• [1]
    Salt, D.E., Blaylock, M., Kumar, N.P.B.A., Dushenkov, V., Ensley, B.D., Chet, I., Raskin, I. (1995) Phytoremediation: a novel strategy for the removal of toxic metals from the environment using plants. Biotechnology 13, 468474.
  • [2]
    Babich, H., Stotzky, G. (1985) Heavy metal toxicity to microbe-mediated ecologic processes: A review and potential application to regulatory policies. Environ. Res. 36, 111137.
  • [3]
    Baath, E. (1989) Effects of heavy metals in soil microbial processes and populations (a review). Water. Air Soil Pollut. 47, 335379.
  • [4]
    Giller, K.E., Witter, E., McGrath, S.P. (1998) Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: a review. Soil Biol. Biochem. 30, 13891414.
  • [5]
    J. Vangronsveld, S.D. Cunningham (1998) Introduction to the concepts. (Eds. J. Vangronsveld, S. Cunningham), Metal-Contaminated Soils: In Situ Inactivation and Phytorestoration. Springer, New York. 1–15.
  • [6]
    Robinson, B.H., Leblanc, M., Petit, D., Brooks, R.R., Kirkman, J.H., Gregg, P.E.H. (1998) The potential of Thlaspi caerulescens for phytoremediation of contaminated soils. Plant Soil 203, 4756.
  • [7]
    Baker, A.J.M., McGrath, S.P., Sidoli, C.D.M., Reeves, R.D. (1994) The possibility of in situ heavy metal decontamination of polluted soils using crops of metal-accumulating plants. Resour. Conser. Recy. 11, 4149.
  • [8]
    Garbisu, C., Alkorta, I. (2001) Phytoextraction: a cost-effective plant-based technology for the removal of metals from the environment. Bioresour. Technol. 77, 229236.
  • [9]
    D.J. Glass (2000) Economic potential of phytoremediation. (Eds. I. Raskin, B. Ensley), Phytoremediation of Toxic Metals: Using Plants to Clean Up the Environment. Wiley, New York. 15–31.
  • [10]
    Mulligan, C.N., Yong, R.N., Gibbs, B.F. (2001) Remediation technologies for metal-contaminated soils and groundwater: an evaluation. Eng. Geol. 60, 193207.
  • [11]
    Baker, A.J.M., Reeves, R.D., Hajar, A.S.M. (1994) Heavy metal accumulation and tolerance in british populations of the metallophyte Thlaspi caerulescens J. &C Presl (Brassicaceae). New Phytol. 127, 6163.
  • [12]
    Brown, S.L., Chaney, R.L., Angle, J.S., Baker, A.J.M. (1994) Phytoremediation potential of Thlaspi caerulescens and Bladder Campion for Zinc- and cadmium-contaminated soil. J. Environ. Qual. 23, 11511157.
  • [13]
    R.D. Reeves, A.J.M. Baker (2000) Metal-accumulating plants. (Eds. I. Raskin, B.D. Ensley), Phytoremediation of Toxic Metals: Using Plants to Clean Up the Environment. Wiley, New York. 193–229.
  • [14]
    De Souza, M.P., Huang, C.P., Chee, N., Terry, N. (1999) Rhizosphere bacteria enhance the accumulation of selenium and mercury in wetland plants. Planta 209, 259263.
  • [15]
    Whiting, S.N., de Souza, M.P., Terry, N. (2001) Rhizosphere bacteria mobilize Zn for hyperaccumulation by Thlaspi caerulescens. Environ. Sci. Technol. 35, 31443150.
  • [16]
    Pawlowska, T.E., Chaney, R.L., Chin, M., Charvat, I. (2000) Effects of metal phytoextraction practices on the indigenous community of arbuscular mycorrhizal fungi at a metal-contaminated landfill. Appl. Environ. Microbiol. 66, 25262530.
  • [17]
    Delorme, T.A., Galiardi, J.V., Angle, J.S., Chaney, R.L. (2001) Influence of the zinc hyperaccumulator Thlaspi caerulescens J. & C. Presl. and the nonmetal accumulator Trifolium pratense L. on soil microbial populations. Can. J. Microbiol. 47, 773776.
