-
1
-
-
0029004313
-
Understanding the diversity of trichloroethene co-oxidations
-
Arp, D.J. (1995) Understanding the diversity of trichloroethene co-oxidations. Curr Biol 6: 352-358.
-
(1995)
Curr Biol
, vol.6
, pp. 352-358
-
-
Arp, D.J.1
-
2
-
-
33748802383
-
Nitrifiers: more than 100 years from isolation to genome sequences
-
Arp, D.J., and Bottomley, P.J. (2006) Nitrifiers: more than 100 years from isolation to genome sequences. Microbe 1: 229-234.
-
(2006)
Microbe
, vol.1
, pp. 229-234
-
-
Arp, D.J.1
Bottomley, P.J.2
-
3
-
-
0036038187
-
Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea
-
Arp, D.J., Sayavedra-Soto, L.A., and Hommes, N.G. (2002) Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea. Arch Microbiol 178: 250-255.
-
(2002)
Arch Microbiol
, vol.178
, pp. 250-255
-
-
Arp, D.J.1
Sayavedra-Soto, L.A.2
Hommes, N.G.3
-
4
-
-
35848950017
-
The impact of genome analyses on our understanding of ammonia-oxidizing bacteria
-
Arp, D.J., Chain, P.S., and Klotz, M.G. (2007) The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annu Rev Microbiol 61: 503-528.
-
(2007)
Annu Rev Microbiol
, vol.61
, pp. 503-528
-
-
Arp, D.J.1
Chain, P.S.2
Klotz, M.G.3
-
5
-
-
77952093872
-
Oxidation of methane by a biological dicopper centre
-
Balasubramanian, R., Smith, S.M., Rawat, S., Yatsunyk, L.A., Stemmler, T.L., and Rosenzweig, A.C. (2010) Oxidation of methane by a biological dicopper centre. Nature 465: 115-119.
-
(2010)
Nature
, vol.465
, pp. 115-119
-
-
Balasubramanian, R.1
Smith, S.M.2
Rawat, S.3
Yatsunyk, L.A.4
Stemmler, T.L.5
Rosenzweig, A.C.6
-
6
-
-
20444375861
-
Expanding the alkane oxygenase toolbox: new enzymes and applications
-
van Beilen, J.B., and Funhoff, E.G. (2005) Expanding the alkane oxygenase toolbox: new enzymes and applications. Curr Opin Biotechnol 16: 308-314.
-
(2005)
Curr Opin Biotechnol
, vol.16
, pp. 308-314
-
-
van Beilen, J.B.1
Funhoff, E.G.2
-
7
-
-
33846621913
-
Alkane hydroxylases involved in microbial alkane degradation
-
van Beilen, J.B., and Funhoff, E.G. (2007) Alkane hydroxylases involved in microbial alkane degradation. Appl Microbiol Biotechnol 74: 13-21.
-
(2007)
Appl Microbiol Biotechnol
, vol.74
, pp. 13-21
-
-
van Beilen, J.B.1
Funhoff, E.G.2
-
8
-
-
76649087327
-
Abundance of ammonia-oxidizing Archaea and Bacteria along an estuarine salinity gradient in relation to potential nitrification rates
-
Bernhard, A.E., Landry, Z.C., Blevins, A., de la Torre, J.R., Giblin, A.E., and Stahl, D.A. (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.E.1
Landry, Z.C.2
Blevins, A.3
de la Torre, J.R.4
Giblin, A.E.5
Stahl, D.A.6
-
9
-
-
77951942938
-
Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea
-
Dang, H., Luan, X.W., Chen, R., Zhang, X., Guo, L., and Klotz, M.G. (2010) Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea. FEMS Microbiol Ecol 72: 370-385.
