Integration of untargeted metabolomics and microbial community analyses to characterize distinct deep-sea methane seeps
Deep-sea methane seeps host highly diverse microbial communities whose biological diversity is distinct from other marine habitats. Coupled with microbial community analysis, untargeted metabolomics of environmental samples using high resolution tandem mass spectrometry provides unprecedented access...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-10-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2023.1197338/full |
| _version_ | 1797655192168038400 |
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| author | Margaret A. Redick Milo E. Cummings George F. Neuhaus Lila M. Ardor Bellucci Andrew R. Thurber Andrew R. Thurber Kerry L. McPhail |
| author_facet | Margaret A. Redick Milo E. Cummings George F. Neuhaus Lila M. Ardor Bellucci Andrew R. Thurber Andrew R. Thurber Kerry L. McPhail |
| author_sort | Margaret A. Redick |
| collection | DOAJ |
| description | Deep-sea methane seeps host highly diverse microbial communities whose biological diversity is distinct from other marine habitats. Coupled with microbial community analysis, untargeted metabolomics of environmental samples using high resolution tandem mass spectrometry provides unprecedented access to the unique specialized metabolisms of these chemosynthetic microorganisms. In addition, the diverse microbial natural products are of broad interest due to their potential applications for human and environmental health and well-being. In this exploratory study, sediment cores were collected from two methane seeps (-1000 m water depth) with very different gross geomorphologies, as well as a non-seep control site. Cores were subjected to parallel metabolomic and microbial community analyses to assess the feasibility of representative metabolite detection and identify congruent patterns between metabolites and microbes. Metabolomes generated using high resolution liquid chromatography tandem mass spectrometry were annotated with predicted structure classifications of the majority of mass features using SIRIUS and CANOPUS. The microbiome was characterized by analysis of 16S rRNA genes and analyzed both at the whole community level, as well as the small subgroup of Actinobacteria, which are known to produce societally useful compounds. Overall, the younger Dagorlad seep possessed a greater abundance of metabolites while there was more variation in abundance, number, and distribution of metabolites between samples at the older Emyn Muil seep. Lipid and lipid-like molecules displayed the greatest variation between sites and accounted for a larger proportion of metabolites found at the older seep. Overall, significant differences in composition of the microbial community mirrored the patterns of metabolite diversity within the samples; both varied greatly as a function of distance from methane seep, indicating a deterministic role of seepage. Interdisciplinary research to understand microbial and metabolic diversity is essential for understanding the processes and role of ubiquitous methane seeps in global systems and here we increase understanding of these systems by visualizing some of the chemical diversity that seeps add to marine systems. |
| first_indexed | 2024-03-11T17:10:38Z |
| format | Article |
| id | doaj.art-a9b66c2d48294754a7d25245256f9327 |
| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-03-11T17:10:38Z |
| publishDate | 2023-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj.art-a9b66c2d48294754a7d25245256f93272023-10-20T06:35:57ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452023-10-011010.3389/fmars.2023.11973381197338Integration of untargeted metabolomics and microbial community analyses to characterize distinct deep-sea methane seepsMargaret A. Redick0Milo E. Cummings1George F. Neuhaus2Lila M. Ardor Bellucci3Andrew R. Thurber4Andrew R. Thurber5Kerry L. McPhail6Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United StatesDepartment of Microbiology, College of Science, Oregon State University, Corvallis, OR, United StatesDepartment of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United StatesCollege of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United StatesDepartment of Microbiology, College of Science, Oregon State University, Corvallis, OR, United StatesCollege of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United StatesDepartment of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United StatesDeep-sea methane seeps host highly diverse microbial communities whose biological diversity is distinct from other marine habitats. Coupled with microbial community analysis, untargeted metabolomics of environmental samples using high resolution tandem mass spectrometry provides unprecedented access to the unique specialized metabolisms of these chemosynthetic microorganisms. In addition, the diverse microbial natural products are of broad interest due to their potential applications for human and environmental health and well-being. In this exploratory study, sediment cores were collected from two methane seeps (-1000 m water depth) with very different gross geomorphologies, as well as a non-seep control site. Cores were subjected to parallel metabolomic and microbial community analyses to assess the feasibility of representative metabolite detection and identify congruent patterns between metabolites and microbes. Metabolomes generated using high resolution liquid chromatography tandem mass spectrometry were annotated with predicted structure classifications of the majority of mass features using SIRIUS and CANOPUS. The microbiome was characterized by analysis of 16S rRNA genes and analyzed both at the whole community level, as well as the small subgroup of Actinobacteria, which are known to produce societally useful compounds. Overall, the younger Dagorlad seep possessed a greater abundance of metabolites while there was more variation in abundance, number, and distribution of metabolites between samples at the older Emyn Muil seep. Lipid and lipid-like molecules displayed the greatest variation between sites and accounted for a larger proportion of metabolites found at the older seep. Overall, significant differences in composition of the microbial community mirrored the patterns of metabolite diversity within the samples; both varied greatly as a function of distance from methane seep, indicating a deterministic role of seepage. Interdisciplinary research to understand microbial and metabolic diversity is essential for understanding the processes and role of ubiquitous methane seeps in global systems and here we increase understanding of these systems by visualizing some of the chemical diversity that seeps add to marine systems.https://www.frontiersin.org/articles/10.3389/fmars.2023.1197338/fullmethane seepdeep-seauntargeted metabolomicsmicrobial communitytandem mass spectrometryenvironmental analysis |
| spellingShingle | Margaret A. Redick Milo E. Cummings George F. Neuhaus Lila M. Ardor Bellucci Andrew R. Thurber Andrew R. Thurber Kerry L. McPhail Integration of untargeted metabolomics and microbial community analyses to characterize distinct deep-sea methane seeps Frontiers in Marine Science methane seep deep-sea untargeted metabolomics microbial community tandem mass spectrometry environmental analysis |
| title | Integration of untargeted metabolomics and microbial community analyses to characterize distinct deep-sea methane seeps |
| title_full | Integration of untargeted metabolomics and microbial community analyses to characterize distinct deep-sea methane seeps |
| title_fullStr | Integration of untargeted metabolomics and microbial community analyses to characterize distinct deep-sea methane seeps |
| title_full_unstemmed | Integration of untargeted metabolomics and microbial community analyses to characterize distinct deep-sea methane seeps |
| title_short | Integration of untargeted metabolomics and microbial community analyses to characterize distinct deep-sea methane seeps |
| title_sort | integration of untargeted metabolomics and microbial community analyses to characterize distinct deep sea methane seeps |
| topic | methane seep deep-sea untargeted metabolomics microbial community tandem mass spectrometry environmental analysis |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2023.1197338/full |
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