1
|
Intrator N, Jayakumar A, Ward BB. Aquatic nitrous oxide reductase gene ( nosZ) phylogeny and environmental distribution. Front Microbiol 2024; 15:1407573. [PMID: 38835481 PMCID: PMC11148229 DOI: 10.3389/fmicb.2024.1407573] [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: 03/26/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and a major cause of ozone depletion. One-third of atmospheric N2O originates in aquatic environments. Reduction of N2O to dinitrogen gas (N2) requires the nitrous oxide reductase enzyme, which is encoded by the gene nosZ. Organisms that contain nosZ are the only known biological sinks of N2O and are found in diverse genera and a wide range of environments. The two clades of nosZ (Clade I and II) contain great diversity, making it challenging to study the population structure and distribution of nosZ containing organisms in the environment. A database of over 11,000 nosZ sequences was compiled from NCBI (representing diverse aquatic environments) and unpublished sequences and metagenomes (primarily from oxygen minimum zones, OMZs, where N2O levels are often elevated). Sequences were clustered into archetypes based on DNA and amino acid sequence identity and their clade, phylogeny, and environmental source were determined. Further analysis of the source and environmental distribution of the sequences showed strong habitat separation between clades and phylogeny. Although there are more Clade I nosZ genes in the compilation, Clade II is more diverse phylogenetically and has a wider distribution across environmental sources. On the other hand, Clade I nosZ genes are predominately found within marine sediment and are primarily from the phylum Pseudonomonadota. The majority of the sequences analyzed from marine OMZs represented distinct phylotypes between different OMZs showing that the nosZ gene displays regional and environmental separation. This study expands the known diversity of nosZ genes and provides a clearer picture of how the clades and phylogeny of nosZ organisms are distributed across diverse environments.
Collapse
Affiliation(s)
- Naomi Intrator
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| |
Collapse
|
2
|
Wei C, Su F, Yue H, Song F, Li H. Spatial distribution characteristics of denitrification functional genes and the environmental drivers in Liaohe estuary wetland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:1064-1078. [PMID: 38030842 DOI: 10.1007/s11356-023-30938-2] [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: 06/27/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Abstract
Genes nirS, nirK, and nosZ are specific for the denitrification process, which is associated with greenhouse gas N2O emission. The abundances and diversities of community containing these three genes are usually used as a common index to reflect the denitrification process, and they would be affected by differences in environmental factors caused by changes from warm to cold conditions. The quantification of denitrification in natural wetlands is complex, and straightforward identification of spatial distribution and drivers affecting the process is still developing. In this study, the bacterial communities, gene diversities, and relative abundances involved in denitrification were investigated in Liaohe Estuary Wetland. We analyzed the relative abundances, diversities, and communities of bacteria containing the three genes at warm and cold conditions using Illumina MiSeq sequencing and detected the potential environmental factors influencing their distribution by using a random forest algorithm. There are great differences in the community composition of the bacteria containing genes nirS, nirK, and nosZ. All the abundant taxa of nirS and nirK communities belonged to phylum Proteobacteria. Compared with the community composition of bacteria containing nirS and nirK, the community of bacteria containing nosZ is more diverse, and the subdivision taxa of phylum Euryarchaeota was also abundant in the community containing nosZ. The distribution characteristics of the relative abundance of nirS and nirK showed obvious differences both at warm and cold climate conditions. The oxidation-reduction potential, nitrite nitrogen, and salinity were detected as potential variables that might explain the diversity of nirS. The total nitrogen and nitrite nitrogen were the important variables for predicting the relative abundance of nirS at warm climate condition, while oxidation-reduction potential and pH contributed to the diversity of nirS at cold condition. The bulk density of sediment was detected as a potential variable affecting the relative abundance of nirK at warm and cold conditions, and diversity of nirK at warm condition, while nitrite nitrogen was detected as an important environmental factor for predicting the diversity of nirK at cold condition. Overall, our results show that the key environmental factors, which affect the relative abundance, diversity, and community of bacteria containing the functional denitrification genes, are not exactly the same, and the diversities of nirS, nirK, and nosZ have a higher environmental sensitivity than their relative abundances.
Collapse
Affiliation(s)
- Chao Wei
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Liaoning Panjin Wetland Ecosystem National Observation and Research Station, Shenyang, 110866, Liaoning, China
- Liaoning Shuangtai Estuary Wetland Ecosystem Research Station, Panjin, 124112, Liaoning, China
- Liaoning Provincial Key Laboratory of Soil Erosion and Ecological Restoration, Shenyang, 110866, Liaoning, China
| | - Fangli Su
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
- Liaoning Panjin Wetland Ecosystem National Observation and Research Station, Shenyang, 110866, Liaoning, China.
