Molecular identification of ectomycorrhizal mycelium in soil horizons

Genomic characterization and identification of candidate genes for putative podophyllotoxin biosynthesis pathway in Penicillium herquei HGN12.1C

Previous studies have reported the functional role, biochemical features and synthesis pathway of podophyllotoxin (PTOX) in plants. In this study, we employed combined morphological and molecular techniques to identify an endophytic fungus and extract PTOX derivatives. Based on the analysis of ITS sequences and the phylogenetic tree, the isolate was classified as Penicillium herquei HGN12.1C, with a sequence identity of 98.58%. Morphologically, the HGN12.1C strain exhibits white colonies, short-branched mycelia and densely packed hyphae. Using PacBio sequencing at an average read depth of 195×, we obtained a high-quality genome for the HGN12.1C strain, which is 34.9 Mb in size, containing eight chromosomes, one mitochondrial genome and a GC content of 46.5%. Genome analysis revealed 10 genes potentially involved in PTOX biosynthesis. These genes include VdtD, Pinoresinollariciresinol reductase (PLR), Secoisolariciresinol dehydrogenase (SDH), CYP719A23, CYP71BE54, O-methyltransferase 1 (OMT1), O-methyltransferase 3 (OMT3), 2-ODD, CYP71CU and CYP82D61. Notably, the VdtD gene in fungi shares functional similarities with the DIR gene found in plants. Additionally, we identified peltatin, a PTOX derivative, in the HGN12.1C extract. Docking analysis suggests a potential role for the 2-ODD enzyme in converting yatein to deoxypodophyllotoxin. These findings offer invaluable insights into the synthesis mechanism of PTOX in fungi, shedding light on the relationship between host plants and endophytes.

Research on the Isolation of Endophytic Fungi from Papaya and the Prevention of Colletotrichum gloeosporioides

Endophytic fungi can be used as a source of herbal antioxidants to overcome the limitations of low yield and lengthy growth cycles associated with using plants as raw materials for antioxidant production. Papaya fruit is often susceptible to infection by Colletotrichum gloeosporioides after harvest, leading to postharvest rot. Endophytic fungi were extracted with ethyl acetate, and the initial screening concentration was 100 mg/L. Seven strains were identified, with scavenging rates exceeding 50% and strong antioxidant activity. The IC50 values in DPPH and ABTS free radical scavenging assays ranged from 19.72 to 84.06 mg/L and from 14.34 to 64.63 mg/L, respectively. Strain Y17 exhibited robust antioxidant activity (IC50 < 20 mg/L) and was identified as Penicillium rolfsii (MT729953) through ITS sequencing. Treatment of papaya fruit wounds with a fermentation broth of strain Y17 significantly inhibited the infection and colonization of anthracnose pathogens, resulting in a slowed disease incidence rate. This promoted the activity of protective enzymes, such as CAT, POD, and SOD, in the papaya fruit and slowed down the rate of MDA accumulation. This strain, which was found to have antioxidant activity in this study, has the potential to control anthracnose in papaya and has value in terms of further development and utilization.

Isolation, screening and characterization of efficient cellulose-degrading fungal and bacterial strains and preparation of their consortium under in vitro studies

In this investigation, cellulose-degrading fungi and bacteria were isolated from different partially decomposed cellulose-rich substrates, such as groundnut residues, rice straw, and rotten wood, following dilution plating techniques on carboxymethyl cellulose agar media and screening for potential cellulose degradation ability. The development of a clear halo zone surrounding the microbial colonies during the initial screening process using the Congo red test (20 isolates) suggested cellulose hydrolysis, and the highest cellulase production activity was implied by the isolates with the largest clear zone ratio (9 isolates). Using both macroscopic and microscopic examinations, as well as standard biochemical tests outlined in Bergey's Manual of Determinative Bacteriology, the genus-level identification of fungi and bacteria was accomplished. In order to molecularly identify the 4 isolated fungal and bacterial strains at the species level after being ultimately selected for cellulase production potential under in vitro studies, fungal and bacterial DNA was extracted and amplified by PCR using the universal primers ITS1 and ITS4 for fungi (ITS rRNA, 5.8S rRNA) and 8F and 1492R for bacterial isolates (16S rRNA). After sequencing, the PCR results were compared to other comparable sequences in GenBank (NCBI). Based on the available NCBI data, phylogenetic analysis of their ribosomal gene partial sequences revealed that DAJ2 (PP086700) shares 100% homology with Aspergillus foetidus, DTJ4 (PP086699) shares 99.74% similarity with Trichoderma atrobrunnium, DBJ6 (PP082584) shares 100% identity with Priestia megaterium, and DMB9 (PP082585) shares 99.88% homology with Micrococcus yunnanensis. The cellulolytic potential of Phanerochaete chrysosporium is well established. Therefore, it was considered a standard culture for comparison and was collected from the MTCC, Chandigarh, India. Overall, all 4 selected isolates and the check organism were mutually compatible or synergistic with each other, and their consortium is useful for the accelerated decomposition of organic constituents during rapid composting.

Isolation, identification, and antibacterial evaluation of endophytic fungi from Gannan navel orange

Gannan navel orange is a famous brand in China but the isolation of its endophytic fungi was rarely reported. In this study, a total of 54 strains of endophytic fungi were successfully isolated from the pulp, peel, twig, and leaf of Gannan navel orange; they were successfully identified to belong to 17 species of 12 genera. All these strains were fermented using potato-dextrose agar (PDA) medium, and their secondary metabolites were then extracted with ethyl acetate (EtOAc). The antibacterial assays of Escherichia coli (E. coli), methicillin-resistant Staphylococcus aureus (MRSA), and Xanthomonas citri subsp. citri (Xcc) were also performed for the EtOAc extracts of these strains. As a result, the extracts of both Geotrichum sp. (gc-1-127-30) and Diaporthe biconispora (gc-1-128-79) demonstrated significant antibacterial activities against Xcc, and the MIC value for the extract of Colletotrichum gloeosporioides against MRSA was low to 62.5 μg/mL. Moreover, the chemical components of the extracts of Colletotrichum sp., Diaporthe biconispora, and Annulohypoxylon atroroseum were primarily investigated, and they successfully led to the isolation of 24 compounds involving a new botryane sesquiterpene. Among the isolated products, compound 2 showed significant inhibitory activities toward SA, MRSA, E. coli, and Xcc with MIC values of 12.5, 3.1, 125, and 12.5 μg/mL, respectively. This study revealed that the endophytic fungi of Gannan navel orange showed high potency to produce secondary metabolites with significant antibacterial effects.

Fungal exposome, human health, and unmet needs: A 2022 update with special focus on allergy

Humans inhale, ingest, and touch thousands of fungi each day. The ubiquity and diversity of the fungal kingdom, reflected by its complex taxonomy, are in sharp contrast with our scarce knowledge about its distribution, pathogenic effects, and effective interventions at the environmental and individual levels. Here, we present an overview of salient features of fungi as permanent players of the human exposome and key determinants of human health, through the lens of fungal allergy and other fungal hypersensitivity reactions. Improved understanding of the fungal exposome sheds new light on the epidemiology of fungal-related hypersensitivity diseases, their immunological substratum, the currently available methods, and biomarkers for environmental and medical fungi. Unmet needs are described and potential approaches are highlighted as perspectives.

Antimicrobial Potential of Endophytic Fungi From Artemisia argyi and Bioactive Metabolites From Diaporthe sp. AC1

Endophytic fungi of medicinal plants are important sources of active natural products. In this study, 26 fungi were isolated from Artemisia argyi, which were belonging to eight genera, namely, Alternaria, Fusarium, Chaetomium, Phoma, Diaporthe, Trichoderma, Gibberella, and Colletotrichum. The antimicrobial activities of all fungal extracts were tested by using the cup-plate method against Staphylococcus aureus, Salmonella enteritidis, and Fusarium graminearum. The results demonstrated that 25 extracts (96%) exhibited inhibitory activity against at least one of the tested pathogenic microorganisms. The strain Diaporthe sp. AC1, which showed good antimicrobial activity and high yield of crude extract from fermentation, was selected for the study of secondary metabolites. The crude extract of strain AC1 was purified by silica gel column chromatography, Sephadex LH-20 gel column chromatography, and HPLC, and finally, a new compound phomopsolide G (1), together with three known phomopsolides (2–4) and four other known compounds (5–8), was obtained. The structures of the compounds were elucidated by NMR and/or HR-MS spectroscopy. Microdilution method and MTT colorimetry were used to determine the bioactivity of the compounds. The study demonstrated that the new compound 1 had moderate antifungal activity against F. graminearum, Fusarium moniliforme, and Botrytis cinerea and weak antibacterial activity against Staphylococcus aureus. Compound 1 also showed weak cytotoxicity against HepG2, A549, and MDA-MB-231, with IC50 values of 89.91, 107.65, and 53.97 μM. Additionally, other compounds also exhibited antimicrobial and/or cytotoxic activities. The findings provided the basis for searching drug and agricultural lead compounds from A. argyi-associated fungi resources.

Fungal-bacterial biofilm mediated heavy metal rhizo-remediation

Heavy metal pollution due to excessive use of chemical fertilizers (CF) causes major damage to the environment. Microbial biofilms, closely associated with the rhizosphere can remediate heavy metal-contaminated soil by reducing plant toxicity. Thus, this study was undertaken to examine the remedial effects of microbial biofilms against contaminated heavy metals. Fungi and bacteria isolated from soil were screened for their tolerance against Cd²⁺, Pb²⁺, and Zn²⁺. Three bacterial and two fungal isolates were selected upon the tolerance index (TI) percentage. Fungal-bacterial biofilms (FBBs) were developed with the most tolerant isolates and were further screened for their bioremediation capabilities against heavy metals. The best biofilm was evaluated for its rhizoremediation capability with different CF combinations using a pot experiment conducted under greenhouse conditions with potatoes. Significantly (P < 0.05), the highest metal removal percentage was observed in Trichoderma harzianum and Bacillus subtilis biofilm under in situ conditions. When compared to the 100% recommended CF, the biofilm with 50% of the recommended CF (50CB) significantly (P < 0.05) reduced soil available Pb²⁺ by 77%, Cd²⁺ by 78% and Zn²⁺ by 62%. In comparison to initial soil, it was 73%, 76%, and 57% lower of Pb²⁺, Cd²⁺, and Zn²⁺, respectively. In addition, 50CB treatment significantly (P < 0.05) reduced the metal penetration into the tuber tissues in comparison with 100 C. Thus, the function of the developed FBB with T. harzianum-B. subtilis can be used as a potential solution to remediate soil polluted with Pb²⁺ Cd²⁺ and Zn²⁺ metal contaminants.

