Encyclopedia of Aquatic Ecotoxicology

2013 Edition
| Editors: Jean-François Férard, Christian Blaise

Monitoring of Oil-Degrading Bacteria by Stable Isotope Probing

  • Caroline Sauret
  • Jean-François Ghiglione
Reference work entry
DOI: https://doi.org/10.1007/978-94-007-5704-2_69


16S rRNA gene

A gene that encodes for the ribosomal RNA of the small subunit of the ribosome involved in the translation of messenger RNA sequences into amino acid chains in prokaryotes. This gene is universally present but sufficiently variant to allow comparison among all bacterial taxa. Many molecular tools are based on its phylogenic resolution capacity.

Bacterial taxon (plural: bacterial taxa)

A population, whether named or not, of organisms which are usually inferred to be phylogenetically related and having characters in common which differentiate the unit (e.g., a geographic population, a genus, a family, an order) from other such units. A taxon encompasses all included taxa of lower rank and individual organisms. Today, bacterial taxa are largely defined by their 16S rRNA gene sequence variations.


Modification of an environment carried out to stimulate indigenous bacteria capable of degrading pollutants. This can be done by addition of various limiting...

This is a preview of subscription content, log in to check access.


  1. Aburto A, Ball AS (2009) Bacterial population dynamics and separation of active degraders by stable isotope probing during benzene degradation in a BTEX-impacted aquifer. Revista Internacional de Contaminacion Ambiental 25:147–156Google Scholar
  2. Atlas RM, Bartha R (1972) Degradation and mineralization of petroleum in seawater: limitation by nitrogen and phosphorus. Biotechnol Bioeng 14:309–317Google Scholar
  3. Bombach P, Chatzinotas A, Neu TR et al (2009) Enrichment and characterization of a sulfate-reducing toluene degrading microbial consortium by combining in situ microcosms and stable isotope probing techniques. FEMS Microbiol Ecol 71:237–246Google Scholar
  4. Bordenave S, Goni-Urriza MS, Caumette P et al (2007) Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat. Appl Environ Microbiol 73:6089–6097Google Scholar
  5. Cébron A, Norini MP, Beguiristain T et al (2008) Real-time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes from Gram positive and Gram negative bacteria in soil and sediment samples. J Microbiol Methods 73:148–159Google Scholar
  6. Chen Y, Murrell JC (2010) When metagenomics meets stable-isotope probing: progress and perspectives. Trends Microbiol 18:157–163Google Scholar
  7. Chen Y, Dumont MG, Neufeld JD et al (2008) Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands. Environ Microbiol 10:2609–2622Google Scholar
  8. Delille D, Pelletier E, Duval A et al (2009) Effects of nutrient and temperature on degradation of petroleum hydrocarbons in subAntarctic seawater. Polar Biol 32:1521–1528Google Scholar
  9. Dumont MG, Murrell JC (2005) Stable isotope probing – linking microbial identity to function. Nat Rev Microbiol 3:499–504Google Scholar
  10. Dumont MG, Radajewski SM, Miguez CB et al (2006) Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomic analysis. Environ Microbiol 8:1240–1250Google Scholar
  11. Frias-Lopez J, Thompson A, Waldbauer J et al (2008) Use of stable isotope-labelled cells to identify active grazers of picocyanobacteria in ocean surface waters. Environ Microbiol 11:512–525Google Scholar
  12. Gallagher E, McGuinness L, Phelps C et al (2005) 13C-carrier DNA shortens the incubation time needed to detect benzoate-utilizing denitrifying bacteria by stable-isotope probing. Appl Environ Microbiol 71:5192–5196Google Scholar
  13. Ghiglione JF, Larcher M, Lebaron P (2005) Spatial and temporal scales of variation in bacterioplankton community structure in the NW Mediterranean Sea. Aquat Microbial Ecol 40:229–240Google Scholar
  14. Ghiglione JF, Mevel G, Pujo-Pay M et al (2007) Diel and seasonal variations in abundance, activity, and community structure of particle-attached and free-living bacteria in NW Mediterranean Sea. Microbial Ecol 54:217–231Google Scholar
  15. Ghiglione JF, Palacios C, Marty JC et al (2008) Role of environmental factors for the vertical distribution (0–1,000 m) of marine bacterial communities in the NW Mediterranean Sea. Biogeoscience 5:1751–1764Google Scholar
  16. Giovannoni SJ, Britschgi TB, Moyer CL et al (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63Google Scholar
  17. Hanson JR, Macalady JL, Harris D et al (1999) Linking toluene degradation with specific microbial populations in soil. Appl Environ Microbiol 65:5403–5408Google Scholar
  18. Head IM, Jones DM, Roling FM (2006) Marine microorganisms make a meal of oil. Nat Rev Microbiol 4:173–182Google Scholar
  19. Herrmann S, Kleinsteube S, Chatzinotas A et al (2009) Functional characterization of an anaerobic benzene-degrading enrichment culture by DNA stable isotope probing. Environ Microbiol 12:401–411Google Scholar
  20. Huang WE, Ferguson A, Singer AC et al (2009) Resolving genetic functions within microbial populations: in situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell Raman-fluorescence in situ hybridization. Appl Environ Microbiol 75:234–241Google Scholar
  21. Jeon CO, Park W, Padmanabhan P et al (2003) Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment. Proc Nat Acad Sci USA 100:13591–13596Google Scholar
  22. Jones MD, Singleton DR, Carstensen DP et al (2008) Effect of incubation conditions on the enrichment of pyrene-degrading bacteria identified by stable-isotope probing in an aged, PAH-contaminated soil. Microbial Ecol 56:341–349Google Scholar
