-
2
-
-
33846923050
-
Genome dynamics in a natural archaeal population
-
Allen, E.E., Tyson, G.W., Whitaker, R., Detter, J.C., Richardson, P.M., and Banfield, J.F. (2007) Genome dynamics in a natural archaeal population. Proc Natl Acad Sci USA 104: 1883-1888.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 1883-1888
-
-
Allen, E.E.1
Tyson, G.W.2
Whitaker, R.3
Detter, J.C.4
Richardson, P.M.5
Banfield, J.F.6
-
3
-
-
0030801002
-
Gapped blast and psi-blast: a new generation of protein database search programs
-
Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. (1997) Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Schaffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
4
-
-
0037033979
-
Unsuspected diversity among marine aerobic anoxygenic phototrophs
-
Béjá, O., Suzuki, M., Heidelberg, J., Nelson, W., Preston, C., Hamada, T., etal. (2002) Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-633.
-
(2002)
Nature
, vol.415
, pp. 630-633
-
-
Béjá, O.1
Suzuki, M.2
Heidelberg, J.3
Nelson, W.4
Preston, C.5
Hamada, T.6
-
5
-
-
37249052742
-
A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea
-
Berg, I.A., Kockelkorn, D., Buckel, W., and Fuchs, G. (2007) A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318: 1782-1786.
-
(2007)
Science
, vol.318
, pp. 1782-1786
-
-
Berg, I.A.1
Kockelkorn, D.2
Buckel, W.3
Fuchs, G.4
-
7
-
-
76649087327
-
Abundance of ammonia-oxidizing archaea and bacteria along an estuarine salinity gradient in relation to potential nitrification rates
-
Bernhard, A., Landry, Z., Blevins, A., De La Torre, J., Giblin, A., and Stahl, D. (2010) Abundance of ammonia-oxidizing archaea and bacteria along an estuarine salinity gradient in relation to potential nitrification rates. Appl Environ Microbiol 76: 1285-1289.
-
(2010)
Appl Environ Microbiol
, vol.76
, pp. 1285-1289
-
-
Bernhard, A.1
Landry, Z.2
Blevins, A.3
De La Torre, J.4
Giblin, A.5
Stahl, D.6
-
8
-
-
36849028589
-
Population level functional diversity in the microbial community revealed by comparative genomic and metagenomic analyses
-
Bhaya, D., Grossman, A., Steunou, A.-S., Khuri, N., Cohan, F., Hamamura, N., etal. (2007) Population level functional diversity in the microbial community revealed by comparative genomic and metagenomic analyses. ISME J 1: 703-713.
-
(2007)
ISME J
, vol.1
, pp. 703-713
-
-
Bhaya, D.1
Grossman, A.2
Steunou, A.-S.3
Khuri, N.4
Cohan, F.5
Hamamura, N.6
-
9
-
-
79952050667
-
Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis
-
Blainey, P., Mosier, A., Potanina, A., Francis, C., and Quake, S. (2011) Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS ONE 6: e16626.
-
(2011)
PLoS ONE
, vol.6
-
-
Blainey, P.1
Mosier, A.2
Potanina, A.3
Francis, C.4
Quake, S.5
-
10
-
-
0029667487
-
Water column nutrients and sedimentary denitrification in the Gulf of Maine
-
Christensen, J., Townsend, D.W., and Montoya, J. (1996) Water column nutrients and sedimentary denitrification in the Gulf of Maine. Cont Shelf Res 16: 489-515.
-
(1996)
Cont Shelf Res
, vol.16
, pp. 489-515
-
-
Christensen, J.1
Townsend, D.W.2
Montoya, J.3
-
11
-
-
79953216726
-
Abundance, diversity, and activity of ammonia-oxidizing prokaryotes in the coastal arctic ocean in summer and winter
-
Christman, G.D., Cottrell, M.T., Popp, B.N., Gier, E., and Kirchman, D.L. (2011) Abundance, diversity, and activity of ammonia-oxidizing prokaryotes in the coastal arctic ocean in summer and winter. Appl Environ Microbiol 77: 2026-2034.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 2026-2034
-
-
Christman, G.D.1
Cottrell, M.T.2
Popp, B.N.3
Gier, E.4
Kirchman, D.L.5
-
12
-
-
77953940648
-
Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean
-
Church, M.J., Wai, B., Karl, D.M., and Delong, E.F. (2010) Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean. Environ Microbiol 12: 679-688.
-
(2010)
Environ Microbiol
, vol.12
, pp. 679-688
-
-
Church, M.J.1
Wai, B.2
Karl, D.M.3
Delong, E.F.4
-
13
-
-
77956193448
-
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement
-
Darling, A.E., Mau, B., and Perna, N.T. (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5: e11147.
