Microbial Ecology

, Volume 60, Issue 4, pp 740–752 | Cite as

Bacterial Diversity of Weathered Terrestrial Icelandic Volcanic Glasses

  • Laura C. Kelly
  • Charles S. Cockell
  • Yvette M. Piceno
  • Gary L. Andersen
  • Thorsteinn Thorsteinsson
  • Viggo Marteinsson
Environmental Microbiology


The diversity of microbial communities inhabiting two terrestrial volcanic glasses of contrasting mineralogy and age was characterised. Basaltic glass from a <0.8 Ma hyaloclastite deposit (Valafell) harboured a more diverse Bacteria community than the younger rhyolitic glass from ∼150-300 AD (Dόmadalshraun lava flow). Actinobacteria dominated 16S rRNA gene clone libraries from both sites, however, Proteobacteria, Acidobacteria and Cyanobacteria were also numerically abundant in each. A significant proportion (15-34%) of the sequenced clones displayed <85% sequence similarities with current database sequences, thus suggesting the presence of novel microbial diversity in each volcanic glass. The majority of clone sequences shared the greatest similarity to uncultured organisms, mainly from soil environments, among these clones from Antarctic environments and Hawaiian and Andean volcanic deposits. Additionally, a large number of clones within the Cyanobacteria and Proteobacteria were more similar to sequences from other lithic environments, included among these Icelandic clones from crystalline basalt and rhyolite, however, no similarities to sequences reported from marine volcanic glasses were observed. PhyloChip analysis detected substantially greater numbers of phylotypes at both sites than the corresponding clone libraries, but nonetheless also identified the basaltic glass community as the richer, containing approximately 29% unique phylotypes compared to rhyolitic glass.


Bacterial Community Clone Library Proteobacteria Actinobacteria Volcanic Glass 
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 work was made possible and supported by the Leverhulme Trust (project number F/00 269/N). We thank Andy Tindle for the provision of the microprobe facilities (Department of Earth Science, Open University, UK). The authors are also grateful to Steve Blake and Steve Self (Earth and Environmental Sciences, Open University, UK) for helpful discussions and advice, and to Steve Summers for performing the analysis of similarity (Planetary and Space Sciences Research Institute, Open University, UK).

Supplementary material

248_2010_9684_Fig6_ESM.gif (78 kb)
Supplemental Information Figure 1

ANOSIM analyis of DGGE profiles. Pal basaltic glass/palagonite samples from Valafell, Obs rhyolitic glass/obsidian samples from Dόmadalshraun. Samples ending in C are composites for the given glass type (GIF 77 kb)

248_2010_9684_MOESM1_ESM.tif (661 kb)
High-resolution image (TIFF 661 kb)


  1. 1.
    Altschul SF, Madden TL, Schäffer AA, Zhang Z, Zhang Z, Miller W, Lipman D (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database serach programs. Nucl Acids Res 25:3389–3402CrossRefPubMedGoogle Scholar
  2. 2.
    Bach W, Edwards KJ (2003) Iron and sulfide oxidation within the basaltic ocean crust: implications for chemolithoautotrophic microbial biomass production. Geochim Cosmochim Acta 67:3871–3887CrossRefGoogle Scholar
  3. 3.
    Brodie EL, DeSantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK et al (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72:6288–6298CrossRefPubMedGoogle Scholar
  4. 4.
    Brodie EL, DeSantis TZ, Parker JPM, Zubietta IX, Piceno YM, Andersen GL (2007) Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci 104:299–304CrossRefPubMedGoogle Scholar
  5. 5.
    Bruce KD, Hiorns WD, Hobman JL, Osborn AM, Strike P, Ritchie DA (1992) Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Appl Environ Microbiol 58:3413–3416PubMedGoogle Scholar
  6. 6.
    Brunauer S, Emmett P, Teller E (1938) Adsorption of gases in multimolar layers. J Am Chem Soc 60:309–319CrossRefGoogle Scholar
  7. 7.
    Caldeira K (1995) Long-term control of atmospheric carbon dioxide; low-temperature seafloor alteration or terrestrial silicate-rock weathering? Am J Sci 295:1077–1114CrossRefGoogle Scholar
  8. 8.
    Chao A, Yang MCK (1993) Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika 80:193–201CrossRefGoogle Scholar
  9. 9.
    Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. Aust J Ecol 18:117–143CrossRefGoogle Scholar
  10. 10.
    Cockell CS, Olsson-Francis K, Herrera A, Kelly L, Thorsteinsson T, Marteinsson V (2009) Bacteria in weathered basaltic glass, Iceland. Geomicrobiol J 26:491–507CrossRefGoogle Scholar
  11. 11.
    Cockell CS, Olsson-Francis K, Herrera A, Meunier A (2009) Alteration textures in terrestrial volcanic glass and the associated bacterial community. Geobiol 7:50–65CrossRefGoogle Scholar
  12. 12.
    Costello EK, Halloy SRP, Reed SC, Sowell P, Schmidt SK (2009) Fumarole-supported islands of biodiversity within a hyperarid, high-elevation landscape on Socompa Volcano, Puna de Atacama, Andes. Appl Environ Microbiol 75:735–747CrossRefPubMedGoogle Scholar
  13. 13.
    Crovisier J-L, Advocat T, Dussossoy J-L (2003) Nature and role of natural alteration gels formed on the surface of ancient volcanic glasses (natural analogs of waste containment glasses). J Nucl Mater 321:91–109CrossRefGoogle Scholar
  14. 14.
    Dahlgren R, Shoji S, Nanzyo M (1993) Mineralogical characteristics of volcanic ash soils. In: Shoji S, Nanzyo M (eds) Volcanic ash soils genesis, properties and utilization. Elsevier, pp 101-143Google Scholar
  15. 15.
    DeSantis T, Brodie E, Moberg J, Zubieta I, Piceno Y, Andersen G (2007) High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microbial Ecol 53:371–383CrossRefGoogle Scholar
  16. 16.
    Dessert C, Dupré B, François LM, Schott J, Gaillardet J, Chakrapani G, Bajpai S (2001) Erosion of Deccan Traps determined by river geochemistry: impact on the global climate and the 87Sr/86Sr ratio of seawater. Earth Planet Sc Lett 188:459–474CrossRefGoogle Scholar
  17. 17.
    Dessert C, Dupré B, Gaillardet J, Francois LM, Allegre CJ (2003) Basalt weathering laws and the impact of basalt weathering on the global carbon cycle. Chem Geol 202:257–273CrossRefGoogle Scholar
  18. 18.
    Edwards KJ, Rogers DR, Wirsen CO, McCollom TM (2003) Isolation and charcterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithotrophic à- and g-Proteobacteria from the deep sea. Appl Environ Microbiol 69:2906–2913CrossRefPubMedGoogle Scholar
  19. 19.
    Gislason SR, Eugster HP (1987) Meteoric water-basalt interactions. II: a field study in N.E. Iceland. Geochim Cosmochim Acta 51:2841–2855CrossRefGoogle Scholar
  20. 20.
    Gomez-Alvarez V, King GM, Nüsslein K (2007) Comparative bacterial diversity in recent Hawaiian volcanic deposits of different ages. FEMS Microbiol Ecol 60:60–73CrossRefPubMedGoogle Scholar
  21. 21.
    Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40:237–264Google Scholar
  22. 22.
    Hall K, Lindgren SB, Jackson P (2005) Rock albedo and monitoring of thermal conditions in respect of weathering: some expected and some unexpected results. Earth Surf Processes and Landf 30:801–811CrossRefGoogle Scholar
  23. 23.
    Herrera A, Cockell CS (2007) Exploring microbial diversity in volcanic environments: a review of methods in DNA extraction. J Microbio Meth 70:1–12CrossRefGoogle Scholar
  24. 24.
    Herrera A, Cockell CS, Self S, Blaxter M, Reitner J (2009) A cryptoendolithic community in volcanic glass. Astrobiol 9:369–382CrossRefGoogle Scholar
  25. 25.
    Herrera A, Cockell CS, Self S, Blaxter M, Reitner J, Arp G, Dröse W, Thorsteinsson T, Tindle AG (2008) Bacterial colonization and weathering of terrestrial obsidian in Iceland. Geomicrobiol J 25:25–37CrossRefGoogle Scholar
  26. 26.
    Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, Wei D, Goldfarb KC, Santee CA, Lynch SV et al (2009) Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139:485–498CrossRefPubMedGoogle Scholar
  27. 27.
    Jackson CRR, Eric E, Churchill PF (2000) Denaturing gradient gel electrophoresis can fail to separate 16S rDNA fragments with multiple base differences. Mol Biol Today 1:49–51Google Scholar
  28. 28.
    Jacobsson SP, Gudmundson MT (2008) Subglacial and intraglacial volcanic formations in Iceland. Jokull 58:179–196Google Scholar
  29. 29.
