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Garcia B, Becker CC, Weber L, Swarr GJ, Kido Soule MC, Apprill A, Kujawinski EB. Benzoyl Chloride Derivatization Advances the Quantification of Dissolved Polar Metabolites on Coral Reefs. J Proteome Res 2024; 23:2041-2053. [PMID: 38782401 PMCID: PMC11166142 DOI: 10.1021/acs.jproteome.4c00049] [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] [Received: 01/22/2024] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Extracellular chemical cues constitute much of the language of life among marine organisms, from microbes to mammals. Changes in this chemical pool serve as invisible signals of overall ecosystem health and disruption to this finely tuned equilibrium. In coral reefs, the scope and magnitude of the chemicals involved in maintaining reef equilibria are largely unknown. Processes involving small, polar molecules, which form the majority components of labile dissolved organic carbon, are often poorly captured using traditional techniques. We employed chemical derivatization with mass spectrometry-based targeted exometabolomics to quantify polar dissolved phase metabolites on five coral reefs in the U.S. Virgin Islands. We quantified 45 polar exometabolites, demonstrated their spatial variability, and contextualized these findings in terms of geographic and benthic cover differences. By comparing our results to previously published coral reef exometabolomes, we show the novel quantification of 23 metabolites, including central carbon metabolism compounds (e.g., glutamate) and novel metabolites such as homoserine betaine. We highlight the immense potential of chemical derivatization-based exometabolomics for quantifying labile chemical cues on coral reefs and measuring molecular level responses to environmental stressors. Overall, improving our understanding of the composition and dynamics of reef exometabolites is vital for effective ecosystem monitoring and management strategies.
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Affiliation(s)
- Brianna
M. Garcia
- Department of Marine Chemistry
and Geochemistry, Woods Hole Oceanographic
Institution, Woods
Hole, Massachusetts 02543, United States
| | | | - Laura Weber
- Department of Marine Chemistry
and Geochemistry, Woods Hole Oceanographic
Institution, Woods
Hole, Massachusetts 02543, United States
| | - Gretchen J. Swarr
- Department of Marine Chemistry
and Geochemistry, Woods Hole Oceanographic
Institution, Woods
Hole, Massachusetts 02543, United States
| | - Melissa C. Kido Soule
- Department of Marine Chemistry
and Geochemistry, Woods Hole Oceanographic
Institution, Woods
Hole, Massachusetts 02543, United States
| | - Amy Apprill
- Department of Marine Chemistry
and Geochemistry, Woods Hole Oceanographic
Institution, Woods
Hole, Massachusetts 02543, United States
| | - Elizabeth B. Kujawinski
- Department of Marine Chemistry
and Geochemistry, Woods Hole Oceanographic
Institution, Woods
Hole, Massachusetts 02543, United States
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2
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Williams J, Pettorelli N, Hartmann AC, Quinn RA, Plaisance L, O'Mahoney M, Meyer CP, Fabricius KE, Knowlton N, Ransome E. Decline of a distinct coral reef holobiont community under ocean acidification. MICROBIOME 2024; 12:75. [PMID: 38627822 PMCID: PMC11022381 DOI: 10.1186/s40168-023-01683-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/28/2023] [Indexed: 04/19/2024]
Abstract
BACKGROUND Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH - an important global coral reef stressor - can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome. RESULTS We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2 seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation. CONCLUSIONS We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem changed. Video Abstract.
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Affiliation(s)
- Jake Williams
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Buckhurst Road, Ascot, SL5 7PY, UK
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Nathalie Pettorelli
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Aaron C Hartmann
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Laetitia Plaisance
- Laboratoire Evolution Et Diversité Biologique, CNRS/UPS, Toulouse, France
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Michael O'Mahoney
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Chris P Meyer
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | | | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Emma Ransome
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Buckhurst Road, Ascot, SL5 7PY, UK.
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3
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Mannochio-Russo H, Swift SOI, Nakayama KK, Wall CB, Gentry EC, Panitchpakdi M, Caraballo-Rodriguez AM, Aron AT, Petras D, Dorrestein K, Dorrestein TK, Williams TM, Nalley EM, Altman-Kurosaki NT, Martinelli M, Kuwabara JY, Darcy JL, Bolzani VS, Wegley Kelly L, Mora C, Yew JY, Amend AS, McFall-Ngai M, Hynson NA, Dorrestein PC, Nelson CE. Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses. Commun Biol 2023; 6:896. [PMID: 37653089 PMCID: PMC10471604 DOI: 10.1038/s42003-023-05230-1] [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] [Received: 12/01/2022] [Accepted: 08/08/2023] [Indexed: 09/02/2023] Open
Abstract
The dominant benthic primary producers in coral reef ecosystems are complex holobionts with diverse microbiomes and metabolomes. In this study, we characterize the tissue metabolomes and microbiomes of corals, macroalgae, and crustose coralline algae via an intensive, replicated synoptic survey of a single coral reef system (Waimea Bay, O'ahu, Hawaii) and use these results to define associations between microbial taxa and metabolites specific to different hosts. Our results quantify and constrain the degree of host specificity of tissue metabolomes and microbiomes at both phylum and genus level. Both microbiome and metabolomes were distinct between calcifiers (corals and CCA) and erect macroalgae. Moreover, our multi-omics investigations highlight common lipid-based immune response pathways across host organisms. In addition, we observed strong covariation among several specific microbial taxa and metabolite classes, suggesting new metabolic roles of symbiosis to further explore.
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Affiliation(s)
- Helena Mannochio-Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, SP, 14800-060, Brazil.
| | - Sean O I Swift
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
| | - Kirsten K Nakayama
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Christopher B Wall
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
- Ecology Behavior and Evolution Section, Department of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Andrés M Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Kathleen Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Taylor M Williams
- Marine Option Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Eileen M Nalley
- Hawai'i Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Noam T Altman-Kurosaki
- School of Biological Sciences, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | | | - Jeff Y Kuwabara
- Marine Option Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - John L Darcy
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Vanderlan S Bolzani
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, SP, 14800-060, Brazil
| | - Linda Wegley Kelly
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, CA, USA
| | - Camilo Mora
- Geography, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Joanne Y Yew
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Anthony S Amend
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Margaret McFall-Ngai
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Nicole A Hynson
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
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4
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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: 6] [Impact Index Per Article: 6.0] [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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5
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Jurburg SD, Buscot F, Chatzinotas A, Chaudhari NM, Clark AT, Garbowski M, Grenié M, Hom EFY, Karakoç C, Marr S, Neumann S, Tarkka M, van Dam NM, Weinhold A, Heintz-Buschart A. The community ecology perspective of omics data. MICROBIOME 2022; 10:225. [PMID: 36510248 PMCID: PMC9746134 DOI: 10.1186/s40168-022-01423-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract.
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Affiliation(s)
- Stephanie D Jurburg
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Institute of Biology, Leipzig University, Leipzig, Germany.
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research- UFZ, Halle, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Narendrakumar M Chaudhari
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Adam T Clark
- Institute of Biology, University of Graz, Graz, Austria
| | - Magda Garbowski
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Botany, University of Wyoming, Wyoming, USA
| | - Matthias Grenié
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Erik F Y Hom
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, Oxford, Mississippi, USA
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Biology, Indiana University, Indiana, USA
| | - Susanne Marr
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle Wittenberg, Halle, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, Halle, Germany
| | - Steffen Neumann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, Halle, Germany
| | - Mika Tarkka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research- UFZ, Halle, Germany
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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6
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Pei J, Chen S, Yu K, Hu J, Wang Y, Zhang J, Qin Z, Zhang R, Kuo TH, Chung HH, Hsu CC. Metabolomics Characterization of Scleractinia Corals with Different Life-History Strategies: A Case Study about Pocillopora meandrina and Seriatopora hystrix in the South China Sea. Metabolites 2022; 12:metabo12111079. [PMID: 36355162 PMCID: PMC9693324 DOI: 10.3390/metabo12111079] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/05/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022] Open
Abstract
Life-history strategies play a critical role in susceptibility to environmental stresses for Scleractinia coral. Metabolomics, which is capable of determining the metabolic responses of biological systems to genetic and environmental changes, is competent for the characterization of species’ biological traits. In this study, two coral species (Pocillopora meandrina and Seriatopora hystrix in the South China Sea) with different life-history strategies (“competitive” and “weedy”) were targeted, and untargeted mass spectrometry metabolomics combined with molecular networking was applied to characterize their differential metabolic pathways. The results show that lyso-platelet activating factors (lyso-PAFs), diacylglyceryl carboxyhydroxymethylcholine (DGCC), aromatic amino acids, and sulfhydryl compounds were more enriched in P. meandrina, whereas new phospholipids, dehydrated phosphoglycerol dihydroceramide (de-PG DHC), monoacylglycerol (MAG), fatty acids (FA) (C < 18), short peptides, and guanidine compounds were more enriched in S. hystrix. The metabolic pathways involved immune response, energy metabolism, cellular membrane structure regulation, oxidative stress system, secondary metabolite synthesis, etc. While the immune system (lysoPAF) and secondary metabolite synthesis (aromatic amino acids and sulfhydryl compounds) facilitates fast growth and resistance to environmental stressors of P. meandrina, the cell membrane structure (structural lipids), energy storage (storage lipids), oxidative stress system (short peptides), and secondary metabolite synthesis (guanidine compounds) are beneficial to the survival of S. hystrix in harsh conditions. This study contributes to the understanding of the potential molecular traits underlying life-history strategies of different coral species.
