Genomic Characterization of Aureimonas altamirensis C2P003—A Specific Member of the Microbiome of Fraxinus excelsior Trees Tolerant to Ash Dieback

Abstract

Some European ash trees show tolerance towards dieback caused by the invasive pathogen Hymenoscyphus fraxineus. The microbiome of these trees harbours a range of specific bacterial groups. One of these groups belonging to the species Aureimonas altamirensis was studied in detail by genome analysis and a plant inoculation trial. The strain group was shown to be phylogenetically distinct from clinical isolates by 16S rRNA analysis and phylogenomics. Genome analysis of a representative strain C2P003 resulted in a large number of unique gene sequences in comparison to other well-studied strains of the species. A functional analysis of the genome revealed features associated with the synthesis of exopolysaccharides, protein secretion and biofilm production as well as genes for stress adaptation, suggesting the ability of C2P003 to effectively colonize ash leaves. The inoculation of ash seedlings with C2P003 showed a significant positive effect on the plant health of the seedlings that were exposed to H. fraxineus infection. This effect was maintained over a period of three years and was accompanied by a significant shift in the bacterial microbiome composition one year after inoculation. Overall, the results indicate that C2P003 may suppress H. fraxineus in or on ash leaves via colonization resistance or indirectly by affecting the microbiome.

Aureimonas altamirensis: First Isolation from a Chicken Slaughterhouse in Italy Followed by Genotype and Phenotype Evaluations

“…However, the obtainment of a single A. altamirensis strain can be associated with the absence of a specific isolation procedure, as the isolation of this bacterium is performed using several nonselective media [10,13,16,19]. The whole-genome analysis (Supplementary Table S1) of the strain isolated in this work (strain AAI) showed a genome of 4.1 Mb with a GC percentage of 64.99%, 4041 coding DNA sequences (CDS), and 3 16S rDNA, 1 23S rRNA, and 47 tRNA demonstrating characteristics comparable to other isolates of the same species [17]. The dendrogram tree (Figure 2) showed a high similarity between AAI and two A. altamirensis strains isolated from the oxygen minimum zone (OMZ) water column and pleural fluid showing the absence of similarity of AAI with isolates from a specific matrix.…”

“…The absence of 16S rRNA and genomes related to A. altamirensis strains isolated from poultry does not allow the evaluation of its contamination route. of 4.1 Mb with a GC percentage of 64.99%, 4041 coding DNA sequences (CDS), and 3 16S rDNA, 1 23S rRNA, and 47 tRNA demonstrating characteristics comparable to other isolates of the same species [17]. The dendrogram tree (Figure 2) showed a high similarity between AAI and two A. altamirensis strains isolated from the oxygen minimum zone (OMZ) water column and pleural fluid showing the absence of similarity of AAI with isolates from a specific matrix.…”

“…The MALDI-TOF MS analysis allowed a fast identification confirmed by PCR and whole-genome analysis, underlying the importance of this method for the identification of A. altamirensis. This is made even more evident by the identification of this species via MALDI-TOF MS reported in the literature [14,17,21]. At the same time, A. butzleri, identified by MALDI-TOF and 16S rDNA, was isolated from the same sample from which A. altamirensis was isolated.…”

“…Aureimonas (formerly Aurantimonas) altamirensis is considered a potential pathogen associated with human illness [10][11][12][13][14], but not yet well considered in the food sector as a foodborne pathogen. This Gram-negative bacterium is included in the Aurantimonadaceae family [15] and was isolated for the first time from the Altamira caves in Spain [16]; later, it was found in plants, like ash tree [17] and rice [18], and from a swollen testicle of a dog [19], while in humans, A. altamirensis was isolated in patients with a dendritic corneal ulcer with perforation, keratitis [20], bacteriemia [12], and a biliary infection [14] and from pleural effusion [13], wound culture [21], and skin [22]. The A. altamirensis strains are normally antibiotic-susceptible [10,14]; however, resistance was observed against erythromycin, clindamycin [19], gentamicin, and tobramycin [23].…”

Quantitative trait loci associated with apple endophytes during pathogen infection

“…This genus has previously been found in increased abundance in the leaf phyllosphere of ash trees tolerant to the fungal disease ash dieback, Hymenoscyphus fraxineus ( Ulrich et al., 2020 ). The inoculation of ash seedlings with Aureimonas altamirensis C2P003 had positive effect on the plant health and reduced ash dieback symptoms ( Becker et al., 2022 ). Furthermore, a study has shown an isolate of Aureimonas to have antifungal activity towards rice blast, Magnaporthe oryzae.…”