Scientists Waited Two and a Half Years to See Whether Bacteria Can Eat Rock

For a substance known for its abundance, persistence, and rock-bottom prices, there is an enduring mystery to dirt: where does it come from?

Generally speaking, it sits at the nexus of geology, meteorology, and time. Rock becomes dirt via weathering. But it is a process that is necessarily difficult for humans to observe.

It’s long been assumed that life is somehow involved (on Earth, there is very little in which life is not involved), and scientists have demonstrated that it is theoretically possible. But no one had ever actually observed this in common types of iron-silicate continental rocks, likely due to the distressingly large gap in weathering’s reaction velocity relative to scientists’ career velocity.

Enter intrepid scientists at the University of Wisconsin-Madison, the University of Bristol, and Pennsylvania State University, who decided to undertake a two and a half year experiment to see how capable microbial life is of taking on rock. To make this possible, they had to think up ways to hit the fast forward button.

One way was to find rock that weathers fast. The Rio Blanco Quartz Diorite bedrock beneath the Rio Icacos watershed in Puerto Rico weathers exceptionally fast, making it a tempting target for an experiment conducted on a publishable timescale. The scientists took samples of pure bedrock from a roadcut as well as long tubes of soil and rock drilled into the formation from above. Included in these cores was the transition zone where fractured bedrock alternates with veins of newborn soil, a region is somewhat oddly called the “rindlet” zone (which sadly does not yield anything crunchy and delicious sold in 99-cent bags).

The scientists found that in this deepest layer of soil, ATP — a chemical generated by metabolizing cells — is more abundant than in any other part of the soil except the surface, where nutritious junk dropped by plants and animals and abundant oxygen fuel ebullient growth. So something is going on down there. The question is: what?

In Search of Electrons

What, if biological weathering is indeed occurring, involves electrons. Electrons are negatively charged particles that orbit the nuclei of atoms. The number of electrons in an atom often varies. Versions containing more electrons are referred to as reduced, while those containing fewer are oxidized.

All living beings juggle electrons, usually by stripping them from sugars and other reduced organic compounds (stuff we call “food”) and using those electrons to power their cells through cellular respiration. But some microbes can use simple inorganic compounds or atoms as electron sources. The ones that can use stone as a source of electrons are called lithotrophs. They eat rocks.

Minerals rich in reduced iron like pyrite (fool’s gold), biotite, and hornblende are potential bacteria chow. The physical changes to these minerals wrought by electron stripping should initiate the process of their chemical dissolution — that is, weathering. This should be visible under the microscope as some sort of physical alteration.

So the scientists took their highly weather-able rock and microbe-laced soil back home and accelerated the proceedings further by grinding the rock, increasing its surface area. They mixed crushed rock with microbes.

Then they waited.

And waited.

And waited some more.

Two birthdays and two Christmases and two income tax filing deadlines passed. And still they waited.

The Ultimate Slow Food

After 30 months, they put their samples under the microscope. The minerals incubated with microbes appeared ragged or pitted — as if they had been dipped in acid, not bacteria — after their 864-day incubation. The sterile control minerals, by contrast, retained sharp, smooth edges.

The scientists also detected abundant ATP in the mixtures that included microbes, indicating feasting. And remember: there was absolutely nothing to feast on except crushed rock.

Another mystery remained: who was eating the rocks? When the scientists checked the DNA of the microbes in their samples, they found almost exclusively bacteria. Missing from the cultures, surprisingly, were fungi. Mycorrhizal fungi that associate with tree roots and generate many familiar forest mushrooms are also known for their ability to mine rock particles in soil, as I discussed with Radiolab a few years ago. The scientists suggest that the amount of fungus food in the rindlet zone is either not enough to support such fungi, or that the culture conditions in their experiments were not sufficient to support any fungi that might have been present in the initial sample.

The lithotrophic bacteria they did find have a special power: the ability to harvest electrons from iron atoms outside their bodies. That is, they can eat without swallowing their food. The bacteria “ingest” the electrons in a technique called external electron transfer. This is vital because the iron atoms are part of the mineral and the bacteria have no crow bars or other means with which to pry them loose. But there is another advantage to doing it this way: if the iron atoms were ingested before oxidation, the microbes would fill with rust, a potentially lethal and definitely embarrassing situation.

So, bacteria indeed appear able to initiate and accelerate the dirt-making process. On land, dirt supports plants, which support most everything else. In this way among many others, life feeds back, yielding the planet we see today in which no surface remains uncolonized, and the height and depth at which life vanishes remain unknown.

Reference

Napieralski, Stephanie A., Heather L. Buss, Susan L. Brantley, Seungyeol Lee, Huifang Xu, and Eric E. Roden. “Microbial chemolithotrophy mediates oxidative weathering of granitic bedrock.” Proceedings of the National Academy of Sciences 116, no. 52 (2019): 26394-26401.