Marine Microbial Bioprospecting References 321
Part B | 11
nobacteria, J. Microbiol. Methods 72, 257–262
(2008)
11.35
S.A. Connon, S.J. Giovannoni: High-throughput
methods for culturing microorganisms in verylow-nutrient media yield diverse new marine
isolates, Appl. Environ. Microbiol. 68, 3878–3885
(2002)
11.36
K. Zengler, G. Toledo, M. Rappó, J. Elkins,
E.J. Mathur, J.M. Short, M. Keller: Cultivating the
uncultured, Proc. Natl. Acad. Sci. USA 99, 15681–
15686 (2002)
11.37
K. Zengler, M. Walcher, G. Clark, I. Haller,
G. Toledo, T. Holland, E.J. Mathur, G. Woodnutt,
J.M. Short, M. Keller: High-throughput cultivation
of microorganisms using microcapsules, Methods
Enzymol. 397, 124–130 (2005)
11.38
K. Zengler, H.H. Richnow, R. Rosselló-Mora,
W. Michaelis, F. Widdel: Methane formation from
long-chain alkanes by anaerobic microorganisms, Nature 401, 266–269 (1999)
11.39
J. Song, H.-M. Oh, J.-C. Cho: Improved
culturability of SAR11 strains in dilution-toextinction culturing from the East Sea, West
Pacific Ocean, FEMS Microbiol. Lett. 295, 141–147
(2009)
11.40
M.S. Rappé, S.A. Connon, K.L. Vergin, S.J. Giovannoni: Cultivation of the ubiquitous SAR11 marine bacterioplankton clade, Nature 418, 630–633
(2002)
11.41
S. Buerger, A. Spoering, E. Gavrish, C. Leslin,
L. Ling, S.S. Epstein: Microbial scout hypothesis
and microbial discovery, Appl. Environ. Microbiol.
78, 3229–3233 (2012)
11.42
J. Houghton, W. Seyfried Jr., A. Banta, A.L. Reysenbach: Continuous enrichment culturing of
thermophiles under sulfate and nitrate-reducing
conditions and at deep-sea hydrostatic pressures, Extremophiles 11, 371–382 (2007)
11.43
A. Postec, F. Lesongeur, P. Pignet, B. Ollivier,
J. Querellou, A. Godfroy: Continuous enrichment
cultures: insights into prokaryotic diversity and
metabolic interactions in deep-sea vent chimneys, Extremophiles 11, 747–757 (2007)
11.44
K. Alain, J. Quérellou: Cultivating the uncultured: Limits, advances and future challenges,
Extremophiles 13, 583–594 (2009)
11.45
K. Alain, M. Zbinden, N. Le Bris, F. Lesongeur,
J. Quérellou, F. Gaill, M.A. Cambon-Bonavita:
Early steps in microbial colonization processes at
deep-sea hydrothermal vents, Environ. Microbiol.
6, 227–241 (2004)
11.46
M. Yasumoto-Hirose, M. Nishijima, M.K. Ngirchechol, K. Kanoh, Y. Shizuri, W. Miki: Isolation of
marine bacteria by in situ culture on mediasupplemented polyurethane foam, Mar. Biotechnol. 8, 227–237 (2006)
11.47
A. Bruns, U. Nübel, H. Cypionka, J. Overmann:
Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton, Appl. Environ. Microbiol. 69, 1980–
1989 (2003)
11.48
D. Nichols, K. Lewis, J. Orjala, S. Mo, R. Ortenberg, P. O’Connor, C. Zhao, P. Vouros, T. Kaeberlein,
S.S. Epstein: Short peptide induces an “uncultivable” microorganism to grow in vitro, Appl.
Environ. Microbiol. 74, 4889–4897 (2008)
11.49
C.J. Ingham, A. Sprenkels, J. Bomer, D. Molenaar, A. van den Berg, J.E.T. van Hylckama Vlieg,
W.M. de Vos: The micro-Petri dish, a million-well
growth chip for the culture and high-throughput
screening of microorganisms, Proc. Natl. Acad.
Sci. USA 104, 18217–18222 (2007)
11.50
D. Nichols, N. Cahoon, E.M. Trakhtenberg,
L. Pham, A. Mehta, A. Belanger, T. Kanigan,
K. Lewis, S.S. Epstein: Use of ichip for highthroughput in situ cultivation of “uncultivable”
microbial species, Appl. Environ. Microbiol. 76,
2445–2450 (2010)
11.51
F. Berrue, S.T. Withers, B. Haltli, J. Withers,
R.G. Kerr: Chemical screening method for the
rapid identification of microbial sources of marine invertebrate-associated metabolites, Mar.
