-
1
-
-
0032898421
-
Butane metabolism by butane-grown 'Pseudomonas butanovora'
-
doi: 10.1099/13500872-145-5-1173
-
Arp, D. J. (1999). Butane metabolism by butane-grown "Pseudomonas butanovora." Microbiology 145, 1173-1180. doi: 10.1099/13500872-145-5-1173
-
(1999)
Microbiology
, vol.145
, pp. 1173-1180
-
-
Arp, D.J.1
-
2
-
-
84865740210
-
Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill
-
doi: 10.1111/j.1462-2920.2012.02780.x
-
Baelum, J., Borglin, S., Chakraborty, R., Fortney, J. L., Lamendella, R., Mason, O. U., et al. (2012). Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ. Microbiol. 14, 2405-2416. doi: 10.1111/j.1462-2920.2012.02780.x
-
(2012)
Environ. Microbiol.
, vol.14
, pp. 2405-2416
-
-
Baelum, J.1
Borglin, S.2
Chakraborty, R.3
Fortney, J.L.4
Lamendella, R.5
Mason, O.U.6
-
3
-
-
84860771820
-
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
-
doi: 10.1089/cmb.2012.0021
-
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. doi: 10.1089/cmb.2012.0021
-
(2012)
J. Comput. Biol.
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
Nurk, S.2
Antipov, D.3
Gurevich, A.A.4
Dvorkin, M.5
Kulikov, A.S.6
-
4
-
-
0031753313
-
Colwellia demingiae s. nov., Colwellia hornerae sp. nov., Colwellia rossensis sp. nov. and Colwellia psychrotropica sp. nov.: psychrophilic Antarctic species with the ability to synthesize docosahexaenoic acid (22:W 63)
-
doi: 10.1099/00207713-48-4-1171
-
Bowman, J. P., Gosinkt, J. J., McCammon, S. A., Skerratt, H., Lewis, T. E., Nichols, D. S., et al. (1997). Colwellia demingiae sp. nov., Colwellia hornerae sp. nov., Colwellia rossensis sp. nov. and Colwellia psychrotropica sp. nov.: psychrophilic Antarctic species with the ability to synthesize docosahexaenoic acid (22:W 63). Int. J. Syst. Bacteriol. 48, 1171-1180. doi: 10.1099/00207713-48-4-1171
-
(1997)
Int. J. Syst. Bacteriol.
, vol.48
, pp. 1171-1180
-
-
Bowman, J.P.1
Gosinkt, J.J.2
McCammon, S.A.3
Skerratt, H.4
Lewis, T.E.5
Nichols, D.S.6
-
5
-
-
67650732640
-
Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly 'Pseudomonas butanovora'
-
doi: 10.1099/mic.0.028175-0
-
Cooley, R. B., Dubbels, B. L., Sayavedra-Soto, L. A., Bottomley, P. J., and Arp, D. J. (2009). Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly "Pseudomonas butanovora." Microbiology 155, 2086-2096. doi: 10.1099/mic.0.028175-0
-
(2009)
Microbiology
, vol.155
, pp. 2086-2096
-
-
Cooley, R.B.1
Dubbels, B.L.2
Sayavedra-Soto, L.A.3
Bottomley, P.J.4
Arp, D.J.5
-
6
-
-
68149126013
-
Thauera butanivorans sp. nov., a C2-C9 alkane-oxidizing bacterium previously referred to as 'Pseudomonas butanovora'
-
doi: 10.1099/ijs.0.000638-0
-
Dubbels, B. L., Sayavedra-Soto, L. A., Bottomley, P. J., and Arp, D. J. (2009). Thauera butanivorans sp. nov., a C2-C9 alkane-oxidizing bacterium previously referred to as "Pseudomonas butanovora." Int. J. Syst. Evol. Microbiol. 59, 1576-8. doi: 10.1099/ijs.0.000638-0
-
(2009)
Int. J. Syst. Evol. Microbiol.