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Affiliation(s)
- Jiying Pei
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530000, China
| | - Shiguo Chen
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530000, China
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530000, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519080, China
- Correspondence:
| | - Junjie Hu
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530000, China
| | - Yitong Wang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530000, China
| | - Jingjing Zhang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530000, China
| | - Zhenjun Qin
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530000, China
| | - Ruijie Zhang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530000, China
| | - Ting-Hao Kuo
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Hsin-Hsiang Chung
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
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7
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MacKnight NJ, Dimos BA, Beavers KM, Muller EM, Brandt ME, Mydlarz LD. Disease resistance in coral is mediated by distinct adaptive and plastic gene expression profiles. SCIENCE ADVANCES 2022; 8:eabo6153. [PMID: 36179017 PMCID: PMC9524840 DOI: 10.1126/sciadv.abo6153] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Infectious diseases are an increasing threat to coral reefs, resulting in altered community structure and hindering the functional contributions of disease-susceptible species. We exposed seven reef-building coral species from the Caribbean to white plague disease and determined processes involved in (i) lesion progression, (ii) within-species gene expression plasticity, and (iii) expression-level adaptation among species that lead to differences in disease risk. Gene expression networks enriched in immune genes and cytoskeletal arrangement processes were correlated to lesion progression rates. Whether or not a coral developed a lesion was mediated by plasticity in genes involved in extracellular matrix maintenance, autophagy, and apoptosis, while resistant coral species had constitutively higher expression of intracellular protein trafficking. This study offers insight into the process involved in lesion progression and within- and between-species dynamics that lead to differences in disease risk that is evident on current Caribbean reefs.
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Affiliation(s)
- Nicholas J. MacKnight
- University of Texas at Arlington, 337 Life Science Building, Arlington, TX 76019, USA
| | - Bradford A. Dimos
- University of Texas at Arlington, 337 Life Science Building, Arlington, TX 76019, USA
| | - Kelsey M. Beavers
- University of Texas at Arlington, 337 Life Science Building, Arlington, TX 76019, USA
| | - Erinn M. Muller
- Mote Marine Laboratory, 1600 Ken Thompson Pkwy, Sarasota, FL 34236, USA
| | - Marilyn E. Brandt
- University of the Virgin Islands, 2 John Brewers Bay, St. Thomas, VI 00802, USA
| | - Laura D. Mydlarz
- University of Texas at Arlington, 337 Life Science Building, Arlington, TX 76019, USA
- Corresponding author.
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8
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Tang CH, Shi SH, Li HH, Lin CY, Wang WH. Lipid profiling of coral symbiosomes in response to copper-induced carbon limitation: A metabolic effect of algal symbionts on the host immune status. CHEMOSPHERE 2022; 293:133673. [PMID: 35063552 DOI: 10.1016/j.chemosphere.2022.133673] [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: 09/22/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Copper micropollutants are known to constrain coral's assimilation of carbonate, affecting the carbon available to algal symbionts and thus inducing a light stress. However, little is known regarding the physiological relevance of lipid metabolism in coral symbiotic algae in a carbon-limited state. Membrane lipids exhibit multiple physicochemical properties that are collectively responsible for the dynamic structure of cells depending on the physiological demands of the circumstances. To gain insight into lipid metabolism's importance in this regard, glycerophosphocholine (GPC) profiling of symbiosomes in coral (Seriatopora caliendrum) exposed to environmentally relevant copper levels (2.2-7.5 μg/L) for 4 days was performed in this study. Notably, reducing the number of 22:6-processing GPCs and increasing that of lyso-GPCs likely addressed the demands of metabolizing excess light energy, such as affecting the membrane dynamics to promote mitochondrial uncoupling. The decrease in 22:6-processing GPCs additionally protected cellular membranes from elevated oxidative stress, reducing their susceptibility to peroxidation and offsetting oxidized lipid-induced effects on membrane dynamics. The change in plasmanylcholines specifically localized within the symbiosome membrane also met the membrane requirements for responding to oxidative stress conditions. Moreover, increasing the 20:4-possessing plasmanylcholines and lysoplasmanylcholines and reducing the 22:6-possessing plasmanylcholines likely resulted in an imbalance of the immune reaction, influencing the coral-algae symbiosis given the role of such plasmanylcholines in cell signaling. In summary, carbon limitations induced by copper enrichment lead to a shift in the membrane lipid profile of coral symbiosomes, accommodating themselves to light stress conditions while compromising the symbiosis's stability.
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Affiliation(s)
- Chuan-Ho Tang
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan; Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan.
| | - Shu-Han Shi
- Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
| | - Hsing-Hui Li
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan; Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Ching-Yu Lin
- Institute of Environmental Health, National Taiwan University, Taipei City, Taiwan
| | - Wei-Hsien Wang
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan; Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
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9
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Abstract
BACKGROUND Marine ecosystems are hosts to a vast array of organisms, being among the most richly biodiverse locations on the planet. The study of these ecosystems is very important, as they are not only a significant source of food for the world but also have, in recent years, become a prolific source of compounds with therapeutic potential. Studies of aspects of marine life have involved diverse fields of marine science, and the use of metabolomics as an experimental approach has increased in recent years. As part of the "omics" technologies, metabolomics has been used to deepen the understanding of interactions between marine organisms and their environment at a metabolic level and to discover new metabolites produced by these organisms. AIM OF REVIEW This review provides an overview of the use of metabolomics in the study of marine organisms. It also explores the use of metabolomics tools common to other fields such as plants and human metabolomics that could potentially contribute to marine organism studies. It deals with the entire process of a metabolomic study, from sample collection considerations, metabolite extraction, analytical techniques, and data analysis. It also includes an overview of recent applications of metabolomics in fields such as marine ecology and drug discovery and future perspectives of its use in the study of marine organisms. KEY SCIENTIFIC CONCEPTS OF REVIEW The review covers all the steps involved in metabolomic studies of marine organisms including, collection, extraction methods, analytical tools, statistical analysis, and dereplication. It aims to provide insight into all aspects that a newcomer to the field should consider when undertaking marine metabolomics.
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Affiliation(s)
- Lina M Bayona
- Natural Products Laboratory, Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Marine Biodiversity, 2333 CR, Leiden, The Netherlands
- Institute of Environmental Sciences, Leiden University, 2333 CC, Leiden, The Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
- College of Pharmacy, Kyung Hee University, 130-701, Seoul, Republic of Korea.
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10
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Zhang S, Song W, Nothias LF, Couvillion SP, Webster N, Thomas T. Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts. MICROBIOME 2022; 10:22. [PMID: 35105377 PMCID: PMC8805237 DOI: 10.1186/s40168-021-01220-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Sponges are ancient sessile metazoans, which form with their associated microbial symbionts a complex functional unit called a holobiont. Sponges are a rich source of chemical diversity; however, there is limited knowledge of which holobiont members produce certain metabolites and how they may contribute to chemical interactions. To address this issue, we applied non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) and gas chromatography mass spectrometry (GC-MS) to either whole sponge tissue or fractionated microbial cells from six different, co-occurring sponge species. RESULTS Several metabolites were commonly found or enriched in whole sponge tissue, supporting the notion that sponge cells produce them. These include 2-methylbutyryl-carnitine, hexanoyl-carnitine and various carbohydrates, which may be potential food sources for microorganisms, as well as the antagonistic compounds hymenialdisine and eicosatrienoic acid methyl ester. Metabolites that were mostly observed or enriched in microbial cells include the antioxidant didodecyl 3,3'-thiodipropionate, the antagonistic compounds docosatetraenoic acid, and immune-suppressor phenylethylamide. This suggests that these compounds are mainly produced by the microbial members in the sponge holobiont, and are potentially either involved in inter-microbial competitions or in defenses against intruding organisms. CONCLUSIONS This study shows how different chemical functionality is compartmentalized between sponge hosts and their microbial symbionts and provides new insights into how chemical interactions underpin the function of sponge holobionts. Video abstract.
