- Short genome report
- Open Access
Complete genome sequence of Paenibacillus yonginensis DCY84T, a novel plant Symbiont that promotes growth via induced systemic resistance
Standards in Genomic Sciences volume 12, Article number: 63 (2017)
This article reports the full genome sequence of Paenibacillus yonginensis DCY84T (KCTC33428, JCM19885), which is a Gram-positive rod-shaped bacterium isolated from humus soil of Yongin Forest in Gyeonggi Province, South Korea. The genome sequence of strain DCY84T provides greater understanding of the Paenibacillus species for practical use. This bacterium displays plant growth promotion via induced systemic resistance of abiotic stresses.
Various Paenibacillus species constitute a large group of facultative anaerobic endospore-forming Gram-positive bacteria that are extensively distributed in nature. Ash et al. proposed that members of ‘group 3’ within the genus Bacillus should be transferred to the genus Paenibacillus , for which they proposed Paenibacillus polymyxa as the type species  Since that time, 174 different type species have been described.
Members of the genus Paenibacillus are well known as PGPR, together with Azotobacter , Azospirillum , Pseudomonas , Acetobacter , and Burkholderia . While many new species from the genus Paenibacillus have been reported , the type species Paenibacillus polymyxa  is considered a PGPR that is widely used in sustainable agriculture and environmental remediation because of its multiple functions [2, 5]. Coupled with many plant species, some Paenibacillus species have been developed as biofertilizers or biocontrol agents and have been used effectively in the control of plant-pathogenic fungi, bacteria, and nematodes [5,6,7]. P. yonginensis DCY84T was isolated from a decomposed humus mixture in South Korea and its plant growth promotion traits have been characterized in vitro . This strain is capable of inducing the defense response of Arabidopsis against several abiotic stresses . Genome sequencing of P. yonginensis DCY84T was conducted to obtain additional insights into the physiological characteristics involved in microbe-plant interactions and to facilitate better understanding of the molecular basis of these traits.
Classification and features
Paenibacillus yonginensis DCY84T was isolated from a decomposed humus mixture collected from Yongin province. It is a Gram-positive bacterium that can grow on Tryptic soy broth agar at 28 °C. Cells of strain DCY84T are rod-shaped with a diameter ranging from 0.7–0.9 μm and length ranging from 3.4 to 4.7 μm. Growth occurs under aerobic conditions with an optimum growth temperature at 25–30 °C and a temperature range of 15–40 °C, general features of strain DCY84T were presented in Table 1. Phylogenetic tree highlighting the position of Paenibacillus yonginensis DCY84T and phylogenetic inferences were obtained using the maximum-likelihood method (Fig. 1). Cell morphology was examined using scanning electron microscopy (Fig. 2).
Genome sequencing information
Genome project history
P. yonginensis DCY84T was selected for genome sequencing because we observed the presence of a unique compatible solute for plant protection from biotic stress and potential plant growth promoting activity with rice in reclaimed paddy soil and Panax ginseng C.A.Mey, respectively. The complete genome sequence has been deposited in the NCBI sequencing read archive under NCBI BioProject PRJNA306396 with BioSample SAMN04419545 and overall sequencing project information was presented in Table 2. Sequencing, annotation, and analysis were performed at LabGenomics (Seongnam, Republic of Korea).
Growth conditions and genomic DNA preparation
For growth and genomic DNA preparation, P. yonginensis DCY84T (KCTC 33428 T=JCM 19885 T) was grown in DSMZ medium 1 (Nutrient Agar) at 28 °C. DNA was isolated from 0.5–1 g of cell paste using the JetFlex genomic protocol as recommended by the manufacturer. For genome sequencing and assembly, the draft genome of P. yonginensis DCY84T was generated using the PacBio platform following the manufacturer’s instructions.
Genome sequencing and assembly
Sequencing produced 74,264 reads with an average length of 7828 bp, which was assembled using the de novo HGAP implemented within the analysis pipeline SMRT Analysis 2.2 (Pacific Biosciences, CA, USA). Ambiguous base and inserted/deleted regions between the PacBio assembled and preassembled high quality draft sequences were manually corrected using consensus sequences for final assembly. Long reads were selected as the seed sequences for constructing preassemblies, and the other short reads were mapped to the seeds using BLASTR software for alignment, which corrected errors in the long reads and thus increased the accuracy rating of bases. The sequencing run yielded 581,398,217 filtered and sub-read bases and a total of 113,985,693 pre-assembled bases were used for deep sequencing. tRNA and rRNA genes were identified by tRNAscan-SE version 1.3  and RNAmmer version 1.2 . The ORFs were predicted using Glimmer 3.02 and the annotation of predicted genes was conducted using Blastall 2.2.26. Protein coding genes were annotated based on the COGs database.
The purpose of the present study was to develop a better understanding of the P. yonginensis DCY84T genetic background to develop more effective utilization of the strain. COGs analysis of strain DCY84T is shown in Fig. 3 and the number of genes associated with the 22 general COGs functional categories presented in Table 3. The analysis of the full P. yonginensis DCY84T genome in comparison with other related Paenibacillus strains is included in Additional file 1: Table S1.
The iaaM gene, also gene responsible for IAA synthesis, siderophores production, phosphate transporter, phosphonate cluster, antimicrobial production, and synthesis of the volatile organic compound bdhA are present in the P. yonginensis DCY84T genome. These genes corroborate with our physiological results demonstrating plant growth promotion and induced systemic resistance in the plant symbiont [9, 10].
Insights from the genome sequence
The completed P. yonginensis DCY84T genome consists of a single circular chromosome of 4,985,901 bp, with a GC content of 51.01%, which is similar to most Paenibacillus strains (45 – 54%) as reported previously  (Fig. 4). The genome size of the strain DCY84T (4.985 Mb) is smaller than the other sequenced members of genus Paenibacillus including P. polymyxa CF05 (5.76 Mb), and P. mucilaginosus 3016 (8.74 Mb) . Full genome of DCY84T was annotated by following NCBI prokaryotic genome annotation pipeline . A total of 4498 genes were predicted for the genome, including 4233 coding sequences (94.1% of total genes) and 147 pseudo genes. Nucleotide content and gene count levels of the chromosome were summarized in Table 4. More detail annotation of the strain DCY84T was available in Additional file 2: Table S5. Most of selected Paenibacillus strain was reported to have plant growth promoting factor traits. The summary features of DCY84T and referred strains are showed on Additional file 1: Table S1 below, including the genome accession number, genome size, GC content, annotation information, protein, Gene, Pseudo gene. The COGs analysis of strain DCY84T and other closely related Paenibacillus strains was provided on Additional file 1: Table S2 (direct plant growth promoting factors) and Additional file 1: Table S3 (indirect plant growth promoting factors). The genome of P. yonginensis DCY84T and P. polymyxa M1 were visualized in Additional file 3: Figure S1 by the comparison using the Artemis software and ACT . Strain DCY84T increased nutrient availability by producing several hydrolyzing enzymes, amino acid transporter proteins (Additional file 1: Table S4). Moreover, Strain DCY84T treatment can induce plant defense mechanism mediated by ABA signal under salinity stress.
Genome analysis showed that P. yonginensis DCY84T contained many genes related to the stress response, such as IAA, choline, glutamate decarboxylase and malate transporters, potassium uptake protein, heat shock proteins, chaperone proteins, and sugar transporters. These genes most likely allow the strain to cope with different environmental stresses. Experimentation and additional analysis of these genes may help to elucidate the mechanisms mediating the stress response and facilitate the development of P. yonginensis DCY84T as a biofertilizer. When the strain DCY84T was used as a treatment for early sprouting rice seeds, several genes responsible for primary metabolism were upregulated in the rice root, which could be related to PGPR. These results indicate that P. yonginensis DCY84T might have the potential for application in industrial biotechnology as a producer of miscellaneous hydrolases.
