Skip to main content
SpringerLink
Log in

Neighbor urban wastewater treatment plants display distinct profiles of bacterial community and antibiotic resistance genes

  • Research Article
  • Published:
Environmental Science and Pollution Research Aims and scope Submit manuscript

Abstract

Urban wastewater treatment plants (UWTPs) are among the major recipients of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antibiotic residues in urban environments. Although during treatment, bacteria of human and animal origin are removed, some are able to survive, persisting in the final effluent. The occurrence of these bacteria, especially those harboring ARGs, may have a direct impact on the quality of the treated wastewater that is returned to the environment. In this study, we aimed to assess if the final effluent bacterial communities of three UWTPs (PT1, PT2, and PT3) located next to each other were distinct and if such differences were related with the antibiotic resistance profiles.

It was observed that the bacterial community (16S rRNA gene Illumina sequencing) and load of selected ARGs of final effluent differed among the three UWTPs, irrespective of sampling time. Members of the families Aeromonadaceae, Campylobacteraceae, Veillonellaceae, [Weeksellaceae], and Porphyromonadaceae were observed to be positively correlated with some ARGs (blaCTX–M, blaOXA-A, blaSHV) and intI1 (p < 0.05), while Intrasporangiaceae were observed to be negatively correlated. While Aeromonadaceae are recognized relevant ARG harbors, the other bacterial families may represent bacteria that co-exist with the ARG hosts, which may belong to minor bacterial groups omitted in the analyses. These findings suggest the importance of bacterial dynamics during treatment to the ARB&ARGs removal, a rationale that may contribute to design new strategies to apply in the UWTPs to prevent the spread of antibiotic resistance.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31:533–538. https://doi.org/10.1038/nbt.2579

    Article  CAS  Google Scholar 

  • Becerra-Castro C, Lopes AR, Teixeira S, Silva MEF, Pimenta E, Manaia CM, Nunes OC (2017) Characterization of bacterial communities from Masseiras, a unique Portuguese greenhouse agricultural system. Antonie van Leeuwenhoek, Int J Gen. Mol Microbiol 110:665–676. https://doi.org/10.1007/s10482-017-0833-7

    Article  Google Scholar 

  • Bengtsson-Palme J, Hammarén R, Pal C, Östman M, Björlenius B, Flach CF, Fick J, Kristiansson E, Tysklind M, Larsson DGJ (2016) Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics. Sci Total Environ 572:697–712. https://doi.org/10.1016/j.scitotenv.2016.06.228

    Article  CAS  Google Scholar 

  • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 57:289–300. https://doi.org/10.2307/2346101

    Article  Google Scholar 

  • Berendonk TU, Manaia CM, Merlin C, Fatta-Kassinos D, Cytryn E, Walsh F, Bürgmann H, Sørum H, Norström M, Pons MN, Kreuzinger N, Huovinen P, Stefani S, Schwartz T, Kisand V, Baquero F, Martinez JL (2015) Tackling antibiotic resistance: the environmental framework. Nat Rev Microbiol 13:310–317. https://doi.org/10.1038/nrmicro3439

    Article  CAS  Google Scholar 

  • Binh CTT, Petrovich ML, Chaudhary A, et al (2018) Metagenomics reveals the impact of wastewater treatment plants on the dispersal of microorganisms and genes in aquatic sediments. 84:1–15 https://doi.org/10.1128/AEM.02168-17

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. https://doi.org/10.1038/nmeth.f.303

    Article  CAS  Google Scholar 

  • Chao A (1984) Non-parametric estimation of the number of classes in a population 11:265–270

  • DeSantis TZ, Hugenholtz P, Larsen N et al (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072. https://doi.org/10.1128/AEM.03006-05

    Article  CAS  Google Scholar 

  • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461

    Article  CAS  Google Scholar 

  • Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 87:1–10. https://doi.org/10.1890/0012-9658(2006)87[1465:ATTFHF]2.0.CO;2

  • Figueira V, Serra E, Manaia CM (2011a) Differential patterns of antimicrobial resistance in population subsets of Escherichia coli isolated from waste- and surface waters. Sci Total Environ 409:1017–1023. https://doi.org/10.1016/j.scitotenv.2010.12.011

