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Sydney sea urchins show how bacteria help make fossils



18 December 2008

New research conducted at the School of Biological Sciences, University of Sydney, has shed light on a palaeontological paradox: how soft animal tissues are able to survive long enough to become fossilised. The secret ingredient is bacteria.

Scanning electron micrograph showing bacterial replaced embryo of Australian sea urchin Heliocidaris erythrogramma.
Scanning electron micrograph showing bacterial replaced embryo of Australian sea urchin Heliocidaris erythrogramma.

The research team of 13 scientists, led by Professor Elizabeth Raff and Professor Rudolf Raff from Indiana University, USA, used embryo cells from Australian sea urchins to demonstrate how bacterial 'decay' can lead to preservation of soft tissue.

Essentially, bacteria invading an embryo will form densely packed biofilms inside the embryo cells. These biofilms can completely replace embryo cell structure and generate a faithful replica of the embryo.

The research, published on 9 December 2008 in the Proceedings of the National Academy of Sciences, provides the first demonstration that soft tissue fossilisation is a biological process which is mediated by bacterial replacement and mineralisation.

"The bacteria consume and replace all the cytoplasm in the cells, generating a little sculpture of the embryo," said Professor Elizabeth Raff, the report's lead author.

The US based biologists, Professors Elizabeth and Rudolf Raff, have been annual visitors to the School of Biological Sciences at the University of Sydney for over 20 years, coming especially to collaborate with Sydney researchers and to study two particular species of Sydney sea urchin that display unique development.

About two years ago, the pair began to investigate whether the embryos of these Sydney sea urchins could serve as models for how fossilisation occurs. In the laboratory, they held newly deceased embryos under a variety of conditions (high or low oxygen, with or without oxygen-poor marine mud, and in the presence or absence of anti-bacterial agents). After a few weeks they examined the embryos under scanning electron microscopes to see the result.

They found that under certain conditions, near-perfect bacterial replicas of the deceased sea urchin embryos were formed. From the laboratory work, the Raffs characterised the fossilisation process in three distinct stages.

Firstly, at the time of its death, the embryo must exist in a low-oxygen or reducing environment - such as the bottom of an anoxic ocean basin or buried in anoxic mud. If significant oxygen is available, the embryo will undergo 'autolysis', or self-destruction, and cellular structures will be rapidly degraded, making preservation impossible.

"The next step, is that bacteria, which are able to survive in low-oxygen conditions, must infest the cells of the dying embryo," explained Professor Elizabeth Raff.

The bacteria form biofilms - crowded assemblies of bacterial cells held together by sticky fibres made of proteins and sugars. As the biofilms fill the embryo cells, the tiny bacteria insinuate themselves between and among the organelles, forming a faithful representation of the cell's innards.

Lastly, the bacteria must leave a permanent record. In the case of finely preserved fossil embryos, the bacteria likely excrete tiny crystals of calcium phosphate (CaPO4), which eventually replace the bacterial sculptures. It is these crystals that provide the support for embryo and soft tissue fossilisation.

"That's a crucial step," said Professor Rudolf Raff. "Deposition of calcium phosphate, which forms very tiny crystals, can show us even minute details of structure and shape, not only of the bacteria laying down the minerals, but also of the embryo cell structures all around them.

"In our experiments, we observed bacteria depositing calcium carbonate (CaCO3), but not calcium phosphate. We'll need to simulate different conditions to fully replicate this step."

For many years, scientists have hypothesised that microbial process are responsible for preservation of soft tissues, given the ubiquitous occurrence of bacterial structures alongside fossils of organic matter.

In the last decade, high-resolution imaging of a trove of half-a-billion-year-old animal embryo fossils from Doushantuo, China, have provided tantalising evidence that bacteria were present during the fossilisation of the delicate cells.

Scanning electron microscopy of the fossil embryos showed filamentous bacteria-like forms on the surface of the embryos, suggesting the cells had been infested with bacteria or bacterial biofilms.

Although it is impossible to know whether bacteria aided the preservation of 550-million-year-old embryo fossils from Doushantuo and elsewhere, the Raffs argue the evidence they gathered strongly favours the view that bacteria are a fundamental force in fossil formation, as rapid biological processes must be available to convert highly delicate cells into a stable form and catalyse mineralisation.

"This work is important because it helps us understand fossilisation as a biological as well as geological process," Professor Elizabeth Raff said. "It gives us a window onto the evolution of the embryos of the earth's first animals."

Professor Rudolf Raff adds that Australia's unique fauna provides invaluable information for evolutionary biologists.

"Australia is blessed with possessing some of the most incredible organisms, that tell a truly amazing story about the evolution of life on earth. This includes a unique marine fauna, precious for its diversity and for what it can teach us."


Contact: Carla Avolio

Phone: 02 9351 4543

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