1
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Coppola AI, Druffel ERM, Broek TA, Haghipour N, Eglinton TI, McCarthy M, Walker BD. Variable aging and storage of dissolved black carbon in the ocean. Proc Natl Acad Sci U S A 2024; 121:e2305030121. [PMID: 38517975 PMCID: PMC10990100 DOI: 10.1073/pnas.2305030121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 02/13/2024] [Indexed: 03/24/2024] Open
Abstract
During wildfires and fossil fuel combustion, biomass is converted to black carbon (BC) via incomplete combustion. BC enters the ocean by rivers and atmospheric deposition contributing to the marine dissolved organic carbon (DOC) pool. The fate of BC is considered to reside in the marine DOC pool, where the oldest BC 14C ages have been measured (>20,000 14C y), implying long-term storage. DOC is the largest exchangeable pool of organic carbon in the oceans, yet most DOC (>80%) remains molecularly uncharacterized. Here, we report 14C measurements on size-fractionated dissolved BC (DBC) obtained using benzene polycarboxylic acids as molecular tracers to constrain the sources and cycling of DBC and its contributions to refractory DOC (RDOC) in a site in the North Pacific Ocean. Our results reveal that the cycling of DBC is more dynamic and heterogeneous than previously believed though it does not comprise a single, uniformly "old" 14C age. Instead, both semilabile and refractory DBC components are distributed among size fractions of DOC. We report that DBC cycles within DOC as a component of RDOC, exhibiting turnover in the ocean on millennia timescales. DBC within the low-molecular-weight DOC pool is large, environmentally persistent and constitutes the size fraction that is responsible for long-term DBC storage. We speculate that sea surface processes, including bacterial remineralization (via the coupling of photooxidation of surface DBC and bacterial co-metabolism), sorption onto sinking particles and surface photochemical oxidation, modify DBC composition and turnover, ultimately controlling the fate of DBC and RDOC in the ocean.
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Affiliation(s)
- Alysha I. Coppola
- Department of Earth Sciences, Geological Institute, ETH Zürich, Zürich8092, Switzerland
| | - Ellen R. M. Druffel
- Department of Earth System Science, University of California, Irvine, CA92697
| | - Taylor A. Broek
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - Negar Haghipour
- Department of Earth Sciences, Geological Institute, ETH Zürich, Zürich8092, Switzerland
- Laboratory of Ion Beam Physics, ETH Zürich, Zürich8093, Switzerland
| | - Timothy I. Eglinton
- Department of Earth Sciences, Geological Institute, ETH Zürich, Zürich8092, Switzerland
| | - Matthew McCarthy
- Department of Ocean Science, University of California, Santa Cruz, CA95064
| | - Brett D. Walker
- Department of Earth System Science, University of California, Irvine, CA92697
- Department of Earth and Environmental Sciences, University of Ottawa, Ottawa, ONK1N 6N5, Canada
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2
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Lodeiro P, Rey-Castro C, David C, Humphreys MP, Gledhill M. Proton Binding Characteristics of Dissolved Organic Matter Extracted from the North Atlantic. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21136-21144. [PMID: 38051294 PMCID: PMC10734258 DOI: 10.1021/acs.est.3c01810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023]
Abstract
Marine dissolved organic matter (DOM) presents key thermodynamic properties that are not yet fully constrained. Here, we report the distribution of binding sites occupied by protons (i.e., proton affinity spectra) and parametrize the median intrinsic proton binding affinities (log K̅H) and heterogeneities (m), for DOM samples extracted from the North Atlantic. We estimate that 11.4 ± 0.6% of C atoms in the extracted marine DOM have a functional group with a binding site for ionic species. The log K̅H of the most acidic groups was larger (4.01-4.02 ± 0.02) than that observed in DOM from coastal waters (3.82 ± 0.02), while the chemical binding heterogeneity parameter increased with depth to values (m1= 0.666 ± 0.009) ca. 10% higher than those observed in surface open ocean or coastal samples. On the contrary, the log K̅H for the less acidic groups shows a difference between the surface (10.01 ± 0.08) and deep (9.22 ± 0.35) samples. The latter chemical groups were more heterogeneous for marine than for terrestrial DOM, and m2 decreased with depth to values of 0.28 ± 0.03. Binding heterogeneity reflects aromatic carbon compounds' persistence and accumulation in diverse, low-abundance chemical forms, while easily degradable low-affinity groups accumulate more uniformly in the deep ocean.
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Affiliation(s)
- Pablo Lodeiro
- Department
of Chemistry, Physics, Environmental and Soil Sciences, University of Lleida − AGROTECNIO-CERCA Center, Rovira Roure 191, 25198 Lleida, Spain
| | - Carlos Rey-Castro
- Department
of Chemistry, Physics, Environmental and Soil Sciences, University of Lleida − AGROTECNIO-CERCA Center, Rovira Roure 191, 25198 Lleida, Spain
| | - Calin David
- Department
of Chemistry, Physics, Environmental and Soil Sciences, University of Lleida − AGROTECNIO-CERCA Center, Rovira Roure 191, 25198 Lleida, Spain
| | - Matthew P. Humphreys
- Department
of Ocean Systems (OCS), NIOZ Royal Netherlands
Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg
(Texel), The Netherlands
| | - Martha Gledhill
- GEOMAR
Helmholtz Centre for Ocean Research Kiel, Wischhofstraße 1-3, 24148 Kiel, Germany
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3
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Liang S, Zhang M, Wang X, Li H, Li S, Ma H, Wang X, Rong Z. Seasonal dynamics of dissolved organic matter bioavailability coupling with water mass circulation in the South Yellow Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166671. [PMID: 37657546 DOI: 10.1016/j.scitotenv.2023.166671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/27/2023] [Accepted: 08/27/2023] [Indexed: 09/03/2023]
Abstract
As a typical shelf-marginal sea, the South Yellow Sea (SYS) is significantly influenced by various factors such as land-based inputs and water mass movements, leading the complex biogeochemical processes of dissolved organic matter (DOM) to become highly dynamic. However, the bioavailability of dissolved organic matter (DOM) coupled with water mass circulation has not been accurately assessed, despite being crucial for understanding the source-sink pattern of organic carbon in marginal sea. In this study, four cruises were conducted in the SYS to analyze the spatial and temporal distribution characteristics of dissolved organic carbon (DOC), dissolved organic nitrogen (DON), and total dissolved amino acids (TDAA). Combined with the bioassay experiments, TDAA carbon normalized yield [TDAA (%DOC)] and TDAA degradation index (DIAA) were used as indicators to explore the bioavailability of DOM across different water masses. Results show that the DOC of the SYS exhibits higher average value in late autumn and early winter, and lower value in spring and summer due to the seasonal alternation of water mass and biological activities. The collective results indicate that DOM bioavailability is higher in the Changjiang River diluted water (CDW) and lower in the Yellow Sea warm current (YSWC) and the Yellow Sea cold water mass (YSCWM). Approximately 20 % of DON can be degraded in the YSCWM during autumn. Notably, although the YSCWM constitutes merely constitutes 10 % of the SYS volume, it stores 18.1 % dissolved inorganic nitrogen (DIN) and 23.9 % PO43- of total nutrients, indicating that the YSCWM is a significant nutrient reservoir within the SYS.
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Affiliation(s)
- Shengkang Liang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China; Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Mingzheng Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Xinke Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Hongguan Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Shanshan Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Haoyang Ma
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Xiulin Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Zengrui Rong
- College of Oceanic and Atmospheric Sciences, Ocean University of China, Qingdao 266100, China.