    Article  CAS  Google Scholar 

  • Figueira V, Vaz-Moreira I, Silva M, Manaia CM (2011b) Diversity and antibiotic resistance of Aeromonas spp. in drinking and waste water treatment plants. Water Res 45:5599–5611. https://doi.org/10.1016/j.watres.2011.08.021

    Article  CAS  Google Scholar 

  • Gatica J, Tripathi V, Green S, Manaia CM, Berendonk T, Cacace D, Merlin C, Kreuzinger N, Schwartz T, Fatta-Kassinos D, Rizzo L, Schwermer CU, Garelick H, Jurkevitch E, Cytryn E (2016) High throughput analysis of integron gene cassettes in wastewater environments. Environ Sci Technol 50:11825–11836. https://doi.org/10.1021/acs.est.6b03188

    Article  CAS  Google Scholar 

  • Ju F, Li B, Ma L, Wang Y, Huang D, Zhang T (2016) Antibiotic resistance genes and human bacterial pathogens: co-occurrence, removal, and enrichment in municipal sewage sludge digesters. Water Res 91:1–10. https://doi.org/10.1016/j.watres.2015.11.071

    Article  CAS  Google Scholar 

  • Kantor RS, Wrighton KC, Handley KM, Sharon I, Hug LA, Castelle CJ, Thomas BC, Banfield JF (2013) Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. MBio 4:e00708–e00713. https://doi.org/10.1128/mBio.00708-13

    Article  CAS  Google Scholar 

  • LaPara TM, Nakatsu CH, Pantea LM, Alleman JE (2002) Stability of the bacterial communities supported by a seven-stage biological process treating pharmaceutical wastewater as revealed by PCR-DGGE. Water Res 36:638–646. https://doi.org/10.1016/S0043-1354(01)00277-9

    Article  CAS  Google Scholar 

  • Leps J, Smilauer P (2014) Multivariate analysis of ecological data using CANOCO 5

  • Lozupone C, Knight R (2005) UniFrac : a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235. https://doi.org/10.1128/AEM.71.12.8228

    Article  CAS  Google Scholar 

  • Manaia CM, Macedo G, Fatta-Kassinos D, Nunes OC (2016) Antibiotic resistance in urban aquatic environments: can it be controlled? Appl Microbiol Biotechnol 100:1543–1557. https://doi.org/10.1007/s00253-015-7202-0

    Article  CAS  Google Scholar 

  • Manaia CM, Rocha J, Scaccia N, Marano R, Radu E, Biancullo F, Cerqueira F, Fortunato G, Iakovides IC, Zammit I, Kampouris I, Vaz-Moreira I, Nunes OC (2018) Antibiotic resistance in wastewater treatment plants: tackling the black box. Environ Int 115:312–324

    Article  CAS  Google Scholar 

  • Michael I, Rizzo L, McArdell CS et al (2013) Urban wastewater treatment plants as hotspots for the release of antibiotics in the environment: a review. Water Res 47:957–995. https://doi.org/10.1016/j.watres.2012.11.027

    Article  CAS  Google Scholar 

  • Moreira NFF, Narciso-da-Rocha C, Polo-López MI, Pastrana-Martínez LM, Faria JL, Manaia CM, Fernández-Ibáñez P, Nunes OC, Silva AMT (2018) Solar treatment (H 2 O 2, TiO 2-P25 and GO-TiO 2 photocatalysis, photo-Fenton) of organic micropollutants, human pathogen indicators, antibiotic resistant bacteria and related genes in urban wastewater. Water Res 135:195–206

    Article  CAS  Google Scholar 

  • Munck C, Albertsen M, Telke A, Ellabaan M, Nielsen PH, Sommer MOA (2015) Limited dissemination of the wastewater treatment plant core resistome. Nat Commun 6:8452. https://doi.org/10.1038/ncomms9452

    Article  CAS  Google Scholar 

  • Narciso-da-Rocha C, Rocha J, Vaz-Moreira I, Lira F, Tamames J, Henriques I, Martinez JL, Manaia CM (2018) Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant. Environ Int 118:179–188. https://doi.org/10.1016/j.envint.2018.05.040

    Article  CAS  Google Scholar 

  • Nelson WC, Stegen JC (2015) The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. Front Microbiol 6. https://doi.org/10.3389/fmicb.2015.00713

