Ancient nickel-eating microbes can teach us valuable biomining techniques – study

Methanogen strain M. barkeri Fusaro, which was was grown with acetate and methanol as substrates and with (Ni,Fe)S2 as the sole source of nickel, iron, and sulfur. (Image from Applied and Environmental Microbiology).

New research produced at Montana State University examines a specific type of ancient microbe that can isolate and bioaccumulate nickel from its surroundings, using minerals as a nutrient source to support growth. 

The recent findings, published in the journal Applied and Environmental Microbiology, help differentiate between two competing hypotheses about the reduction in atmospheric methane billions of years ago.

The microorganisms in question are called methanogens, which are ancient life forms that still exist today. Methanogens are unique because they don’t use sunlight to power their metabolisms like most organisms do, and they are poisoned by oxygen. Instead, their metabolism uses chemicals from their environment, often breaking down rocks and minerals to do so. During the process, the cells produce methane, also known as natural gas.

Pinpointing exactly how methanogens do this could answer questions that reach back more than 3 billion years.

Early earth had no oxygen, and the atmosphere at that time contained a lot more methane and hydrogen,” Eric Boyd, co-author of the study, said in a media statement. “That’s largely due to these methanogens that react hydrogen with carbon dioxide to make methane. And all of a sudden, for reasons that aren’t clear, methane started to decrease and oxygen started to increase. That was about 2.4 billion years ago. So, what happened?”

Microbes taking minerals

According to Boyd, the methane reduction may have been caused by a reduction in the methanogen population.

One hypothesis is that changing environmental conditions led to more competition between methanogens and other organisms for environmental resources, causing a drop in the methanogen population. The other theory suggests that changes in volcanic patterns on early earth led to a decrease in available nickel, leading the methanogens to starve for this essential element.

However, the research contained in the new paper discovered that nickel-dependent methanogens need much less nickel to survive than previously thought. Their ability to accumulate nickel within themselves allows for survival even when nickel is scarce.

To make these observations, Boyd’s team grew methanogens in environments with varying amounts of nickel, observing how they responded to the different conditions. By measuring how much methane the microbes produced, they were able to estimate how well the methanogens were growing and surviving. Using a variety of spectroscopic techniques, the team could identify how much nickel the cells stored.

When life originated, there was no photosynthesis. It was all mineral-based energy that was supporting life,” the scientist said. “And all of a sudden, we stumbled upon this discovery, which is essentially microbes taking minerals and reducing them in a way that was not supposed to be possible. Most of the time, the mineral gets oxidized and generates acidic mine drainage, but this process doesn’t do that.”

In Boyd’s view, a better understanding of this biomining process could allow humans to develop mining technologies that have less environmental impact. 

“There are three elements of this paper that I think are really special,” he said. “One is that we show that the cells can acquire nickel from a mineral, which hasn’t been shown before. The second is that they can acquire it at extremely low concentrations. They don’t need much, and that goes against conventional thought. The third is that they accumulate it, and that just makes sense. If there’s something that you’re very dependent on, and these bugs are so dependent on nickel, that they’ve found some way of ensuring that they’ve got plenty of it for the future.”

While the scientific concepts and research process are extremely complex, Boyd said the larger implications of the work are quite simple, tying directly into the timeless questions of how the planet came to have a habitable environment for other life forms and ultimately humans.