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1 Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan
2 Motobu Noge Hospital, 880-1 Ohama, Motobu-cho, Kunigami-gun, Okinawa, 905-0212, Japan
3 Department of Microbiology, Regeneration and Advanced Medical Science, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu-city, Gifu, 501-1194, Japan
Correspondence
Ken-ichiro Iida
iida{at}bact.med.kyushu-u.ac.jp
| ABSTRACT |
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The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain MC10T is AY741810.
A table of 16S rRNA gene sequence similarities between MC10T and several Paenibacillus species, a transmission electron micrograph showing flagella and an expanded phylogenetic tree are available as supplementary material in IJSEM Online.
| MAIN TEXT |
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Recently, the problems of garbage produced from everyday living have become serious issues, especially in urban areas. Incineration has been used in the past as a common method of waste disposal. However, the production of toxic substances, especially dioxin, during incineration has become a major problem. Alternative methods for waste disposal are needed in order to avoid environmental pollution.
A heat-producing reaction was observed in a mixture of garbage and soil at Motobu-town, Okinawa, Japan. Using this phenomenon, a composting machine was developed by one of us (Y. U.). This machine comprises an airtight container that can withstand three times atmospheric pressure and a motor used for mixing the garbage inside the vessel. After an hour of operation, the temperature in the machine increases to over 130 °C. By using this machine, garbage was broken down and turned into a soil-like substance. The mechanisms by which such high temperatures are produced are not clear and studies to analyse this phenomenon with biological and biochemical techniques have been performed. During a study to identify bacteria in the samples from this machine, a Gram-negative, but spore-forming, strain was isolated. The strain was named MC10T and was considered to represent a Paenibacillus species based on the phylogenetic analysis of the 16S rRNA gene sequence. Based on the 16S rRNA gene sequence, phenotypic characteristics, DNA base composition and cellular fatty acid composition analysis, we propose that strain MC10T is classified as the type strain of Paenibacillus motobuensis sp. nov.
Strain MC10T was isolated from a compost sample collected from a composting machine. Serially-diluted compost suspensions were inoculated onto LuriaBertani agar (pH 6) (Sambrook et al., 1989
). After colony isolation, the strain was cultivated at 37 °C for 48 h on trypticase soy agar (TSA; Difco) for chromosomal DNA extraction and on BUGM medium (Biolog) for the Biolog substrate utilization test. Tests for the utilization of substrates as the sole carbon source were performed with Biolog GP microplates (Biolog) containing 95 different carbon compounds, according to the manufacturer's instructions. Catalase and oxidase activity assays, the nitrate reduction test and the VogesProskauer test were carried out as described previously (Smibert & Krieg, 1994
). Cell morphology was observed using light microscopy and transmission electron microscopy (TEM). Flagellum type was determined by TEM. Bacteria grown statically in trypticase soy broth (TSB; Difco) for 24 h were shadowed with chromium and examined with a JEM2000EX (JEOL) electron microscope. An ultrastructural study was carried out by using colonies and cells grown on TSA at 37 °C for 48 h. The freeze-substitution fixation technique was used for thin sectioning of samples for TEM (Amako et al., 1983
; Amako & Takade, 1985
).
Cells of strain MC10T were rods and approximately 0·61·0x1·03·0 µm in size. The strain was facultatively anaerobic and motile by means of peritrichous flagella (Supplementary Fig. S1 in IJSEM Online). The isolate produced ellipsoidal endospores in swollen sporangia in the terminal region of the cell (Fig. 1
a). Colonies of the isolate grown on TSA were flat, smooth and opaque white. Growth was found to be optimal at 37 °C, with a range from 25 to 55 °C. Although the optimal growth temperature for the majority of the members of the genus Paenibacillus has been reported to be 2830 °C (Shida et al., 1997a
), several novel Paenibacillus species have been described with temperature optima at around 3740 °C (Shida et al., 1997b
; Yoon et al., 1998
; Tcherpakov et al., 1999
; Meehan et al., 2001
; Velázquez et al., 2004
). Strain MC10T was found to be Gram-negative, but no apparent outer membrane structure was observed in the cell wall (Fig. 1b
) and the cell wall structure was more like that of the Gram-positive bacteria. Some members of the genus Paenibacillus, such as Paenibacillus glucanolyticus and Paenibacillus macquariensis, have been known to give a Gram-negative reaction (Marshall & Ohye, 1966
; Dasman et al., 2002
). The endospores had nine projections from the outer spore coat (Fig. 1a
). Strain MC10T showed catalase and oxidase activity and reduced nitrate to nitrite. The utilization of 95 substrates as the sole carbon source was tested using the Biolog GP plate and the results are noted in the description. Physiological characteristics, including selected data from the carbon utilization test for strain MC10T, were compared with those of its closest phylogenetic relatives, Paenibacillus azoreducens, P. cineris, P. cookii, P. favisporus and P. chibensis (Table 1
).
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The DNA G+C content of strain MC10T was 47·0 mol%. The phylogenetic position of the strain, based on the almost-complete 16S rRNA gene sequence of Paenibacillus species, including strain MC10T, shown in Fig. 2
, was constructed from evolutionary distances (Kimura, 1980
) calculated by the neighbour-joining method (Saitou & Nei, 1987
). The 15 strains with the highest binary similarity values of 16S rRNA sequences are presented in Supplementary Table S1 in IJSEM Online. The levels of 16S rRNA gene sequence similarity between strain MC10T and Paenibacillus species ranged from 95·6 % (Paenibacillus azoreducens, DSM 13822T, GenBank accession no. AJ272249) to 90·2 % (Paenibacillus alginolyticus, DSM 5050T, accession no. D78465). The phylogenetic tree (Fig. 2
) constructed from the 16S rRNA gene sequence data shows that strain MC10T appeared within the genus Paenibacillus and occupied a distinct phylogenetic position within the genus (an expanded phylogenetic tree is available as Supplementary Fig. S2 in IJSEM Online). Species found to be closely related to strain MC10T were P. azoreducens, P. chibensis, P. cineris, P. cookii and P. favisporus. The definition of a bacterial species suggests that strains with approximately 70 % or greater DNADNA relatedness are members of the same species (Wayne et al., 1987
). According to the available data (Stackebrandt & Goebel, 1994
), if the 16S rRNA gene sequence similarities are less than 97·0 %, the total chromosomal DNA extracted from two bacterial strains will not reassociate by more than 60 %, regardless of the hybridization method used. Keswani & Whitman (2001)
suggested a threshold value of 98·6 % similarity for taxa where the rRNA gene sequences possess ultrameric properties and Drancourt et al. (2000)
used 99 % for species identification. Our isolate, MC10T, showed less than 95·6 % sequence similarity values among all members of the genus Paenibacillus. A PCR fragment (0·8 kb) could be amplified from the DNA of MC10T using the primer combination of the genus-specific primer PAEN515F and universal primer 1377R (Shida et al., 1997a
).
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The major fatty acids found in isolate MC10T are shown in Table 2
and are compared with values available for phylogenetically related Paenibacillus strains. Anteiso-branched C15 : 0, the major fatty acid in the genus Paenibacillus (Shida et al., 1997a
), was also the major fatty acid component of strain MC10T, comprising 39·8 % of the total. Other major (>10 %) fatty acids were straight-chain C16 : 0 and iso-branched C15 : 0, C16 : 0 and C17 : 0. The fatty acid profile of strain MC10T was similar to those of selected members of the genus Paenibacillus, but there were differences in the proportions of some fatty acids.
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Description of Paenibacillus motobuensis sp. nov.
Paenibacillus motobuensis (mo.to.bu.en'sis. N.L. masc. adj. motobuensis pertaining to Motobu in Okinawa, Japan, where the type strain was isolated).
Rod-shaped cells with a length of approx. 1·03·0 µm and a width of 0·61·0 µm. Cells are motile by means of peritrichous flagella and produce terminally located ellipsoidal spores. Colonies are circular, flat, smooth and opaque white. Facultatively anaerobic. Cells stain Gram-negative; however, the cell wall structure is that of Gram-positive bacteria. Positive catalase and oxidase reactions. Negative VogesProskauer reaction. Nitrate is reduced to nitrite. The temperature range for growth is 2055 °C, with the optimum being 37 °C. The pH range for growth is 6·08·0, the optimum being pH 8·0. Growth occurs in the presence of 5 % NaCl but is inhibited by 10 % NaCl. Anteiso-branched C15 : 0 (39·8 %) represents the major cellular fatty acid. Utilizes
-cyclodextrin,
-cyclodextrin, dextrin, amygdalin, arbutin, cellobiose, D-fructose, D-galactose, gentiobiose, D-gluconic acid,
-D-glucose, maltose, maltotriose, D-mannose, methyl
-D-galactoside, palatinose, D-psicose, salicin, sucrose, D-trehalose, turanose, D-xylose,
-ketovaleric acid, methyl pyruvate, 2,3-butanediol, glycerol and adenosine (utilization data were obtained with Biolog GP microplates). The DNA G+C content of the type strain is 47·0 mol% (determined by HPLC).
The type strain MC10T (=GTC 1835T=JCM 12774T=CCUG 50090T), was isolated from a composting machine containing soil from Motobu, Okinawa, Japan. The 16S rRNA gene sequence of this strain is deposited at DDBJ under accession number AY741810.
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