A collaboration between Teagasc Food Research Centre, Moorepark; Teagasc, Crops, Environment and Land-Use Programme, Johnstown Castle; VistaMilk SFI Research Centre; University of Galway and University College Dublin has recently highlighted the critical need for precise parameters, including the right classifiers, for accurately identifying soil microbiota through shotgun metagenomics. This recently published study pushes the boundaries of what we can understand and achieve through advanced soil studies.
As technology advances, so does our ability to explore the world beneath our feet—specifically, the soil. While projects like the Human Microbiome Project have shown us the hidden complexities of human bodies at a microscopic level, soil remains complex and mysterious. VistaMilk SFI Research Centre, are pioneering new methods to study soil to improve farming methods and shape a healthier planet.
Soil is not just dirt; it is a metropolis of microorganisms that play crucial roles in functions important to agriculture and climate change, including nitrogen fixation and nutrient breakdown. A metagenome is the recovery and complete sequencing of genetic material extracted directly from all environmental samples, providing us with a comprehensive picture of the microbial diversity present in these samples. Understanding these tiny microorganisms can lead to advances in how we grow food and manage natural resources. However, studying these microorganisms is tough due to their vast diversity and the limitations of our current tools.
To tackle this challenge, our team developed a special simulated soil environment—a sort of ‘mock’ soil microbial community—that lets us test and improve tools used to identify and study these microorganisms. By using advanced technologies, we are refining how we analyse soil samples, making our studies more precise than ever.
Niranjana Rose Edwin, a PhD student at our centre, explains, “Until recently, we thought that many soil microbes could not be detected with our tools using metagenomic data, perhaps missing up to 90% of them. Our latest research demonstrate that the issue may lie with the tools themselves, not the soil. By improving these tools, we are starting to reveal the true complexity of soil life.”
Our research is redefining what is possible in soil microbial ecology. By improving how we study soil microbes, VistaMilk are paving the way for advancements in sustainable agriculture and environmental management. This is not just about better farming; it is about creating a sustainable future for all of us, rooted in deep scientific understanding.
The research, published as a full paper by the BMC, Environmental microbiome 2024, can be found here.
This research is supported by Teagasc Walsh Scholarship Programme and VistaMilk SFI Research Centre together with the Irish Department of Agriculture, Food and Marine and is a collaborative effort by Niranjana Rose Edwin; University of Galway and Teagasc Food Research Centre Moorepark; Prof. Orla O’ Sullivan, Teagasc Food Research Centre Moorepark; Dr. Fiona Brennan, Teagasc Crops, Environment and Land-Use Programme, Johnstown Castle; Prof. Florence Abram, University of Galway and Dr. Amy Heather Fitzpatrick, University College Dublin.