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Chapter 1 : DNA Stable Isotope Probing
Authors:
Yin Chen1,
J. Colin Murrell2
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Affiliations:
1: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom;
2: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
Content Type: Monograph
Publication Year:
2011
Category: Environmental Microbiology; Applied and Industrial Microbiology
Book DOI:
10.1128/9781555816896
Chapter DOI:
10.1128/9781555816896.ch1
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Abstract:
The major obstacle for 15N-based DNA stable isotope probing (DNA-SIP) was insufficient separation of 15N-labeled and unlabeled DNA due to the lower nitrogen content in DNA compared with its carbon content. Extracted DNA can be loaded onto a cesium chloride (CsCl) gradient for isopycnic centrifugation and separation of labeled “heavy” DNA from unlabeled background DNA (“light” DNA). DNA-SIP experiments need to be implemented carefully in order to maximize achievable information and to avoid misinterpretation of resulting data. Using DNA-SIP, a study demonstrated the possibility that Candidate phylum TM7 is involved in toluene degradation in soils. Methanol, formaldehyde, and ammonium are the final products of the RDX degradation pathway. It is obvious that microorganisms that only use nitro-nitrogen in the ring-labeled 15N3-RDX would not be seen in this study. In a study, the authors used DNA-SIP to analyze the active methanotroph population in a peatland from the United Kingdom. By using DNA-SIP, the authors demonstrated that Methylocellaand Methylocystisare probably the most active methane utilizers in this peatland. DNA-SIP can be used in combination with metagenomics in a focused way to investigate the function of a subpopulation of environmental microorganisms. It is predicted that this approach will be adopted by more researchers in the near future. The 16S rRNA gene sequences retrieved from the SIP experiments were used to design specific probes targeting 16S rRNA gene of Acidovorax spp. and Pseudomonas spp.
Citation:
Chen Y, Murrell J.
2011.
DNA Stable Isotope Probing,
p 3-24.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch1
Figures
DNA Stable Isotope Probing
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Citation:
Chen Y, Murrell J.
2011.
DNA Stable Isotope Probing,
p 3-24.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch1
/content/10.1128/9781555816896.ch01.ch01fig01
FIGURE 1
The numbers of papers published on stable-isotope probing since the first publication of DNA-SIP in 2000. Search was carried out using the Scopus database using key words “stable isotope probing” or “stable-isotope probing.”
10.1128/9781555816896/f0004-01_thmb.gif
10.1128/9781555816896/f0004-01.gif
FIGURE 1
The numbers of papers published on stable-isotope probing since the first publication of DNA-SIP in 2000. Search was carried out using the Scopus database using key words “stable isotope probing” or “stable-isotope probing.”
Citation:
Chen Y, Murrell J.
2011.
DNA Stable Isotope Probing,
p 3-24.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch1
/content/10.1128/9781555816896.ch01.ch01fig02
FIGURE 2.
An overview of key steps in DNA-SIP.
10.1128/9781555816896/f0011-01_thmb.gif
10.1128/9781555816896/f0011-01.gif
FIGURE 2.
An overview of key steps in DNA-SIP.
Citation:
Chen Y, Murrell J.
2011.
DNA Stable Isotope Probing,
p 3-24.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch1
/content/10.1128/9781555816896.ch01.ch01fig03
FIGURE 3.
DGGE fingerprints of 16S rRNA genes of key fractions from DNA-SIP. Bands that are highlighted were reamplified and sequenced.
10.1128/9781555816896/f0017-01_thmb.gif
10.1128/9781555816896/f0017-01.gif
FIGURE 3.
DGGE fingerprints of 16S rRNA genes of key fractions from DNA-SIP. Bands that are highlighted were reamplified and sequenced.
Citation:
Chen Y, Murrell J.
2011.
DNA Stable Isotope Probing,
p 3-24.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch1
/content/10.1128/9781555816896.ch01.ch01fig04
FIGURE 4.
