Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation.

Institute of Chemical Technology Prague Faculty of Food and Biochemical Technology Department of Biochemistry and Microbiology Technicka 3 166 28 Prague Czech Republic

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Aanderud ZT, Lennon JT. Validation of heavy-water stable isotope probing for the characterization of rapidly responding soil bacteria. Appl Environ Microbiol. 2011;77:4589–4596. PubMed PMC

Adamczyk J, Hesselsoe M, Iversen N, Horn M, Lehner A, Nielsen PH, Schloter M, Roslev P, Wagner M. The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl Environ Microbiol. 2003;69:6875–6887. PubMed PMC

Andreoni V, Gianfreda L. Bioremediation and monitoring of aromatic-polluted habitats. Appl Microbiol Biotechnol. 2007;76:287–308. PubMed

Arai K, Tsubone T, Takechi T, Inoue T. Bioremediation of trichloroethylene and cis-1,2-dichloroethylene-contaminated groundwater by methane-utilizing bacteria. J Vet Med Sci. 1999;61:861–863. PubMed

Barriault D, Plante MM, Sylvestre M. Family shuffling of a targeted bphA region to engineer biphenyl dioxygenase. J Bacteriol. 2002;184:3794–3800. PubMed PMC

Bastida F, Jechalke S, Bombach P, Franchini AG, Seifert J, von Bergen M, Vogt C, Richnow HH. Assimilation of benzene carbon through multiple trophic levels traced by different stable isotope probing methodologies. FEMS Microbiol Ecol. 2011;77:357–369. PubMed

Bastida F, Rosell M, Franchini AG, Seifert J, Finsterbusch S, Jehmlich N, Jechalke S, Von Bergen M, Richnow HH. Elucidating MTBE degradation in a mixed consortium using a multidisciplinary approach. FEMS Microbiol Ecol. 2010;73:370–384. PubMed

Behrens S, Losekann T, Pett-Ridge J, Weber PK, Ng WO, Stevenson BS, Hutcheon ID, Relman DA, Spormann AM. Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS. Appl Environ Microbiol. 2008;74:3143–3150. PubMed PMC

Bell TH, Yergeau E, Martineau C, Juck D, Whyte LG, Greer CW. Identification of nitrogen-incorporating bacteria in petroleum-contaminated Arctic soils by using 15N DNA-based stable isotope probing and pyrosequencing. Appl Environ Microbiol. 2011;77:4163–4171. PubMed PMC

Bertin C, Yang XH, Weston LA. The role of root exudates and allelochemicals in the rhizosphere. Plant Soil. 2003;256:67–83.

Binga EK, Lasken RS, Neufeld JD. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J. 2008;2:233–241. PubMed

Boecklen WJ, Yarnes CT, Cook BA, James AC. On the use of stable isotopes in trophic ecology. Annu Rev Ecol Evol Syst. 2011;42:411–440.

Bombach P, Chatzinotas A, Neu TR, Kästner M, Lueders T, Vogt C. Enrichment and characterization of a sulfate-reducing toluene-degrading microbial consortium by combining in situ microcosms and stable isotope probing techniques. FEMS Microbiol Ecol. 2010;71:237–246. PubMed

Boschker HTS, Nold SC, Wellsbury P, Bos D, de Graaf W, Pel R, Parkes RJ, Cappenberg TE. Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature. 1998;392:801–805.

Braeckevelt M, Fischer A, Kaestner M. Field applicability of Compound-Specific Isotope Analysis (CSIA) for characterization and quantification of in situ contaminant degradation in aquifers. Appl Microbiol Biotechnol. 2012;94:1401–1421. PubMed

Breivik K, Sweetman A, Pacyna JM, Jones KC. Towards a global historical emission inventory for selected PCB congeners - a mass balance approach. 1. Global production and consumption. Sci Total Environ. 2002;290:181–198. PubMed

Brodie EL, Desantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK, Wan JM, Firestone MK. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol. 2006;72:6288–6298. PubMed PMC

Buckley DH, Huangyutitham V, Hsu SF, Nelson TA. Stable isotope probing with 15N2reveals novel noncultivated diazotrophs in soil. Appl Environ Microbiol. 2007a;73:3196–3204. PubMed PMC

