Abstract
The recently discovered complete ammonia oxidizers (comammox Nitrospira) have fundamentally changed the perceptions of two-step nitrification. Previous studies suggest that comammox Nitrospira may outcompete canonical ammonia oxidizers under ammonia-limited conditions (e.g., acidic soils). However, there is no convincing evidence that links comammox Nitrospira activity to nitrification in acidic soils. Here, we report the relative contributions of ammonia-oxidizing bacteria (AOB), archaea (AOA), and comammox Nitrospira to nitrification in four orchard soils with different ages (5Y, 10Y, 20Y, and 30Y) and one adjacent natural forest soil (NF) in China. DNA-based stable-isotope probing demonstrated that both AOA and AOB assimilated 13CO2 in the nonacidic NF, 5Y, and 10Y soils, although a small shift from the light fractions to heavy fractions was observed for comammox Nitrospira clade A in the 10Y soil. Comammox Nitrospira clade A rather than AOA and AOB was labeled by 13CO2 in strongly acidic 30Y soil. In strongly acidic 20Y soil, comammox Nitrospira clade A was much more heavily labeled than AOB. These results suggest the different contributions of ammonia oxidizers to nitrification in orchard soils with different ages and a greater functional importance of comammox Nitrospira than canonical ammonia oxidizers in ammonia oxidation in the tested strongly acidic orchard soils.
Similar content being viewed by others
References
Avrahami S, Liesack W, Conrad R (2003) Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers. Environ Microbiol 5:691–705
Bartelme RP, Mclellan SL, Newton RJ (2017) Freshwater recirculating aquaculture system operations drive biofilter bacterial community shifts around a stable nitrifying consortium of ammonia-oxidizing archaea and comammox Nitrospira. Front Microbiol 8:101
Callahan BP, Yuan Y, Wolfenden R (2005) The burden borne by urease. J Am Chem Soc 127:10828–10829
Cameron KC, Di HJ, Moir JL (2013) Nitrogen losses from the soil/plant system: a review. Ann Appl Biol 162:145–173
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M et al (2010) QIIME allows analysis of highthroughput community sequencing data. Nat Methods 7:335–336
Carson PL (1980) Recommended potassium test. In: Dahnke WC (ed) Recommended chemical soil test procedures for the north central region. Bulletin 499, North Dakota Agricultural Experiment Station, Fargo, ND, pp 17–18
Chu HY, Fujii T, Morimoto S, Lin XG, Yagi K, Hu JL, Zhang JB (2007) Community structure of ammonia-oxidizing bacteria under longterm application of mineral fertilizer and organic manure in a sandy loam soil. Appl Environ Microb 73:485–491
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
Daims H, Lücker S, Wagner M (2016) A new perspective on microbes formerly known as nitrite-oxidizing bacteria. Trends Microbiol 24:699–712
Davidson EA, Hart SC, Firestone MK (1992) Internal cycling of nitrate in soils of a mature coniferous forest. Ecology 73:1148–1156
De Boer W, Kowalchuk GA (2001) Nitrification in acid soils: micro-organisms and mechanisms. Soil Biol Biochem 33:853–866
Di HJ, Cameron KC, Shen JP, Winefield CS, O’Callaghan M, Bowatte S, He JZ (2009) Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils. Nat Geosci 2:621–624
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460
FAO (Food and Agricultural Organization, the United Nations), 2017. FAOSTAT. http://www.fao.org/faostat/en/. Accessed 20 Apr 2021
Fowler SJ, Palomo A, Dechesne A, Mines PD, Smets BF (2018) Comammox Nitrospira are abundant ammonia oxidizers in diverse groundwater-fed rapid sand filter communities. Environ Microbiol 20:1002–1015
Galloway JN, Townsend AR, Erisman JW, Bekunda M, Cai Z, Freney JR, Martinelli LA, Seitzinger SP, Sutton MA (2008) Transformation of the nitrogen cycle: recent trends, questions, and potential solutions. Science 320:889–892