  • [18]
    Gremion, F., Chatzinotas, A., Harms, H. (2003) Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of the metabolically active bacteria in heavy metal-contaminated bulk and rhizosphere soil. Environ. Microbiol. 5, 896907.
  • [19]
    Muyzer, G., Smalla, K. (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Anton. Leeuw. Int. J.G. 73, 127141.
  • [20]
    OIS (1998). Swiss Ordinance relating to Impacts on the Soil; 1st July 1998. SR 814.12, Switzerland
  • [21]
    Hammer, D., Keller, C. (2002) Changes in the rhizosphere of metal-accumulating plants evidenced by chemical extractions. J. Environ. Qual. 31, 15611569.
  • [22]
    Marilley, L., Vogt, G., Blanc, M., Aragno, M. (1998) Bacterial diversity in the bulk soil and rhizosphere fractions of Lolium perenne and Trifolium repens as revealed by PCR restriction analysis of 16S rDNA. Plant Soil 198, 219224.
  • [23]
    Griffiths, R.I., Whiteley, A.S., O'Donnell, A.G., Bailey, M.J. (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66, 54885491.
  • [24]
    G.S.H. Muyzer, A. Teske, C. Wawer (1996) Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA: a new molecular approach to analyze the genetic diversity of mixed microbial communities. (Eds. A.D.L. Akkermans, J.D. Van Elsas, F. De Bruijn), Molecular Microbial Ecology Manual. Kluwer Academic Publishers, Dordrecht, The Netherlands. 3.4.4/1–3.4.4/23.
  • [25]
    D.J. Lane (1991) 16S/23S rRNA sequencing. (Eds. E. Stackebrandt, M. Goodfellow), Nucleic Acid Techniques in Bacterial Systematics. Wiley, New York. 115–175.
  • [26]
    Gomes, N.C.M., Heuer, H., Schönfeld, J., Costa, R., Mendonça-Hagler, L., Smalla, K. (2001) Bacterial diversity of the rhizosphere of maize (Zea mays) grown in tropical soil studied by temperature gradient gel electrophoresis. Plant Soil 232, 167180.
  • [27]
    Heuer, H., Kresk, M., Baker, P., Smalla, K., Wellington, E.M.H. (1997) Analysis of Actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63, 32333241.
  • [28]
    Webster, G., Embley, T.M., Prosser, J.I. (2002) Grassland management regimens reduce small-scale heterogeneity and species diversity of β ammonia oxidizer populations. Appl. Environ. Microbiol. 68, 2030.
  • [29]
    Rotthauwe, J.-H., Witzel, K.-P., Liesack, W. (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63, 47044712.
  • [30]
    Avrahami, S., Liesack, W., Conrad, R. (2003) Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers. Environ. Microbiol. 5, 691705.
  • [31]
    McCaig, A.E., Glover, A.L., Prosser, J.I. (2001) Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl. Environ. Microbiol. 67, 45544559.
  • [32]
    Weinbauer, M.G., Beckmann, C., Höfle, M.G. (1998) Utility of green fluorescent nucleic acid dyes and aluminum oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria. Appl. Environ. Microbiol. 64, 50005003.
  • [33]
    Garland, J.L. (1996) Analytical approaches to the characterization of samples of microbial communities using patterns of potential C source utilization. Soil Biol. Biochem. 28, 213221.
  • [34]
    Hackett, C.A., Griffiths, B.S. (1997) Statistical analysis of the time-course of Biolog substrate utilization. J. Microbiol. Meth. 30, 6369.
  • [35]
    International Organization for Standardisation (ISO) (1999). Ammonium Oxidation, A Rapid Method to Test Potential Nitrification in Soil. ISO/CD 15685. Geneva, Switzerland
  • [36]
    Guckert, J.B., Carr, G.J., Johnson, T.D., Hamm, B.G., Davidson, D.H., Kumagai, Y. (1996) Community analysis by Biolog: curve integration for statistical analysis of activated sludge microbial habitats. J. Microbiol. Meth. 27, 183197.
  • [37]
    Knight, B., Zhao, F.J., Shen, Z.G. (1997) Zinc and cadmium uptake by the hyperaccumulator Thlaspi caerulescens in contaminated soils and its effects on the concentration and chemical speciation of metals in soil solution. Plant Soil 197, 7178.
