Microbial Ecology

, Volume 64, Issue 2, pp 291–310 | Cite as

Local Conditions Structure Unique Archaeal Communities in the Anoxic Sediments of Meromictic Lake Kivu

  • Susma Bhattarai
  • Kelly Ann Ross
  • Martin Schmid
  • Flavio S. Anselmetti
  • Helmut BürgmannEmail author
Microbiology of Aquatic Systems


Meromictic Lake Kivu is renowned for its enormous quantity of methane dissolved in the hypolimnion. The methane is primarily of biological origin, and its concentration has been increasing in the past half-century. Insight into the origin of methane production in Lake Kivu has become relevant with the recent commercial extraction of methane from the hypolimnion. This study provides the first culture-independent approach to identifying the archaeal communities present in Lake Kivu sediments at the sediment-water interface. Terminal restriction fragment length polymorphism analysis suggests considerable heterogeneity in the archaeal community composition at varying sample locations. This diversity reflects changes in the geochemical conditions in the sediment and the overlying water, which are an effect of local groundwater inflows. A more in-depth look at the archaeal community composition by clone library analysis revealed diverse phylogenies of Euryarchaeota and Crenarachaeota. Many of the sequences in the clone libraries belonged to globally distributed archaeal clades such as the rice cluster V and Lake Dagow sediment environmental clusters. Several of the determined clades were previously thought to be rare among freshwater sediment Archaea (e.g., sequences related to the SAGMEG-1 clade). Surprisingly, there was no observed relation of clones to known hydrogentrophic methanogens and less than 2 % of clones were related to acetoclastic methanogens. The local variability, diversity, and novelty of the archaeal community structure in Lake Kivu should be considered when making assumptions on the biogeochemical functioning of its sediments.


Total Organic Carbon Archaea Clone Library Methanogenesis Terminal Restriction Fragment Length Polymorphism 
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.



We would like to thank the following people: Irene Brunner (Eawag) for performing elemental analysis of the sediment samples and Francisco Vazquez for help with molecular analyses. Fabrice Muvundja, Augustin Gafasi, and the crew of the Gloria for support during the sampling campaign. Tina Lösekann (MPI Bremen) and Carsten Schubert (Eawag), for providing the full set of archaeal sequences from Lago Cadagno sediment. We are grateful to the EPP program of the UNESCO-IHE Institute for Water Education in Delft and Eawag for providing S. Bhattarai with the opportunity to perform this research and to Alfred Wüest (Eawag) for scientific discussions and for providing funding for an additional research visit of S. Bhattarai to complete the manuscript. The sampling campaign and the salary of K.A. Ross were financed by the Swiss National Science Foundation grant IZ70Z0_123923.

Supplementary material

248_2012_34_MOESM1_ESM.pdf (201 kb)
ESM 1 (PDF 201 kb)


