Skip to main content
SpringerLink
Log in

Nitrospirillum irinus sp. nov., a diazotrophic bacterium isolated from the rhizosphere soil of Iris and emended description of the genus Nitrospirillum

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

An Erratum to this article was published on 22 September 2015

Abstract

A polyphasic approach was used to characterize a novel nitrogen-fixing bacterial strain, designated YC6995T, isolated from the rhizosphere soil of Iris ensata var. spontanea (Makino) Nakai inhabiting a wetland located at an altitude of 960 m on Jiri Mountain, Korea. Strain YC6995T cells were Gram-negative, and rod-shaped, with motility provided by a single polar flagellum. Optimal growth conditions were 30 °C and pH 7.0. The major fatty acids of strain YC6995T were C18:1 ω7c, C18:1 2-OH and C16:0 3-OH. The major respiratory quinone was ubiquinone-10 (Q-10). The polar lipids were phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified glycolipids. The genomic DNA G+C content was 64.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed strain YC6995T to form a phyletic lineage with Nitrospirillum amazonense DSM 2787T with a high sequence similarity (97.2 %), but it displayed low sequence similarity with other remotely related genera, including Azospirillum (<93 %), Rhodocista (93.1–93.4 %), and Skermanella (91.2–93.3 %) in the family Alphaproteobacteria. Based on the phenotypic, chemotaxonomic, and phylogenetic evidences, strain YC6995T represents a novel species within the genus Nitrospirillum, for which the name Nitrospirillum irinus sp. nov. is proposed. The type strain is YC6995T (= KACC 13777T = DSM 22198T). An emended description of the genus Nitrospirillum is also proposed.

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

  • Atlas RM (1993) Handbook of microbiological media. Mortimer, London

    Google Scholar 

  • Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (1995) Current protocols in molecular biology. Wiley, New York

    Google Scholar 

  • Bally R, Thomas-Bauzon D, Heulin T, Balandreau J (1983) Determination of the most frequent N2-fixing bacteria in a rice rhizosphere. Can J Microbiol 29:881–887

    Article  Google Scholar 

  • Bradford MM (1976) Rapid and sensitive method for quantitation of microgram quantities of protein utilizing principle of protein-dye binding. Anal Biochem 72:248–254

    Article  CAS  PubMed  Google Scholar 

  • Brown AE (2007) Benson’s microbiological applications. In: Laboratory manual in general microbiology. McGraw-Hill, New York

    Google Scholar 

  • Cappuccino JG, Sherman N (2002) Microbiology: a laboratory manual, 6th edn. Benjamin Cummings, San Francisco

    Google Scholar 

  • Dittmer JC, Lester RL (1964) A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 15:126–127

    Google Scholar 

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

    Article  Google Scholar 

  • Fitch WM (1972) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Gallon JR (1992) Reconciling the incompatible—N2 fixation and O2. New Phytol 122:571–609

    Article  CAS  Google Scholar 

  • Gunarto L, Adachi K, Senboku T (1999) Isolation and selection of indigenous Azospirillum spp. from a subtropical island, and effect of inoculation on growth of lowland rice under several levels of N application. Biol Fertil Soils 28:129–135

    Article  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Hardy RWF, Holsten RD, Jackson EK, Burns RC (1968) The acetylene-ethylene assay for N2 fixation: laboratory and field evaluation. Plant Physiol 43:1185–1207

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Jacin H, Mishkin AR (1965) Separation of carbohydrates on borate impregnated silica gel G plates. J Chromatogr 18:170–173

    Article  CAS  PubMed  Google Scholar 

  • Kawasaki H, Hoshino Y, Kuraiski Y, Yamasato K (1992) Rhodocista centenaria gen. nov., sp. nov., a cyst-forming anoxygenic photosynthetic bacterium and its phylogenetic position in the Proteobacteria alpha group. J Gen Appl Microbiol 38:541–551

    Article  CAS  Google Scholar 

  • Khammas KM, Ageron E, Grimont PAD, Kaiser P (1989) Azospirillum irakense sp. nov., a new nitrogen-fixing bacterium associated with rice roots and rhizosphere soil. Res Microbiol 140:679–693

    CAS  PubMed  Google Scholar 

  • Kim OS, Cho YJ, Lee KH, Yoon SH, Kim MC, Na HS, Park SC, Jeon YS, Lee JH, Yi HN, Won SH, Chun JS (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    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 

  • Komagata K, Suzuki K (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207

    Article  CAS  Google Scholar 

  • Ladha JK, So RB, Watanabe I (1987) Composition of Azospirillum species associated with wetland rice plant grown in different soils. Plant Soil 102:127–129

    Article  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175

    Google Scholar 

  • Lavrinenko K, Chernousova E, Gridneva E, Dubinina G, Vladimir A, Kuever J, Lysenko A, Grabovinch M (2010) Azospirillum thiophilum sp. nov., a novel diazotrophic bacterium isolated from a sulfide spring. Int J Syst Evol Microbiol 60:2832–2837

    Article  CAS  PubMed  Google Scholar 

  • Lin SY, Young CC, Hupfer H, Siering C, Arun AB, Chen WM, Lai WA, Shen FT, Rekha PD, Yassin AF (2009) Azospirillum picis sp. nov., isolated from discarded tar. Int J Syst Evol Microbiol 59:761–765

    Article  CAS  PubMed  Google Scholar 

  • Lin SY, Shen FT, Young CC (2011) Rapid detection and identification of the free-living nitrogen fixing genus Azospirillum by 16S rRNA-gene-targeted genus-specific primers. Antonie Van Leeuwenhoek 99:837–844

    Article  CAS  PubMed  Google Scholar 

  • Lin SY, Liu YC, Hameed A, Hsu YH, Lai WA, Shen FT, Young CC (2013) Azospirillum fermentarium sp. nov., a nitrogen-fixing species isolated from a fermenter. Int J Syst Evol Microbiol 63:3762–3768

    Article  CAS  PubMed  Google Scholar 

  • Lin SY, Hameed A, Shen FT, Liu YC, Hsu YH, Shahina M, Lai WA, Young CC (2014) Description of Niveispirillum fermenti gen. nov., sp. nov., isolated from a fermentor in Taiwan, transfer of Azospirillum irakense (1989) as Niveispirillum irakense comb.nov., and reclassification of Azospirillum amazonense (1983) as Nitrospirillum amazonense gen. nov. Antonie Van Leeuwenhoek 105:1149–1162

    Article  CAS  PubMed  Google Scholar 

  • Luo G, Shi Z, Wang H, Wang G (2012) Skermanella stibiiresistens sp. nov., a highly antimony-resistant bacterium isolated from coal-mining soil, and emended description of the genus Skermanella. Int J Syst Evol Microbiol 62:1271–1276

    Article  CAS  PubMed  Google Scholar 

  • Magalhães FM, Baldani JI, Souto M, Kuykendall JR, Dobereiner J (1983) A new acid tolerant Azospirillum species. An Acad Bras Cienc 55:417–430

    Google Scholar 

  • Mehnaz S, Weselowski B, Lazarovits G (2007) Azospirillum canadense sp. nov., a nitrogen-fixing bacterium isolated from corn rhizosphere. Int J Syst Evol Microbiol 57:620–624

    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, 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

    Article  CAS  Google Scholar 

  • Moon SP, Park YJ, Jung JY, Lee SH, Park WJ, Lee KS, Jeon CO (2011) Pusillimonas harenae sp. nov., isolated from a sandy beach, and emended description of the genus Pusillimonas. Int J Syst Evol Microbiol 61:2901–2906

    Article  Google Scholar 

  • Parte AC (2014) LPSN-list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:613–616

    Article  Google Scholar 

  • Peng G, Wang H, Zhang G, Hou W, Liu Y, Wang ET, Tan Z (2006) Azospirillum melinis sp. nov., a group of diazotrophs isolated from tropical molasses grass. Int J Syst Evol Microbiol 56:1263–1271

    Article  CAS  PubMed  Google Scholar 

  • Ross HNM, Grant WD, Harris JE (1985) Lipids in archaebacterial taxonomy. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics. Academic Press, New York, pp 289–300

    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 

  • Short SM, Jenkins BD, Zehr JP (2004) Spatial and temporal distribution of two diazotrophic bacteria in the Chesapeake Bay. Appl Environ Microbiol 70:2186–2192

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sly LI, Stackebrandt E (1999) Description of Skermanella parooensis gen. nov., sp. nov. to accommodate Conglomeromonas largomobilis subsp. largomobilis to the genus Azospirillum. Int J Syst Evol Microbiol 49:541–544

    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 

  • Stewart WDP, Fitzerald GP, Burris RH (1968) Acetylene reduction by nitrogen fixing blue-green algae. Arch Mikrobiol 62:336–348

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tarrand JJ, Krieg NR, Döbereiner J (1978) A taxonomic study of the Spirillum lipoferum group, with descriptions of a new genus, Azospirillum gen. nov., and two species, Azospirillum lipoferum (Beijerinck) comb. nov. and Azospirillum brasilense sp. nov. Can J Microbiol 24:967–980

    Article  CAS  PubMed  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  PubMed Central  CAS  PubMed  Google Scholar 

  • Young CC, Hupfer H, Siering C, Ho MJ, Arun AB, Lai WA, Rekha PD, Shen FT, Hung MH, Yassin AF (2008) Azospirillum rugosum sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 58:959–963

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was carried out with the partial support of “Cooperative Research Program for Agriculture Science & Technology Development (PJ 01104901)” Rural Development Administration, Republic of Korea. E. J. Chung was supported by a scholarship from the BK21 Plus Program, the Ministry of Education, Republic of Korea.

Author information

Authors and Affiliations

  1. Division of Applied Life Science (BK 21 Plus), Plant Molecular Biology & Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea

    Eu Jin Chung, Tae Soon Park & Young Ryun Chung

  2. Department of Life Science, Chung-Ang University, Seoul, 156-756, Republic of Korea

    Kyung Hyun Kim & Che Ok Jeon

  3. Department of Biology, University of Texas-Arlington, Arlington, TX, 760194, USA

    Hae-In Lee & Woo-Suk Chang

  4. Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, 570-752, Republic of Korea

    Woo-Suk Chang

  5. Department of Agronomy, University of Agriculture, Faisalabad, 38040, Pakistan

    Zubair Aslam

Authors
  1. Eu Jin Chung
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tae Soon Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kyung Hyun Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Che Ok Jeon
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hae-In Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Woo-Suk Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Zubair Aslam
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Young Ryun Chung
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Young Ryun Chung.

Additional information

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain YC6995T is GU048666.

Electronic supplementary material

Below is the link to the electronic supplementary material.

10482_2015_528_MOESM1_ESM.docx

Supplementary figures of the transmission electron micrograph and polar lipid analysis of strain YC6995T are available online. (DOCX 2565 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chung, E.J., Park, T.S., Kim, K.H. et al. Nitrospirillum irinus sp. nov., a diazotrophic bacterium isolated from the rhizosphere soil of Iris and emended description of the genus Nitrospirillum . Antonie van Leeuwenhoek 108, 721–729 (2015). https://doi.org/10.1007/s10482-015-0528-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-015-0528-x

Keywords

Search

Navigation