Development and optimization of an 18S rRNA‐based oligonucleotide microarray for the fungal order Eurotiales

Aims: For identification of members of the fungal order Eurotiales, an 18S rRNA gene‐based oligonucleotide microarray was developed and optimized. Methods and Results: Eurotiales‐specific probes covering most members of the Eurotiales as well as species‐specific probes were designed and evaluated with three pure cultures (two fungi from the Eurotiales and one fungus from the Hypocreales). Nearly complete 18S rRNA genes of each reference culture were amplified and fluorescently labelled by random priming. Conclusions: Positive and negative hybridization results confirmed that the Eurotiales probes tested in this study could correctly identify members of the Eurotiales. The species‐specific probes were also capable of species‐level detection. Significance and Impact of the Study: These findings demonstrate the potential applications of a phylogenetic oligonucleotide microarray approach to characterizing fungal species and populations in environmental and other samples.     

Diversity of facultatively anaerobic microscopic mycelial fungi in soils

The numbers of microscopic fungi isolated from soil samples after anaerobic incubation varied from tens to several hundreds of CFU per one gram of soil; a total of 30 species was found. This group is composed primarily of mitotic fungi of the ascomycete affinity belonging to the orders Hypocreales (Fusarium solani, F. oxysporum, Fusarium sp., Clonostachys grammicospora, C. rosea. Acremonium sp., Gliocladium penicilloides, Trichoderma aureoviride, T. harzianum, T. polysporum, T. viride. T. koningii, Lecanicillum lecanii, and Tolypocladium inflatum) and Eurotiales (Aspergillus terreus, A. niger, and Paecilomyces lilacimus), as well as to the phylum Zygomycota, to the order Mucorales (Actinomucor elegans, Absidia glauca, Mucor circinelloides, M. hiemalis, M. racemosus, Mucor sp., Rhizopus oryzae, Zygorrhynchus moelleri, Z. heterogamus, and Umbelopsis isabellina) and the order Mortierellales (Mortierella sp.). As much as 10-30% of the total amount of fungal mycelium remains viable for a long time (one month) under anaerobic conditions.     

虫草属分子系统学研究现状

近年来的分子系统学研究结果表明 ,麦角菌目 (Clavicipitales)与肉座菌目 (Hypocreales)以及虫草属[Cordyceps(Fr.)Link]与麦角菌科 (Clavicipitaceae)内的有关种属关系密切 ,但虫草属为一多系群 ,其中只有新虫草亚属的种类形成单系群。虫草属种类的进化与寄主有一定的关系 ,有关研究显示它们在亲缘关系相差很大的寄主之间多次转移。多个独立的ITS序列研究表明 ,阔孢虫草 (CordycepscrassisporaM .Zangetal.)、甘肃虫草(CordycepsgansuensisK .Y .Zhangetal.)、多轴虫草 (CordycepsmultiaxialisM .Zang&Kinjo)、尼泊尔虫草 (CordycepsnepalensisM .Zang&Kinjo)与冬虫夏草 [Cordycepssinensis(Berk.)Sacc.]为同一物种 ;RAPD和ITS序列分析还显示不同地理分布的冬虫夏草存在明显的遗传分化。分子生物学方法在确定有性型与无性型的关系上已经为多种虫草菌提供了有力的证据。本文主要对虫草属分子系统学研究现状进行了综述 ,同时就分子生物学研究中的取样问题、一些分子方法的适用范围以及有性型与无性型的关系等问题进行了讨论。     

Phylogenetic relationships of the downy mildews (Peronosporales) and related groups based on nuclear large subunit ribosomal DNA sequences

In order to investigate phylogenetic relationships of the Peronosporomycetes (Oomycetes), nuclear large subunit ribosomal DNA sequences containing the D1 and D2 region were analyzed of 92 species belonging to the orders Peronosporales, Pythiales, Leptomitales, Rhipidiales, Saprolegniales and Sclerosporales. The data were analyzed applying methods of neighbor-joining as well as maximum parsimony, both statistically supported using the bootstrap method. The results confirm the major division between the Pythiales and Peronosporales on the one hand and the Saprolegniales, Leptomitales, and Rhipidiales on the other. The Sclerosporales were shown to be polyphyletic; while Sclerosporaceae are nested within the Peronosporaceae, the Verrucalvaceae are merged within the Saprolegniales. Within the Peronosporomycetidae, Pythiales as well as Peronosporales as currently defined are polyphyletic. The well supported Albugo clade appears to be the most basal lineage, followed by a Pythium-Lagenidium clade. The third, highly supported clade comprises the Peronosporaceae together with Sclerospora, Phytophthora, and Peronophythora. Peronophythora is placed within Phytophthora, indicating that both genera should be merged. Bremiella seems to be polyphyletic within the genus Plasmopara, suggesting a transfer to Plasmopara. The species of Peronospora do not appear as a monophyletic group. Peronospora species growing on Brassicaceae form a highly supported clade.     

