e-ISSN 2231-8534
ISSN 0128-7702

Home / Regular Issue / JSSH Vol. 32 (1) Jan. 2024 / JST-3934-2022


Physicochemical Impacts on Bacterial Communities in Putrajaya Lake, Malaysia

Nurul Najwa Farihah Mat Lazim, Afiqah Mohamed, Zana Ruhaizat Zana Rudin, Fatimah Md Yusoff, Ikhsan Natrah and Shahrizim Zulkifly

Pertanika Journal of Social Science and Humanities, Volume 32, Issue 1, January 2024


Keywords: 16S rRNA, bacterial community, engineered wetlands, physicochemical, water quality

Published on: 15 January 2024

This study determines the associations between the bacterial communities and water physicochemical parameters in Putrajaya Lake and Putrajaya Wetlands Park, Malaysia. Bacterial communities were assessed by metagenomics of the 16S rRNA gene from lake water input, central wetlands, and primary lake area. Water samples (n=18) were collected during two different periods: post-high rainfall events (samples collected in May) and dry periods (July). The data revealed that bacterial communities of the three sites were taxonomically distinct and associated with different environmental parameters. However, no significant differences were found between the wet and dry periods. Alpha diversity analyses revealed the highest index in May 2018 in the constructed wetlands (H’= 5.397) than those from water input or primary lake (p<0.05). Overall, 49 phyla, 147 classes, 284 orders, 471 families, 778 genera and 62 species of bacteria were identified. Verrumicrobia and Firmicutes showed a strong positive correlation with ammonia-nitrogen (r = 0.709). Actinobacteria and Cyanobacteria had a moderate positive correlation with nitrate with r value (r = 0.673) and (r = 0.647), respectively. In this study, the metagenomics of the 16S rRNA gene amplicon by Illumina MiSeq has successfully identified the bacterial community assemblage in Putrajaya Lake and wetlands. Bacterial composition was associated with the availability of physicochemical properties of specific sites. The effectiveness of the engineered wetlands of Putrajaya in bioremediation was demonstrated by the marked decrease in certain nutrient concentrations from lake water input to the primary lake area.

  • Abidin, Z. A. Z., Zolkefli, N., Shahari, R., & Chowdhury, A. J. K. (2020). Endophytic bacteria of Anisophyllea disticha (Raja berangkat) from tropical lake environment in Malaysia. Desalination and Water Treatment, 188, 282-287.

  • Al-Sulaiman, S. A. A. W. (2012). Chemical safety of drinking-water: Assessing priorities for risk management. International Journal of Environmental Studies, 69(6), 1001.

  • Anjur, N., Sabran, S. F., Daud, H. M., & Othman, N. Z. (2021). An update on the ornamental fish industry in Malaysia: Aeromonas hydrophila-associated disease and its treatment control. Veterinary World, 14(5), 1143-1152.

  • APHA. (2005). Standard Methods for the Examination of Water and Wastewater (21st ed.). Washington DC. American Public Health Association.

  • Asmat, A., Hazali, N. A., Nor, A. N. M., & Zuhan, F. K. (2018). Seasonal-spatial of Putrajaya Lake Water Quality Parameter (WQP) concentration using geographic information system (GIS). International Journal of Engineering & Technology, 7(3), 176-181.

  • Batrich, M., Maskeri, L., Schubert, R., Ho, B., Kohout, M., Abdeljaber, M., Abuhasna, A., Kholoki, M., Psihogios, P., Razzaq, T., Sawhney, S., Siddiqui, S., Xoubi, E., Cooper, A., Hatzopoulos, T., & Putonti, C. (2019). Pseudomonas diversity within urban freshwaters. Frontiers in Microbiology, 10, Article 195.

  • Briones, A., & Raskin, L. (2003). Diversity and dynamics of microbial communities in engineered environments and their implications for process stability. Current Opinion in Biotechnology, 14(3), 270-276.

  • Chen, Z., Hui, P. C., Hui, M., Yeoh, Y. K., Wong, P. Y., Chan, M. C. W., Wong, M. C. S., Ng, S. C., Chan, F. K. L., & Chan, P. K. S. (2019). Impact of preservation method and 16S rRNA hypervariable region on gut microbiota profiling. MSystems, 4(1), 1-15.

