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Zhao Z, Amano C, Reinthaler T, Baltar F, Orellana MV, Herndl GJ. Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean. Nat Commun 2024; 15:6411. [PMID: 39080340 PMCID: PMC11289388 DOI: 10.1038/s41467-024-50867-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 07/24/2024] [Indexed: 08/02/2024] Open
Abstract
Proteins in the open ocean represent a significant source of organic matter, and their profiles reflect the metabolic activities of marine microorganisms. Here, by analyzing metaproteomic samples collected from the Pacific, Atlantic and Southern Ocean, we reveal size-fractionated patterns of the structure and function of the marine microbiota protein pool in the water column, particularly in the dark ocean (>200 m). Zooplankton proteins contributed three times more than algal proteins to the deep-sea community metaproteome. Gammaproteobacteria exhibited high metabolic activity in the deep-sea, contributing up to 30% of bacterial proteins. Close virus-host interactions of this taxon might explain the dominance of gammaproteobacterial proteins in the dissolved fraction. A high urease expression in nitrifiers suggested links between their dark carbon fixation and zooplankton urea production. In summary, our results uncover the taxonomic contribution of the microbiota to the oceanic protein pool, revealing protein fluxes from particles to the dissolved organic matter pool.
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Affiliation(s)
- Zihao Zhao
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria.
| | - Chie Amano
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Mónica V Orellana
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria.
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands.
- Environmental & Climate Research Hub, University of Vienna, Vienna, Austria.
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2
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Jiao N, Luo T, Chen Q, Zhao Z, Xiao X, Liu J, Jian Z, Xie S, Thomas H, Herndl GJ, Benner R, Gonsior M, Chen F, Cai WJ, Robinson C. The microbial carbon pump and climate change. Nat Rev Microbiol 2024; 22:408-419. [PMID: 38491185 DOI: 10.1038/s41579-024-01018-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 03/18/2024]
Abstract
The ocean has been a regulator of climate change throughout the history of Earth. One key mechanism is the mediation of the carbon reservoir by refractory dissolved organic carbon (RDOC), which can either be stored in the water column for centuries or released back into the atmosphere as CO2 depending on the conditions. The RDOC is produced through a myriad of microbial metabolic and ecological processes known as the microbial carbon pump (MCP). Here, we review recent research advances in processes related to the MCP, including the distribution patterns and molecular composition of RDOC, links between the complexity of RDOC compounds and microbial diversity, MCP-driven carbon cycles across time and space, and responses of the MCP to a changing climate. We identify knowledge gaps and future research directions in the role of the MCP, particularly as a key component in integrated approaches combining the mechanisms of the biological and abiotic carbon pumps for ocean negative carbon emissions.
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Affiliation(s)
- Nianzhi Jiao
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China.
| | - Tingwei Luo
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
| | - Quanrui Chen
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
| | - Zhao Zhao
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
| | - Xilin Xiao
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
| | - Jihua Liu
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Zhimin Jian
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Shucheng Xie
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Helmuth Thomas
- Institute of Carbon Cycles, Helmholtz-Zentrum Hereon, Geesthacht, Germany
- Institut für Chemie und Biologie des Meeres (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Ronald Benner
- Department of Biological Sciences, School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC, USA
| | - Micheal Gonsior
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, MD, USA
| | - Feng Chen
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Wei-Jun Cai
- School of Marine Science and Policy, University of Delaware, Newark, DE, USA
| | - Carol Robinson
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China.
- Centre for Ocean and Atmospheric Sciences (COAS), School of Environmental Sciences, University of East Anglia, Norwich, UK.
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3
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Selden CR, LaBrie R, Ganley LC, Crocker DR, Peleg O, Perry DC, Reich HG, Sasaki M, Thibodeau PS, Isanta-Navarro J. Is our understanding of aquatic ecosystems sufficient to quantify ecologically driven climate feedbacks? GLOBAL CHANGE BIOLOGY 2024; 30:e17351. [PMID: 38837306 DOI: 10.1111/gcb.17351] [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: 01/01/2024] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024]
Abstract
The Earth functions as an integrated system-its current habitability to complex life is an emergent property dependent on interactions among biological, chemical, and physical components. As global warming affects ecosystem structure and function, so too will the biosphere affect climate by altering atmospheric gas composition and planetary albedo. Constraining these ecosystem-climate feedbacks is essential to accurately predict future change and develop mitigation strategies; however, the interplay among ecosystem processes complicates the assessment of their impact. Here, we explore the state-of-knowledge on how ecological and biological processes (e.g., competition, trophic interactions, metabolism, and adaptation) affect the directionality and magnitude of feedbacks between ecosystems and climate, using illustrative examples from the aquatic sphere. We argue that, despite ample evidence for the likely significance of many, our present understanding of the combinatorial effects of ecosystem dynamics precludes the robust quantification of most ecologically driven climate feedbacks. Constraining these effects must be prioritized within the ecological sciences for only by studying the biosphere as both subject and arbiter of global climate can we develop a sufficiently holistic view of the Earth system to accurately predict Earth's future and unravel its past.
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Affiliation(s)
- Corday R Selden
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
- Department of Earth and Planetary Sciences, Rutgers University, Piscataway, New Jersey, USA
| | - Richard LaBrie
- Interdisciplinary Environmental Research Centre, TU Bergakademie Freiberg, Freiberg, Germany
| | - Laura C Ganley
- Anderson Cabot Center for Ocean Life, New England Aquarium, Boston, Massachusetts, USA
| | - Daniel R Crocker
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Ohad Peleg
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Danielle C Perry
- Department of Natural Resources Science, University of Rhode Island, Kingston, Rhode Island, USA
| | - Hannah G Reich
- Department of Biological Sciences, Biological Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Matthew Sasaki
- Department of Marine Sciences, University of Connecticut, Mansfield, Connecticut, USA
| | - Patricia S Thibodeau
- School of Marine and Environmental Programs, University of New England, Biddeford, Maine, USA
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4
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Chen S, Xie ZX, Yan KQ, Chen JW, Li DX, Wu PF, Peng L, Lin L, Dong CM, Zhao Z, Fan GY, Liu SQ, Herndl GJ, Wang DZ. Functional vertical connectivity of microbial communities in the ocean. SCIENCE ADVANCES 2024; 10:eadj8184. [PMID: 38781332 PMCID: PMC11114224 DOI: 10.1126/sciadv.adj8184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Sinking particles are a critical conduit for the transport of surface microbes to the ocean's interior. Vertical connectivity of phylogenetic composition has been shown; however, the functional vertical connectivity of microbial communities has not yet been explored in detail. We investigated protein and taxa profiles of both free-living and particle-attached microbial communities from the surface to 3000 m depth using a combined metaproteomic and 16S rRNA amplicon sequencing approach. A clear compositional and functional vertical connectivity of microbial communities was observed throughout the water column with Oceanospirillales, Alteromonadales, and Rhodobacterales as key taxa. The surface-derived particle-associated microbes increased the expression of proteins involved in basic metabolism, organic matter processing, and environmental stress response in deep waters. This study highlights the functional vertical connectivity between surface and deep-sea microbial communities via sinking particles and reveals that a considerable proportion of the deep-sea microbes might originate from surface waters and have a major impact on the biogeochemical cycles in the deep sea.
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Affiliation(s)
- Shi Chen
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Zhang-Xian Xie
- School of Resource and Environmental Sciences, Quanzhou Normal University, Quanzhou 362000, China
| | - Ke-Qiang Yan
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Wei Chen
- Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Ling Peng
- Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Chun-Ming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen 361005, Fujian, China
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Guang-Yi Fan
- BGI-Shenzhen, Shenzhen 518083, China
- Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China
| | - Si-Qi Liu
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gerhard J. Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, Texel, Netherlands
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
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5
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Zhao Z, Amano C, Reinthaler T, Orellana MV, Herndl GJ. Substrate uptake patterns shape niche separation in marine prokaryotic microbiome. SCIENCE ADVANCES 2024; 10:eadn5143. [PMID: 38748788 PMCID: PMC11095472 DOI: 10.1126/sciadv.adn5143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/11/2024] [Indexed: 05/19/2024]
Abstract
Marine heterotrophic prokaryotes primarily take up ambient substrates using transporters. The patterns of transporters targeting particular substrates shape the ecological role of heterotrophic prokaryotes in marine organic matter cycles. Here, we report a size-fractionated pattern in the expression of prokaryotic transporters throughout the oceanic water column due to taxonomic variations, revealed by a multi-"omics" approach targeting ATP-binding cassette (ABC) transporters and TonB-dependent transporters (TBDTs). Substrate specificity analyses showed that marine SAR11, Rhodobacterales, and Oceanospirillales use ABC transporters to take up organic nitrogenous compounds in the free-living fraction, while Alteromonadales, Bacteroidetes, and Sphingomonadales use TBDTs for carbon-rich organic matter and metal chelates on particles. The expression of transporter proteins also supports distinct lifestyles of deep-sea prokaryotes. Our results suggest that transporter divergency in organic matter assimilation reflects a pronounced niche separation in the prokaryote-mediated organic matter cycles.
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Affiliation(s)
- Zihao Zhao
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Chie Amano
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Mónica V. Orellana
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA 98195, USA
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Gerhard J. Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Environmental and Climate Research Hub, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
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6
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Dang YR, Cha QQ, Liu SS, Wang SY, Li PY, Li CY, Wang P, Chen XL, Tian JW, Xin Y, Chen Y, Zhang YZ, Qin QL. Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench. MICROBIOME 2024; 12:77. [PMID: 38664737 PMCID: PMC11044484 DOI: 10.1186/s40168-024-01789-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/04/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND The deep sea represents the largest marine ecosystem, driving global-scale biogeochemical cycles. Microorganisms are the most abundant biological entities and play a vital role in the cycling of organic matter in such ecosystems. The primary food source for abyssal biota is the sedimentation of particulate organic polymers. However, our knowledge of the specific biopolymers available to deep-sea microbes remains largely incomplete. One crucial rate-limiting step in organic matter cycling is the depolymerization of particulate organic polymers facilitated by extracellular enzymes (EEs). Therefore, the investigation of active EEs and the microbes responsible for their production is a top priority to better understand the key nutrient sources for deep-sea microbes. RESULTS In this study, we conducted analyses of extracellular enzymatic activities (EEAs), metagenomics, and metatranscriptomics from seawater samples of 50-9305 m from the Mariana Trench. While a diverse array of microbial groups was identified throughout the water column, only a few exhibited high levels of transcriptional activities. Notably, microbial populations actively transcribing EE genes involved in biopolymer processing in the abyssopelagic (4700 m) and hadopelagic zones (9305 m) were primarily associated with the class Actinobacteria. These microbes actively transcribed genes coding for enzymes such as cutinase, laccase, and xyloglucanase which are capable of degrading phytoplankton polysaccharides as well as GH23 peptidoglycan lyases and M23 peptidases which have the capacity to break down peptidoglycan. Consequently, corresponding enzyme activities including glycosidases, esterase, and peptidases can be detected in the deep ocean. Furthermore, cell-specific EEAs increased at 9305 m compared to 4700 m, indicating extracellular enzymes play a more significant role in nutrient cycling in the deeper regions of the Mariana Trench. CONCLUSIONS Transcriptomic analyses have shed light on the predominant microbial population actively participating in organic matter cycling in the deep-sea environment of the Mariana Trench. The categories of active EEs suggest that the complex phytoplankton polysaccharides (e.g., cutin, lignin, and hemicellulose) and microbial peptidoglycans serve as the primary nutrient sources available to deep-sea microbes. The high cell-specific EEA observed in the hadal zone underscores the robust polymer-degrading capacities of hadal microbes even in the face of the challenging conditions they encounter in this extreme environment. These findings provide valuable new insights into the sources of nutrition, the key microbes, and the EEs crucial for biopolymer degradation in the deep seawater of the Mariana Trench. Video Abstract.