Production of Mycophenolic Acid by a Newly Isolated Indigenous Penicillium glabrum

Soil-occupant fungi produce a variety of mycotoxins as secondary metabolites, one of which is mycophenolic acid (MPA), an antibiotic and immunosuppressive agent. MPA is mainly produced by several species of Penicillium, especially Penicillium brevicompactum. Here, we present the first report of MPA production by a local strain belonging to Penicillium glabrum species. We screened ascomycete cultures isolated from moldy food and fruits, as well as soils, collected from different parts of Iran. MPA production of one hundred and forty Penicillium isolates was analyzed using HPLC. Three MPA producer isolates were identified, among which the most producer was subjected to further characterization, based on morphological and microscopic analysis, as well as molecular approach (ITS, rDNA and beta-tubulin gene sequences). The results revealed that the best MPA producer belongs to P. glabrum IBRC-M 30518, and can produce 1079 mg/L MPA in Czapek-Dox medium.

Morpho-biochemical and molecular characterization of two new strains of Aspergillus fumigatus nHF-01 and A. fumigatus PPR-01 producing broad-spectrum antimicrobial compounds

The main objective of the study is to characterize two new strains of Aspergillus fumigatus through morphometric, biochemical, molecular methods, and to evaluate their antimicrobial potentiality. The micro-morphotaxonomy, growth, and metabolic behavior of the strains, nHF-01 and PPR-01, were studied in different growth conditions and compared with standard strain. The molecular characterization was done by sequencing the ncrDNA ITS1-5.8S-ITS2 and D1-D2 domains of the nc 28S rDNA region and compared with a secondary structure-based phylogenetic tree. The secretory antimicrobials and pigments were characterized by TLC, UV-Vis, and FT-IR spectroscopy. Both the strains showed distinct growth patterns in different nutritional media and could assimilate a wide range of carbohydrates with distinctive biochemical properties. The molecular characterization revealed the strains, nHF-01 and PPR-01, as Aspergillus fumigatus (GenBank Accession No. MN190286 and MN190284, respectively). It was observed that the strain nHF-01 produces red to brownish pigments having mild antimicrobial activity while the strain PPR-01 does not represent such transformations. The extractable compounds had a significant antimicrobial potentiality against the human pathogenic bacteria. From this analysis, it can be concluded that the nHF-01 and PPR-01 strains are distinct from other A. fumigatus by their unique characters. Large-scale production and detailed molecular elucidation of the antimicrobial compounds may lead to the discovery of new antimicrobial compounds from these strains.

Entomopathogenic Fungi as Endophytes for Biological Control of Subterranean Termite Pests Attacking Cocoa Seedlings

This study was conducted in the scope of developing a sustainable effective approach against subterranean termite pests using entomopathogenic and endophytic fungus-based biopesticides. Termites, Odontotermes spp. workers, were tested for their susceptibility to 15 entomopathogenic fungal isolates through the direct spraying of conidia suspensions at 1 × 108 conidia/mL. In general, all the isolates screened were pathogenic, with 100% mortality 4-7 days post-inoculation. However, the most virulent isolates were Metarhizium brunneum Cb15-III; the M. anisopliae isolates ICIPE 30 and ICIPE 60; Hypocrea lixii F3ST1; and the Beauveria bassiana isolates ICIPE 279, ICIPE 706 and ICIPE 662. These isolates were further tested for their endophytic colonization of cocoa seedlings using seed soaking, soil drench and foliar spray at 1 × 108 conidia/mL. The colonization of the plant tissues by the fungi was determined using a culture-based technique. Only the B. bassiana isolates ICIPE 706 and ICIPE 279, and H. lixii F3ST1 colonized the cocoa seedlings, with varied colonization rates among isolates and inoculation methods. Three naturally occurring endophytes-Trichoderma asperellum, Fusarium solani and F. redolens-were also isolated from the cocoa seedling tissues. These findings suggest that cocoa seedlings are conducive to endophytic fungal growth either occurring naturally or from artificial inoculation Our findings could possibly lead to an innovative approach to the management of herbivory and subterranean termite pests in cocoa agroforests.

Isolation and Identification of Endophytic Fungi in Kernels of Coix lachrymal-jobi L. Cultivars

Coix lachrymal-jobi L. var. ma-yuen Stapf of Gramineae are annual or perennial herbs and an important food-medicine homologous plants of high value in nutrition, health protection, and comprehensive utilization. In recent years, the revival of researches on its roles in food and medicinal applications of this underutilized grass for food security and economic empowerment of rural communities has been seen . In this research, Coix kernel endophytic fungi were isolated and identified by fungal colony morphology observation combined with the PCR-amplified fungal internal transcribed spacer (ITS) sequence analyses. All together six isolates to five species of Coix endophytic fungi and two isolates to the genus level were identified from the kernels of six Coix cultivars: Penicillium expansum, Penicillium polonicum, Cladosporium cladosporioides, Alternaria alternata, Aspergillus flavus, and two genera of Aspergillus and Fusarium. Potential benefits and harms analyses showed that Penicillium expansum, Aspergillus oryzae, and Cladosporium cladosporioides can produce a variety of beneficial composite enzymes and have an extensive application in microbial chemistry, food science, and fermentation, whereas Penicillium, Aspergillus flavus, Alternaria alternate, and Fusarium can produce corresponding toxins harmful to plants, animals, and humans. These results not only provided a basis for the targeted prevention of contamination in the tissue culture of Coix kernels by the addition of specific antibiotics, but also enriched the endophytic fungi resource pool of Gramineae crops and suggested new ideas for the improvement, cultivation, post-harvest seeds/kernels storage, and the development of new natural drugs.

