Microbial Ecology

, Volume 65, Issue 2, pp 405–414 | Cite as

Organic Layer Serves as a Hotspot of Microbial Activity and Abundance in Arctic Tundra Soils

  • Seung-Hoon Lee
  • Inyoung Jang
  • Namyi Chae
  • Taejin Choi
  • Hojeong Kang
Soil Microbiology


Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.


Total Organic Carbon Internal Transcribe Spacer Mineral Soil Terminal Restriction Fragment Length Polymorphism Archaeal Community 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This study was supported by NRF (2010-0028708; 2011-0030838; C1ABA001-2011-0021063).


  1. 1.
    Allison SD, McGuire KL, Treseder KK (2010) Resistance of microbial and soil properties to warming treatment seven years after boreal fire. Soil Biol Biochem 42:1872–1878CrossRefGoogle Scholar
  2. 2.
    Andersson M, Kjller A, Struwe S (2004) Microbial enzyme activities in leaf litter, humus and mineral soil layers of European forests. Soil Biol Biochem 36:1527–1537CrossRefGoogle Scholar
  3. 3.
    Ayton J, Aislabie J, Barker GM, Turner S (2010) Crenarchaeota affiliated with group 1.1b are prevalent in coastal mineral soils of the Ross Sea region of Antarctica. Environ Microbiol 12:689–703PubMedCrossRefGoogle Scholar
  4. 4.
    Campbell BJ, Polson SW, Hanson TE, Mack MC, Schuur EAG (2010) The effect of nutrient deposition on bacterial communities in Arctic tundra soil. Environ Microbiol 12:1842–1854PubMedCrossRefGoogle Scholar
  5. 5.
    Chu H, Fierer N, Lauber CL, Caporaso JG, Knight R, Grogan P (2010) Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ Microbiol 12:2998–3006PubMedCrossRefGoogle Scholar
  6. 6.
    DeBruyn JM, Lauren T, Nixon LT, Mariam N, Fawaz MN, Amy M, Johnson AM, Radosevich M (2011) Global biogeography and quantitative seasonal dynamics of Gemmatimonadetes in soil. Appl Environ Microbiol. doi: 10.1128/AEM.05005-11
  7. 7.
    Dilly O, Bloem J, Vos A, Munch JC (2004) Bacterial diversity in agricultural soils during litter decomposition. Appl Environ Microbiol 70:468–474PubMedCrossRefGoogle Scholar
  8. 8.
    Freeman C, Liska G, Ostle N, Jones SE, Lock MA (1995) The use of fluorogenic substrates for measuring enzyme activity in peatlands. Plant Soil 175:147–152CrossRefGoogle Scholar
  9. 9.
    Ganzert L, Lipski A, Hubberten H-W, Wagner D (2011) The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica. FEMS Microb Ecol 76:476–491CrossRefGoogle Scholar
  10. 10.
    Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes—application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118PubMedCrossRefGoogle Scholar
  11. 11.
    Graef C, Hestnes AG, Svenning MM, Frenzel P (2011) The active methanotrophic community in a wetland from the High Arctic. Environ Microbiol Reports. doi: 10.1111/j.1758-2229.2010.00237.x
  12. 12.
    Hansen AA, Herbert RA, Mikkelsen K, Jensen LL, Kristoffersen T, Tiedje JM, Lomstein BA, Finster KW (2007) Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway. Environ Microbiol 9:2870–2884PubMedCrossRefGoogle Scholar
  13. 13.
    Hinsa-Leasure SM, Bhavaraju L, Rodrigues JLM, Bakermans C, Gilichinsky DA, Tiedje JM (2010) Characterization of a bacterial community from a Northeast Siberian seacoast permafrost sample. FEMS Microb Ecol 74:103–113CrossRefGoogle Scholar
  14. 14.
    Høj L, Olsen RA, Torsvik VL (2008) Effects of temperature on the diversity and community structure of known methanogenic groups and other archaea in high Arctic peat. ISME J 2:37–48PubMedCrossRefGoogle Scholar
  15. 15.
    Kang H, Freeman C (2009) Soil enzyme analysis for leaf litter decomposition in global wetlands. Comm Soil Sci Plant Anal 40:3323–3334CrossRefGoogle Scholar
  16. 16.
    Kim S-Y, Lee S-H, Freeman C, Fenner N, Kang H (2008) Comparative analysis of soil microbial communities and their responses to the short-term drought in bog, fen, and riparian wetlands. Soil Biol Biochem 40:2874–2880CrossRefGoogle Scholar
  17. 17.
    Kobabe S, Wagner D, Pfeiffer EM (2004) Characterisation of microbial community composition of a Siberian tundra soil by fluorescence in situ hybridisation. FEMS Microbiol Ecol 50:13–23PubMedCrossRefGoogle Scholar
  18. 18.
    Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrant E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175Google Scholar
  19. 19.
    LeBauer DS (2010) Litter degradation rate and β-glucosidase activity increase with fungal diversity. Can J Forest Res 40:1076–1085CrossRefGoogle Scholar
  20. 20.
    Leps J, Smilauer P (2003) Multivariate analysis of ecological data using CANOCO. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  21. 21.
    Liebner S, Wagner D (2007) Abundance, distribution and potential activity of methane oxidizing bacteria in permafrost soils from the Lena Delta, Siberia. Environ Microbiol 9:107–117PubMedCrossRefGoogle Scholar
  22. 22.
    Lueders T, Friedrich MW (2003) Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69:320–326PubMedCrossRefGoogle Scholar
