International Journal of Systematic and Evolutionary Microbiology (2013), 63, 2254–2259
DOI 10.1099/ijs.0.046888-0
Geodermatophilus telluris sp. nov., an
actinomycete isolated from Saharan desert sand
Maria del Carmen Montero-Calasanz,1,2 Markus Göker,1 Gabriele Pötter,1
Manfred Rohde,3 Cathrin Spröer,1 Peter Schumann,1 Hans-Peter Klenk1
and Anna A. Gorbushina4
Correspondence
Hans-Peter Klenk
[email protected]
Anna A. Gorbushina
[email protected]
1
Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße
7B, 38124 Braunschweig, Germany
2
IFAPA – Instituto de Investigación y Formación Agraria y Pesquera, Centro Las Torres-Tomejil,
Ctra. Sevilla-Cazalla de la Sierra, Km 12.2, 41200 Alcalá del Rı́o, Sevilla, Spain
3
HZI – Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
4
BAM – Federal Institute for Material Research and Testing, 12205 Berlin, Germany
5
Free University of Berlin, Department of Biology, Chemistry and Pharmacy and Department of
Earth Sciences, 12249 Berlin, Germany
A novel Gram-positive, multiloculated thalli-forming, aerobic, actinobacterial strain, CF9/1/1T, was
isolated in 2007 during environmental screening for xerophilic fungi in arid desert soil from the
Sahara desert, Chad. The isolate grew best at a temperature range of 20–35 6C and at pH 6.0–
8.5 and with 0–4 % (w/v) NaCl, forming black-coloured and irregular colonies on GYM agar.
Chemotaxonomic and molecular characteristics of the isolate matched those described for
members of the genus Geodermatophilus. The DNA G+C content of the novel strain was
75.4 mol%. The peptidoglycan contained meso-diaminopimelic acid as a diagnostic diamino acid.
The main phospholipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, a not yet structurally identified aminophospholipid and a small amount
of phosphatidylglycerol; MK-9(H4) was identified as the dominant menaquinone and galactose
was a diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids: isoC16 : 0 and iso-C15 : 0. The 16S rRNA gene sequence of the isolate showed 94.6–97.0 %
sequence similarities with those of five members of the genus: Geodermatophilus ruber DSM
45317T (94.6 %), Geodermatophilus obscurus DSM 43160T (94.8 %), Geodermatophilus
siccatus DSM 45419T (96.2 %), Geodermatophilus nigrescens DSM 45408T (96.7 %) and
Geodermatophilus arenarius DSM 45418T (97.0 %). Based on the evidence from this polyphasic
taxonomic study, a novel species, Geodermatophilus telluris sp. nov., is proposed; the type strain
is CF9/1/1T (5DSM 45421T5CCUG 62764T).
Although Geodermatophilus obscurus, the type species of the
genus Geodermatophilus (5‘earth Dermatophilus’) was
described 44 years ago by George M. Luedemann
(Luedemann, 1968), the family name Geodermatophilaceae
was first proposed (but at that time not validly published) by
Normand et al. (1996). The name was validly published a
decade later by Normand (2006). In addition to the type
genus Geodermatophilus, the Geodermatophilaceae also contains the genera Blastococcus and Modestobacter. Sharing the
The GenBank/EMBL/DDBJ/International Nucleotide Sequence
Database Collaboration (INSDC) accession number for the 16S rRNA
gene sequence of strain CF9/1/1T is HE815469.
Two supplementary figures are available with the online version of this
paper.
2254
harsh conditions of low availability of water and nutrients,
these two genera are mainly known as inhabitants of rock
surfaces, whereas Geodermatophilus prefers arid soils as
natural habitats (Urzı̀ et al., 2001). The family is rather poorly
sampled and studied, with only one type-strain genome
sequenced, that of G. obscurus (Ivanova et al., 2010), and a
total, at the time of writing of only ten species with validly
published names. In addition to the type species G. obscurus,
the genus Geodermatophilus currently contains the following
species with validly published names: Geodermatophilus ruber
(Zhang et al., 2011), Geodermatophilus nigrescens (Nie et al.,
2012; Euzéby, 2012), Geodermatophilus arenarius (MonteroCalasanz et al., 2012; Euzéby, 2013a) and Geodermatophilus
siccatus (Montero-Calasanz et al., 2013; Euzéby, 2013b). An
analysis of 16S rRNA reference sequences using the
Downloaded from www.microbiologyresearch.org by
046888 G 2013 IUMS
IP: 88.99.165.207
On: Fri, 16 Jun 2017 04:23:46
Printed in Great Britain
Geodermatophilus telluris sp. nov.
