1
|
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.
Collapse
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
| |
Collapse
|
2
|
Delanka-Pedige HMK, Young RB, Abutokaikah MT, Chen L, Wang H, Imihamillage KABI, Thimons S, Jahne MA, Williams AJ, Zhang Y, Xu P. Non-targeted analysis and toxicity prediction for evaluation of photocatalytic membrane distillation removing organic contaminants from hypersaline oil and gas field-produced water. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134436. [PMID: 38688221 DOI: 10.1016/j.jhazmat.2024.134436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/13/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Membrane distillation (MD) has received ample recognition for treating complex wastewater, including hypersaline oil and gas (O&G) produced water (PW). Rigorous water quality assessment is critical in evaluating PW treatment because PW consists of numerous contaminants beyond the targets listed in general discharge and reuse standards. This study evaluated a novel photocatalytic membrane distillation (PMD) process, with and without a UV light source, against a standard vacuum membrane distillation (VMD) process for treating PW, utilizing targeted analyses and a non-targeted chemical identification workflow coupled with toxicity predictions. PMD with UV light resulted in better removals of dissolved organic carbon, ammoniacal nitrogen, and conductivity. Targeted organic analyses identified only trace amounts of acetone and 2-butanone in distillates. According to non-targeted analysis, the number of suspects reduced from 65 in feed to 25-30 across all distillate samples. Certain physicochemical properties of compounds influenced contaminant rejection in different MD configurations. According to preliminary toxicity predictions, VMD, PMD with and without UV distillate samples, respectively contained 21, 22, and 23 suspects associated with critical toxicity concerns. Overall, non-targeted analysis together with toxicity prediction provides a competent supportive tool to assess treatment efficiency and potential impacts on public health and the environment during PW reuse.
Collapse
Affiliation(s)
| | - Robert B Young
- Chemical Analysis and Instrumentation Laboratory, New Mexico State University, Las Cruces, NM 88003, United States
| | - Maha T Abutokaikah
- Chemical Analysis and Instrumentation Laboratory, New Mexico State University, Las Cruces, NM 88003, United States
| | - Lin Chen
- Department of Civil Engineering, New Mexico State University, Las Cruces, NM 88003, United States
| | - Huiyao Wang
- Department of Civil Engineering, New Mexico State University, Las Cruces, NM 88003, United States
| | - Kanchana A B I Imihamillage
- Department of Engineering Technology and Surveying Engineering, New Mexico State University, Las Cruces, NM 88003, United States
| | - Sean Thimons
- Oak Ridge Institute for Science and Education, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Michael A Jahne
- Office of Research and Development, US Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Antony J Williams
- Office of Research and Development, US Environmental Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Yanyan Zhang
- Department of Civil Engineering, New Mexico State University, Las Cruces, NM 88003, United States
| | - Pei Xu
- Department of Civil Engineering, New Mexico State University, Las Cruces, NM 88003, United States.
| |
Collapse
|
3
|
Williams A. Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont. FEMS Microbiol Ecol 2024; 100:fiae058. [PMID: 38653719 PMCID: PMC11067971 DOI: 10.1093/femsec/fiae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/25/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024] Open
Abstract
Since their radiation in the Middle Triassic period ∼240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.
Collapse
Affiliation(s)
- Amanda Williams
- Microbial Biology Graduate Program, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
| |
Collapse
|
4
|
Kuo CH, Xu ZY, Hsiao PZ, Liao PC, Liu CH, Hong MC, Chiu K. Utilizing fish wastewater in aquaponic systems to enhance anti-inflammatory and antioxidant bioactive compounds in Sarcodia suae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169958. [PMID: 38211863 DOI: 10.1016/j.scitotenv.2024.169958] [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: 10/21/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
Aquaculture wastewater, rich in organic nutrients, is an essential environmental factor. When applied to seaweed cultivation systems, this wastewater holds the potential to notably increase the growth rate and carbon capture of Sarcodia suae. Sarcodia suae has the potential to be a healthy food due to its various biological activities; however, its chemical composition has yet to be completely defined. In this study, we applied a UHPLC-HRMS-based foodomics strategy to determine and classify possible bioactive metabolites in S. suae. From pooled seaweed samples (S. suae cultured in filtered running, FR, aquaponic recirculation, AR systems), we identified 179 and 146 compounds in POS and NEG modes, respectively. These compounds were then classified based on their structures using the Classyfire classification. Results show that S. suae in AR exhibited higher growth performance, and ten upregulated metabolites were determined. We also validated the anti-inflammatory and antioxidative bioactivities of some selected compounds. Our study provided important insights into the potential use of fish wastewater in aquaponic systems to profile and produce bioactive compounds in S. suae comprehensively. This has significant implications for the development of sustainable food and the promotion of environmental health.
Collapse
Affiliation(s)
- Chiu-Hui Kuo
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung 811, Taiwan
| | - Zi-Yan Xu
- Tungkang Aquaculture Research Center, Fisheries Research Institute, MOA, Taiwan
| | - Ping-Zu Hsiao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan.
| | - Chun-Hung Liu
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Ming-Chang Hong
- Department and Graduate Institute of Aquaculture, National Kaohsiung University of Science and Technology, Kaohsiung 811, Taiwan
| | - Kuohsun Chiu
- Department and Graduate Institute of Aquaculture, National Kaohsiung University of Science and Technology, Kaohsiung 811, Taiwan; Department of Oceanography, National Sun Yat-sen University, Kaohsiung 804, Taiwan.