  23. 23.
    Marschner P, Yang CH, Lieberei R, Crowley DE (2001) Soil and plant species effects on bacterial community composition in the rhizosphere. Soil Biol Biochem 33:1437–1445CrossRefGoogle Scholar
  24. 24.
    McCune B, Grace JB (2002) Analysis of ecological communities MjM software. Gleneden Beach, Oregon, USAGoogle Scholar
  25. 25.
    Morozova D, Wagner D (2007) Stress response of methanogenic archaea from Siberian permafrost compared to methanogens from non-permafrost habitats. FEMS Microbiol Ecol 61:16–25PubMedCrossRefGoogle Scholar
  26. 26.
    Nadkarni MA, Martin FE, Jacques NA, Hunter N (2002) Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiol 148:257–266Google Scholar
  27. 27.
    Neufeld JD, Mohn WW (2005) Unexpectedly high bacterial diversity in Arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags. Appl Environ Microbiol 71:5710–5718PubMedCrossRefGoogle Scholar
  28. 28.
    Nicol GW, Tscherko D, Chang L, Hammesfahr U, Prosser JI (2006) Crenarchaeal community assembly and microdiversity in developing soils at two sites associated with deglaciation. Environ Microbiol 8:1382–1393PubMedCrossRefGoogle Scholar
  29. 29.
    Noe L, Ascher J, Ceccherini MT, Abril A, Pietramellara G (2012) Molecular discrimination of bacteria (organic versus mineral soil layers) of dry woodlands of Argentina. J Arid Environ 85:18–26CrossRefGoogle Scholar
  30. 30.
    Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schelper C (2003) Diversity and abundances of crenarchaeota in terrestrial habitats studied by 16S rRNA surveys and real time PCR. Environ Microbiol 5:787–797PubMedCrossRefGoogle Scholar
  31. 31.
    Sinsabaugh RL, Hill BH, Follstard Shah JJ (2010) Ecoenzymatic stoichiometry of microbial organic nutrient acquisition in soil and sediment. Nature 462:795–798CrossRefGoogle Scholar
  32. 32.
    Steven B, Briggs G, McKay CP, Pollard WH, Greer CW, Whyte LG (2007) Characterization of the microbial diversity in a permafrost sample from the Canadian high Arctic using culture-dependent and culture-independent methods. FEMS Microbiol Ecol 59:513–523PubMedCrossRefGoogle Scholar
  33. 33.
    Steven B, Pollard WH, Greer CW, Whyte LG (2008) Microbial diversity and activity through a permafrost/ground ice core profile from the Canadian high Arctic. Environ Microbiol 10:3388–3403PubMedCrossRefGoogle Scholar
  34. 34.
    Takai K, Horikoshi K (2000) Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl Environ Microbiol 66:5066–5072PubMedCrossRefGoogle Scholar
  35. 35.
    Tian F, Yu Y, Chen B, Li H, Yao Y-F, Guo X-K (2009) Bacterial, archaeal and eukaryotic diversity in Arctic sediment as revealed by 16S rRNA and 18S rRNA gene clone libraries analysis. Polar Biol 32:93–103CrossRefGoogle Scholar
  36. 36.
    Toberman H, Freeman C, Evans C, Fenner N, Artz RRE (2008) Summer drought decreases soil fungal diversity and associated phenol oxidase activity in upland Calluna heathland soil. FEMS Microbiol Ecol 66:426–436PubMedCrossRefGoogle Scholar
  37. 37.
    Wagner D, Konabe S, Liebner S (2009) Bacterial community structure and carbon turnover in permafrost-affected soils of the Lena Delta, northeastern Siberia. Can J Microbiol 55:73–83PubMedCrossRefGoogle Scholar
  38. 38.
    Wallenstein MD, McMahon SK, Schimel JP (2009) Seasonal variation in enzyme activities and temperature sensitivities in Arctic tundra soils. Glob Change Biol 15:1631–1639CrossRefGoogle Scholar
  39. 39.
    White TJ, Bruns TD, Lee S, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic, New York, pp 315–324Google Scholar
  40. 40.
    Wilhelm RC, Niederberger TD, Greer C, Whyte LG (2011) Microbial diversity of active layer and permafrost in an acidic wetland from the Canadian High Arctic. Can J Microbiol 57:303–315PubMedCrossRefGoogle Scholar
  41. 41.
    Yergeau W, Kowalchuk GA (2008) Responses of Antarctic soil microbial communities and associated functions to temperature and freeze–thaw cycle frequency. Environ Microbiol 10:2223–2235PubMedCrossRefGoogle Scholar
  42. 42.
    Yergeau E, Hogues H, Whyte LG, Greer CW (2010) The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME J 4:1206–1214PubMedCrossRefGoogle Scholar
  43. 43.
    Zak DR, Kling GW (2006) Microbial community composition and function across an arctic tundra landscape. Ecology 87:1659–1670PubMedCrossRefGoogle Scholar
  44. 44.
    Zinger L, Shahnavaz B, Baptist F, Geremia RA, Choler P (2009) Microbial diversity in alpine tundra soils correlates with snow cover dynamics. ISME J 3:850–859PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Seung-Hoon Lee
    • 1
  • Inyoung Jang
    • 1
  • Namyi Chae
    • 1
    • 2
  • Taejin Choi
    • 2
  • Hojeong Kang
    • 1
  1. 1.Yonsei UniversitySeoulRepublic of Korea
  2. 2.Korea Polar Research InstituteIncheonRepublic of Korea

Personalised recommendations