东北黑土区不同纬度农田土壤真菌分子生态网络比较

为了解东北黑土南部、中部和北部3个农田土壤真菌网络结构的异同以及物种之间的相互作用关系,本研究采用Illumina MiSeq技术对东北黑土农田3个长期肥料管理定位试验土壤真菌群落进行测序,并基于随机矩阵理论构建真菌分子生态网络.结果表明: 子囊菌、担子菌和接合菌为优势菌门,肉座菌目、腔菌目和粪壳菌目为优势菌目,但不同地区土壤中一些菌门和菌目的相对丰度存在显著差异.3个地区真菌分子生态网络结构显著不同,北部地区真菌网络更加复杂且物种之间存在更多竞争关系,南部地区真菌网络更不稳定,易受外界环境扰动.3个真菌网络仅有7个共有节点,且共有节点在各地区的连通度存在很大差异.通过亚网络的构建发现,从南到北肉座菌目网络趋于复杂,腔菌网络恰好相反.南部、中部和北部地区真菌网络的关键物种分别为毛壳菌、腔菌和青霉菌.土壤pH值和土壤全氮含量是同时影响3个真菌网络的主要土壤理化因子.     

银叶杜鹃和繁花杜鹃根部真菌的多样性

植物根系与真菌形成菌根, 在自然生态系统的物质能量循环中具有重要的生态功能。作者在四川省的中国杜鹃园选取银叶杜鹃(Rhododendron argyrophyllum)和繁花杜鹃(R. floribundum), 通过直接扩增杜鹃花根部真菌rDNA-ITS区片段, 来揭示该地区杜鹃花属植物根部真菌的多样性。ITS序列分析结果表明: 从两种杜鹃的根部共检测到41个真菌分类单元, 分别属于子囊菌纲的柔膜菌目(Helotiales)、散囊菌目(Eurotiales)、盘菌目(Pezizales)、假球壳目(Pleosporales)和担子菌纲的蜡壳耳目(Sebacinales)、伞菌目(Agaricales)、Erythrobasidiales、线黑粉菌目(Filobasidiales)。银叶杜鹃和繁花杜鹃根部真菌种类丰富, 包括了杜鹃花类菌根真菌、外生菌根真菌和其他类型真菌, 其中担子菌纲的蜡壳耳目和子囊菌纲的柔膜菌目占有较大比例。     

Proteomic analysis of a filamentous fungal endophyte using EST datasets

Proteomic analysis of many species of fungi, particularly filamentous fungi, is difficult due to the lack of publicly available genome sequence data and the problems associated with cross‐species comparisons. Furthermore, the detection of fungal proteins in biological systems where there are a greater number of proteins present from other eukaryote species provides additional challenges. We present an EST‐based approach for identifying proteins from a fungal endophyte of temperate grasses and demonstrate that this method is well suited for fungi with minimal sequence data.     

Host-specific toxins: effectors of necrotrophic pathogenicity

Host-specific toxins (HSTs) are defined as pathogen effectors that induce toxicity and promote disease only in the host species and only in genotypes of that host expressing a specific and often dominant susceptibility gene. They are a feature of a small but well-studied group of fungal plant pathogens. Classical HST pathogens include species of Cochliobolus , Alternaria and Pyrenophora . Recent studies have shown that Stagonospora nodorum produces at least four separate HSTs that interact with four of the many quantitative resistance loci found in the host, wheat. Rationalization of fungal phylogenetics has placed these pathogens in the Pleosporales order of the class Dothideomycetes. It is possible that all HST pathogens lie in this order. Strong evidence of the recent lateral gene transfer of the ToxA gene from S. nodorum to Pyrenophora tritici-repentis has been obtained. Hallmarks of lateral gene transfer are present for all the studied HST genes although definitive proof is lacking. We therefore suggest that the Pleosporales pathogens may have a conserved propensity to acquire HST genes by lateral transfer.     

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.     

Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific

This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs). Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems.     

