Kuypers MMM, Marchant HK, Kartal B (2018) The microbial nitrogen-cycling network. Nat Rev Microbiol 16(5):263–276. https://doi.org/10.1038/nrmicro.2018.9
Article
CAS
Google Scholar
Costa E, Perez J, Kreft JU (2006) Why is metabolic labour divided in nitrification? Trends Microbiol 14(5):213–219. https://doi.org/10.1016/j.tim.2006.03.006
Article
CAS
Google Scholar
Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437(7058):543–546. https://doi.org/10.1038/nature03911
Article
CAS
Google Scholar
Teske A, Alm E, Regan JM, Toze S, Rittmann BE, Stahl DA (1994) Evolutionary relationships among ammonia-oxidizing and nitrite-oxidizing bacteria. J Bacteriol 176(21):6623–6630. https://doi.org/10.1128/jb.176.21.6623-6630.1994
Article
CAS
Google Scholar
Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M (2015) Complete nitrification by Nitrospira bacteria. Nature 528(7583):504. https://doi.org/10.1038/nature16461
Article
CAS
Google Scholar
Van Kessel MAHJ, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJM, Kartal B, Jetten MSM, Lucker S (2015) Complete nitrification by a single microorganism. Nature 528(7583):555. https://doi.org/10.1038/nature16459
Article
CAS
Google Scholar
Xia F, Wang JG, Zhu T, Zou B, Rhee SK, Quan ZX (2018) Ubiquity and diversity of complete ammonia oxidizers (comammox). Appl Environ 84(24):e01390-e1418. https://doi.org/10.1128/aem.01390-18
Article
CAS
Google Scholar
Zhao YX, Hu JJ, Yang WL, Wang JQ, Jia ZJ, Zheng P, Hu BL (2021) The long-term effects of using nitrite and urea on the enrichment of comammox bacteria. Sci Total Environ 755(2):142580. https://doi.org/10.1016/j.scitotenv.2020.142580
Article
CAS
Google Scholar
Wang DQ, Zhou CH, Nie M, Gu JD, Quan ZX (2021) Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants. Sci Total Environ 768:144993. https://doi.org/10.1016/j.scitotenv.2021.144993
Article
CAS
Google Scholar
Wang ZH, Cao YQ, Zhu-Barker X, Nicol GW, Wright AL, Jia ZJ, Jiang XJ (2019) Comammox Nitrospira clade B contributes to nitrification in soil. Soil Biol Biochem 135:392–395. https://doi.org/10.1016/j.soilbio.2019.06.004
Article
CAS
Google Scholar
Wang SY, Wang XM, Jiang YY, Han C, Jetten MSM, Schwark L, Zhu GB (2021) Abundance and functional importance of complete ammonia oxidizers and other nitrifiers in a riparian ecosystem. Environ Sci Technol 55(8):4573–4584. https://doi.org/10.1021/acs.est.0c00915
Article
CAS
Google Scholar
Shi Y, Jiang YY, Wang SY, Wang XM, Zhu GB (2020) Biogeographic distribution of comammox bacteria in diverse terrestrial habitats. Sci Total Environ 717:137257. https://doi.org/10.1016/j.scitotenv.2020.137257
Article
CAS
Google Scholar
Li CY, Hu HW, Chen QL, Chen DL, He JZ (2020) Niche differentiation of clade A comammox Nitrospira and canonical ammonia oxidizers in selected forest soils. Soil Biol Biochem 149:107925. https://doi.org/10.1016/j.soilbio.2020.107925
Article
CAS
Google Scholar
Sun DY, Zhao MY, Tang XF, Liu M, Hou LJ, Zhao Q, Li J, Gu JD, Han P (2021) Niche adaptation strategies of different clades of comammox Nitrospira in the Yangtze Estuary. Int Biodeterior 164:105286. https://doi.org/10.1016/j.ibiod.2021.105286
Article
Google Scholar