Greengenes database (DeSantis et al., 2006) and latest
metagenomic studies on dust originating from deserts
(Giongo et al., 2013) revealed the existence of several more
isolates and as yet uncultured phylotypes in soil and on rock
surfaces (for an overview see Ivanova et al., 2010; Urzı̀ et al.,
2001). The novel organism described in this report
represents a genomically distinct novel lineage from a
screening of Saharan desert sand that falls into the genus
Geodermatophilus in 16S rRNA-based phylogenies.
Representative sand samples were taken in the Saharan
desert of the Republic of Chad near to Vers Ourba and
axenic cultures of xerophiles were isolated from these
samples with classical enrichment procedures (Giongo
et al., 2013). Portions of sand were suspended in
physiological saline, shaken for one hour at 26 uC and
kept overnight at 4 uC and then again shaken for two hours
before being streaked out on R2A and TSA plates and
incubated at 25 uC for 3–10 days (for details see Giongo
et al., 2013). Purified isolates were stored in Microbank
Blue Colour Beads (Pro-Lab Diagnostics) before accession
into the Deutsche Sammlung von. Mikroorganismen und
Zellkulturen (DSMZ) open collection. To determine their
morphological characteristics, strain CF9/1/1T was cultivated on trypticase soy broth agar (DSMZ medium 535)
and GYM Streptomyces medium (DSMZ medium 65). The
colony features were observed under a binocular microscope according to the protocol of Pelczar (1957).
Exponentially growing bacterial cultures were observed
with an optical microscope (AxioScope A1, Zeiss) with
6100 magnification and phase-contrast illumination.
Micrographs of bacterial cells were taken with a fieldemission scanning electron microscope (FE-SEM Merlin,
Zeiss). Gram reaction was performed using the KOH test
described by Gregersen (1978). The motility of the cells was
observed on modified ISP2 (Shirling & Gottlieb, 1966)
swarming agar (0.3 %, w/v) at pH 7.2 that contained (l21)
4.0 g dextrin, 4.0 g yeast extract and 10.0 g malt extract.
Activity of oxidase was analysed using filter-paper disks
(Sartorius grade 388) impregnated with 1 % solution of
N,N,N9,N9,-tetramethyl-p-phenylenediamine (Sigma–Aldrich);
a positive test was indicated by the development of a
blue-purple colour after applying biomass on the filter
paper. Catalase activity was tested by the observation of
bubbles following the addition of drops of 3 % H2O2.
Growth rates were determined on plates of GYM medium
for temperatures from 10 to 50 uC in steps of 5 uC and for
pH values 5.0 to 9.0 (in steps of 0.5 pH units) on modified
ISP2 medium (Shirling & Gottlieb, 1966) by adding NaOH
or HCl, respectively, because the use of a buffer system
inhibited growth of the cultures. Degradation of specific
substrates was examined using agar plates with various basal
media, considering the appearance of clear zones around the
colonies as a positive result: casein degradation was tested on
plates containing milk powder (5 % w/v), NaCl (0.5 %) and
agarose (1 %); tyrosine degradation was investigated as
previously described (Gordon & Smith, 1955) on plates
http://ijs.sgmjournals.org
containing peptone (0.5 %), beef extract (0.3 %), L-tyrosine
(0.5 %) and agarose (1.5 %); the decomposition of xanthine
and hypoxanthine was tested by the same test, replacing Ltyrosine with hypoxanthine or xanthine (0.4 %); starch
degradation was tested on plates containing nutrient broth
(0.8 %), starch (1 %) and agarose (1.5 %), these plates were
developed by flooding with iodine solution (1 %). The
utilization of carbon compounds and acid production were
determined using API 20 NE strips (bioMérieux) and GEN
III Microplates in an OmniLog device (Biolog). The GEN III
Microplates were inoculated with a cell suspension made in
a ‘gelling’ inoculating fluid (IF) at a cell density of 80–83 %
T, except for G. arenarius plates that were filled to a cell
density of 90 % T. As the cultures were respiring (and
growing) comparatively slowly, each plate was measured in
three subsequent runs by restarting the OmniLog device
twice, yielding a total running time of 10 days in phenotype
microarray mode at 28 uC. The exported measurement data
were further analysed with the opm package for R (Vaas
et al., 2012), using its functionality for merging subsequent
measurements of the same plate, statistically estimating
parameters from the respiration curves, such as the
maximum height, and automatically discretizing these
values into negative, weak and positive reactions, respectively. Each strain was studied in two independent repetitions
(yielding a total of six recorded runs per strain), and
reactions with a distinct behaviour between the two
repetitions were regarded as ambiguous. Enzyme activities
were tested using API ZYM galleries according to the
instructions of the manufacturer (bioMérieux). Further
biochemical tests were performed as described by Tindall
et al. (2007), including cellulase activity (15.2.18) and methyl
red and Voges–Proskauer reactions (15.2.52 and 15.2.82).
