Microbes can reduce their need for nickel

Methane-producing archaea are more adaptable to nutrient-poor habitats than previously thought

July 02, 2025

On the left of the image is a natural wetland habitat with water and grasses, with a forest in the background. A laboratory apparatus is shown on the right. — Methanogenic archaea have a major impact on the global climate, as they produce almost all naturally occurring methane. They are usually cultivated and studied under nutrient-rich conditions, especially at high nickel concentrations. A research team led by Dr Seigo Shima at the Max Planck Institute for Terrestrial Microbiology has now investigated methanogenesis under nutrient-poor conditions and discovered a strategy that microbes can use to reduce their nickel requirements.

© MPI f. terrestrische Mikrobiologie/ Nomura&Geisel

Methanogenic archaea have a major impact on the global climate, as they produce almost all naturally occurring methane. They are usually cultivated and studied under nutrient-rich conditions, especially at high nickel concentrations. A research team led by Dr Seigo Shima at the Max Planck Institute for Terrestrial Microbiology has now investigated methanogenesis under nutrient-poor conditions and discovered a strategy that microbes can use to reduce their nickel requirements.

© MPI f. terrestrische Mikrobiologie/ Nomura&Geisel

To the point

Microbes and Nickel: Methanogenic archaea produce nearly all natural methane, thus playing a crucial role in influencing global climate change.

Research Findings: A study revealed that under nutrient-poor conditions, these archaea can replace nickel-dependent enzymes with a non-nickel enzyme system. The research showed that a complex enzyme structure without nickel can still facilitate essential biochemical reactions for methane production.

Adaptation Strategy: This novel methane metabolism may be widespread in nature, allowing organisms to survive in environments with low nickel availability.

Metals play a crucial role in microbial biocatalysis by serving as cofactors for enzymes that facilitate essential biochemical reactions. Metal ions, such as nickel and iron, are often found at the active site of enzymes, where they enable electron transfer and thus the conversion of substrates.

Previous studies have shown that methanogenic archaea that live on hydrogen (H₂) rely on [NiFe]-hydrogenases. In the context of methanogenesis, these enzymes convert hydrogen gas into methane and are involved in the energy-coupling mechanism of the flavin-based electron bifurcation (FBEB) reaction. The Marburg researchers Rolf Thauer and Wolfgang Buckel had discovered this key reaction that enables microbes to efficiently utilise energy.

Nickel levels in natural habitats are low

However, this pathway was identified by culturing methanogenic microorganisms isolated from natural environments using laboratory media with nickel ion concentrations more than 100 times higher than in nature, where habitats are usually strictly nutrient-limited. Indeed, very low concentrations of bioavailable metal ions have been reported in seawater and freshwater environments. Can methane also be produced under these conditions, and if so, how? To address this question, Seigo Shima led a research team at the Max Planck Institute for Terrestrial Microbiology to study methanogenesis under nutrient-limited conditions.

'We were surprised to find that the levels of [NiFe]-hydrogenases in these methanogenic archaea had decreased to almost zero,' says Shunsuke Nomura, the study's lead author. Instead, the catabolic hydrogen pathway appeared to be entirely replaced by a non-nickel enzyme system.

Bonnie Murphy, from the Max Planck Institute for Biophysics in Frankfurt, explains: 'Our cryogenic electron microscopic analysis revealed a complex enzyme structure without nickel that can function as the electron-donating system for the FBEB reaction in the methanogenic pathway, thereby replacing [NiFe] hydrogenases.'

A comparative genomic analysis suggests that this novel methane metabolism is widespread in nature and may help organisms to adapt to their environment and survive in the absence of nickel.

How microbial enzymes influence climate change

“According to traditional textbooks, nickel-containing hydrogenases are the only functioning hydrogenases in methanogenic microbes. However, our findings reveal that this is no longer the case. The complete disappearance and replacement of the nickel-containing hydrogenase enzyme represents a significant paradigm shift in methanogen research and challenges our understanding of methanogenic metabolism in nature”, says Seigo Shima.

This is particularly intriguing because nickel-containing and non-nickel hydrogenases are completely unrelated. They have different protein structures, active site characteristics, reaction mechanisms, and inhibitor sensitivities.

This discovery highlights the importance of understanding the physiological responses of microorganisms in different environments, given that methanogenic activity contributes significantly to greenhouse gas emissions. By further investigating the alternative pathway, the researchers hope to develop more effective strategies for reducing methane's impact on the global climate.