GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage

Applied and Environmental Microbiology

Volumn 77, Issue 3, 2011, Pages 991-999

  Xie, Jianping ^a,b,c   He, Zhili ^b   Liu, Xinxing ^a,c   Liu, Xueduan ^a,c   Van Nostrand, Joy D ^b   Deng, Ye ^b   Wu, Liyou ^b   Zhou, Jizhong ^b   Qiu, Guanzhou ^a,c  

^a CENTRAL SOUTH UNIVERSITY   (China)

^b UNIVERSITY OF OKLAHOMA   (United States)

^c BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACID MINE DRAINAGE; CARBON FIXATION; DIVERSITY INDEX; ENVIRONMENTAL FACTORS; ENVIRONMENTAL VARIABLES; EXTREME ENVIRONMENT; FUNCTIONAL DIVERSITY; FUNCTIONAL GENES; HIGH CONCENTRATION; MANTEL TESTS; METAL RESISTANCES; MICROBIAL COMMUNITIES; NITROGEN REDUCTION; ORGANIC CONTAMINANT; PHYLOGENETIC DIVERSITY;

COPPER MINES; DEGRADATION; DENITRIFICATION; DRAINAGE; ECOLOGY; GENES; METABOLISM; METHANATION; METHANE; SULFUR;

NITROGEN FIXATION;

CARBON; COPPER; HEAVY METAL; METHANE; NITROGEN; SULFITE;

ACID MINE DRAINAGE; CARBON FIXATION; COPPER; GENETIC ANALYSIS; METABOLISM; MICROBIAL COMMUNITY; NITRIFICATION; NITROGEN FIXATION; PH; PHYLOGENETICS;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENE; BACTERIUM; CHINA; DNA MICROARRAY; DRUG EFFECT; ECOSYSTEM; GENETIC VARIABILITY; GENETICS; METABOLISM; METHODOLOGY; MICROBIOLOGY; MINING;

BACTERIA; CARBON; CHINA; COPPER; DRUG RESISTANCE, BACTERIAL; ECOSYSTEM; GENES, BACTERIAL; GENETIC VARIATION; METALS, HEAVY; METHANE; MINING; NITROGEN; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SULFITES; WATER MICROBIOLOGY;

CHINA;

EID: 79551493063     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01798-10     Document Type: Article

References (60)

