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Wan XS, Sheng HX, Liu L, Shen H, Tang W, Zou W, Xu MN, Zheng Z, Tan E, Chen M, Zhang Y, Ward BB, Kao SJ. Particle-associated denitrification is the primary source of N 2O in oxic coastal waters. Nat Commun 2023; 14:8280. [PMID: 38092778 PMCID: PMC10719265 DOI: 10.1038/s41467-023-43997-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
The heavily human-perturbed coastal oceans are hotspots of nitrous oxide (N2O) emission to the atmosphere. The processes underpinning the N2O flux, however, remain poorly understood, leading to large uncertainties in assessing global N2O budgets. Using a suite of nitrogen isotope labeling experiments, we show that multiple processes contribute to N2O production throughout the estuarine-coastal gradient, sustaining intensive N2O flux to the atmosphere. Unexpectedly, denitrification, rather than ammonia oxidation as previously assumed, constitutes the major source of N2O in well-oxygenated coastal waters. Size-fractionated manipulation experiments with gene analysis further reveal niche partitioning of ammonia oxidizers and denitrifiers across the particle size spectrum; denitrification dominated on large particles and ammonia oxidizers on small particles. Total N2O production rate increases with substrate and particle concentrations, suggesting a crucial interplay between nutrients and particles in controlling N2O production. The controlling factors identified here may help understand climate feedback mechanisms between human activity and coastal oceans.
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Affiliation(s)
- Xianhui S Wan
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
| | - Hua-Xia Sheng
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Li Liu
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Hui Shen
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Weiyi Tang
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Wenbin Zou
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Min N Xu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China
| | - Zhenzhen Zheng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China
| | - Ehui Tan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China
| | - Mingming Chen
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Yao Zhang
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Shuh-Ji Kao
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China.
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Abstract
Analysis of nitrogen isotope fractionation effects is useful for tracing biogeochemical nitrogen cycle processes. Nitrification can cause large nitrogen isotope effects through the enzymatic oxidation of ammonia (NH3) via nitrite (NO2−) to nitrate (NO3−) (15εNH4+→NO2- and 15εNO2-→NO3-). The isotope effects of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and of nitrite-oxidizing bacteria (NOB) have been analyzed previously. Here, we studied the nitrogen isotope effects of the complete ammonia oxidizer (comammox) Nitrospira inopinata that oxidizes NH3 to NO3−. At high ammonium (NH4+) availability (1 mM) and pH between 6.5 and 8.5, its 15εNH4+→NO2- ranged from −33.1 to −27.1‰ based on substrate consumption (residual substrate isotopic composition) and −35.5 to −31.2‰ based on product formation (cumulative product isotopic composition), while the 15εNO2-→NO3- ranged from 6.5 to 11.1‰ based on substrate consumption. These values resemble isotope effects of AOB and AOA and of NOB in the genus Nitrospira, suggesting the absence of fundamental mechanistic differences between key enzymes for ammonia and nitrite oxidation in comammox and canonical nitrifiers. However, ambient pH and initial NH4+ concentrations influenced the isotope effects in N. inopinata. The 15εNH4+→NO2- based on product formation was smaller at pH 6.5 (−31.2‰) compared to pH 7.5 (−35.5‰) and pH 8.5 (−34.9‰), while 15εNO2-→NO3- was smaller at pH 8.5 (6.5‰) compared to pH 7.5 (8.8‰) and pH 6.5 (11.1‰). Isotopic fractionation via 15εNH4+→NO2- and 15εNO2-→NO3- was smaller at 0.1 mM NH4+ compared to 0.5 to 1.0 mM NH4+. Environmental factors, such as pH and NH4+ availability, therefore need to be considered when using isotope effects in 15N isotope fractionation models of nitrification. IMPORTANCE Nitrification is an important nitrogen cycle process in terrestrial and aquatic environments. The discovery of comammox has changed the view that canonical AOA, AOB, and NOB are the only chemolithoautotrophic organisms catalyzing nitrification. However, the contribution of comammox to nitrification in environmental and technical systems is far from being completely understood. This study revealed that, despite a phylogenetically distinct enzymatic repertoire for ammonia oxidation, nitrogen isotope effects of 15εNH4+→NO2- and 15εNO2-→NO3- in comammox do not differ significantly from those of canonical nitrifiers. Thus, nitrogen isotope effects are not suitable indicators to decipher the contribution of comammox to nitrification in environmental samples. Moreover, this is the first systematic study showing that the ambient pH and NH4+ concentration influence the isotope effects of nitrifiers. Hence, these key parameters should be considered in comparative analyses of isotope effects of nitrifiers across different growth conditions and environmental samples.
