Abstract:Diverse yet-uncultivated bacteria and archaea, i.e., microbial dark matter, are present in terrestrial hot spring environments. Numerous metagenome-assembled genomes (MAGs) of these uncultivated prokaryotes by short-read metagenomics have been reported so far, suggesting their metabolic potential. However, more reliable MAGs, i.e., circularized complete MAGs (cMAGs), have been rarely reported from hot spring environments. Here, we report 61 high-quality (HQ)-MAGs, including 14 cMAGs, of diverse uncultivated ba… Show more
“…Although the functions of these clusters are unknown, their hypothetical products could be useful molecular biomarkers for the presence of ‘Tectomicrobia’ generally, in the case of the terpenes, or ‘Thalassonella’ specifically, in the case of the other BGCs. Indeed, using the terpene synthase in sequence similarity searches retrieved two MAGs that became publicly available after the completion of this study and that were both classified as ‘Tectomicrobia’ members (Genbank accession VGLS01001192 and [ 75 ]). Fig.…”
Genomic and functional analyses of bacterial sponge symbionts belonging to the uncultivated candidate genus ‘Entotheonella’ has revealed them as the prolific producers of bioactive compounds previously identified from their invertebrate hosts. These studies also suggested ‘Entotheonella’ as the first members of a new candidate phylum, ‘Tectomicrobia’. Here we analyzed the phylogenetic structure and environmental distribution of this as-yet sparsely populated phylum-like lineage. The data show that ‘Entotheonella’ and other ‘Tectomicrobia’ are not restricted to marine habitats but widely distributed among terrestrial locations. The inferred phylogenetic trees suggest several intra-phylum lineages with diverse lifestyles. Of these, the previously described ‘Entotheonella’ lineage can be more accurately divided into at least three different candidate genera with the terrestrial ‘Candidatus Prasianella’, the largely terrestrial ‘Candidatus Allonella’, the ‘Candidatus Thalassonella’ comprising sponge-associated members, and the more widely distributed ‘Candidatus Entotheonella’. Genomic characterization of ‘Thalassonella’ members from a range of sponge hosts did not suggest a role as providers of natural products, despite high genomic similarity to ‘Entotheonella’ regarding primary metabolism and implied lifestyle. In contrast, the analysis revealed a correlation between the revised ‘Entotheonella’ 16S rRNA gene phylogeny and a specific association with sponges and their natural products. This feature might serve as a discovery method to accelerate the identification of new chemically rich ‘Entotheonella’ variants, and led to the identification of the first ‘Entotheonella’ symbiont in a non-tetractinellid sponge, Psammocinia sp., indicating a wide host distribution of ‘Entotheonella’-based chemical symbiosis.
“…Although the functions of these clusters are unknown, their hypothetical products could be useful molecular biomarkers for the presence of ‘Tectomicrobia’ generally, in the case of the terpenes, or ‘Thalassonella’ specifically, in the case of the other BGCs. Indeed, using the terpene synthase in sequence similarity searches retrieved two MAGs that became publicly available after the completion of this study and that were both classified as ‘Tectomicrobia’ members (Genbank accession VGLS01001192 and [ 75 ]). Fig.…”
Genomic and functional analyses of bacterial sponge symbionts belonging to the uncultivated candidate genus ‘Entotheonella’ has revealed them as the prolific producers of bioactive compounds previously identified from their invertebrate hosts. These studies also suggested ‘Entotheonella’ as the first members of a new candidate phylum, ‘Tectomicrobia’. Here we analyzed the phylogenetic structure and environmental distribution of this as-yet sparsely populated phylum-like lineage. The data show that ‘Entotheonella’ and other ‘Tectomicrobia’ are not restricted to marine habitats but widely distributed among terrestrial locations. The inferred phylogenetic trees suggest several intra-phylum lineages with diverse lifestyles. Of these, the previously described ‘Entotheonella’ lineage can be more accurately divided into at least three different candidate genera with the terrestrial ‘Candidatus Prasianella’, the largely terrestrial ‘Candidatus Allonella’, the ‘Candidatus Thalassonella’ comprising sponge-associated members, and the more widely distributed ‘Candidatus Entotheonella’. Genomic characterization of ‘Thalassonella’ members from a range of sponge hosts did not suggest a role as providers of natural products, despite high genomic similarity to ‘Entotheonella’ regarding primary metabolism and implied lifestyle. In contrast, the analysis revealed a correlation between the revised ‘Entotheonella’ 16S rRNA gene phylogeny and a specific association with sponges and their natural products. This feature might serve as a discovery method to accelerate the identification of new chemically rich ‘Entotheonella’ variants, and led to the identification of the first ‘Entotheonella’ symbiont in a non-tetractinellid sponge, Psammocinia sp., indicating a wide host distribution of ‘Entotheonella’-based chemical symbiosis.