  23. Kasai Y, Takahata Y, Manefield M et al (2006) RNA-based stable isotope probing and isolation of anaerobic benzene-degrading bacteria from gasoline-contaminated groundwater. Appl Environ Microbiol 72:3586–3592Google Scholar
  24. Kota S, Borden RC, Barlaz MA (1999) Influence of protozoan grazing on contaminant biodegradation. FEMS Microbiol Ecol 29:179–189Google Scholar
  25. 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 1:643–653Google Scholar
  26. Lami R, Ghiglione JF, Desdevises Y et al (2009) Annual patterns of presence and activity of marine bacteria monitored by 16S rDNA–16S rRNA fingerprints in the coastal NW Mediterranean Sea. Aquat Microbial Ecol 54:199–210Google Scholar
  27. Langenheder S, Prosser JI (2008) Resource availability influences the diversity of a functional group of heterotrophic soil bacteria. Environ Microbiol 10:2245–2256Google Scholar
  28. 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 6:73–78Google Scholar
  29. Luo C, Xie S, Sun W et al (2009) Identification of a novel toluene-degrading bacterium from the candidate phylum TM7, as determined by DNA stable isotope probing. Appl Environ Microbiol 75:4644–4647Google Scholar
  30. Manefield M, Griffiths R, McNamara NP et al (2007) Insights into the fate of a 13C labelled phenol pulse for stable isotope probing (SIP) experiments. J Microbiol Method 69:340–344Google Scholar
  31. Maron PA, Lejon DPH, Carvalho E et al (2005) Assessing genetic structure and diversity of airborne bacterial communities by DNA fingerprinting and 16S rDNA clone library. Atmos Environ 39:3687–3695Google Scholar
  32. Meselson M, Stahl FW (1958) The replication of DNA in Escherichia coli. Proc Nat Acad Sci USA 44:671–682Google Scholar
  33. Neufeld JD, Vohra J, Dumont MG et al (2007) DNA stable-isotope probing. Nat Protoc 2:860–866Google Scholar
  34. Neufeld JD, Chen Y, Dumont MG et al (2008) Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environ Microbiol 10:1526–1535Google Scholar
  35. Padmanabhan P, Padmanabhan S, DeRito C et al (2003) Respiration of 13C-labeled substrates added to soil in the field and subsequent 16S rRNA gene analysis of 13C-labeled soil DNA. Appl Environ Microbiol 69:1614–1622Google Scholar
  36. Prince RC (2005) The microbiology of marine oil spill bioremediation. Pet Microbiol:317–336Google Scholar
  37. Pumphrey GM, Madsen EL (2008) Field-based stable isotope probing reveals the identities of benzoic acid-metabolizing microorganisms and their in situ growth in agricultural soil. Appl Environ Microbiol 74:4111–4118Google Scholar
  38. Ranjard L, Lejon DPH, Mougel C et al (2003) Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environ Microbiol 5:1111–1120Google Scholar
  39. Rodríguez-Blanco A, Ghiglione JF, Catala P et al (2009) Spatial comparison of total vs active bacterial populations by coupling genetic fingerprinting and clone library analyses in the NW Mediterranean Sea. FEMS Microbiol Ecol 67:30–42Google Scholar
  40. Rodríguez-Blanco A, Antoine V, Pelletier E et al (2010a) Effects of temperature and fertilization on total vs. active bacterial communities exposed to crude and diesel oil pollution in NW Mediterranean Sea. Environ Pollut 158:663–673Google Scholar
  41. Rodríguez-Blanco A, Vetion G, Escande ML et al (2010b) Gallaecimonas pentaromativorans gen. nov., sp. nov., a bacterium carrying 16S rRNA gene heterogeneity and able to degrade high-molecular-mass polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 60:504–509Google Scholar
  42. Rogers YH, Venter JC (2005) Genomics: massively parallel sequencing. Nature 437:326–327Google Scholar
  43. Röling WFM, Milner MG, Jones DM et al (2002) Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Appl Environ Microbiol 68:5537–5548Google Scholar
  44. Sakai N, Kurisu F, Yagi O et al (2009) Identification of putative benzene-degrading bacteria in methanogenic enrichment cultures. J Biosci Bioeng 108:501–507Google Scholar
  45. Singleton DR, Powell SN, Sangaiah R et al (2005) Stable-isotope probing of bacteria capable of degrading salicylate, naphthalene, or phenanthrene in a bioreactor treating contaminated soil. Appl Environ Microbiol 71:1202–1209Google Scholar
  46. Singleton DR, Sangaiah R, Gold A et al (2006) Identification and quantification of uncultivated Proteobacteria associated with pyrene degradation in a bioreactor treating PAH-contaminated soil. Environ Microbiol 8:1736–1745Google Scholar
  47. Singleton DR, Hunt M, Powell SN et al (2007) Stable-isotope probing with multiple growth substrates to determine substrate specificity of uncultivated bacteria. J Microbiol Methods 69:180–187Google Scholar
  48. Sul WJ, Park J, Quensen Iii JF et al (2009) DNA-Stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Appl Environ Microbiol 75:5501–5506Google Scholar
  49. Sun W, Xie S, Luo C et al (2010) Direct link between toluene degradation in contaminated-site microcosms and a Polaromonas strain. Appl Environ Microbiol 76:956–959Google Scholar
  50. Whiteley A, Thomson B, Lueders L et al (2007) RNA stable-isotope probing. Nat Protoc 2:838–844Google Scholar
  51. Xie S, Sun W, Luo C et al (2010) Stable isotope probing identifies novel m-xylene degraders in soil microcosms from contaminated and uncontaminated sites. Water Air Soil Pollut 212:113–122Google Scholar
  52. Yu CP, Chu KH (2005) A quantitative assay for linking microbial community function and structure of a naphthalene-degrading microbial consortium. Environ Sci Technol 39:9611–9619Google Scholar