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Affiliation(s)
- Shan Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052 Australia
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, 2052 Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, 2052 Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052 Australia
| | - Louis-Félix Nothias
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | - Sneha P. Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, 2052 Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052 Australia
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11
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Jorissen H, Galand PE, Bonnard I, Meiling S, Raviglione D, Meistertzheim AL, Hédouin L, Banaigs B, Payri CE, Nugues MM. Coral larval settlement preferences linked to crustose coralline algae with distinct chemical and microbial signatures. Sci Rep 2021; 11:14610. [PMID: 34272460 PMCID: PMC8285400 DOI: 10.1038/s41598-021-94096-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
The resilience of coral reefs is dependent on the ability of corals to settle after disturbances. While crustose coralline algae (CCA) are considered important substrates for coral settlement, it remains unclear whether coral larvae respond to CCA metabolites and microbial cues when selecting sites for attachment and metamorphosis. This study tested the settlement preferences of an abundant coral species (Acropora cytherea) against six different CCA species from three habitats (exposed, subcryptic and cryptic), and compared these preferences with the metabolome and microbiome characterizing the CCA. While all CCA species induced settlement, only one species (Titanoderma prototypum) significantly promoted settlement on the CCA surface, rather than on nearby dead coral or plastic surfaces. This species had a very distinct bacterial community and metabolomic fingerprint. Furthermore, coral settlement rates and the CCA microbiome and metabolome were specific to the CCA preferred habitat, suggesting that microbes and/or chemicals serve as environmental indicators for coral larvae. Several amplicon sequence variants and two lipid classes—glycoglycerolipids and betaine lipids—present in T. prototypum were identified as potential omic cues influencing coral settlement. These results support that the distinct microbiome and metabolome of T. prototypum may promote the settlement and attachment of coral larvae.
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Affiliation(s)
- Hendrikje Jorissen
- CRIOBE USR 3278, EPHE-UPVD-CNRS-PSL, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
| | - Pierre E Galand
- CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Sorbonne Université, 66500, Banyuls-sur-Mer, France
| | - Isabelle Bonnard
- CRIOBE USR 3278, EPHE-UPVD-CNRS-PSL, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.,Laboratoire d'Excellence « CORAIL», 98729, Papetoai, Moorea, French Polynesia
| | - Sonora Meiling
- CRIOBE USR 3278, EPHE-UPVD-CNRS-PSL, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.,University of the Virgin Islands, St Thomas, 00802-6004, Virgin Islands (U.S.)
| | - Delphine Raviglione
- CRIOBE USR 3278, EPHE-UPVD-CNRS-PSL, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Anne-Leila Meistertzheim
- CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Sorbonne Université, 66500, Banyuls-sur-Mer, France.,Plastic@Sea, Observatoire Océanologique de Banyuls, 66650, Banyuls-sur-Mer, France
| | - Laetitia Hédouin
- CRIOBE USR 3278, EPHE-UPVD-CNRS-PSL, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.,Laboratoire d'Excellence « CORAIL», 98729, Papetoai, Moorea, French Polynesia
| | - Bernard Banaigs
- CRIOBE USR 3278, EPHE-UPVD-CNRS-PSL, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.,Laboratoire d'Excellence « CORAIL», 98729, Papetoai, Moorea, French Polynesia
| | | | - Maggy M Nugues
- CRIOBE USR 3278, EPHE-UPVD-CNRS-PSL, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.,Laboratoire d'Excellence « CORAIL», 98729, Papetoai, Moorea, French Polynesia
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12
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Geier B, Oetjen J, Ruthensteiner B, Polikarpov M, Gruber-Vodicka HR, Liebeke M. Connecting structure and function from organisms to molecules in small-animal symbioses through chemo-histo-tomography. Proc Natl Acad Sci U S A 2021; 118:e2023773118. [PMID: 34183413 PMCID: PMC8300811 DOI: 10.1073/pnas.2023773118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Our understanding of metabolic interactions between small symbiotic animals and bacteria or parasitic eukaryotes that reside within their bodies is extremely limited. This gap in knowledge originates from a methodological challenge, namely to connect histological changes in host tissues induced by beneficial and parasitic (micro)organisms to the underlying metabolites. We addressed this challenge and developed chemo-histo-tomography (CHEMHIST), a culture-independent approach to connect anatomic structure and metabolic function in millimeter-sized symbiotic animals. CHEMHIST combines chemical imaging of metabolites based on mass spectrometry imaging (MSI) and microanatomy-based micro-computed X-ray tomography (micro-CT) on the same animal. Both high-resolution MSI and micro-CT allowed us to correlate the distribution of metabolites to the same animal's three-dimensional (3D) histology down to submicrometer resolutions. Our protocol is compatible with tissue-specific DNA sequencing and fluorescence in situ hybridization for the taxonomic identification and localization of the associated micro(organisms). Building CHEMHIST upon in situ imaging, we sampled an earthworm from its natural habitat and created an interactive 3D model of its physical and chemical interactions with bacteria and parasitic nematodes in its tissues. Combining MSI and micro-CT, we present a methodological groundwork for connecting metabolic and anatomic phenotypes of small symbiotic animals that often represent keystone species for ecosystem functioning.
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Affiliation(s)
- Benedikt Geier
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany;
| | - Janina Oetjen
- MALDI Imaging Lab, University of Bremen, 28334 Bremen, Germany
| | | | - Maxim Polikarpov
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | | | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany;
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13
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Henry JA, Khattri RB, Guingab-Cagmat J, Merritt ME, Garrett TJ, Patterson JT, Lohr KE. Intraspecific variation in polar and nonpolar metabolite profiles of a threatened Caribbean coral. Metabolomics 2021; 17:60. [PMID: 34143280 DOI: 10.1007/s11306-021-01808-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/29/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Research aimed at understanding intraspecific variation among corals could substantially increase understanding of coral biology and improve outcomes of active restoration efforts. Metabolomics is useful for identifying physiological drivers leading to variation among genotypes and has the capacity to improve our selection of candidate corals that express phenotypes beneficial to restoration. OBJECTIVES Our study aims to compare metabolomic profiles among known, unique genotypes of the threatened coral Acropora cervicornis. In doing so, we seek information related to the physiological characteristics driving variation among genotypes, which could aid in identifying genets with desirable traits for restoration. METHODS We applied proton nuclear magnetic resonance (1H-NMR) and liquid chromatography-mass spectrometry (LC-MS) to identify and compare metabolomic profiles for seven unique genotypes of A. cervicornis that previously exhibited phenotypic variation in a common garden coral nursery. RESULTS Significant variation in polar and nonpolar metabolite profiles was found among A. cervicornis genotypes. Despite difficulties identifying all significant metabolites driving separation among genotypes, our data support previous findings and further suggest metabolomic profiles differ among various genotypes of the threatened species A. cervicornis. CONCLUSION The implementation of metabolomic analyses allowed identification of several key metabolites driving separation among genotypes and expanded our understanding of the A. cervicornis metabolome. Although our research is specific to A. cervicornis, these findings have broad relevance for coral biology and active restoration. Furthermore, this study provides specific information on the understudied A. cervicornis metabolome and further confirmation that differences in metabolome structure could drive phenotypic variation among genotypes.
