Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

Abstract

Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth's environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. Understanding of these microorganisms is important from the perspective of evolutionary studies and because their interactions with other organisms are likely to shape natural microbiome function.

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

“…An interesting aspect of our analysis relates to the detection of a phosphofructokinase-like protein in both genomes (Figures 4 and S1); this enzyme converts fructose 6-phosphate to fructose 1,6-bisphosphate. This finding counters the literature suggesting that a lack of such an enzyme is probably common within members of the CPR/Patescibacteria (Castelle et al, 2018;Wrighton et al, 2012), such as in Saccharimonas aalborgensis (Albertsen et al, 2013) and Teamsevenus rhizospherense (Starr et al, 2018). In addition, an often-missing enzyme in these taxa is enolase.…”

“…Auxotrophy (i.e., the inability to synthesize the cell envelope and to build proteins and nucleic acids) is a clear indication of potential cometabolism interdependencies and symbiotic lifestyles. The metabolic dependence and reduced genome sizes are signatures of CPR/Patescibacteria (Castelle et al, ). We found several pieces of evidence suggesting that Saccharibacter sossegus and Chaer renensis are engaging in symbiosis with other taxa in the AMD system.…”

Ultra‐small and abundant: Candidate phyla radiation bacteria are potential catalysts of carbon transformation in a thermokarst lake ecosystem

“…). Although these results described only a limited part of the CPR bacteria community identified in our samples, these metabolic capabilities align with metabolic functions identified in Parcubacteria bins recovered from other freshwater environments (Nelson and Stegen ; Castelle et al ), and extend our knowledge of CPR bacterial metabolism to thermokarst lakes and ponds, one of the most abundant ecosystem types in the circumpolar North.…”

Clades of huge phage from across Earth’s ecosystems

“…Many phage have genes involved in de novo biosynthesis of purines and pyrimidines, and the interconversion of nucleic and ribonucleic acids and nucleotide phosphorylation states. These gene sets are intriguingly similar to those of bacteria with very small cells and putative symbiotic lifestyles (Castelle et al , 2018) ( Table S4 ).…”