, vol.59
, pp. 1576-1578
-
-
Dubbels, B.L.1
Sayavedra-Soto, L.A.2
Bottomley, P.J.3
Arp, D.J.4
-
7
-
-
84885112335
-
Succession of hydrocarbon-degrading bacteria in the aftermath of the deepwater horizon oil spill in the gulf of Mexico
-
doi: 10.1021/es401676y
-
Dubinsky, E. A., Conrad, M. E., Chakraborty, R., Bill, M., Borglin, S. E., Hollibaugh, J. T., et al. (2013). Succession of hydrocarbon-degrading bacteria in the aftermath of the deepwater horizon oil spill in the gulf of Mexico. Environ. Sci. Technol. 47, 10860-10867. doi: 10.1021/es401676y
-
(2013)
Environ. Sci. Technol.
, vol.47
, pp. 10860-10867
-
-
Dubinsky, E.A.1
Conrad, M.E.2
Chakraborty, R.3
Bill, M.4
Borglin, S.E.5
Hollibaugh, J.T.6
-
8
-
-
0032942360
-
NahY, a catabolic plasmid-encoded receptor required for chemotaxis of pseudomonas putida to the aromatic hydrocarbon naphthalene
-
Grimm, A. C., and Harwood, C. S. (1999). NahY, a catabolic plasmid-encoded receptor required for chemotaxis of pseudomonas putida to the aromatic hydrocarbon naphthalene. J. Bacteriol. 181, 3310.
-
(1999)
J. Bacteriol
, vol.181
, pp. 3310
-
-
Grimm, A.C.1
Harwood, C.S.2
-
9
-
-
84886727312
-
Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP
-
doi: 10.1038/ismej.2013.98
-
Gutierrez, T., Singleton, D. R., Berry, D., Yang, T., Aitken, M. D., and Teske, A. (2013). Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP. ISME J. 7, 2091-2104. doi: 10.1038/ismej.2013.98
-
(2013)
ISME J.
, vol.7
, pp. 2091-2104
-
-
Gutierrez, T.1
Singleton, D.R.2
Berry, D.3
Yang, T.4
Aitken, M.D.5
Teske, A.6
-
10
-
-
77956299931
-
Deep-sea oil plume enriches indigenous oil-degrading bacteria
-
doi: 10.1126/science.1195979
-
Hazen, T. C., Dubinsky, E. A., DeSantis, T. Z., Andersen, G. L., Piceno, Y. M., Singh, N., et al. (2010). Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330, 204-208. doi: 10.1126/science.1195979
-
(2010)
Science
, vol.330
, pp. 204-208
-
-
Hazen, T.C.1
Dubinsky, E.A.2
DeSantis, T.Z.3
Andersen, G.L.4
Piceno, Y.M.5
Singh, N.6
-
11
-
-
84891349082
-
A poor man's BLASTX - high-throughput metagenomic protein database search using PAUDA
-
doi: 10.1093/bioinformatics/btt254
-
Huson, D. H., and Xie, C. (2014). A poor man's BLASTX - high-throughput metagenomic protein database search using PAUDA. Bioinformatics 30, 38-39. doi: 10.1093/bioinformatics/btt254
-
(2014)
Bioinformatics
, vol.30
, pp. 38-39
-
-
Huson, D.H.1
Xie, C.2
-
12
-
-
0038242858
-
Bacterial Adaptation to the Cold: in situ Activities of Extracellular Enzymes in the North Water Polynya and Characterization of a Cold-Active Aminopeptidase from Colwellia Psychrerythraea Strain 34H
-
Ph.D. thesis, Seattle, WA: University of Washington.
-
Huston, A. L. (2003). Bacterial Adaptation to the Cold: in situ Activities of Extracellular Enzymes in the North Water Polynya and Characterization of a Cold-Active Aminopeptidase from Colwellia Psychrerythraea Strain 34H. Ph.D. thesis, Seattle, WA: University of Washington.
-
(2003)
-
-
Huston, A.L.1
-
13
-
-
84874589415
-
Trace element distributions in the water column near the Deepwater Horizon well blowout
-
doi: 10.1021/es303167p
-
Joung, D., and Shiller, A. M. (2013). Trace element distributions in the water column near the Deepwater Horizon well blowout. Environ. Sci. Technol. 47, 2161-2168. doi: 10.1021/es303167p
-
(2013)
Environ. Sci. Technol.