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Affiliation(s)
- Joseph A Henry
- Program in Fisheries and Aquatic Sciences, School of Forest, Fisheries, and Geomatics Sciences, University of Florida/IFAS, 7922 NW 71st Street, Gainesville, FL, 32653, USA.
| | - Ram B Khattri
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Joy Guingab-Cagmat
- Southeast Center for Integrated Metabolomics, Clinical and Translational Science Institute, University of Florida, Gainesville, FL, USA
| | - Matthew E Merritt
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Joshua T Patterson
- Program in Fisheries and Aquatic Sciences, School of Forest, Fisheries, and Geomatics Sciences, University of Florida/IFAS, 7922 NW 71st Street, Gainesville, FL, 32653, USA
- The Florida Aquarium, Center for Conservation, 529 Estuary Shore Ln, Apollo Beach, FL, 33572-2205, USA
| | - Kathryn E Lohr
- Office of National Marine Sanctuaries, National Oceanic and Atmospheric Administration, Silver Spring, MD, USA
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14
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Andrade Rodriguez N, Moya A, Jones R, Miller DJ, Cooke IR. The Significance of Genotypic Diversity in Coral Competitive Interaction: A Transcriptomic Perspective. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.659360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Competitive interactions shape coral assemblages and govern the dynamics of coral ecosystems. Although competition is an ecological concept, the outcomes of competitive interactions are ultimately determined by patterns of gene expression. These patterns are subject to genotypic variation on both sides of any interaction. Such variation is typically treated as “noise”, but it is sometimes possible to identify patterns within it that reveal important hidden factors in an experiment. To incorporate genotypic variation into the investigation of coral competitive interactions, we used RNA-sequencing to study changes in gene expression in a hard coral (Porites cylindrica) resulting from non-contact competition experiment with a soft coral (Lobophytum pauciflorum). Hard coral genotype explained the largest proportion of variation between samples; however, it was also possible to detect gene expression changes in 76 transcripts resulting from interaction with the soft coral. In addition, we found a group of 20 short secreted proteins that were expressed as a coordinated unit in three interacting Porites-Lobophytum pairs. The presence of this secretion response was idiosyncratic in that it could not be predicted based on polyp behaviour, or the genotype of hard or soft coral alone. This study illustrates the significance of individual variation as a determinant of competitive behaviour, and also provides some intriguing glimpses into the molecular mechanisms employed by hard corals competing at a distance.
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15
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Reid T, Bergsveinson J. How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes. Front Mol Biosci 2021; 8:662888. [PMID: 34026835 PMCID: PMC8138469 DOI: 10.3389/fmolb.2021.662888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 12/01/2022] Open
Abstract
Culture-independent and meta-omics sequencing methods have shed considerable light on the so-called “microbial dark matter” of Earth’s environmental microbiome, improving our understanding of phylogeny, the tree of life, and the vast functional diversity of microorganisms. This influx of sequence data has led to refined and reimagined hypotheses about the role and importance of microbial biomass, that paradoxically, sequencing approaches alone are unable to effectively test. Post-genomic approaches such as metabolomics are providing more sensitive and insightful data to unravel the fundamental operations and intricacies of microbial communities within aquatic systems. We assert that the implementation of integrated post-genomic approaches, specifically metabolomics and metatranscriptomics, is the new frontier of environmental microbiology and ecology, expanding conventional assessments toward a holistic systems biology understanding. Progressing beyond siloed phylogenetic assessments and cataloging of metabolites, toward integrated analysis of expression (metatranscriptomics) and activity (metabolomics) is the most effective approach to provide true insight into microbial contributions toward local and global ecosystem functions. This data in turn creates opportunity for improved regulatory guidelines, biomarker discovery and better integration of modeling frameworks. To that end, critical aquatic environmental issues related to climate change, such as ocean warming and acidification, contamination mitigation, and macro-organism health have reasonable opportunity of being addressed through such an integrative approach. Lastly, we argue that the “post-genomics” paradigm is well served to proactively address the systemic technical issues experienced throughout the genomics revolution and focus on collaborative assessment of field-wide experimental standards of sampling, bioinformatics and statistical treatments.
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Affiliation(s)
- Thomas Reid
- Canada Centre for Inland Waters, Environment and Climate Change Canada, Burlington, ON, Canada
| | - Jordyn Bergsveinson
- National Hydrology Research Centre, Environment and Climate Change Canada, Saskatoon, SK, Canada
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16
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Metabolomic signatures of coral bleaching history. Nat Ecol Evol 2021; 5:495-503. [PMID: 33558733 DOI: 10.1038/s41559-020-01388-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/18/2020] [Indexed: 12/13/2022]
Abstract
Coral bleaching has a profound impact on the health and function of reef ecosystems, but the metabolomic effects of coral bleaching are largely uncharacterized. Here, untargeted metabolomics was used to analyse pairs of adjacent Montipora capitata corals that had contrasting bleaching phenotypes during a severe bleaching event in 2015. When these same corals were sampled four years later while visually healthy, there was a strong metabolomic signature of bleaching history. This was primarily driven by betaine lipids from the symbiont, where corals that did not bleach were enriched in saturated lyso-betaine lipids. Immune modulator molecules were also altered by bleaching history in both the coral host and the algal symbiont, suggesting a shared role in partner choice and bleaching response. Metabolomics from a separate set of validation corals was able to predict the bleaching phenotype with 100% accuracy. Experimental temperature stress induced phenotype-specific responses, which magnified differences between historical bleaching phenotypes. These findings indicate that natural bleaching susceptibility is manifested in the biochemistry of both the coral animal and its algal symbiont. This metabolome difference is stable through time and results in different physiological responses to temperature stress. This work provides insight into the biochemical mechanisms of coral bleaching and presents a valuable new tool for resilience-based reef restoration.
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17
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Dittami SM, Arboleda E, Auguet JC, Bigalke A, Briand E, Cárdenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachon CMM, Griffiths SM, Harder T, Kayal E, Kazamia E, Lallier FH, Medina M, Marzinelli EM, Morganti TM, Núñez Pons L, Prado S, Pintado J, Saha M, Selosse MA, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F. A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ 2021; 9:e10911. [PMID: 33665032 PMCID: PMC7916533 DOI: 10.7717/peerj.10911] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/16/2021] [Indexed: 12/19/2022] Open
Abstract
Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
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Affiliation(s)
- Simon M Dittami
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Enrique Arboleda
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - Arite Bigalke
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Enora Briand
- Laboratoire Phycotoxines, Ifremer, Nantes, France
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Ulisse Cardini
- Integrative Marine Ecology Dept, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Johan Decelle
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRA, Grenoble, France
| | | | - Damien Eveillard
- Laboratoire des Sciences Numériques de Nantes (LS2N), Université de Nantes, CNRS, Nantes, France
| | - Claire M M Gachon
- Scottish Marine Institute, Scottish Association for Marine Science, Oban, United Kingdom
| | - Sarah M Griffiths
- School of Science and the Environment, Manchester Metropolitan University, Manchester, United Kingdom
| | | | - Ehsan Kayal
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - François H Lallier
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, United States of America
| | - Ezequiel M Marzinelli
- Ecology and Environment Research Centre, The University of Sydney, Sydney, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Sydney Institute of Marine Science, Mosman, Australia
| | | | - Laura Núñez Pons
- Section Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Soizic Prado
- Molecules of Communication and Adaptation of Microorganisms (UMR 7245), National Museum of Natural History, CNRS, Paris, France
| | - José Pintado
- Instituto de Investigaciones Marinas, CSIC, Vigo, Spain
| | - Mahasweta Saha
- Benthic Ecology, Helmholtz Center for Ocean Research, Kiel, Germany.,Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Plymouth, United Kingdom
| | - Marc-André Selosse
- National Museum of Natural History, Département Systématique et Evolution, Paris, France.,Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Derek Skillings
- Philosophy Department, University of Pennsylvania, Philadelphia, United States of America
| | - Willem Stock
- Laboratory of Protistology & Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Shinichi Sunagawa
- Dept. of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH, Zürich, Switzerland
| | - Eve Toulza
- IHPE, Univ. de Montpellier, CNRS, IFREMER, UPDV, Perpignan, France
| | - Alexey Vorobev
- CEA - Institut de Biologie François Jacob, Genoscope, Evry, France
| | - Catherine Leblanc
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Fabrice Not
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
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18
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Greene A, Leggat W, Donahue MJ, Raymundo LJ, Caldwell JM, Moriarty T, Heron SF, Ainsworth TD. Complementary sampling methods for coral histology, metabolomics and microbiome. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Austin Greene
- Hawai‘i Institute of Marine Biology University of Hawai‘i at Mānoa Kāne‘ohe HI USA
| | - William Leggat
- School of Environmental and Life Sciences The University of Newcastle Ourimbah NSW Australia
| | - Megan J. Donahue
- Hawai‘i Institute of Marine Biology University of Hawai‘i at Mānoa Kāne‘ohe HI USA
| | | | - Jamie M. Caldwell
- Hawai‘i Institute of Marine Biology University of Hawai‘i at Mānoa Kāne‘ohe HI USA
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld Australia
| | - Tess Moriarty
- School of Environmental and Life Sciences The University of Newcastle Ourimbah NSW Australia
- School of Biological, Earth and Environmental Science The University of New South Wales Randwick NSW Australia
| | - Scott F. Heron
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld Australia
- Physics and Marine Geophysical Laboratory College of Science and Engineering James Cook University Townsville Qld Australia
| | - Tracy D. Ainsworth
- School of Biological, Earth and Environmental Science The University of New South Wales Randwick NSW Australia
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19
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A tentacle for every occasion: comparing the hunting tentacles and sweeper tentacles, used for territorial competition, in the coral Galaxea fascicularis. BMC Genomics 2020; 21:548. [PMID: 32770938 PMCID: PMC7430897 DOI: 10.1186/s12864-020-06952-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/27/2020] [Indexed: 12/27/2022] Open
Abstract
Background Coral reefs are among the most diverse, complex and densely populated marine ecosystems. To survive, morphologically simple and sessile cnidarians have developed mechanisms to catch prey, deter predators and compete with adjacent corals for space, yet the mechanisms underlying these functions are largely unknown. Here, we characterize the histology, toxic activity and gene expression patterns in two different types of tentacles from the scleractinian coral Galaxea fascilcularis – catch tentacles (CTs), used to catch prey and deter predators, and sweeper tentacles (STs), specialized tentacles used for territorial aggression. Results STs exhibit more mucocytes and higher expression of mucin genes than CTs, and lack the ectodermal cilia used to deliver food to the mouth and remove debris. STs and CTs also express different sensory rhodopsin-like g-protein coupled receptors, suggesting they may employ different sensory pathways. Each tentacle type has a different complement of stinging cells (nematocytes), and the expression in the two tentacles of genes encoding structural nematocyte proteins suggests the stinging cells develop within the tentacles. CTs have higher neurotoxicity to blowfly larvae and hemolytic activity compared to the STs, consistent with a role in prey capture. In contrast, STs have higher phospholipase A2 activity, which we speculate may have a role in inducing tissue damage during territorial aggression. The expression of genes encoding cytolytic toxins (actinoporins) and phospholipases also differs between the tentacle types. Conclusions These results show that the same organism utilizes two distinct tentacle types, each equipped with a different venom apparatus and toxin composition, for prey capture and defense and for territorial aggression.
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Abstract
Vibrio coralliilyticus and Vibrio mediterranei are important coral pathogens capable of inducing serious coral damage, which increases severely when they infect the host simultaneously. This has consequences related to the dispersion of these pathogens among different locations that could enhance deleterious effects on coral reefs. However, the mechanisms underlying this synergistic interaction are unknown. The work described here provides a new perspective on the complex interactions among these two Vibrio coral pathogens, suggesting that coral infection could be a collateral effect of interspecific competition. Major implications of this work are that (i) Vibrio virulence mechanisms are activated in the absence of the host as a response to interspecific competition and (ii) release of molecules by Vibrio coral pathogens produces changes in the coral microbiome that favor the pathogenic potential of the entire Vibrio community. Thus, our results highlight that social cues and competition sensing are crucial determinants of development of coral diseases. The increase in prevalence and severity of coral disease outbreaks produced by Vibrio pathogens, and related to global warming, has seriously impacted reef-building corals throughout the oceans. The coral Oculina patagonica has been used as a model system to study coral bleaching produced by Vibrio infection. Previous data demonstrated that when two coral pathogens (Vibrio coralliilyticus and Vibrio mediterranei) simultaneously infected the coral O. patagonica, their pathogenicity was greater than when each bacterium was infected separately. Here, to understand the mechanisms underlying this synergistic effect, transcriptomic analyses of monocultures and cocultures as well as experimental infection experiments were performed. Our results revealed that the interaction between the two vibrios under culture conditions overexpressed virulence factor genes (e.g., those encoding siderophores, the type VI secretion system, and toxins, among others). Moreover, under these conditions, vibrios were also more likely to form biofilms or become motile through induction of lateral flagella. All these changes that occur as a physiological response to the presence of a competing species could favor the colonization of the host when they are present in a mixed population. Additionally, during coral experimental infections, we showed that exposure of corals to molecules released during V. coralliilyticus and V. mediterranei coculture induced changes in the coral microbiome that favored damage to coral tissue and increased the production of lyso-platelet activating factor. Therefore, we propose that competition sensing, defined as the physiological response to detection of harm or to the presence of a competing Vibrio species, enhances the ability of Vibrio coral pathogens to invade their host and cause tissue necrosis.
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21
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Roach TNF, Little M, Arts MGI, Huckeba J, Haas AF, George EE, Quinn RA, Cobián-Güemes AG, Naliboff DS, Silveira CB, Vermeij MJA, Kelly LW, Dorrestein PC, Rohwer F. A multiomic analysis of in situ coral-turf algal interactions. Proc Natl Acad Sci U S A 2020; 117:13588-13595. [PMID: 32482859 PMCID: PMC7306781 DOI: 10.1073/pnas.1915455117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.
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Affiliation(s)
- Ty N F Roach
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744;
- Biosphere 2, University of Arizona, Oracle, AZ 85739
- Department of Biology, San Diego State University, San Diego, CA 92182
- Viral Information Institute, San Diego State University, San Diego, CA 92182
| | - Mark Little
- Department of Biology, San Diego State University, San Diego, CA 92182
- Viral Information Institute, San Diego State University, San Diego, CA 92182
| | - Milou G I Arts
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE, Amsterdam, The Netherlands
- Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, 1790 AB, Den Burg, Texel, The Netherlands
- Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T1Z4
| | - Joel Huckeba
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE, Amsterdam, The Netherlands
| | - Andreas F Haas
- Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, 1790 AB, Den Burg, Texel, The Netherlands
| | - Emma E George
- Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T1Z4
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823
| | | | | | - Cynthia B Silveira
- Department of Biology, San Diego State University, San Diego, CA 92182
- Viral Information Institute, San Diego State University, San Diego, CA 92182
| | - Mark J A Vermeij
- Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, 1790 AB, Den Burg, Texel, The Netherlands
- Caribbean Research and Management of Biodiversity (CARMABI), Willemstad, Curaçao
| | | | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA 92182;
- Viral Information Institute, San Diego State University, San Diego, CA 92182
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Stien D, Suzuki M, Rodrigues AMS, Yvin M, Clergeaud F, Thorel E, Lebaron P. A unique approach to monitor stress in coral exposed to emerging pollutants. Sci Rep 2020; 10:9601. [PMID: 32541793 PMCID: PMC7295770 DOI: 10.1038/s41598-020-66117-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 04/15/2020] [Indexed: 11/29/2022] Open
Abstract
Metabolomic profiling of the hexacoral Pocillopora damicornis exposed to solar filters revealed a metabolomic signature of stress in this coral. It was demonstrated that the concentration of the known steroid (3β, 5α, 8α) -5, 8-epidioxy- ergosta- 6, 24(28) - dien- 3- ol (14) increased in response to octocrylene (OC) and ethylhexyl salicylate (ES) at 50 µg/L. Based on the overall coral response, we hypothesize that steroid 14 mediates coral response to stress. OC also specifically altered mitochondrial function at this concentration and above, while ES triggered a stress/inflammatory response at 300 µg/L and above as witnessed by the significant increases in the concentrations of polyunsaturated fatty acids, lysophosphatidylcholines and lysophosphatidylethanolamines. Benzophenone-3 increased the concentration of compound 14 at 2 mg/L, while the concentration of stress marker remained unchanged upon exposition to the other solar filters tested. Also, our results seemed to refute earlier suggestions that platelet-activating factor is involved in the coral inflammatory response.
