Comprehensive assessment of bacterial and functional diversity using next-generation high-throughput sequencing of two crucial lakes of Haryana, India
DOI:
https://doi.org/10.60923/issn.2281-4485/23912Keywords:
Lake Tilyar, Lake Karna, Bacterial profile, Bacterial diversity, 16S rRNA Sequencing, Illumina MiSeq, V3-V4sequenceAbstract
Lakes are dynamic and complex ecosystems where bacterial diversity is a significant biological indicator of water quality. In few decades, in India, several water bodies are reported to have pesticide and heavy metal pollutants. The present study conducted on two substantial lakes of Haryana, India, for analysing bacterial diversity using high-throughput Illumina 16S rRNA sequencing-MiSeq platform. Sequencing analysis showed that, in Karna lake, predominant phylum was Proteobacteria accounting (76.38%), Planctomycetes (6.42%), Verrucomicrobia (5.28 %) and Bacteroidetes (5.06%). Although, in Tilyar lake, predominant phylum was Proteobacteria (46.91%), Verrucobacteria (22.87%), Bacterioidetes (16.34 %), Planctomycetes (8.49%) and Acidobacteria (5.75 %). Tilyar lake exhibited higher alkalinity resulting in dominance of alkaliphilic phyla such as Verrucomicrobia (22.87%) and Bacteroidetes (16.34%). On contrary, Karna Lake with a relatively lower pH, showed a dominance of Proteobacteria (76.38%). The high DO in Tilyar lake, signifies better oxygenation attributing to greater abundance of aerobic bacterial communities. Differences in TDS, TSS and EC between the lakes reflect difference in nutrient influx, pollution sources and pollutant levels. A comparison of bacterial genera revealed 529 (47.4%) shared taxa in both lakes and 232 (20.8%) taxa unique to Karna lake and 356 (31.9%) taxa unique to Tilyar lake. Overall, higher microbial diversity and functional potential observed in Tilyar Lake suggest a more stable and ecologically resilient environment capable of withstanding environmental disturbances. While, dominance of a few specific taxa in Karna Lake indicates potential environmental constraints that may limiting microbial diversity.
References
ALTEIO L.V., SCHULZ F., SESHADRI R., VARGHESE N., RODRIGUEZ R.W., RYAN E., GOUDEAU D., EICHORST S.A., MALMSTROM R.R., BOWERS R.M., KATZ L.A., BLANCHARD J.L., WOYKE T. (2020) Com-plementary metagenomic approaches improve reconstruction of microbial diversity in a forest soil. mSystems 5:e00768-19 https://doi.org/10.1128/mSystems.00768-19
BAG S., BISWAL D., CHATTERJEE S. (2025). Comprehensive Analysis of Salt-Tolerant Extremophilic Bacterial Groups in the Coastal Belt of Digha, India. Geomicrobiology Journal, 42(10), 983–997. https://doi.org/10.1080/01490451.2025.2542863
BANDA J.F., LU Y., HAO C., PEI L., DU Z., ZHANG Y. WEI P., DONG H. (2020). The effects of salinity and pH on microbial community diversity and distribution pattern in the brines of Soda Lakes in Badain Jaran Desert, China. Geomicrobiology Journal, 37(1): 1-12. https://doi.org/10.1080/01490451.2019.1654568
BENSON J., HANLON R., SEIFRIED T.M., BALOH P., POWERS C.W., GROTHE H., DAVID G., SCHMALE D.G. (2019). Microorganisms collected from the surface of freshwater lakes using a drone water sampling system (DOWSE). Water, 11(1): 157. https://doi.org/10.3390/w11010157
BETIKU O.C., SARJEANT K.C., NGATIA L.W., AGHIMIEN M.O., ODEWUMI C.O., LATINWO L.M. (2021) Evaluation of microbial diversity of three recreational water bodies using 16S rRNA metagenomic approach. Science of The Total Environment, 771, 144773. https://doi.org/10.1016/j.scitotenv.2020.144773
CASTRO M.S.O., TOTH V.R., KOLCHANOVA S., WOLFSBERGER W.W., OLEKSYK T.K. (2025) A long-read sequencing approach to high-resolution profiling of bacterioplankton diversity in a shallow freshwater lake. Scientific Reports, 15: 12224. https://doi.org/10.1038/s41598-025-96558-7
CHATTERJEE S., MORE M. (2023) Cyanobacterial Harmful Algal Bloom Toxin Microcystin and Increased Vibrio Occurrence as Climate-Change-Induced Biological Co-Stressors: Exposure and Disease Outcomes via Their Interaction with Gut-Liver-Brain Axis. Toxins (Basel). 17;15(4):289. https://doi.org/10.3390/toxins15040289