This is the first report describing the genome sequence of P. yonginensis DCY84T. When coated on sprouting rice seeds or seedlings directly on paddy soil, strain DCY84T and silica zeolite complex were shown to enhance rice yield and also increase GABA content in brown rice. Treatment was also shown to induce systemic stress resistance responses in rice and Arabidopsis under heavy metal and salty conditions. Furthermore, the sequence of P. yonginensis DCY84T provides useful information and may contribute to agricultural applications of Paenibacillus genera in practical biotechnology. Rice yield was affected by the amount of strain DCY84T administered during the early sprouting stage. Silica zeolite complex and strain DCY84T treatment inhibited the occurrence of fungal infection, and also enhanced rice quality. Silica zeolite complex and two treatments with strain DCY84T resulted in the highest head rice levels (86.8%) compared to a one-time treatment of DCY84T (67.9%), and without strain DCY84T treatment (46.4%). The PGPR treatment enhanced head rice levels by 40.4% . Strain treatment also enhanced nitrogen uptake and increased levels of stored nitrogen in the rice grain, indicating that the strain DCY84T enhanced plant nitrogen utilization with less nitrogen fertilizer application. The most important parameters for economic rice value are head rice rate and good appearance; strain DCY84T treatment enhanced both the rice quality and reduced commercial nitrogen fertilizer usage.
The DCY84T strain was isolated from a decomposed humus mixture. Phylogenetic analysis based on the 16S rRNA gene confirmed its affiliation to the genus Paenibacillus . G + C content, COGs, and average nucleotide identities are presented. The genomic features of strain DCY84T are consistent with the plant growth promoting activity of this strain, including IAA production, phosphate solubilizing activity, and siderophores production. In addition, DCY84T induced systemic stress resistance mechanisms in rice and Arabidopsis under heavy metal and salty conditions.
- bdhA :
Clusters of Orthologous Groups of proteins
Hierarchical Genome Assembly Process
- iaaM :
Open Reading Frames
Plant Growth Promoting Rhizobacteria
Single Molecule, Real-Time
Ash C, Priest FG, Collins MD. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the cr (heading level 1)eation of a new genus Paenibacillus. Antonie Van Leeuwenhoek. 1993;64(3):253–60.
Hayat R, Ali S, Amara U, Khalid R, Ahmed I. Soil beneficial bacteria and their role in plant growth promotion: a review. Ann Microbiol. 2010;60:579–98.
Tindall BJ. What is the type species of the genus Paenibacillus? Request for an opinion. 2005;50:939–40.
Kwak YY, Shin JH. Complete genome sequence of Paenibacillus beijingensis 7188T (=DSM 24997T), a novel rhizobacterium from jujube garden soil. J. Biotechnol. 2016;206:75–6.
Judicial Commission of the International Committee on Systematics of Prokaryotes. The type species of the genus Paenibacillus Ash et al. 1994 is Paenibacillus polymyxa. Opinion 77. IJSEM. 2005;55:513.
Kwon YS, Lee DY, Rakwal R, Baek SB, Lee JH, Kwak YS, Seo JS, Chung WS, Bae DW, Kim SG. Proteomic analyses of the interaction between the plant-growth promoting rhizobacterium Paenibacillus polymyxa E681 and Arabidopsis thaliana. Proteomics. 2016;16(1):122–35.
Lapidot D, Dror R, Vered E, Mishli O, Levy D, Helman Y. Disease protection and growth promotion of potatoes (Solanum tuberosum L.) by Paenibacillus dendritiformis. Plant Pathol. 2015;64(3):545–51.
Goswami D, Parmar S, Vaghela H, Dhandhukia P, Thakker JN. Describing Paenibacillus mucilaginosus strain N3 as an efficient plant growth promoting rhizobacteria (PGPR). Cogent Food Agric. 2015;1:1000714. doi:10.1080/23311932.2014.1000714.
