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Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites

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ABSTRACT

Pseudomonas citronellolis is a Gram negative, motile gammaproteobacterium belonging to the order Pseudomonadales and the family Pseudomonadaceae. We isolated strain P3B5 from the phyllosphere of basil plants (Ocimum basilicum L.). Here we describe the physiology of this microorganism, its full genome sequence, and detailed annotation. The 6.95 Mbp genome contains 6071 predicted protein coding sequences and 96 RNA coding sequences. P. citronellolis has been the subject of many studies including the investigation of long-chain aliphatic compounds and terpene degradation. Plant leaves are covered by long-chain aliphates making up a waxy layer that is associated with the leaf cuticle. In addition, basil leaves are known to contain high amounts of terpenoid substances, hinting to a potential nutrient niche that might be exploited by P. citronellolis. Furthermore, the isolated strain exhibited resistance to several antibiotics. To evaluate the potential of this strain as source of transferable antibiotic resistance genes on raw consumed herbs we therefore investigated if those resistances are encoded on mobile genetic elements. The availability of the genome will be helpful for comparative genomics of the phylogenetically broad pseudomonads, in particular with the sequence of the P. citronellolis type strain PRJDB205 not yet publicly available. The genome is discussed with respect to a phyllosphere related lifestyle, aliphate and terpenoid degradation, and antibiotic resistance.

Electronic supplementary material: The online version of this article (doi:10.1186/s40793-016-0190-6) contains supplementary material, which is available to authorized users.

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Phylogenetic tree of the genus Pseudomonas highlighting the position of P. citronellolis P3B5 relative to other representative Pseudomonas species. Xanthomonas campestris pv. campestris ATCC 33913 was chosen as outgroup. The tree is based on whole genome alignment. The bar reflects normalized pairwise genomic distance between genomes based on their shared genomic content. Accession numbers of the used strains are reported in Additional file 1: Table S1. The overall topology is confirmed by a phylogenetic tree based on MLSA with good bootstrap support (Additional file 2: Figure S2)
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Fig2: Phylogenetic tree of the genus Pseudomonas highlighting the position of P. citronellolis P3B5 relative to other representative Pseudomonas species. Xanthomonas campestris pv. campestris ATCC 33913 was chosen as outgroup. The tree is based on whole genome alignment. The bar reflects normalized pairwise genomic distance between genomes based on their shared genomic content. Accession numbers of the used strains are reported in Additional file 1: Table S1. The overall topology is confirmed by a phylogenetic tree based on MLSA with good bootstrap support (Additional file 2: Figure S2)

Mentions: To phylogenetically place P. citronellolis P3B5, a phylogenetic tree was constructed by multiple genome alignment using the program progressiveMauve with standard parameters [22] (Fig. 2). From each thus far sequenced species one representative strain, if possible a type strain, was chosen. Only complete genomes were considered. As outgroup species Xanthomonas campestris pv. campestrisATCC 33913 was chosen. A summary of the classification and general features of P. citronellolis P3B5 is given in Table 1.Fig. 2


Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites
Phylogenetic tree of the genus Pseudomonas highlighting the position of P. citronellolis P3B5 relative to other representative Pseudomonas species. Xanthomonas campestris pv. campestris ATCC 33913 was chosen as outgroup. The tree is based on whole genome alignment. The bar reflects normalized pairwise genomic distance between genomes based on their shared genomic content. Accession numbers of the used strains are reported in Additional file 1: Table S1. The overall topology is confirmed by a phylogenetic tree based on MLSA with good bootstrap support (Additional file 2: Figure S2)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5037603&req=5

Fig2: Phylogenetic tree of the genus Pseudomonas highlighting the position of P. citronellolis P3B5 relative to other representative Pseudomonas species. Xanthomonas campestris pv. campestris ATCC 33913 was chosen as outgroup. The tree is based on whole genome alignment. The bar reflects normalized pairwise genomic distance between genomes based on their shared genomic content. Accession numbers of the used strains are reported in Additional file 1: Table S1. The overall topology is confirmed by a phylogenetic tree based on MLSA with good bootstrap support (Additional file 2: Figure S2)
Mentions: To phylogenetically place P. citronellolis P3B5, a phylogenetic tree was constructed by multiple genome alignment using the program progressiveMauve with standard parameters [22] (Fig. 2). From each thus far sequenced species one representative strain, if possible a type strain, was chosen. Only complete genomes were considered. As outgroup species Xanthomonas campestris pv. campestrisATCC 33913 was chosen. A summary of the classification and general features of P. citronellolis P3B5 is given in Table 1.Fig. 2

View Article: PubMed Central - PubMed

ABSTRACT

Pseudomonas citronellolis is a Gram negative, motile gammaproteobacterium belonging to the order Pseudomonadales and the family Pseudomonadaceae. We isolated strain P3B5 from the phyllosphere of basil plants (Ocimum basilicum L.). Here we describe the physiology of this microorganism, its full genome sequence, and detailed annotation. The 6.95 Mbp genome contains 6071 predicted protein coding sequences and 96 RNA coding sequences. P. citronellolis has been the subject of many studies including the investigation of long-chain aliphatic compounds and terpene degradation. Plant leaves are covered by long-chain aliphates making up a waxy layer that is associated with the leaf cuticle. In addition, basil leaves are known to contain high amounts of terpenoid substances, hinting to a potential nutrient niche that might be exploited by P. citronellolis. Furthermore, the isolated strain exhibited resistance to several antibiotics. To evaluate the potential of this strain as source of transferable antibiotic resistance genes on raw consumed herbs we therefore investigated if those resistances are encoded on mobile genetic elements. The availability of the genome will be helpful for comparative genomics of the phylogenetically broad pseudomonads, in particular with the sequence of the P. citronellolis type strain PRJDB205 not yet publicly available. The genome is discussed with respect to a phyllosphere related lifestyle, aliphate and terpenoid degradation, and antibiotic resistance.

Electronic supplementary material: The online version of this article (doi:10.1186/s40793-016-0190-6) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus