Omics Approaches: Impact on Bioremediation Techniques

  • Yordanis Pérez-Llano
  • Liliana Martínez-Ávila
  • Ramón Alberto Batista-GarcíaEmail author
Part of the Nanotechnology in the Life Sciences book series (NALIS)


Microbiology has traditionally relied on the culture of microorganisms using general or selective growth media. This methodology allowed the isolation and characterization of a myriad of microbes, but in the past three decades, the disadvantages of this approach have become evident, opening the scope to other methodologies in microbiological research. The uprising of the “omics” techniques has imposed a paradigm shift for biologists, changing the way that we formulate biological questions as well as the data acquisition, manipulation, and interpretation processes. Being a powerful tool as they are, the potential and creative applications of the “omics” methodologies to different fields remain a challenge.

The outcome of “omics” techniques is purely analytical, and therefore it is disputed whether they can be of use to the biotechnological industry. In this chapter, we describe the applications and impact of the different “omics” techniques in the bioremediation of polluted environments and in the generation of novel products that are of interest for this industry.


Omics approach Bioremediation Metagenomic Transcriptomic Proteomic 


  1. Abram F, Enright AM, O’Reilly J, Botting CH, Colling G, O’Flaherty V (2011) A metaproteomic approach gives functional insights into anaerobic digestion. J Appl Microbiol 110:1550–1560CrossRefPubMedGoogle Scholar
  2. Aydin S, Karaçay HA, Shahi A, Gökçe S, Ince B, Ince O (2017) Aerobic and anaerobic fungal metabolism and Omics insights for increasing polycyclic aromatic hydrocarbons biodegradation. Fungal Biol Rev 31:61–72CrossRefGoogle Scholar
  3. Batista-García RA, Sánchez-Carbente MR, Talia P, Jackson SA, O’Leary ND, Dobson ADW, Folch-Mallol JL (2016) From lignocellulosic metagenomes to lignocellulolytic genes: trends, challenges and future prospects. Biofuels, Bioproducts and Biorefining 10 (6):864-882Google Scholar
  4. Benndorf D, Balcke GU, Harms H, von Bergen M (2007) Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J 1:224–234CrossRefPubMedGoogle Scholar
  5. Chauhan A, Jain RK (2010) Biodegradation: gaining insight through proteomics. Biodegradation 21:861–879CrossRefPubMedGoogle Scholar
  6. Desai C, Pathak H, Madamwar D (2010) Advances in molecular and “-omics” technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites. Bioresour Technol 101:1558–1569CrossRefPubMedGoogle Scholar
  7. El Amrani A, Dumas AS, Wick LY, Yergeau E, Berthomé R (2015) “Omics” insights into PAH degradation toward improved green remediation biotechnologies. Environ Sci Technol 49:11281–11291CrossRefPubMedGoogle Scholar
  8. Handelsmanl J, Rondon MR, Goodman RM, Brady SF, Clardy J (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:245–R249CrossRefGoogle Scholar
  9. Hanreich A, Heyer R, Benndorf D, Rapp E, Pioch M, Reichl U, Klocke M (2012) Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass. Can J Microbiol 58:917–922CrossRefPubMedGoogle Scholar
  10. Hernández-López EL, Ramírez-Puebla ST, Vazquez-Duhalt R (2015) Microarray analysis of Neosartorya fischeri using different carbon sources, petroleum asphaltenes and glucose-peptone. Genomics Data 5:235–237CrossRefPubMedPubMedCentralGoogle Scholar
  11. Kan J, Hanson TE, Ginter JM, Wang K, Chen F (2005) Metaproteomic analysis of Chesapeake Bay microbial communities. Saline Syst 1:7–21CrossRefPubMedPubMedCentralGoogle Scholar
  12. Keller M, Hettich R (2009) Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level. Microbiol Mol Biol Rev 73:62–70CrossRefPubMedPubMedCentralGoogle Scholar
  13. Kim SJ, Kweon O, Cerniglia CE (2011) Proteomic applications to elucidate bacterial aromatic hydrocarbon metabolic pathways. Compr Biotechnol 6:105–114Google Scholar
  14. Kuhn R, Benndorf D, Rapp E, Reichl U, Palese LL, Pollice A (2011) Metaproteome analysis of sewage sludge from membrane bioreactors. Proteomics 11:2738–2744CrossRefPubMedGoogle Scholar
  15. Lacerda CMR, Choe LH, Reardon KF (2007) Metaproteomic analysis of a bacterial community response to cadmium exposure. J Proteome Res 6:1145–1152CrossRefPubMedGoogle Scholar
  16. Lin YW, Tuan NN, Huang SL (2016) Metaproteomic analysis of the microbial community present in a thermophilic swine manure digester to allow functional characterization: a case study. Int Biodeterior Biodegrad 115:64–73CrossRefGoogle Scholar
