1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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2
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Manck LE, Coale TH, Stephens BM, Forsch KO, Aluwihare LI, Dupont CL, Allen AE, Barbeau KA. Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron. ISME J 2024; 18:wrae061. [PMID: 38624181 PMCID: PMC11069385 DOI: 10.1093/ismejo/wrae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected insitu. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.
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Affiliation(s)
- Lauren E Manck
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
- Flathead Lake Biological Station, University of Montana, Polson, MT 59860, United States
| | - Tyler H Coale
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, United States
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, United States
| | - Brandon M Stephens
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
- Institute of Oceanography, National Taiwan University, Taipei, 106, Taiwan
| | - Kiefer O Forsch
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
| | - Lihini I Aluwihare
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
| | - Christopher L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, United States
- Department of Human Health, J. Craig Venter Institute, La Jolla, CA 92037, United States
- Department of Synthetic Biology, J. Craig Venter Institute, La Jolla, CA 92037, United States
| | - Andrew E Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, United States
| | - Katherine A Barbeau
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
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3
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James BD, Reddy CM, Hahn ME, Nelson RK, de Vos A, Aluwihare LI, Wade TL, Knap AH, Bera G. Fire and Oil Led to Complex Mixtures of PAHs on Burnt and Unburnt Plastic during the M/V X-Press Pearl Disaster. ACS Environ Au 2023; 3:319-335. [PMID: 37743953 PMCID: PMC10515710 DOI: 10.1021/acsenvironau.3c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/25/2023] [Accepted: 06/29/2023] [Indexed: 09/26/2023]
Abstract
In May 2021, the M/V X-Press Pearl container ship burned for 2 weeks, leading to the largest maritime spill of resin pellets (nurdles). The disaster was exacerbated by the leakage of other cargo and the ship's underway fuel. This disaster affords the unique opportunity to study a time-stamped, geolocated release of plastic under real-world conditions. Field samples collected from beaches in Sri Lanka nearest to the ship comprised nurdles exposed to heat and combustion, burnt plastic pieces (pyroplastic), and oil-plastic agglomerates (petroplastic). An unresolved question is whether the 1600+ tons of spilled and recovered plastic should be considered hazardous waste. Due to the known formation and toxicity of combustion-derived polycyclic aromatic hydrocarbons (PAHs), we measured 20 parent and 21 alkylated PAHs associated with several types of spilled plastic. The maximum PAH content of the sampled pyroplastic had the greatest amount of PAHs recorded for marine plastic debris (199,000 ng/g). In contrast, the sampled unburnt white nurdles had two orders of magnitude less PAH content. The PAH composition varied between the types of spilled plastic and presented features typical of and conflicting with petrogenic and pyrogenic sources. Nevertheless, specific markers and compositional changes for burning plastics were identified, revealing that the fire was the main source of PAHs. Eight months after the spill, the PAH contents of sampled stray nurdles and pyroplastic were reduced by more than 50%. Due to their PAH content exceeding levels allowable for plastic consumer goods, classifying burnt plastic as hazardous waste may be warranted. Following a largely successful cleanup, we recommend that the Sri Lankans re-evaluate the identification, handling, and disposal of the plastic debris collected from beaches and the potential exposure of responders and the public to PAHs from handling it. The maritime disaster underscores pyroplastic as a type of plastic pollution that has yet to be fully explored, despite the pervasiveness of intentional and unintentional burning of plastic globally.
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Affiliation(s)
- Bryan D. James
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
- Biology
Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Christopher M. Reddy
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Mark E. Hahn
- Biology
Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Robert K. Nelson
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Asha de Vos
- Oceanswell, 9 Park Gardens, Colombo 00500, Sri Lanka
- The
Oceans Institute, University of Western
Australia, 35 Stirling
Highway, Perth, WA 6009, Australia
| | - Lihini I. Aluwihare
- Scripps
Institution of Oceanography, University
of California San Diego, La Jolla, California 92093, United States
| | - Terry L. Wade
- Geochemical
and Environmental Research Group, Texas
A&M University, College Station, Texas 77845, United States
- Department
of Oceanography, Texas A&M University, College Station, Texas 77843, United States
| | - Anthony H. Knap
- Geochemical
and Environmental Research Group, Texas
A&M University, College Station, Texas 77845, United States
- Department
of Oceanography, Texas A&M University, College Station, Texas 77843, United States
- Department
of Ocean Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Gopal Bera
- Geochemical
and Environmental Research Group, Texas
A&M University, College Station, Texas 77845, United States
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4
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Koester I, Quinlan ZA, Nothias LF, White ME, Rabines A, Petras D, Brunson JK, Dührkop K, Ludwig M, Böcker S, Azam F, Allen AE, Dorrestein PC, Aluwihare LI. Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations. Environ Microbiol 2022; 24:5408-5424. [PMID: 36222155 PMCID: PMC9707391 DOI: 10.1111/1462-2920.16242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/09/2022] [Indexed: 11/28/2022]
Abstract
The exchange of metabolites mediates algal and bacterial interactions that maintain ecosystem function. Yet, while thousands of metabolites are produced, only a few molecules have been identified in these associations. Using the ubiquitous microalgae Pseudo-nitzschia sp., as a model, we employed an untargeted metabolomics strategy to assign structural characteristics to the metabolites that distinguished specific diatom-microbiome associations. We cultured five species of Pseudo-nitzschia, including two species that produced the toxin domoic acid, and examined their microbiomes and metabolomes. A total of 4826 molecular features were detected by tandem mass spectrometry. Only 229 of these could be annotated using available mass spectral libraries, but by applying new in silico annotation tools, characterization was expanded to 2710 features. The metabolomes of the Pseudo-nitzschia-microbiome associations were distinct and distinguished by structurally diverse nitrogen compounds, ranging from simple amines and amides to cyclic compounds such as imidazoles, pyrrolidines and lactams. By illuminating the dark metabolomes, this study expands our capacity to discover new chemical targets that facilitate microbial partnerships and uncovers the chemical diversity that underpins algae-bacteria interactions.
