History and current taxonomic status of genus Agrobacterium

The genus Agrobacterium was created a century ago by Conn who included it in the family Rhizobiaceae together with the genus Rhizobium. Initially, the genus Agrobacterium contained the non-pathogenic species Agrobacterium radiobacter and the plant pathogenic species Agrobacterium tumefaciens and Agrobacterium rhizogenes. At the end of the past century two new pathogenic species, Agrobacterium rubi and Agrobacterium vitis, were added to the genus. Already in the present century these species plus Agrobacterium larrymoorei were reclassified into genus Rhizobium. This reclassification was controversial and for a time both genus names were used when new species were described. Few years ago, after a taxonomic revision based on genomic data, the old species A. rhizogenes was maintained in the genus Rhizobium, the old species A. vitis was transferred to the genus Allorhizobium and several Rhizobium species were transferred to the genus Agrobacterium, which currently contains 14 species including the old species A. radiobacter, A. tumefaciens, A. rubi and A. larrymoorei. Most of these species are able to produce tumours in different plants, nevertheless the genus Agrobacterium also encompasses non-pathogenic species, one species able to nodulate legumes and one human pathogenic species. Taking into account that the species affiliations to five Agrobacterium genomospecies have not been determined yet, an increase in the number of species within this genus is expected in the near future.     

DNA barcode reveals candidate species of Scinax and Ololygon (Anura: Hylidae) in Atlantic Forest

Molecular species delimitation methods are efficient tools to identify species, including the discovery of new taxa and cryptic organisms, thus being useful to biodiversity studies. In the present work, 16S mitochondrial sequences and cytochrome oxidase I (COI) were used to evaluate the richness of species in the genus Scinax and Ololygon from a biodiversity hotspot in Atlantic Forest. A total of 109 specimens formally belonging to eight species of Scinax and three species of Ololygon were collected in 13 localities along the state of Bahia (northeastern Brazil) and one site in Espírito Santo (southeastern Brazil). Of the Scinax species collected in this study, three were morphologically differentiated from other described species and identified as putative new species (Scinax sp.1, Scinax sp.2 and Scinax sp.3). The species delimitations were inferred using three different methods: ABGD, PTP and mPTP which allowed recognizing 11 Scinax species and five Ololygon species. Scinax sp. 1, Scinax sp. 2 and Scinax sp. 3, have been confirmed as new putative species and Ololygon argyreornata possibly contains cryptic species. We suggest additional studies, including morphological and bioacoustic data to validate these new putative species.     

Hard ticks (Acari,Ixodidae) of Croatia

The present paper is based on original and literature data. In Croatia the first studies on the occurrence of ixodid species were made about 80 years ago. The number of tick species recorded in Croatia considerably increased during the 1950s, 60s, 70s and 80s of the past century. A total of 21 species of hard tick belonging to 5 genera have been recorded in Croatia. Ixodes is the best represented genus, with seven species recorded. Haemaphysalis is represented by six species, followed by Rhipicephalus with four species. Dermacentor and Hyalomma are represented by two species each. The ticks were collected on 47 different host species. Eleven tick species were collected on Bos taurus and Ovis aries, followed by Capra hircus and Equus caballus with 8 species and Canis lupus familiaris with 6 species. On the remaining 42 host species one, two or three tick species were collected. The most widespread tick is Ixodes ricinus which was found on 25 different host species.     

Parallelismic homoplasy of leaf and stipule phenotypes among genetic variants of Pisum sativum and Medicago truncatula and some taxa of Papilionoideae, Caesalpinioideae and Mimosoideae subfamilies of the Leguminosae flora of Delhi

The leguminous flora of Delhi comprises 78 Papilionoideae, 24 Caesalpinioideae and 24 Mimosoideae species; 80 of them are perennials. Five types of imparipinnate and two types of paripinnate compound leaves were observed in the species. The paripinnate leaves are bipinnate in 25 species (mostly mimosoid) and bifoliate in two species. The imparipinnate leaves were trifoliate or multifoliate in 59 papilionoid species and multifoliate in 16 caesalpinioid species; four of the papilionoid species produced leafletted and tendrilled unipinnate leaves. Leaves were bifacially simple in 22 species, simple with ectopic terminal growth in one species and simple tendril in one species. Twenty-one species (mostly mimosoid) were devoid of stipules. In 82 species stipules were small and free. Stipules were large and lobed in 17 species and large and adnate in four species. Two species of Caesalpinioideae produce compound leaf-like stipules. All four stipule phenotypes of 126 species corresponded with stipular phenotypes observed in wild type, coch, st and coch st genotypes of the model legume P. sativum. The seven leaf phenotypes observed in 126 species corresponded with phenotypes expected among combinations of uni (uni-tac), af, ins, mfp and tl mutants of P. sativum and sgl1, cfl1, slm1 and palm1 mutants of M. truncatula, also an IRL model legume. All the variation in leaf and stipule morphologies observed in the leguminous flora of Delhi could be explained in terms of the gene regulatory networks already revealed in P. sativum and M. truncatula. It is hypothesized that the ancestral gene regulatory networks for leaves and stipules produced in Leguminosae were like that prevalent in P. sativum.     

Species of Rhytismatales on Berberis from China

Three species of Rhytismatales on Berberis were found from Sichuan and Yunnan provinces in China. Two of them were described as new species to science, namely Hypoderma minteri and Lophodermium johnstonii. The third one was a known species, Hypoderma berberidis. The phylogenetic relationships of these species within the Rhytismatales were analyzed based on internal transcriber spacer ribosomal DNA. The results showed that the species of the Rhytismatales on Berberis, unlike most species on pines, were not closely related. Three ITS sequences from GenBank, named there as Lirula macrospora, were used in this study, but were found to be from misidentified sources. A key to species of Rhytismatales on Berberis worldwide is also given.     

Halophilic fungi of desert soils in Saudi Arabia

Twenty-five genera and sixty-eight species, in addition to one variety of each of A. chevalieri, A. flavus and A. nidulans were isolated from 40 soil samples collected from desert in Saudi Arabia on 5% sodium chloride-Czapek's agar. The most frequent genera were Aspergillus (20 species + 3 varieties), Penicillium (14 species), Drechslera (2 species) and Ulocladium (3 species), followed by Stemphylium (1 species), Scopulariopsis (2 species), Trichoderma (1 species) Botryotrichum (2 species), Cladosporium (3 species), Myrothecium (1 species) and Alternaria (1 species). From these genra A. amstelodami, A. chevalieri, A. ruber, A. ochraceus, P. brevi-compactum, P. ?cyano-fulvum, P. notatum, D. spicifera, U. consortiale, S. botryosum, S. brevicaulis, T. viride, B. piluliferum, C. herbarum, M. verrucaria and A. alterata were the most common. The results obtained in this investigation reveal that the fungus flora of Saudi Arabian soils is of halophilic nature.     

Trends in the reproductive biology of Venezuelan Melochia (Malvaceae) species

The breeding system, floral morphology, morph frequency, biomass allocation to floral whorls, pollination and reproductive efficiency were examined in four distylous and three monomorphic Melochia species. Monomorphic species were self-compatible and distylous species were self-incompatible. Flowers of homomorphic species were longer than those of distylous species. Herkogamy was significantly higher in pin than in thrum morphs of the two distylous species, and monomorphic species exhibited the lowest values of herkogamy. Pollen/ovule ratios were similar between monomorphic and dimorphic species, irrespective of the self-incompatibility level. Biomass allocation to flowers was biased toward non-sexual structures, attraction and support. Androecium biomass and androecium/gynoecium biomass ratio were larger in thrum than in pin flowers of distylous species indicating maleness in the thrum morph and femaleness in the pin morph. There was no clear difference between fruit set of monomorphic and dimorphic species; however, the greatest fruit set was found in the monomorphic species, M. pyramidata, which is a self-compatible species. Fruit set was significantly higher in pin than in thrum morphs in three out four distylous species and fecundity was only significantly higher in pin morphs of M. caracasana and M. parvifolia. Melochia species have generalist pollination systems. According to the taxonomic classes and number of pollinator species, M. caracasana and M. parvifolia have similar generalist pollination systems. Our comparative analyses of the characters between floral morphs of distylous species and the relationship with these characters in monomorphic species allow divergences and similarities to be established and different evolutionary trends to be postulated in the breeding systems of Melochia species. Specifically, M. parvifolia and M. caracasana are apparently biased toward monomorphy and dioecy, respectively.     

