Part C | 17
472 Part C Marine Genomics
timated to contain substantial anomalies, Appl.
Environ. Microbiol. 71, 7724–7736 (2005)
17.48 L. Krause, N.N. Diaz, A. Goesmann, S. Kelley,
T.W. Nattkemper, F. Rohwer, R.A. Edwards, J. Stoye:
Phylogenetic classification of short environmental
DNA fragments, Nucleic Acids Res. 36, 2230–2239
(2008)
17.49 I.N. Sarkar, M.G. Egan, G. Coruzzi, E.K. Lee, R. DeSalle: Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics,
BMC Bioinformatics 9, 103 (2008)
17.50 G.J. Olsen, H. Matsuda, R. Hagstrom, R. Overbeek:
fastDNAmL: a tool for construction of phylogenetic
trees of DNA sequences using maximum likelihood,
Comput. Appl. Biosci. 10, 41–48 (1994)
17.51 P.D. Schloss, J. Handelsman: Introducing DOTUR, a
computer program for defining operational taxonomic units and estimating species richness, Appl.
Environ. Microbiol. 71, 1501–1506 (2005)
17.52 J. Kamke, K. Bayer, T. Woyke, U. Hentschel: Exploring symbioses by single-cell genomics, Biol. Bull.
223, 30–43 (2012)
17.53 Y. Marcy, T. Ishoey, R.S. Lasken, T.B. Stockwell,
B.P. Walenz, A.L. Halpern, K.Y. Beeson, S.M. Goldberg, S.R. Quake: Nanoliter reactors improve
multiple displacement amplification of genomes
from single cells, PLoS Genetics 3, 1702–1708
(2007)
17.54 C.H. Chen, S.H. Cho, H.I. Chiang, F. Tsai, K. Zhang,
Y.H. Lo: Specific sorting of single bacterial cells with
microfabricated fluorescence-activated cell sorting and tyramide signal amplification fluorescence
in situ hybridization, Anal. Chem. 83, 7269–7275
(2011)
17.55 M.Y. Liu, S. Kjelleberg, T. Thomas: Functional
genomic analysis of an uncultured deltaproteobacterium in the sponge Cymbastela
concentrica, ISME Journal 5, 427–435 (2011)
17.56 T. Kvist, B.K. Ahring, R.S. Lasken, P. Westermann:
Specific single-cell isolation and genomic amplification of uncultured microorganisms, Appl. Microbiol. Biotechnol. 74, 926–935 (2007)
17.57 T. Woyke, D. Tighe, K. Mavromatis, A. Clum,
A. Copeland, W. Schackwitz, A. Lapidus, D. Wu,
J.P. McCutcheon, B.R. McDonald, N.A. Moran,
J. Bristow, J.F. Cheng: One bacterial cell, one complete genome, PLoS ONE 5, e10314 (2010)
17.58 N.S. Webster, M.W. Taylor, F. Behnam, S. Lucker,
T. Rattei, S. Whalan, M. Horn, M. Wagner: Deep sequencing reveals exceptional diversity and modes
of transmission for bacterial sponge symbionts, Environ. Microbiol. 12(8), 2070–2082 (2009)
17.59 M.L. Sogin, H.G. Morrison, J.A. Huber, D.M. Welch,
S.M. Huse, P.R. Neal, J.M. Arrieta, G.J. Herndl: Microbial diversity in the deep sea and the underexplored “rare biosphere”, PNAS 103, 12115–12120
(2006)
17.60 O.O. Lee, Y. Wang, J. Yang, F.F. Lafi, A. Al-Suwailem,
P.Y. Qian: Pyrosequencing reveals highly diverse
and species specific microbial communities in
sponges from the Red Sea, ISME Journal 5, 650–664
(2010)
17.61 N.S. Webster, M.W. Taylor, F. Behnam, S. Lucker,
T. Rattei, S. Whalan, M. Horn, M. Wagner: Deep sequencing reveals exceptional diversity and modes
of transmission for bacterial sponge symbionts, Environ. Microbiol. 12(8), 2070–2082 (2010)
17.62 A.S. Turque, A.M. Cardoso, C.B. Silveira, R.P. Vieira,
F.A.D. Freitas, R.M. Albano, A.M. Gonzalez,
R. Paranhos, G. Muricy, O.B. Martins: Bacterial
communities of the marine sponges Hymeniacidon heliophila and Polymastia janeirensis and
their environment in Rio de Janeiro, Brazil. Mar.