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Affiliation(s)
- Irina Koester
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Zachary A. Quinlan
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
| | - Margot E. White
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Ariel Rabines
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Daniel Petras
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
| | - John K. Brunson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Kai Dührkop
- Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
| | - Marcus Ludwig
- Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
| | - Farooq Azam
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Andrew E. Allen
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
| | - Lihini I. Aluwihare
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
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5
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James BD, de Vos A, Aluwihare LI, Youngs S, Ward CP, Nelson RK, Michel APM, Hahn ME, Reddy CM. Divergent Forms of Pyroplastic: Lessons Learned from the M/V X-Press Pearl Ship Fire. ACS Environ Au 2022; 2:467-479. [PMID: 37101454 PMCID: PMC10125272 DOI: 10.1021/acsenvironau.2c00020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 04/28/2023]
Abstract
In late May 2021, the M/V X-Press Pearl container ship caught fire while anchored 18 km off the coast of Colombo, Sri Lanka and spilled upward of 70 billion pieces of plastic or "nurdles" (∼1680 tons), littering the country's coastline. Exposure to combustion, heat, chemicals, and petroleum products led to an apparent continuum of changes from no obvious effects to pieces consistent with previous reports of melted and burned plastic (pyroplastic) found on beaches. At the middle of this continuum, nurdles were discolored but appeared to retain their prefire morphology, resembling nurdles that had been weathered in the environment. We performed a detailed investigation of the physical and surface properties of discolored nurdles collected on a beach 5 days after the ship caught fire and within 24 h of their arrival onshore. The color was the most striking trait of the plastic: white for nurdles with minimal alteration from the accident, orange for nurdles containing antioxidant degradation products formed by exposure to heat, and gray for partially combusted nurdles. Our color analyses indicate that this fraction of the plastic released from the ship was not a continuum but instead diverged into distinct groups. Fire left the gray nurdles scorched, with entrained particles and pools of melted plastic, and covered in soot, representing partial pyroplastics, a new subtype of pyroplastic. Cross sections showed that the heat- and fire-induced changes were superficial, leaving the surfaces more hydrophilic but the interior relatively untouched. These results provide timely and actionable information to responders to reevaluate cleanup end points, monitor the recurrence of these spilled nurdles, gauge short- and long-term effects of the spilled nurdles to the local ecosystem, and manage the recovery of the spill. These findings underscore partially combusted plastic (pyroplastic) as a type of plastic pollution that has yet to be fully explored despite the frequency at which plastic is burned globally.
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Affiliation(s)
- Bryan D. James
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
- Department
of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Asha de Vos
- Oceanswell, 9 Park Gardens, Colombo 5 00500, Sri Lanka
- The
Oceans Institute, University of Western
Australia, 35 Stirling
Highway, Perth, WA 6009, Australia
| | - Lihini I. Aluwihare
- Scripps
Institution of Oceanography, University
of California San Diego, La Jolla, California 92093, United States
| | - Sarah Youngs
- Department
of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Collin P. Ward
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Robert K. Nelson
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Anna P. M. Michel
- Department
of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Mark E. Hahn
- Department
of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Christopher M. Reddy
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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6
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Wegley Kelly L, Nelson CE, Petras D, Koester I, Quinlan ZA, Arts MGI, Nothias LF, Comstock J, White BM, Hopmans EC, van Duyl FC, Carlson CA, Aluwihare LI, Dorrestein PC, Haas AF. Distinguishing the molecular diversity, nutrient content, and energetic potential of exometabolomes produced by macroalgae and reef-building corals. Proc Natl Acad Sci U S A 2022; 119:2110283119. [PMID: 35101918 PMCID: PMC8812564 DOI: 10.1073/pnas.2110283119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 11/18/2022] Open
Abstract
Metabolites exuded by primary producers comprise a significant fraction of marine dissolved organic matter, a poorly characterized, heterogenous mixture that dictates microbial metabolism and biogeochemical cycling. We present a foundational untargeted molecular analysis of exudates released by coral reef primary producers using liquid chromatography-tandem mass spectrometry to examine compounds produced by two coral species and three types of algae (macroalgae, turfing microalgae, and crustose coralline algae [CCA]) from Mo'orea, French Polynesia. Of 10,568 distinct ion features recovered from reef and mesocosm waters, 1,667 were exuded by producers; the majority (86%) were organism specific, reflecting a clear divide between coral and algal exometabolomes. These data allowed us to examine two tenets of coral reef ecology at the molecular level. First, stoichiometric analyses show a significantly reduced nominal carbon oxidation state of algal exometabolites than coral exometabolites, illustrating one ecological mechanism by which algal phase shifts engender fundamental changes in the biogeochemistry of reef biomes. Second, coral and algal exometabolomes were differentially enriched in organic macronutrients, revealing a mechanism for reef nutrient-recycling. Coral exometabolomes were enriched in diverse sources of nitrogen and phosphorus, including tyrosine derivatives, oleoyl-taurines, and acyl carnitines. Exometabolites of CCA and turf algae were significantly enriched in nitrogen with distinct signals from polyketide macrolactams and alkaloids, respectively. Macroalgal exometabolomes were dominated by nonnitrogenous compounds, including diverse prenol lipids and steroids. This study provides molecular-level insights into biogeochemical cycling on coral reefs and illustrates how changing benthic cover on reefs influences reef water chemistry with implications for microbial metabolism.
