Microbial Ecology

, Volume 78, Issue 3, pp 555–564 | Cite as

Ecological Success of the Nitrosopumilus and Nitrosospira Clusters in the Intertidal Zone

  • Jiajie Hu
  • Shuai Liu
  • Weiling Yang
  • Zhanfei He
  • Jiaqi Wang
  • Huan Liu
  • Ping Zheng
  • Chuanwu Xi
  • Fang MaEmail author
  • Baolan HuEmail author
Microbiology of Aquatic Systems


The intertidal zone is an important buffer and a nitrogen sink between land and sea. Ammonia oxidation is the rate-limiting step of nitrification, conducted by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, it remains a debatable issue regarding dominant ammonia oxidizers in this region, and environmental factors driving their spatiotemporal niche differentiation have yet to be identified. In this study, intertidal and subtidal zones of Zhoushan Islands were selected for seasonal sampling. Ammonia-oxidizing activity, quantitative PCR, and 454 high-throughput sequencing were performed to study the nitrification potential, abundance, and community structure of ammonia-oxidizing archaea and bacteria. AOA and AOB amoA abundance (107–108amoA gene copies/g dry weight sediment) varied spatiotemporally independently of environmental factors. AOA surpassed AOB in most samples, driven by sediment temperature, moisture, and total nitrogen. The diversity of both AOA and AOB differed spatiotemporally. The Nitrosopumilus and Nitrosospira clusters accounted for an absolutely dominant percentage of AOA (> 99%) and AOB (> 99%) respectively, indicating a negligible contribution of other clusters to ammonia oxidation. However, there was no significant correlation between nitrification potential and the abundance of AOA or AOB. Overall, the present study showed that AOA dominated over AOB spatiotemporally in the intertidal zone of Zhoushan Islands due to fluctuations in environmental factors, and the Nitrosopumilus and Nitrosospira clusters ecologically succeeded in the intertidal zone of Zhoushan Islands.


Ammonia-oxidizing archaea Ammonia-oxidizing bacteria Intertidal zone Dominance Nitrosopumilus Nitrosospira 


Funding Information

The authors wish to thank the National Natural Science Foundation of China (No. 41773074, No. 31828001, No. 41641031) and the Open Project of State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (No. QAK201714).

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

248_2019_1359_MOESM1_ESM.docx (2.5 mb)
ESM 1 (DOCX 2543 kb)


