Ammonium-derived nitrous oxide is a global source in streams.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
14 May 2024
14 May 2024
Historique:
received:
30
05
2023
accepted:
29
04
2024
medline:
15
5
2024
pubmed:
15
5
2024
entrez:
14
5
2024
Statut:
epublish
Résumé
Global riverine nitrous oxide (N
Identifiants
pubmed: 38744837
doi: 10.1038/s41467-024-48343-9
pii: 10.1038/s41467-024-48343-9
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
4085Subventions
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 92251304
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 42177063
Informations de copyright
© 2024. The Author(s).
Références
Canadell J. G. et al. In Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (eds Brovkin V. & Feely R. A.) Ch. 5 (Cambridge Univ. Press, 2021).
Tian, H. Q. et al. A comprehensive quantification of global nitrous oxide sources and sinks. Nature 586, 248–256 (2020).
pubmed: 33028999
doi: 10.1038/s41586-020-2780-0
Yao, Y. Z. et al. Increased global nitrous oxide emissions from streams and rivers in the Anthropocene. Nat. Clim. Change. 10, 138–139 (2020).
doi: 10.1038/s41558-019-0665-8
IPCC. in 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories. (2019).
Maavara, T. et al. Nitrous oxide emissions from inland waters: Are IPCC estimates too high? Global Change Biol. 25, 473–488 (2019).
doi: 10.1111/gcb.14504
Beaulieu, J. J. et al. Nitrous oxide emission from denitrification in stream and river networks. Proc. Natl Acad. Sci. USA 108, 214–219 (2011).
pubmed: 21173258
doi: 10.1073/pnas.1011464108
Zhu, X., Burger, M., Doane, T. A. & Horwath, W. R. Ammonia oxidation pathways and nitrifier denitrification are significant sources of N
pubmed: 23576736
pmcid: 3631630
doi: 10.1073/pnas.1219993110
Biddulph, M. In Geomorphological Techniques (eds Clarke, L. & Nield, J.) Ch 3.11.1 (British Society for Geomorphology, 2015).
Kiel, B. A. & Cardenas, M. B. Lateral hyporheic exchange throughout the Mississippi River network. Nat. Geosci. 7, 413–417 (2014).
doi: 10.1038/ngeo2157
Boulton, A. J., Findlay, S., Marmonier, P., Stanley, E. H. & Valett, H. M. The functional significance of the hyporheic zone in streams and rivers. Annu. Rev. Ecol. Syst. 29, 59–81 (1998).
doi: 10.1146/annurev.ecolsys.29.1.59
Reay, D. S. et al. Global agriculture and nitrous oxide emissions. Nat. Clim. Change. 2, 410–416 (2012).
doi: 10.1038/nclimate1458
Tian, H. Q. et al. Food benefit and climate warming potential of nitrogen fertilizer uses in China. Environ. Res. Lett. 7, 044020 (2012).
doi: 10.1088/1748-9326/7/4/044020
Wang, J., Chen, N., Yan, W., Wang, B. & Yang, L. Effect of dissolved oxygen and nitrogen on emission of N
doi: 10.1016/j.atmosenv.2014.12.054
Kumar, A., Yang, T. & Sharma, M. P. Greenhouse gas measurement from chinese freshwater bodies: a review. J. Clean. Prod. 233, 368–378 (2019).
doi: 10.1016/j.jclepro.2019.06.052
Tang, M.-Y. et al. Diffusive fluxes and controls of N
Gong, J.-W. Temporal and spatial distribution of CO
doi: 10.26944/d.cnki.gbfju.2022.000376
Hirayama, J., Eda, S., Mitsui, H. & Minamisawa, K. Nitrate-dependent N
pubmed: 22003029
pmcid: 3233077
doi: 10.1128/AEM.06262-11
Hefting, M. M., Bobbink, R. & Janssens, M. P. Spatial variation in denitrification and N
doi: 10.1007/s10021-006-0160-8
Wrage, N., van Groenigen, J. W., Oenema, O. & Baggs, E. M. A novel dual-isotope labelling method for distinguishing between soil sources of N
pubmed: 16220527
doi: 10.1002/rcm.2191
Kool, D. M. et al. Nitrifier denitrification can be a source of N
doi: 10.1111/j.1365-2389.2010.01270.x
Kool, D. M., Dolfing, J., Wrage, N. & Van Groenigen, J. W. Nitrifier denitrification as a distinct and significant source of nitrous oxide from soil. Soil Biol. Biochem. 43, 174–178 (2011).
