Isolation of a new heterolobosean amoeba from a rice field soil: Vrihiamoeba italica gen. nov., sp. nov.

A heterolobosean amoeba strain 6_5F was isolated from an Italian rice field soil. Although 18S rRNA gene sequence analysis demonstrated that the new isolate was closely related to Stachyamoeba sp. ATCC 50324, further molecular analysis and morphological observation showed distinct differences amongst the two. The 5.8S rRNA gene was successfully amplified and sequenced for strain 6_5F but not for strain ATCC 50324. Trophozoites of strain ATCC 50324 transform into flagellate forms in the late stage of incubation before encystment, while strain 6_5F do not show flagellate forms under different conditions of the flagellation test. Light and electron microscopic observation showed the structural difference of cysts of strain 6_5F from strain ATCC 50324 and also from the type strain Stachyamoeba lipophora. The results show that the strain 6_5F is distinct from Stachyamoeba spp. and we propose a new genus and species for this isolate, Vrihiamoeba italica gen. nov., sp. nov.     

Stenomitos terricola sp. nov. (Leptolyngbyaceae,Cyanobacteria) from the moist soil of Mt. Gwanggyo,Republic of Korea

Stenomitos terricola FBCC-A190 was collected from soils around the trees of Mt. Gwanggyo, located in Yeongtong-gu, Suwon-si, Gyeonggi-do. S. terricola FBCC-A190 is a thin and simple filament with a cell length that is longer than its width. It has a thin and firm sheath, exhibiting a blue-green color. Species belonging to genus Stenomitos is semi-cryptic species with slight morphological differences from each other. They were confirmed as Stenomitos species by analysis using 16S rRNA and 16S–23S ITS. A monophyletic cluster was formed with the previously reported genus Stenomitos, with 16S rRNA gene sequences sharing similarities of 95.9–97.9% except for S. pantisii TAU-MAC 4318. In addition, 16S–23S ITS gene sequencing showed tRNA^Ala, tRNA^Ile and V2, similar to the previously reported genus Stenomitos. From these results, Stenomitos terricola sp. nov. was proposed as a new species belonging to genus Stenomitos.     

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.     

Colletotrichum gigasporum sp. nov., a new species of Colletotrichum producing long straight conidia

A new species of Colletotrichum was described, based on morphology and phylogeny. The fungus was isolated in Madagascar from healthy leaves of Centella asiatica, in Mexico from wild native of Stylosanthes guianensis and in Colombia from Coffea arabica. The fungus differed from the currently related species in the genus by its longer and wider size of conidia. In potato dextrose agar medium supplemented with sterilized leaf powder of Ce. asiatica, the fungus produced fertile perithecia containing asci and unusual long ascospores measuring up to 90 μm. In addition to these morphological characteristics, the maximum parsimony analysis of the ITS region and β-tubulin gene placed the fungus in a distinct clade far from the currently valid Colletotrichum species. Based on the morphological and molecular characterization, Colletotrichum gigasporum sp. nov. was proposed as a new species in the genus Colletotrichum Corda.     

Parablastocatena tetracerae gen. et sp. nov. and Corynesporella licualae sp. nov. from Hainan, China

Parablastocatena tetracerae gen. et sp. nov. and Corynesporella licualae sp. nov., collected on dead branches of Tetracera asiatica and Licuala fordiana, respectively, in tropical forests of China, are described and illustrated. Parablastocatena tetracerae is the type species for a new monotypic genus in possessing macronematous conidiophores forming distinct synnemata with holoblastic conidiogenesis and euseptate, short-chained conidia ending in a paler brown rostrum, whereas C. licualae is distinguished from described species by the smaller conidia with long appendages. A key to currently accepted species of Corynesporella is provided.     

Lecithoceridae (Lepidoptera: Gelechioidea) of New Guinea,Part V: Descriptions of two new genera,Neotimyra gen. nov. and Strombiola gen. nov.

This is the 5th part in a series on the family Lecithoceridae (Lepidoptera, Gelechioidea) of New Guinea. Two new genera, Neotimyra gen. nov. and Strombiola gen. nov. are proposed. There are five new species in the genus Neotimyra (N. senara sp. nov., N. milleri sp. nov., N. gyriola sp. nov., N. warkapiensis sp. nov., and N. nemoralis sp. nov.), and one new species in the genus Strombiola (S. papuana sp. nov.). Adults, heads, labial palpi, venations, and male genitalia are illustrated.     

