Skip to main content
SpringerLink
Log in

Limoniibacter endophyticus gen. nov., sp. nov., an alphaproteobacterium isolated from the roots of Limonium otolepis

  • Original Paper
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

A Gram-negative bacterium, designated as strain YIM 690229T, was isolated from the roots of Limonium otolepis. The strain was able to grow at 10–40 °C (optimum, 28–37 °C), pH 6.0–8.0 (optimum, 7.0) and in the presence of up to 7% NaCl (w/v) (optimum, up to 2.5%). Comparative 16S rRNA gene sequence analysis revealed that strain YIM 690229T shared less than 93.9% sequence similarities with members within the order Rhizobiales, and was remotely related to members of the family Hyphomicrobiaceae. Strain YIM 690229T was characterized by the presence of Q-10 as the predominant respiratory lipoquinone. The major fatty acids (> 10%) detected were C18:1 ω7c, C16:0, anteiso-C15:0 and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B). The polar lipids consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanoamine and two unidentified lipids. The genomic DNA G + C content was 57.2 mol%. Data from this polyphasic taxonomy study suggested that strain YIM 690229T should be classified as a new species of a new genus within the family Hyphomicrobiaceae for which the name Limoniibacter endophyticus gen. nov., sp. nov., is proposed. The type species of the genus Limoniibacter gen. nov. is Limoniibacter endophyticus. The type strain of the species Limoniibacter endophyticus sp. nov. is YIM 690229T (= KCTC 42097T = JCM 30141T = CCTCC AB 2014130T = CGMCC 1.12906T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Buck JD (1982) Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993

    CAS  PubMed  PubMed Central  Google Scholar 

  • Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2,4-diaminobutyric acid. Appl Bacteriol 48:459–470

    Article  CAS  Google Scholar 

  • Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45:316–354

    CAS  PubMed  PubMed Central  Google Scholar 

  • Doronina NV, Braus-Strohmeyer SA, Leisinger T, Trotsenko YA (1995) Isolation and characterization of a new facultatively methylotrophic bacterium: description of Methylorhabdus multivorans gen. nov., sp. nov. Syst Appl Microbiol 18:92–98

    Article  CAS  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  PubMed  Google Scholar 

  • Fritz I, Strömpl C, Abraham WR (2004) Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the ‘Alphaproteobacteria’ and description of the Angulomicrobium amanitiforme sp. nov. Int J Syst Evol Microbiol 54:651–657

    Article  CAS  PubMed  Google Scholar 

  • Fukai Y, Abe M, Kobayashi M, Ishihara K, Oikawa H, Yano Y, Satomi M (2012) Maritalea porphyrae sp. nov., isolated from a red alga (Porphyra yezoensis), and transfer of Zhangella mobilis to Maritalea mobilis comb. nov. Int J Syst Evol Microbiol 62:43–48

    Article  Google Scholar 

  • Gebers R, Beese M (1988) Pedomicrobium americanum sp. nov., and Pedomicrobium australicum sp. nov. from aquatic habitats, Pedomicrobium gen. emend., and Pedomicrobium ferrugineum sp. emend. Int J Syst Bacteriol 38:303–315

    Article  Google Scholar 

  • Geng S, Pan XC, Mei R, Wang YN, Sun JQ, Liu XY, Tang YQ, Wu XL (2015) Paradevosia shaoguanensis gen. nov., sp. nov., isolated from a coking wastewater. Curr Microbiol 70:110–118

    Article  CAS  PubMed  Google Scholar 

  • Hiraishi A (1997) Transfer of the bacteriochlorophyll b-containing phototrophic bacteria Rhodopseudomonas viridis and Rhodopseudomonas sulfoviridis to the genus Blastochloris gen. nov. Int J Syst Bacteriol 47:217–219

    Article  CAS  PubMed  Google Scholar 

  • Hiraishi A, Ueda Y (1994) Rhodoplanes gen. nov., a new genus of phototrophic bacteria including Rhodopseudomonas rosea as Rhodoplanes roseus comb. nov., and Rhodoplanes elegans sp. nov. Int J Syst Bacteriol 44:665–673

    Article  Google Scholar 

  • Hirsch P, Hoffmann B (1989) Dichotomicrobium thermohalophilum gen. nov., spec., nov., budding prosthecate bacteria from the solar lake (Sinai) and some related strains. Syst Appl Microbiol 11:291–301

    Article  Google Scholar 

  • Hwang CY, Cho BC (2008) Cucumibacter marinus gen. nov., sp. nov., a marine bacterium in the family Hyphomicrobiaceae. Int J Syst Evol Microbiol 58:1591–1597

    Article  CAS  PubMed  Google Scholar 

  • Hwang CY, Cho KD, Yih W, Cho BC (2009) Maritalea myrionectae gen. nov., sp. nov., isolated from a culture of the marine ciliate Myrionecta rubra. Int J Syst Evol Microbiol 59:609–614

    Article  CAS  PubMed  Google Scholar 

  • Irgens RL, Kersters K, Segers P, Gillis M, Staley JT (1991) Aquabacter spiritensis gen. nov., sp. nov., an aerobic, gas-vacuolate aquatic bacterium. Arch Microbiol 155:137–142

    Article  Google Scholar 

  • Kim HS, Srinivasan S, Lee SS (2016) Methyloterrigena soli gen. nov., sp. nov., a methanol-utilizing bacterium isolated from chloroethylene-contaminated soil. Int J Syst Evol Microbiol 66:101–106

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703–704

    Article  CAS  PubMed  Google Scholar 

  • Lányí B (1987) Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67

    Google Scholar 

  • Lee JS, Shin YK, Yoon JH, Takeuchi M, Pyun YR, Park YH (2001) Sphingomonas aquatilis sp. nov. Sphingomonas koreensis sp. nov. and Sphingomonas taejonenesis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. Int J Syst Evol Microbiol 51:1491–1498

    Article  CAS  PubMed  Google Scholar 

  • Leifson E (1960) Atlas of bacterial flagellation. Academic Press, London

    Book  Google Scholar 

  • Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57:1424–1428

    Article  PubMed  Google Scholar 

  • Li J, Zhao GZ, Huang HY, Qin S, Zhu WY, Zhao LX, Xu LH, Zhang S, Li WJ, Strobel G (2012) Isolation and characterization of culturable endophytic actinobacteria associated with Artemisia annua L. Antonie Van Leeuwenhoek 101:515–527

    Article  PubMed  Google Scholar 

  • Martineau C, Villeneuve C, Mauffrey F, Villemur R (2013) Hyphomicrobium nitrativorans sp. nov., isolated from the biofilm of a methanol-fed denitrification system treating seawater at the Montreal Biodome. Int J Syst Evol Microbiol 63:3777–3781

    Article  CAS  PubMed  Google Scholar 

  • Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G + C content of deoxyribonucleic acid by high performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

  • 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 47:87–95

    Article  CAS  Google Scholar 

  • Nakagawa Y, Sakane T, Yokota A (1996) Transfer of Pseudomonas riboflavina (Foster 1944). a gram-negative, motile rod with long-chain 3-hydroxy fatty acids to Devosia riboflavina gen. nov., sp. nov., nom. rev. Int J Syst Bacteriol 46:16–22

    Article  CAS  PubMed  Google Scholar 

  • Okamura K, Kanbe T, Hiraishi A (2009) Rhodoplanes serenus sp. nov., a purple non-sulfur bacterium isolated from pond water. Int J Syst Evol Microbiol 59:531–535

    Article  CAS  PubMed  Google Scholar 

  • Oren A, Xu XW (2014) The family Hyphomicrobiaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson S (eds) The Prokaryotes—Alphaproteobacteria and Betaproteobacteria, 4th edn. Springer, Berlin, pp 247–281

    Google Scholar 

  • Ramana VV, Kapoor S, Shobha E, Ramprasad EVV, Sasikala C, Ramana CV (2011) Blastochloris gulmargensis sp. nov., isolated from an epilithic phototrophic biofilm. Int J Syst Evol Microbiol 61:1811–1816

    Article  CAS  PubMed  Google Scholar 

  • Ramana VV, Raj PS, Tushar L, Sasikala C, Ramana CV (2013) Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream. Int J Syst Evol Microbiol 63:2684–2689

    Article  CAS  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI, Inc., Technical Note 101. Newark

    Google Scholar 

  • Schlesner H (1987) Filomicrobium fusiforme gen. nov., sp. nov., a slender budding, hyphal bacterium from brackish water. Syst Appl Microbiol 10:63–67

    Article  Google Scholar 

  • Schmidt JM, Kelly SV (2005) Genus Seliberia Aristovskaya and Prinkina 1963. 56AL. In: Brenner DJ, Krieg NR, Staley JT (eds) Bergey’s manual of systematic bacteriology, Part C, vol 2, 2nd edn. Springer, New York, pp 549–554

    Chapter  Google Scholar 

  • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Article  Google Scholar 

  • Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington DC, pp 607–654

    Google Scholar 

  • Srinivas A, Sasikala C, Ramana CV (2014) Rhodoplanes oryzae sp. nov., a phototrophic alphaproteobacterium isolated from the rhizosphere soil of paddy. Int J Syst Evol Microbiol 64:2196–2203

    Google Scholar 

  • Staley JT (1968) Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. J Bacteriol 95:1921–1942

    CAS  PubMed  PubMed Central  Google Scholar 

  • Staley JT (1984) Prosthecomicrobium hirschii, a new species in a redefined genus. Int J Syst Bacteriol 34:304–308

    Article  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2011) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu XL, Yu SL, Gu J, Zhao GF, Chi CQ (2009) Filomicrobium insigne sp. nov., isolated from an oil-polluted saline soil. Int J Syst Evol Microbiol 59:300–305

    Article  CAS  PubMed  Google Scholar 

  • Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153

    Article  CAS  PubMed  Google Scholar 

  • Xu XW, Huo YY, Wang CS, Oren A, Cui HL, Vedler E, Wu M (2011) Pelagibacterium halotolerans gen. nov., sp. nov., and Pelagibacterium luteolum sp. nov., novel members of the family Hyphomicrobiaceae. Int J Syst Evol Microbiol 61:1817–1822

    Article  CAS  PubMed  Google Scholar 

  • Yokota A, Akagawa-Matsushita M, Hiraishi A, Katayama Y, Urakami T, Yamasato K (1992) Distribution of quinone systems in microorganisms: gram-negative eubacteria. Bull Jpn Fed Cult Coll 8:136–171

    Google Scholar 

  • Yoo SH, Weon HY, Kim BY, Hong SB, Kwon SW, Cho YH, Go SJ, Stackebrandt E (2006) Devosia soli sp. nov., isolated from greenhouse soil in Korea. Int J Syst Evol Microbiol 56:2689–2692

    Article  CAS  PubMed  Google Scholar 

  • Yoon JH, Kang SJ, Park S, Oh TK (2007) Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia. Int J Syst Evol Microbiol 57:1310–1314

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Zahran HH (1999) Rhizobium-legume symbiosis and nitrogen fixation under severe conditions and in an arid climate. Microbiol Mol Biol Rev 63:968–989

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang DC, Redzic M, Liu HC, Zhou YG, Schinner F, Margesin R (2012) Devosia psychrophila sp. nov. and Devosia glacialis sp. nov., from alpine glacier cryoconite, and an emended description of the genus Devosia. Int J Syst Evol Microbiol 62:710–715

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors are grateful to Prof. Aharon Oren for suggesting the Latin name of the species. This research was supported by Xinjiang Uygur Autonomous Region regional coordinated innovation project (Shanghai cooperation organization science and technology partnership program) (no. 2017E01031), West Light Foundation of the Chinese Academy of Sciences (nos. XBBS201305 and XBBS201201) and China Biodiversity Observation Networks (Sino BON). This research was also supported by the State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University (no. PlantKF02). W-J Li was also supported by Guangdong Province Higher Vocational Colleges & Schools Pearl River Scholar Funded Scheme (2014).

Author information

Author notes

  1. Li Li, Ghenijan Osman and Nimaichand Salam contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People’s Republic of China

    Li Li, Osama Abdalla Mohamed, Jinbiao Ma & Wen-Jun Li

  2. Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Ürümqi, 830091, People’s Republic of China

    Ghenijan Osman

  3. State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People’s Republic of China

    Nimaichand Salam, Jianyu Jiao, Mipeshwaree Devi Asem, Min Xiao & Wen-Jun Li

  4. Environmental Science Department, Institute for Post Graduate of Environment Study, Arish University, North Sinai, 45511, Egypt

    Osama Abdalla Mohamed

Authors
  1. Li Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ghenijan Osman
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nimaichand Salam
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Osama Abdalla Mohamed
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jianyu Jiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jinbiao Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Mipeshwaree Devi Asem
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Min Xiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Wen-Jun Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Min Xiao or Wen-Jun Li.

Additional information

Communicated by Erko Stackebrandt.

The GenBank accession number for the 16S rRNA gene sequence of strain YIM 690229T is KM243752. The genus and species information have been submitted to the Digital Protologue Database under the Taxon Numbers GA00048 and TA00322, respectively.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 942 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, L., Osman, G., Salam, N. et al. Limoniibacter endophyticus gen. nov., sp. nov., an alphaproteobacterium isolated from the roots of Limonium otolepis. Arch Microbiol 200, 663–670 (2018). https://doi.org/10.1007/s00203-017-1472-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00203-017-1472-0

Keywords

Search

Navigation