Li CY, Hu HW, Chen QL, Chen DL, He JZ (2019) Comammox Nitrospira play an active role in nitrification of agricultural soils amended with nitrogen fertilizers. Soil Biol Biochem 138:107609. https://doi.org/10.1016/j.soilbio.2019.107609
Article
CAS
Google Scholar
Hu HW, He JZ (2017) Comammox-a newly discovered nitrification process in the terrestrial nitrogen cycle. J Soils Sediments 17(12):2709–2717. https://doi.org/10.1007/s11368-017-1851-9
Article
CAS
Google Scholar
Koch H, Lucker S, Albertsen M, Kitzinger K, Herbold C, Spieck E, Nielsen PH, Wagner M, Daims H (2015) Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. PNAS 112(36):11371–11376. https://doi.org/10.1073/pnas.1506533112
Article
CAS
Google Scholar
Palomo A, Pedersen AG, Fowler SJ, Dechesne A, Sicheritz-Ponten T, Smets BF (2018) Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira. ISME J 12(7):1779–1793. https://doi.org/10.1038/s41396-018-0083-3
Article
Google Scholar
Jiang Y, Pan J, Wang X, Wang Y, Liu S, Zhou J, Zhu G, Liu C, Wang W (2020) Research on abundance, community structure and influencing factors of complete ammonia oxidizing (comammox) bacteria in Chaohu Lake. Acta Sci Circum 40(4):1260–1268
Google Scholar
Wan Q, Wang S, Zhao W, Ma L, Jia Z, Jiang X (2019) Vertical abundance variations of incomplete ammonia oxidizers and comammox in purple paddy soil in Chongqing. Acta Microbiol Sin 59(2):291–302
CAS
Google Scholar
Zeleke J, Lu SL, Wang JG, Huang JX, Li B, Ogram AV, Quan ZX (2013) Methyl coenzyme M reductase A (mcrA) gene-based investigation of methanogens in the mudflat sediments of Yangtze River Estuary, China. Microb Ecol 66(2):257–267. https://doi.org/10.1007/s00248-012-0155-2
Article
CAS
Google Scholar
Wang F, Liang XL, Ma SH, Liu LZ, Wang JK (2021) Ammonia-oxidizing archaea are dominant over comammox in soil nitrification under long-term nitrogen fertilization. J Soils Sediments 21(4):1800–1814. https://doi.org/10.1007/s11368-021-02897-z
Article
CAS
Google Scholar
Hu JJ, Zhao YX, Yao XW, Wang JQ, Zheng P, Xi CAW, Hu BL (2021) Dominance of comammox Nitrospira in soil nitrification. Sci Total Environ 780:146558. https://doi.org/10.1016/j.scitotenv.2021.146558
Article
CAS
Google Scholar
Banning NC, Maccarone LD, Fisk LM, Murphy DV (2015) Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil. Sci Rep 5(1):11146. https://doi.org/10.1038/srep11146
Article
Google Scholar
Liu Y, Zhang JX, Zhang XL, Xie SG (2014) Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland. Appl Microbiol Biotechnol 98(12):5697–5707. https://doi.org/10.1007/s00253-014-5651-5
Article
CAS
Google Scholar
Jiang Q, Xia F, Zhu T, Wang D, Quan Z (2019) Distribution of comammox and canonical ammonia-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary at different depths over four seasons. J Appl Microbiol 127(2):533–543. https://doi.org/10.1111/jam.14337
Article
CAS
Google Scholar
He Q, Peng SJ, Zhai J, Xiao HW (2011) Development and application of a water pollution emergency response system for the Three Gorges Reservoir in the Yangtze River, China. J Environ Sci (China) 23(4):595–600. https://doi.org/10.1016/s1001-0742(10)60424-x
Article
Google Scholar
