Marine Microbial Bioprospecting References 325
Part B | 11
enhanced translational efficiency of high GC
Rhodopseudomonas palustris DNA in Escherichia
coli, J. Biol. Chem. 282, 18929–18936 (2007)
11.137 R. Schmieder, R. Edwards: Insights into antibiotic
resistance through metagenomic approaches, Future Microbiol. 7, 73–89 (2012)
11.138 T. Uchiyama, K. Miyazaki: Product-induced gene
expression, a product-responsive reporter assay used to screen metagenomic libraries for
enzyme-encoding genes, Appl. Environ. Microbiol. 76, 7029–7035 (2010)
11.139 T. Uchiyama, K. Miyazaki: Substrate-induced
gene expression screening: A method for highthroughput screening of metagenome libraries,
Methods Mol. Biol. 668, 153–168 (2010)
11.140 J.H. Kim, Z. Feng, J.D. Bauer, D. Kallifidas,
P.Y. Calle, S.F. Brady: Cloning large natural product
gene clusters from the environment: Piecing environmental DNA gene clusters back together with
TAR, Biopolymers 93(833), 844 (2010)
11.141 M. Ferrer, A. Beloqui, K.N. Timmis, P.N. Golyshin:
Metagenomics for mining new genetic resources
of microbial communities, J. Mol. Microbiol.
Biotechnol. 16, 109–123 (2009)
11.142 B. Temperton, S.J. Giovannoni: Metagenomics:
microbial diversity through a scratched lens, Current Opin. Microbiol. 15, 605–612 (2012)
11.143 R. Mackelprang, M.P. Waldrop, K.M. DeAngelis, M.M. David, K.L. Chavarria, S.J. Blazewicz,
E.M. Rubin, J.K. Jansson: Metagenomic analysis of
a permafrost microbial community reveals a rapid
response to thaw, Nature 480, 368–371 (2011)
11.144 M. Hess, A. Sczyrba, R. Egan, T.W. Kim,
H. Chokhawala, G. Schroth, S. Luo, D.S. Clark,
F. Chen, T. Zhang, R.I. Mackie, L.A. Pennacchio, S.G. Tringe, A. Visel, T. Woyke, Z. Wang,
E.M. Rubin: Metagenomic discovery of biomassdegrading genes and genomes from cow rumen,
Science 331, 463–467 (2011)
11.145 T.S. Bayer, D.M. Widmaier, K. Temme, E.A. Mirsky,
D.V. Santi, C.A. Voigt: Synthesis of methyl hyalides
from biomass using engineered microbes, J. Am.
Chem. Soc. 131, 6508–6515 (2009)
11.146 M.S. Siddiqui, K. Thodey, I. Trenchard,
C.D. Smolke: Advancing secondary metabolite biosynthesis in yeast with synthetic biology
tools, FEMS Yeast Res. 12, 144–170 (2012)
11.147 V.K. Sharma, N. Kumar, T. Prakash, T.D. Taylor:
MetaBioME: A database to explore commercially
useful enzymes in metagenomic datasets, Nucleic
Acids Res. 38, D468–D472 (2010)
11.148 F. Warnecke, M. Hess: A perspective: Metatranscriptomics as a tool for the discovery of novel
biocatalysts, J. Biotechnol. 142, 91–95 (2009)
11.149 J. Wu, W. Gao, W. Zhang, D.R. Meldrum: Optimization of whole-transcriptome amplification from
low cell density deep-sea microbial samples for
metatranscriptomic analysis, J. Microbiol. Methods 84, 88–93 (2011)
11.150 M.A. Moran, B. Satinsky, S.M. Gifford, H. Luo,
A. Rivers, L.-K. Chan, J. Meng, B.P. Durham,
C. Shen, V.A. Varaljay, C.B. Smith, P.L. Yager,
B.M. Hopkinson: Sizing up metatranscriptomics,
ISME Journal 7, 237–243 (2013)
11.151 G. Giannoukos, D.M. Ciulla, K. Huang, B.J. Haas,
J. Izard, J.Z. Levin, J. Livny, A.M. Earl, D. Gevers,
D.V. Ward, C. Nusbaum, B.W. Birren, A. Gnirke: Efficient and robust RNA-seq process for cultured
bacteria and complex community transcriptomes,
Genome Biol. 13, r23 (2012)
11.152 S.M. Gifford, S. Sharma, M. Booth, M.A. Moran:
Expression patterns reveal niche diversification in
a marine microbial assemblage, ISME Journal 7,
281–298 (2013)
11.153 A. Marchetti, D.M. Schruth, C.A. Durkin,
M.S. Parker, R.B. Kodner, C.T. Berthiaume,
R. Morales, A.E. Allen, E.V. Armbrust: Comparative
metatranscriptomics identifies molecular bases
for the physiological responses of phytoplankton
to varying iron availability, Proc. Natl. Acad. Sci.
