Whole-Genome Sequencing of Pseudomonas koreensis Isolated from Diseased Tor tambroides.

Unlike environmental P. koreensis isolated from soil, which has been studied extensively for its role in promoting plant growth, pathogenic P. koreensis isolated from fish has been rarely reported. Therefore, we investigated and isolated the possible pathogen that is responsible for the diseased state of Tor tambroides. Herein, we reported the morphological and biochemical characteristics, as well as whole-genome sequences of a newly identified P. koreensis strain. We assembled a high-quality draft genome of P. koreensis CM-01 with a contig N50 value of 233,601 bp and 99.5% BUSCO completeness. The genome assembly of P. koreensis CM-01 is consists of 6,171,880 bp with a G+C content of 60.5%. Annotation of the genome identified 5538 protein-coding genes, 3 rRNA genes, 54 tRNAs, and no plasmids were found. Besides these, 39 interspersed repeat and 141 tandem repeat sequences, 6 prophages, 51 genomic islands, 94 insertion sequences, 4 clustered regularly interspaced short palindromic repeats, 5 antibiotic-resistant genes, and 150 virulence genes were also predicted in the P. koreensis CM-01 genome. Culture-based approach showed that CM-01 strain exhibited resistance against ampicillin, aztreonam, clindamycin, and cefoxitin with a calculated multiple antibiotic resistance (MAR) index value of 0.4. In addition, the assembled CM-01 genome was successfully annotated against the Cluster of Orthologous Groups of proteins database, Gene Ontology database, and Kyoto Encyclopedia of Genes and Genome pathway database. A comparative analysis of CM-01 with three representative strains of P. koreensis revealed that 92% of orthologous clusters were conserved among these four genomes, and only the CM-01 strain possesses unique elements related to pathogenicity and virulence. This study provides fundamental phenotypic and genomic information for the newly identified P. koreensis strain.

A Pseudomonas taiwanensis malonyl-CoA platform strain for polyketide synthesis.

Malonyl-CoA is a central precursor for biosynthesis of a wide range of complex secondary metabolites. The development of platform strains with increased malonyl-CoA supply can contribute to the efficient production of secondary metabolites, especially if such strains exhibit high tolerance towards these chemicals. In this study, Pseudomonas taiwanensis VLB120 was engineered for increased malonyl-CoA availability to produce bacterial and plant-derived polyketides. A multi-target metabolic engineering strategy focusing on decreasing the malonyl-CoA drain and increasing malonyl-CoA precursor availability, led to an increased production of various malonyl-CoA-derived products, including pinosylvin, resveratrol and flaviolin. The production of flaviolin, a molecule deriving from five malonyl-CoA molecules, was doubled compared to the parental strain by this malonyl-CoA increasing strategy. Additionally, the engineered platform strain enabled production of up to 84 mg L-1 resveratrol from supplemented p-coumarate. One key finding of this study was that acetyl-CoA carboxylase overexpression majorly contributed to an increased malonyl-CoA availability for polyketide production in dependence on the used strain-background and whether downstream fatty acid synthesis was impaired, reflecting its complexity in metabolism. Hence, malonyl-CoA availability is primarily determined by competition of the production pathway with downstream fatty acid synthesis, while supply reactions are of secondary importance for compounds that derive directly from malonyl-CoA in Pseudomonas.

Community Structure of Nitrifying and Denitrifying Bacteria from Effluents Discharged into Lake Victoria, Kenya.

