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Bacterial and eukaryotic microbial communities in urban water systems profiled via Illumina MiSeq platform

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Abstract

Microbial communities from a lake and river flowing through a highly dense urbanized township in Malaysia were profiled by sequencing amplicons of the 16S V3–V4 and 18S V9 hypervariable rRNA gene regions via Illumina MiSeq. Results revealed that Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the dominant prokaryotic phyla; whereas, eukaryotic communities were predominantly of the SAR clade and Opisthokonta. The abundance of Pseudomonas and Flavobacterium in all sites suggested the possible presence of pathogens in the urban water systems, supported by the most probable number (MPN) values of more than 1600 per 100 mL. Urbanization could have impacted the microbial communities as transient communities (clinical, water-borne and opportunistic pathogens) coexisted with common indigenous aquatic communities (Cyanobacteria). It was concluded that in urban water systems, microbial communities vary in their abundance of microbial phyla detected along the water systems. The influences of urban land use and anthropogenic activities influenced the physicochemical properties and the microbial dynamics in the water systems.

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Acknowledgments

We are grateful to Ms. Lee Sze Mei and Ms Lim Shu Yong from Monash University Malaysia Genomics Facility (MUMGF) for carrying out the DNA extraction and library preparation, and the Illumina MiSeq sequencing. This work was supported by the Monash University Malaysia Sustainable Community Grant Scheme 2018 (SDG-2018-01-ENG).

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Authors and Affiliations

  1. School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia

    Adeline Su Yien Ting, Muhammad Zarul Hanifah Md Zoqratt & Hock Siew Tan

  2. Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia

    Muhammad Zarul Hanifah Md Zoqratt

  3. School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia

    Andreas Aditya Hermawan, Amin Talei & Soon Thiam Khu

  4. School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 46150, Bandar Sunway, Selangor Darul Ehsan, Malaysia

    Adeline Su Yien Ting

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  1. Adeline Su Yien Ting
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  2. Muhammad Zarul Hanifah Md Zoqratt
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Contributions

ASYT: Conceptualization, methodology, data organization and interpretation, manuscript writing. HST: Initial mapping of sampling sites, data analysis and interpretation, manuscript review. MZHMZ: Bioinformatics analysis, data visualization and tabulation, manuscript review. AAH: Methodology, project administration, sample collection, investigation, manuscript review. AT: Conceptualization, methodology, resources, funding acquisition, project administration, manuscript review. STK: Conceptualization, methodology, resources, funding, manuscript review.

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Correspondence to Adeline Su Yien Ting.

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This research does not involve human participants and/or animals, therefore no human and/or animal ethical approval is required.

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Additional information

Accession numbers: All Fastq raw data can be accessed through NCBI BioProject accession ID PRJNA624028.

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Ting, A.S.Y., Zoqratt, M.Z.H.M., Tan, H.S. et al. Bacterial and eukaryotic microbial communities in urban water systems profiled via Illumina MiSeq platform. 3 Biotech 11, 40 (2021). https://doi.org/10.1007/s13205-020-02617-3

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