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Microbial Communities’ Characterization in Urban Recreational Surface Waters Using Next Generation Sequencing

  • Microbiology of Aquatic Systems
  • Published:
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Abstract

Microbial communities in surface waters used for recreational purposes are indicators of contamination and risk of contact with human pathogens. Hence, monitoring microbial communities in recreational waters is important for potential public health threats to humans. Such monitoring is rare in Colombia, even in its capital, Bogotá, the most populous city in the country. This city encompasses metropolitan and linear parks with recreational water bodies that are used frequently by the public, and the presence of pathogens can compromise the health of the citizens. Therefore, we examined the bacterial, and eukaryotic communities in urban recreational lakes (URL) in four metropolitan parks in Bogotá, Colombia. Samples from four metropolitan parks (Los Novios, Simon Bolivar, El Tunal, and Timiza) and one stream contaminated with sewage from a linear park (El Virrey) were collected. We used amplicon next-generation sequencing of the 16S-rRNA gene and 18S-rRNA gene to characterize microbial communities followed by bioinformatics analyses. In addition, general water quality parameters—pH, hardness, acidity, alkalinity, dissolved oxygen, and nitrites—were recorded using a commercial kit. Genera of pathogens, including Legionella, Pseudomonas, Mycobacterium, Candida, and Naegleria, were found in lake waters. The stream El Virrey was, however, the only surface water that showed an abundance of fecal bacteria, often associated with low oxygen concentrations. All water bodies showed a predominance of fungal phyla, except for the lake at Timiza. This lake showed the highest pH, and its ecological dynamics are likely different from other water bodies. Likewise, some URLs displayed a greater abundance of cyanobacteria, including toxin-producing species. Algal genera associated with eutrophication were predominant among primary producing microorganisms. This study shows for the first time the description of the bacterial and eukaryotic communities of some URLs and a stream in Bogotá. The URLs and the stream harbored various pathogens that might pose a risk to the citizen’s health.

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Data Availability

The datasets generated and/or analyzed during the current study will be available in the The European Nucleotide Archive (ENA) repository. Study accession number: PRJEB38738.

Abbreviations

MC:

Microbial communities

URL:

Urban recreational lake

NGS:

Next generation sequencing

ASV:

Amplicon sequence variant

NTM:

Nontuberculous mycobacteria

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Acknowledgments

The authors would like to thank to the subdirector of the Instituto Distrital de Recreación y Deporte (IDRD), Javier Suarez, for giving us the authorization to collect the water samples in the water bodies of the metropolitan and linear parks of Bogotá. The authors would also like to thank Milena Camargo for her support in sample transportation to the Laboratory of Microbiology at Universidad del Rosario. Finally, the authors thank Enago editing service for editing a draft of this manuscript that was supported by the Dirección de Investigación e Innovación from Universidad del Rosario.

Funding

This work was funded by DIRECCIÓN DE INVESTIGACIÓN E INNOVACIÓN from Universidad del Rosario.

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Authors and Affiliations

  1. Grupo de Investigaciones Microbiológicas- UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 110221, Colombia

    Laura Vega, Jesús Jaimes, Duvan Morales, David Martínez, Lissa Cruz-Saavedra, Marina Muñoz & Juan David Ramírez

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  1. Laura Vega
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  2. Jesús Jaimes
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  3. Duvan Morales
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  4. David Martínez
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  5. Lissa Cruz-Saavedra
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  6. Marina Muñoz
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  7. Juan David Ramírez
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Contributions

J.D.R and L.C.S designed the experimental design of the present study. J.J., D.M.M, D.M., and L.V collected and processed the samples in the laboratory. M.M and L.V performed the bioinformatic and descriptive analyzes. M.M and J.D.R revised and edited the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Juan David Ramírez.

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The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Supplementary Information

Additional file 1

Description: Environmental parameters of the five sampled water bodies. (CSV 244 bytes)

Additional file 2

Coliform cultures belonging to the four URLs and the stream of the study. Red colonies in the Nutrient-TCC agar of (A) Los Novios, (B) Simon Bolivar, (C) Timiza, (D) El Tunal, and (E) El Virrey confirm the presence of aerobic coliforms. (F) El Virrey stream was the only water body that exhibited bacterial growth in the MacConkey agar. Each cross in the agar surface represents a size of 4 mm. (PDF 1857 kb)

Additional file 3

Heatmap of the relative abundance of the bacterial genera classified as “not identified” and underwent a posterior classification with BLASTn. (PDF 553 kb)

Additional file 4

Representation of relative abundances of (A) fungi genera with a relative abundance higher than 1%, within the five water bodies. (B) Representation of the relative abundance of Candida species found within the water bodies. (PDF 264 kb)

Additional file 5

Photographs taken in the metropolitan park Los Novios where (A) citizens take rides in water bicycles within Los Novios URL and where (B) birds such as ducks and geese are observed inhabiting the URL. (PDF 970 kb)

Additional file 6

Photographs taken in the metropolitan park Simon Bolivar where (A) citizen take rides in boats and (B) in water bicycles within the URL where some waterborne pathogens are present. (PDF 831 kb)

Additional file 7

Photographs taken in the metropolitan park Timiza where (A) birds such as geese and ducks can be seen swimming in the URL. (B) photograph of pets in close contact with the URL. (PDF 954 kb)

Additional file 8

Photographs taken in the metropolitan park El Tunal where (A) pets enter the water of the URL, which shows waterborne pathogens. (B) The fountain at this URL might facilitate the airborne transmission of some pathogens by aerosols or microdroplets. (PDF 750 kb)

Additional file 9

Photographs taken in the linear park El Virrey where (A) El Virrey stream can be visualized as a shallow water body with contamination by sewage water and also (B) the stream contamination by solid waste. (PDF 1014 kb)

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Vega, L., Jaimes, J., Morales, D. et al. Microbial Communities’ Characterization in Urban Recreational Surface Waters Using Next Generation Sequencing. Microb Ecol 81, 847–863 (2021). https://doi.org/10.1007/s00248-020-01649-9

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  • DOI: https://doi.org/10.1007/s00248-020-01649-9

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