Suggested Resources

  1. Friedrich MW (2006) Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes. Curr Opin Biotechnol 17:59–66Google Scholar
  2. Kreuzer-Martin HW (2007) Stable isotope probing: linking functional activity to specific members of microbial communities. Soil Sci Soc Am J 71:611–619Google Scholar
  3. Madsen EL (2006) The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Curr Opin Biotechnol 17:92–97Google Scholar
  4. Radajewski S, McDonald IR, Murrell JC (2003) Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms. Curr Opin Biotechnol 14:296–302Google Scholar
  5. Uhlík O, Jecná K, Leigh MB et al (2009) DNA-based stable isotope probing: a link between community structure and function. Sci Tot Environ 407:3611–3619Google Scholar
  6. Whiteley AS, Manefield M, Lueders T (2006) Unlocking the ‘microbial black box’ using RNA-based stable isotope probing technologies. Curr Opin Biotechnol 17:67–71Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Centre national de la recherché scientifique, UMR 7621, LOMIC, Observatoire OcéanologiqueBanyuls/merFrance
  2. 2.Université Pierre et Marie Curie (Paris VI), UMR 7621, LOMIC, Observatoire OcéanologiqueBanyuls/merFrance
  3. 3.CNRS, UMR 7621, LOMIC, Observatoire OcéanologiqueBanyuls/merFrance
  4. 4.UPMC Univ Paris 06, UMR 7621, LOMIC, Observatoire OcéanologiqueBanyuls/merFrance