Metabolic and evolutionary relationships among Pyrococcus Species: genetic exchange within a hydrothermal vent environment

Pyrococcus furiosus and Pyrococcus woesei grow optimally at temperatures near 100 degrees C and were isolated from the same shallow marine volcanic vent system. Hybridization of genomic DNA from P. woesei to a DNA microarray containing all 2,065 open reading frames (ORFs) annotated in the P. furiosus genome, in combination with PCR analysis, indicated that homologs of 105 ORFs present in P. furiosus are absent from the uncharacterized genome of P. woesei. Pulsed-field electrophoresis indicated that the sizes of the two genomes are comparable, and the results were consistent with the hypothesis that P. woesei lacks the 105 ORFs found in P. furiosus. The missing ORFs are present in P. furiosus mainly in clusters. These clusters include one cluster (Mal I, PF1737 to PF1751) involved in maltose metabolism and another cluster (PF0691 to PF0695) whose products are thought to remove toxic reactive nitrogen species. Accordingly, it was found that P. woesei, in contrast to P. furiosus, is unable to utilize maltose as a carbon source for growth, and the growth of P. woesei on starch was inhibited by addition of a nitric oxide generator. In P. furiosus the ORF clusters not present in P. woesei are bracketed by or are in the vicinity of insertion sequences or long clusters of tandem repeats (LCTRs). While the role of LCTRs in lateral gene transfer is not known, the Mal I cluster in P. furiosus is a composite transposon that undergoes replicative transposition. The same locus in P. woesei lacks any evidence of insertion activity, indicating that P. woesei is a sister or even the parent of P. furiosus. P. woesei may have acquired by lateral gene transfer more than 100 ORFs from other organisms living in the same thermophilic environment to produce the type strain of P. furiosus.     

A proposal to rename the hyperthermophile Pyrococcus woesei as Pyrococcus furiosus subsp. woesei

Pyrococcus species are hyperthermophilic members of the order Thermococcales, with optimal growth temperatures approaching 100 degrees C. All species grow heterotrophically and produce H2 or, in the presence of elemental sulfur (S(o)), H2S. Pyrococcus woesei and P. furiosus were isolated from marine sediments at the same Vulcano Island beach site and share many morphological and physiological characteristics. We report here that the rDNA operons of these strains have identical sequences, including their intergenic spacer regions and part of the 23S rRNA. Both species grow rapidly and produce H2 in the presence of 0.1% maltose and 10-100 microM sodium tungstate in S(o)-free medium. However, P. woesei shows more extensive autolysis than P. furiosus in the stationary phase. Pyrococcus furiosus and P. woesei share three closely related families of insertion sequences (ISs). A Southern blot performed with IS probes showed extensive colinearity between the genomes of P. woesei and P. furiosus. Cloning and sequencing of ISs that were in different contexts in P. woesei and P. furiosus revealed that the napA gene in P. woesei is disrupted by a type III IS element, whereas in P. furiosus, this gene is intact. A type I IS element, closely linked to the napA gene, was observed in the same context in both P. furiosus and P. woesei genomes. Our results suggest that the IS elements are implicated in genomic rearrangements and reshuffling in these closely related strains. We propose to rename P. woesei a subspecies of P. furiosus based on their identical rDNA operon sequences, many common IS elements that are shared genomic markers, and the observation that all P. woesei nucleotide sequences deposited in GenBank to date are > 99% identical to P. furiosus sequences.     

我国大陆细蜉属Caenis 修订及一新种描述(蜉蝣目:细蜉科)

我国大陆细蜉属Caenis共知5种,其中短铗细蜉Caenis parviforcipis(Zhou et al.)n．comb．由短尾蜉属Brachycercus转移而来;中华细蜉Caenis sinensis Gui et al．稚虫形态在本文中首次描述;另外从标本来看,已知的黑铗细蜉Caenis nigroforceps Zhou et al．实际为近岸细蜉Caenis rivulorum Eaton的新异名;本文描述1新种：花斑细蜉Caenis melanoleuca,sp．nov．;第5种黑点细蜉Caenis nigropunctata Klapalek也根据标本得到了确认。文中还给出了以上5种成虫和4种稚虫的检索表。所有标本都保存在南京师范大学生命科学学院。     

Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845)

Capnocytophaga ochracea (Prévot et al. 1956) Leadbetter et al. 1982 is the type species of the genus Capnocytophaga. It is of interest because of its location in the Flavobacteriaceae, a genomically not yet charted family within the order Flavobacteriales. The species grows as fusiform to rod shaped cells which tend to form clumps and are able to move by gliding. C. ochracea is known as a capnophilic (CO(2)-requiring) organism with the ability to grow under anaerobic as well as aerobic conditions (oxygen concentration larger than 15%), here only in the presence of 5% CO(2). Strain VPI 2845(T), the type strain of the species, is portrayed in this report as a gliding, Gram-negative bacterium, originally isolated from a human oral cavity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the flavobacterial genus Capnocytophaga, and the 2,612,925 bp long single replicon genome with its 2193 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

The yeast genus Yarrowia gen. nov.

The ascigerous teleomorph of Candida lipolytica (Harrison) Diddens et Lodder, previously classified as Endomycopsis lipolytica Wickerham et al. and as Saccharomycopsis lipolytica (Wickerham et al.) Yarrow, has been assigned to the new genus Yarrowia. Yarrowia lipolytica (Wickerham et al.) comb. nov. is the type species for the genus.The remaining species of Saccharomycopsis are revised.     

Flagellar Morphology of Vibrio parahaemolyticus (Fujino et al) Sakazaki,Iwanami and Fukumi 19631

The flagellar morphology of 88 Vibrio parahaemolyticus strains, including a strain descended from Fujino's original strain EB101 (= ATCC17802 = KM1339) was studied. EB101 and 83 other strains (95%) showed mixed polar and peritrichous type of flagellation when grown on modified MOF (MMOF) agar after 16-hr incubation at 20 C. Cultures containing numerous peritrichous cells showed wiggly movements in moist preparations and rapidly spreading growth in semisolid agar plates. Peritrichous flagella were easily removed mechanically from the soma. The mean wavelengths of polar and peritrichous flagella were 2.53 μm (normal type) and 1.72 μm (atypical curly type) respectively. Peritrichous cells on solid media appeared after incubation for 2.5 hr at 37 C and 7 hr at 20 C. Overnight incubation at 37 C and acidity of the medium due to fermentation of carbohydrate markedly ruined peritrichous flagella. Electron micrograph of cells grown on MMOF agar revealed a sheathed polar flagellum and unsheathed peritrichous flagella. A hook structure was demonstrated at the proximal end of the latter. Polar monotrichous cultures in MMOF broth sometimes contained some cells having several or many peritrichous flagella of atypical curly type. Seven strains of Vibrio cholerae were exclusively polar monotrichous on solid and in liquid media. The flagellation of V. parahaemolyticus is concluded as being a mixed polar-peritrichous type. This fact would indicate that V. parahaemolyticus should be excluded from the genus Vibrio, since the genus Vibrio was defined as polar monotrichous.     

中国的脊棱齿象属(Stegolophodon)化石

剑齿象属 Stegodon 起源于脊棱齿象属 Stegolophodon,两者都是亚洲大陆晚新生代的特有动物,本文讨论两属中一些种的性质和分类位置问题,并记述了药铺脊棱齿象 Stegolophodon officinalis 的新材料.     

PSEUDOTETRACYSTIS,A NEW CHLOROSARCINACEAN ALGA12

Pseudotetracystis terrestris gen. et sp. nov., a member of the Chlorosarcinaceae, was isolated into axenic culture from dry surface soil collected near Texon in Reagan County, Texas. The characteristics of this presently monotypic genus include vegetative cells with a parietal chloroplast, a single pyrenoid, and polymorphic motile cells which are of the Protosiphon-type (naked with 2 equal flagella); P. terrestris is the type species. Vegetative cell division (desmoschisis) forms diads and tetrahedral or planar tetrads, sometimes aggregated in transitory complexes. Reproduction is by the polymorphic motile cells which may function either as gametes to form zygotes which develop without dormancy directly into vegetative cells, or they may function as zoospores and develop directly into vegetative cells without union.     

