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      Draft Genome Sequence of Pantoea ananatis Strain 1.38, a Bacterium Isolated from the Rhizosphere of Oryza sativa var. Puntal That Shows Biotechnological Potential as an Inoculant

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          ABSTRACT

          Pantoea ananatis 1.38 is a strain isolated from the rhizosphere of irrigated rice in southern Spain. Its genome was estimated at 4,869,281 bp, with 4,644 coding sequences (CDSs). The genome encompasses several CDSs related to plant growth promotion, such as that for siderophore metabolism, and virulence genes characteristic of pathogenic Pantoea spp. are absent.

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          A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.

          Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data.
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            Pantoea agglomerans: a mysterious bacterium of evil and good. Part IV. Beneficial effects.

            Pantoea agglomerans, a gammaproteobacterium of plant origin, possesses many beneficial traits that could be used for the prevention and/or treatment of human and animal diseases, combating plant pathogens, promotion of plant growth and bioremediation of the environment. It produces a number of antibiotics (herbicolin, pantocins, microcin, agglomerins, andrimid, phenazine, among others) which could be used for combating plant, animal and human pathogens or for food preservation. Japanese researchers have demonstrated that the low-molecular-mass lipopolysaccharide of P. agglomerans isolated by them and described as 'Immunopotentiator from Pantoea agglomerans 1 (IP-PA1)' reveals the extremely wide spectrum of healing properties, mainly due to its ability for the maintenance of homeostasis by macrophage activation. IP-PA1 was proved to be effective in the prevention and treatment of a broad range of human and animal disorders, such as tumours, hyperlipidaemia, diabetes, ulcer, various infectious diseases, atopic allergy and stress-induced immunosuppression; it also showed a strong analgesic effect. It is important that most of these effects could be achieved by the safe oral administration of IP-PA1. Taking into account that P. agglomerans occurs commonly as a symbiont of many species of insects, including mosquitoes transmitting the Plasmodium parasites causing malaria, successful attempts were made to apply the strategy of paratransgenesis, in which bacterial symbionts are genetically engineered to express and secrete anti-Plasmodium effector proteins. This strategy shows prospects for a successful eradication of malaria, a deadly disease killing annually over one million people, as well as of other vector-borne diseases of humans, animals and plants. Pantoea agglomerans has been identified as an antagonist of many plant pathogens belonging to bacteria and fungi, as a result of antibiotic production, competition mechanisms or induction of plant resistance. Its use as a biocontrol agent permits the decrease of pesticide doses, being a healthy and environmental-friendly procedure. The application of the preparations of this bacterium efficiently protects the stored pome, stone and citrus fruits against invasion of moulds. P. agglomerans strains associated with both rhizosphere and plant tissues (as endophytes) efficiently promote the growth of many plants, including rice and wheat, which are the staple food for the majority of mankind. The promotion mechanisms are diverse and include fixation of atmospheric nitrogen, production of phytohormones, as well as degradation of phytate and phosphate solubilizing which makes the soil phosphorus available for plants. Accordingly, P. agglomerans is regarded as an ideal candidate for an environmental-friendly bioinoculant replacing chemical fertilizers. It has been documented that the Pantoea strains show biodegradation activity on various chemical pollutants of soil and water, including petroleum hydrocarbons and toxic metals. P. agglomerans prevents the penetration of harmful industrial contaminants into deeper parts of soil by biofilm formation, and has an ability to produce hydrogen from waste. Thus, this bacterium appears as a valuable bioremediator which, in some cases, may be acquired as a cheap form of energy. In conclusion, in spite of the proven pathologic role of P. agglomerans in causing occupational diseases of allergic and/or immunotoxic background and accidental infections, the beneficial traits of this species, and of related species of Pantoea genus, are of great value for potential use in many areas of biotechnology. Hence, any restrictions on the use of these organisms and their products should be declined, providing safety precautions at work with the Pantoea biopreparations are maintained.
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              The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elements

              The seed as a habitat for microorganisms is as yet under-explored and has quite distinct characteristics as compared to other vegetative plant tissues. In this study, we investigated three closely related P. ananatis strains (named S6, S7, and S8), which were isolated from maize seeds of healthy plants. Plant inoculation experiments revealed that each of these strains exhibited a different phenotype ranging from weak pathogenic (S7), commensal (S8), to a beneficial, growth-promoting effect (S6) in maize. We performed a comparative genomics analysis in order to find genetic determinants responsible for the differences observed. Recent studies provided exciting insight into the genetic drivers of niche adaption and functional diversification of the genus Pantoea. However, we report here for the first time on the analysis of P. ananatis strains colonizing the same ecological niche but showing distinct interaction strategies with the host plant. Our comparative analysis revealed that genomes of these three strains are highly similar. However, genomic differences in genes encoding protein secretion systems and putative effectors, and transposase/integrases/phage related genes could be observed.
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                Author and article information

                Journal
                Genome Announc
                Genome Announc
                ga
                ga
                GA
                Genome Announcements
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2169-8287
                25 January 2018
                January 2018
                : 6
                : 4
                : e01547-17
                Affiliations
                [a ]Facultad de Biología, Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
                [b ]Embrapa Cerrados, Soil Microbiology, Planaltina, Federal District, Brazil
                [c ]CNPq, Brasília, Federal District, Brazil
                [d ]Embrapa Soja, Soil Biotechnology, CP 231, Londrina, Paraná, Brazil
                Author notes
                Address correspondence to Mariangela Hungria, mariangela.hungria@ 123456embrapa.br .
                Author information
                https://orcid.org/0000-0002-5132-8685
                Article
                genomeA01547-17
                10.1128/genomeA.01547-17
                5786691
                29371365
                0ece8f6e-133b-4e96-9d03-5982472cf034
                Copyright © 2018 Megías et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 12 December 2017
                : 15 December 2017
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 9, Pages: 2, Words: 1246
                Funding
                Funded by: Ministério de Economía y Competitividad;
                Award ID: Mineco AGL2016-77163-R
                Award Recipient :
                Funded by: CNPq-Universal;
                Award ID: 400468/2016-6
                Award Recipient :
                Funded by: Embrapa;
                Award ID: 02.13.08.001.00.00
                Award Recipient :
                Funded by: INCT-Plant-Growth Promoting Microorganisms for Agricultural Sustainability and Environmental Responsibility;
                Award ID: CNPq 465133/2014-2
                Award ID: Fundação Araucária-SETI
                Award ID: CAPES
                Award Recipient :
                Categories
                Prokaryotes
                Custom metadata
                January 2018

                Genetics
                Genetics

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