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4
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Vemulapalli SPB, Griesinger C, Dittmar T. Expanding the Limits of Structural Characterization of Marine Dissolved Organic Matter Using Nonuniform Sampling Frequency-Reversed Edited HSQC NMR. Anal Chem 2023; 95:14770-14776. [PMID: 37725656 PMCID: PMC10551856 DOI: 10.1021/acs.analchem.3c02923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023]
Abstract
The multiplicity-edited heteronuclear single quantum correlation (ME-HSQC) NMR method is widely used for the structural characterization of marine dissolved organic matter (DOM), which is a complex molecular mixture comprising millions of individual compounds. However, the standard ME-HSQC suffers from significant signal cancellation and subsequent loss of crucial structural information due to the overlap between CH3/CH (positive) and CH2 (negative) cross-peaks in overcrowded regions. This study introduces nonuniform sampling in frequency-reversed ME-HSQC (NUS FR-ME-HSQC), highlighting its remarkable potential for the comprehensive structural characterization of marine DOM. By reversing the frequency of CH2 cross-peaks into an empty region, the FR-ME-HSQC method effectively simplifies the spectra and eliminates signal cancellation. We demonstrate that nonuniform sampling enables the acquisition of comparable spectra in half the time or significantly enhances the sensitivity in time-equivalent spectra. Comparative analysis also identifies vulnerable CH2 cross-peaks in the standard ME-HSQC that coincide with CH3 and CH cross-peaks, resulting in the loss of critical structural details. In contrast, the NUS FR-ME-HSQC retains these missing correlations, enabling in-depth characterization of marine DOM. These findings highlight the potential of NUS FR-ME-HSQC as an advanced NMR technique that effectively addresses challenges such as signal overcrowding and prolonged experimental times, enabling the thorough investigation of complex mixtures with implications in several fields, including chemistry, metabolomics, and environmental sciences. The advantages of NUS FR-ME-HSQC are experimentally demonstrated on two solid-phase-extracted DOM (SPE-DOM) samples from the surface and deep ocean. With this new technology, differences in the composition of DOM from various aquatic environments can be assigned to individual molecules.
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Affiliation(s)
- Sahithya Phani Babu Vemulapalli
- Research
Group for Marine Geochemistry, Institute for Chemistry and Biology
of the Marine Environment (ICBM), University
of Oldenburg, 26129 Oldenburg, Germany
| | - Christian Griesinger
- Department
of NMR Based Structural Biology, Max Planck
Institute (MPI) for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Thorsten Dittmar
- Research
Group for Marine Geochemistry, Institute for Chemistry and Biology
of the Marine Environment (ICBM), University
of Oldenburg, 26129 Oldenburg, Germany
- Helmholtz
Institute for Functional Marine Biodiversity at the University of
Oldenburg (HIFMB), 26129 Oldenburg, Germany
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5
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Li Z, Sinha V, Kuehn S. Constraints on microbial metabolic complexity. Nat Microbiol 2023; 8:1756-1757. [PMID: 37679599 DOI: 10.1038/s41564-023-01466-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Affiliation(s)
- Zeqian Li
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Vaibhhav Sinha
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Seppe Kuehn
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL, USA.
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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6
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Catalá TS, Speidel LG, Wenzel-Storjohann A, Dittmar T, Tasdemir D. Bioactivity profile of dissolved organic matter and its relation to molecular composition. NATURAL PRODUCTS AND BIOPROSPECTING 2023; 13:32. [PMID: 37721596 PMCID: PMC10507005 DOI: 10.1007/s13659-023-00395-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 08/30/2023] [Indexed: 09/19/2023]
Abstract
Dissolved organic matter (DOM) occupies a huge and uncharted molecular space. Given its properties, DOM can be presented as a promising biotechnological resource. However, research into bioactivities of DOM is still in early stages. In this study, the biotechnological potential of terrestrial and marine DOM, its molecular composition and their relationships are investigated. Samples were screened for their in vitro antibacterial, antifungal, anticancer and antioxidant activities. Antibacterial activity was detected against Staphylococcus aureus in almost all DOM samples, with freshwater DOM showing the lowest IC50 values. Most samples also inhibited Staphylococcus epidermidis, and four DOM extracts showed up to fourfold higher potency than the reference drug. Antifungal activity was limited to only porewater DOM towards human dermatophyte Trichophyton rubrum. No significant in vitro anticancer activity was observed. Low antioxidant potential was exerted. The molecular characterization by FT-ICR MS allowed a broad compositional overview. Three main distinguished groups have been identified by PCoA analyses. Antibacterial activities are related to high aromaticity content and highly-unsaturated molecular formulae (O-poor). Antifungal effect is correlated with highly-unsaturated molecular formulae (O-rich). Antioxidant activity is positively related to the presence of double bonds and polyphenols. This study evidenced for the first time antibacterial and antifungal activity in DOM with potential applications in cosmeceutical, pharmaceutical and aquaculture industry. The lack of cytotoxicity and the almost unlimited presence of this organic material may open new avenues in future marine bioprospecting efforts.
