Atopostipes suicloacale gen. nov., sp. nov., isolated from an underground swine manure storage pit

Phenotypic and molecular genetic studies were performed on an unknown facultative anaerobic, catalase-negative, non-spore-forming, rod-shaped bacterium isolated from a pig manure storage pit. The unknown bacterium was nutritionally fastidious with growth enhanced by the addition of rumen fluid and was phenotypically initially identified as an Eubacterium species. Comparative 16S rRNA gene sequencing studies, however, revealed that the unknown bacterium was phylogenetically distant from Eubacterium limosum (the type species of the genus Eubacterium) and related organisms. Phylogenetically, the unknown species displayed a close association with an uncultured organism from human subgingival plaque and formed an unknown sub-line within a cluster of organisms which includes Alloioccoccus otitis, Alkalibacterium olivoapovliticus, Allofustis seminis, Dolosigranulum pigrum, and related organisms, within the low mol% G + C Gram-positive bacteria. Sequence divergence values of > 8% with all known taxonomically recognised taxa, however, clearly indicates the novel bacterium represents a hitherto unknown genus. Based on both phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from pig manure be classified in a new genus and species, as Atopostipes suicloacale gen. nov., sp. nov. The type strain of Atopostipes suicloacale is PPC79(T) = NRRL 23919(T) = DSM 15692(T). Crown Copyright (C) 2004 Published by Elsevier Ltd. All rights reserved.

Atopococcus tabaci gen. nov., sp nov., a novel Gram-positive, catalase-negative, coccus-shaped bacterium isolated from tobacco

A novel Gram-positive, aerobic, catalase-negative, coccus-shaped organism originating from tobacco was characterized using phenotypic and molecular taxonomic methods. The organism contained a cell wall murein based on L-lysine (variation A4 alpha, type L-lysine-L-glutamic acid), synthesized long-chain cellular fatty acids of the straight-chain saturated and monounsaturated types (with C(16:1)omega 9, C-16:0 and C(18:1)omega 9 predominating) and possessed a DNA G+C content of 46 mol%. Based on morphological, biochemical and chemical characteristics, the coccus-shaped organism did not conform to any presently recognized taxon. Comparative 16S rRNA gene sequencing studies confirmed the distinctiveness of the unknown coccus, with the bacterium displaying sequence divergence values of greater than 7% with other recognized Gram-positive taxa. Treeing analysis reinforced its distinctiveness, with the unidentified organism forming a relatively long subline branching at the periphery of an rRNA gene sequence cluster which encompasses the genera Alloiococcus, Allolustis, Alkalibacterium, Atopostipes, Dolosigranulum and Marinilactibacillus. Based on phenotypic and molecular phylogenetic evidence, it is proposed that the unknown organism from tobacco be classified as a new genus and species, Atopococcus tabaci gen. nov., sp. nov. The type strain of Atopococcus tabaci is CCUG 48253(T) (= CIP 108502(T)).

Arsenicicoccus bolidensis gen. nov., sp. nov., a novel actinomycete isolated from contaminated lake sediment

An unknown Gram-positive, catalase-positive, facultatively anaerobic, non-spore-forming, coccus-shaped bacterium originating from sediment was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on LL-diaminopimelic acid (type LL-Dpm-glycine(1)), a complex mixture of saturated, monounsaturated and iso- and anteiso-methyl-branched, non-hydroxylated, long-chain cellular fatty acids and tetrahydrogenated menaquinones with eight isoprene units [MK-8(H-4)] as the major respiratory lipoquinone. This combination of characteristics somewhat resembled members of the suborder Micrococcineae, but did not correspond to any currently described species. Comparative 16S rRNA gene sequencing confirmed that the unidentified coccus-shaped organism is a member of the Actinobacteria and represents a hitherto-unknown subline related to, albeit different from, a number of taxa including Intrasporangium, Janibacter, Terrabacter, Terracoccus and Ornithinicoccus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium originating from lake sediment be classified as a new genus and species, Arsenicicoccus bolidensis gen. nov., sp. nov. (type strain CCUG 47306(T) = DSM 15745(T)).

Allofustis seminis gen. nov., sp. nov., a novel Gram-positive, catalase-negative, rod-shaped bacterium from pig semen

An unknown Gram-positive, catalase-negative, facultatively anaerobic, non-spore-forming, rod-shaped bacterium originating from semen of a pig was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a directly cross-linked cell wall murein based on L-lysine and a DNA G + C content of 39 mol%. Comparative 16S rRNA gene sequencing showed that the unidentified rod-shaped organism formed a hitherto unknown subline related, albeit loosely, to Alkalibacterium olivapovliticus, Alloiococcus otitis, Dolosigranulum pigrum and related organisms, in the low-G + C-content Gram-positive bacteria. However, sequence divergence values of > 11 % from these recognized taxa. clearly indicated that the novel bacterium represents a separate genus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from pig semen be classified as a new genus and species, Allofustis seminis gen. nov., sp. nov. The type strain is strain 01-570-1(T) (=CCUG 45438(T)=CIP 107425(T)).

