Up from the deep: meet the marine bacteria that feed on DNA

Stephen Chen
·3-min read

A team of Chinese marine scientists have found and cultivated a previously unknown bacterial species that, unlike others, feeds on DNA, the building block of life.

In a paper published in the peer-reviewed ISME Journal this month, researchers said understanding of the species could be “crucial for understanding global ocean processes”.

The scientists, led by professor Sun Chaomin at the Institute of Oceanology, Chinese Academy of Sciences in Qingdao in the eastern province of Shandong, named the species Xianfuyuplasma, after the mythical hybrid Yellow River creature with the head of a fish and body of a pig.

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The mythical Xian Fu Yu creature has the head of a fish and the body of a pig. Photo: Handout
The mythical Xian Fu Yu creature has the head of a fish and the body of a pig. Photo: Handout

Bacteria feed on a range of material but they tend to focus on matter that is easy to digest, such as sugars, fats and proteins, rather than DNA, which is more difficult to break down.

Nevertheless, marine researchers had long suspected that DNA could be an important source of food for marine microorganisms, especially at the deep sea where food is scarce.

However, no one had isolated such a strain and cultured it in a laboratory.

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Sun’s team collected the Xianfuyuplasma specimen from a seabed more than 1,000 metres (3,280 feet) beneath the South China Sea in 2017 and took it back to the laboratory.

Most deep sea life species die or become inactive after coming to the surface but Xianfuyuplasma started to reproduce en masse in a petri dish with a few drops of DNA.

Sun’s team then took the bacterium back to the sea in 2020 and conducted an experiment in the waters that confirmed their laboratory observation – Xianfuyuplasma preferred DNA to other nutritions in the dark, cold water.

“DNA is not a typical food. Most laboratories don’t feed DNA to microbes. It is too expensive,” said Professor Zhang Xiaohua, a marine life scientist with Ocean University of China who was not involved in the study.

“It is a surprise to know it makes a top item on the menu.”

The team cultured Xianfuyuplasma in the lab and the deep sea. Photo: Chinese Academy of Science
The team cultured Xianfuyuplasma in the lab and the deep sea. Photo: Chinese Academy of Science

Sun’s team said DNA could be a food source for other deep sea bacteria, a poorly understood area of biology.

They said they named the new species after the monster Xian Fu Yu because it combines the “soft skin” of one phylum with features normally found in bacteria with thick, hard cell walls.

This unique combination could help Xianfuyuplasma better adapt to different environments, according to the researchers.

Sun said the bacterium could also be developed into a new tool for gene editing based on a defence mechanism that recognised and destroyed viral genes.

“It has the potential to outperform CRISPR,” he said, referring to the most popular gene-editing tool in use.

“It took us four years to culture it. But it was worth the effort because it opens a new portal to many exciting possibilities.”

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The research is part of a Chinese government effort to study the world’s uncharted seafloors, which could pave the way for large-scale deep sea activities such as mining.

Unknown species living in extreme environments could provide new tools for biological science.

An oil-eating bacteria recently discovered by another Chinese team in the Mariana Trench, for instance, could become a powerful tool to clean up marine oil spills.

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