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Affiliation(s)
- Linda Wegley Kelly
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037;
| | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI 96822
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
- CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Irina Koester
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037
| | - Zachary A Quinlan
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037
- Department of Biology, San Diego State University, San Diego, CA 92182
| | - Milou G I Arts
- Department of Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Louis-Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Jacqueline Comstock
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106
| | - Brandie M White
- Department of Biology, San Diego State University, San Diego, CA 92182
| | - Ellen C Hopmans
- Department of Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Fleur C van Duyl
- Department of Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Craig A Carlson
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106
| | - Lihini I Aluwihare
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Andreas F Haas
- Department of Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands;
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7
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Aron AT, Petras D, Schmid R, Gauglitz JM, Büttel I, Antelo L, Zhi H, Nuccio SP, Saak CC, Malarney KP, Thines E, Dutton RJ, Aluwihare LI, Raffatellu M, Dorrestein PC. Native mass spectrometry-based metabolomics identifies metal-binding compounds. Nat Chem 2022; 14:100-109. [PMID: 34795435 PMCID: PMC8959065 DOI: 10.1038/s41557-021-00803-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 08/27/2021] [Indexed: 11/09/2022]
Abstract
Although metals are essential for the molecular machineries of life, systematic methods for discovering metal-small molecule complexes from biological samples are limited. Here, we describe a two-step native electrospray ionization-mass spectrometry method, in which post-column pH adjustment and metal infusion are combined with ion identity molecular networking, a rule-based data analysis workflow. This method enabled the identification of metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion species with the same chromatographic profiles. As this native electrospray metabolomics approach is suited to the use of any liquid chromatography-mass spectrometry system to explore the binding of any metal, this method has the potential to become an essential strategy for elucidating metal-binding molecules in biology.
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Affiliation(s)
- Allegra T. Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, USA,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA,Present affiliation: CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, 72076, Germany
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, D-48149, Germany
| | - Julia M. Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, USA,Present affiliation: Sapient Bioanalytics, La Jolla, CA, 92093, USA
| | - Isabell Büttel
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz D-55128, Germany
| | - Luis Antelo
- Institute of Biotechnology and Drug Research (IBWF gGmbH), Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz D-55128, Germany
| | - Hui Zhi
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Sean-Paul Nuccio
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Christina C. Saak
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kien P. Malarney
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eckhard Thines
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz D-55128, Germany,Institute of Biotechnology and Drug Research (IBWF gGmbH), Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz D-55128, Germany
| | - Rachel J. Dutton
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA,Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lihini I. Aluwihare
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA,Chiba University-University of California San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA 92093, United States of America,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA,Correspondence to
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8
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Schmid R, Petras D, Nothias LF, Wang M, Aron AT, Jagels A, Tsugawa H, Rainer J, Garcia-Aloy M, Dührkop K, Korf A, Pluskal T, Kameník Z, Jarmusch AK, Caraballo-Rodríguez AM, Weldon KC, Nothias-Esposito M, Aksenov AA, Bauermeister A, Albarracin Orio A, Grundmann CO, Vargas F, Koester I, Gauglitz JM, Gentry EC, Hövelmann Y, Kalinina SA, Pendergraft MA, Panitchpakdi M, Tehan R, Le Gouellec A, Aleti G, Mannochio Russo H, Arndt B, Hübner F, Hayen H, Zhi H, Raffatellu M, Prather KA, Aluwihare LI, Böcker S, McPhail KL, Humpf HU, Karst U, Dorrestein PC. Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment. Nat Commun 2021; 12:3832. [PMID: 34158495 PMCID: PMC8219731 DOI: 10.1038/s41467-021-23953-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 04/26/2021] [Indexed: 12/21/2022] Open
Abstract
Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.
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Affiliation(s)
- Robin Schmid
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, Germany
| | - Louis-Félix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Annika Jagels
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Johannes Rainer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Mar Garcia-Aloy
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Kai Dührkop
- Chair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany
| | - Ansgar Korf
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Zdeněk Kameník
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | | | - Kelly C Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Melissa Nothias-Esposito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
- Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Andrea Albarracin Orio
- IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina
| | - Carlismari O Grundmann
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
- School of Pharmaceutical Sciences of Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Irina Koester
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Julia M Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Yannick Hövelmann
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | | | - Matthew A Pendergraft
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Richard Tehan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Audrey Le Gouellec
- Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France
| | - Gajender Aleti
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Helena Mannochio Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
- NuBBE, Institute of Chemistry, , São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Birgit Arndt
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Florian Hübner
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Hui Zhi
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA
| | - Kimberly A Prather
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lihini I Aluwihare
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, San Diego, CA, USA.
