Yi, Yanglei

University of Groningen

   University of GroningenBacillus mycoides: novel tools for studying the mechanisms of its interaction with plantsYi, YangleiIMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2018Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Yi, Y. (2018). Bacillus mycoides: novel tools for studying the mechanisms of its interaction with plants.[Groningen]: University of Groningen.CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 12-11-20192Draft genome sequences  of seven Bacillus mycoides strains, isolated from potato endosphere and soil Yanglei Yia, Anne de Jonga, Jan Spoelderb,d, J. Theo M. Elzengab, Jan Dirk van Elsasc, Oscar P. Kuipersa Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlandsa. Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlandsb. Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlandsc.HLB Research & Consultancy in Agriculture,  Kampsweg 27, 9418 PD  Wijster, the Netherlandsd.This chapter is partly based on:Yi, Y., de Jong, A., Spoelder, J., Elzenga, J. T. M., van Elsas, J. D., & Kuipers, O. P. (2016). Draft genome sequence of Bacillus mycoides M2E15, a strain isolated from the endosphere of potato. Genome announcements, 4(1), e00031–16.233Draft genome sequences of seven Bacillus mycoides strains, isolated from potato endosphere and soilBacillus mycoides is a rod-shaped and spore-forming gram-positive bac-terium which is associated with the Bacillus cereus group. On agar plates, it forms unique rhizoid colonies resulting from cells that are linked end-to-end. The  strong intra-cellular connections yield a stable network that favors interactions with other soil inhabitants, such as microbes and plant roots (Turchi et al., 2012). There are several studies showing that B. mycoides is able to promote  the plant growth (Karagöz et  al., 2012), fix N2 (Ambrosini et al., 2016), and control  several plant diseases (Paul et al., 1995; Bargabus et al., 2002; Neher et al., 2009). We found some B. mycoides strains to be present in the endosphere of potato without causing visible signs of disease. In order to understand the genetic make-up of this bac-terium, we present the draft genome of several B. mycoides strains, which was isolated from potato endosphere or soil (Wijster, the Netherlands). Strains were grown overnight in Luria-Bertani (LB) broth at 30 °C, 200 rpm. Bacterial cells were harvested at the exponential growth phase and lysed with lysozyme. After RNase treatment, proteins were removed by proteinase K digestion. DNA was extracted from the lysate by phe-nol-chloroform treatment and recovered by isopropanol precipitation. The extracted DNA was checked for purity by Nanodrop (Thermo Fisher Scientific) and 1% agarose gel, then quantified by Quantus™ Fluorom-eter (Promega). The high-quality DNA was sequenced using the MiSeq sequencing system of Illumina, yielding 250 bp paired-end reads with a mean library size of 400 bp. De novo assembly was performed using Vel-vet (Zerbino and Birney, 2008). Prediction of protein-encoding regions and automatic functional annotation was performed using the Rapid Annotations using Subsystem Technology (RAST) server (Aziz et  al., 2008). Moreover, the bacteriocin identification tool Bagel3 was used (van Heel et al., 2013). The whole genome alignment of the seven strains was performed with GEGENEES tool (Ågren et al. 2012). Phylogram was generated with Neigh-bour joining method and is shown in Figure 1. The resulting phylogenetic tree has two main branches that group the 29 genomes into two species clades: B. mycoides and other B. cereus-group members. For B. mycoides, we selected the 7 strains based on their origin of isolation and plant col-onization ability: four strains isolated from the endosphere that could be endophytic again (EC18, M2E15, S2E19, and S3E15), and three strains iso-lated from soil which could not be endophytic (SB4, SB8, and SB13). The phylogenetic tree showed that the four endophytic strains are clustered together, indicating that the endophytic strains have some common fea-tures. Intriguingly, the soil strain SB8 was also grouped in this putative endophytic clade. 2234 35Draft genome sequences of seven Bacillus mycoides strains, isolated from potato endosphere and soilACKNOWLEDGMENTSTable 1. Genome features and GenBank accession numbers of the strains.Species Strain Source of isolation Accession No.Bacillus mycoides EC18 Endosphere MRWW00000000.1Bacillus mycoides S2E19 Endosphere MRWV00000000.1Bacillus mycoides M2E15 Endosphere LLWA00000000.1Bacillus mycoides S3E15 Endosphere MRWU00000000.1Bacillus mycoides SB4 Soil MRZX00000000.1Bacillus mycoides SB8 Soil MRWS00000000.1Bacillus mycoides SB13 Soil MRWT00000000.1Nucleotide sequence accession number. The genome sequences of the 7 B. mycoides strains have been deposited as whole genome shotgun projects at GenBank under the accession numbers listed in Table 1.ACKNOWLEDGMENTSY.Yi was supported by a scholarship to from the China Scholarship Council (201306300040).REFERENCES Ågren, J., Sundström, A., Håfström, T., &  Segerman, B. (2012). Gegenees: frag-mented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for speci-fied target groups. Plos One 7(6): e39107.Ambrosini, A., Stefanski, T., Lisboa, B.B.,  Beneduzi, A., Vargas, L.K., and Passaglia, L.M.P. (2016) Diazotrophic Bacilli isolated from the sunflower rhizosphere and the potential of Bacillus mycoides B38V as bio-fertiliser. Ann Appl Biol 168: 93-110.Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A. et al. (2008) The RAST Server: rapid annotations using sub-systems technology. BMC Genomics 9: 75.Bargabus, R., Zidack, N., Sherwood, J., and Ja-cobsen, B. (2002) Characterisation of sys-temic resistance in sugar beet elicited by a non-pathogenic, phyllosphere-colonizing Bacillus mycoides, biological control agent. Physiol Mol Plant Pathol 61: 289-298.Karagöz, K., Ateş, F., Karagöz, H., Kotan, R., and Çakmakçı, R. (2012) Characterization of plant growth-promoting traits of bacteria isolated from the rhizosphere of grape-vine grown in alkaline and acidic soils. Eur J Soil Biol 50: 144-150.Neher, O.T., Johnston, M.R., Zidack, N.K., and Jacobsen, B.J. (2009) Evaluation of Bacillus mycoides isolate BmJ and B. mojavensis iso-late 203-7 for the control of anthracnose of cucurbits caused by Glomerella cingu-lata var. orbiculare. Biological Control 48: 140-146.Paul, B., Charles, R., and Bhatnagar, T. (1995) Biological control of Pythium mamilla-tum causing damping-off of cucumber seedlings by a soil bacterium, Bacillus my-coides. Microbiol Res 150: 71-75.Figure 1. Phylogenetic analysis based on the whole genome sequences of the 7 B. my-coides isolates and other representatives of the B. cereus-group: B. cereus, B. anthracis, and B. thuringensis. Turchi, L., Santini, T., Beccari, E., and Di Franco, C. (2012) Localization of new peptidogly-can at poles in Bacillus mycoides, a mem-ber of the Bacillus cereus group. Arch Mi-crobiol 194: 887-892.van Heel, A.J., de Jong, A., Montalbán-López, M., Kok, J., and Kuipers, O.P. (2013) BA-GEL3: automated identification of genes encoding bacteriocins and (non-) bacte-ricidal posttranslationally modified pep-tides. Nucleic Acids Res 41: W448-W453.Zerbino, D.R., and Birney, E. (2008) Velvet: al-gorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.

Bacillus mycoides: novel tools for studying the mechanisms of its interaction with plants

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Bacillus mycoides: novel tools for studying the mechanisms of its interaction with plants

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