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Canonical ammonia oxidizers and comammox Clade A play active roles in nitrification in a black soil at different pH and ammonium concentrations

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Abstract

The discovery of complete ammonia oxidizers (comammox) challenged our cognition of the nitrification process. Ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB) and comammox can carry out soil autotrophic nitrification process together. However, the differentiation of the ecological niche of three types of ammonia oxidizers in different environments has not been fully discovered. In this study, a typical black soil collected from northeast China was adjusted to different pH (original and adjusted pH were 4.29 and 7, respectively) and NH4+-N concentrations (weekly adding and without adding 100 mg NH4+-N kg− 1 soil). The activities of AOA, AOB and comammox were examined using DNA stable isotope probing approach with 13CO2, the phylogenetic information of active ammonia oxidizers was detected by high-throughput sequencing. The results showed that niche differentiation of AOA, AOB and comammox in black soils differed with soil pH. AOA dominated the nitrification process in acidic soils, while AOA, AOB and comammox Clade A taken part in the nitrification process in neutral soils. Among them, AOB showed strong activity in the soils with the high N treatment. The active AOA mainly belonged to Nitrososphaera in acidic and neutral soils. The active AOB and comammox Clade A mainly belonged to Nitrosospira and Clade A.2 in neutral soils, respectively. Taken together, the results highlighted the significance of canonical ammonia oxidizers in nitrification process of black soils, and comammox Clade A played an active role in neutral condition.

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References

  • Anderson CR, Peterson ME, Frampton RA, Bulman SR, Keenan S, Curtin D (2018) Rapid increase in soil pH solubilises organic matter, dramatically increases denitrification potential and strongly stimulates microorganisms from the Firmicutes phylum. Peer J 6:e6090

    Article  PubMed  PubMed Central  Google Scholar 

  • Bai X, Hu X, Liu J, Gu H, Jin J, Liu X, Wang G (2022a) Evaluation of four primer sets for analysis of comammox communities in black soils. Front Microbiol 13:944373

    Article  PubMed  PubMed Central  Google Scholar 

  • Bai X, Hu X, Liu J, Wei D, Zhu P, Cui X, Zhou B, Chen X, Liu J, Jin J, Liu X, Wang G (2022b) Ammonia oxidizing bacteria dominate soil nitrification under different fertilization regimes in black soils of northeast China. Eur J Soil Biol 111:103410

    Article  CAS  Google Scholar 

  • Belser LW (1979) Population ecology of nitrifying bacteria. Annu Rev Microbiol 33:309–333

    Article  CAS  PubMed  Google Scholar 

  • Chen C, Liang H, Gao D (2019) Community diversity and distribution of ammonia-oxidizing archaea in marsh wetlands in the black soil zone in Northeast China. Front Env Sci Eng 13:58

    Article  Google Scholar 

  • Dai S, Liu Q, Zhao J, Zhang J (2018) Ecological niche differentiation of ammonia-oxidising archaea and bacteria in acidic soils due to land use change. Soil Res 56:71–79

    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 528:504–509

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Daims H, Lucker S, Wagner M (2016) A new perspective on microbes formerly known as nitrite-oxidizing bacteria. Trends Microbiol 24:699–712

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • FAO (2022) Global status of black soils. https://doi.org/10.4060/cc3124en. Rome

  • Francis CA, Roberts KJ, Michael Beman J, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaeain water columns and sediments of the ocean. Proc Natl Acad Sci USA 102:14683–14688

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao JF, Fan XY, Pan KL, Li HY, Sun LX (2016) Diversity, abundance and activity of ammonia-oxidizing microorganisms in fine particulate matter. Sci Rep 6:38785

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao W, Fan C, Zhang W, Li N, Liu H, Chen M (2023) Heterotrophic nitrification of organic nitrogen in soils: process, regulation, and ecological significance. Biol Fert Soils 59:261–274

    Article  CAS  Google Scholar 

  • Guo J, Ling N, Chen H, Zhu C, Kong Y, Wang M, Shen Q, Guo S (2017) Distinct drivers of activity, abundance, diversity and composition of ammonia-oxidizers: evidence from a long-term field experiment. Soil Biol Biochem 115:403–414

    Article  CAS  Google Scholar 

  • Hu HW, He JZ (2017) Comammox-a newly discovered nitrification process in the terrestrial nitrogen cycle. J Soil Sediment 17:2709–2717

    Article  CAS  Google Scholar 

  • Hu HW, Zhang LM, Dai Y, Di HJ, He JZ (2013) pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing. J Soil Sediment 13:1439–1449

    Article  Google Scholar 

  • Hu HW, Xu ZH, He JZ (2014) Ammonia-oxidizing archaea play a predominant role in acid soil nitrification. Elsevier Science & Technology, pp 261–302

  • Huang X, Zhao J, Su J, Jia Z, Shi X, Wright AL, Zhu-Barker X, Jiang X (2018) Neutrophilic bacteria are responsible for autotrophic ammonia oxidation in an acidic forest soil. Soil Biol Biochem 119:83–89

