Facchinelli A, Sacchi E, Mallen L. Multivariate statistical and GIS-based approach to identify heavy metal sources in soils. Environ Pollut. 2001;114(3):313–24.
Article
CAS
PubMed
Google Scholar
Solgi E, Esmaili-Sari A, Riyahi-Bakhtiari A, Hadipour M. Soil contamination of metals in the three industrial estates, arak, Iran. Bull Environ Contam Toxicol. 2012;88(4):634–8.
Article
CAS
PubMed
Google Scholar
Dong WQY, Cui Y, Liu X. Instances of soil and crop heavy metal contamination in China. Soil & Sediment Contamination An International Journal. 2001;10(5):497–510.
Article
Google Scholar
Salt DE, Blaylock M, Kumar NPBA, Dushenkov V, Ensley BD, Chet I, Raskin I. Phytoremediation: a novel strategy for the removal of toxic metals from the environment using plants. Nat Biotechnol. 1995;13(5):468–74.
Article
CAS
Google Scholar
Zhuang P, McBride MB, Xia H, Li N, Li Z. Health risk from heavy metals via consumption of food crops in the vicinity of Dabaoshan mine, South China. Sci Total Environ. 2009;407(5):1551–61.
Article
CAS
PubMed
Google Scholar
Li Z, Ma Z, van der Kuijp TJ, Yuan Z, Huang L. A review of soil heavy metal pollution from mines in China: pollution and health risk assessment. Sci Total Environ. 2014;468-469:843–53.
Article
CAS
PubMed
Google Scholar
Fu X, Dou C, Chen Y, Chen X, Shi J, Yu M, Jie X. Subcellular distribution and chemical forms of cadmium in Phytolacca Americana L. J Hazard Mater. 2011;186(1):103–7.
Article
CAS
PubMed
Google Scholar
Maron PA, Mougel C, Ranjard L. Soil microbial diversity: methodological strategy, spatial overview and functional interest. Comptes rendus biologies. 2011;334(5–6):403–11.
Article
PubMed
Google Scholar
Toppi LSD, Gabbrielli R. Response to cadmium in higher plants. Environmental & Experimental Botany. 1999;41(2):105–30.
Article
Google Scholar
Balestrasse KB, Gardey L, ML GSMT. Response of antioxidant defence system in soybean nodules and rootssubjected to cadmium stress. Funct Plant Biol. 2001;28(6):497–504.
Article
CAS
Google Scholar
Fornazier RF, Ferreira RR, Vitória AP, Molina SMG, Lea PJ, Azevedo RA. Effects of cadmium on antioxidant enzyme activities in sugar cane. Biol Plant. 2002;45(1):91–7.
Article
CAS
Google Scholar
Cho UH, Seo NH. Oxidative stress in Arabidopsis Thaliana exposed to cadmium is due to hydrogen peroxide accumulation. Plant Sci. 2005;168(1):113–20.
Article
CAS
Google Scholar
Gao L, Zhang J, Shen G. Effect of cd contamination on soil microbial community structure in flue-cured tobacco rhizosphere. Science News. 2014;164(1):7–9.
Google Scholar
Almås ÅR, Bakken LR, Mulder J. Changes in tolerance of soil microbial communities in Zn and cd contaminated soils. Soil Biol Biochem. 2004;36(5):805–13.
Article
Google Scholar
Ohya H, Komai Y, Yamaguchi M. Zinc effects on a soil bacterial flora characterized by fatty acid composition of the isolates. Biol Fertil Soils. 1986;2(2):59–63.
Article
Google Scholar
Frostegard A, Tunlid A, Bååth E. Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Applied & Environmental Microbiology. 1993;59(11):3605–17.
CAS
Google Scholar
Frostegard A, Tunlid A, Baath E. Changes in microbial community structure during long-term incubation in two soils experimentally contaminated with metals. Soil Biol Biochem. 1996;28(1):55–63.
Article
CAS
Google Scholar
Yang Y, Liu C, Xu L, Wu P, Zhang G. Effects of heavy metal contamination on microbial biomass and community structure in soils. Chin J Geochem. 2004;23(4):319–28.
