Study on Cortinarius subgenus Telamonia section Hydrocybe in Europe, with especial emphasis on Mediterranean taxa

In this paper we have attempted to clarify the taxonomy and nomenclature of thirteen taxa of the genus Cortinarius subgenus Telamonia (sections Hydrocybe, Fraternii) well represented in the southwestern Mediterranean area of Europe (C. atrocoeruleus, C. bombycinus, C casimiri, C. contrarius, C. decipiens, C. fraternus, C. gallurae, C. hoffmannii, C. petroselineus, C. sertipes, C. subturibulosus, C. urdaibaiensis and C. vernus). To this end we have performed a combined study of morphological and molecular data (rDNA ITS sequences). The morphological analysis was carried out on 114 collections and the molecular analysis involved 31 of the 114 collections, including 11 type collections (types for C. casimiri and C. fraternus were not available). In addition, a study of spores under field emission scanning electron microscopy (FESEM) was conducted. The results of the combined analysis allowed us to asign the studied material to five species (C. casimiri s.l., C. decipiens s.l., C. gallurae, C. subturibulosus s.l. and C. vernus s.l.). Thus, all collections from more continental areas, which were originally identified as six different taxa (C. atrocoeruleus, C. contrarius, C. decipiens, C. fraternus, C. sertipes, C. flexipes fo. sertipes) corresponded to C. decipiens sensu lato, a widely distributed, genetically and morphologically variable species. Cortinarius casimiri is also found in such habitats, but it is confirmed as distinct taxon. Collections from Mediterranean sclerophyllous communities correspond to C. gallurae, C. vernus sensu lato and C. subturibulosus sensu lato. Due to close phylogenetic relationships we propose the new combinations C. casimiri var. hoffmannii (=C. decipiens var. hoffmannii non C. hoffmannii) and C. subturibulosus var. bombycinus (=C. bombycinus), and the new variety C. vernus var. nevadavernus (=C. vernus H. Lindstr. & Melot sensu auct.).     

In vitro activity effects of combinations of cephalothin, dicloxacillin, imipenem, vancomycin and amikacin against methicillin-resistantStaphylococcus spp. strains

Background

CHROMagar Candida (CaC) is increasingly being reported as a medium used to differentiate Candida albicans from non-albicans Candida (NAC) species. Rapid identification of NAC can assist the clinician in selecting appropriate antifungal therapy. CaC is a differential chromogenic medium designed to identify C. albicans, C. krusei, and C. tropicalis based on colony color and morphology. Some reports have proposed that CaC can also reliably identify C. dubliniensis and C. glabrata.

Methods

We evaluated the usefulness of CaC in the identification of C. dubliniensis, C. famata, C. firmetaria, C. glabrata, C. guilliermondii, C. inconspicua, C. kefyr, C. lipolytica, C. lusitaniae, C. norvegensis, C. parapsilosis, and C. rugosa.

Results

Most NAC produced colonies that were shades of pink, lavender, or ivory. Several isolates of C. firmetaria and all C. inconspicua produced colonies difficult to differentiate from C. krusei. Most C. rugosa isolates produced unique colonies with morphology like C. krusei except in a light blue-green color. C. glabrata isolates produced small dark violet colonies that could be differentiated from the pink and lavender colors produced by other species. All seventeen isolates of C. dubliniensis produced green colonies similar to those produced by C. albicans.

Conclusion

C. glabrata and C. rugosa appear distinguishable from other species using CaC. Some NAC, including C. firmetaria and C. inconspicua, could be confused with C. krusei using this medium.     

