Indian Institute of Technology Madras (IIT Madras) and US Researchers are studying viruses in Freshwater Lakes. Such research is critical to understanding viruses in nature as it has enormous applications that can benefit society and the environment.
An exciting example is ‘phage therapy’, which uses specific viruses called phages to target and kill disease-causing bacteria. This approach has the potential to combat antibiotic-resistant bacterial infections that are spreading in India and across the world and revolutionize medicine.
The findings of this research reveal the vital roles viruses play in ecosystems, not just by influencing the environment but also by supporting other organisms. This work highlights how viruses are beneficial to the health and stability of natural systems.
This International Team of researchers developed and applied cutting-edge Machine Learning-based tools to uncover the hidden world of viruses in microbiomes. Using these methods, they studied 465 freshwater lake samples from the same location in Madison, Wisconsin, US, collected over a period of more than 20 years. This research represents the longest DNA-based monitoring of a natural environment on Earth.
The Research was led by Dr. Karthik Anantharaman, Visiting Professor, Wadhwani School of Data Science and AI, IIT Madras and an Associate Professor of Microbial and Viral Ecology at University of Wisconsin-Madison, USA.
It was undertaken by an International team of Scientists from the University of Wisconsin-Madison and the University of Texas at Austin. The Research Paper was published in the prestigious Nature Microbiology Journal (https://doi.org/10.1038/s41564-024-01876-7), with the co-authors being Zhichao Zhou, Patricia Q. Tran, Cody Martin, Robin R. Rohwer, Brett J. Baker, Katherine D. McMahon and Karthik Anantharaman.
Elaborating on the need for such Research, Dr. Karthik Anantharaman said, “The COVID-19 pandemic has shown us just how important it is to track viruses. Understanding how viruses emerge, evolve, and interact with their environments is critical — not only for responding to pandemics but also for recognizing the vital roles they play in ecosystems. Yet, long-term studies of viral communities, particularly in natural environments, are rare.”
Dr. Karthik Anantharaman added, “This lack of data creates a significant knowledge gap, hindering our ability to predict how viruses influence both human health and environmental stability. By investing in long-term viral monitoring, we can better prepare for future outbreaks and uncover the complex ways viruses contribute to the health of our planet.”
In addition, studying viruses in freshwater systems can transform how we manage water resources, natural ecosystems, and public health. These findings also open doors to innovative strategies for ecosystem management, such as using viruses to restore balance in disrupted environments such as polluted lakes. For example, viruses could be used to prevent harmful algal blooms or bacterial outbreaks (like the green slime seen in polluted lakes), ensuring safer drinking water and healthier recreational lakes.
Welcoming the research findings, Prof. Karthik Raman, Wadhwani School of Data Science and AI, IIT Madras, said, “Viruses are everywhere in the environment and play essential, yet often underestimated and misunderstood roles in shaping microbiomes and human health. Contrary to common misconceptions, not all viruses are harmful. Many are integral to maintaining ecosystem health and microbiome stability, much like apex predators such as sharks or lions regulate the balance of ecosystems in the oceans or land.”
.png)
This study stands out for its groundbreaking combination of machine learning-based methods and long-term monitoring to study viruses and address global challenges. Such an extended timeline of more than 20 years offers an unprecedented view of how viruses evolve and respond to environmental changes, far beyond the short-term view provided by most previous research.
This unique approach allowed the researchers to study how viruses change with the seasons, over decades, and in response to environmental shifts.
By sequencing all the DNA from the lakes using a method called metagenomics, the researchers uncovered several key findings:
They reconstructed 1.3 million virus genomes, making this the largest study of its kind.
Viruses follow seasonal and yearly cycles, with many reappearing year after year, showing remarkable predictability.
Viruses can “steal” genes from their hosts and repurpose them for their own benefit. Researchers found 578 examples of viral genes that help with critical processes like photosynthesis and methane use.
Viruses evolve over time, with some genes becoming more dominant due to natural selection.
Environmental factors, such as carbon and ammonium levels which are often associated with pollution, influence viral populations – similar to how they would impact other organisms.