Abstract
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.
Keywords
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
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 8:54
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):1919–1925
Amann RI, Ludwig W, Schleifer K-H (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59(1):143–169
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 105–118
Bardgett RD, van der Putten WH (2014) Belowground biodiversity and ecosystem functioning. Nature 515(7528):505
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):440–452
Bordukalo-Nikšić, T. (2007) Reverse transcription-polymerase chain reaction (RT-PCR). Metode u molekularnoj biologiji, Institut Ruđer Bošković
Brady NC, Weil RR (2002) The nature and properties of soils, 13th edn. Agrofor Syst 54(3):249
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 30:101–112
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):2092–2103
Fernández-Arrojo L, Guazzaroni M-E, López-Cortés N, Beloqui A, Ferrer M (2010) Metagenomic era for biocatalyst identification. Curr Opin Biotechnol 21(6):725–733
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):541
Finniss DG, Kaptchuk TJ, Miller F, Benedetti F (2010) Biological, clinical, and ethical advances of placebo effects. Lancet 375(9715):686–695
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):1700198
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):9–15
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68(4):669–685
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):2364–2374
Heacock M, Kelly CB, Suk WA (2016) E-waste: the growing global problem and next steps. Rev Environ Health 31(1):131–135
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 41–66
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):73–81
Jansson JK, Hofmockel KS (2018) The soil microbiome—from metagenomics to metaphenomics. Curr Opin Microbiol 43:162–168
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):1–4
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):169–188
Knowles JG, Cole AL (2008) Handbook of the arts in qualitative research: perspectives, methodologies, examples, and issues. Sage, Thousand Oaks
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):5
Loureiro C, Medema MH, van der Oost J, Sipkema D (2018) Exploration and exploitation of the environment for novel specialized metabolites. Curr Opin Biotechnol 50:206–213
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):363–385
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):247–255
Mastriani M, Giraldez A (2018) Microarrays denoising via smoothing of coefficients in wavelet domain. arXiv preprint arXiv:1807.11571
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):207–218
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):553–564
Mérillon J-M, Riviere C (2018) Natural antimicrobial agents, vol 19. Springer, Cham, Switzerland
Mohanty S, Swain CK (2018) Role of microbes in climate smart agriculture. In: Microorganisms for green revolution. Springer, Singapore, pp 129–140
Morgan XC, Huttenhower C (2012) Human microbiome analysis. PLoS Comput Biol 8(12):e1002808
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 181–196
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):205–210
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):3753–3757
Pernthaler A, Amann R (2004) Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl Environ Microbiol 70(9):5426–5433
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):930–936
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):339–348
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):602–612
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):283
Schloter M, Nannipieri P, Sørensen SJ, van Elsas JD (2018) Microbial indicators for soil quality. Biol Fertil Soils 54(1):1–10
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):159–166
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 3–19
Tansel B (2017) From electronic consumer products to e-wastes: global outlook, waste quantities, recycling challenges. Environ Int 98:35–45
Theron J, Cloete T (2000) Molecular techniques for determining microbial diversity and community structure in natural environments. Crit Rev Microbiol 26(1):37–57
Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6(11):805
Tringe SG, Von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW et al (2005) Comparative metagenomics of microbial communities. Science 308(5721):554–557
UNEP (2005) http://wedocs.unep.org/handle/20.500.11822/183
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG et al (2001) The sequence of the human genome. Science 291(5507):1304–1351
Wilcox TM, Schwartz MK, Lowe WH (2018) Evolutionary community ecology: time to think outside the (taxonomic) box. Trends Ecol Evol 33(4):240–250
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 117–136
Yilmaz A, Javed O, Shah M (2006) Object tracking: a survey. ACM Comput Surv (CSUR) 38(4):13
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):177–183
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):31–48
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Shah, N.A., Kaleem, I., Rasheed, Y. (2019). Metagenomics Approaches to Study Microbes in the E-waste Polluted Environment. In: Hashmi, M., Varma, A. (eds) Electronic Waste Pollution. Soil Biology, vol 57. Springer, Cham. https://doi.org/10.1007/978-3-030-26615-8_11
Download citation
DOI: https://doi.org/10.1007/978-3-030-26615-8_11
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-26614-1
Online ISBN: 978-3-030-26615-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)