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Hu Y, Zhang Z, Sun S, Sun Y, Huang H, Zhou W, Wei F. Toward the generation of pure coral genomes with experimental and bioinformatic improvements. Innovation (N Y) 2024; 5:100643. [PMID: 38912429 PMCID: PMC11192846 DOI: 10.1016/j.xinn.2024.100643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/16/2024] [Indexed: 06/25/2024] Open
Abstract
Stony corals, the primary architects of coral reef ecosystems, are largely underrepresented in omics studies despite their importance. The presence of endosymbiotic Symbiodiniaceae algae complicates the extraction of pure coral DNA, posing a challenge for genomic research. Here, we devised a comprehensive methodological framework that incorporates various experimental treatments to achieve 99% purity in coral DNA extraction and a robust bioinformatics pipeline to guarantee the assembly of high-quality, contamination-free coral genomes. Validation of our framework using Acropora millepora samples demonstrated its efficacy and superiority in obtaining high-quality pure coral genomes using easily accessible adult colony. This integrated framework serves as a critical foundation for large-scale genome-enabled research on stony corals, providing insight into coral evolution and conservation.
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Affiliation(s)
- Yisi Hu
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Zhiwei Zhang
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shuyan Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Youfang Sun
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Hui Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Fuwen Wei
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang 330029, China
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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2
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Khen A, Wall CB, Smith JE. Standardization of in situ coral bleaching measurements highlights the variability in responses across genera, morphologies, and regions. PeerJ 2023; 11:e16100. [PMID: 37810774 PMCID: PMC10552771 DOI: 10.7717/peerj.16100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/25/2023] [Indexed: 10/10/2023] Open
Abstract
Marine heatwaves and regional coral bleaching events have become more frequent and severe across the world's oceans over the last several decades due to global climate change. Observational studies have documented spatiotemporal variation in the responses of reef-building corals to thermal stress within and among taxa across geographic scales. Although many tools exist for predicting, detecting, and quantifying coral bleaching, it remains difficult to compare bleaching severity (e.g., percent cover of bleached surface areas) among studies and across species or regions. For this review, we compiled over 2,100 in situ coral bleaching observations representing 87 reef-building coral genera and 250 species of common morphological groups from a total of 74 peer-reviewed scientific articles, encompassing three broad geographic regions (Atlantic, Indian, and Pacific Oceans). While bleaching severity was found to vary by region, genus, and morphology, we found that both genera and morphologies responded differently to thermal stress across regions. These patterns were complicated by (i) inconsistent methods and response metrics across studies; (ii) differing ecological scales of observations (i.e., individual colony-level vs. population or community-level); and (iii) temporal variability in surveys with respect to the onset of thermal stress and the chronology of bleaching episodes. To improve cross-study comparisons, we recommend that future surveys prioritize measuring bleaching in the same individual coral colonies over time and incorporate the severity and timing of warming into their analyses. By reevaluating and standardizing the ways in which coral bleaching is quantified, researchers will be able to track responses to marine heatwaves with increased rigor, precision, and accuracy.
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Affiliation(s)
- Adi Khen
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Christopher B. Wall
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Jennifer E. Smith
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
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3
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Bay LK, Gilmour J, Muir B, Hardisty PE. Management approaches to conserve Australia's marine ecosystem under climate change. Science 2023; 381:631-636. [PMID: 37561873 DOI: 10.1126/science.adi3023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/23/2023] [Indexed: 08/12/2023]
Abstract
Australia's coastal marine ecosystems have a deep cultural significance to Indigenous Australians, include multiple World Heritage sites, and support the nation's rapidly growing blue economy. Yet, increasing local pressures and global climate change are expected to undermine the biological, social, cultural, and economic value of these ecosystems within a human generation. Mitigating the causes of climate change is the most urgent action to secure their future; however, conventional and new management actions will play roles in preserving ecosystem function and value until that is achieved. This includes strategies codeveloped with Indigenous Australians that are guided by traditional ecological knowledge and a modeling and decision support framework. We provide examples of developments at one of Australia's most iconic ecosystems, the Great Barrier Reef, where recent, large block funding supports research, governance, and engagement to accelerate the development of tools for management under climate change.