COI DNA barcoding for molecular identification of the genus Aphidius (Braconidae: Aphidiinae) in South Korea,with diagnoses of two newly recorded species

The genus Aphidius is one of the most commercially important species in greenhouse for controlling pests, especially aphids. Although 13 Aphidius species had been recorded in South Korea, it was not carefully surveyed yet. In this study, we surveyed and collected 8 Aphidius spp. including two unrecorded species. Using the DNA barcode region of mitochondrial cytochrome c oxidase subunit I (COI), sequences were newly generated for 16 molecular operational taxonomic units (MOTUs) of 8 species, except for 15 duplicates, in addition of 58 MOTUs of 18 species referred from GenBank for comparison and identification, which were reconstructed in a barcode phylogeny with Neighbor-Joining method. Then, to define each species, both Automatic Barcode Gap Discovery (ABGD) and Bayesian Poisson Tree Processes (bPTP) analyses were performed. As results, although most of Aphidius spp. could be identified by clustering into a clade, we recognized that three Aphdius species were placed in a clade, of which each species was not separated as an independent species. Our data suggested that those species demonstrating a species complex were able to be hypothesized as one species. In addition, diagnoses and illustrations of the two newly recorded species in South Korea were provided.     

Larval Chironomidae (Diptera) of the Big Thicket streams

Eighty-seven species of chironomid larvae were collected from streams in the Big Thicket area of southeast Texas. Samples of leaf debris, wood debris, and sand were taken from the streams and the larvae occupying the substrates were analyzed. Four subfamilies were represented including Tanypodinae (12 species), Diamesinae (2 species), Orthocladiinae (30 species), and Chironominae (43 species). Dominant species included Lopescladius sp., Polypedilum ? convictum, Polypedilum ? halterale, Cladotanytarsus sp. group A, Rheotanytarsus sp., and Tanytarsus sp. 2. A brief account of the habitat and the distribution of each species encountered during this study is given.     

广东担杆岛鸟类多样性的季节变化

摘要：2008年5月至2009年11月,采用固定样点法对广东省珠海市担杆岛的鸟类进行了调查。共记录到鸟类74种,其中留鸟29种、候鸟45种。雨季记录到鸟类45种,旱季记录到鸟类48种。雨季与旱季每个样点平均记录到的鸟类种数分别为3.5种(n--80)和3.7种(n=69),差异不显著(Z=-0.86,P=0.39);鸟...     

Occurrence and assemblage composition of millipedes (Myriapoda, Diplopoda) and terrestrial isopods (Crustacea, Isopoda, Oniscidea) in urban areas of Switzerland

Terrestrial isopods and millipedes, members of the invertebrate macro-decomposer guild, were collected through pitfall traps in three Swiss cities (Zurich, Lucerne, Lugano). A total of 7,198 individuals of 17 isopod species (7093 ind.), and 10 millipede species (105 ind.) were captured. Besides the Alpine endemic isopod (Trichoniscus alemannicus) and millipede (Cylindroiulus verhoeffi), urban assemblages were mainly composed of widespread, native European and even cosmopolitan species, which are frequent in anthropogenic areas. Overall species richness (isopods and millipedes combined) was similar in Zurich (17 species) and Lucerne (16), while only 13 species were sampled in Lugano. According to the Sørensen index of similarity, species composition of Zurich and Lucerne were more alike, while the one of Lugano was more distinct from the other two cities. This result can be explained by the spatial proximity of Zurich and Lucerne in the north of the Alps compared to Lugano, which is located more distantly and in the south of the Alps. Dominant isopods and millipedes in Zurich and Lucerne were found to be widespread synanthropic species in temperate Europe(Porcellio scaber, Trachelipus rathkii and Ophyiulus pilosus) while the dominant isopod in Lugano (Trachelipus razzautii) is a species with a north-eastern Mediterranean distribution. Our study reveals that the urban millipede and isopod fauna in Swiss cities mainly consists of widespread species, but species of narrower distribution (e.g. Trichoniscus alemannicus, Cylindroiulus verhoeffi) may also find suitable habitats in cities. Despite some signs of biotic homogenization, our study also found compositional differences of millipede and isopod assemblages between northern and southern cities that suggest geographical effects of the regional species pool.     

A survey on coccidian infection of Lake Biwa fishes in Japan,with the description of four new species of Goussia Labbé, 1896 (Apicomplexa)

Thirty-two specimens of 11 freshwater fish species from Lake Biwa, Japan were surveyed for coccidian infections. Four fish species proved to be infected with apicomplexans belonging to the genus Goussia. Altogether, seven Goussia species were found. Oöcysts of four species inhabiting the intestinal epithelium were shed at the sporulated stage. Two other intestinal species left the fish unsporulated. A few relatively large and aged oöcysts of a further species were found in the renal tubules. The sporulated intestinal species were described as Goussia biwaensis n. sp., G. grygieri n. sp., G. nipponica n. sp. and G. wakabayashii n. sp.     

A null model test of Floristic Quality Assessment: Are plant species’ Coefficients of Conservatism valid?

Floristic Quality Assessment (FQA) was developed as a tool for quantifying the conservation value of natural areas based on their plant species composition and richness. Floristic Quality Assessment is based on Coefficients of Conservatism (C values) assigned to each plant species in a region or state. Each species i, is assigned a value C_i, on a scale of 0–10 by expert botanists, based on its fidelity to undegraded natural areas. A criticism of Floristic Quality Assessment is the subjective nature of these C values. Our objective was to determine if C values of individual species are indicative of the C values of species with which they co-occur. If subjectively assigned species’ C values carry meaningful information about plant assemblages and the conservation value of particular habitats, then individual species should tend to co-occur with species of similar C. We tested this hypothesis using occurrences of 1014 species in 388 forests and wetlands across Illinois, USA. Using a null model approach, we found that species co-occurred with species of similar C far more often than would be expected by chance; affirming the predictive ability of subjectively assigned C values. Furthermore, we quantified the extent to which each species was under- or overvalued relative to its co-occurring species assemblages to assess if any species C values were mis-assigned. Woody plants and perennial herbs, as groups, were undervalued as ecological indicators, i.e. their C values were too low. Several non-native species, which, by convention, are assigned a C of zero, were over- or under-valued relative to native species with a C of zero. Based on species occurrences across hundreds of sites, our results indicated that, despite their subjective basis, C values carry considerable ecological information, such that a given species can be used to predict the C values of its co-occurring assemblage. However, some species C values appeared less accurate than others. Our methodological approach could be applied in other states or regions to validate and refine C value assignments.     

Scanning Electron Microscopy of Xiphinema,Longidorus, and Californidorus Stylet Morphology

Stylet ultrastructure of five Xiphinema, four Longidorus, and three Californidorus species was compared by scanning electron microscopy. Morphological differences were seen in the odontophores and odontostyle bases between the genera and some of the species. All Xiphinema studied had well-developed odontophore flanges; the Longidorus species lacked flanges, except for weakly developed ones in L. diadecturus; and none of the Californidorus had flanges. Three sinuses were present in the odontophores of all species. The sinuses varied in length depending upon species. In Xiphinema and Californidorus the odontostyle bases had distinct overlapping collars, but in Longidorus the collars were absent except for L. diadecturus. The odontostyle-odontophore junction from a lateral view appeared as a slanted transverse line in all the species, but in a dorsal view of Xiphinema and Californidorus it was V-shaped. Dorsal longitudinal seams of the odontostyle and odontophore were observed in all the species. The dorsally located odontostyle aperture was ca. 1 μm from the anterior end in all species, except in one Longidorus sp. it was ca. 4 μm from the end.     

Systematics of the genusCandida Berkhout: Proton magnetic resonance spectra of the mannose-containing polysaccharides of some further species ofCandida as an aid in classification

The proton magnetic resonance spectra of the mannose-containing polysaccharides of 48Candida species were determined. Two other species formed heteropolymers for which p.m.r. spectra could not be obtained. The species were grouped as follows: 17 species formed mannose-containing polysaccharides with spectra like those ofHansenula anomala, Pichia farinosa, Pichia membranaefaciens orPichia robertsii mannans; 12, like those ofMetschnikowia andDebaryomyces mannans; 6, like those of mannans ofSaccharomyces species; 4, like that ofTorulopsis bombicola mannan; and 4, like those ofCandida obtusa andCandida tepae polysaccharides. Five formed mannans whose spectra were unlike those of the mannans of any other yeast species examined.     

