Assessment of bacterial communities in auriferous and non-auriferous soils using genetic and functional fingerprinting

Geomicrobiology Journal

Volumn 25, Issue 3-4, 2008, Pages 203-215

  Reith, F ^a   Rogers, S L ^b  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b Cooperative Research Centre for Landscape Environments and Mineral Exploration Bentley ^*  (Australia)

Author keywords

16S rDNA PCR DGGE; Bacteria; Biolog; CLPP; Gold; Regolith; Soil; Solubilization

Indexed keywords

BACTERIUM; BIOGEOCHEMICAL CYCLE; DNA FINGERPRINTING; GOLD; MICROBIAL ACTIVITY; MICROCOSM; REGOLITH; SOLUBILIZATION;

ARTHROBACTER; ARTHROBACTER SP.; BACILLUS (BACTERIUM); BACILLUS SP.; BACTERIA (MICROORGANISMS); METHYLOCELLA;

EID: 46249115383     PISSN: 01490451     EISSN: 15210529     Source Type: Journal    
DOI: 10.1080/01490450802081846     Document Type: Article

References (46)

1. Amann, R. I., Ludwig, W. and Scheidler, K. H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. FEMS Microbiol Rev, 59, pp. 143-169.
2. Carotti, S., Marcon, G., Marussich, M., Mazzei, T., Messori, L., Mini, E. and Orioli, P. (2000) Cytotoxicity and DNA binding properties of a chloro-glycylhistidinate gold (III) complex (GhAu). Chem Biol Interact, 125, pp. 29-38.
3. Clarke, K. R. (1993) Non-parametric multivariate analysis of changes in community structure. Austral J Ecol, 18, pp. 117-143.
4. Clarke, K. R. and Warwick, R. M. (2001) Change in marine communities: An approach to statistical analysis and interpretation, Primer-E Ltd, Plymouth, UK
5. Dedysh, S. N., Dunfield, P. F., Derakshani, M., Stubner, S., Heyer, J. and Liesack, W. (2003) Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes. FEMS Microbiol Ecol, 43, pp. 299-308.
6. Dobler, R., Saner, M. and Bachofen, R. (2000) Population canges of soil microbial communities induced by hydrocarbon and heavy metal contamination. Bioremed J, 4, pp. 41-56.
7. Ehrlich, H. L. (1996) Geomicrobiology, Marcel Dekker, New York, USA
8. Evans, F. F., Seldin, L., Sebastian, G. V., Kjelleberg, S., Holmstroem, C. and Rosado, A. S. (2004) Influence of petroleum contamination and biostimulation treatment on the diversity of Pseudomonas spp. in soil microcosms as evaluated by 16S rRNA based-PCR and DGGE. L Appl Microbiol, 38, pp. 93-98.
9. Fromin, N., Hamelin, J., Tarnawski, S., Roesti, D., Jourdain-Miserez, K., Forestier, N., Teyssier-Cuvelle, S., Gillet, F., Aragno, M. and Rossi, P. (2002) Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ Microbiol, 4, pp. 634-643.
10. Garland, J. L. (1996) Analytical approaches to the characterisation of samples of microbial communities using patterns of potential C source utilization. Soil Biol Biochem, 28, pp. 223-230.
11. Gray, D. J. and Lintern, M. J. (1998) Further aspects of the chemistry of gold in some Western Australian soils
12. Guckert, J. B., Carr, G. J., Johnson, T. D., Hamm, B. G., Davidson, D. H. and Kumagai, Y. (1996) Community analysis by Biolog: Curve integration for statistical analysis of activated sludge microbial habitats. J Microbiol Meth, 27, pp. 183-197.
13. Kizilkaya, R., Askin, T., Bayrakli, B. and Saglam, M. (2004) Microbial characteristics of soil contaminated with heavy metals. Euro J Soil Biol, 40, pp. 95-102.
14. Korobushkina, E. D., Karavaiko, G. I. and Korobushkin, I. M. (1983) Biochemistry of gold. Environmental Biogeochemistry, pp. 325-333.
15. Kozdroj, J. and van Elsas, J. D. (2000) Response of the bacterial community to root exudates in soil polluted with heavy metals assessed by molecular and cultural approaches. Soil Biol Biochem, 32, pp. 1405-1417.
16. Lane, D. J. (1991) 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics, pp. 115-175. John Wiley & Sons Ltd, Chichester
17. Levchenko, L. A., Sadkov, A. P., Lariontseva, N. V., Koldasheva, E. M., Shilova, A. K. and Shilov, A. E. (2002) Gold helps bacteria to oxidize methane. J Inorg Biochem, 88, pp. 251-253.
18. Lopez, R. (1997) Services Programme, Lloyd A
19. Madigan, M. T. and Martinko, J. M. (2006) Brock-Biology of Microorganisms., Prentice Hall, New York, USA
20. Mann, A. W. (1984) Mobility of gold and silver in lateritic weathering profiles: Some observations from Western Australia. Econ Geol, 79, pp. 38-49.
21. McDonald, R. C., Isbell, R. F., Speight, J. G., Walker, J. and Hopkins, M. S. (1998) Australian Soil and Land Survey Field Handbook., CSIRO Publishing, Australia
22. Melchior, A., Cardenas, J. and Dejonghe, L. (1994) Geomicrobiology applied to mineral exploration in Mexico. J Geochem Explor, 51, pp. 193-212.