Whole-cell amino acids and sugars were prepared according
to the protocol of Lechevalier & Lechevalier (1970) and
analysed by TLC (Staneck & Roberts, 1974). Polar lipids
were extracted, separated by two-dimensional TLC and
identified according to the method of Minnikin et al. (1984)
as modified by Kroppenstedt & Goodfellow (2006). For the
extraction of menaquinones, freeze-dried cell material was
extracted with methanol as described by Collins et al. (1977)
and analysed by HPLC (Kroppenstedt, 1982). For the
extraction and analysis of cellular fatty acids, the physiological age of the strains was standardized by always
choosing the same sector (the last quadrant streak) on
Gym agar plates held at 28 uC (four days). Analysis was
conducted using the Microbial Identification System
(MIDI) Sherlock Version 4.5 (method TSBA40, TSBA6
database) as described by Sasser (1990). The composition of
peptidoglycan hydrolysates (6 M HCl, 100 uC for 16 h) was
examined by TLC according to the protocol of Schleifer &
Kandler (1972). All physiological tests were performed at
28 uC using G. obscurus G-20T (5DSM 43160T), G. ruber
CPCC 201356T (5DSM 45317T), G. nigrescens YIM 75980T
(5DSM 45408T), G. arenarius CF5/4T (5DSM 45418T) and
G. siccatus CF6/1T (5DSM 45419T) in parallel assays. The
G+C content of the chromosomal DNA was determined by
Downloaded from www.microbiologyresearch.org by
IP: 88.99.165.207
On: Fri, 16 Jun 2017 04:23:46
2255
M. C. Montero-Calasanz and others
HPLC according to the protocol of Mesbah et al. (1989).
Genomic DNA extraction, PCR-mediated amplification of
the 16S rRNA gene and purification of the PCR product was
carried out as described by Rainey et al. (1996). Phylogenetic
analysis was based on an alignment inferred with POA
version 2.0 (Lee et al., 2002) and filtered with GBLOCKS
(Castresana, 2000). Phylogenetic trees were inferred under
maximum-likelihood and maximum-parsimony as optimality criteria using RAxML version 7.2.8 (Stamatakis et al.,
2008) and PAUP* 4b10 (Swofford, 2002), respectively.
Bootstrap support values were calculated using the bootstopping criterion (Pattengale et al., 2009) as implemented
in RAxML and 1000 replicates in the case of PAUP*. Rooting
was done using the midpoint method (Hess & De Moraes
Russo, 2007) and then checked for its agreement with the
classification. Pairwise similarities were calculated from
exact pairwise sequence alignments using the Smith–
Waterman algorithm as implemented in the EMBOSS suite
(Rice et al., 2000). To assess the occurrence of the novel
strain in environmental samples, the 16S rRNA sequence
was compared using NCBI BLAST (Altschul et al., 1990)
under default settings (e.g. considering only the high-scoring
segment pairs from the best 250 hits) with the most recent
release of the Greengenes database (DeSantis et al., 2006)
and the relative frequencies of taxa and environmental
samples were determined, weighted by BLAST scores (Ivanova
et al., 2010). DNA–DNA hybridization tests were performed
as described by De Ley et al. (1970) with the modifications
suggested by Huss et al. (1983) using a Cary 100 Bio UV/VIS
instrument.
Cells of strain CF9/1/1T were cuboidal and Gram-positive.
They were observed forming dimers, tetrads and higher
aggregates (Fig. 1). The motile zoospores were elliptical;
septated filaments from zoospore germination were
observed. The colonies were black-coloured, irregular,
multilocular and opaque with a dry surface and an
irregular margin. Strain CF9/1/1T grew best at 20–35 uC;
no growth was observed below 15 uC and above 40 uC.
