- Volume 56, Issue 11, 2006

Two strains of Gram-negative bacteria isolated from soil by selective enrichment with nitroaromatics were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA gene sequence analysis, the two strains were found to belong to the genus Pseudomonas, within the Gammaproteobacteria. Strain 1B4T shared the highest sequence similarity with Pseudomonas koreensis DSM 16610T (99.5 %) and Pseudomonas jessenii CCM 4840T (99.3 %), and strain 2B2T with Pseudomonas asplenii DSM 17133T (98.9 %), Pseudomonas fuscovaginae DSM 7231T (98.9 %) and Pseudomonas putida DSM 291T (98.7 %). On the basis of phylogenetic analysis, DNA–DNA hybridization and phenotype, including chemotaxonomic characteristics, two novel species, Pseudomonas moraviensis sp. nov. with the type strain 1B4T (=CCM 7280T=DSM 16007T) and Pseudomonas vranovensis sp. nov. with the type strain 2B2T (=CCM 7279T=DSM 16006T), are proposed. The description of P. asplenii was emended on the basis of additional data obtained in this study.

An unusual Gram-negative, catalase- and oxidase-positive, rod-shaped bacterium isolated from different clinical samples from two monkeys (Callithrix geoffroyi) was characterized by phenotypic and molecular genetic methods. The micro-organism was tentatively identified as a Pseudomonas species on the basis of the results of cellular morphological and biochemical tests. Fatty acid studies confirmed this generic placement and comparative 16S rRNA gene sequencing studies demonstrated that the unknown isolates were phylogenetically closely related to each other (100 % sequence similarity) and were part of the ‘Pseudomonas fluorescens intrageneric cluster’. The novel bacterium, however, was distinguished from other phylogenetically related species of Pseudomonas by DNA–DNA hybridization studies and biochemical tests. On the basis of both phenotypic and phylogenetic findings, it is proposed that the novel Pseudomonas isolates are classified as Pseudomonas simiae sp. nov. The type strain of P. simiae is OLiT (=CCUG 50988T=CECT 7078T).

A Gram-negative, obligately aerobic, rod-shaped bacterium was isolated from greenhouse soil used to cultivate lettuce. The strain, GH2-10T, was characterized on the basis of phenotypic and genotypic data. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Devosia, with highest sequence similarity (98.5 %) to Devosia riboflavina IFO 13584T. Sequence similarities with other strains tested were below 97.0 %. Strain GH2-10T had Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 59.5 mol%. The results of DNA–DNA hybridization experiments (47 % relatedness between D. riboflavina DSM 7230T and strain GH2-10T) and physiological and biochemical tests suggested that strain GH2-10T represents a novel species of the genus Devosia, for which the name Devosia soli sp. nov. is proposed. The type strain is GH2-10T (=KACC 11509T=DSM 17780T).

Bacterial strain LW36T was isolated from activated sludge of a wastewater-treatment bioreactor. Cells of strain LW36T were Gram-negative coccoids to short rods, 1.0–1.2×0.5 μm in size. Colonies were cream-coloured, smooth and circular. Strain LW36T was hetero-organotrophic and chemolithotrophic and was able to use reduced sulfur as an energy resource. Growth was observed at 25–36 °C and pH 5–10. The most abundant cellular fatty acid of strain LW36T was C18 : 1 ω7c (64.2 %). The sole respiratory quinone was ubiquinone-10. The G+C content of the genomic DNA was 61.3 mol% (T m). 16S rRNA gene sequence analysis indicated that strain LW36T was phylogenetically related to members of the genus Paracoccus, with similarities ranging from 92.4 to 94.9 %. Based on these results, it is concluded that strain LW36T represents a novel species of the genus Paracoccus, for which the name Paracoccus sulfuroxidans is proposed. The type strain is strain LW36T (=CGMCC 1.5364T=JCM 14013T).

A novel black yeast-like fungus, Exophiala crusticola, is described based on two closely related isolates from biological soil crust (BSC) samples collected on the Colorado Plateau (Utah) and in the Great Basin desert (Oregon), USA. Their morphology places them in the anamorphic genus Exophiala, having affinities to the family Herpotrichiellaceae (Ascomycota). Phylogenetic analysis of their D1/D2 large subunit nuclear ribosomal RNA (LSU nrRNA) gene sequences suggests that they represent a distinct species. The closest known putative relative to Exophiala crusticola is Capronia coronata Samuels, isolated from decorticated wood in Westland County, New Zealand. The holotype for Exophiala crusticola anam. nov. is UAMH 10686 and the type strain is CP141bT (=ATCC MYA-3639T=CBS 119970T=DSM 16793T). Dark-pigmented fungi appear to constitute an important heterotrophic component of soil crusts and Exophiala crusticola represents the first description of a dematiaceous fungus isolated from BSCs.

