Enrichment and characterization of a sulfate-reducing toluene-degrading microbial consortium by combining in situ microcosms and stable isotope probing techniques

FEMS Microbiology Ecology

Volumn 71, Issue 2, 2010, Pages 237-246

  Bombach, Petra ^a   Chatzinotas, Antonis ^a   Neu, Thomas R ^a   Kästner, Matthias ^a   Lueders, Tillmann ^b   Vogt, Carsten ^a  

^a HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH UFZ   (Germany)

^b INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

Biodegradation; In situ microcosm; Stable isotope probing (SIP); Sulfate reducing; Toluene

Indexed keywords

CARBON 13; RIBOSOME RNA; STABLE ISOTOPE; TOLUENE;

AQUIFER POLLUTION; BIODEGRADATION; BTEX; ENRICHMENT; FATTY ACID; IDENTIFICATION METHOD; MICROCOSM; PHYLOGENETICS; POLYMORPHISM; RNA; STABLE ISOTOPE; SULFATE-REDUCING BACTERIUM; TOLUENE;

ARTICLE; BIODEGRADATION; BIOMASS; CONTROLLED STUDY; IN SITU HYBRIDIZATION; MICROCOSM; NONHUMAN; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SULFATE REDUCING BACTERIUM;

BIODEGRADATION, ENVIRONMENTAL; CARBON ISOTOPES; FATTY ACIDS; FRESH WATER; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SULFATES; SULFUR-REDUCING BACTERIA; TOLUENE; WATER MICROBIOLOGY; WATER POLLUTANTS, CHEMICAL;

BACTERIA (MICROORGANISMS); DESULFOCAPSA;

EID: 72949090817     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2009.00809.x     Document Type: Article

References (45)

1. Annweiler E, Richnow HH, Antranikian G, Hebenbrock S, Garms C, Franke S, Francke W Michaelis W (2000) Naphthalene degradation and incorporation of naphthalene-derived carbon into biomass by the thermophile Bacillus thermoleovorans. Appl Environ Microb 66 : 518 523.
2. Beller HR, Spormann AM, Sharma PK, Cole JR Reinhard M (1996) Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium. Appl Environ Microb 62 : 1188 1196.
3. 13C) labeling in combination with PLFA analysis. Molecular Microbial Ecology Manual, Vol. 2 (Kowalchuk GA, Bruijn FJD, Head IM, Akkermans ADL Elsas JDV, eds), pp. 1673 1688. Kluwer Academic Publisher, Dordrecht.
4. Dojka MA, Hugenholtz P, Haack SK Pace NR (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microb 64 : 3869 3877.
5. Fang J, Lovanh N Alvarez PJJ (2004) The use of isotopic and lipid analysis techniques linking toluene degradation to specific microorganisms: applications and limitations. Water Res 38 : 2529 2536.
6. 13C-carrier DNA shortens the incubation time needed to detect benzoate-utilizing denitrifying bacteria by stable-isotope probing. Appl Environ Microb 71 : 5192 5196.
7. 13C-labeled benzene or toluene. Environ Sci Technol 39 : 4983 4989.
8. Griebler C Lueders T (2008) Microbial biodiversity in groundwater ecosystems. Freshwater Biol 54 : 649 677.
9. Guckert JB, Antworth CP, Nichols PD White DC (1985) Phospholipid, ester-linked fatty acid profiles as reproducible assays for changes in prokaryotic community structure of estuarine sediments. FEMS Microbiol Ecol 31 : 147 158.
10. Harms G, Zengler K, Rabus R, Aeckersberg F, Minz D, Rossello-Mora R Widdel F (1999) Anaerobic oxidation of o-xylene, m-xylene, and homologous alkylbenzenes by new types of sulfate-reducing bacteria. Appl Environ Microb 65 : 999 1004.
11. Hatamoto M, Imachi H, Yashiro Y, Ohashi A Harada H (2007) Diversity of anaerobic microorganisms involved in long-chain fatty acid degradation in methanogenic sludges as revealed by RNA-based stable isotope probing. Appl Environ Microb 73 : 4119 4127.
12. Heider J (2007) Adding handles to unhandy substrates: anaerobic hydrocarbon activation mechanisms. Curr Opin Chem Biol 11 : 188 194.
13. Heider J, Spormann AM, Beller HR Widdel F (1998) Anaerobic bacterial metabolism of hydrocarbons. FEMS Microbiol Rev 22 : 459 473.
14. Herrmann S, Kleinsteuber S, Neu TR, Richnow HH Vogt C (2008) Enrichment of anaerobic benzene-degrading microorganisms by in situ microcosms. FEMS Microbiol Ecol 63 : 94 106.
15. Herrmann S, Kleinsteuber S, Chatzinotas A, Kuppardt S, Lueders T, Richnow HH Vogt C (2009) Functional characterisation of an anaerobic benzene-degrading enrichment culture by DNA stable isotope probing. Environ Microbiol DOI :.
16. 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 Microb 72 : 3586 3592.
17. Kästner M, Fischer A, Nijenhuis I, Geyer R, Stelzer N, Bombach P, Tebbe CC Richnow HH (2006) Assessment of microbial in situ activity in contaminated aquifers. Eng Life Sci 6 : 234 251.
18. Kaur A, Chaudhary A, Kaur A, Choudhary R Kaushik R (2005) Phospholipid fatty acid - a bioindicator of environment and assessment in soil ecosystem. Curr Sci 89 : 1103 1112.
19. Kleikemper J, Pelz O, Schroth MH Zeyer J (2002) Sulfate-reducing bacterial community response to carbon source amendments in contaminated aquifer microcosms. FEMS Microbiol Ecol 42 : 109 118.
20. Kleinsteuber S, Schleinitz KM, Breitfeld J, Harms H, Richnow HH Vogt C (2008) Molecular characterization of bacterial communities mineralizing benzene under sulfate-reducing conditions. FEMS Microbiol Ecol 66 : 143 157.
21. Kovatcheva-Datchary P, Egert M, Maathuis A, Rajilic-Stojanovic M, de Graaf AA, Smidt H, de Vos WM Venema K (2009) Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing. Environ Microbiol 11 : 914 926.
22. Kunapuli U, Lueders T Meckenstock RU (2007) The use of stable isotope probing to identify key iron-reducing microorganisms involved in anaerobic benzene degradation. ISME J 1 : 643 653.
23. Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt E Goodfellow M, eds), pp. 11 175. Wiley, Chichester, UK.
24. Ludwig W, Strunk O, Westram R et al 2004) ARB: a software environment for sequence data. Nucleic Acids Res 32 : 1363 1371.
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 536 : 1 6.
26. 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 Microb 72 : 5342 5348.
27. 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 Microb 68 : 5367 5373.
28. Meckenstock RU (1999) Fermentative toluene degradation in anaerobic defined syntrophic cocultures. FEMS Microbiol Lett 177 : 67 73.
29. Morasch B, Schink B, Tebbe CC Meckenstock RU (2004) Degradation of o-xylene and m-xylene by a novel sulfate-reducer belonging to the genus Desulfotomaculum. Arch Microbiol 181 : 407 417.
30. Oka AR, Phelps CD, McGuinness LM, Mumford A, Young LY Kerkhof LJ (2008) Identification of critical members in a sulfidogenic benzene-degrading consortium by DNA stable isotope probing. Appl Environ Microb 74 : 6476 6480.
31. Peacock AD, Chang YJ, Istok JD, Krumholz L, Geyer R, Kinsall B, Watson D, Sublette KL White DC (2004) Utilization of microbial biofilms as monitors of bioremediation. Microb Ecol 47 : 284 292.
32. 13C- incorporation in fatty acids and whole-cell hybridization. FEMS Microbiol Ecol 38 : 123 131.
33. 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 Microb 59 : 1444 1451.
34. Radajewski S, Webster G, Reay DS, Morris SA, Ineson P, Nedwell DB, Prosser JI Murrell JC (2002) Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing. Microbiology 148 : 2331 2342. (Pubitemid 34928519)
35. Schirmer M, Dahmke A, Dietrich P, Dietze M, Gödeke S, Richnow HH, Schirmer K, Wei H Teutsch G (2006) Natural attenuation research at the contaminated megasite Zeitz. J Hydrol 328 : 393 407.
36. Schmitt ME, Brown TA Trumpower BL (1990) A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res 18 : 3091 3092.
37. van Agteren MH, Keuning S Janssen DB (1998) Handbook on Biodegradation and Biological Treatment of Hazardous Organic Compounds. Kluwer Academic Publishers, Dordrecht.
38. Vieth A, Kästner M, Schirmer M, Weiss H, Gödeke S, Meckenstock RU Richnow HH (2005) Monitoring in situ biodegradation of benzene and toluene by stable carbon isotope fractionation. Environ Toxicol Chem 24 : 51 60.
39. Vogt C, Lösche A, Kleinsteuber S Müller S (2005) Population profiles of a stable, commensalistic bacterial culture grown with toluene under sulphate-reducing conditions. Cytom Part A 66A : 91 102.
40. Vogt C, Gödeke S, Treutler H-C, Weiß H, Schirmer M Richnow H-H (2007) Benzene oxidation under sulfate-reducing conditions in columns simulating in situ conditions. Biodegradation 18 : 625 636.
41. Whiteley AS, Manefield M Lueders T (2006) Unlocking the 'microbial black box' using RNA-based stable isotope probing technologies. Curr Opin Biotech 17 : 67 71.
42. Whiteley AS, Thomson B, Lueders T Manefield M (2007) RNA stable-isotope probing. Nat Protocol 2 : 838 844.
43. Widdel F Rabus R (2001) Anaerobic biodegradation of saturated and aromatic hydrocarbons. Curr Opin Biotech 12 : 259 276.
44. 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.
45. Winderl C, Anneser B, Griebler C, Meckenstock RU Lueders T (2008) Depth-resolved quantification of anaerobic toluene degraders and aquifer microbial community patterns in distinct redox zones of a tar oil contaminant plume. Appl Environ Microb 74 : 792 801.