Actinobacteria-An Ancient Phylum Active in Volcanic Rock Weathering

Geomicrobiology Journal

Volumn 30, Issue 8, 2013, Pages 706-720

  Cockell, Charles S ^a   Kelly, Laura C ^b,c   Marteinsson, Viggo ^d  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b OPEN UNIVERSITY   (United Kingdom)

^c UNIVERSITÉ DE LORRAINE   (France)

^d Matis ohf Iceland   (Iceland)

Author keywords

actinobacteria; basalt; geomicrobiology; volcanic rock; weathering

Indexed keywords

BACTERIUM; BASALT; GEOMICROBIOLOGY; VOLCANIC ROCK; WEATHERING;

ICELAND;

EID: 84879936504     PISSN: 01490451     EISSN: 15210529     Source Type: Journal    
DOI: 10.1080/01490451.2012.758196     Document Type: Article

References (55)

1. Abdulla, H. 2009. Bioweathering and biotransformation of granitic rock minerals by Actinomycetes. Microbiol Ecol, 58: 753 - 761.
2. Abdulla, H, May, E, Bahgat, M and Dewedar, A. 2008. Characterization of actinomycetes isolated from ancient stone and their potential for destruction. Pol J Miccrobiol, 57: 213 - 220.
3. Alexander, GB. 1953. The reaction of low molecular weight silicic acids with molybdic acid. J Am Chem Soc, 75: 5655 - 5657.
4. Altschul, S F, Madden, T L, Schaffer, A A, Zhang, J, Zhang, Z, Miller, W and Lipman, D J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res, 25: 3389 - 3402.
5. Babalola, O O, Kirby, B M, Le Roes-Hill, M, Cook, A E, Cary, S C, Burton, S G and Cowan, D A. 2009. Phylogenetic analysis of actinobacterial populations associated with Antarctic Dry Valley mineral soils. Environ Microbiol, 11: 566 - 576.
6. Bachar, A, Al-Ashhab, A, Soares, M I, Sklarz, M Y, Angel, R, Ungar, E D and Gillor, O. 2010. Microbial abundance and diversity along a low precipitation gradient. Microb Ecol, 60: 453 - 461.
7. Battistuzzi, F U, Feijao, A and Hedges, S B. 2004. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy and the colonization of land. BMC Evol Biol, 4: 44
8. Battistuzzi, F U and Hedges, S B. 2009. A major clade of prokaryotes with ancient adaptation to life on land. Mol Biol Evol, 26: 335 - 343.
9. Bruce, K D, Hiorns, W D, Hobman, J L, Osborn, A M, Strike, P and Ritchie, D A. 1992. Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Appl Environ Microbiol, 58: 3413 - 3416.
10. Brunauer, S, Emmett, P H and Teller, E. 1938. Adsorption of gases in multimolecular layers. J Am Chem Soc, 60: 309 - 319.
11. Chater, K F. 2006. Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics. Phil Trans Roy Soc, 361: 761 - 768.
12. Chizhikova, N P, Omarova, E O, Lobakova, E S, Zenova, G M and Manucharoc, A S. 2009. Crystallochemical transformation of phyllosilicates under the impact of cyanobacteria and actinomycetes. Euras Soil Sci, 42: 69 - 74.
13. Cockell, C S, Olsson, K, Herrera, A, Kelly, L, Thorsteinsson, T and Marteinsson, V. 2009. Bacteria in weathered basaltic glass, Iceland. Geomicrobiol J, 26: 491 - 507.
14. Costello, E K, Halloy, S RP, Reed, S C, Sowell, P and Schmidt, S K. 2009. Fumarole-supported islands of biodiversity within a hyperarid, high-elevation landscape on Socompa Volcano, Puna de Atacama, Andes. Appl Environ Microbiol, 73: 735 - 747.
15. Dessert, C, Dupré, B, François, L M, Schott, J, Gaillardet, J, Chakrapani, G J and 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 Sci Lett, 188: 459 - 474.
16. Dessert, C, Dupré, B, Gaillardet, J, François, L M and Allègre, C J. 2003. Basalt weathering laws and the impact of basalt weathering on the global carbon cycle. Chem Geol, 202: 257 - 273.
17. Embley, T M and Stackebrandt, E. 1994. The molecular phylogeny and systematics of the Actinomycetes. Ann Rev Microbiol, 48: 257 - 289.
18. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c, Seattle: Department of Genetics, University of Washington.
19. Frey, B, Rieder, S R, Brunner, I, Plötze, M, Koetzsch, S, Lapanje, A, Brandl, H and Furrer, G. 2010. Weathering-associated bacteria from the Damma glacier forefield: physiological capabilities and impact on granite dissolution. Appl Environ Microbiol, 76: 4788 - 4796.
20. Gerber, N N and Lechevalier, H A. 1965. Geosmin, an earthy-smelling substance isolated from Actinomycetes. Appl Microbiol, 13: 935 - 938.
21. Gomez-Alvarez, V, King, G M and Nüsslein, K. 2007. Comparative bacterial diversity in recent Hawaiian volcanic deposits of different ages. FEMS Microbiol Ecol, 60: 60 - 73.
22. Goodfellow, M and Williams, S T. 1983. Ecology of actinomycetes. Ann Rev Microbiol, 37: 189 - 216.
23. Groth, I and Saiz-Jimenez, C. 1999. Actinomycetes in hypogean environments. Geomicrobiol J, 16: 1 - 18.
24. Hall, T A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser, 41: 95 - 98.
25. Herrera, A and Cockell, C S. 2007. Exploring microbial diversity in volcanic environments: A review of methods in DNA extraction. J Microbio Meth, 70: 1 - 12.
26. Herrera, A, Cockell, C S, Self, S, Blaxter, M and Reitner, J. 2009. A cryptoendolithic community in volcanic glass. Astrobiol, 9: 369 - 382.
27. Herrera, A, Cockell, C S, Self, S, Blaxter, M, Reitner, J, Arp, G, Dröse, W, Thorsteinsson, T and Tindle, A G. 2008. Bacterial colonization and weathering of terrestrial obsidian in Iceland. Geomicrobiol J, 25: 25 - 37.
28. Ibekwe, A M, Kennedy, A C, Halvorson, J J and Yang, C-H. 2007. Characterization of developing microbial communities in Mount St. Helens pyroclastic substrate. Soil Biol Biochem, 39: 2496 - 2507.
29. Jacobsson, S P and Gudmundson, M T. 2008. Subglacial and intraglacial volcanic formations in Iceland. Jokull, 58: 179 - 196.
30. Jukes, T H and Cantor, C R. 1969. Evolution of protein molecules. In Munro HN. Mammalian protein metabolism, p21 - 123. New York: Academic Press.
31. Kelly, L C, Cockell, C, Piceno, Y, Andersen, G, Thorsteinsson, T and Marteinsson, V. 2010. Bacterial diversity of weathered terrestrial Icelandic volcanic glasses. Microbial Ecol, 60: 740 - 752.
32. Kelly, L C, Cockell, C S, Herrera-Belaroussi, A, Piceno, Y M, Andersen, G, DeSantis, T Z, Brodie, E L, Thorsteinsson, T, Marteinsson, V, Poly, F and Le Roux, X. 2011. Bacterial diversity of terrestrial crystalline volcanic rocks, Iceland. Microbial Ecol, 62: 69 - 79.
33. Lechevalier, H V and Lechevalier, M P. 1967. Biology of actinomycetes. Ann Rev Microbiol, 21: 121 - 125.
34. 2 affects soil microbial diversity associated with trembling aspen. Environ Microbiol, 10: 926 - 941.
35. Nemergut, D R, Martin, A P and Schmidt, S K. 2004. Integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution. Appl Environ Microbiol, 70: 1160 - 1168.
36. Okoro, C K, Brown, R, Jones, A L, Andrews, B A, Asenjo, J A, Goodfellow, M and Bull, A T. 2009. Diversity of culturable actinomycetes in hyper-arid soils of the Atacama Desert, Chile. Anton van Leeuwen, 95: 121 - 133.
37. Orlando, J, Alfaro, M, Bravo, L, Guevara, R and Caru, M. 2010. Bacterial diversity and occurrence of ammonia-oxidizing bacteria in the Atacama Desert soil during a 'desert bloom' event. Soil Biol Biochem, 42: 1183 - 1188.
38. Roes-Hill, M, Rohland, J, Meyers, P R, Cowan, D A and Burton, SG. 2009. Streptomyces hypolithicus sp. nov. Int J Syst Evol Microbiol, isolated from an Antarctic hypolith community, 59: 2032 - 2035.
39. Rutz, B A and Kieft, T L. 2004. Phylogenetic characterization of dwarf archaea and bacteria from a semiarid soil. Soil Biol Biochem, 36: 825 - 833.
40. Ryan, FJ. 1950. Selected methods of Neurospora genetics. Meth Med Res, 3: 51 - 75.
41. Saitou, N and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol, 4: 406 - 425.
42. Sattin, S R, Cleveland, C C, Hood, E, Reed, S C, King, A J, Schmidt, S K, Robeson, M S, Ascarrunz, N and Nemergut, D R. 2009. Functional shifts in unvegetated, perhumid, recently-deglaciated soils do not correlate with shifts in soil bacterial community composition. J Microbiol, 47: 673 - 681.
43. Stroncik, N A and Schminke, H. 2002. Palagonite - a review. Intern J Earth Sci, 91: 680 - 697.
44. Suihko, M-L, Priha, O, Alakomi, A-L, Thompson, P, Mälarstig, B, Stott, R and Richardson, M. 2009. Detection and molecular characterisation of filamentous Actinobacteria and thermoactinomycetes present in water-damaged building materials. Indoor Air, 19: 268 - 277.
45. Tamura, K, Dudley, J, Nei, M and Kumar, S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol, 24: 1596 - 1599.
46. Thompson, J D, Gibson, T J, Plewniak, F, Jeanmougin, F and Higgins, D G. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res, 25: 4876 - 4882.
47. Ventura, M, Canchaya, C, Taunch, A, Chandra, G, Fitzgerald, G F, Chater, K F and van Sinderen, D. 2007. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev, 71: 495 - 548.
48. Walker, J J and Pace, N R. 2007. Phylogenetic composition of Rocky Mountain endolithic microbial ecosystems. Appl Environ Microbiol, 73: 3497 - 3504.
49. Wang, Q, Garrity, G M, Tiedje, J M and Cole, J R. 2007. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol, 73: 5261 - 5267.
50. Wolff-Boenisch, D, Gíslason, S R, Oelkers, E H and Putnis, C V. 2004. The dissolution rates of natural glasses as a function of their composition at pH 4 and 10, and temperatures from 25 to 74°C. Geochim Cosmochim Acta, 68: 4843 - 4858.
51. oC. Geochim Cosmochim Acta, 71: 2224 - 2239.
52. YanXia, Z, Lin, L, ZongXing, W and LiRong, S. 2009. Isolation, identification and odour-producing abilities of geosmin/2-MIBin actinomycetes from sediments in Lake Lotus, China. J Water Supp Res Technol, 58: 552 - 561.
53. Yergeau, E, Newsham, K K, Pearce, D A and Kowalchuk, G A. 2007. Patterns of bacterial diversity across a range of Antarctic terrestrial habitats. Environ Microbiol, 9: 2670 - 2682.
54. Zeglin, L H, Dahm, C N, Barrett, J E, Gooseff, M N, Fitpatrick, S K and Takacs-Vesbach, C D. 2011. Bacterial community structure along moisture gradients in the parafluvial sediments of two ephemeral desert streams. Microb Ecol, 61: 543 - 556.
55. Zinger, L, Shahnavaz, B, Baptist, F, Geremia, R A and Choler, P. 2009. Microbial diversity in alpine tundra soils correlates with snow cover dynamics. ISME J, 3: 850 - 859.