The use of stable isotope probing to identify key iron-reducing microorganisms involved in anaerobic benzene degradation

ISME Journal

Volumn 1, Issue 7, 2007, Pages 643-653

  Kunapuli, Umakanth ^a   Lueders, Tillmann ^a   Meckenstock, Rainer U ^a  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

Anaerobic benzene degradation; Iron reducing microorganisms; Stable isotope probing; Syntrophic interactions

Indexed keywords

BENZENE; CARBON; IRON; RNA 16S;

ACTINOBACTERIA; ANAEROBIC GROWTH; ARTICLE; CLASSIFICATION; DELTAPROTEOBACTERIA; GENETICS; METABOLISM; OXIDATION REDUCTION REACTION; PEPTOCOCCACEAE; PHYLOGENY;

ACTINOBACTERIA; ANAEROBIOSIS; BENZENE; CARBON ISOTOPES; DELTAPROTEOBACTERIA; IRON; OXIDATION-REDUCTION; PEPTOCOCCACEAE; PHYLOGENY; RNA, RIBOSOMAL, 16S;

ACTINOBACTERIA; CLOSTRIDIA; DELTAPROTEOBACTERIA; DESULFOBULBACEAE; PEPTOCOCCACEAE; POSIBACTERIA; THERMINCOLA;

EID: 35948975729     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2007.73     Document Type: Article

References (54)

