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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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2
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Jamion NA, Rafaai NH, Lee KE, Mokhtar M, Goh TL. Sustaining ex-mining lake-converted constructed wetlands as nature-based solutions: A comprehensive assessment of the carbon-water nexus in Paya Indah Wetlands, Malaysia. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 364:121449. [PMID: 38889647 DOI: 10.1016/j.jenvman.2024.121449] [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: 04/11/2024] [Revised: 05/27/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024]
Abstract
Water and carbon, essential for Earth's well-being, face imminent threats from human activities that fuel climate change. This study investigates nature-based solutions, focusing on the carbon-water nexus of ex-mining lake-converted constructed wetlands, specifically in Malaysia's Paya Indah Wetlands (PIW). Addressing research gaps, it assesses the ecosystem services of these wetlands, emphasising integrated evaluations for informed land management and employing a top-down conservation approach. Methodologically, spatial assessments, soil and water sampling, carbon quantification, water quality index calculations, land cover classification and stakeholder surveys were conducted. Results underscore the significant carbon sequestration and water quality improvement potential of constructed wetlands, with soil and sediment carbon accumulation reaching 1553.11 Mg C ha-1 (equivalent to 5700 Mg CO2 ha-1), translating to an annual sequestration capacity of 67.5 Mg C ha-1 year-1. Water quality index values ranged from 58 to 81 (Classes II to III). PIW's establishment led to a reduction of over 90% in barren land, with increases in water bodies (36%) and vegetation-covered land (38%), boosting wildlife populations by 30%. Spatial variations in organic carbon density and water quality underscore the complexity of the carbon-water nexus and its impacts on ecosystem health and water security. Despite land use changes, PIW demonstrates resilience, contributing to climate change mitigation. Stakeholder perceptions vary, emphasising the need for adaptive strategies. The study proposes transdisciplinary conservation initiatives and adaptive plans, stressing the pivotal role of ex-mining lake-converted constructed wetlands in enhancing climate resilience.
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Affiliation(s)
- Nurul' Ain Jamion
- Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, Malaysia; Universiti Teknologi MARA, Cawangan Negeri Sembilan, Kampus Kuala Pilah, Malaysia
| | - Nur Hairunnisa Rafaai
- Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, Malaysia
| | - Khai Ern Lee
- Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, Malaysia; Integrated Water Research Synergy Consortium (IWaReS), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, Malaysia.
| | - Mazlin Mokhtar
- Sustainable Development Solutions Network Asia (SDSN Asia), Sunway University, Malaysia
| | - Thian Lai Goh
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Malaysia
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3
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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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4
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Rothman DH. Slow closure of Earth's carbon cycle. Proc Natl Acad Sci U S A 2024; 121:e2310998121. [PMID: 38241442 PMCID: PMC10823250 DOI: 10.1073/pnas.2310998121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/07/2023] [Indexed: 01/21/2024] Open
Abstract
Carbon near the Earth's surface cycles between the production and consumption of organic carbon; the former sequesters carbon dioxide while the latter releases it. Microbes attempt to close the loop, but the longer organic matter survives, the slower microbial degradation becomes. This aging effect leaves observable quantitative signatures: Organic matter decays at rates that are inversely proportional to its age, while microbial populations and concentrations of organic carbon in ocean sediments decrease at distinct powers of age. Yet mechanisms that predict this collective organization remain unknown. Here, I show that these and other observations follow from the assumption that the decay of organic matter is limited by progressively rare extreme fluctuations in the energy available to microbes for decomposition. The theory successfully predicts not only observed scaling exponents but also a previously unobserved scaling regime that emerges when microbes subsist on the minimum energy flux required for survival. The resulting picture suggests that the carbon cycle's age-dependent dynamics are analogous to the slow approach to equilibrium in disordered systems. The impact of these slow dynamics is profound: They preclude complete oxidation of organic carbon in sediments, thereby freeing molecular oxygen to accumulate in the atmosphere.
