Baker, Brett J.


Publications
10

Asgard archaea modulate potential methanogenesis substrates in wetland soil

Citation
Valentin-Alvarado et al. (2023).
Names
“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

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

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

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Citation
Baker et al. (2016). Nature Microbiology 1 (3)
Names
Hadarchaeum yellowstonense Ts
Abstract
AbstractThe subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes1. Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface2–4, the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63–90% comp

Enigmatic, ultrasmall, uncultivated Archaea

Citation
Baker et al. (2010). Proceedings of the National Academy of Sciences 107 (19)
Names
Ca. Micrarchaeum Ca. Micrarchaeum acidiphilum
Abstract
Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge—particularly for Archaea—that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete ~1-Mb geno

Extremely Acidophilic Protists from Acid Mine Drainage Host Rickettsiales -Lineage Endosymbionts That Have Intervening Sequences in Their 16S rRNA Genes

Citation
Baker et al. (2003). Applied and Environmental Microbiology 69 (9)
Names
“Captivus acidiprotistae”
Abstract
ABSTRACT During a molecular phylogenetic survey of extremely acidic (pH < 1), metal-rich acid mine drainage habitats in the Richmond Mine at Iron Mountain, Calif., we detected 16S rRNA gene sequences of a novel bacterial group belonging to the order Rickettsiales in the Alphaproteobacteria . The closest known relatives of this group (92% 16S rRNA gene sequence identity) are endosymbionts of the protist Acantham