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0035369375
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Microorganisms relevant to bioremediation
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Watanabe K. Microorganisms relevant to bioremediation. Curr. Opin. Biotechnol. 12:2001;237-241.
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Watanabe, K.1
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0036418192
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Microbial community composition and function in wastewater treatment plants
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Wagner M., Loy A., Nogueira R., Purkhold U., Lee N., Daims H. Microbial community composition and function in wastewater treatment plants. Antonie Van Leeuwenhoek. 81:2002;665-680.
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Antonie Van Leeuwenhoek
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Wagner, M.1
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3
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0036419477
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Understanding the diversity in catabolic potential of microorganisms for the development of bioremediation strategies
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Watanabe K., Futamata H., Harayama S. Understanding the diversity in catabolic potential of microorganisms for the development of bioremediation strategies. Antonie Van Leeuwenhoek. 81:2002;655-663.
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Antonie Van Leeuwenhoek
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Watanabe, K.1
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0036425986
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Synergistic interactions in the microbial world
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Schink B. Synergistic interactions in the microbial world. Antonie Van Leeuwenhoek. 81:2002;257-261.
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Antonie Van Leeuwenhoek
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Schink, B.1
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0034886912
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Quorum-sensing in Gram-negative bacteria
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Whitehead N.A., Barnard A.M., Slater H., Simpson N.J., Salmond G.P. Quorum-sensing in Gram-negative bacteria. FEMS Microbiol. Rev. 25:2001;365-404.
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Whitehead, N.A.1
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6
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0037203773
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Structural identification of a bacterial quorum-sensing signal containing boron
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Chen X., Schauder S., Potier N., Van Dorsselaer A., Pelczer I., Bassler B.L., Hughson F.M. Structural identification of a bacterial quorum-sensing signal containing boron. Nature. 415:2002;545-549.
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Chen, X.1
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Pelczer, I.5
Bassler, B.L.6
Hughson, F.M.7
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7
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0033108071
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Towards elucidation of microbial community metabolic pathways: Unraveling the network of carbon sharing in a pollutant-degrading bacterial consortium by immunocapture and isotopic ratio mass spectrometry
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Pelz O., Tesar M., Wittich R.M., Moore E.R., Timmis K.N., Abraham W.R. Towards elucidation of microbial community metabolic pathways: unraveling the network of carbon sharing in a pollutant-degrading bacterial consortium by immunocapture and isotopic ratio mass spectrometry. Environ. Microbiol. 1:1999;167-174.
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Pelz, O.1
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Abraham, W.R.6
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8
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0036951676
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Rhodanobacter sp. strain BPC1 in a benzo[a]pyrene-mineralizing microbial consortium
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Kanaly R.A., Harayama S., Watanabe K. Rhodanobacter sp. strain BPC1 in a benzo[a]pyrene-mineralizing microbial consortium. Appl. Environ. Microbiol. 68:2002;5826-5833.
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Kanaly, R.A.1
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Watanabe, K.3
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9
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0031887954
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In situ gene expression in mixed-culture biofilms: Evidence of metabolic interactions between community members
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Møller S., Sternberg C., Andersen J.B., Christensen B.B., Ramos J.L., Givskov M., Molin S. In situ gene expression in mixed-culture biofilms: evidence of metabolic interactions between community members. Appl. Environ. Microbiol. 64:1998;721-732.
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Møller, S.1
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Givskov, M.6
Molin, S.7
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10
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0036270295
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Is there a role for quorum sensing signals in bacterial biofilms?
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Kjelleberg S., Molin S. Is there a role for quorum sensing signals in bacterial biofilms? Curr. Opin. Microbiol. 5:2002;254-258.
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Kjelleberg, S.1
Molin, S.2
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11
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0036052116
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Estimation of methanotroph abundance in a freshwater lake sediment
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Costello A.M., Auman A.J., Macalady J.L., Scow K.M., Londstrom M.E. Estimation of methanotroph abundance in a freshwater lake sediment. Environ. Microbiol. 4:2002;443-450.
