Abstract
The taxonomic position of a Gram-stain-negative, rod-shaped bacterial strain, designated PI11T, isolated from the rhizospheric sediment of Phragmites karka was characterized using a polyphasic approach. Strain PI11T could grow optimally at 1.0% NaCl concentration with pH 7.0 at 30°C and was positive for oxidase and catalase but negative for hydrolysis of starch, casein, and esculin ferric citrate. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strain PI11T belonged to the genus Pseudomonas sharing the highest sequence similarities with Pseudomonas indoloxydans JCM 14246T (99.72%), followed by, Pseudomonas oleovorans subsp. oleovorans DSM 1045T (99.29%), Pseudomonas toyotomiensis JCM 15604T (99.15%), Pseudomonas chengduensis DSM 26382T (99.08%), Pseudomonas oleovorans subsp. lubricantis DSM 21016T (99.08%), and Pseudomonas alcaliphila JCM 10630T (99.01%). Experimental DNA-DNA relatedness between strain PI11T and P. indoloxydans JCM 14246T was 49.4%. The draft genome of strain PI11T consisted of 4,884,839 bp. Average nucleotide identity between the genome of strain PI11T and other closely related type strains ranged between 77.25–90.74%. The polar lipid pattern comprised of phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine. The major (> 10%) cellular fatty acids were C18:1ω6c/ω7c, C16:1ω6c/ω7c, and C16:0. The DNA G + C content of strain PI11T was 62.4 mol%. Based on the results of polyphasic analysis, strain PI11T was delineated from other closely related type strains. It is proposed that strain PI11T represents represents a novel species of the genus Pseudomonas, for which the name Pseudomonas sediminis sp. nov. is proposed. The type strain is PI11T (= KCTC 42576T = DSMZ 100245T).
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Angiuoli, S.V., Gussman, A., Klimke, W., Cochrane, G., Field, D., Garrity, G., Kodira, C.D., Kyrpides, N., Madupu, R., Markowitz, V., et al. 2008 Toward an online repository of standard operating procedures (SOPs) for (meta)genomic annotation. OMICS 12, 137–141
Anzai, Y., Kim, H., Park, J.Y., Wakabayashi, H., and Oyaizu, H. 2000 Phylogenetic affliation of the pseudomonads based on 16S rRNA sequence. Int. J. Syst. Evol. Microbiol. 50, 1563–1589
Behera, P., Mahapatra, S., Mohapatra, M., Kim, J.Y., Adhya, T.K., Raina, V., Suar, M., Pattnaik, A.K., and Rastogi, G. 2017a. Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon. Sci. Total Environ. 595, 472–485
Behera, P., Mohapatra, M., Adhya, T.K., Suar, M., Pattnaik, A.K., and Rastogi, G. 2018 Structural and metabolic diversity of rhizosphere microbial communities of Phragmites karka in a tropical coastal lagoon. Appl. Soil Ecol. 125, 202–212
Behera, P., Ramana, V.V., Maharana, B., Joseph, N., Vaishampayan, P., Singh, N.K., Shouche, Y., Bhadury, P., Mishra, S.R., Raina, V., et al. 2017b. Mangrovibacter phragmitis sp. nov., an endophyte isolated from the roots of Phragmites karka. Int. J. Syst. Evol. Microbiol. 67, 1228–1234
Bligh, E.G. and Dyer, W.J. 1959 A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 37, 911–917
De Ley, J., Cattoir, H., and Reynaerts, A. 1970 The quantitative measurement of DNA hybridization from renaturation rates. Eur. J. Biochem. 12, 133–142
Delorme, S., Lemanceau, P., Christen, R., Corberand, T., Meyer, J.M., and Gardan, L. 2002 Pseudomonas lini sp. nov., a novel species from bulk and rhizospheric soils. Int. J. Syst. Evol. Microbiol. 52, 513–523
Driscoll, J.A., Brody, S.L., and Kollef, M.H. 2007 The epidemiology, pathogenesis and treatment of Pseudomonas aeruginosa infections. Drugs 67, 351–368
Gillis, M., De Ley, J., and De Cleene, M. 1970 The determination of molecular weight of bacterial genome DNA from renaturation rates. Eur. J. Biochem. 12, 143–153
Gonzalez, J.M. and Saiz-Jimenez, C. 2002 A fluorimetric method for the estimation of G + C mol% content in microorganisms by thermal denaturation temperature. Environ. Microbiol. 4, 770–773
Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P., and Tiedje, J.M. 2007 DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81–91
Greene, R.A., Blum, E.F., Decoro, C.T., Fairchild, R.B., Kaplan, M.T., Landau, J.L., and Sharp, T.R. 1951 Rapid methods for the detection of motility. J. Bacteriol. 62, 347
He, T., Li, Z., Sun, Q., Xu, Y., and Ye, Q. 2016 Heterotrophic nitrification and aerobic denitrification by Pseudomonas tolaasii Y-11 without nitrite accumulation during nitrogen conversion. Bioresour. Technol. 200, 493–499
Lane, D.J., Pace, B., Olsen, G.J., Stahl, D.A., Sogin, M.L., and Pace, N.R. 1985 Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. USA 82, 6955–6959
Lenaerts, M., Alvarez-Perez, S., de Vega, C., Assche, A.V., Johnson, S.D., Willems, K.A., Herrera, C.M., Jacquemyn, H., and Lievens, B. 2014 Rosenbergiella australoborealis sp. nov., Rosenbergiella collisarenosi sp. nov., and Rosenbergiella epipactidis sp. nov., three novel bacterial species isolated from floral nectar. Syst. Appl. Microbiol. 37, 402–411
Loveland-Curtze, J., Miteva, V.I., and Brenchley, J.E. 2011 Evaluation of a new fluorimetric DNA-DNA hybridization method. Can. J. Microbiol. 57, 250–255
Ma, J., Xu, L., and Jia, L. 2012 Degradation of polycyclic aromatic hydrocarbons by Pseudomonas sp. JM2 isolated from active sewage sludge of chemical plant. J. Environ. Sci. (China) 24, 2141–2148
Majeed, H.A. and AL-Sabhany, R.O.S. 2016 Isolation and identification of Pseudomonas aeruginosa from different sources (soil, wound, urine) and checking its MIC with various antibiotics. Helix 4–5, 795–799
Manickam, N., Ghosh, A., Jain, R.K., and Mayilraj, S. 2008 Description of a novel indole-oxidizing bacterium Pseudomonas indoloxydans sp. nov., isolated from a pesticide-contaminated site. Syst. Appl. Microbiol. 31, 101–107
Marmur, J. 1961 A procedure for isolation of deoxyribonucleic acid from micro-organisms. J. Mol. Biol. 3, 208–218
Miller, J.R., Koren, S., and Sutton, G. 2010 Assembly algorithms for next-generation sequencing data. Genomics 95, 315–327
Minnikin, D.E., O’Donnell, A.G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A., and Parlett, J.H. 1984 An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods 2, 233–241
Morris, C.E., Sands, D.C., Vinatzer, B.A., Glaux, C., Guilbaud, C., Buffiere A., Yan, S., Dominguez, H., and Thompson, B.M. 2008 The life history of the plant pathogen Pseudomonas syringae is linked to the water cycle. ISME J. 2, 321–334
Mulamattathil, S.G., Bezuidenhout, C., Mbewe, M., and Ateba, C.N. 2014 Isolation of environmental bacteria from surface and drinking water in Mafikeng, South Africa, and characterization using their antibiotic resistance profiles. J. Pathog. 2014, 371208
Murray, R.G.E., Doetsch, R.N., and Robinow, C.F. 1994 Determinative and cytological light microscopy, pp. 21–41 In Gerhardt, P., Murray, R.G.E., Wood, W.A., and Krieg, N.R. (ed.), Methods for general and Molecular Bacteriology. American Society for Microbiology, Wahington, DC, USA.
Palleroni, N.J. 2015 Pseudomonas. Bergey’s manual of systematics of archaea and bacteria. John Wiley & Sons, Bergey’s Manual Trust.
Pruesse, E., Peplies, J., and Glöckner, F.O. 2012 SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823–1829
Rodriguez-R, L.M. and Konstantinidis, K.T. 2014 Bypassing cultivation to identify bacterial species. Microbe 9, 111–118
Rogers, J.S. and Swofford, D.L. 1998 A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences. Syst. Biol. 47, 77–89
Rossello, R., Garcia-Valdes, E., Lalucat, J., and Ursing, J. 1991 Genotypic and phenotypic diversity of Pseudomonas stutzeri. Syst. Appl. Microbiol. 14, 150–157
Saitou, N. and Nei, M. 1987 The Neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425
Sasser, M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101 MIDI Inc., Newark, DE, USA.
Simmons, J.S. 1926 A culture medium for differentiating organisms of typhoid-colon aerogenes groups and for isolation of certain fungi. J. Infect. Dis. 39, 209–214
Smibert, R.M. and Krieg, N.R. 1994 Phenotypic characterization, pp. 607–654 In Gerhardt, P., Murray, R.G.E., Wood, W.A., and Krieg, N.R. (eds.), Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, USA.
Srichandan, S., Kim, Y.J., Kumar, A., Mishra, D.R., Bhadury, P., Muduli, P.R., Pattnaik, A.K., and Rastogi, G. 2015 Inter annual and cyclone-driven variability in phytoplankton communities of a tropical coastal lagoon. Mar. Poll. Bull. 101, 39–52
Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. 2013 MEGA6 Molecular Evolutionary Genetics Analysis Version 6.0 Mol. Biol. Evol. 30, 2725–2729
Thompson, C.C., Chimetto, L., Edwards, R.A., Swings, J., Stackebrandt, E., and Thompson, F.L. 2013 Microbial genomic taxonomy. BMC Genomics 14, 913
Toro, M., Ramírez-Bahena, M.H., Velazquez, E., and Peix, A. 2013 Pseudomonas guariconensis sp. nov., isolated from rhizospheric soil. Int. J. Syst. Evol. Microbiol. 63, 4413–4420
Vancanneyt, M., Witt, S., Abraham, W.R., Kersters, K., and Fredrickson, H.L. 1996 Fatty acid content in whole-cell hydrolysates and phospholipid fractions of pseudomonads: a taxonomic evaluation. Sytem. Appl. Microbiol. 19, 528–540
Vessey, J.K. 2003 Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255, 571–586
Wayne, L.G., Brenner, D.J., Colwell, R.R., Grimont, P.A.D., Kandler, O., Krichevsky, M.I., Moore, L.H., Moore, W.E.C., Murray, R.G.E., Stackebrandt, E., et al. 1987 Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37, 463–464
Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. 2017 Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617
Zhu, W., Lomsadze, A., and Borodovsky, M. 2010 Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 38, e132
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Behera, P., Mahapatra, M., Seuylemezian, A. et al. Taxonomic description and draft genome of Pseudomonas sediminis sp. nov., isolated from the rhizospheric sediment of Phragmites karka. J Microbiol. 56, 458–466 (2018). https://doi.org/10.1007/s12275-018-7549-x
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DOI: https://doi.org/10.1007/s12275-018-7549-x