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World's first success in observation of the internal structure of microfossils from 3.4 billion years ago: a clue to the bio-organisms that lived at that early time

  • Read in Japanese
  • 2015/12/10
  • Graduate School of Environmental Studies
  • Prof. Kenichiro Sugitani
  • Associate Prof. Koichi Mimura

Prof. Kenichiro Sugitani and Associate Prof. Koichi Mimura at the Graduate School of Environmental Studies, Nagoya University, with their research groups at the University of Liège, Belgium, and Lille University, France, discovered remarkable microfossils in sedimentary rocks in the Pilbara Craton of Western Australia that were deposited ~3.4 billion years ago. Compared to the contemporaneous typical ones, the microfossils were anomalously large, characterized by unusually complex morphologies and had acid-resistant cell walls; therefore, after separation and extraction of the microfossils, it was possible to observe the complicated forms, and even their internal structures, by using scanning and transmission electron microscopies. The researchers concluded that identified microfossils were more diverse and complex than expected. This means that elaborated ecosystems composed of varieties of microorganisms were already established 3.4 billion years ago. This evidence could lead to a paradigm shift in the earth sciences in terms of our understanding of early life.
This study was published online, Geobiology, on June 13, 2015.→ Nagoya University Press Release

“Why have humans evolved in the way that we have?” By revealing the origin of life, researchers attempt to solve the essential question of humans.

Our planet was formed around 4.6 billion years ago, and life is thought to have originated about 3.8 billion years ago, or earlier—

“We have to be extremely careful, as they are micron-sized fossils,” states Prof. Kenichiro Sugitani, Graduate School of Environmental Studies at Nagoya University, who focuses on research into the evolution of life on the early Earth.

Geologic age from 2.9 to 3.8 billion years ago is called the Archean eon, and microfossils identified in such old age have been suggested to represent living organisms, prokaryotes which are composed of a single cell. However, because of the simple morphology and small size of many of the previously reported microfossils, it is difficult to set criteria for determining their affinities and even their biogenicity. Researchers have produced heated discussions in their quest for the truth.

Prof. Sugitani, whose specialty is geobiology of the Paleoarchean eon, conducted the research with Associate Prof. Koichi Mimura, a specialist in the origin of life, from the Graduate School of Environmental Studies at Nagoya University.

They are old colleagues, belonging to the same laboratory when they were students. Today, although they independently organize their own laboratories in different academic areas, they perform great collaborative work due to their shared interest in primitive life.

In this study, Prof. Sugitani, Associate Prof. Mimura, and their collaborative research groups abroad revealed new evidence that complex organisms had evolved on Earth much earlier than had been thought (3.4 billion years ago). They have pioneered a new way of microfossil research for the Paleoarchean eon.


The Archean eon (between 2.5 and 3.8 billion years ago) is considered to have been as described below:

Approximately 3.8 billion years ago, organisms are generally believed to have originated in the deep sea, escaping from the strong ultraviolet light and frequent volcanic activities. Chemical evolution is thought to be promoted by forming simple organic compounds, such as amino acids, nucleic acid bases, and carbohydrates, from carbon dioxide, nitrogen, and water. Subsequently, living organisms came into being.

All the living organisms at that time were heterotrophic prokaryotes, which are creatures of single cells. They lived on organic compounds present in the sea and performed anaerobic respiration (i.e., obtaining energy without using oxygen). However, the available organic compounds were limited and consumed soon or later, and therefore they had to evolve to produce their own food, which was the start of autotrophy using chemical and subsequently photo energies.

3 billion years ago or earlier, cyanobacteria (prokaryotes that perform photosynthesis) evolved and began producing free oxygen. Oxygen gradually accumulated, and aerobic organisms that made use of the oxygen came into being.

Fossils found in such cherts are usually only micron-sized (1 µm = 1/1000 mm)

Research into early fossils and life began in the 1960s when the Canadian Gunflint microfossil assemblage (around 2 billion years old) was discovered.

In the 1990s, as new measurement technologies developed, our understanding of the evolutionary history of life progressed by means of further studies:

In 1993, using high-magnification microscopes, microfossils 3.465 billion years old from the Pilbara area in Western Australia were discovered (Schopf, Science (1993) 260: 640-6).

In 1996, 3.83-billion-year-evidence of life from Southwest Greenland was reported (Mojzsis, et al., Nature (1996) 384: 55-9).

In the same year, evidence of life was reported in meteors as originated from the Mars 3.9 billion years old that were discovered on the Antarctic continent (McKay, et al., Science (1996) 273: 924-30).

Figure 1.Panoramic view of Western Australia (Figure : by courtesy of Prof. Sugitani)

“I have been researching about the Earth and life in the Archean eon since 1989.”