Bai BW, Wang HY, Li XY, Feng YL, Zhi L (2005) A comparative study of the plant community of the future water-level-fluctuating zone and the natural water-level-fluctuatingzone in the three gorges reservoir. J Southwest Agric Univ 27(5):684
Google Scholar
Guo J, Jiang X, Zhou X, Meng Y, Jia Z (2016) Impact of periodical flooding-drying on nitrification and ammonia oxidizers in hydro-fluctuation belt of the Three Gorges Reservoir. Acta Microbiol Sin 56(6):983–999. https://doi.org/10.13343/j.cnki.wsxb.20150402
Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. PNAS 102(41):14683–14688. https://doi.org/10.1073/pnas.0506625102
Article
CAS
Google Scholar
Meinhardt KA, Bertagnolli A, Pannu MW, Strand SE, Brown SL, Stahl DA (2015) Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria. Environ Microbiol Rep 7(2):354–363. https://doi.org/10.1111/1758-2229.12259
Article
CAS
Google Scholar
Jiang R, Wang JG, Zhu T, Zou B, Wang DQ, Rhee SK, An D, Ji ZY, Quan ZX (2020) Use of newly designed primers for quantification of complete ammonia-oxidizing (Comammox) bacterial clades and strict nitrite oxidizers in the genus Nitrospira. Appl Environ Microbiol 86(20):e01775-e1820. https://doi.org/10.1128/aem.01775-20
Article
CAS
Google Scholar
Li CY, Hu HW, Chen QL, Yan ZZ, Nguyen BAT, Chen DL, He JZ (2021) Niche specialization of comammox Nitrospira clade A in terrestrial ecosystems. Soil Biol Biochem 156:108231. https://doi.org/10.1016/j.soilbio.2021.108231
Article
CAS
Google Scholar
Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016) Vsearch: a versatile open source tool for metagenomics. PeerJ. https://doi.org/10.7717/peerj.2584
Article
Google Scholar
Wang Q, Quensen JF, Fish JA, Lee TK, Sun YN, Tiedje JM, Cole JR (2013) Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using framebot, a New Informatics Tool. MBio 4(5):e00592-e613. https://doi.org/10.1128/mBio.00592-13
Article
CAS
Google Scholar
Jiang P, Shi DM, Hu XQ, Huang XZ, Li YX, Guo TL (2015) Soil stability characteristics of mulberry lands at hydro-fluctuation belt in the Three Gorges Reservoir area, China. Environ Monit Assess 187(10):634. https://doi.org/10.1007/s10661-015-4834-6
Article
CAS
Google Scholar
Cheng RM, Wang XR, Xiao WF, Guo QS, Feng XH (2009) Study on the soil physical properties and metal content in the early submerged water-level-fluctuating zone of Three Gorges reservoir. J Soil Water Conserv 23(5):156–161
Google Scholar
Koch H, van Kessel M, Lucker S (2019) Complete nitrification: insights into the ecophysiology of comammox Nitrospira. Appl Microbiol Biotechnol 103(1):177–189. https://doi.org/10.1007/s00253-018-9486-3
Article
CAS
Google Scholar
Zhu GB, Wang XM, Wang SY, Yu LB, Armanbek G, Yu J, Jiang LP, Yuan DD, Guo ZR, Zhang HR, Zheng L, Schwark L, Jetten MSM, Yadav AK, Zhu YG (2022) Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox). Sci Total Environ 829:154590. https://doi.org/10.1016/j.scitotenv.2022.154590
Article
CAS
Google Scholar
Camejo PY, Domingo JS, McMahon KD, Noguera DR (2017) Genome-enabled insights into the ecophysiology of the comammox bacterium “Candidatus nitrospira nitrosa”. Msystems 2(5):e00059-e117. https://doi.org/10.1128/mSystems.00059-17
Article
CAS
Google Scholar
