Corsini A, Cavalca L, Zaccheo P, Crippa L, Andreoni V (2011) Influence of microorganisms on
arsenic mobilization and speciation in a submerged contaminated soil: effects of citrate. Appl
Soil Ecol 49:99–106
Coulon F, Chronopoulou PM, Fahy A, Paisse S, Goni-Urriza M, Peperzak L (2012) Central role of
dynamic tidal biofilms dominated by aerobic hydrocarbonoclastic bacteria and diatoms in the
biodegradation of hydrocarbons in coastal mudflats. Appl Environ Microbiol 78:3638–3648
Cummings DE, Snoeyenbos-West OL, Newby DT, Niggemyer AM, Lovley DR, Achenbachl LA
(2003) Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments
ascertained by 16S rDNA analyses. Microb Ecol 46:257–269
Cunliffe M, Kertesz M (2006) Effect of Sphingobium yanoikuyae B1 inoculation on bacterial
community dynamics and polycyclic aromatic hydrocarbon degradation in aged and freshly
PAH-contaminated soils. Environ Pollut 144:228–237
Da Silva M, Alvarez P (2004) Enhanced anaerobic biodegradation of benzene-toluene-ethyl
benzene xyleme ethanol mixtures in bioaugmented aquifer columns. Appl Environ Microbiol
70:4720–4726
Dahllof I, Harriet B, Staffan K (2000) rpo B-based microbial community analysis avoids limitations
inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66:3376–3380
DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL (2007) High-density
universal 16S rRNA microarray analysis reveals broader diversity than typical clone library
when sampling the environment. Microb Ecol 53:371–383
Dharmadi Y, Gonzalez R (2004) DNA microarrays: experimental issues, data analysis, and
application to bacterial systems. Biotechnol Prog 20:1309–1324
Diaz E (2004) Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. Int
Microbiol 7:173–180
Dojka MA, Hugenholtz P, Haack SK, Pace NR (1999) Microbial diversity in a hydrocarbon and
chlorinated-solvent contaminated aquifer undergoing intrinsic bioremediation. Appl Environ
Microbiol 64:3869–3877
Dokić L, Savić M, Narančić T, Vasiljević B (2010) Metagenomic analysis of soil microbial
communities. Arch Biol Sci Belgrade 62(3):559–564
Dua M, Singh A, Sethunathan N (2002) Biotechnology and bioremediation: successes and limitations. Appl Microbiol Biotechnol 59:143–152
Dubey SK, Tripathi AK, Upadhyay SN (2006) Exploration of soil bacterial communities for their
potential as bioresource. Bioresour Technol 97:2217–2224
Dunbar J, Ticknor LO, Kuske CR (2000) Assessment of microbial diversity in four southwestern
United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl Environ
Microbiol 66:2943–2950
Edgcomb VP, McDonald JH, Devereux R, Smith DW (1999) Estimation of bacterial cell numbers
in humic acid-rich salt marsh sediments with probes directed to 16S ribosomal DNA. Appl
Environ Microbiol 65:1516–1523
El-Latif Hesham A, Khan S, Liu X, Zhang Y, Wang Z, Yang M (2006) Application of PCRDGGE
to analyse the yeast population dynamics in slurry reactors during degradation of polycyclic
aromatic hydrocarbons in weathered oil. Yeast 23:879–887
Evans FF, Rosado AS, Sebastian GV, Casella R, Machado PLOA, Holmstrom C (2004) Impact of
oil contamination and biostimulation on the diversity of indigenous bacterial communities in
soil microcosms. FEMS Microbiol Ecol 49:295–305
Fahy A, Lethbridge G, Earle R, Ball AS, Timmis KN, McGenity TJ (2005) Effects of long-term
benzene pollution on bacterial diversity and community structure in groundwater. Environ
Microbiol 7:1192–1199
Farrell M, Griffith GW, Hobbs PJ, Perkins WT, Jones DL (2010) Microbial diversity and activity
are increased by compost amendment of metal-contaminated soil. FEMS Microbiol Ecol
71:94–105
Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of
microbial diversity and its application to freshwater bacterial communities. Appl Environ