, vol.47
, pp. 2161-2168
-
-
Joung, D.1
Shiller, A.M.2
-
14
-
-
79952119927
-
Magnitude and oxidation potential of hydrocarbon gases released from the BP oil well blowout
-
doi: 10.1038/ngeo1067
-
Joye, S. B., MacDonald, I. R., Leifer, I., and Asper, V. (2011). Magnitude and oxidation potential of hydrocarbon gases released from the BP oil well blowout. Nat. Geosci. 4, 160-164. doi: 10.1038/ngeo1067
-
(2011)
Nat. Geosci.
, vol.4
, pp. 160-164
-
-
Joye, S.B.1
MacDonald, I.R.2
Leifer, I.3
Asper, V.4
-
15
-
-
84880845008
-
Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica
-
doi: 10.1038/ncomms3156
-
Kube, M., Chernikova, T. N., Al-Ramahi, Y., Beloqui, A., Lopez-Cortez, N., Guazzaroni, M.-E., et al. (2013). Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica. Nat. Commun. 4, 2156. doi: 10.1038/ncomms3156
-
(2013)
Nat. Commun.
, vol.4
, pp. 2156
-
-
Kube, M.1
Chernikova, T.N.2
Al-Ramahi, Y.3
Beloqui, A.4
Lopez-Cortez, N.5
Guazzaroni, M.-E.6
-
16
-
-
38849143173
-
Involvement of BmoR and BmoG in n-alkane metabolism in 'Pseudomonas butanovora'
-
doi: 10.1099/mic.0.2007/012724-0
-
Kurth, E. G., Doughty, D. M., Bottomley, P. J., Arp, D. J., and Sayavedra-Soto, L. A. (2008). Involvement of BmoR and BmoG in n-alkane metabolism in "Pseudomonas butanovora." Microbiology 154, 139-147. doi: 10.1099/mic.0.2007/012724-0
-
(2008)
Microbiology
, vol.154
, pp. 139-147
-
-
Kurth, E.G.1
Doughty, D.M.2
Bottomley, P.J.3
Arp, D.J.4
Sayavedra-Soto, L.A.5
-
17
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
doi: 10.1038/nmeth.1923
-
Langmead, B., and Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359. doi: 10.1038/nmeth.1923
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
18
-
-
0023027071
-
Nucleotide sequence of the gene for the ferrienterochelin receptor FepA in Escherichia coli. Homology among outer membrane receptors that interact with TonB.
-
Lundrigan, M. D., and Kadner, R. J. (1986). Nucleotide sequence of the gene for the ferrienterochelin receptor FepA in Escherichia coli. Homology among outer membrane receptors that interact with TonB. J. Biol. Chem. 261, 10797-10801.
-
(1986)
J. Biol. Chem.
, vol.261
, pp. 10797-10801
-
-
Lundrigan, M.D.1
Kadner, R.J.2
-
19
-
-
84865318505
-
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
-
doi: 10.1038/ismej.2012.59
-
Mason, O. U., Hazen, T. C., Borglin, S., Chain, P. S. G., Dubinsky, E. A., Fortney, J. L., et al. (2012). Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J. 6, 1715-1727. doi: 10.1038/ismej.2012.59
-
(2012)
ISME J.
, vol.6
, pp. 1715-1727
-
-
Mason, O.U.1
Hazen, T.C.2
Borglin, S.3
Chain, P.S.G.4
Dubinsky, E.A.5
Fortney, J.L.6
-
20
-
-
84903393770
-
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill
-
doi: 10.1038/ismej.2013.254
-
Mason, O. U., Scott, N. M., Gonzalez, A., Robbins-Pianka, A., Bælum, J., Kimbrel, J., et al. (2014). Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J. 8, 1464-1475. doi: 10.1038/ismej.2013.254
-
(2014)
ISME J.
