Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Recovery of fen peatland microbiomes and predicted functional profiles after rewetting


Many of the world’s peatlands have been affected by water table drawdown and subsequent loss of organic matter. Rewetting has been proposed as a measure to restore peatland functioning and to halt carbon loss, but its effectiveness is subject to debate. An important prerequisite for peatland recovery is a return of typical microbial communities, which drive key processes. To evaluate the effect of rewetting, we investigated 13 fen peatland areas across a wide (>1500 km) longitudinal gradient in Europe, in which we compared microbial communities between drained, undrained, and rewetted sites. There was a clear difference in microbial communities between drained and undrained fens, regardless of location. Community recovery upon rewetting was substantial in the majority of sites, and predictive functional profiling suggested a concomitant recovery of biogeochemical peatland functioning. However, communities in rewetted sites were only similar to those of undrained sites when soil organic matter quality (as expressed by cellulose fractions) and quantity were still sufficiently high. We estimate that a minimum organic matter content of ca. 70% is required to enable microbial recovery. We conclude that peatland recovery after rewetting is conditional on the level of drainage-induced degradation: severely altered physicochemical peat properties may preclude complete recovery for decades.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Geographical locations of the study sites.
Fig. 2: Nonmetric multidimensional scaling (NMDS, stress = 0.187) of prokaryote community composition at three depths and three drainage stages in 39 fen sites across Europe.
Fig. 3: Prokaryote diversity and biomass at three depths and three drainage stages in 39 fen sites across Europe.
Fig. 4: Relative abundances of a selection of predicted functional genes in the top peat layer (0–5 cm) of 39 fen sites that differ in drainage stage.
Fig. 5: Environmental variables in drained (dots) and rewetted (triangles) fens in relation to microbial community dissimilarity to undrained fens.

Data availability

Sequences are available  in NCBI SRA under project number PRJNA595701.


  1. 1.

    Gorham E. Northern peatlands: role in the carbon cycle and probable responses to climatic warming. Ecol Appl. 1991;1:182–95.

    PubMed  Google Scholar 

  2. 2.

    Yu Z. Northern peatland carbon stocks and dynamics: a review. Biogeosciences. 2012;9:4071–85.

    CAS  Google Scholar 

  3. 3.

    Knox SH, Sturtevant C, Matthes JH, Koteen L, Verfaillie J, Baldocchi D. Agricultural peatland restoration: effects of land-use change on greenhouse gas (CO2 and CH4) fluxes in the Sacramento-San Joaquin Delta. Glob Change Biol. 2015;21:750–65.

    Google Scholar 

  4. 4.

    Fenner N, Freeman C. Drought-induced carbon loss in peatlands. Nat Geosci. 2011;4:895–900.

    CAS  Google Scholar 

  5. 5.

    Freeman C, Ostle N, Kang H. An enzymic ‘latch’ on a global carbon store - a shortage of oxygen locks up carbon in peatlands by restraining a single enzyme. Nature. 2001;409:149.

    CAS  PubMed  Google Scholar 

  6. 6.

    Kwon MJ, Haraguchi A, Kang H. Long-term water regime differentiates changes in decomposition and microbial properties in tropical peat soils exposed to the short-term drought. Soil Biol Biochem. 2013;60:33–44.

    CAS  Google Scholar 

  7. 7.

    Laine J, Vasander H, Sallantaus T. Ecological effects of peatland drainage for forestry. Environ Rev. 1995;3:286–303.

    CAS  Google Scholar 

  8. 8.

    Minayeva TY, Bragg O, Sirin A. Towards ecosystem-based restoration of peatland biodiversity. Mires Peat. 2017;19:1–36.

    Google Scholar 

  9. 9.

    Mälson K, Backéus I, Rydin H. Long-term effects of drainage and initial effects of hydrological restoration on rich fen vegetation. Appl Veg Sci. 2007;11:99–106.

    Google Scholar 

  10. 10.

    Juottonen H, Hynninen A, Nieminen M, Tuomivirta TT, Tuittila ES, Nousiainen H, et al. Methane-cycling microbial communities and methane emission in natural and restored peatlands. Appl Environ Micro. 2012;78:6386–9.

    CAS  Google Scholar 

  11. 11.

    Lamers LP, Vile MA, Grootjans AP, Acreman MC, van Diggelen R, Evans MG, et al. Ecological restoration of rich fens in Europe and North America: from trial and error to an evidence‐based approach. Biol Rev. 2015;90:182–203.

    PubMed  Google Scholar 

  12. 12.

    Joosten H. The Global Peatland CO2 Picture: peatland status and drainage related emissions in all countries of the world. Ede: Wetlands International; 2009.

    Google Scholar 

  13. 13.

    Bardgett RD, Van Der Putten WH. Belowground biodiversity and ecosystem functioning. Nature. 2014;515:505.

    CAS  PubMed  Google Scholar 

  14. 14.