中国种子植物内生真菌资源及菌植协同进化

综述了中国种子植物内生真菌资源研究概况,比较了裸子植物和被子植物内生真菌种类,它们都具有肉座菌目(Hypocreales),粪壳菌目(Sordariales),散囊菌目(Eurotiales),毛霉目(Mucorales)及不产孢类(Myceliasterilia)内生真菌。裸子植物内生真菌涉及52个属,既包括高等的子囊菌和担子菌,也包括低等的卵菌(Oomycetes)和接合菌(Zygomycetes)类。被子植物涉及60个属,主要为高等的子囊菌(Ascomycetes)和担子菌(Basidiomycetes),低等的卵菌和接合菌报道很少。双子叶植物涉及40个属,单子叶植物内生真菌涉及30个属,两类被子植物所报道的内生真菌只有11个属相同。裸子植物与双子叶植物内生真菌相似程度较高,都具有炭角菌目(Xylariales)、格孢腔菌目(Pleosporales)、柔膜菌目(Helotiales)和白粉菌目(Erysiphales),刺盘孢菌属(Colletotrichum)、拟茎点霉属(Phomopsis)、枝孢霉属(Cladosporium)、地霉属(Geotrichum)等内真菌,共20个属相同。各类种子植物具有自己独特的一些内生真菌。还对植物与其内生真菌的协同进化关系进行了分析。     

Ascospore morphology is a poor predictor of the phylogenetic relationships of Neurospora and Gelasinospora

The genera Neurospora and Gelasinospora are conventionally distinguished by differences in ascospore ornamentation, with elevated longitudinal ridges (ribs) separated by depressed grooves (veins) in Neurospora and spherical or oval indentations (pits) in Gelasinospora. The phylogenetic relationships of representatives of 12 Neurospora and 4 Gelasinospora species were assessed with the DNA sequences of four nuclear genes. Within the genus Neurospora, the 5 outbreeding conidiating species form a monophyletic group with N. discreta as the most divergent, and 4 of the homothallic species form a monophyletic group. In combined analysis, each of the conventionally defined Gelasinospora species was more closely related to a Neurospora species than to another Gelasinospora species. Evidently, the Neurospora and Gelasinospora species included in this study do not represent two clearly resolved monophyletic sister genera, but instead represent a polyphyletic group of taxa with close phylogenetic relationships and significant morphological similarities. Ascospore morphology, the character that the distinction between the genera Neurospora and Gelasinospora is based upon,was not an accurate predictor of phylogenetic relationships.     

A molecular systematic investigation of the Acrochaetiales (Florideophycidae,Rhodophyta) and related taxa based on nuclear small-subunit ribosomal DNA sequence data

Small-subunit ribosomal DNA (SSU) sequences for 14 members of the rhodophyte order Acrochaetiales were used to generate phylogenetic trees to determine whether the Acrochaetiales is monophyletic and to assess the relationships of acrochaetioid algae to closely related taxa. Within the Acrochaetiales, two strongly supported groups are recognized: one group that includes, in addition to three other species, the type species of the genera Acrochaetium, Audouinella and Rhodochorton; and a second group that includes an unequivocal representative of Colaconema and nine additional species. The relationships of these groups with the Batrachospermales, Palmariales and Nemaliales were not resolved and the possibility that the Acrochaetiales is polyphyletic was not eliminated. Resolution of relationships for species within these groups was strong in only a few cases, with many of the phylogenetic issues at this level remaining equivocal. Our results do not position Camontagnea in the Acrochaetiales, as has recently been suggested, but strongly ally this genus to the family Rhodothamniellaceae of the Palmariales. The phylogenetic position of Rhododraparnaldia, an alga intermediate between the Acrochaetiales and Batrachospermales, remains unresolved. These molecular results provide a foundation for assessing the taxonomic significance of phenotypic characters (e.g. anatomy, life histories, morphology, phycoerythrin type and plastid details) variously considered taxonomically significant in the Acrochaetiales.     