Eukaryote Culturomics of the Gut Reveals New Species

The repertoire of microeukaryotes in the human gut has been poorly explored, mainly in individuals living in northern hemisphere countries. We further explored this repertoire using PCR-sequencing and culture in seven individuals living in four tropical countries. A total of 41 microeukaryotes including 38 different fungal species and three protists were detected. Four fungal species, Davidiella tassiana, Davidiella sp., Corticiaceae sp., and Penicillium sp., were uniquely detected by culture; 27 fungal species were uniquely detected using PCR-sequencing and Candida albicans, Candida glabrata, Trichosporon asahii, Clavispora lusitaniae, Debaryomyces hansenii, Malassezia restricta, and Malassezia sp. were detected using both molecular and culture methods. Fourteen microeukaryotes were shared by the seven individuals, whereas 27 species were found in only one individual, including 11 species in Amazonia, nine species in Polynesia, five species in India, and two species in Senegal. These data support a worldwide distribution of Malassezia sp., Trichosporon sp., and Candida sp. in the gut mycobiome. Here, 13 fungal species and two protists, Stentor roeseli and Vorticella campanula, were observed for first time in the human gut. This study revealed a previously unsuspected diversity in the repertoire of human gut microeukaryotes, suggesting spots for further exploring this repertoire.     

Species Richness and Host Specificity among Caterpillar Ensembles on Shrubs in the Andes of Southern Ecuador

Caterpillar ensembles were sampled on 16 species of shrubs from the family Asteraceae and the genus Piper (Piperaceae) in open and forest habitats in the Andean montane forest zone of southern Ecuador between August 2007 and May 2009. Trophic affiliations of caterpillars to the host plants were confirmed in feeding trials. Overall, species richness of herbivorous caterpillars was high (191 species across all plants), but varied strongly between ensembles associated with different plant species (2?C96 lepidopteran species per shrub species). Ensembles on Piper species were characterized by low effective species numbers and high dominance of one or two species of the Geometridae genus Eois Hübner. Low species number and high dominance were also found on latex-bearing Erato polymnioides, whereas ensembles on two other Asteraceae species were far more diverse and less strongly shaped by a few dominant species. The observed diversity patterns fit well to the concept that anti-herbivore defenses of plants are the major factors regulating associated insect ensembles. Local abundance and geographic range of host plants appear to have less influence. Lepidopteran species feeding on Asteraceae were found to be more generalistic than those feeding on Piper species. We conclude that caterpillar ensembles on most, but not all, studied plant species are defined by a small number of dominant species, which usually are narrow host specialists. This pattern was more distinct on Piper shrubs in forest understory, whereas Asteraceae in disturbed habitats had more open caterpillar ensembles.     

EPIPHYTE FLORA AND DIVERSITY ON BASAL TRUNKS OF SIX OLD-GROWTH FOREST TREE SPECIES IN SOUTHERN AND MIDDLE BOREAL FINLAND

Epiphytic lichen and bryophyte species composition, richness and diversity were surveyed on basal trunks of six common old-growth forest tree species,Picea abies,Pinus sylvestris,Betula pendula,Alnus incana,Salix capreaandPopulus tremula, in two old-growth forest areas, one in southern and one in middle boreal Finland. The average species numbers per tree ranged from 18 (Picea) to 27 (Salix) in the southern and from 20 (Populus) to 31 (Salix) in the middle boreal area. A few widespread habitat-generalist species, such as the foliose lichensHypogymnia physodesandPlatismatia glauca, were most abundant on all the tree species, exceptPopulus. Most other epiphyte species showed at least a slight preference for one or two tree species.Populusproved to have the most distinct flora characterized by the abundance of certain, rather specialized crustose lichens and bryophytes. The number of species that occurred on only one tree species was highest onPopulus(9) in the southern and onAlnus(18) in the middle boreal area. Differences in bark acidity and structure were the most likely explanations for the differences between tree species in the epiphytic flora and diversity.SalixandPopuluswere the most important of the tree species studied for the conservation of epiphyte diversity in the boreal forests of Finland.