An active microbial community of nitrifying and denitrifying bacteria is needed for efficient utilization of nitrogenous compounds from wastewater. In this study, we explored the bacterial community diversity and structure within rivers, treated and untreated wastewater treatment plants (WWTPs) discharging into Lake Victoria. Water samples were collected from rivers and WWTPs that drain into Lake Victoria. Physicochemical analysis was done to determine the level of nutrients or pollutant loading in the samples. Total community DNA was extracted, followed by Illumina high throughput sequencing to determine the total microbial community and abundance. Enrichment and isolation were then done to recover potential nitrifiers and denitrifiers. Physicochemical analysis pointed to high levels total nitrogen and ammonia in both treated and untreated WWTPs as compared to the samples from the lake and rivers. A total of 1,763 operational taxonomic units (OTUs) spread across 26 bacterial phyla were observed with the most dominant phylum being Proteobacteria. We observed a decreasing trend in diversity from the lake, rivers to WWTPs. The genus Planktothrix constituted 19% of the sequence reads in sample J2 collected from the lagoon. All the isolates recovered in this study were affiliated to three genera: Pseudomonas, Klebsiella and Enterobacter in the phylum Proteobacteria. A combination of metagenomic analysis and a culture-dependent approach helped us understand the relative abundance as well as potential nitrifiers and denitrifiers present in different samples. The recovered isolates could be used for in situ removal of nitrogenous compounds from contaminated wastewater.

Specific Detection of Pseudomonas savastanoi Pathovars: From End-Point PCR to Real-Time PCR and HRMA.

Pseudomonas savastanoi is a phytopathogenic bacterium causing severe disease on olive, oleander, ash, and other Oleaceae. Three main pathovars belong to this species: P. savastanoi pv. savastanoi, pv. nerii, and pv. fraxini. Detection methods are mostly based on the visual inspection of the typical symptoms (i.e., knots and galls). However, this bacterium can survive on the host plant also as an epiphyte without giving any symptom. To avoid the spread of P. savastanoi to areas where it is absent, it is necessary to develop efficient and sensitive detection methods. Here, we reported three different PCR-based techniques, able to discriminate the three P. savastanoi pathovars attacking woody plants.

Functional Genetic Diversity and Plant Growth Promoting Potential of Polyphosphate Accumulating Bacteria in Soil.

Polyphosphate (polyP) accumulation is an important trait of microorganisms. Implication of polyP accumulating bacteria (PAB) in enhanced biological phosphate removal, heavy metal sequestration, and dissolution of dental enamel is well studied. Phosphorous (P) accumulated within microbial biomass also regulates labile P in soil; however, abundance and diversity of the PAB in soil is still unexplored. Present study investigated the genetic and functional diversity of PAB in rhizosphere soil. Here, we report the abundance of Pseudomonas spp. as high PAB in soil, suggesting their contribution to global P cycling. Additional subset analysis of functional genes i.e., polyphosphate kinase (ppk) and exopolyphosphatase (ppx) in all PAB, indicates their significance in bacterial growth and metabolism. Distribution of functional genes in phylogenetic tree represent a more biologically realistic discrimination for the two genes. Distribution of ppx gene disclosed its phylogenetic conservation at species level, however, clustering of ppk gene of similar species in different clades illustrated its environmental condition mediated modifications. Selected PAB showed tolerance to abiotic stress and strong correlation with plant growth promotary (PGP) traits viz. phosphate solubilization, auxin and siderophore production. Interaction of PAB with A. thaliana enhanced the growth and phosphate status of the plant under salinity stress, suggestive of their importance in P cycling and stress alleviation. IMPORTANCE Study discovered the abundance of Pseudomonas genera as a high phosphate accumulator in soil. The presence of functional genes (polyphosphate kinase [ppk] and exopolyphosphatase [ppx]) in all PAB depicts their importance in polyphosphate metabolism in bacteria. Genetic and functional diversity reveals conservation of the ppx gene at species level. Furthermore, we found a positive correlation between PAB and plant growth promotary traits, stress tolerance, and salinity stress alleviation in A. thaliana.

Pseudomonas canavaninivorans sp. nov., isolated from bean rhizosphere.

