Paracoccus binzhouensis sp. nov., isolated from activated sludge

Wang, Fang; Gong, Xiaofan; Meng, Dong; Liu, Yuling; Gu, Pengfei; Fan, Xiangyu; Huang, Zida; Du, Zong‐Jun; Li, Qiang

doi:10.1007/s00203-021-02286-7

Cited by 5 publications

(4 citation statements)

References 23 publications

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“…They consist of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL), and an unidentified lipid (L). These profiles are very similar to the lipid profile of the closely related species P. denitrificans [45]. However, small differences can be found.…”

Section: Phenotypic and Chemotaxonomic Characterizationsupporting

confidence: 71%

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Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov.

Timsy

Behrendt

Ulrich

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate–formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus . Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA–DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L). On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus , for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed.

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Section: Phenotypic and Chemotaxonomic Characterizationsupporting

confidence: 71%

“…These profiles are very similar to the lipid profile of the closely related species P. denitrificans [45]. However, small differences can be found.…”

Section: Taxonomic Characterization By a Polyphasic Approachsupporting

confidence: 69%

Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov.

Timsy

Behrendt

Ulrich

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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“…The complete genome of these methylotrophic strains was organized into multi‐replicon genome structure and interestingly, several methylotrophic genes were identified on extrachromosomal replicons‐plasmid/chromid suggestive of acquisition via HGT as a means of adaptation (Czarnecki et al, 2017). Recently, genome analysis of P. binzhouensis reported the presence of 12 clusters for secondary metabolite synthesis and also highlighted certain deviations in the primary carbon metabolism (Wang et al, 2021). Such studies highlight the usage of genome‐based methods for the identification of prospective functional pathways which can be optimized, modulated and exploited for biosynthetic/degradation activity applications of these isolates.…”

Section: Versatile Genomic Capacity: Multi‐replicon Architecture and ...mentioning

confidence: 99%

Harnessing taxonomically diverse and metabolically versatile genus Paracoccus for bioplastic synthesis and xenobiotic biodegradation

Puri

Bajaj

Singh

et al. 2022

Journal of Applied Microbiology

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The genus Paracoccus represents a taxonomically diverse group comprising more than 80 novel species isolated from various pristine and polluted environments. The species are characterized as coccoid‐shaped Gram‐negative bacteria with versatile metabolic attributes and classified as autotrophs, heterotrophs and/or methylotrophs. The present study highlights the up‐to‐date global taxonomic diversity and critically discusses the significance of genome analysis for identifying the genomic determinants related to functional attributes mainly bioplastic synthesis and biodegradation potential that makes these isolates commercially viable. The analysis accentuates polyphasic and genomic attributes of Paracoccus spp. which could be harnessed for commercial applications and emphasizes the need of integrating genome‐based computational analysis for evolutionary species and functional diversification. The work reflects on the underexplored genetic potential for bioplastic synthesis which can be harnessed using advanced genomic methods. It also underlines the degradation potential and possible use of naturally‐occurring pollutant‐degrading Paracoccus isolates for the development of a biodegradation system and efficient removal of contaminants. The work contemplates plausible use of such potent isolates to establish the plant‐microbe interaction, contributing toward contaminated land reclamation. Overall, the work signifies the need and application of genome analysis to identify and explore the prospective potential of Paracoccus spp. for environmental application toward achieving sustainability.

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“…At the time of writing, there were 95 species with validly published names in the genus Paracoccus according to the List of Prokaryotic names with Standing in Nomenclature (LPSN) (http://www.bacterio.net/) (Parte et al 2020). Recently described species are P. amoyensis isolated from the surface seawater of Xiamen Island (Lyu et al 2021), P. onubensis isolated from the wall of a show cave (Gutierrez-Patricio et al 2021) and P. binzhouensis isolated from the activated sludge (Wang et al 2021). In addition, bacteria of the genus Paracoccus were isolated from other various habitats, such as air (Xue et al 2017), soil (Sun et al 2015), sediment (Zhang et al 2019), seawater (Lyu et al 2021) and sediment of freshwater (Wang et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Paracoccus marinaquae sp. nov., isolated from coastal water of the Yellow Sea

Xue

et al. 2022

Preprint

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A Gram-stain-negative, non-motile and coccoid bacterial strain, designated XHP0099T, was isolated from coastal water of the Yellow Sea, China. Growth occurred at 20–37°C (optimum, 28°C), pH 5.0–9.0 (optimum, pH 7.0–8.0), and with 0–7.0% NaCl (optimum, 2.0–3.0%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XHP0099T was related to members of the genus Paracoccus and shared highest sequence similarity with P. siganidrum M26T (98.2%), followed by P. alkanivorans 4-2T (97.6%) and P. alkenifer DSM 11593T (97.4%). The major cellular fatty acids (＞10%) were summed feature 8 (C18:1 ω7c/C18:1 ω6c), and C18:0. The major isoprenoid quinone was Q-10 and the polar lipids contained diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), aminolipid (AL) and unidentified polar lipid (L). The average nucleotide identity values between strain XHP0099T and P. siganidrum M26T, P. alkanivorans 4-2T, P. alkenifer DSM 11593T and P. saliphilus DSM 18447T were 81.41%, 80.13%, 75.77% and 78.27%, respectively. The digital DNA–DNA hybridization values between strain XHP0099T with P. siganidrum M26T, P. alkanivorans 4-2T, P. alkenifer DSM 11593T and P. saliphilus DSM 18447T were 24.10%, 23.00%, 20.80 % and 21.20%, respectively. The G+C content of the genomic DNA of strain XHP0099T was 66.0%. Based on the phenotypic, phylogenetic, biochemical and chemotaxonomic analysis, strain XHP0099T represents a novel species of the genus Paracoccus, for which the name Paracoccus marinaquae sp. nov. is proposed. The type strain is XHP0099T (=JCM 34661T=GDMCC 1.2414T=MCCC 1K05846T).

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Paracoccus binzhouensis sp. nov., isolated from activated sludge

Cited by 5 publications

References 23 publications

Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov.

Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov.

Harnessing taxonomically diverse and metabolically versatile genus Paracoccus for bioplastic synthesis and xenobiotic biodegradation

Paracoccus marinaquae sp. nov., isolated from coastal water of the Yellow Sea

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