1. Ahn, S. J., J. Costa, and J. R. Emanuel. 1996. PicoGreen quantitation of DNA: effective evaluation of samples pre- or post-PCR. Nucleic Acids Res. 24:2623-2625.
2. Allen, E. E., and J. F. Banfield. 2005. Community genomics in microbial ecology and evolution. Nat. Rev. Microbiol. 3:489-498.
3. Atkinson, T., et al. 2000. A microbiological survey of Montserrat Island hydrothermal biotopes. Extremophiles 4:305-313.
4. Baeseman, J. L., R. L. Smith, and J. Silverstein. 2006. Denitrification potential in stream sediments impacted by acid mine drainage: effects of pH, various electron donors, and iron. Microb. Ecol. 51:232-241.
5. Baker, B. J., and J. F. Banfield. 2003. Microbial communities in acid mine drainage. FEMS Microbiol. Ecol. 44:139-152.
6. Banfield, J. F., N. C. Verberkmoes, R. L. Hettich, and M. P. Thelen. 2005. Proteogenomic approaches for the molecular characterization of natural microbial communities. Omics 9:301-333.
7. Belnap, C. P., et al. 2010. Cultivation and quantitative proteomic analyses of acidophilic microbial communities. ISME J. 4:520-530.
8. Bond, P. L., G. K. Druschel, and J. F. Banfield. 2000. Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems. Appl. Environ. Microbiol. 66:4962-4971.
9. Bond, P. L., S. P. Smriga, and J. F. Banfield. 2000. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl. Environ. Microbiol. 66:3842-3849.
10. Demergasso, C. S., et al. 2005. Molecular characterization of microbial populations in a low-grade copper ore bioleaching test heap. Hydrometal-lurgy 80:241-253.
11. Dsa, J. V., K. S. Johnson, D. Lopez, C. Kanuckel, and J. Tumlinson. 2008. Residual toxicity of acid mine drainage-contaminated sediment to stream macroinvertebrates: relative contribution of acidity versus metals. Water Air Soil Poll. 194:185-197.
12. Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U. S. A. 95:14863-14868.
13. Finney, L. A., and T. V. O'Halloran. 2003. Transition metal speciation in the cell: Insights from the chemistry of metal ion receptors. Science 300:931-936.
14. Garrido, P., et al. 2008. An oligonucleotide prokaryotic acidophile microar-ray: its validation and its use to monitor seasonal variations in extreme acidic environments with total environmental RNA. Environ. Microbiol. 10:836- 850.
15. Gerhardt, A., L. J. de Bisthoven, K. Guhr, A. M. V. M. Soares, and M. J. Pereira. 2008. Phytoassessment of acid mine drainage: Lemna gibba bioassay and diatom community structure. Ecotoxicology 17:47-58.
16. Goltsman, D. S. A., et al. 2009. Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (group II) and "Leptospirillum ferrodiazotrophum" (group III) bacteria in acid mine drainage biofilms. Appl. Environ. Microbiol. 75:4599-4615.
17. He, M., Z. Wang, and H. Tang. 1997. Spatial and temporal patterns of acidity and heavy metals in predicting the potential for ecological impact on the Le An river polluted by acid mine drainage. Sci. Total Environ. 206:67-77.
18. He, Z., et al. 2007. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J. 1:67-77.
19. Kallas, T., M. C. Rebiere, R. Rippka, and N. T. Demarsac. 1983. The structural nif genes of the cyanobacteria Gloeothece sp. and Calothrix sp. share homology with those of Anabaena sp., but the Gloeothece genes have a different arrangement. J. Bacteriol. 155:427-431.
20. Karnachuk, O. V., et al. 2009. Bacteria of the sulfur cycle in the sediments of gold mine tailings, Kuznetsk Basin, Russia. Microbiology 78:483-491.
21. Kim, J., et al. 2009. Influence of acid mine drainage on microbial communities in stream and groundwater samples at Guryong Mine, South Korea. Environ. Geol. 58:1567-1574.
22. Kimes, N. E., J. D. Van Nostrand, E. Weil, J. Z. Zhou, and P. J. Morris. 2010. Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies. Environ. Microbiol. 12:541-556.
23. Krebs, W., C. Brombacher, P. P. Bosshard, R. Bachofen, and H. Brandl. 1997. Microbial recovery of metals from solids. FEMS Microbiol. Rev. 20: 605-617.
24. Lear, G., D. Niyogi, J. Harding, Y. M. Dong, and G. Lewis. 2009. Biofilm bacterial community structure in streams affected by acid mine drainage. Appl. Environ. Microbiol. 75:3455-3460.
25. Leigh, M. B., et al. 2007. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J. 1:134-148.
26. Levings, C. D., et al. 2004. Effects of acid mine drainage on the estuarine food web, Britannia Beach, Howe Sound, British Columbia, Canada. Hy-drobiologia 525:185-202.
27. Li, X. F., and M. Sasaki. 2007. Hydrothermal alteration and mineralization of middle Jurassic Dexing porphyry Cu-Mo deposit, southeastern China. Resource Geol. 57:409-426.
28. Liang, Y. T., et al. 2009. Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS Microbiol. Ecol. 70:324-333.
29. Mahmouda, K. K., L. G. Leducb, and G. D. Ferroni. 2005. Detection of Acidithiobacillus ferrooxidans in acid mine drainage environments using fluorescent in situ hybridization (FISH). J. Microbiol. Methods 61:33-45.
