Joëlle Vinh
- ESPCI ParisTech, CNRS, USR 3149, Spectrométrie de Masse Biologique et Protéomique, 75231, Paris Cedex 05, France
| | - François H Lallier
- Sorbonne Université, CNRS, Lab. Adaptation et Diversité en Milieu Marin, Team ABICE, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Arnaud Tanguy
- Sorbonne Université, CNRS, Lab. Adaptation et Diversité en Milieu Marin, Team ABICE, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Jean Mary
- Sorbonne Université, CNRS, Lab. Adaptation et Diversité en Milieu Marin, Team ABICE, Station Biologique de Roscoff, 29680, Roscoff, France.
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Morse D, Tse SPK, Lo SCL. Exploring dinoflagellate biology with high-throughput proteomics. HARMFUL ALGAE 2018; 75:16-26. [PMID: 29778222 DOI: 10.1016/j.hal.2018.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
Dinoflagellates are notorious for their ability to form the harmful algal blooms known as "red tides," yet the mechanisms underlying bloom formation remain poorly understood. Despite recent advances in nucleic acid sequencing, which have generated transcriptomes from a wide range of species exposed to a variety of different conditions, measuring changes in RNA levels have not generally produced great insight into dinoflagellate cell biology or environmental physiology, nor do we have a thorough grasp on the molecular events underpinning bloom formation. Not only is the transcriptomic response of dinoflagellates to environmental change generally muted, but there is a markedly low degree of congruency between mRNA expression and protein expression in dinoflagellates. Herein we discuss the application of high-throughput proteomics to the study of dinoflagellate biology. By profiling the cellular protein complement (the proteome) instead of mRNA (the transcriptome), the biomolecular events that underlie the changes of phenotypes can be more readily evaluated, as proteins directly determine the structure and the function of the cell. Recent advances in proteomics have seen this technique become a high-throughput method that is now able to provide a perspective different from the more commonly employed nucleic acid sequencing. We suggest that the time is ripe to exploit these new technologies in addressing the many mysteries of dinoflagellate biology, such as how the symbiotic dinoflagellate inhabiting reef corals acclimate to increases in temperature, as well as how harmful algal blooms are initiated at the sub-cellular level. Furthermore, as dinoflagellates are not the only eukaryotes that demonstrate muted transcriptional responses, the techniques addressed within this review are amenable to a wide array of organisms.
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Affiliation(s)
- David Morse
- Institut de Recherche en biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Canada.
| | - Sirius P K Tse
- Shenzhen Key Laboratory of Food Biological Safety Control, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong
| | - Samuel C L Lo
- Shenzhen Key Laboratory of Food Biological Safety Control, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong
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Mayfield AB, Chen YJ, Lu CY, Chen CS. Exploring the Environmental Physiology of the Indo-Pacific Reef Coral <em>Seriatopora hystrix</em> with Differential Proteomics. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/ojms.2018.82012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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