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Affiliation(s)
- Didier Stien
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR3579, Observatoire Océanologique, 66650, Banyuls-sur-mer, France.
| | - Marcelino Suzuki
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR3579, Observatoire Océanologique, 66650, Banyuls-sur-mer, France
| | - Alice M S Rodrigues
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR3579, Observatoire Océanologique, 66650, Banyuls-sur-mer, France
| | - Marion Yvin
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR3579, Observatoire Océanologique, 66650, Banyuls-sur-mer, France
| | - Fanny Clergeaud
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR3579, Observatoire Océanologique, 66650, Banyuls-sur-mer, France
| | - Evane Thorel
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR3579, Observatoire Océanologique, 66650, Banyuls-sur-mer, France
| | - Philippe Lebaron
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR3579, Observatoire Océanologique, 66650, Banyuls-sur-mer, France
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Titus BM, Laroche R, Rodríguez E, Wirshing H, Meyer CP. Host identity and symbiotic association affects the taxonomic and functional diversity of the clownfish-hosting sea anemone microbiome. Biol Lett 2020; 16:20190738. [PMID: 32019466 PMCID: PMC7058955 DOI: 10.1098/rsbl.2019.0738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/09/2020] [Indexed: 12/17/2022] Open
Abstract
All eukaryotic life engages in symbioses with a diverse community of bacteria that are essential for performing basic life functions. In many cases, eukaryotic organisms form additional symbioses with other macroscopic eukaryotes. The tightly linked physical interactions that characterize many macroscopic symbioses create opportunities for microbial transfer, which likely affects the diversity and function of individual microbiomes, and may ultimately lead to microbiome convergence between distantly related taxa. Here, we sequence the microbiomes of five species of clownfish-hosting sea anemones that co-occur on coral reefs in the Maldives. We test the importance of evolutionary history, clownfish symbiont association, and habitat on the taxonomic and predicted functional diversity of the microbiome, and explore signals of microbiome convergence in anemone taxa that have evolved symbioses with clownfishes independently. Our data indicate that host identity and clownfish association shapes the majority of the taxonomic diversity of the clownfish-hosting sea anemone microbiome, and predicted functional microbial diversity analyses demonstrate a convergence among host anemone microbiomes, which reflect increased functional diversity over individuals that do not host clownfishes. Further, we identify upregulated predicted microbial functions that are likely affected by clownfish presence. Taken together our study potentially reveals an even deeper metabolic coupling between clownfishes and their host anemones, and what could be a previously unknown mutualistic benefit to anemones that are symbiotic with clownfishes.
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Affiliation(s)
- Benjamin M. Titus
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Robert Laroche
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Herman Wirshing
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
| | - Christopher P. Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
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Hartmann AC, Marhaver KL, Klueter A, Lovci MT, Closek CJ, Diaz E, Chamberland VF, Archer FI, Deheyn DD, Vermeij MJA, Medina M. Acquisition of obligate mutualist symbionts during the larval stage is not beneficial for a coral host. Mol Ecol 2019; 28:141-155. [PMID: 30506836 DOI: 10.1111/mec.14967] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 09/13/2018] [Accepted: 10/19/2018] [Indexed: 12/31/2022]
Abstract
Theory suggests that the direct transmission of beneficial endosymbionts (mutualists) from parents to offspring (vertical transmission) in animal hosts is advantageous and evolutionarily stable, yet many host species instead acquire their symbionts from the environment (horizontal acquisition). An outstanding question in marine biology is why some scleractinian corals do not provision their eggs and larvae with the endosymbiotic dinoflagellates that are necessary for a juvenile's ultimate survival. We tested whether the acquisition of photosynthetic endosymbionts (family Symbiodiniaceae) during the planktonic larval stage was advantageous, as is widely assumed, in the ecologically important and threatened Caribbean reef-building coral Orbicella faveolata. Following larval acquisition, similar changes occurred in host energetic lipid use and gene expression regardless of whether their symbionts were photosynthesizing, suggesting the symbionts did not provide the energetic benefit characteristic of the mutualism in adults. Larvae that acquired photosymbionts isolated from conspecific adults on their natal reef exhibited a reduction in swimming, which may interfere with their ability to find suitable settlement substrate, and also a decrease in survival. Larvae exposed to two cultured algal species did not exhibit differences in survival, but decreased their swimming activity in response to one species. We conclude that acquiring photosymbionts during the larval stage confers no advantages and can in fact be disadvantageous to this coral host. The timing of symbiont acquisition appears to be a critical component of a host's life history strategy and overall reproductive fitness, and this timing itself appears to be under selective pressure.
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Affiliation(s)
- Aaron C Hartmann
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California
| | | | | | - Michael T Lovci
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
| | - Collin J Closek
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Erika Diaz
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Valérie F Chamberland
- CARMABI Foundation, Willemstad, Curaçao.,Aquatic Microbiology/Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.,SECORE International, Hilliard, Ohio
| | | | - Dimitri D Deheyn
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California
| | - Mark J A Vermeij
- CARMABI Foundation, Willemstad, Curaçao.,Aquatic Microbiology/Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
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25
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Shielding the Next Generation: Symbiotic Bacteria from a Reproductive Organ Protect Bobtail Squid Eggs from Fungal Fouling. mBio 2019; 10:mBio.02376-19. [PMID: 31662458 PMCID: PMC6819662 DOI: 10.1128/mbio.02376-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Organisms must have strategies to ensure successful reproduction. Some animals that deposit eggs protect their embryos from fouling/disease with the help of microorganisms. Although beneficial bacteria are hypothesized to contribute to egg defense in some organisms, the mechanisms of this protection remain largely unknown, with the exception of a few recently described systems. Using both experimental and analytical approaches, we demonstrate that symbiotic bacteria associated with a cephalopod reproductive gland and eggs inhibit fungi. Chemical analyses suggest that these bacteria produce antimicrobial compounds that may prevent overgrowth from fungi and other microorganisms. Given the distribution of these symbiotic glands among many cephalopods, similar defensive relationships may be more common in aquatic environments than previously realized. Such defensive symbioses may also be a rich source for the discovery of new antimicrobial compounds. The importance of defensive symbioses, whereby microbes protect hosts through the production of specific compounds, is becoming increasingly evident. Although defining the partners in these associations has become easier, assigning function to these relationships often presents a significant challenge. Here, we describe a functional role for a bacterial consortium in a female reproductive organ in the Hawaiian bobtail squid, Euprymna scolopes. Bacteria from the accessory nidamental gland (ANG) are deposited into the egg jelly coat (JC), where they are hypothesized to play a defensive role during embryogenesis. Eggs treated with an antibiotic cocktail developed a microbial biomass primarily composed of the pathogenic fungus Fusarium keratoplasticum that infiltrated the JC, resulting in severely reduced hatch rates. Experimental manipulation of the eggs demonstrated that the JC was protective against this fungal fouling. A large proportion of the bacterial strains isolated from the ANG or JC inhibited F. keratoplasticum in culture (87.5%), while a similar proportion of extracts from these strains also exhibited antifungal activity against F. keratoplasticum and/or the human-pathogenic yeast Candida albicans (72.7%). Mass spectral network analyses of active extracts from bacterial isolates and egg clutches revealed compounds that may be involved in preventing microbial overgrowth. Several secondary metabolites were identified from ANG/JC bacteria and egg clutches, including the known antimicrobial lincomycin as well as a suite of glycerophosphocholines and mycinamicin-like compounds. These results shed light on a widely distributed but poorly understood symbiosis in cephalopods and offer a new source for exploring bacterial secondary metabolites with antimicrobial activity.
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26
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Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, Bourdin G, Bowler C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Ghiglione JF, Gilson E, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, de Vargas C, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D. The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean. PLoS Biol 2019; 17:e3000483. [PMID: 31545807 PMCID: PMC6776362 DOI: 10.1371/journal.pbio.3000483] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/03/2019] [Indexed: 02/01/2023] Open
Abstract
Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.
