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Background <p>Khecheopalri Lake, a sacred freshwater body and recently recognized Ramsar Wetland site in Sikkim, India, holds both ecological and cultural significance. The ecological health of this lake is influenced by elemental inputs and environmental parameters, yet its microbial and functional diversity remain poorly characterized. In this study, we employed a multi-omics approach combining shotgun metagenomics, inductively coupled plasma mass spectrometry (ICP-MS), and culture-dependent analyses to provide an integrated understanding of the lake’s microbial ecosystem. Shotgun metagenomics revealed taxonomic diversity and functional gene profiles, ICP-MS quantified elemental composition and its potential role in shaping microbial communities, while culture-dependent methods complemented metagenomic insights by isolating representative taxa. Together, these approaches highlight the interactions between microbes and elemental dynamics, offering new perspectives on the ecological functioning of this Himalayan wetland and its potential vulnerability to environmental change.</p> Results <p>ICP-MS analysis revealed phosphorus (P) as the most abundant element, followed by iron (Fe), sodium (Na), magnesium (Mg), and potassium (K). Elevated BOD and COD levels in sample KES4 indicated organic pollution and coincided with the dominance of <i>Microcystis aeruginosa</i>, a cyanobacterium indicative of eutrophication. Shotgun metagenomic sequencing generated approximately 213 million reads, with bacteria constituting 98.85% of the community. Dominant phyla included <i>Pseudomonadota</i> and <i>Cyanobacteria</i>. Culturable isolates confirmed the presence of genera such as <i>Limnohabitans</i>, <i>Microcystis</i>, and <i>Mycolicibacterium</i>. Functional gene profiling showed that metabolism was the most enriched category (71.64%), with several genes (e.g., <i>xylB</i>, <i>pchF</i>, <i>clcD</i>) associated with xenobiotic degradation pathways.</p> Conclusion <p>This first comprehensive metagenomic assessment of Khecheopalri Lake reveals diverse microbial populations involved in nutrient cycling and pollutant detoxification. The presence of genes linked to aromatic hydrocarbon degradation highlights the ecological potential of native microbes in mitigating environmental stress.</p>

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Metagenomic report of element-microbe synergy and xenobiotic detoxification in the sacred waters of Khecheopalri lake, Eastern Himalaya

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年10月31日

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  • Rohit Das,
  • Bipashna Thatal,
  • Nagendra Thakur,
  • Rakshak Kumar,
  • Buddhiman Tamang

摘要

Background

Khecheopalri Lake, a sacred freshwater body and recently recognized Ramsar Wetland site in Sikkim, India, holds both ecological and cultural significance. The ecological health of this lake is influenced by elemental inputs and environmental parameters, yet its microbial and functional diversity remain poorly characterized. In this study, we employed a multi-omics approach combining shotgun metagenomics, inductively coupled plasma mass spectrometry (ICP-MS), and culture-dependent analyses to provide an integrated understanding of the lake’s microbial ecosystem. Shotgun metagenomics revealed taxonomic diversity and functional gene profiles, ICP-MS quantified elemental composition and its potential role in shaping microbial communities, while culture-dependent methods complemented metagenomic insights by isolating representative taxa. Together, these approaches highlight the interactions between microbes and elemental dynamics, offering new perspectives on the ecological functioning of this Himalayan wetland and its potential vulnerability to environmental change.

Results

ICP-MS analysis revealed phosphorus (P) as the most abundant element, followed by iron (Fe), sodium (Na), magnesium (Mg), and potassium (K). Elevated BOD and COD levels in sample KES4 indicated organic pollution and coincided with the dominance of Microcystis aeruginosa, a cyanobacterium indicative of eutrophication. Shotgun metagenomic sequencing generated approximately 213 million reads, with bacteria constituting 98.85% of the community. Dominant phyla included Pseudomonadota and Cyanobacteria. Culturable isolates confirmed the presence of genera such as Limnohabitans, Microcystis, and Mycolicibacterium. Functional gene profiling showed that metabolism was the most enriched category (71.64%), with several genes (e.g., xylB, pchF, clcD) associated with xenobiotic degradation pathways.

Conclusion

This first comprehensive metagenomic assessment of Khecheopalri Lake reveals diverse microbial populations involved in nutrient cycling and pollutant detoxification. The presence of genes linked to aromatic hydrocarbon degradation highlights the ecological potential of native microbes in mitigating environmental stress.