DATE2021.03.29 #FEATURES

Mysteries in Science: Illuminating the research frontier on the dark biosphere

Yohey Suzuki

(Associate Professor, Department of Earth and Planetary Science)


Scientists investigating organisms living underground and in the deep-sea, the unexplored frontiers of the earth, have discovered that substances produced by water-rock reactions allow life to flourish in the dark biosphere where photosynthetic organic matters are not available. In this area of study, it is believed that for life to thrive, rocky substances are produced effectively at high temperatures and then transported to organisms by heat-driven water movement. This has been demonstrated by intensive research on deep-sea hydrothermal vents and onshore hot springs around the world. When looking at the evolution of life, sequences of a few genes amplified by PCR were used to estimate which microbes are closely related to the universal common ancestor to all living things with the central dogma. The answer was thermophilic microorganisms, which makes many scientists think that microbes living in hot water impose constraints on the early evolution of life.

These textbook-level facts up to now are becoming outdated due to new research findings using the latest scientific technology, in particular genomic analysis. Using sequences of nearly 100 genes in the genome informative of the evolution of organisms, instead of the PCR-amplified sequences of the few genes, we found that the early evolution of life was dramatically different from what we had thought. This genome-wide information revealed that tiny prokaryotes, which inhabit cool water, are organisms that are closely related to our common ancestor. “Tiny” means that their cell and genome sizes are equal to those of some viruses and smaller than those of typical prokaryotes. One common feature in tiny prokaryotes is that they ferment organic matters for energy generation. These tiny prokaryotes that are closely related to our common ancestor have become key members of the dark biosphere where cold water flows through cracks in underground rocks. This suggests that underground environments may have been an important place for the evolution of our common ancestor.

Research findings from our lab are about to change the common view of life when the ecology of underground microbes was unveiled. No life was thought to survive in closed spaces within cold rocks because substances necessary to sustain life are not transported there by water movement. Unexpectedly, however, we discovered microbes in these cold rocks without the evidence of water movement. These microbes were packed together at densities comparable to those in human intestines (this was introduced in an article published in the July 2020 edition of The Rigakubu News). This discovery was made possible because of the development of a new technology, the first in the world that can directly see microbes within rocks. I believe that this technological innovation can be compared to the first observation of microbes by Leeuwenhoek using a microscope in the 17th century.

There are diverse growing conditions within rocks, comparable to the diversity of rock types, and microbes that have adapted to distinct rocky habitats are expected to be revealed one after another. We hope to find primitive life that retains the characteristics of our common ancestor among the newly discovered microbes, like tiny prokaryotes that dominate the cold water in underground rocks. We believe that the hypothesis that life was born on the surface of minerals such as clay and metal sulfides can be proven by finding out whether microbes using these minerals in rocks are closely related to our common ancestor. 

We are looking forward to seeing what we will find by future life explorations.

(Upper right) A thin section of a basaltic rock sample, drilled and cored from the oceanic crust, containing microbes that are as densely packed as those in the human intestine. The larger image is a fluorescent microscopy image of green DNA-stained microbial cells taken from the sample, marked with a light blue box in the upper right image. A 1-mm scale bar is shown at the bottom of the upper right image.


This article is from the "Mysteries in Science" series in The Rigakubu News


Translated by Kristina Awatsu, Office of Communication