A novel yeast strain, CBS 10258T, was isolated from the atmosphere in central South Africa. Sequence analysis of the D1/D2 domain and internal transcribed spacer region of the novel strain indicates that it represents a novel species within the Cryptococcus laurentii complex. Phylogenetic analyses based on the D1/D2 domain revealed that the novel strain occupies a relatively isolated position within this complex with Papiliotrema bandonii, Cryptococcus perniciosus, Cryptococcus nemorosus and Cryptococcus sp. CBS 8363 being the closest relatives. However, the novel strain could be distinguished from related species by standard physiological tests including the inability to assimilate rhamnose, methyl α-d-glucoside, salicin, lactose, erythritol, ribitol, xylitol, citrate and ethanol. In addition, no extracellular starch production was observed and the isolate was able to grow in the absence of additional vitamins. On the basis of these results, we suggest that the new strain represents a novel species for which the name Cryptococcus anemochoreius sp. nov. is proposed [type strain CBS 10258T (=NRRL Y-27920T)].

The taxonomic position of six Lactobacillus amylophilus strains isolated from swine waste-corn fermentations was reinvestigated. All strains were included in a multilocus sequence analysis (MLSA) study for species identification of Lactobacillus using the genes encoding the phenylalanyl-tRNA synthase alpha subunit (pheS) and RNA polymerase alpha subunit (rpoA). Partial pheS and rpoA gene sequences showed that strains LMG 11400 and NRRL B-4435 represent a separate lineage that is distantly related to the type strain of L. amylophilus, LMG 6900T, and to three other strains of the species. The MLSA data showed that the two strains LMG 11400 and NRRL B-4435 constituted a distinct cluster, sharing 100 % pheS and rpoA gene sequence similarity. The other reference strains clustered together with the type strain of L. amylophilus, LMG 6900T, and were clearly differentiated from strains LMG 11400 and NRRL B-4435 (80 and 89 % pheS and rpoA gene sequence similarity, respectively). The 16S rRNA gene sequences of the latter two strains are 100 % identical, with the nearest phylogenetic neighbour L. amylophilus LMG 6900T showing only 97.2 % 16S rRNA gene sequence similarity. Further polyphasic taxonomic study based on whole-cell protein fingerprinting, DNA–DNA hybridization and biochemical features demonstrated that the two strains represent a single, novel Lactobacillus species, for which the name Lactobacillus amylotrophicus sp. nov. is proposed. The type strain is LMG 11400T (=NRRL B-4436T=DSM 20534T).

Two Gram-positive bacilli, designated as strains SMC 4352-1T and SMC 4352-2T, were isolated sequentially from the blood of a newborn child with sepsis. They could not be identified by using conventional clinical microbiological methods. 16S rRNA gene sequencing and phylogenetic analysis revealed that both strains belonged to the genus Bacillus but clearly diverged from known Bacillus species. Strain SMC 4352-1T and strain SMC 4352-2T were found to be closely related to Bacillus firmus NCIMB 9366T (98.2 % sequence similarity) and Bacillus cibi JG-30T (97.1 % sequence similarity), respectively. They also displayed low DNA–DNA reassociation values (less than 40 %) with respect to the most closely related Bacillus species. On the basis of their polyphasic characteristics, strain SMC 4352-1T and strain SMC 4352-2T represent two novel species of the genus Bacillus, for which the names Bacillus infantis sp. nov. (type strain SMC 4352-1T=KCCM 90025T=JCM 13438T) and Bacillus idriensis sp. nov. (type strain SMC 4352-2T=KCCM 90024T=JCM 13437T) are proposed.

Two thermophilic strains, designated 607T and 606b, were isolated from a compost pile in Japan. The novel strains were Gram-positive, aerobic, spore-forming rods. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains 607T and 606b were closely related to Bacillus naganoensis (94.0–94.1 % similarity) and separated from clusters of the related genera Bacillus (<91.9 %) and Sporolactobacillus (91.0–92.5 %). In addition, some chemotaxonomic and physiological characteristics of strains 607T and 606b differed from those of B. naganoensis and the two related genera. Several differences in physiological characteristics and 16S–23S rRNA gene internal transcribed spacer region nucleotide sequences were observed between strains 607T and 606b; however, DNA–DNA hybridization indicated that these two strains belonged to the same species. From these results, it is proposed that strains 607T and 606b represent the type species of a new genus, Tuberibacillus calidus gen. nov., sp. nov., with strain 607T (=JCM 13397T=DSM 17572T) as the type strain. In addition, the results of phylogenetic analyses, as well as chemotaxonomic and physiological characterization, indicated that B. naganoensis and Bacillus laevolacticus did not belong to the genus Bacillus. Based on these results, it is proposed that B. naganoensis and B. laevolacticus should be transferred to Pullulanibacillus naganoensis gen. nov., comb. nov. and Sporolactobacillus laevolacticus comb. nov., respectively.

