Fungal Community Analyses of Endophytic Fungi from Two Oak Species, Quercus mongolica and Quercus serrata, in Korea

Diversity of Endophytic Fungi Isolated from Prunus yedoensis and Their Antifungal Activity Against Wood Decay Fungi

Endophytic fungi play a vital role in protecting and promoting the growth of their host plants. The diversity of fungal endophytes has been documented across different host plant species and varies depending on factors such as the species of the host, ecological conditions, and the health status of the plant. We isolated endophytic fungi from Prunus yedoensis trees with different decay rates. A total of 31 species were isolated from decayed trees, while 33 species were obtained from healthy trees. The number of endophytic fungi exhibiting antifungal activities against wood decay fungi was higher in healthy trees, with 10 species showing activity compared to only 1 species from decayed trees. Endophytic fungus Fusarium acuminatum (BEN48) had the highest inhibition rates against Trametes versicolor, Ganoderma gibbosum, and Vanderbylia fraxinea. Heating conditions did not significantly affect the inhibitory ability of the culture filtrate from BEN48 on wood decay fungi. At 50% concentration, the inhibitory abilities of the culture filtrates against Trametes versicolor, Ganoderma gibbosum, and Vanderbylia fraxinea were 96.5%, 64.1%, and 92.7%, respectively. The inhibitory effects against Trametes versicolor decreased at concentrations of 30% and 10%, resulting in inhibition rates of 83.7% and 50.8%, respectively. For Ganoderma gibbosum, the inhibition rate reduced to 52.6% at 30% concentration and 24.5% at 10% concentration. For Vanderbylia fraxinea, there was no significant difference between the 30% and 10% concentrations, and the inhibition rates for both concentrations were high, measuring 89.9% and 88.8%, respectively. Hence, Fusarium acuminatum (BEN48) has promise as a biocontrol agent for managing wood decay fungi.

Diversity of Endophytic Fungi in Plant Species: Traditional vs. High-Throughput Sequencing Approaches

The plant microbiome significantly impacts plant life, with fungi playing a crucial role in shaping interactions and classifications. Advances in cultivation technologies have refined fungal classification, and research highlights the vital connection between endophytic fungi and their plant hosts. The present study employs morphological and phylogenetic techniques, predicting the Internal Transcribed Spacer 2 (ITS2) secondary structure and using next-generation sequencing (NGS) data to detect fungal endophytes in plant leaves via both traditional and conventional approaches. The research area, with its hot semi-arid environment and red and black soils, supports drought-resistant plants like Senna auriculata, Ziziphus mauritiana, and Catunaregam spinosa, known for their medicinal properties. These plants, rich in antioxidants, play a vital role in traditional medicine and highlight the region's rich ethno-botanical heritage. The culture-dependent study on the foliage yielded a total of 17 isolates from S. auriculata and 16 each from both C. spinosa and Z. mauritiana. The most common genera, Alternaria and Nigrospora, account for 18.3% of all isolated endophytic fungi. Three plants were colonized with Nigrospora and Lasiodiplodia, and their morphotypes were determined using ITS2 secondary structure prediction. Recent ecological studies highlight unculturable taxa, or dark taxa, where many species cannot sporulate or be cultured, emphasizing the need for High - Throughput Sequencing (HTS) approaches. The study gathered 68,791 reads from S. auriculata with 101 operational taxonomic units (OTUs), 58,620 from C. spinosa with 219 OTUs, and 66,087 from Z. mauritiana with 193 OTUs, with the majority of OTUs related to Colletotrichum (69%) and a minimum of Myrmaecium (2%). A total of 49 fungal isolates were obtained from traditional methods, whereas 513 fungal OTUs were retrieved through HTS methods, confirming the presence of a highly abundant fungus population in plant samples. The study reveals that using the ITS short amplicon sequencing technique provides distinct insights into endophytic fungal communities in three plant samples. In conclusion, analyzing plant fungal components using a combination of culture-dependent and culture-independent techniques may be a novel strategy.