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Affiliation(s)
- Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Sha-Sha Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shu-Yan Wang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chun-Yang Li
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Peng Wang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ji-Wei Tian
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yu Xin
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yin Chen
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| | - Yu-Zhong Zhang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China.
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China.
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7
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Craig A, Moodie LWK, Hawkes JA. Preparation of Simple Bicyclic Carboxylate-Rich Alicyclic Molecules for the Investigation of Dissolved Organic Matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7078-7086. [PMID: 38608252 PMCID: PMC11044592 DOI: 10.1021/acs.est.4c00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
Dissolved organic matter (DOM) is a vast and complex chemical mixture that plays a key role in the mediation of the global carbon cycle. Fundamental understanding of the source and fate of oceanic organic matter is obscured due to poor definition of the key molecular contributors to DOM, which limits accurate sample analysis and prediction of the Earth's carbon cycle. Previous work has attempted to define the components of the DOM through a variety of chromatographic and spectral techniques. However, modern preparative and analytical methods have not isolated or unambiguously identified molecules from DOM. Therefore, previously proposed structures are based solely on the mixture's aggregate properties and do not accurately describe any true individual molecular component. In addition to this, there is a lack of appropriate analogues of the individual chemical classes within DOM, limiting the scope of experiments that probe the physical, chemical, and biological contributions from each class. To address these problems, we synthesized a series of analogues of carboxylate-rich alicyclic molecules (CRAM), a molecular class hypothesized to exist as a major contributor to DOM. Key analytical features of the synthetic CRAMs were consistent with marine DOM, supporting their suitability as chemical substitutes for CRAM. This new approach provides access to a molecular toolkit that will enable previously inaccessible experiments to test many unproven hypotheses surrounding the ever-enigmatic DOM.
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Affiliation(s)
- 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 A. Hawkes
- Analytical
Chemistry, Department of Chemistry BMC, Uppsala University, Uppsala 752 37, Sweden
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8
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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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9
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Lechtenfeld OJ, Kaesler J, Jennings EK, Koch BP. Direct Analysis of Marine Dissolved Organic Matter Using LC-FT-ICR MS. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4637-4647. [PMID: 38427796 PMCID: PMC10938638 DOI: 10.1021/acs.est.3c07219] [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: 09/05/2023] [Revised: 01/20/2024] [Accepted: 02/07/2024] [Indexed: 03/03/2024]
Abstract
Marine dissolved organic matter (DOM) is an important component of the global carbon cycle, yet its intricate composition and the sea salt matrix pose major challenges for chemical analysis. We introduce a direct injection, reversed-phase liquid chromatography ultrahigh resolution mass spectrometry approach to analyze marine DOM without the need for solid-phase extraction. Effective separation of salt and DOM is achieved with a large chromatographic column and an extended isocratic aqueous step. Postcolumn dilution of the sample flow with buffer-free solvents and implementing a counter gradient reduced salt buildup in the ion source and resulted in excellent repeatability. With this method, over 5,500 unique molecular formulas were detected from just 5.5 nmol carbon in 100 μL of filtered Arctic Ocean seawater. We observed a highly linear detector response for variable sample carbon concentrations and a high robustness against the salt matrix. Compared to solid-phase extracted DOM, our direct injection method demonstrated superior sensitivity for heteroatom-containing DOM. The direct analysis of seawater offers fast and simple sample preparation and avoids fractionation introduced by extraction. The method facilitates studies in environments, where only minimal sample volume is available e.g. in marine sediment pore water, ice cores, or permafrost soil solution. The small volume requirement also supports higher spatial (e.g., in soils) or temporal sample resolution (e.g., in culture experiments). Chromatographic separation adds further chemical information to molecular formulas, enhancing our understanding of marine biogeochemistry, chemodiversity, and ecological processes.
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Affiliation(s)
- Oliver J. Lechtenfeld
- Department
of Environmental Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research −
UFZ, Permoserstraße
15, 04318 Leipzig, Germany
- ProVIS−Centre
for Chemical Microscopy, Helmholtz Centre
for Environmental Research − UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Jan Kaesler
- Department
of Environmental Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research −
UFZ, Permoserstraße
15, 04318 Leipzig, Germany
| | - Elaine K. Jennings
- Department
of Environmental Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research −
UFZ, Permoserstraße
15, 04318 Leipzig, Germany
| | - Boris P. Koch
- Alfred-Wegener-Institut
Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
- University
of Applied Sciences, An der Karlstadt 8, 27568 Bremerhaven, Germany
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10
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Lau MP, Hutchins RHS, Tank SE, A Del Giorgio P. The chemical succession in anoxic lake waters as source of molecular diversity of organic matter. Sci Rep 2024; 14:3831. [PMID: 38360896 PMCID: PMC10869704 DOI: 10.1038/s41598-024-54387-0] [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: 10/30/2023] [Accepted: 02/12/2024] [Indexed: 02/17/2024] Open
Abstract
The aquatic networks that connect soils with oceans receive each year 5.1 Pg of terrestrial carbon to transport, bury and process. Stagnant sections of aquatic networks often become anoxic. Mineral surfaces attract specific components of organic carbon, which are released under anoxic conditions to the pool of dissolved organic matter (DOM). The impact of the anoxic release on DOM molecular composition and reactivity in inland waters is unknown. Here, we report concurrent release of iron and DOM in anoxic bottom waters of northern lakes, removing DOM from the protection of iron oxides and remobilizing previously buried carbon to the water column. The deprotected DOM appears to be highly reactive, terrestrially derived and molecularly distinct, generating an ambient DOM pool that relieves energetic constraints that are often assumed to limit carbon turnover in anoxic waters. The Fe-to-C stoichiometry during anoxic mobilization differs from that after oxic precipitation, suggesting that up to 21% of buried OM escapes a lake-internal release-precipitation cycle, and can instead be exported downstream. Although anoxic habitats are transient and comprise relatively small volumes of water on the landscape scale, our results show that they may play a major role in structuring the reactivity and molecular composition of DOM transiting through aquatic networks and reaching the oceans.
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Affiliation(s)
- Maximilian P Lau
- Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Brennhausgasse 14, 09599, Freiberg, Germany.
- Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), 141 Avenue du Président-Kennedy, Montreal, QC, H2X 1Y4, Canada.
| | - Ryan H S Hutchins
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2R3, Canada
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
| | - Suzanne E Tank
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Paul A Del Giorgio
- Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), 141 Avenue du Président-Kennedy, Montreal, QC, H2X 1Y4, Canada
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11
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Boiteau RM, Corilo YE, Kew WR, Dewey C, Alvarez Rodriguez MC, Carlson CA, Conway TM. Relating Molecular Properties to the Persistence of Marine Dissolved Organic Matter with Liquid Chromatography-Ultrahigh-Resolution Mass Spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 38335252 DOI: 10.1021/acs.est.3c08245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Marine dissolved organic matter (DOM) contains a complex mixture of small molecules that eludes rapid biological degradation. Spatial and temporal variations in the abundance of DOM reflect the existence of fractions that are removed from the ocean over different time scales, ranging from seconds to millennia. However, it remains unknown whether the intrinsic chemical properties of these organic components relate to their persistence. Here, we elucidate and compare the molecular compositions of distinct DOM fractions with different lability along a water column in the North Atlantic Gyre. Our analysis utilized ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry at 21 T coupled to liquid chromatography and a novel data pipeline developed in CoreMS that generates molecular formula assignments and metrics of isomeric complexity. Clustering analysis binned 14 857 distinct molecular components into groups that correspond to the depth distribution of semilabile, semirefractory, and refractory fractions of DOM. The more labile fractions were concentrated near the ocean surface and contained more aliphatic, hydrophobic, and reduced molecules than the refractory fraction, which occurred uniformly throughout the water column. These findings suggest that processes that selectively remove hydrophobic compounds, such as aggregation and particle sorption, contribute to variable removal rates of marine DOM.
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Affiliation(s)
- Rene M Boiteau
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis Oregon 97330, United States
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Yuri E Corilo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 02543, United States
| | - William R Kew
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 02543, United States
| | - Christian Dewey
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | | | - Craig A Carlson
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Tim M Conway
- College of Marine Science, University of South Florida, St. Petersburg, Florida 33712, United States
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12
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Freeman EC, Emilson EJS, Dittmar T, Braga LPP, Emilson CE, Goldhammer T, Martineau C, Singer G, Tanentzap AJ. Universal microbial reworking of dissolved organic matter along environmental gradients. Nat Commun 2024; 15:187. [PMID: 38168076 PMCID: PMC10762207 DOI: 10.1038/s41467-023-44431-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
Soils are losing increasing amounts of carbon annually to freshwaters as dissolved organic matter (DOM), which, if degraded, can offset their carbon sink capacity. However, the processes underlying DOM degradation across environments are poorly understood. Here we show DOM changes similarly along soil-aquatic gradients irrespective of environmental differences. Using ultrahigh-resolution mass spectrometry, we track DOM along soil depths and hillslope positions in forest catchments and relate its composition to soil microbiomes and physico-chemical conditions. Along depths and hillslopes, we find carbohydrate-like and unsaturated hydrocarbon-like compounds increase in abundance-weighted mass, and the expression of genes essential for degrading plant-derived carbohydrates explains >50% of the variation in abundance of these compounds. These results suggest that microbes transform plant-derived compounds, leaving DOM to become increasingly dominated by the same (i.e., universal), difficult-to-degrade compounds as degradation proceeds. By synthesising data from the land-to-ocean continuum, we suggest these processes generalise across ecosystems and spatiotemporal scales. Such general degradation patterns can help predict DOM composition and reactivity along environmental gradients to inform management of soil-to-stream carbon losses.
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Affiliation(s)
- Erika C Freeman
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
| | - Erik J S Emilson
- Natural Resources Canada, Canadian Forest Service, Great Lakes Forestry Centre, 1219 Queen St. E., Sault Ste, Marie, ON, P6A 2E5, Canada
- Ecosystems and Global Change Group, School of the Environment, Trent University, Peterborough, ON, K9L 0G2, Canada
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, 26129, Oldenburg, Germany
| | - Lucas P P Braga
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Caroline E Emilson
- Natural Resources Canada, Canadian Forest Service, Great Lakes Forestry Centre, 1219 Queen St. E., Sault Ste, Marie, ON, P6A 2E5, Canada
| | - Tobias Goldhammer
- Department of Ecohydrology and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Mueggelseedamm, 301, Berlin, Germany
| | - Christine Martineau
- Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380, Québec, G1V 4C7, Canada
| | - Gabriel Singer
- Department of Ecology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
- Ecosystems and Global Change Group, School of the Environment, Trent University, Peterborough, ON, K9L 0G2, Canada
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13
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Sebastián M, Giner CR, Balagué V, Gómez-Letona M, Massana R, Logares R, Duarte CM, Gasol JM. The active free-living bathypelagic microbiome is largely dominated by rare surface taxa. ISME COMMUNICATIONS 2024; 4:ycae015. [PMID: 38456147 PMCID: PMC10919342 DOI: 10.1093/ismeco/ycae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 03/09/2024]
Abstract
A persistent microbial seed bank is postulated to sustain the marine biosphere, and recent findings show that prokaryotic taxa present in the ocean's surface dominate prokaryotic communities throughout the water column. Yet, environmental conditions exert a tight control on the activity of prokaryotes, and drastic changes in these conditions are known to occur from the surface to deep waters. The simultaneous characterization of the total (DNA) and active (i.e. with potential for protein synthesis, RNA) free-living communities in 13 stations distributed across the tropical and subtropical global ocean allowed us to assess their change in structure and diversity along the water column. We observed that active communities were surprisingly more similar along the vertical gradient than total communities. Looking at the vertical connectivity of the active vs. the total communities, we found that taxa detected in the surface sometimes accounted for more than 75% of the active microbiome of bathypelagic waters (50% on average). These active taxa were generally rare in the surface, representing a small fraction of all the surface taxa. Our findings show that the drastic vertical change in environmental conditions leads to the inactivation and disappearance of a large proportion of surface taxa, but some surface-rare taxa remain active (or with potential for protein synthesis) and dominate the bathypelagic active microbiome.