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Affiliation(s)
- Line K Bay
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - James Gilmour
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Bob Muir
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Paul E Hardisty
- Australian Institute of Marine Science, Townsville, QLD, Australia
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4
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Llamas A, Leon-Miranda E, Tejada-Jimenez M. Microalgal and Nitrogen-Fixing Bacterial Consortia: From Interaction to Biotechnological Potential. PLANTS (BASEL, SWITZERLAND) 2023; 12:2476. [PMID: 37447037 PMCID: PMC10346606 DOI: 10.3390/plants12132476] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
Microalgae are used in various biotechnological processes, such as biofuel production due to their high biomass yields, agriculture as biofertilizers, production of high-value-added products, decontamination of wastewater, or as biological models for carbon sequestration. The number of these biotechnological applications is increasing, and as such, any advances that contribute to reducing costs and increasing economic profitability can have a significant impact. Nitrogen fixing organisms, often called diazotroph, also have great biotechnological potential, mainly in agriculture as an alternative to chemical fertilizers. Microbial consortia typically perform more complex tasks than monocultures and can execute functions that are challenging or even impossible for individual strains or species. Interestingly, microalgae and diazotrophic organisms are capable to embrace different types of symbiotic associations. Certain corals and lichens exhibit this symbiotic relationship in nature, which enhances their fitness. However, this relationship can also be artificially created in laboratory conditions with the objective of enhancing some of the biotechnological processes that each organism carries out independently. As a result, the utilization of microalgae and diazotrophic organisms in consortia is garnering significant interest as a potential alternative for reducing production costs and increasing yields of microalgae biomass, as well as for producing derived products and serving biotechnological purposes. This review makes an effort to examine the associations of microalgae and diazotrophic organisms, with the aim of highlighting the potential of these associations in improving various biotechnological processes.
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Affiliation(s)
- Angel Llamas
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain; (E.L.-M.); (M.T.-J.)
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5
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Elder H, Million WC, Bartels E, Krediet CJ, Muller EM, Kenkel CD. Long-term maintenance of a heterologous symbiont association in Acropora palmata on natural reefs. THE ISME JOURNAL 2023; 17:486-489. [PMID: 36510006 PMCID: PMC9938269 DOI: 10.1038/s41396-022-01349-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
The sensitivity of reef-building coral to elevated temperature is a function of their symbiosis with dinoflagellate algae in the family Symbiodiniaceae. Changes in the composition of the endosymbiont community in response to thermal stress can increase coral thermal tolerance. Consequently, this mechanism is being investigated as a human-assisted intervention for rapid acclimation of coral in the face of climate change. Successful establishment of novel symbioses that increase coral thermal tolerance have been demonstrated in laboratory conditions; however, it is unclear how long these heterologous relationships persist in nature. Here, we test the persistence of a novel symbiosis between Acropora palmata and Durusdinium spp. from Mote Marine Laboratory's ex situ nursery by outplanting clonal replicates (ramets) of five A. palmata host genotypes to natural reefs in the lower Florida Keys. Amplicon sequencing analysis of ITS2-type profiles revealed that the majority of surviving ramets remained dominated by Durusdinium spp. two years after transplantation. However, 15% of ramets, including representatives of all genotypes, exhibited some degree of symbiont shuffling or switching at six of eight sites, including complete takeover by site-specific strains of the native symbiont, Symbiodinium fitti. The predominant long-term stability of the novel symbiosis supports the potential effectiveness of symbiont modification as a management tool. Although, the finding that 6-7 year-old coral can alter symbiont community composition in the absence of bleaching indicates that Symbiodiniaceae communities are indeed capable of great flexibility under ambient conditions.
