Arch Microbiol
DOI 10.1007/s00203-014-1073-0
ORIGINAL PAPER
Paenibacillus ginsengiterrae sp. nov., a ginsenoside-hydrolyzing
bacteria isolated from soil of ginseng field
Md. Amdadul Huq · Yeon-Ju Kim · Van-An Hoang ·
Muhammad Zubair Siddiqi · Deok-Chun Yang
Received: 12 September 2014 / Revised: 5 December 2014 / Accepted: 6 December 2014
© Springer-Verlag Berlin Heidelberg 2014
Abstract A novel bacterial strain DCY89T was isolated
from soil sample of ginseng field and was characterized
using a polyphasic approach. Cells were Gram-reactionpositive, rod-shaped, spore-forming and motile with flagella. The strain was aerobic, esculin and starch positive,
catalase- and oxidase-negative, optimum growth temperature, and pH were 25–30 °C and 6.0–7.5, respectively.
On the basis of 16S rRNA gene sequence analysis, strain
DCY89T was shown to belong to the genus Paenibacillus
and the closest phylogenetic relatives were Paenibacillus
cellulosilyticus KACC 14175T (98.2%), Paenibacillus kobensis KACC 15273T (98.1%), Paenibacillus xylaniclasticus
KCTC 13719T (96.9%), and Paenibacillus curdlanolyticus KCTC 3759T (96.64%). The DNA G+C content was
52.5 mol%, and the predominant respiratory quinone was
Communicated by Erko Stackebrandt.
The GenBank/EMBL/DDBJ accession number for the 16S rRNA
gene sequence of strain DCY89T is KF915799.
Electronic supplementary material The online version of this
article (doi:10.1007/s00203-014-1073-0) contains supplementary
material, which is available to authorized users.
Md. A. Huq · Y.-J. Kim (*) · M. Z. Siddiqi · D.-C. Yang (*)
Graduate School of Biotechnology and Ginseng Bank, College
of Life Science, Kyung Hee University, Seocheon-dong,
Giheung-gu, Yongin-Si, Gyeonggi-do 446-701,
Republic of Korea
e-mail: yeonjukim@khu.ac.kr
D.-C. Yang
e-mail: deokchunyang@yahoo.co.kr
Y.-J. Kim · V.-A. Hoang
Department of Oriental Medicinal Materials and Processing,
College of Life Science, Kyung Hee University, Yongin 449-701,
Republic of Korea
MK-7. The major fatty acids were iso-C15:0, iso-C16:0, and
anteiso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The results of the genotypic analysis in combination
with chemotaxonomic and physiological data demonstrated
that DCY89T represented a novel species within the genus
Paenibacillus, for which we propose the name Paenibacillus ginsengiterrae. The type strain is DCY89T (JCM
19887T = KCTC 33430T).
Keywords Paenibacillus ginsengiterrae · Ginseng soil ·
Taxonomy · Biotransformation
Introduction
The members of the genus Paenibacillus are either Gramreaction-positive or Gram-reaction-negative (Ash et al.
1993; Valverde et al. 2008), facultatively anaerobic or
strictly aerobic, produced ellipsoidal spores, non-pigmented, rod-shaped, and motile (Lim et al. 2006; Zhou
et al. 2012) with a G+C content 39–59 mol % (Yao et al.
2014). The genus Paenibacillus, which belongs to the
family Paenibacillaceae, is a novel group of bacilli first
described by Ash et al. (1993). This genus currently comprises 149 species and 4 subspecies (http://www.bacterio.
cict.fr/p/paenibacillus.html). Members of genus Paenibacillus are widespread microorganisms commonly isolated
from various sources, including food (Berge et al. 2002),
fresh water (Baik et al. 2011), air (Rivas et al. 2005),
human blood (Roux and Raoult 2004), heat-treated milk
(Scheldeman et al. 2004), necrotic wounds (Glaeser et al.
2013), warm springs (Saha et al. 2005), and rhizospheric
soil (Cheong et al. 2005). The cell wall peptidoglycan
diamino acid of the Paenibacillus members is meso-DAP,
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Arch Microbiol
and menaquinone-7 (MK-7) is the predominant menaquinone. Diphosphatidylglycerol (DPG) is the major polar
lipid in all the Paenibacillus members for which polar
lipids data are available (Yao et al. 2014). The predominant
cellular fatty acid is anteiso-C15:0 (Ludwig et al. 2009). In
this study, we describe a novel β-glucosidase producing
bacterium, DCY89T, isolated from soil of a ginseng field
in Kyung Hee University, based on a polyphasic taxonomic
approach.
Methods and materials
Bacterial isolation
Soil samples were collected from a ginseng field, Kyung
Hee University, Republic of Korea (37 ° 14′ 43″N 127 °
04′ 56″E). Under 10 cm depth, around 100 g of the rhizosphere soil were carefully collected without any stones and
particles, zipped lock covers and transferred to the laboratory. For bacterial isolation, five times diluted R2A agar
(Difco) was used. The serial dilution was made up to 10−5
by dissolving of one gram of soil sample in 10 ml of 0.85%
sterile saline, and 100 µl of each dilution was spread on
five times diluted R2A plates. The plates were incubated at
30 °C for 3–5 days. The purification of single colony was
carried out by transferring them to new R2A agar plates.
Isolate was preserved at −70 °C in R2A broth (Difco) supplemented with 25 % (v/v) glycerol. For the comparative
study, Paenibacillus cellulosilyticus KACC 14175T and
Paenibacillus kobensis KACC 15273T were obtained from
the Korean Agricultural Culture Collection (KACC), while
Paenibacillus xylaniclasticus KCTC 13719T and Paenibacillus curdlanolyticus KCTC 3759T were obtained from
Korean Collection for Type Cultures (KCTC) as reference
type strains. These strains were cultured under the same
conditions as strain DCY89T.
Cell growth, physiology, morphology, and biochemical
characteristics
Colonies of strain DCY89T were observed after culturing
on R2A agar plate at 30 °C. Cell morphology and flagella
were examined under microscope (×1,000 magnifications, MBL-2100) and transmission electron microscopy
(LOE912AB) using cells that were grown on TSA broth for
24 h at 30 °C. The motility was checked on TSA broth supplemented with on 0.2 % agar (Weon et al. 2008). Gram
reaction was tested by using a bioMerieux Gram stain kit.
Nitrate reduction was tested in nitrate broth containing
0.2 % KNO3 (Skerman 1967). Different media were tested
for growth such as trypticase soy agar (TSA; Difco), R2A,
MacConkey (Bacto), nutrient agar (NA; Difco), and LB
13
agar (Difco) at 30 °C for 7 days. For checking growth at
different temperature, a range of 5, 10, 15, 20, 25, 30, 37,
and 40 °C were tested for 7 days. Growth at different NaCl
was tested by using of 0–10 % (w/v) NaCl in TSB at 0.5 %
unit interval. Growth of strain DCY89T also checked at different pH values in TSB medium. Different initial pH values (4–10 at intervals of 1 pH units) were adjusted, respectively, by use of Tris HCl 0.1 M and 1N NaOH. According
to the manufacturer’s instruction, 1 % (w/v) N,N,N,Ntetramethyl-1,4-phenylenediamine reagents was used to
test the oxidase activity. Catalase activity was determined
by the production of bubble from 3 % (v/v) H2O2 solution.
Triple sugar iron agar was used to test for H2S production.
Hydrolysis of DNA, gelatin, esculin, Tween 80, starch,
skim milk, and tyrosinase were analyzed as described by
Cowan and Steel (1974). Enzymes production and carbon
source utilization were conducted by using API ZYM, API
20NE, and API 32GN strips according to the manufacturer’s instructions (bioMérieux). 1 % tryptophan broth was
used for indole production by using Kovács’s reagent. To
check anaerobic growth, strain DCY89T was cultured on
TSA plates and incubated in a GasPak EZ (BD) for 14 days
at 30 °C. The antibiotics susceptibility was checked according to Bauer et al. (1966) using Oxoid antibiotic disks, on
Müller-Hinton agar plates incubated at 30 °C for 24–48 h
under aerobic condition. The inhibition zone was measured following manufacturer’s manual. The antibiotics
were used including carbenicillin (CAR100, 100 µg), vancomycin (VA30, 30 µg), ceftazidime (CAZ30, 30 µg), novobiocin (NV30, 30 µg), neomycin (N30, 30 µg), tetracycline
(TE30, 30 µg), cephazolin (KZ30, 30 µg), erythromycin (E15,
15 µg), oleandomycin (OL15, 15 µg), penicillin G (P10,
10 µg), rifampicin (RD5, 5 µg), and lincomycin (MY15,
15 µg).