Growth was observed in the presence of 0–4 % NaCl but
not 8 % NaCl and pH 6.0–8.5. More details about the
strain’s phenotypic features are presented in Table 1 in
comparison with the other species of the genus Geodermatophilus; see also Fig. S1 (available in IJSEM Online) for
the heatmap obtained from the OmniLog phenotyping
results. Analysis of cell-wall components revealed the
presence of meso-diaminopimelic acid (meso-DAP), which
is in line with the other species of the genus Geodermatophilus
(Montero-Calasanz et al., 2013), whose cell-wall type is type
III (Lechevalier & Lechevalier, 1970). Strain CF9/1/1T
displayed MK-9(H4) (84.7 %) as the dominant menaquinone, complemented by small amounts of MK-9 (4.1 %),
MK-8(H4) (3.6 %) and an unknown MK (3.6 %). The major
fatty acids were the saturated branched-chain acids iso-C16 : 0
(44.8 %), iso-C15 : 0 (21.4 %). The phospholipid pattern
consisted of diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidylethanolamine (PE),phosphatidylinositol (PI), an unknown aminophospholipid (PN) and a
small amount of phosphatidylglycerol (PG) (Fig. S2). Wholecell sugar analysis revealed galactose as a diagnostic sugar,
complemented by glucose and traces of ribose and mannose
(Lechevalier & Lechevalier, 1970). The DNA G+C content
was 75.4 mol%.
The almost complete (1528 bp) 16S rRNA gene sequence
of strain CF9/1/1T was determined. The 16S rRNA
sequence of the G. arenarius DSM 45418T was the most
similar sequence (97.0 %) within the members of the genus
Geodermatophilus; G. ruber DSM 45317T (94.6 %), G.
obscurus DSM 43160T (94.8 %), G. siccatus DSM 45419T
(96.2 %) and G. nigrescens DSM 45408T (96.7 %). Both
maximum-likelihood and maximum-parsimony phylogenies placed CF9/1/1T within a group also containing the
type strains of G. arenarius and G. nigrescens with high
support (99 %/100 %) (Fig. 2). The 16S rRNA analysis thus
leaves little doubt that the novel strain belongs to the genus
Geodermatophilus and forms a species of its own. However,
the degree of 16S rRNA gene sequence difference of strain
CF9/1/1T from the type strain of G. arenarius (which is also
the sister group of the novel strain in Fig. 2) indicated the
need to prove the genomic distinctness of the type strain
representing the novel species by DNA–DNA hybridizations. Strain CF9/1/1T displayed a DNA–DNA relatedness
of 34.3±0.7 % with G. arenarius, this value being far below
the threshold value of 70 % recommended by Wayne et al.
(1987) for a decision on the species status of novel strains.
The Greengenes analysis indicated that sequences of this taxon
have not been detected as yet in environmental samples.
Fig. 1. Scanning electron micrograph showing strain CF9/1/1T
grown on glucose-yeast-malt medium (DSMZ medium 65, GYM)
for 4 days at 28 6C. Bar, 2mm.
2256
Several phenotypic characteristics apart from the phylogenetic analysis based on 16S rRNA gene sequences also
support the distinctiveness of strain CF9/1/1T from all
other species of the genus Geodermatophilus (see Table 1).
Based on the phenotypic and genotypic data presented
above, we propose that strain CF9/1/1T represents a novel
species within the genus Geodermatophilus, with the name
Geodermatophilus telluris sp. nov.
Downloaded from www.microbiologyresearch.org by
International Journal of Systematic and Evolutionary Microbiology 63
IP: 88.99.165.207
On: Fri, 16 Jun 2017 04:23:46
http://ijs.sgmjournals.org
Table 1. Differential phenotypic characteristics of strain CF9/1/1T and the type strains of the other species of the genus Geodermatophilus
Strains: 1, G. telluris sp. nov. CF9/1/1T (5DSM 45421T); 2, G. obscurus G-20T (5DSM 43160T); 3, G. ruber CPCC 201356T (5DSM 45317T); 4, G. nigrescens YIM 75980T (5DSM 45408T); 5, G.
arenarius CF5/4T (5DSM 45418T); 6, G. siccatus CF6/1T (5DSM 45419T). All data are from this study. +, Positive reaction; 2, negative reaction; +/2, ambiguous; MK, menaquinones. i-, isobranched, ai-, anteiso-branched; DPG, diphosphatidylglycerol; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PC, phosphatidylcholine; PI, phosphatidylinositol; PL, unknown
phospholipid; PN, unknown aminophospholipid; PGL, unknown phosphoglycolipid.