Nitrogenase activity,hydrogen evolution and biomass production in different Casuarina symbioses

Nitrogenase activity, hydrogen evolution, biomass production and nodulation were studied in threeCasuarina species,C. equisetifolia Forst.,C. glauca Sieber ex Spreng andC. obesa Miq., either inoculated with a crushed nodule inoculum prepared fromC. glauca nodules or inoculated with the pure cultureHFP CcI3. Nodulation was also studied inC. cristata Miq. inoculated with the above mentionedFrankia sources. C. equisetifolia, C. glauca andC. obesa were nodulated when inoculated with both of theFrankia inoculum, whileC. cristata was very poorly nodulated. Nitrogenase activity per plant and on a nodule dry weight basis was significantly highest inC. glauca inoculated withC. glauca inoculum after 150 days from planting. This difference decreased and at 217 days from planting there was no significant difference between the symbioses, except forC. obesa inoculated withC. glauca inoculum which showed the significantly lowest nitrogenase activity. After 150 days from planting relative efficiency of nitrogenase was lowest inC. equisetifolia inoculated withHFP CcI3 and inC. equisetifolia inoculated withC. glauca inoculum. Biomass production was similar inC. glauca inoculated withC. glauca inoculum, inC. equisetifolia inoculated withHFP CcI3 and inC. obesa inoculated withHFP CcI3 at the final harvest. The data presented here show that there is a strong interrelationship between host plant and endobiont. This interrelationship is of considerable importance when introducing Casuarina symbioses for production of fuel wood.     

Extreme diversification driven by parallel events of massive loss of heterozygosity in the hybrid lineage of Candida albicans

Candida albicans is the most commonly reported species causing candidiasis. The taxonomic classification of C. albicans and related lineages is controversial, with Candida africana (syn. C. albicans var. africana) and Candida stellatoidea (syn. C. albicans var. stellatoidea) being considered different species or C. albicans varieties depending on the authors. Moreover, recent genomic analyses have suggested a shared hybrid origin of C. albicans and C. africana, but the potential parental lineages remain unidentified. Although the genomes of C. albicans and C. africana have been extensively studied, the genome of C. stellatoidea has not been sequenced so far. In order to get a better understanding of the evolution of the C. albicans clade, and to assess whether C. stellatoidea could represent one of the unknown C. albicans parental lineages, we sequenced C. stellatoidea type strain (CBS 1905). This genome was compared to that of C. albicans and of the closely related lineage C. africana. Our results show that, similarly to C. africana, C. stellatoidea descends from the same hybrid ancestor as other C. albicans strains and that it has undergone a parallel massive loss of heterozygosity.     

Llandoverian and Wenlockian Cyrtograptus,and some other Wenlockian graptolites from Northern and Arctic Canada

Llandoverian and Wenlockian graptolite zonesin northern and Arctic Canada comprise the Sakmaricus-Laqueus Zone of latest Llandoverian age, Centrifugus Zone of earliest Wenlockian age, Rigidus Zone of about mid-Wenlockian age, possibly the Perneri Zone of late Wenlockian age, and the Testis-Lundgreni Zone of very late Wenlockian age.Species of Cyrtograptus described and illustratedin this study are C. centrifugus, C. cf. insectus, C. aff. lapworthi, C. laqueus, C. lundgreni, C. sp. (aff. C. lundgreni), C. mancki, C. radians, C. rigidus, C. sakmaricus, C. solaris n. subsp.? and C. sp. (similar to C. murchisoni bohemicus). Other taxa comprise Monograptus cf. capillaceus, M.? aff. deubeli, Gothograptus nassa, Plectograptus praemacilentus, Spinograptus cf. spinosus and Retiolites nevadensis.     

Palaearctic species of the ichneumon-fly genus Campodorus Förster (Hymenoptera, Ichneumonidae): III. Species with long-haired ovipositor sheath, species with entirely rufous hind tibia, and species with white-banded tibiae

