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Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology
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Amann R., Ludwig W. Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol Rev. 24:2000;555-565.
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FEMS Microbiol Rev
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Amann, R.1
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Molecular community analysis of microbial diversity
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Dahllöf I. Molecular community analysis of microbial diversity. Curr Opin Biotechnol. 13:2002;213-217.
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Curr Opin Biotechnol
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Dahllöf, I.1
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0028946084
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Phylogenetic identification and in situ detection of individual microbial cells without cultivation
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Amann, R.I.1
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Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity
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Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing
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13C-labelled substrates
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13C-labelled substrates.
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Microbiology
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Radajewski, S.1
Webster, G.2
Reay, D.S.3
Morris, S.A.4
Ineson, P.5
Nedwell, D.B.6
Prosser, J.I.7
Murrell, J.C.8
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11
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0034995535
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13C incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations
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The authors demonstrate how 16S rRNA group-specific primers can be used with DNA-SIP to link taxonomic identity with metabolic activity.
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13C incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations. Lett Appl Microbiol. 32:2001;398-401 The authors demonstrate how 16S rRNA group-specific primers can be used with DNA-SIP to link taxonomic identity with metabolic activity.
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Lett Appl Microbiol
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Whitby, C.B.1
Hall, G.2
Pickup, R.3
Saunders, J.R.4
Ineson, P.5
Parekh, N.R.6
McCarthy, A.7
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12
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0036840287
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RNA stable isotope probing, a novel means of linking microbial community function to phylogeny
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The first paper to demonstrate that stable-isotope labelled RNA can be used as a sensitive biomarker for structure-function studies. This study established that the bacteria dominating phenol degradation in a bioreactor are not those that were suspected from conventional methodologies.
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Manefield M., Whiteley A.S., Griffiths R.I., Bailey M.J. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol. 68:2002;5367-5373 The first paper to demonstrate that stable-isotope labelled RNA can be used as a sensitive biomarker for structure-function studies. This study established that the bacteria dominating phenol degradation in a bioreactor are not those that were suspected from conventional methodologies.
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(2002)
Appl Environ Microbiol
, vol.68
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Manefield, M.1
Whiteley, A.S.2
Griffiths, R.I.3
Bailey, M.J.4
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13
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0036452120
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Technical considerations for RNA-based stable isotope probing: An approach to associating microbial diversity with microbial community function
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The authors use pure cultures to critically evaluate the RNA-SIP approach.
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Manefield M., Whiteley A.S., Ostle N., Ineson P., Bailey M.J. Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function. Rapid Commun Mass Spectrom. 16:2002;2179-2183 The authors use pure cultures to critically evaluate the RNA-SIP approach.
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Rapid Commun Mass Spectrom
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Manefield, M.1
Whiteley, A.S.2
Ostle, N.3
Ineson, P.4
Bailey, M.J.5
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14
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0036281803
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Stable isotopes and biomarkers in microbial ecology
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A nice review on the use of stable isotopes to link microbial function with identity via non-nucleic acid biomarkers.
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Boschker H.T.S., Middelburg J.J. Stable isotopes and biomarkers in microbial ecology. FEMS Microbiol Ecol. 40:2002;85-95 A nice review on the use of stable isotopes to link microbial function with identity via non-nucleic acid biomarkers.
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FEMS Microbiol Ecol
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Boschker, H.T.S.1
Middelburg, J.J.2
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0036470363
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Stable carbon isotopes of lipid biomarkers: Analysis of metabolites and metabolic fates of environmental microorganisms
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Zhang C.L. Stable carbon isotopes of lipid biomarkers: analysis of metabolites and metabolic fates of environmental microorganisms. Curr Opin Biotechnol. 13:2002;25-30.
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Zhang, C.L.1
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16
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18844481026
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A marine microbial consortium apparently mediating anaerobic oxidation of methane
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Boetius A., Ravenschlag K., Schubert C.J., Rickert D., Widdel F., Gieseke A., Amann R., Jørgensen B.B., Witte U., Pfannkuche O. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature. 407:2000;623-626.