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Affiliation(s)
- Daniel H. Rothman
- Lorenz Center, Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA02139
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5
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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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6
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Liang S, Zhang M, Wang X, Li H, Li S, Ma H, Wang X, Rong Z. Seasonal dynamics of dissolved organic matter bioavailability coupling with water mass circulation in the South Yellow Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166671. [PMID: 37657546 DOI: 10.1016/j.scitotenv.2023.166671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/27/2023] [Accepted: 08/27/2023] [Indexed: 09/03/2023]
Abstract
As a typical shelf-marginal sea, the South Yellow Sea (SYS) is significantly influenced by various factors such as land-based inputs and water mass movements, leading the complex biogeochemical processes of dissolved organic matter (DOM) to become highly dynamic. However, the bioavailability of dissolved organic matter (DOM) coupled with water mass circulation has not been accurately assessed, despite being crucial for understanding the source-sink pattern of organic carbon in marginal sea. In this study, four cruises were conducted in the SYS to analyze the spatial and temporal distribution characteristics of dissolved organic carbon (DOC), dissolved organic nitrogen (DON), and total dissolved amino acids (TDAA). Combined with the bioassay experiments, TDAA carbon normalized yield [TDAA (%DOC)] and TDAA degradation index (DIAA) were used as indicators to explore the bioavailability of DOM across different water masses. Results show that the DOC of the SYS exhibits higher average value in late autumn and early winter, and lower value in spring and summer due to the seasonal alternation of water mass and biological activities. The collective results indicate that DOM bioavailability is higher in the Changjiang River diluted water (CDW) and lower in the Yellow Sea warm current (YSWC) and the Yellow Sea cold water mass (YSCWM). Approximately 20 % of DON can be degraded in the YSCWM during autumn. Notably, although the YSCWM constitutes merely constitutes 10 % of the SYS volume, it stores 18.1 % dissolved inorganic nitrogen (DIN) and 23.9 % PO43- of total nutrients, indicating that the YSCWM is a significant nutrient reservoir within the SYS.
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Affiliation(s)
- Shengkang Liang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China; Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Mingzheng Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Xinke Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Hongguan Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Shanshan Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Haoyang Ma
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Xiulin Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Zengrui Rong
- College of Oceanic and Atmospheric Sciences, Ocean University of China, Qingdao 266100, China.
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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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8
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She Z, Wang J, Wang S, He C, Jiang Z, Pan X, Shi Q, Yue Z. Quantifying Stochastic Processes in Shaping Dissolved Organic Matter Pool with High-Resolution Mass Spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16361-16371. [PMID: 37844127 DOI: 10.1021/acs.est.3c07046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Natural dissolved organic matter (DOM) represents a ubiquitous molecular mixture, progressively characterized by spatiotemporal resolution. However, an inadequate comprehension of DOM molecular dynamics, especially the stochastic processes involved, hinders carbon cycling predictions. This study employs ecological principles to introduce a neutral theory to elucidate the fundamental processes involving molecular generation, degradation, and migration. A neutral model is thus formulated to assess the probability distribution of DOM molecules, whose frequencies and abundances follow a β-distribution relationship. The neutral model is subsequently validated with high-resolution mass spectrometry (HRMS) data from various waterbodies, including lakes, rivers, and seas. The model fitting highlights the prevalence of molecular neutral distribution and quantifies the stochasticity within DOM molecular dynamics. Furthermore, the model identifies deviations of HRMS observations from neutral expectations in photochemical and microbial experiments, revealing nonrandom molecular transformations. The ecological null model further validates the neutral modeling results, demonstrating that photodegradation reduces molecular stochastic dynamics at the surface of an acidic pit lake, while random distribution intensifies at the river surface compared with the porewater. Taken together, the DOM molecular neutral model emphasizes the significance of stochastic processes in shaping a natural DOM pool, offering a potential theoretical framework for DOM molecular dynamics in aquatic and other ecosystems.
