IJSEM Papers in Press. Published February 25, 2015 as doi:10.1099/ijs.0.000149
International Journal of Systematic and Evolutionary Microbiology Exiguobacterium enclense sp nov., isolated from sediment sample --Manuscript Draft-Manuscript Number:
IJSEM-D-14-00097R3
Full Title:
Exiguobacterium enclense sp nov., isolated from sediment sample
Short Title:
Exiguobacterium enclense sp nov.,
Article Type:
Note
Section/Category:
New taxa - Firmicutes and related organisms
Corresponding Author:
Syed G Dastager, Ph.D CSIR-National Chemical Laboratory Pune, Maharastra INDIA
First Author:
Syed G Dastager, Ph.D
Order of Authors:
Syed G Dastager, Ph.D Rahul M Mawlankar, M.Sc Vidya V. Sonalkar, M.Sc Meghana N. Thorat, M.Sc Poonam Mual, M.Sc Ashish Verma, M.Sc Srinivasan Krishnamurthi, Ph.D Shu-Kun Tang, Ph.D Wen-Jun Li, Ph.D
Manuscript Region of Origin:
INDIA
Abstract:
Abstract A Gram-stain positve marine bacterium, designated NIO-1109T, was isolated from a marine sediment sample from the Chorao Island Goa, India. Phenotypic and chemotaxonomic characteristics and data from a phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1109T was related to the genus Exiguobacterium. Strain NIO-1109T exhibited >98.0% gene sequence similarity with respect to Exiguobacterium acetylicum DSM 20416T (99.0%), and Exiguobacterium indicum IAM 15368T (98.6 %), other species were showing 98.0% gene sequence similarity with respect to
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Exiguobacterium indicum IAM 15368T (99.5%), and Exiguobacterium acetylicum DSM
40
20416T (99.1%), other species were showing 5%) of strain NIO-1109T were iso-C17:0 (21.8 %), iso-C15:0 (13.0
154
%), iso-C13:0 (12.8 %), C16:0 (11.6 %), C18:0 (8.3 %), and anteiso-C13:0 (7.3%). The complete
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cellular fatty acid composition is given in species description and in Table 2. The peptidoglycan
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of the strain contain L-lysine as the diagnostic diamino acid. The major menaquinone was
157
identified as MK-7 (91.3 %) where as MK-8 (8.4 %) occurs in minor amounts. The polar lipids
158
detected in strain NIO-1109T were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG),
159
and phosphatidylethanolamine (PE) (Online Supplementary Fig. S2).
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The genomic DNA G+C content of the strain NIO-1109T was 46.9 mol%. The
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determined DNA–DNA relatedness value between strain NIO-1109T with Exiguobacterium
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indicum LMG 23471T and Exiguobacterium acetylicum DSM 20416T were 37.0 (±3.2%) and
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33.0 (±2.0%) respectively (with standard deviations in triplicate; Table. 3). DNA hybridization
164
results indicated that, values of hybridizations were well below the 70% cutoff point for
165
recognition of novel genomic species (Wayne et al., 1987), thus suggesting the strain NIO-1109T
166
should be considered as a new species of the genus Exiguobacterium.
167
Therefore, based on phenotypic, chemotaxonomic and phylogenetic analysis strain NIO-
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1109T distinguished from its closest phylogenetic relatives (Table.1). Therefore, strain NIO-
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1109T represents a novel species of the genus Exiguobacterium, for which the name
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Exiguobacterium enclensis sp. nov. is proposed.
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Description of Exiguobacterium enclense sp nov
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Exiguobacterium enclense (en.clen'se. N.L. neut. adj. enclense arbitrary name formed from NCL,
173
the acronym for the National Chemical laboratory, India, where taxonomic studies on this
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species were performed).
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The cells are Gram-positive, motile, non-spore forming rods to cocobacilli. Colonies grown on
176
TSA medium are 1.2–1.8 mm in diameter, yellowish orange, convex with entire margin. Growth
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is observed under aerobic condition between 25 and 42° C (optimum, 28±2°C) and between pH
178
6.0 and 12.0 (optimum, pH 7.0); can tolerate up to 15% NaCl (w/v). Positive for citrate
179
utilization, weakly positive for β-galactosidase, and urease. Negative for lysine and ornithine
180
decarboxylase, indole production, methyl red, Voges-Proskauer’s test, phenyl deamination,
181
hydrogen sulphide (H2S), and aesculin hydrolysis. Strain NIO-1009T negative for starch and urea
182
hydrolysis and positive for Tweens 20, 40, 60 or 80. Adonitol, D-arabinose, L-arabinose,
183
cellobiose, dextrose, fructose, galactose, glucose, glycerol, inulin, maltose, mannitol, melezitose,
184
raffinose, saccharose, salicin, sodium gluconate, sucrose, trehalose and xylitol are utilized as a
185
sole carbon sources, but arabitol, dulicitol, erythritol, lactose, malonate, mannose, melibiose, α-
186
methyl-D-glucoside, α-methyl-D-mannoside, rhamnose, sorbitol, sorbose, and xylose are not
187
utilized. Nitrate is not reduced to nitrite. Acid is produced from D-arabinose, cellobiose,
188
dextrose, fructose, glycerol, inulin, mannitol, maltose, salicin, sucrose and trehalose. API ZYM
189
enzyme assay showed positive for alkaline phosphatase, esterase (C4), esterase lipase (C8), acid
190
phosphatase, naphthol-AS-BI-phosphohydrolase, β-galactosidase, and α-glucosidase, weakly
191
positive for α-galactosidase, β-glucuronidase, and β-glucosidase. Negative for lipase (C14),
192
leucine arylamidase, valine arylamidase, cystine arylamidase, trypsin, α-chymotrypsin, N-acetyl-
193
β-glucosaminidase, α-mannosidase and α-fucosidase. The respiratory quinones are MK-7 and
194
MK-8. The cell-wall peptidoglycan is of the Lys–Gly type. The major polar lipids,
195
phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine are present. The
196
fatty acids (≥1.0%) present are iso-C12:0, iso-C13:0, anteiso-C13:0, iso-C14:0, iso-C15:0, anteiso-C15:0,
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iso-C16:0, C16:0, iso-C17:0, anteiso-C17:0, C18:0, iso-C19:0, C16:1 w7c/w6c, C18:1 w7c/w6c, and C16:0
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10-methyl/iso-C17:1w9c. The DNA G+C content is 46.9 mol%. The type strain, NIO-1109T
199
(=NCIM 5457T=DSM 25128T), isolated from marine sediment sample in Chorao Island, Goa,
200
India.
201 202
Acknowledgement
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Author SGD acknowledges the Director, CSIR-NCL and Council for Scientific and Industrial
204
Research (CSIR), New Delhi for financial support.
205 206 207 208 209 210 211 212 213 214 215 216 217
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Table 1. Phenotypic characteristics that differentiate strain NIO-1109T from its phylogenetic neighbours in the genus Exiguobacterium. All data were generated from present study except otherwise indicated. All of the strains shown are motile, Gram-positive, rod-shaped, do not form endospores and yellowish orange in colour. All are positve for lipase, citrate utilization and cellobiose, negative for urease, H2S production, and the indole test. Characteristic
336 337 338
E. enclense NIO-1109T
E. acetylicum DSM 20416T
E. indicum LMG 23471T
Colony morphology Size (mm) 2-4 2-5 2-4 Shape Round Irregular Round Growth temperature (°C) 5 – – + 37 + W – Optimum growth temp(°C) 28±2.0 37 30 Gelatinase – + – Ornithine decarboxylase – + + Voges–Proskauer test – + + Aesculin hydrolysis – + – Starch hydrolysis – + – Lysine decarboxylase – – + Nitrate reduction – – + Acid produced from D-Glucose, sucrose, + + – D-fructose, D-trehalose, maltose, Inulin + – – D-Mannose – + – D-Cellobiose + + – D-Adonitol – + – Carbon-source utilization D-Galactose + – + L-Rhamnose, L-melibiose, + – + D-xylose L-Xylose – – + D-Mannitol + + – D-Raffinose + – + D-sorbitol, dulcitol – – + DNA G+C content (mol %) 46.9 47.0* 48.0* Quinone(s) MK-7, MK-8 MK-7* MK-7, MK-8* Polar lipids PG, DPG, PE DPG, PS* PG, DPG, PE* Source of Isolation Marine sediment Creamery waste Glacial water DPG, Diphosphatidylglycerol; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PS, phosphatidylserine. * Data from Preeti and Shivaji (2006).
339 340
Table.2. Fatty acid composition of Exiguobacterium NIO-1109T. Fatty acids C11:0 iso C12:0 iso C12:0 C13:0 iso C13:0 anteiso C14:0 iso C14:0 C15:0 iso C15:0 anteiso C15:0 C16:1 w7c alcohol C16:1 iso H C16:0 iso C16:1 w11c C16:0 C17:1 anteiso w9c C17:0 iso C17:0 anteiso C17:0 C18:0 iso C18:1 w9c C18:0 C19:0 iso C19:0 anteiso C20:0 *Summed Feature 1 *Summed Feature 3 *Summed Feature 4 *Summed Feature 8 *Summed Feature 9
341 342 343 344 345 346 347
Percent profile (%) 0.42 1.49 0.36 12.81 7.38 1.74 0.93 13.09 3.28 ---0.20 0.17 2.21 0.97 11.60 0.18 21.87 2.67 0.70 0.76 0.92 8.38 1.06 0.23 0.26 0.26 2.28 0.34 1.65 1.79
*Summed features represent groups of two or three fatty acids that could not be separated by GLC with the MIDI system. Summed feature 1 contained C15:1 iso H/C13:0 3OH, summed feature 3 contained C16:1 w7c/ w6c, summed feature 4 contained C17:1 iso I/anteiso B, summed future 8 contained C18:1 w6c/w7c and summed feature 9 contained C16:0 10-methyl/C17:1 iso w9c.
348 349
Table 3. DNA-DNA relatedness between strain NIO-1109T and Exiguobacterium acetylicum DSM 20416T, and Exiguobacterium indicum LMG 23471T.
350 351 352 353
A: NIO-1109T LMG 23471T.
The two DNAs for DNA-DNA hybridization A and B A and C
B: Exiguobacterium acetylicum DSM 20416T C: Exiguobacterium indicum
The result of DNA-DNA hybridization (%)
The values of three replicates (%)
The DNA as probe
The DNA immobilized
B
A
33.27
33.50
33.26
33.34±2.8
A
B
33.19
33.16
33.08
33.14±3.0
A
C
36.49
37.77
36.82
37.02±2.2
C
A
36.37
37.35
37.27
36.99±2.0
1
2
354 355 356 357 358 359 360 361 362 363 364 365 366 367 368
17
3
Mean 33.24±3.0 37.00±2.0
369
Figure Legends
370 371 372 373 374 375
Fig. 1. Phylogenetic position based on neighbour-joining tree with nearly complete 16S rRNA (1415nt) gene sequences showing NIO-1109T and of the genus Exiguobacterium. Astrikes indicate that the corresponding nodes (groupings) are also recovered in Fitch–Margoliash, maximum-parsimony and maximum-likelihood trees. Bootstrap values (>70 %; 1000 resamplings) are given at branch points. Bacillus idriensis SMC 4352-2T (AY904033) used as outgroup. Bar, 0.01 nucleotide substitutions per position.
376 377 378
18
Figure Click here to download Figure: Figure 1.doc
Fig. 1.
T
100* Exiguobacterium antarcticum DSM 14480 (DQ019164) T
Exiguobacterium soli DVS3Y (AY864633) T
Exiguobacterium undae DSM 14481 (DQ019165)
90*
T
Exiguobacterium sibiricum 255-15 (CP001022)
93* 99*
T
Exiguobacterium artemiae 9AN (AM072763) T
100*
Exiguobacterium oxidotolerans T-2-2 (AB105164) T
Exiguobacterium acetylicum NCIMB 9889 (X70313) 99*
T
Exiguobacterium enclense NIO-1109 (JF893462) T
98* Exiguobacterium indicum HHS31 (AJ846291) T
100*
Exiguobacterium mexicanum 8N (AM072764) T
Exiguobacterium aurantiacum DSM 6208 (DQ019166) T
Exiguobacterium marinum TF-80 (AY594266)
100*
T
97* 75*
Exiguobacterium aestuarii TF-16 (AY594264) T
Exiguobacterium profundum 10C (AY818050) T
Bacillus idriensis SMC 4352-2 (AY904033)
0.01
Supplementary Material Files Click here to download Supplementary Material Files: Supplimentory Figure, Table .pdf