Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past

Abstract

Although the phylum Chloroflexota is ubiquitous, 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 genus Tepidiforma and 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. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. 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. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.

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

“…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 ssn BVMO. 25,30 This sequence was 59% and 41% identical to PAMO and Ac CHMO, respectively. Furthermore, the ssn BVMO sequence bears two Rossman fold motifs (GxGxx[G/A]) that flank the two consensus sequences associated with BVMOs ([A/G]GxWxxxx[F/Y]P[G/M]xxxD and FxGxxxHxxxW[P/D]; Figs S4 – S5).…”

“…Here, we describe the identification and subsequent characterization of one such BVMO from Chloroflexota bacterium strain G233 dubbed ssn BVMO. 25…”

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.…”

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.…”