Abstract
Two bacterial strains, 172606-1T and BT10T, were isolated from soil, Korea. Both strains were Gram-stain-negative and rod-shaped bacteria. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 172606-1T formed a distinct lineage within the family Cytophagaceae (order Cytophagales, class Cytophagia, phylum Bacteroidetes). Strain 172606-1T was most closely related to a member of the genus Rhodocytophaga (93.8% 16S rRNA gene sequence similarity to Rhodocytophaga aerolata 5416T-29T). The complete genome sequence of strain 172606-1T is 8,983,451 bp size. Optimal growth occurred at 25 °C and pH 7.0 without NaCl. The major cellular fatty acids were identified as iso-C15:0 and C16:1 ω5c. The major respiratory quinone was MK-7. The major polar lipid was phosphatidylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BT10T belongs to the genus Nibribacter and is closely related to Nibribacter koreensis GSR 3061T (96.5%), Rufibacter glacialis MDT1-10-3T (95.7%), Rufibacter sediminis H-1T (95.1%) and Rufibacter quisquiliarum CAI-18bT (94.9%). The complete genome sequence of strain BT10T is 4,374,810 bp size. The predominant (> 10%) cellular fatty acids of strain BT10T were iso-C15:0 and summed feature 4 (anteiso-C17:1 B/iso-C17:1 I) and a predominant quinone was MK-7. In addition, strain BT10T has phosphatidylethanolamine (PE) as the major polar lipid. On the basis of biochemical, chemotaxonomic and phylogenetic analyses, strain 172606-1T represents a novel bacterial species of the genus Rhodocytophaga, for which the name Rhodocytophaga rosea is proposed and strain BT10T represents a novel species of the genus Nibribacter, for which the name Nibribacter ruber is proposed. The type strains of Rhodocytophaga rosea and Nibribacter ruber are 172606-1T (= KCTC 62096T = NBRC 114410T) and BT10T (= KCTC 62607T = NBRC 114383T), respectively.
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References
Anandham R, Weon HY, Kim SJ, Kim YS, Kwon SW (2010) Rhodocytophaga aerolata gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from air. Int J Syst Evol Microbiol 60:1554–1558
Bernardet JF, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070
Bowman JP (2000) Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50:1861–1868
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2008) BLAST+: architecture and applications. BMC Bioinform 10:421
Cappuccino JG, Sherman N (2002) Microbiology—a laboratory manual, 6th edn. Pearson Education, Inc., Benjamin Cummings, San Francisco
Chin CS, Alexander DH, Marks P et al (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569
Cox MM, Battista JR (2005) Deinococcus radiodurans—the consummate survivor. Nat Rev Microbiol 3:882–892
Felsenstein J (1985) Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469
Im S, Song D, Joe M, Kim D, Park DH, Lim S (2013) Comparative survival analysis of 12 histidine kinase mutants of Deinococcus radiodurans after exposure to DNA-damaging agents. Bioproc Biosyst Eng 36:781–789
Kang JY, Chun J, Jahng KY (2013) Nibribacter koreensis gen. nov., sp. nov., isolated from estuarine water. Int J Syst Evol Microbiol 63:4663–4668
Komagata K, Suzuki K (1987) 4 Lipid and cell-wall analysis in bacterial systematics. Method Microbiol 19:161–207
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549
Lin P, Yan Z, Li C, Kook M, Yi T (2018) Nibribacter flagellatus sp. nov., isolated from rhizosphere of Hibiscus syriacus and emended description of the genus Nibribacter. Antonie Van Leeuwenhoek 111:1777–1784
Liu Q, Liu H, Zhang J, Zhou Y, Xin Y (2016) Rufibacter glacialis sp. nov., a psychrotolerant bacterium isolated from glacier soil. Int J Syst Evol Microbiol 66:315–318
McBride MJ, Liu W, Lu X, Zhu Y, Zhang W (2014) The family Cytophagaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Springer, Berlin
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241
Saitou N, 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
Selvam K, Duncan JR, Tanaka M, Battista JR (2013) DdrA, DdrD, and PprA: components of UV and mitomycin C resistance in Deinococcus radiodurans R1. PLoS ONE 8:e69007
Smibert RM, Krieg NR (1981) General characterization. Manual of methods for general bacteriology. American Society for Microbiology, Washington, pp 409–442
Spaepen S, Vanderleyden J (2011) Auxin and plant-microbe interactions. Cold Spring Harb Perspect Biol 3:a001438
Tatusova T, DiCuccio M, Badretdin A et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624
Weisburg WG, Barns SM, Pellerier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
Xu L, Xu W, Jiang Y, Hu F, Li H (2015) Effects of interactions of auxin-producing bacteria and bacterial-feeding nematodes on regulation of peanut growths. PLoS ONE 10:e0124361
Acknowledgements
This work was supported by a research grant from Seoul Women’s University (2020) and by a grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR201902111). We are grateful to Dr. Aharon Oren (The Hebrew University of Jerusalem, Israel) for helping with the etymology.
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Park, Y., Maeng, S., Han, J.H. et al. Rhodocytophaga rosea sp. nov. and Nibribacter ruber sp. nov., two radiation-resistant bacteria isolated from soil. Antonie van Leeuwenhoek 113, 2177–2185 (2020). https://doi.org/10.1007/s10482-020-01488-1
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DOI: https://doi.org/10.1007/s10482-020-01488-1