Occurrence of the Japanese seahorse Hippocampus mohnikei Bleeker 1854 from the Palk Bay coast of south-eastern India

The occurrence of the Japanese seahorse, Hippocampus mohnikei is reported for the first time from the Palk Bay coast of south-eastern India.     

Length-weight relationship of coral reef-associated fishes from Gulf of Mannar and Palk Bay,Southeast Coast of India

Length-weight relationship parameter was estimated for eight coral reef-associated finfish species from the Gulf of Mannar and Palk Bay, Eastern Indian Ocean. Fish samples were collected from the landings of trawlers with a cod-end mesh size of 25–35 mm, operated at a depth ranging from 50–70 m off Tuticorin, Rameswaram and Thondi coasts on monthly basis between June-2018 and July-2019. Fish specimens were sampled by measuring total length (TL) and total weight (TW) with precision to 0.1 cm and 0.1 g respectively. A new maximum total length was recorded for Canthigaster solandri, Centriscus scutatus and Halichoeres stigmaticus from this study.     

Morphology and small subunit rDNA phylogeny of a new soil ciliate, Bistichella variabilis n. sp. (Ciliophora, Stichotrichia)

We isolated a new ciliate, Bistichella variabilis n. sp., from slightly saline soil of the Yellow River Delta in China and studied it using live observation, protargol staining, and small subunit (SSU) rRNA gene sequencing. Bistichella variabilis is elongated ellipsoidal and about 220 × 70 μm in vivo, with a variable number and arrangement of cirri- ventral row VI mostly very short, but a long row observed also in one specimen, and an extra row occasionally exists besides the left or the right marginal row. Bistichella variabilis differs from all congeners except Bistichella buitkampi (Foissner, 1982) in the macronuclear pattern (four vs. two or many nodules); and from B. buitkampi by the usual oblique arrangement of transverse cirri (vs. perpendicular); and the ventral row VI mostly restricted in the posterior quarter of the cell (vs. long and stretching to the anterior quarter). Phylogenetic analyses of SSU rDNA sequences indicated that B. variabilis grouped with the clade of Orthoamphisiella breviseries and Uroleptoides magnigranulosus with high support values. Despite their distinct differences in morphology, these three species have sequence similarities of 99.5-99.7%. Nonetheless, it is still premature to assign Bistichella together with Uroleptoides to the family Orthoamphisiellidae because of the taxonomic uncertainties and undersampling.     

基于高通量测序技术大亚湾肥胖软箭虫(Flaccisagitta enflata)的食性分析

采用Illuminate高通量测序技术分析了大亚湾肥胖软箭虫(Flaccisagitta enflata)的食性.在夏季(2017年8月)和冬季(2018年1月)对大亚湾内不同站位拖网采获的四组样品中,分别挑取毛颚类优势种肥胖软箭虫进行18S rDNA V4区扩增;通过高通量测序得到四组样品的序列,经过处理每组样品得到...     

单子叶植物高级分类阶元系统演化: matK、rbcL和18S rDNA序列的证据

基于两个叶绿体基因（matK和rbcL）和一个核糖体基因（18S rDNA）的序列分析,对代表了基部被子植物和单子叶植物主要谱系分支的86科126属151种被子植物（单子叶植物58科86属101种）进行了系统演化关系分析。研究结果表明由胡椒目Piperales、樟目Laurales、木兰目Magnoliales和林仙目Canellales构成的真木兰类复合群是单子叶植物的姐妹群。单子叶植物的单系性在3个序列联合分析中得到98％的强烈自展支持。联合分析鉴定出9个单子叶植物主要谱系（广义泽泻目Alismatales、薯蓣目Dioscorcales、露兜树目Pandanales、天门冬目Asparagalcs、百合目Liliales、棕榈目Arecales、禾本目Poales、姜目Zingiberales、鸭跖草目Commelinales）和6个其他被子植物主要谱系（睡莲目Nymphaeales、真双子叶植物、木兰目、樟目、胡椒目、林仙目）。在单子叶植物内,菖蒲目Acorales（菖蒲属Acorus）是单子叶植物最早分化的一个谱系,广义泽泻目（包括天南星科Araceae和岩菖蒲科Toficldiaccae）紧随其后分化出来,二者依次和其余单子叶植物类群构成姐妹群关系。无叶莲科Petrosaviaceac紧随广义的泽泻目之后分化出来,无叶莲科和剩余的单子叶植物类群形成姐妹群关系,并得到了较高的支持率。继无叶莲科之后分化的类群形成两个大的分支：一支是由露兜树目和薯蓣目构成,二者形成姐妹群关系：另一支是由天门冬目、百合目和鸭跖草类复合群组成,三者之间的关系在单个序列分析和联合分析中不稳定,需要进一步扩大取样范围来确定。在鸭跖草类复合群分支内,鸭跖草目和姜目的姐妹群关系在3个序列联合分析和2个序列联合分析的严格一致树中均得到强烈的自展支持,获得的支持率均是100％。但是,对于棕榈目和禾本目在鸭跖草类中的系统位置以及它们和鸭跖草目-姜目之间的关系,有待进一步解决。值得注意的是,无叶莲科与其他单子叶植物类群（除菖蒲目和泽泻目外）的系统关系在本文中获得较高的自展支持率,薯蓣目和天门冬目的单系性在序列联合分析中都得到了较好的自展支持,而这些在以往的研究中通常支持率较低。鉴于菖蒲科和无叶莲科独特的系统演化位置,本文支持将其分别独立成菖蒲目和无叶莲目Petrosavialcs的分类学界定。     