  • Chokmangmeepisarn, P., Thangsunan, P., Kayansamruaj, P., & Rodkhum, C. (2021). Resistome characterization of Flavobacterium columnare isolated from freshwater cultured Asian sea bass (Lates calcarifer) revealed diversity of quinolone resistance associated genes. Aquaculture, 544, Article 737149.

  • Clarke, K. R., & Gorley, R. N. (2006). Primer v. 6: User manual/Tutorial. Scientific Research Publishing Inc.

  • Colquhoun, D. R., Hartmann, E. M., & Halden, R. U. (2012). Proteomic profiling of the dioxin-degrading bacterium Sphingomonas wittichii RW1. Journal of Biomedicine and Biotechnology, 2012, Article 408690.

  • Cotner, J. B., & Biddanda, B. A. (2002). Small players, large role: Microbial influence on biogeochemical processes in pelagic aquatic ecosystems. Ecosystems, 5(2), 105-121.

  • Davis, H. S. (2011). A New Bacterial Disease of Fresh-Water Fishes. US Government Printing Office.

  • Edgar, R. C. (2013). UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10, 996-998.

  • Elgendy, M. Y., Abdelsalam, M., Mohamed, S. A., & Ali, S. E. (2022). Molecular characterization, virulence profiling, antibiotic susceptibility, and scanning electron microscopy of Flavobacterium columnare isolates retrieved from Nile tilapia (Oreochromis niloticus). Aquaculture International, 30, 845-862.

  • Fadrosh, D. W., Ma, B., Gajer, P., Sengamalay, N., Ott, S., Brotman, R. M., & Ravel, J. (2014). An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome, 2(6), 1-7.

  • Fierer, N., Bradford, M. A., & Jackson, R. B. (2007). Toward an ecological classification of soil bacteria. Ecology, 88(6), 1354-1364.

  • Flynn, J. M., Brown, E. A., Chain, F. J. J., Macisaac, H. J., & Cristescu, M. E. (2015). Toward accurate molecular identification of species in complex environmental samples: Testing the performance of sequence filtering and clustering methods. Ecology and Evolution, 5(11), 2252-2266.

  • Gane, A. (2018). Size selection brings better data to NGS workflows. Cytiva.

  • Glibert, P. M., Wilkerson, F. P., Dugdale, R. C., Raven, J. A., Dupont, C. L., Leavitt, P. R., Parker, A. E., Burkholder, J. M., & Kana, T. M. (2016). Pluses and minuses of ammonium and nitrate uptake and assimilation by phytoplankton and implications for productivity and community composition, with emphasis on nitrogen-enriched conditions. Limnology and Oceanography, 61(1), 165-197.

  • Gomes, G. B., Hutson, K. S., Domingos, J. A., Villamil, S. I., Huerlimann, R., Miller, T. L., & Jerry, D. R. (2019). Parasitic protozoan interactions with bacterial microbiome in a tropical fish farm. Aquaculture, 502, 196-201.

  • Good, C., Davidson, J., Wiens, G. D., Welch, T. J., & Summerfelt, S. (2015). Flavobacterium branchiophilum and F. succinicans associated with bacterial gill disease in rainbow trout Oncorhynchus mykiss (Walbaum) in water recirculation aquaculture systems. Journal of Fish Diseases, 38(4), 409-413.

  • Gupta, V., Ratha, S. K., Sood, A., Chaudhary, V., & Prasanna, R. (2013). New insights into the biodiversity and applications of cyanobacteria (blue-green algae) - Prospects and challenges. Algal Research, 2(2), 79-97.

  • Hach, C. (2002). Water Analysis Handbook. Loveland Publishers & Pioneers.

  • Hakim, M., Heryansyah, A., & Ismail, T. (2016, June 7-8). Sustainability in water resources management in Putrajaya wetland: Impact assessment on new emerging pollutants. In 1st Proceeding of Civil Engineering (pp. 301-317). Universiti Teknologi Malaysia, Malaysia.

  • Hassan, N. L., Kam, K. Y., & Zain, N. A. M. (2020). Isolation of antibiotic resistant bacteria from rivers in Kelantan, Malaysia. International Journal of Life Sciences and Biotechnology, 3(2), 291-307.

  • Huang, W., Chen, X., Jiang, X., & Zheng, B. (2017). Characterization of sediment bacterial communities in plain lakes with different trophic statuses. MicrobiologyOpen, 6(5), 1-14.