A complex of about 40 Palaearctic species of the genus Campodorus with long haired ovipositor sheath and with entirely rufous or white-banded hind tibia is considered and keyed. Twenty-one new species are described. The species with the pale rufous hind tibia have black hind coxa and trochanters, most of them also have rather long genae and scabrous mesopleura. The majority of these species are distributed in subarctic Siberia: C. yakutator sp. n., C. minutor sp. n., C. arctor sp. n., C. atripes sp. n., C. pequenitor sp. n., C. mordax sp. n., C. lucidator sp. n., C. subarctor sp. n., C. nikandrovskii sp. n., and C. genator sp. n. C. suomi sp. n. is described from northern Finland, C. labytnangi sp. n., from Kola Peninsula, the Polar Ural, and Transbaikalia, and only C. gallicator sp. n., from France (? Alps). The species with a white band on the hind tibia are mostly boreal; most of them have red coxae and trochanters (except for C. sakhalinator sp. n. and C. taigator sp. n.), rather short genae, and granulate mesopleura. In this group, eight new species are described: C. atrofemorator sp. n., C. barbator sp. n., C. sakhalinator sp. n. (all from the southern part of the Russian Far East), C. taigator sp. n. (southern Siberian), C. ciliator sp. n., C. melanopygus sp. n., C. marginator sp. n., and C. boreator sp. n. (European-Siberian).     

Isozymes of coreopsis section Calliopsis (Compositae): Genetic variation within and divergence among the species

Enzyme electrophoresis was employed to examine genetic variation within and among the three diploid (n=12) species comprisingCoreopsis sectionCalliopsis: C. leavenworthii, C. paludosa andC. tinctoria. Twelve enzymes specified by 20 genes were included, and those isozymes localized in the plastids were identified for several of the enzymes. Mean genetic identities calculated for pair-wise comparisons of 22 populations (four ofC. leavenworthii, one forC. paludosa, and 17 ofC. tinctoria) reveal no genetic differentiation betweenC. leavenworthii andC. tinctoria, whereasC. paludosa exhibits lowered values with the other two taxa. These results are in general agreement with concepts of relationships inferred from morphological and biosystematic data. That is,C. paludosa has been viewed as more distinct fromC. leavenworthii andC. tinctoria than the latter two are from each other. The high similarity betweenC. leavenworthii andC. tinctoria is somewhat unexpected, however, given the several morphological features that serve consistently to distinguish them.     

A review of Cunaxidae (Acariformes,Trombidiformes): Histories and diagnoses of subfamilies and genera,keys to world species,and some new locality records

Cunaxidae are predaceous mites found in a variety of habitats. This work provides comprehensive keys to world subfamilies, genera, and species. Diagnoses and historical reviews are provided for subfamilies and genera.Cunaxa boneti, C. denmarki, C. exoterica, C. floridanus, C. lehmanae, C. lukoschusi, C. metzi, C. myabunderensis, C newyorkensis, C. rackae, C. reevesi, and C. reticulatus are moved to Rubroscirus and C. otiosus, C. valentis, and C. rasile are returned to Rubroscirus. Cunaxoides neopectinatus is moved to Pulaeus. Neocunaxoides pradhani and N. gilbertoi are transferred to Scutopalus. Pulaeus minutus and P. subterraneus are moved to Lupaeus. Pseudobonzia bakari, P. malookensis, and P. shamshadi are transferred to Neobonzia. Dactyloscirus bifidus is transferred to Armascirus.Scirula papillata is reported from the Western Hemisphere for the first time. Armascirus ozarkensis, A. primigenius, and Dactyloscirus dolichosetosus are reported from new localities.     

Systematics of Crepidostomum species from the Russian Far East and northern Japan,with description of a new species and validation of the genus Stephanophiala

Current article touched upon the issue of the complicated taxonomic status of some species from the genus Crepidostomum collected from the freshwater fish in the rivers of Primorsky region, Sakhalin, and Hokkaido Islands. Primary morphological analyses showed affiliation of the worms to the species C. farionis (Müller, 1784) Lühe, 1909; C. metoecus Braun, 1900b; C. chaenogobii Yamaguti and Matsumura, 1942; C. nemachilus Krotov, 1959. We described the new species Crepidostomum achmerovi sp. nov. that is a sibling species of C. nemachilus. Molecular-genetic investigation have shown that C. nemachilus and C. achmerovi sp. nov. are closely related to C. metoecus in both 28S rDNA and cox1 mtDNA markers. Crepidostomum nemachilus forms a separate branch within the C. metoecus clade on the 28S BI tree with strong statistical support and separate clade in relation to C. metoecus clade on the cox1 BI tree. Values of p-distances between Crepidostomum species were at intergeneric level. Crepidostomum metoecus species complex including five species (C. metoecus, C. nemachilus, C. oschmarini, C. brinkmanni, and C. achmerovi sp. nov.) was reconsidered as independent genus Crepidostomum sensu stricto. Minimum Spanning Network showed that C. nemachilus, C. metoecus and C. achmerovi sp. nov. were separated by large number of mutational events and represent independent phyletic lines. An amended diagnosis is provided for the subfamily Crepidostomatinae, the genera Crepidostomum s. str. and Stephanophiala Nicoll, 1909, along with keys to species of both genera.     

