Biodegradation of pyrene and catabolic genes in contaminated soils cultivated with Lolium multiflorum L

Arthur EL, Rice PJ, Rice PJ, Anderson TA, Baladi SM, Henderson KLD, Coats JR (2005) Phytoremediation—an overview. Crit Rev Plant Sci 24:109–122

Baldwin BR, Nakatsu CH, Nies L (2003) Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR. Appl Environ Microb 69:3350–3358

Brinch UC, Ekelund F, Jacobsen CS (2002) Method for spiking soil samples with organic compounds. Appl Environ Microb 68:1808–1816

Chadhain SMN, Sean Norman R, Pesce KV, Kukor JJ, Zylstra GJ (2006) Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. Appl Environ Microb 72:4078–4087

Hamamura N, Olson SH, Ward DM, Inskeep WP (2006) Microbial population dynamics associated with crude-oil biodegradation in diverse soils. Appl Environ Microb 72:6316–6324

Hamann C, Hegemann J, Hildebrandt A (1999) Detection of polycyclic aromatic hydrocarbon degrading genes in different soil bacteria by polymerase chain reaction and DNA hybridization. FEMS Microbiol Lett 173:255–263

Hatzinger PB, Alexander P (1995) Effect of ageing of chemicals in soil on their biodegradability and extractability. Environ Sci Technol 29:537–545

Hutchinson SL, Schwab AP, Banks HK (2003) Biodegradation of ptroleum hydrocarbons in the rhizosphere. In: McCutcheon SC, Schnoor JL (eds) Phytoremediation: transformation and control of contaminants. Wiley-Interscience, Inc., Hoboken, NJ, pp 355–385

Johnsen AR, Lipthay JR, Sørensen SJ, Ekelund F, Christensen P, Andersen O, Karlson U, Jacobsen CS (2006) Microbial degradation of street dust polycyclic aromatic hydrocarbons in microcosms simulating diffuse pollution of urban soil. Environ Microbiol 8:535–545

Johnsen AR, Schmidt S, Hybholt TK, Henriksen S, Jacobsen CS, Andersen O (2007) Strong impact on the polycyclic aromatic hydrocarbon (PAH)-degrading community of a PAH-polluted soil but marginal effect on PAH degradation when priming with bioremediated soil dominated by mycobacteria. Appl Environ Microbiol 73:1474–1480

Joner EJ, Leyval C (2003) Rhizosphere gradients of polycyclic aromatic hydrocarbon (PAH) dissipation in two industrial soils and the impact of arbuscular Mycorrhiza. Environ Sci Technol 37:2371–2375

Jouanneau Y, Willison JC, Mayer C, Krivobok S, Chevron N, Besombes JL, Blake G (2005) Stimulation of pyrene mineralization in freshwater sediments by bacterial and plant bioaugmentation. Environ Sci Technol 39:5729–5735

Kamath R, Schnoor JL, Alvarez PJJ (2004) Effect of root-derived substrates on the expression of nah-lux genes in pseudomonas fluorescens HK44: implications for PAH biodegradation in the rhizosphere. Environ Sci Technol 38:1740–1745

Kaplan CW, Kitts CL (2004) Bacterial succession in a petroleum land treatment unit. Appl Environ Microbiol 70:1777–1786

Khan AA, Wang RF, Cao WW, Doerge DR, Wennerstrom D, Cerniglia CE (2001) Molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 67:3577–3585

Khan S, Cao Q, Chen B, Zhu YG (2006) Humic acids increase the phytoavailability of Cd and Pb to wheat plants cultivated in freshly spiked, contaminated soil. J Soils Sediments 6:236–242

Khan S, Cao Q, Hesham AB, Xia Y, He J (2007) Soil enzymatic activities and microbial community structure with different application rates of Cd and Pb. J Environ Sci 19:834–840

Khan S, Cao Q, Lin AJ, Zhu YG (2008a) Concentrations and bioaccessibility of polycyclic aromatic hydrocarbons in wastewater-irrigated soil using in vitro gastro-intestinal test. Environ Sci Pollut Res 15:344–353

Khan S, Aijun L, Zhang S, Hu Q, Zhu YG (2008b) Accumulation of polycyclic aromatic hydrocarbons and heavy metals in lettuce grown in contaminated soils from long-term wastewater irrigation. J Hazard Mat 152:506–515

Kim SJ, Kweon O, Freeman JP, Jones RC, Adjei MD, Jhoo JW, Edmondson RD, Cerniglia CE (2006) Molecular cloning and expression of genes encoding a novel dioxygenase involved in low- and high-molecular-weight polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Appl Environ Microbiol 72:1045–1054

