Soil DNA mapping project could prevent disease, improve food security
Researchers at the VistaMilk research centre in Fermoy, Co Cork, in association with researchers in Wexford and Galway, are in the early stages of analysing samples of Irish pasture with the aim of identifying the genetic characteristics of microbes, how they interact with their environment, how they cycle nutrients and help plants grow, and how they develop and transmit anti-microbial resistance – a factor in as many as 700,000 deaths a year globally.
In a first-of-its-kind effort on a national basis, Irish scientists are broadening their focus on soil microbiome – rather than the far better-known human or animal microbiome. This ground-breaking project employs metagenomics, which allows scientists to study all the tiny life forms in the soil at once and provide a more complete picture.
It can be described as the world’s largest jigsaw puzzle, with elements of microbial genetic makeup being categorised and matches sought by machine-learning programmes, aiming to provide a detailed look at the soil’s genetic make-up across Ireland – and ultimately develop a quick system to assess soil health.
Rose Edwin, the PhD student leading the research explained: “Similar to other microbiomes, there are microbes – bacteria, fungi, archaea, protozoa, and viruses – that perform specific tasks and identifying them and their presence in soils is of major importance.
“Microbes have symbiotic relationships with plants, playing a pivotal role not only in their growth, but also in their ability to resist disease and withstand drought conditions. The metagenomic jigsaw – where we’ve sliced and diced the genetic material in a sample and are now using terabytes of computer processing power to put it all back together – is key to this, with the goal being to develop a testing system that can identify the beneficial microbes in any soil sample we receive.”
Edwin said: “We’re also working on identifying anti-microbial resistance (AMR) in the soil microbiome, where through billions of years of evolution, microbes have developed resistance to antibiotics or other drugs. Soils are the source of many of the antibiotics we use clinically and a natural reservoir of AMR but AMR can also be transmitted to the soil, and potentially into the food chain, through human activity.
“The ability to address AMR would prevent large numbers of avoidable deaths and would save billions in medical care costs. A report by the World Bank Group notes that a high-case AMR scenario may cause low-income countries to lose more than 5% of GDP and force more than 28 million people into poverty by 2050.”
Beyond human health, plant growth and soil health – all of which are central to the sustainability of Ireland’s dairy industry – the soil microbiome also holds the key to how much of society’s carbon emissions can be sequestered by the land. Currently it is believed that carbon sequestration in Ireland could be underestimated and an understanding of how microbes work with plants to sequester carbon could be one of the keys to unlocking this puzzle.
“We already know that white clover works with Rhizobium bacteria to fix nitrogen in the soil, reducing the need for chemical fertilisers and thereby helping reduce agricultural emissions.” said Edwin. “Identifying the genetic makeup of the microbes that interact with plant species to cycle carbon would greatly advance our understanding of how to encourage the carbon sequestration process.”
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