Baker, Brett J.


Publications
13

Asgard archaea modulate potential methanogenesis substrates in wetland soil

Citation
Valentin-Alvarado et al. (2023).
Names
“Asgardarchaeota” “Atabeyarchaeia”
Abstract
AbstractThe roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems are unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and the first complete genome of Freyarchaeia, and defined their metabolismin situ. Metatranscriptomics highlights high expressi

Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching

Citation
Tahon et al. (2023).
Names
“Korarchaeum calidifontum” “Caldabyssikora” “Korarchaeum” “Caldabyssikoraceae” “Caldabyssikora taketomiensis” “Caldabyssikora guaymasensis” “Thermotainarokoraceae” “Thermotainarokora guaymasensis” “Thermotainarokora taketomiensis” “Hydrocaminikoraceae”
Abstract
AbstractOur knowledge of archaeal diversity and evolution has expanded rapidly in the past decade. However, hardly any genomes of the phylum Korarchaeota have been obtained due to the difficulty in accessing their natural habitats and – possibly – their limited abundance. As a result, many aspects of Korarchaeota biology, physiology and evolution remain enigmatic. Here, we expand this phylum with five high-quality metagenome-assembled genomes. This improved taxon sampling combined with sophistic

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Citation
Eme et al. (2023). Nature 618 (7967)
Names
“Asgardarchaeota”
Abstract
AbstractIn the ongoing debates about eukaryogenesis—the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors—members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2–4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evalua

Expansion of Armatimonadota through marine sediment sequencing describes two classes with unique ecological roles

Citation
Carlton et al. (2023). ISME Communications 3 (1)
Names
“Hebobacteraceae” “Hebobacterales” “Hebobacteria” “Zipacnadaceae” “Zipacnadales” “Zipacnadia” “Hebobacterum abditum” “Hebobacterum” “Zipacnadum vermilionense” “Zipacnadum”
Abstract
AbstractMarine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. Recent studies using metagenomic techniques have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here, we obtained 77 metagenome-assembled genomes (MAGs) from the bacterial phylum Armatimonadota in the Guaymas Basin, Gulf of California, and the Bohai Sea, China. These MAGs

New globally distributed bacterial phyla within the FCB superphylum

Citation
Gong et al. (2022). Nature Communications 13 (1)
Names
“Orphanbacterum longqiense” “Joyebacterota” “Arandabacteraceae” “Arandabacterota” “Arandabacterales” “Arandabacteria” “Orphanbacterum” “Arandabacterum bohaiense” “Blakebacterota” “Orphanbacteraceae” “Joyebacterum haimaense” “Blakebacterum guaymasense” “Orphanbacterales” “Joyebacterum” “Blakebacterum” “Orphanbacteria” “Joyebacteraceae” “Blakebacteraceae” “Orphanbacterota” “Joyebacterales” “Blakebacterales” “Arandabacterum” “Joyebacteria” “Blakebacteria”
Abstract
AbstractMicrobes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbact

Asgard archaea capable of anaerobic hydrocarbon cycling

Citation
Seitz et al. (2019). Nature Communications 10 (1)
Names
Abstract
AbstractLarge reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbo

A new view of the tree of life

Citation
Hug et al. (2016). Nature Microbiology 1 (5)
Names
“Rokuibacteriota” “Abawacaibacteriota” “Wirthibacterota”
Abstract
AbstractThe tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. These approaches overlook the dramatic change in our understanding o