Drugs 9, 369–381 (2011)
11.52
S.S. Epstein: Microbial awakenings, Nature 457,
1083–1083 (2009)
11.53
P.H. Janssen, A. Schuhmann, E. Mörschel,
F.A. Rainey: Novel anaerobic ultramicrobacteria
belonging to the Verrucomicrobiales lineage of
bacterial descent isolated by dilution culture
from anoxic rice paddy soil, Appl. Environ.
Microbiol. 63, 1382–1388 (1997)
11.54
G.J. Olsen, D.J. Lane, S.J. Giovannoni, N.R. Pace,
D.A. Stahl: Microbial ecology and evolution: A ribosomal RNA approach, Annu. Rev. Microbiol. 40,
337–365 (1986)
11.55
C.R. Woese: Bacterial evolution, Microbiol. Rev. 51,
221–271 (1987)
11.56
M.S. Rappé, S.J. Giovannoni: The uncultured microbial majority, Annu. Rev. Microbiol. 57, 369–
394 (2003)
11.57
L.J. Forney, X. Zhou, C.J. Brown: Molecular microbial ecology: land of the one-eyed king, Current
Opin. Microbiol. 7, 210–220 (2004)
11.58
C. Su, L. Lei, Y. Duan, K.-Q. Zhang, J. Yang:
Culture-independent methods for studying environmental microorganisms: Methods, application, and perspective, Appl. Microbiol. Biotechnol. 93, 993–1003 (2012)
11.59
S.G. Tringe, P. Hugenholtz: A renaissance for the
pioneering 16S rRNA gene, Current Opin. Microbiol. 11, 442–446 (2008)
11.60
J. Pérez-Jiménez, L. Kerkhof: Phylogeography of
sulfate-reducing bacteria among disturbed sediments, disclosed by analysis of the dissimilatory
sulfite reductase genes (dsrAB), Appl. Environ.
Microbiol. 71, 1004–1011 (2005)
11.61
G. Braker, H.C.L. Ayala-del-Río, A.H. Devol, A. Fesefeldt, J.M. Tiedje: Community structure of den-
Part B | 11
nobacteria, J. Microbiol. Methods 72, 257–262
(2008)
11.35
S.A. Connon, S.J. Giovannoni: High-throughput
methods for culturing microorganisms in verylow-nutrient media yield diverse new marine
isolates, Appl. Environ. Microbiol. 68, 3878–3885
(2002)
11.36
K. Zengler, G. Toledo, M. Rappó, J. Elkins,
E.J. Mathur, J.M. Short, M. Keller: Cultivating the
uncultured, Proc. Natl. Acad. Sci. USA 99, 15681–
15686 (2002)
11.37
K. Zengler, M. Walcher, G. Clark, I. Haller,
G. Toledo, T. Holland, E.J. Mathur, G. Woodnutt,
J.M. Short, M. Keller: High-throughput cultivation
of microorganisms using microcapsules, Methods
Enzymol. 397, 124–130 (2005)
11.38
K. Zengler, H.H. Richnow, R. Rosselló-Mora,
W. Michaelis, F. Widdel: Methane formation from
long-chain alkanes by anaerobic microorganisms, Nature 401, 266–269 (1999)
11.39
J. Song, H.-M. Oh, J.-C. Cho: Improved
culturability of SAR11 strains in dilution-toextinction culturing from the East Sea, West
Pacific Ocean, FEMS Microbiol. Lett. 295, 141–147
(2009)
11.40
M.S. Rappé, S.A. Connon, K.L. Vergin, S.J. Giovannoni: Cultivation of the ubiquitous SAR11 marine bacterioplankton clade, Nature 418, 630–633
(2002)
11.41
S. Buerger, A. Spoering, E. Gavrish, C. Leslin,
L. Ling, S.S. Epstein: Microbial scout hypothesis
and microbial discovery, Appl. Environ. Microbiol.