  • [38]
    McGrath, S.P., Shen, Z.G., Zhao, F.J. (1997) Heavy metal uptake and chemical changes in the rhizosphere of Thlaspi caerulescens and Thlaspi ochroleucum grown in contaminated soils. Plant Soil 188, 153159.
  • [39]
    S.N. Whiting, J.R. Leake, S.P. McGrath, A.J.M. Baker (2001) Assessment of Zn mobilization in the rhizosphere of Thlaspi caerulescens by bioassays with non-accumulator plants and soil extraction. Plant Soil. 147156
  • [40]
    Hornburg, V., Brümmer, G.W. (1993) Behaviour of heavy metals in soil 1. Investigations on heavy metal mobility (In German). Z. Pflanz. Bodenkunde 156, 467477.
  • [41]
    Phillips, C.J., Harris, D., Dollhopf, S.L., Gross, K.L., Prosser, J.I., Paul, E.A. (2000) Effects of agronomic treatments on structure and function of ammonia-oxidizing communities. Appl. Environ. Microbiol. 66, 54105418.
  • [42]
    Kowalchuk, G.A., Stephen, J.R. (2001) Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu. Rev. Microbiol. 55, 485529.
  • [43]
    Kowalchuk, G.A., Bodelier, P.L.E., Heilig, G.H.J., Stephen, J.R., Laanbroek, H.J. (1998) Community analysis of ammonia-oxidising bacteria, in relation to oxygen, availability in soils and root-oxygenated sediments, using PCR, DGGE and oligonucleotide probe hybridisation. FEMS Microbiol. Ecol. 27, 339350.
  • [44]
    von Wintzingerode, F., Gobel, U.B., Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21, 213229.
  • [45]
    Müller, A.K., Westergaard, K., Christensen, H., Sorensen, S.J. (2001) The effect of long-term mercury pollution on the soil microbial community. FEMS Microbiol. Ecol. 36, 1119.
  • [46]
    Sandaa, R.A., Enger, O., Torsvik, V. (1999) Abundance and diversity of Archaea in heavy-metal-contaminated soil. Appl. Environ. Microbiol. 65, 32933297.
  • [47]
    Kowalchuk, G., Stienstra, A., Heilig, G., Stephen, J., Woldendorp, J. (2000) Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands. Environ. Microbiol. 2, 99110.
  • [48]
    Klemedtsson, L., Berg, P., Clarholm, M., Schnurer, J., Rosswall, T. (1987) Microbial Nitrogen Transformations in the Root Environment of Barley. Soil Biol Biochem 19, 551558.
  • [49]
    Briones, A.M., Okabe, S., Umemiya, Y., Ramsing, N.B., Reichardt, W., Okuyama, H. (2003) Ammonia-oxidizing bacteria on root biofilms and their possible contribution to N use efficiency of different rice cultivars. Plant Soil 250, 335348.
  • [50]
    Luo, Y.M., Christie, P., Baker, A.J.M. (2000) Soil solution Zn and pH dynamics in non-rhizosphere soil and in the rhizosphere of grown in a Zn/Cd-contaminated soil. Chemosphere 41, 161164.
  • [51]
    Lee, Y.W., Ong, S.K., Sato, C. (1997) Effects of heavy metals on nitrifying bacteria. Water Sci. Technol. 36, 6974.
  • [52]
    Sauve, S., Dumestre, A., McBride, M., Gillett, J.W., Berthelin, J., Hendershot, W. (1999) Nitrification potential in field-collected soils contaminated with Pb or Cu. Appl. Soil Ecol. 12, 2939.
  • [53]
    Gong, P., Siciliano, S.D., Srivastava, S., Greer, C.W., Sunahara, G.I. (2002) Assessment of pollution-induced microbial community tolerance to heavy metals in soil using ammonia-oxidizing bacteria and Biolog assay. Hum. Ecol. Risk Assess. 8, 10671081.
