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HUNGRIA, M.

MEGÍAS, E.

MEGÍAS, M.

OLLERO, F. J.

REIS JUNIOR, F. B. dos

RIBEIRO, R. A.

Portuguese

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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.

Draft Genome Sequence of Pantoea ananatis Strain 1.38, aBacterium Isolated from the Rhizosphere of Oryza sativa var.Puntal That Shows Biotechnological Potential as an InoculantEsaú Megías,a,b,c Fábio Bueno dos Reis Junior,b Renan Augusto Ribeiro,c Francisco Javier Ollero,a Manuel Megías,aMariangela HungriadaFacultad de Biología, Departamento de Microbiología, Universidad de Sevilla, Seville, SpainbEmbrapa Cerrados, Soil Microbiology, Planaltina, Federal District, BrazilcCNPq, Brasília, Federal District, BrazildEmbrapa Soja, Soil Biotechnology, CP 231, Londrina, Paraná, BrazilABSTRACT Pantoea ananatis 1.38 is a strain isolated from the rhizosphere of irri-gated rice in southern Spain. Its genome was estimated at 4,869,281 bp, with 4,644coding sequences (CDSs). The genome encompasses several CDSs related to plantgrowth promotion, such as that for siderophore metabolism, and virulence genescharacteristic of pathogenic Pantoea spp. are absent.The genus Pantoea encompasses plant-pathogenic, commensal, and endophyticspecies, and the beneficial species may promote plant growth (1–3). Our researchgroup isolated and characterized several beneficial Pantoea strains from rice (Oryzasativa L.) paddies of the Guadalquivir River marshes in southern Spain (4–6), and wehave sequenced the genome of Pantoea ananatis strain 1.38, isolated from the rhizo-sphere of the variety Puntal. The bacterium has phosphate solubilization activity,siderophore and auxin production, and cellulose, lipase, and pectinase activities. Inexperiments performed under greenhouse conditions, strain 1.38 increased the bio-masses of rice (5 to 8%), maize (Zea mays L.) (15 to 17%), and, when coinoculated withRhizobium tropici, common bean (Phaseolus vulgaris L.) (35 to 40%).DNA extraction and sequencing were performed as previously described (4–6).Paired-end reads obtained by shotgun sequencing on the MiSeq platform allowed agenome coverage of 230-fold. The FASTQ files were assembled by the A5-miseqpipeline (de novo assembly) (7). The genome was estimated at 4,869,281 bp, assembledin 23 contigs, with a GC content of 53.3 mol%; there are two plasmids of about 180and 60 Mb. The average nucleotide identity (ANI) values of the strain 1.38 genome withthe whole genomes of P. ananatis strains LMG 2665T, AMG 501, and AMG521 were96.41, 96.37, and 99.16%, respectively. Therefore, strains AMG521 and 1.38 mightcomprise a specific group of P. ananatis strains from the marshes of the GuadalquivirRiver.Sequences were submitted to the Rapid Annotations using Subsystems Technology(RAST) server (8), and 4,644 DNA coding sequences (CDSs) were identified, with 58%classified in 530 subsystems. Several genes are related to stress response (166 CDSs,3.5% of the genome), including those for response to osmotic and oxidative stress andto cold and heat shock, and those for choline, betaine, and trehalose biosynthesis.There are several transcriptional regulators, with at least 23 belonging to the LysRfamily.Protein secretion systems (types I to VIII) can play important roles in the interactionof P. ananatis with plants. Strain 1.38 carries genes of types II, IV (pilus type IV, INCconjugal transfer, and conjugal transfer proteins TraI, TraB, TraC, TraK, and TraW), VI,Received 12 December 2017 Accepted 15December 2017 Published 25 January 2018Citation Megías E, dos Reis Junior FB, RibeiroRA, Ollero FJ, Megías M, Hungria M. 2018. Draftgenome sequence of Pantoea ananatis strain1.38, a bacterium isolated from the rhizosphereof Oryza sativa var. Puntal that showsbiotechnological potential as an inoculant.Genome Announc 6:e01547-17. https://doi.org/10.1128/genomeA.01547-17.Copyright © 2018 Megías et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to MariangelaHungria, mariangela.hungria@embrapa.br.PROKARYOTEScrossmVolume 6 Issue 4 e01547-17 genomea.asm.org 1 on September 21, 2018 by guesthttp://mra.asm.org/Downloaded from and VII (fimbrial type I) secretion systems, which are slightly different from those ofstrain AMG521, as the type V is