Pink microbiome

Lake Hillier in Western Australia is one of several sites targeted for microbiome investigation by the eXtreme Microbiome Project (XMP - extrememicrobiome.org).
The lake’s water is about 10 times saltier than sea water and has a bright-pink colour¹.

The unusual colouration was thought to be due to a type of red algae (Dunaliella salina), but no formal investigations had been performed until recently. Dr. Ken McGrath’s team from the Australian Genome Research Facility collected water samples from the top and lower levels of the lake, as well as sediment samples, for metagenomic analysis.

Traditional culture-based analysis managed to resolve 13 different microorganisms, with a culture-dependent bias towards bacterial species¹. A 16S-based microbial profile using short-read sequencing technology built a more complete taxonomic representation, but species-level identification was problematic.

In contrast, a whole-shotgun DNA sequencing approach using nanopore technology resulted in species-level taxonomic classification, with a more complete profile starting to emerge after just 2 hours of sequencing. The final results were available after 24 hours of sequencing, with successful identification of algae, archaea, bacteria and viruses.

The XMP found that the red bacterium Salinibacter ruber dominated the metagenomics profile of the lake, whereas D. salina was present at relatively low levels, and concluded that the pink colour of the lake is produced by the bacteria, and not the algae as previously thought.

The Lake Hillier microbiome study, as well as the rest of the XMP work, has put nanopore sequencing at the forefront of microbiome research in extreme understudied environments.

This case study is taken from the microbiome white paper.