Investigation of Microbial Populations in the Extremely Metal-Contaminated Coeur d'Alene River Sediments

Microbial Ecology

Volumn 62, Issue 1, 2011, Pages 1-13

  Rastogi, Gurdeep ^a,c   Barua, Sutapa ^b,d   Sani, Rajesh K ^a   Peyton, Brent M ^b  

^a South Dakota School of Mines and Technology   (United States)

^b Idaho National Laboratory   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d Arizona State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; HEAVY METAL; RNA 16S;

BACTERIUM; CHEMISTRY; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MINING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; REVIEW; RIVER; SEDIMENT; WATER POLLUTANT; WATER POLLUTION;

BACTERIA; BACTERIAL PROTEINS; GEOLOGIC SEDIMENTS; METALS, HEAVY; MINING; MOLECULAR SEQUENCE DATA; PHYLOGENY; RIVERS; RNA, RIBOSOMAL, 16S; WATER POLLUTANTS, CHEMICAL; WATER POLLUTION, CHEMICAL;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); FIRMICUTES; METHANOSARCINA; NITROSOSPIRA; PROTEOBACTERIA;

EID: 79951552894     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-011-9810-2     Document Type: Review

References (56)

1. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-5741.
2. Baker BJ, Banfield JF (2003) Microbial communities in acid mine drainage. FEMS Microbiol Ecol 44: 139-152.
3. Balistrieri LS, Box SE, Tonkin JW (2003) Modeling precipitation and sorption of elements during mixing of river water and pore water in the Coeur d'Alene river basin. Environ Sci Technol 37: 4694-4701.
4. Besser JM, Brumbaugh WG, Ivey CD, Ingersoll CG, Moran PW (2008) Biological and chemical characterization of metal bioavailability in sediments from Lake Roosevelt, Columbia River, Washington, USA. Arch Environ Contam Toxicol 54: 557-570.
5. Bouskill NJ, Barker-Finkel J, Galloway TS, Handy RD, Ford TE (2010) Temporal bacterial diversity associated with metal-contaminated river sediments. Ecotoxicology 19: 317-328.
6. Brodie EL, DeSantis TZ, Parker JP, Zubietta IX, Piceno YM, Andersen GL (2007) Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci USA 104: 299-304.
7. Chhatwal I (2008) Copper and zinc induced growth inhibition to Coeur d'Alene microbial isolates. Thesis South Dakota School of Mines and Technology, Rapid City, SD USA.
8. Cummings DE, Caccavo F, Stefan S, Rosenzweiz RF (1999) Ferribacterium limneticum, gen. nov., sp. nov., an Fe(III)-reducing microorganism isolated from mining-impacted freshwater lake sediments. Arch Microbiol 171: 183-188.
9. Cummings DE, Caccavo F Jr, Fendorf S, Rosenzweig RF (1999) Arsenic mobilization by the dissimilatory Fe(III)-reducing bacterium Shewanella alga BrY. Environ Sci Technol 33: 723-729.
10. Cummings DE, March AW, Bostick B, Spring S, Caccavo F Jr, Fendorf S, Rosenzweig RF (2000) Evidence for microbial Fe(III) reduction in anoxic, mining-impacted Lake sediments (Lake Coeur d'Alene, Idaho). Appl Environ Microbiol 66: 154-162.
11. Cummings DE, Snoeyenbos-West OL, Newby DT, Niggemyer AM, Lovley DR, Achenbach LA, Rosenzweig RF (2003) Diversity of Geobacteraceae species inhabiting metal-polluted freshwater Lake sediments ascertained by 16S rDNA analyses. Microb Ecol 46: 257-269.
12. DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL (2007) High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53: 371-383.
13. Felsenstein J (1989) PHYLIP-Phylogeny inference package (version 3. 2). Cladistics 5: 164-166.
14. Feris K, Ramsey P, Frazar C, Moore JN, Gannon JE, Holben WE (2003) Differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient. Appl Environ Microbiol 69: 5563-5573.
15. Feris KP, Ramsey PW, Frazar C, Rillig M, Moore JN, Gannon JE, Holben WE (2004) Seasonal dynamics of shallow-hyporheic-zone microbial community structure along a heavy-metal contamination gradient. Appl Environ Microbiol 70: 2323-2331.