  17. Liu D, Li M, Xi B, Zhao Y, Wei Z, Song C, Zhu C (2015) Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant. Microb Biotechnol 8:950–960CrossRefPubMedPubMedCentralGoogle Scholar
  18. Liu S, Guo C, Dang Z, Liang X (2017) Comparative proteomics reveal the mechanism of Tween80 enhanced phenanthrene biodegradation by Sphingomonas sp. GY2B. Ecotoxicol Environ Saf 137:256–264CrossRefPubMedGoogle Scholar
  19. Loh KC, Cao B (2008) Paradigm in biodegradation using Pseudomonas putida-a review of proteomics studies. Enzym Microb Technol 43:1–12CrossRefGoogle Scholar
  20. Lucero Camacho-Morales R, García-Fontana C, Fernández-Irigoyen J, Santamaría E, González-López J, Manzanera M, Aranda E (2018) Anthracene drives sub-cellular proteome-wide alterations in the degradative system of Penicillium oxalicum. Ecotoxicol Environ Saf 159:127–135CrossRefPubMedGoogle Scholar
  21. Morel M, Meux E, Mathieu Y, Thuillier A, Chibani K, Harvengt L, Jacquot JP, Gelhaye E (2013) Xenomic networks variability and adaptation traits in wood decaying fungi. Microb Biotechnol 6:248–263CrossRefPubMedPubMedCentralGoogle Scholar
  22. Nzila A, Ramirez CO, Musa MM, Sankara S, Basheer C, Li QX (2018) Pyrene biodegradation and proteomic analysis in Achromobacter xylosoxidans, PY4 strain. Int Biodeterior Biodegrad 130:40–47CrossRefGoogle Scholar
  23. Oliveira JS, Araújo WJ, Figueiredo RM, Silva-Portela RB, Guerra ADB, Carla S, Minnicelli C, Carlos AC, Tereza A, Vasconcelos RD, Freitas AT, Agnez-Lima L (2017) Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near- equatorial biomes have higher abundance of genes with potential for bioremediation. BMC Microbiol 17:1–10CrossRefGoogle Scholar
  24. Osman C, Wilmes C, Tatsuta T, Langer T (2007) Prohibitins interact genetically with Atp23, a novel processing peptidase and chaperone for the F1Fo-ATP synthase. Mol Biol Cell 18:627–635CrossRefPubMedPubMedCentralGoogle Scholar
  25. Pulleman M, Creamer R, Hamer U, Helder J, Pelosi C, Peres G, Rutgers M (2012) Soil biodiversity, biological indicators and soil ecosystem services – an overview of European approaches. Curr Opin Environ Sustain 4:529–538CrossRefGoogle Scholar
  26. Santos PM, Benndorf D, Sá-Correia I (2004) Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 4:2640–2652CrossRefPubMedGoogle Scholar
  27. Shahi A, Aydin S, Ince B, Ince O (2016a) Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach. Ecotoxicol Environ Saf 125:153–160CrossRefPubMedGoogle Scholar
  28. Shahi A, Aydin S, Ince B, Ince O (2016b) Reconstruction of bacterial community structure and variation for enhanced petroleum hydrocarbons degradation through biostimulation of oil contaminated soil. Chem Eng J 306:60–66CrossRefGoogle Scholar
  29. Solazzo C, Dyer JM, Clerens S, Plowman J, Peacock EE, Collins MJ (2013) Proteomic evaluation of the biodegradation of wool fabrics in experimental burials. Int Biodeterior Biodegrad 80:48–59CrossRefGoogle Scholar
  30. Szewczyk R, Soboń A, Sylwia R, Dzitko K, Waidelich D, Długoński J (2014) Intracellular proteome expression during 4-n-nonylphenol biodegradation by the filamentous fungus Metarhizium robertsii. Int Biodeterior Biodegrad 93:44–53CrossRefGoogle Scholar
  31. Szewczyk R, Soboń A, Słaba M, Długoński J (2015) Mechanism study of alachlor biodegradation by Paecilomyces marquandii with proteomic and metabolomic methods. J Hazard Mater 291:52–64CrossRefPubMedGoogle Scholar
  32. Vandera E, Samiotaki M, Parapouli M, Panayotou G, Koukkou AI (2015) Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose. J Proteomics 113:73–89CrossRefPubMedGoogle Scholar
  33. Verdin A, Lounès-Hadj Sahraoui A, Newsam R, Robinson G, Durand R (2005) Polycyclic aromatic hydrocarbons storage by Fusarium solani in intracellular lipid vesicles. Environ Pollut 133:283–291CrossRefPubMedGoogle Scholar
  34. Wang HB, Zhang ZX, Li H, He HB, Fang CX, Zhang AJ, Li QS, Chen RS, Guo XK, Lin HF, Wu LK, Lin S, Chen T, Lin RY, Peng XX, Lin WX (2011) Characterization of metaproteomics in crop rhizospheric soil. J Proteome Res 10:932–940CrossRefPubMedGoogle Scholar
  35. Wilmes P, Wexler M, Bond PL (2008) Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS One 3:e1778CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Yordanis Pérez-Llano
    • 1
  • Liliana Martínez-Ávila
    • 1
  • Ramón Alberto Batista-García
    • 1
    Email author
  1. 1.Centro de Investigación en Dinámica Celular-IICBAUniversidad Autónoma del Estado de MorelosCuernavacaMexico

Personalised recommendations