Breakthrough gives insight into early complex life on Earth

For the first 2 billion years, life on Earth comprised two microbial kingdoms – bacteria and archaea. They featured an innumerable and diverse variety of species, but, ultimately, life on Earth was not that exciting judged by today’s standards.

Then, the theory goes, a rogue archaeon gobbled up a bacterium to create an entirely new type of cell that would go on to form the basis of all complex life on Earth, from plants to humans.

Now, for the first time, scientists have succeeded in culturing an elusive species of archaea believed to be similar to the ancestor that gave rise to the first sophisticated cells, known as eukaryotes. The work has been described as a “monumental” advance that sheds new light on this evolutionary milestone.

Nick Lane, professor of evolutionary biochemistry at UCL, described the work as “magnificent”, while a commentary by two other experts in the field said it marked a “huge breakthrough for microbiology”.

Like bacteria, archaea continue to thrive on Earth today. But despite the pivotal role they are thought to have played in the emergence of complex life there has been relatively little research on them. Many species are found in inhospitable environments and are incredibly difficult to grow in the lab.

The Japanese team behind the latest advance has dedicated 12 years to the effort, overcoming a series of setbacks along the way.

Their scientific odyssey began in 2006 with the collection of a sample of deep-sea mud, dredged up by a submersible from the 2.5km deep Omine Ridge off the coast of Japan. The mud was placed in a bioreactor and continuously fed with methane for more than five years.

“Most organisms that have been cultured in the lab reproduce rapidly, can live in large numbers, and grow by themselves,” said Masaru Nobu, of the National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan. “The organism we isolated reproduces 1,000 times slower than E. coli, only lives in small numbers, and depends on symbiotic partners to grow.”

Nobu and colleagues then took smaller samples from the reactor and placed them in glass tubes, which sat in the lab for another year before showing any obvious signs of life. The researchers painstakingly coaxed them along, feeding them a blend of nutrients including powdered baby milk. The cells took two to four weeks to replicate and divide, meaning each stage of the study took months.

While the epic experiment was running, a fortuitous discovery was made by a Dutch team, also researching archaea. They sequenced microbial DNA extracted from mud from a hydrothermal vent off the coast of Greenland. One intriguing genome stood out: it was clearly a member of the archaea, but dotted through its DNA were genes similar to those seen in eukaryotic cells.

Scientists called it the Asgard archaea and suggested that the ancestors of this evolutionary branch could have bridged the gap between basic and complex life billions of years earlier.

When the Japanese team sequenced their samples, genetic analysis revealed they had managed to cultivate the same Asgard archaea. Until this point, scientists had found out the genetic code, but had no idea what the organism actually looked like.

The latest work reveals that the Asgard archaea are small simple cells, but feature long tentacle-like structures reaching out of the cells. Not everyone agrees that they represent the origins of complex life. But the theory’s proponents suggest that one of these cells could have engulfed a bacteria, with the bacteria then going on to become structures known as mitochondria, which act as an internal power supply in all complex cells today. Bacteria and archaea lack this internal architecture.

The Japanese team suggest that Asgard’s newly revealed spaghetti-like tendrils could have engulfed a passing bacteria and formed a symbiotic relationship with it. After several evolutionary leaps, the two organisms could have become one, more complex, cell type – a primitive eukaryote.

The scenario is still speculative and is likely to remain under active debate for the next decade. Either way, the advance is likely to trigger a resurgence of interest in these under-explored microbes.

“The importance of this work – it’s hard to describe,” said Lane. “You see these genome sequences and try and reconstruct what the cell might look like, but you can’t do that with any real power. Finally you see what the cell looks like and it’s not what anyone expected.”