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Applied Microbiology and Biotechnology

, Volume 97, Issue 1, pp 369–378 | Cite as

Bacterial biodiversity from anthropogenic extreme environments: a hyper-alkaline and hyper-saline industrial residue contaminated by chromium and iron

  • Elcia M. S. Brito
  • Hilda A. Piñón-Castillo
  • Rémy Guyoneaud
  • César A. Caretta
  • J. Félix Gutiérrez-Corona
  • Robert Duran
  • Georgina E. Reyna-López
  • G. Virginia Nevárez-Moorillón
  • Anne Fahy
  • Marisol Goñi-Urriza
Environmental biotechnology

Abstract

Anthropogenic extreme environments are among the most interesting sites for the bioprospection of extremophiles since the selection pressures may favor the presence of microorganisms of great interest for taxonomical and astrobiological research as well as for bioremediation technologies and industrial applications. In this work, T-RFLP and 16S rRNA gene library analyses were carried out to describe the autochthonous bacterial populations from an industrial waste characterized as hyper-alkaline (pH between 9 and 14), hyper-saline (around 100 PSU) and highly contaminated with metals, mainly chromium (from 5 to 18 g kg−1) and iron (from 2 to 108 g kg−1). Due to matrix interference with DNA extraction, a protocol optimization step was required in order to carry out molecular analyses. The most abundant populations, as evaluated by both T-RFLP and 16S rRNA gene library analyses, were affiliated to Bacillus and Lysobacter genera. Lysobacter related sequences were present in the three samples: solid residue and lixiviate sediments from both dry and wet seasons. Sequences related to Thiobacillus were also found; although strains affiliated to this genus are known to have tolerance to metals, they have not previously been detected in alkaline environments. Together with Bacillus (already described as a metal reducer), such organisms could be of use in bioremediation technologies for reducing chromium, as well as for the prospection of enzymes of biotechnological interest.

Keywords

Landfill Industrial waste DNA extraction optimization Chromium hexavalent T-RFLP 

Notes

Acknowledgements

This work was supported by Grants from ECOS-NORD-SEP-CONACyT-ANUIES (M07A01) and FONCICyT (BIOCHROME project Ref. 95887). We acknowledge the financial support by the Aquitaine Regional Government Council (France). H.A. Piñón-Castillo received a fellowship from CONACyT, Mexico.