    Article  CAS  Google Scholar 

  • Hynes RK, Knowle R (1981) Effect of acetylene on autotrophic and heterotrophic nitrification. Can J Microbiol 28:334–340

    Article  Google Scholar 

  • Jia Z, Conrad R (2009) Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11:1658–1671

    Article  CAS  PubMed  Google Scholar 

  • Jiang QQ, Bakken LR (1999) Comparison of Nitrosospira strains isolated from terrestrial environments. FEMS Microbiol Ecol 30:171–186

    Article  CAS  PubMed  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:e01775–e01720

  • Kim JG, Jung MY, Park SJ, Rijpstra WI, Sinninghe Damste JS, Madsen EL, Min D, Kim JS, Kim GJ, Rhee SK (2012) Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil. Environ Microbiol 14:1528–1543

    Article  CAS  PubMed  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 549:269–272

    Article  CAS  PubMed  PubMed Central  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 437:543–546

    Article  PubMed  Google Scholar 

  • Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW (2011) Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci USA 108:15892–15897

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li C, Hu HW, Chen QL, Chen D, He JZ (2019) Comammox Nitrospira play an active role in nitrification of agricultural soils amended with nitrogen fertilizers. Soil Biol Biochem 138:107609

    Article  CAS  Google Scholar 

  • Li C, Hu HW, Chen QL, Chen D, He JZ (2020) Niche differentiation of clade A comammox Nitrospira and canonical ammonia oxidizers in selected forest soils. Soil Biol Biochem 149:107925

    Article  CAS  Google Scholar 

  • Lin C, Xu H, Qin W, Xu S, Tang X, Kuang L, Wang X, Jiang B, Chen J, Shan J, Adams J, Qin H, Wang B (2020) Evaluation of two primer sets for amplification of comammox Nitrospira amoA genes in wetland soils. Front Microbiol 11:560942

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu X, Zhang X, Herbert SJ (2010) Feeding China’s growing needs for grain. Nature 467:420

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu J, Yu Z, Yao Q, Sui Y, Shi Y, Chu H, Tang C, Franks AE, Jin J, Liu X, Wang G (2018) Ammonia-oxidizing archaea show more distinct biogeographic distribution patterns than ammonia-oxidizing bacteria across the black soil zone of northeast China. Front Microbiol 9:171

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu H, Hu H, Huang X, Ge T, Li Y, Zhu Z, Liu X, Tan W, Jia Z, Di H, Xu J, Li Y (2021) Canonical ammonia oxidizers, rather than comammox Nitrospira, dominated autotrophic nitrification during the mineralization of organic substances in two paddy soils. Soil Biol Biochem 156:108192

    Article  CAS  Google Scholar 

  • Liu H, Qin S, Li Y, Zhao P, Nie Z, Liu H (2023) Comammox Nitrospira and AOB communities are more sensitive than AOA community to different fertilization strategies in a fluvo-aquic soil. Agr Ecosyst Environ 342:108224

    Article  CAS  Google Scholar 

  • Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461:976–979

    Article  CAS  PubMed  Google Scholar 

  • Mertens J, Broos K, Wakelin SA, Kowalchuk GA, Springael D, Smolders E (2009) Bacteria, not archaea, restore nitrification in a zinc-contaminated soil. ISME J 3:916–923

    Article  CAS  PubMed  Google Scholar 

  • Monteiro M, Seneca J, Magalhaes C (2014) The history of aerobic ammonia oxidizers: from the first discoveries to today. J Microbiol 52:537–547

    Article  CAS  PubMed  Google Scholar 

  • Ouyang Y, Norton JM, Stark JM, Reeve JR, Habteselassie MY (2016) Ammonia-oxidizing bacteria are more responsive than archaea to nitrogen source in an agricultural soil. Soil Biol Biochem 96:4–15

    Article  CAS  Google Scholar 

  • Ouyang Y, Norton JM, Stark JM (2017) Ammonium availability and temperature control contributions of ammonia oxidizing bacteria and archaea to nitrification in an agricultural soil. Soil Biol Biochem 113:161–172

    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 12:1779–1793

  • Papen H, von Berg R (1998) A most probable number method (MPN) for the estimation of cell numbers of heterotrophic nitrifying bacteria in soil. Plant Soil 199:123–130

  • Prosser JI, Nicol GW (2012) Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol 20:523–531

    Article  CAS  PubMed  Google Scholar 

  • Rotthauwe JH, Witzel KP, Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol 63:4704–4712

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shen JP, Zhang LM, Di HJ, He JZ (2012) A review of ammonia-oxidizing bacteria and archaea in Chinese soils. Front Microbiol 3:296

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sun P, Zhang S, Wu Q, Zhu P, Ruan Y, Wang Q (2021) pH and ammonium concentration are dominant predictors of the abundance and community composition of comammox bacteria in long-term fertilized Mollisol. Appl Soil Ecol 168:104139