烟草根部内生真菌群落结构和功能特征

烟草内生真菌是烟田生态系统的重要组成,根系是烟草内生真菌重要来源途径。本研究通过高通量测序技术分析了5个品种的烟草根部内生真菌群落结构及功能特征。结果表明,烟草根部内生真菌群落多样性较低;粪壳菌纲Sordariomycetes、座囊菌纲Dothideomycetes、散囊菌纲Eurotiomycetes、伞菌纲Agaricomycetes及锤舌菌纲Leotiomycetes为主要菌群,肉座菌目Hypocreales、煤炱目Capnodiales和散囊菌目Eurotiales为优势真菌目,丛赤壳科Nectriaceae、小戴维霉科Davidiellaceae和发菌科Trichocomaceae为优势真菌科,未定义腐生菌和动物病原菌是主要的生态功能群,但不同品种之间的真菌群落组成和生态功能分布差异显著。本研究为进一步挖掘利用烟草内生真菌资源,阐明烟草内生真菌的生态功能提供了参考。     

Screening of basidiomycetes for antimicrobial activities

As a part of a screening programme developed to evaluate the antimicrobial activity of basidiomycetes, 317 isolates representing 204 species collected in Spain were screened against a range of human clinical pathogens and laboratory controls. Extracts from 45% of the isolates, representing 109 species, showed antimicrobial activity. Antibacterial activity was more pronounced than antifungal activity. The proportion of extracts from basidiomycetes showing antimicrobial activity was similar to or above that obtained for representative orders of Ascomycetes, such as Pezizales and Xylariales, but lower than that produced by members of the orders Diaporthales, Eurotiales, Hypocreales, Leotiales and Sordariales. Suprageneric taxa (orders and families) did not show pronounced differences in their antimicrobial activities though such differences were observed at the genus level, suggesting that the ability to produce these bioactive compounds is not homogenously distributed amongst the basidiomycetes. Isolates from some species showed large differences in their ability to produce metabolites with antimicrobial activity, possibly reflecting genetic differences at the infraspecific level.     

A phylogenetic study of the genus Haligena (Halosphaeriales, Ascomycota)

The genus Haligena (Halosphaeriales, Ascomycota), with two accepted species, is encountered frequently in marine habitats, especially on wood in temperate regions. Phylogenetic analyses of Haligena elaterophora (type species) and H. salina were undertaken, with partial large subunit ribosomal DNA sequences, to determine their relationships with other closely related genera in the order. The genus was shown to be polyphyletic within the Halosphaeriales with the type species forming a basal clade to the order. Haligena salina constituted a sister clade with weak support of Neptunella longirostris in all analyses. Haligena elaterophora and H. salina differ significantly in the nature of their ascospore appendages: wider, more sticky and strap-like in H. elaterophora and spoon-shaped at the point of attachment; in H. salina they are longer and narrower, finely drawn out filaments. A new genus, Morakotiella, is introduced to accommodate H. salina.     

Phylogenetic studies on the Thamnocalamus group and its allies (Gramineae: Bambusoideae) based on its sequence data.

Phylogenetic analyses, using the parsimony method and the neighbor-joining method, of 31 species of the Thamnocalamus group and its allies based on internal transcribed spacer (ITS) sequences in nuclear ribosomal DNA are presented. Two species from Arundinaria and Acidosasa were used as outgroups. The ITS phylogeny strongly supports the monophyly of the Thamnocalamus group and its allies, which have pachymorph rhizomes and semelauctant synflorescences with three stamens. Within this clade, Chimonocalamus pallens was resolved in the basal position. The Thamnocalamus group, including species placed in Thamnocalamus, Fargesia (Sinarundinaria, Borinda), and Yushania, may be polyphyletic/paraphyletic according to the ITS phylogeny, but internal support was relatively low. All three sampled species of Ampelocalamus were resolved as a monophyletic group and may be related to Drepanostachyum hookerianum. Two taxa of Thamnocalamus and the species Gaoligongshania megalothyrsa were resolved as monophyletic despite their different morphological characters, but again with a low bootstrap support. Within the Fargesia yunnanensis subclade, the sister relationship of Fargesia fungosa and Fargesia edulis was supported. Another subclade, the Fargesia communis clade, was also weakly supported as monophyletic. However, further resolution within the Thamnocalamus group has not been provided by this sequence data. The results indicate that reevaluation of relationships within this group is necessary.     

SSU rDNA sequence support for a close relationship between the elaphomycetales and the Eurotiales and Onygenales

Based on parsimony analyses of eight new SSU rDNA sequences and 24 homologous sequences retrieved from the DNA databases, we suggest a possible phylogenetic relationship of Elaphomycetales with Eurotiales and Onygenales. Our three includedElaphomyces sequences strongly cluster together (bootstrap value 100%) within a monophyletic group (100%) of Elaphomycetales, Eurotiales, and Onygenales. Earlier reports that another cleistothecial lineage (Erysiphe) is related to Leotiales, are supported by our discovery that also another cleistothecial species,Amylocarpus encephaloides, shows affinity to Leotiales. Ascosphaeraceae and Eremascaceae are possibly better accommodated in Onygenales. We describe a new DNA extraction method in which sonication is used to disrupt thick-walled spores. It is useful for both fresh and dried fungal material.     