| |
Collapse
|
5
|
Sparagon WJ, Arts MGI, Quinlan ZA, Wegley Kelly L, Koester I, Comstock J, Bullington JA, Carlson CA, Dorrestein PC, Aluwihare LI, Haas AF, Nelson CE. Coral thermal stress and bleaching enrich and restructure reef microbial communities via altered organic matter exudation. Commun Biol 2024; 7:160. [PMID: 38351328 PMCID: PMC10864316 DOI: 10.1038/s42003-023-05730-0] [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: 04/10/2023] [Accepted: 12/16/2023] [Indexed: 02/16/2024] Open
Abstract
Coral bleaching is a well-documented and increasingly widespread phenomenon in reefs across the globe, yet there has been relatively little research on the implications for reef water column microbiology and biogeochemistry. A mesocosm heating experiment and bottle incubation compared how unbleached and bleached corals alter dissolved organic matter (DOM) exudation in response to thermal stress and subsequent effects on microbial growth and community structure in the water column. Thermal stress of healthy corals tripled DOM flux relative to ambient corals. DOM exudates from stressed corals (heated and/or previously bleached) were compositionally distinct from healthy corals and significantly increased growth of bacterioplankton, enriching copiotrophs and putative pathogens. Together these results demonstrate how the impacts of both short-term thermal stress and long-term bleaching may extend into the water column, with altered coral DOM exudation driving microbial feedbacks that influence how coral reefs respond to and recover from mass bleaching events.
Collapse
Affiliation(s)
- Wesley J Sparagon
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
| | - Milou G I Arts
- Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Zachary A Quinlan
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- San Diego State University, San Diego, USA
| | - Linda Wegley Kelly
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- San Diego State University, San Diego, USA
| | - Irina Koester
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Jacqueline Comstock
- Department of Ecology, Evolution and Marine Biology, The Marine Science Institute, University of California Santa Barbara, Santa Barbara, USA
| | - Jessica A Bullington
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Craig A Carlson
- Department of Ecology, Evolution and Marine Biology, The Marine Science Institute, University of California Santa Barbara, Santa Barbara, USA
| | | | - Lihini I Aluwihare
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Andreas F Haas
- Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
- San Diego State University, San Diego, USA
| | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| |
Collapse
|
6
|
Pei P, Aslam M, Wang H, Ye P, Li T, Liang H, Lin Q, Chen W, Du H. Diversity and ecological function of urease-producing bacteria in the cultivation environment of Gracilariopsis lemaneiformis. MICROBIAL ECOLOGY 2024; 87:35. [PMID: 38261068 PMCID: PMC10806000 DOI: 10.1007/s00248-023-02339-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: 08/10/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024]
Abstract
Urease-producing bacteria (UPB) provide inorganic nitrogen for primary producers by hydrolyzing urea, and play an important role in marine nitrogen cycle. However, there is still an incomplete understanding of UPB and their ecological functions in the cultivation environment of the red macroalgae Gracilariopsis lemaneiformis. This study comprehensively analyzed the diversity of culturable UPB and explored their effects on urea uptake by G. lemaneiformis. A total of 34 isolates belonging to four main bacterial phyla i.e. (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) were identified through 16S rRNA sequencing and were screened for UPB by urea agar chromogenic medium assay and ureC gene cloning. Our data revealed that only 8 strains contained urease. All of these UPB exhibited different urease activities, which were determined by the Berthelot reaction colorimetry assay. Additionally, the UPB strain (G13) isolated from G. lemaneiformis with higher urease activity was selected for co-culture with G. lemaneiformis to explore its role in promoting or inhibiting nitrogen uptake by macroalgae. The results showed a significant increase in urea consumption in the culture medium and the total cellular nitrogen in G. lemaneiformis in the UPB-co culture group compared to the sterile group. This suggests that the selected UPB strain positively influences nitrogen uptake by G. lemaneiformis. Similarly, isotopic assays revealed that the δ15N content of G. lemaneiformis was significantly higher in the UPB-co culture than in the control group, where δ15N-urea was the only nitrogen source in the culture medium. This indicates that the UPB helped G. lemaneiformis to absorb more nitrogen from urea. Moreover, the highest content of δ15N was found in G. lemaneiformis with epiphytic bacteria compared to sterilized (i.e. control), showing that epiphytic bacteria, along with UPB, have a compound effect in helping G. lemaneiformis absorb more nitrogen from urea. Taken together, these results provide unique insight into the ecological role of UPB and suggest that urease from macroalgae environment-associated bacteria might be an important player in marine nitrogen cycling.
Collapse
Affiliation(s)
- Pengbing Pei
- Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, China
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, 361000, China
| | - Muhammad Aslam
- Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, China
- Faculty of Marine Sciences, LUAWMS, Lasbela, 90150, Pakistan
| | - Hui Wang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, China
| | - Peilin Ye
- Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, China
| | - Tangcheng Li
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, College of Science, Shantou University, Shantou, 515063, China
| | - Honghao Liang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, 361000, China
| | - Weizhou Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, China
| | - Hong Du
- Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, China.
| |
Collapse
|
7
|
Olander A, Raina JB, Lawson CA, Bartels N, Ueland M, Suggett DJ. Distinct emissions of biogenic volatile organic compounds from temperate benthic taxa. Metabolomics 2023; 20:9. [PMID: 38129550 DOI: 10.1007/s11306-023-02070-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
INTRODUCTION Biogenic volatile organic compounds (BVOCs) are emitted by all organisms as intermediate or end-products of metabolic processes. Individual BVOCs perform important physiological, ecological and climatic functions, and collectively constitute the volatilome-which can be reflective of organism taxonomy and health. Although BVOC emissions of tropical benthic reef taxa have recently been the focus of multiple studies, emissions derived from their temperate counterparts have never been characterised. OBJECTIVES Characterise the volatilomes of key competitors for benthic space among Australian temperate reefs. METHODS Six fragments/fronds of a temperate coral (Plesiastrea versipora) and a macroalga (Ecklonia radiata) from a Sydney reef site were placed within modified incubation chambers filled with seawater. Organism-produced BVOCs were captured on thermal desorption tubes using a purge-and-trap methodology, and were then analysed using GC × GC - TOFMS and multivariate tests. RESULTS Analysis detected 55 and 63 BVOCs from P. versipora and E. radiata respectively, with 30 of these common between species. Each taxon was characterised by a similar relative composition of chemical classes within their volatilomes. However, 14 and 10 volatiles were distinctly emitted by either E. radiata or P. versipora respectively, including the halogenated compounds iodomethane, tribromomethane, carbon tetrachloride and trichloromonofluoromethane. While macroalgal cover was 3.7 times greater than coral cover at the sampling site, P. versipora produced on average 17 times more BVOCs per cm2 of live tissue, resulting in an estimated contribution to local BVOC emission that was 4.7 times higher than E. radiata. CONCLUSION Shifts in benthic community composition could disproportionately impact local marine chemistry and affect how ecosystems contribute to broader BVOC emissions.