16. Field EK, D'Imperio S, Miller AR, VanEngelen MR, Gerlach R, Lee BD, Apel WA, Peyton BM (2010) Application of molecular techniques to elucidate the influence of cellulosic waste on bacterial community structure at a simulated low level radioactive waste Site. Appl Environ Microbiol 76: 3106-3115.
17. Fortin D, Roy M, Rioux JP, Thibault PJ (2000) Occurrence of sulfate-reducing bacteria under a wide range of physico-chemical conditions in Au and Cu-Zn mine tailings. FEMS Microbiol Ecol 33: 197-208.
18. Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM (2008) Towards environmental systems biology of Shewanella. Nat Rev Microbiol 6: 592-603.
19. Gillan DC, Danis B, Pernet P, Joly G, Dubois P (2005) Structure of sediment-associated microbial communities along a heavy-metal contamination gradient in the marine environment. Appl Environ Microbiol 71: 679-690.
20. Hallberg KB, Coupland K, Kimura S, Johnson DB (2006) Macroscopic streamer growths in acidic, metal-rich mine waters in North Wales consist of novel and remarkably simple bacterial communities. Appl Environ Microbiol 72: 2022-2030.
21. Hanbo Z, Changqun D, Qiyong S, Weimin R, Tao S, Lizhong C, Zhiwei Z, Bin H (2004) Genetic and physiological diversity of phylogenetically and geographically distinct groups of Arthrobacter isolated from lead-zinc mine tailings. FEMS Microbiol Ecol 49: 333-341.
22. Hao C, Wang L, Gao Y, Zhang L, Dong H (2010) Microbial diversity in acid mine drainage of Xiang Mountain sulfide mine, Anhui Province, China. Extremophiles 14: 465-474.
23. Harrington JM, Fendorf SE, Rosenzweig RF (1998) Biotic generation of Arsenic(III) in metal(loid)-contaminated freshwater lake sediments. Environ Sci Technol 32: 2425-2430.
24. Harrington JM, Laforce MJ, Rember WC, Fendorf SE, Rosenzweig RF (1998) Phase associations and mobilization of iron and trace elements in Coeur d'Alene Lake, Idaho. Environ Sci Technol 32: 650-656.
25. Hemme CL, Deng Y, Gentry TJ, Fields MW, Wu L, Barua S, Barry K, Tringe SG, Watson DB, He Z, Hazen TC, Tiedje JM, Rubin EM, Zhou J (2010) Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J 4: 660-672.
26. Hernández-Eugenio G, Fardeau ML, Cayol JL, Patel BK, Thomas P, Macarie H, Garcia JL, Ollivier B (2002) Clostridium thiosulfatireducens sp. nov., a proteolytic, thiosulfate-and sulfur-reducing bacterium isolated from an upflow anaerobic sludge blanket (UASB) reactor. Int J Syst Evol Microbiol 52: 1461-1468.
27. Horowitz AJ, Elrick KA (1995) Effect of mining and related activities on the sediment trace element geochemistry of Lake Coeur d'Alene, Idaho, USA Part II: subsurface sediments. Hydrol Process 9: 35-54.
28. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72: 1719-1728.
29. Kim BK, de Macario EC, Nölling J, Daniels L (1996) Isolation and characterization of a copper-resistant methanogen from a copper-mining soil sample. Appl Environ Microbiol 62: 2629-2635.
30. Konstantinidis KT, Isaacs N, Fett J, Simpson S, Long DT, Marsh TL (2003) Microbial diversity and resistance to copper in metal-contaminated lake sediment. Microb Ecol 45: 191-202.
31. Kumar S, Tamura K, Nei M (1993) MEGA: molecular evolutionary genetics analysis. Pennsylvania State University, University Park, PA.
32. Moberly JG (2006) Biogeochemical cycling of toxic metals in Lake Coeur d' Alene sediments. Thesis Washington State University, Pullman USA.
33. Moberly JG, Borch T, Sani RK, Spycher NF, Sengor SS, Ginn TR, Peyton BM (2009) Heavy metal-mineral associations in Coeur d'Alene River sediments: a synchrotron-based analysis. Water Air Soil Pollut 201: 195-208.
34. Moberly JG, Staven A, Sani RK, Peyton BM (2010) Influence of pH and inorganic phosphate on toxicity of zinc to Arthrobacter sp. isolated from heavy-metal contaminated sediments. Environ Sci Technol. doi: 10. 1021/es100117f, In press.
35. Mori K, Yamamoto H, Kamagata Y, Hatsu M, Takamizawa K (2000) Methanocalculus pumilus sp. nov., a heavy-metal-tolerant methanogen isolated from a waste-disposal site. Int J Syst Evol Microbiol 50: 1723-1729.