An overview of conventional DNA-SIP, combining DNA-SIP with metagenomics (“focused metagenomics”) and combining DNA-SIP with single cell analysis techniques.
10.1128/9781555816896/f0018-01_thmb.gif
10.1128/9781555816896/f0018-01.gif
FIGURE 4.
An overview of conventional DNA-SIP, combining DNA-SIP with metagenomics (“focused metagenomics”) and combining DNA-SIP with single cell analysis techniques.
Citation:
Chen Y, Murrell J.
2011.
DNA Stable Isotope Probing,
p 3-24.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch1
References
/content/book/10.1128/9781555816896.ch01
1.
Amann, R. I.,, W. Ludwig, and, K. H. Schleifer. 1995. Identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59 : 143– 169.
2.
Baytshtok, V.,, H. Lu,, H. Park,, S. Kim,, R. Yu, and, K. Chandran. 2009. Impact of varying electron donors on the molecular microbial ecology and biokinetics of methylotrophic denitrifying bacteria. Biotechnol. Bioeng. 102 : 1527– 1536.
3.
Bernard, L.,, Maron, V.,, C. Mougel,, V. Nowak,, J. Leveque,, C. Marol,, J. Balesdent,, F. Gibiat, and, L. Ranjard. 2009. Contamination of soil by copper affects the dynamics, diversity and activity of soil bacterial communities involved in wheat decomposition and carbon storage. Appl. Environ. Microbiol. 75 : 7565– 7569.
4.
Bernard, L.,, C. Mougel,, P.-L. Maron,, V. Nowak,, J. Leveque,, C. Henault,, F., el Zahar haichar,, O. Berge,, C. Marol,, J. Balesdent,, F. Gibiat,, P. Lemanceau, and, L. Ranjard. 2007. Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques. Environ. Microbiol. 9 : 752– 764.
5.
Borodina, E.,, M. J. Cox,, I. R. McDonald, and, J. C. Murrell. 2005. Use of DNA-stable isotope probing and functional gene probes to investigate the diversity of methyl chloride-utilizing bacteria in soil. Environ. Microbiol. 7 : 1318– 1328.
6.
Boschker, H. T. S.,, S. C. Nold,, P. Wellsbury,, D. Bos,, W. de graaf,, R. Pel,, R. J. Parkes, and, T. E. Cappenberg. 1998. Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature 392 : 801– 804.
7.
Bressan, M.,, M. A. Roncato,, F. Bellvert,, G. Comte,, F. Z. Haichar,, W. Achouak, and, O. Berge. 2009. Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots. ISME J. 3 : 1243– 1257.
8.
Buckley, D. H.,, V. Huangyutitham,, S. F. Hsu, and, T. A. Nelson. 2007a. Stable isotope probing with 15N achieved by disentangling the effects of genome G+C content and isotope enrichment on DNA density. Appl. Environ. Microbiol. 73 : 3189– 3195.
9.
Buckley, D. H.,, V. Huangyutitham,, S. F. Hsu, and, T. A. Nelson. 2007b. Stable isotope probing with 15N 2 reveals novel noncultivated diazotrophs in soil. Appl. Environ. Microbiol. 73 : 3196– 3204.
10.
Buckley, D. H.,, V. Huangyutitham,, S. F. Hsu, and, T. A. Nelson. 2008. 15N 2-DNA-stable isotope probing of diazotrophic methanotrophs in soil. Soil Bio. Biochem. 40 : 1272– 1283.
11.
Bull, I. D.,, N. R. Parekh,, G. H. Hall,, P. Ineson, and, R. P. Evershed. 2000. Detection and classification of atmospheric methane oxidizing bacteria in soil. Nature 405 : 175– 178.
12.
Burkhardt, E.,, D. M. Akob,, S. Bischoff,, J. Sitte,, J. E. Kostka,, D. Banerjee,, A. C. Scheinost, and, K. Kusel. 2009. Impact of biostimulated redox processes on metal dynamics in an iron-rich creek soil of a former uranium mining area. Environ. Sci. Technol. 44 : 177– 183.
13.
Cadish, G.,, M. Espana,, R. Causey,, M. Richter,, E. Shaw,, J. A. W. Morgan,, C. Rahn, and, G. D. Bending. 2005. Technical considerations for the use of 15N-DNA stable-isotope probing for functional microbial activity in soils. Rapid Commun. Mass Spectrom. 19 : 1424– 1428.
14.
Cébron, A.,, L. Bodrossy,, Y. Chen,, A. C. Singer,, I. P. Thompson,, J. I. Prosser, and, J. C. Murrell. 2007a. Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probing. FEMS Microbiol. Ecol. 62 : 12– 23.
15.
Cébron, A.,, L. Bodrossy,, N. Stralis-Pavese,, A. C. Singer,, I. P. Thompson,, J. I. Prosser, and, J. C. Murrell. 2007b. Nutrient amendments in soil DNA stable isotope probing experiments reduce the observed methanotroph diversity. Appl. Environ. Microbiol. 73 : 798– 807.
16.
Chauhan, A.,, J. Cherrier, and, H. N. Williams. 2009. Impact of sideways and bottom-up control factors on bacterial community succession over a tidal cycle. Proc. Natl. Acad. Sci. USA. 106 : 4301– 4306.
17.
Chauhan, A., and, A. Ogram. 2006a. Fatty acid-oxidizing consortia along a nutrient gradient in the Florida Everglades. Appl. Environ. Microbiol. 72 : 2400– 2406.
18.
Chauhan, A., and, A. Ogram. 2006b. Phylogeny of acetate-utilizing microorganisms in soils along a nutrient gradient in the Florida everglades. Appl. Environ. Microbiol. 72 : 6837– 6840.
19.
Chen, Y.,, M. G. Dumont,, J. D. Neufeld,, L. Bodrossy,, N. Stralis-Pavese,, N. P. McNamara,, N. Ostle,, M. J. Briones, and, J. C. Murrell. 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– 2622.
20.
Chen, Y., and, J. C. Murrell. 2010. When metagenomics meets stable-isotope probing: progress and perspectives. Trends Microbiol. 18 : 157– 163.
21.
Chen, Y.,, L. Wu,, R. Boden,, A. Hillebrand,, D. Kumaresan,, H. Moussard,, M. Baciu,, Y. Lu, and, J. C. Murrell. 2009. Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave. ISME J. 3 : 1093– 1104.
22.
Cupples, A. M.,, E. A. Shaffer,, J. C. Chee-Sanford, and, G. K. Sims. 2007. DNA buoyant density shifts during 15N-DNA stable isotope probing. Microbiol. Res. 162 : 328– 334.
23.
Cupples, A. M., and, G. K. Sims. 2007. Identification of in situ 2,4-dichlorophenoxyacetic acid-degrading soil microorganisms using DNA-stable isotope probing. Soil Biol. Biochem. 39 : 232– 238.
24.
Derito, C. M., and, E. L. Madsen. 2009. Stable isotope probing reveals Trichosporon yeast to be active in situ in soil phenol metabolism. ISME J. 3 : 477– 485.
25.
Derito, C. M.,, G. M. Pumphrey, and, E. L. Madsen. 2005. 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. 71 : 7858– 7865.
26.
Dumont, M. G., and, J. C. Murrell. 2005. Stable isotope probing—linking microbial identity to function. Nat. Rev. Microbiol. 3 : 499– 504.
27.
Dumont, M. G.,, S. M. Radajewski,, C. B. Miguez,, I. R. McDonald, and, J. C. Murrell. 2006. Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomics analysis. Environ. Microbiol. 8 : 1240– 1250.
28.
