- Volume 58, Issue 4, 2008

A novel species, Aspergillus uvarum sp. nov., is described within Aspergillus section Nigri. This species can be distinguished from other black aspergilli based on internal transcribed spacers (ITS), β-tubulin and calmodulin gene sequences, by AFLP analysis and by extrolite profiles. Aspergillus uvarum sp. nov. isolates produced secalonic acid, common to other Aspergillus japonicus-related taxa, and geodin, erdin and dihydrogeodin, which are not produced by any other black aspergilli. None of the isolates were found to produce ochratoxin A. The novel species is most closely related to two atypical strains of Aspergillus aculeatus, CBS 114.80 and CBS 620.78, and was isolated from grape berries in Portugal, Italy, France, Israel, Greece and Spain. The type strain of Aspergillus uvarum sp. nov. is IMI 388523T=CBS 127591T=ITEM 4834T=IBT26606T.

Dipodascus tetrasporeus sp. nov. is described as a novel yeast species in the family Dipodascaceae to accommodate an isolate recovered from sediments collected on the deep-sea floor in the north-western Pacific Ocean. In the clade comprising the genera Dipodascus, Galactomyces and Geotrichum, this is the only species that forms asci that bear four ascospores. The ascospore is surrounded by an irregular exosporium wall, similar to what is observed in the genus Galactomyces, but they are released by rupture, which is characteristic of Dipodascus and not Galactomyces. D. tetrasporeus is remarkably divergent (>10 % difference) in its D1/D2 26S rDNA sequence from any other known species. Although maximum-likelihood analysis of combined 18S rDNA and D1/D2 26S rDNA sequences cannot elucidate a reliable position for this species, it was placed among Geotrichum carabidarum, Geotrichum cucujoidarum, Geotrichum fermentans and Geotrichum histeridarum, which also have morphological and physiological affinity with the species. The species is homothallic. The type strain of Dipodascus tetrasporeus sp. nov. is strain SY-277T (=NBRC 103136T =CBS 10071T).

A moderately thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterium was isolated from a fluidized-bed reactor treating acidic water containing metal and sulfate. The strain, designated RE35E1T, was rod-shaped and motile. The temperature range for growth was 33–51 °C (optimum 44–46 °C) and the pH range was 6.0–7.5 (optimum pH 6.4–7.3). The strain grew optimally without additional NaCl. The electron acceptors were 10 mM sulfate, thiosulfate and elemental sulfur and 1 mM (but not 10 mM) sulfite. Various alcohols and carboxylic acids were utilized as electron donors. Fermentative growth occurred on pyruvate. The cell wall contained meso-diaminopimelic acid, and the major respiratory isoprenoid quinone was menaquinone MK-7. The major whole-cell fatty acids were iso-C15 : 0, iso-C17 : 1 ω10c and iso-C17 : 0. Strain RE35E1T was related to representatives of the genera Desulfotomaculum and Sporotomaculum, the closest relatives being Desulfotomaculum arcticum DSM 17038T (96.3 % 16S rRNA gene sequence similarity) and Sporotomaculum hydroxybenzoicum DSM 5475T (92.0 % similarity). Strain RE35E1T represents a novel species, for which the name Desulfotomaculum alcoholivorax sp. nov. is proposed. The type strain is RE35E1T (=DSM 16058T=JCM 14019T).

Three alkaliphilic and moderately halophilic strains designated K1-5T, K1-10 and B1-1, characterized by optimal growth at pH 9.0–10.0 and at 3–7 % (w/v) NaCl, were isolated from extremely shallow, alkaline soda lakes located in Hungary. Cells of the strains are Gram-positive, straight rods and form a central to subterminal, ellipsoidal endospore. The isolates are strictly aerobic, catalase-positive, oxidase-negative and contain a peptidoglycan of type A1γ based on meso-diaminopimelic acid. In strain K1-5T, menaquinone-7 (MK-7) is the predominant isoprenoid quinone and anteiso-C15 : 0 is the major cellular fatty acid. The DNA G+C content of strain K1-5T is 42.9 mol%. 16S rRNA gene-based phylogenetic analysis revealed that the strains exhibit levels of sequence similarity of less than 95.8 % to known Bacillus species. According to the polyphasic characterization, the strains represent a novel species, for which the name Bacillus aurantiacus sp. nov. is proposed. The type strain is K1-5T (=DSM 18675T =CCM 7447T =NCAIM B002265T).