Characterization of some strains from human clinical sources which resemble “Leptotrichia sanguinegens”: description of Sneathia sanguinegens sp. nov., gen. nov.

Three strains of a gram-negative, blood or serum requiring, rod-shaped bacterium recovered from human clinical specimens were characterised by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed the unknown rod-shaped strains are members of the same species as some fastidious isolates recovered from human blood specimens and previously designated "Leptotrichia sanguinegens". Based on phylogenetic and phenotypic evidence, it is proposed that the isolates from human sources be classified in a new genus Sneathia, as Sneathia sanguinegens gen. nov., sp. nov. The type strain of Sneathia sanguinegens is CCUG 41628T.

Pleistovultur nevesi gen. et sp nov (Aves: Vulturidae) and the diversity of condors and vultures in the South American Pleistocene

Pleistovultur nevesi, a new genus and species of a large Vulturidae is described from the Upper Pleistocene or beginning of the Holocene, based on a complete and well preserved right tibiotarsus from the Cuvieri cave deposits, one of the hundreds of caves of the Lagoa Santa region in Minas Gerais state, Brazil. Also described here is a distal half of a left tibiotarsus from Gruta dos Brejoes, a cave in Morro do Chapeu, Bahia state, Brazil, which probably belongs to another not-yet-known genus and species of the Vulturidae. The described material, added to prior literature, is proof of the appreciable diversity of the Vulturidae during the Pleistocene in South America.

On the first terrestrial ostracod of the Superfamily Cytheroidea (Crustacea, Ostracoda): description of Intrepidocythere ibipora n. gen. n. sp from forest leaf litter in Sao Paulo State, Brazil

Of the three superfamilies of Ostracoda present in fresh water, only the Cytheroidea had thus far no records in terrestrial environments. Here, we report on a new genus and species, Intrepidocythere ibipora n. gen. n. sp., of the ostracod superfamily Cytheroidea, from forest leaf litter in Sao Paulo State, Brazil. Judging from morphological similarities, this new genus is believed to be closely related to the genus Elpidium. Possible pathways that led to the colonisation of terrestrial habitats are discussed, and an overview is given on the distribution of the known terrestrial ostracod lineages. The present findings strengthen the idea that terrestrial ostracods are more common than previously thought, at least in tropical areas.

Systematics and phylogeny of Cristacoxidae (Copepoda, Harpacticoida): a review

Both sexes of a new species of Noodtorthopsyllus Lang, 1965 (Harpacticoida, Cristacoxidae) from a sandy beach in Sao Paulo State (Brazil) are described using light and scanning electron microscopy. Noodtorthopsyllus tageae sp. nov. displays a mosaic of characters drawn from both Noodtorthopsyllus and Cristacoxa Huys, 1990, blurring the boundaries between both genera. Consequently, Cristacoxa, the type genus of the nominal family-group taxon Cristacoxidae Huys, 1990, is relegated to a junior subjective synonym of Noodtorthopsyllus, and its type species is transferred to the latter as N. petkovskii (Huys, 1990) comb. nov. A new genus Acuticoxa is proposed to accommodate A. ubatubaensis sp. nov. (type species), collected on the northern continental shelf of Sao Paulo State, and A. biarticulata sp. nov., previously identified as Laophontisochra sp., from the Northern Magellan Straits. Amended diagnoses are provided for Noodtorthopsyllus and Laophontisochra. Autapomorphies supporting the monophyly of the Cristacoxidae are re-evaluated, including new data on P3 endopod sexual dimorphism and caudal ramus development. It is concluded that a recently published hypothesis of a deeply rooted split of the family into two highly divergent lineages cannot be supported. Consequently, both Laophontisochra and Acuticoxa gen. nov. are removed from the Cristacoxidae and tentatively assigned to the Nannopodidae (ex Huntemanniidae), forming a clade with three other genera displaying coxal modifications on leg 1 (Rosacletodes Wells, 1985; Huntemannia Poppe, 1884; and an as yet undescribed genus from Brazil). Based on the sexual dimorphism of the P4 endopod, we propose to transfer Metahuntemannia Smirnov, 1946 and Pottekia Huys, 2009 from the Nannopodidae to the Canthocamptidae (subfamily Hemimesochrinae) where they are probably most closely related to Psammocamptus Mielke, 1975; Bathycamptus Huys & Thistle, 1989; Perucamptus Huys & Thistle, 1989; and Isthmiocaris George & Schminke, 2003. An identification key to the genera of the Nannopodidae is presented.