Characteristic
Colony colour on GYM
Colony surface on GYM
Nitrate reduction
Degradation of:
Starch
Growth at
pH 5
Utilization of:
Gentiobiose
D-Salicin
L-Fucose
L-Rhamnose
Inosine
D-Sorbitol
D-Arabitol
myo-Inositol
Glycerol
L-Arginine
Pectin
Quinic acid
Oxidase activity
Catalase activity
Predominant menaquinone(s)*
Major fatty acidsD
2
3
4
5
6
Black
Dry
2
Black
Dry
2
Light-red, red
Moist
2
Light-red, black
Moist
+
Light-red, brown
Moist
2
Light-red, black
Moist
+
+
+
2
+
+
+
2
+
+
2
+
2
2
+
2
+
2
+
+
2
+
+
+
+
2
2
MK-9(H4)
+/2
+/2
+/2
2
2
+
+
+
+
2
+
+
2
+
MK-9(H4), MK-9(H2),
two MK
DPG, PE, PG, PC, PI
+
2
+
2
+
2
2
2
2
2
2
+
+
+
MK-9(H4)
+/2
+
+/2
+
+/2
2
+/2
2
2
2
+
2
2
+
MK-9(H4)
DPG, PE, PG, PC,
PI, PL, PGL
i-C15 : 0, i-C16 : 0,
C17 : 1v8c, ai-C15 : 0
DPG, PE, PG,
PC, PI
i-C15 : 0, i-C16 : 0
+
+
2
+
2
2
2
+
+
2
2
2
2
+
MK-9(H4), MK-9(H0),
MK-8(H4)
DPG, PE, PG, PC, PI
2
2
2
2
2
+
+
+
+
+
+
+
2
+
MK-9(H4), MK-9(H0),
MK-8(H4)
DPG, PE, PG, PC, PI
i-C15 : 0, i-C16 : 0
i-C15 : 0, i-C16 : 0,
C17 : 1v8c
DPG, PE, PG, PC,
PI, PN
i-C15 : 0, i-C16 : 0
i-C15 : 0, i-C16 : 0,
C17 : 1v8c
*Only components with ¢5 % peak area ratio are shown.
DOnly components making up ¢10 % peak area ratio are shown.
2257
Downloaded from www.microbiologyresearch.org by
IP: 88.99.165.207
On: Fri, 16 Jun 2017 04:23:46
Geodermatophilus telluris sp. nov.
Polar lipids
1
M. C. Montero-Calasanz and others
Geodermatophilus telluris CF9/1/1T (HE815469)
Geodermatophilus
arenarius DSM 45418T (HE654547)
0.006
-/67
Geodermatophilus nigrescens DSM 45408T (JN656711)
96/77
Geodermatophilus siccatus DSM 45419T (HE654548)
100/97
Geodermatophilus obscurus DSM 43160T (X92356)
Geodermatophilus
ruber DSM 45317T (EU438905)
100/100
Blastococcus saxobsidens DSM 44509T (FN600641)
85/88
Blastococcus aggregatus DSM 4725T (L40614)
66/81
Blastococcus jejuensis DSM 19597T (DQ200983)
Modestobacter marinus DSM 45201T (EU181225)
68/70
100/100
Modestobacter versicolor DSM 16678T (AJ871304)
Modestobacter multiseptatus DSM 44406T (Y18646)
100/99
Description of Geodermatophilus telluris sp. nov.
Geodermatophilus telluris (tel.lu9ris. L. gen. n. telluris of the
soil or earth, referring to the source of organism).
