Genomic signatures and co‐occurrence patterns of the ultra‐small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle

Abstract

The size of bacterial genomes is often associated with organismal metabolic capabilities determining ecological breadth and lifestyle. The recently proposed Candidate Phyla Radiation (CPR)/Patescibacteria encompasses mostly unculturable bacterial taxa with relatively small genome sizes with potential for co‐metabolism interdependencies. As yet, little is known about the ecology and evolution of CPR, particularly with respect to how they might interact with other taxa. Here, we reconstructed two novel genomes (namely, Candidatus Saccharibacter sossegus and Candidatus Chaer renensis) of taxa belonging to the class Saccharimonadia within the CPR/Patescibacteria using metagenomes obtained from acid mine drainage (AMD). By testing the hypothesis of genome streamlining or symbiotic lifestyle, our results revealed clear signatures of gene losses in these genomes, such as those associated with de novo biosynthesis of essential amino acids, nucleotides, fatty acids and cofactors. In addition, co‐occurrence analysis provided evidence supporting potential symbioses of these organisms with Hydrotalea sp. in the AMD system. Together, our findings provide a better understanding of the ecology and evolution of CPR/Patescibacteria and highlight the importance of genome reconstruction for studying metabolic interdependencies between unculturable Saccharimonadia representatives.

The “Plastisphere” of Biodegradable Plastics Is Characterized by Specific Microbial Taxa of Alpine and Arctic Soils

“…In addition, some Saccharibacteria were shown to take up oleic acid and to possess lipase and other exoenzymatic activities (Kindaichi et al, 2016). Interestingly, many Saccharibacteria seem to possess a D−lactate dehydrogenase−like protein acting in the conversion of pyruvate into lactate in a fermentation pathway (Lemos et al, 2019). Our data implicate that lactate, the monomer of PLA, might be used as a C source instead of being only a final waste product in the metabolism of some Saccharibacteria.…”

“…Very little is known about the ecology of Saccharimonadales, which belongs to the candidate phylum Saccharibacteria (formerly TM7), and knowledge almost exclusively stems from genomic data. Saccharibacteria have been shown to possess very small genomes and cell sizes, and they have therefore been proposed to live in symbiosis with other microorganisms depending on co-metabolism (Lemos et al, 2019). Further, Lemos et al (2019) stated that the majority of unique genes found in nearly complete genomes of two Saccharibacteria are of unknown function, underlining the knowledge gaps existing regarding this bacterial order.…”

“…Saccharibacteria have been shown to possess very small genomes and cell sizes, and they have therefore been proposed to live in symbiosis with other microorganisms depending on co-metabolism (Lemos et al, 2019). Further, Lemos et al (2019) stated that the majority of unique genes found in nearly complete genomes of two Saccharibacteria are of unknown function, underlining the knowledge gaps existing regarding this bacterial order. Several genes involved in the catabolism of complex C sources were identified in TM7 strain RAAC3 and other Saccharibacteria (Kantor et al, 2013;Starr et al, 2018).…”

Complete Genome of a Member of a New Bacterial Lineage in the Microgenomates Group Reveals an Unusual Nucleotide Composition Disparity Between Two Strands of DNA and Limited Metabolic Potential

“…According to the NCBI taxonomy database [7], the Microgenomates group at present comprises 16 phylum-level divisions. However, the recently described Genome Taxonomy Database (GTDB) based on genome phylogeny, collapses all CPR lineages into a single candidate phylum, Patescibacteria, comprising the candidate class Microgenomatia [8].Genomics studies of CPR bacteria [4,[9][10][11][12][13][14][15][16] have revealed that they have relatively small genomes (~1 Mbp or less) and limited metabolic capacities, including the common lack of complete pathways for amino acid, nucleotide and lipid biosynthesis, that suggests a partner-dependent symbiotic or parasitic lifestyle [4,17,18]. Physical associations of CPR bacteria with their hosts have been shown for a member of Saccharibacteria (TM7), which attaches to Actinomyces odontolyticus [19].…”

Long-read shotgun metagenome sequencing using PromethION uncovers novel bacteriophages, their abundance, and interaction with host bacterial immunity in the oral microbiota

“…The taxonomy of the contig was predicted to be the Treponema genus, consisting of dozens of species in the human oral microbiota (41). Predicted taxonomy of another contig containing a jumbo prophage was Patescibacteria , the recently proposed Candidate Phyla Radiation (CPR) lineage that encompasses mostly unculturable bacterial taxa with relatively small genome sizes (42), including ubiquitous members of the human oral microbiota (43). Overall, there was no overlap in the predicted taxonomies among the jumbo phages/prophages carrying the phage hallmark genes, suggesting they are not confined to specific phylogenetic groups in the human oral microbiota.…”