International Journal of Systematic and Evolutionary Microbiology (2013), 63, 2424–2429
DOI 10.1099/ijs.0.042176-0
Rhizobium tarimense sp. nov., isolated from soil in
the ancient Khiyik River
Maripat Turdahon,1 Ghenijan Osman,1 Maryam Hamdun,1 Khayir Yusuf,1
Zumret Abdurehim,1 Gulsumay Abaydulla,1 Muhtar Abdukerim,1
Chengxiang Fang2 and Erkin Rahman1
Correspondence
Erkin Rahman
[email protected]
1
College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046,
PR China
2
College of Life Sciences, Wuhan University, Wuhan 430072, PR China
A Gram-negative, non-motile, pale-yellow, rod-shaped bacterial strain, PL-41T, was isolated from
Populus euphratica forest soil at the ancient Khiyik River valley in Xinjiang Uyghur Autonomous
Region, People’s Republic of China. Strain PL-41T grew optimally at 30 6C and pH 7.0–8.0. The
major quinone was Q-10. The predominant cellular fatty acids of strain PL-41T were summed
feature 8 (comprising C18 : 1v7c and C18 : 1v6c), C16 : 0 and C19 : 0 cyclo v8c. Polar lipids of strain
PL-41T include two unidentified aminophospholipids (APL1, 2), two unidentified phospholipids
(PL1, 2), phosphatidylcholine and three unidentified lipids (L1–3). Strain PL-41T showed 16S
rRNA gene sequence similarity of 97.0–97.5 % to the type strains of recognized species of the
genus Rhizobium. Phylogenetic analysis of strain PL-41T based on the sequences of
housekeeping genes recA and atpD confirmed (similarities are less than 90 %) its position as a
distinct species of the genus Rhizobium. The DNA G+C content was 57.8 mol%. DNA–DNA
relatedness between strain PL-41T and the type strains of Rhizobium huautlense S02T,
Rhizobium alkalisoli CCBAU 01393T, Rhizobium vignae CCBAU 05176T and Rhizobium
loessense CCBAU 7190BT were 33.4, 22.6, 25.5 and 45.1 %, respectively, indicating that strain
PL-41T was distinct from them genetically. Strain PL-41T also can be differentiated from these
four phylogenetically related species of the genus Rhizobium by various phenotypic properties.
On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain PL41T is considered to represent a novel species of the genus Rhizobium, for which the name
Rhizobium tarimense sp. nov. is proposed. The type strain is PL-41T (5CCTCC AB
2011011T5NRRL B-59556T).
The genus Rhizobium was proposed for a group of fastgrowing, nodule-forming bacteria. The first description of
the genus Rhizobium as root and/or stem-nodule bacteria,
was from Frank (1889). Currently, this genus is an
evolutionary lineage within the family Rhizobiaceae of the
Alphaproteobacteria (Lee et al., 2005), and contains more
than 50 species at the time of writing including the latest
described species: Rhizobium soli (Yoon et al., 2010),
Rhizobium vignae (Ren et al., 2011) and Rhizobium vallis
(Wang et al., 2011). Members of the genus Rhizobium have
generally been isolated from nodules in leguminous plants
(Peng et al., 2008; Wei et al., 2003). However, some
Rhizobium species have also been isolated from other
The GenBank/EMBL/DDBJ accession numbers for the partial 16S
rRNA, recA and atpD gene sequences of PL-41T are HM371420,
JF508523 and JF508524, respectively.
Two supplementary figures and a supplementary table are available with
the online version of this paper.
2424
sources recently (Yoon et al., 2010; Zhang et al., 2011) by
means of standard dilution plating technique. In this
study, we report on the taxonomic characterization of a
Rhizobium-like bacterial strain PL-41T, isolated from soil in
Xinjiang (Xinjiang Uyghur Autonomous Region), PR
China. The aim of the present study was to determine
the exact taxonomic position of strain PL-41T by using a
polyphasic approach that included determination of
phenotypic properties, phylogenetic investigations based
on 16S rRNA, atpD and recA gene sequences and genetic
analysis.