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Affiliation(s)
- Marta Sebastián
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Caterina R Giner
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Vanessa Balagué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Markel Gómez-Letona
- Instituto de Oceanografía y Cambio Global, Universidad de Las Palmas de Gran Canaria, Parque Científico Tecnológico Marino de Taliarte, s/n, Telde, Las Palmas 35214, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
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14
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Bercovici SK, Wiemers M, Dittmar T, Niggemann J. Disentangling Biological Transformations and Photodegradation Processes from Marine Dissolved Organic Matter Composition in the Global Ocean. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21145-21155. [PMID: 38065573 PMCID: PMC10734261 DOI: 10.1021/acs.est.3c05929] [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: 07/28/2023] [Revised: 11/03/2023] [Accepted: 11/15/2023] [Indexed: 12/20/2023]
Abstract
Dissolved organic matter (DOM) holds the largest amount of organic carbon in the ocean, with most of it residing in the deep for millennia. Specific mechanisms and environmental conditions responsible for its longevity are still unknown. Microbial transformations and photochemical degradation of DOM in the surface layers are two processes that shape its molecular composition. We used molecular data (via Fourier transform ion cyclotron resonance mass spectrometry) from two laboratory experiments that focused on (1) microbial processing of fresh DOM and (2) photodegradation of deep-sea DOM to derive independent process-related molecular indices for biological formation and transformation (Ibio) and photodegradation (Iphoto). Both indices were applied to a global ocean data set of DOM composition. The distributions of Iphoto and Ibio were consistent with increased photodegradation and biological reworking of DOM in sunlit surface waters, and traces of these surface processes were evident at depth. Increased Ibio values in the deep Southern Ocean and South Atlantic implied export of microbially reworked DOM. Photodegraded DOM (increased Iphoto) in the deep subtropical gyres of Atlantic and Pacific oceans suggested advective transport in warm-core eddies. The simultaneous application of Iphoto and Ibio disentangled and assessed two processes that left unique molecular signatures in the global ocean.
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Affiliation(s)
- Sarah K. Bercovici
- Institute
for Chemistry and Biology of the Marine Environment (ICBM), School
of Mathematics and Science, Carl von Ossietzky
Universität Oldenburg, Ammerländer Heerstraße 114-118, Oldenburg 26129, Germany
- National
Oceanography Centre, European Way, Southampton SO14 3ZH, Hampshire, United Kingdom
| | - Maren Wiemers
- Institute
for Chemistry and Biology of the Marine Environment (ICBM), School
of Mathematics and Science, Carl von Ossietzky
Universität Oldenburg, Ammerländer Heerstraße 114-118, Oldenburg 26129, Germany
| | - Thorsten Dittmar
- Institute
for Chemistry and Biology of the Marine Environment (ICBM), School
of Mathematics and Science, Carl von Ossietzky
Universität Oldenburg, Ammerländer Heerstraße 114-118, Oldenburg 26129, Germany
- Helmholtz
Institute for Functional Marine Biodiversity (HIFMB), Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, Oldenburg 26129, Lower Saxony, Germany
| | - Jutta Niggemann
- Institute
for Chemistry and Biology of the Marine Environment (ICBM), School
of Mathematics and Science, Carl von Ossietzky
Universität Oldenburg, Ammerländer Heerstraße 114-118, Oldenburg 26129, Germany
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15
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Huete-Stauffer TM, Logares R, Ansari MI, Røstad A, Calleja ML, Morán XAG. Increased prokaryotic diversity in the Red Sea deep scattering layer. ENVIRONMENTAL MICROBIOME 2023; 18:87. [PMID: 38098078 PMCID: PMC10722844 DOI: 10.1186/s40793-023-00542-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND The diel vertical migration (DVM) of fish provides an active transport of labile dissolved organic matter (DOM) to the deep ocean, fueling the metabolism of heterotrophic bacteria and archaea. We studied the impact of DVM on the mesopelagic prokaryotic diversity of the Red Sea focusing on the mesopelagic deep scattering layer (DSL) between 450-600 m. RESULTS Despite the general consensus of homogeneous conditions in the mesopelagic layer, we observed variability in physico-chemical variables (oxygen, inorganic nutrients, DOC) in the depth profiles. We also identified distinct seasonal indicator prokaryotes inhabiting the DSL, representing between 2% (in spring) to over 10% (in winter) of total 16S rRNA gene sequences. The dominant indicator groups were Alteromonadales in winter, Vibrionales in spring and Microtrichales in summer. Using multidimensional scaling analysis, the DSL samples showed divergence from the surrounding mesopelagic layers and were distributed according to depth (47% of variance explained). We identified the sources of diversity that contribute to the DSL by analyzing the detailed profiles of spring, where 3 depths were sampled in the mesopelagic. On average, 7% was related to the epipelagic, 34% was common among the other mesopelagic waters and 38% was attributable to the DSL, with 21% of species being unique to this layer. CONCLUSIONS We conclude that the mesopelagic physico-chemical properties shape a rather uniform prokaryotic community, but that the 200 m deep DSL contributes uniquely and in a high proportion to the diversity of the Red Sea mesopelagic.
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Affiliation(s)
- Tamara Megan Huete-Stauffer
- Red Sea Research Center, Blg 2, Level 2, Office 2217-WS05, BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Mohd Ikram Ansari
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, India
| | - Anders Røstad
- Red Sea Research Center, Blg 2, Level 2, Office 2217-WS05, BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Maria Lluch Calleja
- Marine Ecology and Systematics, Biology Department, University of the Balearic Islands (UIB), Palma, Spain
| | - Xosé Anxelu G Morán
- Red Sea Research Center, Blg 2, Level 2, Office 2217-WS05, BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Centro Oceanográfico de Gijón/Xixón (IEO), CSIC, Gijón, Spain
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16
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Broek TAB, McCarthy MD, Ianiri HL, Vaughn JS, Mason HE, Knapp AN. Dominant heterocyclic composition of dissolved organic nitrogen in the ocean: A new paradigm for cycling and persistence. Proc Natl Acad Sci U S A 2023; 120:e2305763120. [PMID: 38015845 PMCID: PMC10710018 DOI: 10.1073/pnas.2305763120] [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: 04/10/2023] [Accepted: 10/24/2023] [Indexed: 11/30/2023] Open
Abstract
Marine dissolved organic nitrogen (DON) is one of the planet's largest reservoirs of fixed N, which persists even in the N-limited oligotrophic surface ocean. The vast majority of the ocean's total DON reservoir is refractory (RDON), primarily composed of low molecular weight (LMW) compounds in the subsurface and deep sea. However, the composition of this major N pool, as well as the reasons for its accumulation and persistence, are not understood. Past characterization of the analytically more tractable, but quantitatively minor, high molecular weight (HMW) DON fraction revealed a functionally simple amide-dominated composition. While extensive work in the past two decades has revealed enormous complexity and structural diversity in LMW dissolved organic carbon, no efforts have specifically targeted LMW nitrogenous molecules. Here, we report the first coupled isotopic and solid-state NMR structural analysis of LMW DON isolated throughout the water column in two ocean basins. Together these results provide a first view into the composition, potential sources, and cycling of this dominant portion of marine DON. Our data indicate that RDON is dominated by 15N-depleted heterocyclic-N structures, entirely distinct from previously characterized HMW material. This fundamentally new view of marine DON composition suggests an important structural control for RDON accumulation and persistence in the ocean. The mechanisms of production, cycling, and removal of these heterocyclic-N-containing compounds now represents a central challenge in our understanding of the ocean's DON reservoir.
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Affiliation(s)
- Taylor A. B. Broek
- Ocean Sciences Department, University of California, Santa Cruz, CA95064
- Atmospheric, Earth, and Energy Division, Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA94550
| | | | - Hope L. Ianiri
- Ocean Sciences Department, University of California, Santa Cruz, CA95064
| | - John S. Vaughn
- Nuclear and Chemical Sciences Division, Center for Nuclear Magnetic Resonance Spectroscopy, Lawrence Livermore National Laboratory, Livermore, CA94550
| | - Harris E. Mason
- Nuclear and Chemical Sciences Division, Center for Nuclear Magnetic Resonance Spectroscopy, Lawrence Livermore National Laboratory, Livermore, CA94550
| | - Angela N. Knapp
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL32304
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17
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Lai D, Hedlund BP, Mau RL, Jiao JY, Li J, Hayer M, Dijkstra P, Schwartz E, Li WJ, Dong H, Palmer M, Dodsworth JA, Zhou EM, Hungate BA. Resource partitioning and amino acid assimilation in a terrestrial geothermal spring. THE ISME JOURNAL 2023; 17:2112-2122. [PMID: 37741957 PMCID: PMC10579274 DOI: 10.1038/s41396-023-01517-7] [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: 05/24/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]
Abstract
High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of 13C-acetate and 13C-aspartate into DNA in 74 °C sediments in Gongxiaoshe Hot Spring, Tengchong, China. This revealed a community-wide preference for aspartate and a tight coupling between aspartate incorporation into DNA and the proliferation of aspartate utilizers during labeling. Both 13C incorporation into DNA and changes in the abundance of taxa during incubations indicated strong resource partitioning and a significant phylogenetic signal for aspartate incorporation. Of the active amplicon sequence variants (ASVs) identified by qSIP, most could be matched with genomes from Gongxiaoshe Hot Spring or nearby springs with an average nucleotide similarity of 99.4%. Genomes corresponding to aspartate primary utilizers were smaller, near-universally encoded polar amino acid ABC transporters, and had codon preferences indicative of faster growth rates. The most active ASVs assimilating both substrates were not abundant, suggesting an important role for the rare biosphere in the community response to organic carbon addition. The broad incorporation of aspartate into DNA over acetate by the hot spring community may reflect dynamic cycling of cell lysis products in situ or substrates delivered during monsoon rains and may reflect N limitation.
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Affiliation(s)
- Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
- Nevada Institute for Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China and Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- School of Resource Environment and Earth Science, Yunnan University, Kunming, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
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18
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Kida M, Merder J, Fujitake N, Tanabe Y, Hayashi K, Kudoh S, Dittmar T. Determinants of Microbial-Derived Dissolved Organic Matter Diversity in Antarctic Lakes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5464-5473. [PMID: 36947486 PMCID: PMC10077579 DOI: 10.1021/acs.est.3c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Identifying drivers of the molecular composition of dissolved organic matter (DOM) is essential to understand the global carbon cycle, but an unambiguous interpretation of observed patterns is challenging due to the presence of confounding factors that affect the DOM composition. Here, we show, by combining ultrahigh-resolution mass spectrometry and nuclear magnetic resonance spectroscopy, that the DOM molecular composition varies considerably among 43 lakes in East Antarctica that are isolated from terrestrial inputs and human influence. The DOM composition in these lakes is primarily driven by differences in the degree of photodegradation, sulfurization, and pH. Remarkable molecular beta-diversity of DOM was found that rivals the dissimilarity between DOM of rivers and the deep ocean, which was driven by environmental dissimilarity rather than the spatial distance. Our results emphasize that the extensive molecular diversity of DOM can arise even in one of the most pristine and organic matter source-limited environments on Earth, but at the same time the DOM composition is predictable by environmental variables and the lakes' ecological history.
