Illumina-based analysis yields new insights into the diversity and composition of endophytic fungi in cultivated Huperzia serrata

Phyllosphere mycobiome in two Lycopodiaceae plant species: unraveling potential HupA-producing fungi and fungal interactions

Huperzine A (HupA), a lycopodium alkaloid with therapeutic potential for neurodegenerative diseases such as Alzheimer's disease, is found exclusively in some species of the Huperzioideae subfamily of Lycopodiaceae. Fungi associated with Huperzioideae species are potential contributors to HupA biosynthesis, offering promising prospects for HupA production. Despite its medical significance, limited knowledge of fungal diversity in lycophytes and the variability of HupA production in fungal strains have impeded the discovery and applications of HupA-producing fungi. Here, we investigated HupA concentrations and the mycobiome across various tissues of two Lycopodiaceae species, Huperzia asiatica (a HupA producer) and Diphasiastrum complanatum (a non-HupA producer). We aim to unveil the distribution of potential HupA-producing fungi in different plant tissues and elucidate fungal interactions within the mycobiome, aiming to uncover the role of HupA-producing fungi and pinpoint their potential fungal facilitators. Among the tissues, H. asiatica exhibited the highest HupA concentration in apical shoots (360.27 μg/g fresh weight) whereas D. complanatum showed no HupA presence in any tissue. We obtained 441 amplicon sequence variants (ASVs) from H. asiatica and 497 ASVs from D. complanatum. The fungal communities in bulbils and apical shoots of H. asiatica were low in diversity and dominated by Sordariomycetes, a fungal class harboring the majority of reported HupA-producing fungi. Integrating bioinformatics with published experimental reports, we identified 27 potential HupA-producing fungal ASVs, primarily in H. asiatica, with 12 ASVs identified as hubs in the fungal interaction network, underscoring their pivotal roles in mycobiome stability. Members of certain fungal genera, such as Penicillium, Trichoderma, Dioszegia, Exobasidium, Lycoperdon, and Cladosporium, exhibited strong connections with the potential HupA producers in H. asiatica's network rather than in D. complanatum's. This study advances our knowledge of fungal diversity in Lycopodiaceae and provides insights into the search for potential HupA-producing fungi and fungal facilitators. It highlights the importance of exploring young tissues and emphasizes the ecological interactions that may promote the fungi-mediated production of complex bioactive compounds, offering new directions for research in fungal ecology and secondary metabolite production.

Continental sampling reveals core bacterial and environmentally driven fungal leaf endophytes in Heuchera

PREMISE

Endophytic plant-microbe interactions range from mutualistic relationships that confer important ecological and agricultural traits to neutral or quasi-parasitic relationships. In contrast to root-associated endophytes, the role of environmental and host-related factors in the acquisition of leaf endophyte communities at broad spatial and phylogenetic scales remains sparsely studied. We assessed endofoliar diversity to test the hypothesis that membership in these microbial communities is driven primarily by abiotic environment and host phylogeny.

METHODS

We used a broad geographic coverage of North America in the genus Heuchera L. (Saxifragaceae), representing 32 species and varieties across 161 populations. Bacterial and fungal communities were characterized using 16S and ITS amplicon sequencing, respectively, and standard diversity metrics were calculated. We assembled environmental predictors for microbial diversity at collection sites, including latitude, elevation, temperature, precipitation, and soil parameters.

RESULTS

Assembly patterns differed between bacterial and fungal endophytes. Host phylogeny was significantly associated with bacteria, while geographic distance was the best predictor of fungal community composition. Species richness and phylogenetic diversity were consistent across sites and species, with only fungi showing a response to aridity and precipitation for some metrics. Unlike what has been observed with root-associated microbial communities, in this system microbes show no relationship with pH or other soil factors.

CONCLUSIONS

Overall, this work improves our understanding of the large-scale patterns of diversity and community composition in leaf endophytes and highlights the relative significance of environmental and host-related factors in driving different microbial communities within the leaf microbiome.

The Fungal, Nutritional, and Metabolomic Diagnostics of the Oil Palm Elaeis guineensis Affected by Bud Rot Disease in Esmeraldas, Ecuador

The oil palm Elaeis guineensis represents one of the most important crops in Ecuador. Considering that bud rot disease is deadly in Ecuador, more attention has been given to identifying possible causes for palm debility from this disease. We studied the involvement of fungi and nutrients in triggering bud rot disease in E. guineensis. Special emphasis was given to the molecules synthesized by the plant to protect against this devastating disease. Techniques like Diagnosis and Recommendation Integrated System (DRIS) and metagenomic analysis were used to understand the possible implications of biotic and abiotic factors in the development of bud rot disease in oil palm in Ecuador. Liquid chromatography-mass spectrometry (LC-MS) analysis was used to identify the phenolic protection barrier of the palm facing the disease. Our results indicate that fungi from Ascomyceta phylum were found in the tested samples. The species directly involved are different in soil compared with plants. The results indicate a deficiency of chemical elements, such as Ca, Mn, Mg, and Fe, which are responsible for palm debility from bud rot disease. More than 30 compounds with protective roles were identified in the leaves of symptomatic plants from the first stage of the infection.