Dunfield, P. F.,, V. N. Khmelenina,, N. E. Suzina,, Y. A. Trotsenko, and, S. N. Dedysh. 2003. Methylocella silvestris sp. Nov., a novel methanotrophic bacterium isolated from an acidic forest cambisol. Int. J. Syst. Evol. Microbiol. 53 : 1231– 1239.
29.
Freitag, T. E.,, L. Chang, and, J. I. Prosser. 2006. Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient. Environ. Microbiol. 8 : 684– 696.
30.
Gallagher, E.,, L. McGuinness,, C. Phelps,, L. Y. Young, and, L. J. Kerkhof. 2005. 13C-carrier DNA shortens the incubation time needed to detect benzoate-utilizing denitrifying bacteria by stable-isotope probing. Appl. Environ. Microbiol. 71 : 5192– 5196.
31.
Ginige, M. P.,, P. Hugenholtz,, H. Daims,, M. Wagner,, J. Keller, and, L. L. Blackall. 2004. Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Appl. Environ. Microbiol. 70 : 588– 596.
32.
Ginige, M. P.,, J. Keller, and, L. L. Blackall. 2005. Investigation of an acetate-fed denitrifying microbial community by stable isotope probing, full-cycle rRNA analysis, and fluorescent in situ hybridization-microautoradiography. Appl. Environ. Microbiol. 71 : 8683– 8691.
33.
Gorham, E. 1991. Northern peatlands: role in the carbon cycle and probable responses to climatic warming. Ecol. Appl. 1 : 182– 195.
34.
Handelsman, J. 2005. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Bio. Rev. 68 : 669– 685.
35.
Handelsman, J.,, M. R. Rondon,, S. F. Brady,, J. Clardy, and, R. M. Goodman. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5 : 245– 249.
36.
Han, B.,, Y. Chen,, G. Abell,, H. Jiang,, L. Bodrossy,, J. Zhao,, J. C. Murrell, and, X. H. Xing. 2008. Diversity and activity of methanotrophs in alkaline soil from a Chinese coal mine. FEMS Microbiol. Ecol. 70 : 40– 51.
37.
Haichar, F. E.,, W. Achouak,, R. Christen,, T. Heulin,, C. Marol,, M. F. Marais,, C. Mougel,, L. Ranjard,, J. Balesdent, and, O. Berge. 2007. Identification of cellulolytic bacteria in soil by stable isotope probing. Environ. Microbiol. 9 : 625– 634.
38.
Haichar, F. E.,, C. Marol,, O. Berge,, J. I., Rangel-Castro, J. I. Prosser,, J. Balesdent,, T. Heulin, and, W. Achouak. 2008. Plant host habitat and root exudates shape soil bacterial community structure. ISME J. 2 : 1221– 1230.
39.
Héry, M.,, A. C. Singer,, D. Kumaresan,, L. Bodrossy,, N. Stralis-Pavese,, J. I. Prosser,, I. P. Tompson, and, J. C. Murrell. 2008. Effect of earthworms on the community structure of active methanotrophic bacteria in a landfill cover soil. ISME J. 2 : 92– 104.
40.
Herrmann, S.,, S. Kleinsteuber,, A. Chatzinotas,, S. Kuppardt,, T. Leuders,, H. H. Richnow, and, C. Vogt. 2009. Functional characterization of an anaerobic benzene-degrading enrichment culture by DNA stable-isotope probing. Environ. Microbiol. 12 : 401– 411.
41.
Huang, W. E.,, A. Ferguson,, A. C. Singer,, K. Lawson,, I. P. Thompson,, R. M. Kalin,, M. J. Larkin,, M. M. Bailey, and, A. S. Whiteley. 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– 241.
42.
Hugenholtz, P.,, G. W. Tyson,, R. I. Webb,, A. M. Wagner, and, L. L. Blackall. 2001. Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Appl. Environ. Microbiol. 67 : 411– 419.
43.
