- Volume 61, Issue 7, 2011

Two isolates, designated CadH11T and Cad448T, representing uncultured purple sulfur bacterial populations H and 448, respectively, in the chemocline of Lake Cadagno, a crenogenic meromictic lake in Switzerland, were obtained using enrichment and isolation conditions that resembled those used for cultured members of the genus Thiocystis. Phenotypic, genotypic and phylogenetic analyses of these isolates confirmed their assignment to the genus Thiocystis. However, 16S rRNA gene sequence similarities of 98.2 % between CadH11T and Cad448T, and similarities of 97.7 and 98.5 %, respectively, with their closest cultured relative Thiocystis gelatinosa DSM 215T, as well as differences in DNA G+C content and carbon source utilization suggested that the isolates belonged to two distinct species. DNA–DNA hybridization of CadH11T and Cad448T with T. gelatinosa DSM 215T showed relatedness values of 46.4 and 60.8 %, respectively; the relatedness value between CadH11T and Cad448T was 59.2 %. Based on this evidence, strains CadH11T and Cad448T represent two novel species within the genus Thiocystis, for which the names Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov. are proposed, respectively. The type strains of T. chemoclinalis sp. nov. and T. cadagnonensis sp. nov. are CadH11T ( = JCM 15112T  = KCTC 5954T) and Cad448T ( = JCM 15111T  = KCTC 15001T), respectively.

Strains T138021-75T, Pg19 and Pg20 (taxon 25 of Bisgaard) were isolated from guinea pigs and characterized. Strains T138021-75T and Pg20 showed identical 16S rRNA gene sequences and were distantly related to the published strain P224 with the highest 16S rRNA similarity of 98.6 %. These two strains showed 97.8 % sequence similarity with the type strain and other strains of Mannheimia glucosida and 97.3 % similarity with the type strain of Mannheimia varigena, but <97 % similarity with all other type strains of the genus Mannheimia, including Mannheimia haemolytica (96.9 %). Phylogenetic analysis of rpoB gene sequences showed that strain P224 had a distant position (89.9 % gene sequence similarity) compared with the three other strains (T138021-75T, Pg20 and Pg19), which had identical gene sequences. These three novel strains also shared identical recN gene sequences. Phylogenetic analysis of the recN gene sequences showed a close relationship between the three novel strains and strain P224. The DNA–DNA reassociation value between strain T138021-75T and P224 was 81.6 % and 40.3 % between strain T138021-75T and the type strain of M. glucosida. Based on the DNA–DNA reassociation data, strain T138021-75T belonged to a separate species that was closely related to strain P224. Strain P224 differed from strains T138021-75T, Pg20 and Pg19 in the following phenotypic characteristics: activity of ornithine carboxylase, hydrolysis of glycosides, and acid formation from maltose, dextrin, melibiose and raffinose, as well as reactions for α-galactosidase and β-xylosidase. Whole genome similarity calculations based on recN gene sequences showed that strains T138021-75T and P224 were related at the species level (0.932), whereas 16S rRNA and partial rpoB gene sequence comparisons showed a more divergent position of strain P224 compared with the novel strains, including a different host of isolation. The results showed that the three strains of taxon 25 represent a novel species for which the name Mannheimia caviae sp. nov. is proposed. The type strain, T138021-75T ( = CCUG 59995T = DSM 23207T) was isolated from purulent conjunctivitis in guinea pigs. Previous publications have documented both ubiquinones and demethylmenaquinone to be present in the type strain. The G+C content of the DNA of the type strain has been found to be 41.4 mol% (T m).

Anamorphic basidiomycetous yeast strains RS090T and RS092 were isolated from a soil sample collected on Rishiri Island in the Rishiri, Rebun, Sarobetsu National Park, Hokkaido, Japan. As the sequences of the D1/D2 domains of their large-subunit rRNA genes were identical and those of the internal transcribed spacer regions differed in only four bases, we conclude that they belong to a single species with intraspecific diversity. Phylogenetically, this species was related to Dioszegia buhagiarii and Dioszegia hungarica, in the Tremellales, Tremellomycetes, Basidiomycota, but was clearly distinct from them. Based on the results of sequence analyses and phenotypic characteristics, we conclude that they belong to a novel species in the genus Dioszegia, for which the name Dioszegia rishiriensis sp. nov. is proposed, with the type strain RS090T ( = JCM 16282T  = CBS 11844T).

Two marine stichotrich ciliates, Metaurostylopsis flavicana spec. nov. and Tunicothrix wilberti (Lin & Song, 2004) Xu et al., 2006, isolated from the Shenzhen Mangrove Protection Area on the coast of the South China Sea, were investigated using live observation and protargol impregnation techniques. Metaurostylopsis flavicana is characterized by its elongate body shape, yellowish body colour and bright-yellow cortical granules that are either grouped around the cirri and the dorsal cilia or aligned between the rows of cirri and dorsal cilia. It has four to eight frontal, two frontoterminal, one buccal and seven to ten transverse cirri, a mid-ventral complex comprising 13–17 midventral cirral pairs in a row that extends about three-fifths of the body length, four left and three right marginal rows and three complete dorsal kineties. The small subunit rRNA gene of this species was sequenced and phylogenetic trees were constructed in which M. flavicana does not group with its congeners, suggesting that the genus Metaurostylopsis is paraphyletic. Some supplementary morphological and morphogenetic traits for Tunicothrix wilberti are also documented.

During a survey of yeasts associated with wood-ingesting insects, six strains of the Sugiyamaella clade were isolated from the gut of passalid and tenebrionid beetles and the decayed wood inhabited by them. Phylogeny based on rRNA gene sequences placed these yeasts as members of Sugiyamaella smithiae, Sugiyamaella americana, Candida lignohabitans and a novel species closely related to Su. americana. The only strain of the novel species, EH008T, could be unquestionably distinguished from its relatives by DNA sequences and other taxonomic characteristics. Ascospore production was not observed under the laboratory conditions tested. Therefore, this novel species is proposed as Candida bullrunensis sp. nov. (type strain EH008T = ATCC MYA-4660T = CBS 11840T).

Lateral gene transfer (LGT) is an important mechanism by which micro-organisms acquire new functions. This process has been suggested to be central to prokaryotic evolution in various environments. However, the influence of geographical constraints on the evolution of laterally acquired genes in microbial metabolic evolution is not yet well understood. In this study, the influence of geographical isolation on the evolution of laterally acquired dissimilatory sulphite reductase (dsr) gene sequences in the sulphate-reducing micro-organisms (SRM) was investigated. Sequences on four continental blocks related to SRM known to have received dsr by LGT were analysed using standard phylogenetic and multidimensional statistical methods. Sequences related to lineages with large genetic diversity correlated positively with habitat divergence. Those affiliated to Thermodesulfobacterium indicated strong biogeographical delineation; hydrothermal-vent sequences clustered independently from hot-spring sequences. Some of the hydrothermal-vent and hot-spring sequences suggested to have been acquired from a common ancestral source may have diverged upon isolation within distinct habitats. In contrast, analysis of some Desulfotomaculum sequences indicated they could have been transferred from different ancestral sources but converged upon isolation within the same niche. These results hint that, after lateral acquisition of dsr genes, barriers to gene flow probably play a strong role in their subsequent evolution.