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9
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Stephens BM, Opalk K, Petras D, Liu S, Comstock J, Aluwihare LI, Hansell DA, Carlson CA. Organic Matter Composition at Ocean Station Papa Affects Its Bioavailability, Bacterioplankton Growth Efficiency and the Responding Taxa. Front Mar Sci 2021; 2021:10.3389/fmars.2020.590273. [PMID: 35004707 PMCID: PMC8740527 DOI: 10.3389/fmars.2020.590273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The bioavailability of organic matter (OM) to marine heterotrophic bacterioplankton is determined by both the chemical composition of OM and the microbial community composition. In the current study, changes in OM bioavailability were identified at Ocean Station Papa as part of the 2018 Export Processes in the Ocean from Remote Sensing (EXPORTS) field study. Removal rates of carbon (C) in controlled experiments were significantly correlated with the initial composition of total hydrolyzable amino acids, and C removal rates were high when the amino acid degradation index suggested a more labile composition. Carbon remineralization rates averaged 0.19 ± 0.08 μmol C L-1 d-1 over 6-10 days while bacterial growth efficiencies averaged 31 ± 7%. Amino acid composition and tandem mass spectrometry analysis of compound classes also revealed transformations to a more degraded OM composition during experiments. There was a log2-fold increase in the relative abundances of 16S rDNA-resolved bacterioplankton taxa in most experiments by members of the Methylophilaceae family (OM43 genus) and KI89A order. Additionally, when OM was more bioavailable, relative abundances increased by at least threefold for the classes Bacteroidetes (Flavobacteriaceae NS2b genus), Alphaproteobacteria (Rhodobacteraceae Sulfitobacter genus), and Gammaproteobacteria (Alteromonadales and Ectothiorhodospiraceae orders). Our data suggest that a diverse group of bacterioplankton was responsible for removing organic carbon and altering the OM composition to a more degraded state. Elevated community diversity, as inferred from the Shannon-Wiener H index, may have contributed to relatively high growth efficiencies by the bacterioplankton. The data presented here shed light on the interconnections between OM bioavailability and key bacterioplankton taxa for the degradation of marine OM.
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Affiliation(s)
- Brandon M. Stephens
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Keri Opalk
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Shuting Liu
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Jacqueline Comstock
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lihini I. Aluwihare
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Dennis A. Hansell
- Department of Ocean Sciences, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL, United States
| | - Craig A. Carlson
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
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10
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Petras D, Minich JJ, Cancelada LB, Torres RR, Kunselman E, Wang M, White ME, Allen EE, Prather KA, Aluwihare LI, Dorrestein PC. Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater. Chemosphere 2021; 271:129450. [PMID: 33460888 PMCID: PMC7969459 DOI: 10.1016/j.chemosphere.2020.129450] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 05/31/2023]
Abstract
Urbanization along coastlines alters marine ecosystems including contributing molecules of anthropogenic origin to the coastal dissolved organic matter (DOM) pool. A broad assessment of the nature and extent of anthropogenic impacts on coastal ecosystems is urgently needed to inform regulatory guidelines and ecosystem management. Recently, non-targeted tandem mass spectrometry approaches are gaining momentum for the analysis of global organic matter composition (chemotypes) including a wide array of natural and anthropogenic compounds. In line with these efforts, we developed a non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) workflow that utilizes advanced data analysis approaches such as feature-based molecular networking and repository-scale spectrum searches. This workflow allows the scalable comparison and mapping of seawater chemotypes from large-scale spatial surveys as well as molecular family level annotation of unknown compounds. As a case study, we visualized organic matter chemotype shifts in coastal environments in northern San Diego, USA, after notable rain fall in winter 2017/2018 and highlight potential anthropogenic impacts. The observed seawater chemotype, consisting of 4384 LC-MS/MS features, shifted significantly after a major rain event. Molecular drivers of this shift could be attributed to multiple anthropogenic compounds, including pesticides (Imazapyr and Isoxaben), cleaning products (Benzyl-tetradecyl-dimethylammonium) and chemical additives (Hexa (methoxymethyl)melamine) and potential degradation products. By expanding the search of identified xenobiotics to other public tandem mass spectrometry datasets, we further contextualized their possible origin and show their importance in other ecosystems. The mass spectrometry and data analysis pipelines applied here offer a scalable framework for future molecular mapping and monitoring of marine ecosystems, which will contribute to a deliberate assessment of how chemical pollution impacts our oceans.
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Affiliation(s)
- Daniel Petras
- University of California San Diego, Collaborative Mass Spectrometry Innovation Center, 9500, Gilman Drive, La Jolla, USA; University of California San Diego, Scripps Institution of Oceanography, 8622 Kennel Way, La Jolla, USA.
| | - Jeremiah J Minich
- University of California San Diego, Scripps Institution of Oceanography, 8622 Kennel Way, La Jolla, USA
| | - Lucia B Cancelada
- University of California San Diego, Department of Chemistry, 9500, Gilman Drive, La Jolla, USA
| | - Ralph R Torres
- University of California San Diego, Scripps Institution of Oceanography, 8622 Kennel Way, La Jolla, USA
| | - Emily Kunselman
- University of California San Diego, Scripps Institution of Oceanography, 8622 Kennel Way, La Jolla, USA
| | - Mingxun Wang
- University of California San Diego, Collaborative Mass Spectrometry Innovation Center, 9500, Gilman Drive, La Jolla, USA
| | - Margot E White
- University of California San Diego, Scripps Institution of Oceanography, 8622 Kennel Way, La Jolla, USA
| | - Eric E Allen
- University of California San Diego, Scripps Institution of Oceanography, 8622 Kennel Way, La Jolla, USA; University of California San Diego, Center for Microbiome Innovation, 9500, Gilman Drive, La Jolla, USA
| | - Kimberly A Prather
- University of California San Diego, Scripps Institution of Oceanography, 8622 Kennel Way, La Jolla, USA; University of California San Diego, Department of Chemistry, 9500, Gilman Drive, La Jolla, USA
| | - Lihini I Aluwihare
- University of California San Diego, Scripps Institution of Oceanography, 8622 Kennel Way, La Jolla, USA
| | - Pieter C Dorrestein
- University of California San Diego, Collaborative Mass Spectrometry Innovation Center, 9500, Gilman Drive, La Jolla, USA; University of California San Diego, Department of Chemistry, 9500, Gilman Drive, La Jolla, USA
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11
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Kharbush JJ, Thompson LR, Haroon MF, Knight R, Aluwihare LI. Hopanoid-producing bacteria in the Red Sea include the major marine nitrite oxidizers. FEMS Microbiol Ecol 2019; 94:4969676. [PMID: 29668882 DOI: 10.1093/femsec/fiy063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 01/26/2023] Open
Abstract
Hopanoids, including the extended side chain-containing bacteriohopanepolyols, are bacterial lipids found abundantly in the geological record and across Earth's surface environments. However, the physiological roles of this biomarker remain uncertain, limiting interpretation of their presence in current and past environments. Recent work investigating the diversity and distribution of hopanoid producers in the marine environment implicated low-oxygen regions as important loci of hopanoid production, and data from marine oxygen minimum zones suggested that the dominant hopanoid producers in these environments are nitrite-utilizing organisms, revealing a potential connection between hopanoid production and the marine nitrogen cycle. Here, we use metagenomic data from the Red Sea to investigate the ecology of hopanoid producers in an environmental setting that is biogeochemically distinct from those investigated previously. The distributions of hopanoid production and nitrite oxidation genes in the Red Sea are closely correlated, and the majority of hopanoid producers are taxonomically affiliated with the major marine nitrite oxidizers, Nitrospinae and Nitrospirae. These results suggest that the relationship between hopanoid production and nitrite oxidation is conserved across varying biogeochemical conditions in dark ocean microbial ecosystems.
