Streptomyces baliensis sp. nov., isolated from Balinese soil

(1)

ＮＺＺｊｕｃｾ

ｉｅ

ｔｙ＠

F OR GENERAL

MICROBIOLOGY

International Journal of Systematic and

Evolutionary Microbiology

International Journal of Systematic and Evolutionary Microbiology (IJSEM) is the leading

forum for the publication of new tax a of bacteria and yeasts, and it is the official journal of

record for bacterial names of the International Committee on Systematics of Prokaryotes

(ICSP) of the International Union of Microbiological Societies (IUMS). The current Impact

Factor for the journal is 2.1 12 (2012).

(2)

•.

IJSEM, formerly

International Journal of Systematic Bacteriology

(IJSB), is the official

journal of record for novel prokaryotic tax.a. Now in its 61 st year (before 1966 it was known

as the

International Bulletin of Bacteriological Nomenclature and Taxonomy),

the journal is

the cornerstone of the dynamic field of microbial systematics.

IJSEM publishes papers dealing with all phases of the systematics of prokaryotes, yeasts and

yeast-like organisms, including taxonomy, nomenclature, identification, phylogeny,

evolution, biodiversity, characterization and culture preservation. Its scope covers

phylogenetic and evolutionary aspects of all micro-organisms, including the protists such as

protozoa and algae, and

it

also publishes molecular environmental papers with a strong

systematics content. Its international Editorial Board ensures the highest standards of peer

review.

IJSEM is published monthly, with over 3000 printed pages per year, and is available in print

or online. Our journals are published online with High Wire Press, in both full HTML and as

downloadable PDFs. Features include journal cross-linking, eTOCS and supplementary data.

The complete archive available back to 1951 is available online.

Journal subscriptions are available in two formats, either Online Only or Print and Online.

SGM operates a tiered pricing structure. For more information please visit our subscriptions

ｾﾷ＠

The Journal's Editorial Board ensures high standards of peer review. Below, Karen Rowlett,

Managing Editor oflJSEM (2012), explains the journal's scope and features and summarises

the benefits for authors of publishing in the journal.

You can find out more about the journal, including how to prepare and submit a manuscript

for publication, by visiting our High Wire-hosted site, and you can submit using our online

submission system.

Join the IJSEM Linkedln group

m

IJSEM features:

• Descriptions of the majority of all new prokaryotic and yeast species

• Validation Lists - to validate officially the publication of names of prokaryotes not

published in the USB/IJSEM

•

Opinions of the Judicial Commission of the International Committee on Svstematics

of Prokaryotes (ICSP)

(3)

Benefits to authors:

•

A distinguished international Editorial Board

•

Straightforward online submission

•

Official journal of record for bacterial names

• Rigorous, high-quality peer review

• Immediate online publication

• High production standards

• No page charges

• Pubmed Central deposition*

• Free colour reproduction*

•

Free supplementary data facility

•

25 free downloads of your published PDF

•

Self-archiving

• Paid immediate open access

*Some conditions apply.

IJSEM's impact

• Impact Factor: 2.798 (2013)

• Eigenfactor: 0.01856

(4)

International Journal of Systematic and Evolutionary Microbiology (2009), 59, 2158-2161 DOI 10.1099/ijs.0.007179-0

Correspondence Misa Otoguro

otoguro-misa@nite.go.jp

Streptomyces ba/iensis

sp. nov., isolated from

Balinese soil

Misa Otoguro,

1

Shanti Ratnakomala,2 Yulin Lestari,

3

Ratih D. Hastuti,

4

Evi Triana,

5

Yantyati Widyastuti

2

and Katsuhiko Ando

1

1 _{NITE Biological Resource Center (NBRC), Department of Biotechnology, National Institute of}

Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan

2_{Research Center for Biotechnology, Indonesian Institute of Sciences, JI. Raya Bogor Km. 46,}

Cibinong 16911, Indonesia

3_{Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Ag ricultural}

University, JI Raya pajajaran, Bogor 16144, Indonesia

4_Soil_{Research Institute, JI. Ir. H. Juanda 98, Bogor 16002, Indonesia}

5_{Research Center for Biology, Indonesian Institute of Sciences, JI. Raya Bogor Km. 46, Cibinong}

16911, Indonesia

The taxonomic positions of actinomycete strains 1003-0915r and 1003-0825, isolated from soil on the Indonesian island of Bali, were examined using a polyphasic taxonomic approach. The morphological and chemotaxonomic characteristics of these organisms are typical of the genus Streptomyces. Phylogenetic analyses performed using almost-complete 16$ rRNA gene sequences demonstrated that the strains were closely related to Streptomyces glauciniger and Streptomyces fi/acinus. However, DNA-DNA hybridization and phenotypic characteristics revealed that the strains differed from known Streptomyces species. Therefore, we conclude that strains ID03-0915r and ID03-0825 (=BTCC B-563) represent a novel species of the genus Streptomyces, for which we propose the name Streptomyces ba/iensis sp. nov. The type strain is strain ID03-0915r (= BTCC B-608r = NBRC 104276r).

The genus Streptomyces was proposed by Waksman &

Henrici (1943) and includes aerobic, spore-forming soil

bacteria

with high

DNA

G+C

contents

(69-78

molo/o);

rod-shaped spores originate from the substrate mycelium, 11-diaminopimelic acid (LL-A2pm) is found in the cell wall and galactose and mannose are found in whole-cell hydrolysates. Although the genus Streptomyces contains more than 500 species (Hain et al., 1997) with validly published names, the genus remains a target for screening for novel secondary metabolites.

taxonomic approach that included phylogenetic analyses, chemotaxonomic characteristics, DNA-DNA hybridization and

physiological properties.

The strains were isolated using the SOS/yeast extract method (Hayakawa & Nonomura, 1989) and humic acid/ vitamin (HV) agar (Hayakawa & Nonomura, 1987) supplemented with cydohe:ximide (SO mg 1-1

) and

nali-dixic acid (20

mg

r

1). Morphological and chemotaxo-nomic studies were performed with the two isolates to confirm whether they exhibited properties similar to those of the genus Streptomyces. Morphology was observed under a light microscope and a scanning electron microscope (SEM model JSM-6060; JEOL) on yeast extract-starch (YS) medium or HV agar incubated for 14 days at 28 °C. Cultural and physiological characteristics were examined as described previously (Shirling & Gottlieb, 1966)

In the course of an investif tion of actinomycetes from Indonesia, strains 1D03-0915 and 1003-0825 were isolated from soil collected from the island of Bali. These isolates formed colonies typical of the genus Streptomyces. The aim of this study was to determine the taxonomic positions of strains ID03-0915T and JD03-0825 by a polyphasic

Abbreviation: A2pm, diaminopimelic acid.

The GenBank/EMBUDDBJ accession numbers for the 16S rRNA gene sequences of strains 1003-0915T (=NBRC 104276T) and 1003-08'25

( =

BTCC 8-563) are AB441718 and AB44 1 719.

Detailed cultural properties of the novel strains are available as supplementary material with the online version of this paper.

2158

A2pm isomers and whole-cell sugar patterns were analysed

according to the procedures developed by Hasegawa et

aC·.

(1983) and Lechevalier & Lechevalier (1980). Fatty acid compositions were analysed by GC using the MIDI system (Sasser, 1990; Kampfer & Kroppenstedt, 1996). Isoprenoid quinones and polar lipids were examined

as

described previously (Schaal, 1985; Minnilcin et al., 1984; Tamura et

(5)

"

M. Otoguro and others

ｾＭＭｓＮ＠ thermotineatus NBRC 14750T (AB184618)

100

S. thioluteus NBRC 133411 _(AY999848)

S. blastmyceticus NBRC 127471 _(AB249910)

S. lilacinus NBRC 12884T (AB249906)

S. abikoensis NBRC 13860T (AB184537)

'----S. maJaysiensis NBRC 164461 _(AB249918)

S. baliensis NBRC 1042761 _(AB441718)

S. glauciniger NBRC 1009 t 3T (AB249964)

S. rubidus CGMCC 4.20261 _{(A Y876941)}

S. yangfinensis 13071 _(AY876940)

S. yeochonensis NBRC 1007821 _(AB249943)

ｾＭＭ S. glaucosporvs NBRC 1541 ST (AB 1 84664)

..----S. megasporus NBRC 147491 _(AB184617)

S. macrosporus NBRC 147481 _(AB184616)

Fig. 1. Phylogenetic tree constructed by the neighbour-joining method (Saitou & Nei, 1987) using almost-complete 16S rRNA gene sequences, showing the relationships of strain NBRC 104276T (=ID03-0915T) with type strains of closely related

Streptomyces species. Numbers on branches indicate percentage bootstrap values determined for 1000 replicates (only values above 60% are indicated). Bar, 0.01

Kr.uc·

Asterisks. indicate branches of the tree that were also recovered using the maximum-parsimony (Fitch, 1971) and maximum-likelihood (Felsenstein, 1981) tree-making algorithms.

Streptomyces

species be recognized as belonging to distinct species of the genus (Labeda, 1993, 1996, 1998).

It is clear from the phenotypic and genotypic data that the two isolates should

be

classified within a novel species of the genus

Streptomyces,

for which we propose the name

Streptomyces baliensis

sp. nov.

Description of Streptomyces baliensls sp. nov.

(ba.li.en' sis. N.L. masc. adj.

baliensis

pertaining to the island of Bali, Indonesia, where the first strains were isolated).

Aerobic and strains Gram-positive. Forms well-branched vegetative hyphae and white to grey aerial mycelium. The substrate mycelium is pale yellow to yellow. The aerial mycelium is moderate white to grey on yeast extract/malt extract agar or oatmeal agar. Spore surface is smooth. Soluble pigments are not produced. Melanin pigments are produced on tyrosine agar. Glucose, galactose, mannose, melibiose and lactose are used as sole carbon sources. Grows at 10-30 °C with an optimum around at 28 °C; no

growth

at 37 °C. Optimum growth around pH 7 .0. No growth in the presence of 2 % NaCl. Additional phenotypic properties are listed in Table 1. Type II phospholipids and menaquinones MK-9(1It;), MK-9(H8) and MK-9(H4) are detected. The major

cellular fatty acids are iso-C16:o and iso-C14 , 0 • The G+C

content of DNA of the type strain is 71.l mol%.

Type strain is strain ID03-0915T (=BTCC B-608T =NBRC 104276T), isolated from a soil sample collected in Eka karya

2160

Botanic Garden on Bali, Indonesia. Strain 1003-0825 ( = BTCC B-563) is a second strain of the species.

Acknowledgements

This study was conducted under the Joint Research Project between Department of Biotechnology, National Institute of Technology and Evaluation, Japan, and the Indonesian Institute of Sciences (UPI) representing Indonesian Government Research Institutes. The authors would Like to thank Ms Yayoi Salciyama for her assistance with the chemotaxonomic analyses, Mr Nobuyu.ki Goto for providing the 16S rRNA gene sequences and Dr Tomohiko Tamura for providing valuable suggestions .

References

ｅｺ｡ｫｾ＠ｔｾ＠ Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in miao-dilution wells as an alternative to membrane filter hybrid.i7.ation in which radioisotopes are used to determine genetic relatedness among bacterial strains. Intl Syrt Bacterial 39, 224-229.

Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.

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. Hain, T., Ward-Rainey, N., Kroppenstedt, R. M., Stackebrandt, E. &

Rainey, F. A. .(1997). Discrimination of StreptQmyces albidojlavus strains based on the size and number of 16S-23S ribosomal DNA intergenic spacers. Intl Syrt Bacterial 47, 202-206.

Hasegawa, T., Taklzawa, M. & Tanlda, S. (1983). A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29, 319-322.

Hatano, K., Nishii, T. & ｋ｡ｳ｡ｾ＠ H. (2003). Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA-DNA hybridization and sequence of gyrB,

and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev. Intl Syst Evol Microbiol 53, 1519-1529.

Hayakawa, M. & Nonomura, H. (1987). Humic acid-vitamin agar, a new medium for selective isolation of soil actinomycetes. J Ferment Technol 65, 501-509.

Hayakawa, M. & Nonomura, H. (1989). A new method for the

intensive isolation of actinomycetes from soil Actinomycetologica 3,

95-104.

Kimpfer, P. & Kroppenstedt, R. M. (1996). Numerical analysis of fatty

acid patterns of corynefonn bacteria and related taxa. Can J Microbiol 42, 989-1005.

Kumar, ｓｾ＠ Tamura, K. & Nel, M. (2004). MEGA3: integrated software

for molecular evolutionary genetics analyses and sequence alignment. Brief Bioinform S, ＱＵｾＱＶＳＮ＠

Labeda, D. P. (1993). DNA relatedness among strains of the Streptomyces lavendulae pbenotypic cluster group. Int J Syrt

Bacterial 43, 822-825. \

Labeda, D. P. (1996). DNA relatedness among verticil-forming Streptomyces species (formerly Streptovertidllium species). Int J Syrt Bacteriol 46, 699-703.

Labeda, D. P. (1998). DNA relatedness among the Streptomyces fulvissimus and Strepwmyces griswviridis phenotypic cluster groups. Int J Syst Bacterial 48, 829-832.

(6)

' .

J .

This Issue

September 2009; 5 9 (Y)

•

Index By Author

•

Cover Image

• TOC

(PDF)

l.

VALIDATION LIST

2.

NOTIFICATION LIST

3.

NEW TAXA:

Archaea

4. NEW TAXA: Actinobacteria

5. NEW TAXA: Firmicutes and Related Organisms

6. NEW T AXA: Proteobacteria

7.

NEW

TAXA: Bacteroidetes

8. NEW TAXA: Eukaryotic Micro-organisms

(7)

..

) ·

International Journal of Systematic and

Evolutionary Microbiology

Table of Contents

September 2009; 59 (9)

VALIDATION LIST

• r

Select this article

L ist of n ew na mes and new combinations previously effectively, but not validly,

published

Int

J

Syst Evol Microbial September 2009 59:2129-2130; doi:J0.1099/ijs.0.017988-0

o

Abstract

o Full Text

o

Full Text (PDF)

OPEN ACCESS ARTICLE

NOTIFICATION LIST

• D

Select this article

Notification that new names and new combinations have appeared in volume 59,

part

6, of the IJSEM

Int

J

Syst Evol Microbial September 2009 59:2131-2132; doi:J0.1099/ijs.0.017921-0

o Abstract

o

Full Text

o

Full Text

<PDF)

OPEN ACCESS ARTICLE

NEW T AXA: Archaea

• D

Select this article

o

Seong Woon Roh,

(8)

..

)·

•

o

Ho-Won Chang,

o Kyoung-Ho

Kim,

o

Youlboong Sung,

o

Min-Soo

Kim,

o

Hee-Mock Oh,

o

and

Jin-Woo

Bae

Haloterrigena jeotgali

sp. nov., an extremely balophilic archaeon from

salt-f

ermented food

Int

J Syst Evol Microbial September 2009 59:2359-2363; published ahead of print

July 20, 2009, doi:J0.1099/ijs.0.008243-0

o

Abstract

o

Full Text

o

Full Text

(PDF)

o

Supplementary Figures

NEW TAXA: Actinobacteria

. r

Select this article

o Misa Otoguro,

o Shanti Ratnakomala,

o

Yulln

ｌ･ｾｴｾｲｩＬ＠

o

Ratih D. Hastuti,

o

Evi Triana,

o

Y

antyati Widyastuti,

o and Katsuhiko Ando

sp. nov., isolated from Balinese soil

Int J Syst Evol Microbial September 2009 59:2158-2161; published ahead of print

July 15, 2009, doi:l0.1099/ijs.0.007179-0

o

Abstract

o

Full Text

o

Full Text (PDF)

o

Supplementary Table

• D

Select this article

o

Sheng Qin,

o Guo-Zhen Zhao,

o

Jie Li,

o

Wen-Yong Zhu,

o Li-HuaXu,

o and Wen-Jun Li

Jiangella alba

sp. nov., an endophytic actinomycete isolated from the stem of