absent in strain 1.38. There are no virulence genestypical of plant-pathogenic strains of P. ananatis (9), such as the YhcA protein of thetype IV secretion system, phage P2 (GpU), or phage P7 (Gp4); in addition, strain 1.38carries chaperones of the PapD family, which are typical of beneficial P. ananatis strains.Strain 1.38 has genes involved in siderophore metabolism (siderophore aerobactinin outer membrane, rhizobactin, IutA receptor, and the iucA, iucB, and iucD genes) anda system of recognition and transport of siderophores (FhuA, FhuD, FhuB, and FhuC).There are also quorum-sensing genes (N-acyl-L-homoserine lactose synthetase, N-acyl-L-homoserine lactose hydrolase, N-3-oxohexanoyl-L-homoserine lactose, and N-3-oxooctanoyl-L-homoserine lactose) similar to those of the AMG 501 and AMG521 strains(4, 6).Accession number(s). The whole-genome shotgun project has been deposited atDDBJ/EMBL/GenBank under the accession number NKXT00000000 (SUBID SUB2841407,BioProject number PRJNA393047, BioSample number SAMN07313992). The versiondescribed in this paper is version NKXT01000000.ACKNOWLEDGMENTSThis work was funded by the Ministerio de Economía y Competitividad (Mineco)(grant AGL2016-77163-R), CNPq-Universal (grant 400468/2016-6), Embrapa (grant02.13.08.001.00.00), and INCT-Plant-Growth Promoting Microorganisms for AgriculturalSustainability and Environmental Responsibility (CNPq grant 465133/2014-2; FundaçãoAraucária-STI, CAPES).REFERENCES1. Castagno LN, Estrella MJ, Sannazzaro AI, Grassano AE, Ruiz OA. 2011.Phosphate-solubilization mechanism and in vitro plant growth promo-tion activity mediated by Pantoea eucalypti isolated from Lotus tenuisrhizosphere in the Salado River basin (Argentina). J Appl Microbiol 110:1151–1165. https://doi.org/10.1111/j.1365-2672.2011.04968.x.2. Dutkiewicz J, Mackiewicz B, Lemieszek MK, Golec M, Milanowski J. 2016.Pantoea agglomerans: a mysterious bacterium of evil and good. Part IV.Beneficial effects. Ann Agric Environ Med 23:206 –222. https://doi.org/10.5604/12321966.1203879.3. Adam Z, Tambong JT, Lewis CT, Lévesque CA, Chen W, Bromfield ESP,Khan IUH, Xu R. 2014. Draft genome sequence of Pantoea ananatis strainLMG 2665T, a bacterial pathogen of pineapple fruitlets. Genome Announc2:e00489-14. https://doi.org/10.1128/genomeA.00489-14.4. Megías E, Megías M, Ollero FJ, Hungria M. 2016. Draft genome sequenceof Pantoea ananatis strain AMG521, a rice plant growth-promoting bac-terial endophyte isolated from the Guadalquivir marshes in southernSpain. Genome Announc 4:e01681-15. https://doi.org/10.1128/genomeA.01681-15.5. Megías E, Reis Junior FB, Ribeiro RA, Ollero FJ, Megías M, Hungria M. 2017.Genome sequence of Pantoea sp. strain F1.19, isolated from rice rhizo-sphere and with the capacity of promoting growth of legumes andnon-legumes. Genome Announc 5:e00707-17. https://doi.org/10.1128/genomeA.00707-17.6. Megías E, Reis Junior FB, Ribeiro RA, Ollero FJ, Megías M, Hungria M.2017. Genome sequence of Pantoea ananatis strain AMG 501, a plant-growth promoting bacterium isolated from rice leaves grown in pad-dies of southern Spain. Genome Announc 5:e00848-17. https://doi.org/10.1128/genomeA.00848-17.7. Coil D, Jospin G, Darling AE. 2015. A5-miseq: an updated pipeline toassemble microbial genomes from Illumina MiSeq data. Bioinformatics31:587–589. https://doi.org/10.1093/bioinformatics/btu661.8. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K,Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL,Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD,Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. TheRAST server: Rapid Annotations using Subsystems Technology. BMCGenomics 9:75. https://doi.org/10.1186/1471-2164-9-75.9. Sheibani-Tezerji R, Naveed M, Jehl MA, Sessitsch A, Rattei T, Mitter B. 2015.The genomes of closely related Pantoea ananatis maize seed endophyteshaving different effects on the host plant differ in secretion system genesand mobile genetic elements. Front Microbiol 6:440. https://doi.org/10.3389/fmicb.2015.00440.Megías et al.Volume 6 Issue 4 e01547-17 genomea.asm.org 2 on September 21, 2018 by guesthttp://mra.asm.org/Downloaded from 

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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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