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Affiliation(s)
- Jenan J Kharbush
- Department of Earth and Plantary Sciences, Harvard University, Cambridge, MA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Luke R Thompson
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Mohamed Fauzi Haroon
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Lihini I Aluwihare
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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12
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Arakawa N, Aluwihare LI, Simpson AJ, Soong R, Stephens BM, Lane-Coplen D. Carotenoids are the likely precursor of a significant fraction of marine dissolved organic matter. Sci Adv 2017; 3:e1602976. [PMID: 28959723 PMCID: PMC5617377 DOI: 10.1126/sciadv.1602976] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 09/06/2017] [Indexed: 05/31/2023]
Abstract
The ocean's biota sequester atmospheric carbon dioxide (CO2) in part by producing dissolved organic matter (DOM) that persists in the ocean for millennia. This long-term accumulation of carbon may be facilitated by abiotic and biotic production of chemical structures that resist degradation, consequently contributing disproportionately to refractory DOM. Compounds that are selectively preserved in seawater were identified in solid-phase extracted DOM (PPL-DOM) using comprehensive gas chromatography (GC) coupled to mass spectrometry (MS). These molecules contained cyclic head groups that were linked to isoprenoid tails, and their overall structures closely resembled carotenoid degradation products (CDP). The origin of these compounds in PPL-DOM was further confirmed with an in vitro β-carotene photooxidation experiment that generated water-soluble CDP with similar structural characteristics. The molecular-level identification linked at least 10% of PPL-DOM carbon, and thus 4% of total DOM carbon, to CDP. Nuclear magnetic resonance spectra of experimental CDP and environmental PPL-DOM overlapped considerably, which indicated that even a greater proportion of PPL-DOM was likely composed of CDP. The CDP-rich DOM fraction was depleted in radiocarbon (14C age > 1500 years), a finding that supports the possible long-term accumulation of CDP in seawater. By linking a specific class of widespread biochemicals to refractory DOM, this work provides a foundation for future studies that aim to examine how persistent DOM forms in the ocean.
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Affiliation(s)
- Neal Arakawa
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0244, USA
| | - Lihini I. Aluwihare
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0244, USA
| | - Andre J. Simpson
- Environmental Nuclear Magnetic Resonance Center, University of Toronto, Scarborough Campus, Toronto, Ontario M1C 1A4, Canada
| | - Ronald Soong
- Environmental Nuclear Magnetic Resonance Center, University of Toronto, Scarborough Campus, Toronto, Ontario M1C 1A4, Canada
| | - Brandon M. Stephens
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0244, USA
| | - Daniel Lane-Coplen
- Environmental Nuclear Magnetic Resonance Center, University of Toronto, Scarborough Campus, Toronto, Ontario M1C 1A4, Canada
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Abstract
Polyhalogenated N-methylbipyrroles of two different structure classes have been detected worldwide in over 100 environmental samples including seawater, bird eggs, fish, dolphin blubber, and in the breast milk of humans that consume seafood. These molecules are concentrated in the fatty tissues in comparable abundance to some of the most important anthropogenic contaminants, such as the halogenated flame-retardants and pesticides. Although the origin of these compounds is still unknown, we present evidence that the production of these materials can involve the direct ozone activated seawater halogenation of N-methylbipyrrole precursors. This observation shows that environmental polyhalogenated bipyrroles can be produced via an abiotic process, and implies that the ozone activated halogenation of a variety of natural and anthropogenic seawater organics may be a significant process occurring in surface ocean waters.
