International Journal of Systematic and Evolutionary Microbiology

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.

An intracellular bacterium with the unique ability to enter mitochondria exists in the European vector of Lyme disease, the hard tick Ixodes ricinus. Previous phylogenetic analyses based on 16S rRNA gene sequences suggested that the bacterium formed a divergent lineage within the Rickettsiales (Alphaproteobacteria). Here, we present additional phylogenetic evidence, based on the gyrB gene sequence, that confirms the phylogenetic position of the bacterium. Based on these data, as well as electron microscopy (EM), in situ hybridization and other observations, we propose the name ‘Candidatus Midichloria mitochondrii’ for this bacterium. The symbiont appears to be ubiquitous in females of I. ricinus across the tick's distribution, while lower prevalence is observed in males (44 %). Based on EM and in situ hybridization studies, the presence of ‘Candidatus M. mitochondrii’ in females appears to be restricted to ovarian cells. The bacterium was found to be localized both in the cytoplasm and in the intermembrane space of the mitochondria of ovarian cells. ‘Candidatus M. mitochondrii’ is the first bacterium to be identified that resides within animal mitochondria.

The taxonomic position of a group of mesophilic actinomycetes isolated from arid Australian soils was determined using a polyphasic approach. The organisms shared chemical and morphological markers typical of members of the genus Amycolatopsis. They had identical 16S rRNA gene sequences and formed a distinct phyletic line in the Amycolatopsis mediterranei clade, being most closely related to A. mediterranei. In addition, they shared a range of phenotypic properties that distinguished them from representatives of all of the species classified in this clade. The combined genotypic and phenotypic data indicate that the strains merit species status within the genus Amycolatopsis. The name proposed for the novel species is Amycolatopsis australiensis sp. nov.; the type strain is GY048T (=DSM 44671T=NCIMB 14142T).

Despite differences in their morphologies, comparative analyses of 16S rRNA gene sequences revealed high levels of similarity (>94 %) between strains of the filamentous bacterium ‘Candidatus Nostocoida limicola’ and the cocci Tetrasphaera australiensis and Tetrasphaera japonica and the rod Tetrasphaera elongata, all isolated from activated sludge. These sequence data and their chemotaxonomic characters, including cell wall, menaquinone and lipid compositions and fingerprints of their 16S–23S rRNA intergenic regions, support the proposition that these isolates should be combined into a single genus containing six species, in the family Intrasporangiaceae in the Actinobacteria. This suggestion receives additional support from DNA–DNA hybridization data and when partial sequences of the rpoC1 gene are compared between these strains. Even though few phenotypic characterization data were obtained for these slowly growing isolates, it is proposed, on the basis of the extensive chemotaxonomic and molecular evidence presented here, that ‘Candidatus N. limicola’ strains Ben 17, Ben 18, Ben 67, Ben 68 and Ben 74 all be placed into the species Tetrasphaera jenkinsii sp. nov. (type strain Ben 74T=DSM 17519T=NCIMB 14128T), ‘Candidatus N. limicola’ strain Ben 70 into Tetrasphaera vanveenii sp. nov. (type strain Ben 70T=DSM 17518T=NCIMB 14127T) and ‘Candidatus N. limicola’ strains Ver 1 and Ver 2 into Tetrasphaera veronensis sp. nov. (type strain Ver 1T=DSM 17520T=NCIMB 14129T).