基于部分18S rDNA, 28S rDNA和COI基因序列的索科线虫亲缘关系

通过PCR扩增获得我国常见昆虫病原索科线虫6属10种18S rDNA、28S rDNA(D3区)和COI基因序列,结合来自GenBank中6属10种索科线虫的18S rDNA同源序列,用邻接法和最大简约法构建系统进化树。结果显示:12属索科线虫分为三大类群,第一大类群是三种罗索属线虫(Romanomermis)先聚在一起,再与两索属(Amphimermis)和蛛索属(Aranimermis)线虫聚为一支;在第二大类群中,六索属(Hexamermis)、卵索属线虫(Ovomermis)和多索属(Agamermis)亲缘关系最近,先聚在一起,再与八腱索属(Octomyomermis)和Thaumamermis线虫聚为一支。第三大类群由索属(Mermis)和异索属(Allomermis)线虫以显著水平的置信度先聚在一起,再与蠓索属(Heleidomermis)和施特克尔霍夫索属(Strelkovimermis)线虫聚为一支。从遗传距离看,基于3个基因的数据集均显示索科线虫属内种间差异明显小于属间差异,武昌罗索线虫(R.wuchangensis)和食蚊罗索线虫(R.culicivorax)同属蚊幼寄生罗索属线虫,其种间的遗传距离最小。     

Identification and phylogeny of eukaryotic 18S rDNA phylotypes detected in chlorinated finished drinking water samples from three Parisian surface water treatment plants

Aims:  We performed a preliminary assessment of the eukaryotic 18S rDNA diversity present in finished drinking water samples from three different surface water treatment plants supplying water to the city of Paris (France).
Methods and Results:  A molecular analysis was performed on a sample from each site based on sequencing of PCR amplified and cloned 18S ribosomal RNA genes. Overall, the 18S rDNA sequences combined from all samples could be affiliated to the Amoebozoa (20·8% of the phylotypes), Ciliophora (25%), Metazoa (33·3%), Fungi (8·3%), Cercozoa (4·2%) and unclassified eukaryotes (8·3%) groups.
Conclusions:  The 18S rDNA sequences affiliated to the Amoebozoa, Ciliophora and Metazoa lineages were found to be the most abundant phylotypes observed in the drinking water samples. Phylotypes found to be present in two, or all three, samples (41·7% of the total) may represent groups with members adapted to drinking water treatment plant (DWTP) ecosystem conditions.
Significance and Impact of the Study:  This study shows that finished drinking water can contain 18S rDNA sequences representing a variety of eukaryotic taxa. Further research is needed to better characterize the eukaryotic biodiversity of DWTPs and the effects of the finished drinking water diversity on the downstream water distribution network.     

Monophyly of the family Desmoscolecidae (Nematoda,Demoscolecida) and Its Phylogenetic position inferred from 18S rDNA sequences

To infer the monophyletic origin and phylogenetic relationships of the order Desmoscolecida, a unique and puzzling group of mainly free-living marine nematodes, we newly determined nearly complete 18S rDNA sequences for six marine desmoscolecid nematodes belonging to four genera (Desmoscolex, Greeffiella, Tricoma and Paratricoma). Based on the present data and those of 72 nematode species previously reported, the first molecular phylogenetic analysis focusing on Desmoscolecida was done by using neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods. All four resultant trees consistently and strongly supported that the family Desmoscolecidae forms a monophyletic group with very high node confidence values. The monophyletic clade of desmocolecid nematodes was placed as a sister group of the clade including some members of Monhysterida and Araeolaimida, Cyartonema elegans (Cyartonematidae) and Terschellingia longicaudata (Linhomoeidae) in all the analyses. However, the present phylogenetic trees do not show any direct attraction between the families Desmoscolecidae and Cyartonematidae. Within the monophyletic clade of the family Desmoscolecidae in all of the present phylogenetic trees, there were consistently observed two distinct sub-groups which correspond to the subfamilies Desmoscolecinae [Greeffiella sp. + Desmoscolex sp.] and Tricominae [Paratricoma sp. + Tricoma sp].     

Interrelationships of Staphyliniform groups inferred from 18S and 28S rDNA sequences, with special emphasis on Hydrophiloidea (Coleoptera, Staphyliniformia)

The series Staphyliniformia is one of the mega‐diverse groups of Coleoptera, but the relationships among the main families are still poorly understood. In this paper we address the interrelationships of staphyliniform groups, with special emphasis on Hydrophiloidea and Hydraenidae, based on partial sequences of the ribosomal genes 18S rDNA and 28S rDNA. Sequence data were analysed with parsimony and Bayesian posterior probabilities, in an attempt to overcome the likely effect of some branches longer than the 95% cumulative probability of the estimated normal distribution of the path lengths of the species. The inter‐family relationships in the trees obtained with both methods were in general poorly supported, although most of the results based on the sequence data are in good agreement with morphological studies. In none of our analyses a close relationship between Hydraenidae and Hydrophiloidea was supported, contrary to the traditional view but in agreement with recent morphological investigations. Hydraenidae form a clade with Ptiliidae and Scydmaenidae in the tree obtained with Bayesian probabilities, but are placed as basal group of Staphyliniformia (with Silphidae as subordinate group) in the parsimony tree. Based on the analysed data with a limited set of outgroups Scarabaeoidea are nested within Staphyliniformia. However, this needs further support. Hydrophiloidea s.str., Sphaeridiinae, Histeroidea (Histeridae + Sphaeritidae), and all staphylinoid families included are confirmed as monophyletic, with the exception of Hydraenidae in the parsimony tree. Spercheidae are not a basal group within Hydrophiloidea, as has been previously suggested, but included in a polytomy with other Hydrophilidae in the Bayesian analyses, or its sistergroup (with the inclusion of Epimetopidae) in the parsimony tree. Helophorus is placed at the base of Hydrophiloidea in the parsimony tree. The monophyly of Hydrophiloidea s.l. (including the histeroid families) and Staphylinoidea could not be confirmed by the analysed data. Some results, such as a placement of Silphidae as subordinate group of Hydraenidae (parsimony tree), or a sistergroup relationship between Ptiliidae and Scydmaenidae, appear unlikely from a morphological point of view.     

Morphological,small subunit rRNA,and physiological characterization of Trimyema minutum (Kahl, 1931), an anaerobic ciliate from submarine hydrothermal vents growing from 28 degrees C to 52 degrees C

A thermophilic strain of Trimyema minutum was isolated from the hydrothermally heated sea floor at Vulcano Island (Italy) and cultivated monoxenically on Marinobacter sp. and Methanococcus thermolithotrophicus. It can be propagated strictly anaerobically and is sensitive to oxygen: if exposed to air at 48 degrees C all cells die within 60 min. It grows from 0.45-7.2% (w/v) salt and at pH 6.0-8.0. The isolate is the most extreme thermophilic ciliate which ever has been cultivated, exhibiting an optimal growth temperature of 48 degrees C (doubling time 6 h). Growth occurs between 28 degrees C and 52 degrees C. Trimyema minutum is redescribed using live observation and silver impregnation. Its morphology and the small subunit ribosomal RNA sequence is distinctly different from that of T. compressum, but morphology is highly similar to that of T. shoalsia Nerad et al. 1995, which is thus probably a junior synonym of T. minutum. To stabilize the bewildering species taxonomy in Trimyema, we suggest to recognize our population as a neotype of T. minutum.     