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Costello, A.M.1
Auman, A.J.2
Macalady, J.L.3
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12
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0035956593
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Molecular diversity of pMMO and sMMO in a TCE-contaminated aquifer during bioremediation
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Baker P.W., Futamata H., Harayama S., Watanabe K. Molecular diversity of pMMO and sMMO in a TCE-contaminated aquifer during bioremediation. FEMS Microbiol. Ecol. 38:2001;161-167.
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Baker, P.W.1
Futamata, H.2
Harayama, S.3
Watanabe, K.4
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13
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0035491632
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Group-specific monitoring of phenol hydroxylase genes for a functional assessment of phenol-stimulated trichloroethylene bioremediation
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A significant achievement of this study was that information obtained from analysis of in situ catabolic genes was successfully used to develop a high-performance microbial community.
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Futamata H., Harayama S., Watanabe K. Group-specific monitoring of phenol hydroxylase genes for a functional assessment of phenol-stimulated trichloroethylene bioremediation. Appl. Environ. Microbiol. 67:2001;4671-4677 A significant achievement of this study was that information obtained from analysis of in situ catabolic genes was successfully used to develop a high-performance microbial community.
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(2001)
Appl. Environ. Microbiol.
, vol.67
, pp. 4671-4677
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Futamata, H.1
Harayama, S.2
Watanabe, K.3
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14
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0033981078
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Development of catechol 2,3-dioxygenase-specific primers for monitoring bioremediation by competitive quantitative PCR
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Mesarch M.B., Nakatsu C.H., Nies L. Development of catechol 2,3-dioxygenase-specific primers for monitoring bioremediation by competitive quantitative PCR. Appl. Environ. Microbiol. 66:2000;678-683.
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Mesarch, M.B.1
Nakatsu, C.H.2
Nies, L.3
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15
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0037104964
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A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene
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This study, for the first time, developed a molecular tool for assessing natural attenuation processes treating alkyl aromatic compounds under anaerobic conditions.
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Beller H.R., Kane S.R., Legler T.C., Alvarez P.J. A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene. Environ. Sci. Technol. 36:2002;3977-3984 This study, for the first time, developed a molecular tool for assessing natural attenuation processes treating alkyl aromatic compounds under anaerobic conditions.
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Environ. Sci. Technol.
, vol.36
, pp. 3977-3984
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Beller, H.R.1
Kane, S.R.2
Legler, T.C.3
Alvarez, P.J.4
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16
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0036793715
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Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA
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Nogales B., Timmis K.N., Nedwell D.B., Osborn A.M. Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA. Appl. Environ. Microbiol. 68:2002;5017-5025.
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Nogales, B.1
Timmis, K.N.2
Nedwell, D.B.3
Osborn, A.M.4
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17
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0032906465
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In situ, real-time catabolic gene expression: Extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater
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Wilson M.S., Bakermans C., Madsen E.L. In situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater. Appl. Environ. Microbiol. 65:1999;80-87.
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Wilson, M.S.1
Bakermans, C.2
Madsen, E.L.3
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18
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0035514155
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Direct detection by in situ PCR of the amoA gene in biofilm resulting from a nitrogen removal process
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This paper presents a good example of the combined use of IS-PCR and FISH, which is applicable to analysing a complex microbial community such as a biofilm.
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Hoshino T., Noda N., Tsuneda S., Hirata A., Inamori Y. Direct detection by in situ PCR of the amoA gene in biofilm resulting from a nitrogen removal process. Appl. Environ. Microbiol. 67:2001;5261-5266 This paper presents a good example of the combined use of IS-PCR and FISH, which is applicable to analysing a complex microbial community such as a biofilm.
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(2001)
Appl. Environ. Microbiol.
, vol.67
, pp. 5261-5266
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Hoshino, T.1
Noda, N.2
Tsuneda, S.3
Hirata, A.4
Inamori, Y.5
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20
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0035512205
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In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants
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Daims H., Nielsen J.L., Nielsen P.H., Schleifer K.H., Wagner M. In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Appl. Environ. Microbiol. 67:2001;5273-5284.
