Bacterial Diversity of Weathered Terrestrial Icelandic Volcanic Glasses

Microbial Ecology

Volumn 60, Issue 4, 2010, Pages 740-752

  Kelly, Laura C ^a   Cockell, Charles S ^a   Piceno, Yvette M ^b   Andersen, Gary L ^b   Thorsteinsson, Thorsteinn ^c   Marteinsson, Viggo ^d  

^a OPEN UNIVERSITY   (United Kingdom)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c National Energy Authority Reykjavik   (Iceland)

^d Matis ohf Iceland   (Iceland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; GLASS; RNA 16S;

ARTICLE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEDIMENT; VOLCANO;

BACTERIA; BIODIVERSITY; DNA, BACTERIAL; GEOLOGIC SEDIMENTS; GLASS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; VOLCANIC ERUPTIONS;

ACIDOBACTERIA; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); CYANOBACTERIA; PROTEOBACTERIA;

EID: 78149465759     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-010-9684-8     Document Type: Article

References (54)

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: 3389-3402.
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: 3871-3887.
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: 6288-6298.
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: 299-304.
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: 3413-3416.
6. Brunauer S, Emmett P, Teller E (1938) Adsorption of gases in multimolar layers. J Am Chem Soc 60: 309-319.
7. Caldeira K (1995) Long-term control of atmospheric carbon dioxide; low-temperature seafloor alteration or terrestrial silicate-rock weathering? Am J Sci 295: 1077-1114.
8. Chao A, Yang MCK (1993) Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika 80: 193-201.
9. Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. Aust J Ecol 18: 117-143.
10. Cockell CS, Olsson-Francis K, Herrera A, Kelly L, Thorsteinsson T, Marteinsson V (2009) Bacteria in weathered basaltic glass, Iceland. Geomicrobiol J 26: 491-507.
11. Cockell CS, Olsson-Francis K, Herrera A, Meunier A (2009) Alteration textures in terrestrial volcanic glass and the associated bacterial community. Geobiol 7: 50-65.
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: 735-747.
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: 91-109.
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 101-143.
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: 371-383.
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: 459-474.
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: 257-273.
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: 2906-2913.
19. Gislason SR, Eugster HP (1987) Meteoric water-basalt interactions. II: a field study in N. E. Iceland. Geochim Cosmochim Acta 51: 2841-2855.
20. Gomez-Alvarez V, King GM, Nüsslein K (2007) Comparative bacterial diversity in recent Hawaiian volcanic deposits of different ages. FEMS Microbiol Ecol 60: 60-73.
21. Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40: 237-264.
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: 801-811.
23. Herrera A, Cockell CS (2007) Exploring microbial diversity in volcanic environments: a review of methods in DNA extraction. J Microbio Meth 70: 1-12.
24. Herrera A, Cockell CS, Self S, Blaxter M, Reitner J (2009) A cryptoendolithic community in volcanic glass. Astrobiol 9: 369-382.
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: 25-37.
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: 485-498.
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: 49-51.
28. Jacobsson SP, Gudmundson MT (2008) Subglacial and intraglacial volcanic formations in Iceland. Jokull 58: 179-196.
29. Jukes TH, Cantor CR, Munro HN (1969) Evolution of protein molecules. In: (eds) Mammalian protein metabolism. Academic Press, pp 21-132.
30. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt EG, M. (eds) Nucleic acid techniques in bacterial systematics. pp 115-148.
31. Legendre P, Legendre L (1998) Numerical ecology. Elsevier Science, Amsterdam.
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: 213-230.
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: 231-242.
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: 695-700.
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: 110-122.
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: 385-390.
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: 3671-3681.
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: 1728-1735.
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: 94-108.
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: 653-656.
41. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
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: 7537-7541.
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: 4870-4876.
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: 4374-4376.
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: 513-556.
46. Stroncik N, Schmincke H-U (2002) Palagonite-a review. Int J Earth Sci 91: 680-697.
47. Tamura KD, J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol 24: 1596-1599.
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: 129-140.
49. Tebo BM, Johnson HA, McCarthy JK, Templeton AS (2005) Geomicrobiology of manganese(II) oxidation. Trends Microbiol 13: 421-428.
50. Templeton A, Staudigel H, Tebo B (2005) Diverse Mn(II)-oxidizing bacteria isolated from submarine basalts at Loihi Seamount. Geomicrobiol J 22: 127-139.
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: 731-749.
52. Thorseth IH, Torsvik T, Torsvik V, Daae FL, Pedersen KSP (2001) Diversity of life in ocean floor basalt. Earth Planet Sc Lett 194: 31-37.
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: 4843-4858.
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: 340-351.