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Biotechnology Reports (Amsterdam,... Mar 2021Environmental abiotic stress conditions, especially drought and salinity, are currently the major factors that reduce crop yields worldwide. It has been reported that...
Environmental abiotic stress conditions, especially drought and salinity, are currently the major factors that reduce crop yields worldwide. It has been reported that plant-associated beneficial bacteria, especially strains resistant to abiotic stresses that could maintain their efficiency under environmental challenging conditions, can contribute to alleviate abiotic stresses of host plants. In this study, we presented the assembly of the whole genome of ANP8, a plant growth-promoting bacterium resistant to salinity and drought stresses. The draft genome assembly contained 4,713,172 bp with 4586 predicted genes. A primary draft genome with a total of 5,115,548 bp and 1916 contigs was obtained (longest contig length being 485,272 bp and smallest contig being 112 bp). Following assembly upgrades, 68 scaffolds and 70 contigs with lengths ≥ 500 bp and an N50 = 209,657 bp were obtained. Number of 5554 and 5472 open reading frames longer than 50 codons were observed in the direct strand and in the reverse strand, respectively. Due to the multiple plant growth-promoting characteristics of this bacterium, genes involved in various indole-3-acetic acid production pathways, e.g., indole-3-pyruvic acid and indole-3-acetamide pathways, were found in the bacterium's genome. In addition, multiple copies of the gene, most important enzymes involvement in the solubilization of phosphates, glucose dehydrogenase, were also observed in this genome. The study provides new genomic information to help understanding the way of action of a stress-tolerant plant growth-promoting bacterium.
PubMed: 33643858
DOI: 10.1016/j.btre.2021.e00600 -
Annals of Agricultural and... Dec 2019Five workers (2 males and 3 females) employed in a furniture factory located in eastern Poland developed hypersensitivity pneumonitis (HP) after the pine wood used for...
CASE DESCRIPTION
Five workers (2 males and 3 females) employed in a furniture factory located in eastern Poland developed hypersensitivity pneumonitis (HP) after the pine wood used for furniture production was replaced by birch wood. All of them reported onset of respiratory and general symptoms (cough, shortness of breath, general malaise) after inhalation exposure to birch dust, showed crackles at auscultation, ground-glass attenuations in HRCT examination, and lymphocytosis in the BAL examination. The diagnosis of acute HP was set in 4 persons and the diagnosis of subacute HP in one.
IDENTIFICATION OF SPECIFIC ALLERGEN
Samples of birch wood associated with evoking disease symptoms were subjected to microbiological analysis with the conventional and molecular methods. Two bacterial isolates were found to occur in large quantities (of the order 10 CFU/g) in examined samples: Gram-negative bacterium of the species and a non-filamentous Gram-positive actinobacterium of the species . In the test for inhibition of leukocyte migration, 4 out of 5 examined patients showed a positive reaction in the presence of and 2 in the presence of . Only one person showed the presence of precipitins to and none to . In the inhalation challenge, which is the most relevant allergological test in the HP diagnostics, all patients reacted positively to and only one to . The results indicate that developing in birch wood was the main agent causing HP in the workers exposed to the inhalation of dust from this wood, while the etiologic role of is probably secondary.
CONCLUSION
The results demonstrate that apart from fungi and filamentous actinobacteria, regarded until recently as causative agents of HP in woodworkers, Gram-negative bacteria and non-filamentous actinobacteria may also elicit disease symptoms in the workers processing wood infected with large amounts of these microorganisms. The results obtained also seem to indicate that cellular-mediated reactions are more significant for causing disease symptoms compared to those that are precipitin-mediated.
Topics: Actinobacteria; Acute Disease; Adult; Air Pollutants, Occupational; Alveolitis, Extrinsic Allergic; Betula; Dust; Female; Humans; Inhalation Exposure; Male; Microbacterium; Middle Aged; Pantoea; Poland; Wood
PubMed: 31885240
DOI: 10.26444/aaem/114931 -
Microbial Biotechnology May 2015Lytic bacteriophages are in development as biological control agents for the prevention of fire blight disease caused by Erwinia amylovora. Temperate phages should be...