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Affiliation(s)
- Abdhesh Kumar
- Scripps Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, United States
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, United States
| | - Miles Borgen
- Scripps Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, United States
- Geoscience Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, United States
| | - Lihini I. Aluwihare
- Scripps Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, United States
- Geoscience Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, United States
| | - William Fenical
- Scripps Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, United States
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, United States
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14
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Mackintosh SA, Dodder NG, Shaul NJ, Aluwihare LI, Maruya KA, Chivers SJ, Danil K, Weller DW, Hoh E. Newly Identified DDT-Related Compounds Accumulating in Southern California Bottlenose Dolphins. Environ Sci Technol 2016; 50:12129-12137. [PMID: 27737539 PMCID: PMC6310127 DOI: 10.1021/acs.est.6b03150] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Nontargeted GC×GC-TOF/MS analysis of blubber from 8 common bottlenose dolphins (Tursiops truncatus) inhabiting the Southern California Bight was performed to identify novel, bioaccumulative DDT-related compounds and to determine their abundance relative to the commonly studied DDT-related compounds. We identified 45 bioaccumulative DDT-related compounds of which the majority (80%) is not typically monitored in environmental media. Identified compounds include transformation products, technical mixture impurities such as tris(chlorophenyl)methane (TCPM), the presumed TCPM metabolite tris(chlorophenyl)methanol (TCPMOH), and structurally related compounds with unknown sources, such as hexa- to octachlorinated diphenylethene. To investigate impurities in pesticide mixtures as possible sources of these compounds, we analyzed technical DDT, the primary source of historical contamination in the region, and technical Dicofol, a current use pesticide that contains DDT-related compounds. The technical mixtures contained only 33% of the compounds identified in the blubber, suggesting that transformation products contribute to the majority of the load of DDT-related contaminants in these sentinels of ocean health. Quantitative analysis revealed that TCPM was the second most abundant compound class detected in the blubber, following DDE, and TCPMOH loads were greater than DDT. QSPR estimates verified 4,4',4″-TCPM and 4,4'4,″-TCPMOH are persistent and bioaccumulative.
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Affiliation(s)
- Susan A. Mackintosh
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Graduate School of Public Health, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, United States
- San Diego State University Research Foundation, 5250 Campanile Drive, San Diego, California 92182, United States
| | - Nathan G. Dodder
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Graduate School of Public Health, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, United States
- San Diego State University Research Foundation, 5250 Campanile Drive, San Diego, California 92182, United States
| | - Nellie J. Shaul
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Lihini I. Aluwihare
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Keith A. Maruya
- Southern California Coastal Water Research Project Authority, 3535 Harbor Boulevard, Suite 110, Costa Mesa, California 92626, United States
| | - Susan J. Chivers
- Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, California 92037, United States
| | - Kerri Danil
- Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, California 92037, United States
| | - David W. Weller
- Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, California 92037, United States
| | - Eunha Hoh
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Graduate School of Public Health, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, United States
- Corresponding Author: Phone: +16195944671. Fax: +16195946112.
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Kharbush JJ, Kejriwal K, Aluwihare LI. Distribution and Abundance of Hopanoid Producers in Low-Oxygen Environments of the Eastern Pacific Ocean. Microb Ecol 2016; 71:401-408. [PMID: 26377203 DOI: 10.1007/s00248-015-0671-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/31/2015] [Indexed: 06/05/2023]
Abstract
Hopanoids are bacterial membrane lipid biomarker molecules that feature prominently in the molecular fossil record. In the modern marine water column, recent reports implicate bacteria inhabiting low-oxygen environments as important sources of hopanoids to marine sediments. However, the preliminary biogeography reported by recent studies and the environmental conditions governing such distributions can only be confirmed when the numerical abundance of these organisms is known with more certainty. In this study, we employ two different approaches to examine the quantitative significance of phylogenetically distinct hopanoid producers in low-oxygen environments. First, we develop a novel quantitative PCR (qPCR) assay for the squalene hopene cyclase (sqhC) gene, targeting a subset of hopanoid producers previously identified to be important in the eastern North Pacific Ocean. The results represent the first quantitative gene abundance data of any kind for hopanoid producers in the marine water column and show that these putative alphaproteobacterial hopanoid producers are rare, comprising at most 0.2 % of the total bacterial community in our samples. Second, a complementary analysis of existing low-oxygen metagenomic datasets further examined the generality of the qPCR observation. We find that the dominant sqhC sequences in these metagenomic datasets are associated with phyla such as Nitrospinae rather than Proteobacteria, consistent with the qPCR finding that alphaproteobacterial hopanoid producers are not very abundant in low-oxygen environments. In fact, positive correlations between sqhC gene abundance and environmental parameters in these samples identify nitrite availability as a potentially important factor in the ecology of hopanoid producers that dominate low-oxygen environments.
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Affiliation(s)
- Jenan J Kharbush
- Scripps Institution of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Kanchi Kejriwal
- Scripps Institution of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Lihini I Aluwihare
- Scripps Institution of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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16
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Shaul N, Dodder NG, Aluwihare LI, Mackintosh S, Maruya K, Chivers SJ, Danil K, Weller DW, Hoh E. Nontargeted biomonitoring of halogenated organic compounds in two ecotypes of bottlenose dolphins (Tursiops truncatus) from the Southern California Bight. Environ Sci Technol 2015; 49:1328-38. [PMID: 25526519 PMCID: PMC4319685 DOI: 10.1021/es505156q] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/08/2014] [Accepted: 12/19/2014] [Indexed: 05/18/2023]
Abstract
Targeted environmental monitoring reveals contamination by known chemicals, but may exclude potentially pervasive but unknown compounds. Marine mammals are sentinels of persistent and bioaccumulative contaminants due to their longevity and high trophic position. Using nontargeted analysis, we constructed a mass spectral library of 327 persistent and bioaccumulative compounds identified in blubber from two ecotypes of common bottlenose dolphins (Tursiops truncatus) sampled in the Southern California Bight. This library of halogenated organic compounds (HOCs) consisted of 180 anthropogenic contaminants, 41 natural products, 4 with mixed sources, 8 with unknown sources, and 94 with partial structural characterization and unknown sources. The abundance of compounds whose structures could not be fully elucidated highlights the prevalence of undiscovered HOCs accumulating in marine food webs. Eighty-six percent of the identified compounds are not currently monitored, including 133 known anthropogenic chemicals. Compounds related to dichlorodiphenyltrichloroethane (DDT) were the most abundant. Natural products were, in some cases, detected at abundances similar to anthropogenic compounds. The profile of naturally occurring HOCs differed between ecotypes, suggesting more abundant offshore sources of these compounds. This nontargeted analytical framework provided a comprehensive list of HOCs that may be characteristic of the region, and its application within monitoring surveys may suggest new chemicals for evaluation.
