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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 -
Plant Disease Apr 2022Onion is among the most consumed vegetables in Uruguay, grown in the northwestern and southern regions of the country. The onion supply presents interannual variations...
Onion is among the most consumed vegetables in Uruguay, grown in the northwestern and southern regions of the country. The onion supply presents interannual variations associated with significant postharvest losses, mainly caused by bacterial rots. Besides bulb rotting, onion leaf lesions as well as infections on seed-stalks during seed production may be devastating for some varieties under conducive conditions. This research aimed to identify the causal agents of bulb rots and leaf blight of onion crops in Uruguay. Symptomatic bulbs, seeds-stalks, and leaves were collected from commercial fields from 2015 to 2020. Bacterial colonies were isolated and identified at genera level using physiological tests and 16S rRNA gene sequence analysis. A collection of 59 spp. isolates was obtained (11 from bulbs and 48 from leaves and seeds-stalks). Multilocus sequence analysis using four housekeeping genes (, , , and ) allowed the assignment of the isolates to five species: , , , , and The last two species were not previously reported as onion pathogens elsewhere. The ability to cause disease symptoms was tested by leaf inoculation and red onion scale assays. isolates showed the highest aggressiveness in both assays. Specific isolates from (MAI 6022), (MAI 6036), (MAI 6050), and sp. (MAI 6049) ranked second in aggressiveness on onion leaves, whereas only three isolates belonging to (MAI 6036 and MAI 6058) and (MAI 6045) exhibited the same scale-clearing phenotype as . Leaf inoculation assays were also performed on a set of eight onion cultivars and breeding lines. Overall, MAI 6032 showed the highest aggressiveness in all tested cultivars, followed by MAI 6036. The presence of new reported bacterial species leads to complex disease management and highlights the need for further studies on virulence factors and the epidemiology of these pathogens.
Topics: Crops, Agricultural; Eucalyptus; Onions; Pantoea; Phylogeny; Plant Breeding; Plant Diseases; RNA, Ribosomal, 16S; Uruguay
PubMed: 34818920
DOI: 10.1094/PDIS-06-21-1140-RE -
Frontiers in Microbiology 2021Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to...
Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), , wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants (Columbia-0) and (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to and . All spermospheres also contained DNA belonging to , , and . Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (, , , , and ) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi ( and ) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.
PubMed: 34745040
DOI: 10.3389/fmicb.2021.737616 -
International Journal of Molecular... Sep 2022Due to the observed climate warming, water deficiency in soil is currently one of the most important stressors limiting the size and quality of plant crops. Drought...
Due to the observed climate warming, water deficiency in soil is currently one of the most important stressors limiting the size and quality of plant crops. Drought stress causes a number of morphological, physiological, and biochemical changes in plants, limiting their growth, development, and yield. Innovative methods of inducing resistance and protecting plants against stressors include the inoculation of crops with beneficial microorganisms isolated from the rhizosphere of the plant species to which they are to be applied. The aim of the present study was to evaluate 12 different strains of rhizosphere bacteria of the genera , , , and by using them to inoculate strawberry plants and assessing their impact on mitigating the negative effects of drought stress. Bacterial populations were assessed by estimates of their size based on bacterial counts in the growth substrate and with bioassays for plant growth-promoting traits. The physiological condition of strawberry plants was determined based on the parameters of chlorophyll fluorescence. The usefulness of the test methods used to assess the influence of plant inoculation with rhizosphere bacteria on the response of plants growing under water deficit was also evaluated. A two-factor experiment was performed in a complete randomization design. The first experimental factor was the inoculation of plant roots with rhizosphere bacteria. The second experimental factor was the different moisture content of the growth substrate. The water potential was maintained at -10 to -15 kPa under control conditions, and at -40 to -45 kPa under the conditions of water deficit in the substrate. The tests on strawberry plants showed that the highest sensitivity to water deficiency, and thus the greatest usefulness for characterizing water stress, was demonstrated by the following indices of chlorophyll "a" fluorescence: F, F, F/F, PI, and Area. Based on the assessment of the condition of the photosynthetic apparatus and the analysis of chlorophyll "a" fluorescence indices, including hierarchical cluster analysis, the following strains of rhizosphere bacteria were found to have favorable effects on strawberry plants under water deficit: the sp. strains DLGB2 and DKB26 and the sp. strains DKB63, DKB70, DKB68, DKB64, and DKB65. In the tests, these strains of sp. exhibited a common trait-the ability to produce siderophores, while those of sp. were notable for phosphate mobilization and ACCD activity.
Topics: Bacillus; Bacteria; Chlorophyll; Crops, Agricultural; Fragaria; Phosphates; Plant Roots; Rhizosphere; Siderophores; Soil; Soil Microbiology
PubMed: 36142361
DOI: 10.3390/ijms231810449 -
Microbiology Resource Announcements Dec 2023Here, we describe draft genome sequences for two bacterial isolates from the genus . ATCC 35400 was originally isolated from honeydew melon and was obtained from the...
Here, we describe draft genome sequences for two bacterial isolates from the genus . ATCC 35400 was originally isolated from honeydew melon and was obtained from the American Type Culture Collection. subspecies ICMP 10132 was originally isolated from sugarcane and classified as , but average nucleotide identity and discriminatory PCR support species reclassification.
PubMed: 37982615
DOI: 10.1128/MRA.00471-23 -
Frontiers in Microbiology 2020The species includes strains that are agronomically relevant for their growth-promoting or biocontrol traits. Molecular analysis demonstrated that the IPDC pathway...
The species includes strains that are agronomically relevant for their growth-promoting or biocontrol traits. Molecular analysis demonstrated that the IPDC pathway involved in the conversion of tryptophan (Trp) to indole-3-acetic acid (IAA) is highly conserved among strains at both gene and protein levels. Results also indicated that the promoter region controlling the inducible expression of gene differs from the model system , which is in accordance with the observation that accumulates higher levels of IAA when cells are collected in the exponential phase of growth. To assess the potential applications of these microorganisms for IAA production, C1, an efficient auxin-producer strain, was cultivated in 5 L fermenter so as to evaluate the effect of the medium formulation, the physiological state of the cells, and the induction timing on the volumetric productivity. Results demonstrated that higher IAA levels were obtained by using a saline medium amended with yeast extract and saccharose and by providing Trp, which acts both as a precursor and an inducer, to a culture in the exponential phase of growth. Untargeted metabolomic analysis revealed a significant effect of the carbon source on the exometabolome profile relative to IAA-related compounds and other plant bioactive signaling molecules. The IAA-enriched metabolites secreted in the culture medium by C1 were used as plant biostimulants to run a series of trials at a large-scale nursery farm. Tests were carried out with and systems following the regular protocols used for large-scale plant tree agamic propagation. Results obtained with 4,540 microcuttings of s rootstock GF/677 and 1,080 plantlets of L. showed that metabolites from strain C1 improved percentage of rooted-explant, number of adventitious root formation, plant survival, and quality of plant as vigor, with an increase in the leaf area between 17.5 and 42.7% compared to IBA-K (indole-3-butyric acid potassium salt)-treated plants.
PubMed: 32765438
DOI: 10.3389/fmicb.2020.01475 -
Microorganisms Jan 2020Distinctive strains of are used as soil inoculants for their ability to promote plant growth. strain C1, previously isolated from the phyllosphere of lettuce, can...
Distinctive strains of are used as soil inoculants for their ability to promote plant growth. strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as . In this paper, the complete genome sequence of strain C1 is reported. In addition, experimental evidence is provided on how the strain tolerates arsenate As (V) up to 100 mM, and on how secreted metabolites like IAA and siderophores act as biostimulants in tomato cuttings. The strain has a circular chromosome and two prophages for a total genome of 4,846,925-bp, with a DNA G+C content of 55.2%. Genes related to plant growth promotion and biocontrol activity, such as those associated with IAA and spermidine synthesis, solubilization of inorganic phosphate, acquisition of ferrous iron, and production of volatile organic compounds, siderophores and GABA, were found in the genome of strain C1. Genome analysis also provided better understanding of the mechanisms underlying strain resistance to multiple toxic heavy metals and transmission of these genes by horizontal gene transfer. Findings suggested that strain C1 exhibits high biotechnological potential as plant growth-promoting bacterium in heavy metal polluted soils.
