Project Description

Dr Christian Rinke

Australian Centre for Ecogenomics
The University of Queensland

Illuminating microbial dark matter via single-cell genomics


Friday 8 July 2016

Christian Rinke is a Research Officer at the Australian Centre for Ecogenomics (ACE), University of Queensland, Australia. He received his PhD in Zoology from the Marine Biology Department at the University of Vienna, Austria and has since shifted his focus to the microbial world.

His research interests include genomics and the phylogeny and ecology of symbiotic and free living microbes. He focuses in particular on the uncultured majority of microbes (99%) which elude current culturing efforts. This so called “Microbial Dark Matter” can only be explored with culture-independent methods. Chris pioneered methods in high throughput single-cell genomics, the separation and sequencing of single bacterial and archaeal cells, and also employs metagenomics (the direct sequencing of environmental samples) to illuminate microbial dark matter.

Our view of microbial genomic diversity is severely skewed with the majority of all sequenced bacterial and archaeal genomes belonging to only four bacterial phyla. This bias results in part from our inability to cultivate most microbes, a necessary step for traditional whole genome sequencing. Through cultivation-independent approaches such as single-cell genomics, one can now explore the genetic diversity and metabolic potential of uncultivated environmental microorganisms. We successfully amplified several hundred single cells from free-living and symbiotic populations without cultured representatives, known as microbial dark matter. The single-cell genomes allowed us to explore their intra- and inter-phylum-level relationships, to decipher encoded pathways, and to discover novel metabolic features. The single- cell reference genomes also facilitate the interpretation of metagenomic data sets and substantially improve phylogenetic anchoring of up to 20% of metagenomic reads in some habitats. While there is still much ground to cover, single-cell-genomics has proven to be a valuable tool to improve our understanding of microbial evolution on earth.