Abstract
A white-coloured, rod-shaped, motile, aerobic, and Gram-stain-positive bacterial strain S3N08T was isolated from agricultural soil. The strain grew at temperature 10–40 °C, at 0–1.0% (w/v) NaCl concentration, and at pH 6.5–8.0. Catalase was negative and oxidase was positive. The phylogenetic analysis inferred that the strain S3N08T belonged to the genus Paenibacillus, with the closest relative being Paenibacillus periandrae PM10T (95.6% 16S rRNA gene sequence similarity). The only menaquinone was MK-7 and the major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylglycerol, and phosphatidylethanolamine. The predominant fatty acids were antiso-C15:0, C16:0, and iso-C15:0. The DNA G + C content was 45.1%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain S3N08T and with closest members were < 72.0% and < 19.0%, respectively. Altogether, the phylogenetic, genomics, phenotypic, and chemotaxonomic evidence illustrated in this study suggested that strain S3N08T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus agricola sp. nov. is proposed. The type strain is S3N08T (= KACC 19666 T = NBRC 113430 T).
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Data availability
The GenBank/EMBL/DDBJ accession number for the 16S rRNA sequence of strain S3N08T is MH159222. The whole genome shotgun sequence of strain S3N08T has been deposited at DDBJ/ENA/GenBank under the accession JAAOIW000000000. The version described in this paper is version JAAOIW010000000.
Abbreviations
- KACC:
-
Korean agricultural culture collection
- KCTC:
-
Korean collection for type cultures
- LMG:
-
Laboratorium voor microbiologie
- DSM:
-
Deutsche Sammlung von Mikroorganismen
- NBRC:
-
NITE biological resource center
- ANI:
-
Average nucleotide identity
- dDDH:
-
Digital DNA-DNA hybridization
References
Ash C, Priest FG, 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. https://doi.org/10.1007/BF00873085
Aziz RK et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75. https://doi.org/10.1186/1471-2164-9-75
Baik KS, Lim CH, Choe HN, Kim EM, Seong CN (2011) Paenibacillus rigui sp. nov., isolated from a freshwater wetland. Int J Syst Evol Microbiol 61:529–534. https://doi.org/10.1099/ijs.0.021485-0
Blin K et al (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:W81–W87. https://doi.org/10.1093/nar/gkz310
Breznak JA, Costilow RN (2007) Physicochemical factors in growth. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Synder LR (eds) Methods gen mol microbiol, 3rd edn. American Society of Microbiology, Washinton, DC, pp 309–329
Chaudhary DK, Dahal RH, Altankhuu K, Kim J (2017) Ravibacter arvi gen. nov., sp. nov., isolated from farmland soil during development of new culture techniques. Int J Syst Evol Microbiol 67:5252–5260. https://doi.org/10.1099/ijsem.0.002456
Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354. https://doi.org/10.1128/mr.45.2.316-354.1981
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461–2470. https://doi.org/10.1128/AEM.02272-07
Gao Q-j, Mo K-l, Hu Y-h, Liu Z-y, Huang H-q (2022) Paenibacillus sabuli sp. Nov., isolated from the South China Sea. Int J Syst Evol Microbiol. 72:005568. https://doi.org/10.1099/ijsem.0.005568
Glaeser SP, Falsen E, Busse H-J, Kämpfer P (2013) Paenibacillus vulneris sp. nov., isolated from a necrotic wound. Int J Syst Evol Microbiol 63:777–782. https://doi.org/10.1099/ijs.0.041210-0
Grady EN, MacDonald J, Liu L, Richman A, Yuan Z-C (2016) Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Factories 15:1–18. https://doi.org/10.1186/s12934-016-0603-7
Kämpfer P et al (2022) Paenibacillus allorhizoplanae sp. nov. from the rhizoplane of a Zea mays root. Arch Microbiol 204:630. https://doi.org/10.1007/s00203-022-03225-w
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. https://doi.org/10.1007/BF01731581
Kriechbaumer V, Glawischnig E (2005) Auxin biosynthesis within the network of tryptophan metabolism. J Nano Bio Tech 2:53–58
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547. https://doi.org/10.1093/molbev/msy096
Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H, Chun J (2017) ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 67:2053–2057. https://doi.org/10.1099/ijsem.0.001872
Lefort V, Desper R, Gascuel O (2015) FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 32:2798–2800. https://doi.org/10.1093/molbev/msv150
Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10:2182. https://doi.org/10.1038/s41467-019-10210-3
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60. https://doi.org/10.1186/1471-2105-14-60
Menendez E et al (2016) Paenibacillus periandrae sp. nov., isolated from nodules of Periandra mediterranea. Int J Syst Evol Microbiol 66:1838–1843. https://doi.org/10.1099/ijsem.0.000953
Minnikin DE et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241. https://doi.org/10.1016/0167-7012(84)90018-6
Oktari A, Supriatin Y, Kamal M, Syafrullah H (2017) The bacterial endospore stain on schaeffer fulton using variation of methylene blue solution. In: Journal of Physics: Conference Series. IOP Publishing. p 012066
Pruesse E, Peplies J, Glöckner FO (2012) SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823–1829. https://doi.org/10.1093/bioinformatics/bts252
Qi SS, Cnockaert M, Carlier A, Vandamme PA (2021) Paenibacillus foliorum sp. nov., Paenibacillus phytohabitans sp. nov., Paenibacillus plantarum sp. nov., Paenibacillus planticolens sp. nov., Paenibacillus phytorum sp. nov., and Paenibacillus germinis sp. nov., isolated from the Arabidopsis thaliana phyllosphere. Int J Syst Evol Microbiol 71:004781. https://doi.org/10.1099/ijsem.0.004781
Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131. https://doi.org/10.1073/pnas.0906412106
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Sasser M (1990) Bacterial identification by gas chromatographic analysis of fatty acid methyl esters (GC-FAME). MIDI technical note 101. Midi Inc, Newark
Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K (1997) Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Evol Microbiol 47:289–298. https://doi.org/10.1099/00207713-47-2-289
Smibert R (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 607–654
Stackebrandt E (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155
Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231. https://doi.org/10.1128/am.28.2.226-231.1974
Tatusova T et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569
Thin KK, He S-W, Ma R, Wang X, Han J-G, Zhang X-X (2023) Paenibacillus rhizolycopersici sp. nov., an oligotrophic bacterium isolated from a tomato plant in China. Int J Syst Evol Microbiol 73:005698. https://doi.org/10.1099/ijsem.0.005698
Tindall B (2000) What is the type species of the genus Paenibacillus? Request for an opinion. Int J Syst Evol Microbiol 50:939–940. https://doi.org/10.1099/00207713-50-2-939
Wang J et al (2022) Paenibacillus hamazuiensis sp. nov., a bacterium isolated from Hamazui hot spring in Yunnan province, south-west China. Arch Microbiol 204:1–5. https://doi.org/10.1007/s00203-022-03282-1
Wayne LG et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464. https://doi.org/10.1099/00207713-37-4-463
Yarza P et al (2008) The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250. https://doi.org/10.1016/j.syapm.2008.07.001
Yoon S-H, Ha S-m, Lim J, Kwon S, Chun J (2017a) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4
Yoon S-H et al (2017b) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755
Acknowledgements
This work was supported by Rural Development Administration, South Korea (Project No. PJ014897032023).
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HL and DK designed the study. HL, DKC and OBL contributed the experimental work, data analysis, and original draft preparation. HL and DKC reviewed and finalized the manuscript. DK supervised the project.
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The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA sequence and whole genome shotgun sequence of strain S3N08T are MH159222 and JAAOIW000000000, respectively.
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Lee, H., Chaudhary, D.K., Lim, O.B. et al. Paenibacillus agricola sp. nov., isolated from agricultural soil. Arch Microbiol 205, 248 (2023). https://doi.org/10.1007/s00203-023-03578-w
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DOI: https://doi.org/10.1007/s00203-023-03578-w