Krivobok S, Kuony S, Meyer C, Louwagie M, Willison JC, Jouanneau Y (2003) Identification of pyrene-induced proteins in Mycobacterium sp strain 6PY1: evidence for two ring-hydroxylating dioxygenases. J Bacteriol 185:3828–3841

Laurie AD, Lloyd-Jones G (1999) The phn genes of Burkholderia sp. strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J Bacteriol 181:531–540

Laurie AD, Lloyd-Jones G (2000) Quantification of phnAc and nahAc in contaminated New Zealand soils by competitive PCR. Appl Environ Microbiol 66:1814–1817

Leys NMEJ, Bastiaens L, Verstraere W, Springael D (2005) Influence of the carbon/nitrogen/phosphorus ratio on polycyclic aromatic hydrocarbons degradation by Mycobacterium and Sphingomonas in soil. Appl Environ Microbiol 66:726–736

Lloyd-Jones G, Laurie AD, Hunter DWF, Fraser R (1999) Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils. FEMS Microbiol Ecol 29:69–79

Luca C, Daniele A, Marisa M, Comi G (2002) An application of DGGE analysis to profile the yeast population in raw milk. Int Dairy J 12:407–411

Macleod CJA, Semple KT (2006) The influence of single and multiple applications of pyrene on the evolution of pyrene catabolism in soil. Environ Pollut 139:455–460

Moreau CJ, Klerks PL, Haas CN (1999) Interaction between phenanthrene and zinc in their toxicity to the sheepshead minnow (Cyprinodon variegatus). Arch Environ Contam Toxicol 37:251–257

Mueller KE, Shann JR (2006) PAH dissipation in spiked soil: impacts of bioavailability, microbial activity, and trees. Chemosphere 64:10061014

Muyzer G, de EC Waal, 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

Rentz JA, Alvarez P, Schnoor JL (2004) Repression of Pseudomonas putida phenanthrene-degrading activity by plant root extracts and exudates. Environ Microbiol 6:574–583

Shen G, Lu Y, Zhou Q, Hong J (2005) Interaction of polycyclic aromatic hydrocarbons and heavy metals on soil enzyme. Chemosphere 61:1175–1182

Shen G, Lu Y, Hong J (2006) Combined effect of heavy metals and polycyclic aromatic hydrocarbons on urease activity in soil. Ecotox Environ Safety 63:474–480

Stapleton RD, Savage DC, Sayler GS, Stacey G (1998) Biodegradation of aromatic hydrocarbons in an extremely acidic environment. Appl Environ Microbiol 64:4180–4184

Stuart-Keil KG, Hohnstock AM, Drees KP, Herrick JB, Madsen EL (1998) Plasmids responsible for horizontal transfer of naphthalene catabolism genes between bacteria at a coal tar-contaminated site are homologous to pDTG1 from Pseudomonas putida NCIB 9816–4. Appl Environ Microbiol 64:3633–3640

Su YH, Zhu YG (2007) Transport mechanisms for the uptake of organic compounds by rice (Oryza sativa) roots. Environ Pollut 148:94–100

Tang L, Tang XY, Zhu YG, Zheng MH, Miao QL (2005) Contamination of polycyclic aromatic hydrocarbons (PAHs) in urban soils in Beijing, China. Environ Int 31:822–828

US-EPA (2000) Introduction to phytoremediation. US Environmental Protection Agency, Publication No. 600/R-99/107

Widada J, Nojiri H, Kasuga K, Yoshida T, Habe H, Omori T (2002) Molecular detection and diversity of polycyclic aromatic hydrocarbon-degrading bacteria isolated from geographically diverse sites. Appl Environ Microbiol 58:202–209

Wu Y, Luo Y, Zou D, Ni J, Liu W, Teng Y, Li Z (2008) Bioremediation of polycyclic aromatic hydrocarbons contaminated soil with Monilinia sp.: degradation and microbial community analysis. Biodegradation 19:247–257

Xu SY, Chen YX, Wu WX, Wang KX, Lin Q, Liang XQ (2006) Enhanced dissipation of phenanthrene and pyrene in spiked soils by combined plants cultivation. Sci Total Environ 363:206–215

Yi H, Crowley DE (2007) Biostimulation of PAH degradation with plants containing high concentrations of linoleic acid. Environ Sci Technol 41:4382–4388

Yoon J, Cao X, Zhou Q, Ma LM (2006) Accumulation of Pb, Cu, and Zn in native plants growing on a contaminated Florida site. Sci Total Environ 368:456–464