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Affiliation(s)
- Teresa S Catalá
- Global Society Institute, Wälderhaus, Hamburg, Germany.
- Organization for Science, Education and Global Society gGmbH, Stuttgart, Germany.
- ICBM-MPI Bridging Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany.
| | - Linn G Speidel
- ICBM-MPI Bridging Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
- Geological Institute, Department of Earth Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Arlette Wenzel-Storjohann
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106, Kiel, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106, Kiel, Germany
- Kiel University, Christian-Albrechts-Platz 4, 24118, Kiel, Germany
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7
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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.
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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
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8
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Boukra A, Masson M, Brosse C, Sourzac M, Parlanti E, Miège C. Sampling terrigenous diffuse sources in watercourse: Influence of land use and hydrological conditions on dissolved organic matter characteristics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162104. [PMID: 36775149 DOI: 10.1016/j.scitotenv.2023.162104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/07/2022] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Diffuse and point sources of dissolved organic matter (DOM) in streams influence its composition, interactions and fate in the aquatic ecosystem. These inputs can be very numerous at the scale of a watershed, and their identification remains a challenge, especially for diffuse sources related to land use. The complexity of the transfer mechanisms and the reactivity of DOM throughout the soil-water column continuum raise questions about the sampling of diffuse sources in watercourses. To answer this issue, we compared the characteristics of soil-extracted DOM influenced by a particular land use (homogenous sub-catchment of forest and vineyard) and DOM collected from the watercourse adjacent to the soil samples. A 28-day incubation experiment of soil extracts was designed to remove the labile fraction of DOM. During the first 3 days, between 40 and 70 % of the DOC mass was lost for both types of soils. A set of optical indicators (UV-Visible, EEM fluorescence and HPSEC/UV-fluorescence) showed that the labile fraction was mostly composed by low (<1 kDa) and high (>10 kDa) protein-like molecules. At the end of the incubation, soil-extracted DOM was mainly composed of medium molecules (1-10 kDa) associated to terrigenous humic-like compounds. Its optical and size molecular signature tended towards that in the adjacent watercourses and was specific to land use. However, the characteristics of DOM in watercourses was also influenced by the hydrological conditions, probably due to a transfer of top soil DOM during high water periods and both deep soil and autochthonous DOM during low water periods. These results were obtained by a set of indicators, including novel ones derived from HPSEC/UV-fluorescence. Finally, this study demonstrated that it is possible to sample the DOM representative of a land use directly in the river downstream of the homogeneous sub-basin by multiplying the samples during contrasting hydrological conditions.
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Affiliation(s)
| | | | | | - Mahaut Sourzac
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Edith Parlanti
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
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9
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Felgate SL, Craig AJ, Moodie LWK, Hawkes J. Characterization of a Newly Available Coastal Marine Dissolved Organic Matter Reference Material (TRM-0522). Anal Chem 2023; 95:6559-6567. [PMID: 37052954 PMCID: PMC10134136 DOI: 10.1021/acs.analchem.2c05304] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Recent methodological advances have greatly increased our ability to characterize aquatic dissolved organic matter (DOM) using high-resolution instrumentation, including nuclear magnetic resonance (NMR) and mass spectrometry (HRMS). Reliable DOM reference materials are required for further method development and data set alignment but do not currently exist for the marine environment. This presents a major limitation for marine biogeochemistry and related fields, including natural product discovery. To fill this resource gap, we have prepared a coastal marine DOM reference material (TRM-0522) from 45 m deep seawater obtained ∼1 km offshore of Sweden's west coast. Over 3000 molecular formulas were assigned by direct infusion HRMS, confirming sample diversity, and the distribution of formulas in van Krevelen space was typical for a marine sample, with the majority of formulas in the region H/C 1-1.5 and O/C 0.3-0.7. The extracted DOM pool was more nitrogen (N)- and sulfur (S)-rich than a typical terrestrial reference material (SRFA). MZmine3 processing of ultrahigh-performance liquid chromatography (UPLC)-HRMS/MS data revealed 494 resolvable features (233 in negative mode; 261 in positive mode) over a wide range of retention times and masses. NMR data indicated low contributions from aromatic protons and, generally speaking, low lignin, humic, and fulvic substances associated with terrestrial samples. Instead, carboxylic-rich aliphatic molecules were the most abundant components, followed by carbohydrates and aliphatic functionalities. This is consistent with a very low specific UV absorbance SUVA254 value of 1.52 L mg C-1 m-1. When combined with comparisons with existing terrestrial reference materials (Suwannee River fulvic acid and Pony Lake fulvic acid), these results suggest that TRM-0522 is a useful and otherwise unavailable reference material for use in marine DOM biogeochemistry.