doi: 10.1016/j.soilbio.2010.09.030
Wang, H. J., Wang, W. D., Yin, C. Q., Wang, Y. C. & Lu, J. W. Littoral zones as the “hotspots” of nitrous oxide (N
doi: 10.1016/j.atmosenv.2006.05.032
Wang, H. J., Yang, L. Y., Wang, W. D., Lu, J. W. & Yin, C. Q. Nitrous oxide (N
Woodward, K. B., Fellows, C. S., Conway, C. L. & Hunter, H. M. Nitrate removal, denitrification and nitrous oxide production in the riparian zone of an ephemeral stream. Soil Biol. Biochem. 41, 671–680 (2009).
doi: 10.1016/j.soilbio.2009.01.002
Qin, Y., Wang, S. Y., Wang, X. M., Liu, C. L. & Zhu, G. B. Contribution of ammonium-induced nitrifier denitrification to N
pubmed: 36719089
doi: 10.1021/acs.est.2c06124
Zhang, G. L. et al. Distribution of concentration and stable isotopic composition of N
doi: 10.1029/2019JC014947
Yuan, D. D. et al. Nitrifiers cooperate to produce nitrous oxide in Plateau wetland sediments. Environ. Sci. Technol. 57, 810–821 (2023).
pubmed: 36459424
doi: 10.1021/acs.est.2c06234
Cao, Y., Wang, X., Zhang, X., Misselbrook, T. & Ma, L. Nitrifier denitrification dominates nitrous oxide production in composting and can be inhibited by a bioelectrochemical nitrification inhibitor. Bioresour. Technol. 341, 125851 (2021).
pubmed: 34523577
doi: 10.1016/j.biortech.2021.125851
Wells, N. S. & Eyre, B. D. Flow regulates biological NO
doi: 10.1016/j.gca.2021.05.026
Daebeler, A. et al. Rapid nitrification involving comammox and canonical Nitrospira at extreme pH in saline-alkaline lakes. Environ. Microbiol. 25, 1055–1067 (2023).
pubmed: 36651641
pmcid: 10947350
doi: 10.1111/1462-2920.16337
Blaszczyk, M. K. Comparison of dentrification by Paracoccus denitrificans, Pseudomonas stutzeri and Pseudomonas aeruginosa. Acta Microbiol. Pol. 41, 203–210 (1992).
pubmed: 1284849
Kowalchuk, G. A. & Stephen, J. R. Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu. Rev. Microbiol. 55, 485–529 (2001).
pubmed: 11544365
doi: 10.1146/annurev.micro.55.1.485
Wang, B. et al. Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils. ISME J. 9, 1062 (2015).
pubmed: 25303715
doi: 10.1038/ismej.2014.194
Wang, B. et al. Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons. ISME J. 13, 3067–3079 (2019).
pubmed: 31462715
pmcid: 6863869
doi: 10.1038/s41396-019-0493-x
Wang, S., Wang, Y., Feng, X., Zhai, L. & Zhu, G. Quantitative analyses of ammonia-oxidizing archaea and bacteria in the sediments of four nitrogen-rich wetlands in China. Appl. Microbiol. Biot. 90, 779–787 (2011).
doi: 10.1007/s00253-011-3090-0
Moir, J. W. & Wood, N. J. Nitrate and nitrite transport in bacteria. Cell Mol. Life Sci. 58, 215–224 (2001).
pubmed: 11289303
doi: 10.1007/PL00000849
Fukuda, M. et al. Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK. Nat. Commun. 6, 7097 (2015).
pubmed: 25959928
doi: 10.1038/ncomms8097
Kim, S. W., Miyahara, M., Fushinobu, S., Wakagi, T. & Shoun, H. Nitrous oxide emission from nitrifying activated sludge dependent on denitrification by ammonia-oxidizing bacteria. Bioresour. Technol. 101, 3958–3963 (2010).