Colonies are black-coloured, multiloculated, of irregular
shape, with a dry surface and an irregular margin. Cells are
Gram-positive, catalase and oxidase-negative. No diffusible
pigments are produced on any medium tested. Utilizes
dextrin, maltose, trehalose, cellobiose, sucrose, turanose, Dsalicin, a-D-glucose, D-mannose, D-fructose, D-galactose, Lrhamnose, L-serine, D-arabitol, D-sorbitol, D-mannitol,
glycerol, L-arginine, pectin, D-gluconic acid, a-ketobutyric
acid, p-hydroxyphenylacetic acid, bromosuccinic acid, Llactic acid, acetic acid, propionic acid, L-glutamic acid,
tween 40, quinic acid, D-saccharic acid, methyl pyruvate, camino-butyric acid, sodium lactate, potassium tellurite,
a,b-hydroxybutyric acid and DL-malic acid as sole carbon
source for energy and growth, but not a-lactose, b-methylD-galactoside, N-acetyl-D-glucosamine, N-acetyl-b-D-mannosamine, N-acetyl-D-galactosamine, 3-O-methyl-glucose,
N-acetyl neuraminic acid, a-ketoglutaric acid, glucuronamide inosine, DL-fucose, gentiobiose, fusidic acid, stachyose, raffinose, melibiose, D-serine, myo-inositol, D-glucose
-6-phosphate, D-fructose-6-phosphate, D-aspartic acid,
glycyl-L-proline, L-alanine, L-histidine, L-pyroglutamic
acid, formic acid, D-galacturonic acid, L-galactonic acidc-lactone, N-acetyl neuraminic acid, D-glucuronic acid, Dlactic acid methyl ester, mucic acid and citric acid. Acid is
produced from L-arginine, L-glutamic acid, c-aminobutyric acid and L-serine, which can be used as sole
nitrogen sources, but not from glycyl-L-proline, L-alanine,
L-histidine, L-pyroglutamic acid, D-serine, inosine, Nacetyl-D-glucosamine, N-acetyl-b-D-mannosamine, Nacetyl-D-galactosamine and D-aspartic acid. Positive for
aesculin and starch degradation but negative for the
reduction of nitrate and denitrification, gelatin hydrolysis,
indole production and casein, tyrosine, xanthine and
hypoxanthine degradation. Tests for alkaline phosphatase,
esterase lipase (C8), esterase (C4), valine arylamidase,
leucine arylamidase, a,b-glucosidase, acid phosphatase and
naphthol-AS-BI-phosphohydrolase are positive. Tests are
negative for lipase (C14), urease, cystine arylamidase,
trypsin, a-chymotrypsin, a-galactosidase, b-galactosidase,
b-glucuronidase, N-acetyl-b-glucosamidase, a-mannosidase
and a-fucosidase. NaCl tolerance ranges from 0 to 4 %
2258
Fig. 2. Maximum-likelihood phylogenetic tree,
inferred from 16S rRNA gene sequences,
showing the phylogenetic position of strain
CF9/1/1T relative to type strains within the
family Geodermatophilaceae. The branches
are scaled in terms of the expected number
of substitutions per site. Support values from
maximum-likelihood (left) and maximum-parsimony (right) bootstrapping are shown above
the branches if equal to or larger than 60 %.
(w/v). Cell growth temperature and pH ranges are from 15
to 40 uC and pH 6.0 to 8.5, respectively. The peptidoglycan in the cell wall contains meso-diaminopimelic acid
as a diamino acid, with galactose as a diagnostic sugar
compound. The predominant menaquinone is MK-9(H4).
The main phospholipids are diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and an unknown amino-phospholipid as well as a
trace of phosphatidyglycerol. Cellular fatty acids consist
mainly of branched-chain saturated acids: iso-C16 : 0 and
iso-C15 : 0.
The type strain, CF9/1/1T (5DSM 45421T5CCUG 62764T),
was isolated in 2007 from sand of the Saharan desert
collected near Vers Ourba, Republic of Chad. The type strain
has a genomic DNA G+C content of 75.4 mol%.
Acknowledgements
We would like to gratefully acknowledge the help of Agathe Stricker
of the International Committee of the Red Cross in Geneva,
Switzerland, for organizing the collection of the sand samples from
which strain 9/1/1T was isolated. Jocelyne Favet, Arlette Cattaneo and
William J. Broughton of the Laboratoire de Biologie Moléculaire de
Plantes Supérieures (University of Geneva, Switzerland) are acknowledged for their contribution to the isolation of the strain, Bettina
Sträubler and Birgit Grün for their help in DNA–DNA hybridization
analysis and Brian J. Tindall (DSMZ, Braunschweig) for his guidance
in chemotaxonomic analyses. M. C. M.-C. is the recipient of a
postdoctoral contract from European Social Fund Operational
Programme (2007–2013) for Andalusia.
References
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J.
(1990). Basic local alignment search tool. J Mol Biol 215, 403–410.
Castresana, J. (2000). Selection of conserved blocks from multiple
alignments for their use in phylogenetic analysis. Mol Biol Evol 17,
540–552.
Collins, M. D., Pirouz, T., Goodfellow, M. & Minnikin, D. E. (1977).
Distribution of menaquinones in actinomycetes and corynebacteria.
J Gen Microbiol 100, 221–230.
De Ley, J., Cattoir, H. & Reynaerts, A. (1970). The quantitative
measurement of DNA hybridization from renaturation rates. Eur J
Biochem 12, 133–142.