Gao WL, Fan CH, Zhang W, Li N, Liu HR, Chen M (2023) Heterotrophic nitrification of organic nitrogen in soils: process, regulation, and ecological significance. Biol Fert Soils 59:261–274
Gubry-Rangin C, Hai B, Quince C, Engel M, Thomson BC, James P, Schloter M, Griffiths RI, Prosser JI, Nicol GW (2011) Niche specialization of terrestrial archaeal ammonia oxidizers. P Natl Acad Sci USA 108:21206–21211
Gubry-Rangin C, Nicol GW, Prosser JI (2010) Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microbiol Ecol 74:566–574
Hu HW, He JZ (2017) Comammox-a newly discovered nitrification process in the terrestrial nitrogen cycle. J Soil Sediment 17:2709–2717
Hu JJ, Zhao YX, Yao XW, Wang JQ, Zheng P, Xi CW, Hu BL (2021) Dominance of comammox Nitrospira in soil nitrification. Sci Total Environ 780:146558
Huang XR, Zhao J, Su J, Jia ZJ, Shi XL, Wright AL, Zhu-Barker X, Jiang XJ (2018) Neutrophilic bacteria are responsible for autotrophic ammonia oxidation in an acidic forest soil. Soil Biol Biochem 119:83–89
Hyman M, Arp D (1992) 14C2H2- and 14CO2-labeling studies of the de novo synthesis of polypeptides by Nitrosomonas europaea during recovery from acetylene and light inactivation of ammonia monooxygenase. J Biol Chem 267:1534–1545
Hyman MR, Wood PM (1985) Suicidal inactivation and labelling of ammonia monooxygenase by acetylene. Biochem J 227:719–725
Jia Z, Conrad R (2009) Bacteria rather than archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11:1658–1671
Jiang XJ, Hou XY, Zhou X, Xin XP, Wright A, Jia ZJ (2015) pH regulates key players of nitrification in paddy soils. Soil Biol Biochem 81:9–16
Kissel DE, Cabrera ML, Ferguson RB (1988) Reactions of ammonia and urea hydrolysis products with soil. Soil Sci Soc Am J 52:1793–1796
Kits KD, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P, Daebeler A, Romano S, Albertsen M, Stein LY (2017) Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature 549:269–272
Kӧnneke 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
Kowalchuk GA, Stienstra AW, Stephen JR, Woldendorp JW (2000) Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands. Environ Microbiol 2:99–110
Lehtovirta-Morley LE, Ge C, Ross J, Yao H, Nicol GW, Prosser JI (2014) Characterisation of terrestrial acidophilic archaeal ammonia oxidisers and their inhibition and stimulation by organic compounds. FEMS Microbiol Ecol 89:542–552
Lehtovirta-Morley LE, Ross J, Hink L, Weber EB, Gubry-Rangin C, Thion C, Prosser JI, Nicol GW (2016) Isolation of 'Candidatus Nitrosocosmicus franklandus', a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS Microbiol Ecol 92:fiw057
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
Li C, Hu HW, Chen QL, Chen D, He JZ (2020a) Niche differentiation of clade A comammox Nitrospira and canonical ammonia oxidizers in selected forest soils. Soil Biol Biochem 149:107925
Li C, Hu HW, Chen QL, Yan ZZ, Nguyen BAT, Chen D, He JZ (2021) Niche specialization of comammox Nitrospira clade A in terrestrial ecosystems. Soil Biol Biochem 156:108231
Li S, Chen DW, Wang C, Chen D, Wang Q (2020b) Reduced nitrification by biochar and/or nitrification inhibitor is closely linked with the abundance of comammox Nitrospira in a highly acidic sugarcane soil. Biol Fert Soils 56:1219–1228
Li Y, Chapman SJ, Nicol GW, Yao H (2018) Nitrification and nitrifiers in acidic soils. Soil Biol Biochem 116:290–301
Lin Y, Fan J, Hu HW, Duan C, Ye G, Wan S, He ZY, Zheng Y, He JZ (2022) Differentiation of individual clusters of comammox Nitrospira in an acidic Ultisol following long-term fertilization. Appl Soil Ecol 170:104267
Lin Y, Ye G, Ding W, Hu HW, Zheng Y, Fan J, Wan S, Duan C, He JZ (2020) Niche differentiation of comammox Nitrospira and canonical ammonia oxidizers in soil aggregate fractions following 27-year fertilizations. Agr Ecosyst Environ 304:107147
Liu HY, Ding Y, Zhang QC, Liu XM, Xu JM, Li Y, Di HJ (2019b) Heterotrophic nitrification and denitrification are the main sources of nitrous oxide in two paddy soils. Plant Soil 445:39–53
Liu HY, Hu HW, Huang X, Ge TD, Li YF, Zhu ZK, Liu XM, Tan WF, Jia ZJ, Di HJ, Xu JM, 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
Liu HY, Pan H, Hu HW, Jia ZJ, Zhang Q, Liu YM, Xu JM, Di HJ, Li Y (2019a) Autotrophic archaeal nitrification is preferentially stimulated by rice callus mineralization in a paddy soil. Plant Soil 445:55–69
Liu S, Wang H, Chen L, Wang J, Ni J (2020) Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers. ISME J 14:2488–2504
Liu TL, Wang ZH, Wang SL, Zhao YP, Wright AL, Jiang XJ (2019c) Responses of ammonia-oxidizers and comammox to different long-term fertilization regimes in a subtropical paddy soil. Eur J Soil Biol 93:103087
Lu L, Han W, Zhang J, Wu Y, Wang B, Lin X, Zhu J, Cai Z, Jia Z (2012) Nitrification of archaeal ammonia oxidizers in acid soils is supported by hydrolysis of urea. ISME J 6:1978–1984
Lu L, Jia Z (2013) Urease gene-containing archaea dominate autotrophic ammonia oxidation in two acid soils. Environ Microbiol 15:1795–1809
Lupo D, Li XD, Durand A, Tomizaki T, Cherif-Zahar B, Matassi G, Merrick M, Winkler FK (2007) The 1.3-A resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins. P Natl Acad Sci USA 104:19303–19308
Martens-HabbenaW BPM, Urakawa H, de la Torre JR, Stahl DA (2009) Ammonia oxidation kinetics determine niche separation of nitrifying archaea and bacteria. Nature 461:976–979
Meng C, Xing Y, Ding Y, Zhang Q, Di H, Tang C, Xu J, Li Y (2023) Soil acidification induced variation of nitrifiers and denitrifiers modulates N2O emissions in paddy fields. Sci Total Environ 882:163623
Nguyen LTT, Broughton K, Osanai Y, Anderson IC, Bange MP, Tissue DT, Singh BK (2019) Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop. Sci Total Environ 675:81–89
Norton JM, Stark JM (2011) Regulation and measurement of nitrification in terrestrial systems. Method Enzymol 486:343–368
Offre P, Kerou M, Spang A, Schleper C (2014) Variability of the transporter gene complement in ammonia-oxidizing archaea. Trends Microbiol 22:665–675
Offre P, Prosser JI, Nicol GW (2009) Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene. FEMS Microbiol Ecol 70:99–108
Olsen SR, Cole CV, Watanbe FS, Dean LA (1954) Estimation of available phosphorus in soils by extraction with sodium bicarbonate. Circular of U.S. Department of Agriculture
Palomo A, Pedersen AG, Fowler SJ, Dechesne A, Sicheritz-Pontén T, Smets BF (2018) Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira. ISME J 12:1779–1793
Pan H, Xie KX, Zhang QC, Jia ZJ, Xu JM, Di HJ, Li Y (2017) Archaea and bacteria respectively dominate nitrification in lightly and heavily grazed soil in a grassland system. Biol Fert Soils 54:41–54
Poghosyan L, Koch H, Lavy A, Frank J, van Kessel M, Jetten MSM, Banfield JF, Lücker S (2019) Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface. Environ Microbiol 21:3627–3637
Prosser JI, Hink L, Gubry-Rangin C, Nicol GW (2020) Nitrous oxide production by ammonia oxidizers: physiological diversity, niche differentiation and potential mitigation strategies. Glob Chang Biol 26:103–118
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner F (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596
Sakoula D, Koch H, Frank J, Jetten M, van Kessel MA, Lücker S (2021) Enrichment and physiological characterization of a novel comammox nitrospira indicates ammonium inhibition of complete nitrification. ISME J 15:1010–1024
Shen JP, Zhang LM, Di HJ, He JZ (2012) A review of ammonia-oxidizing bacteria and archaea in Chinese soils. Front Microbiol 3:296
Sterngren AE, Hallin S, Bengtson P (2015) Archaeal ammonia oxidizers dominate in numbers, but bacteria drive gross nitrification in N-amended grassland soil. Front Microbiol 6:1350