The CpA135 gene as a marker to identify Cryptosporidium species infecting humans

Of the 22 species currently recognized as valid in the Cryptosporidium genus, C. parvum and C. hominis account for most cases of human infections worldwide. However, C. meleagridis, C. canis, C. felis, C. suis, C. muris, as well as the cervine, rabbit and monkey Cryptosporidium genotypes, have also been recognized as the etiologic cause of both sporadic and epidemic cryptosporidiosis in humans. Molecular methods are necessary to distinguish species and genotypes of Cryptosporidium, due to the lack of reliable morphological variations. The aim of this work was to determine the genetic polymorphisms in a fragment of the A135 gene in isolates of C. parvum, C. hominis, C. meleagridis, C. canis, C. muris, C. andersoni and the Cryptosporidium cervine genotype. Primers were designed on conserved regions identified on a multiple alignment of the C. parvum, C. hominis and C. muris sequences, the three species for which information is available at the genome level. PCR amplification and direct sequencing of a 576 bp fragment revealed the presence of numerous single nucleotide polymorphisms (SNPs) among the species/genotype tested. The genetic variability was exploited to design a PCR-RFLP assay useful for a rapid identification of the most important human pathogens in the genus Cryptosporidium.     

Scanning Electron Microscopy of Colonies of Six Species of Candida

Thirty strains of six species of Candida isolated from patients were cultured for 60 h on Sabouraud agar, freeze-dried, and examined with a scanning electron microscope. The colonies were circular (Candida albicans, C. guilliermondii) or oval (C. tropicalis, C. pseudotropicalis, C. krusei, C. parakrusei) in outline, and those of C. pseudotropicalis and C. krusei had an irregular outline due to a peripheral pseudomycelium. The morphology of individual microorganisms was examined at the margins and apex of those species which lacked a surface coat (C. pseudotropicalis, C. krusei, C. parakrusei, C. guilliermondii), and through cracks in the surface coating of those which showed a surface coat (C. albicans, C. tropicalis). All species showed buds, bud scars, and interconnecting intercellular processes, but were generally spherical (C. albicans, C. tropicalis) or ovoid (C. pseudotropicalis, C. krusei, C. parakrusei, C. guilliermondii) in fixed preparations. In unfixed material, individual organisms were almost invariably indented. Fixation with 3% glutaraldehyde and washing before freeze-drying caused partial removal of the surface coating of colonies of C. albicans and C. tropicalis, which persisted only as irregular sheets or as a filamentous meshwork. This filamentous meshwork was also present among the organisms of colonies of C. albicans, C. tropicalis, and C. pseudotropicalis. It is concluded that these filaments represent the precipitation or unmasking of some component of the intercellular matrix of these organisms.     

Multi Locus Sequence Typing of Chlamydia Reveals an Association between Chlamydia psittaci Genotypes and Host Species