Streptomyces erringtonii sp. nov. and Streptomyces kaempferi sp. nov., isolated from a hay meadow soil

Two filamentous actinomycetes isolated from a hay meadow soil were provisionally assigned to the genus Streptomyces based on morphological features. The isolates were found to have chemical and morphological properties typical of the genus Streptomyces and formed distinct phyletic lines in the 16S rRNA gene tree. Isolate I36^T was most closely related to Streptomyces glauciniger NBRC 100913^T and isolate I37^T to Streptomyces mirabilis NBRC 13450^T. Low DNA:DNA relatedness values were recorded between each of the isolates and their closest phylogenetic neighbour. The isolates were also distinguished from their nearest phylogenetic neighbour, and from one another, using a combination of phenotypic properties. These data indicate that the isolates should be recognised as new species in the genus Streptomyces. The names proposed for these new taxa are Streptomyces erringtonii sp. nov. and Streptomyces kaempferi sp. nov. with isolate I36^T (=CGMCC 4.7016^T = KACC 15424^T) and isolate I37^T (=CGMCC 4.7020^T = KACC 15428^T) as the respective type strains.     

Morphological and genetic analysis of the Coolia monotis species complex with the introduction of two new species,Coolia santacroce sp. nov. and Coolia palmyrensis sp. nov. (Dinophyceae)

The dinoflagellate genus Coolia Meunier is an important epi-benthic organism that is commonly found in association with other dinoflagellates known to cause ciguatera. Two closely related taxa, Coolia monotis and Coolia malayensis, make up the C. monotis species complex. In this study we introduce two new toxic species that should be included in that complex, Coolia palmyrensis Karafas, Tomas, York sp. nov. and Coolia santacroce Karafas, Tomas, York sp. nov., collected from the Palmyra Atoll in the Pacific Ocean and Saint Croix, US Virgin Islands, respectively. These two species can be distinguished morphologically by size, pore shape, pore density, and the relative size of the apical pore complex. The ITS1/5.8S/ITS2 and the D1/D2 regions of the LSU rDNA were used to provide molecular support of morphological observations using maximum likelihood and Bayesian analyses. Furthermore, C. palmyrensis and C. santacroce both showed cytotoxic effects on human derived cells in vitro.     

Azospirillum himalayense sp. nov., a nifH bacterium isolated from Himalayan valley soil,India

Gram-negative, free-living bacterial strain ptl-3^T was isolated from Himalayan valley soil, India. Polyphasic taxonomy was performed including morphological characterization, fatty acid analysis, biochemical tests, 16S rRNA and nifH gene sequence analyses. 16S rRNA gene sequence analysis showed that the strain ptl-3^T belonged to the genus Azospirillum and was closely related to A. brasilense (98.7 % similarity) and A. rugosum (97 % similarity). 16S rRNA gene sequence similarity (96–95 %) was shown with other members of the genus Azospirillum. Major fatty acid 18:1ω7c was also similar to the genus Azospirillum. DNA–DNA relatedness value between strain ptl-3^T and A. brasilense was found to be 47 %. Various biochemical tests showed that the strain ptl-3^T differed from its closely related species A. brasilense. On the basis of phenotypic, chemotaxonomic and molecular genetics evidence, a bacterium with the type strain ptl-3^T is proposed as a novel species of the genus Azospirillum. The name of bacterial strain ptl-3^T has been proposed as Azospirillum himalayense sp. nov. The type strain of ptl-3^T (CCUG 58760^T, KCTC 23189^T) has been submitted to two culture collection centres. The accession numbers for 16S rRNA and nifH gene are GQ 284588 and GQ 249665. respectively.     

A widespread cyanobacterium supported by polyphasic approach: proposition of Koinonema pervagatum gen. & sp. nov. (Oscillatoriales)1

Several new genera originally classified as the genus Phormidium, a polyphyletic and taxonomically complex genus within the Oscillatoriales, were recently described. The simple morphology of Phormidium does not reflect its genetic diversity and the delimitation of a natural group is not possible with traditional classification systems based on morphology alone. Therefore, this study used morphological, ecological, and molecular approaches to evaluate four populations morphologically similar to Ammassolinea, Kamptonema, and Ancylothrix (simple, curved, and gradually attenuated at the ends trichome), found in subtropical and tropical Brazilian regions. 16S rRNA gene sequences grouped all the strains in a highly supported clade with other two European strains isolated from thermal springs surrounding areas. The 16S‐23S ITS secondary structure corroborated the phylogenetic analysis with all the strains having similar structures. Consequently, a genetically well‐defined and cryptic new genus, Koinonema gen. nov., is proposed containing the aquatic, mesophilic, and morphologically homogeneous new species, Koinonema pervagatum sp. nov.     

