Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community

Abstract

CPR bacteria are generally predicted to be symbionts due to their extensive biosynthetic deficits. Although monophyletic, they are not monolithic in terms of their lifestyles. The organism described here appears to have evolved an unusual metabolic platform not reliant on glucose or pentose sugars. Its biology appears to be centered around bacterial host-derived compounds and/or cell detritus. Amino acids likely provide building blocks for nucleic acids, peptidoglycan, and protein synthesis. We resolved an unusual repeat region that would be invisible without genome curation. The nucleotide sequence is apparently under strong diversifying selection, but the amino acid sequence is under stabilizing selection. The amino acid repeat also occurs in a surface protein of a coexisting bacterium, suggesting colocation and possibly interdependence.

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

“…Gracilibacteria and Ca. Peregrinibacteria are characterised by typical cumulative GC skew curves with two clearly detectable extremes at the origin and the terminus of replication [13,16]. Therefore, we analysed the GC skew patterns for the three currently known complete genomes of other members of the candidate order UBA1400, representing Ca.…”

“…Alternatively, the Ch65 bacterium could acquire intermediates of the glycolytic pathway (e.g., fructose-1,6-bisphosphate or glyceraldehyde-3-phosphate) from the environment or its host organisms. The near-complete absence of the whole glycolytic pathway in some other CPR bacteria [16,17] suggests that this could be a common strategy in this lineage.…”

“…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].…”

Niche Partitioning in the Rimicaris Exoculata Holobiont: The Case of the First Symbiotic Zetaproteobacteria

“…TAG_MAG_00018, from the same phylum (Gracilibacteria class) was in high abundance at TAG (273X) while in low abundance at Rainbow (max 10X; Additional File 4). The predominance of these groups in the Rimicaris holobiont, associated with small genome size for both TAG_MAG_00007 and TAG_MAG_00018 (1,201735 and 841,694 bp, respectively) adds to recent studies showing widespread CPR organisms often in association with abundant autotrophic taxa involved in nitrogen, sulfur and iron cycling [51,52].…”

Schizasterid Heart Urchins Host Microorganisms in a Digestive Symbiosis of Mesozoic Origin

“…Similar results were obtained for A. cordatus , with Desulfobacterales averaging 31.5% of its microbiome, followed by Bacteroidetes (14.0%) and Spirochaetales (9.5%), with the addition of Rhizobiales (9.5%) and Lentisphaerales (7.0%). The most common phylotypes in A. cordatus were closely related to a recently described genus of the Desulfobacterales thus far known from a single psychrophilic species, Desulfoconvexum algidum , isolated from a fjord in the Svalbard archipelago ( Konneke et al, 2013 ) and members of the bacterial candidate phylum Gracilibacteria, which recent genomic analyses suggest are often symbiotic, displaying limited metabolic capacity ( Sieber et al, 2019 ).…”