Gene Analysis for the Evaluation of the Effect of Environmental Factors

  • Satoshi Wakai


A variety of pollutants are present in natural and artificial environments. These pollutants are divided into two groups, chemical and biological pollutants. They cause various problems such as metal corrosion, environmental damage, and human health issues. Chemical pollutants contain heavy metals, hydrocarbons, exhaust gases, and endocrine disruptors. Such pollutants may possibly be detected by using a biosensor. On the other hand, the main biological pollutants are microorganisms. Microorganisms in environments can be detected by using culture-dependent and molecular biology-dependent methods. In particular, this chapter focuses on the molecular biology-dependent evaluation for biological pollution. First I introduce some methods of gene analysis as molecular biology-dependent evaluation techniques. Then I discuss gene analysis for endocrine disruptor detection and the application of a biosensor. Materials may be exposed to various pollutions in their respective environments so a variety of evaluation techniques for different pollutants exist. Thus, the adoption of a proper evaluation technique would be useful for maintaining the quality of materials.


Amplify Fragment Length Polymorphism Microbial Community Structure Endocrine Disruptor Microbiologically Influence Corrosion Microbial Community Analysis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    Beech IB, Sunner JA, Hiraoka K (2005) Microbe-surface interactions in biofouling and biocorrosion processes. Int Microbiol 8:157–168Google Scholar
  2. 2.
    Coetser SE, Cloete TE (2005) Biofouling and biocorrosion in industrial water systems. Crit Rev Microbiol 31:213–232CrossRefGoogle Scholar
  3. 3.
    Kjellerup BV, Thomsen TR, Nielsen JL, Olesen BH, Frolund B, Nielsen PH (2005) Microbial diversity in biofilms from corroding heating systems. Biofouling 21:19–29CrossRefGoogle Scholar
  4. 4.
    Muthukumar N, Rajasekar A, Ponmariappan S, Mohanan S, Maruthamuthu S, Muralidharan S, Subramanian P, Palaniswamy N, Raghavan M (2003) Microbiologically influenced corrosion in petroleum product pipelines – a review. Indian J Exp Biol 41:1012–1022Google Scholar
  5. 5.
    Videla HA, Herrera LK (2005) Microbiologically influenced corrosion: looking to the future. Int Microbiol 8:169–180Google Scholar
  6. 6.
    Samanta SK, Singh OV, Jain RK (2002) Polycyclic aromatic hydrocarbons: environmental pollution and bioremediation. Trends Biotechnol 20:243–248CrossRefGoogle Scholar
  7. 7.
    Järup L (2003) Hazards of heavy metal contamination. Br Med Bull 68:167–182CrossRefGoogle Scholar
  8. 8.
    Mastrangelo G, Fadda E, Marzia V (1997) Polycyclic aromatic hydrocarbons and cancer in man. Environ Health Perspect 104:1166–1170CrossRefGoogle Scholar
  9. 9.
    Goldman R, Enewold L, Pellizzari E, Beach JB, Bowman ED, Krishnan SS, Shields PG (2001) Smoking increase carcinogenic polycyclic aromatic hydrocarbons in human lung tissue. Cancer Res 61:6367–6371Google Scholar
  10. 10.
    Seidal K, Jorgensen N, Elinder CG, Sjogren B, Vahter M (1993) Fatal cadmium-induced pneumonitis. Scand J Work Environ Health 19:429–431CrossRefGoogle Scholar
  11. 11.
    Barbee JY Jr, Prince TS (1999) Acute respiratory distress syndrome in a welder exposed to metal fumes. South Med J 92:510–512CrossRefGoogle Scholar
  12. 12.
    Weiss B, Clarkson TW, Simon W (2002) Silent latency periods in methylmercury poisoning and in neurodegenerative disease. Environ Health Perspect 110:851–854CrossRefGoogle Scholar
  13. 13.
    Lidsky TI, Schneider JS (2003) Lead neurotoxicity in children: basic mechanisms and clinical correlates. Brain 126:15–19CrossRefGoogle Scholar
  14. 14.
    Wilson SC, Jones KC (1993) Bioremediation of soil contaminated with polynuclear aromatic hydrocarbons (PAHs): a review. Environ Pollut 81:229–249CrossRefGoogle Scholar
  15. 15.