Diversity, Bacterial Symbionts, and Antimicrobial Potential of Termite-Associated Fungi

The phylogenetic diversity of fungi isolated from the Odontotermes formosanus was investigated by dilution-plate method, combined with morphological characteristics and 5.8S rDNA sequencing. Thirty-nine fungi were isolated and purified from O. formosanus, which were belonging to two phyla and four classes (Sordariomycetes, Dothideomycetes, Eurotiomycetes, Agaricomycetes). Furthermore, nine bacterial 16S rRNA sequences were obtained from total fungal genomic DNA. All bacterial symbionts were segmented into four genera: Bacillus, Methylobacterium, Paenibacillus, and Trabulsiella. The antimicrobial activities of all endophytic fungi extracts were tested by using the filter paper method against Escherichia coli (ATCC 8739), Bacillus subtilis (ATCC 6633), Staphylococcus aureus (ATCC 6538), and Canidia albicans (ATCC 10231). The results exhibited that 25 extracts (64%) exhibited antibacterial activity against at least one of the tested bacterial strains. Furthermore, the secondary metabolites 1 [5-hydroxyramulosin (1a):biatriosporin M (1b) = 2:1] from the Pleosporales sp. BYCDW4 exhibited potent antimicrobial activities against E. coli, C. albicans, B. subtilis, and S. aureus with the inhibition zone diameter (IZD) of 13.67, 14.33, 12.17, and 11.33 mm, respectively, which were comparable with those of the positive control. 1-(2,5-Dihydroxyphenyl)-3-hydroxybutan-1-one (2) from the Microdiplodia sp. BYCDW8 showed medium inhibitory activities against B. subtilis and S. aureus, with the IZD range of 8.32–9.13 mm. In conclusion, the study showed the diversity of insect symbionts could be expected to develop the resource of new species and antibiotics.

Distribution patterns of fungal taxa and inferred functional traits reflect the non-uniform vertical stratification of soil microhabitats in a coastal pine forest

In boreal systems, soil profiles typically consist of distinct stratified horizons, with organic layers at the surface overlying deeper mineral horizons providing microhabitat variation along a depth gradient, and vertical stratification of fungal communities along such soil profiles is commonly observed. We studied fungal community structure in a coastal pine forest along a gradient of decreasing influence from the coast. In this system, the vertical stratification pattern of soil microhabitats (defined here as organic, mineral with roots and mineral without roots: O, MR and MN, respectively) is non-uniform; organic horizons are sometimes buried under drifting sand dunes. Our results show that soil microhabitats are distinct with respect to physiochemical characteristics, community composition and OTU richness. While community composition was partly related to depth and distance from the coastal forest edge, microhabitat appeared to have the strongest influence. A closer inspection of the OTUs with the highest relative sequence abundance within each microhabitat revealed that microhabitats support functionally distinct fungal communities with respect to trophic mode and growth morphology. These results suggest that in coastal pine forests, variation in soil microhabitats contributes to the high fungal diversity found belowground and may play an important role in optimizing nutrient cycling.

Fungal evolution: major ecological adaptations and evolutionary transitions

Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.

Biodegradation of asphaltene and petroleum compounds by a highly potent Daedaleopsis sp

Petroleum, as the major energy source, is indispensable from our lives. Presence of compounds resistant to degradation can pose risks for human health and environment. Basidiomycetes have been considered as powerful candidates in biodegradation of petroleum compounds via secreting ligninolytic enzymes. In this study a wood-decaying fungus was isolated by significant degradation ability that was identified as Daedaleopsis sp. by morphological and molecular identification methods. According to GC/MS studies, incubation of heavy crude oil with Daedaleopsis sp. resulted in increased amounts of <C24 hydrocarbons and decreased amounts of >C24 compounds. Degradation of asphaltene, anthracene, and dibenzofuran by the identified fungal strain was determined to evaluate its potential in biodegradation. After 14 days of incubation, Daedaleopsis sp. could degrade 93.7% and 91.2% of anthracene and dibenzofuran, respectively, in pH 5 and 40 °C in optimized medium, as revealed by GC/FID. Notably, analysis of saturates, aromatics, resins, and asphaltenes showed a reduction of 88.7% and 38% in asphaletene and aromatic fractions. Laccase, lignin peroxidase, and manganese peroxidase activities were enhanced from 51.3, 145.2, 214.5 U ml^-1 in the absence to 121.5, 231.4, and 352.5 U ml^-1 in the presence of heavy crude oil, respectively. This is the first report that Daedaleopsis sp. can degrade asphaltene and dibenzofuran. Moreover, compared to the reported results of asphaltene biodegradation, this strain was the most successful. Thus, Daedaleopsis sp. could be a promising candidate for biotransformation of heavy crude oil and biodegradation of recalcitrant toxic compounds.

Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino

Understanding how soil pedogenesis affects microbial communities and their in situ activities according to ecosystem functioning is a central issue in soil microbial ecology, as soils represent essential nutrient reservoirs and habitats for the biosphere. To address this question, soil chronosequences developed from a single, shared mineralogical parent material and having the same climate conditions are particularly useful, as they isolate the factor of time from other factors controlling the character of soils. In our study, we considered a natural succession of uplifted marine terraces in Mendocino, CA, ranging from highly fertile in the younger terrace (about 100,000 years old) to infertile in the older terraces (about 300,000 years old). Using ITS amplicon pyrosequencing, we analysed and compared the diversity and composition of the soil fungal communities across the first terraces (T1 to T3), with a specific focus in the forested terraces (T2 and T3) on soil samples collected below trees of the same species (Pinus muricata) and of the same age. While diversity and richness indices were highest in the grassland (youngest) terrace (T1), they were higher in the older forested terrace (T3) compared to the younger forested terrace (T2). Interestingly, the most abundant ectomycorrhizal (ECM) taxa that we found within these fungal communities showed high homology with ITS Sanger sequences obtained previously directly from ECM root tips from trees in the same study site, revealing a relative conservation of ECM diversity over time. Altogether, our results provide new information about the diversity and composition of the fungal communities as well as on the dominant ECM species in the soil chronosequence of Mendocino in relation to soil age and ecosystem development.