Collapse
Affiliation(s)
- Axel Olander
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, 2007, Australia.
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Caitlin A Lawson
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, 2007, Australia
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, NSW, Australia
| | - Natasha Bartels
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Maiken Ueland
- Centre for Forensic Science, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, 2007, Australia
- KAUST Reefscape Restoration Initiative (KRRI) and Red Sea Research Center (RSRC), King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia
| |
Collapse
|
8
|
Mauduit M, Derrien M, Grenier M, Greff S, Molinari S, Chevaldonné P, Simmler C, Pérez T. In Situ Capture and Real-Time Enrichment of Marine Chemical Diversity. ACS CENTRAL SCIENCE 2023; 9:2084-2095. [PMID: 38033807 PMCID: PMC10683479 DOI: 10.1021/acscentsci.3c00661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Indexed: 12/02/2023]
Abstract
Analyzing the chemical composition of seawater to understand its influence on ecosystem functions is a long-lasting challenge due to the inherent complexity and dynamic nature of marine environments. Describing the intricate chemistry of seawater requires optimal in situ sampling. Here is presented a novel underwater hand-held solid-phase extraction device, I-SMEL (In Situ Marine moleculELogger), which aims to concentrate diluted molecules from large volumes of seawater in a delimited zone targeting keystone benthic species. Marine benthic holobionts, such as sponges, can impact the chemical composition of their surroundings possibly through the production and release of their specialized metabolites, hence termed exometabolites (EMs). I-SMEL was deployed in a sponge-dominated Mediterranean ecosystem at a 15 m depth. Untargeted MS-based metabolomics was performed on enriched EM extracts and showed (1) the chemical diversity of enriched seawater metabolites and (2) reproducible recovery and enrichment of specialized sponge EMs such as aerothionin, demethylfurospongin-4, and longamide B methyl ester. These EMs constitute the chemical identity of each targeted species: Aplysina cavernicola, Spongia officinalis, and Agelas oroides, respectively. I-SMEL concentrated sponge EMs from 10 L of water in a 10 min sampling time. The present proof of concept with I-SMEL opens new research perspectives in marine chemical ecology and sets the stage for further sustainable efforts in natural product chemistry.
Collapse
Affiliation(s)
| | | | | | - Stéphane Greff
- IMBE, UMR CNRS
7263, IRD
237, Aix Marseille Université, Avignon
Université, Station Marine d’Endoume, Chemin de la batterie
des lions, 13007 Marseille, France
| | - Sacha Molinari
- IMBE, UMR CNRS
7263, IRD
237, Aix Marseille Université, Avignon
Université, Station Marine d’Endoume, Chemin de la batterie
des lions, 13007 Marseille, France
| | - Pierre Chevaldonné
- IMBE, UMR CNRS
7263, IRD
237, Aix Marseille Université, Avignon
Université, Station Marine d’Endoume, Chemin de la batterie
des lions, 13007 Marseille, France
| | | | | |
Collapse
|
9
|
Quinlan ZA, Bennett MJ, Arts MGI, Levenstein M, Flores D, Tholen HM, Tichy L, Juarez G, Haas AF, Chamberland VF, Latijnhouwers KRW, Vermeij MJA, Johnson AW, Marhaver KL, Kelly LW. Coral larval settlement induction using tissue-associated and exuded coralline algae metabolites and the identification of putative chemical cues. Proc Biol Sci 2023; 290:20231476. [PMID: 37848062 PMCID: PMC10581770 DOI: 10.1098/rspb.2023.1476] [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: 06/29/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023] Open
Abstract
Reef-building crustose coralline algae (CCA) are known to facilitate the settlement and metamorphosis of scleractinian coral larvae. In recent decades, CCA coverage has fallen globally and degrading environmental conditions continue to reduce coral survivorship, spurring new restoration interventions to rebuild coral reef health. In this study, naturally produced chemical compounds (metabolites) were collected from two pantropical CCA genera to isolate and classify those that induce coral settlement. In experiments using four ecologically important Caribbean coral species, we demonstrate the applicability of extracted, CCA-derived metabolites to improve larval settlement success in coral breeding and restoration efforts. Tissue-associated CCA metabolites induced settlement of one coral species, Orbicella faveolata, while metabolites exuded by CCA (exometabolites) induced settlement of three species: Acropora palmata, Colpophyllia natans and Orbicella faveolata. In a follow-up experiment, CCA exometabolites fractionated and preserved using two different extraction resins induced the same level of larval settlement as the unfractionated positive control exometabolites. The fractionated CCA exometabolite pools were characterized using liquid chromatography tandem mass spectrometry, yielding 145 distinct molecular subnetworks that were statistically defined as CCA-derived and could be classified into 10 broad chemical classes. Identifying these compounds can reveal their natural prevalence in coral reef habitats and facilitate the development of new applications to enhance larval settlement and the survival of coral juveniles.