Hutchens, E.,, S. Radajewski,, M. G. Dumont,, I. R. McDonald, and, J. C. Murrell. 2004. Analysis of methanotrophic bacteria in Movile Cave by stable-isotope probing. Environ. Microbiol. 6 : 111– 120.
44.
Janssen, P. H. 2008. New cultivation strategies for terrestrial microorganisms. In K. Zengler, (ed.), Accessing Uncultivated Microorganisms: from the Environment to Organisms and Genomes and Back. ASM Press, Washington, DC.
45.
Jehmlich, N.,, F. Schmidt,, M. von Bergen,, H. H. Richnow, and, C. Vogt. 2008. Protein-based stable isotope probing (protein-SIP) reveals active species within anoxic mixed cultures. ISME J. 2 : 1122– 1133.
46.
Jensen, S.,, J. D. Neufeld,, N. K. Birkeland,, M. Hovland, and, J. C. Murrell. 2008. Methane assimilation and trophic interaction with marine Methylomicrobium in deep-water coral reef sediment off the coast of Norway. FEMS Microbiol. Ecol. 66 : 320– 330.
47.
Jeon, C. O.,, W. Park,, P. Padmanabhan,, C. De-Rito,, J. R. Snape, and, E. L. Madsen. 2003. Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment. Proc. Natl. Acad. Sci. USA 100 : 13591– 13596.
48.
Jia, Z., and, R. Conrad. 2009. Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ. Microbiol. 11 : 1658– 1671.
49.
Jones, M. D.,, D. R. Singleton,, D. P. Cartensen,, S. N. Powell,, J. S. Swanson,, F. K. Pfaender, and, M. D. Aitken. 2008. Effect of incubation conditions on the enrichment of pyrene-degrading bacteria identifed by stable-isotope probing in an aged, PAH-contaminated soil. Microb. Ecol. 56 : 341– 349.
50.
Kalyuzhnaya, M. G.,, A. Lapidus,, N. Ivanova,, A. C. Copeland,, A. C. McHardy,, E. Szeto,, A. Salamov,, I. V. Grigoriev,, D. Suciu,, S. R. Levine,, V. M. Markowitz,, I. Rigoutsos,, S. G. Tringe,, D. C. Bruce,, P. M. Richardson,, M. E. Lidstrom, and, L. Chistoserdova. 2008. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat. Biotechnol. 26 : 1029– 1034.
51.
Kunapuli, U.,, T. Lueders, and, R. U. Meckenstock. 2007. The use of stable isotope probing to identify key iron-reducing microorganisms involved in anaerobic benzene degradation. ISME J. 1 : 643– 653.
52.
Lasken, R. S., and, T. B. Stockwell. 2007. Mechanism of chimera formation during the multiple displacement amplification reaction. BMC Biotechnol. 7 : 19.
53.
Lear, G., B. Song,, A. G. Gault,, D. A. Polya, and, J. R. Lloyd. 2007. Molecular analysis of arsenate-reducing bacteria within Cambodian sediments following amendment with acetate. Appl. Environ. Microbiol. 73 : 1041– 1048.
54.
Leigh, M. B.,, V. Pellizari,, O. Uhlí-k,, R. Sutka,, J. Rodrigues,, N. E. Ostrom,, J. Zhou, and, J. M. Tiedje. 2007. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J. 1 : 134– 148.
55.
Li, T.,, L. Mazeas,, A. Sghir,, G. Leblon, and, T. Bouchez. 2009. Insights into networks of functional microbes catalyzing methanization of cellulose under mesophilic conditions. Environ. Microbiol. 11 : 889– 904.
56.
Lin, J. L.,, S. Radajewski,, B. T. Eshinimaev,, Y. A. Trotsenko,, I. R. McDonald, and, J. C. Murrell. 2004. Molecular diversity of methanotrophs in Transbaikal soda lake sediments and identification of potential active populations by stable isotope probing. Environ. Microbiol. 6 : 1049– 1060.
57.