- Liaoning Shuangtai Estuary Wetland Ecosystem Research Station, Panjin, 124112, Liaoning, China.
- Liaoning Provincial Key Laboratory of Soil Erosion and Ecological Restoration, Shenyang, 110866, Liaoning, China.
| | - Hangyu Yue
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Fei Song
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Liaoning Panjin Wetland Ecosystem National Observation and Research Station, Shenyang, 110866, Liaoning, China
- Liaoning Shuangtai Estuary Wetland Ecosystem Research Station, Panjin, 124112, Liaoning, China
- Liaoning Provincial Key Laboratory of Soil Erosion and Ecological Restoration, Shenyang, 110866, Liaoning, China
| | - Haifu Li
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Liaoning Panjin Wetland Ecosystem National Observation and Research Station, Shenyang, 110866, Liaoning, China
- Liaoning Shuangtai Estuary Wetland Ecosystem Research Station, Panjin, 124112, Liaoning, China
- Liaoning Provincial Key Laboratory of Soil Erosion and Ecological Restoration, Shenyang, 110866, Liaoning, China
| |
Collapse
|
3
|
Hu Y, Wu J, Ye J, Liu X, Wang Y, Ye F, Hong Y. The imbalance between N 2O production and reduction by multi-microbial communities determines sedimentary N 2O emission potential in the Pearl River Estuary. MARINE ENVIRONMENTAL RESEARCH 2023; 190:106119. [PMID: 37535997 DOI: 10.1016/j.marenvres.2023.106119] [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: 05/22/2023] [Revised: 07/04/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
Denitrification is the dominant process of nitrogen removal and nitrous oxide (N2O) emissions in estuarine ecosystems. However, little is known regarding the microbial mechanism of the production and reduction of N2O in estuaries. We investigated in situ dissolved N2O as well as potential N2O production rate (NPR), reduction rate (NRR), and emission rate (NER), and key functional genes related to N2O transformation of denitrification in the Pearl River Estuary. Higher N2O emission potential was found in the upstream and midstream regions with higher NPR and lower NRR values. In contrast, higher NRR values were detected in downstream. Notably, nirS and nirK type N2O producers dominated the upstream zone, whereas abundant N2O reducers, especially nosZ II type N2O reducers, were observed in downstream. Most importantly, the gene abundance ratio (Rnir/nosZ) was significantly correlated with the N2O emission potential (Re). Niche differentiation between N2O producers and N2O reducers from upstream to downstream affected N2O emission potential. This study highlights the N2O emission potential in estuarine sediments is determined by an imbalance between N2O production and the reduction of multi-bacterial communities.
Collapse
Affiliation(s)
- Yaohao 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, 510006, PR China; State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, 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, 510006, PR China
| | - Jiaqi 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, 510006, PR China
| | - Xiaohan Liu
- 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, 510006, 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, 510006, 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, 510006, 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, 510006, PR China.
| |
Collapse
|
4
|
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: 3] [Impact Index Per Article: 3.0] [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.
Collapse
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.
| |
Collapse
|
5
|
Wu S, Zhang Z, Sun H, Hu H. Responses of Rice Yield, N Uptake, NH 3 and N 2O Losses from Reclaimed Saline Soils to Varied N Inputs. PLANTS (BASEL, SWITZERLAND) 2023; 12:2446. [PMID: 37447008 PMCID: PMC10347052 DOI: 10.3390/plants12132446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023]
Abstract
It is of agronomic importance to apply nitrogen (N), but it has high environmental risks in reclaimed saline soils. Therefore, we should apply N fertilizer at an appropriate rate to increase crop yield but decrease N losses. In this soil column experiment, rice yield, N uptake, and ammonia (NH3) and nitrous oxide (N2O) losses were measured in four treatments with no N application (control) and with N applications of 160, 200, and 240 kg/ha (N160, N200, and N240, respectively). The results show that grain yield, spike number, and thousand-kernel weight increased with increases in N application rate, but there was no significant difference in grain yield between N200 and N240. However, the kernels per spike increased first and then decreased with the increase in N application, of which N200 was recorded to have the highest kernels per spike value, which was 16.8 and 9.8% higher than those of N160 and N240, respectively. Total NH3 volatilization of the rice season increased with increasing N input, especially during the first and second supplementary fertilization stages. The NH4+-N concentration of overlying water was relatively lower under the N200 treatment in these two stages, and the yield-scaled NH3 volatilization and the emission factor were the lowest in N200, which were 26.2-27.8% and 4.0-21.0% lower than those of N160 and N240, respectively. Among the three N-applied treatments, N2O losses and the emission factor as well as the yield-scaled N2O emissions were the lowest under the N200 treatment, which had 34.7% and 78.9% lower N2O emissions and 57.8% and 83.5% lower emission factors than those of the N160 and N240 treatments, respectively. Moreover, the gene copies of AOA and AOB amoA, nirS, and nirK in cultivated layer soils all reached the minimum under the N200 treatment. According to the comprehensive effects of N fertilizer on rice grain yield and NH3 and N2O losses, we recommend applying 200 kg/ha to reclaimed saline soil to ensure crop yield and reduce N losses.