Buckley DH, Huangyutitham V, Hsu SF, Nelson TA. Stable isotope probing with 15N achieved by disentangling the effects of genome G+C content and isotope enrichment on DNA density. Appl Environ Microbiol. 2007b;73:3189–3195. PubMed PMC

Chen Y, Dumont MG, Neufeld JD, Bodrossy L, Stralis-Pavese N, McNamara NP, Ostle N, Briones MJ, Murrell JC. Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands. Environ Microbiol. 2008;10:2609–2622. PubMed

Chen Y, Murrell JC. When metagenomics meets stable-isotope probing: progress and perspectives. Trends Microbiol. 2010;18:157–163. PubMed

Daniel R. The metagenomics of soil. Nat Rev Microbiol. 2005;3:470–478. PubMed

DeAngelis KM, Wu CH, Beller HR, Brodie EL, Chakraborty R, DeSantis TZ, Fortney JL, Hazen TC, Osman SR, Singer ME, Tom LM, Andersen GL. PCR Amplification-Independent Methods for Detection of Microbial Communities by the High-Density Microarray PhyloChip. Appl Environ Microbiol. 2011;77:6313–6322. PubMed PMC

DeRito CM, Pumphrey GM, Madsen EL. Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community. Appl Environ Microbiol. 2005;71:7858–7865. PubMed PMC

Diaz E. Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. Int Microbiol. 2004;7:173–180. PubMed

Dumont MG, Murrell JC. Stable isotope probing - linking microbial identity to function. Nat Rev Microbiol. 2005;3:499–504. PubMed

Dumont MG, Pommerenke B, Casper P, Conrad R. DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment. Environ Microbiol. 2011;13:1153–1167. PubMed

Dumont MG, Radajewski SM, Miguez CB, McDonald IR, Murrell JC. Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomic analysis. Environ Microbiol. 2006;8:1240–1250. PubMed

Dunford EA, Neufeld JD. DNA stable-isotope probing (DNA-SIP) J Vis Exp. 2010;42:2027. PubMed PMC

Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC, Rohwer F. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics. 2006;7 PubMed PMC

Erickson BD, Mondello FJ. Enhanced biodegradation of polychlorinated biphenyls after site-directed mutagenesis of a biphenyl dioxygenase gene. Appl Environ Microbiol. 1993;59:3858–3862. PubMed PMC

Feike J, Jurgens K, Hollibaugh JT, Kruger S, Jost G, Labrenz M. Measuring unbiased metatranscriptomics in suboxic waters of the central Baltic Sea using a new in situ fixation system. ISME J. 2012;6:461–470. PubMed PMC

Filiatrault MJ. Progress in prokaryotic transcriptomics. Curr Opin Microbiol. 2011;14:579–586. PubMed

Friedrich MW. Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes. Curr Opin Biotechnol. 2006;17:59–66. PubMed

Futagami T, Goto M, Furukawa K. Biochemical and genetic bases of dehalorespiration. Chem Rec. 2008;8:1–12. PubMed

Gallagher E, McGuinness L, Phelps C, Young LY, Kerkhof LJ. 13C-carrier DNA shortens the incubation time needed to detect benzoate-utilizing denitrifying bacteria by stable-isotope probing. Appl Environ Microbiol. 2005;71:5192–5196. PubMed PMC

Geoffrey MG. Metals, minerals and microbes: geomicrobiology and bioremediation. Microbiology. 2010;156:609–643. PubMed

Gerhardt KE, Huang XD, Glick BR, Greenberg BM. Phytoremediation and rhizoremediation of organic soil contaminants: Potential and challenges. Plant Sci. 2009;176:20–30.

Gutierrez-Zamora ML, Manefield M. An appraisal of methods for linking environmental processes to specific microbial taxa. Rev Environ Sci Biotechnol. 2010;9:153–185.

Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 1998;5:R245–R249. PubMed

Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P. Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proc Natl Acad Sci USA. 2007;104:13913–13918. PubMed PMC

Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'Haeseleer P, Holman HYN, Osman S, Lu ZM, Van Nostrand JD, Deng Y, Zhou JZ, Mason OU. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science. 2010;330:204–208. PubMed

He Z, Deng Y, Van Nostrand JD, Tu Q, Xu M, Hemme CL, Li X, Wu L, Gentry TJ, Yin Y, Liebich J, Hazen TC, Zhou J. GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J. 2010;4:1167–1179. PubMed

He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Huang Z, Wu W, Gu B, Jardine P, Criddle C, Zhou J. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J. 2007;1:67–77. PubMed

Hesselsoe M, Bjerring ML, Henriksen K, Loll P, Nielsen JL. Method for measuring substrate preferences by individual members of microbial consortia proposed for bioaugmentation. Biodegradation. 2008;19:621–633. PubMed

Huang WE, Ferguson A, Singer AC, Lawson K, Thompson IP, Kalin RM, Larkin MJ, Bailey MJ, Whiteley AS. 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. 2009;75:234–241. PubMed PMC

Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS, Wagner M. Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol. 2007;9:1878–1889. PubMed

Huse SM, Welch DM, Morrison HG, Sogin ML. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol. 2010;12:1889–1898. PubMed PMC

Iwai S, Chai B, Jesus EdC, Penton CR, Lee TK, Cole JR, Tiedje JM. Gene-Targeted Metagenomics (GT Metagenomics) to Explore the Extensive Diversity of Genes of Interest in Microbial Communities. Handbook of Molecular Microbial Ecology I: John Wiley & Sons, Inc.; 2011. pp. 235–243.

Jehmlich N, Schmidt F, Hartwich M, von Bergen M, Richnow HH, Vogt C. Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP) Rapid Commun Mass Spectrom. 2008a;22:2889–2897. PubMed

Jehmlich N, Schmidt F, Taubert M, Seifert J, von Bergen M, Richnow HH, Vogt C. 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. 2009;23:1871–1878. PubMed

Jehmlich N, Schmidt F, von Bergen M, Richnow HH, Vogt C. Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures. ISME J. 2008b;2:1122–1133. PubMed

Jørgensen KS. In Situ Bioremediation. Adv Appl Microbiol. 2007;61:285–305. PubMed

Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, McHardy AC, Szeto E, Salamov A, Grigoriev IV, Suciu D, Levine SR, Markowitz VM, Rigoutsos I, Tringe SG, Bruce DC, Richardson PM, Lidstrom ME, Chistoserdova L. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol. 2008;26:1029–1034. PubMed

Kane SR, Chakicherla AY, Chain PS, Schmidt R, Shin MW, Legler TC, Scow KM, Larimer FW, Lucas SM, Richardson PM, Hristova KR. Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. J Bacteriol. 2007;189:1931–1945. PubMed PMC

Kuiper I, Lagendijk EL, Bloemberg GV, Lugtenberg BJ. Rhizoremediation: a beneficial plant-microbe interaction. Mol Plant Microbe Interact. 2004;17:6–15. PubMed

Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol. 2010;12:118–123. PubMed

Kuypers MMM, Jørgensen BB. The future of single-cell environmental microbiology. Environ Microbiol. 2007;9:6–7. PubMed

Lee N, Nielsen PH, Andreasen KH, Juretschko S, Nielsen JL, Schleifer KH, Wagner M. Combination of fluorescent in situ hybridization and microautoradiography - a new tool for structure-function analyses in microbial ecology. Appl Environ Microbiol. 1999;65:1289–1297. PubMed PMC

Lee TK, Lee J, Sul WJ, Iwai S, Chai BC, Tiedje JM, Park J. Novel biphenyl-oxidizing bacteria and dioxygenase genes from a Korean tidal mudflat. Appl Environ Microbiol. 2011;77:3888–3891. PubMed PMC

Leigh MB, Fletcher JS, Fu X, Schmitz FJ. Root turnover: an important source of microbial substrates in rhizosphere remediation of recalcitrant contaminants. Environ Sci Technol. 2002;36:1579–1583. PubMed

Leigh MB, Pellizari VH, Uhlík O, Sutka R, Rodrigues J, Ostrom NE, Zhou J, Tiedje JM. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs) ISME J. 2007;1:134–148. PubMed

Leigh MB, Prouzová P, Macková M, Macek T, Nagle DP, Fletcher JS. Polychlorinated biphenyl (PCB)-degrading bacteria associated with trees in a PCB-contaminated site. Appl Environ Microbiol. 2006;72:2331–2342. PubMed PMC

