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Bertagnolli AD, Konstantinidis KT, Stewart FJ. Non-denitrifier nitrous oxide reductases dominate marine biomes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:681-692. [PMID: 33459515 DOI: 10.1111/1758-2229.12879] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 06/12/2023]
Abstract
Microbial enzymes often occur as distinct variants that share the same substrate but differ in substrate affinity, sensitivity to environmental conditions, or phylogenetic ancestry. Determining where variants occur in the environment helps identify thresholds that constrain microbial cycling of key chemicals, including the greenhouse gas nitrous oxide (N2O). To understand the enzymatic basis of N2O cycling in the ocean, we mined metagenomes to characterize genes encoding bacterial nitrous oxide reductase (NosZ) catalyzing N2O reduction to N2. We examined data sets from diverse biomes but focused primarily on those from oxygen minimum zones where N2O levels are often elevated. With few exceptions, marine nosZ data sets were dominated by 'atypical' clade II gene variants. Atypical nosZ has been associated with low oxygen, enhanced N2O affinity, and organisms lacking enzymes for complete denitrification, i.e., non-denitrifiers. Atypical nosZ often occurred in metagenome-assembled genomes (MAGs) with nitrate or nitrite respiration genes, although MAGs with genes for complete denitrification were rare. We identified atypical nosZ in several taxa not previously associated with N2O consumption, in addition to known N2O-associated groups. The data suggest that marine environments generally select for high N2O-scavenging ability across diverse taxa and have implications for how N2O concentration may affect N2O removal rates.
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Affiliation(s)
- Anthony D Bertagnolli
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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Wu L, Chen X, Wei W, Liu Y, Wang D, Ni BJ. A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:9175-9190. [PMID: 32657581 DOI: 10.1021/acs.est.0c03948] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The continuous increase of nitrous oxide (N2O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N2O production, a clear understanding of the knowledge on archaeal N2O production is necessary for global N2O mitigation. Compared to bacterial N2O production by ammonia-oxidizing bacteria (AOB), AOA-driven N2O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N2O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N2O production pathways, discussed the relative contribution of AOA to N2O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N2O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N2O production. We, then, put forward perspectives for archaeal N2O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N2O mitigations.
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Affiliation(s)
- Lan Wu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Xueming Chen
- College of Environment and Resources, Fuzhou University, Fujian 350116, PR China
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Yiwen Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Dongbo Wang
- Key Laboratory of Environmental Biology and Pollution Control, College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
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Wang J, Kan J, Qian G, Chen J, Xia Z, Zhang X, Liu H, Sun J. Denitrification and anammox: Understanding nitrogen loss from Yangtze Estuary to the east China sea (ECS). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:1659-1670. [PMID: 31284208 DOI: 10.1016/j.envpol.2019.06.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 05/18/2019] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
The Yangtze River, which is the largest in Euro-Asian, receives tremendous anthropogenic nitrogen input and is typically characterized by severe eutrophication and hypoxia. Two major processes, denitrification and anaerobic ammonium oxidation (anammox), play vital roles for removing nitrogen global in nitrogen cycling. In the current study, sediment samples were collected from both latitudinal and longitudinal transects along the coastal Yangtze River and the East China Sea (ECS). We investigated community composition and distributions of nosZ gene-encoded denitrifiers by high throughput sequencing, and also quantified the relative abundances of both denitrifying and anammox bacteria by q-PCR analysis. Denitrifying communities showed distinct spatial distribution patterns that were impacted by physical (water current and river runoffs) and chemical (nutrient availability and organic content) processes. Both denitrifying and anammox bacteria contributed to the nitrogen removal in Yangtze Estuary and the adjacent ECS, and these two processes shifted from coastal to open ocean with reverse trends: the abundance of nosZ gene decreased from coastal to open ocean while anammox exhibited an increasing trend based on quantifications of hzsB and 16S rRNA genes. Further correspondence correlation analysis revealed that salinity and nutrients were the main factors in structuring composition and distribution of denitrifying and anammox bacteria. This study improved our understanding of dynamic processes in nitrogen removal from estuarine to open ocean. We hypothesize that denitrification is the major nitrogen removal pathway in estuaries, but in open oceans, low nutrient and organic matter concentrations restrict denitrification, thus increasing the importance of anammox as a nitrogen removal process.
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Affiliation(s)
- Jing Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China; Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, SOA, Hangzhou, 310012, PR China
| | - Jinjun Kan
- Stroud Water Research Center, 970 Spencer Road, Avondale, PA, 19311, USA
| | - Gang Qian
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Jianfang Chen
- Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, SOA, Hangzhou, 310012, PR China
| | - Zhiqiang Xia
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Xiaodong Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Haijiao Liu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Jun Sun
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
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Coates CJ, Wyman M. A denitrifying community associated with a major, marine nitrogen fixer. Environ Microbiol 2017; 19:4978-4992. [PMID: 29194965 DOI: 10.1111/1462-2920.14007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022]
Abstract
The diazotrophic cyanobacterium, Trichodesmium, is an integral component of the marine nitrogen cycle and contributes significant amounts of new nitrogen to oligotrophic, tropical/subtropical ocean surface waters. Trichodesmium forms macroscopic, fusiform (tufts), spherical (puffs) and raft-like colonies that provide a pseudobenthic habitat for a host of other organisms including marine invertebrates, microeukaryotes and numerous other microbes. The diversity and activity of denitrifying bacteria found in association with the colonies was interrogated using a series of molecular-based methodologies targeting the gene encoding the terminal step in the denitrification pathway, nitrous oxide reductase (nosZ). Trichodesmium spp. sampled from geographically isolated ocean provinces (the Atlantic Ocean, the Red Sea and the Indian Ocean) were shown to harbor highly similar, taxonomically related communities of denitrifiers whose members are affiliated with the Roseobacter clade within the Rhodobacteraceae (Alphaproteobacteria). These organisms were actively expressing nosZ in samples taken from the mid-Atlantic Ocean and Red Sea implying that Trichodesmium colonies are potential sites of nitrous oxide consumption and perhaps earlier steps in the denitrification pathway also. It is proposed that coupled nitrification of newly fixed N is the most likely source of nitrogen oxides supporting nitrous oxide cycling within Trichodesmium colonies.
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Affiliation(s)
- Christopher J Coates
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.,Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, Wales, UK
| | - Michael Wyman
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
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Sun X, Jayakumar A, Ward BB. Community Composition of Nitrous Oxide Consuming Bacteria in the Oxygen Minimum Zone of the Eastern Tropical South Pacific. Front Microbiol 2017; 8:1183. [PMID: 28702012 PMCID: PMC5487485 DOI: 10.3389/fmicb.2017.01183] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/12/2017] [Indexed: 12/04/2022] Open
Abstract
The ozone-depleting and greenhouse gas, nitrous oxide (N2O), is mainly consumed by the microbially mediated anaerobic process, denitrification. N2O consumption is the last step in canonical denitrification, and is also the least O2 tolerant step. Community composition of total and active N2O consuming bacteria was analyzed based on total (DNA) and transcriptionally active (RNA) nitrous oxide reductase (nosZ) genes using a functional gene microarray. The total and active nosZ communities were dominated by a limited number of nosZ archetypes, affiliated with bacteria from marine, soil and marsh environments. In addition to nosZ genes related to those of known marine denitrifiers, atypical nosZ genes, related to those of soil bacteria that do not possess a complete denitrification pathway, were also detected, especially in surface waters. The community composition of the total nosZ assemblage was significantly different from the active assemblage. The community composition of the total nosZ assemblage was significantly different between coastal and off-shore stations. The low oxygen assemblages from both stations were similar to each other, while the higher oxygen assemblages were more variable. Community composition of the active nosZ assemblage was also significantly different between stations, and varied with N2O concentration but not O2. Notably, nosZ assemblages were not only present but also active in oxygenated seawater: the abundance of total and active nosZ bacteria from oxygenated surface water (indicated by nosZ gene copy number) was similar to or even larger than in anoxic waters, implying the potential for N2O consumption even in the oxygenated surface water.
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Affiliation(s)
- Xin Sun
- Department of Geosciences, Princeton University, PrincetonNJ, United States
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, PrincetonNJ, United States
| | - Bess B Ward
- Department of Geosciences, Princeton University, PrincetonNJ, United States
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Effect of NaCl on aerobic denitrification by strain Achromobacter sp. GAD-3. Appl Microbiol Biotechnol 2017; 101:5139-5147. [DOI: 10.1007/s00253-017-8191-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/08/2017] [Accepted: 02/10/2017] [Indexed: 10/20/2022]
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