New paper on the metabolic diversity of Thorarchaeota

Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota

Thorarchaeota are a new archaeal phylum within the Asg ard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To
provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, x inorganic carbon, reduce sulfur/sulfate and produce acetate. In particular, Thorarchaeota may be involved in ethanol production, nitrogen xation, nitrite reduction, and arsenic detoxication. Inter estingly, these Thorarchaeotal genomes are inferred to
contain the tetrahydromethanopterin and tetrahydrofolate WoodLjungdahl (WL) pathways for COreduction, and the latter WL pathway appears to have originated from bacteria. These archaea are predicted to be able to use various inorganic and organic carbon sources, possessing genes inferred to encode ribulose bisph osphate carboxy lase-like proteins (normally without RuBisCO activity) and a near-complete CalvinBensonBassham cycle. The existence of eukaryotic selen ocysteine insertion sequences and many genes for proteins previously considered eukaryote-specic in Thorarchaeota genomes provide new insights into their evolutionary roles in the origin of eukaryo tic cellular complexity. Resolving the metabolic capacities of these enigmatic archaea and their origins will enhance our understanding of the origins of eukaryotes and their
roles in ecosystems.

New paper detailing hydrocarbon and nutrient cycling in deep sea hydrothermal sediments

New insights into microbial hydrocarbon cycling and metabolic interdependencies in hydrothermal sediments

Congrats Nina and Kiley!

This paper details the genetic diversity of these sediments and describes genomes belonging to a uncultured archaeal group (GoM-Arc1) that contain novel pathways for hydrocarbon cycling, related to ANME (anaerobic methane oxidizers).

 

Introducing a new class in the archaea, Theionarchaea, and several other uncultured lineages

In addition to Theionarchaea, this new paper that appears in ISME Journal also details a variety of archaeal genomes there were obtained from the White Oak River Estuary in North Carolina.  This digram summarizes the ecological roles we have inferred from these genomes. This is important because NONE of these lineages have been grown in a laboratory, so having their genomes has significantly advanced our understanding of what they do in nature.

Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches

screen-shot-2017-01-06-at-9-40-17-am

 

Introducing Asgard! A new superphylum of archaea that are related to eukaryotes.

Asgard archaea illuminate the origin of eukaryotic cellular complexity

czj-dlmukaajrwn-jpg-large

screen-shot-2017-01-11-at-9-08-08-amThis week our new paper describing the discovery of 4 archaea phyla that are related to eukaryotes was published in Nature. These phyla are belong to the same branch of life and have been named after different Norse gods, Thor, Odin, Heimdall, and Loki.  This is a collaboration with Thijs Ettema’s lab in Sweden. Last year we published the discovery of Thorarchaeota in ISME.

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

This paper adds 2 additional phyla, Odinarchaeota and Heimdallarchaeota. The focus of this paper is further resolve the phylogenetic position of eukaryotes in this new superphylum.  It also examines the presence of several new ESPs or eukaryotic signature proteins.  These proteins were mostly thought to exist in eukaryotes, but these genomes contain a variety of them!screen-shot-2017-01-11-at-9-07-09-am

Press releases to accompany this study:

UT press release

The Atlantic article by Ed Yong

Uppsala press release

New paper characterizing the metabolic pathways of bacteria involved in oil degradation in the DWH oil spill

Through a collaboration with the Teske Lab (UNC) and Tony Gutierrez my 2015 REU student and postdoc (Nina Dombrowski) reconstructed several genomes from DNA-SIP experiments run on DWH spill oil in 2010.

Hydrocarbon degradation pathways in uncultured bacteria from the Deep Water Horizon Oil Spill

UT press release

Christian Science Monitor

The genomic hunt for oil-degrading bacteria after the Deepwater Horizon blowout: More than the usual suspects

This cover of The National from Scotland.13177959_10154110138150797_26354218422638703_n