During a study of the diversity and phylogeny of culturable
bacteria in the Populus euphratica forest soil of the ancient
Khiyik River in Xinjiang, PR China, strain PL-41T was
isolated by means of the standard dilution plating
technique at 37 uC on Luria–Bertani (LB) agar (5 g yeast
extract, 10 g peptone, 10 g NaCl, 1000 ml distilled water,
pH 7.0–8.0). The strain was cultured on yeast mannitol
Downloaded from www.microbiologyresearch.org by
042176 G 2013 IUMS
IP: 88.99.165.207
On: Sat, 17 Jun 2017 03:15:02
Printed in Great Britain
Rhizobium tarimense sp. nov.
using primers 27F [59-AGAGTTTGATC (A/C) TGGCTCAG-39] and 1492R [59-ACGG(C/T) TACCTTGTTACGACTT-39] as described previously (Menes & Muxı́, 2002).
Sequencing of the amplified 16S rRNA gene and phylogenetic analysis were performed as described by Yoon et al.
(2003). PCR amplifications of atpD and recA genes were
performed under the conditions described by Yoon et al.
(1998). The 16S rRNA, atpD and recA gene sequences of
strain PL-41T were aligned with relevant sequences
retrieved from GenBank using the CLUSTAL W program
contained in the MEGA4 package. Phylogenetic trees
were constructed by using the neighbour-joining (Saitou
& Nei, 1987) and maximum-parsimony (Fitch, 1971)
methods, with bootstrap values based on 1000 replications
(Felsenstein, 1985). Evolutionary distances were calculated
using Kimura’s two-parameter model (Kimura, 1980,
1983). For phylogenetic analyses, the 16S rRNA gene
sequences of related type strains were obtained from the
EzTaxon server (http://www.eztaxon.org; Kim et al., 2012).
The acquired 1444 bp sequence of the 16S rRNA gene from
strain PL-41T was compared with those of closely related
strains retrieved from GenBank. Strain PL-41T exhibited
16S rRNA gene sequence similarity of 97.5 %, 97.1 %,
97.0 % and 97.0 % to the type strains of R. huautlense S02T,
R. alkalisoli CCBAU 01393T, R. vignae CCBAU 05176T, R.
loessense CCBAU 7190BT, respectively and of 95.71–
96.31 % to the type strains of the other species of the
genus Rhizobium (Table 1). In the neighbour-joining tree
based on 16S rRNA gene sequences, strain PL-41T fell
within the clade comprising species of the genus
Rhizobium, particularly forming a cluster with R.
huautlense S02T, R. alkalisoli CCBAU 01393T, R. vignae
CCBAU 05176T and R. loessense CCBAU 7190BT (Fig. 1).
In phylogenetic trees constructed using the maximumparsimony algorithms, strain PL-41T also fell within the
clade encompassed by the genus Rhizobium (results not
shown). PCR amplification and sequencing of partial
atpD (471 bp) and recA (522 bp) genes were completed,
but the nodD and nifH genes were not detected by PCR in
strain PL-41T. Strain PL-41T exhibited 85.0–90.0 % atpD
gene sequence similarity and 80.1–83.0 % recA gene
sequence similarity to the type strains of species in the
genus Rhizobium used in this study (Table 1). In
agar (YMA) (Vincent, 1970) at 30 uC and maintained at
4 uC for temporary storage. The type strains of five species
of the genus Rhizobium were used as reference strains for
DNA–DNA hybridization, tests of physiology and biochemistry and fatty acid analysis: Rhizobium huautlense
S02T, Rhizobium alkalisoli CCBAU 01393T, Rhizobium vignae
CCBAU 05176T, Rhizobium loessense CCBAU 7190BT and
Rhizobium leguminosarum USDA 2370T (Table 1). These
reference strains were cultivated under the culture conditions
recommended by the culture collections and their features
were compared with those of strain PL-41T under the same
laboratory conditions.
