Part B | 11
322 Part B Tools and Methods in Marine Biotechnology
itrifiers, Bacteria, and Archaea along redox gradients in Pacific Northwest marine sediments
by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase
(nirS) and 16S rRNA genes, Appl. Environ. Microbiol. 67, 1893–1901 (2001)
11.62
J.P. Zehr: Nitrogen fixation by marine cyanobacteria, Trends Microbiol. 19, 162–173 (2011)
11.63
S.-J. Park, B.-J. Park, S.-K. Rhee: Comparative analysis of archaeal 16S rRNA and amoA
genes to estimate the abundance and diversity
of ammonia-oxidizing archaea in marine sediments, Extremophiles 12, 605–615 (2008)
11.64
M.S. Marcos, M. Lozada, W.D. Di Marzio,
H.M. Dionisi: Abundance, dynamics, and biogeographic distribution of seven polycyclic
aromatic hydrocarbon dioxygenase gene variants
in coastal sediments of Patagonia, Appl. Environ.
Microbiol. 78, 1589–1592 (2012)
11.65
L.M. Guibert, C.L. Loviso, M.S. Marcos, M.G. Commendatore, H.M. Dionisi, M. Lozada: Alkane
biodegradation genes from chronically polluted
Subantarctic coastal sediments and their shifts in
response to oil exposure, Microb. Ecol. 64, 605–
616 (2012)
11.66
W.J. Hickey, S. Chen, J. Zhao: The phn island:
A new genomic island encoding catabolism of
polynuclear aromatic hydrocarbons, Front. Microbiol. 3, 125 (2012)
11.67
G. Harms, A.C. Layton, H.M. Dionisi, I.R. Gregory, V.M. Garrett, S.A. Hawkins, K.G. Robinson,
G.S. Sayler: Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant, Environ. Sci. Technol. 37, 343–351
(2003)
11.68
C. Lebron, E. Petrovskis, F. Loffler, K. Henn: Application of nucleic acid-based tools for monitoring monitored natural attenuation (MNA),
biostimulation and bioaugmentation at chlorinated solvent sites (Environmental Security Technology Certification Program US Department of
Defense, ER-0518 Final Report, www.serdp.org,
2011)
11.69
J.D. Neufeld, M. Wagner, J.C. Murrell: Who eats
what, where and when? Isotope-labelling experiments are coming of age, ISME Journal 1, 103–110
(2007)
11.70
M.G. Dumont, J.C. Murrell: Stable isotope probing – Linking microbial identity to function, Nat.
Rev. Microbiol. 3, 499–504 (2005)
11.71
A.S. Whiteley, M. Manefield, T. Lueders: Unlocking
the “microbial black box” using RNA-based stable isotope probing technologies, Current Opin.
Biotechnol. 17, 67–71 (2006)
11.72
G. Webster, L.C. Watt, J. Rinna, J.C. Fry, R.P. Evershed, R.J. Parkes, A.J. Weightman: 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 (2006)
11.73
T.E. Freitag, L. Chang, J.I. Prosser: Changes in
the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater–marine gradient, Environ. Microbiol. 8, 684–696 (2006)
11.74
T. Miyatake, B.J. MacGregor, H.T.S. Boschker:
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. 75,
4927–4935 (2009)
11.75
J.D. Neufeld, Y. Chen, M.G. Dumont, J.C. Murrell: Marine methylotrophs revealed by stableisotope probing, multiple displacement amplification and metagenomics, Environ. Microbiol. 10,
1526–1535 (2008)
11.76
E.L. Madsen: The use of stable isotope probing techniques in bioreactor and field studies on
bioremediation, Current Opin. Biotechnol. 17, 92–
97 (2006)
11.77
R.I. Amann, W. Ludwig, K.H. Schleifer: Phylogenetic identification and in situ detection of
individual microbial cells without cultivation, Microbiol. Reviews 59, 143–169 (1995)
11.78
M. Wagner, M. Horn, H. Daims: Fluorescence in
situ hybridisation for the identification characterisation of prokaryotes, Current Opin. Microbiol. 6,
302–309 (2003)
11.79
K. Ishii, M. Mußmann, B.J. MacGregor, R. Amann:
An improved fluorescence in situ hybridization
protocol for the identification of bacteria and archaea in marine sediments, FEMS Microbiol. Ecol.
50, 203–213 (2004)
11.80
E. Teira, T. Reinthaler, A. Pernthaler, J. Pernthaler, G.J. Herndl: Combining catalyzed reporter
deposition-fluorescence in situ hybridization and
microautoradiography to detect substrate utilization by Bacteria and Archaea in the deep ocean,
Appl. Environ. Microbiol. 70, 4411–4414 (2004)
11.81
S. Behrens, T. Lösekann, J. Pett-Ridge, P.K. Weber, W.-O. Ng, B.S. Stevenson, I.D. Hutcheon,
D.A. Relman, A.M. Spormann: Linking microbial
phylogeny to metabolic activity at the singlecell level by using enhanced element labelingcatalyzed reporter deposition fluorescence in situ
hybridization (EL-FISH) and NanoSIMS, Appl. Environ. Microbiol. 74, 3143–3150 (2008)
11.82
T. Li, T.-D. Wu, L. Mazéas, L. Toffin, J.-L. Guerquin-Kern, G. Leblon, T. Bouchez: Simultaneous
analysis of microbial identity and function using
NanoSIMS, Environ. Microbiol. 10, 580–588 (2008)
11.83
D. Wang, S. Bodovitz: Single cell analysis: The new
frontier in “omics”, Trends Biotechnol. 28, 281–
290 (2010)
11.84
R.D. Fleischmann, M.D. Adams, O. White,
R.A. Clayton, E.F. Kirkness, A.R. Kerlavage,
322 Part B Tools and Methods in Marine Biotechnology
itrifiers, Bacteria, and Archaea along redox gradients in Pacific Northwest marine sediments
by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase
(nirS) and 16S rRNA genes, Appl. Environ. Microbiol. 67, 1893–1901 (2001)
11.62
J.P. Zehr: Nitrogen fixation by marine cyanobacteria, Trends Microbiol. 19, 162–173 (2011)
11.63
S.-J. Park, B.-J. Park, S.-K. Rhee: Comparative analysis of archaeal 16S rRNA and amoA
genes to estimate the abundance and diversity
of ammonia-oxidizing archaea in marine sediments, Extremophiles 12, 605–615 (2008)
11.64
M.S. Marcos, M. Lozada, W.D. Di Marzio,
H.M. Dionisi: Abundance, dynamics, and biogeographic distribution of seven polycyclic
aromatic hydrocarbon dioxygenase gene variants
in coastal sediments of Patagonia, Appl. Environ.