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L.,
Keller, K., Huber, T., Dalevi, D., Hu, P. & Andersen, G. L. (2006).
Downloaded from www.microbiologyresearch.org by
International Journal of Systematic and Evolutionary Microbiology 63
IP: 88.99.165.207
On: Fri, 16 Jun 2017 04:23:46
Geodermatophilus telluris sp. nov.
Greengenes, a chimera-checked 16S rRNA gene database and
workbench compatible with ARB. Appl Environ Microbiol 72, 5069–
5072.
Geodermatophilus siccatus sp. nov., isolated from arid sand of the
Saharan desert in Chad. Antonie van Leeuwenhoek 103, 449–456.
Euzéby, J. (2012). Geodermatophilus nigrescens sp. nov. In List of new
Nie, G. X., Ming, H., Li, S., Zhou, E. M., Cheng, J., Yu, T. T., Zhang, J.,
Feng, H. G., Tang, S. K. & Li, W. J. (2012). Geodermatophilus nigrescens
names and new combinations previously effectively, but not validly
published, list no. 147. Int J Syst Evol Microbiol 62, 2045–2047.
sp. nov., isolated from a dry-hot valley. Antonie van Leeuwenhoek 101,
811–817.
Euzéby, J. (2013a). Geodermatophilus arenarius sp. nov. In List of new
Normand, P. (2006). Geodermatophilaceae fam. nov., a formal
description. Int J Syst Evol Microbiol 56, 2277–2278.
names and new combinations previously effectively, but not validly
published, list no. 150. Int J Syst Evol Microbiol 63, 797–798.
Euzéby, J. (2013b). Geodermatophilus siccatus sp. nov. In List of new
Normand, P., Orso, S., Cournoyer, B., Jeannin, P., Chapelon, C.,
Dawson, J., Evtushenko, L. & Misra, A. K. (1996). Molecular
names and new combinations previously effectively, but not validly
published, list no. 151. Int J Syst Evol Microbiol 62, 1577–1580.
phylogeny of the genus Frankia and related genera and emendation
of the family Frankiaceae. Int J Syst Bacteriol 46, 1–9.
Giongo, A., Favet, J., Lapanje, A., Gano, K. A., Kennedy, S., DavisRichardson, A. G., Brown, C., Beck, A., Farmerie, W. G. & other
authors (2013). Microbial hitchhikers on intercontinental dust: high-
Pattengale, N. D., Alipour, M., Bininda-Emonds, O. R. P., Moret,
B. M. E. & Stamatakis, A. (2009). How many bootstrap replicates
throughput sequencing to catalogue microbes in small sand samples.
Aerobiologia. 29, 71–84.
Pelczar, M. J., Jr (editor) (1957). Manual of Microbiological Methods.
Gordon, R. E. & Smith, M. M. (1955). Proposed group of characters for
the separation of Streptomyces and Nocardia. J Bacteriol 69, 147–150.
Gregersen, T. (1978). Rapid method for distinction of Gram-negative
from positive bacteria. Appl Microbiol Biotechnol 5, 123–127.
Hess, P. N. & De Moraes Russo, C. A. (2007). An empirical test of the
midpoint rooting method. Biol J Linn Soc Lond 92, 669–674.
Huss, V. A. R., Festl, H. & Schleifer, K. H. (1983). Studies on the
spectrophotometric determination of DNA hybridization from
renaturation rates. Syst Appl Microbiol 4, 184–192.
Ivanova, N., Sikorski, J., Jando, M., Munk, C., Lapidus, A., Glavina Del
Rio, T., Copeland, A., Tice, H., Cheng, J. F. & other authors (2010).
are necessary? Lect Notes Comput Sci 5541, 184–200.
New York, NY: McGraw-Hill Book Co.
Rainey, F. A., Ward-Rainey, N., Kroppenstedt, R. M. & Stackebrandt,
E. (1996). The genus Nocardiopsis represents a phylogenetically
coherent taxon and a distinct actinomycete lineage: proposal of
Nocardiopsiaceae fam. nov. Int J Syst Bacteriol 46, 1088–1092.
Rice, P., Longden, I. & Bleasby, A. (2000). EMBOSS: the European
Molecular Biology Open Software Suite. Trends Genet 16, 276–277.
Sasser, M. (1990). Identification of bacteria by gas chromatography
of cellular fatty acids. USFCC Newsl 20, 16.
Schleifer, K. H. & Kandler, O. (1972). Peptidoglycan types of bacterial
cell walls and their taxonomic implications. Bacteriol Rev 36, 407–477.