Collapse
Affiliation(s)
- Zachary A. Quinlan
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Milou G. I. Arts
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute of Sea Research (NIOZ), Den Burg, 1797 SZ, Texel, The Netherlands
| | - Mark Levenstein
- Department of Mechanical Science and Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Institute for Genomic Biology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Daisy Flores
- CARMABI Foundation, Piscaderabaai z/n, Willemstad, Curaçao
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Haley M. Tholen
- Department of Mechanical Science and Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Lucas Tichy
- CARMABI Foundation, Piscaderabaai z/n, Willemstad, Curaçao
- Department of Microbiology, Radboud University, Nijmegen, 6525 XZ, The Netherlands
| | - Gabriel Juarez
- Department of Mechanical Science and Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Andreas F. Haas
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute of Sea Research (NIOZ), Den Burg, 1797 SZ, Texel, The Netherlands
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Valérie F. Chamberland
- CARMABI Foundation, Piscaderabaai z/n, Willemstad, Curaçao
- SECORE International, Hilliard, OH 43026, USA
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, 1012 WP, The Netherlands
| | - Kelly R. W. Latijnhouwers
- CARMABI Foundation, Piscaderabaai z/n, Willemstad, Curaçao
- SECORE International, Hilliard, OH 43026, USA
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, 1012 WP, The Netherlands
| | - Mark J. A. Vermeij
- CARMABI Foundation, Piscaderabaai z/n, Willemstad, Curaçao
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, 1012 WP, The Netherlands
| | - Amy Wagoner Johnson
- Department of Mechanical Science and Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Institute for Genomic Biology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | | | - Linda Wegley Kelly
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
10
|
Becker CC, Weber L, Zgliczynski B, Sullivan C, Sandin S, Muller E, Clark AS, Kido Soule MC, Longnecker K, Kujawinski EB, Apprill A. Microorganisms and dissolved metabolites distinguish Florida's Coral Reef habitats. PNAS NEXUS 2023; 2:pgad287. [PMID: 37719750 PMCID: PMC10504872 DOI: 10.1093/pnasnexus/pgad287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/24/2023] [Indexed: 09/19/2023]
Abstract
As coral reef ecosystems experience unprecedented change, effective monitoring of reef features supports management, conservation, and intervention efforts. Omic techniques show promise in quantifying key components of reef ecosystems including dissolved metabolites and microorganisms that may serve as invisible sensors for reef ecosystem dynamics. Dissolved metabolites are released by reef organisms and transferred among microorganisms, acting as chemical currencies and contributing to nutrient cycling and signaling on reefs. Here, we applied four omic techniques (taxonomic microbiome via amplicon sequencing, functional microbiome via shotgun metagenomics, targeted metabolomics, and untargeted metabolomics) to waters overlying Florida's Coral Reef, as well as microbiome profiling on individual coral colonies from these reefs to understand how microbes and dissolved metabolites reflect biogeographical, benthic, and nutrient properties of this 500-km barrier reef. We show that the microbial and metabolite omic approaches each differentiated reef habitats based on geographic zone. Further, seawater microbiome profiling and targeted metabolomics were significantly related to more reef habitat characteristics, such as amount of hard and soft coral, compared to metagenomic sequencing and untargeted metabolomics. Across five coral species, microbiomes were also significantly related to reef zone, followed by species and disease status, suggesting that the geographic water circulation patterns in Florida also impact the microbiomes of reef builders. A combination of differential abundance and indicator species analyses revealed metabolite and microbial signatures of specific reef zones, which demonstrates the utility of these techniques to provide new insights into reef microbial and metabolite features that reflect broader ecosystem processes.
Collapse
Affiliation(s)
- Cynthia C Becker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
- Biological Oceanography, Massachusetts Institute of Technology-Woods Hole Oceanographic Institution Joint Program in Oceanography/Applied Ocean Science and Engineering,Cambridge, MA 02139, USA
| | - Laura Weber
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Brian Zgliczynski
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Chris Sullivan
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Stuart Sandin
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Erinn Muller
- Elizabeth Moore International Center for Coral Reef Research and Restoration, Mote Marine Laboratory, Summerland Key, FL 33042, USA
- Coral Health and Disease Program, Mote Marine Laboratory, Sarasota, FL 34236, USA
| | - Abigail S Clark
- Elizabeth Moore International Center for Coral Reef Research and Restoration, Mote Marine Laboratory, Summerland Key, FL 33042, USA
- Marine Science and Technology Department, The College of the Florida Keys, Key West, FL 33040, USA
| | - Melissa C Kido Soule
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Krista Longnecker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Elizabeth B Kujawinski
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Amy Apprill
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Stincone P, Pakkir Shah AK, Schmid R, Graves LG, Lambidis SP, Torres RR, Xia SN, Minda V, Aron AT, Wang M, Hughes CC, Petras D. Evaluation of Data-Dependent MS/MS Acquisition Parameters for Non-Targeted Metabolomics and Molecular Networking of Environmental Samples: Focus on the Q Exactive Platform. Anal Chem 2023; 95:12673-12682. [PMID: 37578818 PMCID: PMC10469366 DOI: 10.1021/acs.analchem.3c01202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023]
Abstract
Non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used tool for metabolomics analysis, enabling the detection and annotation of small molecules in complex environmental samples. Data-dependent acquisition (DDA) of product ion spectra is thereby currently one of the most frequently applied data acquisition strategies. The optimization of DDA parameters is central to ensuring high spectral quality, coverage, and number of compound annotations. Here, we evaluated the influence of 10 central DDA settings of the Q Exactive mass spectrometer on natural organic matter samples from ocean, river, and soil environments. After data analysis with classical and feature-based molecular networking using MZmine and GNPS, we compared the total number of network nodes, multivariate clustering, and spectrum quality-related metrics such as annotation and singleton rates, MS/MS placement, and coverage. Our results show that automatic gain control, microscans, mass resolving power, and dynamic exclusion are the most critical parameters, whereas collision energy, TopN, and isolation width had moderate and apex trigger, monoisotopic selection, and isotopic exclusion minor effects. The insights into the data acquisition ergonomics of the Q Exactive platform presented here can guide new users and provide them with initial method parameters, some of which may also be transferable to other sample types and MS platforms.