Horton DJ, Theis KR, Uzarski DG, Learman DR (2019) Microbial community structure and microbial networks correspond to nutrient gradients within coastal wetlands of the Laurentian Great Lakes. Fems Microbiol Ecol 95(4):fiz003. https://doi.org/10.1093/femsec/fiz033
Inceoglu O, Lliros M, Garcia-Armisen T, Crowe SA, Michiels C, Darchambeau F, Descy JP, Servais P (2015) Distribution of bacteria and archaea in meromictic tropical Lake Kivu (Africa). Aquat Microb Ecol 74(3):215–233. https://doi.org/10.3354/ame01737
Article
Google Scholar
Lin YX, Ye GP, Hu HW, Yang P, Wan S, Feng MM, He ZY, He JZ (2022) Plant species-driven distribution of individual clades of comammox Nitrospira in a subtropical estuarine wetland. Microb Ecol. https://doi.org/10.1007/s00248-021-01940-3
Article
Google Scholar
Dai H, Jiang Q, Quan Z (2020) Distribution of complete ammonia oxidizers (Comammox) in different seasons and depths in tidal-flat wetland. J Mirobiol 40(5):35–42
Google Scholar
Kits KD, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P, Daebeler A, Romano S, Albertsen M, Stein LY, Daims H, Wagner M (2017) Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature 549(7671):269. https://doi.org/10.1038/nature23679
Osterholz WR, Rinot O, Liebman M, Castellano MJ (2017) Can mineralization of soil organic nitrogen meet maize nitrogen demand? Plant Soil 415(1–2):73–84. https://doi.org/10.1007/s11104-016-3137-1
Article
CAS
Google Scholar
Anthonisen AC, Loehr RC, Prakasam TBS, Srinath EG (1976) Inhibition of nitrification by ammonia and nitrous-acid. J Water Pollut Control Fed 489(5):835–852
Google Scholar
Park S, Bae W (2009) Modeling kinetics of ammonium oxidation, nitrite oxidation under simultaneous inhibition by free ammonia and free nitrous acid. Process Biochem 44(6):631–640. https://doi.org/10.1016/j.procbio.2009.02.002
Article
CAS
Google Scholar
Herbold CW, Lehtovirta-Morley LE, Jung MY, Jehmlich N, Hausmann B, Han P, Loy A, Pester M, Sayavedra-Soto LA, Rhee SK, Prosser JI, Nicol GW, Wagner M, Gubry-Rangin C (2017) Ammonia-oxidising archaea living at low pH: Insights from comparative genomics. Environ Microbiol 19(12):4939–4952. https://doi.org/10.1111/1462-2920.13971
Article
CAS
Google Scholar
Lehtovirta-Morley LE, Sayavedra-Soto LA, Gallois N, Schouten S, Stein LY, Prosser JI, Nicol GW (2016) Identifying potential mechanisms enabling acidophily in the ammonia-oxidizing archaeon “Candidatus Nitrosotalea devanaterra.” Appl Environ Microbiol 82(9):2608–2619. https://doi.org/10.1128/aem.04031-15
Article
CAS
Google Scholar
Sun DY, Tang XF, Zhao MY, Zhang ZX, Hou LJ, Liu M, Wang BZ, Klumper U, Han P (2020) Distribution and diversity of comammox Nitrospira in coastal wetlands of China. Front Microbiol 11:589268. https://doi.org/10.3389/fmicb.2021.731921
Article
Google Scholar
Xu SY, Wang BZ, Li Y, Jiang DQ, Zhou YT, Ding A, Zong YX, Ling X, Zhang S, Lu H (2020) Ubiquity, diversity, and activity of comammox Nitrospira in agricultural soils. Sci Total Environ 706:135684. https://doi.org/10.1016/j.scitoteuv.2019.136684
Article
CAS
Google Scholar
Osburn ED, Barrett JE (2020) Abundance and functional importance of complete ammonia-oxidizing bacteria (comammox) versus canonical nitrifiers in temperate forest soils. Soil Biol Biochem 145:107801. https://doi.org/10.1016/j.soilbio.2020.107801
Article
CAS
Google Scholar