16S rRNA sequence and phylogenetic analysis
The genomic DNA of strain DCY89T was isolated by using
the DNA isolation kit (Gene All Biotechnology, Republic
of Korea). The bacterial universal primer set 27F, 518F,
800R, and 1492R were used to amplify the 16S rRNA
gene sequence (Lane 1991). The purified PCR product
was sequenced by Genotech (Daejeon, Republic of Korea)
according to Kim et al. (2005). Seq-Man software version 4.1 (DNASTAR, Inc.) was used to compile the nearly
complete sequenced (1495 bp) of strain DCY89T. Then,
the sequence was uploaded to EZTaxon-e server (http://
eztaxon-e.ezbiocloud.net/) to find the pair wise similarity
of the nearly full 16S rRNA gene sequence by performing the identity analysis. The 16S rRNA gene sequences
of closely related strain were collected from gene bank and
then aligned by CLUSTAL X program (Thompson et al.
Arch Microbiol
1997), and distances were calculated according to Kimura
two-parameter model (Kimura 1983). The phylogenetic
tree was constructed with neighbor-joining (Saitou and Nei
1987) and MPM (Fitch 1971) by using the MEGA5 program (Tamura et al. 2011). In order to take the confidential
levels for the branches (Felsenstein 1985), bootstrap analysis with 1,000 replications was also conducted.
G+C content and DNA–DNA hybridization
In order to analyze the G+C mol % of DNA, the genomic
DNA of strain DCY89T was extracted and purified using the
Genomic DNA isolation kit (Gene All, Republic of Korea),
then degraded enzymatically into nucleosides as described
by Mesbah et al. (1989). Subsequently, the obtained nucleoside mixture was separated using a reverse-phase HPLC
column YMC-Triart C18 (4.6 × 250 mm × 5 µm).
DNA–DNA hybridization was performed with photobiotin-labeled probes as described by Ezaki et al. (1989).
Optimal hybridization temperature was at 39.1 °C. Levels of DNA–DNA relatedness were determined by triplicate between strain DCY89T and references type strains
of the closest phylogenetic neighbors P. cellulosilyticus
KACC 14175T; P. kobensis KACC 15273T; P. xylaniclasticus KCTC 13719T; and P. curdlanolyticus KCTC 3759T
(mean ± SD, n = 3).
Chemotaxonomic characteristics
Polar lipids and respiratory quinone
Cells were grown in trypticase soy broth at 30 °C, shaken
at 160 rpm for 1 day, centrifuged, and dried in freeze
drier. Isoprenoid quinone was extracted from 100 mg
freeze-dried cells with chloroform/methanol (2:1, v/v),
and after concentrated at 40 °C using vacuum rotary
evaporator, the residue was subsequently extracted with
10 ml hexane using Sep-Pak®Vac 6 cc silica cartridge for
further purification. Then, the samples were analyzed by
HPLC (Model, NS-6000A Futecs) according to Collins
and Jones (1981).
Polar lipid of strain DCY89T and P. cellulosilyticus
KACC 14175T were extracted from dry cells (100 mg)
(Minnikin et al. 1977). Polar lipids were dissolved in chloroform/methanol (2:1, v/v). The samples were spotted on
the corner of two-dimensional thin layer chromatography
(2D-TLC) using TLC Kiesel gel 60F254 (Merck) plates
(10 × 10 cm) and developed in the first direction by using
chloroform/methanol/water (65:25:4, by v/v/v) while in
the second direction developed by chloroform/acetic acid/
methanol/water (80:15:12:4, by v/v/v) as solvent systems.
The total polar lipids, aminolipids, glycolipids, and phospholipids were detected by staining the plates with 5 %
ethanolic molybdophosphoric acid, ninhydrin, α-naphthol,
and molybdenum blue, respectively.
Peptidoglycan and cell wall sugar analysis
Peptidoglycan and cell wall sugar analysis of strain
DCY89T and reference strain P. cellulosilyticus KACC
14175T was analyzed as mentioned by Schleifer and
Kandler (1972). The hydrolyzed peptidoglycans were
determined by spotting the sample on the TLC plate by
using of TLC cellulose Merck KGaA (20 × 20 cm). The
solvent methanol/pyridine/6N HCl/water (100:12.5:6:32.5,
by vol) was made 1 day before running. The hydrolyzed
sugar was detected by spotting 5 µl sample and 5 µl of the
standard mixture of sugars as a reference on the TLC plate
(by using of TLC cellulose Merck KGaA (20 × 20 cm),
(Staneck and Roberts 1974).
Cellular fatty acid analysis
The strain DCY89T and the four reference type strain cells
(P. cellulosilyticus KACC 14175T; P. kobensis KACC
15273T; P. xylaniclasticus KCTC 13719T; and P. curdlanolyticus KCTC 3759T) were grown on TSA agar at 30 °C for
1 day. Fatty acid was extracted, methylated, and saponified by the method described by Sherlock Microbial Identification System (MIDI) and analyzed by capillary GLC
(Hewlet Packard 6890) using the TSBA library (version
6.1) (Sasser 1990). Then, fatty acid analysis was performed
in duplicate.
Polyamine analysis
Polyamine of strain DCY89T and P. cellulosilyticus KACC
14175T were extracted and analyzed as reported by Taibi
et al. (2000). The polyamine standards spermine, spermidine, and putrescine were purchased from Sigma-Aldrich.
The analysis of polyamine was performed using a HPLC
system (Agilent technology 1260 infinity). The separation was carried out on a Poroshell 120 EC-C18 column
(3.0 × 50 mm, 2.7 µm i.d.) using 60 % MeOH as mobile
phase with flow rate: 0.3 ml/min, and detection was performed by monitoring absorbance at 234 nm, with an injection volume of 5 µl.
Biotransformation of ginsenoside Rb1 by crude enzyme
of strain DCY89T
Strain DCY89 was grown in TSB medium at 30 °C for
overnight, and cells were collected by centrifuging at
5,000×g for 30 min at 4 °C. Then, cells were resuspended
in 20 mM sodium phosphate buffer (pH 7.0) and lysed by
sonication with short pulses, and debris was removed by
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Arch Microbiol
centrifugation (12,000×g, at 4 °C for 30 min). Supernatant
was used as crude enzyme. This is the modification of Quan
et al. (2012) protocol. The biotransformation procedure
was carried out in 15-ml screw-capped tubes. First, 2 ml of
crude enzyme was mixed with an equal volume of ginsenoside Rb1 at 1.0 mg/ml in 20 mM sodium phosphate buffer.
The mixture was then incubated at 37 °C with shaking
(160 rpm). During the reaction period, a 200-µl aliquot was
removed every 1 h. Aliquots were extracted using watersaturated n-butanol and analyzed by TLC, HPLC, and LC/
MS. TLC analysis was carried out using silica gel plates
(60F254; Merck, Darmstadt, Germany) and developed with
a solvent system of CHCl3:CH3OH:H2O (65:35:10 v/v/v).
Spots on TLC plates were detected by spraying with 10 %
(v/v) H2SO4 followed by heating at 110 °C for 10 min.
HPLC analysis was carried out with a C18 (250 × 4.6 mm,
particle size 5 µm) column. LC/MS for the ginsenoside
was analyzed with an Agilent QQQ/MS in positive polarity
mode with an ion trap analyzer.
Results and discussion
Cell growth, morphology, physiology, biochemical tests,
and antibiotic susceptibility
Morphological observation of strain DCY89T colonies on
TSA agar was spherical with beige color and raised colonies with approximate diameters 4–9 mm after incubation at
30 °C for 48 h. Strain DCY89T was found to grow on R2A,
TSA, LB, and NA, but not to grow on MacConkey agar.
The strain was observed to grow best in TSA at temperature 20–37 °C (optimum temp 30 °C); at pH 6–8 (optimum,
pH 7) and up to 2 % NaCl (optimum, 0.5 %). Phenotypic
analysis showed that strain DCY89T cells are Gram-positive, aerobic, rod-shaped, motile with monotrichous flagella
(Fig. S2), and spore-forming (Fig. S3). Tests for catalase
and oxidase activity were negative. Strain DCY89T did
not hydrolyze skim milk, tyrosine, DNA, and Tween 80,
but hydrolyzed starch, esculin, and gelatin after 2 days of
incubation at 30 °C. Nitrate was reduced to nitrite. Indole
was not produced. Other biochemical and physiological
characteristics of strain DCY89T and four references strain
are shown in Table 1. Strain DCY89T was susceptible to
all antibiotics that were used in this study, especially cephazolin (KZ30, 30 µg), ceftazidime (CAZ30, 30 µg), and
rifampicin (RD5, 5 µg).
16S rRNA sequence and phylogenetic analysis
The nearly complete sequence (1,495 bp) of the 16S rRNA
gene was obtained. The comparison of the 16S rRNA
13
Table 1 The biochemical and physiological characteristics of strain
DCY89T and the reference strains of genus Paenibacillus
Characteristics
1
2
3
4
5
Hydrolysis of:
Arginine
Urea
Gelatin
–
–
+
+
+
–
+
–
+
+
+
–
+
+
+
Enzyme activity:
α-Glucosidase
β-Glucosidase
β-Galactosidase
–
+
+
w
+
+
–
–
–
–
+
+
+
–
+
Assimilation of:
L-Rhamnose
+
–
–
+
–
N-Acetyl-glucose
D-Ribose
Inositol
D-Saccharose
Itaconic acid
Suberic acid
Sodium malonate
Sodium acetate
Lactic acid
L-Alanine
Potassium 5-ketogluconate
L-Serine
D-Mannitol
L-Fucose
D-Sorbitol
Valeric acid
Trisodium citrate
L-Histidine
Potassium 2-ketogluconate
3-Hydroxybutyric acid
4-Hydroxybenzoic acid
+
–
+
–
+
+
+
+
w
w
–
w
w
w
w
w
+
w
–
–
w
+
–
–
+
–
–
+
w
w
–
–
–
–
w
–
–
w
–
–
–
–
–
–
w
+
+
+
w
–
w
w
w
w
w
w
+
w
w
w
+
+
+
w
w
–
–
–
–
–
–
–
–
–
–
–
–
–
w
–
–
–
–
w
–
w
+
+
–
–
w
w
–
w
w
–
–
w
w
w
w
+
–
–
–
L-Proline
–
–
w
–
w
Strain: 1, P. ginsengiterrae DCY89T; 2, P. cellulosilyticus KACC
14175T; 3, P. kobensis KACC 15273T; 4, P. xylaniclasticus KCTC
13719T; and 5, P. curdlanolyticus KCTC 3759T
All strains were positive for the following reactions: esterase (C4)
(API ZYM); hydrolysis of esculin, assimilation of D-glucose, L-arabinose (API 20NE); assimilation of D-maltose, glycogen, salicin,
D-melibiose (API 32GN); and negative for the following reactions:
α-mannosidase, α-fucosidase, N-acetyl-D-glucosaminidase (API
ZYM); assimilation of 3-hydroxybenzoic acid, propionic acid, capric
acid (API 32GN)
+, positive; w, weakly positive; −, negative
sequence of strain DCY89T (GenBank/EMBL/DDBJ
accession number KF915799) with other Paenibacillus
strains revealed that strain DCY89T is a novel strain of the
genus Paenibacillus, sharing highest sequence similarity
with P. cellulosilyticus KACC 14175T (98.2 %), P. kobensis
Arch Microbiol
Paenibacillus catalpae D75T (HQ657320)
97
Paenibacillus lupini RLAHU15T (KF769449)
92
Paenibacillus glycanilyticus DS-1T (AB042938)
75
Paenibacillus xinjiangensis B538T (AY839868)
Paenibacillus castaneae Ch-32T (EU099594)
100
Paenibacillus endophyticus PECAE04T (KC447384)
Paenibacillus algorifonticola XJ259T (GQ383922)
Paenibacillus harenae B519T (AY839867)
99
Paenibacillus alkaliterrae KSL-134T (AY960748)
Paenibacillus agarexedens DSM 1327T (AJ345020)
Paenibacillus quercus 1-25T (JX409872)
Paenibacillus thailandensis S3-4AT (AB265205)
Paenibacillus granivorans A30T (AF237682)
72
Paenibacillus agaridevorans DSM 1355T (AJ345023)
Paenibacillus nanensis MX2-3T (AB265206)
71
94
Paenibacillus pinesoli NB5T (KC415175)
DCY89T (KF915799)
91
77
Paenibacillus cellulosilyticus KACC 14175 T (DQ407282)
Paenibacillus kobensis KACC 15273 T (AB073363)
100
Paenibacillus xylaniclasticus KCTC 13719 T (FJ532373)
Paenibacillus curdlanolyticus KCTC 3759T (AB073202)
Paenibacillus mendelii C/2T (AF537343)
93
Paenibacillus phyllosphaerae PALXIL04T (AY598818)
82
Paenibacillus marinum THE22 T (FR865169)
Paenibacillus tarimensis SA-7-6T (EF125184)
Paenibacillus pinihumi S23T (GQ423057)
Paenibacillus wooponensis WPCB018 T (EU939687)
93
Paenibacillus pasadenensis SAFN-007T (AY167820)
Paenibacillus dendritiformis CIP 105967 T (AY359885)
Paenibacillus chibensis JCM 9905 T (AB073194)
Bacillus methylotrophicus CBMB205 T (EU194897)
0.01
Fig. 1 The neighbor-joining tree based on 16S rRNA gene sequence
analysis showing phylogenetic relationships of strain DCY89T and
members of the genus Paenibacillus. Bootstrap values more than
70 % based on 1,000 replications are shown at branching points.
Filled circles indicate that the corresponding nodes were also recovered in the tree constructed with the maximum parsimony (MP) algorithm. Scale bar 0.01 substitutions per nucleotide position
KACC 15273T (98.1 %), P. xylaniclasticus KCTC 13719T
(96.9 %), and P. curdlanolyticus KCTC 3759T (96.6 %).
Strain DCY89T formed a reliable and monopheletic cluster with P. cellulosilyticus PALXIL08T in NJ tree, and filled
circles indicate that the corresponding nodes were also
recovered in the tree constructed with the maximum parsimony (MP) algorithm (Fig. 1). This cluster was also recovered in the trees generated by the ML (Fig. S4).
between strain DCY89T and the closest type strains P. cellulosilyticus KACC 14175T; P. kobensis KACC 15273T;
P. xylaniclasticus KCTC 13719T; and P. curdlanolyticus
KCTC 3759T were 22.7 ± 3.4, 17.8 ± 1.2, 31.3 ± 3.2, and
37.4 ± 1.0, respectively. These values were well below the
70 % threshold proposed for species delineation (Wayne
et al. 1987) suggesting that strain DCY89T represents a distinct genomic species of the genus Paenibacillus.
G+C content and DNA–DNA hybridization
Fatty acid, quinone, polar lipid, polyamine, peptidoglycan,
and cell wall sugar analysis
The DNA G+C content of strain DCY89T was 52.5 mol %,
which is similar to related type strains (Shida et al. 1997;
Rivas et al. 2006). The values for DNA–DNA relatedness
The major fatty acids of strain DCY89T was anteiso-C15:0,
(45.7 %), however, iso-C16:0 (16.4 %), iso-C15:0, (9.4 %),
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Table 2 Fatty acid profiles of strain DCY89T and related species of
the genus Paenibacillus
Fatty acid
1
2
Saturated fatty acid
1.31
0.71
C12:0
1.52
1.01
C14:0
7.95
8.88
C16:0
ND
0.38
C17:0
ND
0.37
C18:0
ND
ND
C20:0
Branched-chain fatty acid (iso)
ND
ND
iso-C13:0
2.89
2.71
iso-C14:0
9.41
6.21
iso-C15:0
16.41
25.37
iso-C16:0
3.43
4.81
iso-C17:0
ND
0.28
iso-C18:0
ND
ND
iso-C19:0
Branched-chain fatty acid (anteiso)
ND
ND
anteiso-C11:0
ND
1.13
anteiso-C13:0
45.68
37.65
anteiso-C15:0
7.09
9.79
anteiso-C17:0
ND
ND
anteiso-C19:0
ND
Summed feature 4a 1.4
Summed feature 5b
0.66
ND
3
4
5
ND
0.66
1.47
ND
4.21
2.71
ND
0.63
11.09
1.48
1.46
ND
0.66
1.07
8.38
0.24
0.45
0.14
0.7
1.25
14.01
0.48
5.36
ND
3.29
ND
0.72
1.53
23.64
1.67
0.37
ND
0.13
3.6
7.24
17.44
3.95
0.15
ND
ND
ND
51.46
9.12
2.53
ND
1.36
ND
35.76
19.51
ND
ND
ND
0.16
49.17
5.02
ND
0.19
ND
ND
0.52
Strain: 1, P. ginsengiterrae DCY89T; 2, P. cellulosilyticus KACC
14175T; 3, P. kobensis KACC 15273T; 4, P. xylaniclasticus KCTC
13719T; and 5, P. curdlanolyticus KCTC3759T
ND not detected
a
Summed feature 4 contained anteiso-C17:1 B and/or iso-C17:1
b
Summed feature 5 contained C18:2 ω6,9c and/or anteiso-C18:0
were identified as ribose, rhamnose, glucose, and galactose,
while P. cellulosilyticus KACC 14175T was found to contain ribose and galactose.
Biotransformation of ginsenoside Rb1
Ginsenoside Rb1 was converted to Rd by hydrolysis of a
glucose unit at the C-20 position of the ginsenoside aglycone. As shown in Fig. S5, the concentrations of ginsenoside Rb1 and the decomposition product Rd exhibited
regular changes with increasing reaction time. Within 3 h,
Rb1 was fully hydrolyzed and converted into ginsenoside
Rd. The conversion of ginsenosides Rb1 by DCY89T was
confirmed by quantitative HPLC analysis (Fig. S6). The
peaks with retention times of 20.68 and 22.59 min correspond to ginsenosides Rb1 and Rd, respectively (Fig. S6A).
Fig. S6B shows the control of ginsenoside Rb1. As shown
in Fig. S6C, the peak for ginsenoside Rb1 was fully disappeared (100 %) within 3 h, and a new peak appeared. The
new peak had retention time consistent with that of ginsenosides Rd. The metabolite was determined as ginsenoside
Rd based on the protonated molecular ion peak (Fig. S7).
All the result of the phylogenetic and phenotypic suggested that strain DCY89T belongs to the genus Paenibacillus. While the phylogenetic and chemotaxonomic distinctiveness of DCY89T supported that strain represents a novel
species that is distinct from previously known Paenibacillus species. Strain DCY89T also can be differentiated from
other related Paenibacillus species based on phenotypic
characteristics. Therefore, on the basis of the data presented, we consider that strain DCY89T represents a novel
species of the genus Paenibacillus, for which name Paenibacillus ginsengiterrae sp. nov, is proposed.
Description of Paenibacillus ginsengiterrae sp. nov.
anteiso-C17:0, (7.0 %), and saturated-C16:0, (8.0 %) were
also found little high amount in strain DCY89T. The isolated strain DCY89T showed a similar major fatty acid
composition to the related type strains of the genus Paenibacillus, but there were significant quantitative differences
when cultivated under the same conditions (Table 2). Thus,
the results indicate that strain DCY89T is a new species in
the genus Paenibacillus. The major menaquinone of strain
DCY89T was MK-7 that was similar to other members
of genus Paenibacillus. The major polar lipids of strain
DCY89T were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG) (Fig. S1),
which have been reported in several members of the genus
Paenibacillus. The major polyamine of strain DCY89T was
spermindine. The peptidoglycan contained the major amino
acid meso-DAP (diaminopimelic acid), also contained glutamic acid and alanine, which is similar with P. cellulosilyticus KACC 14175T. Whole cell sugars of strain DCY89T
13
Paenibacillus ginsengiterrae (gin.sen. gi. térrae. N. L. n.
ginsengum ginseng; L. n. terra soil; N.L. gen. n. ginsengiterrae of soil of a ginseng field, the source of the type
strain).
Cells are Gram-reaction-positive, catalase-negative, oxidase-negative, aerobic, rod-shaped, motile with monotrichous
flagella and spore-forming. Colonies are circular, beige color
on TSB agar and 0.4–0.9 mm in diameter after incubation
for 2 days. Cells grow on TSA, R2A, NA, but not on MacCkonkey agar. Growth occurs at 20–37 °C, at pH 6–8 and
at 0–2 % (w/v) NaCl. Nitrate is reduced to nitrite. Tyrosine,
skim milk, Tween 80, and DNA are not hydrolyzed. Starch,
gelatin, and esculine are hydrolyzed. Acid production from
glucose, sucrose, and lactose is positive. H2S gas is not
produced. In API ZYM tests, enzyme activity shows positive for esterase (C4), esterase lipase (C8), leucine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase,
Arch Microbiol
α-galactosidase, β-galactosidase, and β-glucosidase, but
negative for alkaline phosphatase, lipase (C14), valine
arylamidase, cystine arylamidase, trypsin, α-chymotrypsin,
β-glucuronidase, α-glucosidase, N-acetyl-β-glucosaminidase,
α-mannosidase, α-fucosidase. Positively assimilated compounds are L-rhamnose, N-acetyl-glucose, D-ribose, Inositol,
D-saccharose, D-maltose, Itaconic acid, suberic acid, sodium
acetate, lactic acid, L-alanine, potassium 5-ketogluconate,
glycogen, L-serine, D-mannitol, D-glucose, salicin, D-melibiose, L-fucose, L-arabinose, trisodium citrate, ʟ-histidine, and
4-hydroxybenzoic acid. However, the following are negative
for assimilation: sodium malonate, 3-hydroxybenzoic acid,
D-sorbitol, propionic acid, capric acid, valeric acid, potassium 2-ketogluconate, 3-hydroxybutyric acid, and ʟ-proline
(API 20NE, ID 32GN and traditional methods). Cells are
sensitive to neomycin (N30), tetracycline (TE30), cephazolin
(KZ30), carbenicillin (CAR100), vancomycin (VA30), ceftazidime (CAZ30), novobiocin (NV30), erythromycin (E15), oleandomycin (OL15), penicillin G (P10) rifampicin (RD5), and
lincomycin (MY15) with more sensitive to cephazolin (KZ30),
ceftazidime (CAZ30), and rifampicin (RD5). The predominant quinone is MK-7. The major cellular fatty acid of strain
DCY89T was anteiso-C15:0. Strain DCY89T also contain little high amount of iso-C16:0, iso-C15:0, anteiso-C17:0, and saturated-C16:0. The peptidoglycan contained the amino acids
meso-DAP, glutamic acid, and alanine. The major polar lipids
of strain DCY89T were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG).
Cell wall sugars of strain DCY89T were ribose, rhamnose,
glucose, and galactose. The DNA G+C content of the type
strain is 52.47 mol %.
The type strain DCY89T (KCTC 33430T = JCM
19887T) was isolated from soil of a ginseng field in Kyung
Hee University, Republic of Korea.
Acknowledgments This research was supported by Korea Institute of Planning & Evaluation for Technology in Food, Agriculture,
Forestry & Fisheries (KIPET NO: 309019-03-3-SB010) and NextGeneration BioGreen 21 Program (SSAC, Grant#: PJ009529032014),
Republic of Korea.
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