Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past

Abstract

The phylum Chloroflexota is ubiquitous; however, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility; a peptidoglycan-containing cell envelope; and heterotrophic activity on aromatics and plant-associated compounds. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. This evolutionary past explains the widespread genomic potential to degrade terrestrial organic matter among marine Dehalococcoidia and raises new questions about the timing and selective forces driving their successful niche expansion into the global oceans.

Phylogenomic discernments into Anaerolineaceae thermal adaptations and the proposal of a candidate genus Mesolinea

“…The phylum Chloroflexota constitutes a highly diverse and deeply branching lineage of bacteria. Currently, it is categorized into nine classes (Kochetkova et al, 2020;Yan et al, 2020;Palmer et al, 2023): Anaerolineae, Ardenticatenia, Caldilineae, Chloroflexia, Dehalococcoidia, Ktedonobacteria, Thermoflexia, Thermomicrobia, and a class-level SAR202 cluster of uncultured bacteria. Members of the Anaerolineaceae family exhibit a broad distribution in anaerobic environments, including marine sediments, deep hot aquifers, soils, and anaerobic digesters.…”

Genome mining leads to the identification of a stable and promiscuous Baeyer-Villiger monooxygenase from a thermophilic microorganism

“…Here, we describe the identification and subsequent characterization of one such BVMO from Chloroflexota bacterium strain G233 dubbed ssnBVMO. 25 Following the identification of ssnBVMO, we sought to address another major hurdle for the large-scale implementation of BVMOs: the requirement for stoichiometric quantities of the expensive NADPH cofactor. Previous work has overcome this issue by fusing BVMOs to coenzyme regenerating enzymes (CREs).…”

“…Since this organism grows optimally at a temperature of 75 °C, we tentatively identified the protein encoded by A0A2A9HFE7 as a thermostable BVMO that we dubbed ssnBVMO. 25,30 S5). [31][32][33] The presence of these motifs within the sequence of ssnBVMO strongly suggested that the identified enzyme would catalyze Baeyer-Villiger oxidations.…”

Dynamic evolution of nitrogen cycle and pH homeostasis genes enabled the diversification of Pampinifervens gen. nov. (Aquificaceae)

“…To infer the evolutionary events that gave rise to the current distribution of genes associated with nitrogen metabolism and pH homeostasis, consensus presence/absence KO count pro les for the species with high-quality genomes available were generated from the EggNOG functional annotations as described before (75). From here, a cladogram inferred from the species tree (Fig.…”