-
(2010)
PLoS ONE
, vol.5
-
-
Darling, A.E.1
Mau, B.2
Perna, N.T.3
-
14
-
-
84855284261
-
-
Geneious v4.6 [WWW document]. URL
-
Drummond, A., Ashton, B., Cheung, M., Heled, J., Kearse, M., Moir, R., etal. (2009) Geneious v4.6 [WWW document]. URL:.
-
(2009)
-
-
Drummond, A.1
Ashton, B.2
Cheung, M.3
Heled, J.4
Kearse, M.5
Moir, R.6
-
15
-
-
0037348061
-
Urease activity in cultures and field populations of the toxic dinoflagellate Alexandrium
-
Dyhrman, S.T., and Anderson, D.M. (2003) Urease activity in cultures and field populations of the toxic dinoflagellate Alexandrium. Limnol Oceanogr 48: 647-655.
-
(2003)
Limnol Oceanogr
, vol.48
, pp. 647-655
-
-
Dyhrman, S.T.1
Anderson, D.M.2
-
16
-
-
0031978181
-
Base-calling of automated sequencer traces using Phred. II. Error probabilities
-
Ewing, B., and Green, P. (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 8: 186-194.
-
(1998)
Genome Res
, vol.8
, pp. 186-194
-
-
Ewing, B.1
Green, P.2
-
18
-
-
26844541457
-
Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean
-
Francis, C.A., Roberts, K.J., Beman, J.M., Santoro, A.E., and Oakley, B.B. (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA 102: 14683-14688.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 14683-14688
-
-
Francis, C.A.1
Roberts, K.J.2
Beman, J.M.3
Santoro, A.E.4
Oakley, B.B.5
-
19
-
-
0242578620
-
A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon, S., and Gascuel, O. (2003) A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
-
(2003)
Syst Biol
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
20
-
-
0034658817
-
Biogeographical diversity among marine bacterioplankton
-
Hagström, Ä., Pinhassi, J., and Zweifel, U.L. (2000) Biogeographical diversity among marine bacterioplankton. Aquat Microb Ecol 21: 231-244.
-
(2000)
Aquat Microb Ecol
, vol.21
, pp. 231-244
-
-
Hagström, A.1
Pinhassi, J.2
Zweifel, U.L.3
-
21
-
-
33646260901
-
Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota
-
Hallam, S.J., Mincer, T.J., Schleper, C., Preston, C.M., Roberts, K., Richardson, P.M., and DeLong, E.F. (2006a) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4: 520-536.
-
(2006)
PLoS Biol
, vol.4
, pp. 520-536
-
-
Hallam, S.J.1
Mincer, T.J.2
Schleper, C.3
Preston, C.M.4
Roberts, K.5
Richardson, P.M.6
DeLong, E.F.7
-
22
-
-
33845286513
-
Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum
-
Hallam, S.J., Konstantinidis, K.T., Putnam, N., Schleper, C., Watanabe, Y., Sugahara, J., etal. (2006b) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci USA 103: 18296-18301.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 18296-18301
-
-
Hallam, S.J.1
Konstantinidis, K.T.2
Putnam, N.3
Schleper, C.4
Watanabe, Y.5
Sugahara, J.6
-
23
-
-
41149153310
-
A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring
-
Hatzenpichler, R., Lebedeva, E.V., Spieck, E., Stoecker, K., Richter, A., Daims, H., and Wagner, M. (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci USA 105: 2134-2139.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 2134-2139
-
-
Hatzenpichler, R.1
Lebedeva, E.V.2
Spieck, E.3
Stoecker, K.4
Richter, A.5
Daims, H.6
Wagner, M.7
-
24
-
-
45549103517
-
A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis
-
Huber, H., Gallenberger, M., Jahn, U., Eylert, E., Berg, I.A., Kockelkorn, D., etal. (2008) A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis. Proc Natl Acad Sci USA 105: 7851-7856.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 7851-7856
-
-
Huber, H.1
Gallenberger, M.2
Jahn, U.3
Eylert, E.4
Berg, I.A.5
Kockelkorn, D.6
-
25
-
-
33646262107
-
Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon
-
Ingalls, A.E., Shah, S.R., Hansman, R.L., Aluwihare, L.I., Santos, G.M., Druffel, E.R.M., and Pearson, A. (2006) Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proc Natl Acad Sci USA 103: 6442-6447.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 6442-6447
-
-
Ingalls, A.E.1
Shah, S.R.2
Hansman, R.L.3
Aluwihare, L.I.4
Santos, G.M.5
Druffel, E.R.M.6
Pearson, A.7
-
26
-
-
0035945618
-
Archaeal dominance in the mesopelagic zone of the Pacific Ocean
-
Karner, M.B., DeLong, E.F., and Karl, D.M. (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409: 507-510.
