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Sennett LB, Roco CA, Lim NYN, Yavitt JB, Dörsch P, Bakken LR, Shapleigh JP, Frostegård Å. Determining how oxygen legacy affects trajectories of soil denitrifier community dynamics and N 2O emissions. Nat Commun 2024; 15:7298. [PMID: 39181870 PMCID: PMC11344836 DOI: 10.1038/s41467-024-51688-w] [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: 01/12/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024] Open
Abstract
Denitrification - a key process in the global nitrogen cycle and main source of the greenhouse gas N2O - is intricately controlled by O2. While the transition from aerobic respiration to denitrification is well-studied, our understanding of denitrifier communities' responses to cyclic oxic/anoxic shifts, prevalent in natural and engineered systems, is limited. Here, agricultural soil is exposed to repeated cycles of long or short anoxic spells (LA; SA) or constant oxic conditions (Ox). Surprisingly, denitrification and N2O reduction rates are three times greater in Ox than in LA and SA during a final anoxic incubation, despite comparable bacterial biomass and denitrification gene abundances. Metatranscriptomics indicate that LA favors canonical denitrifiers carrying nosZ clade I. Ox instead favors nosZ clade II-carrying partial- or non-denitrifiers, suggesting efficient partnering of the reduction steps among organisms. SA has the slowest denitrification progression and highest accumulation of intermediates, indicating less functional coordination. The findings demonstrate how adaptations of denitrifier communities to varying O2 conditions are tightly linked to the duration of anoxic episodes, emphasizing the importance of knowing an environment's O2 legacy for accurately predicting N2O emissions originating from denitrification.
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Affiliation(s)
- Louise B Sennett
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Constance A Roco
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Natalie Y N Lim
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY, USA
| | - Peter Dörsch
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway.
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2
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Zhang S, Xia X, Yu L, Liu S, Li X, Wang J, Zheng Y, Han L, Tan Q, Yang Z. Biogeography and impact of nitrous oxide reducers in rivers across a broad environmental gradient on emission rates. Environ Microbiol 2024; 26:e16622. [PMID: 38757466 DOI: 10.1111/1462-2920.16622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 04/04/2024] [Indexed: 05/18/2024]
Abstract
Microbial communities that reduce nitrous oxide (N2O) are divided into two clades, nosZI and nosZII. These clades significantly differ in their ecological niches and their implications for N2O emissions in terrestrial environments. However, our understanding of N2O reducers in aquatic systems is currently limited. This study investigated the relative abundance and diversity of nosZI- and nosZII-type N2O reducers in rivers and their impact on N2O emissions. Our findings revealed that stream sediments possess a high capacity for N2O reduction, surpassing N2O production under high N2O/NO3- ratio conditions. This study, along with others in freshwater systems, demonstrated that nosZI marginally dominates more often in rivers. While microbes containing either nosZI and nosZII were crucial in reducing N2O emissions, the net contribution of nosZII-containing microbes was more significant. This can be attributed to the nir gene co-occurring more frequently with the nosZI gene than with the nosZII gene. The diversity within each clade also played a role, with nosZII species being more likely to function as N2O sinks in streams with higher N2O concentrations. Overall, our findings provide a foundation for a better understanding of the biogeography of stream N2O reducers and their effects on N2O emissions.
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Affiliation(s)
- Sibo Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xinghui Xia
- Key Laboratory of Water and Sediment Sciences of Ministry of Education/State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Leilei Yu
- Key Laboratory of Water and Sediment Sciences of Ministry of Education/State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Shaoda Liu
- Key Laboratory of Water and Sediment Sciences of Ministry of Education/State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Xiaokang Li
- School of Environmental and Material Engineering, Yantai University, Yantai, China
| | - Junfeng Wang
- Key Laboratory of Water and Sediment Sciences of Ministry of Education/State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lanfang Han
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Qian Tan
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhifeng Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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3
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Si Y, Zhu Y, Sanders I, Kinkel DB, Purdy KJ, Trimmer M. Direct biological fixation provides a freshwater sink for N 2O. Nat Commun 2023; 14:6775. [PMID: 37880204 PMCID: PMC10600110 DOI: 10.1038/s41467-023-42481-2] [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: 05/03/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
Nitrous oxide (N2O) is a potent climate gas, with its strong warming potential and ozone-depleting properties both focusing research on N2O sources. Although a sink for N2O through biological fixation has been observed in the Pacific, the regulation of N2O-fixation compared to canonical N2-fixation is unknown. Here we show that both N2O and N2 can be fixed by freshwater communities but with distinct seasonalities and temperature dependencies. N2O fixation appears less sensitive to temperature than N2 fixation, driving a strong sink for N2O in colder months. Moreover, by quantifying both N2O and N2 fixation we show that, rather than N2O being first reduced to N2 through denitrification, N2O fixation is direct and could explain the widely reported N2O sinks in natural waters. Analysis of the nitrogenase (nifH) community suggests that while only a subset is potentially capable of fixing N2O they maintain a strong, freshwater sink for N2O that could be eroded by warming.