USA 109, E317–E325 (2012)
11.154 O.U. Mason, T.C. Hazen, S. Borglin, P.S.G. Chain,
E.A. Dubinsky, J.L. Fortney, J. Han, H.-Y.N. Holman, J. Hultman, R. Lamendella, R. Mackelprang, S. Malfatti, L.M. Tom, S.G. Tringe,
T. Woyke, J. Zhou, E.M. Rubin, J.K. Jansson:
Metagenome, metatranscriptome and single-cell
sequencing reveal microbial response to Deepwater Horizon oil spill, ISME Journal 6, 1715–1727
(2012)
11.155 F.J. Stewart, O. Ulloa, E.F. DeLong: Microbial metatranscriptomics in a permanent marine oxygen
minimum zone, Environ. Microbiol. 14, 23–40
(2012)
11.156 K. Anantharaman, J.A. Breier, C.S. Sheik, G.J. Dick:
Evidence for hydrogen oxidation and metabolic
plasticity in widespread deep-sea sulfuroxidizing bacteria, Proc. Natl. Acad. Sci. USA 110,
330–335 (2013)
11.157 H. Dahle, I. Roalkvam, I.H. Thorseth, R.B. Pedersen, I.H. Steen: The versatile in situ gene expression of an Epsilonproteobacteria-dominated
biofilm from a hydrothermal chimney, Environ.
Microbiol. Rep. 5(2), 282–290 (2013)
11.158 J. Kennedy, B. Flemer, S.A. Jackson, D.P.H. Lejon,
J.P. Morrissey, F. O’Gara, A.D.W. Dobson: Marine
metagenomics: new tools for the study and exploitation of marine microbial metabolism, Mar.
Drugs 8, 608–628 (2010)
11.159 P. Wilmes, P.L. Bond: Microbial community proteomics: Elucidating the catalysts and metabolic
mechanisms that drive the Earth’s biogeochemical cycles, Current Opin. Microbiol. 12, 310–317
(2009)
11.160 M. Keller, R. Hettich: Environmental proteomics:
A paradigm shift in characterizing microbial activities at the molecular level, Microbiol. Mol.
Biol. Rev. 73, 62–70 (2009)
Part B | 11
enhanced translational efficiency of high GC
Rhodopseudomonas palustris DNA in Escherichia
coli, J. Biol. Chem. 282, 18929–18936 (2007)
11.137 R. Schmieder, R. Edwards: Insights into antibiotic
resistance through metagenomic approaches, Future Microbiol. 7, 73–89 (2012)
11.138 T. Uchiyama, K. Miyazaki: Product-induced gene
expression, a product-responsive reporter assay used to screen metagenomic libraries for
enzyme-encoding genes, Appl. Environ. Microbiol. 76, 7029–7035 (2010)
11.139 T. Uchiyama, K. Miyazaki: Substrate-induced
gene expression screening: A method for highthroughput screening of metagenome libraries,
Methods Mol. Biol. 668, 153–168 (2010)
11.140 J.H. Kim, Z. Feng, J.D. Bauer, D. Kallifidas,
P.Y. Calle, S.F. Brady: Cloning large natural product
gene clusters from the environment: Piecing environmental DNA gene clusters back together with
TAR, Biopolymers 93(833), 844 (2010)
11.141 M. Ferrer, A. Beloqui, K.N. Timmis, P.N. Golyshin:
Metagenomics for mining new genetic resources
of microbial communities, J. Mol. Microbiol.
Biotechnol. 16, 109–123 (2009)
11.142 B. Temperton, S.J. Giovannoni: Metagenomics:
microbial diversity through a scratched lens, Current Opin. Microbiol. 15, 605–612 (2012)
11.143 R. Mackelprang, M.P. Waldrop, K.M. DeAngelis, M.M. David, K.L. Chavarria, S.J. Blazewicz,
E.M. Rubin, J.K. Jansson: Metagenomic analysis of
a permafrost microbial community reveals a rapid
response to thaw, Nature 480, 368–371 (2011)
11.144 M. Hess, A. Sczyrba, R. Egan, T.W. Kim,
H. Chokhawala, G. Schroth, S. Luo, D.S. Clark,
F. Chen, T. Zhang, R.I. Mackie, L.A. Pennacchio, S.G. Tringe, A. Visel, T. Woyke, Z. Wang,
E.M. Rubin: Metagenomic discovery of biomassdegrading genes and genomes from cow rumen,
Science 331, 463–467 (2011)
11.145 T.S. Bayer, D.M. Widmaier, K. Temme, E.A. Mirsky,
D.V. Santi, C.A. Voigt: Synthesis of methyl hyalides
from biomass using engineered microbes, J. Am.