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Jiang H, Ma J, Xu H, Xu Z, Liu W, Pan K. Multiple isotopic compositions reveal complex nitrogen cycling in a subtropical estuary. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 272:116410. [PMID: 33433349 DOI: 10.1016/j.envpol.2020.116410] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/09/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Nitrogen (N) pollution and the resulting eutrophication can have deleterious consequences on estuaries, such as hypoxia, fish kills, and loss of biotic diversity. An understanding of N sources and cycling in estuaries is fundamental to determining how to effectively manage these ecologically and commercially important areas. We applied a multiple-isotopic approach to examine the transformations and sources of the N pools in the Pearl River Estuary (PRE) during winter. The surface water in the West PRE was characterized by low salinity and high NO3-, while that in the east had high salinity and low NO3-. The NO3- in the West PRE was largely regulated by a conservative mixing process. In contrast, assimilation and nitrification dominated in the East PRE, which was attributed to the long water-residence time. For the first time, the source contributions of NO3- and NH4+ were estimated by isotope mixing models. Our results suggest that river discharge and nitrification contributed 81% and 12% to the NO3- pool, respectively. A major portion (68%) of the NH4+ was from river discharge, with the remainder likely from sewage and the aquitard-aquifer system. Our study demonstrates that internal nitrification can potentially be of pivotal importance in determining the NO3- level in an estuary and its export to coastal waters.
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Affiliation(s)
- Hao Jiang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China; College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Jie Ma
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Huo Xu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Zhifang Xu
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Wenjing Liu
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Ke Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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Kobayashi K, Fukushima K, Onishi Y, Nishina K, Makabe A, Yano M, Wankel SD, Koba K, Okabe S. Influence of δ 18 O of water on measurements of δ 18 O of nitrite and nitrate. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e8979. [PMID: 33053236 DOI: 10.1002/rcm.8979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Oxygen isotope ratio measurements of NO2 - and NO3 - by the azide method and denitrifier method are sensitive to the δ18 O value of the sample water. However, the influence of δ18 OH2O on those measurements has not been quantitatively evaluated and documented so far. Therefore, we investigated the influence of δ18 OH2O of a sample on the δ18 O analysis of NO2 - and NO3 - . METHODS We prepared NO2 - and NO3 - standards (with known δ18 ONO2- and δ18 ONO3- values) dissolved in waters having different δ18 OH2O values (δ18 OH2O = -12.6, 25.9, 56.7, and 110.1‰). Nitrite and nitrate were converted into N2 O using the azide method and the denitrifier method, respectively. The isotope ratios of the generated N2 O were measured with a Sercon purge-and-trap gas chromatography/isotope ratio mass spectrometry (PT-GC/IRMS) system. The measured δ18 O values of the produced N2 O were plotted against known δ18 ONO2- and δ18 ONO3- values to evaluate the influence of exchange of an oxygen atom with H2 O during the conversion of NO2 - into N2 O and NO3 - into N2 O, respectively. RESULTS The degree of oxygen isotope exchange was 10.8 ± 0.3% in the azide method and 5.5 ± 1.0% in the denitrifier method, indicating that the azide method is more susceptible to artifacts arising from differences in the δ18 OH2O value of water than the denitrifier method. Thus, the intercept of the standard calibration curve must be corrected to account for differences in δ18 OH2O . Abiotic NO2 -H2 O equilibrium isotope effect experiments yielded a rate constant of (1.13 ± 007) × 10-2 (h-1 ) and an equilibrium isotope effect of 11.9 ± 0.1‰ under the condition of pH = 7.5, 30°C, and 2.5% salinity. CONCLUSIONS Oxygen isotope ratio measurements of NO2 - by the azide method are highly sensitive to δ18 OH2O as a result of significant oxygen isotope exchange between NO2 - and H2 O. Therefore, to obtain the most accurate measurements water with the same δ18 OH2O value as that of the sample must be used to make the NO2 - and NO3 - standards.
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Affiliation(s)
- Kanae Kobayashi
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
| | - Keitaro Fukushima
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
| | - Yuji Onishi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
| | - Kazuya Nishina
- Center for Regional Environmental Research, National Institute for Environmental Studies, Onogawa, Tsukuba, 305-8506, Japan
| | - Akiko Makabe
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Midori Yano
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
| | - Scott D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543-1050, USA
| | - Keisuke Koba
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
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Kotajima S, Koba K, Ikeda D, Terada A, Isaka K, Nishina K, Kimura Y, Makabe A, Yano M, Fujitani H, Ushiki N, Tsuneda S, Yoh M. Nitrogen and Oxygen Isotope Signatures of Nitrogen Compounds during Anammox in the Laboratory and a Wastewater Treatment Plant. Microbes Environ 2020; 35. [PMID: 33162466 PMCID: PMC7734408 DOI: 10.1264/jsme2.me20031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Isotopic fractionation factors against 15N and 18O during anammox (anaerobic ammonia oxidization by nitrite) are critical for evaluating the importance of this process in natural environments. We performed batch incubation experiments with an anammox-dominated biomass to investigate nitrogen (N) and oxygen (O) isotopic fractionation factors during anammox and also examined apparent isotope fractionation factors during anammox in an actual wastewater treatment plant. We conducted one incubation experiment with high δ18O of water to investigate the effects of water δ18O. The N isotopic fractionation factors estimated from incubation experiments and the wastewater treatment plant were similar to previous values. We also found that the N isotopic effect (15εNXR of -77.8 to -65.9‰ and 15ΔNXR of -31.3 to -30.4‰) and possibly O isotopic effect (18εNXR of -20.6‰) for anaerobic nitrite oxidation to nitrate were inverse. We applied the estimated isotopic fractionation factors to the ordinary differential equation model to clarify whether anammox induces deviations in the δ18O vs δ15N of nitrate from a linear trajectory of 1, similar to heterotrophic denitrification. Although this deviation has been attributed to nitrite oxidation, the O isotopic fractionation factor for anammox is crucial for obtaining a more detailed understanding of the mechanisms controlling this deviation. In our model, anammox induced the trajectory of the δ18O vs δ15N of nitrate during denitrification to less than one, which strongly indicates that this deviation is evidence of nitrite oxidation by anammox under denitrifying conditions.
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Affiliation(s)
- Shotoku Kotajima
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Keisuke Koba
- Center for Ecological Research, Kyoto University.,Institute of Agriculture, Tokyo University of Agriculture and Technology
| | - Daisuke Ikeda
- Graduate School of Engineering, Tokyo University of Agriculture and Technology
| | - Akihiko Terada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology.,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology
| | - Kazuichi Isaka
- Hitachi, Ltd.,Department of Applied Chemistry, Faculty of Science and Engineering, Toyo University
| | - Kazuya Nishina
- Center for Regional Environmental Research, National Institute of Environmental Sciences
| | | | - Akiko Makabe
- Institute of Agriculture, Tokyo University of Agriculture and Technology.,Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology.,Present address: Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology
| | - Midori Yano
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology.,Center for Ecological Research, Kyoto University
| | - Hirotsugu Fujitani
- Department of Life Science and Medical Bioscience, Waseda University.,Present address: Department of Biological Sciences, Faculty of Science and Engineering, Chuo University
| | - Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University
| | - Muneoki Yoh
- Institute of Agriculture, Tokyo University of Agriculture and Technology
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Kobayashi K, Makabe A, Yano M, Oshiki M, Kindaichi T, Casciotti KL, Okabe S. Dual nitrogen and oxygen isotope fractionation during anaerobic ammonium oxidation by anammox bacteria. ISME JOURNAL 2019; 13:2426-2436. [PMID: 31138875 DOI: 10.1038/s41396-019-0440-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/21/2019] [Accepted: 04/16/2019] [Indexed: 11/09/2022]
Abstract
Natural abundance of stable nitrogen (N) and oxygen (O) isotopes are invaluable biogeochemical tracers for assessing the N transformations in the environment. To fully exploit these tracers, the N and O isotope effects (15ε and 18ε) associated with the respective nitrogen transformation processes must be known. However, the N and O isotope effects of anaerobic ammonium oxidation (anammox), one of the major fixed N sinks and NO3- producers, are not well known. Here, we report the dual N and O isotope effects associated with anammox by three different anammox bacteria including "Ca. Scalindua japonica", a putative marine species, which were measured in continuous enrichment culture experiments. All three anammox species yielded similar N isotope effects of NH4+ oxidation to N2 (15εNH4→N2) ranging from 30.9‰ to 32.7‰ and inverse kinetic isotope effects of NO2- oxidation to NO3- (15εNO2→NO3 = -45.3‰ to -30.1‰). In contrast, 15εNO2→N2 (NO2- reduction to N2) were significantly different among three species, which is probably because individual anammox bacteria species might possess different types of nitrite reductase. We also report the combined O isotope effects for NO2- oxidation (18ENO2→NO3) by anammox bacteria. These obtained dual N and O isotopic effects could provide significant insights into the contribution of anammox bacteria to the fixed N loss and NO2- reoxidation (N recycling) in various natural environments.
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Affiliation(s)
- Kanae Kobayashi
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
| | - Akiko Makabe
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Midori Yano
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
| | - Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, Nagaoka, Niigata, 940-8532, Japan
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, Kagamiyama, Higashihiroshima, 739-8511, Japan
| | - Karen L Casciotti
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan.
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Boshers DS, Granger J, Tobias CR, Böhlke JK, Smith RL. Constraining the Oxygen Isotopic Composition of Nitrate Produced by Nitrification. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:1206-1216. [PMID: 30605314 DOI: 10.1021/acs.est.8b03386] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Measurements of the stable isotope ratios of nitrogen (15N/14N) and oxygen (18O/16O) in nitrate (NO3-) enable identification of sources, dispersal, and fate of natural and contaminant NO3- in aquatic environments. The 18O/16O of NO3- produced by nitrification is often assumed to reflect the proportional contribution of oxygen atom sources, water, and molecular oxygen, in a 2:1 ratio. Culture and seawater incubations, however, indicate oxygen isotopic equilibration between nitrite (NO2-) and water, and kinetic isotope effects for oxygen atom incorporation, which modulate the NO3- 18O/16O produced during nitrification. To investigate the influence of kinetic and equilibrium effects on the isotopic composition of NO3- produced from the nitrification of ammonia (NH3), we incubated streamwater supplemented with ammonium (NH4+) and increments of 18O-enriched water. Resulting NO3- 18O/16O ratios showed (1) a disproportionate sensitivity to the 18O/16O ratio of water, mediated by isotopic equilibration between water and NO2-, as well as (2) kinetic isotope discrimination during O atom incorporation from molecular oxygen and water. Empirically, the NO3- 18O/16O ratios thus produced fortuitously converge near the 18O/16O ratio of water. More elevated NO3- 18O/16O values commonly reported in soils and oxic groundwater may thus derive from processes additional to nitrification, including NO3- reduction.
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Affiliation(s)
- Danielle S Boshers
- Department of Marine Sciences , University of Connecticut , 1080 Shennecossett Road , Groton , Connecticut 06340 , United States
| | - Julie Granger
- Department of Marine Sciences , University of Connecticut , 1080 Shennecossett Road , Groton , Connecticut 06340 , United States
| | - Craig R Tobias
- Department of Marine Sciences , University of Connecticut , 1080 Shennecossett Road , Groton , Connecticut 06340 , United States
| | - John K Böhlke
- U.S. Geological Survey , 431 National Center , Reston , Virginia 20192 , United States
| | - Richard L Smith
- U.S. Geological Survey , 3215 Marine Street , Boulder , Colorado 80303 , United States
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