Kazuo Komagata

Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus

We determined the taxonomic status of six Bacillus species (Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus) by using the results of 16S rRNA gene sequence and cellular fatty acid composition analyses. Phylogenetic analysis clustered these species closely with the Paenibacillus species. Like the Paenibacillus species, the six Bacillus species contained anteiso-C15:0 fatty acid as a major cellular fatty acid. The use of a specific PCR primer designed for differentiating the genus Paenibacillus from other members of the Bacillaceae showed that the six Bacillus species had the same amplified 16S rRNA gene fragment as members of the genus Paenibacillus. Based on these observations and other taxonomic characteristics, the six Bacillus species were transferred to the genus Paenibacillus. In addition, we propose emendation of the genus Paenibacillus.

Proposal for two new genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov.

16S rRNA gene sequences of the type strains of 11 species belonging to the Bacillus brevis and Bacillus aneurinolyticus groups were determined. On the basis of the results of gene sequence analyses, these species were separated into two clusters. The B. brevis cluster included 10 species, namely, Bacillus brevis, Bacillus agri, Bacillus centrosporus, Bacillus choshinensis, Bacillus parabrevis, Bacillus reuszeri, Bacillus formosus, Bacillus borstelensis, Bacillus laterosporus, and Bacillus thermoruber. Bacillus aneurinolyticus and Bacillus migulanus belonged to the B. aneurinolyticus cluster. Moreover, the two clusters were phylogenetically distinct from other Bacillus, Amphibacillus, Sporolactobacillus, Paenibacillus, and Alicyclobacillus species. On the basis of our data, we propose reclassification of the B. brevis cluster as Brevibacillus gen. nov. and reclassification of the B. aneurinolyticus cluster as Aneurinibacillus gen. nov. By using 16S rRNA gene sequence alignments, two specific PCR amplification primers were designed for differentiating the two new genera from each other and from other aerobic, endospore-forming organisms.

Asaia bogorensis gen. nov., sp. nov., an unusual acetic acid bacterium in the alpha-Proteobacteria.

Eight Gram-negative, aerobic, rod-shaped and peritrichously flagellated strains were isolated from flowers of the orchid tree (Bauhinia purpurea) and of plumbago (Plumbago auriculata), and from fermented glutinous rice, all collected in Indonesia. The enrichment culture approach for acetic acid bacteria was employed, involving use of sorbitol medium at pH 3.5. All isolates grew well at pH 3.0 and 30 degrees C. They did not oxidize ethanol to acetic acid except for one strain that oxidized ethanol weakly, and 0.35% acetic acid inhibited their growth completely. However, they oxidized acetate and lactate to carbon dioxide and water. The isolates grew well on mannitol agar and on glutamate agar, and assimilated ammonium sulfate for growth on vitamin-free glucose medium. The isolates produced acid from D-glucose, D-fructose, L-sorbose, dulcitol and glycerol. The quinone system was Q-10. DNA base composition ranged from 59.3 to 61.0 mol% G + C. Studies of DNA relatedness showed that the isolates constitute a single species. Phylogenetic analysis based on their 16S rRNA gene sequences indicated that the isolates are located in the acetic acid bacteria lineage, but distant from the genera Acetobacter, Gluconobacter, Acidomonas and Gluconacetobacter. On the basis of the above characteristics, the name Asaia bogorensis gen. nov., sp. nov. is proposed for these isolates. The type strain is isolate 71T (= NRIC 0311T = JCM 10569T).

Reclassification of Pseudomonas acidovorans den Dooren de Jong 1926 and Pseudomonas testosteroni Marcus and Talalay 1956 as Comamonas acidovorans comb. nov. and Comamonas testosteroni comb. nov., with an Emended Description of the Genus Comamonas

We examined 36 strains of Pseudomonas acidovorans, Pseudomonas testosteroni, and Comamonas terrigena on the basis of phenotypic characters, chemotaxonomic characters, and deoxyribonucleic acid (DNA)-DNA homology. Strains of these three species share many phenotypic characteristics; these organisms exhibit higher levels of DNA-DNA homology and higher levels of electrophoretic enzyme pattern similarity within the three species than with Pseudomonas aeruginosa. The strains in the three species could be differentiated on the basis of carbon compound assimilation patterns, cellular fatty acid composition, and DNA base composition. We propose that Pseudomonas acidovorans and Pseudomonas testosteroni be transferred to the genus Comamonas, as Comamonas acidovorans comb. nov. and Comamonas testosteroni comb, nov., respectively.

Taxonomic Significance of Cellular Fatty Acid Composition in Some Coryneform Bacteria

A total of 76 strains of coryneform bacteria belonging to the genera Arthro-bacter, Brevibacterium, Caseobacter, Cellulomonas, Corynebacterium, and Curtobacterium were divided into four groups on the basis of their cellular fatty acid compositions. Cells with saturated and monounsaturated straight-chain fatty acids were designated type I. Strains in this group had meso-diaminopimelic acid and arabinogalactan in their cell walls. In some strains, 10-methyl fatty acids were found. Type I was divided into six subtypes based on fatty acid composition. Type II cells contained iso-anteiso acids and were found in 43 strains of Arthrobacter, Brevibacterium, Cellulomonas, Curtobacterium, and coryneform bacteria with diaminobutyric acid-peptidoglycan. Small differences in fatty acid composition were found among the strains of this type, and the fatty acid compositions of type II strains varied remarkably depending on the media used. Type III strains were characterized by the presence of ω-cyclohexyl fatty acids. In two strains of Curtobacterium pusillum, approximately 60% of the cellular fatty acid was ω-cyclohexyl undecanoic acid. Type IV strains had highly complex patterns of iso, anteiso, normal, saturated, unsaturated, 10-methyl, and 2-hydroxy fatty acids. Five strains of Arthrobacter simplex, Arthrobacter tumescens, and ”Brevibacterium lipolyticum“ possessed this type of fatty acid composition.