Lytic bacteriophages are in development as biological control agents for the prevention of fire blight disease caused by Erwinia amylovora. Temperate phages should be excluded as biologicals since lysogeny produces the dual risks of host resistance to phage attack and the transduction of virulence determinants between bacteria. The extent of lysogeny was estimated in wild populations of E. amylovora and Pantoea agglomerans with real-time polymerase chain reaction primers developed to detect E. amylovora phages belonging to the Myoviridae and Podoviridae families. Pantoea agglomerans, an orchard epiphyte, is easily infected by Erwinia spp. phages, and it serves as a carrier in the development of the phage-mediated biological control agent. Screening of 161 E. amylovora isolates from 16 distinct geographical areas in North America, Europe, North Africa and New Zealand and 82 P. agglomerans isolates from southern Ontario, Canada showed that none possessed prophage. Unstable phage resistant clones or lysogens were produced under laboratory conditions. Additionally, a stable lysogen was recovered from infection of bacterial isolate Ea110R with Podoviridae phage ΦEa35-20. These laboratory observations suggested that while lysogeny is possible in E. amylovora, it is rare or absent in natural populations, and there is a minimal risk associated with lysogenic conversion and transduction by Erwinia spp. phages.
Topics: Africa; Erwinia amylovora; Europe; Lysogeny; Myoviridae; New Zealand; North America; Pantoea; Podoviridae; Prophages; Real-Time Polymerase Chain Reaction
PubMed: 25678125
DOI: 10.1111/1751-7915.12253 -
Molecular Plant Pathology Feb 2018Pantoea agglomerans, a widespread epiphytic bacterium, has evolved into a hypersensitive response and pathogenicity (hrp)-dependent and host-specific gall-forming...
Pantoea agglomerans, a widespread epiphytic bacterium, has evolved into a hypersensitive response and pathogenicity (hrp)-dependent and host-specific gall-forming pathogen by the acquisition of a pathogenicity plasmid containing a type III secretion system (T3SS) and its effectors (T3Es). Pantoea agglomerans pv. betae (Pab) elicits galls on beet (Beta vulgaris) and gypsophila (Gypsophila paniculata), whereas P. agglomerans pv. gypsophilae (Pag) incites galls on gypsophila and a hypersensitive response (HR) on beet. Draft genome sequences were generated and employed in combination with a machine-learning approach and a translocation assay into beet roots to identify the pools of T3Es in the two pathovars. The genomes of the sequenced Pab4188 and Pag824-1 strains have a similar size (∼5 MB) and GC content (∼55%). Mutational analysis revealed that, in Pab4188, eight T3Es (HsvB, HsvG, PseB, DspA/E, HopAY1, HopX2, HopAF1 and HrpK) contribute to pathogenicity on beet and gypsophila. In Pag824-1, nine T3Es (HsvG, HsvB, PthG, DspA/E, HopAY1, HopD1, HopX2, HopAF1 and HrpK) contribute to pathogenicity on gypsophila, whereas the PthG effector triggers HR on beet. HsvB, HsvG, PthG and PseB appear to endow pathovar specificities to Pab and Pag, and no homologous T3Es were identified for these proteins in other phytopathogenic bacteria. Conversely, the remaining T3Es contribute to the virulence of both pathovars, and homologous T3Es were found in other phytopathogenic bacteria. Remarkably, HsvG and HsvB, which act as host-specific transcription factors, displayed the largest contribution to disease development.
Topics: Bacterial Proteins; DNA Mutational Analysis; Machine Learning; Pantoea; Plant Tumors; Virulence
PubMed: 28019708
DOI: 10.1111/mpp.12528 -
PloS One 2019The Enterobacterial genus Pantoea contains both free-living and host-associating species, with considerable debate as to whether documented reports of human infections...
The Enterobacterial genus Pantoea contains both free-living and host-associating species, with considerable debate as to whether documented reports of human infections by members of this species group are accurate. MALDI-TOF-based identification methods are commonly used in clinical laboratories as a rapid means of identification, but its reliability for identification of Pantoea species is unclear. In this study, we carried out cpn60-based molecular typing of 54 clinical isolates that had been identified as Pantoea using MALDI-TOF and other clinical typing methods. We found that 24% had been misidentified, and were actually strains of Citrobacter, Enterobacter, Kosakonia, Klebsiella, Pseudocitrobacter, members of the newly described Erwinia gerundensis, and even several unclassified members of the Enterobacteriaceae. The 40 clinical strains that were confirmed to be Pantoea were identified as Pantoea agglomerans, Pantoea allii, Pantoea dispersa, Pantoea eucalypti, and Pantoea septica as well as the proposed species group, Pantoea latae. Some species groups considered largely environmental or plant-associated, such as P. allii and P. eucalypti were also among clinical specimens. Our results indicate that MALDI-TOF-based identification methods may misidentify strains of the Enterobacteriaceae as Pantoea.
Topics: Bacterial Typing Techniques; Diagnostic Errors; Enterobacteriaceae Infections; Humans; Pantoea; Phylogeny; Plants; Reproducibility of Results; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 31682625
DOI: 10.1371/journal.pone.0224731 -
Plant Disease Sep 2023Schisandra chinensis (Turcz.) Baill is a perennial liana, which is widely cultivated and used in China. In August 2022, Schisandra chinensis leaves with small light...