    Andersen R, Francez A-J, Rochefort L. The physicochemical and microbiological status of a restored bog in Québec: Identification of relevant criteria to monitor success. Soil Biol Biochem. 2006;38:1375–87.

    CAS  Google Scholar 

  15. 15.

    Putkinen A, Tuittila E-S, Siljanen HM, Bodrossy L, Fritze H. Recovery of methane turnover and the associated microbial communities in restored cutover peatlands is strongly linked with increasing Sphagnum abundance. Soil Biol Biochem. 2018;116:110–9.

    CAS  Google Scholar 

  16. 16.

    Wen X, Unger V, Jurasinski G, Koebsch F, Horn F, Rehder G, et al. Predominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissions. Biogeosciences. 2018;15:6519–36.

    CAS  Google Scholar 

  17. 17.

    Potter C, Freeman C, Golyshin PN, Ackermann G, Fenner N, McDonald JE, et al. Subtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems. Sci Rep. 2017;7:11314.

    PubMed  PubMed Central  Google Scholar 

  18. 18.

    Sinsabaugh RL, Hill BH, Shah JJF. Ecoenzymatic stoichiometry of microbial organic nutrient acquisition in soil and sediment. Nature. 2009;462:795–U117.

    CAS  PubMed  Google Scholar 

  19. 19.

    Larmola T, Leppänen SM, Tuittila E-S, Aarva M, Merilä P, Fritze H, et al. Methanotrophy induces nitrogen fixation during peatland development. PNAS. 2014;111:734–9.

    CAS  PubMed  Google Scholar 

  20. 20.

    Liebner S, Zeyer J, Wagner D, Schubert C, Pfeiffer EM, Knoblauch C. Methane oxidation associated with submerged brown mosses reduces methane emissions from Siberian polygonal tundra. J Ecol. 2011;99:914–22.

    CAS  Google Scholar 

  21. 21.

    Aggenbach CJ, Backx H, Emsens WJ, Grootjans AP, Lamers LP, Smolders AJ, et al. Do high iron concentrations in rewetted rich fens hamper restoration. Preslia. 2013;85:405–20.

    Google Scholar 

  22. 22.

    Myers B, Webster KL, Mclaughlin JW, Basiliko N. Microbial activity across a boreal peatland nutrient gradient: the role of fungi and bacteria. Wetl Ecol Manag. 2012;20:77–88.

    CAS  Google Scholar 

  23. 23.

    Ellenberg H, Leuschner C. Vegetation Mitteleuropas mit den Alpen: in ökologischer, dynamischer und historischer Sicht. Stuttgart: Ulmer Verlag; 2010. Vol. 8104.

  24. 24.

    Schaffers AP, Sýkora KV. Reliability of Ellenberg indicator values for moisture, nitrogen and soil reaction: a comparison with field measurements. J Veg Sci. 2000;11:225–44.

    Google Scholar 

  25. 25.

    Rowland A, Roberts J. Lignin and cellulose fractionation in decomposition studies using acid‐detergent fibre methods. Commun Soil Sci Plan. 1994;25:269–77.

    CAS  Google Scholar 

  26. 26.

    Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. PNAS. 2011;108:4516–22.

    CAS  PubMed  Google Scholar 

  27. 27.

    Frostegard A, Baath E. The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol Fert Soils. 1996;22:59–65.

    Google Scholar 

  28. 28.

    Oravecz O, Elhottová D, Krištůfek V, Šustr V, Frouz J, Tříska J, et al. Application of ARDRA and PLFA analysis in characterizing the bacterial communities of the food, gut and excrement of saprophagous larvae ofPenthetria holosericea (Diptera: Bibionidae): a pilot study. Folia microbiologica. 2004;49:83.

    CAS  PubMed  Google Scholar 

  29. 29.

    Šnajdr J, Valášková V, Merhautová V, Cajthaml T, Baldrian P. Activity and spatial distribution of lignocellulose-degrading enzymes during forest soil colonization by saprotrophic basidiomycetes. Enzym Micro Tech. 2008;43:186–92.

    Google Scholar 

  30. 30.

    Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996.

    CAS  PubMed  Google Scholar 

  31. 31.

    Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  32. 32.

    Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31:814.

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33.

    Douglas GM, Maffei VJ, Zaneveld J, Yurgel SN, Brown JR, Taylor CM et al. PICRUSt2: an improved and extensible approach for metagenome inference. 2019.

  34. 34.

    Luton PE, Wayne JM, Sharp RJ, Riley PW. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology. 2002;148:3521–30.

    CAS  PubMed  Google Scholar 

  35. 35.

    Galand PE, Saarnio S, Fritze H, Yrjälä K. Depth related diversity of methanogen Archaea in Finnish oligotrophic fen. FEMS Microbiol Ecol. 2002;42:441–9.

    CAS  PubMed  Google Scholar 

  36. 36.

    Lüdemann H, Arth I, Liesack W. Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl Environ Microbiol. 2000;66:754–62.

    PubMed  PubMed Central  Google Scholar 

  37. 37.

    Andersen R, Chapman SJ, Artz RRE. Microbial communities in natural and disturbed peatlands: a review. Soil Biol Biochem. 2013;57:979–94.

    CAS  Google Scholar 

  38. 38.

    Morales SE, Mouser PJ, Ward N, Hudman SP, Gotelli NJ, Ross DS, et al. Comparison of bacterial communities in New England Sphagnum bogs using terminal restriction fragment length polymorphism (T-RFLP). Micro Ecol. 2006;52:34–44.

    CAS  Google Scholar 

  39. 39.

    Eilers KG, Debenport S, Anderson S, Fierer N. Digging deeper to find unique microbial communities: the strong effect of depth on the structure of bacterial and archaeal communities in soil. Soil Biol Biochem. 2012;50:58–65.

    CAS  Google Scholar 

  40. 40.

    Jackson CR, Liew KC, Yule CM. Structural and functional changes with depth in microbial communities in a tropical malaysian peat swamp forest. Micro Ecol. 2009;57:402–12.

    Google Scholar 

  41. 41.

    Brune A, Frenzel P, Cypionka H. Life at the oxic–anoxic interface: microbial activities and adaptations. FEMS Microbiol Rev. 2000;24:691–710.

    CAS  PubMed  Google Scholar 

  42. 42.

    Basiliko N, Henry K, Gupta V, Moore T, Driscoll B, Dunfield P. Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands. Front Microbiol. 2013;4:215.

    CAS  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Hooijer A, Page S, Jauhiainen J, Lee WA, Lu XX, Idris A, et al. Subsidence and carbon loss in drained tropical peatlands. Biogeosciences. 2012;9:1053–71.

    CAS  Google Scholar 

  44. 44.

    Minkkinen K, Laine J. Effect of forest drainage on the peat bulk density of pine mires in Finland. Can J For Res. 1998;28:178–86.

    Google Scholar 

  45. 45.

    Pérez J, Munoz-Dorado J, De la Rubia T, Martinez J. Biodegradation and biological treatments of cellulose, hemicellulose and lignin: an overview. Int Microbiol. 2002;5:53–63.

    PubMed  Google Scholar 

  46. 46.

    Borren W, Bleuten W, Lapshina ED. Holocene peat and carbon accumulation rates in the southern taiga of western Siberia. Quat Res. 2004;61:42–51.

    CAS  Google Scholar 

  47. 47.

    Succow M, Joosten H. landschaftsökologische Moorkunde. Stuttgart: E. Schweizerbart’sche Verlagsbuchhandlung; 2012.

    Google Scholar 

  48. 48.

    Raghoebarsing AA, Smolders AJ, Schmid MC, Rijpstra WIC, Wolters-Arts M, Derksen J, et al. Methanotrophic symbionts provide carbon for photosynthesis in peat bogs. Nature. 2005;436:1153.

    CAS  PubMed  Google Scholar 

  49. 49.

    Eilers KG, Lauber CL, Knight R, Fierer N. Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil. Soil Biol Biochem. 2010;42:896–903.

    CAS  Google Scholar 

  50. 50.

    Cleveland CC, Nemergut DR, Schmidt SK, Townsend AR. Increases in soil respiration following labile carbon additions linked to rapid shifts in soil microbial community composition. Biogeochemistry. 2007;82:229–40.

    CAS  Google Scholar 

  51. 51.

    Hiraishi T, Krug T, Tanabe K, Srivastava N, Baasansuren J, Fukuda M et al. 2013 supplement to the 2006 IPCC guidelines for national greenhouse gas inventories: Wetlands. Switzerland: IPCC; 2014.

Download references


We are grateful to Johan de Gruyter for help with operating the sequencer, and we thank Tom van der Spiet, Rebecca White, and Adrita Ballal for their assistance in the lab. We thank Natuurpunt, Staatsbosbeheer, Natagora, Stiftung Naturschutz Schleswig-Holstein, and the districts of Vorpommern-Rügen and Vorpommern-Greifswald for sampling permits, and greatly thank Filip Meysman, Tim Urich, Richard Bardgett, and three anonymous reviewers for critical reading of and input on the manuscript. Finally our gratitude to all field helpers and all members of the REPEAT team. This research was financed by BiodivERsA/BELSPO (BR/175/A1), VBNE/OBN (OBN-2016-80-NZ), and FWO (1214520N).

Author information




W-JE, EV, RvD, CJSA, AK, WK, LK, ES, HS, FT, and MW designed the research. RvD, CJSA, TC, JF, LK, YL, ES, FT, and JV collected the data. W-JE and EV statistically analyzed the data. W-JE led the writing of the manuscript and all authors contributed to drafts and gave approval for publication.

Corresponding author

Correspondence to Willem-Jan Emsens.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

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

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Emsens, WJ., van Diggelen, R., Aggenbach, C.J.S. et al. Recovery of fen peatland microbiomes and predicted functional profiles after rewetting. ISME J 14, 1701–1712 (2020).

Download citation

Further reading


Quick links