1. Alfreider A, Vogt C, Babel W. (2002). Microbial diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16S ribosomal DNA analysis. Syst Appl Microbiol 25: 232-240.
2. Anderson RT, Rooney-Varga JN, Gaw CV, Lovley DR. (1998). Anaerobic benzene oxidation in the Fe(III) reduction zone of petroleum-contaminated aquifers. Environ Sci Technol 32: 1222-1229.
3. Bak F, Widdel F. (1986). Anaerobic degradation of phenol and phenol derivatives by Desulfobacterium phenolicum sp. nov. Arch Microbiol 146: 177-180.
4. Beller HR, Spormann AM, Sharma PK, Cole JR, Reinhard M. (1996). Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium. Appl Environ Microbiol 62: 1188-1196.
5. Burland SM, Edwards EA. (1999). Anaerobic benzene biodegradation linked to nitrate reduction. Appl Environ Microbiol 65: 529-533.
6. Chakraborty R, Coates JD. (2004). Anaerobic degradation of monoaromatic hydrocarbons. Appl Microbiol Biotechnol 64: 437-446.
7. Coates JD, Bhupathiraju VK, Achenbach LA, McInerney MJ, Lovley DR. (2001a). Geobacter hydrogenophilus, Geobacter chapellei and Geobacter grbiciae, three new, strictly anaerobic, dissimilatory Fe(III)-reducers. Int J Syst Evol Microbiol 51: 581-588.
8. Coates JD, Chakraborty R, Lack JG, O'Connor SM, Cole KA, Bender KS et al. (2001b). Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. Nature 411: 1039-1043.
9. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J, Garcia P et al. (1994). The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44: 812-826.
10. Dean BJ. (1985). Recent findings on the genetic toxicology of benzene, toluene, xylenes and phenols. Mut Res 154: 153-181.
11. Eichinger J, Rauert W, Salvamoser J, Wolf M. (1980). Large-volume liquid scintillation counting of carbon-14. Radiocarbon 22: 417-427.
12. Heider J, Spormann AM, Beller HR, Widdel F. (1998). Anaerobic bacterial metabolism of hydrocarbons. FEMS Microbiol Rev 22: 459-473.
13. Jahn MK, Haderlein SB, Meckenstock RU. (2005). Anaerobic degradation of benzene, toluene, ethylbenzene, and o-xylene in sediment-free iron-reducing enrichment cultures. Appl Environ Microbiol 71: 3355-3358.
14. Jeon CO, Park W, Padmanabhan P, DeRito C, Snape JR, Madsen EL. (2003). Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment. Proc Natl Acad Sci 100: 13591-13596.
15. Kasai Y, Takahata Y, Manefield M, Watanabe K. (2006). RNA-based stable isotope probing and isolation of anaerobic benzene-degrading bacteria from gasoline-contaminated groundwater. Appl Environ Microbiol 72: 3586-3592.
16. Kazumi J, Caldwell ME, Suflita JM, Lovley DR, Young LY. (1997). Anaerobic degradation of benzene in diverse anoxic environments. Environ Sci Technol 31: 813-818.
17. Knoblauch C, Sahm K, Jorgensen BB. (1999). Psychrophilic sulfate-reducing bacteria isolated from permanently cold Arctic marine sediments: description of Desulfofrigus oceanense gen. nov., sp. nov., Desulfofrigus fragile sp. nov., Desulfofaba gelida gen. nov., sp. nov., Desulfotalea psychrophila gen. nov., sp. nov. and Desulfotalea arctica sp. nov. Int J Syst Bacteriol 49: 1631-1643.
18. Kuever J, Rainey FA, Widdel F. (2005). Class IV. Deltaproteobacteria class nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds). Bergey's Manual of Systematic Bacteriology. Springer: New York, NY, USA, pp 922-1144.
19. Lonergan DJ, Jenter HL, Coates JD, Phillips EJP, Schmidt TM, Lovley DR. (1996). Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria. J Bacteriol 178: 2402-2408.
20. Lovley DR, Coates JD, Woodward JC, Phillips EJP. (1995). Benzene oxidation coupled to sulfate reduction. Appl Environ Microbiol 61: 953-958.
21. Lovley DR, Giovannoni SJ, White DC, Champine JE, Phillips EJP, Gorby YA et al. (1993). Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Arch Microbiol 159: 336-344.
22. Lovley DR, Phillips EJP. (1986). Organic matter mineralization with reduction of ferric iron in anaerobic sediments. Appl Environ Microbiol 51: 683-689.
23. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar et al. (2004). ARB: a software environment for sequence data. Nucl Acids Res 32: 1363-1371.
24. Lueders T, Kindler R, Miltner A, Friedrich MW, Kaestner M. (2006). Identification of bacterial micropredators distinctively active in a soil microbial food web. Appl Environ Microbiol 72: 5342-5348.
25. Lueders T, Manefield M, Friedrich MW. (2004). Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol 6: 73-78.
26. Madsen EL. (2006). The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Curr Opin Biotechnol 17: 92-97.
27. Mahmood S, Paton GI, Prosser JI. (2005). Cultivation-independent in situ molecular analysis of bacteria involved in degradation of pentachlorophenol in soil. Environ Microbiol 7: 1349-1360.
