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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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Bedard DL, Van Slyke G, Nübel U, Bateson MM, Brumfield S, An YJ, Becraft ED, Wood JM, Thiel V, Ward DM. Geographic and Ecological Diversity of Green Sulfur Bacteria in Hot Spring Mat Communities. Microorganisms 2023; 11:2921. [PMID: 38138064 PMCID: PMC10746008 DOI: 10.3390/microorganisms11122921] [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: 10/29/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Three strains of thermophilic green sulfur bacteria (GSB) are known; all are from microbial mats in hot springs in Rotorua, New Zealand (NZ) and belong to the species Chlorobaculum tepidum. Here, we describe diverse populations of GSB inhabiting Travel Lodge Spring (TLS) (NZ) and hot springs ranging from 36.1 °C to 51.1 °C in the Republic of the Philippines (PHL) and Yellowstone National Park (YNP), Wyoming, USA. Using targeted amplification and restriction fragment length polymorphism analysis, GSB 16S rRNA sequences were detected in mats in TLS, one PHL site, and three regions of YNP. GSB enrichments from YNP and PHL mats contained small, green, nonmotile rods possessing chlorosomes, chlorobactene, and bacteriochlorophyll c. Partial 16S rRNA gene sequences from YNP, NZ, and PHL mats and enrichments from YNP and PHL samples formed distinct phylogenetic clades, suggesting geographic isolation, and were associated with samples differing in temperature and pH, suggesting adaptations to these parameters. Sequences from enrichments and corresponding mats formed clades that were sometimes distinct, increasing the diversity detected. Sequence differences, monophyly, distribution patterns, and evolutionary simulation modeling support our discovery of at least four new putative moderately thermophilic Chlorobaculum species that grew rapidly at 40 °C to 44 °C.
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Affiliation(s)
- Donna L. Bedard
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (D.L.B.); (G.V.S.)
| | - Greta Van Slyke
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (D.L.B.); (G.V.S.)
| | - Ulrich Nübel
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
- Leibniz-Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
| | - Mary M. Bateson
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
| | - Sue Brumfield
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA;
| | - Yong Jun An
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (D.L.B.); (G.V.S.)
| | - Eric D. Becraft
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
- Department of Biology, University of North Alabama, Florence, AL 35632, USA
| | - Jason M. Wood
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
- Research Informatics Core, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Vera Thiel
- Leibniz-Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
| | - David M. Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
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Ehrenfels B, Baumann KBL, Niederdorfer R, Mbonde AS, Kimirei IA, Kuhn T, Magyar PM, Odermatt D, Schubert CJ, Bürgmann H, Lehmann MF, Wehrli B, Callbeck CM. Hydrodynamic regimes modulate nitrogen fixation and the mode of diazotrophy in Lake Tanganyika. Nat Commun 2023; 14:6591. [PMID: 37852975 PMCID: PMC10584864 DOI: 10.1038/s41467-023-42391-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
The factors that govern the geographical distribution of nitrogen fixation are fundamental to providing accurate nitrogen budgets in aquatic environments. Model-based insights have demonstrated that regional hydrodynamics strongly impact nitrogen fixation. However, the mechanisms establishing this physical-biological coupling have yet to be constrained in field surveys. Here, we examine the distribution of nitrogen fixation in Lake Tanganyika - a model system with well-defined hydrodynamic regimes. We report that nitrogen fixation is five times higher under stratified than under upwelling conditions. Under stratified conditions, the limited resupply of inorganic nitrogen to surface waters, combined with greater light penetration, promotes the activity of bloom-forming photoautotrophic diazotrophs. In contrast, upwelling conditions support predominantly heterotrophic diazotrophs, which are uniquely suited to chemotactic foraging in a more dynamic nutrient landscape. We suggest that these hydrodynamic regimes (stratification versus mixing) play an important role in governing both the rates and the mode of nitrogen fixation.
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Affiliation(s)
- Benedikt Ehrenfels
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
- ETH Zurich, Institute of Biogeochemistry and Pollutant Dynamics, Zurich, Switzerland
| | - Kathrin B L Baumann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
- ETH Zurich, Institute of Biogeochemistry and Pollutant Dynamics, Zurich, Switzerland
| | - Robert Niederdorfer
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
| | | | - Ismael A Kimirei
- TAFIRI, Tanzania Fisheries Research Institute, Kigoma, Tanzania
- TAFIRI, Tanzania Fisheries Research Institute, Dar es Salaam, Tanzania
| | - Thomas Kuhn
- University of Basel, Department of Environmental Sciences, Basel, Switzerland
| | - Paul M Magyar
- University of Basel, Department of Environmental Sciences, Basel, Switzerland
| | - Daniel Odermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
| | - Carsten J Schubert
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
- ETH Zurich, Institute of Biogeochemistry and Pollutant Dynamics, Zurich, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
| | - Moritz F Lehmann
- University of Basel, Department of Environmental Sciences, Basel, Switzerland
| | - Bernhard Wehrli
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
- ETH Zurich, Institute of Biogeochemistry and Pollutant Dynamics, Zurich, Switzerland
| | - Cameron M Callbeck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland.
- University of Basel, Department of Environmental Sciences, Basel, Switzerland.
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