Nocardioides sambongensis sp. nov., isolated from Dokdo Islands soil Author Hwang, Ye-Ji Author Son, Jin-Soo Author Lee, Soo-Yeong Author He, Yuxi Author Jo, YoungJae Author Shin, Jae-Ho Author Ghim, Sa-Youl text International Journal of Systematic and Evolutionary Microbiology 2020 2020-01-01 70 1 16 22 http://dx.doi.org/10.1099/ijsem.0.003689 journal article 20669 10.1099/ijsem.0.003689 c13e6420-6bc8-478d-9616-188f27d5c617 1466-5034 6048652 DESCRIPTION OF NOCARDIOIDES SAMBONGENSIS SP. NOV. Nocardioides sambongensis (sam.bong.en′ sis. N.L. masc. adj. sambongensis of or pertaining to Sambong Islands. Sambong, ancient name of the Dokdo Islands, located on the coast of the East Sea in Korea , from where the organism was isolated). Cells are aerobic, Gram-stain-positive, non-motile and nonendospore-forming rods. The cells grow well under aerobic conditions on R2A agar and TSA plates. The individual cells are 0.5–0.6×0.8–1.0 µm in size. Colonies are circular, smooth, pale yellow in colour, and are approximately 1.0– 2.5 mm in diameter after 2 days of incubation on R2A agar at 30 Ǫ C. Growth occurs between 25 and 37 Ǫ C, but not at 40 Ǫ C and above. The pH range for growth is pH 5–12 (optimally at pH 7–8). Grows in the presence of 0–7% NaCl (w/ v; optimally in 0.5–2 %), but not in 8 % NaCl. The cells are catalase- and oxidase-positive. The cells hydrolyse Tween 20, Tween 40, Tween 60 and Tween 80, but not casein, DNA, hypoxanthine, starch, L- tyrosine or xanthine. Fig. 1. Neighbour-joining phylogenetic tree reconstructed based on a comparative analysis of 16S rRNA gene sequences showing the relationships between strain KUDC5002 T and related species. Numbers at the nodes indicate the levels of bootstrap support (%) based on 1000 resampled datasets. The 16S rRNA gene sequence of Kribbella flavida DSM 17836 T was used as an outgroup. Solid circles indicate that the corresponding nodes were also obtained in both the maximum-likelihood and maximum-parsimony trees. Open circles indicate that the corresponding nodes were also obtained from the maximum-likelihood tree. Bar, 0.01 nucleotide substitutions per position. Cells are positive for nitrate reduction, aesculin hydrolysis, gelatin hydrolysisand glucose fermentation, but negative for indole production, arginine dihydrolase and urease (API 20NE). D- Glucose is utilized, but adipate, L- arabinose, caproate, citrate, gluconate, N - acetyl-D- glucosamine, malate, maltose, D- mannitol, D- mannose and phenylacetate are not utilized as sole carbon and energy sources (API 20NE). API 50 CH tests are positive for acid production from aesculin, cellobiose, glucose, 5-ketogluconate, rhamnose, sucrose, trehalose, turanose and D- xylose, but negative for that from 2- ketogluconate, adonitol, amygdalin, D- arabinose, D- arabitol, L- arabinose, L- arabitol, arbutin, dulcitol, erythritol, fructose, D- fucose, L- fucose, galactose, gluconate, glycerol, glycogen, inositol, inulin, lactose, maltose, mannitol, mannose, melezitose, melibiose, methyl a- D- glucoside, methyl a- D-mannoside , methyl b- D- xyloside, N -acetylglucosamine, gentiobiose, D- lyxose, D- tagatose, L- xylose raffinose, ribose, salicin, sorbitol, sorbose, starch and xylitol (API 50 CH ). Test results are positive for cystine arylamidase, esterase, b-galactosidase, a- glucosidase, b- glucuronidase, naphthol-AS-BI-phosphohydrolase, trypsin and valine arylamidase, but negative for acid phosphatase, alkaline phosphatase, a-chymotrypsin, esterase lipase, a- fructosidase, a- galactosidase, b- glucosidase, leucine arylamidase, lipase, a- mannosidase and N -acetyl-b- glucosaminidase activities (API ZYM). The predominant menaquinone is MK-8(H 4 ). The major fatty acids are C 18: 1 ! 9 c , iso-C 16: 0 and iso-C. The DNA G+C content is 71.7 mol%. Table 1. Differential physiological properties of strain KUDC5002T and the type strains of closely related species in the genus Nocardioides Strains: 1, KUDC5002T; 2, Nocardioides humi DCY24T; 3, Nocardioides daecheongensis KIS2-16T; 4, Nocardioides panacisoli GSoil 346T., Negative ‒ result; +, positive result.

1	2	3	4
Habitat	Island soil	Ginseng field	soil*	Forest soil†	Ginseng field soil‡
Colony colour	Pale yellow	Pale yellow		Whitish	Pale yellow
Cell size (m)	0.5–0.6×0.8–1.0	0.3–0.5×0.8–1.0*		0.5–0.7×1.2–2.2†	0.2–0.4×0.8–1.2‡
Growth range:
Temperature (Ǫ C)	25–37	25–42*	10–35†	10–42‡
pH	5–12	5–11*	4–10†	5.5–8.5‡
NaCl (%)	0–7	0–3	0–3†	0–2‡
Motility	‒	+*	‒†	‒‡
Catalase activity	+	‒	+	+
Oxidase activity	+	+	‒	+
Reduction of nitrates to	nitrites	+	‒	+	+
Assimilation of:
Adipic acid	‒	‒	‒	+
D- Mannitol	‒	+	‒	‒
L- Arabinose	‒	‒	+	‒
Malate	‒	+	+	+
Potassium gluconate	‒	+	‒	+
Trisodium citrate	‒	‒	+	+
Enzyme activity:
Acid phosphatase	‒	+	+	+
Alkaline phosphatase	‒	+	‒	+
Cystine arylamidase	+	+	‒	‒
Esterase	+	+	+	‒
Esterase lipase	‒	+	+	‒
Leucine arylamidase	‒	+	+	‒
Lipase	‒	‒	+	‒
Trypsin	+	+	‒	+
Valine arylamidase	+	+	‒	‒
a- Chymotrypsin	‒	+	‒	+
a- Glucosidase	+	+	‒	+
b- Galactosidase	+	+	‒	‒
b- Glucosidase	‒	+	‒	‒
b- Glucuronidase	+	‒	‒	‒
Hydrolysis of:
Casein	‒	‒	+	‒
Aesculin	+	+	+	‒
Gelatine	+	‒	‒	‒
L- Tyrosin	‒	+	+	+
Tween 20	+	‒	‒	‒
Tween 40	+	‒	+	‒
Tween 60	+	+	‒	‒

*Data obtained from Kim et al. [ 54 ]. †Data obtained from Lim et al. [ 55 ]. ‡Data obtained from Cho et al. [ 56 ]. Table 2. Cellular fatty acid profiles of strain KUDC5002T and the type strains of closely related species in the genus Nocardioides Strains: 1, KUDC5002T; 2, Nocardioides humi DCY24T; 3, Nocardioides panacisoli GSoil 346T. Values are percentages of total fatty acids., ‒ Not detected or less than 1 %.

Fatty acid 1 2 3
Saturated:
C16: 0 2.5 5.1 5.7
C17: 0 8.1 1.3 1.5
C18: 0 6.0 6.0 6.5
C19: 0 1.0 ‒ ‒
Branched:
iso-C15: 0 2.3 3.2 3.1
iso-C16: 0 16.0 23.1 22.1
iso-C17: 0 11.4 16.2 12.2
iso-C18: 0 3.8 2.9 2.0
anteiso-C17:0 3.0 4.4 6.1
Unsaturated:
C17: 1 ! 8 c 5.7 1.6 1.5
C18: 1 ! 9 c 17.3 17.8 16.6
10-Methyl:
C16: 0 10-Methyl ‒ 1.4 ‒
C17: 0 10-Methyl 2.2 1.9 1.3
C18: 0 10-Methyl (TBSA) 8.7 9.5 10.0
Hydroxy:
C16: 0 2-OH ‒ ‒ 1.0
C17: 0 2-OH 1.0 ‒ ‒
Summed features:*
3 ‒ 1.6 1.6
6 4.2 ‒ ‒
8 2.5 2.3 4.2

*Summed features represent groups of two or three fatty acids that could not be separated by GLC with the MIDI system. Summed feature 3 comprises C16: 1 ! 6 c and/or C16: 1 ! 7 c . Summed feature 6 comprises C19: 1 ! 9 c and/or C19: 1 ! 11 c . Summed feature 8 comprises C18: 1 ! 6 c and/or C18: 1 ! 7 c . 17: 0 The type strain is KUDC5002 T (= KCTC 39855 T = DSM 106604 T ), which was isolated from soil collected from the Dokdo Islands , Republic of Korea . The 16S rRNA gene sequence and the whole genome sequence of strain KUDC5002 T has been deposited in GenBank / EMBL / DDBJ under the accession numbers KX858534 and CP041091 . General features of the genome assembly are as follows: genome size, 4 434 294 bp; number of contigs, 1; coverage, 111.0× .