Article
CAS
Google Scholar
Wang Y, Shi J, Wang H, Lin Q, Chen X, Chen Y. The influence of soil heavy metals pollution on soil microbial biomass, enzyme activity, and community composition near a copper smelter. Ecotoxicology & Environmental Safety. 2007;67(1):75.
Article
CAS
Google Scholar
Kumpiene J, Guerri G, Landi L, Pietramellara G, Nannipieri P, Renella G. Microbial biomass, respiration and enzyme activities after in situ aided phytostabilization of a Pb- and cu-contaminated soil. Ecotoxicology & Environmental Safety. 2009;72(1):115–9.
Article
CAS
Google Scholar
Navarro-Noya YE, Jan-Roblero J, Gonzalez-Chavez Mdel C, Hernandez-Gama R, Hernandez-Rodriguez C. Bacterial communities associated with the rhizosphere of pioneer plants (Bahia Xylopoda and Viguiera Linearis) growing on heavy metals-contaminated soils. Antonie Van Leeuwenhoek. 2010;97(4):335–49.
Article
CAS
PubMed
Google Scholar
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG, et al. Defining the core Arabidopsis Thaliana root microbiome. Nature. 2012;488(7409):86–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kaschuk G, Alberton O, Hungria M. Three decades of soil microbial biomass studies in Brazilian ecosystems: lessons learned about soil quality and indications for improving sustainability. Soil Biol Biochem. 2010;42(1):1–13.
Article
CAS
Google Scholar
Preston-Mafham J, Boddy L, Randerson PF. Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles–a critique. FEMS Microbiol Ecol. 2002;42(1):1–14.
CAS
PubMed
Google Scholar
Li Y, Chen L, Wen H. Changes in the composition and diversity of bacterial communities 13 years after soil reclamation of abandoned mine land in eastern China. Ecol Res. 2014;30(2):357–66.
Article
Google Scholar
de Campos SB, Youn JW, Farina R, Jaenicke S, Junemann S, Szczepanowski R, Beneduzi A, Vargas LK, Goesmann A, Wendisch VF, et al. Changes in root bacterial communities associated to two different development stages of canola (Brassica Napus L. var oleifera) evaluated through next-generation sequencing technology. Microb Ecol. 2013;65(3):593–601.
Article
PubMed
Google Scholar
Hill G, Mitkowski N, Aldrich-Wolfe L, Emele L, Jurkonie D, Ficke A, Maldonado-Ramirez S, Lynch S, Nelson E. Methods for assessing the composition and diversity of soil microbial communities. Appl Soil Ecol. 2000;15(1):25–36.
Article
Google Scholar
Hong C, Si Y, Xing Y, Li Y. Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas. Environ Sci Pollut Res Int. 2015;22(14):10788–99.
Article
CAS
PubMed
Google Scholar
Tonin C, Vandenkoornhuyse P, Joner E, Straczek J, Leyval C. Assessment of arbuscular mycorrhizal fungi diversity in the rhizosphere of Viola calaminaria and effect of these fungi on heavy metal uptake by clover. Mycorrhiza. 2001;10(4):161–8.
Article
CAS
Google Scholar
Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Rev. 1995;59(1):143–69.
CAS
Google Scholar
Giovannoni SJ, Britschgi TB, Moyer CL, Field KG. Genetic diversity in Sargasso Sea bacterioplankton. Nature. 1990;345(6270):60–3.
Article
CAS
PubMed
Google Scholar
Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol. 1998;180(2):366–76.
CAS
PubMed
PubMed Central
Google Scholar
Torsvik V, Goksøyr J, Daae FL. High diversity in DNA of soil bacteria. Applied & Environmental Microbiology. 1990;56(3):782–7.
CAS
Google Scholar
Bhadra B, Nanda AK, Chakraborty R. Inducible nickel resistance in a river isolate of India phylogenetically ascertained as a novel strain of Acinetobacter Junii. World J Microbiol Biotechnol. 2005;22(3):225–32.