Li T, Wu TD, Mazeas L, Toffin L, Guerquin-Kern JL, Leblon G, Bouchez T. Simultaneous analysis of microbial identity and function using NanoSIMS. Environ Microbiol. 2008;10:580–588. PubMed PMC

Liou JS, DeRito CM, Madsen EL. Field-based and laboratory stable isotope probing surveys of the identities of both aerobic and anaerobic benzene-metabolizing microorganisms in freshwater sediment. Environ Microbiol. 2008;10:1964–1977. PubMed

Little CD, Palumbo AV, Herbes SE, Lidstrom ME, Tyndall RL, Gilmer PJ. Trichloroethylene biodegradation by a methane-oxidizing bacterium. Appl Environ Microbiol. 1988;54:951–956. PubMed PMC

Liu S, Suflita JM. Ecology and evolution of microbial populations for bioremediation. Trends Biotechnol. 1993;11:344–352. PubMed

Lovley DR. Cleaning up with genomics: applying molecular biology to bioremediation. Nat Rev Microbiol. 2003;1:35–44. PubMed

Lozupone CA, Knight R. Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev. 2008;32:557–578. PubMed PMC

Lu ZM, Deng Y, Van Nostrand JD, He ZL, Voordeckers J, Zhou AF, Lee YJ, Mason OU, Dubinsky EA, Chavarria KL, Tom LM, Fortney JL, Lamendella R, Jansson JK, D'Haeseleer P, Hazen TC, Zhou JZ. Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J. 2012;6:451–460. PubMed PMC

Lueders T, Kindler R, Miltner A, Friedrich MW, Kaestner M. Identification of bacterial micropredators distinctively active in a soil microbial food web. Appl Environ Microbiol. 2006;72:5342–5348. PubMed PMC

Macek T, Kotrba P, Svatoš A, Nováková M, Demnerová K, Macková M. Novel roles for genetically modified plants in environmental protection. Trends Biotechnol. 2008;26:146–152. PubMed

Macek T, Macková M, Káš J. Exploitation of plants for the removal of organics in environmental remediation. Biotechnol Adv. 2000;18:23–34. PubMed

Macek T, Uhlík O, Ječná K, Nováková M, Lovecká P, Rezek J, Dudková V, Štursa P, Vrchotová B, Pavlíková D, Demnerová K, Macková M. Advances in phytoremediation and rhizoremediation. In: Varma A, editor. Soil Biology. 17 ed. Berlin, Germany: Springer; 2009. pp. 257–277.

MacGregor BJ, Boschker HT, Amann R. Comparison of rRNA and polar-lipid-derived fatty acid biomarkers for assessment of 13C-substrate incorporation by microorganisms in marine sediments. Appl Environ Microbiol. 2006;72:5246–5253. PubMed PMC

MacGregor BJ, Bruchert V, Fleischer S, Amann R. Isolation of small-subunit rRNA for stable isotopic characterization. Environ Microbiol. 2002;4:451–464. PubMed

Macková M, Dowling D, Macek T. Focus on Biotechnology. Dordrecht, Netherlands: Springer; 2006. Phytoremediation and Rhizoremediation. Theoretical Background; p. 300.

Madsen EL. The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Curr Opin Biotechnol. 2006;17:92–97. PubMed

Madsen EL. Stable Isotope Probing Techniques and Bioremediation. In: Murrell JC, Whiteley A, editors. Stable Isotope Probing and Related Technologies. Washington, DC: ASM Press; 2010. pp. 165–202.

Mahmood S, Paton GI, Prosser JI. Cultivation-independent in situ molecular analysis of bacteria involved in degradation of pentachlorophenol in soil. Environ Microbiol. 2005;7:1349–1360. PubMed

Manefield M, Whiteley AS, Bailey MJ. What can stable isotope probing do for bioremediation? Int Biodeterior Biodegrad. 2004;54:163–166.