-
(2001)
Nature
, vol.409
, pp. 507-510
-
-
Karner, M.B.1
DeLong, E.F.2
Karl, D.M.3
-
27
-
-
53849115701
-
Genomic patterns of recombination, clonal divergence and environment in marine microbial populations
-
Konstantinidis, K.T., and DeLong, E.F. (2008) Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J 2: 1052-1065.
-
(2008)
ISME J
, vol.2
, pp. 1052-1065
-
-
Konstantinidis, K.T.1
DeLong, E.F.2
-
28
-
-
78649450690
-
Relevance of a crenarchaeotal subcluster related to Candidatus Nitrosopumilus maritimus to ammonia oxidation in the suboxic zone of the central Baltic Sea
-
Labrenz, M., Sintes, E., Toetzke, F., Zumsteg, A., Herndl, G.J., Seidler, M., etal. (2010) Relevance of a crenarchaeotal subcluster related to Candidatus Nitrosopumilus maritimus to ammonia oxidation in the suboxic zone of the central Baltic Sea. ISME J 4: 1496-1508.
-
(2010)
ISME J
, vol.4
, pp. 1496-1508
-
-
Labrenz, M.1
Sintes, E.2
Toetzke, F.3
Zumsteg, A.4
Herndl, G.J.5
Seidler, M.6
-
29
-
-
17644441088
-
Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeota reveals multiple horizontal gene transfers
-
Lopez-Garcia, P., Brochier, C., Moreira, D., and Rodriguez-Valera, F. (2004) Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeota reveals multiple horizontal gene transfers. Environ Microbiol 6: 19-34.
-
(2004)
Environ Microbiol
, vol.6
, pp. 19-34
-
-
Lopez-Garcia, P.1
Brochier, C.2
Moreira, D.3
Rodriguez-Valera, F.4
-
30
-
-
33644873697
-
The integrated microbial genome (IMG) system
-
Markowiz, V.M., Korzeniewski, F., Palaniappan, K., Szeto, E., Werner, G., Padki, A., etal. (2006) The integrated microbial genome (IMG) system. Nucleic Acids Res 34: D344-D348.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Markowiz, V.M.1
Korzeniewski, F.2
Palaniappan, K.3
Szeto, E.4
Werner, G.5
Padki, A.6
-
31
-
-
34247847886
-
Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre
-
Mincer, T., Church, M., Taylor, L., Preston, C., Karl, D.M., and DeLong, E. (2007) Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ Microbiol 9: 1162-1175.
-
(2007)
Environ Microbiol
, vol.9
, pp. 1162-1175
-
-
Mincer, T.1
Church, M.2
Taylor, L.3
Preston, C.4
Karl, D.M.5
DeLong, E.6
-
32
-
-
77956256740
-
High diversity of ammonia-oxidizing archaea in permanent and seasonal oxygen-deficient waters of the eastern South Pacific
-
Molina, V., Belmar, L., and Ulloa, O. (2010) High diversity of ammonia-oxidizing archaea in permanent and seasonal oxygen-deficient waters of the eastern South Pacific. Environ Microbiol 12: 2450-2465.
-
(2010)
Environ Microbiol
, vol.12
, pp. 2450-2465
-
-
Molina, V.1
Belmar, L.2
Ulloa, O.3
-
33
-
-
78249268816
-
Gene-FISH - an in situ technique for linking gene presence and cell identity in environmental microorganisms
-
Moraru, C., Lam, P., Fuchs, B.M., Kuypers, M.M.M., and Amann, R. (2010) Gene-FISH - an in situ technique for linking gene presence and cell identity in environmental microorganisms. Environ Microbiol 12: 3057-3073.
-
(2010)
Environ Microbiol
, vol.12
, pp. 3057-3073
-
-
Moraru, C.1
Lam, P.2
Fuchs, B.M.3
Kuypers, M.M.M.4
Amann, R.5
-
34
-
-
0034708758
-
A whole-genome assembly of Drosophila
-
Myers, E.W., Sutton, G., Delcher, A.L., Dew, I.M., and Fasulo, D.P. (2000) A whole-genome assembly of Drosophila. Science 287: 2196-2204.
