RESUMEN

Caves are extreme underground environments colonized by oligotrophic bacterial communities that influence mineral transformations. The identification at the species level is important and this study aims to the taxonomic characterisation of four bacterial strains previously isolated from rock surfaces and water samples from a karstic cave located on Mallorca (Spain) that were assigned to the genus Pseudomonas according to 16S rRNA nucleotide sequence analysis. Sequence analysis of the RNA polymerase sigma factor gene (rpoD) allocated these strains to the P. fluorescens lineage within the P. anguilliseptica phylogenetic group, close to the P. benzenivorans type strain. A polyphasic taxonomic approach included phenotypic characterization, fatty acid composition analysis, and whole-cell protein profiling, together with phylogenomic data. The results supported the proposal of a new species in the Pseudomonas genus. Characteristic fatty acid methyl esters of members of the Pseudomonas genus were present (C16:0, C10:0 3-OH, C12:0 2-OH and C12:0 3-OH) and the C12:1 3OH content differentiated these strains from P. benzenivorans. The genomic G + C mol% content of the four sequenced genomes was 66.9%. The average nucleotide indices based on BLAST analysis and the calculation of genome-to-genome distance with respect to their closest relative were lower than 88% and 30%, respectively. These data confirm that the four isolates, R1b-4, R1b-52A, A2bC-1 and R1b-54T, represent a new species, for which the name Pseudomonas lalucatii is proposed, with strain R1b-54T as the type strain (=CCUG 74754T = CECT 30179T). This is the first species in the P. anguilliseptica group isolated from this extreme habitat.

Asunto(s)

Cuevas/microbiología , Filogenia , Pseudomonas , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Genes Bacterianos , Hibridación de Ácido Nucleico , Pseudomonas/clasificación , Pseudomonas/aislamiento & purificación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , España

RESUMEN

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).

Asunto(s)

Citrus/microbiología , Filogenia , Enfermedades de las Plantas/microbiología , Pseudomonas/clasificación , Antibacterianos/farmacología , ADN Bacteriano/genética , Farmacorresistencia Bacteriana , Ácidos Grasos/análisis , Genes Bacterianos/genética , Genoma Bacteriano/genética , Tipificación de Secuencias Multilocus , Hibridación de Ácido Nucleico , Pseudomonas/química , Pseudomonas/genética , Pseudomonas/patogenicidad , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción , Túnez

RESUMEN

Strains VGXO14(T) and Vi1 were isolated from the Atlantic intertidal shore from Galicia, Spain, after the Prestige oil spill. Both strains were Gram-negative rod-shaped bacteria with one polar inserted flagellum, strictly aerobic, and able to grow at 18-37°C, pH 6-10 and 2-10% NaCl. A preliminary analysis of the 16S rRNA and the partial rpoD gene sequences indicated that these strains belonged to the Pseudomonas genus but were distinct from any known Pseudomonas species. A polyphasic taxonomic approach including phylogenetic, chemotaxonomic, phenotypic and genotypic data confirmed that the strains belonged to the Pseudomonas pertucinogena group. In a multilocus sequence analysis, the similarity of VGXO14(T) and Vi1 to the closest type strain of the group, Pseudomonas pachastrellae, was 90.4%, which was lower than the threshold of 97% established to discriminate species in the Pseudomonas genus. The DNA-DNA hybridisation similarity between strains VGXO14(T) and Vi1 was 79.6%, but below 70% with the type strains in the P. pertucinogena group. Therefore, the strains should be classified within the genus Pseudomonas as a novel species, for which the name Pseudomonas aestusnigri is proposed. The type strain is VGXO14(T) (=CCUG 64165(T)=CECT 8317(T)).

Asunto(s)

Pseudomonas/clasificación , Pseudomonas/aislamiento & purificación , Dióxido de Silicio , Microbiología del Suelo , Bacterias , Técnicas de Tipificación Bacteriana , Análisis por Conglomerados , ADN Bacteriano/química , ADN Bacteriano/genética , ADN Ribosómico/química , ADN Ribosómico/genética , ARN Polimerasas Dirigidas por ADN/genética , Datos de Secuencia Molecular , Hibridación de Ácido Nucleico , Petróleo , Contaminación por Petróleo , Filogenia , Pseudomonas/genética , Pseudomonas/fisiología , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Factor sigma/genética , España