“…Finally, two groups that are more common in invaded range soils could be of interest for their differential associations with each genotype growing in that soil inoculum. Taxa in the Armatimonadales (a group of putatively generalist consumers of organic compounds; (Kato et al 2022;Fickling et al 2024) have also been associated with invasions of Amaranthus palmeri in China (Zhang et al 2023), but were more abundant on native genotypes of C. solstitialis. In contrast, taxa in the Chthonomonadales (a group associated with decomposition of glycine substrates; (Bhatnagar, Peay, and Treseder 2018) were more abundant on invader genotypes.…”
It is increasingly recognized that different genetic variants can uniquely shape their microbiomes. Invasive species often evolve in their introduced ranges, but little is known about the potential for microbial associations to evolve during invasion as a result. We investigated invader genotype (G) and microbial environment (E) interactions in C. solstitialis (yellow starthistle), a Eurasian plant that is known to have evolved novel genotypes, and to have altered microbial interactions, in its severe invasion of California, USA. We conducted an experiment in which native and invading genotypes were inoculated with native and invaded range soil microbial communities. We used amplicon sequencing to characterize rhizosphere bacteria in both the experiment and the field soils from which they were derived. We found that bacterial diversity is higher in invaded soils, but that invading genotypes accumulated a lower diversity of bacteria and unique microbial composition in experimental inoculations, relative to native genotypes. Associations with potentially beneficial Streptomycetaceae were particularly interesting, as these were more abundant in the invaded range and accumulated on invading genotypes. Thus variation in microbial associations of invaders was driven by the interaction of G and E, and microbial communities appear to change in composition along with host evolution during invasion.
“…1,060,366-1,060,464) in R. castenholzii (strain DSM 13941/HLO8) genome, but it was not annotated in the Protein Database of Uniprot and NCBI. The amino acid sequence of subunit X showed strict conservation with a hypothetical protein KatS3mg058_1126 (GenBank: GIV99722.1) from Roseiflexus sp, which was denoted by metagenomic analyses of the uncultivated bacteria in Katase hot spring sediment (Kato, Masuda, Shibata, Shirasu, & Ohkuma, 2022) (Figure 2-figure supplement 5). The resolved subunit X inserted into the LH opening in opposite orientation with that of LHαβ and c-TM, where these TM helices were stabilized by hydrophobic and weak hydrogen bonding interactions (Figure 2G and I).…”
Section: Assignment Of the Subunit X In Nrc-lh Complexmentioning
confidence: 99%
“…The Cryo-EM Map of nRC-LH was used for automated model building in ModelAngelo, a program developed by Professor Sjors Scheres (https://arxiv.org/abs/2210.00006v1). BLAST search of the deduced amino acid sequences of subunit X generated a hint with hypothetical protein KatS3mg058_1126 (GenBank: GIV99722.1) from Roseiflexus sp, which was denoted by metagenomic analyses of the uncultivated bacteria in Katase hot spring sediment (Kato et al, 2022). However, this polypeptide has not been annotated in the Protein Database of R. castenholzii (strain DSM 13941/HLO8).…”
Section: Assignment Of the Subunit X Proteins Y And Zmentioning
Carotenoid (Car) pigments perform central roles in photosynthesis-related light harvesting (LH), photoprotection, and assembly of functional pigment-protein complexes. However, the relationships between Car depletion in the LH, assembly of the prokaryotic reaction center (RC)-LH complex, and quinone exchange are not fully understood. Here, we analyzed native RC-LH (nRC-LH) and Car-depleted RC-LH (dRC-LH) complexes inRoseiflexus castenholzii, a chlorosome-less filamentous anoxygenic phototroph that forms the deepest branch of photosynthetic bacteria. Newly identified exterior Cars functioned with the bacteriochlorophyll B800 to block the proposed quinone channel between LHαβ subunits in the nRC-LH, forming a sealed LH ring that was disrupted by transmembrane helices from cytochrome c and subunit X to allow quinone shuttling. dRC-LH lacked subunit X, leading to an exposed LH ring with a larger opening, which together accelerated the quinone exchange rate. We also assigned amino acid sequences of subunit X and two hypothetical proteins Y and Z that functioned in forming the quinone channel and stabilizing the RC-LH interactions. This study reveals the structural basis by which Cars assembly regulates the architecture and quinone exchange of bacterial RC-LH complexes. These findings mark an important step forward in understanding the evolution and diversity of prokaryotic photosynthetic apparatus.
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