References

  1. Alam MZ, Ahmad S, Malik A (2011) Prevalence of heavy metal resistance in bacteria isolated from tannery effluents and affected soil. Environ Monit Assess 178:281–291CrossRefGoogle Scholar
  2. Armienta MA, Rodríguez R, Queré A, Juárez F, Ceniceros N, Aguayo A (1993) Groundwater pollution with chromium in León Valley, México. J Environ Qual 8:31–35Google Scholar
  3. Barton HA, Taylor NM, Lubbers BR, Pemberton AC (2006) DNA extraction from low-biomass carbonate rock: an improved method with reduced contamination and the low-biomass contaminant database. J Microbiol Methods 66:21–31CrossRefGoogle Scholar
  4. Bopp LH, Ehrlich HL (1988) Chromate resistance and reduction in Pseudomonas fluorescens strain LB300. Arch Microbiol 150:426–431CrossRefGoogle Scholar
  5. Bruce KD, Hiorns WD, Hobman JL, Osborn AM, Strike P, Ritchie DA (1992) Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Appl Environ Microbiol 58:3413–3416Google Scholar
  6. Butcher BG, Deane SM, Rawlings DE (2000) The chromosomal arsenic resistance genes of Thiobacillus ferrooxidans have an unusual arrangement and confer increased arsenic and antimony resistance to Escherichia coli. Appl Environ Microbiol 66:1826–1833CrossRefGoogle Scholar
  7. Campos J, Martinez-Pacheco M, Cervantes C (1995) Hexavalent-chromium reduction by a chromate-resistant Bacillus sp. strain. Ant van Leeuwenhoek 68:203–208CrossRefGoogle Scholar
  8. Caretta CA, Brito EMS (2011) In silico restriction analysis for identifying microbial communities in T-RFLP fingerprints. J Comp Interdisciplinary Sc (in press)Google Scholar
  9. Chen SY, Lin J-G (2001) Bioleaching of heavy metals from sediment: significance of pH. Chemosphere 44(5):1093–1102CrossRefGoogle Scholar
  10. Collmer AR, Temple KT, Hinkle ME (1950) An iron-oxidizing bacterium from the acid mine drainage of some bituminous coal mines. J Bacteriol 59:317–328Google Scholar
  11. Desai C, Madamwar D (2006) Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion-exchange treatments. Bioresource Technol 98:761–768CrossRefGoogle Scholar
  12. Desai C, Parikh RY, Shouche YS, Madamwar D (2009) Tracking the influence of long-term chromium pollution on soil bacterial community structures by comparative analyses of 16S rRNA gene phylotypes. Res Microbiol 160:1–9CrossRefGoogle Scholar
  13. Elangovan R, Abhipsa S, Rohit B, Ligy P, Chandraraj K (2006) Reduction of Cr(VI) by a Bacillus sp. Biotechnol Let 28:247–252CrossRefGoogle Scholar
  14. Environmental Protection Agency (US EPA) Methods (1996) Test methods for evaluating solid waste SW-846, 3rd ed. Washington, DC: Office of Solid Waste. (http://www.veridianenv.com/docs/SW-846-Methodologies/Methods)
  15. Fortin N, Beaumier D, Lee K, Greer CW (2004) Soil washing improves the recovery of total community DNA from polluted and high organic content sediments. J Microbiol Methods 56:181–191CrossRefGoogle Scholar
  16. Fujinami S, Fujisawa M (2010) Industrial applications of alkaliphiles and their enzymes—past, present and future. Environ Technol 31:845–856CrossRefGoogle Scholar
  17. Garbisu C, Alkorta I, Llama MJ, Serra JL (1998) Aerobic chromate reducion by Bacillus subtilis. Biodegradetion 9:133–148CrossRefGoogle Scholar
  18. Good IJ (1953) The population frequencies of species and the estimation of the population parameters. Biometrika 40:237–264Google Scholar
  19. Griffiths RI, Whiteley AS, O’donnell AG, Bailey MJ (2000) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes. Appl Environ Microbiol 68:5064–5081Google Scholar
  20. Hayward AC, Fegan N, Fegan M, Stirling GR (2010) Stenotrophomonas and Lysobacter: ubiquitous plant-associated Gammaproteobacteria of developing significance in applied microbiology. J Appl Microbiol 108:756–770CrossRefGoogle Scholar
  21. Herrera A, Cockell CS (2007) Exploring microbial diversity in volcanic environments: a review of methods in DNA extraction. J Microbiol Methods 70:1–12CrossRefGoogle Scholar