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Daims, H.1
Nielsen, J.L.2
Nielsen, P.H.3
Schleifer, K.H.4
Wagner, M.5
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21
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0036727261
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Abundance and phylogenetic affiliation of iron reducers in activated sludge as assessed by fluorescence in situ hybridization and microautoradiography
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Nielsen J.L., Juretschko S., Wagner M., Nielsen P.H. Abundance and phylogenetic affiliation of iron reducers in activated sludge as assessed by fluorescence in situ hybridization and microautoradiography. Appl. Environ. Microbiol. 68:2002;4629-4636.
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(2002)
Appl. Environ. Microbiol.
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, pp. 4629-4636
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Nielsen, J.L.1
Juretschko, S.2
Wagner, M.3
Nielsen, P.H.4
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22
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0036136673
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Phylogenetic identification and substrate uptake patterns of sulfate-reducing bacteria inhabiting an oxic-anoxic sewer biofilm determined by combining microautoradiography and fluorescent in situ hybridization
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Ito T., Nielsen J.L., Okabe S., Watanabe Y., Nielsen P.H. Phylogenetic identification and substrate uptake patterns of sulfate-reducing bacteria inhabiting an oxic-anoxic sewer biofilm determined by combining microautoradiography and fluorescent in situ hybridization. Appl. Environ. Microbiol. 68:2002;356-364.
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(2002)
Appl. Environ. Microbiol.
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, pp. 356-364
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Ito, T.1
Nielsen, J.L.2
Okabe, S.3
Watanabe, Y.4
Nielsen, P.H.5
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23
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0036024789
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Quantification of functional groups in activated sludge by microautoradiography
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Nielsen J.L., Nielsen P.H. Quantification of functional groups in activated sludge by microautoradiography. Water Sci. Technol. 46:2002;389-395.
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Water Sci. Technol.
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Nielsen, J.L.1
Nielsen, P.H.2
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24
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0035486692
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Stable-isotope-based labeling of styrene-degrading microorganisms in biofilters
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Alexandrino M., Knief C., Lipski A. Stable-isotope-based labeling of styrene-degrading microorganisms in biofilters. Appl. Environ. Microbiol. 67:2001;4796-4804.
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(2001)
Appl. Environ. Microbiol.
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Alexandrino, M.1
Knief, C.2
Lipski, A.3
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25
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0036200066
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Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing
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Morris S.A., Radajewski S., Willison T.W., Murrell J.C. Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing. Appl. Environ. Microbiol. 68:2002;1446-1453.
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(2002)
Appl. Environ. Microbiol.
, vol.68
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Morris, S.A.1
Radajewski, S.2
Willison, T.W.3
Murrell, J.C.4
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27
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0036840287
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RNA stable isotope probing, a novel means of linking microbial community function to phylogeny
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An excellent example of the use of stable-isotope probing coupled to reverse-transcriptase-PCR/DGGE for identifying functionally important microorganisms.
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Manefield M., Whiteley A.S., Griffiths R.I., Bailey M.J. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl. Environ. Microbiol. 68:2002;5367-5373 An excellent example of the use of stable-isotope probing coupled to reverse-transcriptase-PCR/DGGE for identifying functionally important microorganisms.
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(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 5367-5373
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Manefield, M.1
Whiteley, A.S.2
Griffiths, R.I.3
Bailey, M.J.4
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28
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0035486815
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Stable hydrogen and carbon isotope fractionation during microbial toluene degradation: Mechanistic and environmental aspects
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Morasch B., Richnow H.H., Schink B., Meckenstock R.U. Stable hydrogen and carbon isotope fractionation during microbial toluene degradation: mechanistic and environmental aspects. Appl. Environ. Microbiol. 67:2001;4842-4849.
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(2001)
Appl. Environ. Microbiol.