  1. 1.
    Kuypers MMM (2015) Microbiology: a division of labour combined. Nature 528:487–488CrossRefGoogle Scholar
  2. 2.
    Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543–546CrossRefGoogle Scholar
  3. 3.
    Galloway JN, Dentener FJ, Capone DG, Boyer EW, Howarth RW, Seitzinger SP, Asner GP, Cleveland CC, Green PA, Holland EA, Karl DM, Michaels AF, Porter JH, Townsend AR, Vöosmarty CJ (2004) Nitrogen cycles: past, present, and future. Biogeochemistry 70:153–226CrossRefGoogle Scholar
  4. 4.
    Wilms R, Sass H, Kopke B, Koster H, Cypionka H, Engelen B (2006) Specific bacterial, archaeal and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters. Appl Environ Microbiol 72:2756–2764CrossRefGoogle Scholar
  5. 5.
    Gruber N, Galloway JN (2008) An Earth-system perspective of the global nitrogen cycle. Nature 451:293–296CrossRefGoogle Scholar
  6. 6.
    Smith JM, Mosier AC, Francis CA (2015) Spatiotemporal relationships between the abundance, distribution, and potential activities of ammonia-oxidizing and denitrifying microorganisms in intertidal sediments. Microb Ecol 69(1):13–24CrossRefGoogle Scholar
  7. 7.
    Holguin G, Vazquez P, Bashan Y (2001) The role of sediment microorganisms in the productivity, conservation, and rehabilitation of mangrove ecosystems: an overview. Biol Fertil Soils 33:265–278CrossRefGoogle Scholar
  8. 8.
    Lagostina L, Goldhammer T, Røy H, Evans TW, Lever MA, Jørgensen BB, Petersen DG, Schramm A, Schreiber L (2015) Ammonia-oxidizing bacteria of the Nitrosospira cluster 1 dominate over ammonia-oxidizing archaea in oligotrophic surface sediments near the South Atlantic Gyre. Environ Microbiol Rep 7(3):404–413CrossRefGoogle Scholar
  9. 9.
    Zheng YL, Hou LJ, Liu M, Lu M, Zhao H, Yin GY, Zhou JL (2013) Diversity, abundance, and activity of ammonia-oxidizing bacteria and archaea in Chongming eastern intertidal sediments. Appl Microbiol Biotechnol 97(18):8351–8363CrossRefGoogle Scholar
  10. 10.
    Cao HL, Hong YG, Li M, Gu JD (2011) Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River estuary to the South China Sea. Antonie Van Leeuwenhoek 100(4):545–556CrossRefGoogle Scholar
  11. 11.
    Wang HT, Su JQ, Zheng TL, Yang XR (2015) Insights into the role of plant on ammonia-oxidizing bacteria and archaea in the mangrove ecosystem. J Soils Sediments 15(5):1212–1223CrossRefGoogle Scholar
  12. 12.
    Alves RJE, Minh BQ, Urich T, von Haeseler A, Schleper C (2018) Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nat Commun 9(1):1517CrossRefGoogle Scholar
  13. 13.
    Sahan E, Muyzer G (2008) Diversity and spatio-temporal distribution of ammonia-oxidizing archaea and Bacteria in sediments of the Westerschelde estuary. FEMS Microbiol Ecol 64(2):175–186CrossRefGoogle Scholar
  14. 14.
    Beman JM, Francis CA (2006) Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico. Appl Environ Microbiol 72:7767–7777CrossRefGoogle Scholar
  15. 15.
    Hu ZY, Meng H, Shi JH, Bu NS, Fang CM, Quan ZX (2014) Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem. Front Microbiol 5(371):371Google Scholar
  16. 16.
    Marton JM, Roberts BJ, Bernhard AE, Giblin AE (2015) Spatial and temporal variability of nitrification potential and ammonia-oxidizer abundances in Louisiana salt marshes. Estuar Coasts 38(6):1824–1837CrossRefGoogle Scholar
  17. 17.
    Wankel SD, Mosier AC, Hansel CM, Paytan A, Francis CA (2011) Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary, California. Appl Environ Microbiol 77:269–280CrossRefGoogle Scholar
  18. 18.
    Wang YF, Feng YY, Ma XJ, Gu JD (2013) Seasonal dynamics of ammonia/ammonium-oxidizing prokaryotes in oxic and anoxic wetland sediments of subtropical coastal mangrove. Appl Microbiol Biotechnol 97(17):7919–7934CrossRefGoogle Scholar
  19. 19.
    Zheng YL, Hou LJ, Newell S, Liu M, Zhou JL, Zhao H, You LL, Cheng XL (2014) Community dynamics and activity of ammonia-oxidizing prokaryotes in intertidal sediments of the Yangtze estuary. Appl Environ Microbiol 80(1):408–419CrossRefGoogle Scholar
  20. 20.
    He H, Yu Z, Mi TZ, Lu XL, Yu ZG (2015) Seasonal and spatial distribution of ammonia-oxidizing microorganism communities in surface sediments from the East China Sea. Acta Oceanol Sin 34(8):83–92CrossRefGoogle Scholar
  21. 21.
    Zhang L, Duff A, Smith CJ (2018) Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal bay ecosystems. Environ MicrobiolGoogle Scholar
  22. 22.