At that time, Prof. Sugitani was a Ph.D. student, and because of his interest in Archean rocks, he visited Western Australia where many Archean sedimentary rocks occur (Figure 1). Since then, “Study of the Earth and life in the Archean eon has become my life’s work,” he says.

In 2001, when he visited Western Australia again for fieldwork, he had an enormous piece of luck.

In fact, he was not looking for fossils; however, he found microfossils (3 billion years old) by chance. They were different in size from previously reported contemporaneous microfossils, as large as dozens of micrometers. Their morphologies were also diverse, including a considerable number that had been fossilized during the process of cell division.

However, in 2002, immediately after this discovery, researchers on early life in the Archean eon got in the face of a great controversy all over the world.

On the basis of geological information, some researchers pointed out that the reported evidence of life of 3.8 billion years ago was incorrect. For example, Southwest Greenland has very complicated geology due to repeated volcanic activities and diastrophisms. Consequently after the geological reassessment, it was considered that cells could hardly have been preserved in their original state. The results also implied that the carbonaceous matter was produced only by inorganic chemical reactions, not by life.

“When we found the microfossils from 3 billion years ago, this controversy heated all over the world. We then had to continue research to gain further trust.”

Prof. Sugitani had targeted the Pilbara area in Western Australia (Figure 2) because it has been rarely influenced by metamorphisms, and thus the condition of the sedimentary rocks is suitable for studies of ancient life. He involved collaborative researchers in Australia who had sufficient knowledges of the Pilbara rocks to analyze the data thoroughly.

Figure 2. Pilbara Craton in Western Australia (shown in red) (Figure : By User:Hesperian [CC BY-SA 3.0) via Wikimedia Commons])

So far, the research results have been published in 15 articles in total since 2007 (Sugitani, et al.,Precambrian Research (2007) 158: 228-62 was the first).

As a result of the team’s work, the large and diverse morphologies of microfossils from 3 billion years ago (Figure 3), have been widely accepted by the scientific community.

Figure 3. large and diverse morphologies of microfossils from 3 billion years ago (Figure : by courtesy of Prof. Sugitani)

“Furthermore, I realized that the large microfossils or similar ones were already reported from the strata 3.4 billion years old in South Africa.”

Prof. Sugitani and his research group then expected that similar microfossils could also be found in the 3.4-billion-year-old strata in Australia, which is called the Strelley Pool Formation.

As they expected, during their research in 2005 and 2008, they discovered large microfossils from 3.4 billion years ago. Also in 2010, during a re-survey in different areas, they found the same types of microfossils (Sugitani, et al., Astrobiology(2010) 10: 899-920), (Sugitani, et al., Precambrian Research (2013) 226: 59-74).

Furthermore, the internal structure of the microfossils was observed in this study—

“Associate Prof. Mimura can distinguish stones using subtle differences.”

Prof. Sugitani and Associate Prof. Mimura had repeated discussions on the subject of what kind of rocks would contain fossils, imagining the environment at that era from the black-colored rocks (Figure 4). They likely contain fossils since the color is generally attributed to carbon particles originated from organisms.

Figure 4. Excavation site (Figure : by courtesy of Prof. Sugitani)

For about a week, they concentrated on collecting black rocks and then brought them back to the laboratory for separation and extraction of fossils.

The stones, which are of the type called chert, are mainly composed of SiO2 as in microcrystalline quartz. The rocks were dissolved using diluted hydrochloric acid and hydrofluoric acid, and then microfossils were extracted carefully. After that, using a binocular stereoscopic microscope, the microfossils are picked out one by one. Thousands of microfossils can be extracted from only 25 g of rock.

The 3.4-billion-year-old microfossils discovered by Prof. Sugitani and his collaborators showed various morphologies (Figure 5):

In most cases, the size of microfossils from the Archean eon is less than several micrometers, and they are usually spherical or thread-like in appearance. However, the microfossils reported by Prof. Sugitani and his collaborators were shaped like films, small spheres, large spherical spheres, lenses with flange, and filaments. In addition, some of them were more than 80 µm in size.

Figure 5. 3.4-billion-year-old microfossils with various morphologies (Figure : by courtesy of Prof. Sugitani)

In order to observe the internal structures of the microfossils, the lens-shaped type was sliced by a focused ion beam system and examined using a transmission electron microscope (Figure 6). This became a world first achievement in revealing the internal shape of such ancient microfossils, which possessed a three-dimensional mesh structure covered with a tough organic wall.

Figure 6. Internal structure of the 3.4-billion-year-old lens-shaped microfossils. (a) TEM image (b,c) SEM images. (Figure : by courtesy of Prof. Sugitani)

In terms of internal shape, the organism is similar to some of extant cyanobacteria (prokaryotes); on the other hand, the comparatively large size, hard organic wall, and presence of flanges indicate a eukaryotic affinity. Thus, it may also be considered as belonging to an extinct group that does not belong to any of the currently existing three domain organisms (eukaryotes, eubacteria, and archaea). “Still further research is required to assess this possibility,” Prof. Sugitani adds.