  1. 1.
    Kling GW, Evans WC, Tuttle ML, Tanyileke G (1994) Degassing of Lake Nyos. Nature 368:405–406CrossRefGoogle Scholar
  2. 2.
    Sigurdsson H, Devine JD, Tchua FM, Presser FM, Pringle MKW, Evans WC (1987) Origin of the lethal gas burst from Lake Monoun, Cameroun. J Volcanol Geoth Res 31:1–16CrossRefGoogle Scholar
  3. 3.
    Schmid M, Halbwachs M, Wehrli B, Wüest A (2005) Weak mixing in Lake Kivu: new insights indicate increasing risk of uncontrolled gas eruption. Geochem Geophys Geosyst 6:Q07009CrossRefGoogle Scholar
  4. 4.
    Newman FC (1976) Temperature steps in Lake Kivu: a bottom heated saline lake. J Phys Oceanogr 6:157–163CrossRefGoogle Scholar
  5. 5.
    Tietze K (1978) Geophysikalische Untersuchung des Kivusees und seiner ungewöhnlichen Methangaslagerstätte—Schichtung, Dynamik und Gasgehalt des Seewassers. (PhD thesis) Christian-Albrechts-Universität, KielGoogle Scholar
  6. 6.
    IPCC (2007) Climate Change 2007: synthesis report. Contribution of Working Groups I, II and III to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. IPCC, Geneva, SwitzerlandGoogle Scholar
  7. 7.
    Bastviken D, Tranvik LJ, Downing JA, Crill PM, Enrich-Prast A (2011) Freshwater methane emissions offset the continental carbon sink. Science 331:50PubMedCrossRefGoogle Scholar
  8. 8.
    Bastviken D, Cole J, Pace M, Tranvik L (2004) Methane emissions from lakes: dependence of lake characteristics, two regional assessments, and a global estimate. Glob Biogeochem Cycle 18:GB4009CrossRefGoogle Scholar
  9. 9.
    Tranvik LJ, Downing JA, Cotner JB, Loiselle SA, Striegle RG, Ballatore TJ, Dillon P, Finlay K, Fortino K, Knoll LB, Kortelainen PL, Kutser T, Larsen S, Laurion I, Leech DM, McCallister SL, McKnight DM, Melack JM, Overholt E, Porter JA, Prairie Y, Renwick WH, Roland F, Sherman BS, Schindler DW, Sobek S, Tremblay A, Vanni MJ, Verschoor AM, von Wachenfeldt E, Weyhenmeyera GA (2009) Lakes and reservoirs as regulators of carbon cycling and climate. Limnol Oceanogr 54:2298–2314CrossRefGoogle Scholar
  10. 10.
    Nayar A (2009) A lakeful of trouble. Nature 460:321–323PubMedCrossRefGoogle Scholar
  11. 11.
    Pasche N, Schmid M, Vazquez F, Schubert CJ, Wüest A, Kessler JD, Pack MA, Reeburgh WS, Bürgmann H (2011) Methane sources and sinks in Lake Kivu. J Geophys Res 116:G03006CrossRefGoogle Scholar
  12. 12.
    Schoell M, Tietze K, Schoberth SM (1988) Origin of methane in Lake Kivu (East-Central Africa). Chem Geol 71:257–265CrossRefGoogle Scholar
  13. 13.
    Tietze K, Geyh M, Müller H, Schröder L, Stahl W, Wehner H (1980) The genesis of the methane in Lake Kivu (Central Africa). Geol Rundsch 69:452–472CrossRefGoogle Scholar
  14. 14.
    Muvundja FA, Pasche N, Bugenyi FWB, Isumbisho M, Müller B, Namugize J-N, Rinta P, Schmid M, Stierli R, Wüest A (2009) Balancing nutrient inputs to Lake Kivu. J Great Lakes Res 35:406–418CrossRefGoogle Scholar
  15. 15.
    Pasche N, Alunga G, Mills K, Muvundja F, Ryves D, Schurter M, Wehrli B, Schmid M (2010) Abrupt onset of carbonate deposition in Lake Kivu during the 1960s: response to recent environmental changes. J Paleolimnol 44:931–946CrossRefGoogle Scholar
  16. 16.
    Pasche N, Dinkel C, Müller B, Schmid M, Wüest A, Wehrli B (2009) Physical and biogeochemical limits to internal nutrient loading of meromictic Lake Kivu. Limnol Oceanogr 54:1863–1873CrossRefGoogle Scholar
  17. 17.
    Degens E, von Herzen R, Wong H-K, Deuser W, Jannasch H (1973) Lake Kivu: structure, chemistry and biology of an East African rift lake. Geol Rundsch 62:245–277CrossRefGoogle Scholar
  18. 18.
    Burggraf S, Jannasch HW, Nicolaus B, Stetter KO (1990) Archaeoglobus profundus sp. nov., represents a new species within the sulfate-reducing archaebacteria. Syst Appl Microbiol 13:24–28CrossRefGoogle Scholar