  22. Hewson I, Fuhrman JA (2006) Improved strategy for comparing microbial assemblage fingerprints. Microb Ecol 51:147–153CrossRefGoogle Scholar
  23. Hinoue M, Fukuda K, Wan Y, Yamauchi K, Ogawa H, Taniguchi H (2004) An effective method for extracting DNA from contaminated soil due to industrial waste. J Univ Occup Environ Health (Jpn) 26:13–21Google Scholar
  24. Hoshino YT, Matsumoro N (2005) Skim milk drastically improves the efficacy of DNA extraction from andisol, a volcanic ash soil. JARQ 39:247–252, http://www.jircas.affrc.go.jp Google Scholar
  25. Huber H, Stetter KO (1990) Thiobacillus cuprinus sp. nov., a novel facultatively organotrophic metal-mobilizing bacterium. Appl Environ Microbiol 56:315–322Google Scholar
  26. Ishibashi Y, Cervantes C, Silver S (1990) Chromium reduction in Pseudomonas putida. Appl Environ Microbiol 56:2268–2270Google Scholar
  27. Justin P, Kelly DP (1978) Metabolic changes in Thiobacillus denitrificans in anaerobic and aerobic chemostat culture. J Gen Microbiol 107:131–137CrossRefGoogle Scholar
  28. Katz SA, Salem H (1993) The toxicity of chromium with respect to its chemical speciation—a review. J Appl Toxicol 13(3):217–224CrossRefGoogle Scholar
  29. Kelly DP, Wood AP (2000) Confirmation of Thiobacillus denitrificans as a species of the genus Thiobacillus, in the subclass of the Proteobacteria, with strain NCIMB 9548 as the type strain. Int J Syst Evol Microbiol 50:547–550CrossRefGoogle Scholar
  30. La Montagne MG, Michel FC Jr, Holden PA, Reddy CA (2002) Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis. J Microbiol Methods 49:255–264CrossRefGoogle Scholar
  31. Lane DJ (1991) rRNA sequencing. In Stachebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics, John Wiley & Sons, Chichester, pp 115–175Google Scholar
  32. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analysis. Proc Natl Acad Sci USA 82:6955–6959CrossRefGoogle Scholar
  33. Liu M, Liu Y, Wang Y, Luo X, Dai J, Fang C (2011) Lysobacter xinjiangensis sp. nov., a moderately thermotolerant and alkalitolerant bacterium isolated from a gamma-irradiated sand soil sample. Int J Syst Evol Microbiol 61:433–437CrossRefGoogle Scholar
  34. Losi ME, Amrhein C, Frankenberger W Jr (1994) Factors affecting chemical and biological reduction of hexavalent chromium in soil. Environ Toxicol Chem 13:1727–1735CrossRefGoogle Scholar
  35. Mahony J, Chong S, Jang D, Luinstra K, Faught M, Dalby D, Sellors J, Chernesky M (1998) Urine specimens from pregnant and nonpregnant women inhibitory to amplification of Chlamydia trachomatis nucleic acid by PCR, ligase chain reaction, and transcription-mediated amplification: identification of urinary substances associated with inhibition and removal of inhibitory activity. J Clin Microbiol 36:3122–3126Google Scholar
  36. Mera N, Iwasaki K (2007) Use of plate-wash samples to monitor the fates of culturable bacteria in mercury- and trichloroethylene-contaminated soils. Appl Microbiol Biotechnol 77:437–445CrossRefGoogle Scholar
  37. Miller LG, Warner K, Baesman SM, Oremland RS, McDonald IR, Radajewski S, Murrell JC (2004) Degradation of methyl bromide and methyl chloride in soil microcosms: use of stable C isotope fractionation and stable isotope probing to identify reactions and the responsible microorganisms. Geochim Cosmochim Acta 68:3271–3283CrossRefGoogle Scholar
  38. Nies DH (2003) Efflux-mediated heavy metal resistance in prokaryotes. FEMS Microbiol Rev 27:313–339CrossRefGoogle Scholar
  39. Official Mexican Standard (NOM-052-SEMARNAT-2005) (2006) Norma Oficial Mexicana, residuos peligrosos, Diario Oficial, Tomo DCXXXIII No. 17 (http://www.glin.gov/view.action?glinID=181729)
  40. Ogram A, Sayler GS, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Methods 7:57–66CrossRefGoogle Scholar
  41. Paissé S, Coulon F, Goñi-Urriza M, Peperzak L, McGenity TJ, Duran R (2008) Structure of bacterial communities along a hydrocarbon contamination gradient in a coastal sediment. FEMS Microbiol Ecol 66:295–305CrossRefGoogle Scholar