A novel canavanine-degrading bacterium, strain HB002T, was isolated from rhizosphere soil of a catch crop field collected from the island of Reichenau in Konstanz, Germany, and characterized by using polyphasic taxonomy. The facultative aerobe, rod-shaped, Gram-stain-negative bacterium was oxidase- and catalase-positive. The isolate was able to grow on canavanine as a sole carbon and nitrogen source. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed highest similarities to Pseudomonas bijieensis (L22-9T, 99.93 %), Pseudomonas brassicacearum subsp. neoaurantiaca (ATCC 49054T, 99.76 %), Pseudomonas brassicacearum subsp. brassicacearum (DBK 11T, 99.63 %), Pseudomonas thivervalensis (DSM 13194T, 99.51 %), Pseudomonas kilonensis (DSM 13647T, 99.39 %) and Pseudomonas corrugata (ATCC29736T, 99.39 %). Marker gene analysis placed the strain in the intrageneric group of Pseudomonas fluorescens, subgroup P. corrugata. In silico DNA-DNA hybridization and average nucleotide identity values were both under the recommended thresholds for species delineation. The predominant fatty acids of strain HB002T were C16 : 0, C17 : 0 cyclo ω7c and C18 : 1 ω7c. The major respiratory quinone was Q9, followed by Q8 and minor components of Q7 and Q10. Results from the phenotypic characterization showd the strain's inability to hydrolyse gelatin and to assimilate N-acetyl glucosamide and a positive enzymatic activity of acid phosphatase and naphthol-AS-BI phosphohydrolase that distinguish this strain from closely related type strains. Taken together, these results show that strain HB002T represents a novel species in the genus Pseudomonas, for which the name Pseudomonas canavaninivorans sp. nov. is proposed. The type strain is HB002T (=DSM 112525T=LMG 32336T).

Multilocus sequence based identification and adaptational strategies of Pseudomonas sp. from the supraglacial site of Sikkim Himalaya.

Microorganisms inhabiting the supraglacial ice are biotechnologically significant as they are equipped with unique adaptive features in response to extreme environmental conditions of high ultraviolet radiations and frequent freeze-thaw. In the current study, we obtained eleven strains of Pseudomonas from the East Rathong supraglacial site in Sikkim Himalaya that showed taxonomic ambiguity in terms of species affiliation. Being one of the most complex and diverse genera, deciphering the correct taxonomy of Pseudomonas species has always been challenging. So, we conducted multilocus sequence analysis (MLSA) using five housekeeping genes, which concluded the taxonomic assignment of these strains to Pseudomonas antarctica. This was further supported by the lesser mean genetic distances with P. antarctica (0.73%) compared to P. fluorescens (3.65%), and highest ANI value of ~99 and dDDH value of 91.2 of the representative strains with P. antarctica PAMC 27494. We examined the multi-tolerance abilities of these eleven Pseudomonas strains. Indeed the studied strains displayed significant tolerance to freezing for 96 hours compared to the mesophilic control strain, while except for four strains, seven strains exhibited noteworthy tolerance to UV-C radiations. The genome-based findings revealed many cold and radiation resistance-associated genes that supported the physiological findings. Further, the bacterial strains produced two or more cold-active enzymes in plate-based assays. Owing to the polyadaptational attributes, the strains ERGC3:01 and ERGC3:05 could be most promising for bioprospection.

Revisiting the intrageneric structure of the genus Pseudomonas with complete whole genome sequence information: Insights into diversity and pathogen-related genetic determinants.

Pseudomonas spp. exhibit considerable differences in host specificity and virulence. Most Pseudomonas species were isolated exclusively from environmental sources, ranging from soil to plants, but some Pseudomonas species have been detected from versatile sources, including both human host and environmental sources. Understanding genome variations that generate the tremendous diversity in Pseudomonas biology is important in controlling the incidence of infections. With a data set of 704 Pseudomonas complete whole genome sequences representing 186 species, Pseudomonas intrageneric structure was investigated by hierarchical clustering based on average nucleotide identity, and by phylogeny analysis based on concatenated core-gene alignment. Further comparative functional analyses indicated that Pseudomonas species only living in natural habitats lack multiple functions that are important in the regulation of bacterial pathogenesis, indicating the possession of these functions might be characteristic of Pseudomonas human pathogens. Moreover, we have performed pan-genome based homogeneity analyses, and detected genes with conserved structures but diversified functions across the Pseudomonas genomes, suggesting these genes play a role in driving diversity. In summary, this study provided insights into the dynamics of genome diversity and pathogen-related genetic determinants in Pseudomonas, which might help the development of more targeted antibiotics for the treatment of Pseudomonas infections.

Network analysis of ten thousand genomes shed light on Pseudomonas diversity and classification.

The growth of sequenced bacterial genomes has revolutionized the assessment of microbial diversity. Pseudomonas is a widely diverse genus, containing more than 254 species. Although type strains have been employed to estimate Pseudomonas diversity, they represent a small fraction of the genomic diversity at a genus level. We used 10,035 available Pseudomonas genomes, including 210 type strains, to build a genomic distance network to estimate the number of species through community identification. We identified taxonomic inconsistencies with several type strains and found that 25.65 % of the Pseudomonas genomes deposited on Genbank are misclassified. The phylogenetic tree using single-copy genes from representative genomes in each species cluster in the distance network revealed at least 14 Pseudomonas groups, including the P. alcaligenes group proposed here. We show that Pseudomonas is likely an admixture of different genera and should be further divided. This study provides an overview of Pseudomonas diversity from a network and phylogenomic perspective that may help reduce the propagation of mislabeled Pseudomonas genomes.

Occurrence of Pseudomonas spp. in Raw Vegetables: Molecular and Phenotypical Analysis of Their Antimicrobial Resistance and Virulence-Related Traits.

Pseudomonas is characterized by its great capacity to colonize different ecological niches, but also by its antimicrobial resistance and pathogenicity, causing human, animal, or plant diseases. Raw and undercooked food is a potential carrier of foodborne disease. The aim of this study was to determine the occurrence of Pseudomonas spp. among raw vegetables, analysing their antimicrobial resistance, virulence, and molecular typing. A total of 163 Pseudomonas spp. isolates (12 different species) were recovered from 77 of the 145 analysed samples (53.1%) and were classified into 139 different pulsed-field gel electrophoresis patterns. Low antimicrobial resistance levels, but one multidrug-resistant isolate, were found. Among the 37 recovered P. aeruginosa strains, 28 sequence-types and nine serotypes were detected. Eleven OprD patterns and an insertion sequence (ISPa1635) truncating the oprD gene of one imipenem-resistant strain were found. Ten virulotypes were observed, including four exoU-positive and thirty-one exoS-positive strains. The lasR gene was absent in three ST155 strains and was truncated by different insertion sequences (ISPre2, IS1411, and ISPst7) in other three strains. High biofilm, motility, pigment, elastase, and rhamnolipid production were detected. Our study demonstrated a low occurrence of P. aeruginosa (18%) and low antimicrobial resistance, but a high number of virulence-related traits in these P. aeruginosa strains, highlighting their pathological importance.

Pseudomonas guryensis sp. nov. and Pseudomonas ullengensis sp. nov., isolated from soil.

Two Gram-staining-negative, aerobic, rod-shaped bacteria designated strains SR9T and UL070T, were isolated from soil and subjected to taxonomic characterization. Strain SR9T grew at 10-37 °C (optimum 30 °C), at pH 4.0-10.0 (optimum pH 8.0) and in the presence of 0-1 % NaCl (optimum 0 %), and UL070T at 4-33 °C (optimum 30 °C), at pH 4.0-10.0 (optimum pH 7.0) and in the presence of 0-2 % NaCl (optimum 0 %), respectively. Strain UL070T was motile with flagella. Analysis of 16S rRNA gene sequences indicated that the two strains fell into phylogenetic clusters belonging to the genus Pseudomonas. Both strains SR9T and UL070T were mostly related to Pseudomonas campi S1-A32-2T with 99.70 and 99.01% sequence similarities, and the similarity between the two isolates was 98.90 %. The genome-based in silico analyses indicated that each of the strains SR9T and UL070T was clearly separated from other species of Pseudomonas, as the orthologous average nucleotide identity (OrthoANI) and the digital DNA-DNA hybridization (dDDH) values were no higher than 93.09 and 50.03% respectively with any related species, which were clearly below the cutoff for species distinction. The fatty acid profiles of the two strains mainly consisting of unsaturated components, the presence of ubiquinone 9 (Q-9) as the major respiratory quinone, and phosphatidylethanolamine (PE) and diphosphatidylglycerol (DPG) as the diagnostic polar lipids were consistent with their classification into Pseudomonas. The DNA G+C contents of strains SR9T and UL070T were 63.2 mol% and 63.6 mol% respectively. On the basis of both phenotypic and phylogenetic evidences, each of the isolated strains should be classified as a novel species, for which the names Pseudomonas guryensis sp. nov. (type strain=SR9T=KCTC 82228T=JCM 34509T) and Pseudomonas ullengensis sp. nov. (type strain=UL070T=KCTC 82229T=JCM 34510T) are proposed.

Pseudomonas tohonis sp. nov., isolated from the skin of a patient with burn wounds in Japan.

Strain TUM18999T was isolated from the skin of a patient with burn wounds in Japan. The strain was successfully cultured at 20-42 °C (optimum, 30-35 °C) in 1.0-4.0% NaCl (w/v) and at pH 5.5-9.5, optimum pH 5.5-8.5. The phylogenetic tree reconstructed using 16S rRNA, gyrB, rpoB and rpoD gene sequences indicated that strain TUM18999T is closely related to Pseudomonas otitidis MCC10330T. Although the partial 16S rRNA gene sequence (1412 bp) of TUM18999T exhibits high similarity to those of Pseudomonas alcaligenes NBRC 14159T (99.08 %) and Pseudomonas otitidis MCC10330T (98.51 %), multi-locus sequence analysis using 16S rRNA, gyrB, rpoB and rpoD genes reveals a clear distinction between TUM18999T and other Pseudomonas species. In addition, an average nucleotide identity >90 % was not observed in the P. aeruginosa group. Moreover, TUM18999T and P. otitidis can be distinguished based on the minimum inhibitory concentration for carbapenem. Meanwhile, the cellular fatty acids are enriched with C18 : 1 ω7c/C18 : 1 ω6c (34.35 %), C16 : 1 ω7c/C16 : 1 ω6c (24.22 %), C16 : 0 (19.79 %) and C12 : 0 (8.25 %). Based on this evidence, strain TUM18999T can be defined as representing a novel Pseudomonas species, with the proposed name Pseudomonas tohonis sp. nov. The type strain is TUM18999T (GTC 22698T=NCTC 14580T).

Multilocus sequence analysis reveals different lineages of Pseudomonas anguilliseptica associated with disease in farmed lumpfish (Cyclopterus lumpus L.).

The bacterium Pseudomonas anguilliseptica has in recent years emerged as a serious threat to production of lumpfish in Norway. Little is known about the population structure of this bacterium despite its association with disease in a wide range of different fish species throughout the world. The phylogenetic relationships between 53 isolates, primarily derived from diseased lumpfish, but including a number of reference strains from diverse geographical origins and fish species, were reconstructed by Multi-Locus Sequence Analysis (MLSA) using nine housekeeping genes (rpoB, atpD, gyrB, rpoD, ileS, aroE, carA, glnS and recA). MLSA revealed a high degree of relatedness between the studied isolates, altough the seven genotypes identified formed three main phylogenetic lineages. While four genotypes were identified amongst Norwegian lumpfish isolates, a single genotype dominated, irrespective of geographic origin. This suggests the existence of a dominant genotype associated with disease in production of lumpfish in Norwegian aquaculture. Elucidation of the population structure of the bacterium has provided valuable information for potential future vaccine development.

Pseudomonas schmalbachii sp. nov., isolated from the gut of a millipede (Trigoniulus corallinus) from a coconut tree.

During an investigation of microbes associated with arthropods living in decaying coconut trees, a Pseudomonas isolate, Milli4T, was cultured from the digestive tract of the common Asian millipede, Trigoniulus corallinus. Sequence analysis of 16S rRNA and rpoB genes found that Milli4T was closely related but not identical to Pseudomonas panipatensis Esp-1T, Pseudomonas knackmussi B13T and Pseudomonas humi CCA1T. Whole genome sequencing suggested that this isolate represents a new species, with average nucleotide identity (OrthoANIu) values of around 83.9-87.7% with its closest relatives. Genome-to-genome distance calculations between Milli4T and its closest relatives also suggested they are distinct species. The genomic DNA G+C content of Milli4T was approximately 65.0 mol%. Phenotypic and chemotaxonomic characterization and fatty acid methyl ester analysis was performed on Milli4T and its related type strains. Based on these data, the new species Pseudomonas schmalbachii sp. nov. is proposed, and the type strain is Milli4T (=BCRC 81294T=JCM 34414T=CIP 111980T).

Pseudomonas capsici sp. nov., a plant-pathogenic bacterium isolated from pepper leaf in Georgia, USA.

Three phytopathogenic bacterial strains (Pc19-1T, Pc19-2 and Pc19-3) were isolated from seedlings displaying water-soaked, dark brown-to-black, necrotic lesions on pepper (Capsicum annuum) leaves in Georgia, USA. Upon isolation on King's medium B, light cream-coloured colonies were observed and a diffusible fluorescent pigment was visible under ultraviolet light. Analysis of their 16S rRNA gene sequences showed that they belonged to the genus Pseudomonas, with the highest similarity to Pseudomonas cichorii ATCC 10857T (99.7 %). The fatty acid analysis revealed that the majority of the fatty acids were summed feature 3 (C16  :  1 ω7c/C16  :  1 ω6c), C16  :  0 and summed feature 8 (C18  :  1 ω7c/C18  :  1 ω6c). Phylogenomic analyses based on whole genome sequences demonstrated that the pepper strains belonged to the Pseudomonas syringae complex with P. cichorii as their closest neighbour, and formed a separate monophyletic clade from other species. Between the pepper strains and P. cichorii, the average nucleotide identity values were 91.3 %. Furthermore, the digital DNA-DNA hybridization values of the pepper strains when compared to their closest relatives, including P. cichorii, were 45.2 % or less. In addition, biochemical and physiological features were examined in this study and the results indicate that the pepper strains represent a novel Pseudomonas species. Therefore, we propose a new species Pseudomonas capsici sp. nov., with Pc19-1T (=CFBP 8884T=LMG 32209T) as the type strain. The DNA G+C content of the strain Pc19-1T is 58.4 mol%.

Pseudomonas lactucae sp. nov., a pathogen causing bacterial rot of lettuce in Japan.

Two phytopathogenic bacteria, MAFF 301380T and MAFF 301381, isolated from rot lesions of lettuce (Lactuca sativa L. var. capitata L.) in Japan, were characterized using a polyphasic approach. The cells were Gram-reaction-negative, aerobic, non-spore-forming, rod-shaped and motile with one to three polar flagella. Analysis of the 16S rRNA gene sequences showed that the strains belong to the genus Pseudomonas and are closely related to Pseudomonas cedrina subsp. cedrina CFML 96-198T (99.72 %), Pseudomonas cedrina subsp. fulgida P515/12T (99.65 %), Pseudomonas gessardii DSM 17152T (99.51 %), Pseudomonas synxantha DSM 18928T (99.44 %), Pseudomonas libanensis CIP 105460T (99.44 %) and Pseudomonas lactis DSM 29167T (99.44 %). The genomic DNA G+C content was 60.4 mol% and the major fatty acids consisted of summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). Phylogenetic analysis using the rpoD gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas fluorescens subgroup but formed a monophyletic and robust clade separated from their closest relatives. The average nucleotide identity and digital DNA-DNA hybridization values between the strains and their closely related species were 88.65 % or less and 36.3 % or less, respectively. The strains could be distinguished from their closest relatives by phenotypic characteristics, pathogenicity towards lettuce and whole-cell MALDI-TOF MS profiles. The evidence presented in this study supports the classification of the strains as representing a novel Pseudomonas species, for which we propose the name Pseudomonas lactucae sp. nov., with the type strain MAFF 301380T (=ICMP 23838T).