Cell morphology and motility were observed by phasecontrast microscope and transmission electron microscope
using cells from the early exponential phase grown at 30 uC
for 2 days. Strain PL-41T formed circular, smooth, white
colonies after 3 days of incubation on LB medium. Cells
were aerobic, non-motile, non-spore-forming rods, 0.7–
1.2 mm wide and 0.5–0.8 mm long. The colonies on YMA
medium were circular, convex, white and opaque, with a
diameter of 1–2 mm within 2–3 days at 28 uC.
The temperature range for growth was determined between
4 and 45 uC with an interval of 5 uC in LB medium. The
initial growth pH range (3–10, with an interval of 0.5 pH
units) was determined using LB medium. The salinity
range that supported growth was determined at various
NaCl concentrations [0.5–15 % (w/v), with intervals of
0.5 %] in LB medium. The salinity and pH range
experiments were conducted with an incubation temperature of 30 uC. Gram staining was performed as described
by Smibert & Krieg (1994). Physiological and biochemical
tests were performed using API 50CH, API 20NE, API 20E,
API 30GN and API ZYM trips (bioMérieux) according to
the manufacturer’s instructions. Cells were Gram-negative.
Growth occurs on YMA supplied with 0–3 % NaCl
(optimum, 0.5 %); at 20–37 uC and pH 5–8, with optimum
growth at 30 uC and pH 7.0. Other phenotypic properties
of strain PL-41T are given in the species description and in
Table 2.
Extraction of genomic DNA was carried out with the
QIAamp DNA Mini kit (Qiagen) and amplification of
nearly full-length 16S rRNA gene fragments was performed
Table 1. Sequence similarities (%) for 16S rRNA gene, atpD, recA and DNA–DNA relatedness (%) between Rhizobium tarimense
PL-41T and reference strains
NA,
not available; – experiment not performed.
Strain
R.
R.
R.
R.
R.
R.
T
huautlense S02
alkalisoli CCBAU 01393T
vignae CCBAU 05176T
loessense CCBAU 7190BT
cellulosilyticum ALA10B2T
leguminosarum USDA 2370T
http://ijs.sgmjournals.org
16S rRNA
recA
atpD
DNA–DNA relatedness
97.5
97.1
97.0
97.0
96.3
95.7
81.1
80.1
83.0
88.5
90.0
89.4
33.4
22.6
22.5
41.5
–
–
NA
NA
82.7
81.8
89.8
85.0
Downloaded from www.microbiologyresearch.org by
IP: 88.99.165.207
On: Sat, 17 Jun 2017 03:15:02
2425
M. Turdahon and others
Table 2. Phenotypic characteristics of Rhizobium tarimense sp. nov. PL-41Tand type strains of phylogenetically closely related
species of the genus Rhizobium
Strains: 1, Rhizobium tarimense sp. nov. PL-41T; 2, R. huautlense S02T; 3, R. alkalisoli CCBAU 01393T; 4, R. vignae CCBAU 05176T; 5, R. loessense
CCBAU 7190BT; 6, R. leguminosarum USDA 2370T. Data are from this study unless indicated. All strains are Gram-negative, aerobic, rod-shaped
and non-spore-forming. All strains are positive for growth at 1 % (w/v) NaCl, nitrate reduction and hydrolysis of hypoxanthine. All strains were
positive for leucine arylamidase and acid phosphatase, negative for lipase (C14), a-galactosidase, b-galactosidase, b-glucuronidase, N-acetyl-bglucosaminidase, a-fucosidase and a-mannosidase. Utilization of D-xylose, aesculin ferric citrate, L-arabinose, D-glucose, D-mannitol, 2nitrophenyl-b-D-galactopyranoside and amygdalin were positive for all the strains, while sorbose, inositol, L-tryptophan, D-sorbitol, L-rhamnose
and melibiose were negative. Susceptibility to penicillin G and kanamycin were negative for all the strains, but cephalothin was positive. +,
Positive; 2, negative; W, weakly positive; ND, no data available.
Characteristic
Origin
Flagella
pH range for growth
Growth at/in:
40 uC
2 % (w/v) NaCl
Enzyme activity (API ZYM,
API 20E)
Alkaline phosphatase
Esterase (C4)
Esterase lipase (C8)
Valine arylamidase
Cystine arylamidase
a-Glucosidase
b-Glucosidase
Utilization of:
Glycerol
Erythritol
D-Arabinose
D-Ribose
L-Xylose
D-Adonitol
Methyl b-D-xyloside
Rhamnose
Dulcitol
L-Arginine
Urea
Gelatin
D-Mannose
Maltose
D-Lyxose
Sucrose
Susceptibility to:
Chloramphenicol
Ampicillin
Novobiocin
Carbenicillin
Oleandomycin
DNA G+C content (mol%)
1
2
Forest soil
Sesbania herbacea
(Xinjiang, China)
(Mexico)
4
5
6
Root nodules
(China)
Root nodules
(China)
None
4.5–9.0
None
5.0–9.5
Trifolium
polymorphum
(Uruguay)
None
5.0–9.0
2
2
None
5.5–8.5
5.0–9.0
Nodules of
legume species
(China)
None
5.5–9.5
2
+
+
2
2
2
+
2
+
+
+
2
+
+
2
2
2
2
2
2
+
+
+
+
2
+
2
2
2
2
+
+
ND
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
2
+
2
2
2
+
+
+
+
2
+
2
+
2
+
2
2
+
2
2
2
+
+
+
2
+
+
2
2
+
+
+
2
+
2
2
57.8
+
2
+
+
2
57.0
2
+
2
2
2
2
2
+
56.8
+
2
+
+
2
58.2
+
2
2
+
2
52.1
W
W
W
W
W
neighbour-joining trees based on atpD and recA gene
sequences, strain PL-41T formed distinct phylogenetic
lineages within the clade comprising species of the genus
Rhizobium (Fig. S1 available in IJSEM Online). Sequence
2426
3
W
+
60.4
W
W
W
analyses of the 16S rRNA, atpD and recA genes showed
that strain PL-41T was phylogenetically related to the
members of the genus Rhizobium, but distinct from all the
defined species.
Downloaded from www.microbiologyresearch.org by
International Journal of Systematic and Evolutionary Microbiology 63
IP: 88.99.165.207
On: Sat, 17 Jun 2017 03:15:02
Rhizobium tarimense sp. nov.
26 Rhizobium hainanense I66T (U71078)
33 Rhizobium multihospitium CCBAU 83401T (EF035074)
85 Rhizobium miluonense CCBAU 41251T (EF061096)
Rhizobium tropici CIAT 899T (U89832)
98
36 Rhizobium leucaenae CENA 183T (X67234)
Rhizobium lusitanum P1-7T (AY738130)
97
71 Rhizobium rhizogenes ATCC 11325T (D14501)
70 Rhizobium rubi ATCC 13335T (AY626395)
44
Rhizobium vallis CCBAU 65647T (FJ839677)
32
Rhizobium endophyticum CCGE 2052T (EU867317)
Rhizobium tibeticum CCBAU 85039T (EU256404)
66
Rhizobium etli CFN 42T (U28916)
Rhizobium leguminosarum 3Hoq18T (U29386)
98
59
Rhizobium trifolii ATCC 14480T (AY509900)
54 Rhizobium phaseoli ATCC 14482T (EF141340)
43
73 Rhizobium pisi DSM 30132T (AY509899)
88 Rhizobium alamii GBV016T (AM931436)
84
Rhizobium mesosinicum CCBAU 25010T (DQ100063)
Rhizobium sullae IS123T (Y10170)
15
Rhizobium indigoferae AS 1.3054T (AF364068)
94
Rhizobium gallicum R602spT (U86343)
76
Rhizobium yanglingense SH 22623T (AF003375)
91
T
42 Rhizobium loessense AS1.3401 (AF364069)
24
53 Rhizobium mongolense ATCC BAA-116T (U89817)
Rhizobium soli DS-42T (EF363715)
Rhizobium tubonense CCBAU 85046T (EU256434)
Rhizobium tarimense PL-41T (HM371420)
19
Rhizobium huautlense SO2T (AF025852)
27
98
Rhizobium alkalisoli CCBAU 01393T (EU074168)
86
T