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Affiliation(s)
- Morimaru Kida
- Research
Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute
for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, Oldenburg 26129, Germany
- Soil
Science Laboratory, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
| | - Julian Merder
- Department
of Global Ecology, Carnegie Institution
for Science, 260 Panama Street, Stanford, California 94305, United States
| | - Nobuhide Fujitake
- Soil
Science Laboratory, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
| | - Yukiko Tanabe
- National
Institute of Polar Research, Research Organization of Information
and Systems, 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan
- Department
of Polar Science, SOKENDAI (The Graduate
University for Advanced Studies), 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan
| | - Kentaro Hayashi
- Institute
for Agro-Environmental Sciences, NARO, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Sakae Kudoh
- National
Institute of Polar Research, Research Organization of Information
and Systems, 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan
- Department
of Polar Science, SOKENDAI (The Graduate
University for Advanced Studies), 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan
| | - Thorsten Dittmar
- Research
Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute
for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, Oldenburg 26129, Germany
- Helmholtz
Institute for Functional Marine Biodiversity (HIFMB) at the University
of Oldenburg, Oldenburg 26129, Germany
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19
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Bao H, Qiao J, Huang D, Niggemann J, Yi Y, Zhao W, Ni S, Dittmar T, Kao SJ. Molecular level characterization of the biolability of rainwater dissolved organic matter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160709. [PMID: 36493812 DOI: 10.1016/j.scitotenv.2022.160709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The atmospheric wet deposition has been recognized as a significant allochthonous source of dissolved organic carbon (DOC) to the ocean. However, few studies have examined the biolability of rainwater dissolved organic matter (DOM) at the molecular level. Rainwater samples were collected and incubated with ambient microbes. DOC, UV-vis spectroscopy, formic acid (FA), acetic acid (AA), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICRMS) were applied. Approximately 50 ± 16 % of rainwater DOC and ~90 % of FA and AA were bioconsumed within 28 days. The contribution of FA and AA to the total BDOC was ~30 %, which was the largest known biolabile fraction in rainwater DOC. In contrast, only approximately 15 % of formulae identified by FT-ICRMS were consumed, which were characterized by higher saturation, higher heteroatom content and lower modified aromaticity. Among the major high molecular weight secondary organic carbon (HWW-SOC)-like compounds, organosulfate contained the largest fraction of consumed formulae, while biogenic volatile organic-derived CHO compounds had the lowest. Our study for the first time provided both quantitative and qualitative understanding of the bioavailability of rainwater DOM, which is essential for understanding their effects on the biogeochemical cycles and the environmental health in the receiving waters.
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Affiliation(s)
- Hongyan Bao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.
| | - Jing Qiao
- School of Oceanography, Shanghai JiaoTong University, Shanghai, China
| | - Dekun Huang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; Observation and Research Station of Island and Coastal Ecosystem in the Western Taiwan Strait, Ministry of Natural Resources, Xiamen 361005, China
| | - Jutta Niggemann
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Yuanbi Yi
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Department of Ocean Science and the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Weiqiang Zhao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Silin Ni
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Thorsten Dittmar
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany; Helmholtz Institute for Functional Marine Biodiversity (HIFMB) at the University of Oldenburg, Oldenburg, Germany
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
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20
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Arandia-Gorostidi N, Parada AE, Dekas AE. Single-cell view of deep-sea microbial activity and intracommunity heterogeneity. THE ISME JOURNAL 2023; 17:59-69. [PMID: 36202927 PMCID: PMC9750969 DOI: 10.1038/s41396-022-01324-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 12/15/2022]
Abstract
Microbial activity in the deep sea is cumulatively important for global elemental cycling yet is difficult to quantify and characterize due to low cell density and slow growth. Here, we investigated microbial activity off the California coast, 50-4000 m water depth, using sensitive single-cell measurements of stable-isotope uptake and nucleic acid sequencing. We observed the highest yet reported proportion of active cells in the bathypelagic (up to 78%) and calculated that deep-sea cells (200-4000 m) are responsible for up to 34% of total microbial biomass synthesis in the water column. More cells assimilated nitrogen derived from amino acids than ammonium, and at higher rates. Nitrogen was assimilated preferentially to carbon from amino acids in surface waters, while the reverse was true at depth. We introduce and apply the Gini coefficient, an established equality metric in economics, to quantify intracommunity heterogeneity in microbial anabolic activity. We found that heterogeneity increased with water depth, suggesting a minority of cells contribute disproportionately to total activity in the deep sea. This observation was supported by higher RNA/DNA ratios for low abundance taxa at depth. Intracommunity activity heterogeneity is a fundamental and rarely measured ecosystem parameter and may have implications for community function and resilience.
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Affiliation(s)
| | - A E Parada
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - A E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, USA.
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21
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Zheng X, Cai R, Yao H, Zhuo X, He C, Zheng Q, Shi Q, Jiao N. Experimental Insight into the Enigmatic Persistence of Marine Refractory Dissolved Organic Matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17420-17429. [PMID: 36347804 DOI: 10.1021/acs.est.2c04136] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
More than 90% of marine dissolved organic matter (DOM) is biologically recalcitrant. This recalcitrance has been attributed to intrinsically refractory molecules or to low concentrations of molecules, but their relative contributions are a long-standing debate. Characterizing the molecular composition of marine DOM and its bioavailability is critical for understanding this uncertainty. Here, using different sorbents, DOM was solid-phase extracted from coastal, epipelagic, and deep-sea water samples for molecular characterization and was subjected to a 180-day incubation. 1H nuclear magnetic resonance spectroscopy and ultra-high-resolution mass spectrometry (UHRMS) analyses revealed that all of the DOM extracts contained refractory carboxyl-rich alicyclic molecules, accompanied with minor bio-labile components, for example, carbohydrates. Furthermore, dissolved organic carbon concentration analysis showed that a considerable fraction of the extracted DOM (86-95%) amended in the three seawater samples resisted microbial decomposition throughout the 180-day heterotrophic incubation, even when concentrated threefold. UHRMS analysis revealed that DOM composition remained mostly invariant in the 180-day deep-sea incubations. These results underlined that the dilution and intrinsic recalcitrance hypotheses are not mutually exclusive in explaining the recalcitrance of oceanic DOM, and that the intrinsically refractory DOM likely has a relatively high contribution to the solid-phase extractable DOM in the ocean.
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Affiliation(s)
- Xiaoxuan Zheng
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Ruanhong Cai
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Hongwei Yao
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Xiaocun Zhuo
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, Beijing 102249, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, Beijing 102249, China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, Beijing 102249, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
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22
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Duteil T, Bourillot R, Braissant O, Grégoire B, Leloup M, Portier E, Brigaud B, Féniès H, Svahn I, Henry A, Yokoyama Y, Visscher PT. Preservation of exopolymeric substances in estuarine sediments. Front Microbiol 2022; 13:921154. [PMID: 36060749 PMCID: PMC9434125 DOI: 10.3389/fmicb.2022.921154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/29/2022] [Indexed: 11/23/2022] Open
Abstract
The surface of intertidal estuarine sediments is covered with diatom biofilms excreting exopolymeric substances (EPSs) through photosynthesis. These EPSs are highly reactive and increase sediment cohesiveness notably through organo-mineral interactions. In most sedimentary environments, EPSs are partly to fully degraded by heterotrophic bacteria in the uppermost millimeters of the sediment and so they are thought to be virtually absent deeper in the sedimentary column. Here, we present the first evidence of the preservation of EPSs and EPS-mineral aggregates in a 6-m-long sedimentary core obtained from an estuarine point bar in the Gironde Estuary. EPSs were extracted from 18 depth intervals along the core, and their physicochemical properties were characterized by (i) wet chemical assays to measure the concentrations of polysaccharides and proteins, and EPS deprotonation of functional groups, (ii) acid–base titrations, and (iii) Fourier transform infrared spectroscopy. EPS-sediment complexes were also imaged using cryo-scanning electron microscopy. EPS results were analyzed in the context of sediment properties including facies, grain size, and total organic carbon, and of metabolic and enzymatic activities. Our results showed a predictable decrease in EPS concentrations (proteins and polysaccharides) and reactivity from the surface biofilm to a depth of 0.5 m, possibly linked to heterotrophic degradation. Concentrations remained relatively low down to ca. 4.3 m deep. Surprisingly, at that depth EPSs abundance was comparable to the surface and showed a downward decrease to 6.08 m. cryo-scanning electron microscopy (Cryo-SEM) showed that the EPS complexes with sediment were abundant at all studied depth and potentially protected EPSs from degradation. EPS composition did not change substantially from the surface to the bottom of the core. EPS concentrations and acidity were anti-correlated with metabolic activity, but showed no statistical correlation with grain size, TOC, depth or enzymatic activity. Maximum EPS concentrations were found at the top of tide-dominated sedimentary sequences, and very low concentrations were found in river flood-dominated sedimentary sequences. Based on this observation, we propose a scenario where biofilm development and EPS production are maximal when (i) the point bar and the intertidal areas were the most extensive, i.e., tide-dominated sequences and (ii) the tide-dominated deposit were succeeded by rapid burial beneath sediments, potentially decreasing the probability of encounter between bacterial cells and EPSs.
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Affiliation(s)
- Thibault Duteil
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, Pessac, France
- *Correspondence: Thibault Duteil,
| | | | - Olivier Braissant
- Department Biomedical Engineering (DBE), Center for Biomechanics and Biocalorimetry, University of Basel, Allschwil, Switzerland
| | - Brian Grégoire
- Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Centre National de la Recherche Scientifique (CNRS), Université de Poitiers, Poitiers, France
| | - Maud Leloup
- Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Centre National de la Recherche Scientifique (CNRS), Université de Poitiers, Poitiers, France
| | | | | | - Hugues Féniès
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, Pessac, France
| | - Isabelle Svahn
- Bordeaux Imaging Center (BIC), CNRS, Université de Bordeaux, Bordeaux, France
| | - Adrien Henry
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, Pessac, France
| | - Yusuke Yokoyama
- Department of Earth and Planetary Sciences, Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwanoha, Chiba, Japan
| | - Pieter T. Visscher
- Department of Marine Sciences and Geosciences, University of Connecticut, Groton, CT, United States
- CNRS, Biogéosciences, Université de Bourgogne Franche-Comté, Dijon, France
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23
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Ma J, Chen F, Xu H, Liu J, Chen CC, Zhang Z, Jiang H, Li Y, Pan K. Fate of face masks after being discarded into seawater: Aging and microbial colonization. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129084. [PMID: 35596986 PMCID: PMC9069998 DOI: 10.1016/j.jhazmat.2022.129084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 05/06/2023]
Abstract
Billions of discarded masks have entered the oceans since the outbreak of the COVID-19 pandemic. Current reports mostly discuss the potential of masks as plastic pollution, but there has been no study on the fate of this emerging plastic waste in the marine environment. Therefore, we exposed masks in natural seawater and evaluated their aging and effects on the microbial community using a combination of physicochemical and biological techniques. After 30-day exposure in natural seawater, the masks suffered from significant aging. Microbial colonizers such as Rhodobacteraceae Flavobacteriaceae, Vibrionaceae and fouling organisms like calcareous tubeworms Hydroides elegans were massively present on the masks. The roughness and modulus of the mask fiber increased 3 and 5 times, respectively, and the molecular weight decreased 7%. The growth of biofouling organisms caused the masks negatively buoyant after 14-30 days. Our study sheds some light on the fate of discarded masks in a coastal area and provides fundamental data to manage this important plastic waste during COVID-19 pandemic.
