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Searching for the Roots of All Life—from Bacteria to Humans The Origin of Life on Earth and Extremophiles

Satoshi Akanuma
Associate Professor, Faculty of Human Sciences, Waseda University


Schematic phylogenetic tree representing the evolution of life from its origin 4 to 4.2 billion years ago up to the modern era

Life forms on Earth share a common genetic mechanism. From studying the complexity and intricacy of genes, it is difficult to imagine that mass numbers of the same construct were formed independently of each other. In fact, it is logical to hypothesize that all life forms on Earth are descendants of a single common ancestral organism, and that common ancestor already had the genetic mechanism present in organisms today. If this is the case, it can be said that all life on Earth—from bacteria to humans—share the same roots, and can be traced back to a single “origin of life” event. The phylogenetic tree that illustrates the evolutionary paths of organisms in the form of branches shows that all existing life forms stem from a single origin. So, when, where and how did the first-ever life-form come into existence?

The Birthplace of Life: Was it the Geothermally Heated Seafloor? Hot Springs on the Earth’s Surface? Or Was It Outer Space?

The origin of life is still shrouded in mystery. One of those mysteries is exactly where the first life-form was born. There are many pieces of evidence that suggest that living things had already existed on Earth about 3.5 to 4.1 billion years ago. This would mean that life-forms had existed even before then. Whenever I ask students in class where the first life-form was born, 70 to 80 percent of them will answer that it was in the geothermally heated seafloor. The water that gushes out of hydrothermal vents located on the seafloor contains many inorganic substances that are required for creating life and the raw material for life, making it a very likely location from which life originated. However, when considering the discrepancy in the potassium-sodium ratio between ocean water and organisms, the fact that the concentration of molecules that are the building blocks of life is lower in ocean water, and the fact that in environments where water is plentiful, hydrolysis is more likely to occur than dehydration synthesis. The theory that life could have begun on above-ground hot springs, small ponds, or tide pools—where there is a cyclical degree of humidity in which concentration occurs more easily—is becoming more prominent. Furthermore, there is even a theory that life may have originated on a different heavenly body, and was brought to Earth on a meteorite. It has been proven that some bacterial life forms can travel through the void of space while remaining alive. The theory that our ancestors were extraterrestrial organisms is not necessarily a far-fetched fantasy.

As explained above, there are several plausible theories as to where life originated. Today, scientists who focus on planetary science, geochemistry and biology each propose experiments based on their respective expertise to tackle this question.

The three environments that are thought to be the likely places where life first originated. From left to right: seafloor geothermal mineral deposits, above-ground hot springs and tide pools.

Clarifying the Origin of Life

In the past, much of the information on life forms and environments was gained from analyzing rocks and fossils excavated through geological means of research. On the other hand, scientists who are experts in chemistry and biology attempt to answer the questions of life’s origins through a method known as the bottom-up approach—also known as synthetic biology—in which an environment imitating prebiotic conditions on Earth are reproduced in labs, where the raw materials necessary for building life can be synthesized and studied. Moreover, Charles Darwin, who was the originator of the biological theory of evolution and is famously known as the author of On the Origins of Species, explained that common traits among species point to a common ancestor of those species. When applying this theory to the base sequences of DNA and the amino acid sequences of protein in life forms that presently exist, the DNA sequences and protein sequences of past life forms can be hypothesized. By comparing the amino acid sequences of protein in many life forms that presently exist, scientists have been able to reconstruct actual proteins of the past. It is known that protein properties such as heat resistance and pH dependence hold the key to revealing the habitation environments of the life forms carrying the proteins. Therefore, by studying the reconstructed protein properties, scientists can hypothesize what sort of life forms these past organisms were, and what sort of environments they inhabited. Through these methods, the author and coworkers have ascertained that about 3.5 to 4 billion years ago, a life form known as “the last common ancestor of all life forms” existed and inhabited high-temperature environments that exceeded 80°C. However, the appearance of “the last common ancestor of all life forms” was more recent than the origin of life itself. This is where the latest research reaches even further into the past from “the last common ancestor of all life forms,” and attempts to discover the initial stages of life on Earth, in what environment they existed, and how they have evolved.

Extremophiles and the Origin of Life

Even today, there are many microbial life forms on Earth that inhabit environments exceeding 80°C. These microbes are called hyperthermophiles, some of which thrive in extreme environments that exceed 100°C. There are also microbes that inhabit acidic and alkaline environments. There are even microbes that thrive in environments with five to ten times the salt concentration of ocean water. These life forms, which live in environments that are uninhabitable for humans or for familiar creatures around us, are called extremophiles. Hyperthermophiles have extremely durable cellular membranes and proteins, while organisms that live in acidic and alkaline environments have neutralizing mechanisms within their bodies. Microbes that inhabit high salt-concentration environments have intracellular mechanisms that accumulate substances that adjust osmotic pressure. These are a few examples of the variety of biological mechanisms of extremophiles that allow them to survive in extreme environments. However, not everything about extremophiles is known to modern science. Assuming that the first life forms were born in extreme environments, many experiments are being conducted in an attempt to discover the traits of the very first life forms by analyzing the biological mechanisms found in extremophiles.

Satoshi Akanuma
Associate Professor, Faculty of Human Sciences, Waseda University

[Brief Personal Record]

Satoshi Akanuma was born in Yokohama, Kanagawa Prefecture, and earned an Sc.D. from the Graduate School of Bioscience and Biotechnology at Tokyo Institute of Technology in 1998. Before assuming his post as an associate professor in the Faculty of Human Sciences at Waseda University in 2015, he had worked as a special postdoctoral researcher at Riken, a postdoctoral researcher at the University of Cologne, a postdoctoral researcher at the National Food Research Institute, and a research associate/assistant professor in the School of Life Sciences at the Tokyo University of Pharmacy and Life Sciences. He specializes in protein engineering and experimental evolutionary science.

[Main Publications Relating to the Subject in this Article]

Akanuma S., (2016) “Thermophilicity of early life revealed by comparing extant genomes” Geochemistry 50, 199-210
Akanuma S. et al., (2015) “Robustness of predictions of extremely thermally stable proteins in ancient organisms” Evolution 69, 2954-2962
Akanuma S. et al., (2013) “Common ancestor of all life forms” Akihiko Yamagishi Edition, Astrobiology, Kagakudojin, 118-131
Akanuma S. et al., (2013) “Experimental evidence for the thermophilicity of ancestral life” Proc. Natl. Acad. Sci. USA 110, 11067-11072

Laboratory of Satoshi Akanuma