Morphology and molecular phylogeny of the benthic dinoflagellates (Dinophyceae,Peridiniales) Amphidiniopsis crumena n. sp. and Amphidiniopsis nileribanjensis n. sp.

Amphidiniopsis is a benthic, heterotrophic and thecate dinoflagellate genus that has a smaller epitheca and larger hypotheca. The genus contains 24 described species, but is considered to be polyphyletic based on morphological characters and molecular phylogenetics. In this study, two new species were discovered from two distant sampling localities, Amphidiniopsis crumena sp. nov. from Japan, and Amphidiniopsis nileribanjensis sp. nov., from Australia. These species have a uniquely shaped, additional second postcingular plate. Both species are dorsoventrally flattened, an apical hook is present, and have six postcingular plates. The plate formula is: APC 4′ 3a 7″ ?C 4?S 6″′ 2″″. The cells of these species were examined with LM and SEM, and molecular phylogenic analyses were performed using 18S and 28S rDNA. These species are distinguished by the presence of spines on the hypotheca and touching of the sixth postcingular plate and the anterior sulcal plate. Their shape and disposition of several thecal plates also differ. Molecular phylogenetic analyses showed that the two new species formed a monophyletic clade and did not belong to any morphogroup proposed by previous studies. Considering the morphological features and the molecular phylogenetic results, a new morphogroup is proposed, Amphidiniopsis morphogroup VI (‘crumena group’).     

Marichromatium litoris sp. nov. and Marichromatium chrysaorae sp. nov. isolated from beach sand and from a jelly fish (Chrysaora colorata)

Three strains (JA349^T, JA553^T, JA439) of phototrophic sulphur bacteria were isolated from marine habitats of India. 16S rRNA gene sequence of the three strains clustered phylogenetically with members of the genus Marichromatium of the family Chromatiaceae belonging to the class Gammaproteobacteria. All the strains shared highest sequence similarity with the type strains of Marichromatium spp. (96-99% sequence similarity) and the new strains were characterized based on polyphasic taxonomy. Strains JA349^T and JA553^T can be distinguished from closest relative species of the genus Marichromatium with respect to distinct differences in cellular polar lipids, fatty acids and carbon/nitrogen sources utilization. Both strains were distinctly related (<50% based on DNA-DNA hybridization) with the type strains of the genus Marichromatium. Multilocus Sequence Analysis (MLSA) of the concatenated five protein coding genes (fusA, pufM, dnaK, recA, soxB) along with internal transcribed spacer (ITS; 16S-23S rRNA) had sequence similarity of less than 92% with the type strains of Marichromatium spp. Distinct phenotypic, chemotaxonomic and molecular differences allow the separation of strains JA349^T and JA553^T into new species of the genus Marichromatium for which, we propose the names Marichromatium litoris sp. nov. and Marichromatium chrysaorae sp. nov., respectively.     

Peptoniphilus coxii sp. nov. and Peptoniphilus tyrrelliae sp. nov. isolated from human clinical infections

Two groups of previously undescribed anaerobic, gram-positive cocci recovered from human clinical infections were characterized using phenotypic and molecular genotypic methods. Comparative genotypic analysis showed that the strains within each of these two groups were homogeneous within the group and that each group was unique within the genus Peptoniphilus. The first group is most closely related to Peptoniphilus ivorii and the second group to Peptoniphilus harei. Based on these findings we propose two novel species, Peptoniphilus coxii sp. nov. and Peptoniphilus tyrrelliae sp. nov. The type strains are P. coxii sp. nov., RMA 16757^T (= JCM 16892^T = CCUG 59622^T = ATCC BAA-2106^T) and P. tyrrelliae sp. nov., RMA 19911^T (= JCM 16893^T = CCUG 59621^T = ATCC BAA-2105^T).     

Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov

Anaerococcus senegalensis strain JC48^T sp. nov. is the type strain of A. senegalensis sp. nov. a new species within the genus Anaerococcus. This strain whose genome is described here was isolated from the fecal flora of a healthy patient. A. senegalensis is an obligate anaerobic coccus. Here we describe the features of this organism together with the complete genome sequence and annotation. The 1,790,835 bp long genome (1 chromosome but no plasmid) contains 1,721 protein-coding and 53 RNA genes including 5 rRNA genes