62 Rhizobium vignae CCBAU 05176 (GU128881)
78 88 Rhizobium galegae ATCC 43677T (D11343)
Rhizobium cellulosilyticum ALA10B2T (DQ855276)
Rhizobium borbori DN316T (EF125187)
Rhizobium undicola ORS 992T (Y17047)
51
Rhizobium oryzae Alt 505T (EU056823)
47
76
Rhizobium pseudoryzae J3-A127T (DQ454123)
100 Rhizobium giardinii H152T (U86344)
Rhizobium herbae CCBAU 83011T (GU565534)
Rhizobium daejeonense L61T (AY341343)
31
Rhizobium selenitireducens B1T (EF440185)
38
Rhizobium aggregatum 161T (X73041)
85
Rhizobium rosettiformans W3T (EU781656)
63
58
Rhizobium taibaishanense CCNWSX 0483T (HM776997)
100 Rhizobium vitis K309T (U45329)
36
Rhizobium larrymoorei ATCC 51759T (Z30542)
50
Rhizobium pusense NRCPB10T (FJ969841)
92
Rhizobium radiobacter ATCC 19358T (AB247615)
33
Rhizobium skierniewicense Ch11T (HQ823551)
Rhizobium
fredii
PRC
205T (X67231)
99
Rhizobium meliloti ATCC 9930T (D14509)
100 Rhizobium ciceri UPM-Ca7T (U07934)
67
Rhizobium loti ATCC 700743T (D14514)
Rhizobium huakuii 103T (D13431)
100
Rhizobium mediterraneum UPM-Ca36T (AM181745)
49
77
0.005
Rhizobium tianshanense A-1BST (AF041447)
Fig. 1. Phylogenetic tree based on 16S rRNA gene sequences, showing the phylogenetic position of strain PL-41T within the
genus Rhizobium and with respect to former species of the genus Agrobacterium. The tree was constructed by using the
neighbour-joining method with a Jukes–Cantor distance matrix. Bootstrap values (%) based on 1000 replicates are shown at
each node.
http://ijs.sgmjournals.org
Downloaded from www.microbiologyresearch.org by
IP: 88.99.165.207
On: Sat, 17 Jun 2017 03:15:02
2427
M. Turdahon and others
Isoprenoid quinones were extracted according to the
method of Komagata & Suzuki (1987) and analysed using
reversed-phase HPLC and a YMC ODS-A (25064.6 mm)
column. The predominant isoprenoid quinone of strain
PL-41T was Q-10, in line with all members of the family
Rhizobiaceae.
separate from recognized species of the genus Rhizobium
(Stackebrandt & Goebel, 1994). Therefore, on the basis of
the data presented, strain PL-41T is considered to represent
a novel species within the genus Rhizobium, for which the
name Rhizobium tarimense sp. nov. is proposed.
For cellular fatty acid analysis, strain PL-41T and the
reference strains were harvested from TSB plates after
cultivation for 2 days at 30 uC. The fatty acids were
extracted according to the standard protocol of the
Microbial Identification System (MIDI, Sherlock).
Analysis of the fatty acid methyl esters was performed by
GC (6850, Agilent) and peaks were identified with MIDI
software (version 6.0). Strain PL-41T contained C16 : 0
(15.77 %), C19 : 0 cyclo v8c (12.82 %) and summed feature
8 (comprising C18 : 1v7c and/or C18 : 1v6c; 56.74 %) as the
major fatty acids. The fatty acid profiles of strain PL-41T
and of the four reference strains were mostly similar,
although there were some differences in the proportions of
some components (Table S1).
Description of Rhizobium tarimense sp. nov.
The polar lipids of strain PL-41T and the reference strain R.
borbori DN316T were extracted as described by Kates (1986).
The lipids were separated using silica gel TLC by twodimensional chromomatography. Total polar lipids profiles
were detected by spraying with 10 % ethanolic molybdophosphoric acid and further characterized by spraying with
ninhydrin, molybdenum blue and a-naphthol (Kates, 1972;
Oren et al., 1996). Polar lipids of strain PL-41T (Fig. S2)
include two unidentified aminophospho lipids (APL1, 2),
two unidentified phospholipids (PL1, 2), phosphatidyl
choline (PC) and three unidentified lipids (L1–3). Polar
lipids of strain PL-41T were mostly consistent with those of
R. borbori DN316T (Ramana et al., 2013).
The DNA G+C content of strain PL-41T was determined
by reversed-phase HPLC using the method of Mesbah et al.
(1989). DNA G+C content was 57.8 mol%, which is
within the range reported for the genus Rhizobium (57–
66 mol%; Young et al., 2001).
The DNA–DNA hybridization was performed fluorometrically 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 for
each sample were excluded and the means of the remaining
three values are quoted as DNA–DNA relatedness values.
Strain PL-41T exhibited mean DNA–DNA relatedness of
22.5–41.55 % to the type strains of phylogenetically related
species of the genus Rhizobium [R. huautlense S02T
(33.4 %), R. alkalisoli CCBAU 01393T (22.6 %), R. vignae
CCBAU 05176T (22.5 %), R. loessense CCBAU 7190BT
(41.55 %)] (Table 1). These values indicate that strain PL41T represents a genomic species distinct from these four
members of the genus Rhizobium (Wayne et al., 1987). The
phylogenetic distinctiveness, together with the DNA–DNA
relatedness data and differential phenotypic properties, is
sufficient to allocate strain PL-41T to a species that is
2428
Rhizobium tarimense (ta.rim.en9se. N.L. neut. adj. tarimense
pertaining to Tarim basin in Xinjiang Uyghur autonomous
region of China, where the type strain was isolated).
Cells are Gram-negative, non-spore-forming, non-motile,
aerobic rods. Colonies on LB are circular, convex, smooth,
glistening, white and 1.2–2.0 mm in diameter after incubation for 3 days at 30 uC. Growth occurs at 20 and 37 uC,
with optimum growth at 30 uC, but not at 38 uC. Optimal
pH for growth is between 7.0 and 8.0; growth occurs at
pH 5.5 and 8.5, but not at pH 5.0 or 9.0. Growth occurs in
the presence of 0–3.0 % (w/v) NaCl, with optimum growth
in the presence of 0 –0.5 % (w/v) NaCl. The nodD and nifH
genes are not detected by PCR. Positive for catalase
and oxidase. Utilizes urea and positive for nitrate
reduction. H2S and indole are not produced. Aesculin
and hypoxanthine are hydrolysed, but casein, starch,
tyrosine, xanthine and Tweens 20, 40, 60 and 80 are not.
D-Arabinose, L-arabinose, ribose, D-xylose, methyl b-Dxyloside, galactose, glucose, fructose, mannitol, N-acetylglucosamine, aesculin, cellobiose, xylitol, L-fucose, Darabitol, gluconate, L-xylose, adonitol, rhamnose, amygdalin and 2-ketogluconate are utilized, and trehalose and
gentiobiose are utilized weakly, but glycerol, erythritol,
mannose, sorbitol, melibiose, sorbose, dulcitol, inositol,
methyl a-D-mannoside, methyl a-glucoside, salicin, lactose,
sucrose, inulin, melezitose, raffinose, starch, glycogen,
turanose, D-tagatose, D-fucose, L-arabitol, 5-ketogluconate,
maltose and D-lyxose are not utilized. Acid is produced
from D-glucose, L-rhamnose, melibiose and L-arabinose,
but not from D-mannitol, inositol, D-sorbitol, sucrose or
amygdalin. Acid phosphatase, leucine arylamidase, bglucosidase and a-glucosidase activities are present and
esterase (C4), esterase lipase (C8), valine arylamidase and
alkaline phosphatase activities are weak, but arginine
decarboxylase, lysine decarboxylase, ornithine decarboxylase,
tryptophan deaminase, lipase (C14), cystine arylamidase,
trypsin, a-chymotrypsin, naphthol-AS-BI-phosphohydrolase,
a-galactosidase, b-galactosidase, b-glucuronidase, N-acetyl-bglucosaminidase, amannosidase and a-fucosidase activities
are absent. Not susceptible to chloramphenicol, kanamycin,
novobiocin, polymyxin G, streptomycin, gentamicin, tetracycline or neomycin, but susceptible to cephalothin, ampicillin, lincomycin, carbenicillin, oleandomycin and penicillin
G. The predominant ubiquinone is Q-10. The major fatty
acid is summed feature 8 (comprising C18 : 1v7c and
C18 : 1v6c). The known polar lipid is phosphatidylcholine
and several unidentified polar lipids are also present.
The type strain PL-41T (5CCTCC AB 2011011T5NRRL B59556T), was isolated from Populus euphratica forest soil of
Downloaded from www.microbiologyresearch.org by
International Journal of Systematic and Evolutionary Microbiology 63
IP: 88.99.165.207
On: Sat, 17 Jun 2017 03:15:02
Rhizobium tarimense sp. nov.
the ancient Khiyik River in Xinjiang, PR China. The DNA
G+C content of the type strain is 57.8 mol% (from
melting temperature).
Peng, G., Yuan, Q., Li, H., Zhang, W. & Tan, Z. (2008). Rhizobium
oryzae sp. nov., isolated from the wild rice Oryza alta. Int J Syst Evol
Microbiol 58, 2158–2163.
Ramana, Ch. V., Parag, B., Girija, K. R., Ram, B. R., Ramana, V. V. &
Sasikala, Ch. (2013). Rhizobium subbaraonis sp. nov., an endolithic
Acknowledgements
bacterium isolated from beach sand. Int J Syst Evol Microbiol 63, 581–
585.
The authors would like to express our gratitude to Professor Wen Xin
Chen and Xin Hua Sui, culture collection of China Agricultural
University (CCBAU) for kindly gifting the type strains. This work was
supported by the National Natural Science Foundation of China
(31060002), the KJZJ foundation of Xinjiang (201091236) and the
foundation of the State Key Laboratory of Microbial Technology,
Shandong University (M2011-07).
Ren, W., Chen, W. F., Sui, X. H., Wang, E. T. & Chen, W. X. (2011).
Rhizobium vignae sp. nov., a symbiotic bacterium isolated from
multiple legume species. Int J Syst Evol Microbiol 61, 580–586.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new
method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–
425.
Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In
References
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.
Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric
Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for
deoxyribonucleic acid–deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in
which radioisotopes are used to determine genetic relatedness among
bacterial strains. Int J Syst Bacteriol 39, 224–229.
DNA–DNA reassociation and 16S rRNA sequence analysis in the
present species definition in bacteriology. Int J Syst Bacteriol 44, 846–
849.
Felsenstein, J. (1985). Confidence limits on phylogenies: an approach
using the bootstrap. Evolution 39, 783–791.
Fitch, W. M. (1971). Toward defining the course of evolution:
minimum change for a specific tree topology. Syst Zool 20, 406–416.
Frank, B. (1889). Ueber die Pilzsymbiose der Leguminosen. Ber Dtsch
Bot Ges 7, 332–346 (in German).
Kates, M. (1972). Techniques of Lipidology. New York: Elsevier.
Kates, M. (1986). Influence of salt concentration on membrane lipids
of halophilic bacteria. FEMS Microbiol Lett 39, 95–101.
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
represent uncultured species. Int J Syst Evol Microbiol 62, 716–721.
