A new view of the the tree of life
The rapid sequencing of new microbial genomes in recent years has left us wondering what has all this new data done to the tree of life. To address this, a new paper that presents the new view of life diversity in the genomic era has just been published in Nature Microbiology.
This paper is a collaboration with many people namely Laura Hug and Jill Banfield (at UC Berkeley).
UC Berkeley press release
UT press release
Carl Zimmer’s New York Times coverage
Our new paper published in Nature Microbiology, which was a collaboration with the Ettema Lab (Upsalla Univ), and Teske Lab (UNC Chapel Hill), begins to resolve the metabolic capabilities of a group (class) of Archaea (referred to as SAGMEG) that are predominant in the subsurface and have not cultured.Two of the genomes were recovered from this hot spring in Yellowstone National Park (photo by Dan Coleman).
Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea
Press releases about this article.
A deeply-branched widespread new group of Archaea whose genome were recovered from estuary sediments, but are in sediments around the world. Read about their physiologies in this first paper in ISME J.
This paper was highlighted in Nature as well.
For the summer we have John working on assembling genomes of uncultured bacteria that were growing on oil from the Deep Water Horizon spill in the Gulf in 2010. He is about half way through his project and will soon have lot of genomes to look at their metabolisms!
Genomic resolution of linkages in carbon, nitrogen,and sulfur cycling among widespread estuary sediment bacteria
Brett J Baker, Cassandre Sara Lazar, Andreas P Teske, and Gregory J Dick
Background: Estuaries are among the most productive habitats on the planet. Bacteria in estuary sediments control the turnover of organic carbon and the cycling of nitrogen and sulfur. These communities are complex and primarily made up of uncultured lineages, thus little is known about how ecological and metabolic processes are partitioned in sediments.
Results: De novo assembly and binning resulted in the reconstruction of 82 bacterial genomes from different redox regimes of estuary sediments. These genomes belong to 23 bacterial groups, including uncultured candidate phyla (for example, KSB1, TA06, and KD3-62) and three newly described phyla (White Oak River (WOR)-1, WOR-2, and WOR-3). The uncultured phyla are generally most abundant in the sulfate-methane transition (SMTZ) and methane-rich zones, and genomic data predicts that they mediate essential biogeochemical processes of the estuarine environment, including organic carbon degradation and fermentation. Among the most abundant organisms in the sulfate-rich layer are novel Gammaproteobacteria that have genes for the oxidation of sulfur and the reduction of nitrate and nitrite. Interestingly, the terminal steps of denitrification (NO3 to N2O and then N2O to N2) are present in distinct bacterial populations.
Conclusions: This dataset extends our knowledge of the metabolic potential of several uncultured phyla. Within the sediments, there is redundancy in the genomic potential in different lineages, often distinct phyla, for essential biogeochemical processes. We were able to chart the flow of carbon and nutrients through the multiple geochemical layers of bacterial processing and reveal potential ecological interactions within the communities.
Figure1 – showing the phylogeny of bacteria based on multiple genes from the genomes
We are busy sorting through loads of genomic data from the Gulf of Mexico hypoxic dead zone and surrounding water. Here is the tetra nucleotide ESOM clustering map of the assembled genomes from that project. 55 genomes and counting!