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Affiliation(s)
- Zhixiang She
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, Anhui, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, Anhui, China
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, Anhui, China
| | - Jin Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, Anhui, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, Anhui, China
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, Anhui, China
| | - Shu Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, Anhui, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, Anhui, China
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, Anhui, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum Beijing, Changping District, Beijing 102249, China
| | - Zhengfeng Jiang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum Beijing, Changping District, Beijing 102249, China
| | - Xin Pan
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, Anhui, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, Anhui, China
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, Anhui, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum Beijing, Changping District, Beijing 102249, China
| | - Zhengbo Yue
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, Anhui, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, Anhui, China
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, Anhui, China
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9
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Bahadori M, Chen C, Lewis S, Wang J, Shen J, Hou E, Rashti MR, Huang Q, Bainbridge Z, Stevens T. The origin of suspended particulate matter in the Great Barrier Reef. Nat Commun 2023; 14:5629. [PMID: 37699913 PMCID: PMC10497579 DOI: 10.1038/s41467-023-41183-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: 11/27/2022] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
River run-off has long been regarded as the largest source of organic-rich suspended particulate matter (SPM) in the Great Barrier Reef (GBR), contributing to high turbidity, pollutant exposure and increasing vulnerability of coral reef to climate change. However, the terrestrial versus marine origin of the SPM in the GBR is uncertain. Here we provide multiple lines of evidence (13C NMR, isotopic and genetic fingerprints) to unravel that a considerable proportion of the terrestrially-derived SPM is degraded in the riverine and estuarine mixing zones before it is transported further offshore. The fingerprints of SPM in the marine environment were completely different from those of terrestrial origin but more consistent with that formed by marine phytoplankton. This result indicates that the SPM in the GBR may not have terrestrial origin but produced locally in the marine environment, which has significant implications on developing better-targeted management practices for improving water quality in the GBR.
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Affiliation(s)
- Mohammad Bahadori
- Australian Rivers Institute, Griffith University, Nathan, QLD, 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia
| | - Chengrong Chen
- Australian Rivers Institute, Griffith University, Nathan, QLD, 4111, Australia.
- School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia.
| | - Stephen Lewis
- Catchment to Reef Research Group, Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, QLD, Australia
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Jupei Shen
- School of Geographical Sciences, Fujian Normal University, Fuzhou, PR China
| | - Enqing Hou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Mehran Rezaei Rashti
- Australian Rivers Institute, Griffith University, Nathan, QLD, 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Zoe Bainbridge
- Catchment to Reef Research Group, Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, QLD, Australia
| | - Tom Stevens
- Catchment to Reef Research Group, Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, QLD, Australia
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10
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George AB, Wang T, Maslov S. Functional convergence in slow-growing microbial communities arises from thermodynamic constraints. THE ISME JOURNAL 2023; 17:1482-1494. [PMID: 37380829 PMCID: PMC10432562 DOI: 10.1038/s41396-023-01455-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 05/15/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
Abstract
The dynamics of microbial communities is complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to thermodynamic equilibrium and growth is slow. To understand the community structure in these energy-limited environments, we developed a microbial community consumer-resource model incorporating energetic and thermodynamic constraints on an interconnected metabolic network. The central element of the model is product inhibition, meaning that microbial growth may be limited not only by depletion of metabolic substrates but also by accumulation of products. We demonstrate that these additional constraints on microbial growth cause a convergence in the structure and function of the community metabolic network-independent of species composition and biochemical details-providing a possible explanation for convergence of community function despite taxonomic variation observed in many natural and industrial environments. Furthermore, we discovered that the structure of community metabolic network is governed by the thermodynamic principle of maximum free energy dissipation. Our results predict the decrease of functional convergence in faster growing communities, which we validate by analyzing experimental data from anaerobic digesters. Overall, the work demonstrates how universal thermodynamic principles may constrain community metabolism and explain observed functional convergence in microbial communities.
