Applied Microbiology and Biotechnology

, Volume 102, Issue 12, pp 5309–5322 | Cite as

Effects of reforestation on ammonia-oxidizing microbial community composition and abundance in subtropical acidic forest soils

  • Ruo-Nan Wu
  • Han Meng
  • Yong-Feng Wang
  • Ji-Dong Gu
Environmental biotechnology


Forest ecosystems have great ecological values in mitigation of climate change and protection of biodiversity of flora and fauna; re-forestry is commonly used to enhance the sequestration of atmospheric CO2 into forest storage biomass. Therefore, seasonal and spatial dynamics of the major microbial players in nitrification, ammonia-oxidizing archaea (AOA) and bacteria (AOB), in acidic soils of young and matured revegetated forests were investigated to elucidate the changes of microbial communities during forest restoration, and compared to delineate the patterns of community shifts under the influences of environmental factors. AOA were more abundant than AOB in both young and matured revegetated forest soils in both summer and winter seasons. In summer, however, the abundance of amoA-AOA decreased remarkably (p < 0.01), ranging from 1.90 (± 0.07) × 108 copies per gram dry soil in matured forest to 5.04 (± 0.43) × 108 copies per gram dry soil in young forest, and amoA-AOB was below detection limits to obtain any meaningful values. Moreover, exchangeable Al3+ and organic matter were found to regulate the physiologically functional nitrifiers, especially AOA abundance in acidic forest soils. AOB community in winter showed stronger correlation with the restoration status of revegetated forests and AOA community dominated by Nitrosotalea devanaterra, in contrast, was more sensitive to the seasonal and spatial variations of environmental factors. These results enrich the current knowledge of nitrification during re-forestry and provide valuable information to developmental status of revegetated forests for management through microbial analysis.


Ammonia-oxidizing archaea (AOA) Ammonia-oxidizing bacteria (AOB) Ammonia monooxygenase subunit A (amoA) gene Forest restoration Organic matter Aluminum 



This study was funded by National Natural Science Foundation of China (grant no. 31470562 to YFW) and by a PhD Fellowship of The University of Hong Kong (RW).

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.