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(2000)
Nature
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Boetius, A.1
Ravenschlag, K.2
Schubert, C.J.3
Rickert, D.4
Widdel, F.5
Gieseke, A.6
Amann, R.7
Jørgensen, B.B.8
Witte, U.9
Pfannkuche, O.10
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17
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0035035778
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Use of isotopic and molecular techniques to link toluene degradation in denitrifying aquifer microcosms to specific microbial populations
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An example of how stable-isotope labelling and molecular biological techniques can be coupled to overcome some of the taxonomic ambiguities that can be associated with PLFA labelling.
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Pelz O., Chatzinotas A., Andersen N., Bernasconi S.M., Hesse C., Abraham W.-R., Zeyer J. Use of isotopic and molecular techniques to link toluene degradation in denitrifying aquifer microcosms to specific microbial populations. Arch Microbiol. 175:2001;270-281 An example of how stable-isotope labelling and molecular biological techniques can be coupled to overcome some of the taxonomic ambiguities that can be associated with PLFA labelling.
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(2001)
Arch Microbiol
, vol.175
, pp. 270-281
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Pelz, O.1
Chatzinotas, A.2
Andersen, N.3
Bernasconi, S.M.4
Hesse, C.5
Abraham, W.-R.6
Zeyer, J.7
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19
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0035919654
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Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis
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Orphan V.J., House C.H., Hinrichs K.U., McKeegan K.D., DeLong E.F. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science. 293:2001;484-487.
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Science
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Orphan, V.J.1
House, C.H.2
Hinrichs, K.U.3
McKeegan, K.D.4
DeLong, E.F.5
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20
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0037188554
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Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments
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Following the pioneering study of Orphan et al. [19], the identities and arrangement of microorganisms involved in the fascinating process of anaerobic methane oxidation are being elucidated through the coupling of FISH with isotopic analysis of single cells and microbial aggregates.
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Orphan V.J., House C.H., Hinrichs K.U., McKeegan K.D., DeLong E.F. Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc Natl Acad Sci USA. 99:2002;7663-7668 Following the pioneering study of Orphan et al. [19], the identities and arrangement of microorganisms involved in the fascinating process of anaerobic methane oxidation are being elucidated through the coupling of FISH with isotopic analysis of single cells and microbial aggregates.
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Proc Natl Acad Sci USA
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Orphan, V.J.1
House, C.H.2
Hinrichs, K.U.3
McKeegan, K.D.4
DeLong, E.F.5
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21
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0036048586
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Isolation of small-subunit rRNA for stable-isotopic characterization
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These authors describe a method using rRNA capture probes to discriminate between different phylogenetic groups. Subsequent isotopic analysis of rRNA classes holds great promise for linking taxonomic identity with microbial function.
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MacGregor B.J., Brüchert V., Fleischer S., Amann R. Isolation of small-subunit rRNA for stable-isotopic characterization. Environ Microbiol. 4:2002;451-464 These authors describe a method using rRNA capture probes to discriminate between different phylogenetic groups. Subsequent isotopic analysis of rRNA classes holds great promise for linking taxonomic identity with microbial function.
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(2002)
Environ Microbiol
, vol.4
, pp. 451-464
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MacGregor, B.J.1
Brüchert, V.2
Fleischer, S.3
Amann, R.4
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23
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Stable isotope tracers in the life sciences and medicine
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Methane formation from long-chain alkanes by anaerobic microorganisms
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Michaelis, W.4
Widdel, F.5
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25
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0014220756
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A living organism of unusual isotopic composition. Sequential and cumulative replacement of stable isotopes in Chlorella vulgaris
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Uphaus R.A., Flaumenhaft E., Katz J.J. A living organism of unusual isotopic composition. Sequential and cumulative replacement of stable isotopes in Chlorella vulgaris. Biochim Biophys Acta. 141:1967;625-632.
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Uphaus, R.A.1
Flaumenhaft, E.2
Katz, J.J.3
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26
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0034554741
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Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage
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Béjà O., Suzuki M.T., Koonin E.V., Aravind L., Hadd A., Nguyen L.P., Villacorta R., Amajadi M., Garrigues C., Jovanovich S.B.et al. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol. 2:2000;516-529.
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Environ Microbiol
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Béjà, O.1
Suzuki, M.T.2
Koonin, E.V.3
Aravind, L.4
Hadd, A.5
Nguyen, L.P.6
Villacorta, R.7
Amajadi, M.8
Garrigues, C.9
Jovanovich, S.B.10
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27
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18844481269
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Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms
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Rondon M.R., August P.R., Bettermann A.D., Brady S.F., Grossman T.H., Liles M.R., Loiacono K.A., Lynch B.A., MacNeil I.A., Minor C.et al. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol. 66:2000;2541-2547.
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Appl Environ Microbiol
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Rondon, M.R.1
August, P.R.2
Bettermann, A.D.3
Brady, S.F.4
Grossman, T.H.5
Liles, M.R.6
Loiacono, K.A.7
Lynch, B.A.8
MacNeil, I.A.9
Minor, C.10
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28
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0035514941
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Gene cassette PCR: Sequence-independent recovery of entire genes from environmental DNA
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Stokes H.W., Holmes A.J., Nield B.S., Holley M.P., Nevalainen K.M.H., Mabbutt B.C., Gillings M.R. Gene cassette PCR: sequence-independent recovery of entire genes from environmental DNA. Appl Environ Microbiol. 67:2001;5240-5246.
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Appl Environ Microbiol
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Stokes, H.W.1
Holmes, A.J.2
Nield, B.S.3
Holley, M.P.4
Nevalainen, K.M.H.5
Mabbutt, B.C.6
Gillings, M.R.7
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29
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0037043731
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Cultivation of the ubiquitous SAR11 marine bacterioplankton clade
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Representatives of this elusive group of microorganisms were isolated following extensive dilution of seawater samples into very low nutrient media.
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Rappé M.S., Connon S.A., Vergin K.L., Giovannoni S.J. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature. 418:2002;630-633 Representatives of this elusive group of microorganisms were isolated following extensive dilution of seawater samples into very low nutrient media.
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Nature
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Rappé, M.S.1
Connon, S.A.2
Vergin, K.L.3
Giovannoni, S.J.4
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30
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18744382447
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Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys
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Simple changes to common cultivation strategies yielded bacterial isolates that represent new families, orders or subdivisions within well-established phylogenetic groups.
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Sait M., Hugenholtz P., Janssen P.H. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol. 4:2002;654-666 Simple changes to common cultivation strategies yielded bacterial isolates that represent new families, orders or subdivisions within well-established phylogenetic groups.
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(2002)
Environ Microbiol
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, pp. 654-666
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Sait, M.1
Hugenholtz, P.2
Janssen, P.H.3
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31
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0037180507
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Cultivating the uncultured
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A single-cell encapsulation method permits the parallel cultivation of isolated cells under conditions where nutrients and metabolites are readily exchanged. Microcolonies are then sorted by flow cytometry.
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Zengler K., Toledo G., Rappé M., Elkins J., Mathur E.J., Short J.M., Keller M. Cultivating the uncultured. Proc Natl Acad Sci USA. 99:2002;15681-15686 A single-cell encapsulation method permits the parallel cultivation of isolated cells under conditions where nutrients and metabolites are readily exchanged. Microcolonies are then sorted by flow cytometry.
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(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 15681-15686
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Zengler, K.1
Toledo, G.2
Rappé, M.3
Elkins, J.4
Mathur, E.J.5
Short, J.M.6
Keller, M.7
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32
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0036250036
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Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia
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Janssen P.H., Yates P.S., Grinton B.E., Taylor P.M., Sait M. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol. 68:2002;2391-2396.
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(2002)
Appl Environ Microbiol
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Janssen, P.H.1
Yates, P.S.2
Grinton, B.E.3
Taylor, P.M.4
Sait, M.5
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