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Authors Biddle

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Biddle, Jennifer F.


Publications
4

CitationNamesAbstract
Occurrence, Diversity, and Genomes of “ Candidatus Patescibacteria” along the Early Diagenesis of Marine Sediments Zhao et al. (2022). Applied and Environmental Microbiology 88 (24) Ca. Patescibacteria
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“ Sifarchaeota ,” a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy Farag et al. (2021). Applied and Environmental Microbiology 87 (9) “Sifarchaeum” Ca. Sifarchaeum marinoarchaea Ca. Sifarchaeum subterraneus “Sifarchaeota” “Sifarchaeum subterraneum”
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“Sifarchaeota” a novel Asgard phylum capable of polysaccharide degradation and anaerobic methylotrophy Farag et al. (2020). “Sifarchaeum” Ca. Sifarchaeum marinoarchaea Ca. Sifarchaeum subterraneus “Sifarchaeota”
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Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria MacGregor et al. (2013). Applied and Environmental Microbiology 79 (13) Ca. Maribeggiatoa
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Occurrence, Diversity, and Genomes of “ Candidatus Patescibacteria” along the Early Diagenesis of Marine Sediments
Ultrasmall-celled “ Ca. Patescibacteria” have been estimated to account for one-quarter of the total microbial diversity on Earth, the parasitic lifestyle of which may exert a profound control on the overall microbial population size of the local ecosystems. However, their diversity and metabolic functions in marine sediments, one of the largest yet understudied ecosystems on Earth, remain virtually uncharacterized.
“ Sifarchaeota ,” a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy
The exploration of deep marine sediments has unearthed many new lineages of microbes. The finding of this novel phylum of Asgard archaea is important, since understanding the diversity and evolution of Asgard archaea may inform also about the evolution of eukaryotic cells. The comparison of metabolic potentials of the Asgard archaea can help inform about selective pressures the lineages have faced during evolution.
“Sifarchaeota” a novel Asgard phylum capable of polysaccharide degradation and anaerobic methylotrophy
AbstractThe Asgard superphylum is a deeply branching monophyletic group of Archaea, recently described as some of the closest relatives of the eukaryotic ancestor. The wide application of genomic analyses from metagenome sequencing has established six distinct phyla, whose genomes encode for diverse metabolic capacities and play important biogeochemical and ecological roles in marine sediments. Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off Costa Rica margin, defining a novel lineage phylogenetically married to Thorarchaeota, as such we propose the name “Sifarchaeota” for this phylum. The two “Sifarchaeota” MAGs encode for an anaerobic methylotrophy pathway enabling the utilization of C1-C3 compounds (methanol and methylamines) to synthesize acetyl CoA. Also, the MAGs showed a remarkable saccharolytic capabilities compared to other Asgard lineages and encoded for diverse classes of carbohydrate active enzymes (CAZymes) targeting different mono-, di- and oligosaccharides. Comparative genomic analysis based on the full metabolic profiles of Asgard lineages revealed the close relation between “Sifarchaeota” and Odinarchaeota MAGs, which suggested a similar metabolic potentials and ecological roles. Furthermore, we identified multiple potential horizontal gene transfer (HGT) events from different bacterial donors within “Sifarchaetoa” MAGs, which hypothetically expanded “Sifarchaeota” capacities for substrate utilization, energy production and niche adaptation.ImportanceDeep marine sediments are the home of multiple poorly described archaeal lineages, many of which have ecological and evolutionary importance. We recovered metagenome-assembled genomes (MAGs) belonging to a novel Asgard phylum from the deep sediment of the Costa Rica margin. We proposed the name “Sifarchaeota” to describe the members of this phylum. Representative genomes of the “Sifarchaeota” showed remarkable saccharolytic capacities extending the known metabolic features encoded by the Asgard lineages. We attribute its ability to survive under the deep sediment conditions to its putative capacities to utilize different (C1-C3) compounds commonly encountered in deep sediment environments via anaerobic methylotrophy pathway. Also, we showed the importance of horizontal gene transfer in enhancing the “Sifarchaeota” collective adaptation strategies.
Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria
ABSTRACT The draft genome sequence of a single orange Beggiatoa (“ Candidatus Maribeggiatoa”) filament collected from a microbial mat at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and group I intron within the 23S rRNA gene; several group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; multiple copies of sequences similar to the fdxN excision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria); and multiple sequences related to an open reading frame (ORF) (00024_0693) of unknown function all have close non- Beggiatoaceae matches with cyanobacterial sequences. Sequences similar to the uncharacterized ORF and Xis elements are found in other Beggiatoaceae genomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria. We speculate that elements shared among filamentous bacterial species may have been exchanged in microbial mats and that some of them may be involved in cell differentiation.
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