Lysinimonas soli gen. nov., sp. nov., isolated from soil

International Journal of Systematic and Evolutionary Microbiology (2013), 63, 1403–1410

DOI 10.1099/ijs.0.042945-0

Lysinimonas soli gen. nov., sp. nov., isolated from soil, and reclassification of Leifsonia kribbensis Dastager et al. 2009 as Lysinimonas kribbensis sp. nov., comb. nov. Yun-Hee Jang,1 Soo-Jin Kim,1 Tomohiko Tamura,2 Moriyuki Hamada,2 Hang-Yeon Weon,1 Ken-ichiro Suzuki,2 Soon-Wo Kwon1 and Wan-Gyu Kim1 Correspondence Soo-Jin Kim [email protected]

1

Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea

2

NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan

A Gram-stain-positive, non-motile rod, designated strain SGM3-12T, was isolated from paddy soil in Suwon, Republic of Korea. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family Microbacteriaceae. The nearest phylogenetic neighbour was Leifsonia kribbensis MSL-13T (97.4 % 16S rRNA gene sequence similarity). Strain SGM3-12T and Leifsonia kribbensis MSL-13T formed a distinct cluster within the family Microbacteriaceae. Strain SGM3-12T contained MK-12(H2) and MK-11(H2) as the predominant menaquinones with moderate amounts of MK-12 and MK-11; anteiso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids (.10 % of total); and diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids as the polar lipids. The peptidoglycan type of the isolate was B1d with LLys as the diagnostic cell-wall diamino acid. On the basis of these results, strain SGM3-12T represents a novel species within a new genus, for which the name Lysinimonas soli gen. nov., sp. nov. is proposed (the type strain of the type species is SGM3-12T5KACC 13362T5NBRC 107106T). It is also proposed that Leifsonia kribbensis be transferred to this genus as Lysinimonas kribbensis comb. nov. (the type strain is MSL-13T5DSM 19272T5JCM 16015T5KACC 21108T5KCTC 19267T).

The family Microbacteriaceae was first proposed by Park et al. (1993) and then emended by Stackebrandt et al. (1997). At the time of writing, 35 genera are included in the family Microbacteriaceae. The genus Leifsonia within the Microbacteriaceae was established by Evtushenko et al. (2000) and has currently 16 species or subspecies with validly published names, with Leifsonia aquatica as the type species. Members of the genus Leifsonia contain a diagnostic diamino acid of 2,4-diaminobutyric acid in the peptidoglycan, MK-11 as the major menaquinone, phosphatidylglycerol and diphosphatidylglycerol as the principal phospholipids, a high content of anteiso- and iso-branched saturated fatty acids and DNA G+C content in the range 66–73 mol%. Phylogenetic analysis has shown that members of the genus Leifsonia do not form a The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain SGM3-12T is JN378395. Two supplementary figures are available with the online version of this paper.

042945 G 2013 IUMS

coherent group (An et al., 2010; Behrendt et al., 2011) and so they have been under reclassification. Leifsonia aurea was combined with the genus Rhodoglobus (An et al., 2010) and Leifsonia ginsengi was combined with a novel genus, Herbiconiux, of the family Microbacteriaceae (Behrendt et al., 2011). A Gram-stain-positive, non-motile rod, designated SGM312T, was isolated from paddy soil in Suwon, Republic of Korea using the standard dilution-plating technique on R2A agar (Difco) at 28 uC after 6 days. The isolate was maintained at 280 uC as a suspension in R2A broth supplemented with 20 % glycerol. Cell staining was tested according to the method of Hucker (Smibert & Krieg, 1994). Catalase and oxidase activities were examined by observing bubble production in 3 % (v/v) hydrogen peroxide solution and using 1 % (w/v) tetramethyl-p-phenylenediamine (bioMe´rieux), respectively. Cell morphology and motility of strain SGM3-12T was examined by light microscopy (Axio; Zeiss) and

Downloaded from www.microbiologyresearch.org by IP: 52.2.249.46 On: Sat, 07 Nov 2015 12:39:14

Printed in Great Britain

1403

Genera: 1, Lysinimonas gen. nov.; 2, Agreia (Evtushenko et al., 2001; Behrendt et al., 2002, Schumann et al., 2003); 3, Agrococcus (Groth et al., 1996; Wieser et al., 1999; Zlamala et al., 2002; Mayilraj et al., 2006; Bora et al., 2007; Lee, 2008; Behrendt et al., 2008; Zhang et al., 2010; Dhanjal et al., 2011); 4, Chryseoglobus (Baik et al., 2010); 5, Glaciibacter (Katayama et al., 2009); 6, Herbiconiux (Qiu et al., 2007; Behrendt et al., 2011; Kim et al., 2012); 7, Labedella (Lee, 2007); 8, Leifsonia (Leifson, 1962; Davis et al., 1984; Suzuki et al., 1999; Evtushenko et al., 2000; Reddy et al., 2003; An & Yokota, 2007; Qiu et al., 2007; Dastager et al., 2008, 2009; Pindi et al., 2009; An et al., 2009, 2010; Madhaiyan et al., 2010; Ganzert et al., 2011); 9, Microcella (Tiago et al., 2005, 2006); 10, Microterricola (Matsumoto et al., 2008); 11, Phycicola (Lee et al., 2008); 12, Rhodoglobus (Reddy et al., 2003; Sheridan et al., 2003; An et al., 2010); 13, Salinibacterium (Han et al., 2003; Zhang et al., 2008); 14, Schumannella (An et al., 2008); 15, Subtercola (Ma¨nnisto¨ et al., 2000; Behrendt et al., 2002); 16, Yonghaparkia (Yoon et al., 2006). B, Brown; C, cream; O, orange; P, pink; Re, red; R, rod; C, cocci; F, filaments; W, white; Y, yellow; DAB, diaminobutyric acid; DPG, diphosphatidylglycerol; GL, unknown glycolipid; PA, phosphatidic acid; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PI, phosphatidylinositol; PL, unknown phospholipid; UL, unknown lipid; +, positive, 2, negative; ND, not data available. Characteristic Source

