Resolution of natural microbial community dynamics by community fingerprinting, flow cytometry, and trend interpretation analysis

Advances in Biochemical Engineering/Biotechnology

Volumn 124, Issue , 2011, Pages 151-181

  Bombach, Petra ^a   Hübschmann, Thomas ^a   Fetzer, Ingo ^a   Kleinsteuber, Sabine ^a   Geyer, Roland ^b   Harms, Hauke ^a   Müller, Susann ^a  

^a HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH UFZ   (Germany)

^b Tecan Trading AG   (Switzerland)

Author keywords

Bioprocess control; Biostimulation; In situ microcosms; Microbial community analysis; Microbial flow cytometry

Indexed keywords

ARTICLE; BACTERIUM; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; DNA FINGERPRINTING; FLOW CYTOMETRY; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIAL CONSORTIUM; PHYSIOLOGY;

BACTERIA; COMPUTER SIMULATION; DNA FINGERPRINTING; FLOW CYTOMETRY; MICROBIAL CONSORTIA; MODELS, BIOLOGICAL;

BACTERIA (MICROORGANISMS);

EID: 80052744267     PISSN: 07246145     EISSN: None     Source Type: Book Series    
DOI: 10.1007/10_2010_82     Document Type: Article

References (53)

1. Abdo Z, Schüette UME, Bent SJ, Williams CJ, Forney LJ, Joyce P (2006) Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ Microbiol 8:929-938
2. Aksoy M (1985) Benzene as a leukemogenic and carcinogenic agent. Am J Ind Med 8:9-20
3. Beller HR, Kane SR, Legler TC, McKelvie JR, Sherwood Lollar B, Pearson F, Balser L, MacKay DM (2008) Comparative assessments of benzene, toluene, and xylene natural attenuation by quantitative polymerase chain reaction analysis of a catabolic gene, signature metabolites, and compound-specific isotope analysis. Environ Sci Technol 42:6065-6072
4. Bombach P, Chatzinotas A, Neu TR, Kästner M, Lueders T, Vogt C (2010a) Enrichment and characterization of a sulfate-reducing toluene-degrading microbial consortium by combining in situ microcosms and stable isotope probing techniques. FEMS Microbiol Ecol 71:237-246
5. Bombach P, Richnow HH, Kästner M, Fischer A (2010b) Current approaches for the assessment of in situ biodegradation. Appl Microbiol Biotechnol 86:839-852
6. Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. Austral Ecol 18:117-143
7. Da Silva MLB, Alvarez PJJ (2004) Enhanced anaerobic biodegradation of benzene-tolueneethylbenzene-xylene-ethanol mixtures in bioaugmented aquifer columns. Appl Environ Microbiol 70:4720-4726
8. EEA (2007) Progress in management of contaminated sites. European Environment Agency
9. Foght J (2008) Anaerobic biodegradation of aromatic hydrocarbons: pathways and prospects. J Mol Microbiol Biotechnol 15:93-120
10. Geyer R, Peacock AD, Miltner A, Richnow HH, White DC, Sublette KL, Kästner M (2005) In situ assessment of biodegradation potential using biotraps amended with 13C-labeled benzene or toluene. Environ Sci Technol 39:4983-4989
11. Günther S, Hübschmann T, Rudolf M, Eschenhagen M, Röske I, Harms H, Müller S (2008) Fixation procedures for flow cytometric analysis of environmental bacteria. J Microbiol Methods 75:127-134
12. Günther S, Trutnau M, Kleinsteuber S, Hause G, Bley T, Röske I, Harms H, Müller S (2009) Dynamics of polyphosphate-accumulating bacteria in wastewater treatment plant microbial communities detected via DAPI (40,60-diamidino-2-phenylindole) and tetracycline labeling. Appl Environ Microbiol 75:2111-2121
13. Herrmann S, Kleinsteuber S, Chatzinotas A, Kuppardt S, Lueders T, Richnow HH, Vogt C (2010) Functional characterization of an anaerobic benzene-degrading enrichment culture by DNA stable isotope probing. Environ Microbiol 12:401-411
14. Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS, Wagner M (2007) Raman-FISH: Combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol 9:1878-1889
15. Jehmlich N, Schmidt F, Taubert M, Seifert J, von Bergen M, Richnow HH, Vogt C (2009) Comparison of methods for simultaneous identification of bacterial species and determination of metabolic activity by protein-based stable isotope probing (protein-SIP) experiments. Rapid Commun Mass Spectrom 23:1871-1878
16. Jindrova E, Chocova M, Demnerova K, Brenner V (2002) Bacterial aerobic degradation of benzene, toluene, ethylbenzene and xylene. Folia Microbiol 47:83-93
17. 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
18. 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
19. Kleinsteuber S, Riis V, Fetzer I, Harms H, Müller S (2006) Population dynamics within a microbial consortium during growth on diesel fuel in saline environments. Appl Environ Microbiol 72:3531-3542
20. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 11-175
21. Li T, Wu T-D, Mazéas L, Toffin L, Guerquin-Kern J-L, Leblon G, Bouchez T (2008) Simultaneous analysis of microbial identity and function using NanoSIMS. Environ Microbiol 10:580-588
22. Liou JS-C, DeRito CM, Madsen EL (2008) Field-based and laboratory stable isotope probing surveys of the identities of both aerobic and anaerobic benzene-metabolizing microorganisms in freshwater sediment. Environ Microbiol 10:1964-1977
23. 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