, vol.8
, pp. 1464-1475
-
-
Mason, O.U.1
Scott, N.M.2
Gonzalez, A.3
Robbins-Pianka, A.4
Bælum, J.5
Kimbrel, J.6
-
21
-
-
23344439437
-
The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses
-
doi: 10.1073/pnas.0504766102
-
Methé, B. A., Nelson, K. E., Deming, J. W., Momen, B., Melamud, E., Zhang, X., et al. (2005). The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc. Natl. Acad. Sci. U.S.A. 102, 10913-10918. doi: 10.1073/pnas.0504766102
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 10913-10918
-
-
Methé, B.A.1
Nelson, K.E.2
Deming, J.W.3
Momen, B.4
Melamud, E.5
Zhang, X.6
-
22
-
-
0033823554
-
Toluene-Degrading bacteria are chemotactic toward the environmental pollutants benzene, toluene, and trichloroethylene
-
doi: 10.1128/AEM.66.9.4098-4104.20
-
Parales, R. E., Ditty, J. L., and Harwood, C. S. (2000). Toluene-Degrading bacteria are chemotactic toward the environmental pollutants benzene, toluene, and trichloroethylene. Appl. Environ. Microbiol. 66, 4098. doi: 10.1128/AEM.66.9.4098-4104.20
-
(2000)
Appl. Environ. Microbiol.
, vol.66
, pp. 4098
-
-
Parales, R.E.1
Ditty, J.L.2
Harwood, C.S.3
-
23
-
-
0034238097
-
Biodegradation kinetics of benzene, toluene, and phenol as single and mixed substrates for Pseudomonas putida F1
-
doi: 10.1002/1097-0290(20000820)69:4<385::AID-BIT5>3.0.CO;2-Q
-
Reardon, K. F., Mosteller, D. C., and Bull Rogers, J. D. (2000). Biodegradation kinetics of benzene, toluene, and phenol as single and mixed substrates for Pseudomonas putida F1. Biotechnol. Bioeng. 69, 385-400. doi: 10.1002/1097-0290(20000820)69:4<385::AID-BIT5>3.0.CO;2-Q
-
(2000)
Biotechnol. Bioeng.
, vol.69
, pp. 385-400
-
-
Reardon, K.F.1
Mosteller, D.C.2
Bull Rogers, J.D.3
-
24
-
-
84870863360
-
Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill
-
doi: 10.1073/pnas.1108756108
-
Redmond, M. C., and Valentine, D. L. (2012). Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill. Proc. Natl. Acad. Sci. U.S.A. 109, 20292-20297. doi: 10.1073/pnas.1108756108
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 20292-20297
-
-
Redmond, M.C.1
Valentine, D.L.2
-
25
-
-
73149098333
-
Shifting the genomic gold standard for the prokaryotic species definition
-
doi: 10.1073/pnas.0906412106
-
Richter, M., and Rosselló-Móra, R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U.S.A. 106, 19126-19131. doi: 10.1073/pnas.0906412106
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 19126-19131
-
-
Richter, M.1
Rosselló-Móra, R.2
-
26
-
-
84881138595
-
Insights into the phylogeny and coding potential of microbial dark matter
-
doi: 10.1038/nature12352
-
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F., et al. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-437. doi: 10.1038/nature12352
-
(2013)
Nature
, vol.499
, pp. 431-437
-
-
Rinke, C.1
Schwientek, P.2
Sczyrba, A.3
Ivanova, N.N.4
Anderson, I.J.5
Cheng, J.-F.6
-
27
-
-
84888199743
-
Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill
-
doi: 10.1038/ismej.2013.129
-
Rivers, A. R., Sharma, S., Tringe, S. G., Martin, J., Joye, S. B., and Moran, M. A. (2013). Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. ISME J. 7, 2315-2329. doi: 10.1038/ismej.2013.129
-
(2013)
ISME J.
, vol.7
, pp. 2315-2329
-
-
Rivers, A.R.1
Sharma, S.2
Tringe, S.G.3
Martin, J.4
Joye, S.B.5
Moran, M.A.6
-
28
-
-
0029818808
-
The biochemistry and genetics of capsular polysaccharide production in bacteria
-
doi: 10.1146/annurev.micro.50.1.285
-
Roberts, I. S. (1996). The biochemistry and genetics of capsular polysaccharide production in bacteria. Annu. Rev. Microbiol. 50, 285-315. doi: 10.1146/annurev.micro.50.1.285
-
(1996)
Annu. Rev. Microbiol.