Sukweenadhi J, Kim YJ, Lee KJ, Koh SC, Hoang VA, Nguyen NL, Yang DC. Paenibacillus yonginensis sp. nov., a potential plant growth promoting bacterium isolated from humus soil of Yongin forest. Antonie Van Leeuwenhoek. 2014;106(5):935–45.
Sukweenadhi J, Kim YJ, Choi ES, Koh SC, Lee SW, Kim YJ, Yang DC. Paenibacillus yonginensis DCY84T induces changes in Arabidopsis thaliana gene expression against aluminum, drought, and salt stress. Microbiol Res. 2015;172:7–15.
Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. http://dx.doi.org/10.1093/nar/25.5.0955.
Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100 –3108. http://dx.doi.org/10.1093/nar/gkm160.
XF H, Li SX, JG W, Wang JF, Fang QL, Chen JS. Transfer of Bacillus mucilaginosus and Bacillus edaphicus to the genus Paenibacillus as Paenibacillus mucilaginosus comb. nov. and Paenibacillus edaphicus comb. nov. Int J Syst Evol Microbiol. 2010;60:8–14.
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;24:1–11.
Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. ACT: the Artemis Comparison Tool. Bioinformatics. 2005;21(16):3422–3.
Choi ES, Sukweenadhi J, KimYJ JKH, Koh SH, Kang CH, Hoang VA, Yang DC. The effects of rice seed dressing with Paenibacillus yonginensis and Silicon on crop development on South Korea’s reclaimed tidal land. Field Crop Res. 2016;188:121–32.
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci. 1990;87:4576–9.
Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzeby J, Tindall BJ. 2007. Taxonomic Outline of Bacteria and Archaea (TOBA) Release 7.7. Michigan: Michigen State University Board of Trustees; 2001-2007. p. 1–5.
Gibbons NE, Murray RGE. Proposals Concerning the Higher Taxa of Bacteria. Int J Syst Bacteriol. 1978;28:1–6.
Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW, editors. Bergey’s Manual of Systematic Bacteriology, vol. 1. Second ed. New York: Springer; 2001. p. 119–66.
Murray RGE. The Higher Taxa, or, a Place for Everything...? In: Holt JG, editor. Bergey's Manual of Systematic Bacteriology, First Edition, Volume 1, The Williams and Wilkins Co. Baltimore; 1984. p. 31–4.
Ludwig W, Schleifer KH, Whitman WB. Class I. Bacilli class. nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB, editors. Bergey’s Manual of Systematic Bacteriology, vol. 3. Second ed. New York: Springer-Verlag; 2009. p. 19–20.
Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol. 1980;30:225–420.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25–9.
We appreciated to the company, Saturn Bio Tech for rice field trials, they supported for application of the strain DCY84 as bio fertilizer in reclaimed paddy soil.
This study was supported by a grant from the Next-Generation BioGreen 21 (“PJ012034”), Rural Development Administration, in Republic of Korea.
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Genome comparison of strain DCY84T and closest Paenibacillus strains. Table S2. COGs analysis of direct plant growth promoting traits. Table S3. COGs analysis of indirect plant growth promoting traits. Table S4. Some important genes annotated on strain DCY84T genome. (DOCX 81 kb)
Annotation of the Paenibacillus yonginensis DCY84T genome. (XLSX 443 kb)
About this article
Cite this article
Kim, YJ., Sukweenadhi, J., Seok, J.W. et al. Complete genome sequence of Paenibacillus yonginensis DCY84T, a novel plant Symbiont that promotes growth via induced systemic resistance. Stand in Genomic Sci 12, 63 (2017). https://doi.org/10.1186/s40793-017-0277-8
- Paenibacillus yonginensis DCY84T
- Plant growth promoting rhizobacteria (PGPR)