pubmed: 20138758
doi: 10.1016/j.biortech.2010.01.030
Peng, Y. Z. & Zhu, G. B. Biological nitrogen removal with nitrification and denitrification via nitrite pathway. Appl. Microbiol. Biotechnol. 73, 15–26 (2006).
pubmed: 17028876
doi: 10.1007/s00253-006-0534-z
Lu, X. et al. Significant production of nitric oxide by aerobic nitrite reduction at acidic pH. Water Res. 230, 119542 (2023).
pubmed: 36603308
doi: 10.1016/j.watres.2022.119542
Liu, B. et al. High nitrite concentration accelerates nitrite oxidizing organism’s death. Water Sci. Technol. 77, 2812–2822 (2018).
pubmed: 30065133
doi: 10.2166/wst.2018.272
Stein, L. Y. et al. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environ.Microbiol. 9, 2993–3007 (2007).
Kuypers, M., Marchant, H. & Kartal, B. The microbial nitrogen-cycling network. Nat. Rev. Microbiol. 16, 263–276 (2018).
pubmed: 29398704
doi: 10.1038/nrmicro.2018.9
Shaw, L. J. et al. Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway. Environ. Microbiol. 8, 214–222 (2006).
pubmed: 16423010
doi: 10.1111/j.1462-2920.2005.00882.x
Lu, M. et al. A cultivated planet in 2010 – Part 1: the global synergy cropland map. Earth Syst. Sci. Data 12, 1913–1928 (2020).
doi: 10.5194/essd-12-1913-2020
Li, D., Liu, C., Luo, R., Sadakane, K. & Lam, T. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de bruijn graph. Bioinformatics 31, 1674–1676 (2015).
pubmed: 25609793
doi: 10.1093/bioinformatics/btv033
Langmead, B. & Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 9, 357–359 (2012).
pubmed: 22388286
pmcid: 3322381
doi: 10.1038/nmeth.1923
Li, H. et al. The sequence alignment/map format and SAM tools. Bioinformatics 25, 2078–2079 (2009).
pubmed: 19505943
pmcid: 2723002
doi: 10.1093/bioinformatics/btp352
Uritskiy, G. V., DiRuggiero, J. & Taylor, J. MetaWRAP-A flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6, 1–103 (2018).
doi: 10.1186/s40168-018-0541-1
Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2, 1533–1542 (2017).
pubmed: 28894102
doi: 10.1038/s41564-017-0012-7
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome. Res. 25, 1043–1055 (2015).
pubmed: 25977477
pmcid: 4484387
doi: 10.1101/gr.186072.114
Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. Drep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017).
pubmed: 28742071
pmcid: 5702732
doi: 10.1038/ismej.2017.126
Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods. 14, 417–419 (2017).
pubmed: 28263959
pmcid: 5600148
doi: 10.1038/nmeth.4197
Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996–1004 (2018).
pubmed: 30148503
doi: 10.1038/nbt.4229
Tu, Q., Lin, L., Cheng, L., Deng, Y. & He, Z. NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes. Bioinformatics 35, 1040–1048 (2019).
pubmed: 30165481
doi: 10.1093/bioinformatics/bty741
Braker, G., Zhou, J., Wu, L., Devol, A. H. & Tiedje, J. M. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities. Appl. Environ. Microbiol. 66, 2096–2104 (2000).
pubmed: 10788387
pmcid: 101460
doi: 10.1128/AEM.66.5.2096-2104.2000
Braker, G., Fesefeldt, A. & Witzel, K. P. Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl. Environ. Microbiol. 64, 3769–3775 (1998).
pubmed: 9758798
pmcid: 106545
doi: 10.1128/AEM.64.10.3769-3775.1998
Hall, B. G. Building phylogenetic trees from molecular data with MEGA. Mol. Biol. Evol. 30, 1229–1235 (2013).
pubmed: 23486614
doi: 10.1093/molbev/mst012
Wang, S. et al. Microbial nitrogen cycle hotspots in the plant-bed/ditch system of a constructed wetland with N
pubmed: 29750509
doi: 10.1021/acs.est.7b04925
Zhu, G. B. et al. Hotspots of anaerobic ammonium oxidation at land-freshwater interfaces. Nat. Geosci. 6, 103–107 (2013).
doi: 10.1038/ngeo1683