Systematic search for cultivatable fungi that best deconstruct cell walls of Miscanthus and sugarcane in the field

The goals of our project were to document the diversity and distributions of cultivable fungi associated with decaying Miscanthus and sugarcane plants in nature and to further assess biodegradation of host plant cell walls by these fungi in pure cultures. Late in 2008 and early in 2009 we collected decaying Miscanthus and Saccharum from 8 sites in Illinois and 11 sites in Louisiana, respectively. To recover fungi that truly decay plants and to recover slow-growing fungi, we washed the plant material repeatedly to remove spores and cultivated fungi from plant fragments small enough to harbor at most one mycelium. We randomly selected 950 fungal colonies out of 4,560 microwell colonies and used molecular identification to discover that the most frequently recovered fungal species resided in Hypocreales (Sordariomycetes), Pleosporales (Dothideomycetes), and Chaetothryiales (Eurotiomycetes) and that only a few weedy species were recovered. We were particularly interested in Pleosporales and Chaetothyriales, groups that have not been mined for plant decay fungi. To confirm that we had truly recovered fungi that deconstruct plant cell walls, we assayed the capacity of the fungi to consume whole, alkali-pretreated, ground Miscanthus. Solid substrate cultures of the nine most commonly encountered Ascomycota resulted in Miscanthus weight loss of 8 to 13% over 4 weeks. This is the first systematic, high-throughput, isolation and biodegradation assessment of fungi isolated from decaying bioenergy grasses.     

Proteomic studies in biomedically and industrially relevant fungi

Historically, the proteomic investigation of filamentous fungi has been restrained by difficulties associated with efficient protein extraction and the lack of extensive fungal genome sequence databases. The advent of robust protein extraction and separation technologies, combined with protein mass spectrometry and emerging genome sequence data, is leading to the emergence of extensive new knowledge on the nature of these organisms. In this review, we discuss some recent technological advances and their role in exploring the proteome of Aspergillus spp., along with other biotechnologically relevant fungi.     

Fungal endophytes from Acer ginnala Maxim: isolation, identification and their yield of gallic acid

Aims:  The aim of the study was to isolate the endophytic fungi from Acer ginnala and screen isolates rich in gallic acid.
Methods and Results:  After epiphytic sterilization, 145 fungal endophytes were isolated from the stem, annual twig and seed of Acer ginnala . The endophytes were grouped into ten different taxa, Phomopsis sp., Neurospora sp., Phoma sp., Epicoccum sp., Penicillium sp., Alternaria sp., Fusarium sp., Trichoderma sp., Cladosporium sp. and a species of Pleosporales Incertae Sedis , by their morphological traits and ITS-rDNA sequence analysis. The content and yield of gallic acid of 141 isolates were determined by HPLC. On average, the species of Pleosporales Incertae Sedis had the highest content and yield of gallic acid (13·28 mg g⁻¹ DW; 119·62 mg l⁻¹), while Alternaria sp. had the lowest.
Conclusions:  Of 141 fungal endophytes from A. ginnala , Phomopsis sp. isolate SX10 showed both the highest content and the highest yield of gallic acid (29·25 mg g⁻¹ DW; 200·47 mg l⁻¹).
Significance and Impact of the Study:  Endophytic fungi isolated from A. ginnala may be used as potential producers of gallic acid and other compounds with biological activities, or functioned as elicitors to produce natural compounds.     

Genomics of the filamentous fungi - moving from the shadow of the bakers yeast

Fungi have now well and truly entered the genomic age. We currently know the complete DNA sequence for 18 fungal species and many more fungal genome sequencing projects are in progress. Whilst yeasts dominated the early genomic years, recently there has been a dramatic increase in filamentous fungal genome projects. The implications of this wealth of genetic information for mycologists worldwide is immense. In this review we summarise the background to fungal genome projects with an emphasis on the filamentous fungi. We discuss efforts to determine gene function and to compare genomes from different species. Since this is such a fast-moving field, useful web sites are listed that will enable the reader to keep up to date with developments.     

Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics

The fungal population dynamics in soil and in the rhizospheres of two maize cultivars grown in tropical soils were studied by a cultivation-independent analysis of directly extracted DNA to provide baseline data. Soil and rhizosphere samples were taken from six plots 20, 40, and 90 days after planting in two consecutive years. A 1.65-kb fragment of the 18S ribosomal DNA (rDNA) amplified from the total community DNA was analyzed by denaturing gradient gel electrophoresis (DGGE) and by cloning and sequencing. A rhizosphere effect was observed for fungal populations at all stages of plant development. In addition, pronounced changes in the composition of fungal communities during plant growth development were found by DGGE. Similar types of fingerprints were observed in two consecutive growth periods. No major differences were detected in the fungal patterns of the two cultivars. Direct cloning of 18S rDNA fragments amplified from soil or rhizosphere DNA resulted in 75 clones matching 12 dominant DGGE bands. The clones were characterized by their HinfI restriction patterns, and 39 different clones representing each group of restriction patterns were sequenced. The cloning and sequencing approach provided information on the phylogeny of dominant amplifiable fungal populations and allowed us to determine a number of fungal phylotypes that contribute to each of the dominant DGGE bands. Based on the sequence similarity of the 18S rDNA fragment with existing fungal isolates in the database, it was shown that the rhizospheres of young maize plants seemed to select the Ascomycetes order Pleosporales, while different members of the Ascomycetes and basidiomycetic yeast were detected in the rhizospheres of senescent maize plants.     

Seagrasses,seaweeds and plant debris: An extraordinary reservoir of fungal diversity in the Mediterranean Sea

This review gathers data derived from many research efforts on marine fungi associated with plant-origin substrates in the Mediterranean Sea. Overall, the review draws up a list of 378 taxa associated with seagrasses, seaweeds and wood.For each of the three substrates, on average, 92.7% of the taxa belonged to the phylum Ascomycota. Basidiomycota were better represented in seagrasses (9.8%) than in seaweeds (4.9%) and wood (1.2%). Mucoromycota and Mortirellomycota were scarce, while Chytridiomycota was detected only in association with phanerogames (3.7%). Dothideomycetes and Sordariomycetes were the dominant classes, while the orders Pleosporales and Hypocreales were significantly represented in the three sububstrates (42, 37, 10 taxa-30, 40, 16 taxa). Seagrasses with 210 associated taxa were the substrates with the richest fungal communities, immediately followed by seaweeds (180 taxa) and finally by wood (78 taxa). Out of the total, only 12 taxa were shared by the three varieties of substrates, including species that were widespread in marine environments. However, many algal species and seagrasses inhabiting the Mediterranean Sea remain unexplored. This gap indicates the need to apply more extensive surveys to explain the huge fungal biodiversity herein hosted, and increase the chances of describing novel fungal lineages.     

Dynamics of Fungal Communities in Bulk and Maize Rhizosphere Soil in the Tropics

The fungal population dynamics in soil and in the rhizospheres of two maize cultivars grown in tropical soils were studied by a cultivation-independent analysis of directly extracted DNA to provide baseline data. Soil and rhizosphere samples were taken from six plots 20, 40, and 90 days after planting in two consecutive years. A 1.65-kb fragment of the 18S ribosomal DNA (rDNA) amplified from the total community DNA was analyzed by denaturing gradient gel electrophoresis (DGGE) and by cloning and sequencing. A rhizosphere effect was observed for fungal populations at all stages of plant development. In addition, pronounced changes in the composition of fungal communities during plant growth development were found by DGGE. Similar types of fingerprints were observed in two consecutive growth periods. No major differences were detected in the fungal patterns of the two cultivars. Direct cloning of 18S rDNA fragments amplified from soil or rhizosphere DNA resulted in 75 clones matching 12 dominant DGGE bands. The clones were characterized by their HinfI restriction patterns, and 39 different clones representing each group of restriction patterns were sequenced. The cloning and sequencing approach provided information on the phylogeny of dominant amplifiable fungal populations and allowed us to determine a number of fungal phylotypes that contribute to each of the dominant DGGE bands. Based on the sequence similarity of the 18S rDNA fragment with existing fungal isolates in the database, it was shown that the rhizospheres of young maize plants seemed to select the Ascomycetes order Pleosporales, while different members of the Ascomycetes and basidiomycetic yeast were detected in the rhizospheres of senescent maize plants.     

Patterns of diversity for fungal assemblages of biological soil crusts from the southwestern United States

Molecular methodologies were used to investigate fungal assemblages of biological soil crusts (BSCs) from arid lands in the southwestern United States. Fungal diversity of BSCs was assessed in a broad survey that included the Chihuahuan and Sonoran deserts as well as the Colorado Plateau. At selected sites samples were collected along kilometer-scale transects, and fungal community diversity and composition were assessed based on community rRNA gene fingerprinting using PCR-denaturing gradient gel electrophoresis (DGGE). Individual phylotypes were characterized through band sequencing. The results indicate that a considerable diversity of fungi is present within crusted soils, with higher diversity being recovered from more successionally mature BSCs. The overwhelming majority of crust fungi belong to the Ascomycota, with the Pleosporales being widespread and frequently dominant. Beta diversity patterns of phylotypes putatively representing dominant members of BSC fungal communities suggest that these assemblages are specific to their respective geographic regions of origin.     

T‐DNA insertion,plasmid rescue and integration analysis in the model mycorrhizal fungus Laccaria bicolor

Ectomycorrhiza is a mutualistic symbiosis formed between fine roots of trees and the mycelium of soil fungi. This symbiosis plays a key role in forest ecosystems for the mineral nutrition of trees and the biology of the fungal communities associated. The characterization of genes involved in developmental and metabolic processes is important to understand the complex interactions that control the ectomycorrhizal symbiosis. Agrobacterium‐mediated gene transfer (AMT) in fungi is currently opening a new era for fungal research. As whole genome sequences of several fungi are being released studies about T‐DNA integration patterns are needed in order to understand the integration mechanisms involved and to evaluate the AMT as an insertional mutagenesis tool for different fungal species. The first genome sequence of a mycorrhizal fungus, the basidiomycete Laccaria bicolor, became public in July 2006. Release of Laccaria genome sequence and the availability of AMT makes this fungus an excellent model for functional genomic studies in ectomycorrhizal research. No data on the integration pattern in Laccaria genome were available, thus we optimized a plasmid rescue approach for this fungus. To this end the transformation vector (pHg/pBSk) was constructed allowing the rescue of the T‐DNA right border (RB)–genomic DNA junctions in Escherichia coli. Fifty‐one Agrobacterium‐transformed fungal strains, picked up at random from a larger collection of T‐DNA tagged strains (about 500), were analysed. Sixty‐nine per cent were successfully rescued for the RB of which 87% were resolved for genomic integration sequences. Our results demonstrate that the plasmid rescue approach can be used for resolving T‐DNA integration sites in Laccaria. The RB was well conserved during transformation of this fungus and the integration analysis showed no clear sequence homology between different genomic sites. Neither obvious sequence similarities were found between these sites and the T‐DNA borders indicating non‐homologous integration of the transgenes. Majority (75%) of the integrations were located in predicted genes. Agrobacterium‐mediated gene transfer is a powerful tool that can be used for functional gene studies in Laccaria and will be helpful along with plasmid rescue in searching for relevant fungal genes involved in the symbiotic process.     

A dual selection based, targeted gene replacement tool for Magnaporthe grisea and Fusarium oxysporum

Rapid progress in fungal genome sequencing presents many new opportunities for functional genomic analysis of fungal biology through the systematic mutagenesis of the genes identified through sequencing. However, the lack of efficient tools for targeted gene replacement is a limiting factor for fungal functional genomics, as it often necessitates the screening of a large number of transformants to identify the desired mutant. We developed an efficient method of gene replacement and evaluated factors affecting the efficiency of this method using two plant pathogenic fungi, Magnaporthe grisea and Fusarium oxysporum. This method is based on Agrobacterium tumefaciens-mediated transformation with a mutant allele of the target gene flanked by the herpes simplex virus thymidine kinase (HSVtk) gene as a conditional negative selection marker against ectopic transformants. The HSVtk gene product converts 5-fluoro-2'-deoxyuridine to a compound toxic to diverse fungi. Because ectopic transformants express HSVtk, while gene replacement mutants lack HSVtk, growing transformants on a medium amended with 5-fluoro-2'-deoxyuridine facilitates the identification of targeted mutants by counter-selecting against ectopic transformants. In addition to M. grisea and F. oxysporum, the method and associated vectors are likely to be applicable to manipulating genes in a broad spectrum of fungi, thus potentially serving as an efficient, universal functional genomic tool for harnessing the growing body of fungal genome sequence data to study fungal biology.     

Distinguishing plant and fungal sequences in ESTs from infected plant tissues

Expressed sequence tags (ESTs) from fungal-infected plant tissues are composed of a mixture of plant and fungal sequences. Using freely available software and tools, a novel procedure is described for distinguishing plant and fungal DNA sequences. Although the GenBank non-redundant (NR) database is larger and therefore one would presume that BLASTX analysis of it would be more accurate, superior resolution of 700 randomly selected fungal ESTs was found with Standalone TBLASTX analyses with a local matching database composed of a plant and a fungal genome. Standalone TBLASTX analyses of 3,983 ESTs from nine different fungal-infected plant EST libraries also proved to be superior in identifying the origin of sequences as either plant or fungal compared to GenBank BLASTX analysis. Standalone TBLASTX with a matching database comprised of a single plant and a single fungal genome appears to be a faster and more accurate method than BLASTX searches of the GenBank non-redundant database to distinguish fungal and plant sequences in mixed EST collections.     

The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae

Background  

Transposable elements are abundant in the genomes of many filamentous fungi, and have been implicated as major contributors to genome rearrangements and as sources of genetic variation. Analyses of fungal genomes have also revealed that transposable elements are largely confined to distinct clusters within the genome. Their impact on fungal genome evolution is not well understood. Using the recently available genome sequence of the plant pathogenic fungus Magnaporthe oryzae, combined with additional bacterial artificial chromosome clone sequences, we performed a detailed analysis of the distribution of transposable elements, syntenic blocks, and other features of chromosome 7.     

银杏内生真菌多样性研究(英文)

采用组织块分离法,从中国福建、江苏、贵州三省银杏Ginkgo biloba的根、茎、叶、树皮组织中分离内生真菌,利用形态学与ITS rDNA序列分析相结合的方法对所分离的菌株进行鉴定。结果表明从根、茎、叶和树皮分离出175株内生真菌,归为47类,每一类取代表菌株进行ITS测序及系统分析,分别属于子囊菌门的8个目,即Eurotiales、Hypocreales、Xylariales、Trichosphaeriales、Glomerellales、Diaporthales、Botryosphaeriales、Pleosporales,11科,16属。其中刺盘孢属Colletotrichum(19.75%)、链格孢属Alternaria(19.15%)、镰孢菌属Fusarium(10.64%)和拟茎点霉属Phomopsis(10.64%)为优势菌群;并且新丛赤壳属Neonectria和生赤壳属Bionectria为首次从银杏中分离出。Shannon-Wiener指数(H=2.4192)和Simpson指数(1-D=0.8856)的计算结果反应出所获得的银杏内生真菌菌群具有较高的多样性。     

Expansion of the sooty blotch and flyspeck complex on apples based on analysis of ribosomal DNA gene sequences and morphology

Sooty blotch and flyspeck (SBFS) is a late-season disease of apple and pear fruit that cosmetically damages the cuticle, resulting in produce that is unacceptable to consumers. Previous studies reported that four species of fungi comprise the SBFS complex. We examined fungal morphology and the internal transcriber spacer (ITS) and large subunit (LSU) regions of rDNA of 422 fungal isolates within the SBFS complex from nine orchards in four Midwestern states (USA) and compared them to previously identified species. We used LSU sequences to phylogenetically place the isolates at the order or genus level and then used ITS sequences to identify lineages that could be species. We used mycelial and conidial morphology on apple and in culture to delimit putative species. Thirty putative species found among the Midwest samples were shown to cause SBFS lesions on apple fruit in inoculation field trials. Among them Peltaster fructicola and Zygophiala jamaicensis have been associated previously with SBFS in North Carolina. The LSU analyses inferred that all 30 SBFS fungi from Midwestern orchards were Dothideomycetes; one putative species was within the Pleosporales, 27 were within Dothideales, and two putative species could not be placed at the ordinal level. The LSU sequences of 17 Dothideales species clustered with LSU sequences of known species of Mycosphaerella.