Collapse
Affiliation(s)
- Paolo Stincone
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| | - Abzer K. Pakkir Shah
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| | - Robin Schmid
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Praha 6, Czech Republic
| | - Lana G. Graves
- Faculty
of Mathematics and Natural Sciences, Environmental Systems Analysis, University of Tübingen, Tübingen 72076, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin 12587, Germany
| | - Stilianos P. Lambidis
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| | - Ralph R. Torres
- University
of California San Diego, Scripps Institution of Oceanography, La Jolla, California 92093, United States
| | - Shu-Ning Xia
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| | - Vidit Minda
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
- Department
of Pharmacology and Pharmaceutical Sciences, University of Missouri−Kansas City, Kansas City, Missouri 64108, United States
| | - Allegra T. Aron
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
| | - Mingxun Wang
- Department
of Computer Science, University of California
Riverside, Riverside, California 92507, United States
| | - Chambers C. Hughes
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
- Department
of Microbial Bioactive Compounds, Interfaculty Institute for Microbiology
and Infection Medicine, University of Tübingen, Tübingen 72076, Germany
- German
Center for Infection Research, Partner Site
Tübingen, Tübingen 72076, Germany
| | - Daniel Petras
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| |
Collapse
|
13
|
Chase AB, Bogdanov A, Demko AM, Jensen PR. Biogeographic patterns of biosynthetic potential and specialized metabolites in marine sediments. THE ISME JOURNAL 2023:10.1038/s41396-023-01410-3. [PMID: 37061583 DOI: 10.1038/s41396-023-01410-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/17/2023]
Abstract
While the field of microbial biogeography has largely focused on the contributions of abiotic factors to community patterns, the potential influence of biotic interactions in structuring microbial communities, such as those mediated by the production of specialized metabolites, remains largely unknown. Here, we examined the relationship between microbial community structure and specialized metabolism at local spatial scales in marine sediment samples collected from the Long-Term Ecological Research (LTER) site in Moorea, French Polynesia. By employing a multi-omic approach to characterize the taxonomic, functional, and specialized metabolite composition within sediment communities, we find that biogeographic patterns were driven by local scale processes (e.g., biotic interactions) and largely independent of dispersal limitation. Specifically, we observed high variation in biosynthetic potential (based on Bray-Curtis dissimilarity) between samples, even within 1 m2 plots, that reflected uncharacterized chemical space associated with site-specific metabolomes. Ultimately, connecting biosynthetic potential to community metabolomes facilitated the in situ detection of natural products and revealed new insights into the complex metabolic dynamics associated with sediment microbial communities. Our study demonstrates the potential to integrate biosynthetic genes and metabolite production into assessments of microbial community dynamics.
Collapse
Affiliation(s)
- Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, Dallas, TX, USA.
| | - Alexander Bogdanov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA, USA
| |
Collapse
|
14
|
Apprill A, Girdhar Y, Mooney TA, Hansel CM, Long MH, Liu Y, Zhang WG, Kapit J, Hughen K, Coogan J, Greene A. Toward a New Era of Coral Reef Monitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5117-5124. [PMID: 36930700 PMCID: PMC10077584 DOI: 10.1021/acs.est.2c05369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Indexed: 06/18/2023]
Abstract
Coral reefs host some of the highest concentrations of biodiversity and economic value in the oceans, yet these ecosystems are under threat due to climate change and other human impacts. Reef monitoring is routinely used to help prioritize reefs for conservation and evaluate the success of intervention efforts. Reef status and health are most frequently characterized using diver-based surveys, but the inherent limitations of these methods mean there is a growing need for advanced, standardized, and automated reef techniques that capture the complex nature of the ecosystem. Here we draw on experiences from our own interdisciplinary research programs to describe advances in in situ diver-based and autonomous reef monitoring. We present our vision for integrating interdisciplinary measurements for select "case-study" reefs worldwide and for learning patterns within the biological, physical, and chemical reef components and their interactions. Ultimately, these efforts could support the development of a scalable and standardized suite of sensors that capture and relay key data to assist in categorizing reef health. This framework has the potential to provide stakeholders with the information necessary to assess reef health during an unprecedented time of reef change as well as restoration and intervention activities.
Collapse
Affiliation(s)
- Amy Apprill
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Yogesh Girdhar
- Department
of Applied Ocean Sciences and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - T. Aran Mooney
- Biology
Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Colleen M. Hansel
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Matthew H. Long
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Yaqin Liu
- Marine
Policy Center, Woods Hole Oceanographic
Institution, Woods Hole, Massachusetts 02543, United States
| | - W. Gordon Zhang
- Department
of Applied Ocean Sciences and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Jason Kapit
- Department
of Applied Ocean Sciences and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Konrad Hughen
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Jeff Coogan
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Austin Greene
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| |
Collapse
|
15
|
Nelson CE, Wegley Kelly L, Haas AF. Microbial Interactions with Dissolved Organic Matter Are Central to Coral Reef Ecosystem Function and Resilience. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:431-460. [PMID: 36100218 DOI: 10.1146/annurev-marine-042121-080917] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
To thrive in nutrient-poor waters, coral reefs must retain and recycle materials efficiently. This review centers microbial processes in facilitating the persistence and stability of coral reefs, specifically the role of these processes in transforming and recycling the dissolved organic matter (DOM) that acts as an invisible currency in reef production, nutrient exchange, and organismal interactions. The defining characteristics of coral reefs, including high productivity, balanced metabolism, high biodiversity, nutrient retention, and structural complexity, are inextricably linked to microbial processing of DOM. The composition of microbes and DOM in reefs is summarized, and the spatial and temporal dynamics of biogeochemical processes carried out by microorganisms in diverse reef habitats are explored in a variety of key reef processes, including decomposition, accretion, trophictransfer, and macronutrient recycling. Finally, we examine how widespread habitat degradation of reefs is altering these important microbe-DOM interactions, creating feedbacks that reduce reef resilience to global change.