    Haritash AK, Kaushik CP (2009) Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): a review. J Hazard Mater 169:1–15CrossRefGoogle Scholar
  16. 16.
    Liang SH, Kao CM, Kuo YC, Chen KF, Yang BM (2011) In situ oxidation of petroleum-hydrocarbon contaminated groundwater using passive ISCO system. Water Res 45:2496–2506CrossRefGoogle Scholar
  17. 17.
    Depledge MH, Billinghurst Z (1999) Ecological significance of endocrine disruption in marine invertebrates. Mar Pollut Bull 39:32–38CrossRefGoogle Scholar
  18. 18.
    Lutz I, Kloas W (1999) Amphibians as a model to study endocrine disruptors: I. Environmental pollution and estrogen receptor binding. Sci Total Environ 225:49–57CrossRefGoogle Scholar
  19. 19.
    Sun Y, Huang H, Sun Y, Wang C, Shi XL, Hu HY, Kameya T, Fujie K (2013) Ecological risk of estrogenic endocrine disrupting chemicals in sewage plant effluent and reclaimed water. Environ Pollut 180:339–344CrossRefGoogle Scholar
  20. 20.
    Flemming HC (2002) Biofouling in water systems–cases, causes and countermeasures. Appl Microbiol Biotechnol 59:629–640CrossRefGoogle Scholar
  21. 21.
    Huttunen-Saarivirta E, Honkanen M, Lepistö T, Kuokkala VT, Koivisto L, Berg CG (2012) Microbiologically influenced corrosion (MIC) in stainless steel heat exchanger. Appl Surf Sci 258:6512–6526CrossRefGoogle Scholar
  22. 22.
    Almeida MAN, De Franca FP (1999) Thermophilic and mesophilic bacteria in biofilms associated with corrosion in a heat exchanger. World J Microbiol Biotechnol 15:439–442CrossRefGoogle Scholar
  23. 23.
    Xu HS, Roberts N, Singleton FL, Attwell RW, Grimes DJ, Colwell RR (1982) Survival and viability of nonculturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment. Microb Ecol 8:313–323CrossRefGoogle Scholar
  24. 24.
    Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169Google Scholar
  25. 25.
    Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R (1993) Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res 21:3025–3049CrossRefGoogle Scholar
  26. 26.
    Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849CrossRefGoogle Scholar
  27. 27.
    Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P, Maiden MC, Nesme X, Rosselló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047Google Scholar
  28. 28.
    Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Nat Biotechnol 7:257–264CrossRefGoogle Scholar
  29. 29.
    Poly F, Monrozier LJ, Bally R (2001) Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res Microbiol 152:95–103CrossRefGoogle Scholar
  30. 30.
    Osborn AM, Moore ER, Timmis KN (2000) An evaluation of terminal‐restriction fragment length polymorphism (T‐RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2:39–50CrossRefGoogle Scholar
  31. 31.
    Franklin RB, Taylor DR, Mills AL (1999) Characterization of microbial communities using randomly amplified polymorphic DNA (RAPD). J Microbiol Methods 35:225–235CrossRefGoogle Scholar
  32. 32.
    Franklin RB, Garland JL, Bolster CH, Mills AL (2001) Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments. Appl Environ Microbiol 67:702–712CrossRefGoogle Scholar
  33. 33.
    Muyzer G, de Waal EC, 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 59:695–700Google Scholar
  34. 34.
    Heuer H, Krsek M, Baker P, Smalla K, Wellington EM (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63:3233–3241Google Scholar
  35. 35.
    Felske A, Rheims H, Wolterink A, Stackebrandt E, Akkermans AD (1997) Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils. Microbiology 143:2983–2989CrossRefGoogle Scholar
  36. 36.
    Okabayashi A, Wakai S, Kanao T, Sugio T, Kamimura K (2005) Diversity of 16S ribosomal DNA-defined bacterial population in acid rock drainage from Japanese pyrite mine. J Biosci Bioeng 100:644–652CrossRefGoogle Scholar
  37. 37.
    Heid CA, Stevens J, Livak KJ, Williams PM (1996) Real time quantitative PCR. Genome Res 6:986–994CrossRefGoogle Scholar
  38. 38.
