Microbial source tracking using metagenomic analysis from Cochin Estuary

Microbial source tracking (MST) and metagenomics offer powerful insights into microbial ecosystems and pollution sources. This pilot study used metagenomics to identify microbial pollution sources in the Cochin Estuary (CE), a vital coastal ecosystem in southwest India. The CE faces significant microbial pollution, necessitating effective tracking for conservation. Bacterial community analysis via high-throughput sequencing was conducted to determine fecal pollution sources in CE waters. Samples included human, cow, dog, and goat feces, along with sewage, slaughterhouse, and domestic waste, alongside 24 water samples from eight sites across monsoon and non-monsoon seasons. DNA extraction and 16S rRNA (V3-V4) sequencing via Illumina MiSeq enabled MST analysis. Results indicated that sewage and domestic waste were the predominant contaminants, contributing to 50% of bacterial communities. Downstream sites were more polluted than upstream areas. Proteobacteria dominated estuarine waters, whereas Firmicutes and Bacteroidetes were prevalent in source samples. This study highlights the need for targeted remediation to protect the CEs environmental health. Importance of the studyThis study is essential for addressing microbial pollution in the Cochin Estuary (CE), a crucial Ramsar site facing contamination threats. Beyond identifying pollution sources, it provides valuable insights into seasonal variations in microbial composition, highlighting differences between monsoon (wet) and non-monsoon (dry) periods. It emphasizes the role of environmental factors such as conductivity, temperature, dissolved oxygen (DO), and salinity in shaping microbial communities. The study also employs advanced statistical tools like non-metric multidimensional scaling (NMDS) and principal coordinates analysis (PCoA) to assess microbial diversity and pollution patterns. Additionally, it underscores the significance of next-generation sequencing (NGS) in high-resolution microbial source tracking (MST). By integrating environmental parameters and microbial analysis, the study offers a comprehensive approach for monitoring estuarine health. These findings are crucial for policymakers, aiding in the development of targeted wastewater management and pollution mitigation strategies to protect CEs biodiversity and ecological balance.