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Affiliation(s)
- Ashish B George
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tong Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Sergei Maslov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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11
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Panhota RS, da Cunha Santino MB, Bianchini I. Oxygen consumption and formation of recalcitrant organic carbon from the decomposition of free-floating macrophyte leachates. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:101379-101391. [PMID: 37651016 DOI: 10.1007/s11356-023-29473-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 08/19/2023] [Indexed: 09/01/2023]
Abstract
Aquatic macrophytes contain high levels of hydrosoluble compounds. These compounds disproportionately support microbial breakdown and affect biological oxygen demand in eutrophic waters. In this study, we investigated the fate of leachates from free-floating macrophytes (Pistia stratiotes and Eichhornia crassipes) usually present in eutrophic tropical lacustrine environments. After extraction, the leachates were fractioned into high and low molecular weight compounds and incubated under aerobic conditions, in the dark and at 20.0 ± 1.3 °C. The concentrations of dissolved oxygen and the total, dissolved, and particulate organic carbon (TOC, DOC, and POC) were determined during 60 days. The selected leachates supported the detritus trophic chain of the Barra Bonita Reservoir. High rates of carbon transfer were measured, which were ascribed to the temperature selected (20 °C), nutrient availability, and labile fractions of the leachates. Decomposition occurred mainly through catabolic pathways (mineralization), with the formation of POC (immobilization) being only minor. In the early stages of P. stratiotes and E. crassipes decomposition, the mineralization of leachates (mainly the low molecular weight) led to declines in dissolved oxygen. Owing to the low rates of mass loss, the recalcitrant fractions of these leachates should constitute the main forms of organic carbon exported from the reservoir.
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Affiliation(s)
- Rafael Spadaccia Panhota
- Programa de Pós-Graduação Em Ecologia E Recursos Naturais, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, Km 235, Caixa Postal 676, São Carlos, SP, 13565-905, Brazil
- Laboratório de Biologia Geral, Instituto de Física de São Carlos, Universidade de São Paulo (USP), Av. Trabalhador São-Carlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Marcela Bianchessi da Cunha Santino
- Programa de Pós-Graduação Em Ecologia E Recursos Naturais, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, Km 235, Caixa Postal 676, São Carlos, SP, 13565-905, Brazil
- Departamento de Hidrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, Km 235, Caixa Postal 676, São Carlos, SP, 13565-905, Brazil
| | - Irineu Bianchini
- Programa de Pós-Graduação Em Ecologia E Recursos Naturais, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, Km 235, Caixa Postal 676, São Carlos, SP, 13565-905, Brazil.
- Departamento de Hidrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, Km 235, Caixa Postal 676, São Carlos, SP, 13565-905, Brazil.
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12
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Reynolds R, Hyun S, Tully B, Bien J, Levine NM. Identification of microbial metabolic functional guilds from large genomic datasets. Front Microbiol 2023; 14:1197329. [PMID: 37455725 PMCID: PMC10348482 DOI: 10.3389/fmicb.2023.1197329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/26/2023] [Indexed: 07/18/2023] Open
Abstract
Heterotrophic microbes play an important role in the Earth System as key drivers of major biogeochemical cycles. Specifically, the consumption rate of organic matter is set by the interaction between diverse microbial communities and the chemical and physical environment in which they reside. Modeling these dynamics requires reducing the complexity of microbial communities and linking directly with biogeochemical functions. Microbial metabolic functional guilds provide one approach for reducing microbial complexity and incorporating microbial biogeochemical functions into models. However, we lack a way to identify these guilds. In this study, we present a method for defining metabolic functional guilds from annotated genomes, which are derived from both uncultured and cultured organisms. This method utilizes an Aspect Bernoulli (AB) model and was tested on three large genomic datasets with 1,733-3,840 genomes each. Ecologically relevant microbial metabolic functional guilds were identified including guilds related to DMSP degradation, dissimilatory nitrate reduction to ammonia, and motile copiotrophy. This method presents a way to generate hypotheses about functions co-occurring within individual microbes without relying on cultured representatives. Applying the concept of metabolic functional guilds to environmental samples will provide new insight into the role that heterotrophic microbial communities play in setting rates of carbon cycling.