Chem. Soc. 131, 6508–6515 (2009)
11.146 M.S. Siddiqui, K. Thodey, I. Trenchard,
C.D. Smolke: Advancing secondary metabolite biosynthesis in yeast with synthetic biology
tools, FEMS Yeast Res. 12, 144–170 (2012)
11.147 V.K. Sharma, N. Kumar, T. Prakash, T.D. Taylor:
MetaBioME: A database to explore commercially
useful enzymes in metagenomic datasets, Nucleic
Acids Res. 38, D468–D472 (2010)
11.148 F. Warnecke, M. Hess: A perspective: Metatranscriptomics as a tool for the discovery of novel
biocatalysts, J. Biotechnol. 142, 91–95 (2009)
11.149 J. Wu, W. Gao, W. Zhang, D.R. Meldrum: Optimization of whole-transcriptome amplification from
low cell density deep-sea microbial samples for
metatranscriptomic analysis, J. Microbiol. Methods 84, 88–93 (2011)
11.150 M.A. Moran, B. Satinsky, S.M. Gifford, H. Luo,
A. Rivers, L.-K. Chan, J. Meng, B.P. Durham,
C. Shen, V.A. Varaljay, C.B. Smith, P.L. Yager,
B.M. Hopkinson: Sizing up metatranscriptomics,
ISME Journal 7, 237–243 (2013)
11.151 G. Giannoukos, D.M. Ciulla, K. Huang, B.J. Haas,
J. Izard, J.Z. Levin, J. Livny, A.M. Earl, D. Gevers,
D.V. Ward, C. Nusbaum, B.W. Birren, A. Gnirke: Efficient and robust RNA-seq process for cultured
bacteria and complex community transcriptomes,
Genome Biol. 13, r23 (2012)
11.152 S.M. Gifford, S. Sharma, M. Booth, M.A. Moran:
Expression patterns reveal niche diversification in
a marine microbial assemblage, ISME Journal 7,
281–298 (2013)
11.153 A. Marchetti, D.M. Schruth, C.A. Durkin,
M.S. Parker, R.B. Kodner, C.T. Berthiaume,
R. Morales, A.E. Allen, E.V. Armbrust: Comparative
metatranscriptomics identifies molecular bases
for the physiological responses of phytoplankton
to varying iron availability, Proc. Natl. Acad. Sci.
USA 109, E317–E325 (2012)
11.154 O.U. Mason, T.C. Hazen, S. Borglin, P.S.G. Chain,
E.A. Dubinsky, J.L. Fortney, J. Han, H.-Y.N. Holman, J. Hultman, R. Lamendella, R. Mackelprang, S. Malfatti, L.M. Tom, S.G. Tringe,
T. Woyke, J. Zhou, E.M. Rubin, J.K. Jansson:
Metagenome, metatranscriptome and single-cell
sequencing reveal microbial response to Deepwater Horizon oil spill, ISME Journal 6, 1715–1727
(2012)
11.155 F.J. Stewart, O. Ulloa, E.F. DeLong: Microbial metatranscriptomics in a permanent marine oxygen
minimum zone, Environ. Microbiol. 14, 23–40
(2012)
11.156 K. Anantharaman, J.A. Breier, C.S. Sheik, G.J. Dick:
Evidence for hydrogen oxidation and metabolic
plasticity in widespread deep-sea sulfuroxidizing bacteria, Proc. Natl. Acad. Sci. USA 110,
330–335 (2013)
11.157 H. Dahle, I. Roalkvam, I.H. Thorseth, R.B. Pedersen, I.H. Steen: The versatile in situ gene expression of an Epsilonproteobacteria-dominated
biofilm from a hydrothermal chimney, Environ.
Microbiol. Rep. 5(2), 282–290 (2013)
11.158 J. Kennedy, B. Flemer, S.A. Jackson, D.P.H. Lejon,
J.P. Morrissey, F. O’Gara, A.D.W. Dobson: Marine
metagenomics: new tools for the study and exploitation of marine microbial metabolism, Mar.
Drugs 8, 608–628 (2010)
11.159 P. Wilmes, P.L. Bond: Microbial community proteomics: Elucidating the catalysts and metabolic
mechanisms that drive the Earth’s biogeochemical cycles, Current Opin. Microbiol. 12, 310–317
(2009)
11.160 M. Keller, R. Hettich: Environmental proteomics:
A paradigm shift in characterizing microbial activities at the molecular level, Microbiol. Mol.
Biol. Rev. 73, 62–70 (2009)