GUPTA P.K., KUMAR A., SIMON M., MANISHA. (2021). Arsenic Pollution in Groundwater and Its In Situ Microbial Remediation Technologies. Fate and Transport of Subsurface Pollutants. Springer, 183-197. https://doi.org/10.1007/978-981-15-6564-9_10
HAFTU Z., ESTIFANOS S. (2020). Investigation of phy-sico-chemical Characteristics and Heavy Metals Concen-tration Implying to the Effect of Local Geology on Surface Water Quality of Werii Catchment, Tigray, Ethiopia. EQA - International Journal of Environmental Quality, 40, 11–18. https://doi.org/10.6092/issn.2281-4485/10602
HEINO J., ALAHUHTA J., BINI L.M., CAI Y., HEISKANEN A.S., HELLSTEN S., KORTELAINEN P., KOTAMAKI N., TOLONEN K.T., VIHERVAARA P., VILMI A., ANGELER D.G. (2020). Lakes in the era of global change: moving beyond single- lake thinking in maintaining biodiversity and ecosystem services. Biological Reviews, 96 (1): 89-106. https://doi.org/10.1111/brv.12647
JIANG T., SUN S., CHEN Y., QIAN Y., GUO J., DAI R., (2021). Microbial diversity characteristics and the influence of environmental factors in a large drinking-water source. Science of The Total Environment, 769,144698. https://doi.org/10.1016/j.scitotenv.2020.144698
JORDAAN K., BEZUIDENHOUT C.C. (2016). Bacterial community composition of an urban river in the North West Province, South Africa, in relation to physico-chemical water quality. Environmental Science and Pollution Research, 23: 5868-5880. https://doi.org/10.1007/s11356-015-5786-7
KASHYAP U., GARG S., ARORA P. (2024) Pesticide pollution in India: Environmental and health risks, and policy challenges. Toxicological Reports 12(2024)101801. https://doi.org/10.1016/j.toxrep.2024.101801
KIM M.K., LIM B.S., LEE C.S., SRINIVASAN S. (2024). Bacterial Diversity in the Different Ecological Niches Related to the Yonghwasil Pond (Republic of Korea). Microorganisms, 12(12):2547. https://doi.org/10.3390/microorganisms12122547
KUMAR S., DAS S., JIYA N., SHARMA A., SAHA C., SHARMA P., TAMANG S., THAKUR N. (2024). Bacterial diversity along the geothermal gradients: insights from the high-altitude Himalayan hot spring habitats of Sikkim. Current Research in Microbial Sciences, 7,100310 https://doi.org/10.1016/j.crmicr.2024.100310
LAMIM V.B., PROCOPIO L. (2021). Influence of acidification and warming of seawater on biofouling by bacteria grown over API 5L steel. Indian Journal of Microbiology, 61(2):151-159. https://doi.org/10.1007/s12088-021-00925-7
LU G., XIE B., CAGLE G.A., WANG X., HAN G., WANG X. (2020) Effects of simulated nitrogen deposition on soil microbial community diversity in coastal wetland of the Yellow River Delta. Science of The Total Environment, 143825. https://doi.org/ 10.1016/j.scitotenv.2020.143825
NYOYOKO V.F. (2022) Proteobacteria response to heavy metal pollution stress and their bioremediation potential. In Cost effective technologies for solid waste and wastewater treatment. Elsevier, 147-159. https://doi.org/ 10.1016/b978-0-12-822933-0.00010-3
PANWAR A.S., RANA B., SHARMA S., RAWAT N., KHULBE K., SINGH D., JOSHI G.K. (2023) A comparative analysis of the bacterial community structure of freshwater lakes located in the outer Himalayan Region of India. Research Square. https://doi.org/10.21203/rs.3.rs-2409218/v1
PIATKA D.R., VENKITESWARAN J.J., UNIYAL B., KAULE R., GILFEDDER B., BARTH J.A. (2022) Dissolved oxygen isotope modelling refines metabolic state estimates of stream ecosystems with different land use background. Scientific Reports, 12. https://doi.org/ 10.1038/s41598-022-13219-9
PORCHAS M.M., ALBORES F.V. (2017) Microbial Metagenomics in Aquaculture: A Potential Tool for a Deeper Insight into the Activity. Reviews in Aquaculture, 9(1): 42-56. https://doi.org/10.1111/raq.12102
PRAKASH O., NIMONKAR Y., DESAI D. (2020) A Recent Overview of Microbes and Microbiome Preservation. Indian Journal of Microbiology, 60:297–309. https://doi.org/10.1007/s12088-020-00880-9