24. Lovley DR, Phillips EJP (1988) Novel mode of microbial energy-metabolism-organiccarbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl Environ Microbiol 54:1472-1480
25. Lovley DR (2001) Bioremediation: anaerobes to the rescue. Science 293:1444-1446
26. Madsen EL (2005) Identifying microorganisms responsible for ecologically significant biogeochemical processes. Nat Rev Microbiol 3:439-446
27. Maher N, Dillon HK, Vermund SH, Unnasch TR (2001) Magnetic bead capture eliminates PCR inhibitors in samples collected from the airborne environment, permitting detection of Pneumacystis carinii DNA. Appl Environ Microbiol 67:449-452
28. Mandelbaum RT, Shati MR, Ronen D (1997) In situ microcosms in aquifer bioremediation studies. FEMS Microbiol Rev 20:489-502
29. Mou XZ, Moran MA, Stepanauskas R, Gonzalez JM, Hodson RE (2005) Flow-cytometric cell sorting and subsequent molecular analyses for culture-independent identification of bacterioplankton involved in dimethylsulfoniopropionate transformations. Appl Environ Microbiol 71:1405-1416
30. Mueller S et al. (2006) Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl Environ Microbiol 72:1027-1033
31. Müller S, Vogt C, Laube M, Harms H, Kleinsteuber S (2009) Community dynamics within a bacterial consortium during growth on toluene under sulfate-reducing conditions. FEMS Microbiol Ecol 70:586-596
32. Müller S, Harms H, Bley T (2010) Origin and analysis of microbial population heterogeneity in bioprocesses. Curr Opin Biotechnol 21:100-113
33. Müller S, Nebe-von-Caron G (2010) Functional single-cell analyses: Flow cytometry and cell sorting of microbial populations and communities. FEMS Microbiol Rev 34:554-587
34. Neufeld J, Dumont M, Vohra J, Murrell J (2007) Methodological considerations for the use of stable isotope probing in microbial ecology. Microb Ecol 53:435-442
35. Nielsen DR, McLellan PJ, Daugulis AJ (2006) Direct estimation of the oxygen requirements of Achromobacter xylosoxidans for aerobic degradation of monoaromatic hydrocarbons (BTEX) in a bioscrubber. Biotechnol Lett 28:1293-1298
36. Oksanen J, Blanchet FG, Kindt R, Legendre P, O'Hara RG, Simpson GL, Solymos P, Stevens MHH, Wagner H (2010) vegan: Community ecology package. R package version 1.17-1. http://cran.R-project.Org/package=vegan
37. 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
38. Porter J, Edwards C, Morgan JAW, Pickup RW (1993) Rapid, automated separation of specific bacteria from lake water and sewage by flow-cytometry and cell sorting. Appl Environ Microbiol 59:3327-3333
39. Rosselló-Mora R, Lee N, Antón J, Wagner M (2003) Substrate uptake in extremely halophilic microbial communities revealed by microautoradiography and fluorescence in situ hybridization. Extremophiles 7:409-413
40. Sakai N, Kurisu F, Yagi O, Nakajima F, Yamamoto K (2009) Identification of putative benzene-degrading bacteria in methanogenic enrichment cultures. J Biosci Bioeng 108:501-507
41. Schirmer M, Dahmke A, Dietrich P, Dietze M, Gödeke S, Richnow HH, Schirmer K, Weiß H, Teutsch G (2006) Natural attenuation research at the contaminated megasite Zeitz. J Hydrol 328:393-407
42. Scow KM, Hicks KA (2005) Natural attenuation and enhanced bioremediation of organic contaminants in groundwater. Curr Opin Biotechnol 16:246-253
43. Spormann AM, Widdel F (2001) Metabolism of alkylbenzenes, alkanes, and other hydrocarbons in anaerobic bacteria. Biodegradation 11:85-105
44. Strevett K, Davidova I, Suflita JM (2002) A comprehensive review of the screening methodology for anaerobic biodegradability of surfactants. Rev Environ Sci Biotechnol 1:143-167
45. Talbot G, Topp E, Palin MF, Masse DI (2008) Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors. Water Res. 42:513-537
46. US-EPA (2004) Cleaning up the nation's waste sites: Markets and technology trends. Office of Solid Waste and Emergency Response, Washington, DC
47. van Agteren MH, Keuning S, Janssen DB (1998) Handbook on biodegradation and biological treatment of hazardous organic compounds. Kluwer Academic Publishers, Dordrecht
48. VerBerkmoes NC, Hervey WJ, Shah M, Land M, Hauser L, Larimer FW, Van Berkel GJ, Goeringer DE (2005) Evaluation of "Shotgun" Proteomics for identification of biological threat agents in complex environmental matrixes: experimental simulations. Anal Chem 77:923-932
49. 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
50. Vogt C, Lösche A, Kleinsteuber S, Müller S (2005) Population profiles of a stable, commensalistic bacterial culture grown with toluene under sulphate-reducing conditions. Cytometry Part A 66A:91-102
51. Wang YY, Hammes F, Boon N, Chami M, Egli T (2009) Isolation and characterization of low nucleic acid (LNA)-content bacteria. ISME J 3:889-902
52. Wiacek C, Mueller S, Benndorf D (2006) A cytomic approach reveals population heterogeneity of Cupriavidus necator in response to harmful phenol concentrations. Proteomics 6:5983-5994
53. Wiedemeier TD, Rifai HS, Newell CJ, Wilson JT (1999) Natural attenuation of fuels and chlorinated solvents in the subsurface. Wiley Inc., London