Bacteria-like endosymbionts of females of the plant-parasitic nematodes Globodera rostochiensis and Heterodera goettingiana and juveniles of Heterodera glycines were first observed during transmission electron microscopy (TEM) studies conducted in the 1970s. These organisms were characterized as being rod-shaped, ranging in size from 0.3 to 0.5 μm in diameter and 1.8 to 3 μm in length and containing structures labelled as striated inclusion bodies or tubular structures. A population of H. glycines was obtained from the soybean field where infected nematodes were first discovered in order to conduct TEM studies of females and males and to determine the phylogenetic position of the H. glycines endosymbiont among bacteria by studying the 16S rRNA and gyrB gene sequences. The bacterium was observed in the pseudocoelom and intestine of juveniles, females and males, in hypodermal chords of juveniles and males, in ovary walls and in oocytes and spermatozoa. The bacterium was polymorphic, measuring 0.4–0.8×2.5–4.5 μm, and many specimens contained an array of microfilament-like structures similar to those observed in ‘Candidatus Cardinium hertigii’, the endosymbiont of Encarsia spp. wasps. Phylogenetic analysis of the 16S rRNA and gyrB genes of the H. glycines-infecting bacterium revealed 93 % and 81 % sequence identity, respectively, to the homologous genes in ‘Candidatus C. hertigii’. Thus, the name ‘Candidatus Paenicardinium endonii’ is proposed for the bacterial endosymbiont of the plant-parasitic nematode H. glycines.

Potato purple top wilt (PPT) is a devastating disease that occurs in various regions of North America and Mexico. At least three distinct phytoplasma strains belonging to three different phytoplasma groups (16SrI, 16SrII and 16SrVI) have been associated with this disease. A new disease with symptoms similar to PPT was recently observed in Texas and Nebraska, USA. Two distinct phytoplasma strain clusters were identified. One belongs to the 16SrI phytoplasma group, subgroup A, and the other is a novel phytoplasma that is most closely related to, and shares 96.6 % 16S rRNA gene sequence similarity with, a member of group 16SrXII. Phylogenetic analysis of 16S rRNA gene sequences of the novel PPT-associated phytoplasma strains, previously described ‘Candidatus Phytoplasma’ organisms and other distinct unnamed phytoplasmas indicated that the novel phytoplasma, termed American potato purple top wilt (APPTW) phytoplasma, represents a distinct lineage and shares a common ancestor with stolbur phytoplasma, ‘Candidatus Phytoplasma australiense’, ‘Candidatus Phytoplasma japonicum’, ‘Candidatus Phytoplasma fragariae’, bindweed yellows phytoplasma (IBS), ‘Candidatus Phytoplasma caricae’ and ‘Candidatus Phytoplasma graminis’. On the basis of unique 16S rRNA gene sequences and biological properties, it is proposed that the APPTW phytoplasma represents ‘Candidatus Phytoplasma americanum’, with APPTW12-NE as the reference strain.

The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

One thermophilic (strain IMO-1T) and two mesophilic (strains KIBI-1T and YMTK-2T) non-spore-forming, non-motile, Gram-negative, multicellular filamentous micro-organisms, which were previously isolated as members of the tentatively named class ‘Anaerolineae’ of the phylum Chloroflexi, were characterized. All isolates were strictly anaerobic micro-organisms. The length of the three filamentous isolates was greater than 100 μm and the width was 0.3–0.4 μm for strain IMO-1T, 0.4–0.5 μm for strain KIBI-1T and thinner than 0.2 μm for strain YMTK-2T. Strain IMO-1T could grow at pH 6.0–7.5 (optimum growth at pH 7.0). The optimal temperature for growth of strain IMO-1T was around 50 °C (growth occurred between 42 and 55 °C). Growth of the mesophilic strains KIBI-1T and YMTK-2T occurred at pH 6.0–7.2 with optimal growth at pH 7.0. Both of the mesophilic strains were able to grow in a temperature range of 25–50 °C with optimal growth at around 37 °C. Yeast extract was required for growth of all three strains. All the strains could grow with a number of carbohydrates in the presence of yeast extract. The G+C contents of the DNA of strains IMO-1T, KIBI-1T and YMTK-2T were respectively 53.3, 59.5 and 48.2 mol%. Major fatty acids for thermophilic strain IMO-1T were anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and anteiso-C15 : 0, whereas those for mesophilic strains KIBI-1T and YMTK-2T were branched C14 : 0, iso-C15 : 0, C16 : 0 and branched C17 : 0, and branched C17 : 0, C16 : 0, C14 : 0 and C17 : 0, respectively. Detailed phylogenetic analyses based on their 16S rRNA gene sequences indicated that the isolates belong to the class-level taxon ‘Anaerolineae’ of the bacterial phylum Chloroflexi, which for a long time had been considered as a typical uncultured clone cluster. Their morphological, physiological, chemotaxonomic and genetic traits strongly support the conclusion that these strains should be described as three novel independent taxa in the phylum Chloroflexi. Here, Anaerolinea thermolimosa sp. nov. (type strain IMO-1T=JCM 12577T=DSM 16554T), Levilinea saccharolytica gen. nov., sp. nov. (type strain KIBI-1T=JCM 12578T=DSM 16555T) and Leptolinea tardivitalis gen. nov., sp. nov. (type strain YMTK-2T=JCM 12579T=DSM 16556T) are proposed. In addition, we formally propose to subdivide the tentative class-level taxon ‘Anaerolineae’ into Anaerolineae classis nov. and Caldilineae classis nov. We also propose the subordinate taxa Anaerolineales ord. nov., Caldilineales ord. nov., Anaerolineaceae fam. nov. and Caldilineaceae fam. nov.

Symbiotic interactions with bacteria are essential for the survival and reproduction of many insects. The European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae) engages in a highly specific association with bacteria of the genus Streptomyces that appears to protect beewolf offspring against infection by pathogens. Using transmission and scanning electron microscopy, the bacteria were located in the antennal glands of female wasps, where they form dense cell clusters. Using genetic methods, closely related streptomycetes were found in the antennae of 27 Philanthus species (including two subspecies of P. triangulum from distant localities). In contrast, no endosymbionts could be detected in the antennae of other genera within the subfamily Philanthinae (Aphilanthops, Clypeadon and Cerceris). On the basis of morphological, genetic and ecological data, ‘Candidatus Streptomyces philanthi’ is proposed. 16S rRNA gene sequence data are provided for 28 ecotypes of ‘Candidatus Streptomyces philanthi’ that reside in different host species and subspecies of the genus Philanthus. Primers for the selective amplification of ‘Candidatus Streptomyces philanthi’ and an oligonucleotide probe for specific detection by fluorescence in situ hybridization (FISH) are described.

A moderately thermophilic, anaerobic bacterium (strain SB91T) was isolated from a freshwater hot spring at Barguzin Valley, Buryatiya, Russia. Cells of strain SB91T were straight to slightly curved rods, 0·5–0·6 μm in diameter and 3·0–7·0 μm in length. Formation of endospores was not observed. The temperature range for growth was 26–62 °C, with an optimum at 50 °C. The pH range for growth was 5·5–9·5, with an optimum at pH 7·5–8·0. The substrates utilized by strain SB91T in the presence of 9,10-anthraquinone 2,6-disulfonate included peptone, tryptone, Casamino acids, yeast extract, beef extract, casein hydrolysate, alanine plus glycine, alanine plus proline, l-valine and n-propanol. Carbohydrates were not utilized. Strain SB91T reduced amorphous Fe(III) oxide, Fe(III) citrate, Fe(III) EDTA or Fe(III) nitrilotriacetate with peptone, l-valine or n-propanol as an electron donor. Strain SB91T reduced 9,10-anthraquinone 2,6-disulfonate, thiosulfate, elemental sulfur, fumarate and selenite. Strain SB91T survived after exposure to gamma-radiation at a dose of 5·4 kGy. The G+C content of the DNA of strain SB91T was 33 mol%. Analysis of the 16S rRNA gene sequence revealed that the isolated organism belonged to cluster XII of the clostridia. On the basis of its physiological properties and the results of phylogenetic analyses, it is proposed that strain SB91T represents the sole species of a novel genus, Tepidimicrobium; the name Tepidimicrobium ferriphilum gen. nov., sp. nov. is proposed, with strain SB91T (=DSM 16624T=VKM B-2348T) as the type strain.