A low-G+C-content Gram-positive bacterium, designated CV53T, phylogenetically related to species of the genus Bacillus, was isolated from a highly alkaline non-saline groundwater environment (pH 11.4). This organism comprised rod-shaped cells, was aerobic, did not display spore formation, was catalase- and oxidase-negative, had an optimum growth temperature of 40 °C and had an optimum pH of approximately 7.0–8.5. Optimal growth was observed in the absence of NaCl, but growth did occur at NaCl concentrations up to 3.0 %. The strain possessed an A1γ-type peptidoglycan cell wall and the major respiratory quinone was MK-7. The predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The G+C content of the DNA was 43.1 mol%. Phylogenetic analyses of the 16S rRNA gene sequence revealed that the novel isolate is closely related to the type strain of Bacillus jeotgali, forming a coherent cluster supported by bootstrap analysis at a confidence level of 90 %. The pairwise similarity of the 16S rRNA gene sequences of the two strains is 97.7 %. On the basis of the phylogenetic analyses and the distinct phenotypic characteristics, strain CV53T represents a novel species within the genus Bacillus, for which we propose the name Bacillus foraminis sp. nov. The type strain is CV53T (=LMG 23174T=CIP 108889T).

Strain B538T is a Gram-positive, motile, rod-shaped bacterium, which was isolated from Xinjiang province in China. This organism grew optimally at 30–35 °C and pH 8.0–8.5. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B538T belonged to the genus Paenibacillus and chemotaxonomic data (DNA G+C content, 47.0 mol%; major isoprenoid quinone, MK-7; cell wall type, A1γ meso-diaminopimelic acid; major fatty acids, anteiso-C15 : 0 and C16 : 0) supported affiliation of the isolate with the genus Paenibacillus. Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to Paenibacillus glycanilyticus DS-1T, with 16S rRNA gene sequence similarity of 98.1 %; sequence similarities to other members of the genus Paenibacillus used in the phylogenetic tree were less than 96.5 %. The DNA–DNA relatedness between strain B538T and P. glycanilyticus DS-1T was about 8.0 %. On the basis of physiological and molecular properties, strain B538T (=KCTC 3952T=DSM 16970T) is proposed as the type strain of a novel species within the genus Paenibacillus, for which the name Paenibacillus xinjiangensis sp. nov. is proposed.

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterium was isolated from an underground mine in a geothermally active area in Japan. Cells of this strain, designated RL50JIIIT, were rod-shaped and motile. The temperature range for growth was 50–72 °C (optimum growth at 61–66 °C) and the pH range was 6.4–7.8 (optimum at pH 7.2–7.4). Strain RL50JIIIT tolerated up to 1.5 % NaCl, but optimum growth occurred in the presence of 0–1 % NaCl. Electron acceptors utilized were sulfate, sulfite, thiosulfate and elemental sulfur. Electron donors utilized were H2 in the presence of CO2, alanine, various carboxylic acids and alcohols. Fermentative growth occurred on lactate and pyruvate. The cell wall contained mesodiaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone 7 (MK-7). Major whole-cell fatty acids were iso-C15 : 0, iso-C17 : 0 DMA (dimethyl acetal), iso-C15 : 0 DMA and iso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed 98.7 % similarity with Desulfotomaculum solfataricum DSM 14956T. However, DNA–DNA hybridization experiments with Desulfotomaculum kuznetsovii, Desulfotomaculum luciae and D. solfataricum and the G+C content of the DNA (54.4 mol%) allowed the differentiation of strain RL50JIIIT from the recognized species of the genus Desulfotomaculum. Strain RL50JIIIT therefore represents a novel species, for which the name Desulfotomaculum thermosubterraneum sp. nov. is proposed. The type strain is RL50JIIIT (=DSM 16057T=JCM 13837T).