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Affiliation(s)
- Ryan Reynolds
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Sangwon Hyun
- Department of Data Sciences and Operations, University of Southern California, Los Angeles, CA, United States
| | - Benjamin Tully
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
- Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Jacob Bien
- Department of Data Sciences and Operations, University of Southern California, Los Angeles, CA, United States
| | - Naomi M. Levine
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
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13
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Klawonn I, Van den Wyngaert S, Iversen MH, Walles TJW, Flintrop CM, Cisternas-Novoa C, Nejstgaard JC, Kagami M, Grossart HP. Fungal parasitism on diatoms alters formation and bio-physical properties of sinking aggregates. Commun Biol 2023; 6:206. [PMID: 36810576 PMCID: PMC9944279 DOI: 10.1038/s42003-023-04453-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023] Open
Abstract
Phytoplankton forms the base of aquatic food webs and element cycling in diverse aquatic systems. The fate of phytoplankton-derived organic matter, however, often remains unresolved as it is controlled by complex, interlinked remineralization and sedimentation processes. We here investigate a rarely considered control mechanism on sinking organic matter fluxes: fungal parasites infecting phytoplankton. We demonstrate that bacterial colonization is promoted 3.5-fold on fungal-infected phytoplankton cells in comparison to non-infected cells in a cultured model pathosystem (diatom Synedra, fungal microparasite Zygophlyctis, and co-growing bacteria), and even ≥17-fold in field-sampled populations (Planktothrix, Synedra, and Fragilaria). Additional data obtained using the Synedra-Zygophlyctis model system reveals that fungal infections reduce the formation of aggregates. Moreover, carbon respiration is 2-fold higher and settling velocities are 11-48% lower for similar-sized fungal-infected vs. non-infected aggregates. Our data imply that parasites can effectively control the fate of phytoplankton-derived organic matter on a single-cell to single-aggregate scale, potentially enhancing remineralization and reducing sedimentation in freshwater and coastal systems.
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Affiliation(s)
- Isabell Klawonn
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), 18119, Rostock, Germany.
| | - Silke Van den Wyngaert
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Morten H Iversen
- Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Centre for Marine Environmental Sciences (MARUM) and University of Bremen, 28359, Bremen, Germany
| | - Tim J W Walles
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
| | - Clara M Flintrop
- Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Centre for Marine Environmental Sciences (MARUM) and University of Bremen, 28359, Bremen, Germany
- The Inter-University Institute for Marine Sciences in Eilat, Eilat, 8810302, Israel
| | - Carolina Cisternas-Novoa
- Helmholtz Centre for Ocean Research (GEOMAR), 24148, Kiel, Germany
- Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Jens C Nejstgaard
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
| | - Maiko Kagami
- Faculty of Science, Toho University, Funabashi, Chiba, 274‑8510, Japan
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, 240‑8502, Japan
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, 14469, Potsdam, Germany
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14
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Harjung A, Schweichhart J, Rasch G, Griebler C. Large-scale study on groundwater dissolved organic matter reveals a strong heterogeneity and a complex microbial footprint. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158542. [PMID: 36087677 DOI: 10.1016/j.scitotenv.2022.158542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/11/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Dissolved organic matter (DOM) in terrestrial groundwater is generally low in concentration compared to inland surface waters. However, the overall amount of groundwater DOM is huge, as there is 100 times more fresh groundwater than fresh surface water. To date, research on groundwater DOM has merely focused on specific threats to humans such as e.g. DOM and heavy metal complexations and DOM from hydrocarbon contamination. A comprehensive, large-scale study of groundwater is still missing. Here, we examine DOM properties in a large-scale approach with regards to surface characteristics such as land use and altitude, aquifer characteristics as well as microbial features. We analyzed 1600 water samples from 100 groundwater bodies all over Austria with regards to their DOM quantity, quality and bacterial abundance (BA). DOM quality was evaluated with self-organizing maps on fluorescence excitation-emission-matrices (EEMs) combined with Ward clustering and subsequent parallel factor analysis to describe DOM properties of each cluster. We evaluated how these clusters differed among each other, based on DOC and nitrate concentrations, BA and selected environmental characteristics. Our results show that fluorescence components in groundwater resemble components found in other groundwater studies, in studies from forest streams, the dark ocean, agricultural catchments and wastewater treatment plants. The latter fluorescence components were associated with a cluster that is characterized by agricultural and urban land use, as well as by high nitrate concentrations. Clusters with an increased abundance of high-molecular weight and humic components, commonly associated with vascular plant and soil origin, correlated with a higher bacterial abundance. This observation provides evidence that elevated numbers of suspended bacteria mainly originate from the surface. Our study shows that DOM fluorescence can be a fast monitoring tool to identify aquifers under anthropogenic stress and delineate sensitive recharge areas with high surface-groundwater interaction.