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Affiliation(s)
- Jie Ma
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Fengyuan Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Huo Xu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Jingli Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Ciara Chun Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Zhen Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Hao Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 Hubei, China
| | - Yanping Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Ke Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China.
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24
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Xia F, Liu Z, Zhao M, Li Q, Li D, Cao W, Zeng C, Hu Y, Chen B, Bao Q, Zhang Y, He Q, Lai C, He X, Ma Z, Han Y, He H. High stability of autochthonous dissolved organic matter in karst aquatic ecosystems: Evidence from fluorescence. WATER RESEARCH 2022; 220:118723. [PMID: 35696806 DOI: 10.1016/j.watres.2022.118723] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/20/2022] [Accepted: 06/06/2022] [Indexed: 05/26/2023]
Abstract
Biological carbon pump (BCP) in karst areas has received intensive attention for years due to their significant contribution to the global missing carbon sink. The stability of autochthonous dissolved organic matter (Auto-DOM) produced by BCP in karst aquatic ecosystems may play a critical role in the missing carbon sink. However, the source of dissolved organic matter (DOM) in inland waters and its consumption by planktonic bacteria have not been thoroughly examined. Recalcitrant dissolved organic matter (RDOM) may exist in karst aquatic ecosystem as in the ocean. Through the study of the chromophoric dissolved organic matter (CDOM) and the interaction between CDOM and the planktonic bacterial community under different land uses at the Shawan Karst Water-carbon Cycle Test Site, SW China, we found that C2, as the fluorescence component of Auto-DOM mineralised by planktonic bacteria, may have some of the characteristics of RDOM and is an important DOM source in karst aquatic ecosystems. The stability ratio (Fmax(C2/(C1+C2))) of Auto-DOM reached 89.6 ± 6.71% in winter and 64.1 ± 7.19% in spring. Moreover, correlation-based network analysis determined that the planktonic bacterial communities were controlled by different fluorescence types of CDOM, of which C1 (fresh Auto-DOM), C3 (conventional allochthonous DOM (Allo-DOM)) and C4 (the Allo-DOM mineralised by bacteria) were clustered in one module together with prevalent organic-degrading planktonic bacteria; C2 was clustered in another tightly combined module, suggesting specific microbial utilization strategies for the C2 component. In addition, some important planktonic bacterium and functional genes (including chemotrophic heterotrophs and photosynthetic bacteria) were found to be affected by high Ca2+ and dissolved inorganic carbon (DIC) concentrations in karst aquatic ecosystems. Our research showed that Auto-DOM may be as an important carbon sink as the Allo-DOM in karst ecosystems, the former generally being neglected based on a posit that it is easily and first mineralized by planktonic bacteria.
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Affiliation(s)
- Fan Xia
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Zaihua Liu
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China; CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, China.
| | - Min Zhao
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Qiang Li
- Key Laboratory of Karst Dynamics, Ministry of Nature Resources/Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China
| | - Dong Li
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfang Cao
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China
| | - Cheng Zeng
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Yundi Hu
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Bo Chen
- Guizhou University of Finance and Economics, Guiyang 550025, China
| | - Qian Bao
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Key Laboratory of Land Resources Evaluation and Monitoring in Southwest China of Ministry of Education, Sichuan Normal University, Chengdu 610066, China
| | - Yi Zhang
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Resources and Environmental Engineering, Guizhou Institute of Technology, Guiyang 550008, China
| | - Qiufang He
- Chongqing Key Laboratory of Karst Environment, School of Geographical Sciences, Southwest University, Chongqing 400700, China; Key Laboratory of Karst Dynamics, Ministry of Nature Resources/Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China
| | - Chaowei Lai
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Xuejun He
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Zhen Ma
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China
| | - Yongqiang Han
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Haibo He
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China
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25
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Chen X, Liu J, Chen J, Wang J, Xiao X, He C, Shi Q, Li G, Jiao N. Oxygen availability driven trends in DOM molecular composition and reactivity in a seasonally stratified fjord. WATER RESEARCH 2022; 220:118690. [PMID: 35661504 DOI: 10.1016/j.watres.2022.118690] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Ocean deoxygenation could potentially trigger substantial changes in the composition and reactivity of dissolved organic matter (DOM) pool, which plays an important role in the global carbon cycle. To evaluate links between DOM dynamics and oxygen availability, we investigated the DOM composition under varying levels of oxygen in a seasonally hypoxic fjord through a monthly time-series over two years. We used ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to characterize DOM on a molecular level. We find a clear trend both in diversity and molecular composition of the DOM along the oxygen gradient. As oxygen decreased, the chemodiversity was significantly increased, along with accumulation of relatively high-molecular-weight, reduced and unsaturated compounds enriched with carboxyl-group structures, which were also thermodynamically less favorable to biodegradation. Our results suggested that oxygen depletion selectively protected otherwise bioavailable compounds from decomposition and may promote the accumulation of a larger recalcitrant DOM pool in the global ocean, which could provide negative feedback to the ocean carbon sequestration and climate change.
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Affiliation(s)
- Xiao Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, Canada, Qingdao, China and Xiamen, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, Canada, Qingdao, China and Xiamen, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China.
| | - Junfeng Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, Canada, Qingdao, China and Xiamen, China
| | - Jianning Wang
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, Canada, Qingdao, China and Xiamen, China; State Key Laboratory for Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xilin Xiao
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, Canada, Qingdao, China and Xiamen, China; State Key Laboratory for Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Nianzhi Jiao
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, Canada, Qingdao, China and Xiamen, China; State Key Laboratory for Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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26
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LaBrie R, Péquin B, Fortin St-Gelais N, Yashayaev I, Cherrier J, Gélinas Y, Guillemette F, Podgorski DC, Spencer RGM, Tremblay L, Maranger R. Deep ocean microbial communities produce more stable dissolved organic matter through the succession of rare prokaryotes. SCIENCE ADVANCES 2022; 8:eabn0035. [PMID: 35857452 PMCID: PMC11323801 DOI: 10.1126/sciadv.abn0035] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The microbial carbon pump (MCP) hypothesis suggests that successive transformation of labile dissolved organic carbon (DOC) by prokaryotes produces refractory DOC (RDOC) and contributes to the long-term stability of the deep ocean DOC reservoir. We tested the MCP by exposing surface water from a deep convective region of the ocean to epipelagic, mesopelagic, and bathypelagic prokaryotic communities and tracked changes in dissolved organic matter concentration, composition, and prokaryotic taxa over time. Prokaryotic taxa from the deep ocean were more efficient at consuming DOC and producing RDOC as evidenced by greater abundance of highly oxygenated molecules and fluorescent components associated with recalcitrant molecules. This first empirical evidence of the MCP in natural waters shows that carbon sequestration is more efficient in deeper waters and suggests that the higher diversity of prokaryotes from the rare biosphere holds a greater metabolic potential in creating these stable dissolved organic compounds.
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Affiliation(s)
- Richard LaBrie
- Département des sciences biologiques, Université de Montréal, Pavillon MIL C. P. 6128, succ. Centre-ville, Montréal, QC H3C 3J7, Canada
- Groupe de recherche interuniversitaire en limnologie et environnement aquatique (GRIL), Université de Montréal, C. P. 6128, succ. Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Bérangère Péquin
- Département des sciences biologiques, Université de Montréal, Pavillon MIL C. P. 6128, succ. Centre-ville, Montréal, QC H3C 3J7, Canada
- Groupe de recherche interuniversitaire en limnologie et environnement aquatique (GRIL), Université de Montréal, C. P. 6128, succ. Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Nicolas Fortin St-Gelais
- Département des sciences biologiques, Université de Montréal, Pavillon MIL C. P. 6128, succ. Centre-ville, Montréal, QC H3C 3J7, Canada
- Groupe de recherche interuniversitaire en limnologie et environnement aquatique (GRIL), Université de Montréal, C. P. 6128, succ. Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Igor Yashayaev
- Department of Fisheries and Ocean Canada, Bedford Institute of Oceanography, 1 Challenger Dr., Dartmouth, NS B2Y 4A2, Canada
| | - Jennifer Cherrier
- Department of Earth and Environmental Sciences, Brooklyn College–The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
| | - Yves Gélinas
- Geotop and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke W., Montréal, QC H4B 1R6, Canada
| | - François Guillemette
- Groupe de recherche interuniversitaire en limnologie et environnement aquatique (GRIL), Université de Montréal, C. P. 6128, succ. Centre-ville, Montréal, QC H3C 3J7, Canada
- Département des sciences de l’environnement, Université du Québec à Trois-Rivières, 3351 Boulevard des Forges, Trois-Rivières, QC G8Z 4M3, Canada
| | - David C. Podgorski
- Pontchartrain Institute for Environmental Sciences, Department of Chemistry, The University of New Orleans, 2000 Lakeshore Dr., New Orleans, LA 70148, USA
| | - Robert G. M. Spencer
- National High Magnetic Field Laboratory, Geochemistry Group, Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, USA
| | - Luc Tremblay
- Département de chimie et biochimie, Université de Moncton, 18, avenue Antonine-Maillet, Moncton, NB E1A 3E9, Canada
| | - Roxane Maranger
- Département des sciences biologiques, Université de Montréal, Pavillon MIL C. P. 6128, succ. Centre-ville, Montréal, QC H3C 3J7, Canada
- Groupe de recherche interuniversitaire en limnologie et environnement aquatique (GRIL), Université de Montréal, C. P. 6128, succ. Centre-ville, Montréal, QC H3C 3J7, Canada
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Wang Y, Xie R, Shen Y, Cai R, He C, Chen Q, Guo W, Shi Q, Jiao N, Zheng Q. Linking Microbial Population Succession and DOM Molecular Changes in Synechococcus-Derived Organic Matter Addition Incubation. Microbiol Spectr 2022; 10:e0230821. [PMID: 35380472 PMCID: PMC9045170 DOI: 10.1128/spectrum.02308-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/10/2022] [Indexed: 12/04/2022] Open
Abstract
The molecular-level interactions between phytoplankton-derived dissolved organic matter (DOM) and heterotrophic prokaryotes represent a fundamental and yet poorly understood component of the marine elemental cycle. Here, we investigated the degradation of Synechococcus-derived organic matter (SynOM) by coastal microorganisms using spectroscopic and ultrahigh-resolution mass spectrometry analyses coupled with high-throughput sequencing. The added SynOM showed a spectrum of reactivity during a 180-day dark incubation experiment. Along with the decrease in DOM bioavailability, the chemical properties of DOM molecules overall showed increases in oxidation state and aromaticity. Both the microbial community and DOM molecular compositions became more homogeneous toward the end of the incubation. The experiment was partitioned into three phases (I, II, and III) based on the total organic carbon consumption rates from 7.0 ± 1.0 to 1.0 ± 0.1 and to 0.1 ± 0.0 μmol C L-1 day-1, respectively. Diverse generalists with low abundance were present in all three phases of the experiment, while a few abundant specialists dominated specific phases, suggesting their diverse roles in the transformation of DOM molecules from labile and semilabile to recalcitrant. The changes of organic molecules belonging to CHO, CHNO, and CHOS containing formulas were closely associated with specific microbial populations, suggesting close interactions between the different bacterial metabolic potential for substrates and DOM molecular compositional characteristics. This study sheds light on the interactions between microbial population succession and DOM molecular changes processes and collectively advances our understanding of microbial processing of the marine elemental cycle. IMPORTANCE Phytoplankton are a major contributor of labile dissolved organic matter (DOM) in the upper ocean, fueling tremendous marine prokaryotic activity. Interactions between microorganisms and algae-derived DOM regulate biogeochemical cycles in the ocean, but key aspects of their interactions remain poorly understood. Under global warming and eutrophication scenarios, Synechococcus blooms are commonly observed in coastal seawaters, and they significantly influence the elemental biogeochemistry cycling in eutrophic ecosystems. To understand the interactions between Synechococcus-derived DOM and heterotrophic prokaryotes as well as their influence on the coastal environment, we investigated the degradation of DOM by coastal microbes during a 180-day dark incubation. We showed substantial DOM compositional changes that were closely linked to the developments of microbial specialists and generalists. Our study provides information on the interactions between microbial population succession and DOM molecular changes, thereby advancing our understanding of microbial processing of the marine DOM pool under the influence of climate change.
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Affiliation(s)
- Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Rui Xie
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Yuan Shen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ruanhong Cai
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Qi Chen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Weidong Guo
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Key Laboratory of Coastal and Wetland Ecosystems, Ministry of Education, Xiamen University, Xiamen, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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28
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Riemann L, Rahav E, Passow U, Grossart HP, de Beer D, Klawonn I, Eichner M, Benavides M, Bar-Zeev E. Planktonic Aggregates as Hotspots for Heterotrophic Diazotrophy: The Plot Thickens. Front Microbiol 2022; 13:875050. [PMID: 35464923 PMCID: PMC9019601 DOI: 10.3389/fmicb.2022.875050] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 11/26/2022] Open
Abstract
Biological dinitrogen (N2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N2 fixation by NCDs and propose a conceptual framework for aggregate-associated N2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments.
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Affiliation(s)
- Lasse Riemann
- Marine Biology Section, University of Copenhagen, Helsingør, Denmark
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Uta Passow
- Ocean Science Centre, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Hans-Peter Grossart
- Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany.,Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Isabell Klawonn
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Meri Eichner
- Institute of Microbiology CAS, Centre ALGATECH, Třeboň, Czechia
| | - Mar Benavides
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France.,Turing Center for Living Systems, Aix-Marseille University, Marseille, France
| | - Edo Bar-Zeev
- The Jacob Blaustein Institutes for Desert Research, Zuckerberg Institute for Water Research (ZIWR), Ben-Gurion University of the Negev, Be'er Sheva, Israel
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29
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30
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Seidel M, Vemulapalli SPB, Mathieu D, Dittmar T. Marine Dissolved Organic Matter Shares Thousands of Molecular Formulae Yet Differs Structurally across Major Water Masses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3758-3769. [PMID: 35213127 DOI: 10.1021/acs.est.1c04566] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Most oceanic dissolved organic matter (DOM) is still not fully molecularly characterized. We combined high-field nuclear magnetic resonance (NMR) and ultrahigh-resolution mass spectrometry (Fourier-transform ion cyclotron resonance mass spectrometry, FT-ICR-MS) for the structural and molecular formula-level characterization of solid-phase extracted (SPE) DOM from surface, mesopelagic, and bathypelagic Atlantic and Pacific Ocean samples. Using a MicroCryoProbe, unprecedented low amounts of SPE-DOM (∼1 mg carbon) were sufficient for two-dimensional NMR analysis. Low proportions of olefinic and aromatic relative to aliphatic and carboxylated structures (NMR) at the sea surface were likely related to photochemical transformations. This was consistent with lower molecular masses and higher degrees of saturation and oxygenation (FT-ICR-MS) compared to those of the deep sea. Carbohydrate structures in the mesopelagic North Pacific Ocean suggest export and release from sinking particles. In our sample set, the universal molecular DOM composition, as captured by FT-ICR-MS, appears to be structurally more diverse when analyzed by NMR, suggesting DOM variability across oceanic provinces to be more pronounced than previously assumed. As a proof of concept, our study takes advantage of new complementary approaches resolving thousands of structural and molecular DOM features while applying reasonable instrument times, allowing for the analysis of large oceanic data sets to increase our understanding of marine DOM biogeochemistry.
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Affiliation(s)
- Michael Seidel
- Research Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, 26129 Oldenburg, Germany
| | - 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
| | - Daniel Mathieu
- Magnetic Resonance Spectroscopy, NMR Applications, Bruker BioSpin GmbH, 76287 Rheinstetten, 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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31
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Kundu K, Melsbach A, Heckel B, Schneidemann S, Kanapathi D, Marozava S, Merl-Pham J, Elsner M. Linking Increased Isotope Fractionation at Low Concentrations to Enzyme Activity Regulation: 4-Cl Phenol Degradation by Arthrobacter chlorophenolicus A6. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3021-3032. [PMID: 35148097 PMCID: PMC8892832 DOI: 10.1021/acs.est.1c04939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 01/23/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Slow microbial degradation of organic trace chemicals ("micropollutants") has been attributed to either downregulation of enzymatic turnover or rate-limiting substrate supply at low concentrations. In previous biodegradation studies, a drastic decrease in isotope fractionation of atrazine revealed a transition from rate-limiting enzyme turnover to membrane permeation as a bottleneck when concentrations fell below the Monod constant of microbial growth. With degradation of the pollutant 4-chlorophenol (4-CP) by Arthrobacter chlorophenolicus A6, this study targeted a bacterium which adapts its enzyme activity to concentrations. Unlike with atrazine degradation, isotope fractionation of 4-CP increased at lower concentrations, from ε(C) = -1.0 ± 0.5‰ in chemostats (D = 0.090 h-1, 88 mg L-1) and ε(C) = -2.1 ± 0.5‰ in batch (c0 = 220 mg L-1) to ε(C) = -4.1 ± 0.2‰ in chemostats at 90 μg L-1. Surprisingly, fatty acid composition indicated increased cell wall permeability at high concentrations, while proteomics revealed that catabolic enzymes (CphCI and CphCII) were differentially expressed at D = 0.090 h-1. These observations support regulation on the enzyme activity level─through either a metabolic shift between catabolic pathways or decreased enzymatic turnover at low concentrations─and, hence, reveal an alternative end-member scenario for bacterial adaptation at low concentrations. Including more degrader strains into this multidisciplinary analytical approach offers the perspective to build a knowledge base on bottlenecks of bioremediation at low concentrations that considers bacterial adaptation.
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Affiliation(s)
- Kankana Kundu
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
- Center
for Microbial Ecology and Technology (CMET), Faculty of Bioscience
Engineering, University of Ghent, Coupure Links 653, 9000 Ghent, Belgium
| | - Aileen Melsbach
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, D-85748 Garching, Germany
| | - Benjamin Heckel
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
| | - Sarah Schneidemann
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
| | - Dheeraj Kanapathi
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
| | - Sviatlana Marozava
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
| | - Juliane Merl-Pham
- Core
Facility Proteomics, Helmholtz Zentrum München, Heidemannstr. 1, 80939 Munich, Germany
| | - Martin Elsner
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, D-85748 Garching, Germany
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32
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Li L, Li Y, Fang Z, He C. Study on molecular structure characteristics of natural dissolved organic nitrogen by use of negative and positive ion mode electrospray ionization Orbitrap mass spectrometry and collision-induced dissociation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152116. [PMID: 34871689 DOI: 10.1016/j.scitotenv.2021.152116] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
Dissolved organic nitrogen (DON) in aquatic systems is an important component of the global nitrogen cycle. However, the molecular structural information of DON in natural water is still unknown. In this study, the molecular structural characteristics of DON molecules in three natural waters were studied by using negative and positive ion mode electrospray ionization (ESI) Orbitrap mass spectrometry and collision-induced dissociation (CID). The DON compounds in these natural water samples could be selectively ionized by a positive ESI source with formic acid as the ionization promoter. A fraction of DON may exist as amphoteric substance. Then, possible chemical structures were assigned for some of these DON molecules by CID. Possible O-containing functional groups could be assigned as carboxyl, hydroxyl, carbonyl and methoxyl in negative/positive ESI tandem mass spectra, and neutral loss of NH3 corresponding to amino groups was observed for the first time in a positive ESI CID MSMS analysis, which demonstrated that a fraction of DON in natural water may exist as amino acid-like compounds. The results demonstrate that the positive/negative ESI CID Orbitrap MSMS method could provide valuable molecular structure information on DON in natural water.
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Affiliation(s)
- Lijie Li
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing 102249, China; Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, China.
| | - Yunyun Li
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing 102249, China
| | - Zhi Fang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing 102249, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing 102249, China.
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33
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Cooper WT, Chanton JC, D'Andrilli J, Hodgkins SB, Podgorski DC, Stenson AC, Tfaily MM, Wilson RM. A History of Molecular Level Analysis of Natural Organic Matter by FTICR Mass Spectrometry and The Paradigm Shift in Organic Geochemistry. MASS SPECTROMETRY REVIEWS 2022; 41:215-239. [PMID: 33368436 DOI: 10.1002/mas.21663] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/16/2020] [Accepted: 09/16/2020] [Indexed: 06/12/2023]
Abstract
Natural organic matter (NOM) is a complex mixture of biogenic molecules resulting from the deposition and transformation of plant and animal matter. It has long been recognized that NOM plays an important role in many geological, geochemical, and environmental processes. Of particular concern is the fate of NOM in response to a warming climate in environments that have historically sequestered carbon (e.g., peatlands and swamps) but may transition to net carbon emitters. In this review, we will highlight developments in the application of high-field Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) in identifying the individual components of complex NOM mixtures, focusing primarily on the fraction that is dissolved in natural waters (dissolved organic matter or DOM). We will first provide some historical perspective on developments in FTICR technology that made molecular-level characterizations of DOM possible. A variety of applications of the technique will then be described, followed by our view of the future of high-field FTICR MS in carbon cycling research, including a particularly exciting metabolomic approach.
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Affiliation(s)
- William T Cooper
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL
| | - Jeffrey C Chanton
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL
| | | | | | | | | | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, Tucson, AZ
| | - Rachel M Wilson
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL
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Morán XAG, García FC, Røstad A, Silva L, Al-Otaibi N, Irigoien X, Calleja ML. Diel dynamics of dissolved organic matter and heterotrophic prokaryotes reveal enhanced growth at the ocean's mesopelagic fish layer during daytime. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150098. [PMID: 34508930 DOI: 10.1016/j.scitotenv.2021.150098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/12/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Contrary to epipelagic waters, where biogeochemical processes closely follow the light and dark periods, little is known about diel cycles in the ocean's mesopelagic realm. Here, we monitored the dynamics of dissolved organic matter (DOM) and planktonic heterotrophic prokaryotes every 2 h for one day at 0 and 550 m (a depth occupied by vertically migrating fishes during light hours) in oligotrophic waters of the central Red Sea. We additionally performed predator-free seawater incubations of samples collected from the same site both at midnight and at noon. Comparable in situ variability in microbial biomass and dissolved organic carbon concentration suggests a diel supply of fresh DOM in both layers. The presence of fishes in the mesopelagic zone during daytime likely promoted a sustained, longer growth of larger prokaryotic cells. The specific growth rates were consistently higher in the noon experiments from both depths (surface: 0.34 vs. 0.18 d-1, mesopelagic: 0.16 vs. 0.09 d-1). Heterotrophic prokaryotes in the mesopelagic layer were also more efficient at converting extant DOM into new biomass. These results suggest that the ocean's twilight zone receives a consistent diurnal supply of labile DOM from the diel vertical migration of fishes, enabling an unexpectedly active community of heterotrophic prokaryotes.