Collapse
Affiliation(s)
- Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, and Sea Grant College Program, School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA;
| | - Linda Wegley Kelly
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA;
| | - Andreas F Haas
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands;
| |
Collapse
|
16
|
ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction. Metabolites 2022; 12:metabo12121275. [PMID: 36557313 PMCID: PMC9786801 DOI: 10.3390/metabo12121275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify molecular networks; however, currently no annotation propagation tools leverage consensus confidence strategies enabled by hierarchical chemical ontologies or enable the use of new in silico tools without significant modification. Herein we present ConCISE (Consensus Classifications of In Silico Elucidations) which is the first tool to fuse molecular networking, spectral library matching and in silico class predictions to establish accurate putative classifications for entire subnetworks. By limiting annotation propagation to only structural classes which are identical for the majority of ion features within a subnetwork, ConCISE maintains a true positive rate greater than 95% across all levels of the ChemOnt hierarchical ontology used by the ClassyFire annotation software (superclass, class, subclass). The ConCISE framework expanded the proportion of reliable and consistent ion feature annotation up to 76%, allowing for improved assessment of the chemo-diversity of dissolved organic matter pools from three complex marine metabolomics datasets comprising dominant reef primary producers, five species of the diatom genus Pseudo-nitzchia, and stromatolite sediment samples.
Collapse
|
17
|
Mauduit M, Greff S, Herbette G, Naubron JV, Chentouf S, Huy Ngo T, Nam JW, Molinari S, Mabrouki F, Garayev E, Baghdikian B, Pérez T, Simmler C. Diving into the Molecular Diversity of Aplysina cavernicola's Exometabolites: Contribution of Bromo-Spiroisoxazoline Alkaloids. ACS OMEGA 2022; 7:43068-43083. [PMID: 36467926 PMCID: PMC9713894 DOI: 10.1021/acsomega.2c05415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Sponges are prolific producers of specialized metabolites with unique structural scaffolds. Their chemical diversity has always inspired natural product chemists working in drug discovery. As part of their metabolic filter-feeding activities, sponges are known to release molecules, possibly including their specialized metabolites. These released "Exo-Metabolites" (EMs) may be considered as new chemical reservoirs that could be collected from the water column while preserving marine biodiversity. The present work aims to determine the proportion and diversity of specialized EMs released by the sponge Aplysina cavernicola (Vacelet 1959). This Mediterranean sponge produces bromo-spiroisoxazoline alkaloids that are widely distributed in the Aplysinidae family. Aquarium experiments were designed to facilitate a continuous concentration of dissolved and diluted metabolites from the seawater around the sponges. Mass Spectrometry (MS)-based metabolomics combined with a dereplication pipeline were performed to investigate the proportion and identity of brominated alkaloids released as EMs. Chemometric analysis revealed that brominated features represented 12% of the total sponge's EM features. Consequently, a total of 13 bromotyrosine alkaloids were reproducibly detected as EMs. The most abundant ones were aerothionin, purealidin L, aerophobin 1, and a new structural congener, herein named aplysine 1. Their structural identity was confirmed by NMR analyses following their isolation. MS-based quantification indicated that these major brominated EMs represented up to 1.0 ± 0.3% w/w of the concentrated seawater extract. This analytical workflow and collected results will serve as a stepping stone to characterize the composition of A. cavernicola's EMs and those released by other sponges through in situ experiments, leading to further evaluate the biological properties of such EMs.
Collapse
Affiliation(s)
- Morgane Mauduit
- IMBE,
UMR CNRS 7263, IRD 237, Aix Marseille Université, Avignon Université,
Endoume Marine Station, Chemin de la batterie des lions, 13007 Marseille, France
| | - Stéphane Greff
- IMBE,
UMR CNRS 7263, IRD 237, Aix Marseille Université, Avignon Université,
Endoume Marine Station, Chemin de la batterie des lions, 13007 Marseille, France
| | - Gaëtan Herbette
- Aix
Marseille Université, CNRS, Centrale Marseille, FSCM-Spectropole,Service 511, Campus Saint-Jérome, 13397 Marseille, France
| | - Jean-Valère Naubron
- Aix
Marseille Université, CNRS, Centrale Marseille, FSCM-Spectropole,Service 511, Campus Saint-Jérome, 13397 Marseille, France
| | - Sara Chentouf
- Aix
Marseille Université, CNRS, Centrale Marseille, FSCM-Spectropole,Service 511, Campus Saint-Jérome, 13397 Marseille, France
| | - Trung Huy Ngo
- College
of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, South Korea
| | - Joo-Won Nam
- College
of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, South Korea
| | - Sacha Molinari
- IMBE,
UMR CNRS 7263, IRD 237, Aix Marseille Université, Avignon Université,
Endoume Marine Station, Chemin de la batterie des lions, 13007 Marseille, France
| | - Fathi Mabrouki
- IMBE,
UMR CNRS 7263, IRD 237, Aix Marseille Université, Avignon Université,
Faculté de Pharmacie, 27 Boulevard Jean Moulin, 13385 Marseille, Cedex 5, France
| | - Elnur Garayev
- IMBE,
UMR CNRS 7263, IRD 237, Aix Marseille Université, Avignon Université,
Faculté de Pharmacie, 27 Boulevard Jean Moulin, 13385 Marseille, Cedex 5, France
| | - Béatrice Baghdikian
- IMBE,
UMR CNRS 7263, IRD 237, Aix Marseille Université, Avignon Université,
Faculté de Pharmacie, 27 Boulevard Jean Moulin, 13385 Marseille, Cedex 5, France
| | - Thierry Pérez
- IMBE,
UMR CNRS 7263, IRD 237, Aix Marseille Université, Avignon Université,
Endoume Marine Station, Chemin de la batterie des lions, 13007 Marseille, France
| | - Charlotte Simmler
- IMBE,
UMR CNRS 7263, IRD 237, Aix Marseille Université, Avignon Université,
Endoume Marine Station, Chemin de la batterie des lions, 13007 Marseille, France
| |
Collapse
|
18
|