Chlamydia comprises a group of obligate intracellular bacterial parasites responsible for a variety of diseases in humans and animals, including several zoonoses. Chlamydia trachomatis causes diseases such as trachoma, urogenital infection and lymphogranuloma venereum with severe morbidity. Chlamydia pneumoniae is a common cause of community-acquired respiratory tract infections. Chlamydia psittaci, causing zoonotic pneumonia in humans, is usually hosted by birds, while Chlamydia abortus, causing abortion and fetal death in mammals, including humans, is mainly hosted by goats and sheep. We used multi-locus sequence typing to asses the population structure of Chlamydia. In total, 132 Chlamydia isolates were analyzed, including 60 C. trachomatis, 18 C. pneumoniae, 16 C. abortus, 34 C. psittaci and one of each of C. pecorum, C. caviae, C. muridarum and C. felis. Cluster analyses utilizing the Neighbour-Joining algorithm with the maximum composite likelihood model of concatenated sequences of 7 housekeeping fragments showed that C. psittaci 84/2334 isolated from a parrot grouped together with the C. abortus isolates from goats and sheep. Cluster analyses of the individual alleles showed that in all instances C. psittaci 84/2334 formed one group with C. abortus. Moving 84/2334 from the C. psittaci group to the C. abortus group resulted in a significant increase in the number of fixed differences and elimination of the number of shared mutations between C. psittaci and C. abortus. C. psittaci M56 from a muskrat branched separately from the main group of C. psittaci isolates. C. psittaci genotypes appeared to be associated with host species. The phylogentic tree of C. psittaci did not follow that of its host bird species, suggesting host species jumps. In conclusion, we report for the first time an association between C. psittaci genotypes with host species.     

Comparative mitochondrial genomics and phylogenetic relationships of the Crossoptilon species (Phasianidae,Galliformes)

Background

Phasianidae is a family of Galliformes containing 38 genera and approximately 138 species, which is grouped into two tribes based on their morphological features, the Pheasants and Partridges. Several studies have attempted to reconstruct the phylogenetic relationships of the Phasianidae, but many questions still remain unaddressed, such as the taxonomic status and phylogenetic relationships among Crossoptilon species. The mitochondrial genome (mitogenome) has been extensively used to infer avian genetic diversification with reasonable resolution. Here, we sequenced the entire mitogenomes of three Crossoptilon species (C. harmani, C. mantchuricum and C. crossoptilon) to investigate their evolutionary relationship among Crossoptilon species.

Results

The complete mitogenomes of C. harmani, C. mantchuricum and C. crossoptilon are 16682 bp, 16690 bp and 16680 bp in length, respectively, encoding a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a putative control region. C. auritum and C. mantchuricum are more closely related genetically, whereas C. harmani is more closely related to C. crossoptilon. Crossoptilon has a closer relationship with Lophura, and the following phylogenetic relationship was reconstructed: ((Crossoptilon + Lophura) + (Phasianus + Chrysolophus)). The divergence time between the clades C. harmani-C. crossoptilon and C. mantchuricum-C. auritum is consistent with the uplift of the Tibetan Plateau during the Tertiary Pliocene. The Ka/Ks analysis showed that atp8 gene in the Crossoptilon likely experienced a strong selective pressure in adaptation to the plateau environment.

Conclusions

C. auritum with C. mantchuricum and C. harmani with C. crossoptilon form two pairs of sister groups. The genetic distance between C. harmani and C. crossoptilon is far less than the interspecific distance and is close to the intraspecific distance of Crossoptilon, indicating that C. harmani is much more closely related to C. crossoptilon. Our mito-phylogenomic analysis supports the monophyly of Crossoptilon and its closer relationship with Lophura. The uplift of Tibetan Plateau is suggested to impact the divergence between C. harmani-C. crossoptilon clade and C. mantchuricum-C. auritum clade during the Tertiary Pliocene. Atp8 gene in the Crossoptilon species might have experienced a strong selective pressure for adaptation to the plateau environment.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1234-9) contains supplementary material, which is available to authorized users.     

Chromosome numbers for native North American unifoliolate species of Crotalaria (Leguminosae)

Chromosome counts are reported for nine taxa of the genusCrotalaria. Previous reports ofn = 16 are confirmed forC. sagittalis L. andC. stipularia Desv. First counts ofn = 16 are reported forC. bupleurifolia var.bupleurifolia, C. nayaritensis, C. polyphylla,C. purshii, C. quercetorum, C. rotundifolia var.rotundifolia, andC. rotundifolia var.vulgaris.     