Re-evaluation on the diversity of the polyphyletic genus Metaurostylopsis (Ciliophora, Hypotricha): ontogenetic, morphologic, and molecular data suggest the establishment of a new genus Apourostylopsis n. g

The urostylid genus Metaurostylopsis Song et al., 2001 was considered to be a well-outlined taxon. Nevertheless, recent evidence, including morphological, ontogenetic, and molecular information, have consistently revealed conflicts among congeners, regarding their systematic relationships, ciliature patterns, and origins of ciliary organelles. In the present work, the morphogenetic and morphogenetic features were re-checked and compared, and the phylogeny of nominal species was analysed based on information inferred from the small subunit ribosomal RNA (SS rRNA) gene sequence. In addition, the binary divisional process in a new isolate of Metaurostylopsis struederkypkeae Shao et al., 2008 is described. All results obtained reveal that the genus is a polyphyletic assemblage whose nominal congeners fall into three clades within the core Urostylida, based on SS rRNA gene sequences. These three clades not match the groups inferred from morphological/morphogenetical evidences. Some conflicting data from molecular and ontogenetic studies also indicate that single-gene information might not be consistently reliable in detecting the phylogenetic relationships among closely related groups and comprehensive multi-gene analyses are necessary to give a more exact evaluation for this divergent assemblage. According to our new understandings, five forms are confirmed to be true Metaurostylopsis. The morphotype Metaurostylopsis sinica Shao et al., 2008 should be excluded from the genus and represents a distinct type, and, thus, a new genus Apourostylopsis n. g. with it as the type specie, i.e. Apourostylopsis sinica (Shao et al., 2008) n. comb.     

论泥盆纪腕足动物Yunnanella和Nayunnella属

腕足动物Yunnanella和Nayunnella两属在我国分布很广 ,是晚泥盆世法门期重要的带化石之一。由于命名等问题 ,迄今 ,这两属的使用在国内外仍比较混乱。Sartenaer (196 1a ,196 2 )根据国际动物命名法规提出 ,YunnanellaGrabau ,192 3和NayunnellaSartenaer ,196 1两属的命名是有效的 ,它们的模式种分别是Yunnanellahanburii (Davidson ,185 3)和YunnanellasynplicataGrabau ,1931。YunnanellaGrabau ,1931是YunnanellaGrabau ,192 3的异物同名 ,YunnanellinaGrabau ,1931是YunnanellaGrabau ,192 3的同物异名。研究认为 ,Sartenaer(196 1a ,196 2 )的观点符合国际动物命名法规的优先原则 ,应予采纳     

Complete genome sequence of Arcobacter nitrofigilis type strain (CI)

Arcobacter nitrofigilis (McClung et al. 1983) Vandamme et al. 1991 is the type species of the genus Arcobacter in the family Campylobacteraceae within the Epsilonproteobacteria. The species was first described in 1983 as Campylobacter nitrofigilis [1] after its detection as a free-living, nitrogen-fixing Campylobacter species associated with Spartina alterniflora Loisel roots [2]. It is of phylogenetic interest because of its lifestyle as a symbiotic organism in a marine environment in contrast to many other Arcobacter species which are associated with warm-blooded animals and tend to be pathogenic. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a type stain of the genus Arcobacter. The 3,192,235 bp genome with its 3,154 protein-coding and 70 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas.

Based on the results of a phylogenetic analysis of 16S rRNA and the presence of sphingoglycolipid in cellular lipids of the type strains, transfer of "Rhizomonas" suberifaciens, Blastomonas natatoria and Erythromonas ursincola to the genus Sphingomonas as Sphingomonas suberifaciens (van Bruggen et al 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., and Sphingomonas ursincola (Yurkov et al 1997) comb. nov. are herein proposed together with the emendation of genus Sphingomonas. The type strain of S. suberifaciens is van Bruggen Cal=ATCC 49382=NCPPB 3629=IFO 15211=JCM 8521, that of S. natatoria is ATCC 35951 =DSM 3183=NCIMB 12085=JCM10396, and that of S. ursincola is DSM 9006= KR-99.     