International Journal of Systematic and Evolutionary Microbiology 63

1

2

3

4

5

6

7

Soil

Leaf galls, phyllosphere

Soil, air, cheese, ice glacier, phyllosphere, wall paintings

Watercooling system

Ice wedge

Phyllosphere, tissue

Seaweed

Y, BO, O, RO

C, O, P, W, Y

Y

W

W, Y

Y

R

R, C

R

R

R

R

+ ND–37

2 10–40

+ 20–40

+ 25–25

2 4–37

2 10–37

L-DAB,

L-DAB

Lys

DAB

DL-DAB

Orn

Colony colour B, Y Morphology R Motility 2 Temperature 20–37 range (uC) Diagnostic Lys, DAB diamino acid Peptidoglycan B1d type Major fatty acids ai-C15 : 0, (.10 %) i-C16 : 0

Major menaquinones Polar lipids

DNA G+C content (mol%)

12(H2), 11(H2) 13(H2) DPG, PG, GL, PL 67–74

8

Water Diverse sources including soil, water, lichen, nematode, glacier, sugar cane RE, W, Y Y R, F R 2/+ 2 26–37 10–45 DL-DAB

D-Orn

B

Lys,

10

11

12

13

14

15

16

Soil

Seawater

Lake, pond

Seawater, glacier

Lichen

Water, phyllosphere

Soil

Y

W, Y

RE

Y

Y

Y

Y

R

R, C

R

R

R

R

R

+ 10–38

+ 4–30

+ 22–30

2 4–37

2 8–35

2 22–28

2 10–37

DAB

DAB

Orn,

Lys, Orn B

DAB

DAB,

DL-DAB

D-Orn

B, B2c

B2b

B2c

ai-C15 : 0, i-C16 : 0, ai-C17 : 0, i-C15 : 0, C16 : 0, C17 : 0

i-C16 : 0, ai-C15 : 0, i-C14 : 0, C16 : 0

ai-C15 : 0, ai-C17 : 0, i-C16 : 0

10, 11

11, 12, 10, 9

12, 13, 14

PG, DPG

PG, DPG, GL, UL, UP

DPG, PG

ND

65–67

73–76

68

65

ai-C15 : 0, i-C16 : 0, ai-C17 : 0

9

B2c

ai-C15 : 0, ai-C17 : 0, v-cyclohexylundecanoic acid, cyclohexyl-C17 : 0, i-C16 : 0 11, 12, 13 11

ND

ai-C15 : 0, i-C16 : 0

B, 2Bc

B, B2b

DL-DAB ND

ai-C15 : 0, ai-C15 : 0, ai-C15 : 0, ai-C17 : 0, i-C16 : 0, ai-C17 : 0 i-C16 : 0 i-C14 : 0, i-C15 : 0,

10, 11

11, 12, 10, 9

13, 12, 14

12

DPG, PG, UPL, GL

PG, DPG

ND

ND

66–70

68

DPG, PG, GL, PE, UL, PA 62–73

67–69

70


B

B2a

D-Orn ND

B2c

B2c

ai-C15 : 0, ai-C15 : 0, ai-C15 : 0, ai-C15 : 0, ai-C15 : 0, ai-C15 : 0, ai-C17 : 0 i-C16 : 0, i-C16 : 0, i-C16 : 0 i-C16 : 0, i-C16 : 0, ai-C17 : 0 i-C14 : 0 ai-C17 : 0 ai-C17 : 0

11

11, 12

11, 10

DPG, PC, PG, DPG PG, DPG PG, PI 70

62–64

61–64

11, 10

ND

59

9, 10, 11

12, 11

PG, DPD, DPG, PG, PL, GL UPL, GL 64–68

71–72

Y.-H. Jang and others

1404

Table 1. Differential characteristics of closely related genera of the family Microbacteriaceae

Lysinimonas soli. gen. nov., sp. nov.

transmission electron microscopy (model 912AB; Leo) using cells grown for 3 days on R2A agar at 28 uC. For transmission electron microscopy, cells were negatively stained with 0.5 % (w/v) uranyl acetate. Optimum conditions for growth were determined by culture for up to 14 days in R2A broth. Growth was determined at 4, 10, 15, 20, 25, 28, 30, 35, 37, 40 and 45 uC. Growth at pH 4–11 (at intervals of 1 pH unit) was determined in R2A broth that was buffered with citrate/phosphate buffer or Tris/hydrochloride buffer (Breznak & Costilow, 1994). Growth was determined with 0, 1, 3, 5 and 7 % (w/v) NaCl. Casein degradation was tested on R2A agar containing milk powder (5 %, w/v). Starch degradation was tested on R2A agar containing starch (1 %, w/v). Tyrosine degradation was tested on R2A agar containing tyrosine (0.1 %, w/v). CM-cellulose and Tween 80 was examined on R2A agar amended with 1 % (w/v) substrate (Teather & Wood, 1982; Gerhardt et al., 1994). DNase activity was determined on DNase test agar (Difco). Anaerobic growth was assessed on R2A agar containing 0.5 % Na2SO4, 0.5 % NaNO3, 0.5 % NaHCO3 or 0.02 % FeCl3. Growth was incubated for 14 days at 28 uC in air-tight jars containing a BBL GasPak Anaerobic System (Difco). Strain SGM3-12T was also characterized using the whole test spectra of the API ZYM, API 20 NE and API ID 32 GN identification systems (bioMe´rieux) according to the manufacturer’s instructions. As strain SGM3-12T did not grow in the AUX medium supplied on API 20 NE and API ID 32 GN kit, cells were suspended in modified AUX medium [containing l21 distilled water: 0.728 g yeast nitrogen base (Difco), 5.4 mg yeast extract (Difco), 1.072 g K2HPO4, 0.524 KH2PO4 and 0.15 g agar]. Cells of strain SGM3-13T were Gram-stainpositive, aerobic, non-motile rods (Fig. S1, available in IJSEM Online). Colonies were light brown, round and convex after 3 days of growth at 28 uC on R2A agar. Growth occurred on trypticase soy agar, but not on nutrient agar or MacConkey agar (all from Difco). The detailed phenotypic characteristics of strain SGM3-12T are given in the genus and species descriptions and Tables 1 and 2. Genomic DNA extraction and amplification of the 16S rRNA gene of strain SGM3-12T was carried out as described by Weon et al. (2006). PCR products were sequenced by Geno Tech (Korea). The resultant 16S rRNA sequence was aligned using ARB (Ludwig et al., 2004) and was added to the alignment of the SILVA SSURef 106 database (release April 2011; Pruesse et al., 2007). The aligned nucleotide positions with 30 and 50 % conservation filters and without filter were used for phylogenetic analysis in MEGA version 4.0 (Tamura et al., 2007). Phylogenetic trees were inferred using neighbour joining with Kimura’s two-parameter model and maximum parsimony. To determine the closest phylogenetic neighbours of strain SGM3-12T, a continuous stretch (1466 bp) of its 16S rRNA gene sequence was analysed using the EzTaxon-e server (http://eztaxon-e.ezbiocloud.net/; Kim et al., 2012). For the comparison of signature sequences, several sequences, http://ijs.sgmjournals.org

including those from strain SGM3-12T, Escherichia coli K12 (GenBank accession number J01695), Leifsonia aquatica JCM 1368T (D45057) and Microbacterium lacticum DSM 20427T, were aligned using both CLUSTAL W of MEGALIGN (Lasergene software; DNASTAR) and ARB (Ludwig et al., 2004). Similarity values indicated that the novel strain was a member of the family Microbacteriaceae, with Leifsonia kribbensis MSL-13T as the closest relative (97.4 % 16S rRNA gene sequence similarity). The isolate exhibited ,97 % sequence similarity with all other members of the family Microbacteriaceae, such as Labedella gwakjiensis KSW2-17T (96.5 %), Cryobacterium psychrotolerans 0549T (96.4 %) and Herbiconiux ginsengi wged11T (96.1 %). According to the neighbour-joining phylogenetic tree, strain SGM3-12T formed a robust cluster with Leifsonia kribbensis MSL-13T (bootstrap value 97 %) and the two strains were clearly separable from the type strain of the type species of the genus Leifsonia (Fig. 1). The cluster was also recovered in the maximum-parsimony tree. The position of strain SGM3-12T in the family Microbacteriaceae was further supported by the presence of a set of family-specific signature nucleotides (Zhi et al., 2009) that was complete except for one signature nucleotide (position 131) in its 16S rRNA gene sequence. According to our analysis, the nucleotide of position 131 was U or C which is different from the G reported by Zhi et al. (2009). This discrepancy was supposed to occur because of either an error in the previous literature or differences in the analytical method. Analysis of the cell wall and the fatty acids was conducted using cells grown for 48 h on R2A agar at 28 uC. GC/MS (model 6890; Hewlett Packard) of fatty acid methyl esters was performed according to the protocol of the Sherlock Microbial Identification System (MIDI; Sasser, 1990). The fatty acid methyl esters were identified and quantified using TSBA 6 database version 6.10 (MIDI). Menaquinones and polar lipids were extracted and analysed according to Minnikin et al. (1984). Menaquinones were further determined by LC-MS (models LCMS-8030 and LC20AD; Shimadzu, Kyoto, Japan) equipped with a SenshuPak Pegasil ODS-SP-100 column (10062.0 mm i.d.; Senshu Scientific, Tokyo, Japan). For the peptidoglycan analysis, the preparation of cell walls and determination of molar ratio and isomers of amino acids in the cell-wall hydrolysates were performed using the method described in Hamada et al. (2010) by LC-MS (model LCMS-2020; Shimadzu). The acyl type of the cell wall was analysed according to the method of Uchida & Aida (1984). The major fatty acids of strain SGM3-12T were anteiso-C15 : 0 (47.8 %), iso-C16 : 0 (39.5 %), anteiso-C17 : 0 (5.0 %), isoC15 : 0 (4.2 %) and iso-C14 : 0 (3.5 %) (Table 2). The menaquinones of strain SGM3-12T were MK-12(H2) (48.7 %), MK-11(H2) (24.5 %), MK-12 (10.0 %) and MK11 (6.3 %), with MK-10, MK-10(H2), MK-13 and MK13(H2) as trace components. Dastager et al. (2009) reported that the menaquinone composition of Leifsonia kribbensis MSL-13T was composed of MK-12 and MK-11.


1405


Table 2. Characteristics that differentiate Lysinimonas soli sp. nov., Lysinimonas kribbensis comb. nov. and Labedella gwakjiensis Strains: 1, Lysinimonas soli sp. nov. SGM3-12T; 2, Lysinimonas kribbensis comb. nov. MSL-13T; 3, Labedella gwakjiensis KSW2-17T. Data were taken from this study unless otherwise mentioned. Fatty acids were analysed using cells grown on R2A agar at 28 uC for 48 h; fatty acids representing ,1.0 % are omitted. All strains are positive for aesculin hydrolysis (API 20 NE), utilization of N-acetylglucosamine, L-arabinose, D-glucose, lactic acid, D-maltose, D-mannose, Dmelibiose, L-rhamnose, D-ribose and D-sucrose (API 20 NE and API ID 32 GN) and a-galactosidase, b-galactosidase, a-glucosidase, esterase, esterase lipase, leucine arylamidase and naphthol-AS-BIphosphohydrolase activities (API ZYM). All strains are negative for indole production, arginine dihydrolase and urease (API 20 NE), utilization of N-acetylglucosamine, adipic acid, capric acid, Lhistidine, 4-hydroxybenzoic acid, 3-hydroxybutyric acid, itaconic acid, L-proline, phenylacetic acid, potassium 5-ketogluconate, propionic acid, L-serine, sodium malonate, D-sorbitol, suberic acid and valeric acid (API 20 NE and API ID 32 GN) and a-chymotrypsin, afucosidase, lipase, trypsin and valine arylamidase activities (API ZYM). +, Positive; 2, negative; ND, no data available. Characteristic Reduction of nitrate to nitrite Glucose fermentation Catalase/oxidase pH range Hydrolysis of: Casein Gelatin Tyrosine Tween 80 Assimilation of: N-Acetylglucosamine L-Alanine L-Fucose Glycogen 4-Hydroxybenzoic acid Inositol Malic acid D-Maltose D-Mannitol Potassium gluconate Potassium 2-ketogluconate Salicin Sodium acetate Trisodium citrate Enzyme activities: N-Acetyl-b-glucosaminidase Alkaline phosphatase Acid phosphatase Cystine arylamidase, b-Glucosidase b-Glucuronidase a-Mannosidase Fatty acids (%)

1406

1

2

3

2 + 2 /+ 5–9

+ + 2/2D 6–11D

2* 2 +/2* 5–10*

2 2 2 2

+D 2 +D +D

2* +

2 2 + + + 2 2 2 2 2 2 2 + 2

2 2 2 2 2 2 2 2 2 2 + + 2 2

+ + + 2 2 + + + + + 2 + + +

2 2 2 2 2 2 2

2 2 + 2 + 2 +

+ + + + + + 2

ND ND

Table 2. cont. Characteristic iso-C14 : 0 iso-C15 : 0 C16 : 0 anteiso-C15 : 0 iso-C16 : 0 anteiso-C17 : 0

1

2

3

3.5 4.2 2 47.8 39.5 5.0

2.7 5.4 2 52.4 35.2 4.3

5.0 4.9 1.4 49.9 29.7 7.8

*Data from Lee (2007). DData from Dastager et al. (2009).

However, our study showed that Leifsonia kribbensis MSL13T contained MK-12(H2) and MK-13(H2) (approx. 7 : 3) as the predominant menaquinones. Both strains, SGM312T and Leifsonia kribbensis MSL-13T, are the first within the family Microbacteriaceae to be found to contain partially unsaturated menaquinones. The polar lipid profile of strain SGM3-12T consisted of diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and three unknown glycolipids, while Leifsonia kribbensis MSL-13T revealed a polar lipid profile similar to strain SGM3-12T except for an additional unknown glycolipid (Fig. S2). The peptidoglycan of strain SGM3-12T contained glutamic acid, glycine, alanine and lysine in the molar ratio of 1.0 : 1.1 : 1.9 : 1.0. Enantiomeric analysis of the peptidoglycan amino acids revealed the presence of Gly, D-Glu, D-Ala, L-Ala and L-Lys. These data suggested that the cell-wall peptidoglycan of strain SGM3-12T was type B1d. DNA–DNA hybridization was carried out according to the method of Seldin & Dubnau (1985). Probe labelling was conducted using the nonradioactive DIG High Prime DNA Labelling and Detection Starter kit II (Roche Molecular Biochemicals, USA). The hybridized DNA was visualized using the DIG luminescent detection kit (Roche Molecular Biochemicals). DNA–DNA relatedness was quantified using a densitometer (Bio-Rad). The G+C content of the DNA was determined by HPLC (Mesbah et al., 1989). DNA–DNA relatedness between strain SGM3-12T and Leifsonia kribbensis MSL-13T was 32 % (reciprocal 29 %). The DNA G+C content of strain SGM3-12T was 67.3 mol%. Phylogenetic analysis clearly revealed that strain SGM3-12T belongs to the family Microbacteriaceae and that strain SGM3-12T and Leifsonia kribbensis MSL-13T comprise a cluster separate from other members of the family. Strain SGM3-12T can be differentiated from closely related genera on the basis of chemotaxonomic characteristics such as fatty acids, polar lipids, menaquinones and peptidoglycan structure (Table 1). Especially, strain SGM3-12T has a unusual peptidoglycan structure (type B1d) and both SGM3-12T and Leifsonia kribbensis MSL-13T contain the partially saturated menaquinones MK-12(H2), MK-11(H2)

Downloaded from www.microbiologyresearch.org by International Journal of Systematic and Evolutionary Microbiology 63 IP: 52.2.249.46 On: Sat, 07 Nov 2015 12:39:14

Lysinimonas soli. gen. nov., sp. nov.

71

Agreia bicolorata VKM Ac-1804T (AF159363) Subtercola boreus K300T (AF224722) Glaciibacter superstes AHU1791T (AB378301) Herbiconiux ginsengi wged11T (DQ473536) Microterricola viridarii KV-677T (AB282862) Phycicola gilvus SSWW-21T (AM286414) 99 Agrococcus jenensis DSM 9580T (X92492) Microbacterium lacticum DSM 20427T (X77441) Okibacterium fritillariae VKM Ac-2059T (AB042094) Plantibacter flavus P 297/02 T (AJ310417) 60 Amnibacterium kyonggiense KSL51201-037T (FJ527819) 78 Labedella gwakjiensis KSW2-17T (DQ533552) Lysinimonas soli SGM3-12T (JN378395) Lysinimonas kribbensis MSL-13T (EF466129) 97 Rhodoglobus vestalii LV3T (AJ459101) 99 Salinibacterium amurskyense KMM 3673T (AF539697) Chryseoglobus frigidaquae CW1T (EF373534) Microcella putealis CV-2T (AJ717388) 83 Yonghaparkia alkaliphila KSL-113T (DQ256087) 94 Schumannella luteola KHIAT (AB362159) Leifsonia aquatica JCM 1368T (D45057) Agromyces ramosus DSM 43045T (X77447) Humibacter albus SC-083T (AM494541) 90 Leucobacter komagatae JCM 9414T (D45063) Curtobacterium citreum DSM 20528T (X77436) Gryllotalpicola koreensis RU-16T (HQ832501) Gulosibacter molinativorax ON4T (AJ306835) Pseudoclavibacter helvolus DSM 20419T (X77440) 92 Mycetocola saprophilus CM-01T (AB012647) Rathayibacter rathayi DSM 7485T (X77439) Alpinimonas psychrophila Cr8-25T (GU784868) Klugiella xanthotipulae 44C3T (AY372075) Cryobacterium psychrophilum DSM 4854T (AJ544063) Clavibacter michiganensis subsp. michiganensis DSM 46364T (X77435) Compostimonas suwonensis SMC46T (JN000316) Marisediminicola antarctica ZS314T (GQ496083) Frigoribacterium faeni 801T (Y18807) Frondihabitans australicus E1HC-02T (DQ525859) 97

•

0.005

•

52

•

•

•

•

•

• 66

•

•

•

•

•

• 87

•

•

74

Fig. 1. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing the position of strain SGM3-12T in the family Microbacteriaceae. Bootstrap values (.50 %) based on 1000 replications are shown at branch nodes. Filled squares indicate that the corresponding branches were also recovered in the maximum-parsimony tree. Bar, 0.005 substitutions per nucleotide position.

and/or MK-13(H2) as the predominant menaquinones, which makes these two strains differentiable from other members of the family Microbacteriaceae. Furthermore, a comparison of characteristics of the two strains and Labedella gwakjiensis is shown in Table 2. On the basis of the phylogenetic analysis and chemotaxonomic characteristics, strain SGM3-12T represents a novel genus and species, for which the name Lysinimonas soli sp. nov. is proposed. It is also proposed that Leifsonia kribbensis be transferred to this genus as Lysinimonas kribbensis comb. nov. Description of Lysinimonas gen. nov. Lysinimonas (Ly.si.ni.mo9nas. N.L. n. lysinum lysine; L. fem. n. monas a unit, monad; N.L. fem. n. Lysinimonas lysine monad, referring to the presence of lysine in the cell wall). Cells are aerobic, Gram-stain-positive, non-spore-forming, non-motile rods. The major fatty acids (.10 % of the total) are anteiso-C15 : 0 and iso-C16 : 0. The polar lipid profiles are dominated by diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids. The predominant respiratory menaquinones are MK-12(H2) and MK11(H2). The DNA G+C content is 67–74 mol%. The type species is Lysinimonas soli sp. nov. http://ijs.sgmjournals.org

Description of Lysinimonas soli sp. nov. Lysinimonas soli (so9li. L. gen. n. soli of soil). Cells are Gram-stain-positive, non-spore-forming, nonmotile, aerobic rods. Colonies are light brown, round and convex after 3 days of growth at 28 uC on R2A agar. Cells are usually 0.4–0.5 mm wide and 1.2–3.0 mm long. Growth occurs at 10–37 uC (optimum 28 uC) and at pH 5–9 (optimum pH 7.0). Growth does not occur in the presence of 2 % (w/v) NaCl. Oxidase-positive and catalase-negative. Does not hydrolyse CM-cellulose, chitin, DNA, hypoxanthine, pectin, starch, tyrosine, Tween 80 or xanthine. Other physiological characteristics are given in Table 2. The fatty acids are anteisoC15 : 0, iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C14 : 0. The type strain, SGM3-12T (5KACC 13362T5NBRC 107106T), was isolated from paddy soil in Suwon, Republic of Korea. The G+C content of the DNA of type strain is 67.3 mol%. Description of Lysinimonas kribbensis comb. nov. Lysinimonas kribbensis (krib.ben9sis. N.L. fem. adj. kribbensis pertaining to KRIBB, an arbitrary adjective formed from the acronym of the Korea Research Institute of Bioscience and Biotechnology, where taxonomic studies on the type strain were performed).


1407


Basonym: Leifsonia kribbensis Dastager et al. 2009. The description of Lysinimonas kribbensis is as given for Leifsonia kribbensis Dastager et al. 2009 with the following additional characteristics. The predominant respiratory menaquinones are MK-12(H2) and MK-13(H2). The type strain, MSL-13T (5DSM 19272T5JCM 16015T 5KACC 21108T5KCTC 19267T), was isolated from soil on Bigeum Island, Republic of Korea.

Acknowledgements This study was carried out with the support of the Research Program for Agricultural Science & Technology Development, National Academy of Agricultural Science, Rural Development Administration, Republic of Korea (project no. PJ008666). The authors thank Professor J. P. Euze´by of the Ecole Nationale Ve´te´rinaire in Toulouse for advice concerning the etymology.

References An, S.-Y. & Yokota, A. (2007). The status of the species Leifsonia rubra

Reddy et al. 2003. Request for an opinion. Int J Syst Evol Microbiol 57, 1163. An, S.-Y., Xiao, T. & Yokota, A. (2008). Schumannella luteola gen. nov.,

sp. nov., a novel genus of the family Microbacteriaceae. J Gen Appl Microbiol 54, 253–258.

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. Dastager, S. G., Lee, J.-C., Ju, Y.-J., Park, D.-J. & Kim, C.-J. (2009).

Leifsonia kribbensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 59, 18–21. Davis, M. J., Gillaspie, A. G., Vidaver, A. K. & Harris, R. W. (1984).

Clavibacter: a new genus containing some hytopathogenic coryneform bacteria, 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 stunting disease. Int J Syst Bacteriol 34, 107–117. Dhanjal, S., Kaur, I., Korpole, S., Schumann, P., Cameotra, S. S., Pukall, R., Klenk, H.-P. & Mayilraj, S. (2011). Agrococcus carbonis sp.

nov., isolated from soil of a coal mine. Int J Syst Evol Microbiol 61, 1253–1258. Evtushenko, L. I., Dorofeeva, L. V., Subbotin, S. A., Cole, J. R. & Tiedje, J. M. (2000). Leifsonia poae gen. nov., sp. nov., isolated from

nematode galls on Poa annua, and reclassification of ‘Corynebacterium aquaticum’ Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli Davis 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. Evtushenko, L. I., Dorofeeva, L. V., Dobrovolskaya, T. G., Streshinskaya, G. M., Subbotin, S. A. & Tiedje, J. M. (2001). Agreia

bicolorata gen. nov., sp. nov., to accommodate actinobacteria isolated from narrow reed grass infected by the nematode Heteroanguina graminophila. Int J Syst Evol Microbiol 51, 2073–2079. Ganzert, L., Bajerski, F., Mangelsdorf, K., Lipski, A. & Wagner, D. (2011). Leifsonia psychrotolerans sp. nov., a psychrotolerant species of

An, S.-Y., Xiao, T. & Yokota, A. (2009). Leifsonia lichenia sp. nov., isolated from lichen in Japan. J Gen Appl Microbiol 55, 339–343.

the family Microbacteriaceae from Livingston Island, Antarctica. Int J Syst Evol Microbiol 61, 1938–1943.

An, S.-Y., Xiao, T. & Yokota, A. (2010). Reclassification of Leifsonia

Gerhardt, P., Murray, R. G. E., Wood, W. A. & Krieg, N. R. (editors) (1994). Methods for General and Molecular Bacteriology. Washington,

aurea to the genus Rhodoglobus as Rhodoglobus aureus comb. nov., and emended description of Rhodoglobus vestalii Sheridan et al. 2003. J Gen Appl Microbiol 56, 53–55. Baik, K. S., Park, S. C., Kim, H. J., Lee, K. H. & Seong, C. N. (2010).

DC: American Society for Microbiology. Groth, I., Schumann, P., Weiss, N., Martin, K. & Rainey, F. A. (1996).

Chryseoglobus frigidaquae gen. nov., sp. nov., a novel member of the family Microbacteriaceae. Int J Syst Evol Microbiol 60, 1311–1316.

Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 46, 234– 239.

Behrendt, U., Ulrich, A., Schumann, P., Naumann, D. & Suzuki, K. (2002). Diversity of grass-associated Microbacteriaceae isolated from

Hamada, M., Iino, T., Iwami, T., Harayama, S., Tamura, T. & Suzuki, K. (2010). Mobilicoccus pelagius gen. nov., sp. nov. and Piscicoccus

the phyllosphere and litter layer after mulching the sward; polyphasic characterization of Subtercola pratensis sp. nov., Curtobacterium herbarum sp. nov. and Plantibacter flavus gen. nov., sp. nov. Int J Syst Evol Microbiol 52, 1441–1454.

intestinalis gen. nov., sp. nov., two new members of the family Dermatophilaceae, and reclassification of Dermatophilus chelonae (Masters et al. 1995) as Austwickia chelonae gen. nov., comb. nov. J Gen Appl Microbiol 56, 427–436.

Behrendt, U., Schumann, P. & Ulrich, A. (2008). Agrococcus versicolor

Han, S. K., Nedashkovskaya, O. I., Mikhailov, V. V., Kim, S. B. & Bae, K. S. (2003). Salinibacterium amurskyense gen. nov., sp. nov., a novel

sp. nov., an actinobacterium associated with the phyllosphere of potato plants. Int J Syst Evol Microbiol 58, 2833–2838. Behrendt, U., Schumann, P., Hamada, M., Suzuki, K.-i., Spro¨er, C. & Ulrich, A. (2011). Reclassification of Leifsonia ginsengi (Qiu et al.

2007) as Herbiconiux ginsengi gen. nov., comb. nov. and description of Herbiconiux solani sp. nov., an actinobacterium associated with the phyllosphere of Solanum tuberosum L. Int J Syst Evol Microbiol 61, 1039–1047. Bora, N., Vancanneyt, M., Gelsomino, R., Swings, J., Brennan, N., Cogan, T. M., Larpin, S., Desmasures, N., Lechner, F. E. & other authors (2007). Agrococcus casei sp. nov., isolated from the surfaces of

smear-ripened cheeses. Int J Syst Evol Microbiol 57, 92–97. Breznak, J. A. & Costilow, R. N. (1994). Physicochemical factors in

growth. 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. 1408

genus of the family Microbacteriaceae from the marine environment. Int J Syst Evol Microbiol 53, 2061–2066. Katayama, T., Kato, T., Tanaka, M., Douglas, T. A., Brouchkov, A., Fukuda, M., Tomita, F. & Asano, K. (2009). Glaciibacter superstes gen.

nov., sp. nov., a novel member of the family Microbacteriaceae isolated from a permafrost ice wedge. Int J Syst Evol Microbiol 59, 482–486. Kim, B.-C., Park, D.-S., Kim, H., Oh, H.-W., Lee, K. H., Shin, K.-S. & Bae, K. S. (2012). Herbiconiux moechotypicola sp. nov., a xylanolytic

bacterium isolated from the gut of hairy long-horned toad beetles, Moechotypa diphysis (Pascoe). Int J Syst Evol Microbiol 62, 90– 95. Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S., Lee, J. H. & other authors (2012). Introducing EzTaxon-e:

a prokaryotic 16S rRNA gene sequence database with phylotypes that


Lysinimonas soli. gen. nov., sp. nov. represent uncultured species. Int J Syst Evol Microbiol 62, 716– 721.

Sasser, M. (1990). Identification of bacteria by gas chromatography of

Lee, S. D. (2007). Labedella gwakjiensis gen. nov., sp. nov., a novel actinomycete of the family Microbacteriaceae. Int J Syst Evol Microbiol 57, 2498–2502.

Schumann, P., Behrendt, U., Ulrich, A. & Suzuki, K. (2003).

cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.

Lee, S. D. (2008). Agrococcus jejuensis sp. nov., isolated from dried

Reclassification of Subtercola pratensis Behrendt et al. 2002 as Agreia pratensis comb. nov. Int J Syst Evol Microbiol 53, 2041– 2044.

seaweed. Int J Syst Evol Microbiol 58, 2297–2300.

Seldin, L. & Dubnau, D. (1985). Deoxyribonucleic acid homology

Lee, D. W., Lee, J. M., Seo, J. P., Schumann, P., Kim, S. J. & Lee, S. D. (2008). Phycicola gilvus gen. nov., sp. nov., an actinobacterium

among Bacillus polymyxa, Bacillus macerans, Bacillus azotofixans, and other nitrogen-fixing Bacillus strains. Int J Syst Bacteriol 35, 151– 154.

isolated from living seaweed. Int J Syst Evol Microbiol 58, 1318– 1323. Leifson, E. (1962). The bacterial flora of distilled and stored water. III.

New species of the genera Corynebacterium, Flavobacterium, Spirillum and Pseudomonas. Int J Syst Evol Microbiol 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 Acids

Res 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 J Syst Evol Microbiol 60, 1322–1327. Ma¨nnisto¨, M. K., Schumann, P., Rainey, F. A., Ka¨mpfer, P., Tsitko, I., Tiirola, M. A. & Salkinoja-Salonen, M. S. (2000). Subtercola boreus

gen. nov., sp. nov. and Subtercola frigoramans sp. nov., two new psychrophilic actinobacteria isolated from boreal groundwater. Int J Syst Evol Microbiol 50, 1731–1739. Matsumoto, A., Yamada, M., Omura, S. & Takahashi, Y. (2008).

Microterricola viridarii gen. nov., sp. nov., a new member of the family Microbacteriaceae. Int J Syst Evol Microbiol 58, 1019–1023. Mayilraj, S., Suresh, K., Schumann, P., Kroppenstedt, R. M. & Saini, H. S. (2006). Agrococcus lahaulensis sp. nov., isolated from a cold desert of

the Indian Himalayas. Int J Syst Evol Microbiol 56, 1807– 1810. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise

measurement of the G+C content of deoxyribonucleic acid by highperformance 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 integrated

procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.

Sheridan, P. P., Loveland-Curtze, J., Miteva, V. I. & Brenchley, J. E. (2003). Rhodoglobus vestalii gen. nov., sp. nov., a novel psychrophilic

organism isolated from an Antarctic Dry Valley lake. Int J Syst Evol Microbiol 53, 985–994. Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In

Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology. Stackebrandt, E., Rainey, F. A. & Ward-Rainey, N. L. (1997). Proposal

for 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. K. (1999). Leifsonia gen. nov., a genus for 2, 4-diaminobutyric acid-

containing actinomycetes to accommodate ‘Corynebacterium aquaticum’ Leifson 1962 and Clavibacter xyli subsp. cynodontis Davis et al. 1984. J Gen Appl Microbiol 45, 253–262. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596–1599.

Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007).

Teather, R. M. & Wood, P. J. (1982). Use of Congo red-polysaccharide

interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 43, 777– 780. Tiago, I., Pires, C., Mendes, V., Morais, P. V., da Costa, M. & Verı´ssimo, A. (2005). Microcella putealis gen. nov., sp. nov., a gram-

positive alkaliphilic bacterium isolated from a nonsaline alkaline groundwater. Syst Appl Microbiol 28, 479–487. Tiago, I., Morais, P. V., da Costa, M. S. & Verı´ssimo, A. (2006).

Microcella alkaliphila sp. nov., a novel member of the family Microbacteriaceae isolated from a non-saline alkaline groundwater, and emended description of the genus Microcella. Int J Syst Evol Microbiol 56, 2313–2316. Uchida, K. & Aida, K. (1984). An improved method for the glycolate

Park, Y.-H., Suzuki, K.-i., Yim, D.-G., Lee, K.-C., Kim, E., Yoon, J.-s., Kim, S., Kho, Y.-H., Goodfellow, M. & Komagata, K. (1993).

test for simple identification of acyl type of bacterial cell walls. J Gen Appl Microbiol 30, 131–134.

Suprageneric classification of peptidoglycan group B actinomycetes by nucleotide sequencing of 5S ribosomal RNA. Antonie van Leeuwenhoek 64, 307–313.

Weon, H.-Y., Kim, B.-Y., Yoo, S.-H., Lee, S.-Y., Kwon, S.-W., Go, S.-J. & Stackebrandt, E. (2006). Niastella koreensis gen. nov., sp. nov.

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. & Glo¨ckner, F. O. (2007). SILVA: a comprehensive online resource

for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35, 7188–7196. Qiu, F., Huang, Y., Sun, L., Zhang, X., Liu, Z. & Song, W. (2007).

andNiastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microbiol 56, 1777–1782. Wieser, M., Schumann, P., Martin, K., Altenburger, P., Burghardt, J., Lubitz, W. & Busse, H.-J. (1999). Agrococcus citreus sp. nov., isolated

from a medieval wall painting of the chapel of Castle Herberstein (Austria). Int J Syst Bacteriol 49, 1165–1170. Yoon, J.-H., Kang, S.-J., Schumann, P. & Oh, T.-K. (2006).

Leifsonia ginsengi sp. nov., isolated from ginseng root. Int J Syst Evol Microbiol 57, 405–408.

Yonghaparkia alkaliphila gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an alkaline soil. Int J Syst Evol Microbiol 56, 2415–2420.

Reddy, G. S. N., Prakash, J. S. S., Srinivas, R., Matsumoto, G. I. & Shivaji, S. (2003). Leifsonia rubra sp. nov. and Leifsonia aurea sp.

Zhang, D.-C., Liu, H.C., Xin, Y.-H., Yu, Y., Zhou, P.-J. & Zhou, Y.-G. (2008). Salinibacterium xinjiangense sp. nov., a psychrophilic

nov., psychrophiles from a pond in Antarctica. Int J Syst Evol Microbiol 53, 977–984.

bacterium isolated from the China No. 1 glacier. Int J Syst Evol Microbiol 58, 2739–2742.

http://ijs.sgmjournals.org


1409

Y.-H. Jang and others Zhang, J.-Y., Liu, X.-Y. & Liu, S.-J. (2010). Agrococcus terreus sp. nov. and Micrococcus terreus sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 60, 1897–1903.

suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 59, 589–608.

Zhi, X.-Y., Li, W.-J. & Stackebrandt, E. (2009). An update of the

Zlamala, C., Schumann, P., Ka¨mpfer, P., Rossello´-Mora, R., Lubitz, W. & Busse, H.-J. (2002). Agrococcus baldri sp. nov., isolated from the air

structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new

in the ‘Virgilkapelle’ in Vienna. Int J Syst Evol Microbiol 52, 1211– 1216.

1410