A phylogenetic hypothesis for the Aizoaceae (Caryophyllales) based on four plastid DNA regions

The Aizoaceae is the largest family of leaf succulent plants, and most of its species are endemic to southern Africa. To evaluate subfamilial, generic, and tribal relationships, we produced two plastid DNA data sets for 91 species of Aizoaceae and four outgroups: rps16 intron and the trnL-F gene region (both the trnL intron and the trnL-F intergenic spacer). In addition, we generated two further plastid data sets for 56 taxa restricted to members of the Ruschioideae using the atpB-rbcL and the psbA-trnH intergenic spacers. In the combined tree of the rps16 intron and trnL-F gene region, three of the currently recognized subfamilies (Sesuvioideae, Mesembryanthemoideae, and Ruschioideae) are each strongly supported monophyletic groups. The subfamily Tetragonioideae is polyphyletic, with Tribulocarpus as sister to the Sesuvioideae and Tetragonia embedded in the Aizooideae. Our study showed that the group consisting of the Sesuvioideae, Aizooideae, and Tetragonioideae does not form a monophyletic entity. Therefore, it cannot be recognized as a separate family in order to accommodate the frequently used concept of the Mesembryanthemaceae or "Mesembryanthema," in which the subfamilies Mesembryanthemoideae and Ruschioideae are included. We also found that several genera within the Mesembryanthemoideae (Mesembryanthemum, Phyllobolus) are not monophyletic. Within the Ruschioideae, our study retrieved four major clades. However, even in the combined analysis of all four plastid gene regions, relationships within the largest of these four clades remain unresolved. The few nucleotide substitutions that exist among taxa of this clade point to a rapid and recent diversification within the arid winter rainfall area of southern Africa. We propose a revised classification for the Aizoaceae.     

Phylogeny of mitosporic entomopathogenic fungi: is the genus Paecilomyces polyphyletic?

We analyzed sequences of the divergent domain at the 5' end of the large subunit rRNA gene from the mitosporic entomopathogenic fungi Paecilomyces sp., Paecilomyces fumosoroseus, Paecilomyces farinosus, Paecilomyces lilacinus, Verticillium lecanii, Verticillium psalliotae, Beauveria bassiana, Aschersonia sp., Aschersonia placenta, ascomycetous Cordyceps sp., and Cordyceps militaris. Phylogenetic analysis showed P. fumosorseus as the best characterized out of the analyzed species with the B. bassiana clade as its sister group. Two of the P. farinosus isolates were invariably placed within the Verticillium cluster, which also contained C. militaris. The only analyzed P. lilacinus isolate appeared on the root of the hyphomycetous fungi and was characterized as the most distinct from all the hyphomycetous fungi tested. Polyphyly of the genus Paecilomyces was well supported by the Kishino-Hasegawa test. In all trees based on the small subunit rRNA gene sequences obtained from the GenBank, V. lecanii, V. psalliotae, P. fumosoroseus, P. tenuipes and B. bassiana form, together with that of C. militaris, the best supported cluster in the tree. The rest of Cordyceps spp. constitute a distinct clade. Phylogenetic relationships derived from both tested DNA regions show polyphyly of the genus Paecilomyces and close relationships among entomopathogenic species of the genera Verticillium, Paecilomyces, and Beauveria.     

A phylogeny of the schoenoid sedges (Cyperaceae: Schoeneae) based on plastid DNA sequences, with special reference to the genera found in Africa

Despite its large size (about 700 species), the australy-centred sedge tribe Schoeneae has received little explicit phylogenetic study, especially using molecular data. As a result, generic relationships are poorly understood, and even the monophyly of the tribe is open to question. In this study, plastid DNA sequences (rbcL, trnL-trnF, and rps16) drawn from a broad array of Schoeneae are analysed using Bayesian and parsimony-based approaches to infer a framework phylogeny for the tribe. Both analytical methods broadly support the monophyly of Schoeneae, Bayesian methods doing so with good support. Within the schoenoid clade, there is strong support for a series of monophyletic generic groupings whose interrelationships are unclear. These lineages form a large polytomy at the base of Schoeneae that may be indicative of past radiation, probably following the fragmentation of Gondwana. Most of these lineages contain both African and non-African members, suggesting a history of intercontinental dispersal. The results of this study clearly identify the relationships of the African-endemic schoenoid genera and demonstrate that the African-Australasian genus Tetraria, like Costularia, is polyphyletic. This pattern is morphologically consistent and suggests that these genera require realignment.     

Spatio-temporal,environmental factors,and host identity shape culturable-epibiotic fungi of seaweeds in the Red Sea,Egypt

The study of fungal species diversity from marine algae is in its infancy; as now no studies have been carried out on the distribution and diversity of fungi on the surfaces of marine macroalgae where all fungal–algal interactions tend to begin. The aim of this study was to isolate and describe the culturable part of mycobiota associated with the surface of benthic marine macroalgae (epiphytic or epibiotic fungi). This is an important step in understanding their abundance, diversity and factors influencing their variability and composition. The fungal community was dominated by Ascomycetes (89%) with Eurotiales as the most abundant fungal order followed by Capnodiales, Pleosporales, and Hypocreales, while Zygomycetes was less frequent. The nature of occurrence of fungal genera on different macroalgal hosts suggests that a mix of generalists’ framework applies to fungal epiphytes of seaweeds, but the abundance of fungal taxa varied among ecological functional groups of algae, as well as macroalgal taxonomic groups, which imply host filtering. The fungal assemblages were also characterized by temporal variation with variation in temperature, pH, and salinity as the most important abiotic factors. The structure of fungal assemblages showed high beta diversity and low similarity between hosts.     

Phylogeny of Dendroctonus bark beetles (Coleoptera: Curculionidae: Scolytinae) inferred from morphological and molecular data

Bark beetles in the genus Dendroctonus may attack and kill several species of coniferous trees, some of them causing major economic losses in temperate forests throughout North and Central America. For this reason, they have been widely studied. However, various aspects of the taxonomy and evolutionary history of the group remain contentious. The genus has been subdivided in species groups according to morphological, biological, karyological or molecular attributes, but the evolutionary affinities among species and species groups within the genus remain uncertain. In this study, phylogenetic relationships among Dendroctonus species were reassessed through parsimony‐based cladistic analysis of morphological and DNA sequence data. Phylogenetic inference was based on 36 morphological characters and on mitochondrial DNA sequences of the cytochrome oxidase I (COI) gene. Analyses were carried out for each dataset, as well as for the combined data analysed simultaneously, under equal and implied weights. According to the combined analysis, the genus Dendroctonus is a monophyletic group defined by at least three synapomorphic characters and there are four main lineages of varied composition and diversity within the genus. Within these lineages, several monophyletic groups match, to some extent, species groups defined by previous authors, but certain groups proposed by those authors are polyphyletic or paraphyletic.     

粉拟青霉种内RAPD多态性分析

对来自不同地理来源和不同寄主的 １３株粉拟青霉Ｐａｅｃｉｌｏｍｙｃｅｓ ｆａｎｉｎｏｓｕｓ和其他３种拟青霉及１株球孢白僵菌进行ＲＡＰＤ分析,从ＲＡＰＤ扩增结果可知粉拟青霉种内具丰富的遗传多样型。ＲＡＰＤ扩增指纹图谱能有效地分辨不同菌株的基因型,可用于监测生防效果的菌株示踪。聚类分析结果表明种间的遗传差异要明显大于种内的差异。菌株间差异是和地理来源相关,而和寄主不相关。     

菝葜科基于形态学证据的系统发育分析

对全世界范围分布的菝葜科Smilacaceae的79个代表种(包括了全部的属和组), 以分布于南美洲的Philesia Comm. ex Juss.和Lapageria Ruiz &; Pav.属为外类群, 选取包括花粉和染色体性状在内的47个广义的形态学性状进行了分支分类系统发育分析, 同时以表征分类的方法构建了距离树(NJ)辅助分析, 首次对世界分布的菝葜科各属间及属内的系统发育关系作了探讨。(1)Ripogonum与菝葜属Smilax +肖菝葜属Heterosmilax互为姐妹群, 但是距离较远, 支持将类菝葜属(新拟中文名)Ripogonum独立为科的观点; (2)肖菝葜属在菝葜科内处于较为进化的分支上, 并与菝葜属土茯苓组sect. Coilanthus的部分种组成一个具较高支持率(88%)的单系分支, 分析表明肖菝葜属并非是一个好属, 应归入菝葜属; (3)菝葜属6个组的划分大都没有得到支持, 只有东亚北美间断分布的草本菝葜组sect. Nemexia的单系得到很好的支持(93%); (4)分布于南美洲巴西的种类聚为一个单系类群, 表明它们可能有共同的起源, 但由于取样局限, 南美洲种类的系统地位有待进一步研究。