Liou, J. S.-C.,, C. M. DeRito, and, E. L. Madsen. 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. 74 : 4111– 4118.
58.
Longnecker, K.,, A. Da Costa,, M. Bhatia, and, E. B. Kujawinski. 2009. Effect of carbon addition and predation on acetate-assimilating bacterial cells in groundwater. FEMS Microbiol. Ecol. 70 : 124– 138.
59.
Lu, Y.,, T. Lueders,, W. Michael,, M. W. Friedrich, and, R. Conrad. 2005. Detecting active methanogenic populations on rice roots using stable isotope probing. Environ. Microbiol. 7 : 326– 336.
60.
Lueders, T.,, M. Manefield, and, M. W. Friedrich. 2004a. Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ. Microbiol. 6 : 73– 78.
61.
Lueders, T.,, B. Wagner,, P. Claus, and, M. W. Friedrich. 2004b. Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil. Environ. Microbiol. 6 : 60– 72.
62.
Luo, C.,, S. Xie,, W. Sun,, X. Li, and, A. M. Cupples. 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– 4647.
63.
Manefield, M.,, A. S. Whiteley,, R. I. Griffiths, and, M. Bailey. 2002. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl. Environ. Microbiol. 68 : 5367– 5373.
64.
Martineau, C.,, L. G. Whyte, and, C. W. Greer. 2008. Development of SYBR safe TM technique for the sensitive detection of DNA in cesium chloride density gradient for stable isotope probing assays. J. Microbiol. Methods. 73 : 199– 202.
65.
McCormick, N. G.,, J. H. Cornell, and, A. M. Kaplan. 1981. Biodegradation of hexahydro-1,3,5-trinitro-1,3,5-triazine. Appl. Environ. Microbiol. 42 : 817– 823.
66.
Miller, L. G.,, K. L. Warner,, S. M. Baesman,, R. S. Oremland,, I. R. McDonald,, S. Radajewski, and, J. C. Murrell. 2004. Degradation of methyl bromide and methyl chloride in soil microcosms: use of stable C isotope fractionation and stable isotope probing to identify reactions and the responsible microorganisms. Geochim. Cosmochim. Acta 68 : 3271– 3283.
67.
Morris, S. A.,, S. Radajewski,, T. W. Willison, and, J. C. Murrell. 2002. Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing. Appl. Environ. Microbiol. 68 : 1446– 1453.
68.
Moussard, H.,, N. Stralis-Pavese,, L. Bodrossy,, J. D. Neufeld, and, J. C. Murrell. 2009. Identification of active methylotrophic bacteria inhabiting surface sediment of a marine estuary. Environ. Microbio. Rep. 1 : 424– 433.
69.
Muyzer, G.,, E. C. De Waal, and, A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59 : 695– 700.
70.
Nercessian, O.,, E. Noyes,, M. G. Kalyuzhnaya,, M. E. Lidstrom, and, L. Chistoserdova. 2005. Bacterial populations active in metabolism of C1 compounds in the sediment of Lake Washington, a freshwater lake. Appl. Environ. Microbiol. 71 : 6885– 6899.
71.
Neufeld, J. D.,, R. Boden,, H. Moussard,, H. Schäfer, and, J. C. Murrell. 2008b. Substrate-specific clades of active marine methylotrophs associated with a phytoplankton bloom in a temperate coastal environment. Appl. Environ. Microbiol. 74 : 7321– 7328.
72.
Neufeld, J. D.,, Y. Chen,, M. G. Dumont,, J. C. Murrell. 2008a. Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environ. Microbiol. 10 : 1526– 1535.
73.
Neufeld, J. D.,, M. G., Dumont,, J. Vohra, and, J. C. Murrell. 2007a. Methodological considerations for the use of stable isotope probing in microbial ecology. Microb. Ecol. 53 : 435– 442.
74.
