International Journal of Systematic and Evolutionary Microbiology (2010), 60, 291–295
DOI 10.1099/ijs.0.009837-0
Virgibacillus byunsanensis sp. nov., isolated from a
marine solar saltern
Jung-Hoon Yoon, So-Jung Kang, Yong-Taek Jung, Keun Chul Lee,
Hyun Woo Oh and Tae-Kwang Oh
Correspondence
Jung-Hoon Yoon
Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon,
Republic of Korea
jhyoon@kribb.re.kr
A Gram-variable, motile, endospore-forming and rod-shaped bacterial strain, ISL-24T, was
isolated from a marine solar saltern of the Yellow Sea, Korea, and its taxonomic position was
investigated by a polyphasic study. Strain ISL-24T grew optimally at pH 7.0–8.0, at 30–37 6C
and in the presence of 8 % (w/v) NaCl. It contained MK-7 as the predominant menaquinone and
anteiso-C15 : 0 as the predominant fatty acid. The DNA G+C content was 37.6 mol%. A
phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-24T fell within
the genus Virgibacillus, clustering with Virgibacillus carmonensis LMG 20964T and Virgibacillus
necropolis LMG 19488T, with a bootstrap resampling value of 92.3 %, and exhibiting 97.3 and
97.4 % 16S rRNA gene sequence similarity, respectively, to these strains. Strain ISL-24T
exhibited 94.8–96.8 % 16S rRNA gene sequence similarity to the type strains of the other
Virgibacillus species. Mean DNA–DNA relatedness values between strain ISL-24T and V.
carmonensis DSM 14868T and V. necropolis DSM 14866T were 11 and 19 %, respectively.
Differential phenotypic properties of strain ISL-24T, together with the phylogenetic and genetic
distinctiveness, revealed that this strain is different from recognized Virgibacillus species. On the
basis of phenotypic, phylogenetic and genetic data, strain ISL-24T represents a novel species of
the genus Virgibacillus, for which the name Virgibacillus byunsanensis sp. nov. is proposed. The
type strain is ISL-24T (5KCTC 13259T 5CCUG 56754T).
The genus Virgibacillus was proposed by Heyndrickx et al.
(1998) for Bacillus pantothenticus and, at the time of
writing, the genus comprises at least 16 species with validly
published names, including the recently described species
Virgibacillus chiguensis (Wang et al., 2008), V. kekensis
(Chen et al., 2008), V. salarius (Hua et al., 2008), V.
sediminis (Chen et al., 2009) and V. arcticus (Niederberger
et al., 2009). Members of the genus Virgibacillus are Grampositive or variable, endospore-forming and motile rods
that are characterized chemotaxonomically by having
meso-diaminopimelic acid or L-lysine as the diagnostic
diamino acid in the peptidoglycan, MK-7 as the predominant menaquinone and iso-C15 : 0, and sometimes also
anteiso-C17 : 0, as the major fatty acid (Chen et al., 2008,
2009; Hua et al., 2008; Niederberger et al., 2009).
Virgibacillus species have been isolated from a variety of
habitats, including soils, antacids, food, bile, mural
paintings, salterns, seawater, freshwater, waste water of
green-olive processing, salt lakes and the Arctic (Chen et al.,
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene
sequence of strain ISL-24T is FJ357159.
Differential phenotypic characteristics of strain ISL-24T and other
Virgibacillus species are available as supplementary material with the
online version of this paper.
009837 G 2010 IUMS
2009; Heyndrickx et al., 1999; Heyrman et al., 2003;
Niederberger et al., 2009; Quesada et al., 2007; Wang et al.,
2008; Yoon et al., 2005). In this study, we report the
taxonomic characterization of a Virgibacillus-like bacterial
strain, ISL-24T, which was isolated from a marine solar
saltern of the Yellow Sea in Korea.
Strain ISL-24T was isolated by means of the standard
dilution-plating technique at 30 uC on marine agar 2216
(MA; Difco) supplemented with 6 % (w/v) NaCl.
Virgibacillus carmonensis DSM 14868T and Virgibacillus
necropolis DSM 14866T, which were used as reference
strains for DNA–DNA hybridization and fatty acid
analysis, were obtained from the Deutsche Sammlung
von Mikroorganismen und Zellkulturen (DSMZ),
Braunschweig, Germany. Virgibacillus pantothenticus
KCTC 3539T, which was used as a reference strain for
fatty acid analysis, was obtained from the Korean
Collection for Type Cultures (KCTC), Taejon, South
Korea. The morphological, physiological and biochemical
characteristics of strain ISL-24T were investigated using
routine cultivation on MA supplemented with 6 % (w/v)
NaCl (6 % NaCl MA) at 30 uC. The cell morphology was
examined by light microscopy (Nikon E600) and transmission electron microscopy. Flagellation was determined
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291
J.-H. Yoon and others
using a Philips CM-20 transmission electron microscope
with cells from exponentially growing cultures. For this
purpose, the cells were negatively stained with 1 % (w/v)
phosphotungstic acid and the grids were examined after
being air-dried. Growth under anaerobic conditions was
determined after incubation in a Forma anaerobic chamber
on 6 % NaCl MA and on 6 % NaCl MA supplemented with
potassium nitrate (0.1 %, w/v), both of which had been
prepared anaerobically under a nitrogen atmosphere.
Growth in the absence of NaCl was investigated using
trypticase soy broth, both with and without 0.45 % (w/v)
MgCl2 . 6H2O, prepared according to the formula of the
Difco medium except that NaCl was omitted. Growth in
the presence of 0.5, 1.0 and 2.0 % (w/v) NaCl was
investigated by using trypticase soy broth supplemented
with 0.45 % (w/v) MgCl2 . 6H2O and growth between 2.0
and 22.0 % (w/v) NaCl (in increments of 1.0 %) was
investigated in marine broth 2216 (MB; Difco). The pH
range for growth was determined in MB supplemented
with 6 % (w/v) NaCl (6 % NaCl MB) adjusted to pH 4.5–
9.5 (at intervals of 0.5 pH units) by the addition of HCl or
Na2CO3. Growth at 4, 10, 20, 25, 28, 30, 35, 37, 40 and
45 uC was measured on 6 % NaCl MA. Catalase and
oxidase activities and hydrolysis of casein, starch and
Tweens 20, 40, 60 and 80 were determined as described by
Cowan & Steel (1965). Hydrolysis of hypoxanthine,
tyrosine and xanthine was tested on 6 % NaCl MA using
the substrate concentrations described by Cowan & Steel
(1965). Hydrolysis of aesculin, gelatin and urea and
reduction of nitrate were investigated as described by
Lányı́ (1987) with the modification that artificial seawater
supplemented with 6 % (w/v) NaCl was used for
preparation of media. The artificial seawater contained
(l21 distilled water) 23.6 g NaCl, 0.64 g KCl, 4.53 g
5.94 g
MgSO4 . 7H2O
and
1.3 g
MgCl2 . 6H2O,
CaCl2 . 2H2O (Bruns et al., 2001). H2S production was
tested as described by Bruns et al. (2001). Susceptibility to
antibiotics was investigated on 6 % NaCl MA plates by
using antibiotic discs containing the following (mg per disc
unless otherwise stated): polymyxin B (100 U), streptomycin (50), penicillin G (20 U), chloramphenicol (100),
ampicillin (10), cephalothin (30), gentamicin (30), novobiocin (5), tetracycline (30), kanamycin (30), lincomycin
(15), oleandomycin (15), neomycin (30) and carbenicillin
(100). Acid production from carbohydrates was tested as
described by Leifson (1963) with the modification that 6 %
(w/v) NaCl was added for preparation of media. Utilization
of various substrates for growth was determined as
described by Baumann & Baumann (1981), using supplementation with 6 % (w/v) NaCl, 2 % (v/v) Hutner’s
mineral salts solution (Cohen-Bazire et al., 1957) and
1 % (v/v) vitamin solution (Staley, 1968). Enzyme activities
were determined by using the API ZYM system
(bioMérieux).
Cell biomass for DNA extraction and for the analysis of
cell-wall isoprenoid quinones and polar lipids was obtained
from cultures grown in 6 % NaCl MB at 30 uC.
292
Chromosomal DNA was isolated and purified according
to the method described by Yoon et al. (1996), with the
exception that RNase T1 was used in combination with
RNase A to minimize contamination with RNA. The 16S
rRNA gene sequence was amplified by PCR using two
universal primers, 9F (59-GAGTTTGATCCTGGCTCAG39) and 1542R (59-AGAAAGGAGGTGATCCAGCC-39), as
described previously (Yoon et al., 1998). Sequencing of the
amplified gene fragments and phylogenetic analysis were
performed as described by Yoon et al. (2003). The isomer
type of the diamino acid in the cell-wall peptidoglycan was
analysed using TLC according to the method described by
Komagata & Suzuki (1987). Isoprenoid quinones were
analysed as described by Komagata & Suzuki (1987) using
reversed-phase HPLC and a YMC ODS-A (25064.6 mm)
column. For cellular fatty acid analysis, cell mass of strain
ISL-24T, V. carmonensis DSM 14868T, V. necropolis DSM
14866T and V. pantothenticus KCTC 3539T was harvested
from MA plates after cultivation for 3 days at 30 uC. The
fatty acids were extracted and fatty acid methyl esters were
prepared according to the standard protocol of the MIDI/
Hewlett Packard Microbial Identification System (Sasser,
1990). The DNA G+C content was determined by the
method of Tamaoka & Komagata (1984) with the
modification that DNA was hydrolysed using nuclease P1
(Sigma) and the resultant nucleotides were analysed by
reversed-phase HPLC. DNA–DNA hybridization was
performed fluorometrically at 55 uC by the method of
Ezaki et al. (1989) using photobiotin-labelled DNA probes
and microdilution wells. Hybridization was performed
with five replications for each sample. The highest and
lowest values obtained in each sample were excluded, and
the means of the remaining three values are quoted as
DNA–DNA relatedness values.
Morphological, cultural, physiological and biochemical
properties of the newly isolated strain are given in the
species description and in Table 1. The almost-complete
16S rRNA gene sequence of strain ISL-24T determined in
this study comprised 1518 nt, representing approximately
96 % of the Escherichia coli 16S rRNA gene sequence. In the
phylogenetic tree (1381 nt) based on the neighbour-joining
algorithm, strain ISL-24T fell within the clade comprising
Virgibacillus species, clustering with V. carmonensis LMG
20964T and V. necropolis LMG 19488T with a bootstrap
resampling value of 92.3 % (Fig. 1). This cluster was also
found in trees constructed using the maximum-likelihood
and maximum-parsimony algorithms (Fig. 1). Strain ISL24T exhibited 16S rRNA gene sequence similarity of 97.3
and 97.4 % to V. carmonensis LMG 20964T and V.
necropolis LMG 19488T, respectively, and 94.8–96.8 % to
the type strains of the other Virgibacillus species.
Strain ISL-24T had meso-diaminopimelic acid as the
diagnostic diamino acid in the cell-wall peptidoglycan.
The predominant menaquinone detected in strain ISL-24T
was MK-7. Strain ISL-24T contained large amounts of
branched fatty acids; the fatty acids constituting .10 % of
total fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0
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Virgibacillus byunsanensis sp. nov.
Table 1. Differential phenotypic characteristics of strain ISL24T and the type strains of phylogenetically related
Virgibacillus species
Strains: 1, Virgibacillus byunsanensis sp. nov. ISL-24T (data from this
study); 2, V. carmonensis DSM 14868T (Heyrman et al., 2003); 3, V.
necropolis DSM 14866T (Heyrman et al., 2003). All strains are rodshaped, motile and positive for catalase and nitrate reduction and the
presence of diphosphatidylglycerol, phosphatidylglycerol and unidentified phospholipids, but negative for anaerobic growth, growth at
25 % (w/v) NaCl, H2S production, growth on D-arabinose, D-fructose
and D-xylose, acid production from D-galactose, melibiose, Lrhamnose and D-mannitol and the presence of an unknown
aminophospholipid. +, Positive; 2, negative; W, weakly positive;
V, variable.
Characteristic
Spore shape*
Spore positionD
Gram stain
Pigmentation
Growth at 0.5 % (w/v) NaCl
Temperature range (uC)
Hydrolysis of:
Aesculin
Casein
Gelatin
Growth on:
D-Glucose
Sucrose
Acid production from:
D-Fructose
D-Glucose
D-Mannose
Trehalose
DNA G+C content (mol%)
1
2
S, O
S, E
E
T
ST
C, T, ST
2
+
4–45
+
Pink
2
10–40
+
2
2
2
2
+
2
2
2
2
+
+
+
W
2
2
2
2
38.9
W
V
2
2
2
37.6
W
3
W
10–40
2
+
W
W
W
W
37.3
*E, Ellipsoidal; O, oval; S, spherical.
DC, Central; ST, subterminal; T, terminal.
(Table 2). This fatty acid profile was similar to those of the
type strains of the two closest phylogenetically related
Virgibacillus species and V. pantothenticus, the type species
of the genus, in that the predominant fatty acid is anteisoC15 : 0 (Table 2). The DNA G+C content of strain ISL-24T
was 37.6 mol%. The chemotaxonomic analyses show that
strain ISL-24T shares properties exhibited by Virgibacillus
species and were in agreement with the result of
phylogenetic analysis, i.e. that strain ISL-24T is a member
of the genus Virgibacillus.
Strain ISL-24T did not show clear phenotypic differentiation from its closest phylogenetic neighbours, V. carmonensis and V. necropolis, although some properties were
different, including growth at 4 uC, hydrolysis of casein and
growth on sucrose. However, strain ISL-24T was distinguished genetically from V. carmonensis DSM 14868T and
V. necropolis DSM 14866T as it exhibited low mean DNA–
http://ijs.sgmjournals.org
Fig. 1. Neighbour-joining phylogenetic tree based on 16S rRNA
gene sequences showing the positions of strain ISL-24T,
Virgibacillus species and some other related taxa. Bootstrap
values (.50 %) based on 1000 replications are shown at branch
nodes. Filled circles indicate that the corresponding nodes were
also recovered in trees generated with the maximum-likelihood and
maximum-parsimony algorithms. The sequence of Alicyclobacillus
acidocaldarius DSM 446T was used as an outgroup. Bar, 0.01
substitutions per nucleotide position.
DNA relatedness values of 11 and 19 %, respectively. Strain
ISL-24T was also distinguishable from other recognized
Virgibacillus species through differences in several phenotypic characteristics (Supplementary Table S1, available in
IJSEM Online). The phylogenetic and genetic distinctiveness and differential phenotypic properties of strain ISL24T are sufficient to categorize it as a member of a species
that is distinct from the recognized Virgibacillus species
(Wayne et al., 1987; Stackebrandt & Goebel, 1994).
On the basis of the data presented, strain ISL-24T is
considered to represent a novel species of the genus
Virgibacillus, for which the name Virgibacillus byunsanensis
sp. nov. is proposed.
Description of Virgibacillus byunsanensis sp. nov.
Virgibacillus byunsanensis (byun.san.en9sis. N.L. masc. adj.
byunsanensis of Byunsan, from where the type strain was
isolated).
Cells are Gram-variable and rod-shaped (0.2–0.461.0–
5.0 mm). A few cells longer than 10.0 mm may occur.
Motile by means of peritrichous flagella. Terminal spherical
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J.-H. Yoon and others
Table 2. Cellular fatty acid compositions of strain ISL-24T and
the type strains of three Virgibacillus species
Strains: 1, Virgibacillus byunsanensis sp. nov. ISL-24T; 2, V.
carmonensis DSM 14868T; 3, V. necropolis DSM 14866T; 4, V.
pantothenticus KCTC 3539T. All data were taken from this study.
Values are percentages of total fatty acids; fatty acids that represented
,0.5 % in all strains are not shown. 2, Not detected (,0.5 %).
Fatty acid
Straight-chain
C15 : 0
C16 : 0
Unsaturated
C16 : 1v7c alcohol
Branched
anteiso-C13 : 0
iso-C14 : 0
iso-C15 : 0
anteiso-C15 : 0
iso-C16 : 0
iso-C17 : 0
anteiso-C17 : 0
Summed feature 4*
diaminopimelic acid as the diamino acid. The predominant
menaquinone is MK-7. The predominant fatty acid is
anteiso-C15 : 0. Other phenotypic characteristics are given in
Table 1 and Supplementary Table S1. The DNA G+C
content of the type strain is 37.6 mol% (determined by
HPLC).
The type strain, ISL-24T (5KCTC 13259T 5CCUG
56754T), was isolated from a marine solar saltern of the
Yellow Sea, Korea.
1
2
3
4
0.5
0.9
0.9
1.3
0.5
1.7
0.3
0.9
Acknowledgements
0.3
6.1
1.0
2
0.7
7.6
1.2
71.7
5.2
2
10.3
1.1
0.3
8.9
2.6
58.7
11.7
0.2
6.8
1.6
0.3
3.3
2.2
73.0
4.9
0.4
11.0
0.9
0.3
1.1
4.8
50.4
5.5
2.1
34.5
2
This work was supported by the 21C Frontier program of Microbial
Genomics and Applications (grant MG05-0401-2-0) from the
Ministry of Education, Science and Technology (MEST) of the
Republic of Korea.
*Summed features represent two or three fatty acids that cannot be
separated by the Microbial Identification System. Summed feature 4
consisted of iso-C17 : 1 I and/or anteiso-C17 : 1 B.
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