Mycobiota of the giant oyster <Emphasis Type="Italic">Crassostrea gigas</Emphasis> (Thunberg, 1787) (Bivalvia) from the Peter the Great Bay of the Sea of Japan

Mycological investigation of the Pacific (giant) oyster Crassostrea gigas (Thunberg, 1793) (Bivalvia) from the Peter the Great Bay of the Sea of Japan was carried out. The taxonomic composition of filamentous fungi associated with C. gigas was studied. The taxonomic composition of the fungi associated with the giant oyster included 22 species of filamentous fungi of which 17 species were identified. The latter belonged to six genera: Alternaria, Aspergillus, Botrytis, Fusarium, Penicillium, and Trichoderma. The distribution of filamentous fungi in the internal organs of the bivalve mollusk was studied.     

Fungi recovered from root-knot nematodes infecting vegetables under protected cultivation

A survey was conducted in root-knot nematode-infested plastic houses to determine the diversity and frequency of occurrence of fungi associated with the nematode. The relationships between percentage fungal parasitism and physicochemical properties of soil were also investigated. Fifty-nine plastic houses were sampled in southeastern Spain, 42 treated with nematicides and 17 left untreated. Eleven fungal genera and unidentified fungi were isolated from nematode eggs or juveniles. Fungal parasitism occurred more frequently in untreated (82.4%) than treated (50%) soils. The species richness in untreated soils ranged from 0 to 5, the Shannon–Wiener diversity index (a measurement of how many different fungi there are in site taking into account how evenly they are distributed among the site) from 0 to 2.01, and the evenness index from 0.46 to 0.99. In treated soils, species richness ranged from 0 to 4, the Shannon–Wiener diversity index from 0 to 1.61, and the evenness index from 0.81 to 1. Of the sites with nematophagous fungi, Arthrobotrys dactyloides (34%), Cylindrocarpon sp., Neosartoria hiratsukae (17%), and Fusarium solani (14%) were the fungi most frequently found. Physicochemical properties of soil were similar in nematicide treated and untreated soils. Percent fungal parasitism in untreated soils correlated positively with lime, silt and carbonate content of soil.     

Comparison of the Yeast Proteome to Other Fungal Genomes to Find Core Fungal Genes

The purpose of this research was to search for evolutionarily conserved fungal sequences to test the hypothesis that fungi have a set of core genes that are not found in other organisms, as these genes may indicate what makes fungi different from other organisms. By comparing 6355 predicted or known yeast (Saccharomyces cerevisiae) genes to the genomes of 13 other fungi using Standalone TBLASTN at an e-value <1E-5, a list of 3340 yeast genes was obtained with homologs present in at least 12 of 14 fungal genomes. By comparing these common fungal genes to complete genomes of animals (Fugu rubripes, Caenorhabditis elegans), plants (Arabidopsis thaliana, Oryza sativa), and bacteria (Agrobacterium tumefaciens, Xylella fastidiosa), a list of common fungal genes with homologs in these plants, animals, and bacteria was produced (938 genes), as well as a list of exclusively fungal genes without homologs in these other genomes (60 genes). To ensure that the 60 genes were exclusively fungal, these were compared using TBLASTN to the major sequence databases at GenBank: NR (nonredundant), EST (expressed sequence tags), GSS (genome survey sequences), and HTGS (unfinished high-throughput genome sequences). This resulted in 17 yeast genes with homologs in other fungal genomes, but without known homologs in other organisms. These 17 core, fungal genes were not found to differ from other yeast genes in GC content or codon usage patterns. More intensive study is required of these 17 genes and other common fungal genes to discover unique features of fungi compared to other organisms.Reviewing Editor: Prof. David Gottman     

豚草种带内生真菌及其对种子发芽和幼苗生长的影响

内生真菌是一类共生于植物体内,能够不同程度影响宿主植物生态适应性和竞争能力的微生物。分析内生真菌在豚草种子中的分布、种群结构,以及内生真菌发酵液对种子发芽和幼苗生长的作用。结果显示:发生于6个地区的豚草种子均能分离获得内生真菌,分离率在19%—92.63%之间,不同地区之间差异极显著(P0.01)。内生真菌主要存在于种子的总苞部位,分离率达到65.52%。发生于福建省长乐市松下镇的豚草种带内生真菌种群包含5个属,以链格孢属(Alternaria)真菌为优势菌群,占82.26%;其次为镰孢属(Fusarium)真菌,占9.68%;其它3个属的真菌发生较少,均低于5%。内生真菌主要以水平传播方式在豚草不同世代之间传播。供试的7个内生真菌菌株的发酵液均不同程度地抑制豚草种子发芽,降低幼苗地上部高度、根长度、根数量和总生物量,但不同菌株发酵液之间抑制程度差异明显,显示不同菌株对豚草种子发芽和幼苗生长产生不同的影响。内生真菌发酵液处理后的种子仍然保持较高程度的活力;不同内生真菌发酵液处理后,有活力的种子维持在50%—87.5%之间,均高于(或等于)清水处理的种子,说明内生真菌代谢产物只是抑制种子的发芽,但并不导致种子的腐烂和死亡。这些研究结果初步显示种子携带的内生真菌可能在豚草入侵生物学中发挥重要的作用。     

Restriction fragment length polymorphisms distinguish ectomycorrhizal fungi

Basidiomycetous fungi, two saprophytes and three mycorrhizal, were used to assess the specificity of DNA hybridization for distinguishing genera from one another. Interspecific comparisons were done with several isolates of mycorrhizal fungi,Laccaria bicolor andL. laccata, collected from diverse geographical sites. The DNAs were digested with four restriction nucleases and separated by gel electrophoresis into patterns of DNA fragments called restriction fragment length polymorphisms (RFLPs). The RFLPs were hybridized with a radioactively-labeled DNA probe encoding Basidiomycetous ribosomal RNA genes. The five genera were discernable using both unprobed and probed RFLPs. Hybridization of probe DNA with RFLPs was isolate-specific for all nine Laccaria isolates examined. The reclassification of aL. bicolor isolate is supported, demonstrating that hybridization of RFLPs offers an additional tool for taxonomy of ectomycorrhizal fungi. The method may have field application for distinguishing known isolates if their DNA fingerprints are previously ascertained and are distinct from RFLPs of indigenous organisms.     

Genetic transformation of a Rhizomucor pusillus mutant defective in asparagine-linked glycosylation: production of a milk-clotting enzyme in a less-glycosylated form

Rhizomucor pusillus 1116R3 has a defect in alg2 encoding a mannosyltransferase in the asparagine (N)-linked oligosaccharide biosynthetic pathway and produces proteins in less-glycosylated forms. For development of a genetic transformation system for this zygomycete, an uracil auxotroph (mutant 1116U17) as the host strain was derived by ultraviolet (UV) mutagenesis as 5-fluoroorotic acid-resistant colonies and the orotidine-5′-monophosphate (OMP) decarboxylase (pyr4) gene as a selection marker was cloned from the wild-type strain R. pusillus F27 by the polymerase chain reaction with primers designed on the basis of the pyr4 sequences from other fungi. The amino acid sequence of R. pusillus Pyr4 deduced from the nucleotide sequence showed high homology with the OMP decarboxylases from various fungi. The pyr4 gene on pUC19 (plasmid pRPPyr4) was introduced into protoplasts of R. pusillus 1116U17 by polyethylene glycol-assisted transformation. Transformation under optimized conditions yielded 5 Ura⁺ transformants with 1 μg pRPPyr4 DNA and 1 × 10⁷ viable protoplasts. Southern blot analysis of the genomic DNA from the transformants showed that multiple copies of the pRPPyr4 sequence were integrated into the genome by homologous recombination at the pyr4 locus. For the purpose of production of a milk-clotting aspartic proteinase (MPP) in a less-glycosylated form, mpp from the wild-type strain was cloned in pRPPyr4 and introduced into protoplasts of R. pusillus 1116U17. Transformants obtained in this way contained multiple copies of mpp at the chromosomal mpp locus and produced MPP as a mixture of molecules having no sugar chains and Man_0∼1GlcNAc₂ at the two N-linked glycosylation sites in an amount about 12 times larger than the parent strain. The transformation system for R. pusillus 1116U17 would be useful for production of proteins with truncated N-linked oligosaccharide chains. Received: 1 February 1999 / Received revision: 26 February 1999 / Accepted: 20 March 1999     

Community analysis of arbuscular mycorrhizal fungi in a warm-temperate deciduous broad-leaved forest and introduction of the fungal community into the seedlings of indigenous woody plants

A community of arbuscular mycorrhizal (AM) fungi was investigated in a warm-temperate deciduous broad-leaved forest using a molecular analysis method. Root samples were obtained from the forest, and DNA was extracted from the samples. Partial 18S rDNA of AM fungi were amplified from the extracted DNA by polymerase chain reaction using a universal eukaryotic primer NS31 and an AM fungal-specific primer AM1. After cloning the PCR products, 394 clones were obtained in total, which were divided into five types by restriction fragment length polymorphism (RFLP) with HinfI, RsaI, and Hsp92II. More than 20% of the clones were randomly selected from each RFLP type and sequenced. Phylogenetic analysis showed that all the obtained clones belonged to Glomus but could not be identified at species level. Topsoil of the forest containing plant roots was inoculated to nonmycorrhizal seedlings of indigenous woody plants, Rhus javanica var. roxburghii and Clethra barvinervis, to introduce the community of AM fungi into the seedlings. Among these five RFLP types, four types were detected from both seedlings, which indicates that the AM fungal community in the forest root samples was introduced at least partly into the seedlings. Meanwhile, an additional four types that were not found in the forest root samples were newly detected in the seedlings, these types were closely related to one another and close to G. fasciculatum or G. intraradices. It is expected that a community of indigenous diverse AM fungi could be introduced into target fields by planting these mycorrhizal seedlings.     

Isolation and identification of mycorrhizal fungi associated with <Emphasis Type="Italic">Stigmatodactylus sikokianus</Emphasis> (Maxim. ex Makino) Rauschert (Orchidaceae)

The mycorrhizal fungi of Stigmatodactylus sikokianus (Orchidaceae) were isolated and identified to be nearly related to Sebacina spp. in Sebacinaceae (Basidiomycota) by a neighbor-joining phylogenetic analysis based on the sequences of the ITS region of nuclear rDNA. In spite of the geographically separated samplings, high sequence similarity was found among the obtained DNA sequences, which suggested that S. sikokianus might be highly specialized to the group of fungi. It is known that Sebacina spp. are saprobes or ectomycorrhiza-forming fungi. The mycorrhizal fungi of S. sikokianus were regarded to be saprobic from the environment of their habitats.     

Isolation and identification of mycorrhizal fungi associating with an achlorophyllous plant, Epipogium roseum (Orchidaceae)

The identity of mycorrhizal fungi associated with the achlorophyllous orchid Epipogium roseum was investigated by DNA analysis. The fungi were isolated from each coiled hypha (peloton), and the ITS region of nuclear rDNA was sequenced. Phylogenetic analysis based on the neighbor-joining method showed that all the isolates clustered with fungi belonging to Psathyrella or Coprinus in Coprinaceae. Those fungi are known as saprobes, using dead organic materials for a nutritive source. Large colonies of this orchid were frequently found around tree stumps or fallen logs. In such colonies, these decaying wood materials would be used as a large and persistent carbon source for the growth of this orchid. This is the first report of Coprinaceae as an orchid mycorrhizal fungi.     

Community of arbuscular mycorrhizal fungi in drought-resistant plants, <Emphasis Type="Italic">Moringa</Emphasis> spp., in semiarid regions in Madagascar and Uganda

The community structure of arbuscular mycorrhizal (AM) fungi in the roots of drought-resistant trees, Moringa spp., was examined in semiarid regions in Madagascar and Uganda. Root samples were collected from 8 individuals of M. hildebrandtii and 2 individuals of M. drouhardii in Madagascar and from 21 individuals of M. oleifera in Uganda. Total DNA was extracted from the root samples, and partial nSSU rDNA of AM fungi was amplified using a universal eukaryotic primer NS31 and an AM fungalspecific primer AM1. The PCR products were cloned and divided by restriction fragment length polymorphism (RFLP) analysis with HinfI and RsaI. Some representatives in each RFLP types were sequenced, and a neighbor-joining phylogenetic analysis was conducted for the obtained sequences with analogous sequences of AM fungi. The RFLP and phylogenetic analyses showed that AM fungi closely related to Glomus intraradices or G. sinuosum were detected in many samples. The AM fungal groups frequently detected in the Moringa spp. might be widely distributed species in semiarid environments.     

Co-occurrence of Arum- and Paris-type morphologies of arbuscular mycorrhizae in cucumber and tomato

Colonization by arbuscular mycorrhizal (AM) fungi was investigated in cucumber (Cucumis sativus), tomato (Lycopersicon esculentum) and Clethra barbinervis (Ericales) grown in field-collected soil known from previous studies to generate Paris-type arbuscular mycorrhizae in C. barbinervis. Spores of Paraglomus, Acaulospora, Glomus, and Gigaspora were found in the soil. Formation of hyphal coils and arbusculate coils of Paris-type mycorrhizae and of arbuscules of Arum-type mycorrhizae in roots raised in this soil in the growth chamber were compared with the detection of DNA of AM fungi from the same root systems using Glomales-specific primers. Only Paris-type mycorrhizae with extensive arbusculate coils developed in C. barbinervis, but cucumber and tomato developed both Paris- and Arum-types in the same root systems. Glomaceae and Archaeosporaceae and/or Paraglomaceae were detected strongly in the DNA from both cucumber and tomato roots, in which Arum-type mycorrhizae were observed. In contrast, DNA of Glomaceae was detected more sparingly in C. barbinervis, in which Paris-type mycorrhizae dominated. Acaulosporaceae and Gigasporaceae were strongly detected in the DNA from both C. barbinervis and tomato, whereas they were more weakly detected in cucumber. These results indicate that the morphology of colonization is strongly influenced by the selection of fungi to colonize the host plant from among those in the soil environment.     

Diversity and Antimicrobial and Plant-Growth-Promoting Activities of Endophytic Fungi in Dendrobium loddigesii Rolfe

Endophytic fungi are ubiquitously distributed in orchids and have a great impact on the host plant. The diversity of endophytic fungi in the medicinal orchid Dendrobium loddigesii Rolfe was investigated and their bioactivities in microbe and plant growth were explored here. Endophytic fungi were identified by using morphological and molecular biological methods. Antimicrobial activity was determined by a standard disk assay. Activity in promoting plant growth was confirmed by root inoculation of endophytic fungi in seedling tray and pot experiments. Overall, 48 isolates were isolated from D. loddigesii and identified to belong to 18 genera, with Fusarium and Acremonium being the most dominant populations. A total of 17 isolates belonging to 9 genera were screened for their antimicrobial activity, and Fusarium spp., 8 of the 17 isolates, was also the dominant population. In the seedling tray experiment, two isolates, one of Fusarium named DL26 and the other of Pyrenochaeta named DL351, were shown to enhance plant growth in alder bark–humus medium, and the latter displayed weak activity against Bacillus subtilis (As 1.308) and Aspergillus fumigatus (As 3.2910). In the pot experiment, after inoculation of DL26 and DL351, five out of seven media were fit for plant-endophyte symbionts. Medium #1 of red brick fragments and sphagna was optimal in accelerating plant growth. In conclusion, a great diversity of endophytic fungi in D. loddigesii was first confirmed in a considerable proportion of antimicrobial isolates. Furthermore, two endophytes exhibited the ability to enhance plant growth although their activities were influenced by the growth media.     

Isolation and characterisation of Isaria farinosa and Purpureocillium lilacinum associated with emerald ash borer,Agrilus planipennis in Canada

Entomopathogenic fungi of the genera Isaria and Purpureocillium were recovered from infestation sites of emerald ash borer (EAB) in Southern Ontario, Canada. Isolates were identified using morphological characters and by sequencing the ITS1-5.8S-ITS2 ribosomal DNA gene and partial β-tubulin gene. Phylogenetic analysis and constructed trees based on the ITS and β-tubulin gene explicitly confirm isolates L66B, SY17-a and LHY46-a as Isaria farinosa and B3A, B59A and SY45B-a as Purpureocillium lilacinum. Pathogenicity was tested in the laboratory against adult EAB using a single concentration (2.0×10⁷ conidia/ml) applied topically to adults. Controls included three commercial isolates: Isaria fumosorosea LRC176, Metarhizium brunneum LRC187 and Beauveria bassiana strain GHA. The native isolates I. farinosa L66B and P. lilacinum SY45B-a killed 75 and 50% of the beetles 14 days post-inoculation. Although these indigenous entomogenous fungi were less virulent compared with the commercial isolates, yearly isolation from EAB populations suggests they are one of the natural mortality factors of EAB in Canada.     

Ectomycorrhizae associated with Castanopsis fargesii (Fagaceae) in a subtropical forest, China

Ectomycorrhizal (ECM) trees were commonly distributed in subtropical forest ecosystems, but we know little of below-ground ECM status. The ECM community composition and anatomical structure of Castanopsis fargesii were investigated in a subtropical evergreen broad-leaved forest of southwest China. Twelve root samples of C. fargesii were collected from a 2-ha plot and a total of 19 ECM morphotypes were obtained based on morphological characters. Furthermore, a total of 17 ECM fungi were identified from the 19 morphotypes based on the analysis of ITS sequences. Of these fungi, 14 belonged to Basidiomycetes and 3 were Ascomycetes. Taxa in Russulaceae and Thelephoraceae were frequent. Lactarius sp., Russula sp.1, Tomentella sp.2 and Boletus sp. were the dominant fungi occurred in more than four samples with importance values of 31.5, 29.4, 23.4 and 22.9%, respectively. The other 13 ECM fungi were rare. Anatomical structures of the 17 ECMs were described. This is the first study to characterize the below-ground ECM communities and anatomical structures in a subtropical evergreen broad-leaved forest.     

Contrasting root associated fungi of three common oak-woodland plant species based on molecular identification: host specificity or non-specific amplification?

An increasingly popular approach used to identify arbuscular mycorrhizal (AM) fungi in planta is to amplify a portion of AM fungal small subunit ribosomal DNA (SSU-rDNA) from whole root DNA extractions using the primer pair AM1-NS31, followed by cloning and sequencing. We used this approach to study the AM fungal community composition of three common oak-woodland plant species: a grass (Cynosurus echinatus), blue oak (Quercus douglasii), and a forb (Torilis arvensis). Significant diversity of AM fungi were found in the roots of C. echinatus, which is consistent with previous studies demonstrating a high degree of AM fungal diversity from the roots of various hosts. In contrast, clones from Q. douglasii and T. arvensis were primarily from non-AM fungi of diverse origins within the Ascomycota and Basidiomycota. This work demonstrates that caution must be taken when using this molecular approach to determine in planta AM fungal diversity if non-sequence based methods such as terminal restriction fragment length polymorphisms, denaturing gradient gel electrophoresis, or temperature gradient gel electrophoresis are used.     

Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms

A modification of the amplified fragment length polymorphism technique was developed for the determination of DNA methylation in dimorphic fungi representative of three of the major fungal taxa: Mucor rouxii, a zygomycete; Yarrowia lipolytica, an ascomycete; and Ustilago maydis, a basidiomycete. DNA obtained from the yeast or mycelial stages of the fungi was digested with a mixture of EcoRI, and one of the isoschizomers MspI and HpaII, whose ability to cleave at the sequence CpCpGpG is affected by the methylation state. The resulting fragments were ligated to primers and subjected to a double round of amplification by the polymerase chain reaction, radiolabeled in the second round, and separated by polyacrylamide gel electrophoresis. Comparison of patterns revealed differences indicative of fragments whose methylation state did or did not change during the dimorphic transition. These results indicate the usefulness of the method for the study of DNA methylation, demonstrate the universality of DNA methylation in fungi, and confirm that differential DNA methylation occurs during fungal morphogenesis. Received: 3 May 1996 / Accepted: 19 September 1996     

三种红树林植物健康与非健康叶片中真菌的比较

红树林叶片感染真菌后可能会向非健康状态变化,为了比较三种红树林植物海漆、秋茄和桐花树健康与非健康叶片真菌类群,明确其中真菌类群的差异,该研究从广西茅尾海红树林自然保护区采集海漆、秋茄和桐花树健康与非健康叶片,对叶片中真菌分离纯化并进行形态学鉴定,提取真菌的DNA,采用RAPD多样性、ITS序列对真菌进行分子鉴定。经过初步分析,从海漆、秋茄和桐花树中共分离到157株真菌,经过形态学和RAPD分析,可能为19种不同的真菌。采用真菌ITS序列对19种真菌代表性菌株进行分析,结果表明:19种真菌都属于子囊菌门,有15株与已有的真菌ITS序列相似性在97%以上;有4株相似性低于95%,可能为新种。海漆健康和非健康叶片分别分离到真菌7种和5种,健康叶片含了非健康叶片中所有真菌;秋茄健康和非健康叶片分离到真菌1种和9种,且健康叶片中分离到的内生真菌Dothiorella aegiceri也包含于非健康叶片分离的真菌中;桐花树健康和非健康叶片分离到真菌1种和3种,且桐花树分离的内生真菌也是Dothiorella aegiceri,其包含于非健康叶片中分离到的真菌。该研究证明,海漆内生真菌同时也可能是植物病原菌,内生真菌与植物病原菌没有明显界限;另一方面,该研究发现秋茄和桐花树叶片的病变是由外部的病原真菌感染引起,感染的原因可能是昆虫叮咬红树林植物后留下了创口,这些创口有利于真菌的感染。     

Genetic evidence for the occurrence of assimilatory nitrate reductase in arbuscular mycorrhizal and other fungi

Using primers synthesized from two conserved regions and employing PCR, a DNA segment coding for part of the apoprotein of assimilatory nitrate reductase could be amplified from the fungi Aspergillus nidulans, Pythium intermedium, Phytophthora infestans, Phytophthora megasperma and Glomus D13. Sequencing of the amplificates as well as DNA hybridization revealed strong homologies with the nitrate reductase gene in all cases. The digoxigenin-labeled amplificate from Glomus hybridized with DNA isolated from Glomus spores. The data from these gene probing experiments are generally in accord with the published results from enzyme measurements. Thus assimilatory nitrate reductase occurs in saprophytic, parasitic as well as arbuscular mycorrhizal fungi. No amplificates with these primers were obtained with DNA isolated from Mucor mucedo and Saprolegnia ferax. Such results agree with the failure to detect nitrate assimilation physiologically in these two organisms.