Providencia manganoxydans sp. nov., a Mn(II)-oxidizing bacterium isolated from heavy metal contaminated soils in Hunan Province, China

Li, Zongpei; Liao, Fengfeng; Ding, Zhexu; Chen, Sha; Li, Ding

doi:10.1099/ijsem.0.005474

Cited by 14 publications

(8 citation statements)

References 53 publications

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“… a Strains: 1, P. manganoxydans LLDRA6; 2, P. alcalifaciens DSM 30120; 3, P. burhodogranariea DSM 19968; 4, P. heimbachae DSM 3591; 5, P. huaxiensis KCTC 62577; 6, P. rettgeri DSM4542; 7, P. rustigianii DSM 4541; 8, P. sneebia DSM 19967; 9, P. stuartii DSM 4539; 10, P. thailandensis KCTC 23281; 11, P. vermicola DSM 17385; 12, P. hangzhouensis PR-310; 13, P. entomophila IO-23; 14, P. wenzhouensis R33. Data for species other than P. zhijiangensis D4759 are from references ( 8 , 17 ). (+), 90% to 100% positive reaction; (−), 0% to 10% positive reaction; ND, not determined.…”

Section: Resultsmentioning

confidence: 99%

Genomic revisitation and reclassification of the genus Providencia

Dong,

Jia,

et al. 2024

mSphere

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Members of Providencia , although typically opportunistic, can cause severe infections in immunocompromised hosts. Recent advances in genome sequencing provide an opportunity for more precise study of this genus. In this study, we first identified and characterized a novel species named Providencia zhijiangensis sp. nov. It has ≤88.23% average nucleotide identity (ANI) and ≤31.8% in silico DNA-DNA hybridization (dDDH) values with all known Providencia species, which fall significantly below the species-defining thresholds. Interestingly, we found that Providencia stuartii and Providencia thailandensis actually fall under the same species, evidenced by an ANI of 98.59% and a dDDH value of 90.4%. By fusing ANI with phylogeny, we have reclassified 545 genomes within this genus into 20 species, including seven unnamed taxa (provisionally titled Taxon 1–7), which can be further subdivided into 23 lineages. Pangenomic analysis identified 1,550 genus-core genes in Providencia , with coenzymes being the predominant category at 10.56%, suggesting significant intermediate metabolism activity. Resistance analysis revealed that most lineages of the genus (82.61%, 19/23) carry a high number of antibiotic-resistance genes (ARGs) and display diverse resistance profiles. Notably, the majority of ARGs are located on plasmids, underscoring the significant role of plasmids in the resistance evolution within this genus. Three species or lineages ( P. stuartii , Taxon 3, and Providencia hangzhouensis L12) that possess the highest number of carbapenem-resistance genes suggest their potential influence on clinical treatment. These findings underscore the need for continued surveillance and study of this genus, particularly due to their role in harboring antibiotic-resistance genes. IMPORTANCE The Providencia genus, known to harbor opportunistic pathogens, has been a subject of interest due to its potential to cause severe infections, particularly in vulnerable individuals. Our research offers groundbreaking insights into this genus, unveiling a novel species, Providencia zhijiangensis sp. nov., and highlighting the need for a re-evaluation of existing classifications. Our comprehensive genomic assessment offers a detailed classification of 545 genomes into distinct species and lineages, revealing the rich biodiversity and intricate species diversity within the genus. The substantial presence of antibiotic-resistance genes in the Providencia genus underscores potential challenges for public health and clinical treatments. Our study highlights the pressing need for increased surveillance and research, enriching our understanding of antibiotic resistance in this realm.

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Section: Resultsmentioning

confidence: 99%

Genomic revisitation and reclassification of the genus Providencia

Dong,

Jia,

et al. 2024

mSphere

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“… a Strains: 1, P. manganoxydans LLDRA6; 2, P. alcalifaciens DSM 30120; 3, P. burhodogranariea DSM 19968; 4, P. heimbachae DSM 3591; 5, P. huaxiensis KCTC 62577; 6, P. rettgeri DSM4542; 7, P. rustigianii DSM 4541; 8, P. sneebia DSM 19967; 9, P. stuartii DSM 4539; 10, P. thailandensis KCTC 23281; 11, P. vermicola DSM 17385. Data for species other than P. hangzhouensis PR-310 are from reference ( 14 ). + represents 90 to 100% positive reaction and − represents 0 to 10% positive reaction.…”

Section: Resultsmentioning

confidence: 99%

Whole-genome sequencing provides insights into a novel species: Providencia hangzhouensis associated with urinary tract infections

