A Gram-negative rod, designated strain 1N-3T, was isolated from a rhizome of Phragmites australis grown in Kumtag Desert, China. Phylogenetic analysis showed that the strain is closely related to Phyllobacterium salinisoli LMG 30173T with 99.0% sequence similarity in the 16S rRNA gene and 92.9% in the atpD gene. Growth was observed at salinities of 0–4% (w/v), over a pH range of 5.0–10.0 (optimum 8.0) and at temperatures of 15–40 °C (optimum 30 °C). The predominant cellular fatty acids were identified as summed feature 8 (C18:1ω7c/C18:1ω6c). The G+C content of strain 1N-3T was determined to be 60.1%. Based on phenotypic, chemotaxonomic, phylogenetic properties and genomic comparison, it is concluded that strain 1N-3T represents a novel species of the genus Phyllobacterium, for which the name Phyllobacterium phragmitis sp. nov. is proposed. The type strain is 1N-3T (=KCTC 62183T =ACCC 60071T).
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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Auch AF, Jan M, Klenk HP, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117
Dees PM, Ghiorse WC (2001) Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol Ecol 35:207–216
Flores-Félix JD, Carro L, Velázquez E, Valverde Á, Cerda-Castillo E, García-Fraile P, Rivas R (2013) Phyllobacterium endophyticum sp. nov., isolated from nodules of Phaseolus vulgaris. Int J Syst Evol Microbiol 63:821–826
Holt J (2000) Bergey’s manual of determinative bacteriology. Lippincott Williams & Wilkins, Philadelphia
Jiao YS, Yan H, Ji ZJ, Liu YH, Sui XH, Zhang XX, Wang ET, Chen WX, Chen WF (2015) Phyllobacterium sophorae sp. nov., a symbiotic bacterium isolated from root nodules of Sophora flavescens. Int J Syst Evol Microbiol 65:399–406
Jurado V, Laiz L, Gonzalez JM, Hernandez-Marine M, Valens M, Saiz-Jimenez C (2005) Phyllobacterium catacumbae sp. nov., a member of the order ‘Rhizobiales’ isolated from Roman catacombs. Int J Syst Evol Microbiol 55:1487–1490
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
Knösel D (1962) Prüfung von bakterien auf fähigkeit zur sternbildung. Zentralbl Bakteriol Parasitenkd Infektionskr Hyg II Abt 116:79–100
Lee I, Kim YO, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103
León-Barrios M, Ramírez-Bahena MH, Igual JM, Peix Á, Velázquez E (2018) Phyllobacterium salinisoli sp. nov., isolated from a Lotus lancerottensis root nodule in saline soil from Lanzarote. Int J Syst Evol Microbiol 68:1085–1089
Li B, Yang X, Tan H, Ke B, He D, Ke CW, Zhang YH (2017) Vibrio parahaemolyticus O4:K8 forms a potential predominant clone in southern China as detected by whole-genome sequence analysis. Int J Food Microbiol 244:90–95
Liu L, Li LB, Song Z, Wang SY, Zhang J, Zhang XX, Sun QW (2017) Parapedobacter deserti sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems. Int J Syst Evol Microbiol 67:2148–2152
Mantelin S, Saux MF, Zakhia F, Béna G, Bonneau S, Jeder H, Lajudie P, Cleyet-Marel JC (2006) Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov. Int J Syst Evol Microbiol 56:827–839
Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60–73
Mergaert J, Swings J (2015) Phyllobacterium. In: Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J, DeVos P, Hedlund B, Dedysh S (eds) Bergey’s manual of systematics of archaea and bacteria. Wiley, New York
Mergaert J, Cnockaert MC, Swings J (2002) Phyllobacterium myrsinacearum (subjective synonym Phyllobacterium rubiacearum) emend. Int J Syst Evol Microbiol 52:1821–1823
Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131
Rogers JS, Swofford DL (1998) A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences. Syst Biol 47:77–89
Rosselló-Móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria. Antonie Van Leeuwenhoek 110:455–456
Safronova VI, Sazanova AL, Kuznetsova IG, Belimov AA, Andronov EE, Chirak ER, Popova JP, Verkhozina AV, Willems A, Tikhonovich IA (2018) Phyllobacterium zundukense sp. nov. a novel species of rhizobia isolated from root nodules of the legume species oxytropis triphylla (pall.) pers. Int J Syst Evol Microbiol 68:1644–1651
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sánchez M, Ramírez-Bahena MH, Peix A, Lorite MJ, Sanjuán J, Velázquez E, Monza J (2014) Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus. Int J Syst Evol Microbiol 64:781–786
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc
Smibert RM (1994) Phenotypic characterization. Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 607–654
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
Tatusova T, Dicuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624
Valverde A, Velázquez E, Fernández-Santos F, Vizcaíno N, Rivas R, Mateos PF, Martínez-Molina E, Igual JM, Willems A (2005) Phyllobacterium trifolii sp. nov., nodulating Trifolium and Lupinus in Spanish soils. Int J Syst Evol Microbiol 55:1985–1989
Weir BS, Turner SJ, Silvester WB, Park DC, Young JM (2004) Unexpectedly diverse Mesorhizobium strains and Rhizobium leguminosarum nodulate native legume genera of New Zealand, while introduced legume weeds are nodulated by Bradyrhizobium species. Appl Environ Microbiol 70:5980–5987
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617
This work was supported by The State Key Research and Development Program of China (2016YFC0500801).
Conflict of interest
The authors declare that there are no conflicts of interest.
No specific ethical or institutional permits were required to conduct sampling and the experimental studies did not involve endangered or protected species.
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Liang, Lx., Sun, Qw., Hui, N. et al. Phyllobacterium phragmitis sp. nov., an endophytic bacterium isolated from Phragmites australis rhizome in Kumtag Desert. Antonie van Leeuwenhoek 112, 661–668 (2019). https://doi.org/10.1007/s10482-018-1195-5
- Phragmites australis
- Novel species