    Caffrey JM, Bano N, Kalanetra K, Hollibaugh JT (2007) Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia. ISME J 1:660–662CrossRefGoogle Scholar
  23. 23.
    Tait K, Kitidis V, Ward BB, Cummings DG, Jones MR, Somerfield PJ, Widdicombe S (2014) Spatio-temporal variability in ammonia oxidation and ammonia oxidising bacteria and archaea in coastal sediments of the Western English Channel. Mar Ecol Prog 511(511):41–58CrossRefGoogle Scholar
  24. 24.
    Bernhard AE, Bollmann A (2010) Estuarine nitrifiers: estuarine nitrifiers: new players, patterns and processes. Estuar Coast Shelf Sci 88:1–11CrossRefGoogle Scholar
  25. 25.
    Hu BL, Liu S, Shen LD, Zheng P, Xu XY, Lou LP (2012) Effect of different ammonia concentrations on community succession of ammonia-oxidizing microorganisms in a simulated paddy soil column. PLoS One 7(8):e44122CrossRefGoogle Scholar
  26. 26.
    Hu BL, Liu S, Wang W, Shen LD, Lou LP, Liu WP, Tian GM, Xu XY, Zheng P (2014) pH-dominated niche segregation of ammonia-oxidising microorganisms in Chinese agricultural soils. FEMS Microbiol Ecol 90(1):290–299CrossRefGoogle Scholar
  27. 27.
    He ZF, Geng S, Cai CY, Liu S, Liu Y, Pan YW, Lou LP, Zheng P, Xu XH, Hu BL (2015) Anaerobic oxidation of methane coupled to nitrite reduction by halophilic marine NC10 bacteria. Appl Environ Microbiol 81(16):5538–5545CrossRefGoogle Scholar
  28. 28.
    Hu BL, Shen LD, Du P, Zheng P, Xu XY, Zeng JN (2012) The influence of intense chemical pollution on the community composition, diversity and abundance of anammox bacteria in the Jiaojiang estuary (China). PLoS One 7:3Google Scholar
  29. 29.
    Liu S, Hu BL, He ZF, Zhang B, Tian GM, Zheng P, Fang F (2015) Ammonia-oxidizing archaea have better adaptability in oxygenated/hypoxic alternant conditions compared to ammonia-oxidizing bacteria. Appl Microbiol Biotechnol 99:8587–8596CrossRefGoogle Scholar
  30. 30.
    He ZF, Cai CY, Shen LD, Lou LP, Zheng P, Xu XH, Hu BL (2015) Effect of inoculum sources on the enrichment of nitrite-dependent anaerobic methane-oxidizing bacteria. Appl Microbiol Biotechnol 99(2):939–946CrossRefGoogle Scholar
  31. 31.
    Shen LD, Huang Q, He ZF, Lian X, Liu S, He YF, Lou LP, Xu XY, Zheng P, Hu BL (2015) Vertical distribution of nitrite-dependent anaerobic methane-oxidising bacteria in natural freshwater wetland soils. Appl Microbiol Biotechnol 99(1):349–357CrossRefGoogle Scholar
  32. 32.
    Zhong WH, Bian BY, Gao N, Min J, Shi WM, Lin XG, Shen WS (2015) Nitrogen fertilization induced changes in ammonia oxidation are attributable mostly to bacteria rather than archaea in greenhouse-based high N input vegetable soil. Soil Biol Biochem 93:150–159CrossRefGoogle Scholar
  33. 33.
    Liu S, Shen LD, Lou LP, Tian GM, Zheng P, Hu BL (2013) Spatial distribution and factors shaping the niche segregation of ammonia-oxidizing microorganisms in the Qiantang River, China. Appl Environ Microbiol 79:4065–4071CrossRefGoogle Scholar
  34. 34.
    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 63:4704–4712Google Scholar
  35. 35.
    Pester M, Rattei T, Flechl S, Gröngröft A, Richter A, Overmann J, Reinhold-Hurek B, Loy A, Wagner M (2012) amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ Microbiol 14(2):525–539CrossRefGoogle Scholar
  36. 36.
    Coci M, Nicol GW, Pilloni GN, Schmid M, Kamst-van Agterveld MP, Bodelier PLE, Laanbroek HJ (2010) Quantitative assessment of ammonia-oxidizing bacterial communities in the epiphyton of submerged macrophytes in shallow lakes. Appl Environ Microbiol 76(6):1813–1821CrossRefGoogle Scholar
  37. 37.
    Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537–7541CrossRefGoogle Scholar
  38. 38.
    Liu S, Ren HX, Shen LD, Lou LP, Tian GM, Zheng P, Hu BL (2015) pH levels drive bacterial community structure in sediments of the Qiantang River as determined by 454 pyrosequencing. Front Microbiol 6:285Google Scholar
  39. 39.
    Ye L, Zhang T (2011) Ammonia-oxidizing bacteria dominates over ammonia-oxidizing archaea in a saline nitrification reactor under low DO and high nitrogen loading. Biotechnol Bioeng 108(11):2544–2552CrossRefGoogle Scholar
  40. 40.
    Shen LD, Zhu Q, Liu S, Du P, Zeng JN, Cheng DQ, Xu XY, Zheng P, Hu BL (2014) Molecular evidence for nitrite-dependent anaerobic methane-oxidising bacteria in the Jiaojiang estuary of the East Sea (China). Appl Microbiol Biotechnol 98(11):5029–5038CrossRefGoogle Scholar
  41. 41.
