Three New Species of Brevibacteria,Brevibacterium antiquum sp. nov., Brevibacterium aurantiacum sp. nov., and Brevibacterium permense sp. nov.

This work deals with the taxonomic study of orange-pigmented bacteria isolated from permafrost sediments, rice plots, and soils contaminated with wastes from the chemical and salt industries that were assigned to the genus Brevibacterium on the basis of phenotypic characteristics, as well as of some strains described previously as Brevibacterium linens. The study revealed three genomic species, whose members and the type strains of the closest species of Brevibacterium had DNA similarity levels between 24 and 59%. The strains of the genomic species differed from each other and from the known species of Brevibacterium in some physiological and biochemical characteristics, as well as in the sugar and polyol composition of their teichoic acids. The 16S rDNA sequence analysis confirmed the assignment of the environmental isolates to the genus Brevibacterium and showed the phylogenetic distinction of the three genomic species. The results obtained in this study allow three new Brevibacterium species to be described: Brevibacterium antiquum (type strain VKM Ac-2118^T = UCM Ac-411^T), Brevibacterium aurantiacum (type strain VKM Ac-2111^T = NCDO 739^T = ATCC 9175^T), and Brevibacterium permense (type strain VKM Ac-2280^T = UCM Ac-413^T).     

Rahnella victoriana sp. nov., Rahnella bruchi sp. nov., Rahnella woolbedingensis sp. nov., classification of Rahnella genomospecies 2 and 3 as Rahnella variigena sp. nov. and Rahnella inusitata sp. nov., respectively and emended description of the genus Rahnella

Isolations from oak symptomatic of Acute Oak Decline, alder and walnut log tissue, and buprestid beetles in 2009–2012 yielded 32 Gram-negative bacterial strains showing highest gyrB sequence similarity to Rahnella aquatilis and Ewingella americana. Multilocus sequence analysis (using partial gyrB, rpoB, infB and atpD gene sequences) delineated the strains into six MLSA groups. Two MLSA groups contained reference strains of Rahnella genomospecies 2 and 3, three groups clustered within the Rahnella clade with no known type or reference strains and the last group contained the type strain of E. americana. DNA–DNA relatedness assays using both the microplate and fluorometric methods, confirmed that each of the five Rahnella MLSA groups formed separate taxa. Rahnella genomospecies 2 and 3 were previously not formally described due to a lack of distinguishing phenotypic characteristics. In the present study, all five Rahnella MLSA groups were phenotypically differentiated from each other and from R. aquatilis. Therefore we propose to classify the strains from symptomatic oak, alder and walnut and buprestid beetles as: Rahnella victoriana sp. nov. (type strain FRB 225^T = LMG 27717^T = DSM 27397^T), Rahnella variigena sp. nov. (previously Rahnella genomosp. 2, type strain CIP 105588^T = LMG 27711^T), Rahnella inusitata sp. nov. (previously Rahnella genomosp. 3, type strain DSM 30078^T = LMG 2640^T), Rahnella bruchi sp. nov. (type strain FRB 226^T = LMG 27718^T = DSM 27398^T) and Rahnella woolbedingensis sp. nov. (type strain FRB 227^T = LMG 27719^T = DSM 27399^T).     

A new genus of male cones of voltzialean affinity,Uralostrobus voltzioides nov. gen., nov. sp., from the Lower Permian of the Urals (Russia)

A new genus and species of male cones of coniferophyte from the Lower Permian (Artinskian and Kungurian) deposits of the Urals, Russia is described: Uralostrobus voltzioides Naugolnykh nov. gen., nov. sp. The cone shows characters typical of some representatives of conifers belonging to the order Voltziales: more or less isometrical bracts of rhombic shape, prolonged sporangia with attenuate apices, and bisaccate pollen of Illinites-type. General information on the associated female seed scales and vegetative leafy shoots is given as well.     

Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium

Fenollaria massiliensis strain 9401234^T, is the type strain of Fenollaria massiliensis gen. nov., sp. nov., a new species within a new genus Fenollaria. This strain, whose genome is described here, was isolated from an osteoarticular sample. F. massiliensis strain 9401234^T is an obligate anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1.71 Mbp long genome exhibits a G+C content of 34.46% and contains 1,667 protein-coding and 30 RNA genes, including 3 rRNA genes.     

Phylogenetic classification of ten novel species belonging to the genus Bifidobacterium comprising B. phasiani sp. nov., B. pongonis sp. nov., B. saguinibicoloris sp. nov., B. colobi sp. nov., B. simiiventris sp. nov., B. santillanense sp. nov., B. miconis sp. nov., B. amazonense sp. nov., B. pluvialisilvae sp. nov., and B. miconisargentati sp. nov

Ten Bifidobacterium strains, i.e., 6T3, 64T4, 79T10, 80T4, 81T8, 82T1, 82T10, 82T18, 82T24, and 82T25, were isolated from mantled guereza (Colobus guereza), Sumatran orangutan (Pongo abeli), silvery marmoset (Mico argentatus), golden lion tamarin (Leontopithecus rosalia), pied tamarin (Saguinus bicolor), and common pheasant (Phaisanus colchinus). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic, and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on the core genome sequences revealed that isolated strains exhibit close phylogenetic relatedness with Bifidobacterium genus members belonging to the Bifidobacterium bifidum, Bifidobacterium longum, Bifidobacterium pullorum, and Bifidobacterium tissieri phylogenetic groups. Phenotypic characterization and genotyping based on the genome sequences clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, B. phasiani sp. nov. (6T3 = LMG 32224^T = DSM 112544^T), B. pongonis sp. nov. (64T4 = LMG 32281^T = DSM 112547^T), B. saguinibicoloris sp. nov. (79T10 = LMG 32232^T = DSM 112543^T), B. colobi sp. nov. (80T4 = LMG 32225^T = DSM 112552^T), B. simiiventris sp. nov. (81T8 = LMG 32226^T = DSM 112549^T), B. santillanense sp. nov. (82T1 = LMG 32284^T = DSM 112550^T), B. miconis sp. nov. (82T10 = LMG 32282^T = DSM 112551^T), B. amazonense sp. nov. (82T18 = LMG 32297^T = DSM 112548^T), pluvialisilvae sp. nov. (82T24 = LMG 32229^T = DSM 112545^T), and B. miconisargentati sp. nov. (82T25 = LMG 32283^T = DSM 112546^T) are proposed as novel Bifidobacterium species.     

Parahaliea maris sp. nov., isolated from surface seawater and emended description of the genus Parahaliea

Journal of Microbiology - A Gram-stain-negative strictly aerobic, short-rod-shaped, and non-motile bacterial strain designated HSLHS9T was isolated from surface seawater collected from the South...     

Actinomycetospora atypica sp. nov., a novel soil actinomycete and emended description of the genus Actinomycetospora

A novel actinomycete, designated strain NEAU-st4^T, was isolated from a soil sample collected from Shaanxi province, Northwest China and characterized using a polyphasic approach. 16S rRNA gene sequence analysis revealed that strain NEAU-st4^T has the highest sequence similarities with Actinomycetospora rishiriensis RI109-Li102^T (99.4 %), Actinomycetospora corticicola 014-5^T (99.1 %), Actinomycetospora chiangmaiensis YIM 0006^T (98.8 %) and Actinomycetospora iriomotensis IR73-Li102^T (98.2 %). However, the low level of DNA–DNA relatedness differentiated strain NEAU-st4^T from its closest phylogenetic neighbours. The main chemotaxonomic properties of strain NEAU-st4^T, such as the diamino acid of the peptidoglycan, the whole-cell hydrolysates, the predominant menaquinones and the phospholipid profile, supported its classification within the genus Actinomycetospora. The distinctive morphology of this strain compared with that of other members in the genus Actinomycetospora is the formation of sporangia directly on the substrate hyphae. Phenotypic and genotypic differences also allowed the distinction of the strain from closely related species. Consequently, strain NEAU-st4^T represents a new species of the genus Actinomycetospora, for which the name Actinomycetospora atypica sp. nov. is proposed. The type strain is NEAU-st4^T (=CGMCC 4.7093^T = DSM 45873^T).     