PRASANNA K., SARKAR A., SHARMA A., MANOJ M.C., TRIPATHI S., THAKUR B., BASUMATARY S.K., KUMAR K., RANHOTRA P.S., PANDEY S., TRIVEDI A., QUAMAR M.F., SRIVASTAVA J., RAHI I.C. (2025) Heavy Metal Pollutants and Their Spatial Distribution in Surficial Sediments from the Gangetic Plains, Central, and Western Parts of India. Soil and Sediment Contamination: An International Journal, 34(5):981-1001. https://doi.org/10.1080/15320383.2024.2395948
PU H., YUAN Y., QIN L., LIU X. (2023) pH Drives differences in bacterial community β-diversity in hydrolo-gically connected lake sediments. Microorganisms, 11(3): 676. https://doi.org/ 10.3390/microorganisms11030676
SHI Y.J., LI W.B., GUO X. (2023) Composition, interaction networks, and nitrogen metabolism patterns of bacterioplankton communities in a grassland type Lake: a case of Hulun lake, China. Frontiers in Microbiology, 14:1305345. https://doi.org/10.3389/fmicb.2023.1305345
SIRBU T., BURTEVA S., BIRSA M., BALAN L., SLANINA V., TURCAN O., MOLDOVAN C. (2022). Study of the microbial biodiversity of the lake La Izvor, Chisinau municipality. ACROSS, 6(2). https://doi.org/10.35219/across.2022.2.08
SMITH R.J., JEFRIES T.C., ROUDNEW B., FITCH A.J., SEYMOUR J.R., DELPIN M.W., NEWTON K., BROWN M.H., MITCHELL J.G. (2012) Metagenomic comparison of microbial communities in habiting confned and unconfned aquifer ecosystems. Environmental Microbiology, 14(1):240–253. https://doi.org/10.1111/j.1462-2920.2011.02614.x
TRINGE S.G., MERING C.V., KOBAYASHI A., SALAMOV A.A., CHEN K., CHANG H.W., PODAR M., SHORT J.M., MATHUR E.J. DETTER J.C., BORK P., HUGENHOLTZ P., RUBIN E.M. (2005). Comparative metagenomics of microbial communities. Science. https://doi.org/10.1126/science.1107851
VASISTHA P., GANGULY R. (2020). Water quality assessment of natural lakes and its importance: An overview. Materials Today: Proceedings, 32: 544-552. https://doi.org/ 10.1016/j.matpr.2020.02.092
VESAMAKI J.S., LAINE M.B., NISSINEN R., TAIPALE S.J. (2024). Plastic and terrestrial organic matter degradation by the humic lake microbiome continues throughout the seasons. Environ Microbiological Reports, 16(3): e13302. https://doi.org/ 10.1111/1758-2229.13302
WANG W., WENG Y., LUO T., WANG Q., YANG G., JIN Y. (2023). Antimicrobial and the Resistances in the Environment: Ecological and Health Risks, Influencing Factors, and Mitigation Strategies. Toxics, 11(2):185. https://doi.org/10.3390/toxics11020185
XIN G., XIAOHONG S., YUJIAO S., WENBAO L., YANJUM W., ZHIMOU C., ARVOLAB L. (2024). Characterization of bacterial community dynamics dominated by salinity in lakes of the Inner Mongolian Plateau, China. Frontiers in Microbiology, 15-20224. https://doi.org/10.3389/fmicb.2024.1448919
XU M., ZHANG K., WANG Y., ZHANG B., MAO K., ZHANG H. (2022) Health Risk Assessments and Microbial Community Analyses of Groundwater from a Heavy Metal-Contaminated Site in Hezhou City, Southwest China. Int J Environ Res Public Health, 20(1):604. https://doi.org/ 10.3390/ijerph20010604.
YADAV A., GAUTAM K.A. (2025). Physiochemical Profile of Tilyar Lake – Essential Parameters for Sustainable Biodiversity. Indian Journal of Science and Technology, 18(4): 268-274. https://doi.org/10.17485/IJST/v18i4.3134
ZHANG H., HUANG Y., LIU X., MA B., AN S. (2025). Exploring bacteria communities in lakes and reservoirs: a global perspective. Biocontaminant 1: e003. https://doi.org/ 10.48130/biocontam-0025-0003
ZHAO D., ZHANG S., XUE Q., CHEN J., ZHOU J., CHENG F., LI M., ZHU Y., YU H., HU S., ZHENG Y., LIU S., XIANG H. (2020). Abundant taxa and favorable pathways in the microbiome of soda-saline lakes in Inner Mongolia. Frontiers in Microbiology, 11:1740. https://doi.org/ 10.3389/fmicb.2020.01740
ZHU W., LIU J., LI Q., GU P., GU X., WU L., GAO Y., SHAN J., ZHENG Z., ZHANG W. (2022). Effects of nutrient levels on microbial diversity in sediments of a eutrophic shallow lake. Frontiers in Ecology and Evolution, 10: 909983. https://doi.org/ 10.3389/fevo.2022.909983
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