Carbon fixation pathways across the bacterial and archaeal tree of life

Abstract

Carbon fixation is a critical process for our planet, however, its distribution across the bacterial and archaeal domains of life has not been comprehensively studied. Here, we performed an analysis of 52,515 metagenome-assembled genomes (MAGs) and discover carbon fixation pathways in 1007 bacteria and archaea. We reveal the genomic potential for carbon fixation through the reverse tricarboxylic acid cycle in previously unrecognised archaeal and bacterial phyla (ie. Thermoplasmatota and Elusimicrobiota) and show that the 3-hydroxypropionate bi-cycle is not, as previously thought, restricted to the phylum Chloroflexota. The data also substantially expands the phylogenetic breadth for autotrophy through the dicarboxylate/4-hydroxybutyrate cycle and the Calvin-Benson-Bassham cycle. Finally, the genomic potential for carbon fixation through the 4-hydroxybutyrate/3-hydroxypropionate cycle, previously exclusively found in Archaea, was also detected in the Bacteria. Carbon fixation appears thus to be much more widespread than previously known and this study lays the foundation to better understand the role of archaea and bacteria in global primary production and how they contribute to microbial carbon sinks.

Tripartite interaction of a patescibacterial epibiont, a methylotrophic gammaproteobacterial host and a jumbo phage

“…S9). Another Methylophilaceae MAG encoding a complete CBB cycle has been recently reported (63), which supports that the presence of these genes in our host MAGs is not artifactual and that these Methylophilaceae might have the capacity to synthesize 3-phosphoglycerate using various pathways. An interesting point to notice is that, to date, all identified hosts of Absconditicoccaceae epibionts possess RuBisCO (13,14), suggesting that carbon fixation may be advantageous for the establishment of this symbiotic interaction.…”

A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene‐tetrahydrofolate reductase mutant of Acetobacterium woodii

“…The Wood–Ljungdahl pathway (WLP) is one of the seven known pathways for the fixation of carbon dioxide found in nature (Garritano et al, 2022). It is present in strictly anaerobic microorganisms such as methanogenic archaea, sulphate reducing and acetogenic bacteria and catalyses the anabolic formation of acetyl‐CoA from two molecules of CO 2 (Schauder et al, 1988; Wolfe, 1993; Wood et al, 1986).…”

Aquificae overcomes competition by archaeal thermophiles, and crowding by bacterial mesophiles, to dominate the boiling vent-water of a Trans-Himalayan sulfur-borax spring

“…In contrast, the 3-hydroxypropionate bi-cycle, discovered in the green non-sulfur bacterium called Chloroflexus aurantiacus [107, 108], has long been considered as an exclusive feature of Chloroflexi. Recent studies, however, have shown that the pathway, or its analogous variants, could exist beyond this single phylum [109, 110]. The present investigation of the Lotus Pond metagenome showed that genes for a few key enzymes of the 3-hydroxypropionate bi-cycle were present in the MAGs affiliated to Aquificae.…”