-
(2000)
Science
, vol.287
, pp. 2196-2204
-
-
Myers, E.W.1
Sutton, G.2
Delcher, A.L.3
Dew, I.M.4
Fasulo, D.P.5
-
35
-
-
33747341311
-
Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors
-
Park, H., Wells, G.F., Bae, H., Criddle, C.S., and Francis, C.A. (2006) Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Appl Environ Microbiol 72: 5643-5647.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 5643-5647
-
-
Park, H.1
Wells, G.F.2
Bae, H.3
Criddle, C.S.4
Francis, C.A.5
-
36
-
-
33947238287
-
The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
-
Rusch, D.B., Halpern, A.L., Sutton, G., Heidelberg, K.B., Williamson, S., Yooseph, S., etal. (2007) The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 5: 398-431.
-
(2007)
PLoS Biol
, vol.5
, pp. 398-431
-
-
Rusch, D.B.1
Halpern, A.L.2
Sutton, G.3
Heidelberg, K.B.4
Williamson, S.5
Yooseph, S.6
-
37
-
-
78049432317
-
Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current
-
Santoro, A., Casciotti, K., and Francis, C. (2010) Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current. Environ Microbiol 12: 1989-2006.
-
(2010)
Environ Microbiol
, vol.12
, pp. 1989-2006
-
-
Santoro, A.1
Casciotti, K.2
Francis, C.3
-
38
-
-
33747847779
-
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
-
Suyama, M., Torrents, D., and Bork, P. (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34: W609-W612.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Suyama, M.1
Torrents, D.2
Bork, P.3
-
39
-
-
4344670204
-
Application of tetranucleotide frequencies for the assignment of genomic fragments
-
Teeling, H., Meyedierks, A., Bauer, M., Amann, R., and Glockner, F.O. (2004) Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol 6: 938-947.
-
(2004)
Environ Microbiol
, vol.6
, pp. 938-947
-
-
Teeling, H.1
Meyedierks, A.2
Bauer, M.3
Amann, R.4
Glockner, F.O.5
-
40
-
-
0027968068
-
clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994) clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
41
-
-
38549131184
-
Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol
-
de la Torre, J., Walker, C., Ingalls, A., Könneke, M., and Stahl, D. (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 10: 810-818.
-
(2008)
Environ Microbiol
, vol.10
, pp. 810-818
-
-
de la Torre, J.1
Walker, C.2
Ingalls, A.3
Könneke, M.4
Stahl, D.5
-
42
-
-
79957684288
-
Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil
-
Tourna, M., Stieglmeier, M., Spang, A., Konneke, M., Schintlmeister, A., Urich, T., etal. (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci USA 108: 8420-8425.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 8420-8425
-
-
Tourna, M.1
Stieglmeier, M.2
Spang, A.3
Konneke, M.4
Schintlmeister, A.5
Urich, T.6
-
43
-
-
33745025682
-
Sulfolipids dramatically decrease phosphorus demand by picocyanobacteria in oligotrophic marine environments
-
Van Mooy, B.A.S., Rocap, G., Fredricks, H.F., Evans, C.T., and Devol, A.H. (2006) Sulfolipids dramatically decrease phosphorus demand by picocyanobacteria in oligotrophic marine environments. Proc Natl Acad Sci USA 103: 8607-8612.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 8607-8612
-
-
Van Mooy, B.A.S.1
Rocap, G.2
Fredricks, H.F.3
Evans, C.T.4
Devol, A.H.5
-
44
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
Venter, J.C., Remington, K., Heidelberg, J., Halpern, A.L., Rusch, D., Eisen, J., etal. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.3
Halpern, A.L.4
Rusch, D.5
Eisen, J.6
-
45
-
-
77952739182
-
Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea
-
Walker, C.B., de la Torre, J.R., Klotz, M.G., Urakawa, H., Pinel, N., Arp, D.J., etal. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci USA 107: 8818-8823.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 8818-8823
-
-
Walker, C.B.1
de la Torre, J.R.2
Klotz, M.G.3
Urakawa, H.4
Pinel, N.5
Arp, D.J.6
-
46
-
-
0037469625
-
Bicarbonate uptake by marine Crenarchaeota
-
Wuchter, C., Schouten, S., Boschker, H., and Damste, J.S. (2003) Bicarbonate uptake by marine Crenarchaeota. FEMS Microbiol Lett 219: 203-207.
-
(2003)
FEMS Microbiol Lett
, vol.219
, pp. 203-207
-
-
Wuchter, C.1
Schouten, S.2
Boschker, H.3
Damste, J.S.4
-
47
-
-
34547803197
-
paml 4: phylogenetic analysis by maximum likelihood
-
Yang, Z. (2007) paml 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
|