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Affiliation(s)
- A Harjung
- University of Vienna, Department of Functional & Evolutionary Ecology, Division Limnology, Djerassiplatz 1, 1030 Vienna, Austria
| | | | - G Rasch
- University of Vienna, Department of Functional & Evolutionary Ecology, Division Limnology, Djerassiplatz 1, 1030 Vienna, Austria
| | - C Griebler
- University of Vienna, Department of Functional & Evolutionary Ecology, Division Limnology, Djerassiplatz 1, 1030 Vienna, Austria.
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15
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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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16
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Historical contingencies and phage induction diversify bacterioplankton communities at the microscale. Proc Natl Acad Sci U S A 2022; 119:e2117748119. [PMID: 35862452 PMCID: PMC9335236 DOI: 10.1073/pnas.2117748119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In many natural environments, microorganisms decompose microscale resource patches made of complex organic matter. The growth and collapse of populations on these resource patches unfold within spatial ranges of a few hundred micrometers or less, making such microscale ecosystems hotspots of heterotrophic metabolism. Despite the potential importance of patch-level dynamics for the large-scale functioning of heterotrophic microbial communities, we have not yet been able to delineate the ecological processes that control natural populations at the microscale. Here, we address this challenge by characterizing the natural marine communities that assembled on over 1,000 individual microscale particles of chitin, the most abundant marine polysaccharide. Using low-template shotgun metagenomics and imaging, we find significant variation in microscale community composition despite the similarity in initial species pools across replicates. Chitin-degrading taxa that were rare in seawater established large populations on a subset of particles, resulting in a wide range of predicted chitinolytic abilities and biomass at the level of individual particles. We show, through a mathematical model, that this variability can be attributed to stochastic colonization and historical contingencies affecting the tempo of growth on particles. We find evidence that one biological process leading to such noisy growth across particles is differential predation by temperate bacteriophages of chitin-degrading strains, the keystone members of the community. Thus, initial stochasticity in assembly states on individual particles, amplified through ecological interactions, may have significant consequences for the diversity and functionality of systems of microscale patches.
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17
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Hu A, Jang KS, Meng F, Stegen J, Tanentzap AJ, Choi M, Lennon JT, Soininen J, Wang J. Microbial and Environmental Processes Shape the Link between Organic Matter Functional Traits and Composition. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10504-10516. [PMID: 35737964 DOI: 10.1021/acs.est.2c01432] [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] [Indexed: 06/15/2023]
Abstract
Dissolved organic matter (DOM) is a large and complex mixture of molecules that fuels microbial metabolism and regulates biogeochemical cycles. Individual DOM molecules have unique functional traits, but how their assemblages vary deterministically under global change remains poorly understood. Here, we examine DOM and associated bacteria in 300 aquatic microcosms deployed on mountainsides that span contrasting temperatures and nutrient gradients. Based on molecular trait dimensions of reactivity and activity, we partition the DOM composition into labile-active, recalcitrant-active, recalcitrant-inactive, and labile-inactive fractions and quantify the relative influences of deterministic and stochastic processes governing the assembly of each. At both subtropical and subarctic study sites, the assembly of labile or recalcitrant molecules in active fractions is primarily governed by deterministic processes, while stochastic processes are more important for the assembly of molecules within inactive fractions. Surprisingly, the importance of deterministic selection increases with global change gradients for recalcitrant molecules in both active and inactive fractions, and this trend is paralleled by changes in the deterministic assembly of microbial communities and environmental filtering, respectively. Together, our results highlight the shift in focus from potential reactivity to realized activity and indicate that active and inactive fractions of DOM assemblages are structured by contrasting processes, and their recalcitrant components are consistently sensitive to global change. Our study partitions the DOM molecular composition across functional traits and links DOM with microbes via a shared ecological framework of assembly processes. This integrated approach opens new avenues to understand the assembly and turnover of organic carbon in a changing world.
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Affiliation(s)
- Ang Hu
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing 210008, China
| | - Kyoung-Soon Jang
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Cheongju 28119, South Korea
| | - Fanfan Meng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - James Stegen
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, U.K
| | - Mira Choi
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Cheongju 28119, South Korea
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, Helsinki, FIN 00014, Finland
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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18
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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 DOI: 10.1126/sciadv.abn0035] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [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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19
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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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20
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Wang B, Allison SD. Climate-Driven Legacies in Simulated Microbial Communities Alter Litter Decomposition Rates. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.841824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mechanisms underlying diversity-functioning relationships have been a consistent area of inquiry in biogeochemistry since the 1950s. Though these mechanisms remain unresolved in soil microbiomes, many approaches at varying scales have pointed to the same notion—composition matters. Confronting the methodological challenge arising from the complexity of microbiomes, this study used the model DEMENTpy, a trait-based modeling framework, to explore trait-based drivers of microbiome-dependent litter decomposition. We parameterized DEMENTpy for five sites along a climate gradient in Southern California, United States, and conducted reciprocal transplant simulations analogous to a prior empirical study. The simulations demonstrated climate-dependent legacy effects of microbial communities on plant litter decomposition across the gradient. This result is consistent with the previous empirical study across the same gradient. An analysis of community-level traits further suggests that a 3-way tradeoff among resource acquisition, stress tolerance, and yield strategies influences community assembly. Simulated litter decomposition was predictable with two community traits (indicative of two of the three strategies) plus local environment, regardless of the system state (transient vs. equilibrium). Although more empirical confirmation is still needed, community traits plus local environmental factors (e.g., environment and litter chemistry) may robustly predict litter decomposition across spatial-temporal scales. In conclusion, this study offers a potential trait-based explanation for climate-dependent community effects on litter decomposition with implications for improved understanding of whole-ecosystem functioning across scales.
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21
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Moran MA, Kujawinski EB, Schroer WF, Amin SA, Bates NR, Bertrand EM, Braakman R, Brown CT, Covert MW, Doney SC, Dyhrman ST, Edison AS, Eren AM, Levine NM, Li L, Ross AC, Saito MA, Santoro AE, Segrè D, Shade A, Sullivan MB, Vardi A. Microbial metabolites in the marine carbon cycle. Nat Microbiol 2022; 7:508-523. [PMID: 35365785 DOI: 10.1038/s41564-022-01090-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/23/2022] [Indexed: 01/08/2023]
Abstract
One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.
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Affiliation(s)
- Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA.
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Shady A Amin
- Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Nicholas R Bates
- Bermuda Institute of Ocean Sciences, St George's, Bermuda.,School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Rogier Braakman
- Departments of Earth, Atmospheric and Planetary Sciences, and Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Titus Brown
- Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Scott C Doney
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA, USA
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Science, Columbia University, Palisades, NY, USA
| | - Arthur S Edison
- Departments of Biochemistry and Genetics, Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.,Helmholtz-Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Oldenburg, Germany
| | - Naomi M Levine
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Mak A Saito
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Daniel Segrè
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
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22
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Wu Z, Aharonovich D, Roth-Rosenberg D, Weissberg O, Luzzatto-Knaan T, Vogts A, Zoccarato L, Eigemann F, Grossart HP, Voss M, Follows MJ, Sher D. Single-cell measurements and modelling reveal substantial organic carbon acquisition by Prochlorococcus. Nat Microbiol 2022; 7:2068-2077. [PMID: 36329198 PMCID: PMC9712107 DOI: 10.1038/s41564-022-01250-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/13/2022] [Indexed: 11/06/2022]
Abstract
Marine phytoplankton are responsible for about half of the photosynthesis on Earth. Many are mixotrophs, combining photosynthesis with heterotrophic assimilation of organic carbon, but the relative contribution of these two lifestyles is unclear. Here single-cell measurements reveal that Prochlorococcus at the base of the photic zone in the Eastern Mediterranean Sea obtain only ~20% of carbon required for growth by photosynthesis. This is supported by laboratory-calibrated calculations based on photo-physiology parameters and compared with in situ growth rates. Agent-based simulations show that mixotrophic cells could grow tens of metres deeper than obligate photo-autotrophs, deepening the nutricline by ~20 m. Time series from the North Atlantic and North Pacific indicate that, during thermal stratification, on average 8-10% of the Prochlorococcus cells live without enough light to sustain obligate photo-autotrophic populations. Together, these results suggest that mixotrophy underpins the ecological success of a large fraction of the global Prochlorococcus population and its collective genetic diversity.