28. Manefield M, Whiteley AS, Griffiths RI, Bailey MJ. (2002). RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68: 5367-5373.
29. Meckenstock RU. (1999). Fermentative toluene degradation in anaerobic defined syntrophic cocultures. FEMS Microbiol Lett 177: 67-73.
30. Meckenstock RU, Safinowski M, Griebler C. (2004). Anaerobic degradation of polycyclic aromatic hydrocarbons. FEMS Microbiol Ecol 49: 27-36.
31. 13C-labeled soil DNA. Appl Environ Microbiol 69: 1614-1622.
32. Phelps CD, Kerkhof LJ, Young LY. (1998). Molecular characterization of a sulfate-reducing consortium which mineralizes benzene. FEMS Microbiol Ecol 27: 269-279.
33. Phelps CD, Young LY. (1999). Anaerobic biodegradation of BTEX and gasoline in various aquatic sediments. Biodegradation 10: 15-25.
34. Rabus R, Nordhaus R, Ludwig W, Widdel F. (1993). Complete oxidation of toluene under strictly anoxic conditions by a new sulfate-reducing bacterium. Appl Environ Microbiol 59: 1444-1451.
35. Radajewski S, Ineson P, Parekh NR, Murrell JC. (2000). Stable-isotope probing as a tool in microbial ecology. Nature 403: 646-649.
36. Robertson WJ, Bowman JP, Franzmann PD, Mee BJ. (2001). Desulfosporosinus meridiei sp. nov., a spore-forming sulfate-reducing bacterium isolated from gasolene-contaminated groundwater. Int J Syst Evol Microbiol 51: 133-140.
37. Rooney-Varga JN, Anderson RT, Fraga JL, Ringelberg D, Lovley DR. (1999). Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Appl Environ Microbiol 65: 3056-3063.
38. Schink B. (1997). Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61: 262-280.
39. Schlötelburg C, von Wintzingerode F, Hauck R, Hegemann W, Göbel UB. (2000). Bacteria of an anaerobic 1,2-dichloropropane-dechlorinating mixed culture are phylogenetically related to those of other anaerobic dechlorinating consortia. Int J Syst Evol Microbiol 50: 1505-1511.
40. Slobodkin A, Reysenbach AL, Mayer F, Wiegel J. (1997). Isolation and characterization of the homoacetogenic thermophilic bacterium Moorella glycerini sp. nov. Int J Syst Bacteriol 47: 969-974.
41. Sokolova TG, Kostrikina NA, Chernyh NA, Kolganova TV, Tourova TP, Bonch-Osmolovskaya EA. (2005). Thermincola carboxydiphila gen. nov., sp. nov., a novel anaerobic, carboxydotrophic hydrogenogenic bacterium from a hot spring of the Lake Baikal area. Int J Syst Evol Microbiol 55: 2069-2073.
42. Stookey LL. (1970). Ferrozine-a new spectrophotometric reagent for iron. Anal Chem 42: 779-781.
43. Straub KL, Schink B. (2004). Ferrihydrite-dependent growth of Sulfurospirillum deleyianum through electron transfer via sulfur cycling. Appl Environ Microbiol 70: 5744-5749.
44. Szewzyk R, Pfennig N. (1987). Complete oxidation of catechol by the strictly anaerobic sulfate-reducing Desulfobacterium catecholicum sp. nov. Arch Microbiol 147: 163-168.
45. Ulrich AC, Edwards EA. (2003). Physiological and molecular characterization of anaerobic benzene-degrading mixed cultures. Environ Microbiol 5: 92-102.
46. Villemur R, Lanthier M, Beaudet R, Lepine F. (2006). The Desulfitobacterium genus. FEMS Microbiol Rev 30: 706-733.
47. Weiner JM, Lovley DR. (1998). Rapid benzene degradation in methanogenic sediments from a petroleum-contaminated aquifer. Appl Environ Microbiol 64: 1937-1939.
48. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. (1991). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173: 697-703.
49. Widdel F, Bak F. (1992). Gram-negative mesophilic sulfate-reducing bacteria. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer K-H (eds). The Prokaryotes. Springer: New York, NY, USA, pp 3352-3378.
50. Winderl C, Schaefer S, Lueders T. (2007). Detection of anaerobic toluene and hydrocarbon degraders in contaminated aquifers using benzylsuccinate synthase (bssA) genes as a functional marker. Environ Microbiol 9: 1035-1046.
51. Yi H, Schumann P, Chun J. (2007). Demequina aestuarii gen. nov., sp. nov., a novel actinomycete of the suborder Micrococcineae, and reclassification of Cellulomonas fermentans Bangara et al. 1985 as Actinotalea fermentans gen. nov., comb. nov. Int J Syst Evol Microbiol 57: 151-156.
52. Yu C-P, Chu K-H. (2005). A quantitative assay for linking microbial community function and structure of a naphthalene-degrading microbial consortium. Environ Sci Technol 39: 9611-9619.
53. Zavarzina DG, Sokolova TG, Tourova TP, Chernyh NA, Kostrikina NA, Bonch-Osmolovskaya EA. (2007). Thermincola ferriacetica sp. nov., a new anaerobic, thermophilic, facultatively chemolithoautotrophic bacterium capable of dissimilatory Fe(III) reduction. Extremophiles 11: 1-7.
54. Zengler K, Richnow HH, Rosello-Mora R, Michaelis M, Widdel F. (1999). Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401: 466-469.