  • [54]
    Stephen, J.R., Chang, Y.-J, Macnaughton, S.J., Kowalchuk, G.A., Leung, K.T., Fleming, C.A., White, D.C. (1999) Effect of toxic metals on indigenous soil β-proteobacterium ammonia oxidizer community structure and protection against toxicity by inoculated metal-resistant bacteria. Appl. Environ. Microbiol. 65, 95101.
  • [55]
    Smalla, K., Wachtendorf, U., Heuer, H., Liu, W.T., Forney, L. (1998) Analysis of BIOLOG GN substrate utilization patterns by microbial communities. Appl. Environ. Microbiol. 64, 12201225.
  • [56]
    Preston-Mafham, J., Boddy, L., Randerson, P.F. (2002) Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles - a critique. FEMS Microbiol. Ecol. 42, 114.
  • [57]
    Knight, B.P., McGrath, S.P., Chaudri, A.M. (1997) Biomass carbon measurements and substrate utilization patterns of microbial populations from soils amended with cadmium, copper, or zinc. Appl. Environ. Microbiol. 63, 3943.
  • [58]
    Kelly, J.J., Tate, R.L. (1998) Effects of heavy metal contamination and remediation on soil microbial communities in the vicinity of a zinc smelter. J. Environ. Qual. 27, 609617.
  • [59]
    Dobler, R., Saner, M., Bachofen, R. (2000) Population changes of soil microbial communities induced by hydrocarbon and heavy metal contamination. Biorem. J. 4, 4156.
  • [60]
    Ellis, R.J., Neish, B., Trett, M.W., Best, J.G., Weightman, A.J., Morgan, P., Fry, J.C. (2001) Comparison of microbial and meiofaunal community analyses for determining impact of heavy metal contamination. J. Microbiol. Meth. 45, 171185.
  • [61]
    Garland, J.L., Mills, A.L. (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl. Environ. Microbiol. 57, 23512359.
  • [62]
    Reber, H.H. (1992) Simultaneous estimates of the diversity and the degradative capability of heavy-metal-affected soil bacterial communities. Soil Biol. Biochem. 13, 181186.
  • [63]
    Doelman, P., Jansen, E., Michels, M., van Til, M. (1994) Effects of heavy metals in soil on microbial diversity and activity as shown by the sensitivity-resistance index, an ecologically relevant parameter. Biol. Fert. Soils 17, 177184.
  • [64]
    Wenderoth, D.F., Reber, H.H. (1999) Correlation between structural diversity and catabolic versatility of metal-affected prototrophic bacteria in soil. Soil Biol. Biochem. 31, 345352.
  • [65]
    Wenderoth, D.F., Stackebrandt, E., Reber, H.H. (2001) Metal stress selects for bacterial ARDRA-types with a reduced catabolic versatility. Soil Biol. Biochem. 33, 667670.
  • [66]
    Obbard, J.P., Jones, K.C. (1993) The use of the cotton-strip assay to assess cellulose decomposition in heavy metal-contaminated sewage sludge-amended soils. Environ. Pollut. 81, 173178.
  • [67]
    Heinonsalo, J., Jorgensen, K.S., Haahtela, K., Sen, R. (2000) Effects of Pinus sylvestris rooth growth and mycorrhizosphere development on bacterial carbon source utilization and hydrocarbon oxidation in forest and petroleum-contaminated soils. Can. J. Microbiol. 46, 451464.
  • [68]
    Kozdrój, J., van Elsas, J.D. (2000) Response of the bacterial community to root exudates in soil polluted with heavy metal assessed by molecular and cultural approaches. Soil Biol. Biochem. 32, 14051417.
  • [69]
    Campbell, C.D., Grayston, S.J., Hirst, D.J. (1997) Use of rhizosphere carbon sources in sole carbon source tests to discriminate soil microbial communities. J. Microbiol. Meth. 30, 3341.
  • [70]
    S.E. Smith, D.J. Read (1997) Mycorrhizal Symbiosis. second ed.) Academic Press, San Diego, London.
  • [71]
    Regvar, M., Vogel, K., Irgel, N., Wraber, T., Hildebrandt, U., Wilde, P., Bothe, H. (2003) Colonization of pennycresses (Thlaspi spp.) of the Brassicaceae by arbuscular mycorrhizal fungi. J. Plant Physiol. 160, 615626.