Novel Species Of Pseudomonas Research Articles

Characterization of Pseudomonas sp. En3, an Endophytic Bacterium from Poplar Leaf Endosphere with Plant Growth-Promoting Properties

Growth-promoting endophytic bacteria possess substantial potential for sustainable agriculture. Here, we isolated an endophytic bacterium, Pseudomonas sp. En3, from the leaf endosphere of Populus tomentosa and demonstrated its significant growth-promoting effects on both poplar and tomato seedlings. The phosphorus solubilization and nitrogen fixation abilities of strain En3 were confirmed via growth experiments on NBRIP and Ashby media, respectively. Salkowski staining and HPLC-MS/MS confirmed that En3 generated indole-3-acetic acid (IAA). The infiltration of En3 into leaf tissues of multiple plants did not induce discernible disease symptoms, and a successful replication of En3 was observed in both poplar and tobacco leaves. Combining Illumina and Nanopore sequencing data, we elucidated that En3 possesses a circular chromosome of 5.35 Mb, exhibiting an average G + C content of 60.45%. The multi-locus sequence analysis (MLSA) and genome average nucleotide identity (ANI) supported that En3 is a novel species of Pseudomonas and constitutes a distinct phylogenetic branch with P. rhizosphaerae and P. coleopterorum. En3 genome annotation analysis revealed the presence of genes associated with nitrogen fixation, phosphate solubilization, sulfur metabolism, siderophore biosynthesis, synthesis of IAA, and ethylene and salicylic acid modulation. The findings suggest that Pseudomonas sp. En3 exhibits significant potential as a biofertilizer for crop and tree cultivation.

CRISPR/Cas9-Mediated Genome Editing for Pseudomonas fulva, a Novel Pseudomonas Species with Clinical, Animal, and Plant-Associated Isolates.

As one of the most widespread groups of Gram–negative bacteria, Pseudomonas bacteria are prevalent in almost all natural environments, where they have developed intimate associations with plants and animals. Pseudomonas fulva is a novel species of Pseudomonas with clinical, animal, and plant–associated isolates, closely related to human and animal health, plant growth, and bioremediation. Although genetic manipulations have been proven as powerful tools for understanding bacterial biological and biochemical characteristics and the evolutionary origins, native isolates are often difficult to genetically manipulate, thereby making it a time–consuming and laborious endeavor. Here, by using the CRISPR–Cas system, a versatile gene–editing tool with a two–plasmid strategy was developed for a native P. fulva strain isolated from the model organism silkworm (Bombyx mori) gut. We harmonized and detailed the experimental setup and clarified the optimal conditions for bacteria transformation, competent cell preparation, and higher editing efficiency. Furthermore, we provided some case studies, testing and validating this approach. An antibiotic–related gene, oqxB, was knocked out, resulting in the slow growth of the P. fulva deletion mutant in LB containing chloramphenicol. Fusion constructs with knocked–in gfp exhibited intense fluorescence. Altogether, the successful construction and application of new genetic editing approaches gave us more powerful tools to investigate the functionalities of the novel Pseudomonas species.

Pseudomonas eucalypticola sp. nov., a producer of antifungal agents isolated from Eucalyptus dunnii leaves

Pseudomonas are ubiquitously occurring microorganisms and are known for their ability to produce antimicrobials. An endophytic bacterial strain NP-1 T, isolated from Eucalyptus dunnii leaves, exhibits antifungal properties against five tested phytopathogenic fungi. The strain is a Gram-negative rod-shaped bacterium containing a single polar flagellum. It is strictly aerobic, grows at 4–37 °C, 2–5% NaCl, and pH 3–7. The 16S rRNA sequence analysis showed that NP-1 T belongs to the Pseudomonas genus. Phylogenetic analysis based on four concatenated partial genes (16S rDNA, gyrB, rpoB and rpoD) and the phylogenomic tree indicated that NP-1 T belongs to Pseudomonas fluorescens lineage but is distinct from any known Pseudomonas species. The G + C mol % of NP-1 T genome is 63.96, and the differences between NP-1 T and related species are larger than 1. The digital DNA-DNA hybridization and tetranucleotide signatures are 23.8 and 0.97, which clearly separates strain NP-1 T from its closest neighbours, Pseudomonas coleopterorum and Pseudomonas rhizosphaerae. Its phenotypic and chemotaxonomic features confirmed its differentiation from related taxa. The results from this polyphasic approach support the classification of NP-1 T as a novel species of Pseudomonas, and the name of Pseudomonas eucalypticola is thus proposed for this strain, whose type is NP-1 T (= CCTCC M2018494T = JCM 33572 T).

New species of pathogenic Pseudomonas isolated from citrus in Tunisia: Proposal of Pseudomonas kairouanensis sp. nov. and Pseudomonas nabeulensis sp. nov.

