Phylogenetic relationships of xenodontine snakes inferred from 12S and 16S ribosomal RNA sequences

The phylogenetic relationships of xenodontine snakes are inferred from sequence analyses of portions of two mitochondrial genes (12S and 16S ribosomal RNA) in 85 species. Although support values for most of the basal nodes are low, the general pattern of cladogenesis observed is congruent with many independent molecular, morphological, and geographical data. The monophyly of xenodontines and the basal position of North American xenodontines in comparison with Neotropical xenodontines are favored, suggesting an Asian-North American origin of xenodontines. West Indian xenodontines (including endemic genera and members of the genus Alsophis) appear to form a monophyletic group belonging to the South American clade. Their mid-Cenozoic origin by dispersal using ocean currents is supported. Within South American mainland xenodontines, the tribes Hydropsini, Pseudoboini, and Xenodontini are monophyletic. Finally, our results suggest that some morphological and ecological traits concerning maxillary dentition, macrohabitat use, and foraging strategy have appeared multiple times during the evolution of xenodontine snakes.     

Morphology and phylogeny of Bryophryoides ocellatus n. g., n. sp. (Ciliophora,Colpodea) from in situ soil percolates of Idaho,U.S.A.

We describe the morphology and 18S rDNA phylogeny of Bryophryoides ocellatus n. g., n. sp., a bryophryid ciliate inhabiting in situ soil percolates from Idaho, U.S.A. The new genus is distinguished from other bryophryid genera by a combination of the following features: (1) kreyellid (irregularly meshed) silverline pattern, (2) polymorphic adoral organelles in the preoral suture, (3) absence of vestibular kineties. In phylogenetic analyses, Bryophryoides ocellatus is most closely related to Bryophrya gemmea. The 18S rDNA sequence pairwise distance of 2% between these genera, while similar to that between many colpodidan species, exceeds that between some colpodidan genera (e.g. Mykophagophrys and Pseudoplatyophrya, 1.1%), further supporting establishment of the new genus. Topology hypothesis testing strongly supports the monophyly of the Colpodida including the bryophryids. Despite weak nodal support, tests of topology constraints narrowly reject the non-monophyly of the sequenced Bryophryidae (Bryophrya + Bryophryoides + Notoxoma). Likewise, the monophyletic origin of the sequenced Bryophryidae is indicated in the phylogenetic networks though with low support.     

Nomenclature of tribes within the Urticaceae

Summary  As part of systematic studies of the genus Elatostema (Urticaceae) and its sister genera, it was apparent that different names had been applied at the tribal level for these genera. This paper proposes that the tribal name Elatostemeae be used for the genera currently delineated as belonging to tribe Lecantheae (Friis 1993). It is also proposed that the authorship of the currently recognised tribes in the Urticaceae should be attributed to Charles Gaudichaud-Beaupres as described in H. L. C. de Freycinet’s Voyage autour du monde…executé sur les corvettes de S. M. l’Uranie et la Physiciene, published in 1830.     

普洱地区茶叶内生细菌与根际土壤细菌群落结构分析

[目的]茶叶内生细菌、根际土壤细菌在普洱茶的发酵中起着重要的作用,还可以促进茶树生长,诱导茶树抗病性.研究其群落结构组成及相互关系可为微生物资源开发利用提供理论依据.[方法]本研究以普洱地区茶树叶片和根际土壤为材料,采用高通量测序技术,对茶叶及根际土壤细菌的16S核糖体RNA基因(16S rRNA)进行测序,比较分析茶...     

Morphological and molecular characterization within 26 strains of the genus Cylindrospermum (Nostocaceae,Cyanobacteria), with descriptions of three new species

Twenty‐six strains morphologically identified as Cylindrospermum as well as the closely related taxon Cronbergia siamensis were examined microscopically as well as phylogenetically using sequence data for the 16S rRNA gene and the 16S‐23S internal transcribed spacer (ITS) region. Phylogenetic analysis of the 16S rRNA revealed three distinct clades. The clade we designate as Cylindrospermum sensu stricto contained all five of the foundational species, C. maius, C. stagnale, C. licheniforme, C. muscicola, and C. catenatum. In addition to these taxa, three species new to science in this clade were described: C. badium, C. moravicum, and C. pellucidum. Our evidence indicated that Cronbergia is a later synonym of Cylindrospermum. The phylogenetic position of Cylindrospermum within the Nostocaceae was not clearly resolved in our analyses. Cylindrospermum is unusual among cyanobacterial genera in that the morphological diversity appears to be more evident than sequence divergence. Taxa were clearly separable using morphology, but had very high percent similarity among ribosomal sequences. Given the high diversity we noted in this study, we conclude that there is likely much more diversity remaining to be described in this genus.     