  • Huang, Y. F., Ang, S. Y., Lee, K. M., & Lee, T. S. (2015). Quality of water resources in Malaysia. In Research and Practices in Water Quality (pp. 65-94). InTech.

  • Iliev, I., Yahubyan, G., Marhova, M., Apostolova, E., Gozmanova, M., Gecheva, G., Kostadinova, S., Ivanova, A., & Baev, V. (2017). Metagenomic profiling of the microbial freshwater communities in two Bulgarian reservoirs. Journal of Basic Microbiology, 57(8), 669-679.

  • Jaapar, A. R., Ahba, N. A., & Hussin, A. (2002, May 26). The occurrence and classification of hard rock body in Putrajaya and its implication to construction activities. Bulletin of the Geological Society of Malaysia, 45, 123-128.

  • Jamal, A., Yusoff, F. M., Banerjee, S., & Shariff, M. (2014). Littoral and limnetic phytoplankton distribution and biodiversity in a tropical man-made lake, Malaysia. Advanced Studies in Biology, 6(4), 149-168.

  • Jo, J. H., Kennedy, E. A., & Kong, H. H. (2016). Research techniques made simple: Bacterial 16S ribosomal RNA gene sequencing in cutaneous research. Journal of Investigative Dermatology, 136(3), e23-e27.

  • Kragh, T., Martinsen, K. T., Kristensen, E., & Sand-Jensen, K. (2020). From drought to flood: Sudden carbon inflow causes whole-lake anoxia and massive fish kill in a large shallow lake. Science of the Total Environment, 739, Article 140072.

  • Kuczynski, J., Stombaugh, J., Walters, W. A., González, A., Caporaso, J. G., & Knight, R. (2012). Using QIIME to analyze 16s rRNA gene sequences from microbial communities. Current Protocols in Microbiology, 27(1), 1E.5.1-1E.5.20.

  • LaFrentz, B. R., García, J. C., Waldbieser, G. C., Evenhuis, J. P., Loch, T. P., Liles, M. R., Wong, F. S., & Chang, S. F. (2018). Identification of four distinct phylogenetic groups in Flavobacterium columnare with fish host associations. Frontiers in Microbiology, 9, Article 452.

  • Lange, M. D., Abernathy, J., & Farmer, B. D. (2019). Evaluation of a recombinant flavobacterium columnare DnaK protein vaccine as a means of protection against columnaris disease in channel catfish (Ictalurus punctatus). Frontiers in Immunology, 10, Article 1175.

  • Lange, M. D., Abernathy, J., Farmer, B. D., & Beck, B. H. (2021). Use of an immersion adjuvant with a Flavobacterium columnare recombinant protein vaccine in channel catfish. Fish and Shellfish Immunology, 117, 136-139.

  • Lau, N. S., Zarkasi, K. Z., Sah, A. S. R. M., & Shu-Chien, A. C. (2019). Diversity and coding potential of the microbiota in the photic and aphotic zones of tropical man-made lake with intensive aquaculture activities: A case study on Temengor Lake, Malaysia. Microbial Ecology, 78, 20-32.

  • Li, Q., Huang, Y., Wen, D., Fu, R., & Feng, L. (2020). Application of alkyl polyglycosides for enhanced bioremediation of petroleum hydrocarbon-contaminated soil using Sphingomonas changbaiensis and Pseudomonas stutzeri. Science of the Total Environment, 719, Article 137456.

  • Liles, M. R., Manske, B. F., Bintrim, S. B., Handelsman, J., & Goodman, R. M. (2003). A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Applied and Environmental Microbiology, 69(5), 2684-2691.

  • Loch, T. P., & Faisal, M. (2015). Emerging flavobacterial infections in fish: A review. Journal of Advanced Research, 6(3), 283-300.

  • Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J., & Knight, R. (2011). UniFrac: An effective distance metric for microbial community comparison. The ISME Journal, 5, 169-172.

  • Majizat, A., Ahmad, B., Noordin, N., & Sharip, Z. (2016). Adopting an integrated catchment-based management approach for Putrajaya Lake and Wetlands. International Journal of Water, 10(4), 343-358.

  • Mohamad, N. H. N. (2012). Ecological approaches in designing neighbourhood green spaces as urban wildlife habitat in the Klang valley, Peninsular Malaysia. International Journal of Applied Science and Technology, 2(3), 192-213.