A moderately thermophilic, anaerobic bacterium (strain SG 508T) was isolated from a hydrothermal vent chimney located at 1 ° N on the East Pacific Rise at a depth of 2650 m. Cells of strain SG 508T were straight to slightly curved rods, 0.4–0.6 μm in diameter and 2.0–3.0 μm in length. Spore formation was observed only below pH 5.5. The temperature range for growth was 22–60 °C, with optimum growth at 50 °C. The pH range for growth was 4.0–8.5, with optimum growth at pH 6.0–6.8. Growth of strain SG 508T was observed at NaCl concentrations ranging from 1.0 to 6.0 % (w/v), with optimum growth at 2.5 % (w/v). Substrates utilized by strain SG 508T included casein, peptone, tryptone, yeast extract, beef extract, starch, maltose and glucose. The products of glucose fermentation were ethanol, acetate, H2, formate and CO2. Strain SG 508T was able to reduce elemental sulfur to hydrogen sulfide. The DNA G+C content of strain SG 508T was 30.9 mol%. 16S rRNA gene sequence analysis revealed that the isolated organism belonged to cluster I of the genus Clostridium. On the basis of its physiological properties and data from phylogenetic analyses, strain SG 508T is considered to represent a novel species of the genus Clostridium, for which the name Clostridium tepidiprofundi sp. nov. is proposed. The type strain is SG 508T (=DSM 19306T =VKM B-2459T).

A Gram-positive, spore-forming, halophilic bacterial strain, FP5T, was isolated from a salt lake in southern Spain and subjected to a polyphasic taxonomic study. Strain FP5T was strictly aerobic. Cells were coccoidal, occurring singly or in clusters. The cell-wall peptidoglycan type of strain FP5T was A4β based on l-Orn–d-Asp. Strain FP5T was characterized chemotaxonomically by having MK-7 as the major menaquinone and anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C16 : 0 as the main fatty acids. The isolate grew optimally at 37 °C and in presence of 10 % NaCl; no growth was observed in the absence of NaCl. The DNA G+C content was 43.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FP5T falls within the evolutionary radiation of species of the genus Halobacillus. Levels of 16S rRNA gene sequence similarity between strain FP5T and the type strains of nine recognized Halobacillus species were in the range 97.0–99.0 %. Levels of DNA–DNA relatedness indicated that strain FP5T represents a genomic species that is distinct from recognized Halobacillus species. Strain FP5T could be differentiated from recognized Halobacillus species based on several phenotypic characteristics. On the basis of phenotypic, phylogenetic and genomic data, strain FP5T is considered to represent a novel species of the genus Halobacillus, for which the name Halobacillus alkaliphilus sp. nov. is proposed. The type strain is FP5T (=DSM 18525T =ATCC BAA-1361T).

Biochemical and molecular genetic studies were performed on three isolates of an unknown Gram-positive, catalase-negative and rod-shaped organism isolated from the lungs and liver of two beaked whales. The organisms were tentatively identified as Lactobacillus spp. based on cellular morphology and biochemical tests. 16S rRNA gene sequencing studies confirmed the provisional identification of the novel isolates as members of the genus Lactobacillus, but the isolates did not correspond to any recognized species of this genus. The novel strains shared the same phenotypic characteristics and exhibited 100 % 16S rRNA gene sequence similarity. The nearest phylogenetic relatives of the novel isolates were Lactobacillus satsumensis DSM 16230T (94.2 % 16S rRNA gene sequence similarity), Lactobacillus salivarius JCM 1047 (94.0 %), Lactobacillus nagelii ATCC 700692T (94.0 %) and Lactobacillus saerimneri DSM 16049T (93.8 %). The novel isolates could be distinguished from these species and other related species of the genus Lactobacillus by physiological and biochemical tests. On the basis of these phenotypic, physiological and phylogenetic findings, it is proposed that the new isolates from whales be classified as a novel species of the genus Lactobacillus, Lactobacillus ceti sp. nov. The type strain is 142-2T (=CECT 7185T=CCUG 53626T).

Indigo-reducing, obligately alkaliphilic strains A11T, F11 and F12 were isolated from indigo fermentation liquor obtained from Tokushima Prefecture, Shikoku, Japan. The isolates grew at pH 9.0–12.3, but not at pH 7.0–8.0. The optimum pH range for growth was 9.5–11.5. They were Gram-negative, facultatively anaerobic, rod-shaped strains with peritrichous flagella. The isolates grew in 0–14 % (w/v) NaCl, with optimum growth at 1–11 %. They grew at temperatures of 15–35 °C with optimum growth at around 20–30 °C. dl-Lactate was the major end product from d-glucose. No quinones were detected. The peptidoglycan type was A4α, l-Lys (l-Orn)–d-Asp. The major cellular fatty acids were C16 : 0, C16 : 17c and C18 : 19c. The DNA G+C contents were 47.0–47.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence data indicated that the isolates belong to the genus Alkalibacterium. DNA–DNA hybridization revealed low relatedness values between the isolates and the three phylogenetically most closely related species, Alkalibacterium olivapovliticus, Alkalibacterium psychrotolerans and Alkalibacterium iburiense (<41 %). On the basis of phenotypic characteristics, including hydrolysis of cellulose and fermentation of carbohydrates, and chemotaxonomic characteristics, phylogenetic data and DNA–DNA relatedness data, it is concluded that the isolates merit classification as representatives of a novel species of the genus Alkalibacterium, for which the name Alkalibacterium indicireducens sp. nov. is proposed. The type strain of this species is A11T (=JCM 14232T=NCIMB 14253T).

