Genomic and genetic sequence information of strains assigned to the genus Rhodopseudomonas reveal the great heterogeneity of the group and identify strain Rhodopseudomonas palustris DSM 123T as the authentic type strain of this species

Imhoff, Johannes F.; Meyer, Terrance E.; Kyndt, John A.

doi:10.1099/ijsem.0.004077

Cited by 17 publications

(10 citation statements)

References 22 publications

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“…The Rhodopseudomonas was identified as a strain of Rps. palustris having ANI of 98% to the neotype strain DSM 123 (Imhoff et al 2020). The other contaminant in the culture was found to have ANI of 82% to Rfx.…”

Section: Resultsmentioning

confidence: 91%

The genome sequence of the giant phototrophic gammaproteobacterium Thiospirillum jenense gives insight into its physiological properties and phylogenetic relationships

2020

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In a conserved culture of the purple sulfur bacterium Thiospirillum jenense DSM216 T , cells of this species were easily recognized by cell morphology, large-size spirilla and visible flagellar tuft. The Tsp. jenense genome is 3.22 Mb in size and has a GC content of 48.7 mol%. It was readily identified as a member of the Chromatiaceae by the complement of proteins in its genome. A whole genome comparison clearly placed Tsp. jenense near Thiorhodovibrio and Rhabdochromatium species and somewhat more distant from Thiohalocapsa and Halochromatium species. This relationship was also found with the sequences of the photosynthetic reaction center protein PufM. The genome sequence supported important properties of this bacterium: the presence of ribulose-bisphosphate carboxylase and enzymes of the Calvin cycle of autotrophic carbon dioxide fixation but the absence of carboxysomes, an incomplete tricarboxylic acid cycle and the lack of malate dehydrogenase, the presence of a sulfur oxidation pathway including adenylylsulfate reductase (aprAB) but absence of assimilatory sulfate reduction, the presence of hydrogenase (hoxHMFYUFE), nitrogenase and a photosynthetic gene cluster (pufBALMC). The FixNOP type of cytochrome oxidase was notably lacking, which may be the reason that renders the cells highly sensitive to oxygen. Two minor phototrophic contaminants were found using metagenomic binning: one was identified as a strain of Rhodopseudomonas palustris and the second one has an average nucleotide identity of 82% to the nearest neighbor Rhodoferax antarcticus. It should be considered as a new species of this genus and Rhodoferax jenense is proposed as the name.

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Section: Resultsmentioning

confidence: 91%

The genome sequence of the giant phototrophic gammaproteobacterium Thiospirillum jenense gives insight into its physiological properties and phylogenetic relationships

2020

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“…Since there appeared to be much heterogeneity within the Rhodopsuedomonas genus [ 25 ], we decided to perform a more in-depth whole genome comparison of this new isolate to obtain a more complete phylogenetic analysis. Average percentage nucleotide identity (ANIb) between our genome and the whole genomes of other Rhodopseudomonas species was calculated using JSpecies ( Table 2 ) [ 34 ].…”

Section: Resultsmentioning

confidence: 99%

“…rhenobascensis , and Rps. telluris [ 23 , 24 , 25 ]. Several genomes of different strains of Rhodopseudomonas have been sequenced.…”

Section: Introductionmentioning

confidence: 99%

“…Since Rhodopseudomonas is widely distributed in soil and water environments it is frequently found in metagenomic analyses and correct taxonomic information is important to derive detailed conclusions from such broad metagenomic studies. Therefore, an updated phylogenetic analysis of the genus, based on whole genome comparisons and 16S rRNA comparisons, was published recently [ 25 ], and revealed that the genus shows great heterogenicity at the species level. That study also showed that Rhodopseudomonas palustris DSM 123 is the authentic type strain for that species, which had previously been debated, but previous confusion was shown to be due to errors in strain transfers over time.…”

Section: Introductionmentioning

confidence: 99%

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Genomic and Phylogenetic Characterization of Rhodopseudomonas infernalis sp. nov., Isolated from the Hell Creek Watershed (Nebraska)

et al. 2022

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The genus Rhodopseudomonas is known for its versatile metabolic capabilities and has been proposed to be used in a wide variety of innovative applications, ranging from biohydrogen and electricity production, bioremediation and as biostimulant in agriculture. Here, we report the isolation, characterization and genome sequence analysis of a novel Rhodopseudomonas species, strain HC1, isolated from the Hell Creek urban native restoration area. Whole genome-based analysis, average nucleotide identity (ANI) comparison, and growth characteristics identified this isolate as a new species of the Rhodopseudomonas genus, for which we propose the name Rhodopseudomonas infernalis sp. nov. Besides containing several nitrogenases for nitrogen fixation and hydrogen production, the HC1 genome encodes a unique gene cluster, not found in any other Rhodopseudomonas species, which encodes genes for the degradation of yet-unidentified aromatic PCB-type chemicals with potentially interesting biotechnological applications. The genomic features of Rps. infernalis HC1 indicate that it plays a positive role in the degradation of anthropogenic substances and aids the restoration of the Hell Creek watershed by contributing to N2 and carbon fixation and plant growth; however, the genome also contains several antibiotic resistance genes, indicating a broad range of antibiotic resistance in this environmental isolate.

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“…As before, the concentration of added DMSO (Sigma Life Sciences, molecular biology grade) was 40 mM, the concentration of added sodium bicarbonate was 10 mM, and the concentration of added ammonium sulfate was 7.5 mM. We note that, though we continue to refer to the cultures as R. palustris , a recent phylogenetic analysis has suggested that strain CGA009 and its mutant derivatives may in fact be more closely related to R. rutila (Imhoff et al ., 2020). This phylogenic reclassification does not impact our studies.…”

Section: Methodsmentioning

confidence: 99%

Carbon substrate re‐orders relative growth of a bacterium using Mo‐, V‐, or Fe‐nitrogenase for nitrogen fixation

Luxem¹,

Kraepiel²,

Zhang³

et al. 2022

Environmental Microbiology

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Genomic and genetic sequence information of strains assigned to the genus Rhodopseudomonas reveal the great heterogeneity of the group and identify strain Rhodopseudomonas palustris DSM 123T as the authentic type strain of this species

Abstract: The genus Rhodopseudomonas , containing purple nonsulfur photosynthetic Proteobacteria, has a number of strains that belong to different species, although many of them are c… Show more

Cited by 17 publications

References 22 publications

The genome sequence of the giant phototrophic gammaproteobacterium Thiospirillum jenense gives insight into its physiological properties and phylogenetic relationships

The genome sequence of the giant phototrophic gammaproteobacterium Thiospirillum jenense gives insight into its physiological properties and phylogenetic relationships

Genomic and Phylogenetic Characterization of Rhodopseudomonas infernalis sp. nov., Isolated from the Hell Creek Watershed (Nebraska)

Carbon substrate re‐orders relative growth of a bacterium using Mo‐, V‐, or Fe‐nitrogenase for nitrogen fixation

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