Nevskia aquatilis sp. nov. and Nevskia persephonica sp. nov., isolated from a mineral water aquifer and the emended description of the genus Nevskia

Four isolates, with an optimum temperature of about 30°C and an optimum pH for growth of 6.0-6.5, were recovered from a borehole head of a mineral water aquifer in Portugal and from the stored bottles produced on site. Strains F2-63(T) and F2-178 were yellow-pigmented and formed non-motile rod-shaped cells. Strains G6M-30(T) and G6-54 were whitish-pigmented, translucent and form rod-shaped cells with a polar flagellum. The four strains were strictly aerobic, oxidase and catalase positive. The major fatty acids of strains F2-63(T) and F2-178 were C(18:1)ω7c and C(16:0), and the major fatty acids of strains G6M-30(T) and G6-54 were C(18:1)ω7c and C(16:1)ω7c. Ubiquinone 8 was the major respiratory quinone. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics two new species of the genus Nevskia are described; Nevskia aquatilis represented by strains F2-63(T) (=LMG 26345 =CECT 7897) and F2-178 (=LMG 26344 =CECT 7898) and Nevskia persephonica represented by strains G6M-30(T) (=DSM 24987 =CECT 7975) and G6-54 (=DSM 25048 =CECT 7976).     

Rouxiella aceris sp. nov., isolated from tree sap and the emended description of the genus Rouxiella

Antonie van Leeuwenhoek - Polyphasic taxonomic studies were performed for the seven strains, which were isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea. Cells...     

Description of five novel thermophilic species of the genus Thermus: Thermus hydrothermalis sp. nov., Thermus neutrinimicus sp. nov., Thermus thalpophilus sp. nov., Thermus albus sp. nov., and Thermus altitudinis sp. nov., isolated from hot spring sediments

Biological denitrification is a significant process in nitrogen biogeochemical cycle of terrestrial geothermal environments, and Thermus species have been shown to be crucial heterotrophic denitrifier in hydrothermal system. Five Gram-stain negative, aerobic and rod-shaped thermophilic bacterial strains were isolated from hot spring sediments in Tibet, China. Phylogenetic analysis based on 16S rRNA gene and whole genome sequences indicated that these isolates should be assigned to the genus Thermus and were most closely related to Thermus caldifontis YIM 73026^T, and Thermus brockianus YS38^T. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the five strains and the type strains of the genus Thermus were lower than the threshold values (95% and 70%, respectively) recommended for bacterial species, which clearly distinguished the five isolates from other species of the genus Thermus and indicated that they represent independent species. Colonies are circular, convex, non-transparent. Cell growth occurred at 37–80 °C (optimum, 60–65 °C), pH 6.0–8.0 (optimum, pH 7.0) and with 0–2.0% (w/v) NaCl (optimum, 0–0.5%). Denitrification genes (narG, nirK, nirS, and norB genes) detected in their genomes indicated their potential function in nitrogen metabolism. The obtained results combined with those of morphological, physiological, and chemotaxonomic characteristics, including the menaquinones, polar lipids, and cellular fatty acids showed that the isolates are proposed as representing five novel species of the genus Thermus, which are proposed as Thermus hydrothermalis sp. nov. SYSU G00291^T, Thermus neutrinimicus sp. nov. SYSU G00388^T, Thermus thalpophilus sp. nov. SYSU G00506^T, Thermus albus sp. nov. SYSU G00608^T, Thermus altitudinis sp. nov. SYSU G00630^T.     

