Part B | 11
324 Part B Tools and Methods in Marine Biotechnology
11.111 A. Bankevich, S. Nurk, D. Antipov, A.A. Gurevich, M. Dvorkin, A.S. Kulikov, V.M. Lesin, S.I. Nikolenko, S. Pham, A.D. Prjibelski, A.V. Pyshkin,
A.V. Sirotkin, N. Vyahhi, G. Tesler, M.A. Alekseyev,
P.A. Pevzner: SPAdes: A new genome assembly
algorithm and its applications to single-cell sequencing, J. Comput. Biol. 19, 455–477 (2012)
11.112 T. Woyke, A. Sczyrba, J. Lee, C. Rinke, D. Tighe,
S. Clingenpeel, R. Malmstrom, R. Stepanauskas,
J.-F. Cheng: Decontamination of MDA reagents for
single cell whole genome amplification, PLoS One
6, e26161 (2011)
11.113 A.E.K. Dichosa, M.S. Fitzsimons, C.-C. Lo, L.L. Weston, L.G. Preteska, J.P. Snook, X. Zhang, W. Gu,
K. McMurry, L.D. Green, P.S. Chain, J.C. Detter,
C.S. Han: Artificial polyploidy improves bacterial
single cell Genome recovery, PLoS One 7, e37387
(2012)
11.114 R. Stepanauskas: Single cell genomics: an individual look at microbes, Current Opin. Microbiol.
15, 613–620 (2012)
11.115 H.S. Yoon, D.C. Price, R. Stepanauskas, V.D. Rajah, M.E. Sieracki, W.H. Wilson, E.C. Yang, S. Duffy,
D. Bhattacharya: Single-cell genomics reveals
organismal interactions in uncultivated marine
protists, Science 332, 714–717 (2011)
11.116 J. Kamke, K. Bayer, T. Woyke, U. Hentschel: Exploring symbioses by single-cell genomics, Biol.
Bulletin 223, 30–43 (2012)
11.117 K. Bayer, M. Scheuermayer, L. Fieseler,
U. Hentschel: Genomic mining for novel FADH 2 -
dependent halogenases in marine spongeassociated microbial consortia, Mar. Biotechnol.
15, 63–72 (2013)
11.118 M. Martinez-Garcia, D.M. Brazel, B.K. Swan,
C. Arnosti, P.S.G. Chain, K.G. Reitenga, G. Xie,
N.J. Poulton, M.L. Gomez, D.E.D. Masland,
B. Thompson, W.K. Bellows, K. Ziervogel, C.C. Lo, S. Ahmed, C.D. Gleasner, C.J. Detter,
R. Stepanauskas: Capturing single cell genomes
of active polysaccharide degraders: An unexpected contribution of Verrucomicrobia, PLoS One
7, e35314 (2012)
11.119 R.R. Malmstrom, S. Rodrigue, K.H. Huang,
L. Kelly, S.E. Kern, A. Thompson, S. Roggensack,
P.M. Berube, M.R. Henn, S.W. Chisholm: Ecology
of uncultured Prochlorococcus clades revealed
through single-cell genomics and biogeographic
analysis, ISME Journal 7, 184–198 (2013)
11.120 J.A. Gilbert, C.L. Dupont: Microbial metagenomics: beyond the genome, Annu. Rev. Mar. Sci.
3, 347–371 (2011)
11.121 W.R. Streit, R. Daniel: Metagenomics: Methods
and protocols. In: Methods in Molecular Biology,
Vol. 668 (Humana, New York 2010)
11.122 S. Shokralla, J.L. Spall, J.F. Gibson, M. Hajibabaei:
Next-generation sequencing technologies for environmental DNA research, Mol. Ecol. 21, 1794–
1805 (2012)
11.123 C. Simon, R. Daniel: Metagenomic analyses: past
and future trends, Appl. Environ. Microbiol. 77,
1153–1161 (2011)
11.124 D.M. Ekkers, M.S. Cretoiu, A.M. Kielak, J.D. van Elsas: The great screen anomaly – A new frontier
in product discovery through functional metagenomics, Appl. Microbiol. Biotechnol. 93, 1005–
1020 (2012)
11.125 J. Kennedy, N.D. O’Leary, G.S. Kiran, J.P. Morrissey, F. O’Gara, J. Selvin, A.D.W. Dobson: Functional
metagenomic strategies for the discovery of novel
enzymes and biosurfactants with biotechnological applications from marine ecosystems, J. Appl.
Microbiol. 111, 787–799 (2011)
11.126 R. Cavicchioli, T. Charlton, H. Ertan, S. Mohd Omar,
K.S. Siddiqui, T.J. Williams: Biotechnological uses
of enzymes from psychrophiles, Microb. Biotechnol. 4, 449–460 (2011)
11.127 J. Kennedy, J.R. Marchesi, A.D.W. Dobson: Marine metagenomics: Strategies for the discovery
of novel enzymes with biotechnological applications from marine environments, Microb. Cell
Fact. 7, 27 (2008)
11.128 J. Piel: Approaches to capturing and designing
biologically active small molecules produced by
uncultured microbes, Annu. Rev. Microbiol. 65,
431–453 (2011)
11.129 T. Uchiyama, K. Miyazaki: Functional metagenomics for enzyme discovery: Challenges to efficient screening, Current Opin. Biotechnol. 20,
616–622 (2009)
11.130 F.-X. Lussier, O. Chambenoit, A. Côté, J.-F. Hupé,
F. Denis, P. Juteau, R. Beaudet, F. Shareck: Construction and functional screening of a metagenomic library using a T7 RNA polymerase-based
expression cosmid vector, J. Ind. Microbiol.
Biotechnol. 38, 1321–1328 (2011)
11.131 M. Taupp, K. Mewis, S.J. Hallam: The art and design of functional metagenomic screens, Current
Opin. Biotechnol. 22, 465–472 (2011)
11.132 G. Hannig, S.C. Makrides: Strategies for optimizing
heterologous protein expression in Escherichia
coli, Trends Biotechnol. 16, 54–60 (1998)
11.133 R.L. Warren, J.D. Freeman, R.C. Levesque,
D.E. Smailus, S. Flibotte, R.A. Holt: Transcription
of foreign DNA in Escherichia coli, Genome Res.
18, 1798–1805 (2008)
11.134 M.D. McMahon, C. Guan, J. Handelsman,
M.G. Thomas: Metagenomic analysis of Streptomyces lividans reveals host-dependent
functional expression, Appl. Environ. Microbiol. 78, 3622–3629 (2012)
11.135 K.S. Kakirde, J. Wild, R. Godiska, D.A. Mead,
A.G. Wiggins, R.M. Goodman, W. Szybalski,
M.R. Liles: Gram negative shuttle BAC vector
for heterologous expression of metagenomic libraries, Gene 475, 57–62 (2011)
11.136 J.R. Bernstein, T. Bulter, C.R. Shen, J.C. Liao:
Directed evolution of ribosomal protein S1 for
324 Part B Tools and Methods in Marine Biotechnology
11.111 A. Bankevich, S. Nurk, D. Antipov, A.A. Gurevich, M. Dvorkin, A.S. Kulikov, V.M. Lesin, S.I. Nikolenko, S. Pham, A.D. Prjibelski, A.V. Pyshkin,
A.V. Sirotkin, N. Vyahhi, G. Tesler, M.A. Alekseyev,
P.A. Pevzner: SPAdes: A new genome assembly
algorithm and its applications to single-cell sequencing, J. Comput. Biol. 19, 455–477 (2012)
11.112 T. Woyke, A. Sczyrba, J. Lee, C. Rinke, D. Tighe,
S. Clingenpeel, R. Malmstrom, R. Stepanauskas,
J.-F. Cheng: Decontamination of MDA reagents for
single cell whole genome amplification, PLoS One
6, e26161 (2011)
11.113 A.E.K. Dichosa, M.S. Fitzsimons, C.-C. Lo, L.L. Weston, L.G. Preteska, J.P. Snook, X. Zhang, W. Gu,
K. McMurry, L.D. Green, P.S. Chain, J.C. Detter,
C.S. Han: Artificial polyploidy improves bacterial
single cell Genome recovery, PLoS One 7, e37387
(2012)
11.114 R. Stepanauskas: Single cell genomics: an individual look at microbes, Current Opin. Microbiol.
15, 613–620 (2012)
11.115 H.S. Yoon, D.C. Price, R. Stepanauskas, V.D. Rajah, M.E. Sieracki, W.H. Wilson, E.C. Yang, S. Duffy,
D. Bhattacharya: Single-cell genomics reveals
organismal interactions in uncultivated marine
protists, Science 332, 714–717 (2011)
11.116 J. Kamke, K. Bayer, T. Woyke, U. Hentschel: Exploring symbioses by single-cell genomics, Biol.
Bulletin 223, 30–43 (2012)
11.117 K. Bayer, M. Scheuermayer, L. Fieseler,
U. Hentschel: Genomic mining for novel FADH 2 -
dependent halogenases in marine spongeassociated microbial consortia, Mar. Biotechnol.