Complete genome sequence of Geodermatophilus obscurus type strain
(G-20). Stand Genomic Sci 2, 158–167.
Shirling, E. B. & Gottlieb, D. (1966). Methods for characterization of
Kroppenstedt, R. M. (1982). Separation of bacterial menaquinones by
Stamatakis, A., Hoover, P. & Rougemont, J. (2008). A rapid
HPLC using reverse phase (RP18) and a silver loaded ion exchanger.
J Liq Chromatogr 5, 2359–2367.
bootstrap algorithm for the RAxML Web servers. Syst Biol 57, 758–
771.
Kroppenstedt, R. M. & Goodfellow, M. (2006). The family
Staneck, J. L. & Roberts, G. D. (1974). Simplified approach to
Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillispora
and Thermomonospora. In The Prokaryotes, Archaea and Bacteria:
Firmicutes, Actinomycetes, 3rd edn, vol. 3, pp. 682–724. Edited by
M. Dworkin, S. Falkow, K. H. Schleifer & E. Stackebrandt. New York:
Springer.
identification of aerobic actinomycetes by thin-layer chromatography.
Appl Microbiol 28, 226–231.
Lechevalier, M. P. & Lechevalier, H. A. (1970). Chemical composition
as a criterion in the classification of aerobic actinomycetes. Int J Syst
Bacteriol 20, 435–443.
Lee, C., Grasso, C. & Sharlow, M. F. (2002). Multiple sequence
alignment using partial order graphs. Bioinformatics 18, 452–464.
Luedemann, G. M. (1968). Geodermatophilus, a new genus of the
Streptomyces species. Int J Syst Bacteriol 16, 313–340.
PAUP*: Phylogenetic analysis using parsimony
(and other methods), version 4. Sunderland, MA: Sinauer Associates.
Swofford, D. L. (2002).
Tindall, B. J., Sikorski, J., Smibert, R. A. & Krieg, N. R. (2007).
Phenotypic characterization and the principles of comparative
systematics. In Methods for General and Molecular Microbiology, pp.
330–393. Edited by T. J. Beveridge, J. A. Breznak, G. A. Marzluf,
T. M. Schmidt & L. R. Snyder. Washington: American Society for
Microbiology.
Dermatophilaceae (Actinomycetales). J Bacteriol 96, 1848–1858.
Urzı̀, C., Brusetti, L., Salamone, P., Sorlini, C., Stackebrandt, E. &
Daffonchio, D. (2001). Biodiversity of Geodermatophilaceae isolated
Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise
from altered stones and monuments in the Mediterranean basin.
Environ Microbiol 3, 471–479.
measurement of the G + C content of deoxyribonucleic acid by highperformance liquid chromatography. Int J Syst Bacteriol 39, 159–167.
Vaas, L. A. I., Sikorski, J., Michael, V., Göker, M. & Klenk, H. P. (2012).
Minnikin, D. E., O’Donnell, A. G., Goodfellow, M., Alderson, G.,
Athalye, M., Schaal, K. & Parlett, J. H. (1984). An integrated
Visualization and curve-parameter estimation strategies for efficient
exploration of phenotype microarray kinetics. PLoS ONE 7, e34846.
procedure for the extraction of bacterial isoprenoid quinones and
polar lipids. J Microbiol Methods 2, 233–241.
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
Montero-Calasanz, M. C., Göker, M., Pötter, G., Rohde, M., Spröer,
C., Schumann, P., Gorbushina, A. A. & Klenk, H. P. (2012).
Geodermatophilus arenarius sp. nov., a xerophilic actinomycete
isolated from Saharan desert sand in Chad. Extremophiles 16, 903–
909.
Montero-Calasanz, M. C., Göker, M., Rohde, M., Schumann, P.,
Pötter, G., Spröer, C., Gorbushina, A. A. & Klenk, H. P. (2013).
http://ijs.sgmjournals.org
Bacteriology. Report of the ad hoc committee on reconciliation of
approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–
464.
Zhang, Y.-Q., Chen, J., Liu, H.-Y., Zhang, Y.-Q., Li, W.-J. & Yu, L.-Y.
(2011). Geodermatophilus ruber sp. nov., isolated from rhizosphere
soil of a medical plant. Int J Syst Evol Microbiol 61, 190–193.
Downloaded from www.microbiologyresearch.org by
IP: 88.99.165.207
On: Fri, 16 Jun 2017 04:23:46
2259