There are abundant records of fossil from 3.4 billion years ago, indeed much more than we expected. Even in the Archean eon, diverse groups of organisms may already have created complex ecosystems. These researchers have pioneered the evidence of bio-organisms that lived at this early time.


Evolution of life, the essential question of humans—

Expanding these research results, Prof. Sugitani raised three discussion points:

  • In the Archaeon eon, were there only prokaryotes?
  • How different were organisms between 3 billion and 3.4 billion years ago?

  • Is it possible to establish the criteria to distinguish similar fossils (but different in shape), or not?

“An important key is to understand the chemical composition of chert.”

Prof. Sugitani refers to geochemistry as a necessity for future discussion. In addition to study of the Earth, researchers aim to solve cosmic questions, such as whether there is or was life on the Mars.

In space, do living organisms exist?

—We may yet solve this question, too.

(Ayako Umemura)

Researchers featured in this article

Dr. Kenichiro SugitaniProfessor, Graduate School of Environmental Studies, Nagoya University

Dr. Sugitani graduated from the School of Science, Nagoya University, in 1986. In 1992, he completed his doctorate degree at Earth Sciences, Graduate School of Science, Nagoya University. He worked as an assistant professor from 1991 to 2000, and then as an associate professor at the School of Informatics and Sciences at Nagoya University. In 2001, he became an associate professor at the Graduate School of Environmental Studies, Nagoya University. Since 2006, he has been a professor and remains in that position.


To solve the mystery of organisms on the early Earth and their evolution, Dr. Sugitani has driven the microfossil research. He expects that the research can also lead to discussion about the evolution of life in space.
While going beyond space, Dr. Sugitani is interested in local environmental issues as well. He wants to maintain, recover, and rebuild the aquatic environment of the Kushida and Inabe rivers in Mie Prefecture, where his hometown is, as well as the Kiso River, running through the Nobi plain in this local area. I expect that further achievements will be produced from his lifework (by AU)

Dr. Koichi Mimura【Associate Professor, Graduate School of Environmental Studies, Nagoya University

Dr. Mimura completed his master’s course at the Graduate School of Science at Nagoya University in 1992. Between 1994 and 2000, he worked as an assistant professor at the Graduate School of Science, and in 1995, he obtained his doctorate degree from Nagoya University. In 2001, he became an assistant professor at the Graduate School of Environmental Studies at Nagoya University. Since 2004, he has worked as an associate professor at the same school.


“I want to find out when and how life appeared on the Earth,” says Dr. Mimura. Finding the oldest fossils gives us a clue to the question of “when.” For the “how,” he studies meteorite impacts as a supplier of organic materials on the primitive Earth. When meteorites containing organic materials impacted on the Earth, these materials reacted to produce complex organics useful for the formation of life.
With his interesting research theme, his talk at the science café has been well received. I am looking forward to further results from him (by AU)


K. Sugitani, K. Mimura, M. Takeuchi, K. Lepot, S. Ito, and E. J. Javaux.

Early evolution of large micro-organisms with cytological complexity revealed by microanalyses of 3.4 Ga organic-walled microfossils.

Geobiology. (2015).

(First published on June 13, 2015; doi: 10.1111/gbi.12148)

Kenichiro Sugitani, Kathleen Grey, Abigail Allwood, Tsutomu Nagaoka, Koichi Mimura, Masayo Minami, Craig P. Marshall, Martin J. Van Kranendonk, and Malcolm R. Walter.

Diverse microstructures from Archaean chert from the Mount Goldsworthy–Mount Grant area, Pilbara Craton, Western Australia: Microfossils, dubiofossils, or pseudofossils?

Precambrian Research. 158: 228 (2007).
(First published on October 5, 2007; doi: 10.1016/j.precamres.2007.03.006)

Kenichiro Sugitani, Kevin Lepot, Tsutomu Nagaoka, Koichi Mimura, Martin Van Kranendonk, Dorothy Z. Oehler, and Malcolm R. Walter.
Biogenicity of Morphologically Diverse Carbonaceous Microstructures from the ca.3400 Ma Strelley Pool Formation, in the Pilbara Craton, Western Australia.

Astrobiology. 10: 899 (2010).
(First published on December 1, 2010; doi: 10.1089/ast.2010.0513)

Kenichiro Sugitani, Koichi Mimura, Tsutomu Nagaoka, Kevin Lepot, and Makoto Takeuchi.

Microfossil assemblage from the 3400 Ma Strelley Pool Formation in the Pilbara Craton, Western Australia: Results form a new locality.

Precambrian Research. 226: 59 (2013).

(First published in March, 2013; doi: 10.1016/j.precamres.2012.11.005)


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