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<p>A multi-marker sequencing approach was applied to characterize the eukaryotic microbial community of the Najafgarh Drain. It will provide the first comprehensive view of eukaryotic diversity in this system, highlighting both its ecological significance and pathogenic potential. We combined 18S rRNA, internal transcribed spacer (ITS), and whole-metagenome shotgun (WMS) sequencing; 18S rRNA captured broad protist diversity but offered limited fungal resolution, which was complemented by ITS, while WMS provided higher, often species level resolution across kingdoms. To improve WMS classification, a dual-database strategy was employed, sequences were first classified using a eukaryote-filtered NCBI clustered nr database, unclassified sequences were subsequently analyzed with a combined database comprising of SILVA, MIDORI2, PlantITS, and COInr. This approach consistently increased the number of identified genera and species compared with using a single database. Using the multi-marker and dual database approach, multiple phyla were detected, including Chlorophyta (55.72%), Ciliophora (21.46%), Ascomycota (6.44%), Mucoromycota (1.35%), and Nematoda (0.80%). Beneficial taxa such as <i>Chlorella</i>, members of Ciliophora, and <i>Penicillium</i>, known for organic-matter degradation, nutrient cycling, and heavy-metal remediation, were observed. Additionally, human pathogens such as <i>Pneumocystis jirovecii</i>, <i>Rhizopus arrhizus</i> and <i>Trichuris trichiura</i> along with plant pathogenic fungi such as <i>Fusarium</i>, <i>Sporisorium</i>, and <i>Rhizopus</i> were also observed. These findings underscore the need to incorporate eukaryotic pathogen surveillance into water quality monitoring and environmental policy frameworks. Such measures would contribute to more resilient water management practices and support broader public health protection goals.</p>

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Multi-marker metagenomic assessment of eukaryotic communities in Najafgarh Drain reveals public health and ecological risks

  • 期刊论文

  • 发表日期：

    2025年11月19日

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  • Gaurav Singh,
  • Inderjeet Tyagi,
  • Kaomud Tyagi,
  • Vikas Kumar,
  • Ravi Kiran Donthu

摘要

A multi-marker sequencing approach was applied to characterize the eukaryotic microbial community of the Najafgarh Drain. It will provide the first comprehensive view of eukaryotic diversity in this system, highlighting both its ecological significance and pathogenic potential. We combined 18S rRNA, internal transcribed spacer (ITS), and whole-metagenome shotgun (WMS) sequencing; 18S rRNA captured broad protist diversity but offered limited fungal resolution, which was complemented by ITS, while WMS provided higher, often species level resolution across kingdoms. To improve WMS classification, a dual-database strategy was employed, sequences were first classified using a eukaryote-filtered NCBI clustered nr database, unclassified sequences were subsequently analyzed with a combined database comprising of SILVA, MIDORI2, PlantITS, and COInr. This approach consistently increased the number of identified genera and species compared with using a single database. Using the multi-marker and dual database approach, multiple phyla were detected, including Chlorophyta (55.72%), Ciliophora (21.46%), Ascomycota (6.44%), Mucoromycota (1.35%), and Nematoda (0.80%). Beneficial taxa such as Chlorella, members of Ciliophora, and Penicillium, known for organic-matter degradation, nutrient cycling, and heavy-metal remediation, were observed. Additionally, human pathogens such as Pneumocystis jirovecii, Rhizopus arrhizus and Trichuris trichiura along with plant pathogenic fungi such as Fusarium, Sporisorium, and Rhizopus were also observed. These findings underscore the need to incorporate eukaryotic pathogen surveillance into water quality monitoring and environmental policy frameworks. Such measures would contribute to more resilient water management practices and support broader public health protection goals.