    Article  Google Scholar 

  • Sun X, Zhao J, Bei Q, Xia W, Zhou X, Zhao B, Zhang J, Jia Z (2022) Niche specialization and ecophysiological adaptation strategies of salt–tolerant nitrite oxidizers in soil. Biol Fert Soils 58:815–825

    Article  CAS  Google Scholar 

  • Tamura K, Stecher G, Kumar S (2021) MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 38:3022–3027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van Kessel MA, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJ, Kartal B, Jetten MS, Lucker S (2015) Complete nitrification by a single microorganism. Nature 528:555–559

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Z, Cao Y, Wright AL, Shi X, Jiang X (2019a) Different ammonia oxidizers are responsible for nitrification in two neutral paddy soils. Soil till Res 195:104433

    Article  Google Scholar 

  • Wang Z, Cao Y, Zhu-Barker X, Nicol GW, Wright AL, Jia Z, Jiang X (2019b) Comammox Nitrospira clade B contributes to nitrification in soil. Soil Biol Biochem 135:392–395

    Article  CAS  Google Scholar 

  • Wang X, Lu L, Zhou X, Tang X, Kuang L, Chen J, Shan J, Lu H, Qin H, Adams J, Wang B (2020) Niche differentiation of comammox Nitrospira in the mudflat and reclaimed aagricultural soils along the north branch of Yangtze River Estuary. Front Microbiol 11:618287

    Article  PubMed  Google Scholar 

  • Ward BB, Glover HE, Lipschultz F (1989) Chemoautotrophic activity and nitrification in the oxygen minimum zone off Peru. Deep-Sea Res PT I 36:1031–1051

    Article  CAS  Google Scholar 

  • Xia W, Zhang C, Zeng X, Feng Y, Weng J, Lin X, Zhu J, Xiong Z, Xu J, Cai Z, Jia Z (2011) Autotrophic growth of nitrifying community in an agricultural soil. ISME J 5:1226–1236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu Y, Yu W, Ma Q, Zhou H (2012) Responses of bacterial and archaeal ammonia oxidisers of an acidic luvisols soil to different nitrogen fertilization rates after 9 years. Biol Fert Soils 48:827–837

    Article  CAS  Google Scholar 

  • Xu S, Wang B, Li Y, Jiang D, Zhou Y, Ding A, Zong Y, Ling X, Zhang S, Lu H (2020a) Ubiquity, diversity, and activity of comammox Nitrospira in agricultural soils. Sci Total Environ 706:135684

    Article  CAS  PubMed  Google Scholar 

  • Xu Y, Lu J, Wang Y, Liu G, Wan X, Hua Y, Zhu D, Zhao J (2020b) Diversity and abundance of comammox bacteria in the sediments of an urban lake. J Appl Microbiol 128:1647–1657

    Article  CAS  PubMed  Google Scholar 

  • Zhang LM, Hu HW, Shen JP, He JZ (2012) Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils. ISME J 6:1032–1045

    Article  CAS  PubMed  Google Scholar 

  • Zhang Q, Li Y, He Y, Brookes PC, Xu J (2019a) Elevated temperature increased nitrification activity by stimulating AOB growth and activity in an acidic paddy soil. Plant Soil 445:71–83

    Article  CAS  Google Scholar 

  • Zhang Q, Li Y, He Y, Liu H, Dumont MG, Brookes PC, Xu J (2019b) Nitrosospira Cluster 3-like bacterial ammonia oxidizers and Nitrospira-like nitrite oxidizers dominate nitrification activity in acidic terrace paddy soils. Soil Biol Biochem 131:229–237

  • Zhang C, Ju X, Zhang J, Rees RM, Muller C, Müller C (2023) Soil pH and long–term fertilization affect gross N transformation and N2O production pathways in Chinese and UK croplands. Biol Fert Soils 59:527–539

  • Zhao J, Meng Y, Drewer J, Skiba UM, Prosser JI, Gubry-Rangin C (2020) Differential ecosystem function stability of ammonia-oxidizing archaea and bacteria following short-term environmental perturbation. mSystems 5:e00309–e00320

  • Zou W, Lang M, Zhang L, Liu B, Chen X (2022) Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea dominate nitrification in a nitrogen-fertilized calcareous soil. Sci Total Environ 811:151402

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This study was financially supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA28020201), the National Natural Science Foundation of China (41977202) and International Partnership Project of Chinese Academy of Sciences (131323KYSB20210004).

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  1. Xin Bai and Xiaojing Hu contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China

    Xin Bai, Xiaojing Hu, Junjie Liu, Zhenhua Yu, Jian Jin, Xiaobing Liu & Guanghua Wang

  2. College of Life Science and Technology, Heilongjiang Province Key Laboratory of Plant Biology, Harbin Normal University, Harbin, 150025, China

    Xin Bai

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  1. Xin Bai
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Bai, X., Hu, X., Liu, J. et al. Canonical ammonia oxidizers and comammox Clade A play active roles in nitrification in a black soil at different pH and ammonium concentrations. Biol Fertil Soils 60, 471–481 (2024). https://doi.org/10.1007/s00374-024-01812-1

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