GANGA PROJECT

GIS-based Mapping of Microbial Diversity across the Ganges for Ecosystem Services

Project No: TE-16015/11/2019-TECH5 NMCG

Coordinating Institute

1. CSIR-National Environmental Engineering Research Institute, Nagpur.

Partner Institutes:

1. PhiXgen Pvt. Ltd., Gurugram.
2. Motilal Nehru National Institute of Technology Allahabad.
3. Charotar University of Science and Technology, Anand.
4. Xcelris Labs Limited, Ahmedabad.

Introduction

Microbes play a key role in regulating the ecosystem of any niche in the environment. Their adaptability to diverse conditions and their unique genotype, provide ecosystem services that contribute in maintaining a healthy niche and stability of an ecosystem. This project aims to understand the ecosystem services of microbes in a river niche, taking the river Ganga as a specific target. The Ganga river is a lifeline for those living along its path; it provides freshwater and is a water resource for agriculture, fisheries, industries, energy and tourism. Besides, this river has a deep social, cultural and religious footprint in India and houses a wide biodiversity. Microbes are one of the key drivers that maintain the health of the river. They help regulate the bio-geochemical cycles, carry out biodegradation of harmful organics (anthropogenic and natural), provide nutrients and growth factors to sustain aquatic life and are an indicator of pollution levels. Since 95% of the microbial world is unreported via culture-based studies, this project has used metagenomics to analyze microbes in the river Ganga based on their DNA.

Methodology

Results

• The microbial diversity within the river ecosystem harbors essential genes critical for nutrient recycling and organic biodegradation, with detailed analyses of the carbon, nitrogen, and sulfur cycles. Genes coding for CAZy enzymes are abundant in rivers and hold potential for future applications in biomass and bioenergy. Additionally, genes associated with the denitrification cycle are prevalent in the river.
• Metagenomic studies have revealed a diverse bacterial community, including unique species like hydrogen-oxidizing bacteria that are gaining attention for their CO₂ fixation capabilities. Rare phyla, such as Gemmatimonadetes, which play roles in nutrient recycling, were also identified among other unique taxa.
• The impact of domestic sewage and other human activities is evident from the presence of E. coli, pathogens, and antimicrobial resistance (AMR) genes—AMR being one of the top ten health risks identified by the WHO. AMR abundance was higher in biomat samples than in the water, with genes conferring resistance to 18 antibiotic classes identified. Special attention was given to detecting E. coli, a fecal contamination indicator, with sequence data tracing its origin to either human or animal sources. E. coli abundance was low, ranging from 0.005% to 0.31% of bacterial taxa. Locations such as Haridwar, Bijnor, Narora, and Badaun exhibited relatively higher levels of E. coli, including strains originating from cattle.
• While dissolved oxygen (DO) levels in most rivers range from 5-7 mg/L, the Ganga exhibits notably high DO levels. The river’s upper stretch maintains a uniform DO of 7-9 mg/L in winter, while the middle segments show super-saturation, with DO levels between 10-12 mg/L, possibly due to natural turbulence and oxygen-releasing bio-processes. In the lower segments, DO levels reach up to 6 mg/L in both winter and summer.
• Sampling took place in two seasons: winter (November 2020), when human activity was minimal due to COVID-19, and summer (May 2022), post-COVID. This comprehensive study, covering the entire stretch of the Ganga from Gangotri to Diamond Harbor, provides a baseline for future studies on the river. GIS maps were developed, plotting major physico-chemical parameters and microbial taxa, which can be updated with additional bacterial data as needed.
• In total, 22 locations across seven segments of the river were analyzed, generating approximately 8 TB of metagenomic sequence data. This data offers extensive information on microbial identification and functional genes in the river, with potential applications in biomass conversion, renewable energy, drug discovery, and secondary metabolites. The data will be deposited with the National Mission for Clean Ganga (NMCG) and, with permission, may be made available in public databases.

Figure 1: Distribution of the top ten genera in of the microbiome of River Ganga at different locations from Summer sampling time point

Figure 2: Heatmap showing the number of AMR associated genes determined in each sample for resistance to different classes of antibiotics. KA- Katwa, HW- Howrah, DH diamod Harbor. B stands Biomat, S- for Sediment and W for water samples.