Open access
Announcement
10 April 2014

Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. P22, Isolated from Populus

ABSTRACT

Paenibacillus sp. P22 is a Gram-negative facultative anaerobic endospore-forming bacterium isolated from poplar hybrid 741 (♀[Populus alba × (P. davidiana + P. simonii) × P. tomentosa]). This bacterium shows strong similarities to Paenibacillus humicus, and important growth-promoting effects on in vitro grown explants of poplar hybrid 741 have been described.

GENOME ANNOUNCEMENT

Bacillus is a phylogenetically heterogeneous taxon, and Paenibacillus was classified as a new genus in 1993 (13). The rod-shaped cells are motile, have peritrichous flagella, and show variable Gram staining. They form ellipsoidal endospores (4). Species of this genus are known to produce hormones that stimulate plant growth, like cytokinin (5), and antibiotic peptides as well as different (6) hydrolyzing enzymes, which are responsible for antagonistic behavior against many plant pathogens. Thus, many species of the genus have been described as plant growth-promoting bacteria. Paenibacillus sp. P22 was isolated by Ulrich et al. (7) from the poplar hybrid 741 [Populus alba × (P. davidiana + P. simonii) × P. tomentosa] (8). The phylogenetic analysis of the strain was based on 16S rRNA gene sequencing and showed that Paenibacillus sp. P22 has strong 16S rRNA gene sequence similarity to Paenibacillus humicus (99.5%) (7). Former experiments have shown that in vitro grown explants of hybrid 741 inoculated with Paenibacillus sp. P22 exhibited significantly more root growth and root length than noninoculated explants (7). The pure culture of the bacterial strain was grown under aerobic conditions on tryptic soy broth agar plates. The DNA extraction was performed with a DNA GeneJET gel extraction kit according to the manufacturer's instructions. Application of the 454 GS FLX Titanium sequencing technology and sequencing of an 8-kb paired-end library resulted in 561,213 reads and 61,143,112 nucleotides. In an Ion Torrent PGM sequencing approach, 1,978,332 reads and 343,311,791 nucleotides were gathered. Consensus assembly using MIRA (9) yielded 5,443,257 bp in 297 contigs (>300 bp), with an overall GC content of 58%. Coding sequences (CDS) were predicted based on an in-house workflow that integrates ab initio predictions from Glimmer (10), Genemark (11), Prodigal (12), and Critica (13) with homology information derived from a BLAST search against NCBI nr (14). Noncoding RNAs were identified by tRNAscanSE (15), RNAmmer (16), and Infernal (17). Predicted CDS were compared to the databases InterPro (18), Swissprot (19), and trEMBL (19) for functional annotation and mapped to KEGG pathways.
The genome of Paenibacillus sp. P22 contains 5,224 protein-coding genes, 65 tRNAs, and 1 16S rRNA. Presence of tRNAs for all 20 proteinogenic amino acids as well as 31 out of 31 phylogenetic marker proteins (AMPHORA2 software) (20) that are essential in prokaryotes indicates an estimated completeness of the genome of about 99%. Further investigation of the metabolic capabilities of Paenibacillus sp. P22 yielded two particularly interesting findings. We found a gene encoding a nitrogenase (EC 1.19.6.1) for nitrogen fixation coinciding with the observation that Paenibacillus sp. P22 is able to grow without nitrogen in the medium (21). Accordingly, metabolite profiles of poplar plants which were inoculated with Paenibacillus sp. P22 showed a strongly altered C/N homeostasis as a result of the endophyte-plant interaction (21). Genes of the auxine-pathway were also detected, suggesting growth-promoting effects by hormone secretion. This finding was indeed confirmed by the detection of auxin in a metabolite profile of a Paenibacillus sp. P22 culture.

Nucleotide sequence accession numbers.

The genome sequence of Paenibacillus sp. P22 has been deposited in the European Nucleotide Archive under the accession numbers CBRA020000001 through CBRA020000297.

ACKNOWLEDGMENTS

We thank the University of Vienna, Faculty of Life Science, for financial support. M.N. is funded by the DFG within the project “Identification of in vivo Substrates of MEK-MPK Modules in Arabidopsis.”