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Affiliation(s)
- Xosé Anxelu G Morán
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Science & Engineering Division, 23955-6900 Thuwal, Saudi Arabia.
| | - Francisca C García
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Science & Engineering Division, 23955-6900 Thuwal, Saudi Arabia; Environment and Sustainability Institute, University of Exeter, TR10 9FE Penryn, United Kingdom
| | - Anders Røstad
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Science & Engineering Division, 23955-6900 Thuwal, Saudi Arabia
| | - Luis Silva
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Science & Engineering Division, 23955-6900 Thuwal, Saudi Arabia
| | - Najwa Al-Otaibi
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Science & Engineering Division, 23955-6900 Thuwal, Saudi Arabia; Department of Biology, College of Science, Taif University, Al-Hawiya 888, Saudi Arabia
| | | | - Maria Ll Calleja
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Science & Engineering Division, 23955-6900 Thuwal, Saudi Arabia; Max Planck Institute for Chemistry, 55128 Mainz, Germany
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35
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De Corte D, Muck S, Tiroch J, Mena C, Herndl GJ, Sintes E. Microbes mediating the sulfur cycle in the Atlantic Ocean and their link to chemolithoautotrophy. Environ Microbiol 2021; 23:7152-7167. [PMID: 34490972 DOI: 10.1111/1462-2920.15759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 08/18/2021] [Accepted: 09/03/2021] [Indexed: 11/26/2022]
Abstract
Only about 10%-30% of the organic matter produced in the epipelagic layers reaches the dark ocean. Under these limiting conditions, reduced inorganic substrates might be used as an energy source to fuel prokaryotic chemoautotrophic and/or mixotrophic activity. The aprA gene encodes the alpha subunit of the adenosine-5'-phosphosulfate (APS) reductase, present in sulfate-reducing (SRP) and sulfur-oxidizing prokaryotes (SOP). The sulfur-oxidizing pathway can be coupled to inorganic carbon fixation via the Calvin-Benson-Bassham cycle. The abundances of aprA and cbbM, encoding RuBisCO form II (the key CO2 fixing enzyme), were determined over the entire water column along a latitudinal transect in the Atlantic from 64°N to 50°S covering six oceanic provinces. The abundance of aprA and cbbM genes significantly increased with depth reaching the highest abundances in meso- and upper bathypelagic layers. The contribution of cells containing these genes also increased from mesotrophic towards oligotrophic provinces, suggesting that under nutrient limiting conditions alternative energy sources are advantageous. However, the aprA/cbbM ratios indicated that only a fraction of the SOP is associated with inorganic carbon fixation. The aprA harbouring prokaryotic community was dominated by Pelagibacterales in surface and mesopelagic waters, while Candidatus Thioglobus, Chromatiales and the Deltaproteobacterium_SCGC dominated the bathypelagic realm. Noticeably, the contribution of the SRP to the prokaryotic community harbouring aprA gene was low, suggesting a major utilization of inorganic sulfur compounds either as an energy source (occasionally coupled with inorganic carbon fixation) or in biosynthesis pathways.
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Affiliation(s)
- Daniele De Corte
- Institute for Chemistry and Biology of the Marine Environment, Carl Von Ossietzky University, Oldenburg, Germany
| | - Simone Muck
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Johanna Tiroch
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Catalina Mena
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
| | - Eva Sintes
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
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36
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A largely invariant marine dissolved organic carbon reservoir across Earth's history. Proc Natl Acad Sci U S A 2021; 118:2103511118. [PMID: 34580216 DOI: 10.1073/pnas.2103511118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/18/2022] Open
Abstract
Marine dissolved organic carbon (DOC), the largest pool of reduced carbon in the oceans, plays an important role in the global carbon cycle and contributes to the regulation of atmospheric oxygen and carbon dioxide abundances. Despite its importance in global biogeochemical cycles, the long-term history of the marine DOC reservoir is poorly constrained. Nonetheless, significant changes to the size of the oceanic DOC reservoir through Earth's history have been commonly invoked to explain changes to ocean chemistry, carbon cycling, and marine ecology. Here, we present a revised view of the evolution of marine DOC concentrations using a mechanistic carbon cycle model that can reproduce DOC concentrations in both oxic and anoxic modern environments. We use this model to demonstrate that the overall size of the marine DOC reservoir has likely undergone very little variation through Earth's history, despite major changes in the redox state of the ocean-atmosphere system and the nature and efficiency of the biological carbon pump. A relatively static marine DOC reservoir across Earth's history renders it unlikely that major changes in marine DOC concentrations have been responsible for driving massive repartitioning of surface carbon or the large carbon isotope excursions observed in Earth's stratigraphic record and casts doubt on previously hypothesized links between marine DOC levels and the emergence and radiation of early animals.
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37
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Marine dissolved organic matter: a vast and unexplored molecular space. Appl Microbiol Biotechnol 2021; 105:7225-7239. [PMID: 34536106 PMCID: PMC8494709 DOI: 10.1007/s00253-021-11489-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 01/02/2023]
Abstract
Abstract Marine dissolved organic matter (DOM) comprises a vast and unexplored molecular space. Most of it resided in the oceans for thousands of years. It is among the most diverse molecular mixtures known, consisting of millions of individual compounds. More than 1 Eg of this material exists on the planet. As such, it comprises a formidable source of natural products promising significant potential for new biotechnological purposes. Great emphasis has been placed on understanding the role of DOM in biogeochemical cycles and climate attenuation, its lifespan, interaction with microorganisms, as well as its molecular composition. Yet, probing DOM bioactivities is in its infancy, largely because it is technically challenging due to the chemical complexity of the material. It is of considerable interest to develop technologies capable to better discern DOM bioactivities. Modern screening technologies are opening new avenues allowing accelerated identification of bioactivities for small molecules from natural products. These methods diminish a priori the need for laborious chemical fractionation. We examine here the application of untargeted metabolomics and multiplexed high-throughput molecular-phenotypic screening techniques that are providing first insights on previously undetectable DOM bioactivities. Key points • Marine DOM is a vast, unexplored biotechnological resource. • Untargeted bioscreening approaches are emerging for natural product screening. • Perspectives for developing bioscreening platforms for marine DOM are discussed.
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38
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Wang L, Lin Y, Ye L, Qian Y, Shi Y, Xu K, Ren H, Geng J. Microbial Roles in Dissolved Organic Matter Transformation in Full-Scale Wastewater Treatment Processes Revealed by Reactomics and Comparative Genomics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:11294-11307. [PMID: 34338502 DOI: 10.1021/acs.est.1c02584] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Understanding the degradation of dissolved organic matter (DOM) is vital for optimizing DOM control. However, the microbe-mediated DOM transformation during wastewater treatment remains poorly characterized. Here, microbes and DOM along full-scale biotreatment processes were simultaneously characterized using comparative genomics and high-resolution mass spectrometry-based reactomics. Biotreatments significantly increased DOM's aromaticity and unsaturation due to the overproduced lignin and polyphenol analogs. DOM was diversified by over five times in richness, with thousands of nitrogenous and sulfur-containing compounds generated through microbe-mediated oxidoreduction, functional group transfer, and C-N and C-S bond formation. Network analysis demonstrated microbial division of labor in DOM transformation. However, their roles were determined by their functional traits rather than taxa. Specifically, network and module hubs exhibited rapid growth potentials and broad substrate affinities but were deficient in xenobiotics-metabolism-associated genes. They were mainly correlated to liable DOM consumption and its transformation to recalcitrant compounds. In contrast, connectors and peripherals were potential degraders of recalcitrant DOM but slow in growth. They showed specialized associations with fewer DOM molecules and probably fed on metabolites of hub microbes. Thus, developing technologies (e.g., carriers) to selectively enrich peripheral degraders and consequently decouple the liable and recalcitrant DOM transformation processes may advance DOM removal.
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Affiliation(s)
- Liye Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Yuan Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Yuli Qian
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Yufei Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Ke Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
| | - Jinju Geng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, No. 163, Xianlin Avenue, Nanjing 210023, Jiangsu, P. R. China
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39
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From Nano-Gels to Marine Snow: A Synthesis of Gel Formation Processes and Modeling Efforts Involved with Particle Flux in the Ocean. Gels 2021; 7:gels7030114. [PMID: 34449609 PMCID: PMC8395865 DOI: 10.3390/gels7030114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 11/24/2022] Open
Abstract
Marine gels (nano-, micro-, macro-) and marine snow play important roles in regulating global and basin-scale ocean biogeochemical cycling. Exopolymeric substances (EPS) including transparent exopolymer particles (TEP) that form from nano-gel precursors are abundant materials in the ocean, accounting for an estimated 700 Gt of carbon in seawater. This supports local microbial communities that play a critical role in the cycling of carbon and other macro- and micro-elements in the ocean. Recent studies have furthered our understanding of the formation and properties of these materials, but the relationship between the microbial polymers released into the ocean and marine snow remains unclear. Recent studies suggest developing a (relatively) simple model that is tractable and related to the available data will enable us to step forward into new research by following marine snow formation under different conditions. In this review, we synthesize the chemical and physical processes. We emphasize where these connections may lead to a predictive, mechanistic understanding of the role of gels in marine snow formation and the biogeochemical functioning of the ocean.
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40
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Investigation of the molecular structure complexity of dissolved organic matter by UPLC-orbitrap MS/MS. Talanta 2021; 230:122320. [PMID: 33934784 DOI: 10.1016/j.talanta.2021.122320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/24/2022]
Abstract
The complex natural organic matter of the Suwannee River fulvic acid (SRFA) standard was analyzed by online reversed-phase chromatography with Orbitrap MS/MS using collision-induced dissociation (CID). The number of isobars per nominal mass could be reduced to a single dominantly abundant species in a chromatographic run, sharing some ions with signals having the identical molecular formula in adjacent chromatographic segments and later serving as a precursor ion for fragmentation. A very large proportion of the same fragment ions existed in adjacent chromatographic fractions. The difference in the fragment ions in adjacent chromatographic fractions could be attributed to a gradual change in the formula composition of precursor ions in a chromatographic run. It could be concluded that dissolved organic matter (DOM) molecules with the same elemental composition in different chromatographic fractions may have very similar molecular structures. In addition, we propose a possible DOM model that might greatly deepen our understanding of the behavior of DOM in aquatic matrices.
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41
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Cyanobacteria and biogeochemical cycles through Earth history. Trends Microbiol 2021; 30:143-157. [PMID: 34229911 DOI: 10.1016/j.tim.2021.05.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022]
Abstract
Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis, transforming the biology and chemistry of our planet. Genomic and evolutionary studies have revolutionized our understanding of early oxygenic phototrophs, complementing and dramatically extending inferences from the geologic record. Molecular clock estimates point to a Paleoarchean origin (3.6-3.2 billion years ago, bya) of the core proteins of Photosystem II (PSII) involved in oxygenic photosynthesis and a Mesoarchean origin (3.2-2.8 bya) for the last common ancestor of modern cyanobacteria. Nonetheless, most extant cyanobacteria diversified after the Great Oxidation Event (GOE), an environmental watershed ca. 2.45 bya made possible by oxygenic photosynthesis. Throughout their evolutionary history, cyanobacteria have played a key role in the global carbon cycle.