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Affiliation(s)
- Stacey L Felgate
- Analytical Chemistry, Department of Chemistry BMC, Uppsala University, Uppsala 752 37, Sweden
| | - Alexander J Craig
- Analytical Chemistry, Department of Chemistry BMC, Uppsala University, Uppsala 752 37, Sweden
- Drug Design and Discovery, Department of Medicinal Chemistry, Uppsala University, Uppsala 752 37, Sweden
| | - Lindon W K Moodie
- Drug Design and Discovery, Department of Medicinal Chemistry, Uppsala University, Uppsala 752 37, Sweden
| | - Jeffrey Hawkes
- Analytical Chemistry, Department of Chemistry BMC, Uppsala University, Uppsala 752 37, Sweden
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10
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Verma A, Amnebrink D, Pinhassi J, Wikner J. Prokaryotic maintenance respiration and growth efficiency field patterns reproduced by temperature and nutrient control at mesocosm scale. Environ Microbiol 2023; 25:721-737. [PMID: 36511634 DOI: 10.1111/1462-2920.16300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The distribution of prokaryotic metabolism between maintenance and growth activities has a profound impact on the transformation of carbon substrates to either biomass or CO2 . Knowledge of key factors influencing prokaryotic maintenance respiration is, however, highly limited. This mesocosm study validated the significance of prokaryotic maintenance respiration by mimicking temperature and nutrients within levels representative of winter and summer conditions. A global range of growth efficiencies (0.05-0.57) and specific growth rates (0.06-2.7 d-1 ) were obtained. The field pattern of cell-specific respiration versus specific growth rate and the global relationship between growth efficiency and growth rate were reproduced. Maintenance respiration accounted for 75% and 15% of prokaryotic respiration corresponding to winter and summer conditions, respectively. Temperature and nutrients showed independent positive effects for all prokaryotic variables except abundance and cell-specific respiration. All treatments resulted in different taxonomic diversity, with specific populations of amplicon sequence variants associated with either maintenance or growth conditions. These results validate a significant relationship between specific growth and respiration rate under productive conditions and show that elevated prokaryotic maintenance respiration can occur under cold and oligotrophic conditions. The experimental design provides a tool for further study of prokaryotic energy metabolism under realistic conditions at the mesocosm scale.
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Affiliation(s)
- Ashish Verma
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Hörnefors, Sweden
| | - Dennis Amnebrink
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Johan Wikner
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Hörnefors, Sweden
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11
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Westall F, Brack A, Fairén AG, Schulte MD. Setting the geological scene for the origin of life and continuing open questions about its emergence. FRONTIERS IN ASTRONOMY AND SPACE SCIENCES 2023; 9:1095701. [PMID: 38274407 PMCID: PMC7615569 DOI: 10.3389/fspas.2022.1095701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
The origin of life is one of the most fundamental questions of humanity. It has been and is still being addressed by a wide range of researchers from different fields, with different approaches and ideas as to how it came about. What is still incomplete is constrained information about the environment and the conditions reigning on the Hadean Earth, particularly on the inorganic ingredients available, and the stability and longevity of the various environments suggested as locations for the emergence of life, as well as on the kinetics and rates of the prebiotic steps leading to life. This contribution reviews our current understanding of the geological scene in which life originated on Earth, zooming in specifically on details regarding the environments and timescales available for prebiotic reactions, with the aim of providing experimenters with more specific constraints. Having set the scene, we evoke the still open questions about the origin of life: did life start organically or in mineralogical form? If organically, what was the origin of the organic constituents of life? What came first, metabolism or replication? What was the time-scale for the emergence of life? We conclude that the way forward for prebiotic chemistry is an approach merging geology and chemistry, i.e., far-from-equilibrium, wet-dry cycling (either subaerial exposure or dehydration through chelation to mineral surfaces) of organic reactions occurring repeatedly and iteratively at mineral surfaces under hydrothermal-like conditions.