Kimura, M. (1980). A simple method for estimating evolutionary rates
of base substitutions through comparative studies of nucleotide
sequences. J Mol Evol 16, 111–120.
Kimura, M. (1983). The Neutral Theory of Molecular Evolution.
Cambridge: Cambridge University Press.
Komagata, K. & Suzuki, K. (1987). Lipid and cell-wall analysis in
bacterial systematics. Methods Microbiol 19, 161–207.
Lee, K. B., Liu, C. T., Anzai, Y., Kim, H., Aono, T. & Oyaizu, H. (2005).
Vincent, J. M. (1970). The cultivation, isolation and maintenance of
rhizobia. In A Manual for the Practical Study of the Root-Nodule
Bacteria, pp. 1–13. Edited by J. M. Vincent. Oxford: Blackwell
Scientific.
Wang, F., Wang, E. T., Wu, L. J., Sui, X. H., Li, Y., Jr & Chen, W. X.
(2011). Rhizobium vallis sp. nov., isolated from nodules of three
leguminous species. Int J Syst Evol Microbiol 61, 2582–2588.
Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler,
O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. &
other authors (1987). International Committee on Systematic
Bacteriology. Report of the ad hoc committee on reconciliation of
approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.
Wei, G. H., Tan, Z. Y., Zhu, M. E., Wang, E. T., Han, S. Z. & Chen, W. X.
(2003). Characterization of rhizobia isolated from legume species
within the genera Astragalus and Lespedeza grown in the Loess Plateau
of China and description of Rhizobium loessense sp. nov.. Int J Syst
Evol Microbiol 53, 1575–1583.
Yoon, J. H., Lee, S. T. & Park, Y. H. (1998). Inter- and intraspecific
phylogenetic analysis of the genus Nocardioides and related taxa based
on 16S rDNA sequences. Int J Syst Bacteriol 48, 187–194.
Yoon, J. H., Kim, I. G., Shin, D. Y., Kang, K. H. & Park, Y. H. (2003).
Microbulbifer salipaludis sp. nov., a moderate halophile isolated from
a Korean salt marsh. Int J Syst Evol Microbiol 53, 53–57.
Yoon, J. H., Kang, S. J., Yi, H. S., Oh, T. K. & Ryu, C. M. (2010).
The hierarchical system of the ‘Alphaproteobacteria’: description of
Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and
Erythrobacteraceae fam. nov.. Int J Syst Evol Microbiol 55, 1907–1919.
Rhizobium soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 60,
1387–1393.
Menes, R. J. & Muxı́, L. (2002). Anaerobaculum mobile sp. nov., a novel
Young, J. M., Kuykendall, L. D., Martı́nez-Romero, E., Kerr, A. &
Sawada, H. (2001). A revision of Rhizobium Frank 1889, with an
anaerobic, moderately thermophilic, peptide-fermenting bacterium
that uses crotonate as an electron acceptor, and emended description
of the genus Anaerobaculum. Int J Syst Evol Microbiol 52, 157–164.
Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise
emended description of the genus, and the inclusion of all species of
Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al.
1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R.
rubi, R. undicola and R. vitis. Int J Syst Bacteriol 51, 89–103.
measurement of the G+C content of deoxyribonucleic acid by highperformance liquid chromatography. Int J Syst Bacteriol 39, 159–167.
Zhang, G. X., Ren, S. Z., Xu, M. Y., Zeng, G. Q., Luo, H. D., Chen, J. L.,
Tan, Z. Y. & Sun, G. P. (2011). Rhizobium borbori sp. nov., aniline-
Oren, A., Duker, S. & Ritter, S. (1996). The polar lipid composition of
Walsby’s square bacterium. FEMS Microbiol Lett 138, 135–140.
http://ijs.sgmjournals.org
degrading bacteria isolated from activated sludge. Int J Syst Evol
Microbiol 61, 816–822.
Downloaded from www.microbiologyresearch.org by
IP: 88.99.165.207
On: Sat, 17 Jun 2017 03:15:02
2429