Schisandra chinensis (Turcz.) Baill is a perennial liana, which is widely cultivated and used in China. In August 2022, Schisandra chinensis leaves with small light brown spots were found on plants growing in Fusong (127°28'E, 42°33'N) of China. There was 15% disease incidence and 50% disease severity of Schisandra chinensis in 2-ha fields of S. chinensis. As the disease progressed, the spots become darker and form round or irregular concentric circles. Leaves with brown spot symptoms were collected from the field. Leaf pieces (5 mm × 5 mm) were excised from lesion margins, surface disinfected with 75% ethanol for 1 min, followed by 1.5% sodium hypochlorite for 3 min, and incubated on Luria Bertani (LB) solid medium at 28°C for 24 hours. Eight cultures were isolated, and representative single colony (XWWZH) was selected from the pure cultures according to colony characteristics for observation The purified colonies were round, yellow, and slimy, cells were straight rod-shaped (0.40 to 0.52 × 1.12 to 1.69 µm) were observed. The isolate was Gram negative. It was positive for methyl red reaction, lysine decarboxylase reaction, gelatin hydrolysis reactionand sucrose utilization. It was negative for indole reaction and produced H2S. The bacterium was preliminarily identified as Pantoea agglomerans based on morphological and biochemical tests (Baird et al. 2007). The 16S rDNA and a portion of rpoB of strain XWWZH were amplified and sequenced. The sequences were submitted to GenBank. (Accession OP763753 and OQ813505, respectively). Phylogenetic trees were constructed based on the 16S rDNA and rpoB gene sequences. The sequences of strain XWWZH clustered with strains P. agglomerans deposited in GenBank. The pathogenicity was verified with non-wounded S. chinensis seedlings by punching holes with sterile needles and injecting a solution of 1 × 108 CFU/ml solution. Sterile ddH2O was injected in the control experiment. The inoculated seedlings were incubated in a greenhouse at 25°C with a relative humidity of 65 to 70%. Five to eight days after inoculation, inoculated leaves, exhibited symptoms which were morphologically identical to those of the originally infected leaves whereas control plants remained asymptomatic. The pathogenicity assays were repeated twice with the same results. The re-isolated pathogen had the same morphology and DNA sequences as the original isolate obtained from the field samples, completing Koch's postulates. Strains of P. agglomerans have been reported to severely infect many plants (Ren et al.2008; Lee et al. 2010; Yang et al. 2011; Guo et al. 2019; Gao et al, 2022), but to the best of our knowledge, this is the first report of a strain of P. agglomerans causing leaf blight on Schisandra chinensis in China. The identification of leaf blight caused by P. agglomerans will enable farmers to prevent and manage it ahead of time to reduce losses.
PubMed: 37729653
DOI: 10.1094/PDIS-07-23-1258-PDN -
International Journal of Molecular... Aug 2019In the arid region Bou-Saâda at the South of Algeria, durum wheat L. cv Waha production is severely threatened by abiotic stresses, mainly drought and salinity. Plant...
In the arid region Bou-Saâda at the South of Algeria, durum wheat L. cv Waha production is severely threatened by abiotic stresses, mainly drought and salinity. Plant growth-promoting rhizobacteria (PGPR) hold promising prospects towards sustainable and environmentally-friendly agriculture. Using habitat-adapted symbiosis strategy, the PGPR strain Pa was recovered from wheat roots sampled in Bou-Saâda, conferred alleviation of salt stress in durum wheat plants and allowed considerable growth in this unhostile environment. Strain Pa showed growth up to 35 °C temperature, 5-10 pH range, and up to 30% polyethylene glycol (PEG), as well as 1 M salt concentration tolerance. Pa strain displayed pertinent plant growth promotion (PGP) features (direct and indirect) such as hormone auxin biosynthesis, production of 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and ammonia and phosphate solubilization. PGPR features were stable over wide salt concentrations (0-400 mM). Pa strain was also able to survive in seeds, in the non-sterile and sterile wheat rhizosphere, and was shown to have an endophytic life style. Phylogenomic analysis of strain Pa indicated that genus suffers taxonomic imprecision which blurs species delimitation and may have impacted their practical use as biofertilizers. When applied to plants, strain Pa promoted considerable growth of wheat seedlings, high chlorophyll content, lower accumulation of proline, and favored K accumulation in the inoculated plants when compared to Na in control non-inoculated plants. Metabolomic profiling of strain Pa under one strain many compounds (OSMAC) conditions revealed a wide diversity of secondary metabolites (SM) with interesting salt stress alleviation and PGP activities. All these findings strongly promote the implementation of strain Pa as an efficient biofertilizer in wheat plants culture in arid and salinity-impacted regions.