    Moin NS, Nelson KA, Bush A, Bernhard AE (2009) Distribution and diversity of archaeal and bacterial ammonia oxidizers in salt marsh sediments. Appl Environ Microbiol 75(23):7461–7468CrossRefGoogle Scholar
  42. 42.
    He H, Zhen Y, Mi TZ, Yu ZG (2016) Community composition and abundance of ammonia-oxidizing archaea in sediments from the Changjiang estuary and its adjacent area in the East China Sea. Geomicrobiol J 33(5):416–425CrossRefGoogle Scholar
  43. 43.
    de la Torre JR, Walker CB, Ingalls AE, Könneke M, Stahl DA (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 10(3):810–818CrossRefGoogle Scholar
  44. 44.
    Paine RT (1974) Intertidal community structure: experimental studies on relationship between a dominant competitor and its principal predator. Oecologia 15(2):93–120CrossRefGoogle Scholar
  45. 45.
    Hatzenpichler R (2012) Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl Environ Microbiol 78(21):7501–7510CrossRefGoogle Scholar
  46. 46.
    Erguder TH, Boon N, Wittebolle L, Marzorati M, Verstraete W (2009) Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiol Rev 33(5):855–869CrossRefGoogle Scholar
  47. 47.
    He ZF, Wang JQ, Hu JJ, Yu HQ, Jetten MSM, Liu H, Cai CY, Liu Y, Ren HX, Zhang X, Hua ML, Xu XH, Zheng P, Hu BL (2019) Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers. Environ Pollut 244:228–237. CrossRefGoogle Scholar
  48. 48.
    Wang JQ, Cai CY, Li YF, Hua ML, Wang JR, Yang HR, Zheng P, Hu BL (2019) Denitrifying anaerobic methane oxidation: a previously overlooked methane sink in intertidal zone. Environ Sci Technol 53:203–212. CrossRefGoogle Scholar
  49. 49.
    Jung MY, Kim JG, Sinninghe Damsté JS, Rijpstra WIC, Madsen EL, Kim SJ, Hong H, Si OJ, Kerou M, Schleper C, Rhee SK (2016) A hydrophobic ammonia-oxidizing archaeon of the Nitrosocosmicus clade isolated from coal tar-contaminated sediment. Environ Microbiol Rep 8(6):983–992CrossRefGoogle Scholar
  50. 50.
    Fan XY, Gao JF, Pan KL, Li DC, Dai HH (2017) Temporal dynamics of bacterial communities and predicted nitrogen metabolism genes in a full-scale wastewater treatment plant. RSC Adv 7(89):56317–56327CrossRefGoogle Scholar
  51. 51.
    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):269–272CrossRefGoogle Scholar
  52. 52.
    Koops HP, Purkhold U, Pommerening-Röser A, Timmermann G, Wagner M (2006) The lithoautotrophic ammonia-oxidizing bacteria. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes. Proteobacteria: alpha and beta subclasses, vol 5. Springer, New York, pp 778–811CrossRefGoogle Scholar
  53. 53.
    Laanbroek HJ, Speksnijder AG (2008) Niche separation of ammonia-oxidizing bacteria across a tidal freshwater marsh. Environ Microbiol 10:3017–3025CrossRefGoogle Scholar
  54. 54.
    Hunik JH, Meijer HJG, Tramper J (1992) Kinetics of Nitrosomonas europaea at extreme substrate, product and salt concentrations. Appl Microbiol Biotechnol 37(6):802–807Google Scholar
  55. 55.
    Schramm A, de Beer D, van den Heuvel JC, Ottengraf S, Amann R (1999) Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor quantification by in situ hybridization and the use of microelectrodes. Appl Environ Microbiol 65:3690–3696Google Scholar
  56. 56.
    Yu SL, Yao P, Liu JW, Zhao B, Zhang GL, Zhao MX, Yu ZG, Zhang XH (2016) Diversity, abundance, and niche differentiation of ammonia-oxidizing prokaryotes in mud deposits of the eastern China marginal seas. Front Microbiol 7(137):137Google Scholar
  57. 57.
    Hu BL, Shen LD, Lian X, Zhu Q, Liu S, Huang Q, He ZF, Geng S, Cheng DQ, Lou LP, Xu XY, Zheng P, He YF (2014) Evidence for nitrite-dependent anaerobic methane oxidation as a previously overlooked microbial methane sink in wetlands. Proc Natl Acad Sci U S A 111(12):4495–4500CrossRefGoogle Scholar
  58. 58.
    Yu CD, Hou LJ, Zheng YL, Liu M, Yin GY, Gao J, Liu C, Chang YK, Han P (2018) Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira, in natural environments. Appl Microbiol Biotechnol:1–15Google Scholar

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Authors and Affiliations

  1. 1.Department of Environmental EngineeringZhejiang UniversityHangzhouChina
  2. 2.Department of Environmental Health Sciences, School of Public HealthUniversity of MichiganAnn ArborUSA
  3. 3.State Key Laboratory of Urban Water Resource and EnvironmentHarbin Institute of TechnologyHarbinChina
  4. 4.Zhejiang Province Key Laboratory for Water Pollution Control and Environmental SafetyHangzhouChina

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