Manefield M, Whiteley AS, Griffiths RI, Bailey MJ. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol. 2002;68:5367–5373. PubMed PMC

Marchetti A, Schruth DM, Durkin CA, Parker MS, Kodner RB, Berthiaume CT, Morales R, Allen AE, Armbrust EV. Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. Proc Natl Acad Sci USA. 2012;109:E317–E325. PubMed PMC

Maxfield PJ, Dildar N, Hornibrook ERC, Stott AW, Evershed RP. Stable isotope switching (SIS): a new stable isotope probing (SIP) approach to determine carbon flow in the soil food web and dynamics in organic matter pools. Rapid Commun Mass Spectrom. 2012;26:997–1004. PubMed

McGuinness M, Dowling D. Plant-associated bacterial degradation of toxic organic compounds in soil. Int J Environ Res Public Health. 2009;6:2226–2247. PubMed PMC

Miyatake T, MacGregor BJ, Boschker HT. Linking microbial community function to phylogeny of sulfate-reducing Deltaproteobacteria in marine sediments by combining stable isotope probing with magnetic-bead capture hybridization of 16S rRNA. Appl Environ Microbiol. 2009;75:4927–4935. PubMed PMC

Mondello FJ, Turcich MP, Lobos JH, Erickson BD. Identification and modification of biphenyl dioxygenase sequences that determine the specificity of polychlorinated biphenyl degradation. Appl Environ Microbiol. 1997;63:3096–3103. PubMed PMC

Morales SE, Holben WE. Linking bacterial identities and ecosystem processes: can ‘omic’ analyses be more than the sum of their parts? FEMS Microbiol Ecol. 2011;75:2–16. PubMed

Mou XZ, Vila-Costa M, Sun SL, Zhao WD, Sharma S, Moran MA. Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton. Environ Microbiol Rep. 2011;3:798–806. PubMed

Mulligan CN, Yong RN. Natural attenuation of contaminated soils. Environ Int. 2004;30:587–601. PubMed

Nakatsu CH, Hristova K, Hanada S, Meng XY, Hanson JR, Scow KM, Kamagata Y. Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria. Int J Syst Evol Microbiol. 2006;56:983–989. PubMed

Neufeld JD, Chen Y, Dumont MG, Murrell JC. Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environ Microbiol. 2008;10:1526–1535. PubMed

Neufeld JD, Dumont MG, Vohra J, Murrell JC. Methodological considerations for the use of stable isotope probing in microbial ecology. Microb Ecol. 2007a;53:435–442. PubMed

Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW, Murrell JC. DNA stable-isotope probing. Nat Protoc. 2007b;2:860–866. PubMed

Neufeld JD, Wagner M, Murrell JC. Who eats what, where and when? Isotope-labelling experiments are coming of age. ISME J. 2007c;1:103–110. PubMed

Newman LA, Reynolds CM. Bacteria and phytoremediation: new uses for endophytic bacteria in plants. Trends Biotechnol. 2005;23:6–8. PubMed

Nikolausz M, Palatinszky MA, Rusznyak A, Richnow HH, Kappelmeyer U, Kastner M. Novel approach using substrate-mediated radiolabelling of RNA to link metabolic function with the structure of microbial communities. FEMS Microbiol Lett. 2007;274:154–161. PubMed

Nováková M, Macková M, Chrastilová Z, Viktorová J, Szekeres M, Demnerová K, Macek T. Cloning the bacterial bphC gene into Nicotiana tabacum to improve the efficiency of PCB phytoremediation. Biotechnol Bioeng. 2009;102:29–37. PubMed

Orphan VJ, House CH, Hinrichs KU, McKeegan KD, DeLong EF. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science. 2001;293:484–487. PubMed

Ottesen EA, Marin R, Preston CM, Young CR, Ryan JP, Scholin CA, DeLong EF. Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. ISME J. 2011;5:1881–1895. PubMed PMC

Pace NR, Stahl DA, Lane DJ, Olsen GJ. Analyzing natural microbial populations by rRNA sequences. ASM News. 1985;51:4–12.

Padmanabhan P, Padmanabhan S, DeRito C, Gray A, Gannon D, Snape JR, Tsai CS, Park W, Jeon C, Madsen EL. 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. 2003;69:1614–1622. PubMed PMC

Pan CL, Fischer CR, Hyatt D, Bowen BP, Hettich RL, Banfield JF. Quantitative tracking of isotope flows in proteomes of microbial communities. Mol Cell Proteomics. 2011;10 PubMed PMC

Pei AY, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, Gerz EA, Jin Z, Lee P, Yang L, Poles M, Brown SM, Sotero S, Desantis T, Brodie E, Nelson K, Pei Z. Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol. 2010;76:3886–3897. PubMed PMC

Pernthaler A, Dekas AE, Brown CT, Goffredi SK, Embaye T, Orphan VJ. Diverse syntrophic partnerships from-deep-sea methane vents revealed by direct cell capture and metagenomics. Proc Natl Acad Sci USA. 2008;105:7052–7057. PubMed PMC

Pilloni G, von Netzer F, Engel M, Lueders T. Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil-contaminated aquifer by Pyro-SIP. FEMS Microbiol Ecol. 2011;78:165–175. PubMed

Prosser JI, Rangel-Castro JI, Killham K. Studying plant-microbe interactions using stable isotope technologies. Curr Opin Biotechnol. 2006;17:98–102. PubMed

Pumphrey GM, Madsen EL. Field-based stable isotope probing reveals the identities of benzoic acid-metabolizing microorganisms and their in situ growth in agricultural soil. Appl Environ Microbiol. 2008;74:4111–4118. PubMed PMC

Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods. 2009;6:639–641. PubMed

Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ. Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 2011;12 PubMed PMC

Radajewski S, Ineson P, Parekh NR, Murrell JC. Stable-isotope probing as a tool in microbial ecology. Nature. 2000;403:646–649. PubMed

Radajewski S, McDonald IR, Murrell JC. Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms. Curr Opin Biotechnol. 2003;14:296–302. PubMed

Radajewski S, Webster G, Reay DS, Morris SA, Ineson P, Nedwell DB, Prosser JI, Murrell JC. Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing. Microbiology. 2002;148:2331–2342. PubMed

Reeder J, Knight R. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods. 2010;7:668–669. PubMed PMC

Rezek J, Macek T, Macková M, Tríska J, Růžičková K. Hydroxy-PCBs, methoxy-PCBs and hydroxy-methoxy-PCBs: metabolites of polychlorinated biphenyls formed in vitro by tobacco cells. Environ Sci Technol. 2008;42:5746–5751. PubMed

Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet. 2004;38:525–552. PubMed

Rinta-Kanto JM, Sun SL, Sharma S, Kiene RP, Moran MA. Bacterial community transcription patterns during a marine phytoplankton bloom. Environ Microbiol. 2012;14:228–239. PubMed

Roh H, Yu CP, Fuller ME, Chu KH. Identification of hexahydro-1,3,5-trinitro-1,3,5-triazinedegrading microorganisms via 15N-stable isotope probing. Environ Sci Technol. 2009;43:2505–2511. PubMed

Ruess L, Chamberlain PM. The fat that matters: Soil food web analysis using fatty acids and their carbon stable isotope signature. Soil Biol Biochem. 2010;42:1898–1910.

Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 2011;6:e27310. PubMed PMC

Schloss PD, Handelsman J. Biotechnological prospects from metagenomics. Curr Opin Biotechnol. 2003;14:303–310. PubMed

Schloss PD, Handelsman J. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol. 2005;6 229-. PubMed PMC

Schmeisser C, Steele H, Streit WR. Metagenomics, biotechnology with non-culturable microbes. Appl Microbiol Biotechnol. 2007;75:955–962. PubMed

Schnoor JL, Licht LA, Mccutcheon SC, Wolfe NL, Carreira LH. Phytoremediation of organic and nutrient contaminants. Environ Sci Technol. 1995;29:A318–A323. PubMed

Schwarz S, Waschkowitz T, Daniel R. Enhancement of gene detection frequencies by combining DNA-based stable-isotope probing with the construction of metagenomic DNA libraries. World J Microbiol Biotechnol. 2006;22:363–367.

Shigematsu T, Hanada S, Eguchi M, Kamagata Y, Kanagawa T, Kurane R. Soluble methane monooxygenase gene clusters from trichloroethylene-degrading Methylomonas sp. strains and detection of methanotrophs during in situ bioremediation. Appl Environ Microbiol. 1999;65:5198–5206. PubMed PMC

Simon C, Daniel R. Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol. 2009;85:265–276. PubMed PMC

Simon C, Daniel R. Metagenomic analyses: Past and future trends. Appl Environ Microbiol. 2011;77:1153–1161. PubMed PMC

Singer AC, Crowley DE, Thompson IP. Secondary plant metabolites in phytoremediation and biotransformation. Trends Biotechnol. 2003;21:123–130. PubMed