Collapse
Affiliation(s)
- Si Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (S.W.); (H.H.)
| | - Zhenhua Zhang
- Jiangsu Key Laboratory for Bioresource of Saline Soils, School of Wetlands, Yancheng Teachers University, Yancheng 224007, China;
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia
| | - Haijun Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (S.W.); (H.H.)
| | - Haibo Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (S.W.); (H.H.)
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Vuillemin A. Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia. Front Microbiol 2023; 14:1101902. [PMID: 36846760 PMCID: PMC9950273 DOI: 10.3389/fmicb.2023.1101902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes, and stable-isotope probing incubations from the water column and subseafloor of the Benguela upwelling system. The taxonomic composition of 16S rRNA genes and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity toward mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria, and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification is fueled by fixed and organic nitrogen dissolved in dysoxic waters, and prevails over canonical denitrification and anaerobic oxidation of ammonia when the Namibian coastal waters and sediment-water interface on the shelf are ventilated by lateral currents during austral winter.
Collapse
|
8
|
Pan Y, She D, Shi Z, Cao T, Xia Y, Shan J. Salinity and high pH reduce denitrification rates by inhibiting denitrifying gene abundance in a saline-alkali soil. Sci Rep 2023; 13:2155. [PMID: 36750752 PMCID: PMC9905596 DOI: 10.1038/s41598-023-29311-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Denitrification, as the main nitrogen (N) removal process in farmland drainage ditches in coastal areas, is significantly affected by saline-alkali conditions. To elucidate the effects of saline-alkali conditions on denitrification, incubation experiments with five salt and salt-alkali gradients and three nitrogen addition levels were conducted in a saline-alkali soil followed by determination of denitrification rates and the associated functional genes (i.e., nirK/nirS and nosZ Clade I) via N2/Ar technique in combination with qPCR. The results showed that denitrification rates were significantly decreased by 23.83-50.08%, 20.64-57.31% and 6.12-54.61% with salt gradient increasing from 1 to 3‰, 8‰, and 15‰ under 0.05‰, 0.10‰ and 0.15‰ urea addition conditions, respectively. Similarly, denitrification rates were significantly decreased by 44.57-63.24% with an increase of the salt-alkali gradient from 0.5 to 8‰. The abundance of nosZ decreased sharply in the saline condition, while a high salt level significantly decreased the abundance of nirK and nirS. In addition, the increase of nitrogen concentration attenuated the reduction of nirK, nirS and nosZ gene abundance. Partial least squares regression (PLSR) models demonstrated that salinity, dissolved oxygen (DO) in the overlying water, N concentration, and denitrifying gene abundance were key determinants of the denitrification rate in the saline environment, while pH was an additional determinant in the saline-alkali environment. Taken together, our results suggest that salinity and high pH levels decreased the denitrification rates by significantly inhibiting the abundance of the denitrifying genes nirK, nirS, and nosZ, whereas increasing nitrogen concentration could alleviate this effect. Our study provides helpful information on better understanding of reactive N removal and fertilizer application in the coastal areas.