Transfer of pseudomonas plantarii and Pseudomonas glumae to Burkholderia as Burkholderia spp. and description of Burkholderia vandii sp. nov

Plant-associated bacteria were characterized and are discussed in relation to authentic members of the genus Pseudomonas sensu stricto. Bacteria belonging to Pseudomonas rRNA group II are separated clearly from members of the genus Pseudomonas sensu stricto (Pseudomonas fluorescens rRNA group) on the basis of plant association characteristics, chemotaxonomic characteristics, DNA-DNA hybridization data, rRNA-DNA hybridization data, and the sequences of 5S and 16S rRNAs. The transfer of Pseudomonas cepacia, Pseudomonas mallei, Pseudomonas pseudomallei, Pseudomonas caryophylli, Pseudomonas gladioli, Pseudomonas pickettii, and Pseudomonas solanacearum to the new genus Burkholderia is supported; we also propose that Pseudomonas plantarii and Pseudomonas glumae should be transferred to the genus Burkholderia. Isolate VA-1316T (T = type strain) was distinguished from Burkholderia species on the basis of physiological characteristics and DNA-DNA hybridization data. A new species, Burkholderia vandii sp. nov. is proposed for this organism; the type strain of B. vandii is VA-1316 (= JCM 7957).

Lactobacillus acidipiscis sp. nov. and Weissella thailandensis sp. nov., isolated from fermented fish in Thailand

Eleven strains of homofermentative, rod-shaped lactic acid bacteria and five strains of heterofermentative, sphere-shaped lactic acid bacteria were isolated from fermented fish (pla-ra and pla-chom) in Thailand. They were identified as new species and named Lactobacillus acidipiscis sp. nov. and Weissella thailandensis sp. nov., respectively, on the basis of phylogenetic analysis of the 16S rRNA gene sequences, DNA relatedness and phenotypic characteristics. The type strain of L. acidipiscis is FS60-1T (= PCU 207T = NRIC 0300T = HSCC 1411T = JCM 10692T = TISTR 1386T) and the type strain of Weissella thailandensis is FS61-1T (= PCU 210T = NRIC 0298T = HSCC 1412T = JCM 10695T = TISTR 1384T).

Emended description of Paenibacillus amylolyticus and description of Paenibacillus illinoisensis sp. nov. and Paenibacillus chibensis sp. nov.

The taxonomic position of unidentified group 6 of Bacillus circulans as described by Nakamura and Swezey (L.K. Nakamura and J. Swezey, Int. J. Syst. Bacteriol. 33:46-52, 1983) was determined, and the taxonomy of Paenibacillus amylolyticus was reexamined. The results of PCR amplification of a 16S rRNA gene fragment with a specific primer and comparative analysis of 16S rRNA gene sequences warranted placing the two taxa in the genus Paenibacillus. The levels of DNA reassociation among the strains revealed four groups (designated groups I, II, III, and 6), each with a high level of intragroup relatedness (> 72%). Clustering based on phenotypic characteristics correlated well with DNA relatedness grouping. P. amylolyticus strains were scattered in groups I, II, and III. Strains labeled the type strain of P. amylolyticus from different culture collections appeared in groups I and III. Strains found in group I were identified as P. amylolyticus sensu stricto, and the one strain found in group III was identified as Paenibacillus lautus. Group 6 encompassed strains formerly assigned to B. circulans group 6, and group II contained other strains identified as P. amylolyticus. Groups 6 and II were phenotypically and genetically distinct taxa that were distinguishable from the previously described species. These findings showed that groups 6 and II were new species, for which we propose the names Paenibacillus illinoisensis and Paenibacillus chibensis, respectively.

Asaia siamensis sp. nov., an acetic acid bacterium in the alpha-proteobacteria.

Five bacterial strains were isolated from tropical flowers collected in Thailand and Indonesia by the enrichment culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were located within the cluster of the genus Asaia. The isolates constituted a group separate from Asaia bogorensis on the basis of DNA relatedness values. Their DNA G+C contents were 58.6-59.7 mol%, with a range of 1.1 mol%, which were slightly lower than that of A. bogorensis (59.3-61.0 mol%), the type species of the genus Asaia. The isolates had morphological, physiological and biochemical characteristics similar to A. bogorensis strains, but the isolates did not produce acid from dulcitol. On the basis of the results obtained, the name Asaia siamensis sp. nov. is proposed for these isolates. Strain S60-1T, isolated from a flower of crown flower (dok rak, Calotropis gigantea) collected in Bangkok, Thailand, was designated the type strain ( = NRIC 0323T = JCM 10715T = IFO 16457T).

Protomonas, a New Genus of Facultatively Methylotrophic Bacteria

A new genus and species of facultatively methylotrophic bacteria are described. These bacteria are polarly flagellated, gram-negative, nonsporeforming, rod-shaped organisms that occur singly and in pairs. Carotenoid pigment and bacteriochlorophyll are formed in the cells. The deoxyribonucleic acid base composition is 65 to 67 mol% guanine plus cytosine. The cellular fatty acids consist of a large amount of straight-chain unsaturated C18:1 acid and small amounts of straight-chain saturated C16:1 acid, C19:0 cyclopropane acid, and 3-OH-C14:0 hydroxy acid. The major ubiquinone is Q-10. Ubiquinones Q-8, Q-9, and Q-11 are present as minor components. A new genus, Protomonas, is proposed to include this group of methylotropic bacteria. The type species of the genus Protomonas is Protomonas extorquens comb. nov., with type strain TK 0001 (=DSM 1337 = NCIB 9399).