Applied Microbiology and Biotechnology

, Volume 100, Issue 12, pp 5313–5321 | Cite as

Microbial sequencing methods for monitoring of anaerobic treatment of antibiotics to optimize performance and prevent system failure

  • Sevcan AydinEmail author


As a result of developments in molecular technologies and the use of sequencing technologies, the analyses of the anaerobic microbial community in biological treatment process has become increasingly prevalent. This review examines the ways in which microbial sequencing methods can be applied to achieve an extensive understanding of the phylogenetic and functional characteristics of microbial assemblages in anaerobic reactor if the substrate is contaminated by antibiotics which is one of the most important toxic compounds. It will discuss some of the advantages and disadvantages associated with microbial sequencing techniques that are more commonly employed and will assess how a combination of the existing methods may be applied to develop a more comprehensive understanding of microbial communities and improve the validity and depth of the results for the enhancement of the stability of anaerobic reactors.


Anaerobic treatment process Anaerobic microbial community Microbial sequencing techniques Antibiotics 



The authors thank Republic of Turkey Ministry of Science, Industry and Technology (Project No: 0328.TGSD.2015) for their support of this research.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical statement

This article does not contain any studies with human participants or animals performed by any of the authors.


  1. Abbassi-Guendouz A, Trably E, Hamelin J, Dumas C, Steyer JP, Delgenès JP, Escudié R (2013) Microbial community signature of high-solid content methanogenic ecosystems. Bioresour Technol 133:256–262CrossRefPubMedGoogle Scholar
  2. Amin MM, Zilles JL, Greiner J, Charbonneau S, Raskin L, Morgenroth E (2006) Influence of the antibiotic erythromycin on anaerobic treatment of a pharmaceutical wastewater. Environ Sci Technol 40:3971–3977CrossRefPubMedGoogle Scholar
  3. Aydin S, Shahi A, Ozbayram EG, Ince B, Ince O (2015a) Use of PCR-DGGE based molecular methods to assessment of microbial diversity during anaerobic treatment of antibiotic combinations. Bioresour Technol 192:735–740CrossRefPubMedGoogle Scholar
  4. Aydin S, Ince B, Ince O (2015b) Development of antibiotic resistance genes in microbial communities during long-term operation of anaerobic reactors in the treatment of pharmaceutical wastewater. Water Res 83:337–344CrossRefPubMedGoogle Scholar
  5. Aydin S, Ince B, Ince O (2015c) Application of real-time PCR to determination of combined effect of antibiotics on bacteria, methanogenic archaea. Archaea in anaerobic sequencing batch reactors. Water Res 76:88–98CrossRefPubMedGoogle Scholar
  6. Aydin S, Ince B, Ince O (2016a) Assessment of anaerobic bacterial diversity and its effects on the anaerobic system stability and the occurrence of resistance genes. Bioresour Technol 207:332–338CrossRefPubMedGoogle Scholar
  7. Aydin S (2016b) Enhanced biodegradation of antibiotic combinations via the sequential treatment of the sludge resulting from pharmaceutical wastewater treatment using white-rot fungi Trametes versicolor and Bjerkandera adusta. Appl Microbiol Biotechnol 1–9Google Scholar
  8. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Anastasi C (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59CrossRefPubMedPubMedCentralGoogle Scholar
  9. Camarinha-Silva A, Jáuregui R, Chaves-Moreno D, Oxley A, Schaumburg F, Becker K, Pieper DH (2014) Comparing the anterior nare bacterial community of two discrete human populations using Illumina amplicon sequencing. Environ Microbiol 16:2939–2952CrossRefPubMedGoogle Scholar
  10. Cardenas E, Tiedje JM (2008) New tools for discovering and characterizing microbial diversity. Curr Opin Biotechnol 19:544–549CrossRefPubMedGoogle Scholar
  11. Cetecioglu Z, Ince B, Gros M, Rodriguez-Mozaz S, Barceló D, Orhon D, Ince O (2013) Chronic impact of tetracycline on the biodegradation of an organic substrate mixture under anaerobic conditions. Water Res 47:2959–2969CrossRefPubMedGoogle Scholar
  12. Christgen B, Yang Y, Ahammad SZ, Li B, Rodriquez DC, Zhang T, Graham DW (2015) Metagenomics shows that low-energy anaerobic-aerobic treatment reactors reduce antibiotic resistance Gene levels from domestic wastewater. Environ Sci Technol 49:2577–2584CrossRefPubMedGoogle Scholar
  13. Hamady M, Knight R (2009) Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res 19:1141–1152CrossRefPubMedPubMedCentralGoogle Scholar
  14. Hayes JL, Tzika A, Thygesen H, Berri S, Wood HM, Hewitt S, Taylor GR (2013) Diagnosis of copy number variation by Illumina next generation sequencing is comparable in performance to oligonucleotide array comparative genomic hybridisation. Genomics 102:174–181CrossRefPubMedGoogle Scholar
  15. Kim J, Lim J, Lee C (2013) Quantitative real-time PCR approaches for microbial community studies in wastewater treatment systems: applications and considerations. Biotechnol Adv 31:1358–1373CrossRefPubMedGoogle Scholar
