rudaibacter terrae gen. nov., sp. nov., isolated from greenhouse soil
TRANSCRIPT
Rudaibacter terrae gen. nov., sp. nov., isolated fromgreenhouse soil
Soo-Jin Kim,1 Ji-Young Moon,1 Moriyuki Hamada,2 Tomohiko Tamura,2
Hang-Yeon Weon,1 Ken-ichiro Suzuki2 and Soon-Wo Kwon1
Correspondence
Soon-Wo Kwon
1Agricultural Microbiology Division, National Academy of Agricultural Science, Rural DevelopmentAdministration, Suwon 441-707, Republic of Korea
2NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation,2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
A novel Gram-stain-positive, non-motile, rod-shaped bacterium, designated 5GHs34-4T, was
isolated from greenhouse soil in Yongin, Republic of Korea. Growth occurred in the temperature
range of 10–37 6C (optimum 28–30 6C) and at pH 5.0–9.0 (optimum pH 7.0). It can tolerate up
to 3 % (w/v) NaCl. The strain showed 16S rRNA gene sequence similarity levels of 95.1–97.0 %
with species of the genus Leifsonia, 95.7–96.7 % with species of the genus Herbiconiux, 95.1–
96.4 % with species of the genus Salinibacterium and 96.1 % with Labedella gwakjiensis and
Homoserinimonas aerilata. The highest sequence similarities (97.0 %) were with Leifsonia
aquatica JCM 1368T, Leifsonia poae VKM Ac-1401T and Leifsonia psychrotolerans LI1T. The
peptidoglycan type determined for strain 5GHs34-4T was B2c with DL-2,4-diaminobutyric acid at
position 3. The murein was of the acetyl type. The polar lipids consisted of diphosphatidylglycerol,
phosphatidylglycerol and two unknown glycolipids. The menaquinones detected were MK-13,
MK-12 and MK-14, and the major fatty acids were summed feature 8 (C18 : 1v7c and/or
C18 : 1v6c), anteiso-C17 : 0 and anteiso-C15 : 0. The phenotypic and phylogenetic traits of strain
5GHs34-4T differed in some respects from those of members of the family Microbacteriaceae.
Therefore, strain 5GHs34-4T is considered to represent a novel species of a new genus in the
family Microbacteriaceae, for which the name Rudaibacter terrae gen. nov., sp. nov. is proposed.
The type strain is 5GHs34-4T (5KACC 15523T5NBRC 108754T).
The family Microbacteriaceae consists of actinobacteria thatare aerobic, motile or non-motile, non-spore-forming andGram-stain-positive and have G+C-rich genomic DNA(Park et al., 1993; Stackebrandt et al., 1997). At the time ofwriting, 39 genera are classified as members of the familyMicrobacteriaceae (http://www.bacterio.net/). Members ofthe family Microbacteriaceae have been found in diverseenvironments of plants, soil, air, dairy products, sewage,mushrooms, compost, insects and groundwater. Recently,new genera such as Homoserinimonas, Compostimonas,Lysinimonas and Naasia, which have been isolated fromenvironments such as air, soil and cotton composts, havebeen reported to be members of the family Microbac-teriaceae (Kim et al., 2012b, c; . Weon et al., 2013; Janget al., 2013)
We isolated one bacterial strain, 5GHs34-4T, from a soilsample from a greenhouse used to cultivate cucumbers in
the Yongin region, Republic of Korea. The soil sample wasserially diluted with 0.85 % saline and the suspension wasplated on R2A agar (Difco). Several strains were collectedand purified and their 16S rRNA gene sequences weredetermined. According to the phylogenetic analysis, strain5GHs34-4T could be classified as a member of the familyMicrobacteriacea.
The 16S rRNA gene sequence of the strain 5GHs34-4T wasdetermined by PCR amplification (Kwon et al., 2003).Identification of phylogenetic neighbours and calculationof pairwise levels of 16S rRNA gene sequence similaritywere achieved by using the EzTaxon server (http://www.eztaxon.org/; Chun et al., 2007). Sequence alignment andanalysis of the data were performed using the ARB softwarepackage (version December 2007; Ludwig et al., 2004) andthe corresponding SILVA SSURef 100 database (releaseAugust 2009; Pruesse et al., 2007). Phylogenetic trees werereconstructed using MEGA version 5.0 (Tamura et al., 2011)on the basis of the neighbour-joining (Saitou & Nei, 1987),maximum-parsimony (Kluge & Farris, 1969) and max-imum-likelihood (Felsenstein, 1981) algorithms. Strain5GHs34-4T showed 16S rRNA gene sequence similarity
The GenBank/EMBL/DDBJ accession number for the 16S rRNA genesequence of 5GHs34-4T is JQ639054.
Four supplementary figures are available with the online version of thispaper.
International Journal of Systematic and Evolutionary Microbiology (2013), 63, 4052–4057 DOI 10.1099/ijs.0.049817-0
4052 049817 G 2013 IUMS Printed in Great Britain
levels of 95.1–97.0 % with species of the genus Leifsonia,95.7–96.7 % with species of the genus Herbiconiux, 95.1–96.4 % with species of the genus Salinibacterium and96.1 % with Labedella gwakjiensis and Homoserinimonasaerilata, revealing the highest sequence similarity (97.0 %)with Leifsonia aquatica JCM 1368T, Leifsonia poae VKMAc-1401T and Leifsonia psychrotolerans LI1T. Maximum-likelihood, neighbour-joining and maximum-parsimonytrees indicated that strain 5GHs34-4T clustered with somemembers of the genus Leifsonia, Homoserinimonas aerilata,Salinibacterium amurskyense, Rhodoglobus vestalii andSchumannella luteola (Fig. 1, Figs S1 and S2 available inIJSEM Online). However, this cluster was not highlysupported on the basis of bootstrap value. Because 16S
rRNA gene-based trees have shown that the genus Leifsonia
is a heterogeneous group that is divided at least into three
subgroups (Ganzert et al., 2011; Madhaiyan et al., 2010;
Pindi et al., 2009), the grouping of strain 5GHs34-4T into
the genus Leifsonia could not be supported. The taxonomic
position of strain 5GHs34-4T could not be specifically
determined at the genus level.
Cell morphology and presence of flagella was observed by
electron microscope (model 912AB; LEO) at the exponen-
tial phase of growth. A Gram-staining kit (Difco) was used
for testing the Gram reaction. The pH range for growth
was determined using R2A broth medium. The pH wasadjusted prior to sterilization to pH 4–10 (at intervals of
Leifsonia naganoensis JCM 10592T (DQ232612) Leifsonia aquatica JCM 1368T (D45057)
Leifsonia xyli subsp. cynodontis JCM 9733T (AB016985) Leifsonia shinshuensis JCM 10591T (DQ232614)
Leifsonia soli TG-S248T (EU912483) Leifsonia lichenia 2SbT (AB278552)
Leifsonia poae VKM Ac-1401T (AF116342) Rudaibacter terrae 5GHs34-4T (JQ639054)
Leifsonia bigeumensis MSL-27T (EF466124) Homoserinimonas aerilata 5317J-19T (JQ639053)
Salinibacterium amurskyense KMM 3673T (AF539697) Rhodoglobus vestalii LV3T (AJ459101)
Leifsonia rubra CMS 76rT (AJ438585) Herbiconiux ginsengi wged11T (DQ473536)
Microcella putealis CV-2T (AJ717388) Chryseoglobus frigidaquae CW1T (EF373534)
Agrococcus jenensis DSM 9580T (X92492) Lysinimonas soli SGM3-12T (JN378395)
Lysinimonas kribbensis MSL-13T (EF466129) Leifsonia psychrotolerans LI1T (GQ406810) Leifsonia kafniensis KFC-22T (AM889135)
Leifsonia antarctica SPC-20T (AM931710) Phycicola gilvus SSWW-21T (AM286414)
Microterricola viridarii KV-677T (AB282862) Leifsonia pindariensis PON10T (AM900767)
Glaciibacter superstes AHU1791T (AB378301) Agreia bicolorata VKM Ac-1804T (AF159363)
Labedella gwakjiensis KSW2-17T (DQ533552) Amnibacterium kyonggiense KSL51201-037T (FJ527819)
Klugiella xanthotipulae 44C3T (AY372075) Cryobacterium psychrophilum DSM 4854T (AJ544063)
Rathayibacter rathayi DSM 7485T (X77439) Frondihabitans australicus E1HC-02T (DQ525859)
Frigoribacterium faeni 801T (Y18807) Clavibacter michiganensis subsp. michiganensis DSM 46364T (X77435)
Mycetocola saprophilus CM-01T (AB012647) Marisediminicola antarctica ZS314T (GQ496083) Curtobacterium citreum DSM 20528T (X77436)
Pseudoclavibacter helvolus DSM 20419T (X77440)Gulosibacter molinativorax ON4T (AJ306835)
Microbacterium lacticum DSM 20427T (X77441) Plantibacter flavus P 297/02T (AJ310417)
Okibacterium fritillariae VKM Ac-2059T (AB042094) Schumannella luteola KHIAT (AB362159)
Humibacter albus SC-083T (AM494541) Brevibacterium linens DSM 20425T (X77451)
Agromyces ramosus DSM 43045T (X77447)
100
99
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97
89
85
94
93
79
80
79
0.01
Fig. 1. Maximum-likelihood (ML) phylogenetic tree based on concatenated 16Sr RNA gene sequence comparisons, showingthe phylogenetic relationship between members of the family Microbacteriaceae. Bootstrap percentages (based on 1000replications) .70 % are shown at branching points. Bar, 0.01 substitutions per nucleotide position.
Rudaibacter terrae sp. nov.
http://ijs.sgmjournals.org 4053
1.0 pH unit) using appropriate biological buffers (Breznak& Costilow, 1994). Incubation temperatures varied from4 uC to 40 uC. To investigate the tolerance to NaCl, R2Abroth was prepared with NaCl concentrations adjusted to0–5 %, w/v (at intervals of 1.0 %). Growth under anaerobicconditions was determined after incubating strain 5GHs34-4T on the BBL GasPak Anaerobic System (Difco) for14 days at 28 uC on R2A agar. Catalase and oxidaseactivities were examined by bubble production in 3 % (v/v)hydrogen peroxide solution and 1 % (w/v) tetramethyl-p-phenylenediamine (bioMerieux), respectively. Casein,starch and tyrosine degradations were examined on R2Aplates containing milk powder [5 % (w/v)], starch [1 % (w/v)] and tyrosine [0.1 % (w/v)], respectively. CM-celluloseand Tween 80 degradation was examined using R2Asupplemented with 1 % (w/v) of each substrate. DNaseactivity was determined with DNase test agar (Difco).Enzyme activity, utilization of various substrates and otherphysiological properties were tested in duplicate withcommercial API ZYM, API 20NE and API ID 32GN(bioMerieux) strips according to the manufacturer’sprotocols. API ZYM test strips were checked after 4 h,and API 20NE and API ID 32GN test strips were recordedafter 10 days incubation. The strain was Gram-stain-positive, aerobic, non-spore-forming, non-motile androd-shaped (0.661.2–1.7 mm) (Fig. S3). The colonies areirregular, convex, yellowish to deep yellow with age. Strain5GHs34-4T grew on R2A, trypticase soy agar (TSA) andnutrient agar (NA), but did not grow on MacConkey agar(all from Difco). Growth occurred on the range of 10–37 uC (optimum 28–30 uC) and pH 5.0–9.0 (optimumpH 7.0). The strain can tolerate up to 3 % (w/v) NaCl.
For the analysis of whole-cell fatty acids, strain 5GHs34-4T,Leifsonia aquatica KACC 20649T, Leifsonia naganoensisKACC 14398T and Leifsonia poae KACC 14399T weregrown for 2 days at 28 uC on R2A while Leifsoniabigeumensis KACC 21122T was cultivated for 4 days at28 uC on R2A to the stationary phase of growth. Cellularfatty acids were extracted, methylated and analysed byusing the Sherlock Microbial Identification System (MIDI)according to the manufacturer’s instructions. Fatty acidmethyl esters were analysed by using the MicrobialIdentification software package (Sherlock Version 6.1;MIDI database: TSBA6). Menaquinones and polar lipidswere extracted and analysed by the method of Minnikinet al. (1984) using cells grown on R2A. The acyl type of thecell wall was analysed according to the method of Uchida &Aida (1984). For peptidoglycan analysis, cells were grownin shake flasks containing liquid NBRC medium 802[1.0 % polypeptone (Wako), 0.2 % yeast extract, 0.1 %MgSO4 . 7H2O; pH 7.0] on a rotary shaker for 72 h at30 uC Cell-wall samples were prepared from approximately1 g of wet cells by mechanical disruption with an ultrasonicoscillator and glass beads. The cell walls were separatedfrom unbroken cells by 3, 000 g centrifugation in distilledwater and further purified in boiling 4 % SDS (100 uC,40 min), followed by several washings with distilled water.
Molar ratios of the amino acids in cell-wall hydrolysates(4 M HCl, 16 h) were determined using the methoddescribed by Hamada et al. (2010). The amino acid isomersin cell-wall hydrolysates were examined using the methoddescribed by Nozawa et al. (2007) using a liquidchromatograph–mass spectrometer (LC–MS; modelLCMS-2020; Shimadzu). The DNA G+C content wasdetermined by HPLC (Mesbah et al., 1989). The majorfatty acids of strain 5GHs34-4T were summed feature 8(C18 : 1v7c and/or C18 : 1v6c) (69.1 %), anteiso-C17 : 0
(13.1 %) and anteiso-C15 : 0 (10.8 %), which is quitedifferent from the profile for species of the genusLeifsonia, which have anteiso-C15 : 0, iso-C16 : 0 and ante-iso-C17 : 0 as the major fatty acids (Table 1). Polar lipids ofstrain 5GHs34-4T were diphosphatidylglycerol, phosphati-dylglycerol and two unknown glycolipids (Fig. S4). Themurein was of the acetyl type. The menaquinonecomposition of strain 5GHs34-4T was MK-13 (56 %),
Table 1. Fatty acid compositions of strain 5GHs34-4T andsome species of the genus Leifsonia
Strains: 1, 5GHs34-4T; 2, Leifsonia aquatica KACC 20649T; 3, Leifsonia
bigeumensis KACC 21122T; 4, Leifsonia naganoensis KACC 14398T; 5,
Leifsonia poae KACC 14399T; 6, Leifsonia psychrotolerans KACC
15592T. Data are from this study. All strains except Leifsonia
bigeumensis KACC 21122T and Leifsonia psychrotolerans KACC
15592T were grown on R2A medium for 2 days at 28 uC. Leifsonia
bigeumensis KACC 21122T was grown on R2A for 4 days at 28 uC,
and Leifsonia psychrotolerans KACC 15592T was grown for 4 days at
15 uC and 28 uC. 2, Not detected.
Fatty acids 1 2 3 4 5 6
15 6C 28 6C
iso-C14 : 0 2 1.3 1.5 1.3 0.5 0.9 0.3
C14 : 0 0.2 0.3 0.4 0.2 0.2 2 0.3
iso-C15 : 0 0.7 1.5 2.0 2.1 2.5 0.6 0.6
anteiso-
C15 : 0
10.8 36.0 42.1 35.3 42.2 71.2 70.2
anteiso-
C15 : 1 A
2 2 2 2 2 7.9 2
iso-C16 : 0 2.8 35.9 33.4 31.2 30.9 8.4 5.3
C16 : 1v11c 0.3 2 2 2 2 2 2
C16 : 0 1.9 1.4 1.8 1.0 1.3 2.7 4.1
iso-C17 : 0 0.6 0.6 0.7 0.7 1.0 2 2
anteiso-
C17 : 0
13.1 23.0 17.9 28.0 21.2 8.3 18.7
C17 : 1v7c 2 2 0.1 2 2 2 2
iso-C18 : 0 2 2 0.1 0.1 0.1 2 2
C18 : 1v9c 2 2 2 2 0.1 2 0.3
C18 : 0 0.6 2 0.1 2 0.1 2 2
C20 : 0 2 2 2 2 2 2 0.3
Summed
feature 8*
69.1 2 2 2 2 2 2
*Summed feature 8 consists of C18 : 1v7c and/or C18 : v6c.
S.-J. Kim and others
4054 International Journal of Systematic and Evolutionary Microbiology 63
MK-12 (36 %) and MK-14 (8 %). The menaquinonecomposition is also very different from that of the closelyrelated genera such as Leifsonia and Herbiconiux (Table 2).The peptidoglycan of strain 5GHs34-4T contained D-alanine, D-glutamic acid, glycine and DL-2,4-diaminobu-tyric acid at a molar ratio of 0.8 : 1.0 : 1.2 : 1.6. Thepeptidoglycan was determined to be B2c (Schleifer &Kandler, 1972). The peptidoglycan type is the same as thoseof members of the genera Herbiconiux and Leifsonia. TheDNA G+C content of strain 5GHs34-4T was 64.0 mol%.
In conclusion, strain 5GHs34-4T can be classified as amember of the family Microbacteriaceae on the basis of thephylogenetic analysis. Strain 5GHs34-4T was phylogeneti-cally related to the genera Leifsonia, Homoserinimonas,Herbiconiux and Labedella. It can be also clearly differ-entiated from those genera in the light of the fatty acid andmenaquinone compositions (Table 1 and 2). On the basisof the data presented here, strain 5GHs34-4T is consideredto represent a novel species of a new genus in the familyMicrobacteriaceae, for which the name Rudaibacter terraegen. nov., sp. nov. is proposed.
Description of Rudaibacter gen. nov.
Rudaibacter (Ru.da.i.bac9ter. N.L. n. RuDA, acronym forRural Development Administration; N.L. masc. n. bacter, arod; N.L. masc. n. Rudaibacter, a rod named after RDA).
Cells are Gram-stain-positive, aerobic, mesophilic, non-motile rods. No spores are observed. The major fatty acidsare summed feature 8 (C18 : 1v7c and/or C18 : 1v6c), anteiso-C17 : 0 and anteiso-C15 : 0. The polar lipids consist of dipho-sphatidylglycerol, phosphatidylglycerol and two unknownglycolipids. The dominant menaquinones are MK-13 andMK-12. The murein is of the acetyl type. The peptidoglycancontains D-alanine, D-glutamic acid, glycine and DL-2,4-diaminobutyric acid at a molar ratio of 0.8 : 1.0 : 1.2 : 1.6.The peptidoglycan type is B2c. Phylogenetically, thegenus belongs to the family Microbacteriaceae, suborderMicrococcineae, within the order Actinomycetales. The typespecies is Rudaibacter terrae.
Description of Rudaibacter terrae sp. nov.
Rudaibacter terrae (ter9rae. L. gen. n. terrae of the soil).
The species displays the following characteristics inaddition to those given for the genus. Cells are 0.6 mmwide and 1.2–1.7 mm long. The colonies are irregular,convex, yellowish to deep yellow with age. Grows on R2A,TSA and NA but does not on MacConkey agar. Growthoccurs in the temperature range of 10–37 uC (optimum28–30 uC) and at pH 5.0–9.0 (optimum pH 7.0). It cantolerate up to 3 % (w/v) NaCl. Oxidase- and catalase-negative. Hydrolyses tyrosine, but does not hydrolysecasein, chitin, CM-cellulose, DNA, hypoxanthine, starch,Tween 80 and xanthine. Positive for nitrate reduction,aesculin hydrolysis and b-galactosidase (PNG), but nega-tive for indole production, glucose fermentation, arginineT
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Rudaibacter terrae sp. nov.
http://ijs.sgmjournals.org 4055
dihydrolase, urease and gelatin hydrolysis (API 20NE teststrip). Assimilates D-glucose, L-arabinose, D-mannose, D-mannitol, maltose, potassium gluconate, D-ribose, sucrose,melibiose and potassium 2-ketogluconate, but does notassimilate N-acetylglucosamine, capric acid, adipic acid,malic acid, trisodium citrate, phenylacetic acid, L-rham-nose, inositol, itaconic acid, suberic acid, sodium mal-onate, sodium acetate, lactic acid, L-alanine, potassium5-ketogluconate, glycogen, 3-hydroxybenzoic acid, L-ser-ine, salicin, L-fucose, D-sorbitol, propionic acid, valericacid, L-histidine, 3-hydroxybutyric acid, 4-hydroxybenzoicacid or L-proline. Positive for activities of esterase (C4),esterase lipase (C8), leucine arylamidase, acid phosphatase,naphthol-AS-BI-phosphohydrolase, a-galactosidase, b-galactosidase, a-glucosidase, b-glucosidase, N-acetyl-b-glucosaminidase and a-mannosidase, but negative foractivities of alkaline phosphatase, lipase (C14), valinearylamidase, cystine arylamidase, trypsin, a-chymotrypsin,b-glucuronidase and a-fucosidase (API ZYM test strip).
The type strain, 5GHs34-4T (5KACC 15523T5NBRC108754T), was isolated from greenhouse soil in theYongin region, Republic of Korea. The DNA G+C contentof the type strain is 64.0 mol%.
Acknowledgements
This study was carried out with the support of the National Academyof Agricultural Science, Rural Development Administration, Republicof Korea (project no. PJ9017121703). The authors thank ProfessorJ. P. Euzeby of the Ecole Nationale Veterinaire in Toulouse for adviceconcerning naming.
References
An, S. Y., Xiao, T. & Yokota, A. (2008). Schumannella luteola gen. nov.,sp. nov., a novel genus of the family Microbacteriaceae. J Gen ApplMicrobiol 54, 253–258.
An, S. Y., Xiao, T. & Yokota, A. (2009). Leifsonia lichenia sp. nov.,isolated from lichen in Japan. J Gen Appl Microbiol 55, 339–343.
Behrendt, U., Schumann, P., Hamada, M., Suzuki, K., Sproer, C. &Ulrich, A. (2011). Reclassification of Leifsonia ginsengi (Qiu et al. 2007) asHerbiconiux ginsengi gen. nov., comb. nov. and description of Herbiconiuxsolani sp. nov., an actinobacterium associated with the phyllosphere ofSolanum tuberosum L. Int J Syst Evol Microbiol 61, 1039–1047.
Breznak, J. A. & Costilow, R. N. (1994). Physicochemical factors ingrowth. In Methods for General and Molecular Bacteriology, pp. 137–154. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood &N. R. Krieg. Washington, DC: American Society for Microbiology.
Chun, J., Lee, J. H., Jung, Y., Kim, M., Kim, S., Kim, B. K. & Lim, Y. W.(2007). EzTaxon: a web-based tool for the identification ofprokaryotes based on 16S ribosomal RNA gene sequences. Int J SystEvol Microbiol 57, 2259–2261.
Dastager, S. G., Lee, J. C., Ju, Y. J., Park, D. J. & Kim, C. J. (2008).Leifsonia bigeumensis sp. nov., isolated from soil on Bigeum Island,Korea. Int J Syst Evol Microbiol 58, 1935–1938.
Davis, M. J., Gillaspie, A. G., Vidaver, A. K. & Harris, R. W. (1984).Clavibacter: a new genus containing some hytopathogenic coryneformbacteria, including Clavibacter xyli subsp. xyli sp. nov., subsp. nov.and Clavibacter xyli subsp. cynodontis subsp. nov., pathogens that
cause ratoon stunting disease of sugarcane and bermudagrass stuntingdisease. Int J Syst Bacteriol 34, 107–117.
Evtushenko, L. I., Dorofeeva, L. V., Subbotin, S. A., Cole, J. R.& Tiedje, J. M. (2000). Leifsonia poae gen. nov., sp. nov., isolatedfrom nematode galls on Poa annua, and reclassification of‘Corynebacterium aquaticum’ Leifson 1962 as Leifsonia aquatica (exLeifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyliDavis et al. 1984 with two subspecies as Leifsonia xyli (Davis et al.1984) gen. nov., comb. nov. Int J Syst Evol Microbiol 50, 371–380.
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: amaximum likelihood approach. J Mol Evol 17, 368–376.
Ganzert, L., Bajerski, F., Mangelsdorf, K., Lipski, A. & Wagner, D.(2011). Leifsonia psychrotolerans sp. nov., a psychrotolerant species ofthe family Microbacteriaceae from Livingston Island, Antarctica. Int JSyst Evol Microbiol 61, 1938–1943.
Hamada, M., Iino, T., Iwami, T., Harayama, S., Tamura, T. & Suzuki,K. (2010). Mobilicoccus pelagius gen. nov., sp. nov. and Piscicoccusintestinalis gen. nov., sp. nov., two new members of the familyDermatophilaceae, and reclassification of Dermatophilus chelonae(Masters et al. 1995) as Austwickia chelonae gen. nov., comb. nov.J Gen Appl Microbiol 56, 427–436.
Han, S. K., Nedashkovskaya, O. I., Mikhailov, V. V., Kim, S. B. & Bae,K. S. (2003). Salinibacterium amurskyense gen. nov., sp. nov., a novelgenus of the family Microbacteriaceae from the marine environment.Int J Syst Evol Microbiol 53, 2061–2066.
Jang, Y. H., Tamura, T., Hamada, M., Weon, H. Y., Suzuki, K., Kwon,S. W. & Kim, W. G. (2013). Lysinimonas soli gen. nov., sp. nov., isolatedfrom soil, and reclassification of Leifsonia kribbensis Dastager et al.2009 as Lysinimonas kribbensis sp. nov., comb. nov. Int J Syst EvolMicrobiol 63, 1403–1410.
Kim, B. C., Park, D. S., Kim, H., Oh, H. W., Lee, K. H., Shin, K. S. & Bae,K. S. (2012a). Herbiconiux moechotypicola sp. nov., a xylanolyticbacterium isolated from the gut of hairy long-horned toad beetles,Moechotypa diphysis (Pascoe). Int J Syst Evol Microbiol 62, 90–95.
Kim, S. J., Jang, Y. H., Hamada, M., Tamura, T., Ahn, J. H., Weon, H. Y.,Suzuki, K. & Kwon, S. W. (2012b). Homoserinimonas aerilata gen.nov., sp. nov., a novel member of the family Microbacteriaceaeisolated from an air sample in Korea. J Microbiol 50, 673–679.
Kim, S. J., Tamura, T., Hamada, M., Ahn, J. H., Weon, H. Y., Park, I. C.,Suzuki, K. & Kwon, S. W. (2012c). Compostimonas suwonensis gen.nov., sp. nov., isolated from spent mushroom compost. Int J Syst EvolMicrobiol 62, 2410–2416.
Kluge, A. G. & Farris, F. S. (1969). Quantitative phyletics and theevolution of anurans. Syst Zool 18, 1–32.
Kwon, S. W., Kim, J. S., Park, I. C., Yoon, S. H., Park, D. H., Lim, C. K. &Go, S. J. (2003). Pseudomonas koreensis sp. nov., Pseudomonasumsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novelspecies from farm soils in Korea. Int J Syst Evol Microbiol 53, 21–27.
Lee, S. D. (2007). Labedella gwakjiensis gen. nov., sp. nov., a novelactinomycete of the family Microbacteriaceae. Int J Syst Evol Microbiol57, 2498–2502.
Leifson, E. (1962). The bacterial flora of distilled and stored water. III.New species of the genera Corynebacterium, Flavobacterium, Spirillumand Pseudomonas. Int Bull Bacteriol Nomencl Taxon 12, 161–170.
Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H.,Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors(2004). ARB: a software environment for sequence data. Nucleic AcidsRes 32, 1363–1371.
Madhaiyan, M., Poonguzhali, S., Lee, J. S., Senthilkumar, M., Lee,K. C. & Sundaram, S. (2010). Leifsonia soli sp. nov., a yellow-pigmented actinobacterium isolated from teak rhizosphere soil. Int JSyst Evol Microbiol 60, 1322–1327.
S.-J. Kim and others
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Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precisemeasurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159–167.
Minnikin, D. E., O’Donnell, A. G., Goodfellow, M., Alderson, G.,Athalye, M., Schaal, A. & Parlett, J. H. (1984). An integratedprocedure for the extraction of bacterial isoprenoid quinones andpolar lipids. J Microbiol Methods 2, 233–241.
Nozawa, Y., Sakai, N., Arai, K., Kawasaki, Y. & Harada, K. (2007).Reliable and sensitive analysis of amino acids in the peptidoglycan ofactinomycetes using the advanced Marfey’s method. J MicrobiolMethods 70, 306–311.
Park, Y. H., Suzuki, K., Yim, D. G., Lee, K. C., Kim, E., Yoon, J., Kim, S.,Kho, Y. H., Goodfellow, M. & Komagata, K. (1993). Supragenericclassification of peptidoglycan group B actinomycetes by nucleotidesequencing of 5S ribosomal RNA. Antonie van Leeuwenhoek 64, 307–313.
Pindi, P. K., Kishore, K. H., Reddy, G. S. N. & Shivaji, S. (2009).Description of Leifsonia kafniensis sp. nov. and Leifsonia antarctica sp.nov. Int J Syst Evol Microbiol 59, 1348–1352.
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies,J. & Glockner, F. O. (2007). SILVA: a comprehensive online resourcefor quality checked and aligned ribosomal RNA sequence datacompatible with ARB. Nucleic Acids Res 35, 7188–7196.
Qiu, F., Huang, Y., Sun, L., Zhang, X., Liu, Z. & Song, W. (2007).Leifsonia ginsengi sp. nov., isolated from ginseng root. Int J Syst EvolMicrobiol 57, 405–408.
Reddy, G. S. N., Prakash, J. S. S., Srinivas, R., Matsumoto, G. I. &Shivaji, S. (2003). Leifsonia rubra sp. nov. and Leifsonia aurea sp.nov., psychrophiles from a pond in Antarctica. Int J Syst EvolMicrobiol 53, 977–984.
Reddy, G. S. N., Prabagaran, S. R. & Shivaji, S. (2008). Leifsoniapindariensis sp. nov., isolated from the Pindari glacier of the Indian
Himalayas, and emended description of the genus Leifsonia. Int J SystEvol Microbiol 58, 2229–2234.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a newmethod for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
Schleifer, K. H. & Kandler, O. (1972). Peptidoglycan types of bacterialcell walls and their taxonomic implications. Bacteriol Rev 36, 407–477.
Stackebrandt, E., Rainey, F. A. & Ward-Rainey, N. L. (1997). Proposalfor a new hierarchic classification system, Actinobacteria classis nov.Int J Syst Bacteriol 47, 479–491.
Suzuki, K. I., Suzuki, M., Sasaki, J., Park, Y. H. & Komagata, K.(1999). Leifsonia gen. nov., a genus for 2,4-diaminobutyric acid-containing actinomycetes to accommodate ‘‘Corynebacterium aqua-ticum’’ Leifson 1962 and Clavibacter xyli subsp. cynodontis Davis et al.1984. J Gen Appl Microbiol 45, 253–262.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar,S. (2011). MEGA5: molecular evolutionary genetics analysis usingmaximum likelihood, evolutionary distance, and maximum par-simony methods. Mol Biol Evol 28, 2731–2739.
Uchida, K. & Aida, K. (1984). An improved method for the glycolatetest for simple identification of the acyl type of bacterial cell walls.J Gen Appl Microbiol 30, 131–134.
Weon, H.-Y., Kim, S.-J., Jang, Y.-H., Hamada, M., Tamura, T., Ahn,J.-H., Suzuki, K.-i. & Kwon, S.-W. (2013). Naasia aerilata gen. nov., sp.nov., a member of the family Microbacteriaceae isolated from air. Int JSyst Evol Microbiol 63, 2436–2441. .
Zhang, D. C., Liu, H. C., Xin, Y. H., Yu, Y., Zhou, P. J. & Zhou, Y. G.(2008). Salinibacterium xinjiangense sp. nov., a psychrophilicbacterium isolated from the China No. 1 glacier. Int J Syst EvolMicrobiol 58, 2739–2742.
Rudaibacter terrae sp. nov.
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