  19. 19.
    Tourna M, Stieglmeier M, Spang A, Könneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci U S A 108:8420–8425PubMedCrossRefGoogle Scholar
  20. 20.
    Rudd JWM, Hamilton RD (1978) Methane cycling in a eutrophic shield lake and its effects on whole lake metabolism. Limnol Oceanogr 23:337–348CrossRefGoogle Scholar
  21. 21.
    Banning N, Brock F, Fry JC, Parkes RJ, Hornibrook ERC, Weightman AJ (2005) Investigation of the methanogen population structure and activity in a brackish lake sediment. Environ Microbiol 7:947–960PubMedCrossRefGoogle Scholar
  22. 22.
    Schleper C (2007) Diversity of uncultivated Archaea: perspectives from microbial ecology and metagenomics. Archaea. Blackwell, New York, pp 39–50Google Scholar
  23. 23.
    Casamayor EO, Borrego CM (2009) Archaea in inland waters. In: Likens GE (ed) Encyclopedia of inland waters, vol 3. Elsevier, Oxford, pp 167–181CrossRefGoogle Scholar
  24. 24.
    Galand PE, Casamayor EO, Kirchman DL, Potvin M, Lovejoy C (2009) Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing. ISME J 3:860–869PubMedCrossRefGoogle Scholar
  25. 25.
    Karner MB, DeLong EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507–510PubMedCrossRefGoogle Scholar
  26. 26.
    Lliros M, Gich F, Plasencia A, Auguet J-C, Darchambeau F, Casamayor EO, Descy J-P, Borrego C (2010) Vertical distribution of ammonia-oxidizing crenarchaeota and methanogens in the epipelagic waters of Lake Kivu (Rwanda-Democratic Republic of the Congo). Appl Environ Microbiol 76:6853–6863PubMedCrossRefGoogle Scholar
  27. 27.
    Bochem HP, Schoberth SM, Sprey B, Wengler P (1982) Thermophilic biomethanation of acetic acid: morphology and ultrastructure of a granular consortium. Can J Microbiol/Rev Can Microbiol 28:500–510CrossRefGoogle Scholar
  28. 28.
    Meyers PA, Teranes JL (2001) Sediment organic matter. In: Last WM, Smol JP (eds) Tracking environmental change using lake sediments, vol 3, Physical and geochemical methods. Kluwer Academic, Dordrecht, pp 239–269Google Scholar
  29. 29.
    DEW (2004) Deutsche Einheitsverfahren zur Wasseruntersuchung (DEW). Wiley, New YorkGoogle Scholar
  30. 30.
    Hönerlage W, Hahn D, Zeyer J (1995) Detection of mRNA of nprM in Bacillus megaterium ATCC 14581 grown in soil by whole-cell hybridization. Arch Microbiol 163:235–241CrossRefGoogle Scholar
  31. 31.
    Schwarz JIK, Eckert W, Conrad R (2007) Community structure of Archaea and Bacteria in a profundal lake sediment Lake Kinneret (Israel). Syst Appl Microbiol 30:239–254PubMedCrossRefGoogle Scholar
  32. 32.
    Grosskopf R, Stubner S, Liesack W (1998) Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl Environ Microbiol 64:4983–4989Google Scholar
  33. 33.
    Lueders T, Friedrich M (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
  34. 34.
    Ramette A (2009) Quantitative molecular community fingerprinting for estimating the abundance of operational taxonomic units in natural microbial communities. Appl Environ Microbiol 75:10CrossRefGoogle Scholar
  35. 35.
    Junier P, Junier T, Witzel K-P (2008) TRiFLe, a program for in silico terminal restriction fragment length polymorphism analysis with user-defined sequence sets. Appl Environ Microbiol 74:6452–6456PubMedCrossRefGoogle Scholar
  36. 36.
    Kaplan CW, Kitts CL (2003) Variation between observed and true terminal restriction fragment length is dependent on true TRF length and purine content. J Microbiol Methods 54:121–125PubMedCrossRefGoogle Scholar
  37. 37.
    R Development Core Team (2011) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, AustriaGoogle Scholar
  38. 38.
    Oksanen J, Blanchet FG, Kindt R, Legendre P, O’Hara RB, Simpson GL, Solymos P, Henry M, Stevens H, Wagner H (2011) vegan: community ecology package. R package version 1.17-6.
  39. 39.
    Kindt R, Coe R (2005) Tree diversity analysis. A manual and software for common statistical methods for ecological and biodiversity studies. World Agroforestry Centre (ICRAF), Nairobi. ISBN 92-9059-179-XGoogle Scholar
  40. 40.
    Borcard D, Gillet F, Legendre P (2011) Numerical Ecology with R. Springer, New York. ISBN 978-1-4419-7975-9CrossRefGoogle Scholar
  41. 41.
    Legendre P, Gallagher E (2001) Ecologically meaningful transformations for ordination of species data. Oecologia 129:271–280CrossRefGoogle Scholar
  42. 42.
    Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317–2319PubMedCrossRefGoogle Scholar
  43. 43.
    Wang Q, Garrity G, Tiedje J, Cole J (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267PubMedCrossRefGoogle Scholar
  44. 44.
    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739PubMedCrossRefGoogle Scholar
  45. 45.
    Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedCrossRefGoogle Scholar
  46. 46.
    Barberán A, Fernández-Guerra A, Auguet J-C, Galand PE, Casamayor EO (2011) Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota. Mol Ecol 20:1988–1996PubMedCrossRefGoogle Scholar
  47. 47.
    Sneath PHA (2005) Numerical taxonomy. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual® of systematic bacteriology. Springer, New York, pp 39–42CrossRefGoogle Scholar
  48. 48.
    Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120PubMedCrossRefGoogle Scholar
  49. 49.
    Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar BA, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüßmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371PubMedCrossRefGoogle Scholar
  50. 50.
    McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and Archaea. ISME J 6:610–618PubMedCrossRefGoogle Scholar
  51. 51.
    Schubert CJ, Vazquez F, Lösekann-Behrens T, Knittel K, Tonolla M, Boetius A (2011) Evidence for anaerobic oxidation of methane in sediments of a freshwater system (Lago di Cadagno). FEMS Microbiol Ecol 76:26–38PubMedCrossRefGoogle Scholar
  52. 52.
    MacGregor BJ, Moser DP, Alm EW, Nealson KH, Stahl DA (1997) Crenarchaeota in Lake Michigan sediment. Appl Environ Microbiol 63:1178–1181PubMedGoogle Scholar
  53. 53.
    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 75:7537–7541PubMedCrossRefGoogle Scholar
  54. 54.
    Sayeh R, Birrien J, Alain K, Barbier G, Hamdi M, Prieur D (2010) Microbial diversity in Tunisian geothermal springs as detected by molecular and culture-based approaches. Extremophiles 14:501–514PubMedCrossRefGoogle Scholar
  55. 55.
    Sahl JW, Gary MO, Harris JK, Spear JR (2010) A comparative molecular analysis of water-filled limestone sinkholes in north-eastern Mexico. Environ Microbiol 13:226–240PubMedCrossRefGoogle Scholar
  56. 56.
    Takai K, Moser DP, DeFlaun M, Onstott TC, Fredrickson JK (2001) Archaeal diversity in waters from deep South African gold mines. Appl Environ Microbiol 67:5750–5760PubMedCrossRefGoogle Scholar
  57. 57.
    Lösekann T, Knittel K, Nadalig T, Fuchs B, Niemann H, Boetius A, Amann R (2007) Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby mud volcano, Barents Sea. Appl Environ Microbiol 73:3348–3362PubMedCrossRefGoogle Scholar
  58. 58.
    Conrad R (2005) Quantification of methanogenic pathways using stable carbon isotopic signatures: a review and a proposal. Org Geochem 36:739–752CrossRefGoogle Scholar
  59. 59.
    Auguet J-C, Barberan A, Casamayor EO (2010) Global ecological patterns in uncultured Archaea. ISME J 4:182–190PubMedCrossRefGoogle Scholar
  60. 60.
    Schleper C, Holben W, Klenk H (1997) Recovery of crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments. Appl Environ Microbiol 63:321–323PubMedGoogle Scholar
  61. 61.
    Falz KZ, Holliger C, Großkopf R, Liesack W, Nozhevnikova AN, Müller B, Wehrli B, Hahn D (1999) Vertical distribution of methanogens in the anoxic sediment of Rotsee (Switzerland). Appl Environ Microbiol 65(6):2402–2408Google Scholar
  62. 62.
    Koizumi Y, Takii S, Nishino M, Nakajima T (2003) Vertical distributions of sulfate-reducing bacteria and methane-producing Archaea quantified by oligonucleotide probe hybridization in the profundal sediment of a mesotrophic lake. FEMS Microbiol Ecol 44:101–108PubMedCrossRefGoogle Scholar
  63. 63.
    Luna G, Stumm K, Pusceddu A, Danovaro R (2009) Archaeal diversity in deep-sea sediments estimated by means of different terminal-restriction fragment length polymorphisms (T-RFLP) protocols. Curr Microbiol 59:356–361PubMedCrossRefGoogle Scholar
  64. 64.
    Lloyd KG, Alperin MJ, Teske A (2011) Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) Archaea. Environ Microbiol 13:2548–2564PubMedCrossRefGoogle Scholar
  65. 65.
    Glissman K, Chin KJ, Casper P, Conrad R (2004) Methanogenic pathway and archaeal community structure in the sediment of eutrophic Lake Dagow: effect of temperature. Microb Ecol 48:389–399PubMedCrossRefGoogle Scholar
  66. 66.
    Galand P, Lovejoy C, Jrm P, Garneau M, Vincent W (2008) Microbial community diversity and heterotrophic production in a coastal Arctic ecosystem: a stamukhi lake and its source waters. Limnol Oceanogr 53:813–823CrossRefGoogle Scholar
  67. 67.
    Galand PE, Lovejoy C, Vincent WF (2006) Remarkably diverse and contrasting archaeal communities in a large arctic river and the coastal Arctic Ocean. Aquat Microb Ecol 44:115–126CrossRefGoogle Scholar
  68. 68.
    Zemskaya T, Pogodaeva T, Shubenkova O, Chernitsina S, Dagurova O, Buryukhaev S, Namsaraev B, Khlystov O, Egorov A, Krylov A, Kalmychkov G (2010) Geochemical and microbiological characteristics of sediments near the Malenky mud volcano (Lake Baikal, Russia), with evidence of Archaea intermediate between the marine anaerobic methanotrophs ANME-2 and ANME-3. Geo-Mar Lett 30:411–425CrossRefGoogle Scholar
  69. 69.
    Lahmeyer O (1998) Bathymetric survey of Lake Kivu. Final report. Republic of Rwanda, Ministry of Public Work, Directory of Energy and Hydrocarbons, KigaliGoogle Scholar
  70. 70.
    Conrad R, Chan O-C, Claus P, Casper P (2007) Characterization of methanogenic Archaea and stable isotope fractionation during methane production in the profundal sediment of an oligotrophic lake (Lake Stechlin, Germany). Limnol Oceanogr 52:1393–1406CrossRefGoogle Scholar
  71. 71.
    Chan OC, Claus P, Casper P, Ulrich A, Lueders T, Conrad R (2005) Vertical distribution of structure and function of the methanogenic archaeal community in Lake Dagow sediment. Environ Microbiol 7:1139–1149PubMedCrossRefGoogle Scholar
  72. 72.
    Ye W, Liu X, Lin S, Tan J, Pan J, Li D, Yang H (2009) The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu. FEMS Microbiol Ecol 70:263–276CrossRefGoogle Scholar
  73. 73.
    Jiang H, Dong H, Zhang G, Yu B, Chapman LR, Fields MW (2006) Microbial diversity in water and sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China. Appl Environ Microbiol 72:3832–3845PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Susma Bhattarai
    • 1
  • Kelly Ann Ross
    • 1
  • Martin Schmid
    • 1
  • Flavio S. Anselmetti
    • 1
  • Helmut Bürgmann
    • 1
    Email author
  1. 1.Department of Surface Waters-Research and ManagementEawag, Swiss Federal Institute for Aquatic Science and TechnologyKastanienbaumSwitzerland

Personalised recommendations