-
(2010)
FEMS Microbiol Ecol
, vol.72
, pp. 370-385
-
-
Dang, H.1
Luan, X.W.2
Chen, R.3
Zhang, X.4
Guo, L.5
Klotz, M.G.6
-
10
-
-
34247347786
-
Biodegradability of chlorinated solvents and related chlorinated aliphatic compounds
-
Field, J.A., and Sierra-Alvarez, R. (2004) Biodegradability of chlorinated solvents and related chlorinated aliphatic compounds. Rev Environ Sci Bio/Technol 3: 185-254.
-
(2004)
Rev Environ Sci Bio/Technol
, vol.3
, pp. 185-254
-
-
Field, J.A.1
Sierra-Alvarez, R.2
-
11
-
-
34548628155
-
The biochemistry of methane oxidation
-
Hakemian, A.S., and Rosenzweig, A.C. (2007) The biochemistry of methane oxidation. Annu Rev Biochem 76: 223-241.
-
(2007)
Annu Rev Biochem
, vol.76
, pp. 223-241
-
-
Hakemian, A.S.1
Rosenzweig, A.C.2
-
12
-
-
0034194873
-
Isolation and characterization of alkane-utilizing Nocardioides sp. strain CF8
-
Hamamura, N., and Arp, D.J. (2000) Isolation and characterization of alkane-utilizing Nocardioides sp. strain CF8. FEMS Microbiol Lett 186: 21-26.
-
(2000)
FEMS Microbiol Lett
, vol.186
, pp. 21-26
-
-
Hamamura, N.1
Arp, D.J.2
-
13
-
-
0030799165
-
Chloroform cometabolism by butane-grown CF8, Pseudomonas butanovora, and Mycobacterium vaccae JOB5 and methane-grown Methylosinus trichosporium OB3b
-
Hamamura, N., Page, C., Long, T., Semprini, L., and Arp, D.J. (1997) Chloroform cometabolism by butane-grown CF8, Pseudomonas butanovora, and Mycobacterium vaccae JOB5 and methane-grown Methylosinus trichosporium OB3b. Appl Environ Microbiol 63: 3607-3613.
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 3607-3613
-
-
Hamamura, N.1
Page, C.2
Long, T.3
Semprini, L.4
Arp, D.J.5
-
14
-
-
0032832635
-
Diversity in butane monooxygenases among butane-grown bacteria
-
Hamamura, N., Storfa, R.T., Semprini, L., and Arp, D.J. (1999) Diversity in butane monooxygenases among butane-grown bacteria. Appl Environ Microbiol 65: 4586-4593.
-
(1999)
Appl Environ Microbiol
, vol.65
, pp. 4586-4593
-
-
Hamamura, N.1
Storfa, R.T.2
Semprini, L.3
Arp, D.J.4
-
15
-
-
0035511721
-
Two distinct monooxygenases for alkane oxidation in Nocarioides sp. strain CF8
-
Hamamura, N., Yeager, C., and Arp, D.J. (2001) Two distinct monooxygenases for alkane oxidation in Nocarioides sp. strain CF8. Appl Environ Microbiol 67: 4992-4998.
-
(2001)
Appl Environ Microbiol
, vol.67
, pp. 4992-4998
-
-
Hamamura, N.1
Yeager, C.2
Arp, D.J.3
-
16
-
-
26844561468
-
Diversity and functional analysis of bacterial communities associated with natural hydrocarbon seeps in acidic soils at Rainbow Springs, Yellowstone National Park
-
Hamamura, N., Olson, S.H., Ward, D.M., and Inskeep, W.P. (2005) Diversity and functional analysis of bacterial communities associated with natural hydrocarbon seeps in acidic soils at Rainbow Springs, Yellowstone National Park. Appl Environ Microbiol 71: 5943-5950.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 5943-5950
-
-
Hamamura, N.1
Olson, S.H.2
Ward, D.M.3
Inskeep, W.P.4
-
17
-
-
0026610274
-
2-labeling studies of the de novo synthesis of polypeptides by Nitrosomonas europaea during recovery from acetylene and light inactivation of ammonia monooxygenase
-
2-labeling studies of the de novo synthesis of polypeptides by Nitrosomonas europaea during recovery from acetylene and light inactivation of ammonia monooxygenase. J Biol Chem 267: 1534-1545.