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Affiliation(s)
- Nellie
J. Shaul
- Center
for Oceans and Human Health, Scripps Institution of Oceanography, University of California—San Diego, 9500 Gilman Drive, La Jolla, California 92037, United States
- Scripps
Institution of Oceanography, University
of California—San Diego, 9500 Gilman Drive, La Jolla, California 92037, United States
| | - Nathan G. Dodder
- Southern
California Coastal Water Research Project Authority, 3535 Harbor Boulevard, Suite 110, Costa Mesa, California 92626, United States
| | - Lihini I. Aluwihare
- Center
for Oceans and Human Health, Scripps Institution of Oceanography, University of California—San Diego, 9500 Gilman Drive, La Jolla, California 92037, United States
- Scripps
Institution of Oceanography, University
of California—San Diego, 9500 Gilman Drive, La Jolla, California 92037, United States
| | - Susan
A. Mackintosh
- Center
for Oceans and Human Health, Scripps Institution of Oceanography, University of California—San Diego, 9500 Gilman Drive, La Jolla, California 92037, United States
- Graduate
School of Public Health, San Diego State
University, 5500 Campanile
Drive, San Diego, California 92182, United States
- San
Diego State University Research Foundation, 5250 Campanile Drive, San
Diego, California 92182, United States
| | - Keith
A. Maruya
- Southern
California Coastal Water Research Project Authority, 3535 Harbor Boulevard, Suite 110, Costa Mesa, California 92626, United States
| | - Susan J. Chivers
- Marine Mammal
& Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic
and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, California 92037, United States
| | - Kerri Danil
- Marine Mammal
& Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic
and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, California 92037, United States
| | - David W. Weller
- Marine Mammal
& Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic
and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, California 92037, United States
| | - Eunha Hoh
- Center
for Oceans and Human Health, Scripps Institution of Oceanography, University of California—San Diego, 9500 Gilman Drive, La Jolla, California 92037, United States
- Graduate
School of Public Health, San Diego State
University, 5500 Campanile
Drive, San Diego, California 92182, United States
- Phone: +16195944671; fax: +16195946112; e-mail:
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Agarwal V, Li J, Rahman I, Borgen M, Aluwihare LI, Biggs JS, Paul VJ, Moore BS. Complexity of naturally produced polybrominated diphenyl ethers revealed via mass spectrometry. Environ Sci Technol 2015; 49:1339-46. [PMID: 25559102 PMCID: PMC4358748 DOI: 10.1021/es505440j] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs) are persistent and bioaccumulative anthropogenic and natural chemicals that are broadly distributed in the marine environment. PBDEs are potentially toxic due to inhibition of various mammalian signaling pathways and enzymatic reactions. PBDE isoforms vary in toxicity in accordance with structural differences, primarily in the number and pattern of hydroxyl moieties afforded upon a conserved core structure. Over four decades of isolation and discovery-based efforts have established an impressive repertoire of natural PBDEs. Based on our recent reports describing the bacterial biosyntheses of PBDEs, we predicted the presence of additional classes of PBDEs to those previously identified from marine sources. Using mass spectrometry and NMR spectroscopy, we now establish the existence of new structural classes of PBDEs in marine sponges. Our findings expand the chemical space explored by naturally produced PBDEs, which may inform future environmental toxicology studies. Furthermore, we provide evidence for iodinated PBDEs and direct attention toward the contribution of promiscuous halogenating enzymes in further expanding the diversity of these polyhalogenated marine natural products.
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Affiliation(s)
- Vinayak Agarwal
- Scripps Center for Oceans and Human Health, University of California at San Diego, San Diego, California 92037, United States
| | - Jie Li
- Center for Marine Biotechnology and Biomedicine, University of California at San Diego, San Diego, California 92037, United States
| | - Imran Rahman
- Scripps Center for Oceans and Human Health, University of California at San Diego, San Diego, California 92037, United States
| | - Miles Borgen
- Scripps Center for Oceans and Human Health, University of California at San Diego, San Diego, California 92037, United States
| | - Lihini I. Aluwihare
- Scripps Center for Oceans and Human Health, University of California at San Diego, San Diego, California 92037, United States
- Geoscience Research Division, Scripps Institution of Oceanography, University of California at San Diego, San Diego, California 92037, United States
| | - Jason S. Biggs
- University of Guam Marine Laboratory, UoG Station, Mangilao, Guam 96923, United States
| | - Valerie J. Paul
- Center for Marine Biotechnology and Biomedicine, University of California at San Diego, San Diego, California 92037, United States
- Smithsonian Marine Station at Fort Pierce, Fort Pierce, Florida 34949, United States
| | - Bradley S. Moore
- Scripps Center for Oceans and Human Health, University of California at San Diego, San Diego, California 92037, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, San Diego, California 92037, United States
- Corresponding Author: Phone: 858-822-6650; fax: 858-534-1318;
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Eglinton TI, Aluwihare LI, Bauer JE, Druffel ER, McNichol AP. Gas chromatographic isolation of individual compounds from complex matrices for radiocarbon dating. Anal Chem 2012; 68:904-12. [PMID: 21619188 DOI: 10.1021/ac9508513] [Citation(s) in RCA: 277] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes the application of a novel, practical approach for isolation of individual compounds from complex organic matrices for natural abundance radiocarbon measurement. This is achieved through the use of automated preparative capillary gas chromatography (PCGC) to separate and recover sufficient quantities of individual target compounds for (14)C analysis by accelerator mass spectrometry (AMS). We developed and tested this approach using a suite of samples (plant lipids, petroleums) whose ages spanned the (14)C time scale and which contained a variety of compound types (fatty acids, sterols, hydrocarbons). Comparison of individual compound and bulk radiocarbon signatures for the isotopically homogeneous samples studied revealed that Δ(14)C values generally agreed well (±10%). Background contamination was assessed at each stage of the isolation procedure, and incomplete solvent removal prior to combustion was the only significant source of additional carbon. Isotope fractionation was addressed through compound-specific stable carbon isotopic analyses. Fractionation of isotopes during isolation of individual compounds was minimal (<5‰ for δ(13)C), provided the entire peak was collected during PCGC. Trapping of partially coeluting peaks did cause errors, and these results highlight the importance of conducting stable carbon isotopic measurements of each trapped compound in concert with AMS for reliable radiocarbon measurements. The addition of carbon accompanying derivatization of functionalized compounds (e.g., fatty acids and sterols) prior to chromatographic separation represents a further source of potential error. This contribution can be removed using a simple isotopic mass balance approach. Based on these preliminary results, the PCGC-based approach holds promise for accurately determining (14)C ages on compounds specific to a given source within complex, heterogeneous samples.