PubMed: 31979031
DOI: 10.3390/microorganisms8020153 -
Microbial Cell Factories Mar 2023The lipopeptide herbicolin A (HA) secreted by the biocontrol agent Pantoea agglomerans ZJU23 is a promising antifungal drug to combat fungal pathogens by targeting lipid...
BACKGROUND
The lipopeptide herbicolin A (HA) secreted by the biocontrol agent Pantoea agglomerans ZJU23 is a promising antifungal drug to combat fungal pathogens by targeting lipid rafts, both in agricultural and clinical settings. Improvement of HA production would be of great significance in promoting its commercialization. This study aims to enhance the HA production in ZJU23 by combining fermentation optimization and strain engineering.
RESULTS
Based on the results in the single-factor experiments, corn steep liquor, temperature and initial pH were identified as the significant affecting factors by the Plackett-Burman design. The fermentation medium and conditions were further optimized using the Box-Behnken response surface method, and the HA production of the wild type strain ZJU23 was improved from ~ 87 mg/mL in King's B medium to ~ 211 mg/mL in HA induction (HAI) medium. A transposon library was constructed in ZJU23 to screen for mutants with higher HA production, and two transcriptional repressors for HA biosynthesis, LrhA and PurR, were identified. Disruption of the LrhA gene led to increased mRNA expression of HA biosynthetic genes, and subsequently improved about twofold HA production. Finally, the HA production reached ~ 471 mg/mL in the ΔLrhA mutant under optimized fermentation conditions, which is about 5.4 times higher than before (~ 87 mg/mL). The bacterial suspension of the ΔLrhA mutant fermented in HAI medium significantly enhanced its biocontrol efficacy against gray mold disease and Fusarium crown rot of wheat, showing equivalent control efficacies as the chemical fungicides used in this study. Furthermore, HA was effective against fungicide resistant Botrytis cinerea. Increased HA production substantially improved the control efficacy against gray mold disease caused by a pyrimethanil resistant strain.
CONCLUSIONS
This study reveals that the transcriptional repressor LrhA negatively regulates HA biosynthesis and the defined HAI medium is suitable for HA production. These findings provide an extended basis for large-scale production of HA and promote biofungicide development based on ZJU23 and HA in the future.
Topics: Pantoea; Fermentation; Genetic Engineering; Antifungal Agents; Biological Control Agents; Temperature; Hydrogen-Ion Concentration; Gene Expression Regulation, Bacterial; Culture Media; Bioreactors; Regression Analysis; Analysis of Variance; Reproducibility of Results; Repressor Proteins; Mycoses; Crops, Agricultural; Plant Diseases; Humans; Animals
PubMed: 36915090
DOI: 10.1186/s12934-023-02051-z -
Microorganisms Sep 2023Cuban rice cultivars INCA LP-5 and INCA LP-7 are widely distributed in Cuba and Caribbean countries. Although there are studies about rhizospheric bacteria associated...
Cuban rice cultivars INCA LP-5 and INCA LP-7 are widely distributed in Cuba and Caribbean countries. Although there are studies about rhizospheric bacteria associated with these cultivars, there are no reports about their seed-associated bacteria. This study aimed to isolate endophytic bacteria from rice seeds and select those with the greatest plant growth-promoting traits. A total of nineteen bacterial strains from the genera , , , and were isolated from the husk and endosperm of rice seeds. The strains sp. S5-1, sp. S5-38, and sp. S7-1 were classified as the most promissory to increase rice growth as they demonstrated the presence of multiple plant growth-promoting traits such as the production of auxins, phosphate, and potassium solubilization, the production of siderophores, and the inhibition of the phytopathogen . The inoculation of strains of sp. and spp. in rice improves the height, root length, fresh weight, and dry weight of the shoot and root after 21 days post-inoculation in hydroponic assays. This study constitutes the first report on Cuban rice cultivars about the presence of endophytes in seeds and their potential to promote seedling growth. sp. S5-1, sp. S5-38, and sp. S7-1 were selected as the more promising strains for the development of bio-stimulators or bio-inoculants for Cuban rice crops.
PubMed: 37764161
DOI: 10.3390/microorganisms11092317