A novel, alkaliphilic, obligately anaerobic bacterium, strain SCAT, was isolated from mud sediments of a soda lake in California, USA. The rod-shaped cells were motile, Gram-positive, formed spores and were 0.4–0.5×2.5–5.0 μm in size. Growth occurred within the pH range 6.7–10.0 and was optimal at pH 8.5. The temperature range for growth was 10–45 °C, with optimal growth at 35 °C. NaCl was required for growth. Growth occurred at 0.5–9.0 % (w/v) NaCl and was optimal at 1–2 % (w/v). The novel isolate was a catalase-negative chemo-organoheterotroph that fermented sugars, proteolysis products, some organic and amino acids, glycerol, d-cellobiose and cellulose. It was also capable of growth by the Stickland reaction. Strain SCAT was sensitive to tetracycline, chloramphenicol, rifampicin and gentamicin, but it was resistant to ampicillin and kanamycin. The G+C content of the genomic DNA was 34.2 mol%. Major fatty acid components were C14 : 0, iso-C15 : 0, C16 : 1 ω9c and C16 : 0. 16S rRNA gene sequence analysis of strain SCAT showed a similarity of approximately 97 % with the type strains of Clostridium formicaceticum and Clostridium aceticum in clostridial cluster XI and a similarity of less than 94.2 % to any other recognized Clostridium species and those of related genera in this cluster. Strain SCAT was clearly differentiated from C. formicaceticum and C. aceticum based on comparison of their phenotypic properties and fatty acid profiles, as well as low levels of DNA–DNA relatedness between strain SCAT and the type strains of these two species. Therefore, strain SCAT is considered to represent a novel species of a new genus, Anaerovirgula multivorans gen. nov., sp. nov., in clostridial cluster XI. The type strain is SCAT (=ATCC BAA-1084T=JCM 12857T=DSM 17722T=CIP 107910T).

A Gram-positive, rod-shaped, spore-forming bacterium, Gsoil 3088T, was isolated from soil from a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 3088T was shown to belong to the family Paenibacillaceae, being related to Brevibacillus centrosporus (96.6 %), Brevibacillus borstelensis (96.3 %), Brevibacillus parabrevis (96.1 %), Brevibacillus formosus (96.1 %), Brevibacillus brevis (96.1 %) and Brevibacillus laterosporus (96.0 %). The phylogenetic distances from other validly described species within the genus Brevibacillus were greater than 4.0 % (i.e. there was less than 96.0 % similarity). The G+C content of the genomic DNA was 52.1 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; fatty acid profile, iso-C15 : 0, iso-C14 : 0 and anteiso-C15 : 0) supported the affiliation of strain Gsoil 3088T to the genus Brevibacillus. The results of physiological and biochemical tests allowed strain Gsoil 3088T to be distinguished genotypically and phenotypically from Brevibacillus species with validly published names. Strain Gsoil 3088T, therefore, represents a novel species of the genus Brevibacillus, for which the name Brevibacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3088T (=KCTC 13938T=LMG 23403T).

A Gram-positive, facultatively anaerobic, motile, spore-forming bacterium, designated Gsoil 1411T, was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 1411T belongs to the family Paenibacillaceae, with closest sequence similarity to the type strains of Paenibacillus xylanilyticus (95.7 %), Paenibacillus illinoisensis (95.2 %) and Paenibacillus pabuli (94.8 %). Strain Gsoil 1411T showed less than 94 % sequence similarity to the type strains of other recognized members of the genus Paenibacillus. In addition, the presence of MK-7 as the major menaquinone, anteiso-C15 : 0 as a major fatty acid (44.8 %) and the presence of PAEN513F and PAEN862F signature sequences suggest that it is affiliated to the genus Paenibacillus. The G+C content of the genomic DNA was 53.9 mol%. On the basis of its phenotypic characteristics and phylogenetic distinctiveness, strain Gsoil 1411T is suggested to represent a novel species within the genus Paenibacillus, for which the name Paenibacillus panacisoli sp. nov. is proposed. The type strain is Gsoil 1411T (=KCTC 13020T=LMG 23405T).

Lysobacter enzymogenes subsp. enzymogenes Christensen and Cook 1978 , L. enzymogenes subsp. cookii Christensen 1978 and Streptococcus casseliflavus ( Mundt and Graham 1968 ) Vaughan et al. 1978 were inadvertently omitted from the Approved Lists of Bacterial Names. According to Rule 24a, Note 1, the authors request that these names be considered as included in these Lists.

The prokaryotic, generic names Micromonas Murdoch and Shah 2000 and Quadricoccus Maszenan et al. 2002 are illegitimate* because they are later homonyms of the names Micromonas Manton and Parke 1960 (alga) and Quadricoccus Fott 1948 (alga). [Principle 2, Rule 51b(4) of the Bacteriological Code (1990 Revision)]. Such names have no claim to be correct names (Principle 6) and, therefore, replacement generic names must be proposed (Rule 54).

It is now 30 years since the concept of valid publication was introduced into prokaryote systematics in such a way that a system of registration/indexing was integrated. Despite the success of this system and the introduction of the Approved Lists of Bacterial Names, accompanied by a new starting date in prokaryote nomenclature, there is a need to review both the historical aspects and current practices so that the current generation of prokaryote systematists have an up-to-date overview of some of the key elements.