Early carboniferous athyridid brachiopods from the Qaidam Basin, Northwest China

Four new Early Carboniferous athyridid species in three genera, including one new genus, Bruntonathyris, are described from the Qaidam Basin, northwest China: Lamellosathyris qaidamensis, Bruntonathyris amunikeensis, Bruntonathyris? heijianshanensis, and Lochengia qinghaiensis. Based on the new material and also on published information, we also reviewed the taxonomic composition and the stratigraphic and paleogeographic distributions of the three genera. As a result, Lamellosathyris is considered to be indicative of late Famennian to Viséan age, originating in late Famennian in central North America and Armenia of Russia, respectively. Later, the genus appears to have two migratory directions: one branch rapidly dispersed over Mississippi Valley, Oklahoma, Texas and New Mexico of central North America in Tournaisian; alternatively, another branch from Armenia migrated westerly to Belgium, France, Spain, Britain, Ireland, via the Moscow Basin and Ural seaway, eastward to the Tienshan Mountains and Qaidam Basin of northwest China during the Tournaisian to Viséan, and easterly along the southern shelves of the Paleo-Tethys to Iran and western Yunnan of southwestern China in Tournaisian. Both Bruntonathyris and Lochengia are restrictedly Tournaisian to Viséan in age, and probably originated in the Qaidam Basin. Later, Bruntonathyris migrated easterly to South China and Japan, and westerly to Urals, Moscow Basin, Donetsk Basin and Britain; Lochengia migrated easterly to South China and westerly to the Urals seaway and the adjoined Russian Platform (i.e., both the Moscow and Donetsk Basins).

Permian brachiopoda from China and Malaysia : palaeoecology, palaeobiogeography and extinctions

The systematics, palaeoecology, palaeobiogeography and patterns of faunal change of Permian brachiopods from Sichuan, China and Pahang, Malaysia were investigated. The brachiopods from Pahang were systematically described for the first time. Five new species and one new genus were found in Sichuan, and two extinction and five origination events were recognised.

Implications of Kungurian (Early Permian) conodonts from Hatahoko, Japan, for correlation between the Tethyan and international timescales

The correlation between the fusulinid-based Tethyan and the conodont-based international timescales of the Permian System has become one of themost disputed issues among the Permian community during the past two decades. In this paper,we document a conodont fauna consisting of four species including Sweetognathus guizhouensis, Pseudohindeodus augustus, Hindeodus permicus and a new genus Meiognathus pustulus from the lower part of a large exotic limestone block at Hatahoko in the Nyukawa area, Gifu Prefecture, central Japan, which all suggest aKungurian age. The Kungurian age indicated by the conodonts is consistent with the age of the associated brachiopods, but conflicts with the Murgabian age indicated by the associated fusulinids including Cancellina nipponica, Neoschwagerina simplex, Neofusulinella praecursor etc. This co-occurrence of Kungurian conodonts and Murgabian fusulinids in central Japan suggests that previously unrecognized temporal distributions of some key fusulinid or conodont elements need to be clarified and that the intensively-disputed correlation problem between theKungurian containing theMurgabian fusulinids at the Luodian section in Guizhou, South China with the strata containing the ammonoid Waagenoceras in Oman and Sicily was caused by artificial conodont taxonomic discrepancies. The Luodian section in South China could serve as a key reference section for the correlation of the Kungurian Stage (late Early Permian) between the Tethyan and international timescales. 

First report of a phytogeographically mixed (transitional) Middle-Late Permian fossil wood assemblage from the Hami area, northwest China, and implications for Permian phytogeographical, paleogeographical and paleoclimatic evolution in central Asia

A diverse and well-preserved fossil wood assemblage is described, for the first time, from the Middle Permian Taerlang Formation and the Upper Permian Quanzijie Formation in the vicinity of the Tianshan Town, Hami City of northwestern China. On the basis of wood microstructure, the fossil woods are classified into three genera and five species, including one new genus: Prototianshanoxylon gen. nov. and two new species: Prototianshanoxylon erdaogouense sp. nov., Prototianshanoxylon hamiense sp. nov. The new genus is characterized by window-like cross-field pitting and mixed tracheid radial wall pitting that suggest a transitional type between araucarioid-type and protopinoid-type pittings.Phytogeographically, the fossil wood assemblage is characterized by an admixture of elements of both temperate Angaran (represented by wood specimens with moderately to well defined growth rings in their secondary xylem) and tropical-subtropical north subregion of the Cathaysian floras (with wood specimens lacking well-defined growth rings). Such a phytogeographically mixed fossil wood assemblage is interpreted to represent a transitional and complex climate condition between a cool temperate and tropical to subtropical zones, showing both seasonal variation and unstable climate conditions. Previously, similarly mixed floras have already been found to exist widely in northern China ranging in age from Early to Late Permian, but the mechanisms thought to be responsible for their formation were varied and remain controversial. In this study, the formation of these mixed Permian floras of North China is linked to the closure of the Tianshan-Hingan seaway coupled with the collision and amalgamation of Siberia with North China and the Tarim block, in a manner much like closing a pair of scissors with the closure of the seaway proceeding gradually and progressively from west to the east.