Diversity of basidiomycetous phylloplane yeasts belonging to the genus Dioszegia (Tremellales) and description of Dioszegia athyri sp. nov., Dioszegia butyracea sp. nov. and Dioszegia xingshanensis sp. nov

From approximately 200 basidiomycetous yeast isolates forming orange or orange-red colonies isolated from senescent leaves collected in different regions of China, 29 representative strains varying in their geographic distribution and ballistoconidium forming ability were selected for further phenotypic and molecular taxonomic studies. Sequence analysis of the large subunit (26S) rDNA D1/D2 domain and the internal transcribed spacer (ITS) region including 5.8S rRNA from the strains resulted in the recognition of seven Dioszegia species, including four described species, namely D. aurantiaca, D. fristingensis, D. hungarica and D. zsoltii var. zsoltii and D. zsoltii var. yunnanensis, and three undescribed species. The three new species are described as Dioszegia athyri sp. nov. (type strain: CB 159(T) = AS 2.2559(T) = CBS 10119(T)), Dioszegia butyracea sp. nov. (type strain: CB 261(T) = AS 2.2600(T) = CBS 10122(T)) and Dioszegia xingshanensis sp. nov. (type strain: HB 1.4(T) = AS 2.2481(T) = CBS 10120(T)) in the present study.     

Leonophyllum tenellum nov. gen., nov. sp., an enigmatic plant from the Early Jurassic of the Mecsek Mts (Hungary)

The Early Jurassic flora of the Mecsek Mountains is diverse, with numerous representatives of ferns, seed ferns, cycadophytes, ginkgophytes, and conifers. Its (para-)autochthonous deposition, good preservation and low collection bias has permitted researchers to save delicate, small plant remains that would generally be missing from the fossil record. These plant fossils are characterized by having a “filmy” (probably unilayered) structure, thin stalks with flat leaf-like branches and ultimate irregular segments with streamlined epidermal cells having thick cell walls. Due to the absence of sporangia, the plant remains cannot be confidently assigned to any higher plant group, although they show some similarities to thalloid liverworts with raised vegetative bodies and also have some resemblance to the fern family Hymenophyllaceae. The new genus and species Leonophyllum tenellum Barbacka et Kustatscher is erected.     

Characterization of Bifidobacterium apousia sp. nov., Bifidobacterium choladohabitans sp. nov., and Bifidobacterium polysaccharolyticum sp. nov., three novel species of the genus Bifidobacterium from honey bee gut

Bifidobacterium is one of the dominating bacterial genera in the honey bee gut, and they are the key degrader of diet polysaccharides for the host. Previous genomic analysis shows that they belong to separate phylogenetic clusters and exhibited different functional potentials in hemicellulose digestion. Here, three novel strains from the genus Bifidobacterium were isolated from the guts of the honey bee (Apis mellifera). Phylogenomic analysis showed that the isolates could be grouped into four phylogenetic clusters. The average nucleotide identity values between strains from different clusters are <95%, while strains in Cluster IV belong to the characterized species Bifidobacterium asteroides. Carbohydrate-active enzyme annotation confirmed that the metabolic capacity for carbohydrates varied between clusters of strains. Cells are Gram-positive rods; they grew both anaerobically and in a CO₂-enriched atmosphere. All strains grew at a temperature range of 20–42 °C, with optimum growth at 35 °C. The pH range for growth was 5–9. Strains from different phylogenetic clusters varied in multiple phenotypic and chemotaxonomic characterizations. Thus, we propose three novel species Bifidobacterium apousia sp. nov. whose type strain is W8102^T (=CGMCC 1.18893 ^T = JCM 34587 ^T), Bifidobacterium choladohabitans sp. nov., whose type strain is B14384H11^T (=CGMCC 1.18892 ^T = JCM 34586 ^T), and Bifidobacterium polysaccharolyticum sp. nov. whose type strain is W8117^T (=CGMCC 1.18894 ^T = JCM 34588 ^T).     

Rectogerochammina eugubina nov. gen., nov. sp., a new agglutinated foraminifer from the Upper Cretaceous of Gubbio, Italy

We describe the new agglutinated foraminiferal genus and species Rectogerochammina eugubina nov. gen., nov. sp. from the Upper Cretaceous Scaglia Rossa Formation of the Umbria-Marche Basin in Italy. The genus differs from Gerochammina (Neagu, 1990) in the presence of a terminal uniserial part.