Mineral-extracting microorganism could solve early Earth’s nitrogen-fixing mystery

Nitrogen fixation – a key step for complex life’s evolution – could have been helped along by ancient bacteria living in shallow water that were able to extract molybdenum from rocks. That’s according to researchers who have demonstrated how this offers a plausible explanation to the paradox of how molybdenum-nitrogenase, the predominant nitrogen-fixing enzyme, could have evolved 3.2 billion years ago when Earth’s supply of dissolved molybdenum was scarce.

DNA and proteins all need nitrogen. Without it, life as we know it could not have begun or evolved. However, on early Earth, most nitrogen was locked up in the atmosphere as highly stable and unreactive dinitrogen gas. Volcanic lightning is suspected to have kickstarted the availability of nitrogen for ancient life by zapping apart the triple bond of dinitrogen to form nitrates that rained down on Earth at least 3.7 billion years ago.

By 3.2 billion years ago, according to a 2015 study that analysed the chemistry of such ancient rocks, lifeforms had already evolved the ability to pull nitrogen from the air and convert it into ammonia using a molybdenum-based enzyme. This was around a billion years before the two other nitrogenase enzymes that use different metals, namely iron or vanadium, are thought to have evolved.

However, this presented a conundrum. At the time, dissolved molybdenum was scarce due to a lack of atmospheric oxygen to react with molybdenum-containing rocks and wash it into the ocean. So how did molybdenum-nitrogenase evolve as the prevailing nitrogen-fixing enzyme?

Hailiang Dong at China University of Geosciences and colleagues have now shown in the lab that an ancient photosynthesising microorganism could have extracted the required molybdenum from molybdenite, or molybdenum disulfide, a mineral present in rocks on early Earth. This, they say, could have promoted the rise of nitrogen fixation via molybdenum-nitrogenase.

To help solve the puzzle, the team looked to the ancient anoxygenic photosynthesising microbe Rhodopseudomonas palustris – a purple, rod-shaped bacterium found in marshy habitats. This has all three nitrogenase enzymes – molybdenum, vanadium and iron – and switches between them depending on metal availability.

To study if R. palustris could extract molybdenum from molybdenite, the researchers first created a mutant strain with its iron-nitrogenase removed. This was because the molybdenum-nitrogenase contains and needs a supply of iron, which could have skewed results by the microbe switching to iron-nitrogenase.

The mutant strain was then incubated with millimetre-sized pieces of molybdenite. Results revealed that the microbe extracted molybdenum from molybdenite by secreting two high-affinity ligands, or molybdophores, and by expressing molybdenum transport proteins. The team also observed significant changes in the surface chemistry of molybdenite after being incubated with these cells, suggesting that organic compounds had attached to the mineral.

‘Our findings demonstrate that molybdenite can indeed support nitrogen fixation by R. palustris, with the rate of nitrogen fixation increasing in correlation with the concentration of molybdenite,’ says Dong. The results highlight that molybdenum-bearing minerals could have provided a crucial source of molybdenum for photosynthesising microbes in early, low-oxygen environments, such as shallow waters near land.

‘The results look convincing to me and definitely offer a plausible mechanism for life to obtain molybdenum on the Archean Earth,’ comments Eva Stüeken, at the University of St Andrews, UK, who co-authored the 2015 study that discovered molybdenum-nitrogenase 3.2 billion years ago. However, she points out that other molybdenum sources, particularly in deep-sea hydrothermal vents, remain to be investigated for their potential importance for early life in the open ocean. ‘Nevertheless, the work definitely addresses an important biogeochemical problem,’ she says. ‘It is undoubtedly thought-provoking.’