Hohnstock-Ashe AM, Plummer SM, Yager RM, Baveye P, Madsen EL (2001) Further biogeochemical characterization of a trichloroethene-contaminated fractured dolomite aquifer: electron
source and microbial communities involved in reductive dechlorination. Environ Sci Technol
35:4449–4456
Huang L-N, Zhou W-H, Hallberg KB, Wan C-Y, Li J, Shu W-S (2011) Spatial and temporal
analysis of the microbial community in the tailings of a Pb-Zn mine generating acidic drainage.
Appl Environ Microbiol 77:5540–5544
HuiJie L, Caiyun Y, Yun T, Tianling Z (2011) Using population dynamics analysis by DGGE to
design the bacterial consortium isolated from mangrove sediments for biodegradation of PAHs.
Int Biodeterior Biodegrad 65:269–275
Jakobs-Schonwandt D, Mathies H, Abraham W-R, Pritzkow W, Stephan I, Noll M (2010) Biodegradation of a biocide (Cu-N-cyclohexyldiazenium dioxide) component of a wood preservative
by a defined soil bacterial community. Appl Environ Microbiol 78:8076–8083
Jardillier L, Boucher D, Personnic S, Jacquet S, Thenot A, Sargos D (2005) Relative importance of
nutrients and mortality factors on prokaryotic community composition in two lakes of different
trophic status: microcosm experiments. FEMS Microbiol Ecol 53:429–443
Kauppinen J, Pelkonen J, Katila MJ (1994) RFLP analysis of Mycobacterium malmoense strains
using ribosomal RNA gene probes: an additional tool to examine intraspecies variation. J
Microbiol Methods 19:261–267
Kent AD, Smith DJ, Benson BJ, Triplett EW (2003) Web-based phylogenetic assignment tool for
analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Appl Environ Microbiol 69:6768–6776
Keum YS, Seo JS, Qing XL, Kim JH (2008) Comparative metabolomic analysis of Sinorhizobium
sp. C4 during the degradation of phenanthrene. Appl Microbiol Biotechnol 80:863–872
Kikuchi T, Iwasaki K, Nishihara H, Takamura Y, Yagi O (2002) Quantitative and rapid detection of
the trichloroethylene-degrading bacterium Methylocystis sp. M in groundwater by real-time
PCR. Appl Microbiol Biotechnol 59:731–736
Kim S II, Kim SJ, Nam MH (2002) Proteome analysis of aniline-induced proteins in Acinetobacter
lwoffi K24. Curr Microbiol 44:61–66
Kim J, Koo S-Y, Kim J-Y, Lee E-H, Lee S-D, Ko K-S, Ko D-C, Cho K-S (2009) Influence of acid
mine drainage on microbial communities in stream and groundwater samples at Guryong Mine,
South Korea. Environ Geol 58:1567–1574
Kimura S, Bryan CG, Hallberg KB, Johnson DB (2011) Biodiversity and geochemistry of an
extremely acidic, low-temperature subterranean environment sustained by chemolithotrophy.
Environ Microbiol 13:2092–2104
Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H (2004) Methods of studying
soil microbial diversity. J Microbiol Methods 58:169–188
Kita-Tsukamoto K, Wada M, Yao K, Kamiya A, Yoshizawa S, Uchiyama N (2006) Rapid
identification of marine bioluminescent bacteria by amplified 16S ribosomal RNA gene restriction analysis. FEMS Microbiol Lett 256:298–303
Kjoller R, Rosendahl S (2000) Detection of arbuscular mycorrhizal fungi (Glomales) in roots by
nested PCR and SSCP (single stranded conformation polymorphism). Plant Soil 226:189–196
Kleikemper J, Schroth MH, Sigler WV, Schmucki M, Bernasconi SM, Zeyer J (2002) Activity and
diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer. Appl
Environ Microbiol 68:1516–1523
Kotsyurbenko OR, Chin KJ, Glagolev MV, Stubner S, Simankova MV, Nozhevnikova AN (2004)
Acetoclastic and hydrogenotrophic methane production and methanogenic populations in an
acidic West-Siberian peat bog. Environ Microbiol 6:1159–1173
Krizova J, Spanova A, Rittich B (2006) Evaluation of amplified ribosomal DNA restriction analysis
(ARDRA) and species-specific PCR for identification of Bifidobacterium species. Syst Appl
Microbiol 29:36–44
Kuhner S, Wohlbrand L, Fritz I (2005) Substrate-dependent regulation of anaerobic degradation
pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J Bacteriol
187:1493–1503
18 Molecular Technologies for Assessment of Bioremediation and. . .
469
source and microbial communities involved in reductive dechlorination. Environ Sci Technol
35:4449–4456
Huang L-N, Zhou W-H, Hallberg KB, Wan C-Y, Li J, Shu W-S (2011) Spatial and temporal
analysis of the microbial community in the tailings of a Pb-Zn mine generating acidic drainage.