Diversity, chemical constituents and biological activities of endophytic fungi from Alisma orientale (Sam.) Juzep

The dried tuber of Alisma orientale (Sam.) Juzep. (AOJ) is a traditional Chinese medicine with high medicinal value. The endophytic fungi of medicinal plants are a treasure house of natural compounds. However, there is a lack of research on the diversity and biological activity of endophytic fungi of AOJ. In this study, high-throughput sequencing technology was used to study the diversity of endophytic fungi in the roots and stems of AOJ, and endophytic fungi with a high output of phenols and flavonoids were screened by chromogenic reaction, and the antioxidant and antibacterial activities and chemical constituents of crude extracts of their fermentation broth were studied. A total of 3,426 amplicon sequence variants (ASVs) belonging to 9 phyla, 27 classes, 64 orders, 152 families, and 277 genera were identified from AOJ. There were significant differences in the endophytic fungal communities of AOJ roots and stems, as well as in the endophytic fungal communities of triangular AOJ and circular AOJ. In addition, 31 strains of endophytic fungi were isolated from AOJ, of which 6 strains had good antioxidant and antibacterial activities. The crude extract of YG-2 had the strongest free radical scavenging ability and bacteriostatic ability, and its IC50 DPPH, IC50 ABTS, and IC50⋅OH values were 0.009 ± 0.000 mg/mL, 0.023 ± 0.002 mg/mL, and 0.081 ± 0.006 mg/mL, respectively. The results of LC-MS showed that the main component of the crude extract of YG-2 was caffeic acid (10.12 μmol/g). Overall, the results of this study preliminarily elucidated the diversity and community composition of endophytic fungi of AOJ, indicating that AOJ endophytic fungi have abundant secondary metabolites and good antioxidant and antibacterial activities. This study provides an important reference for further research, development and utilization of AOJ endophytic fungi and a theoretical basis for the further development of the endophytic fungus YG-2 (Chaetomium globosum) as a source of antioxidants.

The temporal and spatial endophytic fungal community of Huperzia serrata: diversity and relevance to huperzine A production by the host

BACKGROUND

Plants maintain the steady-state balance of the mutually beneficial symbiosis relationship with their endophytic fungi through secondary metabolites. Meanwhile endophytic fungi can serve as biological inducers to promote the biosynthesis and accumulation of valuable secondary metabolites in host plants through a variety of ways. The composition and structure of endophytic fungal community are affected by many factors, including tissues, seasons and so on. In this work, we studied the community diversity, temporal and spatial pattern of endophytic fungi detected from the roots, stems and leaves of Huperzia serrata in different seasons. The correlation between endophytic fungi and huperzine A (HupA) content in plants was analyzed.

RESULTS

A total of 7005 operational taxonomic units were detected, and all strains were identified as 14 phyla, 54 classes, 140 orders, 351 families and 742 genera. Alpha diversity analysis showed that the diversity of endophytic fungi in stem and leaf was higher than that in root, and the diversity in summer (August) was lower than that in other months. NMDS analysis showed that the endophytic fungal communities of leaves, stems and roots were significantly different, and the root and leaf communities were also different between four seasons. Through correlation analysis, it was found that 33 genera of the endophytic fungi of H. serrata showed a significant positive correlation with the content of HupA (p < 0.05), of which 13 genera (Strelitziana, Devriesia, Articulospora, Derxomyces, Cyphellophora, Trechispora, Kurtzmanomyces, Capnobotryella, Erythrobasidium, Camptophora, Stagonospora, Lachnum, Golubevia) showed a highly significant positive correlation with the content of HupA (p < 0.01). These endophytic fungi may have the potential to promote the biosynthesis and accumulation of HupA in plant.

CONCLUSIONS

This report is the first time to analyze the diversity of endophytic fungi in tissues of H. serrata in different seasons, which proves that there is variability in different tissues and seasonal distribution patterns. These findings provide references to the study of endophytic fungi of H. serrata.

Methods used for the study of endophytic fungi: a review on methodologies and challenges, and associated tips

Endophytic fungi are microorganisms that colonize the interior of plant tissues (e.g. leaves, seeds, stem, trunk, roots, fruits, flowers) in intracellular and/or extracellular spaces without causing symptoms of disease in host plants. These microorganisms have been isolated from plant species in a wide variety of habitats worldwide, and it is estimated that all terrestrial plants are colonized by one or more species of endophytic fungus. In addition, these microorganisms have been drawing the attention of researchers because of their ability to synthesize a wide range of bioactive molecules with potential for applications in agriculture, medicine and biotechnology. However, several obstacles come up when studying the diversity and chemical potential of endophytic fungi. For example, the usage of an inappropriate surface disinfection method for plant tissue may not eliminate the epiphytic microbiota or may end up interfering with the endophytic mycobiota, which consequently generates erroneous results. Moreover, the composition of the culture medium and the culture conditions can favor the growth of certain species and inhibit others, which generates underestimated results. Other inconsistencies can arise from the fungus misidentification and consequent exploration of its chemical potential. Based on the methodological biases that may occur at all stages of studies dealing with endophytic fungi, the objective of this review is to discuss the main methods employed in these studies as well as highlight the challenges derived from the different approaches. We also report associated tips to help future studies on endophytic fungi as a contribution.