-
(1992)
J Biol Chem
, vol.267
, pp. 1534-1545
-
-
Hyman, M.R.1
Arp, D.J.2
-
18
-
-
0027165601
-
An electrophoretic study of the thermal-dependent and reductant-dependent aggregation of the 27kDa component of ammonia monooxygenase from Nitrosomonas europaea
-
Hyman, M.R., and Arp, D.J. (1993) An electrophoretic study of the thermal-dependent and reductant-dependent aggregation of the 27kDa component of ammonia monooxygenase from Nitrosomonas europaea. Electrophoresis 14: 619-627.
-
(1993)
Electrophoresis
, vol.14
, pp. 619-627
-
-
Hyman, M.R.1
Arp, D.J.2
-
19
-
-
0343958771
-
Bromocarbon oxidations by Nitrosomonas europaea
-
In . Crawford, R.L., and Hanson, R.S. (eds). Washington, DC, USA: American Society for Microbiology -.
-
1 compounds: Proceedings of the 4th International Symposium. Crawford, R.L., and Hanson, R.S. (eds). Washington, DC, USA: American Society for Microbiology, pp. 49-52.
-
(1984)
1 compounds: Proceedings of the 4th International Symposium
, pp. 49-52
-
-
Hyman, M.R.1
Wood, P.M.2
-
20
-
-
0027374388
-
Inhibition of ammonia oxidation in nitrosomonas europaea by sulfur compounds: thioethers are oxidized to sulfoxides by ammonia monooxygenase
-
Juliette, L.Y., Hyman, M.R., and Arp, D.J. (1993) Inhibition of ammonia oxidation in nitrosomonas europaea by sulfur compounds: thioethers are oxidized to sulfoxides by ammonia monooxygenase. Appl Environ Microbiol 59: 3718-3727.
-
(1993)
Appl Environ Microbiol
, vol.59
, pp. 3718-3727
-
-
Juliette, L.Y.1
Hyman, M.R.2
Arp, D.J.3
-
21
-
-
0028200507
-
Transformations of aromatic compounds by Nitrosomonas europaea
-
Keener, W.K., and Arp, D.J. (1994) Transformations of aromatic compounds by Nitrosomonas europaea. Appl Environ Microbiol 60: 1914-1920.
-
(1994)
Appl Environ Microbiol
, vol.60
, pp. 1914-1920
-
-
Keener, W.K.1
Arp, D.J.2
-
22
-
-
0031732063
-
Multiple copies of ammonia monooxygenase (amo) operons have evolved under biased AT/GC mutational pressure in ammonia-oxidizing autotrophic bacteria
-
Klotz, M.G., and Norton, J.M. (1998) Multiple copies of ammonia monooxygenase (amo) operons have evolved under biased AT/GC mutational pressure in ammonia-oxidizing autotrophic bacteria. FEMS Microbiol Lett 168: 303-311.
-
(1998)
FEMS Microbiol Lett
, vol.168
, pp. 303-311
-
-
Klotz, M.G.1
Norton, J.M.2
-
23
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., etal. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
-
24
-
-
15044356424
-
Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane
-
Lieberman, R.L., and Rosenzweig, A.C. (2005) Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane. Nature 434: 177-182.
-
(2005)
Nature
, vol.434
, pp. 177-182
-
-
Lieberman, R.L.1
Rosenzweig, A.C.2
-
25
-
-
0027153142
-
Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea
-
McTavish, H., Fuchs, J.A., and Hooper, A.B. (1993) Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea. J Bacteriol 175: 2436-2444.