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Morasch, B.1
Richnow, H.H.2
Schink, B.3
Meckenstock, R.U.4
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29
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0036795084
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Carbon and hydrogen stable isotope fractionation during aerobic bacterial degradation of aromatic hydrocarbons
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Morasch B., Richnow H.H., Schink B., Vieth A., Meckenstock R.U. Carbon and hydrogen stable isotope fractionation during aerobic bacterial degradation of aromatic hydrocarbons. Appl. Environ. Microbiol. 68:2002;5191-5194.
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(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 5191-5194
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Morasch, B.1
Richnow, H.H.2
Schink, B.3
Vieth, A.4
Meckenstock, R.U.5
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30
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0035206821
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Isolate PM1 populations are dominant and novel methyl tert-butyl ether-degrading bacterial in compost biofilter enrichments
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Bruns M.A., Hanson J.R., Mefford J., Scow K.M. Isolate PM1 populations are dominant and novel methyl tert-butyl ether-degrading bacterial in compost biofilter enrichments. Environ. Microbiol. 3:2001;220-225.
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Environ. Microbiol.
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Bruns, M.A.1
Hanson, J.R.2
Mefford, J.3
Scow, K.M.4
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31
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0036135280
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Isolation and characterization of Novosphingobium sp. strain MT1, a dominant polychlorophenol-degrading strain in a groundwater bioremediation system
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Tiirola M.A., Mannisto M.K., Puhakka J.A., Kulomaa M.S. Isolation and characterization of Novosphingobium sp. strain MT1, a dominant polychlorophenol-degrading strain in a groundwater bioremediation system. Appl. Environ. Microbiol. 68:2002;173-180.
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(2002)
Appl. Environ. Microbiol.
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Tiirola, M.A.1
Mannisto, M.K.2
Puhakka, J.A.3
Kulomaa, M.S.4
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32
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0031734089
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Molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge
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Watanabe K., Teramoto M., Futamata H., Harayama S. Molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge. Appl. Environ. Microbiol. 64:1998;4396-4402.
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Watanabe, K.1
Teramoto, M.2
Futamata, H.3
Harayama, S.4
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33
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0036001073
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Enrichment versus biofilm culture: A functional and phylogenetic comparison of polycyclic aromatic hydrocarbon-degrading microbial communities
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The implication that changes in growth modes (e.g. from attached to suspended) may be one reason why environmentally relevant microorganisms are not easily enriched and isolated is interesting and useful for designing new isolation strategies.
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Stach J.E., Burns R.G. Enrichment versus biofilm culture: a functional and phylogenetic comparison of polycyclic aromatic hydrocarbon-degrading microbial communities. Environ. Microbiol. 4:2002;169-182 The implication that changes in growth modes (e.g. from attached to suspended) may be one reason why environmentally relevant microorganisms are not easily enriched and isolated is interesting and useful for designing new isolation strategies.
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Environ. Microbiol.
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Stach, J.E.1
Burns, R.G.2
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34
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0036324056
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High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates
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Connon S.A., Giovannoni S.J. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68:2002;3878-3885.
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(2002)
Appl. Environ. Microbiol.
, vol.68
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Connon, S.A.1
Giovannoni, S.J.2
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35
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0036250036
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Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia
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Janssen P.H., Yates P.S., Grinton B.E., Taylor P.M., Sait M. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl. Environ. Microbiol. 68:2002;2391-2396.
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(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 2391-2396
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Janssen, P.H.1
Yates, P.S.2
Grinton, B.E.3
Taylor, P.M.4
Sait, M.5
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36
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0036323967
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Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea
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The methods described in this paper are considered to be widely and easily applicable to the isolation of new types of microorganism from the environment.
-
Bruns A., Cypionka H., Overmann J. Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Appl. Environ. Microbiol. 68:2002;3978-3987 The methods described in this paper are considered to be widely and easily applicable to the isolation of new types of microorganism from the environment.
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(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 3978-3987
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Bruns, A.1
Cypionka, H.2
Overmann, J.3
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37
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0033678838
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Reclamation of an activated-sludge microbial consortium by selective biostimulation
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Watanabe K., Miyashita M., Harayama S. Reclamation of an activated-sludge microbial consortium by selective biostimulation. Appl. Microbiol. Biotechnol. 54:2000;719-723.