Collapse
Affiliation(s)
- Yongchun Pan
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China.,Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Nanjing, 210098, China
| | - Dongli She
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China. .,Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Nanjing, 210098, China.
| | - Zhenqi Shi
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China.,Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Nanjing, 210098, China
| | - Taohong Cao
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China.,Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Nanjing, 210098, China
| | - Yongqiu Xia
- Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jun Shan
- Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| |
Collapse
|
9
|
Wang J, Guo X, Li Y, Song G, Zhao L. Understanding the Variation of Bacteria in Response to Summertime Oxygen Depletion in Water Column of Bohai Sea. Front Microbiol 2022; 13:890973. [PMID: 35756048 PMCID: PMC9221365 DOI: 10.3389/fmicb.2022.890973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/05/2022] [Indexed: 11/14/2022] Open
Abstract
Aiming to reveal the variation in bacteria community under oxygen depletion formed every summer in water column of central Bohai Sea, a time-scenario sampling from June to August in 2018 at a 20-day interval along one inshore-offshore transect was settled. Water samples were collected at the surface, middle, and bottom layer and then analyzed by high-throughput sequencing targeting both 16S rRNA and nosZ genes. Compared to the surface and middle water, oxygen depletion occurred at bottom layer in August. In top two layers, Cyanobacteria dominated the bacterial community, whereas heterotrophic bacteria became dominant in bottom water of Bohai Sea. Based on the time scenario, distinct community separation was observed before (June and July) and after (August) oxygen depletion (p = 0.003). Vertically, strict stratification of nosZ gene was stably formed along 3 sampling layers. As a response to oxygen depletion, the diversity indices of both total bacteria (16S rRNA) and nosZ gene-encoded denitrification bacteria all increased, which indicated the intense potential of nitrogen lose when oxygen depleted. Dissolved oxygen (DO) was the key impacting factor on the community composition of total bacteria in June, whereas nutrients together with DO play the important roles in August for both total and denitrifying bacteria. The biotic impact was revealed further by strong correlations which showed between Cyanobacteria and heterotrophic bacteria in June from co-occurrence network analysis, which became weak in August when DO was depleted. This study discovered the variation in bacteria community in oxygen-depleted water with further effort to understand the potential role of denitrifying bacteria under oxygen depletion in Bohai Sea for the first time, which provided insights into the microbial response to the world-wide expanding oxygen depletion and their contributions in the ocean nitrogen cycling.
Collapse
Affiliation(s)
- Jing Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Xiaoxiao Guo
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Yanying Li
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Guisheng Song
- School of Marine Science and Technology, Tianjin University, Tianjin, China
| | - Liang Zhao
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| |
Collapse
|
10
|
Pan Y, She D, Chen X, Xia Y, Timm LC. Elevation of biochar application as regulator on denitrification/NH 3 volatilization in saline soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:41712-41725. [PMID: 33786768 DOI: 10.1007/s11356-021-13562-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Denitrification and NH3 volatilization are the main removal processes of nitrogen in coastal saline soils. In this incubation study, the effects of wheat straw biochar application at rates of 0, 2, 5, 10 and 15% by weight to saline soil with two salt gradients of 0 and 1‰ on denitrification and NH3 volatilization were investigated. The results showed that the denitrification rates with 2, 5 and 10% biochar amendments decreased by 25.26, 33.07 and 17.50%, respectively, under salt-free conditions, and the denitrification rates with 2 and 5% biochar amendments under 1‰ salt conditions decreased by 17.74 and 17.39%, respectively. However, the NH3 volatilization rates increased by 8.05-61.73% after biochar application. The path analysis revealed the interactions of overlying water-sediment system environmental factors in biochar-amended saline soils and their roles in denitrification and NH3 volatilization. Environmental factors in sediment exerted much greater control over denitrification than those in overlying water. In addition, environmental factors exhibited an indirect negative influence on denitrification by negatively influencing the abundance of the nosZ gene. The comprehensive effects of the environmental factors in overlying water on NH3 volatilization were greater than those in sediment. The NH4+-N content, pH of overlying water and sediment salinity were the main controlling factors for NH3 volatilization in saline soils. Biochar application effectively regulated the denitrification rate by changing the environmental factors and denitrifying functional gene abundance, but its application posed a risk of increased NH3 volatilization mainly by increasing NH4+-N, EC and pH in overlying water.
Collapse
Affiliation(s)
- Yongchun Pan
- College of Agricultural Sciences and Engineering, Hohai University, Nanjing, 210098, China
| | - Dongli She
- College of Agricultural Sciences and Engineering, Hohai University, Nanjing, 210098, China.
| | - Xinyi Chen
- College of Agricultural Sciences and Engineering, Hohai University, Nanjing, 210098, China
| | - Yongqiu Xia
- Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Luís Carlos Timm
- Department of Rural Engineering, Faculty of Agronomy, Federal University of Pelotas, Campus Universitário s/n, CEP, Capão do Leão, Rio Grande do Sul, 96010-900, Brazil
| |
Collapse
|
11
|
Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones. THE ISME JOURNAL 2021; 15:1317-1329. [PMID: 33408366 PMCID: PMC8114937 DOI: 10.1038/s41396-020-00852-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/13/2020] [Accepted: 11/20/2020] [Indexed: 01/29/2023]
Abstract
Nitrite is a pivotal component of the marine nitrogen cycle. The fate of nitrite determines the loss or retention of fixed nitrogen, an essential nutrient for all organisms. Loss occurs via anaerobic nitrite reduction to gases during denitrification and anammox, while retention occurs via nitrite oxidation to nitrate. Nitrite oxidation is usually represented in biogeochemical models by one kinetic parameter and one oxygen threshold, below which nitrite oxidation is set to zero. Here we find that the responses of nitrite oxidation to nitrite and oxygen concentrations vary along a redox gradient in a Pacific Ocean oxygen minimum zone, indicating niche differentiation of nitrite-oxidizing assemblages. Notably, we observe the full inhibition of nitrite oxidation by oxygen addition and nitrite oxidation coupled with nitrogen loss in the absence of oxygen consumption in samples collected from anoxic waters. Nitrite-oxidizing bacteria, including novel clades with high relative abundance in anoxic depths, were also detected in the same samples. Mechanisms corresponding to niche differentiation of nitrite-oxidizing bacteria across the redox gradient are considered. Implementing these mechanisms in biogeochemical models has a significant effect on the estimated fixed nitrogen budget.
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Zhang X, Ward BB, Sigman DM. Global Nitrogen Cycle: Critical Enzymes, Organisms, and Processes for Nitrogen Budgets and Dynamics. Chem Rev 2020; 120:5308-5351. [DOI: 10.1021/acs.chemrev.9b00613] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Bess B. Ward
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Daniel M. Sigman
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
14
|
Chee-Sanford JC, Connor L, Krichels A, Yang WH, Sanford RA. Hierarchical detection of diverse Clade II (atypical) nosZ genes using new primer sets for classical- and multiplex PCR array applications. J Microbiol Methods 2020; 172:105908. [PMID: 32234512 DOI: 10.1016/j.mimet.2020.105908] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 11/27/2022]
Abstract
The reduction of nitrous oxide (N2O) to N2 represents the key terminal step in canonical denitrification. Nitrous oxide reductase (NosZ), the enzyme associated with this biological step, however, is not always affiliated with denitrifying microorganisms. Such organisms were shown recently to possess a Clade II (atypical) nosZ gene, in contrast to Clade I (typical) nosZ harbored in more commonly studied denitrifiers. Subsequent phylogenetic analyses have shown that Clade II NosZ are affiliated with a much broader diversity of microorganisms than those with Clade I NosZ, the former including both non-denitrifiers and denitrifiers. Most studies attempting to characterize the nosZ gene diversity using DNA-based PCR approaches have only focused on Clade I nosZ, despite recent metagenomic sequencing studies that have demonstrated the dominance of Clade II nosZ genes in many ecosystems, particularly soil. As a result, these studies have greatly underestimated the genetic potential for N2O reduction present in ecosystems. Because the high diversity of Clade II NosZ makes it impossible to design a universal primer set that would effectively amplify all nosZ genes in this clade, we developed a suite of primer sets to specifically target seven of ten designated subclades of Clade II nosZ genes. The new primer sets yield suitable product sizes for paired end amplicon sequencing and qPCR, demonstrated here in their use for both conventional single-reaction and multiplex array platforms. In addition, we show the utility of these primers for detecting nosZ gene transcripts from mRNA extracted from soil.
Collapse
Affiliation(s)
| | | | - Alexander Krichels
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wendy H Yang
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
15
|
Sun X, Kop LFM, Lau MCY, Frank J, Jayakumar A, Lücker S, Ward BB. Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones. THE ISME JOURNAL 2019; 13:2391-2402. [PMID: 31118472 PMCID: PMC6776041 DOI: 10.1038/s41396-019-0443-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 01/05/2023]
Abstract
Oxygen minimum zones (OMZs) are marine regions where O2 is undetectable at intermediate depths. Within OMZs, the oxygen-depleted zone (ODZ) induces anaerobic microbial processes that lead to fixed nitrogen loss via denitrification and anammox. Surprisingly, nitrite oxidation is also detected in ODZs, although all known marine nitrite oxidizers (mainly Nitrospina) are aerobes. We used metagenomic binning to construct metagenome-assembled genomes (MAGs) of nitrite oxidizers from OMZs. These MAGs represent two novel Nitrospina-like species, both of which differed from all known Nitrospina species, including cultured species and published MAGs. Relative abundances of different Nitrospina genotypes in OMZ and non-OMZ seawaters were estimated by mapping metagenomic reads to newly constructed MAGs and published high-quality genomes of members from the Nitrospinae phylum. The two novel species were present in all major OMZs and were more abundant inside ODZs, which is consistent with the detection of higher nitrite oxidation rates in ODZs than in oxic seawaters and suggests novel adaptations to anoxic environments. The detection of a large number of unclassified nitrite oxidoreductase genes in the dataset implies that the phylogenetic diversity of nitrite oxidizers is greater than previously thought.