Microbiol. 78, 1589–1592 (2012)
11.65
L.M. Guibert, C.L. Loviso, M.S. Marcos, M.G. Commendatore, H.M. Dionisi, M. Lozada: Alkane
biodegradation genes from chronically polluted
Subantarctic coastal sediments and their shifts in
response to oil exposure, Microb. Ecol. 64, 605–
616 (2012)
11.66
W.J. Hickey, S. Chen, J. Zhao: The phn island:
A new genomic island encoding catabolism of
polynuclear aromatic hydrocarbons, Front. Microbiol. 3, 125 (2012)
11.67
G. Harms, A.C. Layton, H.M. Dionisi, I.R. Gregory, V.M. Garrett, S.A. Hawkins, K.G. Robinson,
G.S. Sayler: Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant, Environ. Sci. Technol. 37, 343–351
(2003)
11.68
C. Lebron, E. Petrovskis, F. Loffler, K. Henn: Application of nucleic acid-based tools for monitoring monitored natural attenuation (MNA),
biostimulation and bioaugmentation at chlorinated solvent sites (Environmental Security Technology Certification Program US Department of
Defense, ER-0518 Final Report, www.serdp.org,
2011)
11.69
J.D. Neufeld, M. Wagner, J.C. Murrell: Who eats
what, where and when? Isotope-labelling experiments are coming of age, ISME Journal 1, 103–110
(2007)
11.70
M.G. Dumont, J.C. Murrell: Stable isotope probing – Linking microbial identity to function, Nat.
Rev. Microbiol. 3, 499–504 (2005)
11.71
A.S. Whiteley, M. Manefield, T. Lueders: Unlocking
the “microbial black box” using RNA-based stable isotope probing technologies, Current Opin.
Biotechnol. 17, 67–71 (2006)
11.72
G. Webster, L.C. Watt, J. Rinna, J.C. Fry, R.P. Evershed, R.J. Parkes, A.J. Weightman: 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 (2006)
11.73
T.E. Freitag, L. Chang, J.I. Prosser: Changes in
the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater–marine gradient, Environ. Microbiol. 8, 684–696 (2006)
11.74
T. Miyatake, B.J. MacGregor, H.T.S. Boschker:
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. 75,
4927–4935 (2009)
11.75
J.D. Neufeld, Y. Chen, M.G. Dumont, J.C. Murrell: Marine methylotrophs revealed by stableisotope probing, multiple displacement amplification and metagenomics, Environ. Microbiol. 10,
1526–1535 (2008)
11.76
E.L. Madsen: The use of stable isotope probing techniques in bioreactor and field studies on
bioremediation, Current Opin. Biotechnol. 17, 92–
97 (2006)
11.77
R.I. Amann, W. Ludwig, K.H. Schleifer: Phylogenetic identification and in situ detection of
individual microbial cells without cultivation, Microbiol. Reviews 59, 143–169 (1995)
11.78
M. Wagner, M. Horn, H. Daims: Fluorescence in
situ hybridisation for the identification characterisation of prokaryotes, Current Opin. Microbiol. 6,
302–309 (2003)
11.79
K. Ishii, M. Mußmann, B.J. MacGregor, R. Amann:
An improved fluorescence in situ hybridization
protocol for the identification of bacteria and archaea in marine sediments, FEMS Microbiol. Ecol.
50, 203–213 (2004)
11.80
E. Teira, T. Reinthaler, A. Pernthaler, J. Pernthaler, G.J. Herndl: Combining catalyzed reporter
deposition-fluorescence in situ hybridization and
microautoradiography to detect substrate utilization by Bacteria and Archaea in the deep ocean,
Appl. Environ. Microbiol. 70, 4411–4414 (2004)
11.81
S. Behrens, T. Lösekann, J. Pett-Ridge, P.K. Weber, W.-O. Ng, B.S. Stevenson, I.D. Hutcheon,
D.A. Relman, A.M. Spormann: Linking microbial
phylogeny to metabolic activity at the singlecell level by using enhanced element labelingcatalyzed reporter deposition fluorescence in situ
hybridization (EL-FISH) and NanoSIMS, Appl. Environ. Microbiol. 74, 3143–3150 (2008)
11.82
T. Li, T.-D. Wu, L. Mazéas, L. Toffin, J.-L. Guerquin-Kern, G. Leblon, T. Bouchez: Simultaneous
analysis of microbial identity and function using
NanoSIMS, Environ. Microbiol. 10, 580–588 (2008)
11.83
D. Wang, S. Bodovitz: Single cell analysis: The new
frontier in “omics”, Trends Biotechnol. 28, 281–
290 (2010)
11.84
R.D. Fleischmann, M.D. Adams, O. White,
R.A. Clayton, E.F. Kirkness, A.R. Kerlavage,