30. Mantel, N. 1967. Detection of disease clustering and a generalized regression approach. Cancer Res. 27:209-220.
31. Mason, O. U., et al. 2009. Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts. ISME J. 3:231-242.
32. Morel, F. M. M., and N. M. Price. 2003. The biogeochemical cycles of trace metals in the ocean. Science 300:944-947.
33. Nordstrom, D. K., and C. N. Alpers. 1999. Negative pH, efflorescent mineralogy, and consequences for environmental restoration at the Iron Mountain superfund site, California. Proc. Natl. Acad. Sci. U. S. A. 96:3455-3462.
34. Nordstrom, D. K., C. N. Alpers, C. J. Ptacek, and D. W. Blowes. 2000. Negative pH and extremely acidic mine waters from Iron Mountain, California. Environ. Sci. Technol. 34:254-258.
35. Norris, P. R., J. C. Murrell, and D. Hinson. 1995. The potential for diazo-trophy in iron-oxidizing and sulfur-oxidizing acidophilic bacteria. Arch. Mi-crobiol. 164:294-300.
36. Qiu, G. Z., et al. 2008. Archaeal diversity in acid mine drainage from Dabaoshan Mine, China. J. Basic Microbiol. 48:401-409.
37. Ram, R. J., et al. 2005. Community proteomics of a natural microbial biofilm. Science 308:1915-1920.
38. Rodríguez-Martínez, E. M., E. X. Perez, C. W. Schadt, J. Zhou, and A. A. Massol-Deya. 2006. Microbial diversity and bioremediation of a hydrocarbon-contaminated aquifer (Vega Baja, Puerto Rico). Int. J. Environ. Res. Public Health 3:292-300.
39. Sand, W., K. Rohde, B. Sobotke, and C. Zenneck. 1992. Evaluation of Leptospirillum ferrooxidans for leaching. Appl. Environ. Microbiol. 58: 85-92.
40. Schippers, A., A. A. Nagy, D. Kock, F. Melcher, and E.-D. Gock. 2008. The use of FISH and real-time PCR to monitor the biooxidation and cyanidation for gold and silver recovery from a mine tailings concentrate (Ticapampa, Peru). Hydrometallurgy 94:77-81.
41. Sokal, R. R., and F. J. Rohlf. 1994. Biometry: the principles and practices of statistics in biological research, 3rd ed. W. H. Freeman, New York, NY.
42. Tas, N., et al. 2009. Tracking functional guilds: " Dehalococcoides" spp. in European river basins contaminated with hexachlorobenzene. Appl. Environ. Microbiol. 75:4696-4704.
43. Tiwary, R. K. 2001. Environmental impact of coal mining on water regime and its management. Water Air Soil Poll. 132:185-199.
44. Tremaine, S. C., and A. L. Mills. 1991. Impact of water column acidification on protozoan bacterivory at the lake sediment-water interface. Appl. Environ. Microbiol. 57:775-784.
45. Tyson, G. W., et al. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
46. Van Nostrand, J. D., et al. 2009. GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. Environ. Microbiol. 11:2611-2626.
47. Waldron, P. J., et al. 2009. Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels. Environ. Sci. Technol. 43:3529-3534.
48. Wang, F. P., et al. 2009. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc. Natl. Acad. Sci. U. S. A. 106:4840-4845.
49. Wu, L., L. Kellogg, A. H. Devol, J. M. Tiedje, and J. Zhou. 2008. Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the gulf of Mexico. Appl. Environ. Microbiol. 74:4516-4529.
50. Wu, L. Y., X. Liu, C. W. Schadt, and J. Z. Zhou. 2006. Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl. Environ. Microbiol. 72:4931- 4941.
51. Xie, B., D. Xi, and J. Chen. 2002. Effects of heavy metals on activated sludge microorganism. J. DongHua Univ. 19:132-137.
52. Xie, X. H., S. M. Xiao, and J. S. Liu. 2009. Microbial communities in acid mine drainage and their interaction with pyrite surface. Curr. Microbiol. 59:71-77.
53. Yergeau, E., S. Kang, Z. He, J. Zhou, and G. A. Kowalchuk. 2007. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J. 1:163-179.
54. Yin, H., et al. 2008. Molecular diversity of 16S rRNA and gyrB genes in copper mines. Arch. Microbiol. 189:101-110.
55. Yin, H., et al. 2008. Bacterial diversity based on 16S rRNA and gyrB genes at Yinshan mine, China. Syst. Appl. Microbiol. 31:302-311.
56. Yin, H. Q., et al. 2007. Development and evaluation of 50-mer oligonucle-otide arrays for detecting microbial populations in acid mine drainages and bioleaching systems. J. Microbiol. Methods 70:165-178.
57. Yin, H. Q., et al. 2008. Microbial community diversity and changes associated with a mine drainage gradient at the Dexing copper mine, China. Aquat. Microb. Ecol. 51:67-76.
58. Zhang, D., G. Xu, W. Zhang, and S. D. Golding. 2007. High salinity fluid inclusions in the Yinshan polymetallic deposit from the Le-De metallogenic belt in Jiangxi Province, China: their origin and implications for ore genesis. Ore Geol. Rev. 31:247-260.
59. Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.
60. Zhou, J. Z., S. Kang, C. W. Schadt, and C. T. Garten. 2008. Spatial scaling of functional gene diversity across various microbial taxa. Proc. Natl. Acad. Sci. U. S. A. 105:7768-7773.