Metagenomics Approaches to Study Microbes in the E-waste Polluted Environment

  • Naseer Ali ShahEmail author
  • Imdad Kaleem
  • Yasir Rasheed
Part of the Soil Biology book series (SOILBIOL, volume 57)


Metagenomics approaches have tremendous application in encompassing ecological sustainability along with biotic and abiotic factors. The significance of metagenomics is well seen in establishing the role of microbes in sustainable environmental management tools such as bioremediation. This chapter highlights the recent innovative metagenomic techniques in determining the substantial role of microbes in environmental systems contaminated by e-waste dumping. We also describe modern metagenomic analysis for a variety of microbial communities and their key functions in e-waste soil. Moreover, culture-based and culture-independent integrated metagenomic analyses are discussed to authenticate microbial community taxonomic profiling and characterization of sustainable ecological development.


Metagenomics Microbes E-waste Pollution Environment 


  1. Albuquerque P, Ribeiro N, Almeida A, Panschin I, Porfirio A, Vales M, Tavares F (2017) Application of a dot blot hybridization platform to assess Streptococcus uberis population structure in dairy herds. Front Microbiol 8:54PubMedPubMedCentralCrossRefGoogle Scholar
  2. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56(6):1919–1925PubMedPubMedCentralGoogle Scholar
  3. Amann RI, Ludwig W, Schleifer K-H (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59(1):143–169PubMedPubMedCentralGoogle Scholar
  4. Balkwill DL, Boone DR (2018) Identity and diversity of microorganisms cultured from subsurface environments. In: Microbiology of the terrestrial deep subsurface. CRC, Boca Raton, pp 105–118CrossRefGoogle Scholar
  5. Bardgett RD, van der Putten WH (2014) Belowground biodiversity and ecosystem functioning. Nature 515(7528):505PubMedCrossRefGoogle Scholar
  6. Bender SF, Wagg C, van der Heijden MG (2016) An underground revolution: biodiversity and soil ecological engineering for agricultural sustainability. Trends Ecol Evol 31(6):440–452PubMedCrossRefGoogle Scholar
  7. Bordukalo-Nikšić, T. (2007) Reverse transcription-polymerase chain reaction (RT-PCR). Metode u molekularnoj biologiji, Institut Ruđer BoškovićGoogle Scholar
  8. Brady NC, Weil RR (2002) The nature and properties of soils, 13th edn. Agrofor Syst 54(3):249CrossRefGoogle Scholar
  9. Camus C, Faugeron S, Buschmann AH (2018) Assessment of genetic and phenotypic diversity of the giant kelp, Macrocystis pyrifera, to support breeding programs. Algal Res 30:101–112CrossRefGoogle Scholar
  10. De Vries FT, Hoffland E, van Eekeren N, Brussaard L, Bloem J (2006) Fungal/bacterial ratios in grasslands with contrasting nitrogen management. Soil Biol Biochem 38(8):2092–2103CrossRefGoogle Scholar
  11. Fernández-Arrojo L, Guazzaroni M-E, López-Cortés N, Beloqui A, Ferrer M (2010) Metagenomic era for biocatalyst identification. Curr Opin Biotechnol 21(6):725–733PubMedCrossRefGoogle Scholar
  12. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Angiuoli SV (2008) The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 26(5):541PubMedPubMedCentralCrossRefGoogle Scholar
  13. Finniss DG, Kaptchuk TJ, Miller F, Benedetti F (2010) Biological, clinical, and ethical advances of placebo effects. Lancet 375(9715):686–695PubMedPubMedCentralCrossRefGoogle Scholar
  14. Grattepanche JD, Walker LM, Ott BM, Paim Pinto DL, Delwiche CF, Lane CE, Katz LA (2018) Microbial diversity in the eukaryotic SAR clade: illuminating the darkness between morphology and molecular data. Bioessays 40(4):1700198CrossRefGoogle Scholar
  15. Ha NN, Agusa T, Ramu K, Tu NPC, Murata S, Bulbule KA, Tanabe S (2009) Contamination by trace elements at e-waste recycling sites in Bangalore, India. Chemosphere 76(1):9–15PubMedCrossRefGoogle Scholar
