The marine pathogenic genotype of Spironucleus barkhanus from farmed salmonids redescribed as Spironucleus salmonicida n. sp

There are two genotypes of the diplomonad Spironucleus barkhanus. Based on sequence data from the small subunit ribosomal RNA gene the conspecificity of these two genotypes has been questioned. Therefore, we have sampled Spironucleus from 27 fish, representing 14 populations, five species, and four genera. Partial nucleotide sequences from the three genes; small subunit ribosomal DNA, glutamate dehydrogenase 1 and alpha-tubulin were compared. The pathogenic isolates of S. barkhanus, which causes systemic spironucleosis in Atlantic salmon, Chinook salmon, and Arctic charr, all farmed in sea water, were genetically very different from the commensal isolate found in wild freshwater populations of Arctic charr and grayling. The genetic distances between the genotypes were of the same magnitude as those separating species of Giardia. Based on these genetic and ecological data, the pathogenic genotype from farmed salmonids is described as a new species, Spironucleus salmonicida n. sp. Scanning and transmission electron microscopy showed no specific morphological or ultrastructural features distinguishing S. salmonicida n. sp. from S. barkhanus. The present study clearly demonstrates the value of applying genetics in identification of Spironucleus species. Phylogenetic analyses that included the isolates of S. salmonicida n. sp. did not change the phylogenetic relationship within the genus Spironucleus.     

Description of Hemicaloosia graminis n. sp. (Nematoda: Caloosiidae) Associated with Turfgrasses in North and South Carolina,USA

A new nematode species was discovered during a diversity survey of plant-parasitic nematodes on turfgrass conducted in North and South Carolina in 2010 and 2011. It is described herein as Hemicaloosia graminis n. sp. and is characterized by two annuli in the lip region, one lateral line, body 610.0–805.0 μm long, stylet 65.0–74.6 μm long, vulva at 84.1% –85.8% of the body , 254–283 annuli, vulva at the 38–53^rd annulus from tail terminus, 12–14 annuli between vulva and anus, tail elongate-pointed, 67.5–84.8 μm long in females and spicule straight, 31.0 μm long, caudal alae well developed, two lateral lines in males. The newly described species is morphologically closest to H. paradoxa, but has a longer stylet (65.0–74.6 vs 61.0–65.0 μm) and a higher V-value (84.1–85.8 vs 78.1–84.0%), less RV (38–53 vs 50–56), higher RVan (12–14 vs 10) in females, and a shorter tail (30.1 vs 36.7 μm) and more anteriorly located excretory pore (105.9 vs 140.0 μm) in the male. It was easily differentiated from other species based on near-full-length small subunit rRNA gene (SSU) and ITS1 sequences. Phylogenetic analysis from SSU supports placement in a monophyletic clade with the genus Caloosia. An identification key and a table of distinguishing characteristics are presented for all seven species of Hemicaloosia.     

MORPHOLOGY AND MOLECULAR PHYLOGENY OF ANKISTRODINIUM GEN. NOV. (DINOPHYCEAE), A NEW GENUS OF MARINE SAND‐DWELLING DINOFLAGELLATES FORMERLY CLASSIFIED WITHIN AMPHIDINIUM1

The classical athecate dinoflagellate genera (Amphidinium, Gymnodinium, Gyrodinium) have long been recognized to be polyphyletic. Amphidinium sensu lato is the most diverse of all marine benthic dinoflagellate genera; however, following the redefinition of this genus ～100 species remain now of uncertain or unknown generic affiliation. In an effort to improve our taxonomic and phylogenetic understanding of one of these species, namely Amphidinium semilunatum, we re‐investigated organisms from several distant sites around the world using light and scanning electron microscopy and molecular phylogenetic methods. Our results enabled us to describe this species within a new heterotrophic genus, Ankistrodinium. Cells of A. semilunatum were strongly laterally flattened, rounded‐quadrangular to oval in lateral view, and possessed a small asymmetrical epicone. The sulcus was wide and characteristically deeply incised on the hypocone running around the antapex and reaching the dorsal side. The straight acrobase with hook‐shaped end started at the sulcal extension and continued onto the epicone. The molecular phylogenetic results clearly showed that A. semilunatum is a distinct taxon and is only distantly related to species within the genus Amphidinium sensu stricto. The nearest sister group to Ankistrodinium could not be reliably determined.     

Host genetic and environmental effects on mouse intestinal microbiota

The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived from a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strain-specific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel.     