    Duck P, Alvarado-Urbina G, Burdick B, Collier B (1990) Probe amplifier system based on chimeric cycling oligonucleotides. Biotechniques 9:142–148Google Scholar
  39. 39.
    Harvey JJ, Lee SP, Chan EK, Kim JH, Hwang ES, Cha CY, Knutson JR, Han MK (2004) Characterization and applications of CataCleave probe in real-time detection assays. Anal Biochem 333:246–255CrossRefGoogle Scholar
  40. 40.
    Zhou J (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6:288–294CrossRefGoogle Scholar
  41. 41.
    Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH, Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68:5064–5081CrossRefGoogle Scholar
  42. 42.
    Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55:641–658CrossRefGoogle Scholar
  43. 43.
    Nyrén P (1987) Enzymatic method for continuous monitoring of DNA polymerase activity. Anal Biochem 167:235–238CrossRefGoogle Scholar
  44. 44.
    Harrington CT, Lin EI, Olson MT, Eshleman JR (2013) Fundamentals of pyrosequencing. Arch Pathol Lab Med 137:1296–1303CrossRefGoogle Scholar
  45. 45.
    Ferrer M, Martínez-Abarca F, Golyshin PN (2005) Mining genomes and ‘metagenomes’ for novel catalysts. Curr Opin Biotechnol 16:588–593CrossRefGoogle Scholar
  46. 46.
    Ferrer M, Golyshina O, Beloqui A, Golyshin PN (2007) Mining enzymes from extreme environments. Curr Opin Microbiol 10:207–214CrossRefGoogle Scholar
  47. 47.
    Ducey TF, Hunt PG (2013) Microbial community analysis of swine wastewater anaerobic lagoons by next-generation DNA sequencing. Anaerobe 21:50–57CrossRefGoogle Scholar
  48. 48.
    Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017CrossRefGoogle Scholar
  49. 49.
    Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336CrossRefGoogle Scholar
  50. 50.
    Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7341CrossRefGoogle Scholar
  51. 51.
    Kiyama R, Wada-Kiyama Y (2015) Estrogenic endocrine disruptors: molecular mechanisms of action. Environ Int 83:11–40CrossRefGoogle Scholar
  52. 52.
    Mikkelsen SR (1996) Electrochecmical biosensors for DNA sequence detection. Electroanalysis 8:15–19CrossRefGoogle Scholar
  53. 53.
    Gracey AY, Cossins AR (2003) Application of microarray technology in environmental and comparative physiology. Annu Rev Physiol 65:231–259CrossRefGoogle Scholar
  54. 54.
    Oleksiak MF, Kolell KJ, Crawford DL (2001) Utility of natural populations for microarray analyses: isolation of genes necessary for functional genomic studies. Mar Biotechnol (NY) 3(Supplement 1):S203–S211CrossRefGoogle Scholar
  55. 55.
    Kanesaki Y, Suzuki I, Allakhverdiev SI, Mikami K, Murata N (2002) Salt stress and hyperosmotic stress regulate the expression of different sets of genes in Synechocystis sp. PCC 6803. Biochem Biophys Res Commun 290:339–348CrossRefGoogle Scholar
  56. 56.
    AlAbbas FM, Williamson C, Bhola SM, Spear JR, Olson DL, Mishra B, Kakpovbia AE (2013) Influence of sulfate reducing bacterial biofilm on corrosion behavior of low-alloy, high-strength steel (API-5L X80). Int Biodeterior Biodegrad 78:34–42CrossRefGoogle Scholar
  57. 57.
    Duncan KE, Perez-Ibarra BM, Jenneman G, Harris JB, Webb R, Sublette K (2014) The effect of corrosion inhibitors on microbial communities associated with corrosion in a model flow cell system. Appl Microbiol Biotechnol 98:907–918CrossRefGoogle Scholar
  58. 58.
    Murali Mohan A, Hartsock A, Hammack RW, Vidic RD, Gregory KB (2013) Microbial communities in flowback water impoundments from hydraulic fracturing for recovery of shale gas. FEMS Microbiol Ecol 86:567–580CrossRefGoogle Scholar
  59. 59.
    Wakai S, Ito K, Iino T, Tomoe Y, Mori K, Harayama S (2014) Corrosion of iron by iodide-oxidizing bacteria isolated from brine in an iodine production facility. Microb Ecol 68:519–527CrossRefGoogle Scholar

Copyright information

© Springer Japan 2016

Authors and Affiliations

  1. 1.Organization of Advanced Science and TechnologyKobe UniversityKobeJapan

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