Seed structure in Crocus sativus L. ×, C. cartwrightianus Herb., C. thomasii Ten., and C. hadriaticus Herb. at SEM

Crocus sativus L. (Iridaceae) is a sterile triploid geophyte widely cultivated for the production of the spice saffron and only reproduced by means of corms. Extensive research has identified Crocus cartwrightianus Herb. as being a probable progenitor of C. sativus. However, other diploid Crocus species of the same C. sativus group, such as C. thomasii Ten. and C. hadriaticus Herb., have been considered as possible progenitors of saffron. Of the characteristics for distinguishing critical genera, species and intraspecific taxa of angiosperms, the most widely adopted have been seed organisation and patterns of spermoderma microstructure detected at SEM. The aim of this study is to use SEM to analyse the seeds of C. sativus ×, a cross obtained by C. sativus with pollen of C. cartwrightianus Herb. and the seeds of allopollinated C. cartwrightianus, C. thomasii Ten., and C. hadriaticus Herb. Results indicate that the seed surface microstructure of C. sativus × is very similar to that of C. cartwrightianus while being different from those of C. thomasii and C. hadriaticus.     

SNP Mining in Crassostrea gigas EST Data: Transferability to Four Other Crassostrea Species,Phylogenetic Inferences and Outlier SNPs under Selection

Oysters, with high levels of phenotypic plasticity and wide geographic distribution, are a challenging group for taxonomists and phylogenetics. Our study is intended to generate new EST-SNP markers and to evaluate their potential for cross-species utilization in phylogenetic study of the genus Crassostrea. In the study, 57 novel SNPs were developed from an EST database of C. gigas by the HRM (high-resolution melting) method. Transferability of 377 SNPs developed for C. gigas was examined on four other Crassostrea species: C. sikamea, C. angulata, C. hongkongensis and C. ariakensis. Among the 377 primer pairs tested, 311 (82.5%) primers showed amplification in C. sikamea, 353 (93.6%) in C. angulata, 254 (67.4%) in C. hongkongensis and 253 (67.1%) in C. ariakensis. A total of 214 SNPs were found to be transferable to all four species. Phylogenetic analyses showed that C. hongkongensis was a sister species of C. ariakensis and that this clade was sister to the clade containing C. sikamea, C. angulata and C. gigas. Within this clade, C. gigas and C. angulata had the closest relationship, with C. sikamea being the sister group. In addition, we detected eight SNPs as potentially being under selection by two outlier tests (fdist and hierarchical methods). The SNPs studied here should be useful for genetic diversity, comparative mapping and phylogenetic studies across species in Crassostrea and the candidate outlier SNPs are worth exploring in more detail regarding association genetics and functional studies.     

Does heterospecific seminal fluid reduce fecundity in interspecific copulation between seed beetles?

Reproductive interference through mating between related species can cause fitness reduction and affect population dynamics of the interacting species. In experimental matings between two seed beetles, Callosobruchus chinensis and Callosobruchus maculatus, C. maculatus females, but not C. chinensis females, suffer from significant loss of fecundity when conspecific mating is followed by heterospecific mating. We hypothesized that male traits associated with sexual conflict, which are often harmful to females, pleiotropically affect fitness of heterospecific females through interspecific mating. We examined the effect of ejaculate of C. chinensis males on C. maculatus females as the cause of the fecundity loss in C. maculatus females due to interspecific copulation. We found that frequent interspecific copulation occurred between C. maculatus females and C. chinensis males, but not between C. chinensis females and C. maculatus males, resulting in frequent interspecific ejaculate transfer from C. chinensis males to C. maculatus females. However, injection of the extract from C. chinensis male reproductive organs into C. maculatus females did not significantly affect C. maculatus fecundity compared with saline injection, indicating that the effect of the heterospecific ejaculate transfer on fecundity is negligible. We suggest that other harmful male traits such as genital spines of C. chinensis males are mainly responsible for the fecundity reduction in C. maculatus females that have experienced interspecific mating.