Singer AC, Thompson IP, Bailey MJ. The tritrophic trinity: a source of pollutant-degrading enzymes and its implications for phytoremediation. Curr Opin Microbiol. 2004;7:239–244. PubMed

Smidt H, de Vos WM. Anaerobic microbial dehalogenation. Annu Rev Microbiol. 2004;58:43–73. PubMed

Stewart FJ, Ulloa O, DeLong EF. Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environ Microbiol. 2012;14:23–40. PubMed

Su C, Lei LP, Duan YQ, Zhang KQ, Yang JK. Culture-independent methods for studying environmental microorganisms: methods, application, and perspective. Appl Microbiol Biotechnol. 2012;93:993–1003. PubMed

Suenaga H, Koyama Y, Miyakoshi M, Miyazaki R, Yano H, Sota M, Ohtsubo Y, Tsuda M, Miyazaki K. Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis. ISME J. 2009;3:1335–1348. PubMed

Sul WJ, Park J, Quensen JF, III, Rodrigues JL, Seliger L, Tsoi TV, Zylstra GJ, Tiedje JM. DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Appl Environ Microbiol. 2009;75:5501–5506. PubMed PMC

Sylvestre M, Macek T, Macková M. Transgenic plants to improve rhizoremediation of polychlorinated biphenyls (PCBs) Curr Opin Biotechnol. 2009;20:242–247. PubMed

Takeuchi M, Nanba K, Iwamoto H, Nirei H, Kusuda T, Kazaoka O, Owaki M, Furuya K. In situ bioremediation of a cis-dichloroethylene-contaminated aquifer utilizing methane-rich groundwater from an uncontaminated aquifer. Water Res. 2005;39:2438–2444. PubMed

Taubert M, Jehmlich N, Vogt C, Richnow HH, Schmidt F, von Bergen M, Seifert J. Time resolved protein-based stable isotope probing (Protein-SIP) analysis allows quantification of induced proteins in substrate shift experiments. Proteomics. 2011;11:2265–2274. PubMed

Tobino T, Kurisu F, Kasuga I, Furumai H. Shotgun isotope array for rapid, substrate-specific detection of microorganisms in a microbial community. Appl Environ Microbiol. 2011;77:7430–7432. PubMed PMC

Topp E, Hanson RS, Ringelberg DB, White DC, Wheatcroft R. Isolation and characterization of an N-methylcarbamate insecticide-degrading methylotrophic bacterium. Appl Environ Microbiol. 1993;59:3339–3349. PubMed PMC

Torsvik V, Øvreås L. Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol. 2002;5:240–245. PubMed

Toussaint J-P, Pham T, Barriault D, Sylvestre M. Plant exudates promote PCB degradation by a rhodococcal rhizobacteria. Appl Microbiol Biotechnol. 2012;95:1589–1603. PubMed

Uhlík O, Ječná K, Leigh MB, Macková M, Macek T. DNA-based stable isotope probing: a link between community structure and function. Sci Total Environ. 2009a;407:3611–3619. PubMed

Uhlík O, Ječná K, Macková M, Vlček C, Hroudová M, Demnerová K, Pačes V, Macek T. Biphenyl-metabolizing bacteria in the rhizosphere of horseradish and bulk soil contaminated by polychlorinated biphenyls as revealed by stable isotope probing. Appl Environ Microbiol. 2009b;75:6471–6477. PubMed PMC

Uhlík O, Wald J, Strejček M, Musilová L, Rídl J, Hroudová M, Vlček Č, Cardenas E, Macková M, Macek T. Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil. PLoS ONE. 2012;7:e40653. PubMed PMC

Van Aken B, Correa PA, Schnoor JL. Phytoremediation of polychlorinated biphenyls: new trends and promises. Environ Sci Technol. 2010;44:2767–2776. PubMed PMC

Van Aken B, Yoon JM, Schnoor JL. Biodegradation of nitro-substituted explosives 2,4,6-trinitrotoluene, hexahydro-1,3,5-trinitro-1,3,5-triazine, and octahydro-1,3,5,7-tetranitro-1,3,5-tetrazocine by a phytosymbiotic Methylobacterium sp. associated with poplar tissues (Populus deltoides x nigra DN34) Appl Environ Microbiol. 2004;70:508–517. PubMed PMC

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004;304:66–74. PubMed

Vézina J, Barriault D, Sylvestre M. Family shuffling of soil DNA to change the regiospecificity of Burkholderia xenovorans LB400 biphenyl dioxygenase. J Bacteriol. 2007;189:779–788. PubMed PMC

Vézina J, Barriault D, Sylvestre M. Diversity of the C-terminal portion of the biphenyl dioxygenase large subunit. J Mol Microbiol Biotechnol. 2008;15:139–151. PubMed

Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M. Metagenomics approaches in systems microbiology. FEMS Microbiol Rev. 2009;33:236–255. PubMed

Wagner M, Horn M, Daims H. Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr Opin Microbiol. 2003;6:302–309. PubMed

Wagner M, Nielsen PH, Loy A, Nielsen JL, Daims H. Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. Curr Opin Biotechnol. 2006;17:83–91. PubMed

Warner KL, Larkin MJ, Harper DB, Murrell JC, McDonald IR. Analysis of genes involved in methyl halide degradation in Aminobacter lissarensis CC495. FEMS Microbiol Lett. 2005;251:45–51. PubMed

Wellington EMH, Berry A, Krsek M. Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. Curr Opin Microbiol. 2003;6:295–301. PubMed

Weyens N, Truyens S, Saenen E, Boulet J, Dupae J, Taghavi S, van der Lelie D, Carleer R, Vangronsveld J. Endophytes and their potential to deal with co-contamination of organic contaminants (toluene) and toxic metals (nickel) during phytoremediation. Int J Phytoremediat. 2011;13:244–255. PubMed

Weyens N, van der Lelie D, Taghavi S, Vangronsveld J. Phytoremediation: plant-endophyte partnerships take the challenge. Curr Opin Biotechnol. 2009;20:248–254. PubMed

Whiteley AS, Manefield M, Lueders T. Unlocking the 'microbial black box' using RNA-based stable isotope probing technologies. Curr Opin Biotechnol. 2006;17:67–71. PubMed

Wiegel J, Wu Q. Microbial reductive dehalogenation of polychlorinated biphenyls. FEMS Microbiol Ecol. 2000;32:1–15. PubMed

Winderl C, Penning H, von Netzer F, Meckenstock RU, Lueders T. DNA-SIP identifies sulfate-reducing Clostridia as important toluene degraders in tar-oil-contaminated aquifer sediment. ISME J. 2010;4:1314–1325. PubMed

Woods A, Watwood M, Schwartz E. Identification of a toluene-degrading bacterium from a soil sample through H2 18O DNA stable isotope probing. Appl Environ Microbiol. 2011;77:5995–5999. PubMed PMC

Yang YR, Zarda A, Zeyer J. Combination of microautoradiography and fluorescence in situ hybridization for identification of microorganisms degrading xenobiotic contaminants. Environ Toxicol Chem. 2003;22:2840–2844. PubMed

Yi H, Crowley DE. Biostimulation of PAH degradation with plants containing high concentrations of linoleic acid. Environ Sci Technol. 2007;41:4382–4388. PubMed

Yun J, Ryu S. Screening for novel enzymes from metagenome and SIGEX, as a way to improve it. Microb Cell Fact. 2005;4:8. PubMed PMC

Zhang L, Xu Z. Assessing bacterial diversity in soil. J Soil Sediment. 2008;8:379–388.

DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

DNA stable isotope probing on soil treated by plant biostimulation and flooding revealed the bacterial communities involved in PCB degradation

Predominant Biphenyl Dioxygenase From Legacy Polychlorinated Biphenyl (PCB)-Contaminated Soil Is a Part of Unusual Gene Cluster and Transforms Flavone and Flavanone

Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation

The stimulating role of syringic acid, a plant secondary metabolite, in the microbial degradation of structurally-related herbicide, MCPA

Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

Synergistic Processing of Biphenyl and Benzoate: Carbon Flow Through the Bacterial Community in Polychlorinated-Biphenyl-Contaminated Soil

Hunting Down Frame Shifts: Ecological Analysis of Diverse Functional Gene Sequences

Pseudomonads Rule Degradation of Polyaromatic Hydrocarbons in Aerated Sediment