Collapse
Affiliation(s)
- Xin Sun
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA.
| | - Linnea F M Kop
- Department of Microbiology, Radboud University, Nijmegen, AJ, 6525, the Netherlands
| | - Maggie C Y Lau
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
- Laboratory of Extraterrestrial Ocean Systems, Institute of Deep-Sea Science and Engineering, Chinese Academic of Sciences, Sanya, Hainan, 572000, China
| | - Jeroen Frank
- Department of Microbiology, Radboud University, Nijmegen, AJ, 6525, the Netherlands
| | - Amal Jayakumar
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
| | - Sebastian Lücker
- Department of Microbiology, Radboud University, Nijmegen, AJ, 6525, the Netherlands
| | - Bess B Ward
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
| |
Collapse
|
16
|
Pitt A, Schmidt J, Koll U, Hahn MW. Aquirufa antheringensis gen. nov., sp. nov. and Aquirufa nivalisilvae sp. nov., representing a new genus of widespread freshwater bacteria. Int J Syst Evol Microbiol 2019; 69:2739-2749. [DOI: 10.1099/ijsem.0.003554] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Martin W. Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Nakagawa T, Tsuchiya Y, Ueda S, Fukui M, Takahashi R. Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan. Microbes Environ 2018; 34:13-22. [PMID: 30504642 PMCID: PMC6440730 DOI: 10.1264/jsme2.me18103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N2O only. Collectively, these results suggest that the N2O-reducing microbiome in eelgrass meadows is largely responsible for coastal N2O mitigation.
Collapse
Affiliation(s)
| | | | - Shingo Ueda
- College of Bioresource Sciences, Nihon University
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University
| | | |
Collapse
|
19
|
Otwell AE, López García de Lomana A, Gibbons SM, Orellana MV, Baliga NS. Systems biology approaches towards predictive microbial ecology. Environ Microbiol 2018; 20:4197-4209. [DOI: 10.1111/1462-2920.14378] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 01/17/2023]
Affiliation(s)
| | | | - Sean M. Gibbons
- Institute for Systems Biology Seattle WA USA
- eScience Institute, University of Washington Seattle WA USA
- Molecular and Cellular Biology Program University of Washington Seattle WA USA
| | - Mónica V. Orellana
- Institute for Systems Biology Seattle WA USA
- Polar Science Center Applied Physics Lab, University of Washington Seattle WA
| | - Nitin S. Baliga
- Institute for Systems Biology Seattle WA USA
- Molecular and Cellular Biology Program University of Washington Seattle WA USA
- Departments of Biology and Microbiology University of Washington Seattle WA USA
- Lawrence Berkeley National Lab Berkeley CA USA
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Genomics and Ecology of Novel N 2O-Reducing Microorganisms. Trends Microbiol 2017; 26:43-55. [PMID: 28803698 DOI: 10.1016/j.tim.2017.07.003] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/29/2017] [Accepted: 07/14/2017] [Indexed: 11/22/2022]
Abstract
Microorganisms with the capacity to reduce the greenhouse gas nitrous oxide (N2O) to harmless dinitrogen gas are receiving increased attention due to increasing N2O emissions (and our need to mitigate climate change) and to recent discoveries of novel N2O-reducing bacteria and archaea. The diversity of denitrifying and nondenitrifying microorganisms with capacity for N2O reduction was recently shown to be greater than previously expected. A formerly overlooked group (clade II) in the environment include a large fraction of nondenitrifying N2O reducers, which could be N2O sinks without major contribution to N2O formation. We review the recent advances about fundamental understanding of the genomics, physiology, and ecology of N2O reducers and the importance of these findings for curbing N2O emissions.
Collapse
|