Hu IH, Hemond HF. Benthic Fluxes of Fluorescent Dissolved Organic Material, Salt, and Heat Measured by Multiple-Sensor Aquatic Eddy Covariance. SENSORS (BASEL, SWITZERLAND) 2022; 22:8984. [PMID: 36433578 PMCID: PMC9696887 DOI: 10.3390/s22228984] [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: 08/30/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Aquatic eddy covariance (AEC) is an in situ technique for measuring fluxes in marine and freshwater systems that is based on the covariance of velocity and concentration measurements. To date, AEC has mainly been applied to the measurement of benthic oxygen fluxes. Here, development of a fast multiple-channel sensor enables the use of AEC for measurement of benthic fluxes of fluorescent material, salt, and heat at three distinct sites in Massachusetts, USA, including the Connecticut River, the Concord River, and Upper Mystic Lake. Benthic fluxes of salt, useful as a tracer for groundwater input (submarine groundwater discharge), were consistent with independent measurements made with seepage meters. Eddy fluxes of heat were consistent with the balance of incoming solar radiation and thermal conduction at the sediment surface. Benthic eddy fluxes of fluorescent dissolved organic material (FDOM) revealed a substantial net downward flux in the humic-rich Concord River, suggesting that microbial consumption of dissolved organic carbon in the sediment was significant. Simultaneous measurement of several fluxes expands the utility of AEC as a biogeochemical tool while enabling checks for mutual consistency among data channels.
Collapse
Affiliation(s)
- Irene H. Hu
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Harold F. Hemond
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
19
|
Weber L, Soule MK, Longnecker K, Becker CC, Huntley N, Kujawinski EB, Apprill A. Benthic exometabolites and their ecological significance on threatened Caribbean coral reefs. ISME COMMUNICATIONS 2022; 2:101. [PMID: 37938276 PMCID: PMC9723752 DOI: 10.1038/s43705-022-00184-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 09/02/2023]
Abstract
Benthic organisms are the architectural framework supporting coral reef ecosystems, but their community composition has recently shifted on many reefs. Little is known about the metabolites released from these benthic organisms and how compositional shifts may influence other reef life, including prolific microorganisms. To investigate the metabolite composition of benthic exudates and their ecological significance for reef microbial communities, we harvested exudates from six species of Caribbean benthic organisms including stony corals, octocorals, and an invasive encrusting alga, and subjected these exudates to untargeted and targeted metabolomics approaches using liquid chromatography-mass spectrometry. Incubations with reef seawater microorganisms were conducted to monitor changes in microbial abundances and community composition using 16 S rRNA gene sequencing in relation to exudate source and three specific metabolites. Exudates were enriched in amino acids, nucleosides, vitamins, and indole-based metabolites, showing that benthic organisms contribute labile organic matter to reefs. Furthermore, exudate compositions were species-specific, and riboflavin and pantothenic acid emerged as significant coral-produced metabolites, while caffeine emerged as a significant invasive algal-produced metabolite. Microbial abundances and individual microbial taxa responded differently to exudates from stony corals and octocorals, demonstrating that exudate mixtures released from different coral species select for specific bacteria. In contrast, microbial communities did not respond to individual additions of riboflavin, pantothenic acid, or caffeine. This work indicates that recent shifts in benthic organisms alter exudate composition and likely impact microbial communities on coral reefs.
Collapse
Affiliation(s)
- Laura Weber
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.
| | - Melissa Kido Soule
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Krista Longnecker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Cynthia C Becker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA
| | - Naomi Huntley
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- Marine and Environmental Science Department, University of the Virgin Islands, Charlotte Amalie West, St Thomas, Charlotte Amalie, VI, 00802, USA
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Elizabeth B Kujawinski
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Amy Apprill
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.
| |
Collapse
|
20
|
Campana S, Riesgo A, Jongepier E, Fuss J, Muyzer G, de Goeij JM. Meta-transcriptomic comparison of two sponge holobionts feeding on coral- and macroalgal-dissolved organic matter. BMC Genomics 2022; 23:674. [PMID: 36175840 PMCID: PMC9520939 DOI: 10.1186/s12864-022-08893-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 09/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background Sponge holobionts (i.e., the host and its associated microbiota) play a key role in the cycling of dissolved organic matter (DOM) in marine ecosystems. On coral reefs, an ecological shift from coral-dominated to algal-dominated ecosystems is currently occurring. Given that benthic corals and macroalgae release different types of DOM, in different abundances and with different bioavailability to sponge holobionts, it is important to understand how the metabolic activity of the host and associated microbiota change in response to the exposure to both DOM sources. Here, we look at the differential gene expression of two sponge holobionts 6 hours after feeding on naturally sourced coral- and macroalgal-DOM using RNA sequencing and meta-transcriptomic analysis. Results We found a slight, but significant differential gene expression in the comparison between the coral- and macroalgal-DOM treatments in both the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Haliclona vansoesti. In the hosts, processes that regulate immune response, signal transduction, and metabolic pathways related to cell proliferation were elicited. In the associated microbiota carbohydrate metabolism was upregulated in both treatments, but coral-DOM induced further lipid and amino acids biosynthesis, while macroalgal-DOM caused a stress response. These differences could be driven by the presence of distinct organic macronutrients in the two DOM sources and of small pathogens or bacterial virulence factors in the macroalgal-DOM. Conclusions This work provides two new sponge meta-transcriptomes and a database of putative genes and genetic pathways that are involved in the differential processing of coral- versus macroalgal-DOM as food source to sponges with high and low abundances of associated microbes. These pathways include carbohydrate metabolism, signaling pathways, and immune responses. However, the differences in the meta-transcriptomic responses of the sponge holobionts after 6 hours of feeding on the two DOM sources were small. Longer-term responses to both DOM sources should be assessed to evaluate how the metabolism and the ecological function of sponges will be affected when reefs shift from coral towards algal dominance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08893-y.
