| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Northwest Institute of Plateau Biology, CAS, Xining, Qinghai, 810008, People's Republic of China
2 The Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
3 Graduate School of the Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
Correspondence
Li-Hua Xu
wjli{at}ynu.edu.cn or
lihxu{at}ynu.edu.cn
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
8c (9·37 %). The G+C content of the DNA was 70 mol%. Phylogenetic analysis and signature nucleotide data based on 16S rRNA gene sequences showed that strain YIM 002T is distinct from all recognized genera of the family Nocardioidaceae in the suborder Propionibacterineae. On the basis of the phenotypic and genotypic characteristics, it is proposed that isolate YIM 002T be classified as a novel species in a new genus, Jiangella gansuensis gen. nov., sp. nov. The type strain is YIM 002T (=DSM 44835T=CCTCC AA 204001T=KCTC 19044T).
Published online ahead of print on 29 October 2004 as DOI 10.1099/ijs.0.63353-0.
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain YIM 002T is AY631071.
Scanning electron micrographs of substrate and aerial mycelia of strain YIM 002T are available as supplementary material in IJSEM Online.
These authors contributed equally to this work. 
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
to accommodate two genera, Nocardioides Prauser 1976 and Pimelobacter Suzuki and Komagata 1983. Collins et al. (1989) transferred the Pimelobacter species to the genera Terrabacter and Nocardioides. Currently, the family Nocardioidaceae comprises five genera: Nocardioides (Prauser, 1976), Aeromicrobium (Miller et al., 1991), Kribbella (Park et al., 1999; Sohn et al., 2003), Marmoricola (Urzì et al., 2000) and Actinopolymorpha (Wang et al., 2001). During a project to screen bioactive actinomycete strains from soils, one actinomycete strain, designated YIM 002T, was isolated from a desert soil sample collected in Sunan county, Gansu Province, north-west China. It contained LL-2,6-diaminopimelic acid (LL-A2pm) as the diagnostic amino acid in the peptidoglycan and formed well-differentiated aerial and substrate mycelia; the substrate mycelia had a tendency to fragment in the early stages of growth. In order to determine the taxonomic and phylogenetic position of this organism, we examined its morphological, physiological and biochemical characteristics and analysed its chemotaxonomic compositions and 16S rRNA gene sequence. The results indicated that strain YIM 002T should be placed in a novel species of a new genus, for which the name Jiangella gansuensis gen. nov., sp. nov. is proposed.
Strain YIM 002T was isolated from the soil sample by using the dilution plating method. The medium used for selective isolation was glycerol–asparagine agar (ISP5 medium; Shirling & Gottlieb, 1966), which was incubated at 28 °C for about 2 weeks. Following purification, the organism was maintained on yeast extract–malt extract agar (ISP2 medium; Shirling & Gottlieb, 1966) at 28 °C.
Strain YIM 002T was grown on ISP2, ISP3, ISP4, ISP5, nutrient agar and Czapek's agar plates at 28 °C. Colour determination was performed with colour chips from the ISCC-NBS Colour Charts Standard Samples no. 2106 (Kelly, 1964). Morphological characteristics were examined by light microscopy with a model BH-2 microscope (Olympus) and scanning electron microscopy with a JEOL model JSM5600LV. Morphological features were observed on ISP2 medium at 28 °C. Growth was tested over a range of temperatures (4–45 °C) and pH values (6·0–12·0). Strain YIM 002T grew well on ISP2 agar but only slowly on the other media tested. Substrate mycelium of YIM 002T fragmented into short or elongated rods; aerial mycelium developed well on ISP2 agar plates (see Supplementary Fig. A in IJSEM Online). The colour of the colonies was white on ISP3 medium and yellow–white on ISP2, ISP4 and ISP5 media, nutrient agar and Czapek's agar plates. No diffusible pigment was produced on any of the media tested. The optimal temperature and pH for growth were 28 °C and 7·0–8·0, respectively.
Physiological and biochemical characteristics of strain YIM 002T are given in the genus and species descriptions below. All tests were performed at 28 °C and properties were recorded after 7, 14, 20 and 30 days, except for the nitrate reduction test, which was recorded after 1, 3 and 5 days. Carbon source utilization and sugar fermentation tests were carried out according to the method of Kämpfer et al. (1991).
Procedures for identification of cell-wall amino acids and sugars followed those described by Stanek & Roberts (1974). Polar lipids were extracted, examined by two-dimensional TLC and identified using the procedures of Minnikin et al. (1984). Menaquinones were isolated using the methods of Minnikin et al. (1984) and separated by HPLC (Kroppenstedt, 1982). Cellular fatty acid composition was determined as described by Sasser (1990) using the Microbial Identification System (MIDI, Inc.). Amino acids in the peptidoglycan layer of strain YIM 002T were LL-A2pm, alanine, glycine and glutamic acid, indicating a type I wall chemotype according to the classification of Lechevalier & Lechevalier (1970). Cell-wall sugars were glucose and ribose. The predominant menaquinone was MK-9(H4). Phospholipids of strain YIM 002T present were phosphatidylinositol mannosides, phosphatidylinositol and diphosphatidylglycerol. The cellular fatty acid composition of strain YIM 002T is given in the genus and species descriptions.