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Affiliation(s)
- T I Eglinton
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543
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19
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Ball GI, Xu L, McNichol AP, Aluwihare LI. A two-dimensional, heart-cutting preparative gas chromatograph facilitates highly resolved single-compound isolations with utility towards compound-specific natural abundance radiocarbon (14C) analyses. J Chromatogr A 2012; 1220:122-31. [DOI: 10.1016/j.chroma.2011.11.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 10/26/2011] [Accepted: 11/14/2011] [Indexed: 10/15/2022]
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20
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Gaston CJ, Furutani H, Guazzotti SA, Coffee KR, Bates TS, Quinn PK, Aluwihare LI, Mitchell BG, Prather KA. Unique ocean-derived particles serve as a proxy for changes in ocean chemistry. ACTA ACUST UNITED AC 2011. [DOI: 10.1029/2010jd015289] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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McNichol AP, Aluwihare LI. The Power of Radiocarbon in Biogeochemical Studies of the Marine Carbon Cycle: Insights from Studies of Dissolved and Particulate Organic Carbon (DOC and POC). Chem Rev 2007; 107:443-66. [PMID: 17300140 DOI: 10.1021/cr050374g] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ann P McNichol
- NOSAMS/Department of Marine Geochemistry and Geology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USA
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22
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Ingalls AE, Shah SR, Hansman RL, Aluwihare LI, Santos GM, Druffel ERM, Pearson A. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proc Natl Acad Sci U S A 2006; 103:6442-7. [PMID: 16614070 PMCID: PMC1564200 DOI: 10.1073/pnas.0510157103] [Citation(s) in RCA: 366] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An ammonia-oxidizing, carbon-fixing archaeon, Candidatus "Nitrosopumilus maritimus," recently was isolated from a salt-water aquarium, definitively confirming that chemoautotrophy exists among the marine archaea. However, in other incubation studies, pelagic archaea also were capable of using organic carbon. It has remained unknown what fraction of the total marine archaeal community is autotrophic in situ. If archaea live primarily as autotrophs in the natural environment, a large ammonia-oxidizing population would play a significant role in marine nitrification. Here we use the natural distribution of radiocarbon in archaeal membrane lipids to quantify the bulk carbon metabolism of archaea at two depths in the subtropical North Pacific gyre. Our compound-specific radiocarbon data show that the archaea in surface waters incorporate modern carbon into their membrane lipids, and archaea at 670 m incorporate carbon that is slightly more isotopically enriched than inorganic carbon at the same depth. An isotopic mass balance model shows that the dominant metabolism at depth indeed is autotrophy (83%), whereas heterotrophic consumption of modern organic carbon accounts for the remainder of archaeal biomass. These results reflect the in situ production of the total community that produces tetraether lipids and are not subject to biases associated with incubation and/or culture experiments. The data suggest either that the marine archaeal community includes both autotrophs and heterotrophs or is a single population with a uniformly mixotrophic metabolism. The metabolic and phylogenetic diversity of the marine archaea warrants further exploration; these organisms may play a major role in the marine cycles of nitrogen and carbon.
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Affiliation(s)
- Anitra E. Ingalls
- *Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138
| | - Sunita R. Shah
- *Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138
| | - Roberta L. Hansman
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093; and
| | - Lihini I. Aluwihare
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093; and
| | - Guaciara M. Santos
- Department of Earth System Science, University of California, Irvine, CA 92697
| | - Ellen R. M. Druffel
- Department of Earth System Science, University of California, Irvine, CA 92697
| | - Ann Pearson
- *Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138
- To whom correspondence should be addressed. E-mail:
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Abstract
The chemical dynamics of marine dissolved organic nitrogen (DON), a reservoir featuring surface accumulations even in areas where nitrogen limits productivity, have yet to be resolved. We exploited differences in the acid lability of amide bonds within high-molecular-weight (HMW) DON to show that vertical DON profiles result in part from the presence of two chemically distinct pools of amide. Half of HMWDON in surface waters is present as N-acetyl amino polysaccharides. In contrast, nearly all deep-sea HMWDON, and therefore, most HMWDON, is present in amides that resist both chemical hydrolysis and biological degradation.
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Affiliation(s)
- Lihini I Aluwihare
- Geosciences Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093, USA.
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