    Jukes TH, Cantor CR, Munro HN (1969) Evolution of protein molecules. In: (eds) Mammalian protein metabolism. Academic Press, pp 21-132Google Scholar
  30. 30.
    Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt EG, M. (eds) Nucleic acid techniques in bacterial systematics. pp 115-148Google Scholar
  31. 31.
    Legendre P, Legendre L (1998) Numerical ecology. Elsevier Science, AmsterdamGoogle Scholar
  32. 32.
    Lysnes K, Thorseth IH, Steinsbu BO, Øvreås L, Torsvik T, Pedersen RB (2004) Microbial community diversity in seafloor basalt from the Arctic spreading ridges. FEMS Microbiol Ecol 50:213–230CrossRefPubMedGoogle Scholar
  33. 33.
    Mason OU, Di Meo-Savoie CA, Van Nostrand JD, Zhou J, Fisk MR, Giovannoni SJ (2008) Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts. ISME J 3:231–242CrossRefPubMedGoogle Scholar
  34. 34.
    Muyzer G, DeWaal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700PubMedGoogle Scholar
  35. 35.
    Nemergut D, Anderson S, Cleveland C, Martin A, Miller A, Seimon A, Schmidt S (2007) Microbial community succession in an unvegetated, recently deglaciated soil. Microbial Ecol 53:110–122CrossRefGoogle Scholar
  36. 36.
    Nikolausz M, Sipos R, Révész S, Székely A, Márialigeti K (2005) Observation of bias associated with re-amplification of DNA isolated from denaturing gradient gels. FEMS Microbiol Lett 244:385–390CrossRefPubMedGoogle Scholar
  37. 37.
    Oelkers EH, Gislason SR (2001) The mechanism, rates and consequences of basaltic glass dissolution: I. An experimental study of the dissolution rates of basaltic glass as a function of aqueous Al, Si and oxalic acid concentration at 25 °C and pH = 3 and 11. Geochim Cosmochim Acta 65:3671–3681CrossRefGoogle Scholar
  38. 38.
    Orcutt B, Bailey B, Staudigel H, Tebo BM, Edwards KJ (2009) An interlaboratory comparison of 16S rRNA gene-based terminal restriction fragment length polymorphism and sequencing methods for assessing microbial diversity of seafloor basalts. Environ Microbiol 11:1728–1735CrossRefPubMedGoogle Scholar
  39. 39.
    Rastogi G, Osman S, Vaishampayan P, Andersen G, Stetler L, Sani R (2010) microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library. Microbial Ecol 59:94–108CrossRefGoogle Scholar
  40. 40.
    Santelli CM, Orcutt BN, Banning E, Bach W, Moyer CL, Sogin ML, Staudigel H, Edwards KJ (2008) Abundance and diversity of microbial life in ocean crust. Nature 453:653–656CrossRefPubMedGoogle Scholar
  41. 41.
    Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501–1506CrossRefPubMedGoogle Scholar
  42. 42.
    Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541CrossRefPubMedGoogle Scholar
  43. 43.
    Schwieger F, Tebbe CC (1998) A new approach to utilize PCR single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol 64:4870–4876PubMedGoogle Scholar
  44. 44.
    Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001) Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67:4374–4376CrossRefPubMedGoogle Scholar
  45. 45.
    Stefansson A, Gislason SR (2001) Chemical weathering of basalts, Southwest Iceland: effect of rock crystallinity and secondary minerals on chemical fluxes to the ocean. Am J Sci 301:513–556CrossRefGoogle Scholar
  46. 46.
    Stroncik N, Schmincke H-U (2002) Palagonite—a review. Int J Earth Sci 91:680–697CrossRefGoogle Scholar
  47. 47.
    Tamura KD, J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599Google Scholar
  48. 48.
    Tarlera S, Jangid K, Ivester AH, Whitman WB, Williams MA (2008) Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development. FEMS Microbiol Ecol 64:129–140CrossRefPubMedGoogle Scholar
  49. 49.
    Tebo BM, Johnson HA, McCarthy JK, Templeton AS (2005) Geomicrobiology of manganese(II) oxidation. Trends Microbiol 13:421–428CrossRefPubMedGoogle Scholar
  50. 50.
    Templeton A, Staudigel H, Tebo B (2005) Diverse Mn(II)-oxidizing bacteria isolated from submarine basalts at Loihi Seamount. Geomicrobiol J 22:127–139CrossRefGoogle Scholar
  51. 51.
    Thorseth IH, Furnes H, Tumyr O (1991) A textural and chemical study of Icelandic palagonite of varied composition and its bearing on the mechanism of the glass-palagonite transformation. Geochim Cosmochim Acta 55:731–749CrossRefGoogle Scholar
  52. 52.
    Thorseth IH, Torsvik T, Torsvik V, Daae FL, Pedersen KSP (2001) Diversity of life in ocean floor basalt. Earth Planet Sc Lett 194:31–37CrossRefGoogle Scholar
  53. 53.
    Wolff-Boenisch D, Gislason SR, Oelkers EH, Putnis CV (2004) The dissolution rates of natural glasses as a function of their composition at pH 4 and 10.6, and temperatures from 25 to 74 °C. Geochim Cosmochim Acta 68:4843–4858CrossRefGoogle Scholar
  54. 54.
    Yergeau E, Schoondermark-Stolk SA, Brodie EL, Dejean S, DeSantis TZ, Goncalves O, Piceno YM, Andersen GL, Kowalchuk GA (2008) Environmental microarray analyses of Antarctic soil microbial communities. ISME J 3:340–351CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Laura C. Kelly
    • 1
  • Charles S. Cockell
    • 1
  • Yvette M. Piceno
    • 2
  • Gary L. Andersen
    • 2
  • Thorsteinn Thorsteinsson
    • 3
  • Viggo Marteinsson
    • 4
  1. 1.Geomicrobiology Research Group, Planetary and Space Sciences Research InstituteOpen UniversityMilton KeynesUK
  2. 2.Ecology Department, Earth Sciences DivisionLawrence Berkeley National LaboratoryBerkeleyUSA
  3. 3.Hydrology DivisionNational Energy AuthorityReykjavikIceland
  4. 4.Matís ohf./Icelandic Food and Biotech R&DReykjavikIceland

Personalised recommendations