-
(1993)
J Bacteriol
, vol.175
, pp. 2436-2444
-
-
McTavish, H.1
Fuchs, J.A.2
Hooper, A.B.3
-
26
-
-
70350052417
-
Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria
-
Martens-Habbena, W., Berube, P.M., Urakawa, H., Torre, J.R., and Stahl, D.A. (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461: 976-979.
-
(2009)
Nature
, vol.461
, pp. 976-979
-
-
Martens-Habbena, W.1
Berube, P.M.2
Urakawa, H.3
Torre, J.R.4
Stahl, D.A.5
-
27
-
-
13844292651
-
Physiological and molecular genetic analyses of vinyl chloride and ethene biodegradation in Nocardioides sp. strain JS614
-
Mattes, T.E., Coleman, N.V., Spain, J.C., and Gossett, J.M. (2005) Physiological and molecular genetic analyses of vinyl chloride and ethene biodegradation in Nocardioides sp. strain JS614. Arch Microbiol 183: 95-106.
-
(2005)
Arch Microbiol
, vol.183
, pp. 95-106
-
-
Mattes, T.E.1
Coleman, N.V.2
Spain, J.C.3
Gossett, J.M.4
-
28
-
-
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
-
29
-
-
0004136246
-
-
Cold Springs Harbor, NY, USA: Cold Springs Harbor Laboratory Press.
-
Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Springs Harbor, NY, USA: Cold Springs Harbor Laboratory Press.
-
(1989)
Molecular Cloning: A Laboratory Manual
-
-
Sambrook, J.1
Fritsch, E.F.2
Maniatis, T.3
-
30
-
-
77952295773
-
A comparative study of most probable number (MPN)-PCR vs. real-time-PCR for the measurement of abundance and assessment of diversity of alkB homologous genes in soil
-
Schulz, S., Pérez-de-Mora, A., Engel, M., Munch, J.C., and Schloter, M. (2010) A comparative study of most probable number (MPN)-PCR vs. real-time-PCR for the measurement of abundance and assessment of diversity of alkB homologous genes in soil. J Microbiol Methods 80: 295-298.
-
(2010)
J Microbiol Methods
, vol.80
, pp. 295-298
-
-
Schulz, S.1
Pérez-de-Mora, A.2
Engel, M.3
Munch, J.C.4
Schloter, M.5
-
31
-
-
0029055846
-
Particulate methane monooxygenase genes in methanotrophs
-
Semrau, J.D., Chistoserdov, A., Lebron, J., Costello, A., Davagnino, J., Kenna, E., etal. (1995) Particulate methane monooxygenase genes in methanotrophs. J Bacteriol 177: 3071-3079.
-
(1995)
J Bacteriol
, vol.177
, pp. 3071-3079
-
-
Semrau, J.D.1
Chistoserdov, A.2
Lebron, J.3
Costello, A.4
Davagnino, J.5
Kenna, E.6
-
32
-
-
0022033560
-
Spectroscopic evidence for a photosensitive oxygenated state of ammonia mono-oxygenase
-
Shears, J.H., and Wood, P.M. (1985) Spectroscopic evidence for a photosensitive oxygenated state of ammonia mono-oxygenase. Biochem J 226: 499-507.
-
(1985)
Biochem J
, vol.226
, pp. 499-507
-
-
Shears, J.H.1
Wood, P.M.2
-
33
-
-
33644778038
-
4 gaseous hydrocarbons and isoprene by microorganisms
-
4 gaseous hydrocarbons and isoprene by microorganisms. J Chem Technol Biotechnol 81: 237-256.
-
(2006)
J Chem Technol Biotechnol
, vol.81
, pp. 237-256
-
-
Shennan, J.L.1
-
34
-
-
0031752797
-
Something from almost nothing: carbon dioxide fixation in chemoautotrophs
-
Shively, J.M., van Keulen, G., and Meijer, W.G. (1998) Something from almost nothing: carbon dioxide fixation in chemoautotrophs. Annu Rev Microbiol 52: 191-230.