  • Mueller-Spitz, S. R., Goetz, G. W., & McLellan, S. L. (2009). Temporal and spatial variability in nearshore bacterioplankton communities of Lake Michigan. FEMS Microbiology Ecology, 67(3), 511-522.

  • Najah, A., Teo, F. Y., Chow, M. F., Huang, Y. F., Latif, S. D., Abdullah, S., Ismail, M., & El-Shafie, A. (2021). Surface water quality status and prediction during movement control operation order under COVID-19 pandemic: Case studies in Malaysia. International Journal of Environmental Science and Technology, 18, 1009-1018.

  • Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D., & Bertilsson, S. (2011). A guide to the natural history of freshwater lake bacteria. Microbiology and Molecular Biology Reviews, 75(1), 14-49.

  • Oksanen, J. (2008). Vegan: An Introduction to Ordination.

  • Pernthaler, J., & Amann, R. (2005). Fate of heterotrophic microbes in pelagic habitats: Focus on populations. Microbiology and Molecular Biology Reviews, 69(3), 440-461.

  • Ponpukdee, N., Wangman, P., Rodkhum, C., Pengsuk, C., Chaivisuthangkura, P., Sithigorngul, P., & Longyant, S. (2021). Detection and identification of a fish pathogen Flavobacterium columnare using specific monoclonal antibodies. Aquaculture, 545, Article 737231.

  • Sabkie, N., Zulkifly, S., Lazim, N., Rosli, N., & Yong, C. (2020). Physico-chemical influence on the diversity of phytoplankton at Putrajaya Lake and Wetlands, Putrajaya, Malaysia. Malayan Nature Journal, 72(2), 153-163.

  • Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011). Metagenomic biomarker discovery and explanation. Genome Biology, 12, Article R60.

  • Sharip, Z., Saman, J. M., Noordin, N., Majizat, A., Suratman, S., & Shaaban, A. J. (2016). Assessing the spatial water quality dynamics in Putrajaya Lake: A modelling approach. Modeling Earth Systems and Environment, 2, Article 46.

  • Singh, S., Mallik, S. K., Kala, K., Shahi, N., Pathak, R., Giri, A. K., Chandra, S., Pant, K., & Patiyal, R. S. (2021). Characterization of Flavobacterium columnare from farmed infected rainbow trout, Oncorhynchus mykiss (Walbaum, 1792) of Central Indian Himalayan region, India. Aquaculture, 544, Article 737118.

  • Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. M., Huse, S. M., Neal, P. R., Arrieta, J. M., & Herndl, G. J. (2006). Microbial diversity in the deep sea and the underexplored “rare biosphere.” Proceedings of the National Academy of Sciences of the United States of America, 103(32), 12115-12120.

  • Staley, C., Unno, T., Gould, T. J., Jarvis, B., Phillips, J., Cotner, J. B., & Sadowsky, M. J. (2013). Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River. Journal of Applied Microbiology, 115(5), 1147-1158.

  • Struyf, E., van Damme, S., & Meire, P. (2004). Possible effects of climate change on estuarine nutrient fluxes: A case study in the highly nutrified Schelde estuary (Belgium, the Netherlands). Estuarine, Coastal and Shelf Science, 60(4), 649-661.

  • Suratman, S., Hussein, A. N. A. R., Tahir, N. M., Latif, M. T., Mostapa, R., & Weston, K. (2016). Seasonal and spatial variability of selected surface water quality parameters in Setiu Wetland, Terengganu, Malaysia. Sains Malaysiana, 45(4), 551-558.

  • Tan, G., Opitz, L., Schlapbach, R., & Rehrauer, H. (2019). Long fragments achieve lower base quality in Illumina paired-end sequencing. Scientific Reports, 9, Article 2856.

  • Viet, N. D., Bac, N. A., & Huong, H. T. T. (2016). Dissolved oxygen as an indicator for eutrophication in freshwater lakes. In Proceedings of International Conference on Environmental Engineering and Management for Sustainable Development (pp. 1-6). ResearchGate.

  • Vymazal, J. (2007). Removal of nutrients in various types of constructed wetlands. Science of the Total Environment, 380(1-3), 48-65.

  • Wan, Y., Ruan, X., Zhang, Y., & Li, R. (2017). Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes. MicrobiologyOpen, 6(4), Article e00450.

ISSN 0128-7702

e-ISSN 2231-8534

Article ID


Download Full Article PDF

Share this article

Related Articles