Neufeld, J. D.,, H. Schafer,, M. J. Cox,, R. Boden,, I. R. McDonald, and, J. C. Murrell. 2007c. Stable-isotope probing implicates Methylophaga spp. and novel Gammaproteobacteria in marine methanol and methylamine metabolism. ISME J. 1 : 480– 491.
75.
Neufeld, J. D.,, J. Vohra,, M. G. Dumont,, T. Lueers,, M. Manefield,, M. W. Friedrich,, J. C. Murrell. 2007b. DNA stable-isotope probing. Nat. Protoc. 2 : 860– 866.
76.
Oka, A. R.,, C. D. Phelps,, L. M. McGuinness,, A. Mumford,, L. Y. Young, and, L. J. Kerkhof. 2008. Identification of critical members in a sulfidogenic benzene-degrading consortium by DNA stable isotope probing. Appl. Environ. Microbiol. 74 : 6476– 6480.
77.
Osaka, T.,, Y. Ebie,, S. Tsuneda, and, Y. Ianamori. 2008. Identification of the bacterial community involved in methane-dependent denitrification in activated sludge using DNA stable-isotope probing. FEMS Microbiol. Ecol. 64 : 494– 506.
78.
Osaka, T.,, S. Yoshie,, S. Tsuneda,, A. Hirata,, N. Iwami, and, Y. Inamori. 2006. Identification of acetate- or methanol-assimilating bacteria under nitrate-reducing conditions by stable-isotope probing. Microb. Ecol. 52 : 253– 266.
79.
Pace, N. R. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173 : 4371– 4378.
80.
Padmanabhan, P.,, S. Padmanabhan,, C. DeRito,, A. Gray,, D. Gannon,, J. R. Snape,, C. S. Tsai,, W. Park,, C. Jeon, and, E. L. Madsen. 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– 1622.
81.
Powell, S. N.,, D. R. Singleton, and, M. D. Aitken. 2008. Effects of enrichment with salicylate on bacterial selection and PAH mineralization in a microbial community from a bioreactor treating contaminated soil. Environ. Sci. Technol. 42 : 4099– 4105.
82.
Pumphrey, G. M., and, E. L. Madsen. 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– 4118.
83.
Rasche, F.,, T. Leuders,, M. Schloter,, S. Schaefer,, F. Buegger,, A. Gattinger,, R. C., Hood-Nowotny, and, A. Sessitsch. 2009. DNA-stable isotope probing enables the identification of active bacterial endophytes in potatoes. New Phytologist. 181 : 802– 807.
84.
Radajewski, S.,, P. Ineson,, N. R. Parekh, and, J. C. Murrell. 2000. Stable-isotope probing as a tool in microbial ecology. Nature 403 : 646– 649.
85.
Radajewski, S.,, G. Webster,, D. S. Reay,, S. A. Morris,, P. Ineson,, D. B. Nedwell,, J. I. Prosser, and, J. C. Murrell. 2002. Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing. Microbiology 148 : 2331– 2342.
86.
Roh, H.,, C. Yu,, M. E. Fuller, and, K. Chu. 2009. Identification of hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading microorganisms via 15N-stable isotope probing. Environ. Sci. Technol. 43 : 2505– 2511.
87.
Schwartz, E. 2007. Characterization of growing microorganisms in soil by stable isotope probing with H 2 18O . Appl. Environ. Microbiol. 73 : 2541– 2546.
88.
Schwarz, S.,, T. Waschkowitz, and, R. Daniel. 2006. Enhancement of gene detection frequencies by combining DNA-based stable-isotope probing with the construction of metagenomic DNA libraries. World J. Microb. Biotech. 22 : 363– 367.
89.
Singleton, D. R.,, M. Hunt,, S. N. Powell,, R. Frontera-Suau, and, M. D. Aitken. 2007. Stable-isotope probing with multiple growth substrates to determine substrate specificity of uncultivated bacteria. J. Microbiol. Methods 69 : 180– 187.
90.
