Crenobacter oryzisoli sp. nov., a novel phosphate-solubilizing bacterium isolated from the paddy soil.

Publisher: Springer-Verlag Country of Publication: Germany NLM ID: 0410427 Publication Model: Electronic Cited Medium: Internet ISSN: 1432-072X (Electronic) Linking ISSN: 03028933 NLM ISO Abbreviation: Arch Microbiol Subsets: MEDLINE

Original Publication: Berlin, New York, Springer-Verlag.

Soil Microbiology* ; Phylogeny* ; RNA, Ribosomal, 16S*/genetics ; DNA, Bacterial*/genetics ; Base Composition* ; Fatty Acids*/analysis ; Fatty Acids*/metabolism ; Fatty Acids*/chemistry ; Phosphates*/metabolism; China ; Nucleic Acid Hybridization ; Bacterial Typing Techniques ; Phospholipids/analysis ; Sequence Analysis, DNA ; Oryza/microbiology ; Oryza/growth & development

Two Gram-staining-negative, facultative anaerobic, rod-shaped and phosphate-solubilizing strains designated SG2303 ^T and SG2305, were isolated from paddy soil in China. Phylogenetic analysis based on 16 S rRNA gene sequences indicated that SG2303 ^T and SG2305 represented a member of the genus Crenobacter within the family Neisseriaceae of the phylum Pseudomonadota. Strain SG2303 ^T displayed higher 16 S rRNA gene sequence similarities with members of the genus Crenobacter ranging from 93.5 to 94.0%. Strains C. luteus YIM 78141 ^T and C. cavernae K1W11S-77 ^T were closest related to the isolated strains and were considered as type strains. Growth of strain SG2303 ^T occurred at 10-55 °C (optimum 37 °C), pH 5.0-9.0 (optimum pH 6.0-7.0) and 0-1% (w/v) NaCl (optimum 0%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG2303 ^T and its closely related taxa were 76.1-78.2% and 20.5-22.1%, respectively. The genomic DNA G + C content was 62.2%. The quinone of strain SG2303 ^T was Q-8. The major fatty acids (> 10%) of strain SG2303 ^T were C 16:0 (30.6%), summed feature 3 (C 16:1 ω7c and/or C 16:1 ω6c) (26.0%) and C 12:0 3OH (12.1%). The polar lipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phospholipids (PL), glycolipid (GL) and unidentified lipids (UL). Based on the results of the phylogenetic, physiological, biochemical, and morphological analysis, strain SG2303 ^T is recognized as a novel species of the genus Crenobacter, for which the name Crenobacter oryzisoli sp. nov. is proposed. The type strain is SG2303 ^T (= GDMCC 1.3970 ^T  = JCM 36468 ^T ). In addition, SG2303 ^T was also able of phosphorus solubilization and promoting the growth of rice seeds. Strain SG2303 ^T exhibited a relatively high dissolvable phosphorus content of 2.52 µg·mL ^- 1 .
(© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29(12):2607–2618. https://doi.org/10.1093/nar/29.12.2607. (PMID: 10.1093/nar/29.12.26071141067055746)
Castagno LN, Estrella MJ, Sannazzaro AI, Grassano AE, Ruiz OA (2011) Phosphate-solubilization mechanism and in vitro plant growth promotion activity mediated by Pantoea eucalypti isolated from Lotus tenuis rhizosphere in the Salado River Basin (Argentina). J Appl Microbiol 110(5):1151–1165. https://doi.org/10.1111/j.1365-2672.2011.04968.x. (PMID: 10.1111/j.1365-2672.2011.04968.x21299771)
Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2,4-diaminobutyric acid. J Appl Microbiol 48:459–470. https://doi.org/10.1111/j.1365-2672.1980.tb01036.x. (PMID: 10.1111/j.1365-2672.1980.tb01036.x)
Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100(2):221–230. https://doi.org/10.1099/00221287-100-2-221. (PMID: 10.1099/00221287-100-2-221894261)
Dong L, Ming H, Zhou EM, Yin YR, Liu L et al (2015) Crenobacter luteus gen. nov., sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 65(1):214–219. https://doi.org/10.1099/ijs.0.060996-0. (PMID: 10.1099/ijs.0.060996-025332210)
Dong ZY, Narsing Rao MP, Wang HF, Fang BZ, Liu YH et al (2019) Transcriptomic analysis of two endophytes involved in enhancing salt stress ability of Arabidopsis thaliana. Sci Total Environ 686:107–117. https://doi.org/10.1016/j.scitotenv.2019.05.483. (PMID: 10.1016/j.scitotenv.2019.05.48331176810)
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376. https://doi.org/10.1007/BF01734359. (PMID: 10.1007/BF017343597288891)
Felsenstein J (1985) Confidence limits on phylogenies: an approach using. Bootstrap Evol 39(4):783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x. (PMID: 10.1111/j.1558-5646.1985.tb00420.x)
Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416. https://doi.org/10.1093/sysbio/20.4.406. (PMID: 10.1093/sysbio/20.4.406)
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57(Pt 1):81–91. https://doi.org/10.1099/ijs.0.64483-0. (PMID: 10.1099/ijs.0.64483-017220447)
Gregersen T (1978) Rapid method for distinction of Gram negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5:123–127. https://doi.org/10.1007/BF00498806. (PMID: 10.1007/BF00498806)
Han XJ, Zeng QW, Zhao YP (2020) Identification of inorganic phosphate-solubilizing bacterium Mp1-Ha4 in poplar rhizosphere and its phosphate-solubilizing mechanism. Biotechnol Bull 36(3):141–147. https://doi.org/10.13560/j.cnki.biotech.bull.1985.2019-0952. (PMID: 10.13560/j.cnki.biotech.bull.1985.2019-0952)
He K, Li XP, Dong LL (2018) The effects of flue gas desulfurization gypsum (FGD gypsum) on P fractions in a coastal plain soil. J Soils Sediments 18:804–815. https://doi.org/10.1007/s11368-017-1821-2. (PMID: 10.1007/s11368-017-1821-2)
Hsieh YJ, Wanner BL (2010) Global regulation by the seven-component pi signaling system. Curr Opin Microbiol 13(2):198–203. https://doi.org/10.1016/j.mib.2010.01.014. (PMID: 10.1016/j.mib.2010.01.014201719282847643)
Itoh H, Xu Z, Masuda Y, Ushijima N, Hayakawa C et al (2021) Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas. Int J Syst Evol Microbiol 71(1). https://doi.org/10.1099/ijsem.0.004607.
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32(Database issue):D277–D280. https://doi.org/10.1093/nar/gkh063. (PMID: 10.1093/nar/gkh06314681412308797)
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M et al (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34(Database issue):D354–D357. https://doi.org/10.1093/nar/gkj102. (PMID: 10.1093/nar/gkj10216381885)
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120. https://doi.org/10.1007/BF01731581. (PMID: 10.1007/BF017315817463489)
Kirui CK, Njeru EM, Runo S (2022) Diversity and phosphate solubilization efficiency of phosphate solubilizing bacteria isolated from semi-arid agroecosystems of Eastern Kenya. Microbiol Insights 15:11786361221088991. https://doi.org/10.1177/11786361221088991. (PMID: 10.1177/11786361221088991354641209019392)
Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178(4535):703. https://doi.org/10.1038/178703a0. (PMID: 10.1038/178703a013369512)
Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded Ion exchanger as stationary phases. J Liq Chromatogr 5(12):2359–2367. https://doi.org/10.1080/01483918208067640. (PMID: 10.1080/01483918208067640)
Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108. https://doi.org/10.1093/nar/gkm160. (PMID: 10.1093/nar/gkm160174523651888812)
Li Y, Yu J, Guo Z, Song X, Xu M et al (2023) First report of peanut root rot caused by Fusarium acuminatum in Shandong Province, China. Plant Dis 107(9):2882. https://doi.org/10.1094/PDIS-11-22-2681-PDN.
Liu JY, Li YH, Liu JJ, Wang SW, Liu HQ et al (2023) Grazing promotes soil phosphorus cycling by enhancing soil microbial functional genes for phosphorus transformation in plant rhizosphere in a semi-arid natural grassland. Geoderma 430:116303. https://doi.org/10.1016/j.geoderma.2022.116303. (PMID: 10.1016/j.geoderma.2022.116303)
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):955–964. https://doi.org/10.1093/nar/25.5.955. (PMID: 10.1093/nar/25.5.9559023104146525)
Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M (2022) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 50(D1):D801–D807. https://doi.org/10.1093/nar/gkab902. (PMID: 10.1093/nar/gkab90234634793)
Minnikin DE, Collins MD, Goodfellow M (1979) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47(1):87–95. https://doi.org/10.1111/j.1365-2672.1979.tb01172.x. (PMID: 10.1111/j.1365-2672.1979.tb01172.x)
Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al (2018) UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56(4):280–285. https://doi.org/10.1007/s12275-018-8014-6. (PMID: 10.1007/s12275-018-8014-629492869)
Narsing Rao MP, Dong ZY, Kan Y, Dong L, Li S et al (2020) Description of Paenibacillus tepidiphilus sp. nov., isolated from a tepid spring. Int J Syst Evol Microbiol 70(3):1977–1981. https://doi.org/10.1099/ijsem.0.004004.
Ren Y, Yu G, Shi CP, Zhang D, Liu LM et al (2022) Majorbio Cloud: a one-stop, comprehensive bioinformatic platform for multi-omics analyses. iMeta 1(2):e12. https://doi.org/10.1002/imt2.12. (PMID: 10.1002/imt2.123886857310989754)
Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106(45):19126–19131. https://doi.org/10.1073/pnas.0906412106.
Rodriguez -RLM, Konstantinidis KT (2014) By passing cultivation to identify bacterial species. Microbe Magazine 9(3):111–118. https://doi.org/10.1128/microbe.9.111.1. (PMID: 10.1128/microbe.9.111.1)
Rodriguez -RLM, Konstantinidis KT (2016) The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ 4:e1900v1. https://doi.org/10.7287/peerj.preprints.1900v1.
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454. (PMID: 10.1093/oxfordjournals.molbev.a0404543447015)
Sang Y, Jin L, Zhu R, Yu XY, Hu S et al (2022) Phosphorus-solubilizing capacity of Mortierella species isolated from Rhizosphere Soil of a Poplar Plantation. Microorganisms 10(12):2361. https://doi.org/10.3390/microorganisms10122361. (PMID: 10.3390/microorganisms10122361365576159785298)
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News 20:16.
Shi SB, Wu JF, Yang LF, Jiang MG, Gao CM et al (2021) Crenobacter intestini sp. nov., isolated from the intestinal tract of Konosirus punctatus. Curr Microbiol 78(4):1686–1691. https://doi.org/10.1007/s00284-021-02372-5. (PMID: 10.1007/s00284-021-02372-533683417)
Solari AA, Herrero MM, Painceira MT (1968) Use of malachite green for staining flagella in bacteria. Appl Microbiol 16(5):792. https://doi.org/10.1128/am.16.5.792-.1968. (PMID: 10.1128/am.16.5.792-.19684173339547519)
Tamura K, Stecher G, Kumar S (2021) MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 38(7):3022–3027. https://doi.org/10.1093/molbev/msab120. (PMID: 10.1093/molbev/msab120338924918233496)
Wang S, Liu W, He Y et al (2021) bZIP72 promotes submerged rice seed germination and coleoptile elongation by activating ADH1. Plant Physiol Biochem 169:112–118. https://doi.org/10.1016/j.plaphy.2021.11.005. (PMID: 10.1016/j.plaphy.2021.11.00534775177)
Yang Z, Xu J, Sheng M, Qiu J, Zhu J et al (2020) Crenobacter caeni sp. nov. isolated from sludge. Curr Microbiol 77(12):4180–4185. https://doi.org/10.1007/s00284-020-02233-7. (PMID: 10.1007/s00284-020-02233-733047166)
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al (2017a) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67(5):1613–1617. https://doi.org/10.1099/ijsem.0.001755. (PMID: 10.1099/ijsem.0.001755280055265563544)
Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110(10):1281–1286. https://doi.org/10.1007/s10482-017-0844-4. (PMID: 10.1007/s10482-017-0844-428204908)
Yuan L, Ju F (2023) Potential auxiliary metabolic capabilities and activities reveal biochemical impacts of viruses in municipal Wastewater treatment plants. Environ Sci Technol 57(13):5485–5498. https://doi.org/10.1021/acs.est.2c07800. (PMID: 10.1021/acs.est.2c0780036947091)
Zhang Q, Zhang C, Zhu Y, Yuan C, Zhao T (2021) Effect of bacteria-to-algae volume ratio on treatment performance and microbial community of a novel heterotrophic nitrification-aerobic denitrification bacteria-chlorella symbiotic system. Bioresour Technol 342:126025. https://doi.org/10.1016/j.biortech.2021.126025. (PMID: 10.1016/j.biortech.2021.12602534600093)
Zhu HZ, Jiang CY, Liu SJ (2019) Crenobacter cavernae sp. nov., isolated from a karst cave, and emended description of the genus Crenobacter. Int J Syst Evol Microbiol 69(2):476–480. https://doi.org/10.1099/ijsem.0.003179. (PMID: 10.1099/ijsem.0.00317930556805)

FJHYF-L-2023-37 Special Funds Program for Promoting High-Quality Development of Marine and Fishery Industry in Fujian Province; GJYS202306 Fujian Academy of Agricultural Sciences; 2021YFD1900400 National Key Research and Development Program of China; 2023350000200089 Fujian Provincial Tobacco Monopoly Bureau

Keywords: Crenobacter oryzisoli sp. nov.; Paddy soil.; Phosphate-solubilizing ability

0 (RNA, Ribosomal, 16S)
0 (DNA, Bacterial)
0 (Fatty Acids)
0 (Phosphates)
0 (Phospholipids)

Date Created: 20240702 Date Completed: 20240702 Latest Revision: 20240806

20240806

10.1007/s00203-024-04070-9

38954015