Phenotypic and genetic diversity of rice seed-associated bacteria and their role in pathogenicity and biological control
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To study the phenotypic and genetic diversity of culturable bacteria associated with rice seed and to asses the antagonistic and pathogenic potential of the isolated bacteria.Seed of rice cultivar PSBRc14 was collected from farmers' fields of irrigated lowland in southern Luzon, Philippines. Isolations of distinct colonies yielded 498 isolates. Classification of the isolates according to similarities in cellular characteristics, whole-cell fatty acid composition, and colony appearance differentiated 101 morphotype groups. Predominant bacteria were Coryneform spp., Pantoea spp. and Pseudomonas spp. Other bacteria regularly present were Actinomycetes spp., Bacillus pumilus, B. subtilis, Burkholderia glumae, Enterobacter cloacae, Paenibacillus polymyxa, Staphylococcus spp. and Xanthomonas spp. The genetic diversity among isolates was assessed by BOX-PCR fingerprinting of genomic DNA and represented 284 fingerprint types (FPTs). Most FPTs (78%) were not shared among samples, while eight FPTs occurred frequently in the samples. Seven of these FPTs also occurred frequently in a previous collection made from rainfed lowlands of Iloilo island, Philippines. Sixteen per cent of the isolates inhibited in vitro the mycelial growth of the rice pathogens Rhizoctonia solani and Pyricularia grisea, whereas 4% were pathogens identified as Burkholderia glumae, Burkholderia gladioli and Acidovorax avenae ssp. avenae.This study reveals a broad morphological and genetic diversity of bacteria present on seed of a single rice cultivar.This line of work contributes to a better understanding of the microbial diversity present on rice seed and stresses its importance as a carrier of antagonists and pathogens.Keywords:
Pantoea
The endophytes were separated from Xinjiang carrots using gradient dilution method. There were 59 endophytes obtained by the separation and purification method, including 49 strains of endophytic bacteria, 10 strains of endophytic fungi. These endophytes incorporated 10 strains isolated from the head skin, 18 strains separated from central skin, 13 strains segregated from the tail skin, 9 strains derived from shallow meat, and 9 strains did from deep meat, which of the most number belonged to 30.5% of central skin. Gram staining experiment of endophytic bacteria authenticated 43 strains of gram-positive bacterium and 6 strains of gram-negative bacterium. Through observing the strain of morphological characteristics under a microscope, and identification of physiology and biochemistry as well as molecular biology, some strains were classified, for example 3 strains of Enterobacter cloacae strains, 5 strains of Enterobacter ludwigii strain, 1 strains of Pantoea dispersa strain, 2 strains of Pantoea, 1 strains of Enterobacter, 1 strains of Raoultella, 1 strains of Enterobacteriales bacterium, 4 strains of Enterobacter asburiae strain, 3 strains of Enterobacter aerogenes strain, 2 strains of Pantoea vagans partial, 1 strains of Pantoea agglomerans strain, 1 strains of Kluyvera cryocrescens, 1 strains of Enterobacter asburiae, 1 strains of Enterobacter cloacae subsp, 1 strains of Enterobacter mori strain. 1 strains of Aspergillus niger strain. 1 strains of Ciadosporium. 1 strains of Corynespora torulosa. Among these strains, enterobacterium was the largest, accounting for 17.9% of the total number.
Pantoea
Enterobacter cloacae
Enterobacter aerogenes
Strain (injury)
Pantoea agglomerans
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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.
Pantoea
Pantoea agglomerans
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Crop diseases are responsible for considerable yield losses worldwide and particularly in sub-Saharan Africa. To implement efficient disease control measures, detection of the pathogens and understanding pathogen spatio-temporal dynamics is crucial and requires the use of molecular detection tools, especially to distinguish different pathogens causing more or less similar symptoms. We report here the design a new molecular diagnostic tool able to simultaneously detect five bacterial taxa causing important diseases on rice in Africa: (1) Pseudomonas fuscovaginae, (2) Xanthomonas oryzae, (3) Burkholderia glumae and Burkholderia gladioli, (4) Sphingomonas and (5) Pantoea species. This new detection tool consists of a multiplex PCR, which is cost effective and easily applicable. Validation of the method is presented through its application on a global collection of bacterial strains. Moreover, sensitivity assessment for the detection of all five bacteria is reported to be at 0.5 ng DNA by μl. As a proof of concept, we applied the new molecular detection method to a set of 256 rice leaves collected from 16 fields in two irrigated areas in western Burkina Faso. Our results show high levels of Sphingomonas spp. (up to 100% of tested samples in one field), with significant variation in the incidence between the two sampled sites. Xanthomonas oryzae incidence levels were mostly congruent with bacterial leaf streak (BLS) and bacterial leaf blight (BLB) symptom observations in the field. Low levels of Pantoea spp. were found while none of the 256 analysed samples was positive for Burkholderia or Pseudomonas fuscovaginae. Finally, many samples (up to 37.5% in one studied field) were positive for more than one bacterium (co-infection). Documenting co-infection levels are important because of their drastic consequences on epidemiology, evolution of pathogen populations and yield losses. The newly designed multiplex PCR for multiple bacterial pathogens of rice is a significant improvement for disease monitoring in the field, thus contributing to efficient disease control and food safety.
Pantoea
Xanthomonas
Burkholderia cepacia complex
Sphingomonas
Bacterial disease
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Pantoea
Pantoea agglomerans
Kanamycin
Operational taxonomic unit
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To isolate and identify diazotrophic endophytes in the stem of Japanese sweetpotato cv. Koganesengan.Surface-sterilized and thinly sliced (1-2 mm) sweetpotato stem samples were incubated in test tubes with semi-solid modified Rennie (MR) medium. The test tubes were assayed for acetylene reduction activity (ARA) 5 days after incubation at 30 degrees C. Twelve isolates were obtained from MR plates inoculated with a loop of semi-solid MR medium from ARA+ tubes. However, ARA test showed that only nine isolates were diazotrophic and three were nondiazotrophic strains. Using the API 20E diagnostic kit, four diazotrophic isolates were identified as strains of Pantoea spp. and five isolates as Klebsiella spp. The nondiazotrophic bacteria were strains of Enterobacter spp. A diazotrophic isolate Pantoea sp. MY1 and nondiazotrophic isolate Enterobacter sp. MY2 were identified to the species level by full sequence analysis of 16S rRNA gene. The results showed that MY1 had 99.2% similarity to Pantoea agglomerans ATCC 27155 and MY2 had 99.5% similarity to Enterobacter asburiae ATCC 35953.The stem of sweetpotato cv. Koganesengan was colonized by diazotrophic endophyte P. agglomerans and nondiazotrophic endophyte E. asburiae.This study is an essential step toward understanding the ecology and interaction between endophytic bacteria and sweetpotato.
Pantoea agglomerans
Pantoea
Endophyte
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Pantoea
Serratia
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Pantoea
Cronobacter
Cronobacter sakazakii
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Investigations of microbial contamination and species composition of the Enterobacteriaceae family in fresh vegetables and lettuce has been conducted. The objects of study were new types of fresh ready-to-eat vegetable foods - salads, sliced vegetables and mixtures thereof, sampled at the main stages of production, including washing, antimicrobial treatment with sodium hypochlorite, and packaging in the film under vacuum. Quantitative analysis of Enterobacteriaceae levels in fresh and packaged vegetables and salads showed that their part in the total amount of microbial contaminants is large enough. Average Enterobacteriaceae content ranged from 2,14 to 3,34 lg cfu/g, reaching in some samples values 4,38-4,74 lg, comparable with the levels of total bacteria. Considerable species diversity of microflora contaminating ready-to-eat vegetable products has been found. Bacteria of the genera Enterobactel; Pantoea, Citrobacter, Serratia, Pseudomonas, Kluyvera, Klebsiella, Escherichia, Rahnella, Acinetobacter were found in the salads and sliced vegetables. In the tested samples most frequently detected Enterobacter spp. - 37% of identified strains and Pantoea spp - 25% of strains. The data on the composition and levels of microbial contaminants in vegetable and salad products highlight not only the need to monitor coliform bacteria - traditional indicators of faecal contamination of raw materials, but also the need to introduce criteria for the amount of Enterobacteriaceae.
Pantoea
Citrobacter
Serratia
Pantoea agglomerans
Klebsiella
Sodium hypochlorite
Food contaminant
Coliform bacteria
Food microbiology
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Pantoea
Pantoea agglomerans
Serratia
Citrobacter
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Pantoea
Cronobacter
Cronobacter sakazakii
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