Culture-dependent and -independent molecular analysis of the bacterial community within uranium ore

Journal of Basic Microbiology

Volumn 51, Issue 4, 2011, Pages 372-384

  Islam, Ekramul ^a   Sar, Pinaki ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY   (India)

Author keywords

16S rRNA gene; Bacterial community; Heavy metals; Uranium ore; Uranium resistance

Indexed keywords

BACTERIAL DNA; HEAVY METAL; RIBOSOME DNA; RNA 16S; URANIUM;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIUM; BACTERIUM IDENTIFICATION; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA SEQUENCE; DRUG EFFECT; GENETICS; INDIA; ISOLATION AND PURIFICATION; MICROBIOLOGY; MINING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYSICAL CHEMISTRY; SOIL;

BACTERIA; BACTERIAL TYPING TECHNIQUES; BASE SEQUENCE; BIODIVERSITY; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA, BACTERIAL; DNA, RIBOSOMAL; DRUG RESISTANCE, BACTERIAL; INDIA; METALS, HEAVY; MINING; MOLECULAR SEQUENCE DATA; PHYLOGENY; PHYSICOCHEMICAL PHENOMENA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY; URANIUM;

ACINETOBACTER; ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BURKHOLDERIACEAE; ENTEROBACTER; EXIGUOBACTERIUM; FIRMICUTES; MICROBACTERIACEAE; MICROBACTERIUM; MORAXELLACEAE; PROTEOBACTERIA; PSEUDOMONAS; STENOTROPHOMONAS; UNIDENTIFIED BACTERIUM; XANTHOMONADACEAE;

EID: 79961187998     PISSN: 0233111X     EISSN: 15214028     Source Type: Journal    
DOI: 10.1002/jobm.201000327     Document Type: Article

References (33)

1. Dong, H., 2008. Microbial life in extreme environments: Linking geological and microbiological processes. In: Dilek, Y., Furnes, H., Muehlenbachs, K., (eds.), Links between Geological Processes, Microbial Activities and Evolution of Life., Springer, Berlin, pp. 237-280.
2. Rastogi, G., Osman, S., Kukkadapu, R., Engelhard, M. et al., 2010. Microbial and mineralogical characterizations of soils collected from the deep biosphere of the former Homestake gold mine, South Dakota. Microb. Ecol., DOI: 10.1007/s00248-010-9657-y.
3. Wanger, G., Onstott, T.C., Southam, G., 2008. Stars of the terrestrial deep subsurface: A novel 'star-shaped' bacterial morphotype from a South African platinum mine. Geobiology, 6, 325-30.
4. Southam, G., Saunders, J.A., 2005. The geomicrobiology of ore deposits. Econ. Geol., 100, 1067-1084.
5. Pfiffner, S.M., Cantu, J.M., Smithgall, A., Peacock, A.D. et al., 2006. Deep subsurface microbial biomass and community structure in Witwatersrand Basin mines. Geomicrobiol. J., 23, 431-442.
6. Fukuda, A., Hagiwara, H., Ishimura, T., Kouduka, M., Ioka, S., Amano, Y., Tsunogai, U., Suzuki, Y., Mizuno, T., 2010. Geomicrobiological properties of ultra-deep granitic groundwater from the Mizunami Underground Research Laboratory (MIU), central Japan. Microb. Ecol., 60, 214-225.
7. Papineau, D., Walker, J.J., Mojzsis, S.J., Pace, N.R., 2005. Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia. Appl. Environ. Microbiol., 71, 4822-4832.
8. Valenzuela, L., Chi, A., Beard, S., Orell, A. et al., 2006. Genomics, metagenomics and proteomics in biomining microorganisms. Biotechnol. Adv., 24, 197-211.
9. Rastogi, G., Osman, S., Vaishampayan, P.A., Andersen, G.L., Stetler, L.D., Sani, R.K., 2010. Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library. Microb. Ecol., 59, 94-108.
10. Akob, D.M., Mills, H.J., Kostka, J.E., 2007. Metabolically active microbial communities in uranium-contaminated subsurface sediments. FEMS Microbiol. Ecol., 59, 95-107.
11. Merroun, M.L., Selenska-Pobell, S., 2008. Bacterial interactions with uranium: An environmental perspective. J. Contam. Hydrol., 102, 285-295.
12. Radeva, G., Selenska-Pobell, S., 2005. Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals. Can. J. Microbiol., 51, 910-923.
13. Gadd, G.M., Metals, minerals and microbes: Geomicrobiology and bioremediation. Microbiology, 156, 609-643.
14. Oremland, R.S., Capone, D.G., Stolz, J.F., Fuhrman., J., 2005. Whither or wither geomicrobiology in the era of 'community metagenomics';. Nat. Rev. Microbiol., 3, 572-578.
15. Rawlings, D.E., Johnson, D.B., 2007. The microbiology of biomining: development and optimization of mineral-oxidizing microbial consortia. Microbiology, 153, 315-324.
16. Jackson, M.L., 1967. Soil Chemical Analysis. Prentice Hall of India Pvt. Ltd., New Delhi.
17. Kepner, R.L., Pratt, J.R., 1994. Use of fluorochromes for direct enumeration of total bacteria in environmental samples: Past and present. Microbiol. Rev., 58, 603-615.
18. Martinez, R.J., Wang, Y., Raimondo, M.A., Coombs, J.M., Barkay, T., Sobecky, P.A., 2006. Horizontal gene transfer of PIB-type ATPases among bacteria isolated from radionuclide- and metal-contaminated subsurface soils. Appl. Environ. Microbiol., 72, 3111-3118.
19. Bhattacharyya, S., Chakrabarti, B.K., Das, A., Kundu, P.N., Banerjee, P.C., 1991. Acidiphilium symbioticum sp. nov., an acidophilic heterotrophic bacterium from Thiobacillus ferrooxidans cultures isolated from Indian mines. Can. J. Microbiol., 37, 78-85.
20. Olson, G.J., McFeters, G.A., Temple, K.L., 1981. Occurrence and activity of iron- and sulfur-oxidizing microorganisms in alkaline coal strip mine spoils. Mirob. Ecol., 7, 39-50.
21. Reardon, C.L., Cummings, D.E., Petzke, L.M., Kinsall, B.L. et al., 2004. Composition and diversity of microbial communities recovered from surrogate minerals incubated in an acidic uranium-contaminated aquifer. Appl. Environ. Microbiol., 70, 6037-6046.
22. Muyzer, G., de Waal, E.C., 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, 695-700.
23. Tamura, K., Dudley, J., Nei, M., Kumar, S., 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24, 1596-1599.
24. Suzuki, Y., Banfield, J.F., 2004. Resistance to, and accumulation of, uranium by bacteria from a uranium-contaminated site. J. Geomicrobiol., 21, 113-121.
25. Kieft, T.L., Kovacik, W.P., Ringelberg, D.B., White, D.C., Haldeman, D.L., Amy, P.S., Hersman, L.E., 1997. Factors limiting microbial growth and activity at a proposed high-level nuclear repository, Yucca Mountain, Nevada. Appl. Environ. Microbiol., 63, 3128-3133.
26. Janssen, P.H., Yates, P.S., Grinton, B.E., Taylor, P.M., Sait, M., 2002. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl. Environ. Microbiol., 68, 2391-2396.
27. Fierer, N., Jackson, R.B., 2006. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA, 103, 626-631.
28. Fields, M.W., Yan, T., Rhee, S.K., Carroll, S.L. et al., 2005. Impacts on microbial communities and cultivable isola- tes from groundwater contaminated with high levels of nitric acid-uranium waste. FEMS Microbiol. Ecol., 53, 417-428.
29. Peix, A., Ramirez-Bahena, M.H., Velazquez, E., 2009. Historical evolution and current status of the taxonomy of genus Pseudomonas. Infect. Genet. Evol., 9, 1132-1147.
30. OECD, 2008. Consensus document on information used in the assessment of environmental applications involving Acinetobacter. Series on Harmonization of Regulatory Oversight in Biotechnology No. 46. Organisation for Economic Co-operation and Development (OECD), Paris.
31. Nedelkova, M., Merroun, M.L., Rossberg, A., Hennig, C., Selenska-Pobell, S., 2007. Microbacterium isolates from the vicinity of a radioactive waste depository and their interactions with uranium. FEMS Microbiol. Ecol., 59, 694-705.
32. Chen, S., Shao, Z., 2009. Isolation and diversity analysis of arsenite-resistant bacteria in communities enriched from deep-sea sediments of the Southwest Indian Ocean Ridge. Extremophiles, 13, 39-48.
33. Chaudhary, S., 2010. Uranium and other heavy metal resistance and accumulation in a Pseudomonas aeruginosa strain: Potential in bioremediation. Ph.D. thesis, Indian Institute of Technology Kharagpur, Kharagpur, India.