RubisCO‐based CO₂ fixation and C₁ metabolism in the actinobacterium Pseudonocardia dioxanivorans CB1190

Abstract

Pseudonocardia is an actinobacterial genus of interest due to its potential biotechnological, medical and environmental remediation applications, as well as for the ecologically relevant symbiotic relationships it forms with attine ants. Some Pseudonocardia spp. can grow autotrophically, but the genetic basis of this capability has not previously been reported. In this study, we examined autotrophy in Pseudonocardia dioxanivorans CB1190, which can grow using H2 and CO2, as well as heterotrophically. Genomic and transcriptomic analysis of CB1190 cells grown with H2/bicarbonate implicated the Calvin-Benson-Bassham (CBB) cycle in growth-supporting CO2 fixation, as well as a [NiFe] hydrogenase-encoding gene cluster in H2 oxidation. The CBB cycle genes are evolutionarily most related to actinobacterial homologues, although synteny has not been maintained. Ribulose-1,5-bisphosphate carboxylase activity was confirmed in H2/bicarbonate-grown CB1190 cells and was detected in cells grown with the C1 compounds formate, methanol and carbon monoxide. We also demonstrated the upregulation of CBB cycle genes upon exposure of CB1190 to these C1 substrates, and identified genes putatively involved in generating CO2 from the C1 substrates by using RT-qPCR. Finally, the potential for autotrophic growth of other Pseudonocardia spp. was explored, and the ecological implications of autotrophy in attine ant- and plant root-associated Pseudonocardia discussed.

Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy

“…3). The Calvin cycle is typical of photosynthetic organisms, including Cyanobacteria (35), but is also found in bacteria of the phyla Verrucomicrobia (74), Proteobacteria (77), Actinobacteria (78), and Firmicutes (79). All of these phyla were detected in the metagenome (Fig.…”

A widely distributed hydrogenase oxidises atmospheric H2during bacterial growth

“…S3) ; this constitutes a 3.2-fold increase in the number of genera and 1.4-fold increase in the number of phyla reported to encode this enzyme [4, 26]. The HucL-encoding bacteria include various known hydrogenotrophic aerobes, such as Nitrospira moscoviensis (Nitrospirota) [31], Hydrogenobacter thermophilus (Aquificota) [48], Kyrpidia tusciae (Firmicutes) [49], Sulfobacillus acidophilus (Firmicutes) [50], and Pseudonocardia dioxanivorans (Actinobacteriota) [51], suggesting these strains may also consume atmospheric H 2 . The hydrogenase was also distributed in various lineages of Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, and Deinococcota for which H 2 oxidation has not, to our knowledge, been reported.…”

Streptomyces thermoautotrophicus does not fix nitrogen

“…The high number of CODH enzymes encoded by the S. thermoautotrophicus genomes and the purported identity of the St1 nitrogenase as a modified CODH prompted us to examine other published genomes containing high numbers of such enzymes. We identified Pseudonocardia dioxanivorans CB1190 as another strain whose sequenced genome encodes multiple molybdenum hydroxylase enzymes (10 operons, two of which are putative type I CODH enzymes 34 ), and which has been reported to be a diazotroph 35 . The strain CB1190 similarly lacks nif , anf , and vnf genes, yet reportedly displayed a similar ability to grow on media lacking NH 4 + as an additive.…”