The Populations of Two Differently Medicine-Used Plants of Hedyotis diffusa and Hedyotis corymbosa Shoot-Assembling Rich Bacterial and Fungal Communities with Varied Compositions but Conserved Structures

The plant-colonized microbial communities have closely micro-ecological effects on host plant growth and health. There are many medicinal plants in the genus Hedyotis, but it is yet unclear about the shoot-assembled bacterial and fungal communities (SBFC) of Hedyotis plants. Hence, eight plant populations of Hedyotis diffusa (HD) and H. corymbosa (HC) were evaluated with 16S rRNA gene and ITS sequences, for comparing the types, abundance, or/and potential functions of SBFC at plant species- and population levels. In tested HD- and HC-SBFC, 682 fungal operational taxonomic units and 1,329 bacterial zero-radius operational taxonomic units were identified, with rich species compositions and varied alpha diversities. Notably, the SBFC compositions of HD and HC plant populations were exhibited with partly different types and abundances at phylum and genus levels but without significantly different beta diversities at plant species and population levels. Typically, the SBFC of HD and HC plant populations were presented with abundance-different biomarkers, such as Frankiaceae and Bryobacteraceae, and with similar micro-ecological functions of microbial metabolisms of lipids, terpenoids,and xenobiotics. Taken together, HD- and HC-SBFC possessed with varied rich compositions, conservative taxonomic structures, and similar metabolic functions, but with small-scale type and abundance differences at plant species- and population- levels.

Foliar mycobiome remains unaltered under urban air-pollution but differentially express stress-related genes

Air pollution caused by tropospheric ozone contributes to the decline of forest ecosystems; for instance, sacred fir, Abies religiosa (Kunth) Schltdl. & Cham. forests in the peri-urban region of Mexico City. Individual trees within these forests exhibit variation in their response to ozone exposure, including the severity of visible symptoms in needles. Using RNA-Seq metatranscriptomic data and ITS2 metabarcoding, we investigated whether symptom variation correlates with the taxonomic and functional composition of fungal mycobiomes from needles collected in this highly polluted area in the surroundings of Mexico City. Our findings indicate that ozone-related symptoms do not significantly correlate with changes in the taxonomic composition of fungal mycobiomes. However, genes coding for 30 putative proteins were differentially expressed in the mycobiome of asymptomatic needles, including eight genes previously associated with resistance to oxidative stress. These results suggest that fungal communities likely play a role in mitigating the oxidative burst caused by tropospheric ozone in sacred fir. Our study illustrates the feasibility of using RNA-Seq data, accessible from global sequence repositories, for the characterization of fungal communities associated with plant tissues, including their gene expression.

Why Are There So Few Basidiomycota and Basal Fungi as Endophytes? A Review

A review of selected studies on fungal endophytes confirms the paucity of Basidiomycota and basal fungi, with almost 90% attributed to Ascomycota. Reasons for the low number of Basidiomycota and basal fungi, including the Chytridiomycota, Mucoromycota, and Mortierellomycota, are advanced, including isolation procedure and media, incubation period and the slow growth of basidiomycetes, the identification of non-sporulating isolates, endophyte competition, and fungus-host interactions. We compare the detection of endophytes through culture-dependent methods and culture-independent methods, the role of fungi on senescence of the host plant, and next-generation studies.

Antifungal Activity and Effect of Plant-Associated Bacteria on Phenolic Synthesis of Quercus robur L