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42
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Baetge N, Behrenfeld MJ, Fox J, Halsey KH, Mojica KDA, Novoa A, Stephens BM, Carlson CA. The Seasonal Flux and Fate of Dissolved Organic Carbon Through Bacterioplankton in the Western North Atlantic. Front Microbiol 2021; 12:669883. [PMID: 34220753 PMCID: PMC8249739 DOI: 10.3389/fmicb.2021.669883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/20/2021] [Indexed: 11/13/2022] Open
Abstract
The oceans teem with heterotrophic bacterioplankton that play an appreciable role in the uptake of dissolved organic carbon (DOC) derived from phytoplankton net primary production (NPP). As such, bacterioplankton carbon demand (BCD), or gross heterotrophic production, represents a major carbon pathway that influences the seasonal accumulation of DOC in the surface ocean and, subsequently, the potential vertical or horizontal export of seasonally accumulated DOC. Here, we examine the contributions of bacterioplankton and DOM to ecological and biogeochemical carbon flow pathways, including those of the microbial loop and the biological carbon pump, in the Western North Atlantic Ocean (∼39-54°N along ∼40°W) over a composite annual phytoplankton bloom cycle. Combining field observations with data collected from corresponding DOC remineralization experiments, we estimate the efficiency at which bacterioplankton utilize DOC, demonstrate seasonality in the fraction of NPP that supports BCD, and provide evidence for shifts in the bioavailability and persistence of the seasonally accumulated DOC. Our results indicate that while the portion of DOC flux through bacterioplankton relative to NPP increased as seasons transitioned from high to low productivity, there was a fraction of the DOM production that accumulated and persisted. This persistent DOM is potentially an important pool of organic carbon available for export to the deep ocean via convective mixing, thus representing an important export term of the biological carbon pump.
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Affiliation(s)
- Nicholas Baetge
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Michael J. Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - James Fox
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Kimberly H. Halsey
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Kristina D. A. Mojica
- Division of Marine Science, School of Ocean Science and Engineering, The University of Southern Mississippi, John C. Stennis Space Center, Hattiesburg, MS, United States
| | - Anai Novoa
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Brandon M. Stephens
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, 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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43
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Lian J, Zheng X, Zhuo X, Chen YL, He C, Zheng Q, Lin TH, Sun J, Guo W, Shi Q, Jiao N, Cai R. Microbial transformation of distinct exogenous substrates into analogous composition of recalcitrant dissolved organic matter. Environ Microbiol 2021; 23:2389-2403. [PMID: 33559211 DOI: 10.1111/1462-2920.15426] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 01/24/2021] [Accepted: 02/04/2021] [Indexed: 01/02/2023]
Abstract
Oceanic dissolved organic matter (DOM) comprises a complex molecular mixture which is typically refractory and homogenous in the deep layers of the ocean. Though the refractory nature of deep-sea DOM is increasingly attributed to microbial metabolism, it remains unexplored whether ubiquitous microbial metabolism of distinct carbon substrates could lead to similar molecular composition of refractory DOM. Here, we conducted microbial incubation experiments using four typically bioavailable substrates (L-alanine, trehalose, sediment DOM extract, and diatom lysate) to investigate how exogenous substrates are transformed by a natural microbial assemblage. The results showed that although each-substrate-amendment induced different changes in the initial microbial assemblage and the amended substrates were almost depleted after 90 days of dark incubation, the bacterial community compositions became similar in all incubations on day 90. Correspondingly, revealed by ultra-high resolution mass spectrometry, molecular composition of DOM in all incubations became compositionally consistent with recalcitrant DOM and similar toward that of DOM from the deep-sea. These results indicate that while the composition of natural microbial communities can shift with substrate exposures, long-term microbial transformation of distinct substrates can ultimately lead to a similar refractory DOM composition. These findings provide an explanation for the homogeneous and refractory features of deep-sea DOM.
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Affiliation(s)
- Jie Lian
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.,Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, WE, 6708, Netherlands
| | - Xiaoxuan Zheng
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Xiaocun Zhuo
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, Beijing, 102249, China
| | - Yi-Lung Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, Beijing, 102249, China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361005, China
| | - Ta-Hui Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361005, China
| | - Weidong Guo
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, Beijing, 102249, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361005, China
| | - Ruanhong Cai
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361005, China
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44
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Trembath-Reichert E, Shah Walter SR, Ortiz MAF, Carter PD, Girguis PR, Huber JA. Multiple carbon incorporation strategies support microbial survival in cold subseafloor crustal fluids. SCIENCE ADVANCES 2021; 7:7/18/eabg0153. [PMID: 33910898 PMCID: PMC8081358 DOI: 10.1126/sciadv.abg0153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/09/2021] [Indexed: 05/03/2023]
Abstract
Biogeochemical processes occurring in fluids that permeate oceanic crust make measurable contributions to the marine carbon cycle, but quantitative assessments of microbial impacts on this vast, subsurface carbon pool are lacking. We provide bulk and single-cell estimates of microbial biomass production from carbon and nitrogen substrates in cool, oxic basement fluids from the western flank of the Mid-Atlantic Ridge. The wide range in carbon and nitrogen incorporation rates indicates a microbial community well poised for dynamic conditions, potentially anabolizing carbon and nitrogen at rates ranging from those observed in subsurface sediments to those found in on-axis hydrothermal vent environments. Bicarbonate incorporation rates were highest where fluids are most isolated from recharging bottom seawater, suggesting that anabolism of inorganic carbon may be a potential strategy for supplementing the ancient and recalcitrant dissolved organic carbon that is prevalent in the globally distributed subseafloor crustal environment.
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Affiliation(s)
| | - Sunita R Shah Walter
- School of Marine Science and Policy, University of Delaware, Lewes, DE 19958, USA
| | | | - Patrick D Carter
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Applied Ocean Engineering and Physics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Julie A Huber
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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45
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Ofaim S, Sulheim S, Almaas E, Sher D, Segrè D. Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus. Front Genet 2021; 12:586293. [PMID: 33633777 PMCID: PMC7900632 DOI: 10.3389/fgene.2021.586293] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 01/14/2021] [Indexed: 12/02/2022] Open
Abstract
Microbial life in the oceans impacts the entire marine ecosystem, global biogeochemistry and climate. The marine cyanobacterium Prochlorococcus, an abundant component of this ecosystem, releases a significant fraction of the carbon fixed through photosynthesis, but the amount, timing and molecular composition of released carbon are still poorly understood. These depend on several factors, including nutrient availability, light intensity and glycogen storage. Here we combine multiple computational approaches to provide insight into carbon storage and exudation in Prochlorococcus. First, with the aid of a new algorithm for recursive filling of metabolic gaps (ReFill), and through substantial manual curation, we extended an existing genome-scale metabolic model of Prochlorococcus MED4. In this revised model (iSO595), we decoupled glycogen biosynthesis/degradation from growth, thus enabling dynamic allocation of carbon storage. In contrast to standard implementations of flux balance modeling, we made use of forced influx of carbon and light into the cell, to recapitulate overflow metabolism due to the decoupling of photosynthesis and carbon fixation from growth during nutrient limitation. By using random sampling in the ensuing flux space, we found that storage of glycogen or exudation of organic acids are favored when the growth is nitrogen limited, while exudation of amino acids becomes more likely when phosphate is the limiting resource. We next used COMETS to simulate day-night cycles and found that the model displays dynamic glycogen allocation and exudation of organic acids. The switch from photosynthesis and glycogen storage to glycogen depletion is associated with a redistribution of fluxes from the Entner–Doudoroff to the Pentose Phosphate pathway. Finally, we show that specific gene knockouts in iSO595 exhibit dynamic anomalies compatible with experimental observations, further demonstrating the value of this model as a tool to probe the metabolic dynamic of Prochlorococcus.
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Affiliation(s)
- Shany Ofaim
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Snorre Sulheim
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Daniel Sher
- Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Daniel Segrè
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Biomedical Engineering, Boston University, Boston, MA, United States.,Department of Physics, Boston University, Boston, MA, United States.,Department of Biology, Boston University, Boston, MA, United States
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46
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Abstract
Organic matter in the global ocean, soils, and sediments stores about five times more carbon than the atmosphere. Thus, the controls on the accumulation of organic matter are critical to global carbon cycling. However, we lack a quantitative understanding of these controls. This prevents meaningful descriptions of organic matter cycling in global climate models, which are required for understanding how changes in organic matter reservoirs provide feedbacks to past and present changes in climate. Currently, explanations for organic matter accumulation remain under debate, characterized by seemingly competing hypotheses. Here, we develop a quantitative framework for organic matter accumulation that unifies these hypotheses. The framework derives from the ecological dynamics of microorganisms, the dominant consumers of organic matter. Organic matter constitutes a key reservoir in global elemental cycles. However, our understanding of the dynamics of organic matter and its accumulation remains incomplete. Seemingly disparate hypotheses have been proposed to explain organic matter accumulation: the slow degradation of intrinsically recalcitrant substrates, the depletion to concentrations that inhibit microbial consumption, and a dependency on the consumption capabilities of nearby microbial populations. Here, using a mechanistic model, we develop a theoretical framework that explains how organic matter predictably accumulates in natural environments due to biochemical, ecological, and environmental factors. Our framework subsumes the previous hypotheses. Changes in the microbial community or the environment can move a class of organic matter from a state of functional recalcitrance to a state of depletion by microbial consumers. The model explains the vertical profile of dissolved organic carbon in the ocean and connects microbial activity at subannual timescales to organic matter turnover at millennial timescales. The threshold behavior of the model implies that organic matter accumulation may respond nonlinearly to changes in temperature and other factors, providing hypotheses for the observed correlations between organic carbon reservoirs and temperature in past earth climates.
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47
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Su HN, Zhang YZ. Lifestyle of bacteria in deep sea. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:15-17. [PMID: 33006410 DOI: 10.1111/1758-2229.12891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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48
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Kothawala DN, Kellerman AM, Catalán N, Tranvik LJ. Organic Matter Degradation across Ecosystem Boundaries: The Need for a Unified Conceptualization. Trends Ecol Evol 2021; 36:113-122. [DOI: 10.1016/j.tree.2020.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 10/23/2022]
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49
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Chen S, Xu K, Ji D, Wang W, Xu Y, Chen C, Xie C. Release of dissolved and particulate organic matter by marine macroalgae and its biogeochemical implications. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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50
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Sebastián M, Forn I, Auladell A, Gómez-Letona M, Sala MM, Gasol JM, Marrasé C. Differential recruitment of opportunistic taxa leads to contrasting abilities in carbon processing by bathypelagic and surface microbial communities. Environ Microbiol 2020; 23:190-206. [PMID: 33089653 DOI: 10.1111/1462-2920.15292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/20/2020] [Indexed: 01/04/2023]
Abstract
Different factors affect the way dissolved organic matter (DOM) is processed in the ocean water column, including environmental conditions and the functional capabilities of the communities. Recent studies have shown that bathypelagic prokaryotes are metabolically flexible, but whether this versatility translates into a higher ability to process DOM has been barely explored. Here we performed a multifactorial transplant experiment to compare the growth, activity and changes in DOM quality in surface and bathypelagic waters inoculated with either surface or bathypelagic prokaryotic communities. The effect of nutrient additions to surface waters was also explored. Despite no differences in the cell abundance of surface and deep ocean prokaryotes were observed in any of the treatments, in surface waters with nutrients the heterotrophic production of surface prokaryotes rapidly decreased. Conversely, bathypelagic communities displayed a sustained production throughout the experiment. Incubations with surface prokaryotes always led to a significant accumulation of recalcitrant compounds, which did not occur with bathypelagic prokaryotes, suggesting they have a higher ability to process DOM. These contrasting abilities could be explained by the recruitment of a comparatively larger number of opportunistic taxa within the bathypelagic assemblages, which likely resulted in a broader community capability of substrate utilization.
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Affiliation(s)
- Marta Sebastián
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, 08003, Spain.,Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, 35214, Spain
| | - Irene Forn
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, 08003, Spain
| | - Adrià Auladell
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, 08003, Spain
| | - Markel Gómez-Letona
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, 35214, Spain
| | - M Montserrat Sala
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, 08003, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, 08003, Spain
| | - Cèlia Marrasé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, 08003, Spain
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