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Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements
(2023)bioRxivMethane emissions that contribute to climate change can be mitigated by anaerobic methane-oxidizing archaea such as Methanoperedens. Some Methanoperedens have huge extrachromosomal genetic elements (ECEs) called Borgs that may modulate their activity, yet the broader diversity of Methanoperedens ECEs is little studied. Here, we report small enigmatic linear ECEs, circular viruses and unclassified ECEs, that we predict replicate within ...Working Paper -
Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires
(2023)bioRxivBorgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes. 13 complete and four near-complete linear genomes share 40 genes that define a largely syntenous genome backbone. We use these conserved genes to identify new Borgs from peatland soil and to ...Working Paper -
Genomic analysis of cultivated infant microbiomes identifies Bifidobacterium 2’-fucosyllactose utilization can be facilitated by co-existing species
(2023)Human milk oligosaccharides (HMOs) ensure proper infant gut microbiome establishment. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigated microbiome responses to 2'-fucosyllactose (2’FL), a prevalent HMO and infant formula additive, by establishing individualized microbiomes using fecal ...Working Paper -
Long-term incubation of lake water enables genomic sampling of consortia involving Planctomycetes and Candidate Phyla Radiation bacteria
(2021)bioRxivMicrobial communities in lakes can profoundly impact biogeochemical processes through their individual activities and collective interactions. However, the complexity of these communities poses challenges, particularly for studying rare members. Laboratory enrichments can select for subsystems of interacting organisms and enable genome recovery for enriched populations. Here, a reactor inoculated with water from Lake Fargette, France, and ...Working Paper -
The Chloroflexi supergroup is metabolically diverse and representatives have novel genes for non-photosynthesis based CO2 fixation
(2021)bioRxivThe Chloroflexi superphylum have been investigated primarily from the perspective of reductive dehalogenation of toxic compounds, anaerobic photosynthesis and wastewater treatment, but remain relatively little studied compared to their close relatives within the larger Terrabacteria group, including Cyanobacteria, Actinobacteria, and Firmicutes. Here, we conducted a detailed phylogenetic analysis of the phylum Chloroflexota, the ...Working Paper -
Borgs are giant extrachromosomal elements with the potential to augment methane oxidation
(2021)bioRxivAnaerobic methane oxidation exerts a key control on greenhouse gas emissions 1, yet factors that modulate the activity of microorganisms performing this function remain little explored. In studying groundwater, sediments, and wetland soil where methane production and oxidation occur, we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins. Four curated, complete genomes are linear, up to ~1 ...Working Paper