Eukaryotic molecular diversity at different steps of the wastewater treatment plant process reveals more phylogenetic novel lineages

  • Rakia ChouariEmail author
  • Marie Leonard
  • Moez Bouali
  • Sonda Guermazi
  • Naima Rahli
  • Ines Zrafi
  • Loïc Morin
  • Abdelghani Sghir
Original Paper


Wastewater microbiota represents important actors of organic depollution. Nowadays, some species used as bioindicators of the effluent quality are still identified by microscopy. In the present study, we investigated eukaryotic diversity at the different steps of the treatment process of a wastewater treatment plant (aerobic, anaerobic, clarifier basins and anaerobic digester) using the 18S rRNA gene sequencing approach. Of the 1519 analysed sequences, we identified 160 operational taxonomic units. Interestingly, 56.9% of the phylotypes were assigned to novel phylogenetic molecular species since they show <97% sequence identity with their nearest affiliated representative within public databases. Peritrichia ciliates were the most predominant group, with Epistylis as the most common genus. Although anaerobic, the digester appears to harbor many unclassified phylotypes of protozoa species. Novel lineages such as LKM11 and LKM118 were widely represented in the digester. Diversity values given by Shannon indexes show that the clarifier is the most diversified. This work will help designing molecular tools that are fast, reliable, and reproducible for monitoring wastewater depollution and studying phylogenetic relationships among the wonderful world of protists within this anthropogenic ecosystem.


Activated sludge Ciliates Cryptomycota LKM118 Wastewater microbiota 18S rRNA gene 



We are very grateful to Susan Cure for reading the manuscript, the excellent technical assistance of the Genoscope sequencing team, Stephane Frenette for giving access to the Evry WWTP, M. Trouvé and D. Dehon for providing samples from the WWTP.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


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Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  • Rakia Chouari
    • 1
    Email author
  • Marie Leonard
    • 2
  • Moez Bouali
    • 3
  • Sonda Guermazi
    • 6
  • Naima Rahli
    • 5
  • Ines Zrafi
    • 4
  • Loïc Morin
    • 2
  • Abdelghani Sghir
    • 5
    • 7
    • 8
  1. 1.Faculté des Sciences de Bizerte, UR11ES32 Toxicologie Végétale et Biologie Moléculaire des Micro-organismesUniversité de CarthageBizerteTunisia
  2. 2.IBCI: Institut de Biologie Cellulaire Intégrative, UMR 9198, CEA-CNRS-UPSud, Université Paris-SudOrsay CedexFrance
  3. 3.Laboratoire d’Analyses, Traitement et Valorisation des Polluants de l’Environnement et des Produits, Faculté de PharmacieUniversité de MonastirMonastirTunisia
  4. 4.Technopole de Borj CedriaCERTESoliman, Hammam LifTunisia
  5. 5.Université d’Evry Val d’EssonneEvryFrance
  6. 6.Faculté des Sciences de GafsaUniversité de GafsaGafsaTunisia
  7. 7.Laboratoire de métagénomique des procaryotesCEA-GenoscopeEvryFrance
  8. 8.CNRS-UMR 8030EvryFrance

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