Topics: Droughts; Endophytes; Pantoea; Plant Roots; Rhizosphere; Salinity; Salt Tolerance; Secondary Metabolism; Stress, Physiological; Symbiosis; Triticum
PubMed: 31426312
DOI: 10.3390/ijms20163989 -
Standards in Genomic Sciences 2016The genus Pantoea incorporates many economically and clinically important species. The plant-associated species, Pantoea agglomerans and Pantoea vagans, are closely...
The genus Pantoea incorporates many economically and clinically important species. The plant-associated species, Pantoea agglomerans and Pantoea vagans, are closely related and are often isolated from similar environments. Plasmids conferring certain metabolic capabilities are also shared amongst these two species. The genomes of two isolates obtained from fungus-growing termites in South Africa were sequenced, assembled and annotated. A high number of orthologous genes are conserved within and between these species. The difference in genome size between P. agglomerans MP2 (4,733,829 bp) and P. vagans MP7 (4,598,703 bp) can largely be attributed to the differences in plasmid content. The genome sequences of these isolates may shed light on the common traits that enable P. agglomerans and P. vagans to co-occur in plant- and insect-associated niches.
PubMed: 26937267
DOI: 10.1186/s40793-016-0144-z -
Journal of Clinical Microbiology Feb 2009Pantoea agglomerans and other Pantoea species cause infections in humans and are also pathogenic to plants, but the diversity of Pantoea strains and their possible...
Pantoea agglomerans and other Pantoea species cause infections in humans and are also pathogenic to plants, but the diversity of Pantoea strains and their possible association with hosts and disease remain poorly known, and identification of Pantoea species is difficult. We characterized 36 Pantoea strains, including 28 strains of diverse origins initially identified as P. agglomerans, by multilocus gene sequencing based on six protein-coding genes, by biochemical tests, and by antimicrobial susceptibility testing. Phylogenetic analysis and comparison with other species of Enterobacteriaceae revealed that the genus Pantoea is highly diverse. Most strains initially identified as P. agglomerans by use of API 20E strips belonged to a compact sequence cluster together with the type strain, but other strains belonged to diverse phylogenetic branches corresponding to other species of Pantoea or Enterobacteriaceae and to probable novel species. Biochemical characteristics such as fosfomycin resistance and utilization of d-tartrate could differentiate P. agglomerans from other Pantoea species. All 20 strains of P. agglomerans could be distinguished by multilocus sequence typing, revealing the very high discrimination power of this method for strain typing and population structure in this species, which is subdivided into two phylogenetic groups. PCR detection of the repA gene, associated with pathogenicity in plants, was positive in all clinical strains of P. agglomerans, suggesting that clinical and plant-associated strains do not form distinct populations. We provide a multilocus gene sequencing method that is a powerful tool for Pantoea species delineation and identification and for strain tracking.
Topics: Bacterial Typing Techniques; Cluster Analysis; Genotype; Gram-Negative Bacterial Infections; Humans; Microbial Sensitivity Tests; Molecular Sequence Data; Pantoea; Phylogeny; Plant Diseases; Plants; Sequence Analysis, DNA
PubMed: 19052179
DOI: 10.1128/JCM.01916-08 -
Microorganisms Dec 2022, the causative agent of fire blight, leads to important economic losses of apple and pear crops worldwide. This study aimed to investigate the potential of the resident...
, the causative agent of fire blight, leads to important economic losses of apple and pear crops worldwide. This study aimed to investigate the potential of the resident microbiota of the apple blossom in combatting plant disease-causing organisms, with a focus on controlling fire blight. We obtained 538 isolates from sites around Canton Zurich, which we tested for activity against and We also evaluated the isolates' activity against oomycete and fungal pathogens. Nine isolates showed activity against , and eight of these against . Furthermore, 117 showed antifungal, and 161 anti-oomycete, activity. We assigned genera and in some cases species to 238 of the isolates by sequencing their 16S RNA-encoding gene. Five strains showed activity against all pathogens and were tested in a detached apple model for anti- activity. Of these five strains, two were able to antagonize , namely #124 and #378. We sequenced the #378 genome and analyzed it for secondary metabolite clusters using antiSMASH, revealing the presence of a putative bacteriocin cluster. We also showed that #124 exhibits strong activity against three different fungi and two oomycetes in vitro, suggesting a broader capacity for biocontrol. Our results showcase the protective potential of the natural apple blossom microbiota. We isolated two candidate biocontrol strains from apple blossoms, suggesting that they might persist at the most common entry point for the causative agent of fire blight. Furthermore, they are probably already part of the human diet, suggesting they might be safe for consumption, and thus are promising candidates for biocontrol applications.
PubMed: 36557734
DOI: 10.3390/microorganisms10122480