Article
Google Scholar
Rhee SK, Liu X, Wu L, Chong SC, Wan X, Zhou J. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol. 2004;70(7):4303–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trajanovska S, Britz ML, Bhave M. Detection of heavy metal ion resistance genes in gram-positive and gram-negative bacteria isolated from a lead-contaminated site. Biodegradation. 1997;8(2):113–24.
Article
CAS
PubMed
Google Scholar
Jones DS, Albrecht HL, Dawson KS, Schaperdoth I, Freeman KH, Pi Y, Pearson A, Macalady JL. Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm. The ISME journal. 2012;6(1):158–70.
Article
CAS
PubMed
Google Scholar
Mason OU, Hazen TC, Borglin S, Chain PS, Dubinsky EA, Fortney JL, Han J, Holman HY, Hultman J, Lamendella R, et al. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater horizon oil spill. The ISME journal. 2012;6(9):1715–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci U S A. 2006;103(32):12115–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun. 2013;4:2120.
Article
PubMed
PubMed Central
Google Scholar
Kantor RS, Wrighton KC, Handley KM, Sharon I, Hug LA, Castelle CJ, Thomas BC, Banfield JF. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. MBio. 2013;4(5):e00708–13.
Article
PubMed
PubMed Central
Google Scholar
Musat N, Halm H, Winterholler B, Hoppe P, Peduzzi S, Hillion F, Horreard F, Amann R, Jorgensen BB, Kuypers MM. A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc Natl Acad Sci U S A. 2008;105(46):17861–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, Verberkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science. 2012;337(6102):1661–5.
Article
CAS
PubMed
Google Scholar
Hole JA, Ryberg T, Fuis GS, Bleibinhaus F, Sharma AK. Microbial population structures in the deep marine biosphere. Science. 2007;318(5847):97–100.
Article
Google Scholar
Altimira F, Yáñez C, Bravo G, González M, Rojas LA, Seeger M. Characterization of copper-resistant bacteria and bacterial communities from copper-polluted agricultural soils of central Chile. BMC Microbiol. 2012;12(1):193.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dopson M, Baker-Austin C, Koppineedi PR, Bond PL. Growth in sulfidic mineral environments: metal resistance mechanisms in acidophilic micro-organisms. Microbiology. 2003;149(Pt 8):1959–70.
Article
CAS
PubMed
Google Scholar
Bloem J, Hopkins DW, Benedetti A: Microbiological methods for assessing soil quality. Microbiological Methods for Assessing Soil Quality 2006, 36(1995):249-259.: CABI Pub 2006, 36(1995): 249–259.
Sun JY, Li MZ, Zheng LH, Hu YG, Zhang XJ. Real-time analysis of soil moisture, soil organic matter, and soil total nitrogen with NIR spectra. Spectroscopy & Spectral Analysis. 2006;26(3):426–9.
CAS
Google Scholar
Curtius AJ, Schlemmer G, Welz B. Determination of phosphorus by graphite furnace atomic absorption spectrometry. Part 2. Comparison of different modifiers. J Anal At Spectrom. 1987;2(2):115–24.
Article
CAS
Google Scholar
Bao SD. Soil and agricultural chemistry analysis. Beijing: China Agriculture Press; 2000.
Google Scholar
Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011;29(10):908–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma J, Wang Z, Li H, Park H-D, Zhichao W. Metagenomes reveal microbial structures, functional potentials, and biofouling-related genes in a membrane bioreactor. Applied Microbiology & Biotechnology. 2016;100(11):5109–21.
Article
CAS
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with burrows–wheeler transform. Bioinformatics. 2009;25(14):1754–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parks DH, Beiko RG. Identifying biologically relevant differences between metagenomic communities. Bioinformatics. 2010;26(6):715–21.
Article
CAS
PubMed
Google Scholar
Albertsen M, Hansen LB, Saunders AM, Nielsen PH, Nielsen KL. A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal. The ISME journal. 2012;6(6):1094–106.
Article
CAS
PubMed
Google Scholar
Ter BJ, Guskov A, Slotboom DJ. Structural diversity of ABC transporters. J Gen Physiol. 2014;143(4):419.