While studying the taxonomy of six lactic acid bacterium isolates from Finnish porcine intestine and faeces, the taxonomic positions of Lactobacillus sobrius type strain DSM 16698T and strain AD5 based on comparative 16S rRNA sequence analysis were found to be controversial, as they showed high similarity to Lactobacillus amylovorus strains. Therefore, the taxonomy of these species was addressed in a polyphasic taxonomy study that included, in addition to re-evaluating the 16S rRNA gene sequence and DNA–DNA reassociation results, multilocus sequence analysis (MLSA) of the housekeeping genes encoding the phenylalanyl-tRNA synthase alpha subunit (pheS) and RNA polymerase alpha subunit (rpoA) as well as numerical analysis of HindIII and EcoRI ribotypes. 16S rRNA gene sequence analysis demonstrated a very high similarity between the L. sobrius and L. amylovorus type and reference strains and representative Finnish porcine isolates (99.6–99.9 %). The MLSA data showed the close phylogenetic relationship of these strains; pheS and rpoA gene sequence similarities were 98.5–100 % and 99.6–99.8 %, respectively. Numerical analyses of HindIII/EcoRI ribotypes placed these strains in a single cluster by both enzymes. Finally, the DNA–DNA reassociation experiments revealed high reassociation levels (higher than 79 %) between the strains. These results indicate that DSM 16698T, AD5 and the related porcine lactobacilli strains from Finland constitute a single species, Lactobacillus amylovorus, and that the name Lactobacillus sobrius should be considered as a later synonym of Lactobacillus amylovorus.

Two strains of lactic acid bacteria were isolated from faeces of two actively racing thoroughbred horses. The isolates formed a subcluster in the Lactobacillus reuteri phylogenetic group, closely related to Lactobacillus fermentum, L. gastricus, L. ingluviei and L. mucosae, by phylogenetic analysis based on 16S rRNA gene sequences. Levels of DNA–DNA relatedness revealed that the isolates belonged to the same taxon and were genetically separated from their phylogenetic relatives. Biochemical and physiological characteristics also distinguished the isolates from their phylogenetic relatives. The isolates produced spherical or oval cells, and tetrad-like cells were rarely seen. To the best of our knowledge, this is the first report of this morphological characteristic within the genus Lactobacillus. Thus, the isolates represent an atypical novel species of the genus Lactobacillus, for which the name Lactobacillus equigenerosi sp. nov. is proposed. The type strain is NRIC 0697T (=JCM 14505T =DSM 18793T).

A moderately halophilic, Gram-positive and rod-shaped bacterium, strain m4-4T, was isolated from a Chihuahuan desert lagoon in Cuatro Ciénegas, Coahuila, Mexico. Strain m4-4T was found to grow optimally at 30–37 °C, pH 7.0–8.0 and 5 % NaCl and to tolerate from 0.5 % to 10 % NaCl. It was shown to be aerobic. The genomic DNA G+C content was about 37 mol%. Strain m4-4T exhibited minimal or no growth on most sugars tested. Its major cellular fatty acids were C14 : 0, C16 : 0 and C18 : 1. Based on phylogenetic analysis of 16S rRNA and recA gene sequences, we observed that the closest relatives of the isolate are moderately halophilic Bacillus species, with 16S rRNA gene sequence similarity ranging from 96.6 to 97.4 % (Bacillus marisflavi, Bacillus aquimaris and Bacillus vietnamensis). Additionally, using genomic data it was determined that the type strain contains a total of nine rRNA operons with three slightly different sequences. On the basis of phenotypic and molecular properties, strain m4-4T represents a novel species within the genus Bacillus, for which the name Bacillus coahuilensis sp. nov. is proposed, with the type strain m4-4T (=NRRL B-41737T =CECT 7197T).