, vol.50
, pp. 285-315
-
-
Roberts, I.S.1
-
29
-
-
70149108769
-
Whole genome amplification and de novo assembly of single bacterial cells
-
doi: 10.1371/journal.pone.0006864
-
Rodrigue, S., Malmstrom, R. R., Berlin, A. M., Birren, B. W., Henn, M. R., and Chisholm, S. W. (2009). Whole genome amplification and de novo assembly of single bacterial cells. PLoS ONE 4:e6864. doi: 10.1371/journal.pone.0006864
-
(2009)
PLoS ONE
, vol.4
-
-
Rodrigue, S.1
Malmstrom, R.R.2
Berlin, A.M.3
Birren, B.W.4
Henn, M.R.5
Chisholm, S.W.6
-
30
-
-
0031279440
-
Psychrophilic bacteria-molecular adaptations of membrane lipids
-
doi: 10.1016/S0300-9629(97)87354-9
-
Russell, N. J. (1997). Psychrophilic bacteria-molecular adaptations of membrane lipids. Comp. Biochem. Physiol. A Physiol. 118, 489-493. doi: 10.1016/S0300-9629(97)87354-9
-
(1997)
Comp. Biochem. Physiol. A Physiol.
, vol.118
, pp. 489-493
-
-
Russell, N.J.1
-
31
-
-
78651266825
-
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
-
doi: 10.1093/nar/gkq1102
-
Sun, S., Chen, J., Li, W., Altintas, I., Lin, A., Peltier, S., et al. (2011). Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res. 39, D546-D551. doi: 10.1093/nar/gkq1102
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Sun, S.1
Chen, J.2
Li, W.3
Altintas, I.4
Lin, A.5
Peltier, S.6
-
32
-
-
0001074279
-
Production of intracellular protein from n-butane by Pseudomonas butanovora sp
-
Takahashi, J. (1980). Production of intracellular protein from n-butane by Pseudomonas butanovora sp. nov. Adv. Appl. Microbiol. 26, 117-128.
-
(1980)
nov. Adv. Appl. Microbiol.
, vol.26
, pp. 117-128
-
-
Takahashi, J.1
-
33
-
-
77957750550
-
Propane respiration jump-starts microbial response to a deep oil spill
-
doi: 10.1126/science.1196830
-
Valentine, D. L., Kessler, J. D., Redmond, M. C., Mendes, S. D., Heintz, M. B., Farwell, C., et al. (2010). Propane respiration jump-starts microbial response to a deep oil spill. Science 330, 208-211. doi: 10.1126/science.1196830
-
(2010)
Science
, vol.330
, pp. 208-211
-
-
Valentine, D.L.1
Kessler, J.D.2
Redmond, M.C.3
Mendes, S.D.4
Heintz, M.B.5
Farwell, C.6
-
34
-
-
80054791084
-
Decontamination of MDA reagents for single cell whole genome amplification
-
doi: 10.1371/journal.pone.0026161
-
Woyke, T., Sczyrba, A., Lee, J., Rinke, C., Tighe, D., Clingenpeel, S., et al. (2011). Decontamination of MDA reagents for single cell whole genome amplification. PLoS ONE 6:e26161. doi: 10.1371/journal.pone.0026161
-
(2011)
PLoS ONE
, vol.6
-
-
Woyke, T.1
Sczyrba, A.2
Lee, J.3
Rinke, C.4
Tighe, D.5
Clingenpeel, S.6
-
35
-
-
70349687228
-
Atmosphere. Nitrous oxide: no laughing matter.
-
doi: 10.1126/science.1179571
-
Wuebbles, D. J. (2009). Atmosphere. Nitrous oxide: no laughing matter. Science 326, 56-57. doi: 10.1126/science.1179571
-
(2009)
Science
, vol.326
, pp. 56-57
-
-
Wuebbles, D.J.1
|