Abstract
A short rod-shaped, yellow–orange pigmented, strictly aerobic bacterium, designated as strain H2T, was isolated from the wetland soil of Halla Mountain, Jeju-island, South Korea. Growth was observed at temperatures of 10–30 °C (optimum at 25–30 °C), pH of 6–8 (optimum at pH 7), and salt concentrations of 0–1% (w/v) NaCl (optimum at 0%). The strain H2T was found to be a catalase and oxidase-positive, non-motile, Gram-negative bacterium. On the basis of 16S rRNA gene sequence similarity and phylogenetic analysis, strain H2T was found to be related to the members of the Chitinophagaceae family, being closely related to Taibaiella chishuiensis AY17T (94.3% sequence similarity). The major polar lipids are phosphatidylethanolamine and glycolipid. Strain H2T contained MK-7 as the only menaquinone as well as iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH as the major fatty acids (> 15%). The DNA G+C content of strain H2T was determined to be 48.3 mol%. Based on the phylogenetic, phenotypic characteristics and chemotaxonomic analysis data, strain H2T (= KCTC 62115T = JCM 32353T) should be classified as representative of a novel species of a novel genus within the family Chitinophagaceae, for which the name Edaphocola aurantiacus gen. nov., sp. nov., is proposed.
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Albert RA, Zitomer D, Dollhopf M, Schauer-Gimenez AE, Struble C, King M, Son S, Langer S, Busse HJ (2014) Proposal of Vibrionimonas magnilacihabitans gen. nov., sp. nov., a curved Gram-stain-negative bacterium isolated from lake water. Int J Syst Evol Microbiol 64:613–620
Anders H, Dunfield PF, Lagutin K, Houghton KM, Power JF, Mackenzie AD, Vyssotski M, Ryan JL, Hanssen EG, Moreau JW, Stott MB (2014) Thermoflavifilum aggregans gen. nov., sp. nov., a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteroidetes. Int J Syst Evol Microbiol 64:1264–1270
Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman J (eds) (1995) Short protocols in molecular biology: a compendium of methods from current protocols in molecular biology, 3rd edn. Wiley, New York
Chaudhary DK, Kim J (2016) Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 66:4347–4354
Chung EJ, Park TS, Jeon CO, Chung YR (2012) Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.). Int J Syst Evol Microbiol 62:3030–3035
Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354
Eder W, Peplies J, Wanner G, Fruhling A, Verbarg S (2015) Hydrobacter penzbergensis gen. nov., sp. nov., isolated from purified water. Int J Syst Evol Microbiol 65:920–926
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Gonzalez JM, 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
Hall T (1997) BioEdit. Biological sequence alignment editor for Win 95/98/NT/2K/XP. Ibis Therapeutics, Carlsbad
Han JH, Baek K, Lee MH (2017) Lacibacter nakdongensis sp. nov., isolated from river sediment. Int J Syst Evol Microbiol 67:352–356
Hanada S, Tamaki H, Nakamura K, Kamagata Y (2014) Crenotalea thermophila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a hot spring. Int J Syst Evol Microbiol 64:1359–1364
Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by highperformance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469
Jin L, Shin SY, Lee HG, Ahn CY, Oh HM (2013) Lacibacter daechungensis sp. nov., isolated from deep freshwater of a reservoir. Int J Syst Evol Microbiol 63:4519–4523
Kampfer P, Young CC, Sridhar KR, Arun AB, Lai WA, Shen FT, Rekha PD (2006) Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov. Int J Syst Evol Microbiol 56:2223–2228
Kampfer P, Lodders N, Falsen E (2011) Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. Int J Syst Evol Microbiol 61:518–523
Kang H, Kim H, Joung Y, Joh K (2016) Parasediminibacterium paludis gen. nov., sp. nov., isolated from wetland. Int J Syst Evol Microbiol 66:326–331
Kim MK, Kim TS, Joung Y, Han JH, Kim SB (2016) Taibaiella soli sp. nov., isolated from pine forest soil. Int J Syst Evol Microbiol 66:3230–3234
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
Komagata K, Suzuki KI (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–205
Krieg NR, Ludwig W, Whitman W, Hedlund BP, Paster BJ, Staley JT, Ward N, Brown D, Parte A (eds) (2010) Bergey’s manual of systematic bacteriology, volume 4. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes, vol 4. Springer, Berlin, pp 351–358
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
Kuykendall LD, Roy MA, O’Neill JJ, Devine TE (1988) Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 38:358–361
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
Lee HG, An DS, Im WT, Liu QM, Na JR, Cho DH, Jin CW, Lee ST, Yang DC (2007) Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 57:1396–1401
Madhaiyan M, Poonguzhali S, Senthilkumar M, Pragatheswari D, Lee JS, Lee KC (2015) Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil. Int J Syst Evol Microbiol 65:578–586
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241
Powers EM (1995) Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61:3756–3758
Qu JH, Yuan HL, Yang JS, Li HF, Chen N (2009) Lacibacter cauensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from sediment of a eutrophic lake. Int J Syst Evol Microbiol 59:1153–1157
Rosselló-Móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: timely move towards a database-driven systematics of archaea and bacteria. Syst Appl Microbiol 40:121–122
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT (2016) Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 66:4039–4045
Siddiqi MZ, Aslam Z, Im WT (2017) Arachidicoccus ginsenosidivorans sp. nov., with ginsenoside-converting activity isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 67:1005–1010
Singh H, Du J, Won K, Yang JE, Akter S, Kim KY, Yin C, Yi TH (2015) Taibaiella yonginensis sp. nov., a bacterium isolated from soil of Yongin city. Antonie Van Leeuwenhoek 108:517–524
Sly LI, Taghavi M, Fegan M (1999) Phylogenetic position of Chitinophaga pinensis in the Flexibacter-Bacteroides-Cytophaga phylum. Int J Syst Bacteriol 49(Pt 2):479–481
Son HM, Kook M, Kim JH, Yi TH (2014) Taibaiella koreensis sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 64:1018–1023
Szabo I, Szoboszlay S, Tancsics A, Szerdahelyi SG, Szucs A, Rado J, Benedek T, Szabo L, Daood HG, Cserhati M, Kriszt B (2016) Taibaiella coffeisoli sp. nov., isolated from the soil of a coffee plantation. Int J Syst Evol Microbiol 66:1627–1632
Tan X, Zhang RG, Meng TY, Liang HZ, Lv J (2014) Taibaiella chishuiensis sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 64:1795–1801
Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
Weon HY, Yoo SH, Kim YJ, Son JA, Kim BY, Kwon SW, Koo BS (2009) Chitinophaga niabensis sp. nov. and Chitinophaga niastensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 59:1267–1271
Weon HY, Kwon SW, Son JA, Kim SJ, Kim YS, Kim BY, Ka JO (2010) Adhaeribacter aerophilus sp. nov., Adhaeribacter aerolatus sp. nov. and Segetibacter aerophilus sp. nov., isolated from air samples. Int J Syst Evol Microbiol 60:2424–2429
Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12:635–645
Yasir M, Chung EJ, Song GC, Bibi F, Jeon CO, Chung YR (2011) Chitinophaga eiseniae sp. nov., isolated from vermicompost. Int J Syst Evol Microbiol 61:2373–2378
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617
Zhang L, Wang Y, Wei L, Wang Y, Shen X, Li S (2013) Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus. Int J Syst Evol Microbiol 63:3769–3776
Zhao R, Chen XY, Li XD, Tian Y, Kong BH, Chen ZL, Li YH (2014) Cnuella takakiae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from Takakia lepidozioides. Int J Syst Evol Microbiol 64:607–612
Acknowledgements
We are grateful to Dr. Bernhard Schink for helping us with etymology. This research was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (MIST) (NRF-2017R1A2B4009448).
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JC isolated the bacterium, designed the study, performed the phenotypic and biochemical characterization, wrote the original draft; SC, GC and DY helped the analysis of taxonomic data; TS designed and supervised the study, edited the original draft.
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Choi, J., Cha, S., Chhetri, G. et al. Edaphocola aurantiacus gen. nov., sp. nov., a new member of the family Chitinophagaceae isolated from wetland soil in South Korea. Antonie van Leeuwenhoek 112, 687–694 (2019). https://doi.org/10.1007/s10482-018-1199-1
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DOI: https://doi.org/10.1007/s10482-018-1199-1