Biol. 155, 135–146 (2008)
17.63 A.S. Turque, D. Batista, C.B. Silveira, A.M. Cardoso,
R.P. Vieira, F.C. Moraes, M.M. Clementino, R.M. Albano, R. Paranhos, O.B. Martins, G. Muricy: Environmental shaping of sponge associated archaeal
communities, PLoS ONE 5, e15774 (2010)
17.64 A.E.T. Silva, C. Rua, G.G.Z. Silva, B.E. Dutilh,
A.P.B. Moreira, R.A. Edwards, E. Hajdu, G.L. Hajdu,
A.T. Vasconcelo, R.G.S. Berlinck, F.L. Thompson:
Taxonomic and functional microbial signatures of
the endemic marine sponge Arenosclerabrasiliensis, PLoS ONE 7(7), e39905 (2012)
17.65 N.S. Webster, R.T. Hill: The culturable microbial community of the Great Barrier Reef sponge
Rhopaloeides odorabile is dominated by an alpha Proteobacterium, Mar. Biol. 138, 843–851
(2001)
17.66 A. Schirmer, R. Gadkari, C.D. Reeves, F. Ibrahim,
E.F. DeLong, C.R. Hutchinson: Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine
sponge Discodermia dissoluta, Appl. Environ. Microbiol. 71, 4840–4849 (2005)
17.67 J. Piel, D. Hui, G. Wen, D. Butzke, M. Platzer,
N. Fusetani, S. Matsunaga: Antitumor polyketide
biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei, Proc. Natl. Acad. Sci. USA 101, 16222–16227
(2004)
17.68 M.D. Unson, D.J. Faulkner: A brominated secondary
metabolite synthesized by the cyanobacterial symbiont of a marine sponge and accumulation of the
crystalline metabolite in the sponge tissue, Experientia 49, 349–353 (1993)
17.69 Z. Chang, P. Flatt, W.H. Gerwick, V.A. Nguyen,
C.L. Willis, D.H. Sherman: The barbamide biosynthetic gene cluster: a novel marine cyanobacterial
system of mixed polyketide synthase (PKS) non ribosomal peptide synthetase (NRPS) origin involving
an unusual trichloroleucyl starter unit, Gene 296,
235–247 (2002)
17.70 K.M. Fisch, C. Gurgui, N. Heycke, S.A. van der Sar,
S.A. Anderson, V.L. Webb, S. Taudien, M. Platzer,
B.K. Rubio, S.J. Robinson, P. Crews, J. Piel: Polyketide assembly lines of uncultivated sponge sym-
472 Part C Marine Genomics
timated to contain substantial anomalies, Appl.
Environ. Microbiol. 71, 7724–7736 (2005)
17.48 L. Krause, N.N. Diaz, A. Goesmann, S. Kelley,
T.W. Nattkemper, F. Rohwer, R.A. Edwards, J. Stoye:
Phylogenetic classification of short environmental
DNA fragments, Nucleic Acids Res. 36, 2230–2239
(2008)
17.49 I.N. Sarkar, M.G. Egan, G. Coruzzi, E.K. Lee, R. DeSalle: Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics,
BMC Bioinformatics 9, 103 (2008)
17.50 G.J. Olsen, H. Matsuda, R. Hagstrom, R. Overbeek:
fastDNAmL: a tool for construction of phylogenetic
trees of DNA sequences using maximum likelihood,
Comput. Appl. Biosci. 10, 41–48 (1994)
17.51 P.D. Schloss, J. Handelsman: Introducing DOTUR, a
computer program for defining operational taxonomic units and estimating species richness, Appl.
Environ. Microbiol. 71, 1501–1506 (2005)