贵州福泉分布桃花水母的形态特征及分子鉴定

2017年10月,在贵州省福泉县发现了桃花水母(Craspedacusta)。观察其形态结构,福泉的桃花水母与索氏桃花水母(C. sowerbyi)高度相似。采用PCR和DNA测序技术扩增和测定了福泉采集桃花水母的核糖体小亚基rRNA基因(18SrRNA)、核糖体RNA基因内转录间隔区(ITS)及线粒体细胞色素氧化酶亚基基因(COI),并与GenBank上已有的桃花水母18S rRNA、ITS、COI基因序列进行了比对。分子鉴定结果显示,福泉的桃花水母18SrRNA、ITS、COI基因序列与索氏桃花水母相似度分别为100%、92%、99%,确定贵州省福泉市发现的桃花水母样品在种分类水平上为索氏桃花水母。并就桃花水母的某些形态学分类指标的标准、不同伞径之间的差值是否能作为桃花水母形态分类的一个新指标这些问题做了讨论。     

Identification of Anguilla anguilla (L.) and Anguilla rostrata (Le Sueur) and their hybrids based on a diagnostic single nucleotide polymorphism in nuclear 18S rDNA

The variability of the nuclear 18S rDNA was examined for 10 species of freshwater eels: Anguilla anguilla, A. australis, A. dieffenbachii, A. japonica, A. marmorata, A. mossambica, A. nebulosa labiata, A. obscura, A. reinhardtii and A. rostrata. We observed that a single nucleotide polymorphism (SNP) separated A. anguilla and A. japonica from the remaining taxa. While this SNP marker may be used to identify hypothetical hybrids of A. japonica and sympatric eel species, we focused on Atlantic eels to evaluate the potential for this diagnostic chromosomal marker to discriminate between individuals of A. anguilla, A. rostrata and their hybrids.     

Small subunit rDNA and Bayesian inference reveal Pectenophilus ornatus (Copepoda incertae sedis) as highly transformed Mytilicolidae, and support assignment of Chondracanthidae and Xarifiidae to Lichomolgoidea (Cyclopoida)

Phylogenetic analysis of newly obtained data from the complete small subunit rDNA (18S) nuclear gene of a wide range of copepods placed the enigmatic Pectenophilus ornatus firmly in the Cyclopoida. Both maximum parsimony tree reconstruction, and Bayesian analysis operating under the GTR + I + Γ model of nucleotide substitution, gave identical solutions and placed P. ornatus at the base of the poecilostome families, in apposition to the mytilicolid taxa. The recently suggested assignment to the Siphonostomatoida on the basis of a tubular mouth cone in the pygmy male was rejected not only by the molecular data but also by new morphological observations. Scanning electron microscopy revealed that the appendage previously interpreted as the mandible was in reality the maxilla, the presumptive ‘labium’ only an intermaxillary outgrowth of the ventral cephalic sclerite bearing the widely separated paragnaths, and that there was no basal fusion between the labrum and the ‘posterior lip’ as in genuine siphonostomatoids. Absence of mandibles and their functional replacement by the anteriorly displaced maxillae is a unique and robust apomorphy for the Mytilicolidae and placed unequivocally P. ornatus in that family. The morphology of male Pectenophilus probably evolved as a result of global progenesis, involving early sexual maturation at the metanauplius stage and the complete cessation of somite and limb development. The molecular data were also employed to examine the relationships of two other highly modified parasitic families, the Xarifiidae (inhabiting hard corals) and the Chondracanthidae (parasitic on marine demersal fishes). Our analyses rejected the previously proposed relationship between Xarifiidae and Vahiniidae and strongly supported an Anchimolgidae + (Rhynchomolgidae + Xarifiidae) clade as sister group to the Sabelliphilidae within a monophyletic Lichomolgoidea. The obtained topology suggests that the common ancestor of this clade had already established a symbiotic relationship with scleractinian corals and that host switching occurred only secondarily in the Rhynchomolgidae, involving predominantly other cnidarian and occasionally noncnidarian hosts. Reassessment of the morphology of Parangium provided new evidence for a relationship with the xarifiids, rendering its current position in the Serpulidicolidae extremely unlikely. Both parsimony and Bayesian analyses revealed an unexpected but strongly supported relationship between the Chondracanthidae and Pseudanthessiidae. This result contrasts with earlier views advocating affinity to the Synapticolidae or Lichomolgidae, but was congruent with the previously unnoticed morphological similarity in antennary armature patterns in the first copepodid stage. The morphological grounds used to establish the Lernaeosoleidae were shown to be secondarily derived characters shared with one or several chondracanthid genera. Particularly the similarity between the Lernaeosoleidae and Markevitchielinus demonstrated that the former evolved from a mesoparasitic ancestor within the Chondracanthidae and consequently should sink as a synonym of the latter. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87 , 403–425.     

Identification of Yersinia pestis as the causative organism of plague in India as determined by 16S rDNA sequencing and RAPD-based genomic fingerprinting

Eighteen isolates of bacteria obtained from the sputum of pneumonic plague patients and from the liver and spleen of rodents from the plague-affected areas of India during 1994-1995 when analyzed by 16S rDNA analysis clearly demonstrated that all 18 isolates exhibit an average similarity of 98.5% with the genus Yersinia and 99.1% with Yersinia pestis, thus identifying the isolates as Y. pestis. The isolates from the human plague patients were found to be genetically more homogeneous compared to the isolates from the rodents which were more heterogeneous. An epidemiological linkage among the rodents and human patients is also indicated by 16S rDNA analysis, which suggests that only a sub-population of the rodents was probably the source of the infectious pathogen to the humans initiating the outbreak of the epidemic. The results of the randomly amplified DNA polymorphisms (RAPD)-based DNA fingerprinting are in agreement with the above conclusions.     

Identification of Lactobacillus alimentarius and Lactobacillus farciminis with 16S-23S rDNA intergenic spacer region polymorphism and PCR amplification using species-specific oligonucleotide

AIMS: The restriction fragment length polymorphism (RFLP) method was used to differentiate Lactobacillus species having closely related identities in the 16S-23S rDNA intergenic spacer region (ISR). Species-specific primers for Lact. farciminis and Lact. alimentarius were designed and allowed rapid identification of these species. METHODS AND RESULTS: The 16S-23S rDNA spacer region was amplified by primers tAla and 23S/p10, then digested by HinfI and TaqI enzymes and analysed by electrophoresis. Digestion by HinfI was not sufficient to differentiate Lact. sakei, Lact. curvatus, Lact. farciminis, Lact. alimentarius, Lact. plantarum and Lact. paraplantarum. In contrast, digestion carried out by TaqI revealed five different patterns allowing these species to be distinguished, except for Lact. plantarum from Lact. paraplantarum. The 16S-23S rDNA spacer region of Lact. farciminis and Lact. alimentarius were amplified and then cloned into vector pCR(R)2.1 and sequenced. The DNA sequences obtained were analysed and species-specific primers were designed from these sequences. The specificity of these primers was positively demonstrated as no response was obtained for 14 other species tested. RESULTS AND CONCLUSIONS: The species-specific primers for Lact. farciminis and Lact. alimentarius were shown to be useful for identifying these species among other lactobacilli. The RFLP profile obtained upon digestion with HinfI and TaqI enzymes can be used to discriminate Lact. farciminis, Lact. alimentarius, Lact. sakei, Lact. curvatus and Lact. plantarum. SIGNIFICANCE AND IMPACT OF THE STUDY: In this paper, we have established the first species-specific primer for PCR identification of Lact. farciminis and Lact. alimentarius. Both species-specific primer and RFLP, could be used as tools for rapid identification of lactobacilli up to species level.     

Identification and control of bacterial contaminants from Ilex dumosa nodal segments culture in a temporal immersion bioreactor system using 16S rDNA analysis

Endogenous bacterial contaminants isolated from infected cultures of Ilex dumosa nodal segments were identified as Stenotrophomonas maltophilia and Achromobacter sp. using 16S rDNA analysis. A range of antibiotics with different mechanism of actions and the commercial biocide PPM™ were tested for their capacity to repress the growth of Gram negative bacteria grown in liquid medium during the establishment phase of temporal immersion systems. The best results were obtained with the addition of 0.5 mg ml⁻¹ cefotaxime to the culture media obtaining 100% of uncontaminated cultures without suppress of shoot growth.     

基于16S rDNA序列探讨中国剑角蝗科的单系性及其六属的系统发育关系

在中国学者夏凯龄的分类系统中,剑角蝗科Acrididae一直被看作是单系群,包含6个亚科。但是,近年来的研究对其单系性争议较大。为探讨其单系性和剑角蝗属等6属的系统发育关系,我们测定了剑角蝗科14种蝗虫的16S rRNA基因部分序列,并从GenBank中下载了1种蝗虫的同源序列。以蚱科的2个种作外群,用NJ、MP及ML法重建系统发生树。由三棵分子系统树中得出的系统发生关系与中国的分类系统差别较大,都不支持剑角蝗科是单系群,但与国外Kevan的系统相一致,提示我们国内的分类系统亟待修改和完善。长腹蝗亚科与斑腿蝗科的亲缘关系要近于与剑角蝗科的其他种类的关系。另外,尽管所测的红足剑角蝗和上海剑角蝗的16S rDNA的片段序列完全相同,我们仍不能断定二者是同一个物种[动物学报52 (2) : 302 -308 , 2006]。