Europe's forests, particularly in Ukraine, are highly vulnerable to climate change. The maintenance and improvement of forest health are high-priority issues, and various stakeholders have shown an interest in understanding and utilizing ecological interactions between trees and their associated microorganisms. Endophyte microbes can influence the health of trees either by directly interacting with the damaging agents or modulating host responses to infection. In the framework of this work, ten morphotypes of endophytic bacteria from the tissues of unripe acorns of Quercus robur L. were isolated. Based on the results of the sequenced 16S rRNA genes, four species of endophytic bacteria were identified: Bacillus amyloliquefaciens, Bacillus subtilis, Delftia acidovorans, and Lelliottia amnigena. Determining the activity of pectolytic enzymes showed that the isolates B. subtilis and B. amyloliquefaciens could not cause maceration of plant tissues. Screening for these isolates revealed their fungistatic effect against phytopathogenic micromycetes, namely Fusarium tricinctum, Botrytis cinerea, and Sclerotinia sclerotiorum. Inoculation of B. subtilis, B. amyloliquefaciens, and their complex in oak leaves, in contrast to phytopathogenic bacteria, contributed to the complete restoration of the epidermis at the sites of damage. The phytopathogenic bacteria Pectobacterium and Pseudomonas caused a 2.0 and 2.2 times increase in polyphenol concentration in the plants, respectively, while the ratio of antioxidant activity to total phenolic content decreased. Inoculation of Bacillus amyloliquefaciens and Bacillus subtilis isolates into oak leaf tissue were accompanied by a decrease in the total pool of phenolic compounds. The ratio of antioxidant activity to total phenolic content increased. This indicates a qualitative improvement in the overall balance of the oak leaf antioxidant system induced by potential PGPB. Thus, endophytic bacteria of the genus Bacillus isolated from the internal tissues of unripe oak acorns have the ability of growth biocontrol and spread of phytopathogens, indicating their promise for use as biopesticides.

Fungal Communities in Leaves and Roots of Healthy-Looking and Diseased Ulmusglabra

The aim of this study was to investigate fungal communities associated with leaves and roots of healthy-looking and declining U. glabra trees. The study was expected to demonstrate whether and how the diversity and composition of fungal communities change in these functional tissues following the infection by Dutch elm disease-causing fungi. The study sites included six U. glabra sites in Lithuania, where leaves and roots were sampled. DNA was isolated from individual samples, amplified using ITS2 rRNA as a marker, and subjected to high-throughput sequencing. The sequence analysis showed the presence of 32,699 high-quality reads, which following clustering, were found to represent 520 non-singleton fungal taxa. In leaves, the fungal species richness was significantly higher in healthy-looking trees than in diseased ones (p < 0.05). In roots, a similar comparison showed that the difference was insignificant (p > 0.05). The most common fungi in all samples of roots were Trichocladium griseum (32.9%), Penicillium restrictum (21.2%), and Unidentified sp. 5238_7 (12.6%). The most common fungi in all samples of leaves were Trichomerium sp. 5238_8 (12.30%), Aureobasidium pullulans (12.03%), Cladosporium sp. 5238_5 (11.73%), and Vishniacozyma carnescens (9.86%). The results showed that the detected richness of fungal taxa was higher in samples collected from healthy-looking trees than from diseased ones, thereby highlighting the negative impact of the Dutch elm disease on the overall fungal diversity.

Dendrobine biosynthesis in Dendrobium nobile in four different habitats is affected by the variations in the endophytic fungal community

Dendrobium nobile, an epiphytic plant, is a traditional medicinal herb with abundant endophytes. It is unclear whether the variation in the diversity and abundance of endophytes could stimulate the biosynthesis of medicinal compounds in the plant. In this study, we collected fresh stems of D. nobile from four habitats for investigating the fungal community structure, dendrobine content, and environment factors and their correlations. The results indicated no significant difference in endophytic fungal diversity among the habitats; however, different dominant or special endophytic genera were observed in the hosts from different habitats. The altitude was observed to be positively related to the dendrobine content, as the stems collected from the altitude of 692 m exhibited the highest level of dendrobine. Furthermore, the relative abundance of Toxicocladosporium was found to be positively correlated with the altitude and dendrobine content. The epiphytic matrix exhibited a significant negative correlation with the relative abundance of the endophytic fungus Gibberella but did not exhibit any significant correlation with the dendrobine content. The results indicated that the abundance of endophytes in D. nobile was affected by the altitude and epiphytic matrix and that high Toxicocladosporium abundance and high altitude were conducive to dendrobine production.