Calcaridorylaimus castaneae sp. n. (Nematoda,Dorylaimidae) from Bulgaria with an identification key to the species of the genus

An unknown species belonging to the genusCalcaridorylaimus Andrássy, 1986 was collected from the litter of broadleaf forests dominated by Castanea sativa Mill. and mixed with Quercus daleshampii Ten. and Fagus sylvatica L. on Belasitsa Mountain, south-western Bulgaria. Calcaridorylaimus castaneae sp. n. is characterised by its long body (1.4–2.1 mm), lip region practically not offset, vulva transverse, short odontostyle (14.5–16 μm) and tail (75.5–110.5 μm, c=14.7–23.6; c’=2.9–4.4) in females and 38–46 μm long spicules with small spur before their distant end in males. It is most similar to C. andrassyi Ahmad & Shaheen, 2004, but differs in having transverse vs pore-like vulva and shorter spicules (38–46 μm vs 52–57 μm). An identification key to the species of the genus Calcaridorylaimus is proposed. Phylogenetic analyses were performed on 18S and D2-D3 expansion domains of 28S rRNA genes by Neighbor-Joining, Maximum Likelihood and Bayesian Inference methods. The phylograms inferred from 18S sequences showed closest relationships of the new species with some species belonging to the genus Mesodorylaimus. However, insufficient molecular data for members of both genera do not allow the phylogenetic relationships of Calcaridorylaimus and the new species described herein to be elucidated.     

New contributions to the taxonomy of urostylid ciliates (Ciliophora,Hypotrichia), with establishment of a new genus and new species

Hypotrichia, one of the most complex and highly differentiated groups in Ciliophora, has been the object of extensive studies, especially in recent years. Nevertheless, methodological difficulties and insufficient faunistic studies have limited our understanding of their biodiversity and phylogeny. In this study, one novel urostylid ciliate, Pseudoholosticha zhaoi nov. gen., nov. spec. and two populations of Anteholosticha monilata (Kahl, 1928) Berger, 2003, type species of the latter genus, are studied using an integrative approach (live observation, protargol impregnation, scanning electron microscopy, and phylogenetic analysis) to provide further insights into the diversity, classification, and phylogeny of this group of ciliates. Pseudoholosticha nov. gen. can be separated from other morphologically similar genera mainly by the absence of buccal and caudal cirri. A key to 12 morphologically similar genera and illustrations of their cirral patterns are provided. The validation of the new genus and new species is supported by both morphological and phylogenetic analyses. The first 18S rRNA gene sequence of A. monilata, with detailed morphological data, provided a reliable clarification of A. monilata populations and corroborated the phylogenetic position of the type species of the polyphyletic genus Anteholosticha.     

Isolation and functional analysis of denitrifiers in an aquifer with high potential for denitrification

Aquifers are among the main freshwater sources. The Raigón aquifer is susceptible to contamination, mainly by nitrate and pesticides, such as atrazine, due to increasing agricultural activities in the area. The capacity of indigenous bacteria to attenuate nitrate contamination in different wells of this aquifer was assessed by measuring denitrification rates with either acetate plus succinate or nitrate amendments. Denitrification activity in nitrate-amended assays was significantly higher than in unamended assays, particularly in groundwater from wells where nitrate concentration was 33.5 mg L⁻¹ or lower. Furthermore, groundwater denitrifiers capable of using acetate or succinate as electron donors were isolated, identified by 16S rRNA gene sequencing and evaluated for functional denitrification genes (nirS, nirK and nosZ). Phylogenetic affiliation of 54 isolates showed that all members belonged to nine different genera within the Proteobacteria (Bosea, Ochrobactrum, Azospira, Zoogloea, Acidovorax, Achromobacter, Vogesella, Stenotrophomonas and Pseudomonas). In addition, isolate AR28 that clustered separately from validly described species could potentially belong to a new genus. The majority of the isolates were related to species belonging to previously reported denitrifying genera. However, the phylogeny of the nirS and nosZ genes revealed new sequences of these functional genes. To our knowledge, this is the first isolation and sequencing of the nirS gene from the genus Vogesella, as well as the nosZ gene from the genera Acidovorax and Zoogloea. The results indicated that indigenous bacteria in the Raigón aquifer had the capacity to overcome high nitrate contamination and exhibited functional gene diversity.     

Isolation and identification of gastrointestinal microbiota from the short-nosed fruit bat Cynopterus brachyotis brachyotis

Studies on the microbial ecology of gut microbiota in bats are limited and such information is necessary in determining the ecological significance of these hosts. Short-nosed fruit bats (Cynopterus brachyotis brachyotis) are good candidates for microbiota studies given their close association with humans in urban areas. Thus, this study explores the gut microbiota of this species from Peninsular Malaysia by means of biochemical tests and 16S rRNA gene sequences analysis. The estimation of viable bacteria present in the stomach and intestine of C. b. brachyotis ranged from 3.06 × 10¹⁰ to 1.36 × 10¹⁵ CFU/ml for stomach fluid and 1.92 × 10¹⁰ to 6.10 × 10¹⁵ CFU/ml for intestinal fluid. A total of 34 isolates from the stomach and intestine of seven C. b. brachyotis were retrieved. A total of 16 species of bacteria from eight genera (Bacillus, Enterobacter, Enterococcus, Escherichia, Klebsiella, Pantoea, Pseudomonas and Serratia) were identified, Enterobacteriaceae being the most prevalent, contributing 12 out of 16 species isolated. Most isolates from the Family Enterobacteriaceae have been reported as pathogens to humans and wildlife. With the possibility of human wildlife transmission, the findings of this study focus on the importance of bats as reservoirs of potential bacterial pathogens.     

A molecular and morphological reassessment of the phylogeny of the subfamily Ophioninae (Hymenoptera: Ichneumonidae)

The phylogeny of the subfamily Ophioninae (Hymenoptera: Ichneumonidae) is investigated using molecular markers and morphological characters. We analysed the mitochondrial DNA CO1 and the nuclear 28S D2–D3 gene fragments for 74 species of Ophioninae from 25 out of the 32 recognized genera, which collectively represent 98% of described species diversity of the subfamily. Molecular markers were analysed separately and combined, with or without the adjunction of a matrix of 62 morphological characters using Bayesian inference. Our results reveal three distinct lineages, each including one of most speciose genera: Ophion, Enicospilus and Thyreodon. The comparison of the molecular data, and combined molecular plus morphological data led to the definition of the three tribes: Ophionini stat. rev. (Ophion + Alophophion + Rhopalophion + Xylophion + Afrophion); Enicospilini stat. rev. (Enicospilus + Laticoleus + Dicamptus + Hellwigiella); and Thyreodonini tribe nov. (Thyreodon + Dictyonotus + Rhynchophion). The possible association of other genera to one or another of these lineages is discussed. Ophion is a polyphyletic assemblage and requires a further revision to define the delimitation with close genera. The enigmatic Old World genus Skiapus is strongly supported as belonging to the Ophioninae, although its placement within the subfamily is ambiguous as a result of its derived genotype and phenotype. Finally, we propose a biogeographical scenario supported by this phylogeny and based on the limited available fossil data.     

Culturable bacterial diversity at the Princess Elisabeth Station (Utsteinen, Sør Rondane Mountains, East Antarctica) harbours many new taxa

We studied the culturable heterotrophic bacterial diversity present at the site of the new Princess Elisabeth Station at Utsteinen (Dronning Maud Land, East Antarctica) before construction. About 800 isolates were picked from two terrestrial microbial mat samples after incubation on several growth media at different temperatures. They were grouped using rep-PCR fingerprinting and partial 16S rRNA gene sequencing. Phylogenetic analysis of the complete 16S rRNA gene sequences of 93 representatives showed that the isolates belonged to five major phyla: Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes and Deinococcus-Thermus. Isolates related to the genus Arthrobacter were the most prevalent whereas the genera Hymenobacter, Deinococcus, Cryobacterium and Sphingomonas were also recovered in high numbers in both samples. A total of 35 different genera were found, the majority of which has previously been reported from Antarctica. For the genera Aeromicrobium, Aurantimonas, Rothia, Subtercola, Tessaracoccus and Xylophilus, this is the first report in Antarctica. In addition, numerous potential new species and new genera were recovered; many of them currently restricted to Antarctica, particularly in the phyla Bacteroidetes and Deinococcus-Thermus.     