A collection of Pseudomonas strains was isolated in different regions of Tunisia in the period 2016–2017 from the fruits and leaves of Citrus sinensis cv. ‘Valencia Late’ and Citrus limon cv. ‘Eureka’ plants with symptoms of blast and black pit disease. A phylogenetic analysis of the housekeeping gene rpoD was used for strain identification at the species level. The results demonstrated the affiliation of these strains with the genus Pseudomonas and revealed the presence of 11 strains representing two putative new species in two monophyletic branches. These strains were analyzed morphologically and genotypically by multilocus sequence analyses of the rpoD, gyrB and 16S rRNA (rrs) gene sequences, and their phenotypic characteristics by API 20NE and Biolog GEN III. Plant pathogenic properties were confirmed on fruits and detached leaves of C. limon cv. ‘Eureka’. Fatty acids and WC MALDI-TOF MS major protein profiles were determined. The genomes of both representatives were sequenced. The average nucleotide index and genome-to-genome distance from KC12T and E10BT are below the cut-off established for a described species. These results support the conclusion that the strains KC12T, KC17, KC20, KC22, KC24A, KC25 and KC26 represent a novel species of Pseudomonas, for which the name of Pseudomonas kairouanensis is proposed. The type strain is KC12T (=CECT9766 and CFBP 8662). The strains E10BT, E10AB, E10CB1 and Iy3BA represent another novel species of Pseudomonas for which the name of Pseudomonas nabeulensis is proposed; the type strain is E10BT (=CECT9765 and CFBP 8661).

Pseudomonas asiatica sp. nov., isolated from hospitalized patients in Japan and Myanmar.

A novel Gram-negative, aerobic, rod-shaped, non-spore-forming bacterial strain, RYU5T, was isolated from a stool sample of an inpatient at a hospital in Okinawa, Japan. The optimal growth temperature of RYU5T was 30 °C. Phylogenetic analysis based on the sequences of housekeeping genes, including the 16S rRNA, rpoB, rpoD and gyrB genes, showed that RYU5T was a member of the Pseudomonas putida group and was located close to Pseudomonas monteilii and P. putida. Whole-genome comparisons, using average nucleotide identity and digital DNA-DNA hybridization, confirmed that strain RYU5T should be classified as a novel species of Pseudomonas. Phenotypic characterization tests showed that utilization of d-mannose, d-serine, l-arabinose and d-fructose could distinguish this strain from other related species of the genus Pseudomonas. Based on genetic and phenotypic evidence, strain RYU5T should be classified as a novel species, for which the name Pseudomonas asiatica sp. nov. is proposed. The type strain is RYU5T (=DSM 107182T, =JCM 32716T), with a DNA G+C content of 62.25 mol%.

Pseudomonas laurylsulfatovorans sp. nov., sodium dodecyl sulfate degrading bacteria, isolated from the peaty soil of a wastewater treatment plant

Pseudomonas are known from their flexible degradation capabilities and their engagement in xenobiotic biotransformation and bioremediation in habitats like soil, active sludge, plant surfaces, and freshwater or marine environments. Here we present taxonomic characterization of three efficient sodium dodecyl sulfate degrading strains: AP3_10, AP3_20 and AP3_22T belonging to the genus Pseudomonas, recently isolated from peaty soil used in a biological wastewater treatment plant. Sequence analyses of 16S rRNA and housekeeping genes: gyrB, rpoD and rpoB showed that the three closely related isolates classify within the Pseudomonas jessenii subgroup. ANIb or dDDH genomic comparisons of AP3_22T (type strain DSM 105098T=PCM 2904T) supported by biochemical tests showed that the isolates differ significantly from their closest relatives. The combined genotypic, phenotypic and chemotaxonomic data strongly support the classification of the three strains: AP3_10, AP3_20 and AP3_22T as a novel species of Pseudomonas, for which we propose the name Pseudomonas laurylsulfatovorans sp. nov. with AP3_22T as the type strain.

Pseudomonas gallaeciensis sp. nov., isolated from crude-oil-contaminated intertidal sand samples after the Prestige oil spill

Strains V113T, V92 and V120 have been isolated from sand samples taken at the Atlantic intertidal shore in Galicia, Spain, after the Prestige oil spill. A preliminary analysis of the 16S rRNA and the partial rpoD gene sequences indicated that these strains belonged to the Pseudomonas genus, but they were distinct from any known Pseudomonas species. They were extensively characterized by a polyphasic taxonomic approach and phylogenetic data that confirmed that these strains belonged to the Pseudomonas pertucinogena group. Phylogenetic analysis of 16S rRNA, gyrB and rpoD gene sequences showed that the three strains were 99% similar and were closely related to members of the P. pertucinogena group, with less than 94% similarity to strains of established species; Pseudomonas pachastrellae was the closest relative. The Average Nucleotide Index based on blast values was 89.0% between V113T and the P. pachastrellae type strain, below the accepted species level (95%). The predominant cellular fatty acid contents and whole cell protein profiles determined by MALDI-TOF mass spectrometry also differentiated the studied strains from known Pseudomonas species. We therefore conclude that strains V113T, V92 and V120 represent a novel species of Pseudomonas, for which the name Pseudomonas gallaeciensis is proposed; the type strain is V113T (=CCUG 67583T=LMG 29038T).