Collapse
Affiliation(s)
- Sara Campana
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Post Office Box 94240, 1090, Amsterdam, GE, Netherlands.
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Evelien Jongepier
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Post Office Box 94240, 1090, Amsterdam, GE, Netherlands
| | - Janina Fuss
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Post Office Box 94240, 1090, Amsterdam, GE, Netherlands
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Post Office Box 94240, 1090, Amsterdam, GE, Netherlands.,CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
| |
Collapse
|
21
|
Xu N, Wang W, Xu K, Xu Y, Ji D, Chen C, Xie C. Cultivation of different seaweed species and seasonal changes cause divergence of the microbial community in coastal seawaters. Front Microbiol 2022; 13:988743. [PMID: 36160253 PMCID: PMC9490310 DOI: 10.3389/fmicb.2022.988743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/17/2022] [Indexed: 12/02/2022] Open
Abstract
Although the effects of certain species of seaweed on the microbial community structure have long been a research focus in marine ecology, the response of the microbial community to seasons and different seaweed species is poorly understood. In the present study, a total of 39 seawater samples were collected during 3 months from three zones: Neoporphyra haitanensis cultivation zones (P), Gracilaria lemaneiformis-Saccharina japonica mixed cultivation zones (G), and control zones (C). These samples were then analyzed using 18S and 16S rRNA gene sequencing to ascertain the fungal and bacterial communities, respectively, along with the determination of environmental factors. Our results showed that increased dissolved oxygen (DO), decreased inorganic nutrients, and released dissolved organic matter (DOM) in seaweed cultivation zone predominantly altered the variability of eukaryotic and prokaryotic microbial communities. Certain microbial groups such as Aurantivirga, Pseudomonas, and Woeseia were stimulated and enriched in response to seaweed cultivation, and the enriched microorganisms varied across seaweed cultivation zones due to differences in the composition of released DOM. In addition, seasonal changes in salinity and temperature were strongly correlated with microbial community composition and structure. Our study provides new insights into the interactions between seaweed and microbial communities.
Collapse
Affiliation(s)
- Ningning Xu
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Wenlei Wang
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Kai Xu
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Yan Xu
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Dehua Ji
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Changsheng Chen
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Chaotian Xie
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
- *Correspondence: Chaotian Xie,
| |
Collapse
|
22
|
Simon C, Dührkop K, Petras D, Roth VN, Böcker S, Dorrestein PC, Gleixner G. Mass Difference Matching Unfolds Hidden Molecular Structures of Dissolved Organic Matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11027-11040. [PMID: 35834352 PMCID: PMC9352317 DOI: 10.1021/acs.est.2c01332] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/20/2022] [Accepted: 06/30/2022] [Indexed: 05/30/2023]
Abstract
Ultrahigh-resolution Fourier transform mass spectrometry (FTMS) has revealed unprecedented details of natural complex mixtures such as dissolved organic matter (DOM) on a molecular formula level, but we lack approaches to access the underlying structural complexity. We here explore the hypothesis that every DOM precursor ion is potentially linked with all emerging product ions in FTMS2 experiments. The resulting mass difference (Δm) matrix is deconvoluted to isolate individual precursor ion Δm profiles and matched with structural information, which was derived from 42 Δm features from 14 in-house reference compounds and a global set of 11 477 Δm features with assigned structure specificities, using a dataset of ∼18 000 unique structures. We show that Δm matching is highly sensitive in predicting potential precursor ion identities in terms of molecular and structural composition. Additionally, the approach identified unresolved precursor ions and missing elements in molecular formula annotation (P, Cl, F). Our study provides first results on how Δm matching refines structural annotations in van Krevelen space but simultaneously demonstrates the wide overlap between potential structural classes. We show that this effect is likely driven by chemodiversity and offers an explanation for the observed ubiquitous presence of molecules in the center of the van Krevelen space. Our promising first results suggest that Δm matching can both unfold the structural information encrypted in DOM and assess the quality of FTMS-derived molecular formulas of complex mixtures in general.
Collapse
Affiliation(s)
- Carsten Simon
- Molecular
Biogeochemistry, Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
| | - Kai Dührkop
- Chair
for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Daniel Petras
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California
San Diego, 9500 Gilman Drive, MC 0657, La Jolla, California 92093-0657, United States of America
- CMFI
Cluster of Excellence, Interfaculty Institute of Microbiology and
Medicine, University of Tübingen, Auf der Morgenstelle 24, 72076 Tübingen, Germany
| | - Vanessa-Nina Roth
- Molecular
Biogeochemistry, Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
| | - Sebastian Böcker
- Chair
for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Pieter C. Dorrestein
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California
San Diego, 9500 Gilman Drive, MC 0657, La Jolla, California 92093-0657, United States of America
| | - Gerd Gleixner
- Molecular
Biogeochemistry, Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
| |
Collapse
|