78, 3229–3233 (2012)
11.42
J. Houghton, W. Seyfried Jr., A. Banta, A.L. Reysenbach: Continuous enrichment culturing of
thermophiles under sulfate and nitrate-reducing
conditions and at deep-sea hydrostatic pressures, Extremophiles 11, 371–382 (2007)
11.43
A. Postec, F. Lesongeur, P. Pignet, B. Ollivier,
J. Querellou, A. Godfroy: Continuous enrichment
cultures: insights into prokaryotic diversity and
metabolic interactions in deep-sea vent chimneys, Extremophiles 11, 747–757 (2007)
11.44
K. Alain, J. Quérellou: Cultivating the uncultured: Limits, advances and future challenges,
Extremophiles 13, 583–594 (2009)
11.45
K. Alain, M. Zbinden, N. Le Bris, F. Lesongeur,
J. Quérellou, F. Gaill, M.A. Cambon-Bonavita:
Early steps in microbial colonization processes at
deep-sea hydrothermal vents, Environ. Microbiol.
6, 227–241 (2004)
11.46
M. Yasumoto-Hirose, M. Nishijima, M.K. Ngirchechol, K. Kanoh, Y. Shizuri, W. Miki: Isolation of
marine bacteria by in situ culture on mediasupplemented polyurethane foam, Mar. Biotechnol. 8, 227–237 (2006)
11.47
A. Bruns, U. Nübel, H. Cypionka, J. Overmann:
Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton, Appl. Environ. Microbiol. 69, 1980–
1989 (2003)
11.48
D. Nichols, K. Lewis, J. Orjala, S. Mo, R. Ortenberg, P. O’Connor, C. Zhao, P. Vouros, T. Kaeberlein,
S.S. Epstein: Short peptide induces an “uncultivable” microorganism to grow in vitro, Appl.
Environ. Microbiol. 74, 4889–4897 (2008)
11.49
C.J. Ingham, A. Sprenkels, J. Bomer, D. Molenaar, A. van den Berg, J.E.T. van Hylckama Vlieg,
W.M. de Vos: The micro-Petri dish, a million-well
growth chip for the culture and high-throughput
screening of microorganisms, Proc. Natl. Acad.
Sci. USA 104, 18217–18222 (2007)
11.50
D. Nichols, N. Cahoon, E.M. Trakhtenberg,
L. Pham, A. Mehta, A. Belanger, T. Kanigan,
K. Lewis, S.S. Epstein: Use of ichip for highthroughput in situ cultivation of “uncultivable”
microbial species, Appl. Environ. Microbiol. 76,
2445–2450 (2010)
11.51
F. Berrue, S.T. Withers, B. Haltli, J. Withers,
R.G. Kerr: Chemical screening method for the
rapid identification of microbial sources of marine invertebrate-associated metabolites, Mar.
Drugs 9, 369–381 (2011)
11.52
S.S. Epstein: Microbial awakenings, Nature 457,
1083–1083 (2009)
11.53
P.H. Janssen, A. Schuhmann, E. Mörschel,
F.A. Rainey: Novel anaerobic ultramicrobacteria
belonging to the Verrucomicrobiales lineage of
bacterial descent isolated by dilution culture
from anoxic rice paddy soil, Appl. Environ.
Microbiol. 63, 1382–1388 (1997)
11.54
G.J. Olsen, D.J. Lane, S.J. Giovannoni, N.R. Pace,
D.A. Stahl: Microbial ecology and evolution: A ribosomal RNA approach, Annu. Rev. Microbiol. 40,
337–365 (1986)
11.55
C.R. Woese: Bacterial evolution, Microbiol. Rev. 51,
221–271 (1987)
11.56
M.S. Rappé, S.J. Giovannoni: The uncultured microbial majority, Annu. Rev. Microbiol. 57, 369–
394 (2003)
11.57
L.J. Forney, X. Zhou, C.J. Brown: Molecular microbial ecology: land of the one-eyed king, Current
Opin. Microbiol. 7, 210–220 (2004)
11.58
C. Su, L. Lei, Y. Duan, K.-Q. Zhang, J. Yang:
Culture-independent methods for studying environmental microorganisms: Methods, application, and perspective, Appl. Microbiol. Biotechnol. 93, 993–1003 (2012)
11.59
S.G. Tringe, P. Hugenholtz: A renaissance for the
pioneering 16S rRNA gene, Current Opin. Microbiol. 11, 442–446 (2008)
11.60
J. Pérez-Jiménez, L. Kerkhof: Phylogeography of
sulfate-reducing bacteria among disturbed sediments, disclosed by analysis of the dissimilatory
sulfite reductase genes (dsrAB), Appl. Environ.
Microbiol. 71, 1004–1011 (2005)
11.61
G. Braker, H.C.L. Ayala-del-Río, A.H. Devol, A. Fesefeldt, J.M. Tiedje: Community structure of den-