A novel anaerobic, moderately thermophilic, spore-forming, rod-shaped bacterium (strain EBR46T) was isolated from an enrichment culture derived from an anaerobic thermophilic (55 °C) methanogenic bioreactor treating artificial solid wastes. Phylogeny based on 16S rRNA gene sequence analysis placed strain EBR46T within a distinct lineage between Clostridium clusters II and III. The closest recognized relative of strain EBR46T was Gracilibacter thermotolerans DSM 17427T (85.3 % 16S rRNA gene sequence similarity). The DNA G+C content of strain EBR46T was 36.2 mol%. The novel strain grew optimally at 55–58 °C and at pH 7.5–8.0 and was able to grow on peptone, tryptone, Casamino acids, casein hydrolysate, methionine, threonine, tryptophan, cysteine, lysine and serine in the presence of 0.2 % yeast extract. Carbohydrates were not utilized. The main products from tryptone utilization were acetate, iso-butyrate, propionate and iso-valerate. Strain EBR46T produced hydrogen sulfide from cysteine. The major fatty acids were iso-C15 : 0, C14 : 0, C16 : 0 DMA (dimethyl acetal) and iso-C15 : 0 DMA. Based on its unique phylogenetic and physiological features, strain EBR46T is considered to represent a novel species of a new genus, for which the name Lutispora thermophila gen. nov., sp. nov. is proposed. The type strain of the type species is EBR46T (=NBRC 102133T=DSM 19022T).

Three strains of anaerobic, non-spore-forming, Gram-negative coccobacilli (YIT 11816T, YIT 11817 and YIT 11818) were isolated from human faeces. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the family Alcaligenaceae and to be related to the type strain of Sutterella stercoricanis (94.9 %) and to Sutterella wadsworthensis WAL 7877 (94.3 %); the similarity to strains of any other species with a validly published name within the family Alcaligenaceae was less than 92 %. Biochemical data supported the affiliation of these strains to the genus Sutterella. These strains therefore represent a novel species, for which the name Sutterella parvirubra sp. nov. is proposed; the type strain is YIT 11816T (=DSM 19354T =JCM 14724T). The cells of another isolate, strain YIT 11815T, were non-spore-forming, Gram-negative, very large rods, 1×5–200 μm in size, with or without a central, subterminal or terminal swelling of 2–4 μm diameter when grown in a broth medium supplemented with glucose. Based on comparative 16S rRNA gene sequencing, this bacterium is a member of the family Acidaminococcaceae, and most closely related to Megamonas hypermegale (95.3 % similarity to the type strain). Interestingly, the 16S rRNA gene sequence of strain YIT 11815T showed 99 % similarity to sequences of uncultured colonic bacteria. A 16S rRNA gene sequence divergence value of >3 % from known cultured species suggested that isolate YIT 11815T represents a novel species, for which the name Megamonas funiformis sp. nov. is proposed; the type strain is YIT 11815T (=DSM 19343T =JCM 14723T).

‘Rickettsiella melolonthae’ is an intracellularly multiplying bacterial pathogen of European cockchafers, Melolontha melolontha (Linnaeus, 1758) and Melolontha hippocastani (Fabricius, 1801) (Coleoptera: Scarabaeidae). We report the first determination of nucleotide sequences from this organism, i.e. the 16S rRNA encoding rrs gene, the chaperonin encoding groEL gene and the mucZ gene encoding the orthologue of a capsule synthesis-inducing factor of Coxiella burnetii. Within the genus Rickettsiella, the pathotype ‘Rickettsiella melolonthae’ is currently classified as a synonym of the nomenclatural type species Rickettsiella popilliae. Previous sequencing of a 16S rRNA gene from a different species, Rickettsiella grylli, has motivated the transfer of the entire genus from the alphaproteobacterial order Rickettsiales to the gammaproteobacterial order Legionellales, family Coxiellaceae. We investigated the validity of this taxonomic reorganization beyond the species Rickettsiella grylli by reconstructing the organismal phylogeny from comparisons of 16S rRNA gene and GroEL and MucZ protein sequences from a selected set of alpha- and gammaproteobacteria as well as bacterial pathogens from the order Chlamydiales. Our analysis strongly supported the transfer of the genus Rickettsiella to the order Legionellales, but not its classification in one of the recognized families present in this order. Furthermore, our results substantiated inconsistencies in the internal organization of the genus. In particular, the currently accepted delineation of Rickettsiella species and the claimed synonymy of ‘Rickettsiella melolonthae’ with Rickettsiella popilliae are not simultaneously consistent with our findings.

The prokaryotic, generic name Goodfellowia Labeda and Kroppenstedt 2006 is illegitimate because it is a later homonym of the name Goodfellowia Hartert, 1903 (Animalia, Chordata, Aves, Passeriformes, Sturnidae) [Principle 2 of the Bacteriological Code (1990 Revision)]. A new genus name, Goodfellowiella, is therefore proposed for this taxon (Rule 54). This also requires that a new combination, Goodfellowiella coeruleoviolacea comb. nov., be proposed for the type species to replace the illegitimate combination Goodfellowia coeruleoviolacea (Preobrazhenskaya and Terekhova 1987) Labeda and Kroppenstedt 2006.