Moriya Y, Shigemizu D, Hattori M, Tokimatsu T, Kotera M, Goto S, Kanehisa M (2010) PathPred:
an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res 38:1–6
Moyer CL, Tiedje JM, Dobbs FC, Karl DM (1996) A computer-simulated restriction fragment
length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected
tetraneric restriction enzymes for studies of microbial diversity in nature. Appl Environ
Microbiol 62:2501–2507
Muffler A, Bettermann S, Haushalter M (2002) Genomewide transcription profiling of Corynebacterium glutamicum after heat shock and during growth on acetate and glucose. J Biotechnol
98:255–268
Muyzer G, de Waal DC, Uitterlinden AG (1993) Profiling of complex microbial populations by
denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes
coding for 16S rRNA. Appl Environ Microbiol 59:695–700
Nancucheo I, Johnson DB (2011) Selective removal of transition metals from acidic mine waters by
novel consortia of acidophilic sulfidogenic bacteria. Microb Biotechnol 5:34–44
Nyyssönen M, Piskonen R, Itävaara M (2006) A targeted real-time PCR assay for studying
naphthalene degradation in the environment. Microb Ecol 52:533–543
Onda S, Hiraishi A, Matsuo Y, Takii S (2002) Polyphasic approaches to the identification of
predominant polyphosphate-accumulating organisms in a laboratory-scale anaerobic/aerobic
activated sludge system. J Gen Appl Microbiol 48:43–54
Osborn AM, Moore ERB, Timmis KN (2000) An evaluation of terminal-restriction fragment length
polymorphisms (TRFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2:39–50
Palleroni NJ (1993) Structure of the bacterial genome. In: Goodfellow M, O’Donnell AG (eds)
Handbook of new bacterial systematic. Academic Press, London, pp 57–151
Park SJ, Lee SY, Cho J (2005) Global physiological understanding and metabolic engineering of
microorganisms based on omics studies. Appl Microbiol Biotechnol 68:567–579
Pazos F, Valencia A, De Lorenzo V (2003) The organization of the microbial biodegradation
network from a systems-biology perspective. EMBO Rep 4:994–999
Pazos F, Guijas D, Valencia A, De Lorenzo V (2005) Meta Router: bioinformatics for bioremediation. Nucleic Acids Res 33:D588–D592
Peters S, Koschinsky S, Schwieger F, Tebbe CC (2000) Succession of microbial communities
during hot composting as detected by PCR-single-strand-conformation polymorphism based
genetic profiles of small-subunit rRNA genes. Appl Environ Microbiol 66:930–936
Pieper DH, Reineke W (2000) Engineering bacteria for bioremediation. Curr Opin Biotechnol
11:262–270
Popp J, Peto K, Nagy J (2013) Pesticide productivity and food security: a review. Agron Sustain
Dev 33:243–255
Queyrel W, Habets F, Blanchoud H, Ripoche D, Launay M (2016) Pesticide fate modeling in soils
with the crop model STICS: feasibility for assessment of agricultural practices. Sci Total
Environ 542:787–802
Rajendhran J, Gunasekaran P (2011) Microbial phylogeny and diversity: small subunit ribosomal
RNA sequence analysis and beyond. Microbiol Res 166:99–110
Ralebitso TK, Roling WF, Braster M, Senior E, van Verseveld HW (2000) 16S rDNA based
characterization of BTX-catabolizing microbial associations isolated from a South African
sandy soil. Biodegradation 11:351–357
Ranjard L, Brothier E, Nazaret S (2000) Sequencing bands of ribosomal intergenic spacer analysis
fingerprints for characterization and microscale distribution of soil bacterium populations
responding to mercury spiking. Appl Environ Microbiol 66:5334–5339
Reardon CL, Cummings DE, Petzke LM, Kinsall BL, Watson DB, Peyton BM (2004) Composition
and diversity of microbial communities recovered from surrogate minerals incubated in an