Article
Google Scholar
Higgins CF. ABC transporters: from microorganisms to man. Annu Rev Cell Biol. 1992;8(1):67–113.
Article
CAS
PubMed
Google Scholar
Finlayson JC, Liao B, Droppo IG, Leppard GG, Liss SN. The relationship between the structure of activated sludge flocs and the sorption of hydrophobic pollutants. Water Science & Technology. 1998;37(4–5):353–7.
CAS
Google Scholar
Kurek E, Francis AJ, Bollag JM. Immobilization of cadmium by microbial extracellular products. Archives of Environmental Contamination & Toxicology. 1991;21(1):106–11.
Article
CAS
Google Scholar
Demanou J, Sharma S, Weber A, Wilke BM, Njine T, Monkiedje A, Munch JC, Schloter M. Shifts in microbial community functions and nitrifying communities as a result of combined application of copper and mefenoxam. FEMS Microbiol Lett. 2006;260(1):55–62.
Article
CAS
PubMed
Google Scholar
Mertoglu B, Semerci N, Guler N, Calli B, Cecen F, Saatci AM. Monitoring of population shifts in an enriched nitrifying system under gradually increased cadmium loading. J Hazard Mater. 2008;160(2–3):495–501.
Article
CAS
PubMed
Google Scholar
Carmalin Sophia A, Swaminathan K, Sandhya S. Microbially-influenced degradation of solidified/stabilized metal waste. Bioresour Technol. 2007;98(13):2562–7.
Article
CAS
PubMed
Google Scholar
Seviour RJ, Mino T, Onuki M. The microbiology of biological phosphorus removal in activated sludge systems. FEMS Microbiol Rev. 2003;27(1):99–127.
Article
CAS
PubMed
Google Scholar
Vandamme P, Coenye T. Taxonomy of the genus Cupriavidus: a tale of lost and found. Int J Syst Evol Microbiol. 2004;54(Pt 6):2285–9.
Article
PubMed
Google Scholar
Chang IS, Kim BH. Effect of sulfate reduction activity on biological treatment of hexavalent chromium [Cr(VI)] contaminated electroplating wastewater under sulfate-rich condition. Chemosphere. 2007;68(2):218–26.
Article
CAS
PubMed
Google Scholar
Cook WJ, Kar SR, Taylor KB, Hall LM. Crystal structure of the cyanobacterial metallothionein repressor SmtB: a model for metalloregulatory proteins 1. J Mol Biol. 1998;275(2):337–46.
Article
CAS
PubMed
Google Scholar
Goulhen F, Gloter A, Guyot F, Bruschi M. Cr(VI) detoxification by Desulfovibrio Vulgaris strain Hildenborough: microbe-metal interactions studies. Appl Microbiol Biotechnol. 2006;71(6):892–7.
Article
CAS
PubMed
Google Scholar
Bauer BE, Wolfger H, Kuchler K. Inventory and function of yeast ABC proteins: about sex, stress, pleiotropic drug and heavy metal resistance. Biochim Biophys Acta. 2000;1461(2):217–36.
Article
Google Scholar
Lee JY, Yang JG, Zhitnitsky D, Lewinson O, Rees DC. Structural basis for heavy metal detoxification by an Atm1-type ABC exporter. Science. 2014;343(6175):1133–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee J, Yang J, Zhitnitsky D, Lewinson O, Rees D. Structural and functional characterization of a heavy metal detoxifying ABC transporter. Sci-Tech Information Development & Economy. 2014;24(3):308–13.
Google Scholar
Nies DH: Bacterial transition metal homeostasis. Springer Berlin Heidelberg 2007, 3(2):117–142.
Prange A, Modrow H. Rev Environ Sci Biotechnol. 2015;
Silver S, Le TP. Bacterial Heavy Metal Resistance: new surprises. Annu Rev Microbiol. 1996;50(50):753.
Article
CAS
PubMed
Google Scholar
Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics. 2010;95(6):315–27.
Article
CAS
PubMed
PubMed Central
Google Scholar