Searching for the 4th domain

This past weekend I participated in the first sampling for Phase II of the Microbial Dark Matter (MDM) project.  For this project we are searching for deep branching microbes with no cultured representatives that may reveal new phyla or domains of life using single cell genomics.  Prior to this study, Phase I of the MDM project identified genomes of microorganisms belonging to, what scientists proposed to be, two new super phyla and generated over 200 previously-unidentified genomes to help improve the taxonomic assignment of metagenomic reads.

With Phase II of this project, we want to continue the exploration of enigmatic members of the tree of life through an increased sequencing effort in sites where MDM are abundant. One environment of particular interest is the under-explored terrestrial subsurface where, in some sites, MDM taxa have been found to account for over 40% of the microbial population! Over the weekend, myself and other members from the Phase II team ventured into Death Valley in the hopes of capturing some elusive and undocumented microbes.

During this trip, we sampled 4 different high diversity springs/wells; however, my favorite subsurface window during the sampling was Devil’s Hole, a geothermal aquifer fed pool.  Notably, this pool has made headlines as the home to a species of fish found only on the shallow bank of Devil’s Hole: The Devil’s Hole Pupfish.  Our hope is that, like this special species of pupfish, we will find several microorganisms that have not been identified anywhere else (and, potentially, of novel lineages).  Due to the endangered status of the pupfish, a lot of precautions were taken to ensure that our sampling in Devil’s Hole would not disrupt the pupfish habitat.  To sample the pool, the National Parks Service required a series of metal walkways, that never touch the water, to be placed along the walls of the pool (below).  From these walkways, we set up tubing to pump geothermal water out the pool and onto our workspace on top of the rocks.

Devil's Hole Setup

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Sampling at Devil’s Hole.  Courtesy of Jonathon Eisen

I was surprised to find that the sampling procedure in Death Valley was rather similar to sampling done in South African mines.  As in the mines, we set up some filters to collect biomass for metagenomic sequencing, collected water for chemical and isotopic analysis, prepared and filled biovials (evacuated serum vials) for culturing, and preserved unfiltered water for single sorting and sequencing.  All in all, it was a great trip out to Death Valley and a chance to capture some really special organisms — not to mention a ton of great views!

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