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Affiliation(s)
- Serge Planes
- Laboratoire d’Excellence “CORAIL,” PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- * E-mail:
| | - Denis Allemand
- Centre Scientifique de Monaco, Monte Carlo, Principality of Monaco
| | | | - Bernard Banaigs
- Laboratoire d’Excellence “CORAIL,” PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Emilie Boissin
- Laboratoire d’Excellence “CORAIL,” PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, Maine, United States of America
| | - Guillaume Bourdin
- School of Marine Sciences, University of Maine, Orono, Maine, United States of America
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l’Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - J. Michel Flores
- Weizmann Institute of Science, Dept. Earth and Planetary Science, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur-CNRS-INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, Nice, France
| | - Paola Furla
- Université Côte d'Azur-CNRS-INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, Nice, France
| | - Pierre E. Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université, CNRS, Laboratoire d’Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur mer, France
| | - Jean-François Ghiglione
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université Laboratoire d’Océanographie Microbienne LOMIC, UMR 7621, Observatoire Océanologique de Banyuls, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur-CNRS-INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | | | - Stephane Pesant
- PANGEA, Data Publisher for Earth and Environment Science, Bremen, Germany
- MARUM—Center for Marine Environmental Sciences, Universität Bremen, Bremen, Germany
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | | | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, United States of America
| | - Shinichi Sunagawa
- Department of Biology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Olivier P. Thomas
- Marine Biodiscovery Laboratory, School of Chemistry and Ryan Institute, National University of Ireland, Galway (NUI Galway), Galway, Ireland
| | - Romain Troublé
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- La Fondation Tara Expéditions, “Base Tara” 11, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | | | - Patrick Wincker
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, Monte Carlo, Principality of Monaco
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Metabolomic profiles differ among unique genotypes of a threatened Caribbean coral. Sci Rep 2019; 9:6067. [PMID: 30988456 PMCID: PMC6465396 DOI: 10.1038/s41598-019-42434-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 04/01/2019] [Indexed: 11/20/2022] Open
Abstract
Global threats to reefs require urgent efforts to resolve coral attributes that affect survival in a changing environment. Genetically different individuals of the same coral species are known to exhibit different responses to the same environmental conditions. New information on coral physiology, particularly as it relates to genotype, could aid in unraveling mechanisms that facilitate coral survival in the face of stressors. Metabolomic profiling detects a large subset of metabolites in an organism, and, when linked to metabolic pathways, can provide a snapshot of an organism’s physiological state. Identifying metabolites associated with desirable, genotype-specific traits could improve coral selection for restoration and other interventions. A key step toward this goal is determining whether intraspecific variation in coral metabolite profiles can be detected for species of interest, however little information exists to illustrate such differences. To address this gap, we applied untargeted 1H-NMR and LC-MS metabolomic profiling to three genotypes of the threatened coral Acropora cervicornis. Both methods revealed distinct metabolite “fingerprints” for each genotype examined. A number of metabolites driving separation among genotypes were identified or putatively annotated. Pathway analysis suggested differences in protein synthesis among genotypes. For the first time, these data illustrate intraspecific variation in metabolomic profiles for corals in a common garden. Our results contribute to the growing body of work on coral metabolomics and suggest future work could identify specific links between phenotype and metabolite profile in corals.
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Vohsen SA, Fisher CR, Baums IB. Metabolomic richness and fingerprints of deep-sea coral species and populations. Metabolomics 2019; 15:34. [PMID: 30830472 PMCID: PMC6469635 DOI: 10.1007/s11306-019-1500-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/22/2019] [Indexed: 10/27/2022]
Abstract
INTRODUCTION From shallow water to the deep sea, corals form the basis of diverse communities with significant ecological and economic value. These communities face many anthropogenic stressors including energy and mineral extraction activities, ocean acidification and rising sea temperatures. Corals and their symbionts produce a diverse assemblage of compounds that may help provide resilience to some of these stressors. OBJECTIVES We aim to characterize the metabolomic diversity of deep-sea corals in an ecological context by investigating patterns across space and phylogeny. METHODS We applied untargeted Liquid Chromatography-Mass Spectrometry to examine the metabolomic diversity of the deep-sea coral, Callogorgia delta, across three sites in the Northern Gulf of Mexico as well as three other deep-sea corals, Stichopathes sp., Leiopathes glaberrima, and Lophelia pertusa, and a shallow-water species, Acropora palmata. RESULTS Different coral species exhibited distinct metabolomic fingerprints and differences in metabolomic richness including core ions unique to each species. C. delta was generally least diverse while Lophelia pertusa was most diverse. C. delta from different sites had different metabolomic fingerprints and metabolomic richness at individual and population levels, although no sites exhibited unique core ions. Two core ions unique to C. delta were putatively identified as diterpenes and thus may possess a biologically important function. CONCLUSION Deep-sea coral species have distinct metabolomic fingerprints and exhibit high metabolomic diversity at multiple scales which may contribute to their capabilities to respond to both natural and anthropogenic stressors, including climate change.
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Affiliation(s)
- Samuel A Vohsen
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA.
| | - Charles R Fisher
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
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Evaluation of Sample Preparation Methods for the Analysis of Reef-Building Corals Using ¹H-NMR-Based Metabolomics. Metabolites 2019; 9:metabo9020032. [PMID: 30781808 PMCID: PMC6410050 DOI: 10.3390/metabo9020032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/08/2019] [Accepted: 02/10/2019] [Indexed: 11/21/2022] Open
Abstract
The field of metabolomics generally lacks standardized methods for the preparation of samples prior to analysis. This is especially true for metabolomics of reef-building corals, where the handful of studies that were published employ a range of sample preparation protocols. The utilization of metabolomics may prove essential in understanding coral biology in the face of increasing environmental threats, and an optimized method for preparing coral samples for metabolomics analysis would aid this cause. The current study evaluates three important steps during sample processing of stony corals: (i) metabolite extraction, (ii) metabolism preservation, and (iii) subsampling. Results indicate that a modified Bligh and Dyer extraction is more reproducible across multiple coral species compared to methyl tert-butyl ether and methanol extractions, while a methanol extraction is superior for feature detection. Additionally, few differences were detected between spectra from frozen or lyophilized coral samples. Finally, extraction of entire coral nubbins increased feature detection, but decreased throughput and was more susceptible to subsampling error compared to a novel tissue powder subsampling method. Overall, we recommend the use of a modified Bligh and Dyer extraction, lyophilized samples, and the analysis of brushed tissue powder for the preparation of reef-building coral samples for 1H NMR metabolomics.
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Gaubert J, Payri CE, Vieira C, Solanki H, Thomas OP. High metabolic variation for seaweeds in response to environmental changes: a case study of the brown algae Lobophora in coral reefs. Sci Rep 2019; 9:993. [PMID: 30700781 PMCID: PMC6353962 DOI: 10.1038/s41598-018-38177-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/12/2018] [Indexed: 02/02/2023] Open
Abstract
In the marine environment, macroalgae face changing environmental conditions and some species are known for their high capacity to adapt to the new factors of their ecological niche. Some macroalgal metabolites play diverse ecological functions and belong to the adaptive traits of such species. Because algal metabolites are involved in many processes that shape marine biodiversity, understanding their sources of variation and regulation is therefore of utmost relevance. This work aims at exploring the possible sources of metabolic variations with time and space of four common algal species from the genus Lobophora (Dictyotales, Phaeophyceae) in the New Caledonian lagoon using a UHPLC-HRMS metabolomic fingerprinting approach. While inter-specific differences dominated, a high variability of the metabolome was noticed for each species when changing their natural habitats and types of substrates. Fatty acids derivatives and polyolefins were identified as chemomarkers of these changing conditions. The four seaweeds metabolome also displayed monthly variations over the 13-months survey and a significant correlation was made with sea surface temperature and salinity. This study highlights a relative plasticity for the metabolome of Lobophora species.
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Affiliation(s)
- Julie Gaubert
- Sorbonne Universités, Collège Doctoral, F-75005, Paris, France.
- UMR ENTROPIE (IRD, UR, CNRS), Institut de Recherche pour le Développement, B.P. A5, 98848, Nouméa Cedex, Nouvelle-Calédonie, France.
| | - Claude E Payri
- UMR ENTROPIE (IRD, UR, CNRS), Institut de Recherche pour le Développement, B.P. A5, 98848, Nouméa Cedex, Nouvelle-Calédonie, France
| | - Christophe Vieira
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), 9000, Gent, Belgium
| | - Hiren Solanki
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33, Galway, Ireland
| | - Olivier P Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33, Galway, Ireland
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Lohr KE, Camp EF, Kuzhiumparambil U, Lutz A, Leggat W, Patterson JT, Suggett DJ. Resolving coral photoacclimation dynamics through coupled photophysiological and metabolomic profiling. J Exp Biol 2019; 222:jeb.195982. [DOI: 10.1242/jeb.195982] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/11/2019] [Indexed: 11/20/2022]
Abstract
Corals continuously adjust to short term variation in light availability on shallow reefs. Long-term light alterations can also occur due to natural and anthropogenic stressors, as well as management interventions such as coral transplantation. Although short term photophysiological responses are relatively well-understood in corals, little information is available regarding photoacclimation dynamics over weeks of altered light availability. We coupled photophysiology and metabolomic profiling to explore changes that accompany longer-term photoacclimation in a key Great Barrier Reef coral species (Acropora muricata). High (HL) and low light (LL) acclimated corals were collected from the reef and reciprocally exposed to high and low light ex situ. Rapid light curves using Pulse Amplitude Modulation (PAM) fluorometry revealed photophysiological acclimation of LL to HL and HL to LL shifted corals within 21 days. A subset of colonies sampled at 7 and 21 days for untargeted LC-MS and GC-MS metabolomic profiling revealed metabolic reorganization before acclimation was detected using PAM fluorometry. Metabolomic shifts were more pronounced for LL to HL treated corals than their HL to LL counterparts. Compounds driving metabolomic separation between HL-exposed and LL control colonies included amino acids, organic acids, fatty acids and sterols. Reduced glycerol and campesterol suggest decreased translocation of photosynthetic products from symbiont to host in LL to HL shifted corals, with concurrent increases in fatty acid abundance indicating reliance on stored lipids for energy. We discuss how these data provide novel insight into environmental regulation of metabolism and implications for management strategies that drive rapid changes in light availability.