Microbiol 65:4630–4636
18 Molecular Technologies for Assessment of Bioremediation and. . .
467
arsenic mobilization and speciation in a submerged contaminated soil: effects of citrate. Appl
Soil Ecol 49:99–106
Coulon F, Chronopoulou PM, Fahy A, Paisse S, Goni-Urriza M, Peperzak L (2012) Central role of
dynamic tidal biofilms dominated by aerobic hydrocarbonoclastic bacteria and diatoms in the
biodegradation of hydrocarbons in coastal mudflats. Appl Environ Microbiol 78:3638–3648
Cummings DE, Snoeyenbos-West OL, Newby DT, Niggemyer AM, Lovley DR, Achenbachl LA
(2003) Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments
ascertained by 16S rDNA analyses. Microb Ecol 46:257–269
Cunliffe M, Kertesz M (2006) Effect of Sphingobium yanoikuyae B1 inoculation on bacterial
community dynamics and polycyclic aromatic hydrocarbon degradation in aged and freshly
PAH-contaminated soils. Environ Pollut 144:228–237
Da Silva M, Alvarez P (2004) Enhanced anaerobic biodegradation of benzene-toluene-ethyl
benzene xyleme ethanol mixtures in bioaugmented aquifer columns. Appl Environ Microbiol
70:4720–4726
Dahllof I, Harriet B, Staffan K (2000) rpo B-based microbial community analysis avoids limitations
inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66:3376–3380
DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL (2007) High-density
universal 16S rRNA microarray analysis reveals broader diversity than typical clone library
when sampling the environment. Microb Ecol 53:371–383
Dharmadi Y, Gonzalez R (2004) DNA microarrays: experimental issues, data analysis, and
application to bacterial systems. Biotechnol Prog 20:1309–1324
Diaz E (2004) Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. Int
Microbiol 7:173–180
Dojka MA, Hugenholtz P, Haack SK, Pace NR (1999) Microbial diversity in a hydrocarbon and
chlorinated-solvent contaminated aquifer undergoing intrinsic bioremediation. Appl Environ
Microbiol 64:3869–3877
Dokić L, Savić M, Narančić T, Vasiljević B (2010) Metagenomic analysis of soil microbial
communities. Arch Biol Sci Belgrade 62(3):559–564
Dua M, Singh A, Sethunathan N (2002) Biotechnology and bioremediation: successes and limitations. Appl Microbiol Biotechnol 59:143–152
Dubey SK, Tripathi AK, Upadhyay SN (2006) Exploration of soil bacterial communities for their
potential as bioresource. Bioresour Technol 97:2217–2224
Dunbar J, Ticknor LO, Kuske CR (2000) Assessment of microbial diversity in four southwestern
United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl Environ
Microbiol 66:2943–2950
Edgcomb VP, McDonald JH, Devereux R, Smith DW (1999) Estimation of bacterial cell numbers
in humic acid-rich salt marsh sediments with probes directed to 16S ribosomal DNA. Appl
Environ Microbiol 65:1516–1523
El-Latif Hesham A, Khan S, Liu X, Zhang Y, Wang Z, Yang M (2006) Application of PCRDGGE
to analyse the yeast population dynamics in slurry reactors during degradation of polycyclic
aromatic hydrocarbons in weathered oil. Yeast 23:879–887
Evans FF, Rosado AS, Sebastian GV, Casella R, Machado PLOA, Holmstrom C (2004) Impact of
oil contamination and biostimulation on the diversity of indigenous bacterial communities in
soil microcosms. FEMS Microbiol Ecol 49:295–305
Fahy A, Lethbridge G, Earle R, Ball AS, Timmis KN, McGenity TJ (2005) Effects of long-term
benzene pollution on bacterial diversity and community structure in groundwater. Environ
Microbiol 7:1192–1199
Farrell M, Griffith GW, Hobbs PJ, Perkins WT, Jones DL (2010) Microbial diversity and activity
are increased by compost amendment of metal-contaminated soil. FEMS Microbiol Ecol
71:94–105
Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of
microbial diversity and its application to freshwater bacterial communities. Appl Environ
Microbiol 65:4630–4636
18 Molecular Technologies for Assessment of Bioremediation and. . .
467