Pseudomonas arcuscaelestis sp. nov., isolated from rainbow trout and water.

Cells of strains P66T, V1 and W15Feb18 are Gram-stain-negative short rods and motile by one polar flagellum. Strain P66T was isolated from rainbow trout (Oncorhynchus mykiss) cultivated at a fish farm in Turkey. Strain V1 was isolated from sand of an intertidal shore on the Galicia coast in Spain and strain W15Feb18 was isolated from water collected at the Woluwe River in Belgium. Based on 16S rRNA sequence similarity values, the strains were grouped under the genus Pseudomonas and the Pseudomonas putida phylogenetic group of species. The DNA G+C content ranged from 58.5 to 58.9 mol%. The strains were characterized phenotypically by the API 20NE and Biolog GEN III tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. The absence of the hydrolysis of gelatin and the assimilation of arabinose, mannose and mannitol differentiated these strains from the closest species, Pseudomonas alkylphenolica. The major fatty acid components were C16:0 (29.91-31.68 %) and summed feature 3 (36.44-37.55 %). Multilocus sequence analysis with four and 83 housekeeping gene sequences and a core proteome analysis showed that these strains formed a phylogenetic cluster in the P. putida group of species. Genome comparisons by the average nucleotide identity based on blast and the Genome-to-Genome Distance Calculator demonstrated that the three strains belonged to the same genomic species and were distant from any known species, with similarity values lower than the thresholds established for species in the genus Pseudomonas. These data permitted us to conclude that strains P66T, V1 and W15Feb18 belong to a novel species in the genus Pseudomonas, for which the name Pseudomonas arcuscaelestis sp. nov. is proposed. The type strain is P66T (=CECT 30176T=CCUG 74872T). The other strains have been deposited in the CECT with the corresponding collection numbers: V1 (=CECT 30356) and W15Feb18 (=CECT 30355).

Biodegradation of binary mixtures of octane with benzene, toluene, ethylbenzene or xylene (BTEX): insights on the potential of Burkholderia, Pseudomonas and Cupriavidus isolates.

The contamination of the environment by crude oil and its by-products, mainly composed of aliphatic and aromatic hydrocarbons, is a widespread problem. Biodegradation by bacteria is one of the processes responsible for the removal of these pollutants. This study was conducted to determine the abilities of Burkholderia sp. B5, Cupriavidus sp. B1, Pseudomonas sp. T1, and another Cupriavidus sp. X5 to degrade binary mixtures of octane (representing aliphatic hydrocarbons) with benzene, toluene, ethylbenzene, or xylene (BTEX as aromatic hydrocarbons) at a final concentration of 100 ppm under aerobic conditions. These strains were isolated from an enriched bacterial consortium (Yabase or Y consortium) that prefer to degrade aromatic hydrocarbon over aliphatic hydrocarbons. We found that B5 degraded all BTEX compounds more rapidly than octane. In contrast, B1, T1 and X5 utilized more of octane over BTX compounds. B5 also preferred to use benzene over octane with varying concentrations of up to 200 mg/l. B5 possesses alkane hydroxylase (alkB) and catechol 2,3-dioxygenase (C23D) genes, which are responsible for the degradation of alkanes and aromatic hydrocarbons, respectively. This study strongly supports our notion that Burkholderia played a key role in the preferential degradation of aromatic hydrocarbons over aliphatic hydrocarbons in the previously characterized Y consortium. The preferential degradation of more toxic aromatic hydrocarbons over aliphatics is crucial in risk-based bioremediation.

Evolutionary history expands the range of signaling interactions in hybrid multikinase networks.

Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonical TCS signaling pathways, with transmitter and receiver domains within a single protein communicating via intramolecular phosphotransfer. Here, we report how evolutionary relationships between hybrid HKs can be used as predictors of potential intermolecular and intramolecular interactions ('phylogenetic promiscuity'). We used domain-swap genes chimeras to investigate the specificity of phosphotransfer within hybrid HKs of the GacS-GacA multikinase network of Pseudomonas brassicacearum. The receiver domain of GacS was replaced with those from nine donor hybrid HKs. Three chimeras with receivers from other hybrid HKs demonstrated correct functioning through complementation of a gacS mutant, which was dependent on strains having a functional gacA. Formation of functional chimeras was predictable on the basis of evolutionary heritage, and raises the possibility that HKs sharing a common ancestor with GacS might remain components of the contemporary GacS network. The results also demonstrate that understanding the evolutionary heritage of signaling domains in sophisticated networks allows their rational rewiring by simple domain transplantation, with implications for the creation of designer networks and inference of functional interactions.

Inhibition of Three Potato Pathogens by Phenazine-Producing Pseudomonas spp. Is Associated with Multiple Biocontrol-Related Traits.

Phenazine-producing Pseudomonas spp. are effective biocontrol agents that aggressively colonize the rhizosphere and suppress numerous plant diseases. In this study, we compared the ability of 63 plant-beneficial phenazine-producing Pseudomonas strains representative of the worldwide diversity to inhibit the growth of three major potato pathogens: the oomycete Phytophthora infestans, the Gram-positive bacterium Streptomyces scabies, and the ascomycete Verticillium dahliae. The 63 Pseudomonas strains are distributed among four different subgroups within the P. fluorescens species complex and produce different phenazine compounds, namely, phenazine-1-carboxylic acid (PCA), phenazine-1-carboxamide (PCN), 2-hydroxyphenazine-1-carboxylic acid, and 2-hydroxphenazine. Overall, the 63 strains exhibited contrasted levels of pathogen inhibition. Strains from the P. chlororaphis subgroup inhibited the growth of P. infestans more effectively than strains from the P. fluorescens subgroup. Higher inhibition was not associated with differential levels of phenazine production nor with specific phenazine compounds. The presence of additional biocontrol-related traits found in P. chlororaphis was instead associated with higher P. infestans inhibition. Inhibition of S. scabies by the 63 strains was more variable, with no clear taxonomic segregation pattern. Inhibition values did not correlate with phenazine production nor with specific phenazine compounds. No additional synergistic biocontrol-related traits were found. Against V. dahliae, PCN producers from the P. chlororaphis subgroup and PCA producers from the P. fluorescens subgroup exhibited greater inhibition. Additional biocontrol-related traits potentially involved in V. dahliae inhibition were identified. This study represents a first step toward harnessing the vast genomic diversity of phenazine-producing Pseudomonas spp. to achieve better biological control of potato pathogens. IMPORTANCE Plant-beneficial phenazine-producing Pseudomonas spp. are effective biocontrol agents, thanks to the broad-spectrum antibiotic activity of the phenazine antibiotics they produce. These bacteria have received considerable attention over the last 20 years, but most studies have focused only on the ability of a few genotypes to inhibit the growth of a limited number of plant pathogens. In this study, we investigated the ability of 63 phenazine-producing strains, isolated from a wide diversity of host plants on four continents, to inhibit the growth of three major potato pathogens: Phytophthora infestans, Streptomyces scabies, and Verticillium dahliae. We found that the 63 strains differentially inhibited the three potato pathogens. These differences are in part associated with the nature and the quantity of the phenazine compounds being produced but also with the presence of additional biocontrol-related traits. These results will facilitate the selection of versatile biocontrol agents against pathogens.