中国鸡皮衣属二新记录种

1 INTRODUCTION Pertusaria is a fairly large genus of Pertusariaceae with around 170 species recognized(Kirk et al.2001).The genus is characterized by the verrucose thallus,and the large spores(often longer than 30μm)with a conspicuously thick wall(more than 2.5μm thick).Both morphology and chemistry are essential for identifying species in this genus(Oshio 1968; Dibben 1980; Archer 1991,1997;Lumbsch et al.1999).Studies of the Chinese Pertusaria have been extensively developed with 45taxa accepted to data(Zhao et al.2004).A considerable portion of these taxa are difficult to be distinguished without chemical data which,however,have been detected for only a handful of species (Yu et al.1999; Zhao et al.2004).     

Application of stains-all staining to the analysis of axonemal tubulins: identification of beta-tubulin and beta-isotubulins.

The cationic dye, Stains-all, is known to stain brain beta-tubulin blue and alpha-tubulin red (Serrano, L. et al. (1986) J. Biochem. Biophys. Methods 12, 281-287; Serrano, L. et al. (1989) Biochem. Int., 19, 235-246). The present experiments show that this stain can also be applied to detect beta-tubulin in axonemal tubulins from various sources such as cilia of protozoa, sperm flagella of echinoderm, and sperm flagella of mollusc. Furthermore, these experiments showed that it selectively stains isoforms of axonemal beta-tubulin blue following isoelectric focusing, whereas those of alpha-tubulin are stained red. These results indicate that Stains-all staining is a useful tool for electrophoretic analysis of axonemal tubulins.     

再论三叶虫Megapalaeolenus Chang,1966属的无效地位

作者2004年根据保存于法国的模式标本和产自我国三峡地区的新材料以及对以往所发现的化石材料的研究,认为Megapalaeolenus Chang,1966一属不能成立,是Palaeolenus Mansuy,1912的晚出异名;其模式种Palaeolenus deprati Mansuy,1912也是Palaeolenus的模式种Palaeolenus douvillei,Mansuy,1912的晚出异名.提出属名Megapalaeolenus Chang和种名Palaeolenusdeprati Mansuy均应废弃的结论.最近,罗惠麟等发表了一系列采自模式标本产地附近的标本,为笔者的上述结论提供了更有力的证据.根据这些新材料,笔者不同意罗惠麟等认为Megapalaeolenus继续有效、Palaeolenusdeprati能够成立的观点.     

Complete genome sequence of Meiothermus ruber type strain (21)

Meiothermus ruber (Loginova et al. 1984) Nobre et al. 1996 is the type species of the genus Meiothermus. This thermophilic genus is of special interest, as its members share relatively low degrees of 16S rRNA gene sequence similarity and constitute a separate evolutionary lineage from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. The temperature related split is in accordance with the chemotaxonomic feature of the polar lipids. M. ruber is a representative of the low-temperature group. This is the first completed genome sequence of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,097,457 bp long genome with its 3,052 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Studies on woloszynskioid dinoflagellates V. Ultrastructure of Biecheleriopsis gen. nov., with description of Biecheleriopsis adriatica sp. nov.

An isolate of the very small marine dinoflagellate Biecheleriopsis adriatica gen. et sp. nov. (12–15 µm long) has been examined by light, scanning and transmission electron microscopy, combined with partial sequencing of nuclear-encoded large subunit rRNA. Biecheleriopsis is a genus of thin-walled dinoflagellates, related to Biecheleria and the taxonomic group of Polarella , Protodinium and Symbiodinium , the latter comprising mainly symbionts of marine invertebrates. The mixotrophic Biecheleriopsis adriatica is characterized by: (i) a special type of apical furrow apparatus; (ii) an eyespot of Type E sensu Moestrup and Daugbjerg; (iii) an unusual type of pyrenoid; and (iv) a spiny resting cyst. Thin sections showed the presence a fibrous connection between the flagellar apparatus and a finger-like extension of the nucleus ('rhizoplast'). It forms a physical connection between the flagella and the nucleus. This unusual structure has previously been considered to characterize the 'true' gymnodinioids, represented by Gymnodinium sensu Daugbjerg et al. and related forms. However, the apical furrow apparatus and the nuclear envelope of Biecheleriopsis are woloszynskioid rather than gymnodinioid. The related genus Biecheleria lacks a rhizoplast, and it also lacks a 51-base pair fragment of domain D2 of the large subunit rRNA, which is present in other woloszynskioids. A physical connection between the flagellar apparatus and the nucleus mediated by a fibrous structure is known in other groups of protists, for example, the 'rhizoplast' of many heterokont flagellates, some green algal flagellates, etc. The phylogenetic significance of a rhizoplast in two groups of dinoflagellates that are only distantly related is presently difficult to assess.     