  42. Pal A, Paul AK (2004) Aerobic chromate reduction by chromium-resistant bacteria isolated from serpentine soil. Microbiol Res 159:347–354CrossRefGoogle Scholar
  43. Piñon-Castillo HA, Brito EMS, Goñi-Urriza M, Guyoneaud R, Duran R, Nevarez-Moorillon G, Gutiérrez-Corona JF, Caretta CA, Reyna-López GH (2010) Hexavalent chromium reduction by bacterial consortia and pure strains from an alkaline industrial effluent. J Appl Microbiol 109:2173–2182CrossRefGoogle Scholar
  44. Rajendhrana J, Gunasekaran P (2008) Strategies for accessing soil metagenome for desired applications. Biotechnol Adv 26:576–590CrossRefGoogle Scholar
  45. Rochelle PA, Fry JC, Parkes RJ, Weightman AW (1992) DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities. FEMS Microbiol Lett 100:59–66Google Scholar
  46. Sand W, Rhode K, Sobotke B, Zenneck C (1992) Evaluation of Leptospirillum ferrooxidans for leaching. Appl Environ Microbiol 58:85–92Google Scholar
  47. Shen H, Wang Y-T (1994) Biological reduction of chromium by E. coli. J Environ Eng 120:560–572CrossRefGoogle Scholar
  48. Sorokin DY, Lysenko AM, Mityushina LL, Tourova TP, Jones BE, Rainey FA, Robertson LA, Kuenen GJ (2001) Thioalkalimicrobium aerophilum gen. nov., sp nov and Thioalkalimicrobium sibericum sp nov., and Thioalkalivibrio versutus gen. nov., sp nov., Thioalkalivibrio nitratis sp nov and Thioalkalivibrio denitrificans sp nov., novel obligately alkaliphilic and obligately chemolithoautotrophic sulfur-oxidizing bacteria from soda lakes. Int J Sys Evol Microbiol, 51: 565-580Google Scholar
  49. Sorokin ID, Kravchenko IK, Doroshenko EV, Boulygina ES, Zadorina EV, Tourova TP, Sorokin DY (2008) Haloalkaliphilic diazotrophs in soda solonchak soils. FEMS Microbiol Ecol 65: 425–433Google Scholar
  50. Torsvik V, Goksyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787Google Scholar
  51. Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57:1070–1074Google Scholar
  52. Tsai YL, Olson BH (1992) Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. App Environ Microbiol 58:2292–2295Google Scholar
  53. Tuovinen OH, Niemelä SI, Gyllenberg HG (1971) Tolerance of Thiobacillus ferrooxidans to some metals. Ant van Leeuwenhoek 37:489–496CrossRefGoogle Scholar
  54. Van Elsas JD, Mäntynen V, Wolters AC (1997) Soil DNA extraction and assessment of the fate of Mycobacterium chlorophenolicum strain PCP-1 in different soils by 16S ribosomal RNA gene sequence based most-probable-number PCR and immunofluorescence. Biol Fertil Soils 24:188–195CrossRefGoogle Scholar
  55. Whitehouse CA, Hotte HE (2007) Comparison of five commercial DNA extraction kits for the recovery of Francisella tularensis DNA from spiked soil samples. Mol Cell Probes 21:92–96CrossRefGoogle Scholar
  56. Yassin AF, Chen W-M, Hupfer H, Siering C, Kroppenstedt RM, Arun AB, Lai W-A, Shen F-T, Rekha PD, Young CC (2007) Lysobacter defluvii sp. nov., isolated from municipal solid waste. Int J Sys Evol Microbiol 57:1131-1136Google Scholar
  57. Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322Google Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Elcia M. S. Brito
    • 1
  • Hilda A. Piñón-Castillo
    • 2
  • Rémy Guyoneaud
    • 3
  • César A. Caretta
    • 4
  • J. Félix Gutiérrez-Corona
    • 2
  • Robert Duran
    • 3
  • Georgina E. Reyna-López
    • 2
  • G. Virginia Nevárez-Moorillón
    • 5
  • Anne Fahy
    • 3
  • Marisol Goñi-Urriza
    • 3
  1. 1.Grupo de Ingeniería Ambiental, Departamento de Ingeniería Civil, División de IngenieríasUniversidad de GuanajuatoGuanajuatoMexico
  2. 2.Departamento de Biología, División de Ciencias Naturales y ExactasUniversidad de GuanajuatoGuanajuatoMexico
  3. 3.Equipe Environnement et Microbiologie—UMR IPREM5254Université de Pau et des Pays de l’AdourPau CedexFrance
  4. 4.Departamento de Astronomía, División de Ciencias Naturales y ExactasUniversidad de GuanajuatoGuanajuatoMexico
  5. 5.Facultad de Ciencias QuímicasUniversidad Autónoma de ChihuahuaChihuahuaMexico

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