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We need new ways of mitigating the effects of climate change by reducing the amount of greenhouse gas in the atmosphere. Methane (CH4) is a potent greenhouse gas which is contributing to global climate change. It is far more powerful than carbon dioxide when it comes to trapping the sun's heat, and is increasing in abundance .
Several years ago, scientists discovered that methane can be broken down – or oxidised – by microorganisms in the absence of oxygen.
The EU’s ECO-MOM project, funded by the European Research Council, studied how the methane, nitrogen and iron cycles are connected. It focused on how these unique and unusual microorganisms simultaneously break down methane and cleanse water of pollutants such as nitrates, which damage aquatic ecosystems and are known to be toxic to infants.
If these natural processes could be industrialised, they may offer a way of reducing methane emissions and cleaning wastewater cheaply and with low energy demands.
‘By surveying several different oxygen-limited ecosystems – from Italian paddy fields to Finnish peatlands and Dutch wetlands – we were able to discover several new methane-oxidising microbes and elucidate some of their key properties,’ says principal investigator Mike Jetten of Radboud University in the Netherlands.
‘The discovery of iron-dependent methane oxidation by a complex community of archaea (single-celled organisms) and bacteria was a surprising highlight.’
Unravelling complex interactions
With a huge amount of ground to cover, ECO-MOM researchers followed seven complementary lines of enquiry. They investigated the detection, adaptation, ecophysiology, biochemistry, cell biology, metabolism, and potential applications of methane-oxidising microorganisms.
The team developed new molecular diagnostic tools to detect and quantify the anaerobic methane-oxidising microbes Methylomirabilis and Methanoperedens in various oxygen-poor sediments around Europe. They identified a new Methylomirabilis species and also found new bacteria that completely break down ammonium to nitrate.
Another surprise was the discovery of a new species of bacterium, Nitrobium versatile; its role in geochemical cycles has yet to be determined.
The microorganisms collected were enriched in bioreactors and microcosm systems in the laboratory. Researchers examined their metabolism and behaviour to reveal an intricate interplay between the various archaea and bacteria. In another bioreactor experiment, mimicking brackish sediments showed that, under the right conditions, the microbial community could use nitrite to break down sulphide, ammonium and methane at the same time.
In addition, the team demonstrated that Methanoperedens archaea use iron oxides to oxidise methane. They then sequenced and analysed the genomes of several species, revealing various enzymes of interest involved in breaking down methane, nitrates and nitrites.
Further laboratory work showed that the cultured bacteria and archaea can remove these common pollutants from synthetic wastewater.
Commercial biofilters
‘A linked European Research Council Proof of Concept grant was used to make a business case for using the newly discovered microbes to remove methane, nitrates and ammonium from water in a more sustainable manner,’ says Jetten.
‘We are now in close contact with wastewater biotechnology companies and a plant producing drinking water to see how this could approach be implemented in the next three to six years.’
The success of the ECO-MOM project has led to an ongoing collaboration with Utrecht University to further explore the biogeochemistry of nitrogen and methane removal in coastal sediments in the ERC-funded MARIX project, which began in March 2020.