Abstract
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.
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References
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Baker BJ, Hugenholtz P, Dawson SC, Banfield JF (2003) Extremely acidophilic protists from acid mine drainage host brichettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Appl Environ Microbiol 69:5512–5518
Chen SG, Xu MQ, Cao H, Zhu J, Zhou KX, Xu J et al (2004) The activated-sludge fauna and performance of five sewage treatment plants in Beijing, China. Eur J Protistol 40:147–152
Chouari R, Le Paslier D, Daegelen P, Ginestet P, Weissenbach J, Sghir A (2003) Molecular evidence for novel planctomycete diversity in a municipal wastewater treatment plant. Appl Environ Microbiol 69:7354–7363
Chouari R, Le Paslier D, Daegelen P, Ginestet P, Weissenbach J, Sghir A (2005) Novel predominant archaeal and bacterial groups revealed by molecular analysis of anaerobic sludge digester. Environ Microbiol 7:1104–1115
Curds CR (1982) The ecology and role of protozoa in aerobic sewage treatment processes. Ann Rev Microbiol 36:27–46
Curds CR, Cockburn A (1970) Protozoa in biological sewage treatment processes-II. Protozoa as indicators in the activated-sludge process. Water Res 4:237–249
Dopheide A, Lear G, Stott R, Lewis G (2011) Preferential feeding by the ciliates Chilodonella and Tetrahymena spp. and effects of these protozoa on bacterial biofilm structure and composition. Appl Environ Microbiol 77:4564–4572
Drzewicki A, Kulikowska D (2011) Limitation of sludge biotic index application for control of a wastewater treatment plant working with shock organic and ammonium loadings. Eur J. Protistol 47:287–294
Dubber D, Gray NF (2011) The effect of anoxia and anaerobia on ciliate community in biological nutrient removal systems using laboratory-scale sequencing batch reactors (SBRs). Water Res 45:2213–2226
Evans TN, Seviour RJ (2012) Estimating biodiversity of fungi in activated sludge communities using culture-independent methods. Microb Ecol 63:773–786
Fialkowska E, Pajdak-Stós A (2008) The role of Lecane rotifers in activated sludge bulking control. Water Res 42:2483–2490
Foissner W, Blatterer H, Berger H, Kohmann F (1991) Taxonomische und Ökologische Revision der Ciliaten des Saprobiensystems—Band I: Cyrtophorida, Oligotrichida, Hypotrichida, Colpodea. Informationsber. des Bayer. Landesamtes f. Wasserwirtschaft, Heft 1/91, München
Foissner W, Berger H, Kohmann F (1992). Taxonomische und Ökologische Revision der Ciliaten des Saprobiensystems—Band II: Peritrichia, Heterotrichida, Odontostomatida. Informationsber. des Bayer. Landesamtes f. Wasserwirtschaft, Heft 5/92, München
Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40:237–264
Hu B, Qi R, An W, Xu M, Zhang Y, Bai X, Bao H, Wen Y, Gu J, Yang M (2013) Dynamics of the microfauna community in a full-scale municipal wastewater treatment plant experiencing sludge bulking. Eur J Protistol 49:491–499
Jiang JG, Shen YF (2003) Development of a biotic index using the correlation of protozoan communities with chemical water quality. NZ J Mar Freshw Res 37:777–792.
Juretschko S, Timmermann G, Schmid M, Schleifer KH, Pommerening-Roser A, Koops HP et al (1998) Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations. Appl Environ Microbiol 64:3042–3051
Lara E, Moreira D, López-García P (2010) The environmental clade LKM11 and Rozella form the deepest branching clade of Fungi. Protist 161:116–121
Liu J, Yang M, Qi R, An W, Zhou J (2008) Comparative study of protozoan communities in full-scale MWTPs in Beijing related to treatment processes. Water Res 42:1907–1918
Lopez-Garcia P, Rodriguez-Valera F, Pedros-Alio C, Moreira D (2001) Unexpected diversity of small eucaryotes in deep sea Antarctic plankton. Nature 409:603–607
Madoni P (1988) I protozoi ciliati nel controllo di efficienza dei fanghi attivi. CISBA, Reggio Emilia, pp 1–82
Madoni P (1994) A sludge biotic index (SBI) for the evaluation of the biological performance of activated sludge plants based on the microfauna analysis. Water Res 28:67–75
Madoni P (2003) Protozoa as indicators of wastewater treatment efficiency. In: Mara D, Horan N (eds) The handbook of water and wastewater microbiology. Academic Press, London, pp 361–373
Madoni P, Davoli D, Chierici E (1993) Comparative analysis of the activated sludge microfauna in several sewage treatment works. Water Res 27:1485–1491
Marsh TL, Liu WT, Forney LJ, Cheng H (1998) Beginning a molecular analysis of the eukaryal community in activated sludge. Water Sci Technol 37:455–460
Martin-Cereceda M, Pérez-Uz B, Serrano S, Guinea A (2001) Dynamics of protozoan and metazoan communities in a full scale wastewater treatment plant by rotating biological contactors. Microbiol Res 156:225–238
Martínez ÁT, Speranza M, Ruiz-Dueñas FJ, Ferreira P, Camarero S, Guillén F, Martínez MJ, Gutiérrex A, del Río JC (2005) Biodegradation of lignocellulosics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin. Int J Microbiol 8:195–204
Matsunaga K, Kubota K, Harada H (2014) Molecular diversity of eukaryotes in municipal waste water treatment processes as revealed by 18S rRNA gene analysis. Microbes Environ 29:401–407
Moreno AM, Matz C, Kjelleberg S, Manefield M (2010) Identification of ciliate grazers of autotrophic bacteria in ammonia-oxidizing activated sludge by RNA stable isotope probing. Appl Environ Microbiol 76:2203–2211
Ntougias S, Tanasidis S, Melidis P (2011) Microfaunal indicators, Ciliophora phylogeny and protozoan populations shifts in an intermittently aerated and fed bioreactor. J Hazard Mater 186:1862–1869
Papadimitriou CA, Papatheodoulou A, Takavakoglou V, Zdragas A, Samaras P, Sakellaropoulos GP, Lazaridou M, Zalidis G (2010) Investigation of protozoa as indicators of wastewater treatment efficiency in constructed wetlands. Desalin J 250:378–382
Priya M, Haridas A, Manilal VB (2007) Involvement of protozoa in anaerobic wastewater treatment process. Water Res 41:4639–4645
Rivière D, Desvignes V, Pelletier E, Chaussonnerie S, Guermazi S, Weissenbach J, Li T, Camacho P, Sghir A (2009) Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME J 3:700–714
Salvado H, Gracia MP, Amigo JM (1995) Capability of ciliated protozoa as indicators of effluent quality in activated-sludge plants. Water Res 29:1041–1050
Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
van Hannen EJ, Mooij W, van Agterveld MP, Gons HJ, Laanbroek HJ (1999) Detritus-dependent development of the microbial community in an experimental system: qualitative analysis by denaturing gradient gel electrophoresis. Appl Environ Microbiol 65:2478–2484
Yiannakopoulou TV, Kaimakamidou V (2009) Testing the reliability of protozoa as indicators of wastewater treatment plant performance. Fresenius Environ Bull 18:146–157
Acknowledgements
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.
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Rakia Chouari, Marie Leonard, Moez Bouali and Sonda Guermazi have contributed equally to this work.
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Chouari, R., Leonard, M., Bouali, M. et al. Eukaryotic molecular diversity at different steps of the wastewater treatment plant process reveals more phylogenetic novel lineages. World J Microbiol Biotechnol 33, 44 (2017). https://doi.org/10.1007/s11274-017-2217-6
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DOI: https://doi.org/10.1007/s11274-017-2217-6