  1. Amazonas N, Martinelli L, de Cássia Piccolo M, Rodrigues R (2011) Nitrogen dynamics during ecosystem development in tropical forest restoration. Forest Ecol Manag 262(8):1551–1557CrossRefGoogle Scholar
  2. Baker-Austin C, Dopson M (2007) Life in acid: pH homeostasis in acidophiles. Trends Microbiol 15(4):165–171. CrossRefPubMedGoogle Scholar
  3. Booth M, Stark J, Rastetter E (2005) Controls on nitrogen cycling in terrestrial ecosystems: a synthetic analysis of literature data. Ecol Monogr 75(2):139–157. CrossRefGoogle Scholar
  4. Carnol M, Kowalchuk G, De Boer W (2002) Nitrosomonas europaea-like bacteria detected as the dominant β-subclass Proteobacteria ammonia oxidisers in reference and limed acid forest soils. Soil Biol Biochem 34(7):1047–1050CrossRefGoogle Scholar
  5. Chen Y, Yu S, Liu S, Wang X, Zhang Y, Liu T, Zhou L, Zhang W, Fu S (2017) Reforestation makes a minor contribution to soil carbon accumulation in the short term: evidence from four subtropical plantations. Forest Ecol Manag 384:400–405CrossRefGoogle Scholar
  6. De Camargo P, Trumbore S, Martinelli L, Davidson E, Nepstad D, Victoria R (1999) Soil carbon dynamics in regrowing forest of eastern Amazonia. Glob Chang Biol 5(6):693–702CrossRefGoogle Scholar
  7. Fish J, Chai B, Wang Q, Sun Y, Brown C, Tiedje J, Cole J (2013) FunGene: the functional gene pipeline and repository. Front Microbiol 4:291. CrossRefPubMedPubMedCentralGoogle Scholar
  8. Flannigan M, Logan K, Amiro B, Skinner W, Stocks B (2005) Future area burned in Canada. Clim Chang 72:1), 1–1),16CrossRefGoogle Scholar
  9. Francis C, Roberts K, Beman J, Santoro A, Oakley B (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. P Natl Acad Sci USA 102(41):14683–14688. CrossRefGoogle Scholar
  10. Gan X, Zhang F, Gu J, Guo Y, Li Z, Zhang W, Xu X, Zhou Y, Wen X, Xie G, Wang Y (2016) Differential distribution patterns of ammonia-oxidizing archaea and bacteria in acidic soils of Nanling National Nature Reserve forests in subtropical China. Antonie Van Leeuwenhoek 109(2):237–251CrossRefPubMedGoogle Scholar
  11. Gillett N, Weaver A, Zwiers F, Flannigan M (2004) Detecting the effect of climate change on Canadian forest fires. Geophys Res Lett 31(18):L18211. CrossRefGoogle Scholar
  12. Gubry-Rangin C, Nicol G, Prosser J (2010) Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microbiol Ecol 74(3):566–574CrossRefPubMedGoogle Scholar
  13. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenetics: assessing the performance of PhyML 3.0. Syst Biol 59(3):307–321CrossRefPubMedGoogle Scholar
  14. Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe Y, Sugahara J, Preston C, de la Torre J, Richardson PM, DeLong EF (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. P Natl Acad Sci USA 103(48):18296–18301. CrossRefGoogle Scholar
  15. Hankinson T, Schmidt E (1988) An acidophilic and a neutrophilic nitrobacter strain isolated from the numerically predominant nitrite-oxidizing population of an acid forest soil. Appl Environ Microbiol 54(6):1536–1540PubMedPubMedCentralGoogle Scholar
  16. He J, Shen J, Zhang L, Zhu Y, Zheng Y, Xu M, Di H (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9(9):2364–2374CrossRefPubMedGoogle Scholar
  17. Horz H, Barbrook A, Field C, Bohannan B (2004) Ammonia-oxidizing bacteria respond to multifactorial global change. P Natl Acad Sci USA 101(42):15136–15141. CrossRefGoogle Scholar
  18. Jiang Q, Bakken L (1999) Comparison of Nitrosospira strains isolated from terrestrial environments. FEMS Microbiol Ecol 30(2):171–186. CrossRefPubMedGoogle Scholar
  19. Kochian L, Piñeros M, Liu J, Magalhaes J (2015) Plant adaptation to acid soils: the molecular basis for crop aluminum resistance. Annu Rev Plant Biol 66:571–598CrossRefPubMedGoogle Scholar
  20. Konneke M, Bernhard A, de la Torre J, Walker C, Waterbury J, Stahl D (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437(7058):543–546. CrossRefPubMedGoogle Scholar
  21. Laurance W (1999) Reflections on the tropical deforestation crisis. Biol Conserv 91(2):109–117CrossRefGoogle Scholar
  22. Lehtovirta-Morley L, Ge C, Ross J, Yao H, Nicol G, Prosser J (2014) Characterisation of terrestrial acidophilic archaeal ammonia oxidisers and their inhibition and stimulation by organic compounds. FEMS Microbiol Ecol 89(3):542–552. CrossRefPubMedPubMedCentralGoogle Scholar
  23. Lehtovirta-Morley L, Stoecker K, Vilcinskas A, Prosser J, Nicol G (2011) Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. P Natl Acad Sci USA 108(38):15892–15897. CrossRefGoogle Scholar
  24. Liu Y, Chen J, Liu Q, Wu Y (2007) Nitrification and denitrification in subalpine coniferous forests of different restoration stages in western Sichuan, China. Frontiers of Forestry in China 2(3):260–265CrossRefGoogle Scholar
  25. Lu R (2000) Agricultural chemical analysis methods of soil. China Agricultural Science and Technology Press, Beijing, China 107–108Google Scholar
