A 2-billion-year-old Rock Is Home To Living Microbes

Pockets of microbes have been found living within a sealed fracture in 2-billion-year-old rock. The rock was excavated from the Bushveld Igneous Complex in South Africa, an area known for its rich ore deposits. This is the oldest example of living microbes being found within ancient rock so far discovered.

The team involved in the study built on its previous work to perfect a technique involving three types of imaging – infrared spectroscopy, electron microscopy and fluorescent microscopy – to confirm that the microbes were indigenous to the ancient core sample and not caused by contamination during the retrieval and study process. Research on these microbes could help us better understand the very early evolution of life, as well as the search for extraterrestrial life in similarly aged rock samples brought back from Mars.

Deep in the earth lies something ancient and alive. Colonies of microbes live in rocks far beneath the surface, somehow managing to survive for thousands, even millions of years. These tiny, resilient organisms appear to live life at a slower pace, scarcely evolving over geological time spans and so offering us a chance to peek back in time. Now, researchers have found living microbes in a rock sample dated to be 2 billion years old.

“We didn’t know if 2-billion-year-old rocks were habitable. Until now, the oldest geological layer in which living microorganisms had been found was a 100-million-year-old deposit beneath the ocean floor, so this is a very exciting discovery. By studying the DNA and genomes of microbes like these, we may be able to understand the evolution of very early life on Earth,” said Yohey Suzuki, lead author and associate professor from the Graduate School of Science at the University of Tokyo.

This picture was taken on site when the drill core sample was washed, flamed and then cracked. The 30-centimeter-long, 85-millimeter-diameter core was taken back to Japan for further study. — Credit Y. Suzuki

The rock sample was taken from the Bushveld Igneous Complex (BIC), a rocky intrusion in northeastern South Africa which formed when magma slowly cooled below the Earth’s surface. The BIC covers an area of approximately 66,000 square kilometers (roughly the size of Ireland), varies in thickness by up to 9 km, and contains some of the richest ore deposits on Earth including about 70% of the world’s mined platinum.

Due to the way it was formed and minimal deformation or change occurring to it since then, the BIC is believed to have provided a stable habitat for ancient microbial life to continue until today.

With the aid of the International Continental Scientific Drilling Program, a nonprofit organization that funds exploration at geological sites, the team obtained a 30-centimeter-long rock core sample from about 15 meters belowground. The rock was cut into thin slices and analyzed, which is when the team discovered living microbial cells densely packed into cracks in the rock. Any gaps near these cracks were clogged with clay, making it impossible for the organisms to leave or for other things to enter.

The team built on a technique they had previously developed to confirm that the microbes were native to the rock sample, and not due to contamination during the drilling or examination process. By staining the DNA of the microbial cells and using infrared spectroscopy to look at the proteins in the microbes and surrounding clay, the researchers could confirm that the microorganisms were both alive and not contaminated.

“I am very interested in the existence of subsurface microbes not only on Earth, but also the potential to find them on other planets,” said Suzuki. NASA’s Mars rover Perseverance is currently due to bring back rocks that are a similar age to those we used in this study. Finding microbial life in samples from Earth from 2 billion years ago and being able to accurately confirm their authenticity makes me excited for what we might be able to now find in samples from Mars.”

Characterization of a section from the fracture surface to the rock interior. A Photo of the section with a yellow arrow pointing to the fracture surface. B Microscopic image of a region of the section highlighted in a yellow rectangle in A. C Fluorescence microscopy image of the region highlighted by orange rectangle in B. Intensity maps of the section at 1000 cm−1 (D), 1530 cm−1 (E), and 1640 cm−1 (F) obtained by optical photothermal infrared (O-PTIR) spectroscopy. The intensity maps were obtained from the area highlighted with a yellow square in B. G RGB color synthesis of the three intensity maps. A yellow rectangle in G indicates an area where the intensity maps for RGB color synthesis are obtained in Fig. 5A — Microbial Ecology via PubMed

Visualization of microbial cells after SYBR Green I staining. A Fluorescence microscopic images of the large area from the section highlighted by an orange rectangle in Fig. 4B, and B the small area highlighted by a yellow rectangle in Fig. 5A. The yellow rectangle in A is the same as shown in Fig. 5A, and the orange square in B is the same as in Fig. 5B. Pink arrows in A point to the veins shown in Fig. 4 — Microbial Ecology via PubMed

Paper

Yohey Suzuki, Susan J. Webb, Mariko Kouduka, Hanae Kobayashi, Julio Castillo, Jens Kallmeyer, Kgabo Moganedi, Amy J. Allwright, Reiner Klemd, Frederick Roelofse, Mabatho Mapiloko, Stuart J. Hill, Lewis D. Ashwal, Robert B. Trumbull. Subsurface Microbial Colonization at Mineral‐Filled Veins in 2‐Billion‐Year‐Old Mafic Rock from the Bushveld Igneous Complex, South Africa. Microbial Ecology. 2nd October 2024. doi: 10.1007/s00248-024-02434-8, via PubMed

Astrobiology