  • Parks DH, Tyson GW, Hugenholtz P, Beiko RG (2014) STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30:3123–3124

    Article  CAS  Google Scholar 

  • Paulson JN, Stine CO, Bravo HC, Pop M (2014) Robust methods for differential abundance analysis in marker gene surveys. Nat Methods 10:1200–1202. https://doi.org/10.1038/nmeth.2658.Robust

    Article  Google Scholar 

  • Rizzo L, Manaia C, Merlin C, Schwartz T, Dagot C, Ploy MC, Michael I, Fatta-Kassinos D (2013) Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review. Sci Total Environ 447:345–360. https://doi.org/10.1016/j.scitotenv.2013.01.032S0048-9697(13)00042-9 [pii]

    Article  CAS  Google Scholar 

  • Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863–864. https://doi.org/10.1093/bioinformatics/btr026

    Article  CAS  Google Scholar 

  • Shannon CE, Weaver W (1963) The mathematical theory of communication. University of Illinois Press, Urbana

    Google Scholar 

  • Simpson EH (1949) Measurement of diversity. Nature

  • Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL, A Weitz D, Pitkänen LK, Vigneault F, Virta MPJ, Alm EJ (2016) Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME J 10:427–436. https://doi.org/10.1038/ismej.2015.124

    Article  CAS  Google Scholar 

  • van den Wollenberg AL (1977) Redundancy analysis an alternative for canonical correlation analysis. Psychometrika 42:207–219

    Article  Google Scholar 

  • Vaz-Moreira I, Nunes OC, Manaia CM (2014) Bacterial diversity and antibiotic resistance in water habitats: searching the links with the human microbiome. FEMS Microbiol Rev 38:761–778

    Article  CAS  Google Scholar 

  • Vikesland PJ, Pruden A, Alvarez PJJ, Aga D, Bürgmann H, Li XD, Manaia CM, Nambi I, Wigginton K, Zhang T, Zhu YG (2017) Toward a comprehensive strategy to mitigate dissemination of environmental sources of antibiotic resistance. Environ Sci Technol 51:13061–13069. https://doi.org/10.1021/acs.est.7b03623

    Article  CAS  Google Scholar 

  • Wu D, Dolfing J, Xie B (2018) Bacterial perspectives on the dissemination of antibiotic resistance genes in domestic wastewater bio-treatment systems: beneficiary to victim. Appl Microbiol Biotechnol 102:597–604. https://doi.org/10.1007/s00253-017-8665-y

    Article  CAS  Google Scholar 

  • Ye L, Zhang T (2013) Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing. Appl Microbiol Biotechnol 97:2681–2690. https://doi.org/10.1007/s00253-012-4082-4

    Article  CAS  Google Scholar 

  • Zhang T, Shao M-F, Ye L (2012) 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J 6:1137–1147. https://doi.org/10.1038/ismej.2011.188

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors gratefully acknowledge the support of the staff of the UWTPs and supplying entities that made this study possible by providing the water samples; Christophe Merlin that kindly provided the integrase gene qPCR protocol and Gonçalo Macedo and Jaqueline Rocha for technical assistance on sampling, DNA extraction, and qPCR analysis.

Funding

This work was funded by National Funds from FCT – Fundação para a Ciência e a Tecnologia through project WaterJPI/0001/2013 STARE – “Stopping Antibiotic Resistance Evolution,” and UID/Multi/50016/2013. IVM was supported by the FCT grant (SFRH/BPD/87360/2012).

Author information

Author notes

  1. Telma Fernandes

    Present address: Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal

Authors and Affiliations

  1. Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal

    Telma Fernandes, Ivone Vaz-Moreira & Célia M. Manaia

Authors
  1. Telma Fernandes
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ivone Vaz-Moreira
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Célia M. Manaia
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Célia M. Manaia.

Ethics declarations

Conflict of interest statement

The authors declare that they have no conflict of interest.

Additional information

Responsible editor: Diane Purchase

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fernandes, T., Vaz-Moreira, I. & Manaia, C.M. Neighbor urban wastewater treatment plants display distinct profiles of bacterial community and antibiotic resistance genes. Environ Sci Pollut Res 26, 11269–11278 (2019). https://doi.org/10.1007/s11356-019-04546-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11356-019-04546-y

Keywords

Search

Navigation