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Affiliation(s)
- Holland Elder
- University of Southern California, 3616 Trousdale Parkway, AHF 231, Los Angeles, CA, 90089, USA.
| | - Wyatt C Million
- University of Southern California, 3616 Trousdale Parkway, AHF 231, Los Angeles, CA, 90089, USA
| | - Erich Bartels
- Mote Marine Laboratory, 24244 Overseas Hwy, Summerland Key, FL, 33042, USA
| | - Cory J Krediet
- Eckerd College, 4200 54th Ave., St. Petersburg, FL, 33711, USA
| | - Erinn M Muller
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA
| | - Carly D Kenkel
- University of Southern California, 3616 Trousdale Parkway, AHF 231, Los Angeles, CA, 90089, USA
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6
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Bove CB, Ingersoll MV, Davies SW. Help Me, Symbionts, You're My Only Hope: Approaches to Accelerate our Understanding of Coral Holobiont Interactions. Integr Comp Biol 2022; 62:1756-1769. [PMID: 36099871 DOI: 10.1093/icb/icac141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/24/2022] [Accepted: 09/05/2022] [Indexed: 01/05/2023] Open
Abstract
Tropical corals construct the three-dimensional framework for one of the most diverse ecosystems on the planet, providing habitat to a plethora of species across taxa. However, these ecosystem engineers are facing unprecedented challenges, such as increasing disease prevalence and marine heatwaves associated with anthropogenic global change. As a result, major declines in coral cover and health are being observed across the world's oceans, often due to the breakdown of coral-associated symbioses. Here, we review the interactions between the major symbiotic partners of the coral holobiont-the cnidarian host, algae in the family Symbiodiniaceae, and the microbiome-that influence trait variation, including the molecular mechanisms that underlie symbiosis and the resulting physiological benefits of different microbial partnerships. In doing so, we highlight the current framework for the formation and maintenance of cnidarian-Symbiodiniaceae symbiosis, and the role that immunity pathways play in this relationship. We emphasize that understanding these complex interactions is challenging when you consider the vast genetic variation of the cnidarian host and algal symbiont, as well as their highly diverse microbiome, which is also an important player in coral holobiont health. Given the complex interactions between and among symbiotic partners, we propose several research directions and approaches focused on symbiosis model systems and emerging technologies that will broaden our understanding of how these partner interactions may facilitate the prediction of coral holobiont phenotype, especially under rapid environmental change.
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Affiliation(s)
- Colleen B Bove
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA 02215, USA
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Sheahan K, Zarate D, Chalifour B, Li J. Intraspecific transfer of algal symbionts can occur in photosymbiotic Exaiptasia sea anemones. Symbiosis 2022. [DOI: 10.1007/s13199-022-00891-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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8
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Puntin G, Sweet M, Fraune S, Medina M, Sharp K, Weis VM, Ziegler M. Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont. Microbiol Mol Biol Rev 2022; 86:e0005322. [PMID: 36287022 PMCID: PMC9769930 DOI: 10.1128/mmbr.00053-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.
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Affiliation(s)
- Giulia Puntin
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Sebastian Fraune
- Institute for Zoology and Organismic Interactions, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Koty Sharp
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, Rhode Island, USA
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
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9
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Grupstra CGB, Lemoine NP, Cook C, Correa AMS. Thank you for biting: dispersal of beneficial microbiota through 'antagonistic' interactions. Trends Microbiol 2022; 30:930-939. [PMID: 35393166 DOI: 10.1016/j.tim.2022.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/23/2022]
Abstract
Multicellular organisms harbor populations of microbial symbionts; some of these symbionts can be dispersed through the feeding activities of consumers. Studies of consumer-mediated microbiota dispersal generally focus on pathogenic microorganisms; the dispersal of beneficial microorganisms has received less attention, especially in the context of 'antagonistic' trophic interactions (e.g., herbivory, parasitism, predation). Yet, this 'trophic transmission' of beneficial symbionts has significant implications for microbiota assembly and resource species (e.g., prey) health. For example, trophic transmission of microorganisms could assist with environmental acclimatization and help resource species to suppress other consumers or competitors. Here, we highlight model systems and approaches that have revealed these potential 'silver-linings' of antagonism as well as opportunities and challenges for future research.
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Affiliation(s)
- C G B Grupstra
- BioSciences Department, Rice University, Houston, TX 77098, USA.
| | - N P Lemoine
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; Department of Zoology, Milwaukee Public Museum, Milwaukee, WI 53233, USA
| | - C Cook
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - A M S Correa
- BioSciences Department, Rice University, Houston, TX 77098, USA
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