Subbarao GV, Ito O, Sahrawat KL, Berry WL, Nakahara K, Ishikawa T, Watanabe T, Suenaga K, Rondon M, Rao IM (2006) Scope and strategies for regulation of nitrification in agricultural systems-challenges and opportunities. Crit Rev Plant Sci 25:303–335
Takahashi Y, Fujitani H, Hirono Y, Tago K, Wang Y, Hayatsu M, Tsuneda S (2020) Enrichment of comammox and nitrite-oxidizing Nitrospira from acidic soils. Front Microbiol 11:1737
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599
Tan C, Yin C, Li W, Fan X, Jiang Y, Liang Y (2022) Comammox Nitrospira play a minor role in N2O emissions from an alkaline arable soil. Soil Biol Biochem 171:108720
van Kessel MV, 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
Wang B, Zhao J, Guo Z, Ma J, Xu H, Jia Z (2015) Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils. ISME J 9:1062–1075
Wang B, Zheng Y, Huang R, Zhou X, Wang D, He Y, Jia Z (2014) Active ammonia oxidizers in an acidic soil are phylogenetically closely related to neutrophilic archaeon. Appl Environ Microb 80:1684–1691
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
Wang J, Huang Q, Li Y, Tu X, Chen Z, Elrys AS, Cheng Y, Ma L (2023) A shift from nitrification to denitrification-dominated N2O emission in an acidic soil following organic amendment. Biol Fert Soils 59:117–122
Wang Q, Zhang LM, Shen JP, Du S, Han LL, He JZ (2016) Nitrogen fertiliser-induced changes in N2O emissions are attributed more to ammonia-oxidising bacteria rather than archaea as revealed using 1-octyne and acetylene inhibitors in two arable soils. Biol Fert Soils 52:1163–1171
Wang Z, Cao Y, Wright AL, Shi X, Jiang X (2019b) Different ammonia oxidizers are responsible for nitrification in two neutral paddy soils. Soil Till Res 195:104433
Wang Z, Cao Y, Zhu-Barker X, Nicol G, Wright AL, Jia Z, Jiang X (2019a) Comammox Nitrospira clade B contributes to nitrification in soil. Soil Biol Biochem 135:392–395
Weidinger K, Neuhäuser B, Gilch S, Ludewig U, Meyer O, Schmidt I (2007) Functional and physiological evidence for a rhesus-type ammonia transporter in Nitrosomonas europaea. FEMS Microbiol Ecol 273:260–267
Xia F, Wang JG, Zhu T, Zou B, Rhee SK, Quan ZX (2018) Ubiquity and diversity of complete ammonia oxidizers (comammox). Appl Environ Microb 84:e01390–e01318
Xia W, Zhang C, Zeng X, Feng Y, Weng J, Lin X, Zhu J, Xiong Z, Xu J, Cai Z (2011) Autotrophic growth of nitrifying community in an agricultural soil. ISME J 5:1226–1236
Xu S, Wang B, Li Y, Jiang D, Zhou Y, Ding A, Zong Y, Ling X, Zhang S, Lu H (2020) Ubiquity, diversity, and activity of comammox Nitrospira in agricultural soils. Sci Total Environ 706:135684
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
Zhang LM, Offre RR, He RZ, Verhamme RT, Nicol RW, Prosser RI (2010) Autotrophic ammonia oxidation by soil thaumarchaea. P Natl Acad Sci USA 107:17240–17245
Zhang Q, Li Y, He Y, Liu HY, Dumont MG, Brookes PC, Xu JM (2019) 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
Zhao J, Meng Y, Drewer J, Skiba UM, Gubry-Rangin C (2020) Differential ecosystem function stability of ammonia-oxidizing archaea and bacteria following short-term environmental perturbation. mSystems 5:e00309–e00320
Funding
This work was supported by the National Key Research and Development Program of China (2021YFD1901205), National Natural Science Foundation of China (42007033 and 32061123007) and Natural Science Foundation of Hubei province (No. 2020CFA013).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Liu, H., Zhang, S., Xu, W. et al. The active role of comammox Nitrospira in nitrification in acidic orchard soils revealed by DNA-SIP. Biol Fertil Soils 59, 819–832 (2023). https://doi.org/10.1007/s00374-023-01749-x
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00374-023-01749-x