Flagellar membrane proteins of Tetraselmis striata butcher (Chlorophyta)

Highly purified flagella of the green alga Tetraselmis striata (Chlorophyta) were extracted by Triton X-114 phase partitioning. SDS-PAGE analysis revealed that most proteins were present in the aqueous phase, only two prominent flagellar membrane proteins (fmp) of apparent molecular weight 145 and 57 kDa (fmp145 and fmp57) were enriched in the detergent phase. Fmp145 was purified by gel permeation chromatography. Glycosidase treatment in combination with lectin blot analysis showed that fmp145 is a glycoprotein containing 3-5 N-glycans of the high mannose and/or hybrid type. A polyclonal antibody (anti-fmp136) was raised against the deglycosylated form of fmp145 and used to localize fmp145 by immunofluorescence and immunoelectron microscopy. Immunogold labeling showed fmp145 to be present between the scale layers and the flagellar membrane. During flagellar regeneration fmp145 is incorporated evenly and rapidly into the newly developing flagella. Anti-fmp136 specifically cross-reacted with flagella of only a subgroup of Tetraselmis strains characterized by a specific flagellar hair type (type II according to Marin et al. 1993) and thus could be a useful immunomarker for the identification of Tetraselmis strains by fluorescence microscopy.     

云南鲤属(Cyprinus)鱼类的分类整理

关于鲤属鱼类的分类,过去已有两次比较系统的研究,但对亚属的划分、种下阶元的判定等仍有争议。原因是分类所循的外形性状变异较大,且多互相重叠。本文试从骨骼比较入手,寻找新的、较为稳定的分类依据。经比较分析,鲤属鱼类的第一脊椎横突、上颌骨、上筛骨、额骨、枕骨突、犁骨、下咽骨和下颌骨等存在明显差异,可作为划分亚属和种的鉴别特征。据此重新分类整理,认为Mesocyprinus亚属仍能成立,首次把产于洱海的厚唇鲤cyprinus crassilabris Chen et Hwang归入杞麓鲤Cyprinus carpio chilia Wu et al.的同物异名;Cyprinus pellegrini pellegrini Tchang,Cyprinus pellegrini barbatus Chen et Hwang,Cyprinns yunnanensis yunnanensis Tchang和Cyprinus yunnanensis daliensis Chen et Hwang在骨骼上有明显分化,由亚种提升为各自独立的种。整理后云南共有鲤属鱼类12个种和亚种,以骨骼特征做出检索表。     

Cryothecomonas aestivalis sp. nov., a colourless nanoflagellate feeding on the marine centric diatomGuinardia delicatula (Cleve) Hasle

The vegetative life cycle, host specificity, morphology, and ultrastructure of a new phagotrophic nanoflagellate are described:Cryothecomonas aestivalis Drebes, Kühn & Schnepf sp. nov. During summer and autumn it is frequently found in the North Sea phytoplankton feeding on the centric diatomGuinardia delicatula. The flagellate penetrates the diatom cell and phagocytizes the host cytoplasm by means of a pseudopodium that emerges from the posterior cell pole. The mature trophont gives rise to eight or more biflagellate swarmers which leave the emptied diatom frustule. Transmission electron microscopy revealed a delicate theca surrounding the swarmers. The pseudopodium protrudes through a gap in the theca. The cytostome consists of a membranous labyrinth. The mitochondria are of the tubular type. The two apically inserted flagella are heterodynamic and of unequal length. They are smooth, and their basal bodies are surrounded by satellites and fibrous strands (“transitional fibres” sensu Thomsen et al., 1990). In the trophonts and dividing flagellates the transition region between the flagellum and the basal body ends apically with a massive transitional cylinder instead of distinct microtubules, and is surrounded by a funnel of the theca. The nuclear envelope disintegrates during mitosis. Due to the fine structural details the new flagellate is placed in the genusCryothecomonas Thomsen et al., a genus of still uncertain position.