-
(1998)
Annu Rev Microbiol
, vol.52
, pp. 191-230
-
-
Shively, J.M.1
van Keulen, G.2
Meijer, W.G.3
-
35
-
-
0034986949
-
Carbon cycling: the prokaryotic contribution
-
Shively, J.M., English, R.S., Baker, S.H., and Cannon, G.C. (2001) Carbon cycling: the prokaryotic contribution. Curr Opin Microbiol 4: 301-306.
-
(2001)
Curr Opin Microbiol
, vol.4
, pp. 301-306
-
-
Shively, J.M.1
English, R.S.2
Baker, S.H.3
Cannon, G.C.4
-
36
-
-
46949088787
-
Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American margin
-
Tavormina, P.L., Ussler, W., 3rd, and Orphan, V.J. (2008) Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American margin. Appl Environ Microbiol 74: 3985-3995.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 3985-3995
-
-
Tavormina, P.L.1
Ussler 3rd, W.2
Orphan, V.J.3
-
37
-
-
77951498451
-
Distributions of putative aerobic methanotrophs in diverse pelagic marine environments
-
Tavormina, P.L., Ussler, W., 3rd, Joye, S.B., Harrison, B.K., and Orphan, V.J. (2010) Distributions of putative aerobic methanotrophs in diverse pelagic marine environments. ISME J 4: 700-710.
-
(2010)
ISME J
, vol.4
, pp. 700-710
-
-
Tavormina, P.L.1
Ussler 3rd, W.2
Joye, S.B.3
Harrison, B.K.4
Orphan, V.J.5
-
38
-
-
79955945981
-
-
and Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics Chapter 2: Unit 2 3.
-
Thompson, J.D., Gibson, T.J., and Higgins, D.G. (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics Chapter 2: Unit 2 3.
-
(2002)
-
-
Thompson, J.D.1
Gibson, T.J.2
Higgins, D.G.3
-
39
-
-
77950273400
-
High abundance of ammonia-oxidizing archaea in coastal waters determined using a modified DNA extraction method
-
Urakawa, H., Martens-Habbena, W., and Stahl, D.A. (2010) High abundance of ammonia-oxidizing archaea in coastal waters determined using a modified DNA extraction method. Appl Environ Microbiol 76: 2129-2135.
-
(2010)
Appl Environ Microbiol
, vol.76
, pp. 2129-2135
-
-
Urakawa, H.1
Martens-Habbena, W.2
Stahl, D.A.3
-
40
-
-
77952739182
-
Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea
-
Walker, C.B., 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
Torre, J.R.2
Klotz, M.G.3
Urakawa, H.4
Pinel, N.5
Arp, D.J.6
-
41
-
-
34748892898
-
Bacterial metabolism of long-chain n-alkanes
-
Wentzel, A., Ellingsen, T.E., Kotlar, H.K., Zotchev, S.B., and Throne-Holst, M. (2007) Bacterial metabolism of long-chain n-alkanes. Appl Microbiol Biotechnol 76: 1209-1221.
-
(2007)
Appl Microbiol Biotechnol
, vol.76
, pp. 1209-1221
-
-
Wentzel, A.1
Ellingsen, T.E.2
Kotlar, H.K.3
Zotchev, S.B.4
Throne-Holst, M.5
-
42
-
-
0001279038
-
Preparation of genomic DNA from bacteria
-
In . Ausubel, F.M., Brent, R., Kingstone, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. (eds). New York, NY, USA: John Wiley & Sons -.
-
Wilson, K. (1995) Preparation of genomic DNA from bacteria. In Current Protocols in Molecular Biology. Ausubel, F.M., Brent, R., Kingstone, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. (eds). New York, NY, USA: John Wiley & Sons, pp. 2.4.1-2.4.5.
-
(1995)
Current Protocols in Molecular Biology
, pp. 241-245
-
-
Wilson, K.1
-
43
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino, D.R., and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
|