Molecular typing and genetic relatedness of 72 clinical Candida albicans isolates from poultry

Candida albicans is the most prevalent opportunistic fungus of humans and animals. While most studies focus on human isolates, they rarely focus on poultry isolates. In this study, C. albicans strains were recovered from poultry in the southern Hebei Province (China) and identified. Molecular typing and analyses were performed to understand the molecular epidemiology and genetic relatedness of the strains. The fungi were isolated from live birds with presumed candidiasis or their corpses. The isolates were identified based on morphology, differential medium culture, and rDNA internal transcribed spacer sequencing. The identified C. albicans strains were analyzed by ABC genotyping and multilocus sequence typing. Clonal groups were identified using the eBURST (version 3.0) software, and an UPGMA phylogenetic tree was constructed using the MEGA (version 6.06) software. Overall, 72 isolates were divided into three genotypes (A, B, and C), 48 novel sequence types (STs), five groups with 10 singletons, and four clades. Results indicated that candidiasis is common in poultry in the southern Hebei Province, and that the genetic composition of the C. albicans poultry population from the area is relatively complicated. Based on the eBURST analysis for the STs in this study and others, we suggest that C. albicans poultry isolates were relatively independent but not completely separated from human isolates. The strains with the same or closely related genotypes but recovered from both birds and humans could have transferred and evolved between the two types of host.

Seasonal dynamics of extraradical mycelium and mycorrhizas in a black truffle (Tuber melanosporum) plantation

Seasonal dynamics of black truffle (Tuber melanosporum) extraradical mycelium as well as the associated mycorrhizal community have been evaluated in a 16-year-old plantation with productive and non-productive trees. Mycelium biomass was seasonally quantified by real-time PCR over two consecutive years and the correlation with environmental variables explored. Extraradical mycelium biomass varied seasonally and between the two consecutive years, being correlated with the precipitation that occurred 1 month before sampling. In addition, productive trees had more mycelium in the brûlé area than non-productive trees did. The ectomycorrhizal community composition inside the burnt areas was seasonally evaluated during a year. Ten mycorrhizal morphotypes were detected; T. melanosporum was the most abundant in productive and non-productive trees. Black truffle mycorrhizas were more abundant (mycorrhizal tips per unit of soil volume) in productive trees, and no seasonal variation was observed. The occurrence of black truffle mycorrhizas was significantly and positively correlated with the biomass of extraradical mycelium. The mycorrhizal community within the brûlé areas was significantly different between productive and non-productive trees, and no variation was detected between seasons. The assessment of the fungal vegetative structures in a mature plantation is of paramount importance to develop trufficulture methods based on the knowledge of the biological cycle of the fungus and its relationships with the associated ectomycorrhizal communities.

Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile

Our study reports the diversity of culturable mycoplankton in the eastern South Pacific Ocean off Chile to contribute with novel knowledge on taxonomy of filamentous fungi isolated from distinct physicochemical and biological marine environments. We characterized spatial distribution of isolates, evaluated their viability and assessed the influence of organic substrate availability on fungal development. Thirty-nine Operational Taxonomic Units were identified from 99 fungal strains isolated from coastal and oceanic waters by using Automatic Barcode Gap Discovery. All Operational Taxonomic Units belonged to phylum Ascomycota and orders Eurotiales, Dothideales, Sordariales and Hypocreales, mainly Penicillium sp. (82%); 11 sequences did not match existing species in GenBank, suggesting occurrence of novel fungal taxa. Our results suggest that fungal communities in the South Pacific Ocean off Chile appear to thrive in a wide range of environmental conditions in the ocean and that substrate availability may be a factor influencing fungal viability in the ocean.

Sources of varieties and quality of circular Fructus Ligustri Lucidi

This study aimed to trace sources and quantitatively analyze the specnuezhenide content of circular Fructus Ligustri Lucidi for clinical use. Different specifications of Fructus Ligustri Lucidi were identified using DNA barcoding technology and the specnuezhenide content was analyzed by High Performance Liquid Chromatography (HPLC). The ITS sequence of circular Fructus Ligustri Lucidi was identical to that of standard privet, which was determined through botanical identification. ITS sequence similarity between circular Fructus Ligustri Lucidi and Fructus Ligustri Lucidi which was registered in NCBI ranged from 99.5% to 100%. The sequences of circular and other Fructus Ligustri Lucidi were clustered in a Neighbor-Joining tree with bootstrap value of 95, and these sequences could be distinguished from adulterants. Conforming to pharmacopoeia standard, the average specnuezhenide content of circular Fructus Ligustri Lucidi was higher than that of chicken waist Fructus Ligustri Lucidi. Circular Fructus Ligustri Lucidi derived from Ligustrum lucidum Ait. and the specnuezhenide content was higher in circular Fructus Ligustri Lucidi than that in chicken waist Fructus Ligustri Lucidi.