Pseudomonas versuta sp. nov., isolated from Antarctic soil

In this study we analysed three bacterial strains coded L10.10T, A4R1.5 and A4R1.12, isolated in the course of a study of quorum-quenching bacteria occurring in Antarctic soil. The 16S rRNA gene sequence was identical in the three strains and showed 99.7% pairwise similarity with respect to the closest related species Pseudomonas weihenstephanensis WS4993T. Therefore, the three strains were classified within the genus Pseudomonas. Analysis of housekeeping genes (rpoB, rpoD and gyrB) sequences showed similarities of 84-95% with respect to the closest related species of Pseudomonas, confirming its phylogenetic affiliation. The ANI values were less than 86% to the closest related species type strains. The respiratory quinone is Q9. The major fatty acids are C16:0, C16:1 ω7c/ C16:1 ω6c in summed feature 3 and C18:1 ω7c / C18:1 ω6c in summed feature 8. The strains are oxidase- and catalase-positive. Growth occurs at 4–30°C, and at pH 4.0–10. The DNA G+C content is 58.2–58.3mol %. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strains L10.10T, A4R1.5 and A4R1.12 into a novel species of Pseudomonas, for which the name P. versuta sp. nov. is proposed. The type strain is L10.10T (LMG 29628T, DSM 101070T).

Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment

Pseudomonas sp. 10B238 was a putatively novel species of Pseudomonas, isolated from a deep-sea sediment of the South China Sea, which had the genetic potential to produce secondary metabolites related to nonribosomal peptides (NRPs), as well as showed moderate antimicrobial activities. Here we report a high quality draft genome of Pseudomonas sp. 10B238, which comprises 4,933,052bp with the G+C content of 60.23%. A total of 11 potential secondary metabolite biosynthetic gene clusters were predicted, including a NRP for new peptide siderophore. And many anaerobic respiratory terminal enzymes were found for life in deep-sea environments. Our results may provide insights into biosynthetic pathway for antimicrobial bioactive compounds and be helpful to understand the physiological characteristic of this species.

High-Quality Draft Genome Sequence of Pseudomonas sp. BRG100, a Strain with Bioherbicidal Properties against Setaria viridis (Green Foxtail) and Other Pests of Agricultural Significance.

Pseudomonas sp. BRG100 inhibits the growth of certain agricultural pests and is a potentially useful biopesticide for weeds and plant diseases. We have sequenced the 6.25-Mbp genome of this strain and assembled it into 4 scaffolds. Genome sequence comparisons revealed that this strain may represent a novel species of Pseudomonas.

Pseudomonas litoralis sp. nov., isolated from Mediterranean seawater

Strains 2SM5(T) and 2SM6, two strictly aerobic chemo-organotrophic gammaproteobacteria, were isolated from Mediterranean seawater off the coast of Vinaroz, Castellón, Spain, in February, 1990. They were extensively characterized by a polyphasic study that placed them in the genus Pseudomonas. Phylogenetic analysis of 16S rRNA gene sequences showed that both strains shared 100 % sequence similarity and were closely related to members of the Pseudomonas pertucinogena clade, with less than 97.3 % similarity to strains of established species; Pseudomonas xiamenensis was the closest relative. Analysis of sequences of three housekeeping genes, rpoB, rpoD and gyrB, further confirmed the phylogenetic assignment of the Mediterranean isolates. Chemotaxonomic traits such as quinone and polar lipid composition also corroborated the placement of strains 2SM5(T) and 2SM6 in the gammaproteobacteria. Other phenotypic traits, including fatty acid composition, enabled clear differentiation of both isolates from other species of Pseudomonas. We therefore conclude that strains 2SM5(T) and 2SM6 represent a novel species of Pseudomonas, for which the name Pseudomonas litoralis is proposed; the type strain is 2SM5(T) ( = CECT 7670(T) = KCTC 23093(T)).

Extremophilic orgainisms as and unexplored source fo antifungal compounds.

Extracts of the biomasses and fermentation broths of 217 extremophilic microorganisms isolated from a number of locales were screened for antifungal activity using whole-cell and mechanism-based in vitro assays. Importantly, eleven broth extracts had activity against several Candida species and Aspergillus fumigatus in whole-cell in vitro assays. One broth specifically inhibited (1,3)beta-glucan synthase activity and four specifically inhibited ketol-isomerase activity, suggesting a mode of action of the antifungal compound(s) present in these extracts. The extract from one thermophile, a novel species of Pseudomonas, was fractionated, an active compound purified and its structure determined. The compound was identified as pyochelin, a previously identified iron-binding compound with heretofore undescribed antifungal activity. To our knowledge, this is the first report demonstrating that extremophiles synthesize compounds that have antifungal activity.