Dong,

Yu,

Liu

et al. 2023

Microbiol Spectr

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Providencia rettgeri is a clinically significant opportunistic pathogen that is involved in urinary tract infections. Due to the resolution limitations of identification, distinguishing P. rettgeri from closely related species is challenging by commercial biochemical test systems. Here, we first reported a novel species, Providencia hangzhouensis , which had been misidentified as P. rettgeri . Exhibiting ≤91.97% average nucleotide identity (ANI) and ≤46.10% in silico DNA-DNA hybridization values with all known Providencia species, P. hangzhouensis falls well beneath the established species-defining thresholds. We conducted a population genomics analysis of P. hangzhouensis isolates worldwide. Our study revealed that P. hangzhouensis has emerged in many countries and has formed several transmission clusters. We found that P. hangzhouensis shared the highest ANI values (91.54% and 91.97%) with P. rettgeri and P. huaxiensis , respectively. The pan-genome analysis revealed that these three species possessed a similar component of pan-genomes. Two genes associated with metabolism, folE2 and ccmM , were identified to be specific to P. hangzhouensis . Furthermore, we also observed that carbapenem-resistance genes frequently occur in P. hangzhouensis with the bla IMP-27 being the most prevalent (46.15%; 36/78). The emergence of P. hangzhouensis is often accompanied by extended-spectrum β-lactamase and carbapenem-resistance genes, and calls for tailored surveillance of this species as a clinically relevant species in the future. IMPORTANCE Our study has identified and characterized a novel species, Providencia hangzhouensis , which is associated with urinary tract infections and was previously misidentified as Providencia rettgeri . Through this study, we have identified specific genes unique to P. hangzhouensis , which could serve as marker genes for rapid PCR identification. Additionally, our findings suggest that the emergence of P. hangzhouensis is often accompanied by extended-spectrum β-lactamase and carbapenem-resistance genes, emphasizing the need for attention to clinical management and the importance of accurate species identification and proper drug use.

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“…The genomic DNA of strain L3, prepared from a pure culture using an Ezup Column Bacteria Genomic DNA Puri cation Kit (Sangon Biotech), was used as the PCR template to amplify the 16S rRNA gene, via a pair of universal primers, 27F (5 -AGAGTTTGATCCTGGCTCAG-3 ) and 1492R (5 -GGTTACCTTGTTACGACTT-3 ) (Weisburg et al, 1991). The sequenced ampli cation fragments of 16S rRNA gene were subject to phylogenetic identi cation by using the BLAST search program (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and MEGA X software (Li et al, 2022). Brie y, the phylogenetic tree was constructed by employing the neighbour-joining (NJ) method in MEGA X software to analyze the evolutionary relationship between strain L3 and close bacterial species.…”

Section: Phylogenetic Identi Cation Of Strain L3mentioning

confidence: 99%

The formation of bixbyite-type Mn2O3 via pyocyanin-dependent Mn(II) oxidation of soil-derived Pseudomonas aeruginosa

Xue,

Liao,

Tang

et al. 2024

Preprint

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Bacterial Mn(II) oxidation is believed to play a dominant role in accelerating the rate of Mn biomineralization in nature. Commonly, bacteria adopt two ways concerning Mn(II) oxidases and reactive oxygen species to oxidize Mn(II). In this study, a new strategy for bacterial Mn(II) oxidation involving the pyocyanin, a greenish blue phenazine pigment from Pseudomonas aeruginosa, was discovered. To begin with, a bacterial strain L3 was isolate from soils and identified as Pseudomonas aeruginosa, which exhibited the ability of Mn(II) oxidation. Next, the pyocyanin was purified from strain L3 cultures and proven to be involved in Mn(II) oxidation. Particularly, the oxidation of Mn(II) by pyocyanin was dependent on its ambient pH. In comparison with pH of 5 and 7, pyocyanin (the initial value of OD387 was 0.56 at pH 2) showed a stronger capability of oxidizing Mn(II) at pH of 9, reaching 144.03 µg L− 1 of Mn oxides after 108 h of Mn(II) oxidation, while pyocyanin ultimately produced 43.81 µg L− 1 at pH of 7 and 3.32 µg L− 1 at pH of 5, respectively. Further, strain L3 cultures were fractionated into three parts, i.e., the cell culture solution, fermentation supernatant, and cell suspension, and the Mn(II)-oxidizing activity was found to be distributed in the cell culture solution and fermentation supernatant, as evidenced by the formation of blackish glossy Mn oxides. Specifically, in the first half, the rate of Mn(II) oxidation by the fermentation supernatant was higher than that by the cell culture solution, whereas in the second half, the cell culture solution showed the much higher Mn(II)-oxidizing activity than did the fermentation supernatant. Last but not least, the collective results from mineral characterization demonstrated that, the Mn oxides produced by P. aeruginosa strain L3, either by the cell culture solution or by the fermentation supernatant, were bixbyite-type Mn2O3 with poor crystallinity.

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Providencia manganoxydans sp. nov., a Mn(II)-oxidizing bacterium isolated from heavy metal contaminated soils in Hunan Province, China

Cited by 14 publications

References 53 publications

Genomic revisitation and reclassification of the genus Providencia

Genomic revisitation and reclassification of the genus Providencia

Whole-genome sequencing provides insights into a novel species: Providencia hangzhouensis associated with urinary tract infections

The formation of bixbyite-type Mn2O3 via pyocyanin-dependent Mn(II) oxidation of soil-derived Pseudomonas aeruginosa

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