ANALYSIS OF ANCIENT DNA FROM FOSSIL CORALLINES (CORALLINALES,RHODOPHYTA)1

The field of molecular paleontology has recently made significant contributions to anthropology and biology. Hundreds of ancient DNA studies have been published, but none has targeted fossil coralline algae. Using regions of the SSU gene, we analyzed rDNA from fossil coralline algae of varying ages and states of preservation from Spain, Papua New Guinea (PNG), and the Great Barrier Reef (GBR). Specimens from PNG, GBR, and some localities from Spain did not contain endogenous ancient DNA. Reproducible sequence data were obtained from specimens ～550 years old from near Cadiz, Spain, and from rocky‐shore deposits in Carboneras, Almeria Province of Spain (～78,000 years before present [YBP]). Based on BLAST searches and a phylogenetic analysis of sequences, an undescribed coralline alga belonging to the Melobesioideae was discovered in the Carboneras material as well as the following coralline genera: Jania, Lithophyllum, Lithothamnion, Mesophyllum, and Phymatolithon. DNA from fleshy brown and red macroalgae was also discovered in the specimens from Carboneras. The coralline algae identified using molecular techniques were in agreement with those based on morphological methods. The identified taxa are common in the present‐day southeastern Spain littoral zone. Amino acid racemization, concentration ratios, and specific concentrations failed to show a correlation between biomolecular preservation and PCR amplification success. Results suggest that molecular investigations on fossil algae, although limited by technical difficulties, are feasible. Validity of our results was established using authentication criteria and a self‐critical approach to compliance.     

Impact of soil warming and shading on colonization and community structure of arbuscular mycorrhizal fungi in roots of a native grassland community

Arbuscular mycorrhizal (AM) fungi have a major influence on the structure, responses and below‐ground C allocation of plant communities. Our lack of understanding of the response of AM fungi to factors such as light and temperature is an obstacle to accurate prediction of the impact of global climate change on ecosystem functioning. In order to investigate this response, we divided a grassland site into 24 plots, each either unshaded or partly shaded with soil either unheated or heated by 3°C at 2 cm depth. In both short‐term studies in spring and autumn, and in a 1‐year‐long study, we measured root length colonization (L_RC) by AM and non‐AM fungi. For selected root samples, DNA sequences were amplified by PCR with fungal‐specific primers for part of the small sub‐unit (SSU) rRNA gene. In spring, the total L_RC increased over 6 weeks from 12% to 25%. Shading significantly reduced AM but increased non‐AM fungal colonization, while soil warming had no effect. In the year‐long study, colonization by AM fungi peaked in summer, whereas non‐AM colonization peaked in autumn, when there was an additive effect of shading and soil warming that reduced AM but increased non‐AM fungi. Stepwise regression revealed that light received within the 7 days prior to sampling was the most significant factor in determining AM L_RC and that mean temperature was the most important influence on non‐AM L_RC. Loglinear analysis confirmed that there were no seasonal or treatment effects on the host plant community. Ten AM fungal sequence types were identified that clustered into two families of the Glomales, Glomaceae and Gigasporaceae. Three other sequence types were of non‐AM fungi, all Ascomycotina. AM sequence types showed seasonal variation and shading impacts: loglinear regression analysis revealed changes in the AM fungal community with time, and a reduction of one Glomus sp. under shade, which corresponded to a decrease in the abundance of Trifolium repens. We suggest that further research investigating any impacts of climate change on ecosystem functioning must not only incorporate their natural AM fungal communities but should also focus on niche separation and community dynamics of AM fungi.     

裳卷蛾变形孢虫SSU rRNA核心序列的克隆与系统发育分析

[目的]利用分子生物学手段探索裳卷蛾变形孢虫的遗传发育地位.[方法]微孢子虫的SSUrRNA序列是构建系统发育进化树的重要工具.试验通过T-A克隆法对裳卷蛾变形孢虫(Vairimorphaceraces)SSU rRNA核心序列进行了克隆,并采用近邻法构建了系统发育进化树.[结果]克隆得到了长为1228bp的核苷酸序列(GenBank EU267796).系统发育分析结果表明:裳卷蛾变形孢虫与分离于小菜蛾(Plutella xylostella)的Vairimorpha sp.Germany(GenBank AF124331)和Vairimorphaimperyecta(GenBank AJ131645)相似性最高,它们在系统发育进化树中与寄主为鳞翅目昆虫的Nosema属聚为一类,与纳卡变形孢虫(Vairimorpha necatrix)为代表的Vairimorpha属为相邻集.[结论]结合其生物学特征,裳卷蛾变形孢虫确实为Vairimorph a属的成员,但根据系统发育分析归入Nosematidae科可能更为合适.     

Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences

The origin of the anomalodesmatan bivalves and the relationships of the constituent families are far from being settled. Phylogenetic uncertainties result from the morphological heterogeneity of the Anomalodesmata and from parallel/convergent evolution of several character complexes due to similar life habits. Here, we assess these problems with 26 near-complete anomalodesmatan 18S rRNA sequences from 12 out of 15 families and a selection of heteroconch outgroup taxa. The robustly monophyletic Anomalodesmata share insertions in the V2 and V4 expansion regions. Both parsimony and maximum-likelihood analyses confirm their position among the basal heterodonts rooting between Carditidae and Lucinidae or, together with the latter, between Carditidae and the remaining Heterodonta. There is no support for monophyletic Myoida, nor for a close relationship of Anomalodesmata with any myoid taxon. At the base of the Anomalodesmata is an unstable cluster of long-branch species belonging to the Poromyidae, Verticordiidae, Lyonsiellidae and Thraciidae. The remaining Anomalodesmata split consistently but with varying branch support into three major clades: the Cuspidariidae excluding Myonera ; a 'thraciid' clade consisting of (Euciroidae, ( Myonera ( Thracia, Cleidothaerus , Myochamidae))); and a 'lyonsiid' clade with Laternulidae, Pandoridae, diphyletic Lyonsiidae due to a robust clade of Lyonsia norwegica and the clavagellid Brechites vaginiferus . Tests of various alternative topologies showed that all are significantly longer but optimal likelihood trees with monophyletic carnivorous taxa and/or Thraciidae are not significantly less likely. These results differ greatly from previous morphological studies. Palaeontological data and homology decisions for selected characters are evaluated in the light of the molecular trees.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 229–246.     

Assessment of arbuscular mycorrhizal fungi diversity in the rhizosphere of <Emphasis Type="Italic">Viola calaminaria</Emphasis> and effect of these fungi on heavy metal uptake by clover

 The ability of arbuscular mycorrhizal (AM) fungi from a metal-tolerant plant (Viola calaminaria, violet) to colonise and reduce metal uptake by a non-tolerant plant (Trifolium subterraneum, subterranean clover) in comparison to a metal-tolerant AM fungus isolated from a non-tolerant plant was studied. AM spores from the violet rhizosphere and from violet roots were characterised by polymerase chain reaction (PCR) amplification of the SSU rDNA, and sequencing. Subterranean clover was grown in pots containing a soil supplemented with Cd and Zn salts and inoculated either with a mixture of spores extracted from the violet rhizosphere or with spores of a Cd-tolerant Glomus mosseae P2 (BEG 69), or non-inoculated. The diversity of fungi, including AM fungi, colonising clover roots was assessed and analysed using terminal-restriction fragment length polymorphism. At least four different Glomus species were found in the violet rhizosphere. After 8 weeks in a growth chamber, colonisation of clover roots with spores from the violet rhizosphere increased Cd and Zn concentrations in clover roots without significantly affecting the concentrations of metals in the shoot and plant growth. G. mosseae P2 reduced plant growth and slightly increased the Cd concentration. Only one AM fungus (Glomus b) from the violet rhizosphere colonised clover roots, but other fungi were present. AM fungi from heavy metal-contaminated soils and associated with metal-tolerant plants may be effective in accumulating heavy metals in roots in a non-toxic form. Accepted: 7 July 2000     

Phylogenetic relationships ofPelvetia andPelvetiopsis (Phaeophyceae) based on small subunit ribosomal DNA sequences

Nucleotide sequences of the small-subunit (SSU) ribosomal DNA were determined forPelvetia babingtonii, P. canaliculate, Pelvetiopsis limitata, andAscophyllum nodosum in the family Fucaceae. A total of 1755 positions were aligned for the whole sequence. The positional differences in the primary structure among the taxa ranged from 16 to 30 nucleotide changes in pairwise comparisons. There was a minimum divergence betweenPs. limitata andP. babingtonii while a maximum betweenPs. limitata andP. canaliculata. The SSU rDNA trees showed that the genusPelvetia was not monophyletic and the genusPelvetiopsis was not closely related toPelvetia. Our results suggest that the taxonomic revision of the genusPelvetia as well as the family Fucaceae is needed based on detailed morphological observations.