Application of Locked Nucleic Acid (LNA) Primer and PCR Clamping by LNA Oligonucleotide to Enhance the Amplification of Internal Transcribed Spacer (ITS) Regions in Investigating the Community Structures of Plant-Associated Fungi

The simultaneous extraction of host plant DNA severely limits investigations of the community structures of plant-associated fungi due to the similar homologies of sequences in primer-annealing positions between fungi and host plants. Although fungal-specific primers have been designed, plant DNA continues to be excessively amplified by PCR, resulting in the underestimation of community structures. In order to overcome this limitation, locked nucleic acid (LNA) primers and PCR clamping by LNA oligonucleotides have been applied to enhance the amplification of fungal internal transcribed spacer (ITS) regions. LNA primers were designed by converting DNA into LNA, which is specific to fungi, at the forward primer side. LNA oligonucleotides, the sequences of which are complementary to the host plants, were designed by overlapping a few bases with the annealing position of the reverse primer. Plant-specific DNA was then converted into LNA at the shifted position from the 3' end of the primer-binding position. PCR using the LNA technique enhanced the amplification of fungal ITS regions, whereas those of the host plants were more likely to be amplified without the LNA technique. A denaturing gradient gel electrophoresis (DGGE) analysis displayed patterns that reached an acceptable level for investigating the community structures of plant-associated fungi using the LNA technique. The sequences of the bands detected using the LNA technique were mostly affiliated with known isolates. However, some sequences showed low similarities, indicating the potential to identify novel fungi. Thus, the application of the LNA technique is considered effective for widening the scope of community analyses of plant-associated fungi.

Temporal distance decay of similarity of ectomycorrhizal fungal community composition in a subtropical evergreen forest in Japan

Community compositions of ectomycorrhizal (ECM) fungi are known to show spatial distance decay of similarity, which arises from both deterministic niche-based processes and stochastic spatial-based processes (e.g. dispersal limitation). Recent studies have highlighted the importance of incorporating the spatial-based processes in the study of community ecology of ECM fungi. However, few studies have investigated the temporal distance decay of similarity of ECM fungal communities. More specifically, the role of stochastic temporal-based processes, which could drive the temporal distance decay of similarity independently of niche-based processes, in the temporal variation of the communities remains unclear. Here we investigated ECM fungi associated with roots of Castanopsis sieboldii at 3-month intervals over a 2-year period. We found that dissimilarity of the ECM fungal community composition was significantly correlated with temporal distance but not with environmental distance among sampling dates. Both climatic and temporal variables significantly explained the temporal variation of the community composition. These results suggest that temporal variations of ECM fungi can be affected not only by niche-based processes but also by temporal-based processes. Our findings imply that priority effects may play important roles in the temporal turnover of ECM fungal community at the site.

Ectomycorrhizal Fungal Protein Degradation Ability Predicted by Soil Organic Nitrogen Availability

In temperate and boreal forest ecosystems, nitrogen (N) limitation of tree metabolism is alleviated by ectomycorrhizal (ECM) fungi. As forest soils age, the primary source of N in soil switches from inorganic (NH4 (+) and NO3 (-)) to organic (mostly proteins). It has been hypothesized that ECM fungi adapt to the most common N source in their environment, which implies that fungi growing in older forests would have greater protein degradation abilities. Moreover, recent results for a model ECM fungal species suggest that organic N uptake requires a glucose supply. To test the generality of these hypotheses, we screened 55 strains of 13 Suillus species with different ecological preferences for their in vitro protein degradation abilities. Suillus species preferentially occurring in mature forests, where soil contains more organic matter, had significantly higher protease activity than those from young forests with low-organic-matter soils or species indifferent to forest age. Within species, the protease activities of ecotypes from soils with high or low soil organic N content did not differ significantly, suggesting resource partitioning between mineral and organic soil layers. The secreted protease mixtures were strongly dominated by aspartic peptidases. Glucose addition had variable effects on secreted protease activity; in some species, it triggered activity, but in others, activity was repressed at high concentrations. Collectively, our results indicate that protease activity, a key ectomycorrhizal functional trait, is positively related to environmental N source availability but is also influenced by additional factors, such as carbon availability.

Fungal biodiversity in the periglacial soil of Dosdè Glacier (Valtellina, Northern Italy)

Periglacial areas are one of the least studied habitats on Earth, especially in terms of their fungal communities. In this work, both molecular and culture-dependent methods have been used to analyse the microfungi in soils sampled on the front of the East Dosdè Glacier (Valtellina, Northern Italy). Although this survey revealed a community that was rich in fungal species, a distinct group of psychrophilic microfungi has not been detected. Most of the isolated microfungi were mesophiles, which are well adapted to the sensitive climatic changes that occur in this alpine environment. A discrepancy in the results that were obtained by means of the two diagnostic approaches suggests that the used molecular methods cannot entirely replace traditional culture-dependent methods, and vice versa.

Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR-DGGE

Both the internal transcribed spacer (ITS) region and 18S rRNA genes are broadly applied in molecular fingerprinting studies of fungi. However, the differences in those two ribosomal RNA regions are still largely unknown. In the current study, three sets of most suitable subunit ribosomes in ITS and 18S rRNA were compared using denaturing gradient gel electrophoresis (DGGE) under the optimum experimental conditions. Ten samples from both aquatic and soil environments were tested. The results revealed that the ITS region produced range-weighted richness in the range 36-361, which was significantly higher than that produced by 18S rDNA. There was a similar tendency in terms of the Shannon-Weaver diversity index and community dynamics in both water and soil samples. Samples from water and soil were better separated using ITS than 18S rDNA in principal component analysis of DGGE bands. Our study suggests that the ITS region is more precise and has more potential than 18S rRNA genes in fungal community analysis.