Filogenia molecular de fungos gasteroides das ordens Phallales e Geastrales (Phallomycetidae)

Gasteroids fungi are characterized by the basidiospores maturation inside the basidioma, from which spores liberation occurs in a passive manner. These fungi were once seen as a well definite class of Basidiomycota, but nowadays they are considered an artificial assemblage, because the organisms have independent evolutionary histories forming a polyphyletic group with a vast morphological variety. Despite their diversity, studies with this group in the tropics are incipient, and the phylogenetic relationships of the species from temperate climate remain unknown. Thus, this work aimed to elucidate the phylogenetic relationships of gasteroids fungi from the Geastrales and Phallales orders, with the inclusion of tropical and temperate species, and with these analyses suggest a systematic position of species like Aseroë floriformis and Phallus roseus, as well as to verify if the lignicolous habit can indicate parental relationship in the Geastrum genus. For this, basidiomata were collected at Atlantic rain forest areas, during the rainy season, and the specimen identification followed specific literature for gasteroid fungi. The phylogenetic analyses were performed with Maximum Parsimony and Bayesian Analysis, making use of RPB2 and 28S nuclear genes and atp6 mitochondrial gene. It could be observed on the Phallales dendogram, that Aseroë floriformis did not cluster with A. rubra, and that it has an anterior divergence from all others species of the family Clathraceae used in this analysis, assuming a basal position in the clade. Phallus roseus, which once was recognized as Itajahya, has previous divergence from the group formed by Phallus species. At the Geastrales dendogram, in the group corresponding to Geastrum genus, it could be observed that species with lignicolous habitat clustered in a clade with high support values. So, the results suggest the creation of a new genus to accommodate A. floriformis, and the revalidation of Itajahya, as well as it can be affirmed that the lignicolous habitat on the Geastrum genus in fact indicates parental relationships, and that it has arised only once at the evolutionary history of the genus

Dinâmica sazional de fungos micorrízicos arbusculares (Glomeromycota) em cerradão e brejo de altitude na Chapada do Araripe, CE

Arbuscular mycorrhizal fungi (AMF) are obligatory symbiotic organisms that associate with roots of a large number of plant taxa, and are found in all terrestrial ecosystems. These fungi promote greater tolerance to environmental stresses to associated plant, favoring the establishment of plant communities, especially where soil fertility is a limiting factor, as in the Caatinga, an exclusively Brazilian domain that has been focus of research due to its great biodiversity that can help clarify the history of vegetation in South America. Because of the ecological importance of AMF, the limited number of jobs and the potential diversity of the Caatinga, this work aims to inventory the diversity and determine AMF communities in areas with different faces occurrent in FLONA Araripe, Ceará (CE). The sample collection occurred in four periods at the beginning and end of the dry season (August and December 2011, respectively) and rainy (February and June 2012, respectively) in an area of marsh and woodland altitude of the Araripe, Crato, CE. The glomerosporos were extracted by wet sieving and centrifugation in water and sucrose (50%) mounted between slide and coverslip using PVLG and PVLG + Reagent Melzer. In total, we found 46 species of AMF distributed in eight families and 16 genera: Acaulospora (6), Ambispora (1), Cetraspora (2), Dentiscutata (5), Fuscutata (2), Gigaspora (6), Glomus (13) Intraornatospora (1), Kuklospora (1), Orbispora (1), Paradentiscutata (1), Quatunica (1), Racocetra (1), Scutellospora (2), Septoglomus (2) and a new genus. analysis showed that ecological each area of study has its own seasonal dynamics, with an area of woodland with a greater diversity of species throughout the year, while the marsh elevation showed greater variation in species found among the collection periods, showing that vegetation and rainfall has strong influence on the seasonal dynamics of AMF, as well as the availability of nutrients and soil pH so

Evolutionary and biogeographic history of the subfamily Neoplecostominae (Siluriformes: Loricariidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)