Morphological and molecular characterization of the name-bearing type species Rimaleptus binucleatus (Kahl, 1931), with a phylogenetic re-analysis of dileptid evolutionary history (Ciliophora: Litostomatea: Rhynchostomatia)

We collected Rimaleptus binucleatus from soil in the surroundings of the town of Ulsan, South Korea. Its morphology and 18S rRNA gene were studied using standard methods. This possibly widely distributed species is characterized by: (i) a size of about 170–400 × 20–65 μm; (ii) a narrowly to cylindrically dileptid body with proboscis occupying about 30–65% of body length; (iii) two dorsal contractile vacuoles; (iv) two size groups of rod-shaped extrusomes; and (v) about 18–29 ciliary rows, 4–6 of them anteriorly differentiated into a staggered dorsal brush. Phylogenetic analyses of five new rhynchostomatian 18S rRNA gene sequences supported monophylies of the orders Tracheliida and Dileptida, but revealed that the genera Rimaleptus and Pseudomonilicaryon are polyphyletic. Monophyly of genera with two macronuclear nodules was consistently rejected, but monophylies of dileptids with many scattered macronuclear nodules and of dileptids with moniliform macronucleus and multi-rowed dorsal brush could not be excluded by statistical topology tests. Nevertheless, phylogenetic network analyses indicated considerable conflict in the phylogenetic signal provided by the 18S rRNA gene to resolve unambiguously relationships among dileptid genera.     

基于28S rRNA D2序列的内茧蜂亚科的分子系统发育

首次利用同源28S rRNA D2基因序列对内茧蜂亚科Rogadinae （昆虫纲Insecta：膜翅目Hymenoptera：茧蜂科Braconidae）进行了分子系统学研究。本研究从95%～100%乙醇浸渍保存的标本中提取基因组DNA并扩增了10种内群种类和5种外群种类的28S rDNA D2片段并测序（GenBank序列号AY167645-AY167659）,利用BLAST搜索相关的同源序列, 采用了GenBank中13个种类的28S rRNA D2同源序列,然后据此进行分子分析。利用3个外群（共8个种类）和3种建树方法 (距离邻近法distance based neighbor joining, NJ; 最大俭约法maximum parsimony, MP; 和最大似然法maximum likelihood, ML)分析了内茧蜂亚科内的分子系统发育关系。结果表明,由分子数据产生的不同的分子系统树均显示内茧蜂亚科是一个单系群。内茧蜂亚科内依据形态和生物学特征的分群（族和亚族）及其系统发育关系得到部分支持。NJ、MP和ML分析结果均表明内茧蜂族Rogadini不是一个单系,而是一个并系,其余3族则得到不同程度的支持。内茧蜂族可分成2个分支：“脊茧蜂属Aleiodes+弓脉茧蜂属Arcaleiodes”和“沟内茧蜂属Canalirogas+锥齿茧蜂属Conspinaria+刺茧蜂属Spinaria+内茧蜂属Rogas”,二者不是姐妹群。脊茧蜂属Aleiodes和弓脉茧蜂属Arcaleiodes始终是姐妹群。脊茧蜂属Aleiodes是一个单系,并可分成2个姐妹分支,这与依据形态和生物学特征的亚属分群相一致。弓脉茧蜂属Arcaleiodes Chen et He,1991是一个独立的属。分支“沟内茧蜂属Canalirogas+锥齿茧蜂属Conspinaria+刺茧蜂属Spinaria+内茧蜂属Rogas”的单系性仅得到部分分子数据的支持;因形态特异（腹部成甲壳状）而列为亚族级的刺茧蜂属Spinaria,分子分析没有证实这一点。横纹茧蜂族Clinocentrini是个单系,并在内茧蜂亚科的系统发育中处于基部（原始）的位置。我们研究结果还表明,阔跗茧蜂属Yelicones和潜蛾茧蜂属Stiropius相对应的阔跗茧蜂族Yeliconini和潜蛾茧蜂族Stiropiini为2个独立的分支, 与形态和生物学的结果一致,但它们在内茧蜂亚科的系统发育的位置不明,有待今后进一步研究。     

A widespread cyanobacterium supported by polyphasic approach: proposition of Koinonema pervagatum gen. & sp. nov. (Oscillatoriales)1

Several new genera originally classified as the genus Phormidium, a polyphyletic and taxonomically complex genus within the Oscillatoriales, were recently described. The simple morphology of Phormidium does not reflect its genetic diversity and the delimitation of a natural group is not possible with traditional classification systems based on morphology alone. Therefore, this study used morphological, ecological, and molecular approaches to evaluate four populations morphologically similar to Ammassolinea, Kamptonema, and Ancylothrix (simple, curved, and gradually attenuated at the ends trichome), found in subtropical and tropical Brazilian regions. 16S rRNA gene sequences grouped all the strains in a highly supported clade with other two European strains isolated from thermal springs surrounding areas. The 16S‐23S ITS secondary structure corroborated the phylogenetic analysis with all the strains having similar structures. Consequently, a genetically well‐defined and cryptic new genus, Koinonema gen. nov., is proposed containing the aquatic, mesophilic, and morphologically homogeneous new species, Koinonema pervagatum sp. nov.     

16S rRNA-Targeted identification of cyanobacterial genera using oligonucleotide-probes immobilized on bacterial magnetic particles

16S rRNA-targeted identification of cyanobacterial genera, Anabaena,Microcystis, Nostoc, Oscillatoria, Synechococcus wasdeveloped using bacterial magnetic particles (BMPs). 16S rRNA-targetedcapture probes designed from the genus specific region of the 16S rRNAsequence were immobilized on BMPs. Identification of cyanobacteria wasperformed by a sandwich hybridization using the capture probes – BMPconjugates and a digoxigenin (DIG)-labeled detector probe complementaryto the highly conserved 16S rRNA sequence for cyanobacteria. Theluminescence intensity of the probe/target-BMP hybrids was measured afterreaction with alkaline phosphatase conjugated anti-DIG antibody. Fivespecies of cyanobacteria from five different genera were successfullydiscriminated using this magnetic capture system.     

DNA barcodes for marine fungal identification and discovery

We employed DNA barcodes for identification of fungal species in marine sediments. Sediments were collected seasonally along the Southeast coast of India from which a culturable fungal library was constructed. All cultured species were morphologically documented using microscopical analysis. A maximum population density of 19.3 × 10³ CFU/g was recorded in monsoon and minimum of 3 × 10³ CFU/g in premonsoon season. Two-way analysis of variance suggests that the fungal community varied significantly between the seasons (F = 9.543, P < 0.001) and at various depths sampled (F = 4.655, P < 0.05). In total, 54 fungal species belonging to 13 different families were documented and all species were sequenced for internal transcribed spacer genes. Each species was represented by at least two specimens constituting a total of 171 specimens for DNA barcoding. Twelve species of a marine fungi were sequenced for the first time. Branching patterns of phylogenetic tree strongly supported the sequence variations within and between all species barcoded. Based on the pairwise distance model we suggest barcode gaps of 15 %, 21 %, 30 %, 35 % and 51 % for genera, family, order, class and phyla respectively.     

Phylogenetic Analysis of the Spider Mite Sub-Family Tetranychinae (Acari: Tetranychidae) Based on the Mitochondrial COI Gene and the 18S and the 5′ End of the 28S rRNA Genes Indicates That Several Genera Are Polyphyletic

The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825–1,901 bp) and 28S (the 5′ end of 646–743 bp) rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp). As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus) appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered.     

Early social contact alters the community structure and functions of the faecal microbiome in suckling-growing piglets

Social contact during suckling, in an enriched social environment, can reduce the aggressive behaviours of piglets during regrouping at weaning, and improve their production performance and welfare. The aim of this study was to determine the possible impact of suckling social contact on gut microbes. We performed 16S rRNA sequencing to measure the faecal microbial structure and function in piglets experiencing social contact. Eighteen-litter piglets were allocated to two treatments: an early continuous social contact (CSC) group where piglets from adjacent pens shared a mutual pen starting at 14 days postpartum and a control (CON) group where piglets had no contact with individuals from adjacent pens during the suckling period. The piglets were regrouped at 36 days of age. The litter weights at 35 and 63 days of age were measured. Faecal samples were randomly collected at 16, 35, 42, and 63 days of age and faecal DNA was determined. The results showed that the litter weight of piglets in the CSC group was significantly decreased at 63 days compared with the CON group. Continuous social contact also significantly decreased the microbial richness at 16 and 35 days of age (P < 0.05). Firmicutes was the most abundant bacterial phylum in both groups at all detected time-points and the abundance increased with social contact. At the genus level, Lactobacillus was the most abundant bacterium after weaning and the abundance increased in the piglets with social contact. Compared with the faecal microbiota of control piglets, a total of 22 genera at 16 days, 20 genera at 35 days, 12 genera at 42 days, and 27 genera at 63 days in the faeces of CSC piglets were observed to be significantly different in abundance (linear discriminant analysis score > 3, P < 0.05). Furthermore, functional analysis of the microbial composition showed that the changes induced by early CSC mainly altered the relative abundance of metabolic and related pathways. The social contact notably had an effect on the abundance of microbial pathways for amino acid and carbohydrate metabolism. In conclusion, CSC changed the microbial composition in the faeces of piglets, which might have a negative effect on nutrient metabolism for the suckling-growing piglets. Our study provided new insight into the influence of social contact on the suckling-growing piglets.