Chromosomal DNA from strain YIM 002T was prepared following the method of Marmur (1961). The G+C content of the DNA was determined using the thermal denaturation method of Marmur & Doty (1962); a value of 70 mol% was measured.
Amplification of the 16S rRNA gene sequence was performed as described by Cui et al. (2001). Database searching was carried out using the BLAST program. The 16S rRNA gene sequence of strain YIM 002T and previously published sequences of reference actinomycetes were aligned using the CLUSTAL X program (Thompson et al., 1997). A phylogenetic tree was constructed using the neighbour-joining method of Saitou & Nei (1987) from Knuc values (Kimura, 1980, 1983). The reliability of the phylogenetic tree was evaluated using the bootstrap resampling method of Felsenstein (1985) with 1000 replicates.
The almost complete 16S rRNA gene sequence (1497 nt) of strain YIM 002T was obtained (Escherichia coli numbering 29–1542), and BLAST search comparisons were made against the GenBank/EMBL/DDBJ databases. A sequence of 1466 nt was compared after elimination of all sites for which nucleotides were not determined in any sequences. The phylogenetic tree shown in Fig. 1 includes sequences of representative members of the family Nocardioidaceae.
|
). Strain YIM 002T formed a monophyletic clade with Actinopolymorpha singaporensis at a low nucleotide sequence similarity (92·3 %). The relationship was confirmed in all three tree-making analyses [least-squares (Fitch & Margoliash, 1967) and maximum-likelihood (Felsenstein, 1981) (data not shown) as well as neighbour-joining (Fig. 1)] and by the high bootstrap value (>80 %), based on the neighbour-joining algorithm. The next closest neighbours were Kribbella species, sharing only 91·6–92·3 % 16S rRNA gene sequence similarities. Strain YIM 002T had no more than 92 % sequence similarity to all other taxa within the family Nocardioidaceae.
Additionally, there are significant differences in morphology and chemotaxonomic characteristics between strain YIM 002T and related genera of the family Nocardioidaceae (Table 1). We also compared the nucleotide signatures of strain YIM 002T against those specific to the family Nocardioidaceae (Stackebrandt et al., 1997). The results indicated the presence of most of the specific nucleotide signatures in the sequence of strain YIM 002T, except for variations at some positions (see under the genus description below).
|
Description of Jiangella gen. nov.
Jiangella [Ji.ang.el'la. N.L. fem. dim. n. Jiangella after Cheng-Lin Jiang (1942–), a Chinese microbiologist, in recognition of his work on actinomycete taxonomy].
Strictly aerobic and Gram-positive. Substrate mycelium fragments into short or elongated rods in the early stages of growth. Aerial mycelium differentiates well and no spores are formed. Grow very well on ISP2 medium. Cell wall contains LL-A2pm as the diamino acid in the peptidoglycan. MK-9(H4) is the predominant menaquinone; cell-wall sugars are glucose and ribose. Phosphatidylinositol mannosides, phosphatidylinositol and diphosphatidylglycerol are present. Major cellular fatty acids are anteiso C15 : 0, anteiso C17 : 0, iso C15 : 0, iso C16 : 0 and C17 : 18c. DNA G+C content is 70 mol%. Phylogenetically, the genus is placed in the family Nocardioidaceae. All family-specific nucleotide signatures (Stackebrandt et al., 1997) are present except for a C : G pair at nucleotide positions 370 : 391 instead of G : C, a C : G pair at positions 602 : 636 instead of G : U and a U : U pair at positions 658 : 748 instead of U : A. The type species is Jiangella gansuensis.
Description of Jiangella gansuensis sp. nov.
Jiangella gansuensis (gan.su.en'sis. N.L. fem. adj. gansuensis pertaining to Gansu, a province of north-west China from where the type strain was isolated).
Morphological, chemotaxonomic and general characteristics are as given above for the genus. Colonies are white on ISP3 and yellow–white on ISP2, ISP4 and ISP5 media and nutrient and Czapek's agar plates. No diffusible pigment is produced on these agar plates. Optimal temperature and pH for growth are 28 °C and 7·0–8·0, respectively. Utilizes glucose, fructose, xylose, rhamnose, mannitol, sucrose, inositol, galactose, mannose, mannitol, arabinose, xylitol, melibiose, maltose, lactose, raffinose, cellobiose, dextrin and glycerol as sole carbon sources, but not ribose. Positive for gelatin hydrolysis, urease, milk coagulation and peptonization, but negative for cellulose hydrolysis, production of H2S, starch hydrolysis and nitrate reduction. Fatty acids present are anteiso C15 : 0 (35·92 %), anteiso C17 : 0 (15·84 %), iso C15 : 0 (10·40 %), C17 : 18c (9·37 %), iso C16 : 0 (7·07 %), C17 : 0 (3·39 %), iso C17 : 0 (3·09 %), iso G-C16 : 1 (2·90 %), anteiso A C17 : 1 (2·86 %), C15 : 0 2-OH (2·28 %), iso C14 : 0 2-OH (2·23 %), anteiso A C15 : 1 (1·31 %), C18 : 19c (1·24 %), iso C17 : 19c (1·05 %) and C15 : 0 (1·05 %). DNA G+C content is 70 mol%.