Appl Environ Microbiol 77:5540–5544
HuiJie L, Caiyun Y, Yun T, Tianling Z (2011) Using population dynamics analysis by DGGE to
design the bacterial consortium isolated from mangrove sediments for biodegradation of PAHs.
Int Biodeterior Biodegrad 65:269–275
Jakobs-Schonwandt D, Mathies H, Abraham W-R, Pritzkow W, Stephan I, Noll M (2010) Biodegradation of a biocide (Cu-N-cyclohexyldiazenium dioxide) component of a wood preservative
by a defined soil bacterial community. Appl Environ Microbiol 78:8076–8083
Jardillier L, Boucher D, Personnic S, Jacquet S, Thenot A, Sargos D (2005) Relative importance of
nutrients and mortality factors on prokaryotic community composition in two lakes of different
trophic status: microcosm experiments. FEMS Microbiol Ecol 53:429–443
Kauppinen J, Pelkonen J, Katila MJ (1994) RFLP analysis of Mycobacterium malmoense strains
using ribosomal RNA gene probes: an additional tool to examine intraspecies variation. J
Microbiol Methods 19:261–267
Kent AD, Smith DJ, Benson BJ, Triplett EW (2003) Web-based phylogenetic assignment tool for
analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Appl Environ Microbiol 69:6768–6776
Keum YS, Seo JS, Qing XL, Kim JH (2008) Comparative metabolomic analysis of Sinorhizobium
sp. C4 during the degradation of phenanthrene. Appl Microbiol Biotechnol 80:863–872
Kikuchi T, Iwasaki K, Nishihara H, Takamura Y, Yagi O (2002) Quantitative and rapid detection of
the trichloroethylene-degrading bacterium Methylocystis sp. M in groundwater by real-time
PCR. Appl Microbiol Biotechnol 59:731–736
Kim S II, Kim SJ, Nam MH (2002) Proteome analysis of aniline-induced proteins in Acinetobacter
lwoffi K24. Curr Microbiol 44:61–66
Kim J, Koo S-Y, Kim J-Y, Lee E-H, Lee S-D, Ko K-S, Ko D-C, Cho K-S (2009) Influence of acid
mine drainage on microbial communities in stream and groundwater samples at Guryong Mine,
South Korea. Environ Geol 58:1567–1574
Kimura S, Bryan CG, Hallberg KB, Johnson DB (2011) Biodiversity and geochemistry of an
extremely acidic, low-temperature subterranean environment sustained by chemolithotrophy.
Environ Microbiol 13:2092–2104
Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H (2004) Methods of studying
soil microbial diversity. J Microbiol Methods 58:169–188
Kita-Tsukamoto K, Wada M, Yao K, Kamiya A, Yoshizawa S, Uchiyama N (2006) Rapid
identification of marine bioluminescent bacteria by amplified 16S ribosomal RNA gene restriction analysis. FEMS Microbiol Lett 256:298–303
Kjoller R, Rosendahl S (2000) Detection of arbuscular mycorrhizal fungi (Glomales) in roots by
nested PCR and SSCP (single stranded conformation polymorphism). Plant Soil 226:189–196
Kleikemper J, Schroth MH, Sigler WV, Schmucki M, Bernasconi SM, Zeyer J (2002) Activity and
diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer. Appl
Environ Microbiol 68:1516–1523
Kotsyurbenko OR, Chin KJ, Glagolev MV, Stubner S, Simankova MV, Nozhevnikova AN (2004)
Acetoclastic and hydrogenotrophic methane production and methanogenic populations in an
acidic West-Siberian peat bog. Environ Microbiol 6:1159–1173
Krizova J, Spanova A, Rittich B (2006) Evaluation of amplified ribosomal DNA restriction analysis
(ARDRA) and species-specific PCR for identification of Bifidobacterium species. Syst Appl
Microbiol 29:36–44
Kuhner S, Wohlbrand L, Fritz I (2005) Substrate-dependent regulation of anaerobic degradation
pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J Bacteriol
187:1493–1503
18 Molecular Technologies for Assessment of Bioremediation and. . .
469