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Affiliation(s)
| | - André Brack
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
| | - Alberto G. Fairén
- Centro de Astrobiología (CAB, CSIC-INTA), Madrid, Spain
- Cornell University, Ithaca, NY, United States
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12
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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.
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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
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13
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Gonsior M, Powers L, Lahm M, McCallister SL. New Perspectives on the Marine Carbon Cycle-The Marine Dissolved Organic Matter Reactivity Continuum. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:5371-5380. [PMID: 35442650 PMCID: PMC9069685 DOI: 10.1021/acs.est.1c08871] [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: 12/28/2021] [Indexed: 05/08/2023]
Abstract
This perspective challenges our current understanding of the marine carbon cycle, including an alternative explanation of bulk 14C-DOM measurements. We propose the adoption of the carbon reactivity continuum concept previously established for lakes and sediments for the oceans using kinetic data and term this the marine DOM reactivity continuum. We need to gain a fundamental understanding of the biogeochemical drivers of surface water DOM concentrations and reactivity, biological carbon pump efficiency, and the autotrophic communities that are the ultimate but variable sources of marine DOM. This perspective is intended to shift our focus to a more inclusive kinetic model and may lead us to a more accurate assessment of the active and dynamic role marine DOM plays in the global carbon cycle. Currently, the kinetic data to establish and validate such a marine DOM reactivity continuum model are still lacking, and their resolution depends on the discovery of new organic tracers that span large differences in reactivity and microbial degradation rates. We may need to refocus our efforts in deciphering the structure and reactivity of marine organic molecules in a kinetic context, including the microbial and physicochemical constraints on molecular reactivity that are present in the deep ocean.
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Affiliation(s)
- Michael Gonsior
- Chesapeake
Biological Laboratory, University of Maryland
Center for Environmental Science, 146 Williams Street, Solomons, Maryland 20688, United
States
| | - Leanne Powers
- Chesapeake
Biological Laboratory, University of Maryland
Center for Environmental Science, 146 Williams Street, Solomons, Maryland 20688, United
States
| | - Madeline Lahm
- Chesapeake
Biological Laboratory, University of Maryland
Center for Environmental Science, 146 Williams Street, Solomons, Maryland 20688, United
States
| | - Shannon Leigh McCallister
- Biology
Department, College of Humanities and Sciences, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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Luo J, Zhou Q, Hu X, Zeng H, Deng P, He C, Shi Q. Lake Chemodiversity Driven by Natural and Anthropogenic Factors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:5910-5919. [PMID: 35389635 DOI: 10.1021/acs.est.1c08148] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
As extremely active sites processing terrestrially derived dissolved organic matter (DOM), lakes deserve sufficient attention. Because of high-complexity interactions between DOM and the surrounding environment, the natural and anthropogenic drivers controlling the composition and chemodiversity of DOM molecules in lakes remain unclear. Here, 13,952 DOM molecules were identified and assessed in 45 lakes across China via ultrahigh-resolution mass spectrometry. Furthermore, the effects of both natural and anthropogenic factors on the DOM composition, DOM chemodiversity, and greenhouse gas emissions were investigated. The majority of the variations in DOM chemical composition could be attributed to the differences in the hydrology and nutrient concentrations of the lakes, and human activities also played a role, mainly through atmospheric pollution. Environmental factors mainly influenced DOM chemodiversity in the form of S-containing compounds. N-containing compounds exhibited a positive correlation with CO2 emissions, while N- and S-free compounds exhibited a positive correlation with N2O emissions. These results facilitate a comprehensive understanding of the interactions between lake DOM and the surrounding environment, thereby providing a reference for the formulation of strategies aimed at the harmonious development of human and natural environments.
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Affiliation(s)
- Jiwei Luo
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Hui Zeng
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Peng Deng
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, Petroleum Molecular Engineering Center (PMEC), China University of Petroleum, Beijing 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, Petroleum Molecular Engineering Center (PMEC), China University of Petroleum, Beijing 102249, China
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