REFERENCES

1.
Aguilera M, Monteoliva-Sánchez M, Suárez A, Guerra V, Lizama C, Bennasar A, and Ramos-Cormenzana A. 2001. Paenibacillus jamilae sp. nov., an exopolysaccharide-producing bacterium able to grow in olive-mill wastewater. Int. J. Syst. Evol. Microbiol. 51:1687–1692.
2.
Lebuhn M, Heulin T, and Hartmann A. 1997. Production of auxin and other indolic and phenolic compounds by Paenibacillus polymyxa strains isolated from different proximity to plant roots. FEMS Microbiol. Ecol. 22:325–334.
3.
Ash C, Priest FG, and Collins MD. 1993. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie Van Leeuwenhoek 64:253–260.
4.
Vaz-Moreira I, Faria C, Nobre MF, Schumann P, Nunes OC, and Manaia CM. 2007. Paenibacillus humicus sp. nov., isolated from poultry litter compost. Int. J. Syst Evol. Microbiol. 57:2267–2271.
5.
Timmusk S, Nicander B, Granhall U, and Tillberg E. 1999. Cytokinin production by Paenibacillus polymyxa. Soil Biol. Biochem. 31:1847–1852.
6.
Dluzniewska P, Gessler A, Dietrich H, Schnitzler JP, Teuber M, and Rennenberg H. 2007. Nitrogen uptake and metabolism in Populus x canescens as affected by salinity. New Phytol. 173:279–293.
7.
Ulrich K, Stauber T, and Ewald D. 2008. Paenibacillus—a predominant endophytic bacterium colonising tissue cultures of woody plants. Plant Cell Tissue Organ Cult. 93:347–351.
8.
Su X. 2003. Advances in tree genetic engineering in China. World Forestry Congress XII, Québec, Canada.
9.
Chevreux B, Wetter T, and Suhai S. 1999. Computer Science and Biology, p 45–56. Proceedings of the German Conference on Bioinformatics(GCB), Hannover, Germany.
10.
Delcher AL, Bratke KA, Powers EC, and Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679.
11.
Lukashin AV and Borodovsky M. 1998. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26:1107–1115.
12.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, and Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119.
13.
Badger JH and Olsen GJ. 1999. CRITICA: coding region identification tool invoking comparative analysis. Mol. Biol. Evol. 16:512–524.
14.
Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, and Ye J. 2009. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 37:D5–15.
15.
Lowe TM and Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964.
16.
Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, and Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100–3108.
17.
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, and Bateman A. 2005. Rfam: annotating noncoding RNAs in complete genomes. Nucleic Acids Res. 33:D121–D124.
18.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, and Yong SY. 2012. Interpro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 40:D306–D312.
19.
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, and Schneider M. 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:365–370.
20.
Wu M and Scott AJ. 2012. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 28:1033–1034.
21.
Scherling C, Ulrich K, Ewald D, and Weckwerth W. 2009. A metabolic signature of the beneficial interaction of the endophyte Paenibacillus sp. Isolate and in vitro–grown poplar plants revealed by metabolomics. Mol. Plant. Microbe. Interact. 22:1032–1037.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 2Number 21 May 2014
eLocator: 10.1128/genomea.00276-14

History

Received: 13 March 2014
Accepted: 18 March 2014
Published online: 10 April 2014

Contributors

Authors

Anne M. Hanak
Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
Matthias Nagler
Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
Thomas Weinmaier
Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
Xiaoliang Sun
Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
Lena Fragner
Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
Clarissa Schwab
Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
Thomas Rattei
Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
Kristina Ulrich
Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Institute of Forest Genetics, Waldsieversdorf, Germany
Dietrich Ewald
Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Institute of Forest Genetics, Waldsieversdorf, Germany
Marion Engel
Research Unit Environmental Genomics, Helmholtz Zentrum Munich, Neuherberg, Germany
Michael Schloter
Research Unit Environmental Genomics, Helmholtz Zentrum Munich, Neuherberg, Germany
Romana Bittner
Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
Christa Schleper
Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
Wolfram Weckwerth
Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria

Notes

Address correspondence to Wolfram Weckwerth, [email protected].

Metrics & Citations

Metrics

Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download.

View Options

Figures and Media

Figures

Media

Tables

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy