Probing microbial dark matter

A new method for sequencing the genomes of cells found in the environment without cultivating them in a lab has been developed by Australian and US researchers.

Associate Professor Aaron Darling from the ithree institute at the University of Technology, Sydney (UTS) and colleagues from the US Department of Energy Joint Genome Institute (DOE) and the University of Queensland developed the first enabling technology and new method of single cell genomic sequencing on a large number of cells.

With over 200 uncultivated genomes from nine diverse habitats, this single cell sequencing methodology allowed the discovery and a first ever view of the genomes and lifestyle of 29 major groups of bacteria that are widespread in the oceans and the environment.

By analysing the sequencing data, Assoc Prof Darling reconstructed the evolutionary history of the microbes and mapped out where the sampled organisms lay on the tree of life and confirmed they were like nothing previously described by science.

“We were able to characterise 29 major groups of bacteria that had never been characterised before,” Assoc Prof Darling said.

“This is an amazing discovery because we’ve never been able to do single cell sequencing on a large number of cells before and this is a new technical advance.

“It’s an exciting time to be working in the field of microbiology,” Assoc Prof Darling said. “Every surface of the planet is covered with microbes - they’re in the atmosphere, in the deep ocean subfloor and they’re in and on our bodies.

“Before DNA sequencing was developed we had no way of knowing the intricate details of these microbes, but now [through this research] we have the ability to gain a greater understanding about the importance of microbial evolution on our planet and in everyday life.”

This work was published in Nature.