15, 63–72 (2013)
11.118 M. Martinez-Garcia, D.M. Brazel, B.K. Swan,
C. Arnosti, P.S.G. Chain, K.G. Reitenga, G. Xie,
N.J. Poulton, M.L. Gomez, D.E.D. Masland,
B. Thompson, W.K. Bellows, K. Ziervogel, C.C. Lo, S. Ahmed, C.D. Gleasner, C.J. Detter,
R. Stepanauskas: Capturing single cell genomes
of active polysaccharide degraders: An unexpected contribution of Verrucomicrobia, PLoS One
7, e35314 (2012)
11.119 R.R. Malmstrom, S. Rodrigue, K.H. Huang,
L. Kelly, S.E. Kern, A. Thompson, S. Roggensack,
P.M. Berube, M.R. Henn, S.W. Chisholm: Ecology
of uncultured Prochlorococcus clades revealed
through single-cell genomics and biogeographic
analysis, ISME Journal 7, 184–198 (2013)
11.120 J.A. Gilbert, C.L. Dupont: Microbial metagenomics: beyond the genome, Annu. Rev. Mar. Sci.
3, 347–371 (2011)
11.121 W.R. Streit, R. Daniel: Metagenomics: Methods
and protocols. In: Methods in Molecular Biology,
Vol. 668 (Humana, New York 2010)
11.122 S. Shokralla, J.L. Spall, J.F. Gibson, M. Hajibabaei:
Next-generation sequencing technologies for environmental DNA research, Mol. Ecol. 21, 1794–
1805 (2012)
11.123 C. Simon, R. Daniel: Metagenomic analyses: past
and future trends, Appl. Environ. Microbiol. 77,
1153–1161 (2011)
11.124 D.M. Ekkers, M.S. Cretoiu, A.M. Kielak, J.D. van Elsas: The great screen anomaly – A new frontier
in product discovery through functional metagenomics, Appl. Microbiol. Biotechnol. 93, 1005–
1020 (2012)
11.125 J. Kennedy, N.D. O’Leary, G.S. Kiran, J.P. Morrissey, F. O’Gara, J. Selvin, A.D.W. Dobson: Functional
metagenomic strategies for the discovery of novel
enzymes and biosurfactants with biotechnological applications from marine ecosystems, J. Appl.
Microbiol. 111, 787–799 (2011)
11.126 R. Cavicchioli, T. Charlton, H. Ertan, S. Mohd Omar,
K.S. Siddiqui, T.J. Williams: Biotechnological uses
of enzymes from psychrophiles, Microb. Biotechnol. 4, 449–460 (2011)
11.127 J. Kennedy, J.R. Marchesi, A.D.W. Dobson: Marine metagenomics: Strategies for the discovery
of novel enzymes with biotechnological applications from marine environments, Microb. Cell
Fact. 7, 27 (2008)
11.128 J. Piel: Approaches to capturing and designing
biologically active small molecules produced by
uncultured microbes, Annu. Rev. Microbiol. 65,
431–453 (2011)
11.129 T. Uchiyama, K. Miyazaki: Functional metagenomics for enzyme discovery: Challenges to efficient screening, Current Opin. Biotechnol. 20,
616–622 (2009)
11.130 F.-X. Lussier, O. Chambenoit, A. Côté, J.-F. Hupé,
F. Denis, P. Juteau, R. Beaudet, F. Shareck: Construction and functional screening of a metagenomic library using a T7 RNA polymerase-based
expression cosmid vector, J. Ind. Microbiol.
Biotechnol. 38, 1321–1328 (2011)
11.131 M. Taupp, K. Mewis, S.J. Hallam: The art and design of functional metagenomic screens, Current
Opin. Biotechnol. 22, 465–472 (2011)
11.132 G. Hannig, S.C. Makrides: Strategies for optimizing
heterologous protein expression in Escherichia
coli, Trends Biotechnol. 16, 54–60 (1998)
11.133 R.L. Warren, J.D. Freeman, R.C. Levesque,
D.E. Smailus, S. Flibotte, R.A. Holt: Transcription
of foreign DNA in Escherichia coli, Genome Res.
18, 1798–1805 (2008)
11.134 M.D. McMahon, C. Guan, J. Handelsman,
M.G. Thomas: Metagenomic analysis of Streptomyces lividans reveals host-dependent
functional expression, Appl. Environ. Microbiol. 78, 3622–3629 (2012)
11.135 K.S. Kakirde, J. Wild, R. Godiska, D.A. Mead,
A.G. Wiggins, R.M. Goodman, W. Szybalski,
M.R. Liles: Gram negative shuttle BAC vector
for heterologous expression of metagenomic libraries, Gene 475, 57–62 (2011)
11.136 J.R. Bernstein, T. Bulter, C.R. Shen, J.C. Liao:
Directed evolution of ribosomal protein S1 for