Molecular Commerce on Coral Reefs: Using Metabolomics to Reveal Biochemical Exchanges Underlying Holobiont Biology and the Ecology of Coastal Ecosystems
The rapidly advancing field of metabolomics encompasses a diverse suite of powerful analytical and bioinformatic tools that can help to reveal the diversity and activity of chemical compounds in individual organisms, species interactions, and entire ecosystems. In this perspective we use examples fr...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-07-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2021.630799/full |
| _version_ | 1818618605207552000 |
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| author | Linda Wegley Kelly Linda Wegley Kelly Craig E. Nelson Lihini I. Aluwihare Milou G. I. Arts Pieter C. Dorrestein Irina Koester Shayle B. Matsuda Daniel Petras Daniel Petras Zachary A. Quinlan Zachary A. Quinlan Andreas F. Haas |
| author_facet | Linda Wegley Kelly Linda Wegley Kelly Craig E. Nelson Lihini I. Aluwihare Milou G. I. Arts Pieter C. Dorrestein Irina Koester Shayle B. Matsuda Daniel Petras Daniel Petras Zachary A. Quinlan Zachary A. Quinlan Andreas F. Haas |
| author_sort | Linda Wegley Kelly |
| collection | DOAJ |
| description | The rapidly advancing field of metabolomics encompasses a diverse suite of powerful analytical and bioinformatic tools that can help to reveal the diversity and activity of chemical compounds in individual organisms, species interactions, and entire ecosystems. In this perspective we use examples from studies of coral reefs to illustrate ways in which metabolomics has been and can be applied to understand coastal ecosystems. Examples of new insights that can be provided by metabolomics include resolving metabolite exchange between plants, animals and their microbiota, identifying the relevant metabolite exchanges associated with the onset and maintenance of diverse, microbial mutualisms characterizing unknown molecules that act as cues in coral, reproduction, or defining the suites of compounds involved in coral-algal competition and microbialization of algal-dominated ecosystems. Here we outline sampling, analytical and informatic methods that marine biologists and ecologists can apply to understand the role of chemical processes in ecosystems, with a focus on open access data analysis workflows and democratized databases. Finally, we demonstrate how these metabolomics tools and bioinformatics approaches can provide scientists the opportunity to map detailed metabolic inventories and dynamics for a holistic view of the relationships among reef organisms, their symbionts and their surrounding marine environment. |
| first_indexed | 2024-12-16T17:24:15Z |
| format | Article |
| id | doaj.art-111bdc15334344b7b76a53dc55067e13 |
| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-12-16T17:24:15Z |
| publishDate | 2021-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj.art-111bdc15334344b7b76a53dc55067e132022-12-21T22:23:05ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452021-07-01810.3389/fmars.2021.630799630799Molecular Commerce on Coral Reefs: Using Metabolomics to Reveal Biochemical Exchanges Underlying Holobiont Biology and the Ecology of Coastal EcosystemsLinda Wegley Kelly0Linda Wegley Kelly1Craig E. Nelson2Lihini I. Aluwihare3Milou G. I. Arts4Pieter C. Dorrestein5Irina Koester6Shayle B. Matsuda7Daniel Petras8Daniel Petras9Zachary A. Quinlan10Zachary A. Quinlan11Andreas F. Haas12Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United StatesDepartment of Biology, San Diego State University, San Diego, CA, United StatesDepartment of Oceanography and Sea Grant College Program, Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology, University of Hawai‘i at Mānoa, Honolulu, HI, United StatesScripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United StatesDepartment of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Den Burg, NetherlandsCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United StatesScripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United StatesDepartment of Oceanography and Sea Grant College Program, Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology, University of Hawai‘i at Mānoa, Honolulu, HI, United StatesScripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United StatesCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United StatesScripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United StatesDepartment of Biology, San Diego State University, San Diego, CA, United StatesDepartment of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Den Burg, NetherlandsThe rapidly advancing field of metabolomics encompasses a diverse suite of powerful analytical and bioinformatic tools that can help to reveal the diversity and activity of chemical compounds in individual organisms, species interactions, and entire ecosystems. In this perspective we use examples from studies of coral reefs to illustrate ways in which metabolomics has been and can be applied to understand coastal ecosystems. Examples of new insights that can be provided by metabolomics include resolving metabolite exchange between plants, animals and their microbiota, identifying the relevant metabolite exchanges associated with the onset and maintenance of diverse, microbial mutualisms characterizing unknown molecules that act as cues in coral, reproduction, or defining the suites of compounds involved in coral-algal competition and microbialization of algal-dominated ecosystems. Here we outline sampling, analytical and informatic methods that marine biologists and ecologists can apply to understand the role of chemical processes in ecosystems, with a focus on open access data analysis workflows and democratized databases. Finally, we demonstrate how these metabolomics tools and bioinformatics approaches can provide scientists the opportunity to map detailed metabolic inventories and dynamics for a holistic view of the relationships among reef organisms, their symbionts and their surrounding marine environment.https://www.frontiersin.org/articles/10.3389/fmars.2021.630799/fullbiogeochemistrycoral reefscoral holobiontdissolved organic mattermetabolomicsmicrobial ecology |
| spellingShingle | Linda Wegley Kelly Linda Wegley Kelly Craig E. Nelson Lihini I. Aluwihare Milou G. I. Arts Pieter C. Dorrestein Irina Koester Shayle B. Matsuda Daniel Petras Daniel Petras Zachary A. Quinlan Zachary A. Quinlan Andreas F. Haas Molecular Commerce on Coral Reefs: Using Metabolomics to Reveal Biochemical Exchanges Underlying Holobiont Biology and the Ecology of Coastal Ecosystems Frontiers in Marine Science biogeochemistry coral reefs coral holobiont dissolved organic matter metabolomics microbial ecology |
| title | Molecular Commerce on Coral Reefs: Using Metabolomics to Reveal Biochemical Exchanges Underlying Holobiont Biology and the Ecology of Coastal Ecosystems |
| title_full | Molecular Commerce on Coral Reefs: Using Metabolomics to Reveal Biochemical Exchanges Underlying Holobiont Biology and the Ecology of Coastal Ecosystems |
| title_fullStr | Molecular Commerce on Coral Reefs: Using Metabolomics to Reveal Biochemical Exchanges Underlying Holobiont Biology and the Ecology of Coastal Ecosystems |
| title_full_unstemmed | Molecular Commerce on Coral Reefs: Using Metabolomics to Reveal Biochemical Exchanges Underlying Holobiont Biology and the Ecology of Coastal Ecosystems |
| title_short | Molecular Commerce on Coral Reefs: Using Metabolomics to Reveal Biochemical Exchanges Underlying Holobiont Biology and the Ecology of Coastal Ecosystems |
| title_sort | molecular commerce on coral reefs using metabolomics to reveal biochemical exchanges underlying holobiont biology and the ecology of coastal ecosystems |
| topic | biogeochemistry coral reefs coral holobiont dissolved organic matter metabolomics microbial ecology |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2021.630799/full |
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