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Affiliation(s)
- Kathryn E. Lohr
- Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - Emma F. Camp
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Adrian Lutz
- Metabolomics Australia, University of Melbourne, Parkville, VIC, Australia
| | - William Leggat
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW, Australia
| | - Joshua T. Patterson
- Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
- Center for Conservation, The Florida Aquarium, Apollo Beach, FL, USA
| | - David J. Suggett
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
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A High-Content Screening Assay for the Discovery of Novel Proteasome Inhibitors from Formosan Soft Corals. Mar Drugs 2018; 16:md16100395. [PMID: 30347865 PMCID: PMC6213913 DOI: 10.3390/md16100395] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/17/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is a major proteolytic pathway that safeguards protein homeostasis. The main 26S proteasome consists of a 20S catalytic core proteasome and a 19S substrate recognition proteasome. UPS dysfunction underlies many important clinical diseases involving inflammation, tumors, and neurodegeneration. Currently, three 20S proteasome inhibitors, bortezomib, carfilzomib, and ixazomib, have been approved for the treatment of multiple myeloma. We aim to screen UPS inhibitors for biomedical purposes. The protein interaction network of human cytomegalovirus UL76 targets UPS, resulting in aggregations of ubiquitinated proteins termed aggresomes. In this study, we demonstrated that cell-based high-content measurements of EGFP-UL76 aggresomes responded to bortezomib and MG132 treatment in a dose-dependent manner. Employing this high-content screening (HCS) assay, we screened natural compounds purified from Formosan soft corals. Four cembrane-based compounds, sarcophytonin A (1), sarcophytoxide (2), sarcophine (3), and laevigatol A (4), were found to enhance the high-content profiles of EGFP-UL76 aggresomes with relative ratios of 0.2. By comparison to the mechanistic action of proteasome inhibitors, compounds 1 and 3 modulated the accumulation of ubiquitinated proteins, with a unique pattern likely targeting 19S proteasome. We confirmed that the EGFP-UL76 aggresome-based HCS system greatly improves the efficacy and sensitivity of the identification of proteasome inhibitors.
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Galtier d'Auriac I, Quinn RA, Maughan H, Nothias LF, Little M, Kapono CA, Cobian A, Reyes BT, Green K, Quistad SD, Leray M, Smith JE, Dorrestein PC, Rohwer F, Deheyn DD, Hartmann AC. Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism. Proc Biol Sci 2018; 285:rspb.2018.1307. [PMID: 30111600 PMCID: PMC6111180 DOI: 10.1098/rspb.2018.1307] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/20/2018] [Indexed: 11/17/2022] Open
Abstract
Corals and humans represent two extremely disparate metazoan lineages and are therefore useful for comparative evolutionary studies. Two lipid-based molecules that are central to human immunity, platelet-activating factor (PAF) and Lyso-PAF were recently identified in scleractinian corals. To identify processes in corals that involve these molecules, PAF and Lyso-PAF biosynthesis was quantified in conditions known to stimulate PAF production in mammals (tissue growth and exposure to elevated levels of ultraviolet light) and in conditions unique to corals (competing with neighbouring colonies over benthic space). Similar to observations in mammals, PAF production was higher in regions of active tissue growth and increased when corals were exposed to elevated levels of ultraviolet light. PAF production also increased when corals were attacked by the stinging cells of a neighbouring colony, though only the attacked coral exhibited an increase in PAF. This reaction was observed in adjacent areas of the colony, indicating that this response is coordinated across multiple polyps including those not directly subject to the stress. PAF and Lyso-PAF are involved in coral stress responses that are both shared with mammals and unique to the ecology of cnidarians.
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Affiliation(s)
| | - Robert A Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA 92093, USA
| | | | - Louis-Felix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA 92093, USA
| | - Mark Little
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Clifford A Kapono
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA 92093, USA
| | - Ana Cobian
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Brandon T Reyes
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Kevin Green
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Steven D Quistad
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA.,Laboratoire de Génétique de l'Evolution (LGE), Institute of Chemistry, Biology, and Innovation, ESPCI ParisTech/CNRS UMR 8231/PSL Research University, Paris, France
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Smithsonian Institution, Panama City, Republic of Panama
| | - Jennifer E Smith
- Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA 92093, USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Dimitri D Deheyn
- Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA
| | - Aaron C Hartmann
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA .,National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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Ecosystem Microbiology of Coral Reefs: Linking Genomic, Metabolomic, and Biogeochemical Dynamics from Animal Symbioses to Reefscape Processes. mSystems 2018; 3:mSystems00162-17. [PMID: 29556542 PMCID: PMC5850082 DOI: 10.1128/msystems.00162-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/30/2017] [Indexed: 01/01/2023] Open
Abstract
Over the past 2 decades, molecular techniques have established the critical role of both free-living and host-associated microbial partnerships in the environment. Advancing research to link microbial community dynamics simultaneously to host physiology and ecosystem biogeochemistry is required to broaden our understanding of the ecological roles of environmental microbes. Over the past 2 decades, molecular techniques have established the critical role of both free-living and host-associated microbial partnerships in the environment. Advancing research to link microbial community dynamics simultaneously to host physiology and ecosystem biogeochemistry is required to broaden our understanding of the ecological roles of environmental microbes. Studies on coral reefs are actively integrating these data streams at multiple levels, from the symbiotic habitat of the coral holobiont to microbially mediated interactions between corals and algae to the effects of these interactions on the microbial community structure, metabolism, and organic geochemistry of the reef ecosystem. Coral reefs endure multiple anthropogenic impacts, including pollution, overfishing, and global change. In this context, we must develop ecosystem microbiology with an eye to providing managers with microbial indicators of reef ecosystem processes, coral health, and resilience to both local and global stressors.
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The Importance of Experimental Design, Quality Assurance, and Control in Plant Metabolomics Experiments. Methods Mol Biol 2018; 1778:3-17. [PMID: 29761427 DOI: 10.1007/978-1-4939-7819-9_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The output of metabolomics relies to a great extent upon the methods and instrumentation to identify, quantify, and access spatial information on as many metabolites as possible. However, the most modern machines and sophisticated tools for data analysis cannot compensate for inappropriate harvesting and/or sample preparation procedures that modify metabolic composition and can lead to erroneous interpretation of results. In addition, plant metabolism has a remarkable degree of complexity, and the number of identified compounds easily surpasses the number of samples in metabolomics analyses, increasing false discovery risk. These aspects pose a large challenge when carrying out plant metabolomics experiments. In this chapter, we address the importance of a proper experimental design taking into consideration preventable complications and unavoidable factors to achieve success in metabolomics analysis. We also focus on quality control and standardized procedures during the metabolomics workflow.
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Abstract
Untargeted metabolomics of environmental samples routinely detects thousands of small molecules, the vast majority of which cannot be identified. Meta-mass shift chemical (MeMSChem) profiling was developed to identify mass differences between related molecules using molecular networks. This approach illuminates metabolome-wide relationships between molecules and the putative chemical groups that differentiate them (e.g., H2, CH2, COCH2). MeMSChem profiling was used to analyze a publicly available metabolomic dataset of coral, algal, and fungal mat holobionts (i.e., the host and its associated microbes and viruses) sampled from some of Earth's most remote and pristine coral reefs. Each type of holobiont had distinct mass shift profiles, even when the analysis was restricted to molecules found in all samples. This result suggests that holobionts modify the same molecules in different ways and offers insights into the generation of molecular diversity. Three genera of stony corals had distinct patterns of molecular relatedness despite their high degree of taxonomic relatedness. MeMSChem profiles also partially differentiated between individuals, suggesting that every coral reef holobiont is a potential source of novel chemical diversity.
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Quinn RA, Vermeij MJA, Hartmann AC, d'Auriac IG, Benler S, Haas A, Quistad SD, Lim YW, Little M, Sandin S, Smith JE, Dorrestein PC, Rohwer F. Correction to 'Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence'. Proc Biol Sci 2016; 283:rspb.2016.1485. [PMID: 27559065 DOI: 10.1098/rspb.2016.1485] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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