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Affiliation(s)
- Yueyue Si
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London, E1 4NS, UK
| | - Yizhu Zhu
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London, E1 4NS, UK
| | - Ian Sanders
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London, E1 4NS, UK
| | - Dorothee B Kinkel
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London, E1 4NS, UK
| | - Kevin J Purdy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Mark Trimmer
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London, E1 4NS, UK.
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4
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Zhang IH, Sun X, Jayakumar A, Fortin SG, Ward BB, Babbin AR. Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones. ISME COMMUNICATIONS 2023; 3:76. [PMID: 37474642 PMCID: PMC10359470 DOI: 10.1038/s43705-023-00284-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.
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Affiliation(s)
- Irene H Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Xin Sun
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | | | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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5
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Chen X, Zhang S, Liu J, Wang J, Xin Y, Sun S, Xia X. Tracing Microbial Production and Consumption Sources of N 2O in Rivers on the Qinghai-Tibet Plateau via Isotopocule and Functional Microbe Analyses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7196-7205. [PMID: 37097256 DOI: 10.1021/acs.est.3c00950] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nitrous oxide (N2O), a potent greenhouse gas, is produced in rivers through a series of microbial metabolic pathways. However, the microbial source of N2O production and the degree of N2O reduction in river systems are not well understood and quantified. This work investigated isotopic compositions (δ15N-N2O and δ18O-N2O) and N2O site preference as well as N2O-related microbial features, thereby differentiating the importance of nitrification, denitrification, and N2O reduction in controlling N2O emissions from five rivers on the eastern Qinghai-Tibet Plateau (EQTP). The average N2O concentration in overlying water (15.2 nmol L-1) was close to that in porewater (17.5 nmol L-1), suggesting that both overlying water and sediment are potentially important sources of N2O. Canonical and nitrifier denitrification dominated riverine N2O production, with contribution being approximately 90%. Nitrification is a non-negligible source of N2O production, and N2O concentration was positively correlated with nitrification genetic potential. The degree of N2O reduction ranged from 78.1 to 94.1% (averaging 90%), significantly exceeding the reported values (averaging 70%) in other freshwaters, which was attributed to the higher ratios of organic carbon to nitrogen and lower ratio of (nirS + nirK)/nosZ in EQTP rivers. This study indicates that a combination of isotopic and isotopocule values with functional microbe analysis is useful for quantifying the microbial sources of N2O in rivers, and the intense microbial reduction of N2O significantly accounts for the low N2O emissions observed in EQTP rivers, suggesting that both the production and consumption of N2O in rivers should be considered in the future.
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Affiliation(s)
- Xin Chen
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Sibo Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Jiao Liu
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Junfeng Wang
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yuan Xin
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Siyue Sun
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xinghui Xia
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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6
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Xiang H, Hong Y, Wu J, Wang Y, Ye F, Hu Z, Qu Z, Long A. NosZ-II-type N 2O-reducing bacteria play dominant roles in determining the release potential of N 2O from sediments in the Pearl River Estuary, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121732. [PMID: 37116571 DOI: 10.1016/j.envpol.2023.121732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/09/2023] [Accepted: 04/26/2023] [Indexed: 05/04/2023]
Abstract
The microbial reduction of N2O serves as a "gatekeeper" for N2O emissions, determining the flux of N2O release into the atmosphere. Estuaries are active regions for N2O emissions, but the microbial functions of N2O-reducing bacteria in estuarine ecosystems are not well understood. In this study, the 15N isotope tracer method, qPCR, and high-throughput sequencing were used to analyze N2O production, reduction, and emission processes in surface sediments of the Pearl River Estuary. The 15N isotope tracer experiment showed that the N2O production rates declined and the N2O reduction potential (Rr, the ratio of N2O reduction rates to N2O production rates) increased from upstream to downstream of the Pearl River Estuary, leading to a corresponding decrease of the N2O emission rates from upstream to downstream. The gene abundance ratio of nosZ/nir gradually increased from upstream to downstream and was negatively correlated with the water N2O saturation. The gene abundance of nosZ II was significantly higher than that of nosZ I in the estuary, and the nosZ II/nosZ I abundance ratio was positively correlated with N2O reduction potential. Furthermore, the community composition of NosZ-I- and NosZ-II-type N2O-reducing bacteria shifted from upstream to downstream. NosZ-II-type N2O-reducing bacteria, especially Myxococcales, Thiotrichales, and Gemmatimonadetes species, contributed to the high N2O reduction potential in the downstream. Our results suggest that NosZ-II-type N2O-reducing bacteria play a dominant role in determining the release potential of N2O from sediments in the Pearl River Estuary. This study provides a new insight into the function of microbial N2O reduction in estuarine ecosystems.
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Affiliation(s)
- Hua Xiang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China; State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China.
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China
| | - Zheng Hu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China
| | - Zhiming Qu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China
| | - Aimin Long
- State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
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7
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Shao B, Zhang R, Xu X, Niu L, Fan K, Lin Z, Zhao L, Zhou X, Ren N, Lee DJ, Chen C. Cryptic Sulfur and Oxygen Cycling Potentially Reduces N 2O-Driven Greenhouse Warming: Underlying Revision Need of the Nitrogen Cycle. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:5960-5972. [PMID: 35416037 DOI: 10.1021/acs.est.1c08113] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Increasing global deoxygenation has widely formed oxygen-limited biotopes, altering the metabolic pathways of numerous microbes and causing a large greenhouse effect of nitrous oxide (N2O). Although there are many sources of N2O, denitrification is the sole sink that removes N2O from the biosphere, and the low-level oxygen in waters has been classically thought to be the key factor regulating N2O emissions from incomplete denitrification. However, through microcosm incubations with sandy sediment, we demonstrate here for the first time that the stress from oxygenated environments does not suppress, but rather boosts the complete denitrification process when the sulfur cycle is actively ongoing. This study highlights the potential of reducing N2O-driven greenhouse warming and fills a gap in pre-cognitions on the nitrogen cycle, which may impact our current understanding of greenhouse gas sinks. Combining molecular techniques and kinetic verification, we reveal that dominant inhibitions in oxygen-limited environments can interestingly undergo triple detoxification by cryptic sulfur and oxygen cycling, which may extensively occur in nature but have been long neglected by researchers. Furthermore, reviewing the present data and observations from natural and artificial ecosystems leads to the necessary revision needs of the global nitrogen cycle.
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Affiliation(s)
- Bo Shao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ruochen Zhang
- School of Civil and Transportation, Hebei University of Technology, Tianjin 300401, China
| | - Xijun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Li Niu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kaili Fan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhengda Lin
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150090, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xu Zhou
- Engineering Laboratory of Microalgal Bioenergy, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen 518055, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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Song W, Liu J, Qin W, Huang J, Yu X, Xu M, Stahl D, Jiao N, Zhou J, Tu Q. Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean. mBio 2022; 13:e0383221. [PMID: 35285696 PMCID: PMC9040759 DOI: 10.1128/mbio.03832-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/02/2022] [Indexed: 12/22/2022] Open
Abstract
Microorganisms drive much of the marine nitrogen (N) cycle, which jointly controls the primary production in the global ocean. However, our understanding of the microbial communities driving the global ocean N cycle remains fragmented. Focusing on "who is doing what, where, and how?", this study draws a clear picture describing the global biogeography of marine N-cycling microbial communities by utilizing the Tara Oceans shotgun metagenomes. The marine N-cycling communities are highly variable taxonomically but relatively even at the functional trait level, showing clear functional redundancy properties. The functional traits and taxonomic groups are shaped by the same set of geo-environmental factors, among which, depth is the major factor impacting marine N-cycling communities, differentiating mesopelagic from epipelagic communities. Latitudinal diversity gradients and distance-decay relationships are observed for taxonomic groups, but rarely or weakly for functional traits. The composition of functional traits is strongly deterministic as revealed by null model analysis, while a higher degree of stochasticity is observed for taxonomic composition. Integrating multiple lines of evidence, in addition to drawing a biogeographic picture of marine N-cycling communities, this study also demonstrated an essential microbial ecological theory-determinism governs the assembly of microbial communities performing essential biogeochemical processes; the environment selects functional traits rather than taxonomic groups; functional redundancy underlies stochastic taxonomic community assembly. IMPORTANCE A critical question in microbial ecology is how the complex microbial communities are formed in natural ecosystems with the existence of thousands different species, thereby performing essential ecosystem functions and maintaining ecosystem stability. Previous studies disentangling the community assembly mechanisms mainly focus on microbial taxa, ignoring the functional traits they carry. By anchoring microbial functional traits and their carrying taxonomic groups involved in nitrogen cycling processes, this study demonstrated an important mechanism associated with the complex microbial community assembly. Evidence shows that the environment selects functional traits rather than taxonomic groups, and functional redundancy underlies stochastic taxonomic community assembly. This study is expected to provide valuable mechanistic insights into the complex microbial community assembly in both natural and artificial ecosystems.
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Affiliation(s)
- Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - Wei Qin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Jun Huang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Mengzhao Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - David Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
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9
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The marine nitrogen cycle: new developments and global change. Nat Rev Microbiol 2022; 20:401-414. [PMID: 35132241 DOI: 10.1038/s41579-022-00687-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 12/25/2022]
Abstract
The ocean is home to a diverse and metabolically versatile microbial community that performs the complex biochemical transformations that drive the nitrogen cycle, including nitrogen fixation, assimilation, nitrification and nitrogen loss processes. In this Review, we discuss the wealth of new ocean nitrogen cycle research in disciplines from metaproteomics to global biogeochemical modelling and in environments from productive estuaries to the abyssal deep sea. Influential recent discoveries include new microbial functional groups, novel metabolic pathways, original conceptual perspectives and ground-breaking analytical capabilities. These emerging research directions are already contributing to urgent efforts to address the primary challenge facing marine microbiologists today: the unprecedented onslaught of anthropogenic environmental change on marine ecosystems. Ocean warming, acidification, nutrient enrichment and seawater stratification have major effects on the microbial nitrogen cycle, but widespread ocean deoxygenation is perhaps the most consequential for the microorganisms involved in both aerobic and anaerobic nitrogen transformation pathways. In turn, these changes feed back to the global cycles of greenhouse gases such as carbon dioxide and nitrous oxide. At a time when our species casts a lengthening shadow across all marine ecosystems, timely new advances offer us unique opportunities to understand and better predict human impacts on nitrogen biogeochemistry in the changing ocean of the Anthropocene.
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10
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Su X, Wen T, Wang Y, Xu J, Cui L, Zhang J, Xue X, Ding K, Tang Y, Zhu YG. Stimulation of N 2 O emission via bacterial denitrification driven by acidification in estuarine sediments. GLOBAL CHANGE BIOLOGY 2021; 27:5564-5579. [PMID: 34453365 DOI: 10.1111/gcb.15863] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/04/2021] [Accepted: 08/16/2021] [Indexed: 05/02/2023]
Abstract
Ocean acidification in nitrogen-enriched estuaries has raised global concerns. For decades, biotic and abiotic denitrification in estuarine sediments has been regarded as the major ways to remove reactive nitrogen, but they occur at the expense of releasing greenhouse gas nitrous oxide (N2 O). However, how these pathways respond to acidification remains poorly understood. Here we performed a N2 O isotopocules analysis coupled with respiration inhibition and molecular approaches to investigate the impacts of acidification on bacterial, fungal, and chemo-denitrification, as well as N2 O emission, in estuarine sediments through a series of anoxic incubations. Results showed that acidification stimulated N2 O release from sediments, which was mainly mediated by the activity of bacterial denitrifiers, whereas in neutral environments, N2 O production was dominated by fungi. We also found that the contribution of chemo-denitrification to N2 O production cannot be ignored, but was not significantly affected by acidification. The mechanistic investigation further demonstrated that acidification changed the keystone taxa of sedimentary denitrifiers from N2 O-reducing to N2 O-producing ones and reduced microbial electron-transfer efficiency during denitrification. These findings provide novel insights into how acidification stimulates N2 O emission and modulates its pathways in estuarine sediments, and how it may contribute to the acceleration of global climate change in the Anthropocene.
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Affiliation(s)
- Xiaoxuan Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Teng Wen
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Yingmu Wang
- College of Civil Engineering, Fuzhou University, Fuzhou, China
| | - Junshi Xu
- Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing, China
- Key Laboratory of Virtual Geographic Environment, Ministry of Education, Nanjing Normal University, Nanjing, China
| | - Ximei Xue
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Kai Ding
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yijia Tang
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Institute of Agriculture, Sydney, New South Wales, Australia
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of the Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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