  26. Matson P, Lohse K, Hall S (2002) The globalization of nitrogen deposition: consequences for terrestrial ecosystems. Ambio 31(2):113–119CrossRefPubMedGoogle Scholar
  27. Meng H, Wang Y, Chan H, Wu R, Gu J (2016) Co-occurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in subtropical acidic forest soils. Appl Microbiol Biotechnol 100(17):7727–7739CrossRefPubMedGoogle Scholar
  28. Mo Q, Li Z, Zhu W, Zou B, Li Y, Yu S, Ding Y, Chen Y, Li X, Wang F (2016) Reforestation in southern China: revisiting soil N mineralization and nitrification after 8 years restoration. Sci Rep 6:19770. CrossRefPubMedPubMedCentralGoogle Scholar
  29. Nelson D, Sommers L (1996) Total carbon, organic carbon, and organic matter. Methods of soil analysis: part 3: chemical methods. Soil Science Society of America, Madison, Wisconsin, pp 961–1010Google Scholar
  30. Nicol G, Leininger S, Schleper C, Prosser J (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol 10(11):2966–2978CrossRefPubMedGoogle Scholar
  31. Norton J, Alzerreca J, Suwa Y, Klotz M (2002) Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch Microbiol 177(2):139–149. CrossRefPubMedGoogle Scholar
  32. Parolari A, Mobley M, Bacon A, Katul G, Porporato A (2017) Boom and bust carbon-nitrogen dynamics during reforestation. Ecol Model 360:108–119. CrossRefGoogle Scholar
  33. Paul M, Catterall C, Pollard P, Kanowski J (2010) Recovery of soil properties and functions in different rainforest restoration pathways. Forest Ecol Manag 259(10):2083–2092CrossRefGoogle Scholar
  34. Pedersen H, Dunkin K, Firestone M (1999) The relative importance of autotrophic and heterotrophic nitrification in a conifer forest soil as measured by 15N tracer and pool dilution techniques. Biogeochem 44(2):135–150Google Scholar
  35. Pennington P, Ellis R (1993) Autotrophic and heterotrophic nitrification in acidic forest and native grassland soils. Soil Biol Biochem 25(10):1399–1408. CrossRefGoogle Scholar
  36. Prosser J, Nicol G (2012) Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol 20(11):523–531. CrossRefPubMedGoogle Scholar
  37. Schmidt C, Hultman K, Robinson D, Killham K, Prosser J (2007) PCR profiling of ammonia-oxidizer communities in acidic soils subjected to nitrogen and sulphur deposition. FEMS Microbiol Ecol 61(2):305–316CrossRefPubMedGoogle Scholar
  38. Rotthauwe J-H, Witzel K-P, Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microb 63(12):4704–4712Google Scholar
  39. Stopnisek N, Gubry-Rangin C, Hofferle S, Nicol G, Mandic-Mulec I, Prosser J (2010) Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment. Appl Environ Microbiol 76(22):7626–7634. CrossRefPubMedPubMedCentralGoogle Scholar
  40. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729. CrossRefPubMedPubMedCentralGoogle Scholar
  41. Thompson J, Higgins D, Gibson T (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680CrossRefPubMedPubMedCentralGoogle Scholar
  42. Tian H, Chen L, Xing F (2013) Species diversity and conservation of orchids in Nanling National Nature Reserve, Guangdong. Biodivers Sci 21:224–231CrossRefGoogle Scholar
  43. van Hoek A, van Alen T, Sprakel V, Hackstein J, Vogels G (1998) Evolution of anaerobic ciliates from the gastrointestinal tract: phylogenetic analysis of the ribosomal repeat from Nyctotherus ovalis and its relatives. Mol Biol Evol 15(9):1195–1206CrossRefPubMedGoogle Scholar
  44. Venter J, Remington K, Heidelberg J, Halpern A, Rusch D, Eisen J, Wu D, Paulsen I, Nelson K, Nelson W, Fouts D (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304(5667):66–74. CrossRefPubMedGoogle Scholar
  45. Wu R, Meng H, Wang Y, Lan W, Gu J-D (2017) A more comprehensive community of ammonia-oxidizing archaea (AOA) revealed by genomic DNA and RNA analyses of amoA gene in subtropical acidic forest soils. Microb Ecol 74(4):910–922. CrossRefPubMedGoogle Scholar
  46. Yao H, Gao Y, Nicol G, Campbell C, Prosser J, Zhang L, Han W, Singh B (2011) Links between ammonia oxidizer community structure, abundance, and nitrification potential in acidic soils. Appl Environ Microb 77(13):4618–4625CrossRefGoogle Scholar
  47. Zhang L, Li Z, Su Z, Chen B (2007) Quantitative classification and ordination of forest communities in Nanling National Nature Reserve. J South China Agr Univ 3:017Google Scholar
  48. Zhang L, Hu H, Shen J, He J (2012) Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils. ISME J 6(5):1032–1045. CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of ScienceThe University of Hong KongHong Kong SARPeople’s Republic of China
  2. 2.Guangdong Provincial Key Laboratory of Silviculture, Protection and UtilizationGuangdong Academy of ForestryGuangzhouPeople’s Republic of China
  3. 3.Laboratory of Microbial Ecology and ToxicologyGuangdong Academy of ForestryGuangzhouPeople’s Republic of China
  4. 4.State Key Laboratory in Marine PollutionCity University of Hong KongKowloonPeople’s Republic of China

Personalised recommendations