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Appl. Microbiol. Biotechnol.
, vol.54
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Watanabe, K.1
Miyashita, M.2
Harayama, S.3
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38
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0036801608
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Stable augmentation of activated sludge with foreign catabolic genes harboured by an indigenous dominant bacterium
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Watanabe K., Teramoto M., Harayama S. Stable augmentation of activated sludge with foreign catabolic genes harboured by an indigenous dominant bacterium. Environ. Microbiol. 4:2002;577-583.
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(2002)
Environ. Microbiol.
, vol.4
, pp. 577-583
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Watanabe, K.1
Teramoto, M.2
Harayama, S.3
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39
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0035476674
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Gene expression monitoring in soils by mRNA analysis and gene lux fusions
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Sayler G.S., Fleming J.T., Nivens D.E. Gene expression monitoring in soils by mRNA analysis and gene lux fusions. Curr. Opin. Biotechnol. 12:2001;455-460.
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(2001)
Curr. Opin. Biotechnol.
, vol.12
, pp. 455-460
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Sayler, G.S.1
Fleming, J.T.2
Nivens, D.E.3
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41
-
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0035291227
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Biological sensor for sucrose availability: Relative sensitivities of various reporter genes
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This study showed that sensitivities to a substrate and the minimum numbers of cells required for bioreporting are different in different reporting systems, suggesting the need for careful selection of bioreporting systems in the environment.
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Miller W.G., Brandl M.T., Quinones B., Lindow S.E. Biological sensor for sucrose availability: relative sensitivities of various reporter genes. Appl. Environ. Microbiol. 67:2001;1308-1317 This study showed that sensitivities to a substrate and the minimum numbers of cells required for bioreporting are different in different reporting systems, suggesting the need for careful selection of bioreporting systems in the environment.
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(2001)
Appl. Environ. Microbiol.
, vol.67
, pp. 1308-1317
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Miller, W.G.1
Brandl, M.T.2
Quinones, B.3
Lindow, S.E.4
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42
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0036300648
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Solid-phase contact assay that uses a lux-marked Nitrosomonas europaea reporter strain to estimate toxicity of bioavailable linear alkylbenzene sulfonate in soil
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Brandt K.K., Pedersen A., Sorensen J. Solid-phase contact assay that uses a lux-marked Nitrosomonas europaea reporter strain to estimate toxicity of bioavailable linear alkylbenzene sulfonate in soil. Appl. Environ. Microbiol. 68:2002;3502-3508.
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(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 3502-3508
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Brandt, K.K.1
Pedersen, A.2
Sorensen, J.3
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44
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0036210998
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Development and characterization of a green fluorescent protein-based bacterial biosensor for bioavailable toluene and related compounds
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Stiner L., Halverson L.J. Development and characterization of a green fluorescent protein-based bacterial biosensor for bioavailable toluene and related compounds. Appl. Environ. Microbiol. 68:2002;1962-1971.
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(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 1962-1971
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Stiner, L.1
Halverson, L.J.2
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45
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0036245081
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Assessing the role of Pseudomonas aeruginosa surface-active gene expression in hexadecane biodegradation in sand
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Holden P.A., LaMontagne M.G., Bruce A.K., Miller W.G., Lindow S.E. Assessing the role of Pseudomonas aeruginosa surface-active gene expression in hexadecane biodegradation in sand. Appl. Environ. Microbiol. 68:2002;2509-2518.
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(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 2509-2518
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Holden, P.A.1
LaMontagne, M.G.2
Bruce, A.K.3
Miller, W.G.4
Lindow, S.E.5
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46
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0036727219
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Construction and characterization of a proU-gfp transcriptional fusion that measures water availability in a microbial habitat
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Axtell C.A., Beattie G.A. Construction and characterization of a proU-gfp transcriptional fusion that measures water availability in a microbial habitat. Appl. Environ. Microbiol. 68:2002;4604-4612.
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