Elevated CO2 and O3 effects on ectomycorrhizal fungal root tip communities in consideration of a post-agricultural soil nutrient gradient legacy

Despite the critical role of EMF in nutrient and carbon (C) dynamics, combined effects of global atmospheric pollutants on ectomycorrhizal fungi (EMF) are unclear. Here, we present research on EMF root-level community responses to elevated CO2 and O3. We discovered that belowground EMF community richness and similarity were both negatively affected by CO2 and O3, but the effects of CO2 and O3 on EMF communities were contingent on a site soil pH and cation availability gradient. These results contrast with our previous work showing a strong direct effect of CO2 and O3 on sporocarp community dynamics and production. We discuss the possible role of carbon demand and allocation by EMF taxa in the discrepancy of these results. EMF communities were structured by a legacy of spatially defined soil properties, changing atmospheric chemistry and temporal dynamics. It is therefore necessary to understand global change impacts across multiple environmental gradients and spatiotemporal scales.

Effects of soil tillage on Tuber magnatum development in natural truffières

Tuber magnatum Pico, the Italian white truffle, commands the highest prices of any truffle. Despite its commercial value, it is the only edible European truffle which has not yet been successfully cultivated. Because of this, it is essential to safeguard natural truffières and to identify cultural practices to maximize their productivity. Soil tillage is successfully and extensively used in black truffle cultivation to enhance productivity, but its effects are not known on the development of T. magnatum. A recently developed real-time PCR assay was applied to evaluate the effects of tillage (10-15 cm depth) on T. magnatum mycelium in two different natural truffle grounds located in Tuscany and Emilia-Romagna. Tillage effects on bulk density, ectomycorrhizal fungal communities, and ascoma production were also assessed. Tilling significantly increased the quantity of T. magnatum mycelium which seemed to be related to an increase in soil porosity by up to 34%, and the diversity of ectomycorrhizal fungal communities. On the contrary, no significant effects were found on ascoma production. The results highlight that real-time PCR is the most reliable method for evaluating the effects of cultural practices on the development of T. magnatum in soil avoiding long-term studies on fruiting body production.

Fine-scale diversity and distribution of ectomycorrhizal fungal mycelium in a Scots pine forest

Ectomycorrhizal (ECM) mycelium is a key component of the ectomycorrhizal symbiosis, yet we know little regarding the fine-scale diversity and distribution of mycelium in ECM fungal communities. We collected four 20 × 20 × 2-cm(3) (800-cm(3)) slices of Scots pine (Pinus sylvestris) forest soil and divided each into 100 2 × 2 × 2-cm(3) (8-cm(3)) cubes. The presence of mycelium of ECM fungi was determined using an internal transcribed spacer (ITS) database terminal restriction fragment length polymorphism (T-RFLP) approach. As expected, many more ECM fungi were detected as mycelium than as ectomycorrhizas in a cube or slice. More surprisingly, up to one-quarter of the 43 species previously detected as ectomycorrhizas over an area of 400 m(2) could be detected in a single 8-cm(3) cube, and up to three-quarters in a single 800-cm(3) slice. ECM mycelium frequency decreased markedly with depth and there were distinct 'hotspots' of mycelium in the moss/F1 layer. Our data demonstrate a high diversity of ECM mycelium in a small (8-cm(3) ) volume of substrate, and indicate that the spatial scale at which ECM species are distributed as mycelium may be very different from the spatial scale at which they are distributed as tips.

Genetic Variability in Puccinia psidii Populations as Revealed by PCR-DGGE and T-RFLP Markers

Eucalyptus rust caused by Puccinia psidii is responsible for losses of approximately 20% of young Eucalyptus plants, depending on the environmental conditions and the geographic location. Despite its economic importance, there are few studies describing the genetic variability in P. psidii populations that infect different host plants. In the present study, we evaluated the ribosomal DNA internal transcribed spacer region (rDNA-ITS) using polymerase chain reaction denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism to assess the genetic variability in P. psidii populations infecting different Eucalyptus spp. and hybrids, as well as guava, jabuticaba, and syzygium. These culture-independent methods were efficient in differentiating populations based on the host species from which they were collected. In general, the results from both techniques showed that the populations collected from guava, jabuticaba, and syzygium were different from and had a greater level of diversity than the Eucalyptus rust populations. The sequencing of cloned rDNA-ITS fragments confirmed that the vast majority of the profiles generated were from P. psidii. This analysis also revealed interesting single-nucleotide polymorphisms. Therefore, these culture-independent methods are suitable for the rapid assessment of genetic variability within and between populations of this biotrophic fungus on a variety of host species and could be a tool to study the evolution of this pathogen and its interactions with host plants.

From genus to phylum: large-subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition

We compared the classification accuracy of two sections of the fungal internal transcribed spacer (ITS) region, individually and combined, and the 5' section (about 600 bp) of the large-subunit rRNA (LSU), using a naive Bayesian classifier and BLASTN. A hand-curated ITS-LSU training set of 1,091 sequences and a larger training set of 8,967 ITS region sequences were used. Of the factors evaluated, database composition and quality had the largest effect on classification accuracy, followed by fragment size and use of a bootstrap cutoff to improve classification confidence. The naive Bayesian classifier and BLASTN gave similar results at higher taxonomic levels, but the classifier was faster and more accurate at the genus level when a bootstrap cutoff was used. All of the ITS and LSU sections performed well (>97.7% accuracy) at higher taxonomic ranks from kingdom to family, and differences between them were small at the genus level (within 0.66 to 1.23%). When full-length sequence sections were used, the LSU outperformed the ITS1 and ITS2 fragments at the genus level, but the ITS1 and ITS2 showed higher accuracy when smaller fragment sizes of the same length and a 50% bootstrap cutoff were used. In a comparison using the larger ITS training set, ITS1 and ITS2 had very similar accuracy classification for fragments between 100 and 200 bp. Collectively, the results show that any of the ITS or LSU sections we tested provided comparable classification accuracy to the genus level and underscore the need for larger and more diverse classification training sets.

Studies on the ectomycorrhizal community in a declining Quercus suber L. stand

This survey was carried out in a Quercus suber L. stand with many trees affected by the disease "oak decline". Its aim was to obtain information about both the belowground ectomycorrhizal fungal community in a declining Q. suber stand as a whole, and the ectomycorrhizal fungal community of individual tree (EFT) detected in healthy and diseased plants. To this end, we first categorized the trees into four different decline classes (one for healthy plants and three for diseased plants) and then, by using morphological and molecular tools, we identified the ectomycorrhizas isolated from samples collected near the trees with different declining classes. The ectomycorrhizal community as a whole was seen to be composed of numerous ectomycorrhizal fungal species, only some of which appeared to be dominant (Cenococcum geophilum, Lactarius chrysorrheus, and some species of Tomentella genus), while most occurred sporadically. Results show that all root tips observed are mycorrhized and that decline class does not influence the number of ectomycorrhizal root tips found in the EFTs, thus oak decline does not impact the investment in ectomycorrhizal symbiosis. However, some statistical differences can be observed in the values of evenness and taxonomic distinctness in the EFT associated with trees with different states of health. Finally, both the analysis of similarity test and the ordination technique highlight a compositional difference between the EFT associated with trees in different health conditions, but also suggest that other factors may play a role in causing these differences.

Assessment of ectomycorrhizal fungal communities in the natural habitats of Tuber magnatum (Ascomycota, Pezizales)

The ectomycorrhizal (ECM) fungal communities of four natural Tuber magnatum truffle grounds, located in different Italian regions (Abruzzo, Emilia-Romagna, Molise, and Tuscany), were studied. The main objective of this study was to characterize and compare the ECM fungal communities in the different regions and in productive (where T. magnatum ascomata were found) and nonproductive points. More than 8,000 (8,100) colonized root tips were counted in 73 soil cores, and 129 operational taxonomic units were identified using morphological and molecular methods. Although the composition of the ECM fungal communities studied varied, we were able to highlight some common characteristics. The most plentiful ECM fungal taxa belong to the Thelephoraceae and Sebacinaceae families followed by Inocybaceae and Russulaceae. Although several ectomycorrhizas belonging to Tuber genus were identified, no T. magnatum ectomycorrhizas were found. The putative ecological significance of some species is discussed.

The distribution of the thermally tolerant symbiont lineage (Symbiodinium clade D) in corals from Hawaii: correlations with host and the history of ocean thermal stress

Spatially intimate symbioses, such as those between scleractinian corals and unicellular algae belonging to the genus Symbiodinium, can potentially adapt to changes in the environment by altering the taxonomic composition of their endosymbiont communities. We quantified the spatial relationship between the cumulative frequency of thermal stress anomalies (TSAs) and the taxonomic composition of Symbiodinium in the corals Montipora capitata, Porites lobata, and Porites compressa across the Hawaiian archipelago. Specifically, we investigated whether thermally tolerant clade D Symbiodinium was in greater abundance in corals from sites with high frequencies of TSAs. We recovered 2305 Symbiodinium ITS2 sequences from 242 coral colonies in lagoonal reef habitats at Pearl and Hermes Atoll, French Frigate Shoals, and Kaneohe Bay, Oahu in 2007. Sequences were grouped into 26 operational taxonomic units (OTUs) with 12 OTUs associated with Montipora and 21 with Porites. Both coral genera associated with Symbiodinium in clade C, and these co-occurred with clade D in M. capitata and clade G in P. lobata. The latter represents the first report of clade G Symbiodinium in P. lobata. In M. capitata (but not Porites spp.), there was a significant correlation between the presence of Symbiodinium in clade D and a thermal history characterized by high cumulative frequency of TSAs. The endogenous community composition of Symbiodinium and an association with clade D symbionts after long-term thermal disturbance appear strongly dependent on the taxa of the coral host.

Quantification of ectomycorrhizal mycelium in soil by real-time PCR compared to conventional quantification techniques

Mycelial biomass estimates in soils are usually obtained by measuring total hyphal length or by measuring the amount of fungal-specific biomarkers such as ergosterol and phospholipid fatty acids (PLFAs). These methods determine the biomass of the fungal community as a whole and do not allow species-specific identification. Molecular methods based on the extraction of total soil DNA and the use of genes as biomarkers enable identification of mycelia directly from the environment. Three molecular techniques were compared to determine the most reliable method for determining the biomass of individual fungal species in soil. The growth of extramatrical mycelium of two ectomycorrhizal (EM) fungal species (Suillus bovinus and Paxillus involutus) in soil was monitored by denaturing gradient gel electrophoresis, a cloning technique and real-time quantitative polymerase chain reaction, and the results were compared with those obtained with hyphal length determination and PLFA analysis. The molecular methods enabled identification and relative quantification of both species separately in an environment with several fungal species present and showed consistent results. Amounts of target DNA per gram soil were used to quantitatively compare soil samples. Increasing amounts of S. bovinus DNA and decreasing amounts of P. involutus DNA were detected over time in an environment containing a more complex community. This work demonstrates that molecular methods provide tools to determine the biomass of individual fungal species in soil.