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      Development of a New Semi-Selective Lysine-Ornithine-Mannitol-Arginine-Charcoal Medium for the Isolation of Pantoea Species from Environmental Sources in Japan

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          Abstract

          Although Pantoea species are widely distributed among plants, water, soils, humans, and animals, due to a lack of efficient isolation methods, the clonality of Pantoea species is poorly characterized. Therefore, we developed a new semi-selective medium designated ‘lysine-ornithine-mannitol-arginine-charcoal’ (LOMAC) to isolate these species. In an inclusive and exclusive study examining 94 bacterial strains, all Pantoea strains exhibited yellow colonies on LOMAC medium. The performance of the medium was assessed using Pantoea-spiked soils. Percent average agreement relative to the Api20E biochemical test was 97%. A total of 24 soil spot samples and 19 plant types were subjected to practical trials. Of the 91 yellow colonies selected on LOMAC medium, 81 were correctly identified as Pantoea species using the biochemical test. The sequencing of 16S rRNA ( rrs) and gyrB from these isolates confirmed that Pantoea agglomerans, P. vagans, P. ananatis, and P. deleyi were present in Japanese fields. A phylogenetic analysis using rrs enabled only the limited separation of strains within each Pantoea spp., whereas an analysis using gyrB revealed higher variability and enabled the finer resolution of distinct branches. P. agglomerans isolates were divided into 3 groups, 2 of which were new clades, with the other comprising a large group including biocontrol strains. P. vagans was also in one of the new clades. The present results indicate that LOMAC medium is useful for screening Pantoea species. The use of LOMAC medium will provide new opportunities for identifying the beneficial properties of Japanese Pantoea isolates.

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          Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae.

          The bacterial genus Pantoea comprises many versatile species that have been isolated from a multitude of environments. Pantoea was delineated as a genus approximately 25 years ago, but since then, approximately 20 species have been identified having a diversity of characteristics. Isolates from water and soil have been harnessed for industrial purposes including bioremediation, and the degradation of herbicides and other toxic products. Other isolates possess nitrogen fixation and plant growth-promoting capabilities, which are currently being explored for agricultural applications. Some isolates are antibiotic producers, and have been developed into biocontrol agents for the management of plant diseases. Pantoea is also known to form host associations with a variety of hosts, including plants, insects and humans. Although often thought of as a plant pathogen, recent evidence suggests that Pantoea is being frequently isolated from the nosocomial environment, with considerable debate as to its role in human disease. This review will explore this highly versatile group and its capabilities, its known associations, and the underlying genetic and genomic determinants that drive its diversity and adaptability.
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            WWW-query: an on-line retrieval system for biological sequence banks.

            We have developed a World Wide Web (WWW) version of the sequence retrieval system Query: WWW-Query. This server allows to query nucleotide sequence banks in the EMBL/GenBank/DDBJ formats and protein sequence banks in the NBRF/PIR format. WWW-Query includes all the features of the on-line sequences browsers already available: possibility to build complex queries, integration of cross-references with different data banks, and access to the functional zones of biological interest. It also provides original services not available elsewhere: introduction of the notion of re-usable sequence lists, integration of dedicated helper applications for visualizing alignments and phylogenetic trees and links with multivariate methods for studying codon usage or for complementing phylogenies.
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              Solubilization of insoluble inorganic phosphates by a novel salt- and pH-tolerant Pantoea agglomerans R-42 isolated from soybean rhizosphere.

              To develop environment-friendly biofertilizer solubilizing insoluble phosphates, salt- and pH-tolerant, insoluble inorganic phosphate-solubilizing bacterium was isolated from soybean rhizosphere. On the basis of its physiological characteristics and Vitek analysis, this bacterium was identified as Pantoea agglomerans. The optimal medium composition and cultural conditions for the solubilization of insoluble phosphate by P. agglomerans R-42 were 3% (w/v) of glucose, 0.1% (w/v) of NH4NO3, 0.02% (w/v) of MgSO4 x 7H2O, and 0.06% (w/v) of CaCl2 x 2H2O along with initial pH 7.5 at 30 degree C. The soluble phosphate production under optimal condition was around 900 mg/l, which was approximately 4.6-fold higher than the yield in the MPVK medium. The solubilization of insoluble phosphate was associated with a drop in the pH of the culture medium. P. agglomerans R-42 showed resistance against different environmental stresses like 5-45 degrees C temperature, 1-5% salt concentration and 3-11 pH range. Insoluble phosphate solubilization was highest from CaHPO4 (1367 mg/l), hydroxyapatite (1357 mg/l) and Ca3(PO4)2 (1312 mg/l). However, the strain produced soluble phosphate to the culture broth with the concentrations of 28 mg/l against FePO4, and 19 mg/l against AlPO4, respectively.
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                Author and article information

                Journal
                Microbes Environ
                Microbes Environ
                Microbes and Environments
                the Japanese Society of Microbial Ecology (JSME)/the Japanese Society of Soil Microbiology (JSSM)/the Taiwan Society of Microbial Ecology (TSME)/the Japanese Society of Plant Microbe Interactions (JSPMI)
                1342-6311
                1347-4405
                June 2019
                28 March 2019
                : 34
                : 2
                : 136-145
                Affiliations
                [1 ] Microbiology Research Division Kohjin Bio Co., Ltd. 5–1–3 Chiyoda, Sakado, Saitama 350–0214 Japan
                [2 ] Department of Health and Nutrition, Faculty of Human Life, Jumonji University 2–1–28 Sugasawa, Niiza, Saitama 352–8510 Japan
                Author notes
                [* ]Corresponding author. E-mail: toku169@ 123456jumonji-u.ac.jp ; Tel: +81–48–478–9367; Fax: +81–48–478–9367.
                Article
                34_136
                10.1264/jsme2.ME18128
                6594737
                30918162
                2f66e6fb-2e3c-4f36-8ade-53a4d19f3696
                Copyright © 2019 by Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 14 September 2018
                : 10 January 2019
                Categories
                Articles

                pantoea sp.,isolation,semi-selective medium,environment,phylogenetic analysis

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