Singleton, D. R.,, S. N. Powell,, R. Sangaiah,, A. Gold,, L. M. Ball, and, M. D. Aitken. 2005. Stable-isotope probing of bacteria capable of degrading salicylate, naphthalene, or phenanthrene in a bioreactor treating contaminated soil. Appl. Environ. Microbiol. 71 : 1202– 1209.
91.
Singleton, D. R.,, R. Sangaiah,, A. Gold,, L. M. Ball, and, M. D. Aitken. 2006. Identification and quantification of uncultivated Proteobacteria associated with pyrene degradation in a bioreactor treating PAH-contaminated soil. Environ. Microbiol. 10 : 1736– 1745.
92.
Sul, W. J.,, J. Park,, J. F. Quensen, III,, J. L. Eodrigues,, L. Seliger,, T. V. Tsoi,, G. J. Zylstra, and, J. M. Tiedje. 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– 5506.
93.
Uhlik, O.,, K. Jecna,, M. Mackova,, C. Vlcek,, M. Hroudova,, K. Demnerova,, V. Paces, and, T. Macek. 2009. Biphenyl-metabolizing bacteria in the rhizosphere of horseradish and bulk soil contaminated by polychlorinated biphenyls as revealed by stable isotope probing. Appl. Environ. Microbiol. 75 : 6471– 6477.
94.
Vorob'ev, A. V.,, W. De Boer,, L. B. Folman,, P. L. Bodelier,, N. V. Doronina,, N. E. Zuzina,, Y. A. Trosenko, and, S. N. Dedysh. 2009. Methylovirgula ligni gen. Nov., sp. Nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene. Int. J. Syst. Evol. Microbiol. 59 : 2538– 2545.
95.
Wagner, M. 2009. Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging. Annu. Rev. Microbiol. 63 : 411– 429.
96.
Wawrik, B.,, A.V. Callaghan, and, D.A. Bronk. 2009. Use of inorganic and organic nitrogen by Synechococcus spp. and diatoms on the West Florida shelf as measured using stable isotope probing. Appl. Environ. Microbiol. 75 : 6662– 6670.
97.
Webster, G.,, L. C. Watt,, J. Rinna,, J. C. Fry,, R. P. Evershed,, R. J. Parkes, and, A. J. Weightman. 2006. A comparison of stable-isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate-reducing marine sediment enrichment slurries. Environ. Microbiol. 8 : 1575– 1589.
98.
Whitby, C. B.,, G. Hall,, R. Pickup,, J. R. Saunders,, P. Ineson,, N. R. Parekh, and, A. McCarthy. 2001. 13C incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations. Lett. Appl. Microbiol. 32 : 398– 401.
99.
Yu, C. P., and, K. H. Chu. 2005. A quantitative assay for linking microbial community function and structure of a naphthalene-degrading microbial consortium. Environ. Sci. Technol. 39 : 9611– 9619.
100.
Zengler, K. 2009. Central role of the cell in microbial ecology. Microbiol. Mol. Bio. Rev. 73 : 712– 729.
Tables
DNA Stable Isotope Probing
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Citation:
Chen Y, Murrell J.
2011.
DNA Stable Isotope Probing,
p 3-24.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch1
/content/10.1128/9781555816896.ch01.ch01tab01
TABLE 1
Key studies using DNA-SIP for identifying active microorganisms from diverse habitats
TABLE 1
Key studies using DNA-SIP for identifying active microorganisms from diverse habitats
Citation:
Chen Y, Murrell J.
2011.
DNA Stable Isotope Probing,
p 3-24.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch1
/content/10.1128/9781555816896.ch01.ch01tab02
TABLE 2
Comparison of DNA-, RNA-, PLFA- and Protein-SIP
TABLE 2
Comparison of DNA-, RNA-, PLFA- and Protein-SIP
Citation:
Chen Y, Murrell J.
2011.
DNA Stable Isotope Probing,
p 3-24.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch1