Chiho Suzuki-Minakuchi

Enock Mpofu

Felipe Vejarano

Hideaki Nojiri

Joydeep Chakraborty

Kazunori Okada

Masataka Tsuda

Masatoshi Nakajima

Nobuki Tada

Toshiaki Kimura

Yoshiyuki Ohtsubo

Microbiology Resource Announcements

Enock, Mpofu

Felipe, Vejarano

Chiho, Suzuki-Minakuchi

Yoshiyuki, Ohtsubo

Masataka, Tsuda

Joydeep, Chakraborty

Masatoshi, Nakajima

Kazunori, Okada

Nobuki, Tada

Toshiaki, Kimura

Hideaki, Nojiri

Tohoku University Repository (TOUR) / 東北大学機関リポジトリ

Complete Genome Sequence of Bacilluslicheniformis TAB7, a Compost-DeodorizingStrain with Potential for Plant GrowthPromotion著者 Enock Mpofu, Felipe Vejarano, ChihoSuzuki-Minakuchi, Yoshiyuki Ohtsubo, MasatakaTsuda, Joydeep Chakraborty, MasatoshiNakajima, Kazunori Okada, Nobuki Tada,Toshiaki Kimura, Hideaki Nojirijournal orpublication titleMicrobiology Resource Announcementsvolume 8number 4page range 01659year 2019-01-24URL http://hdl.handle.net/10097/00126937doi: 10.1128/MRA.01659-18.Creative Commons : 表示http://creativecommons.org/licenses/by/3.0/deed.jaComplete Genome Sequence of Bacillus licheniformis TAB7, aCompost-Deodorizing Strain with Potential for Plant GrowthPromotionEnock Mpofu,a Felipe Vejarano,a Chiho Suzuki-Minakuchi,a,b Yoshiyuki Ohtsubo,c Masataka Tsuda,c Joydeep Chakraborty,aMasatoshi Nakajima,d Kazunori Okada,a Nobuki Tada,e Toshiaki Kimura,e Hideaki Nojiria,baBiotechnology Research Center, The University of Tokyo, Tokyo, JapanbCollaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, JapancGraduate School of Life Sciences, Tohoku University, Sendai, JapandDepartment of Applied Biological Chemistry, The University of Tokyo, Tokyo, JapaneToyota Motor Corporation, Nagoya, JapanABSTRACT Bacillus licheniformis strain TAB7 degrades short-chain fatty acids re-sponsible for offensive odor in manure and is used as a deodorant in a compost-deodorizing technology. Here, we report the complete genome sequence ofstrain TAB7, which consists of a 4.37-Mb chromosome and two plasmids (42 kband 31 kb).TAB7 is a thermophilic Bacillus licheniformis strain isolated as a Tween 20 (a surfac-tant with a fatty acid side chain) degrader from composting manure in Japan (1). Itdegrades short-chain fatty acids responsible for the offensive odor in compost and iscommercially available as a deodorizing agent for composts (2). Several Bacillus spp.can produce indole-3-acetic acid (IAA) and promote plant growth (3–5). Our cultivationsof TAB7 in lysogeny broth (LB) (6), with and without tryptophan, resulted in productionof IAA in both cases (Fig. 1). Thus, TAB7 may not only deodorize compost but may alsopromote plant growth. Therefore, its genome sequence will be useful in comparativegenomic studies with known plant growth-promoting bacteria.For genome sequencing, TAB7 cells were grown overnight in 10 ml of LB at 30°Cwith shaking (300 strokes/min). DNA was extracted and purified using a Wizardgenomic DNA purification kit (Promega) following the manufacturer’s instructions.Sequencing with a v3 chemistry 600-cycle kit (Illumina) was done using a MiSeqsequencer with PCR-free paired-end (PE) and mate pair (MP) libraries that were pre-pared with TruSeq DNA PCR-free and Nextera mate pair library preparation kits(Illumina), respectively, following the manufacturer’s instructions. Obtained reads wereprocessed with ShortReadManager 0.995 (7) to extract paired reads, perform low-abundance 21-mer-read trimming, and discard reads shorter than 150 and 100 