17.52 J. Kamke, K. Bayer, T. Woyke, U. Hentschel: Exploring symbioses by single-cell genomics, Biol. Bull.
223, 30–43 (2012)
17.53 Y. Marcy, T. Ishoey, R.S. Lasken, T.B. Stockwell,
B.P. Walenz, A.L. Halpern, K.Y. Beeson, S.M. Goldberg, S.R. Quake: Nanoliter reactors improve
multiple displacement amplification of genomes
from single cells, PLoS Genetics 3, 1702–1708
(2007)
17.54 C.H. Chen, S.H. Cho, H.I. Chiang, F. Tsai, K. Zhang,
Y.H. Lo: Specific sorting of single bacterial cells with
microfabricated fluorescence-activated cell sorting and tyramide signal amplification fluorescence
in situ hybridization, Anal. Chem. 83, 7269–7275
(2011)
17.55 M.Y. Liu, S. Kjelleberg, T. Thomas: Functional
genomic analysis of an uncultured deltaproteobacterium in the sponge Cymbastela
concentrica, ISME Journal 5, 427–435 (2011)
17.56 T. Kvist, B.K. Ahring, R.S. Lasken, P. Westermann:
Specific single-cell isolation and genomic amplification of uncultured microorganisms, Appl. Microbiol. Biotechnol. 74, 926–935 (2007)
17.57 T. Woyke, D. Tighe, K. Mavromatis, A. Clum,
A. Copeland, W. Schackwitz, A. Lapidus, D. Wu,
J.P. McCutcheon, B.R. McDonald, N.A. Moran,
J. Bristow, J.F. Cheng: One bacterial cell, one complete genome, PLoS ONE 5, e10314 (2010)
17.58 N.S. Webster, M.W. Taylor, F. Behnam, S. Lucker,
T. Rattei, S. Whalan, M. Horn, M. Wagner: Deep sequencing reveals exceptional diversity and modes
of transmission for bacterial sponge symbionts, Environ. Microbiol. 12(8), 2070–2082 (2009)
17.59 M.L. Sogin, H.G. Morrison, J.A. Huber, D.M. Welch,
S.M. Huse, P.R. Neal, J.M. Arrieta, G.J. Herndl: Microbial diversity in the deep sea and the underexplored “rare biosphere”, PNAS 103, 12115–12120
(2006)
17.60 O.O. Lee, Y. Wang, J. Yang, F.F. Lafi, A. Al-Suwailem,
P.Y. Qian: Pyrosequencing reveals highly diverse
and species specific microbial communities in
sponges from the Red Sea, ISME Journal 5, 650–664
(2010)
17.61 N.S. Webster, M.W. Taylor, F. Behnam, S. Lucker,
T. Rattei, S. Whalan, M. Horn, M. Wagner: Deep sequencing reveals exceptional diversity and modes
of transmission for bacterial sponge symbionts, Environ. Microbiol. 12(8), 2070–2082 (2010)
17.62 A.S. Turque, A.M. Cardoso, C.B. Silveira, R.P. Vieira,
F.A.D. Freitas, R.M. Albano, A.M. Gonzalez,
R. Paranhos, G. Muricy, O.B. Martins: Bacterial
communities of the marine sponges Hymeniacidon heliophila and Polymastia janeirensis and
their environment in Rio de Janeiro, Brazil. Mar.
Biol. 155, 135–146 (2008)
17.63 A.S. Turque, D. Batista, C.B. Silveira, A.M. Cardoso,
R.P. Vieira, F.C. Moraes, M.M. Clementino, R.M. Albano, R. Paranhos, O.B. Martins, G. Muricy: Environmental shaping of sponge associated archaeal
communities, PLoS ONE 5, e15774 (2010)
17.64 A.E.T. Silva, C. Rua, G.G.Z. Silva, B.E. Dutilh,
A.P.B. Moreira, R.A. Edwards, E. Hajdu, G.L. Hajdu,
A.T. Vasconcelo, R.G.S. Berlinck, F.L. Thompson:
Taxonomic and functional microbial signatures of
the endemic marine sponge Arenosclerabrasiliensis, PLoS ONE 7(7), e39905 (2012)
17.65 N.S. Webster, R.T. Hill: The culturable microbial community of the Great Barrier Reef sponge
Rhopaloeides odorabile is dominated by an alpha Proteobacterium, Mar. Biol. 138, 843–851
(2001)
17.66 A. Schirmer, R. Gadkari, C.D. Reeves, F. Ibrahim,
E.F. DeLong, C.R. Hutchinson: Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine
sponge Discodermia dissoluta, Appl. Environ. Microbiol. 71, 4840–4849 (2005)
17.67 J. Piel, D. Hui, G. Wen, D. Butzke, M. Platzer,
N. Fusetani, S. Matsunaga: Antitumor polyketide
biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei, Proc. Natl. Acad. Sci. USA 101, 16222–16227
(2004)
17.68 M.D. Unson, D.J. Faulkner: A brominated secondary
metabolite synthesized by the cyanobacterial symbiont of a marine sponge and accumulation of the
crystalline metabolite in the sponge tissue, Experientia 49, 349–353 (1993)
17.69 Z. Chang, P. Flatt, W.H. Gerwick, V.A. Nguyen,
C.L. Willis, D.H. Sherman: The barbamide biosynthetic gene cluster: a novel marine cyanobacterial
system of mixed polyketide synthase (PKS) non ribosomal peptide synthetase (NRPS) origin involving
an unusual trichloroleucyl starter unit, Gene 296,
235–247 (2002)
17.70 K.M. Fisch, C. Gurgui, N. Heycke, S.A. van der Sar,
S.A. Anderson, V.L. Webb, S. Taudien, M. Platzer,
B.K. Rubio, S.J. Robinson, P. Crews, J. Piel: Polyketide assembly lines of uncultivated sponge sym-