The type strain, YIM 002T (=DSM 44835T=CCTCC AA 204001T=KCTC 19044T), was isolated from a desert soil sample from Gansu Province, China.
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Cui, X. L., Mao, P. H., Tseng, M., Li, W. J., Zhang, L. P., Xu, L. H. & Jiang, C. L. (2001). Streptomonospora salina gen. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 51, 357–363.[Abstract]
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.[CrossRef][Medline]
Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
Fitch, W. M. & Margoliash, E. (1967). Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome c sequences is of general applicability. Science 155, 279–284.
Kämpfer, P., Steiof, M. & Dott, W. (1991). Microbiological characterization of a fuel oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 21, 227–251.
Kelly, K. L. (1964). Inter-Society Color Council – National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors. Washington, DC: US Government Printing Office.
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.[CrossRef][Medline]
Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
Kroppenstedt, R. M. (1982). Separation of bacterial menaquinones by HPLC using reverse phase (RP 18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5, 2359–2387.[CrossRef]
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.
Marmur, J. (1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.
Marmur, J. & Doty, P. (1962). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5, 109–118.[Medline]
Miller, E. S., Woese, C. R. & Brenner, S. (1991). Description of the erythromycin-producing bacterium Arthrobacter sp. strain NRRL B-3381 as Aeromicrobium erythreum gen. nov., sp. nov. Int J Syst Bacteriol 41, 363–368.
Minnikin, D. E. O'Donnell A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. & Parlett, J. H. (1984). An integrated procedure for the extraction of isoprenoid quinines and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef]
Nesterenko, O. A., Kvasnikov, E. I. & Nogina, T. M. (1985). Nocardioidaceae fam. nov., a new family of the order Actinomycetales Buchanan 1917. Mikrobiol Zh 47, 3–12.
O'Donnell, A. G., Goodfellow, M. & Minnikin, D. E. (1982). Lipids in the classification of Nocardioides: reclassification of Arthrobacter simplex (Jensen) Lochhead in the genus Nocardioides (Prauser) emend. O'Donnell et al. as Nocardioides simplex comb. nov. Arch Microbiol 133, 323–329.[CrossRef][Medline]
Park, Y.-H., Yoon, J.-H., Shin, Y. K., Suzuki, K., Kudo, T., Seino, A., Kim, H.-J., Lee, J.-S. & Lee, S. T. (1999). Classification of ‘Nocardioides fulvus’ IFO 14399 and Nocardioides sp. ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov. Int J Syst Bacteriol 49, 743–752.
Prauser, H. (1976). Nocardioides, a new genus of the order Actinomycetales. Int J Syst Bacteriol 26, 58–65.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20, 16.
Shirling, E. B. & Gottlieb, D. (1966). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.
Sohn, K., Hong, S. G., Bae, K. S. & Chun, J. (2003). Transfer of Hongia koreensis Lee et al. 2000 to the genus Kribbella Park et al. 1999 as Kribbella koreensis comb. nov. Int J Syst Evol Microbiol 53, 1005–1007.
Stackebrandt, E., Rainey, F. A. & Ward-Rainey, N. L. (1997). Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47, 479–491.
Stanek, J. L. & Roberts, G. D. (1974). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28, 226–231.[Medline]
Suzuki, K. & Komagata, K. (1983). Pimelobacter gen. nov., a new genus of coryneform bacteria with LL-diaminopimelic acid in the cell wall. J Gen Appl Microbiol 29, 59–71.
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.
Urzì, C., Salamone, P., Schumann, P. & Stackebrandt, E. (2000). Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue. Int J Syst Evol Microbiol 50, 529–536.[Abstract]
Wang, Y. M., Zhang, Z. S., Xu, X. L., Ruan, J. S. & Wang, Y. (2001). Actinopolymorpha singaporensis gen. nov., sp. nov., a novel actinomycete from the tropical rainforest of Singapore. Int J Syst Evol Microbiol 51, 467–473.[Abstract]
This article has been cited by other articles:
|
|
 |
|
  J. Zhang, D. Wu, J. Zhang, Z. Liu, and F. Song Saccharopolyspora shandongensis sp. nov., isolated from wheat-field soil Int J Syst Evol Microbiol, May 1, 2008; 58(5): 1094 - 1099. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. D. Lee Jiangella alkaliphila sp. nov., an actinobacterium isolated from a cave Int J Syst Evol Microbiol, May 1, 2008; 58(5): 1176 - 1179. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. W. Griffin Atmospheric Movement of Microorganisms in Clouds of Desert Dust and Implications for Human Health Clin. Microbiol. Rev., July 1, 2007; 20(3): 459 - 477. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