36. Nevin KP, Finneran KT, Lovley DR (2003) Microorganisms associated with uranium bioremediation in a high-salinity subsurface sediment. Appl Environ Microbiol 69: 3672-3675.
37. Niggemyer A, Spring S, Stackebrandt E, Rosenzweig RF (2001) Isolation and characterization of a novel As(V)-reducing bacterium: implications for arsenic mobilization and the genus Desulfitobacterium. Appl Environ Microbiol 67: 5568-5580.
38. Nold SC, Zhou J, Devol AH, Tiedje JM (2000) Pacific Northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the Proteobacteria. Appl Environ Microbiol 66: 4532-4535.
39. Petrie L, North NN, Dollhopf SL, Balkwill DL, Kostka JE (2003) Enumeration and characterization of iron(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium(VI). Appl Environ Microbiol 69: 7467-7479.
40. Purdy KJ, Nedwell DB, Embley TM (2003) Analysis of the sulfate-reducing bacterial and methanogenic archaeal populations in contrasting Antarctic sediments. Appl Environ Microbiol 69: 3181-3191.
41. Ramamoorthy S, Piotrowski JS, Langner HW, Holben WE, Morra MJ, Rosenzweig RF (2009) Ecology of sulfate-reducing bacteria in an iron-dominated, mining-impacted freshwater sediment. J Environ Qual 38: 675-684.
42. Rastogi G, Osman S, Kukkadapu R, Engelhard M, Vaishampayan PA, Andersen GL, Sani RK (2010) Microbial and mineralogical characterizations of soils collected from the deep biosphere of the former Homestake Gold Mine, South Dakota. Microb Ecol. (In press. doi: 10. 1007/s00248-010-9657-y).
43. Rastogi G, Osman S, Vaishampayan PA, Andersen GL, Stetler LD, Sani RK (2010) Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library. Microb Ecol 59: 94-108.
44. Rastogi G, Ranade DR, Yeole TY, Patole MS, Shouche YS (2008) Investigation of methanogen population structure in biogas reactor by molecular characterization of methyl-coenzyme M reductase A (mcrA) genes. Bioresour Technol 99: 5317-5326.
45. Rastogi G, Sani RK, Peyton BM, Moberly JG, Ginn TR (2009) Molecular studies on the microbial diversity associated with mining-impacted Coeur d'Alene river sediments. Microb Ecol 58: 129-139.
46. Roane TM (1999) Lead resistance in two bacterial isolates from heavy metal-contaminated soils. Microb Ecol 37: 218-224.
47. Sani RK, Rastogi G, Moberly JG, Dohnalkova A, Ginn TR, Spycher N, Shende N, Peyton BM (2010) The toxicity of lead to Desulfovibrio desulfuricans G20 in the presence of goethite and quartz. J Basic Microbiol 50: 160-170.
48. Sass H, Ramamoorthy S, Yarwood C, Langner H, Schumann P, Kroppenstedt RM, Spring S, Rosenzweig RF (2009) Desulfovibrio idahonensis sp. nov., sulfate-reducing bacteria isolated from a metal(loid)-contaminated freshwater sediment. Int J Syst Evol Microbiol 59: 2208-2214.
49. 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.
50. Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil. PLoS Comput Biol 2: e92.
51. Sevinc Sengor S, Sengor S, Spycher NF, Sani GTR, RK PB (2007) Biogeochemical reactive-diffusive transport of heavy metals in Lake Coeur d'Alene sediments. Appl Geochem 22: 2569-2594.
52. Simankova MV, Parshina SN, Tourova TP, Kolganova TV, Zehnder AJ, Nozhevnikova AN (2001) Methanosarcina lacustris sp. nov., a new psychrotolerant methanogenic archaeon from anoxic lake sediments. Syst Appl Microbiol 24: 362-367.
53. Sprenke KF, Rember WC, Bender SF, Hoffman ML, Rabbi F, Chamberlain VE (2000) Toxic metal contamination in the lateral lakes of the Coeur d'Alene River valley, Idaho. Environ Geol 39: 575-586.
54. Stein LY, La Duc MT, Grundl TJ, Nealson KH (2001) Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments. Environ Microbiol 3: 10-18.
55. von Wintzingerode F, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
56. Wang H, Wang FY, Wei ZQ, Hu HY (2010) Quinone profiles of microbial communities in sediments of Haihe River-Bohai Bay as influenced by heavy metals and environmental factors. Environ Monit Assess. doi: 10. 1007/s10661-010-1573-6.