  16. Lautenschlager K, Hwang C, Ling F, Liu WT, Boon N, Köster O, Hammes F (2014) Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant. Water Res 62:40–52CrossRefPubMedGoogle Scholar
  17. Ma J, Frear C, Wang ZW, Yu L, Zhao Q, Li X, Chen S (2013) A simple methodology for rate-limiting step determination for anaerobic digestion of complex substrates and effect of microbial community ratio. Bioresour Technol 134:391–395CrossRefPubMedGoogle Scholar
  18. Meng LW, Li XK, Wang K, Ma KL, Zhang J (2015) Influence of the amoxicillin concentration on organics removal and microbial community structure in an anaerobic EGSB reactor treating with antibiotic wastewater. Chem Eng J 274:94–101CrossRefGoogle Scholar
  19. Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11:31–46CrossRefPubMedGoogle Scholar
  20. Nagarajan K, Loh KC (2014) Molecular biology-based methods for quantification of bacteria in mixed culture: perspectives and limitations. Appl Microbiol Biotechnol 98:6907–6919CrossRefPubMedGoogle Scholar
  21. Ng KK, Shi X, Ng HY (2015) Evaluation of system performance and microbial communities of a Bioaugmented anaerobic membrane bioreactor treating pharmaceutical wastewater. Water Res 81:311–324CrossRefPubMedGoogle Scholar
  22. Ng KK, Shi X, Ong SL, Ng HY (2016) Pyrosequencing reveals microbial community profile in anaerobic bio-entrapped membrane reactor for pharmaceutical wastewater treatment. Bioresour Technol 200:1076–1079CrossRefPubMedGoogle Scholar
  23. Oktem YA, Ince O, Sallis P, Donnelly T, Ince BK (2008) Anaerobic treatment of a chemical synthesis-based pharmaceutical wastewater in a hybrid upflow anaerobic sludge blanket reactor. Bioresour Technol 99:1089–1096CrossRefPubMedGoogle Scholar
  24. Parson W, Strobl C, Huber G, Zimmermann B, Gomes SM, Souto L, Lagacé R (2013) Evaluation of next generation mtGenome sequencing using the ion torrent personal genome machine (PGM). Forensic Sci Int Genet 7:543–549CrossRefPubMedPubMedCentralGoogle Scholar
  25. Prest EI, El-Chakhtoura J, Hammes F, Saikaly PE, Van Loosdrecht MCM, Vrouwenvelder JS (2014) Combining flow cytometry and 16S rRNA gene pyrosequencing: a promising approach for drinking water monitoring and characterization. Water Res 63:179–189CrossRefPubMedGoogle Scholar
  26. Rastogi G, Sani RK (2011) Molecular techniques to assess microbial community structure, function, and dynamics in the environment. In Microbes and microbial technology (pp. 29–57). Springer New York.Google Scholar
  27. Resende JA, Silva VL, de Oliveira TLR, de Oliveira FS, da Costa CJ, Otenio MH, Diniz CG (2014) Prevalence and persistence of potentially pathogenic and antibiotic resistant bacteria during anaerobic digestion treatment of cattle manure. Bioresour Technol 153:284–291CrossRefPubMedGoogle Scholar
  28. Rothberg JM, Leamon JH (2008) The development and impact of 454 sequencing. Nat Biotechnol 26:1117–1124CrossRefPubMedGoogle Scholar
  29. Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, Clinton SM (2009) Molecular diversity of a North Carolina wastewater treatment plant as revealed by pyrosequencing. Appl Environ Microbiol 75:1688–1696CrossRefPubMedPubMedCentralGoogle Scholar
  30. Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14:303–310CrossRefPubMedGoogle Scholar
  31. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145CrossRefPubMedGoogle Scholar
  32. Simon C, Daniel R (2009) Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol 85:265–276CrossRefPubMedPubMedCentralGoogle Scholar
  33. Stams AJ, Sousa DZ, Kleerebezem R, Plugge CM (2012) Role of syntrophic microbial communities in high-rate methanogenic bioreactors. Water Sci Technol 66:352–362CrossRefPubMedGoogle Scholar
  34. Smith CJ, Osborn AM (2009) Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiol Ecol 67:6–20CrossRefPubMedGoogle Scholar
  35. Taupp M, Mewis K, Hallam SJ (2011) The art and design of functional metagenomic screens. Curr Opin Biotechnol 22:465–472CrossRefPubMedGoogle Scholar
  36. Tringe SG, Hugenholtz P (2008) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11:442–446CrossRefPubMedGoogle Scholar
  37. Vanwonterghem I, Jensen PD, Ho DP, Batstone DJ, Tyson GW (2014) Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Curr Opin Biotechnol 27:55–64CrossRefPubMedGoogle Scholar
  38. Wittwer CT, Herrmann MG, Moss AA, Rasmussen RP (1997) Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotech 22:130–139Google Scholar
  39. Yang Y, Li B, Zou S, Fang HH, Zhang T (2014) Fate of antibiotic resistance genes in sewage treatment plant revealed by metagenomic approach. Water Res 62:97–106CrossRefPubMedGoogle Scholar
  40. Yu Y, Kim J, Hwang S (2006) Use of real-time PCR for group-specific quantification of aceticlastic methanogens in anaerobic processes: population dynamics and community structures. Biotechnol Bioeng 93:424–433CrossRefPubMedGoogle Scholar
  41. Zhang T, Yang Y, Pruden A (2015) Effect of temperature on removal of antibiotic resistance genes by anaerobic digestion of activated sludge revealed by metagenomic approach. Appl Microbiol Biotechnol 99:7771–7779CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.BioCore Biotechnology Environmental and Energy Technologies R&D Ltd.IstanbulTurkey

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