  16. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68(4):669–685PubMedPubMedCentralCrossRefGoogle Scholar
  17. He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG, Di H (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9(9):2364–2374PubMedCrossRefGoogle Scholar
  18. Heacock M, Kelly CB, Suk WA (2016) E-waste: the growing global problem and next steps. Rev Environ Health 31(1):131–135PubMedCrossRefGoogle Scholar
  19. Horwath WR (2017) The role of the soil microbial biomass in cycling nutrients. In: Microbial bio mass: a paradigm shift in terrestrial biogeochemistry. World Scientific, London, pp 41–66CrossRefGoogle Scholar
  20. Inbar E, Green SJ, Hadar Y, Minz D (2005) Competing factors of compost concentration and proximity to root affect the distribution of streptomycetes. Microb Ecol 50(1):73–81PubMedCrossRefGoogle Scholar
  21. Jansson JK, Hofmockel KS (2018) The soil microbiome—from metagenomics to metaphenomics. Curr Opin Microbiol 43:162–168PubMedCrossRefGoogle Scholar
  22. Kardol P, Veen G, Teste FP, Perring MP (2015) Peeking into the black box: a trait-based approach to predicting plant–soil feedback. New Phytol 206(1):1–4PubMedCrossRefGoogle Scholar
  23. Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H, Trevors JT (2004) Methods of studying soil microbial diversity. J Microbiol Methods 58(2):169–188PubMedCrossRefGoogle Scholar
  24. Knowles JG, Cole AL (2008) Handbook of the arts in qualitative research: perspectives, methodologies, examples, and issues. Sage, Thousand OaksCrossRefGoogle Scholar
  25. Liu Y-F, Galzerani DD, Mbadinga SM, Zaramela LS, Gu J-D, Mu B-Z et al (2018) Metabolic capability and in situ activity of microorganisms in an oil reservoir. Microbiome 6(1):5PubMedPubMedCentralCrossRefGoogle Scholar
  26. Loureiro C, Medema MH, van der Oost J, Sipkema D (2018) Exploration and exploitation of the environment for novel specialized metabolites. Curr Opin Biotechnol 50:206–213PubMedCrossRefGoogle Scholar
  27. Lynch J, Benedetti A, Insam H, Nuti M, Smalla K, Torsvik V, Nannipieri P (2004) Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms. Biol Fertil Soils 40(6):363–385CrossRefGoogle Scholar
  28. Martinez-Murcia A, Acinas S, Rodriguez-Valera F (1995) Evaluation of prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments. FEMS Microbiol Ecol 17(4):247–255CrossRefGoogle Scholar
  29. Mastriani M, Giraldez A (2018) Microarrays denoising via smoothing of coefficients in wavelet domain. arXiv preprint arXiv:1807.11571Google Scholar
  30. Matt M, Gaunand A, Joly PB, Colinet L (2017) Opening the black box of impact: ideal-type impact pathways in a public agricultural research organization. Res Policy 46(1):207–218CrossRefGoogle Scholar
  31. Meert JG, Torsvik TH, Eide EA, Dahlgren S (1998) Tectonic significance of the Fen Province, S. Norway: constraints from geochronology and paleomagnetism. J Geol 106(5):553–564CrossRefGoogle Scholar
  32. Mérillon J-M, Riviere C (2018) Natural antimicrobial agents, vol 19. Springer, Cham, SwitzerlandCrossRefGoogle Scholar
  33. Mohanty S, Swain CK (2018) Role of microbes in climate smart agriculture. In: Microorganisms for green revolution. Springer, Singapore, pp 129–140CrossRefGoogle Scholar
  34. Morgan XC, Huttenhower C (2012) Human microbiome analysis. PLoS Comput Biol 8(12):e1002808PubMedPubMedCentralCrossRefGoogle Scholar
  35. Nanda DK, Chaudhary R, Kumar D (2018) Molecular approaches for identification of lactobacilli from traditional dairy products. In: Advances in animal biotechnology and its applications. Springer, Singapore, pp 181–196CrossRefGoogle Scholar
  36. Oguntoyinbo FA, Tourlomousis P, Gasson MJ, Narbad A (2011) Analysis of bacterial communities of traditional fermented West African cereal foods using culture independent methods. Int J Food Microbiol 145(1):205–210PubMedCrossRefGoogle Scholar
