Why might metabolomics be showing us the Next Big Thing in agriculture? Ute Roessner weighs in.
I was always interested in chemistry, but when I went to university in Potsdam, back in Germany, there was a lot of plant biology research happening. They even opened an institute right there on the campus in the time I was there, the Max Planck Institute for Molecular Plant Physiology.
That gave me an opportunity to get my hands dirty in the lab, which I loved. I was just there as a casual, doing a lot of analytical measurements of single metabolites – small molecules like glucose, fructose, sucrose and ATP. It was very laborious work measuring every metabolite individually with a different enzymatic assay, but it was a lot of fun to be in the lab and part of a science community.
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Then my boss at the time bought a new toy, a gas chromatograph coupled to a mass spectrometer (GC-MS). He promised me that it could measure all these metabolites in one go in one sample, which sounded super exciting. I remember the moment we first analysed plant samples on this high-end instrument, and got thousands of peaks which we started to identify in a one hour run. These days, you can get that down to 20 minutes – and with the GC-MS or complementary LC-MS (liquid chromatography coupled to mass spectrometry) it could be up to 2,500 compounds. That was the moment I realised that the chemistry of life is just amazing. We knew it before but we couldn’t really measure it until then.
That’s when I signed up to do my PhD at the Max Planck Institute to develop the methods. And that’s how metabolomics was born.
Metabolomics is a super useful tool. It’s the plant side that particularly interests me, but I love applying this science for people who work in all kinds of other biological areas, like biomedicine. They tell me about a big question they have, that I probably didn’t even know about, then I play my part measuring something that helps them to go ahead with their science to develop a new drug or disease treatment, for instance. It’s so cool. We’ve done a lot of metabolomics for cancer, diabetes, and a number of other diseases. Metabolomics is perfect as a monitoring tool for the progression of diseases – that’s a growing area at the moment.
My personal research has mainly focused on things you can eat. In Germany, that was potato and tomato, then when I came to Australia I joined the Australian Centre for Plant Functional Genomics, focusing on cereals – grains like wheat, barley and oats. How can a plant better survive changing climates – heat stress, salinity, drought, nitrogen deficiency, boron toxicity? We measure how the environment influences the chemical makeup of the plant.
You could for instance compare a plant which grows really well with water deficiency to a crop plant which doesn’t sustain drought very well. Ideally, they’re from the same kind of family or genetically related, so you can potentially identify metabolites which might infer the drought tolerance in that variety or species. That can then lead you to a gene which is needed in order to produce that particular metabolite. Then you use those genes to put them into your commercial crop and hopefully induce drought tolerance or at least improve drought tolerance. That’s a good thing.
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We’re recently focusing on nitrogen as a very important nutrient. Farmers heavily fertilise their crops, and these fertilisers can be ridiculously expensive – even more so with increasing energy costs. Broadacre crops, in particular, use a lot of nitrogen. Yet 50% of what the farmer applies on the field gets lost – the plant simply can’t take it up. So either the timing of the application isn’t quite right, or the fertiliser has degraded and been made volatile. Then you have nitrogen leaching into the waterways, which is very bad for the environment. Or when it’s volatilised, it creates greenhouse gases based on nitrogen oxide, which is even worse than CO2.
Everyone talks about CO2, and no one talks about nitrogen. It’s actually much worse.
So on one hand we’re trying to create plants which are more efficient at taking up nitrogen, leading to less loss. And on the other hand, we’re trying to develop new fertiliser technologies to inhibit the degradation processes. We’re not just trying to increase agricultural production – that’s great, we need to do that anyway. But we also want to reduce the environmental impact of agriculture.
Some of my latest work is looking at what these new fertiliser technologies do to the plant by looking at the metabolites. Are they toxic? Are they taken up? Are they actually improving nitrogen uptake? Are they doing anything else to the plant which might be not wanted? Or are they good technology? We’re working with the chemists and chemical engineers who produce these kinds of chemicals. I partner with them and say, ‘Give me your new fertiliser technology chemicals’. And we’ll put them together with the plant and look at what happens at the molecular level to see if these new chemistries actually do the right thing.
First, we take those chemicals and put them together with plants in very small growth chambers so we can study them on a daily basis, looking at the roots, how they grow, and how they are impacted. At the end of a growth cycle, which is probably about four weeks, we take the roots and root exudates – everything that’s around the roots – and measure the metabolites to see what happened to those plants compared to when treated with other fertilisers.
We then go to the glasshouse and create a more real-life growth situation, and the next step after that is to go to the fields to test if there’s a benefit in nitrogen uptake by the plant. And do we have less loss to the environment, which is the big issue.
We have to improve the environmental aspect of agriculture. Otherwise, this world is going to go under.
Professor Ute Roessner AM FAA is one of Australia's leading plant scientists and a pioneer in the field of metabolomics. She is the newly appointed Academic Director, Research Initiatives and Infrastructure at the ANU, having come from the University of Melbourne, where she was Head of the School of BioSciences.