23. Melchior, A., Dejonghe, L. and Hughesa, G. (1996) A geomicrobiological study of soils collected from auriferous areas of Argentina. J Geochem Explor, 56, pp. 219-227.
24. Muyzer, G., de Waal, E. C. and Uitterlinden, A. G. (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, pp. 695-700.
25. Muyzer, G., Hottentrager, S., Teske, A. and Wawer, C. (1996) Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA-A new molecular approach to analyse the genetic diversity of mixed microbial communities. Molecular Microbial Manual, pp. 1-23. Kluwer Academic Publishers, Dordrecht, The Netherlands
26. Muyzer, G. and Smalla, K. (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek, 73, pp. 127-141.
27. Neybergh, H. Z., Moureau, G. P., Verraes, G. and Sulten, E. (1991) Utilisation des concentrations de Bacillus cereus dans les sols comme technique de prospection des gites auriferes. Chronique de la Recherche Miniere, 502, pp. 37-46.
28. Nies, D. H. (1999) Microbial heavy-metal resistance. Appl Microbiol Biotech, 51, pp. 730-750.
29. Nikolausz, M., Sipos, R., Revesz, S., Szekely, A. and Marialigeti, K. (2005) Observation of bias associated with re-amplification of DNA isolated from denaturing gradient gels. FEMS Microbiol Lett, 244, pp. 385-390.
30. Paul, E. A. and Clark, F. E. (1996) Soil microbiology and biochemistry, Academic Press, San Diego, USA
31. Powell, S. M., Bowman, J. P., Snape, I. and Stark, J. S. (2003) Microbial community variation in pristine and polluted near shore Antarctic sediments. FEMS Microbiol Ecol, 45, pp. 135-145.
32. Ranjard, L., Poly, F. and Nazaret, S. (2000) Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment. Res Microbiol, 151, pp. 167-177.
33. Rasmussen, L. D. and Sorensen, S. J. (2001) Effect of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil. FEMS Microbiol Ecol, 36, pp. 1-9.
34. Reith, F., Lengke, M. F., Falconer, D., Craw, D. and Southam, G. (2007) Winogradski review-The geomicrobiology of gold. ISME J, 1, pp. 567-584.
35. Reith, F. and McPhail, D. C. (2006) Effect of resident microbiota on the solubilization of gold in soil from the Tomakin Park Gold Mine, New South Wales, Australia. Geochim Cosmochim Acta, 70, pp. 1421-1438.
36. Reith, F. and McPhail, D. C. (2007) Microbial influences on solubilisation and mobility of gold and arsenic in regolith samples from two gold mines in semi-arid and tropical Australia. Geochim Cosmochim Acta, 71, pp. 1183-1196.
37. Reith, F., McPhail, D. C. and Christy, A. G. (2005) Bacillus cereus, gold and associated elements in soil and other regolith samples from Tomakin Park Gold Mine in south-eastern New South Wales, Australia. J Geochem Explor, 85, pp. 81-98.
38. Reith, F., Rogers, S. L., McPhail, D. C. and Webb, D. (2006) Biomineralization of Gold: Biofilms on bacterioform gold. Science, 313, pp. 333-336.
39. Reith, F. and Rogers, S. L. (2007) Exploration Geomicrobiology-The New Frontier. Handbook of Exploration and Environmental Geochemistry 9: Biogeochemistry in Mineral Exploration, pp. 393-413. Elsevier, Amsterdam, The Netherlands
40. Selvakannan, P. R., Mandal, S., Gole, A., Pasricha, R., Adyanthaya, S. D. and Sastry, M. (2004) Water-dispersible tryptophan-protected gold nanoparticles prepared by the spontaneous reduction of aqueous chloroaurate ions by the amino acid. J Coll Interf Sci, 269, pp. 97-102.
41. Southam, G. and Saunders, J. A. (2005) The geomicrobiology of ore deposits. Econ Geol, 100, pp. 1067-1084.
42. von Wintzingerode, F., Gobel, U. B. and Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev, 21, pp. 213-229.
43. Wang, H. M., Yang, F. Q., Xie, S. C. and Zhou, Q. W. (1999) Soil Bacillus cereus serving as an indicator of gold mineralization related to underlying gold deposits in northwestern Sichuan province. Earth Sci J China Univ Geosci, 24, pp. 78-82.
44. Widmer, F., Fliessbach, A., Laczko, E., Schulze-Aurich, J. and Zeyer, J. (2001) Assessing soil biological characteristics: A comparison of bulk soil community DNA-, PFLA-, and BiologTM-analyses. Soil Biol Biochem, 33, pp. 1029-1036.
45. Witkiewicz, P. L. and Shaw, C. F. (1981) Oxidative cleavage of peptide and protein disulphide bonds by gold(III): A mechanism for gold toxicity. J Chem Soc Chem Comm, 21, pp. 1111-1114.
46. Zak, J. C., Willig, M. R., Moorhead, D. L. and Wildman, H. G. (1994) Functional diversity of microbial communities: A quantitative approach. Soil Biol Biochem, 26, pp. 1101-1108.