acidic uranium-contaminated aquifer. Appl Environ Microbiol 70:6037–6046
18 Molecular Technologies for Assessment of Bioremediation and. . .
471
an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res 38:1–6
Moyer CL, Tiedje JM, Dobbs FC, Karl DM (1996) A computer-simulated restriction fragment
length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected
tetraneric restriction enzymes for studies of microbial diversity in nature. Appl Environ
Microbiol 62:2501–2507
Muffler A, Bettermann S, Haushalter M (2002) Genomewide transcription profiling of Corynebacterium glutamicum after heat shock and during growth on acetate and glucose. J Biotechnol
98:255–268
Muyzer G, de Waal DC, Uitterlinden AG (1993) Profiling of complex microbial populations by
denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes
coding for 16S rRNA. Appl Environ Microbiol 59:695–700
Nancucheo I, Johnson DB (2011) Selective removal of transition metals from acidic mine waters by
novel consortia of acidophilic sulfidogenic bacteria. Microb Biotechnol 5:34–44
Nyyssönen M, Piskonen R, Itävaara M (2006) A targeted real-time PCR assay for studying
naphthalene degradation in the environment. Microb Ecol 52:533–543
Onda S, Hiraishi A, Matsuo Y, Takii S (2002) Polyphasic approaches to the identification of
predominant polyphosphate-accumulating organisms in a laboratory-scale anaerobic/aerobic
activated sludge system. J Gen Appl Microbiol 48:43–54
Osborn AM, Moore ERB, Timmis KN (2000) An evaluation of terminal-restriction fragment length
polymorphisms (TRFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2:39–50
Palleroni NJ (1993) Structure of the bacterial genome. In: Goodfellow M, O’Donnell AG (eds)
Handbook of new bacterial systematic. Academic Press, London, pp 57–151
Park SJ, Lee SY, Cho J (2005) Global physiological understanding and metabolic engineering of
microorganisms based on omics studies. Appl Microbiol Biotechnol 68:567–579
Pazos F, Valencia A, De Lorenzo V (2003) The organization of the microbial biodegradation
network from a systems-biology perspective. EMBO Rep 4:994–999
Pazos F, Guijas D, Valencia A, De Lorenzo V (2005) Meta Router: bioinformatics for bioremediation. Nucleic Acids Res 33:D588–D592
Peters S, Koschinsky S, Schwieger F, Tebbe CC (2000) Succession of microbial communities
during hot composting as detected by PCR-single-strand-conformation polymorphism based
genetic profiles of small-subunit rRNA genes. Appl Environ Microbiol 66:930–936
Pieper DH, Reineke W (2000) Engineering bacteria for bioremediation. Curr Opin Biotechnol
11:262–270
Popp J, Peto K, Nagy J (2013) Pesticide productivity and food security: a review. Agron Sustain
Dev 33:243–255
Queyrel W, Habets F, Blanchoud H, Ripoche D, Launay M (2016) Pesticide fate modeling in soils
with the crop model STICS: feasibility for assessment of agricultural practices. Sci Total
Environ 542:787–802
Rajendhran J, Gunasekaran P (2011) Microbial phylogeny and diversity: small subunit ribosomal
RNA sequence analysis and beyond. Microbiol Res 166:99–110
Ralebitso TK, Roling WF, Braster M, Senior E, van Verseveld HW (2000) 16S rDNA based
characterization of BTX-catabolizing microbial associations isolated from a South African
sandy soil. Biodegradation 11:351–357
Ranjard L, Brothier E, Nazaret S (2000) Sequencing bands of ribosomal intergenic spacer analysis
fingerprints for characterization and microscale distribution of soil bacterium populations
responding to mercury spiking. Appl Environ Microbiol 66:5334–5339
Reardon CL, Cummings DE, Petzke LM, Kinsall BL, Watson DB, Peyton BM (2004) Composition
and diversity of microbial communities recovered from surrogate minerals incubated in an
acidic uranium-contaminated aquifer. Appl Environ Microbiol 70:6037–6046
18 Molecular Technologies for Assessment of Bioremediation and. . .
471