  37. Parsley LC, Consuegra EJ, Kakirde KS, Land AM, Harper WF, Liles MR (2010) Identification of diverse antimicrobial resistance determinants carried on bacterial, plasmid, or viral metagenomes from an activated sludge microbial assemblage. Appl Environ Microbiol 76(11):3753–3757PubMedPubMedCentralCrossRefGoogle Scholar
  38. Pernthaler A, Amann R (2004) Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl Environ Microbiol 70(9):5426–5433PubMedPubMedCentralCrossRefGoogle Scholar
  39. Peters S, Koschinsky S, Schwieger F, Tebbe CC (2000) Succession of microbial communities during hot composting as detected by PCR–single-strand-conformation polymorphism-based genetic profiles of small-subunit rRNA genes. Appl Environ Microbiol 66(3):930–936PubMedPubMedCentralCrossRefGoogle Scholar
  40. Petersen DG, Dahllöf I (2005) Improvements for comparative analysis of changes in diversity of microbial communities using internal standards in PCR-DGGE. FEMS Microbiol Ecol 53(3):339–348PubMedCrossRefGoogle Scholar
  41. Rangel DE, Finlay RD, Hallsworth JE, Dadachova E, Gadd GM (2018) Fungal strategies for dealing with environment- and agriculture-induced stresses. Fungal Biol 122(6):602–612PubMedCrossRefGoogle Scholar
  42. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, Kent AD et al (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1(4):283PubMedPubMedCentralCrossRefGoogle Scholar
  43. Schloter M, Nannipieri P, Sørensen SJ, van Elsas JD (2018) Microbial indicators for soil quality. Biol Fertil Soils 54(1):1–10CrossRefGoogle Scholar
  44. Sunamura M, Maruyama A (2006) A digital imaging procedure for seven-probe-labeling FISH (rainbow-FISH) and its application to estuarine microbial communities. FEMS Microbiol Ecol 55(1):159–166PubMedCrossRefGoogle Scholar
  45. Taketani RG, Kavamura VN, dos Santos SN (2017) Diversity and technological aspects of microorganisms from semiarid environments. In: Diversity and benefits of microorganisms from the tropics. Springer, Cham, pp 3–19CrossRefGoogle Scholar
  46. Tansel B (2017) From electronic consumer products to e-wastes: global outlook, waste quantities, recycling challenges. Environ Int 98:35–45PubMedCrossRefGoogle Scholar
  47. Theron J, Cloete T (2000) Molecular techniques for determining microbial diversity and community structure in natural environments. Crit Rev Microbiol 26(1):37–57PubMedCrossRefGoogle Scholar
  48. Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6(11):805PubMedCrossRefGoogle Scholar
  49. Tringe SG, Von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW et al (2005) Comparative metagenomics of microbial communities. Science 308(5721):554–557PubMedCrossRefGoogle Scholar
  50. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG et al (2001) The sequence of the human genome. Science 291(5507):1304–1351PubMedCrossRefGoogle Scholar
  51. Wilcox TM, Schwartz MK, Lowe WH (2018) Evolutionary community ecology: time to think outside the (taxonomic) box. Trends Ecol Evol 33(4):240–250PubMedCrossRefGoogle Scholar
  52. Wood SA, Bradford MA (2018) Leveraging a new understanding of how belowground food webs stabilize soil organic matter to promote ecological intensification of agriculture. In: Soil carbon storage. Elsevier, Amsterdam, pp 117–136CrossRefGoogle Scholar
  53. Yilmaz A, Javed O, Shah M (2006) Object tracking: a survey. ACM Comput Surv (CSUR) 38(4):13CrossRefGoogle Scholar
  54. Zhang L, Dai Y, Chen J, Hong L, Liu Y, Ke Q, Chen Z (2018) Comparison of the performance in detection of HPV infections between the high-risk HPV genotyping real time PCR and the PCR-reverse dot blot assays. J Med Virol 90(1):177–183PubMedCrossRefGoogle Scholar
  55. Zoetendal EG, Cheng B, Koike S, Mackie RI (2004) Molecular microbial ecology of the gastrointestinal tract: from phylogeny to function. Curr Issues Intest Microbiol 5(2):31–48PubMedGoogle Scholar

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of BiosciencesCOMSATS University IslamabadIslamabadPakistan

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