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Affiliation(s)
- Zhen Wu
- grid.116068.80000 0001 2341 2786Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Dikla Aharonovich
- grid.18098.380000 0004 1937 0562Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dalit Roth-Rosenberg
- grid.18098.380000 0004 1937 0562Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Osnat Weissberg
- grid.18098.380000 0004 1937 0562Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Tal Luzzatto-Knaan
- grid.18098.380000 0004 1937 0562Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Angela Vogts
- grid.423940.80000 0001 2188 0463Leibniz-Institute for Baltic Sea Research, Warnemuende, Germany
| | - Luca Zoccarato
- grid.419247.d0000 0001 2108 8097Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Falk Eigemann
- grid.423940.80000 0001 2188 0463Leibniz-Institute for Baltic Sea Research, Warnemuende, Germany
| | - Hans-Peter Grossart
- grid.419247.d0000 0001 2108 8097Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany ,grid.11348.3f0000 0001 0942 1117Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Maren Voss
- grid.423940.80000 0001 2188 0463Leibniz-Institute for Baltic Sea Research, Warnemuende, Germany
| | - Michael J. Follows
- grid.116068.80000 0001 2341 2786Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Daniel Sher
- grid.18098.380000 0004 1937 0562Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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23
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Harms TK, Groffman PM, Aluwihare L, Craft C, Wieder WR, Hobbie SE, Baer SG, Blair JM, Frey S, Remucal CK, Rudgers JA, Collins SL, Kominoski JS, Ball BA. Patterns and trends of organic matter processing and transport: Insights from the US long-term ecological research network. CLIMATE CHANGE ECOLOGY 2021. [DOI: 10.1016/j.ecochg.2021.100025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Sichert A, Cordero OX. Polysaccharide-Bacteria Interactions From the Lens of Evolutionary Ecology. Front Microbiol 2021; 12:705082. [PMID: 34690949 PMCID: PMC8531407 DOI: 10.3389/fmicb.2021.705082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022] Open
Abstract
Microbes have the unique ability to break down the complex polysaccharides that make up the bulk of organic matter, initiating a cascade of events that leads to their recycling. Traditionally, the rate of organic matter degradation is perceived to be limited by the chemical and physical structure of polymers. Recent advances in microbial ecology, however, suggest that polysaccharide persistence can result from non-linear growth dynamics created by the coexistence of alternate degradation strategies, metabolic roles as well as by ecological interactions between microbes. This complex "landscape" of degradation strategies and interspecific interactions present in natural microbial communities appears to be far from evolutionarily stable, as frequent gene gain and loss reshape enzymatic repertoires and metabolic roles. In this perspective, we discuss six challenges at the heart of this problem, ranging from the evolution of genetic repertoires, phenotypic heterogeneity in clonal populations, the development of a trait-based ecology, and the impact of metabolic interactions and microbial cooperation on degradation rates. We aim to reframe some of the key questions in the study of polysaccharide-bacteria interactions in the context of eco-evolutionary dynamics, highlighting possible research directions that, if pursued, would advance our understanding of polysaccharide degraders at the interface between biochemistry, ecology and evolution.
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25
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Unifying chemical and biological perspectives of carbon accumulation in the environment. Proc Natl Acad Sci U S A 2021; 118:2100935118. [PMID: 33622800 PMCID: PMC7980461 DOI: 10.1073/pnas.2100935118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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