bp inthe PE and MP data sets, respectively. One million PE (273 Mb) and 0.7 million MP(128 Mb) reads were assembled with Newbler 2.8 (Roche) into three scaffolds, two ofwhich consisted of single circular contigs without gaps (plasmids). A total of 29repeat-induced gaps in the remaining scaffold (chromosome) were identified usingGenoFinisher 2.1 (7), and their precise sequences and locations with respect to othercontigs were determined with AceFileViewer 1.5 (7), using the MP data. Assembledreplicons were checked for errors with the GenoFinisher tool FinishChecker (8), con-firming complete gap resolution.A 4,367,367-bp chromosome (85 coverage) and two circular plasmids, pTAB7A andpTAB7B (42,138 bp and 31,204 bp, with 290 and 400 coverage, respectively) wereassembled. Open reading frame (ORF) prediction and annotation were done using theCitation Mpofu E, Vejarano F, Suzuki-Minakuchi C, Ohtsubo Y, Tsuda M, ChakrabortyJ, Nakajima M, Okada K, Tada N, Kimura T, NojiriH. 2019. Complete genome sequence ofBacillus licheniformis TAB7, a compost-deodorizing strain with potential for plantgrowth promotion. Microbiol Resour Announc8:e01659-18. https://doi.org/10.1128/MRA.01659-18.Editor Julia A. Maresca, University of DelawareCopyright © 2019 Mpofu et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Hideaki Nojiri,anojiri@mail.ecc.u-tokyo.ac.jp.Received 8 December 2018Accepted 19 December 2018Published 24 January 2019GENOME SEQUENCEScrossmVolume 8 Issue 4 e01659-18 mra.asm.org 1 on November 14, 2019 at TOHOKU UNIVERSITYhttp://mra.asm.org/Downloaded from Microbial Genome Annotation Pipeline (MiGAP) (9) and the NCBI Prokaryotic GeneAnnotation Pipeline (PGAP) (10). The two annotation results were compared andmanually corrected using GenomeMatcher (11) and then merged. The Kyoto Encyclo-pedia of Genes and Genomes (KEGG) pathway database (12) was used to predictmetabolic pathways.The chromosome of TAB7 has a GC content of 45.82% and bears 4,429 codingDNA sequences (CDS). It contains 85 tRNA genes and 7 rRNA operons. pTAB7A (51 CDS)and pTAB7B (33 CDS) have GC contents of 40.10% and 38.61%, respectively. The TAB7chromosome harbors nitrilase (yhcX) and IAA-acetyl-transferase (ysnE) (4) genes thatmay be involved in IAA biosynthesis. It also has genes encoding phenolic acid decar-boxylase (padC) (13), vanillic acid decarboxylase (vdcC) (14), and protocatechuic acid-degrading enzymes (praABCDEHI) (15), which are involved in catabolism of phenoliccompounds known to have negative allelopathy on some plants (16–18). Furthermore,putative genes involved in the production of other plant growth-promoting com-pounds, such as bacillibactin (dhbABCEF), and acetoin (alsDRS) (4, 19) were found,further suggesting TAB7 involvement in plant growth promotion.Data availability. The genome sequence of Bacillus licheniformis strain TAB7 hasbeen deposited in DDBJ/ENA/GenBank under the accession numbers CP027789 (chro-mosome), CP027790 (pTAB7A), and CP027791 (pTAB7B). Raw sequencing data havebeen deposited under BioProject accession number PRJNA438467. Details of theassembly procedure for the generation of the complete sequences and the parametersused with each software are available in the comment section of each submission aspart of the metadata.ACKNOWLEDGMENTWe thank Yurika Takahashi of Toyama Prefectural University for kindly sequencingour DNA libraries.REFERENCES1. Kimura T. 2015. Aerobic composting of livestock manure by thermophileand enzymes. J Environ Biotechnol 15:23–28.2. Tada N, Matsushita H, Kimura T. June 2014. Microorganism and deodor-izer containing the same. US patent US8741625B2.3. Shao JH, Li SQ, Zhang N, Cui XS, Zhou X, Zhang GS, Shen QR, Zhang RF.2015. Analysis and cloning of the synthetic pathway of the phytohor-mone indole-3-acetic acid in the plant-beneficial Bacillus amyloliquefa-ciens SQR9. Microb Cell Fact 14:130. https://doi.org/10.1186/s12934-015-0323-4.4. Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heine-meyer I, Morgenstern B, Voss B, Hess WR, Reva O, Junge H, Voigt B,Jungblut PR, Vater J, Sussmuth R, Liesegang H, Strittmatter A,Gottschalk G, Borriss R. 2007. Comparative analysis of the completegenome sequence of the plant growth-promoting bacterium Bacillusamyloliquefaciens FZB42. Nat Biotechnol 25:1007–1014. https://doi.org/10.1038/nbt1325.5. Santoyo G, Orozco-Mosqueda MC, Govindappa M. 2012. Mechanisms ofbiocontrol and plant growth-promoting activity in soil bacterial speciesFIG 1 IAA production by Bacillus licheniformis TAB7. TAB7 cells were grown in LB at 30°C for 24 h with shaking(300 strokes/min) and then centrifuged. The supernatant was then acidified, and IAA was extracted byacetonitrile. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was performed on aXevo TQ (Waters) platform using an Acquity ultraperformance liquid chromatography (UPLC) ethylenebridged hybrid (BEH) C18 column (1.7 m, 2.1 by 50 mm; Waters). A 10-ng aliquot of 13C-labeled IAA was usedas an internal standard. 1, sterile LB (control); 2, sterile LB with 300 g/ml of tryptophan (Trp, control); 3,extracts from the TAB7 culture; 4, extracts from the TAB7 culture supplemented with 300 g/ml of trypto-phan. Data are expressed as means  standard deviation of results from technical triplicates.Mpofu et al.Volume 8 Issue 4 e01659-18 mra.asm.org 2 on November 14, 2019 at TOHOKU UNIVERSITYhttp://mra.asm.org/Downloaded from of Bacillus and Pseudomonas: a review. Biocontrol Sci Technol 22:855– 872. https://doi.org/10.1080/09583157.2012.694413.6. Sambrook J, Russell D. 2001. Molecular cloning: a laboratory manual, 3rded. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.7. 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Khang DT, Anh LH, Ha PTT, Tuyen PT, Quan NV, Minh LT, Quan NT, MinhTN, Xuan TD, Khanh TD, Trung KH. 2016. Allelopathic activity of dehulledrice and its allelochemicals on weed germination. Int Lett Nat Sci58:1–10. https://doi.org/10.18052/www.scipress.com/ILNS.58.1.17. Li ZH, Wang Q, Ruan X, Pan CD, Jiang DA. 2010. Phenolics and plantallelopathy. Molecules 15:8933– 8952. https://doi.org/10.3390/molecules15128933.18. Blum U. 1996. Allelopathic interactions involving phenolic acids. J Nema-tol 28:259 –267.19. Bruto M, Priget-Combaret C, Muller D, Moenne-Loccoz V. 2014. Analysisof genes contributing to plant-beneficial functions of plant growth-promoting rhizobacteria and related proteobacteria. Sci Rep 4:6261.Microbiology Resource AnnouncementVolume 8 Issue 4 e01659-18 mra.asm.org 3 on November 14, 2019 at TOHOKU UNIVERSITYhttp://mra.asm.org/Downloaded from 

Complete Genome Sequence of Bacillus licheniformis TAB7, a Compost-Deodorizing Strain with Potential for Plant Growth Promotion

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Complete Genome Sequence of Bacillus licheniformis TAB7, a Compost-Deodorizing Strain with Potential for Plant Growth Promotion

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