Diversity of endophytic fungal community in Huperzia serrata from different ecological areas and their correlation with Hup A content

Background

Huperzine A (Hup A) has attracted considerable attention as an effective therapeutic candidate drug used to treat Alzheimer’s disease. Whereas, the production of Hup A from wild plants faced a major challenge, which is the wild Huperzia Serrata harbor a low Hup A content, has a long-life cycle, and has a small yield. At present, several reports showed that Hup A is produced by various endophytic fungal strains isolated from H. serrata, thereby providing an alternative method to produce the compound and reduce the consumption of this rare and endangered plant. However, till now, very few comprehensive studies are available on the biological diversity and structural composition of endophytic fungi and the effects of endophytic fungi on the Hup A accumulation in H. serrata.

Results

In this research, the composition and diversity of fungal communities in H. serrata were deciphered based on high-throughput sequencing technology of fungal internal transcribed spacer regions2 (ITS2). The correlation between endophytic fungal community and Hup A content was also investigated. Results revealed that the richness and the diversity of endophytic fungi in H. serrata was various according to different tissues and different ecological areas. The endophytic fungal communities of H. serrata exhibit species-specific, ecological-specific, and tissue-specific characteristics. There are 6 genera (Ascomycota_unclassified, Cyphellophora, Fungi_unclassified, Sporobolomyces, and Trichomeriaceae_unclassified) were significantly positively correlated with Hup A content in all two areas, whereas, there are 6 genera (Auricularia, Cladophialophora, Cryptococcus, Mortierella, and Mycena) were significantly negatively correlated with Hup A content of in all two areas.

Conclusions

This study indicated a different composition and diverse endophytic fungal communities in H. serrata from different organs and ecological areas. The current study will provide the realistic basis and theoretical significance for understanding the biological diversity and structural composition of endophytic fungal communities in H. serrata, as well as providing novel insights into the interaction between endophytic fungi and Hup A content.

Microeukaryotic Communities on the Fruit of Gardenia thunbergia Thunb. with a Focus on Pathogenic Fungi

Woody fruit which stay on ornamental plants for a long time may present a risk of infection to other organisms due to the presence of pathogens on their surface. We compared the microbe communities on the fruit surfaces of garden ornamental Gardenia thunbergia Thunb. with those on other surfaces in the study region. As Gardenia fruit contain antifungal substances, the focus of this study was on the fungal communities that exist thereon. We used Illumina sequencing to identify Amplicon Sequence Variants (ASV) of the internal transcribed spacer 2 (ITS2) of the ribosomal RNA. The microbial communities of the Gardenia fruit are distinct from the communities from the surrounding environments, indicating a specialized microhabitat. We employed clustering methods to position unidentified ASVs relative to known ASVs. We identified a total of 56 ASVs representing high risk fungal species as putative plant pathogens exclusively found on the fruit of Gardenia. Additionally, we found several ASVs representing putative animal or human pathogens. Those pathogens were distributed over distinct fungi clades. The infection risk of the high diversity of putative pathogens represented on the Gardenia fruit needs to be elucidated in further investigations.

Endophytic Fungal Community of Huperzia serrata: Diversity and Relevance to the Production of Huperzine A by the Plant Host

As the population ages globally, there seem to be more people with Alzheimer's disease. Unfortunately, there is currently no specific treatment for the disease. At present, Huperzine A (HupA) is one of the best drugs used for the treatment of Alzheimer's disease and has been used in clinical trials for several years in China. HupA was first separated from Huperzia serrata, a traditional medicinal herb that is used to cure fever, contusions, strains, hematuria, schizophrenia, and snakebite for several hundreds of years in China, and has been confirmed to have acetylcholinesterase inhibitory activity. With the very slow growth of H. serrata, resources are becoming too scarce to meet the need for clinical treatment. Some endophytic fungal strains that produce HupA were isolated from H. serrate in previous studies. In this article, the diversity of the endophytic fungal community within H. serrata was observed and the relevance to the production of HupA by the host plant was further analyzed. A total of 1167 strains were obtained from the leaves of H. serrata followed by the stems (1045) and roots (824). The richness as well as diversity of endophytic fungi within the leaf and stem were higher than in the root. The endophytic fungal community was similar within stems as well as in leaves at all taxonomic levels. The 11 genera (Derxomyces, Lophiostoma, Cyphellophora, Devriesia, Serendipita, Kurtzmanomyces, Mycosphaerella, Conoideocrella, Brevicellicium, Piskurozyma, and Trichomerium) were positively correlated with HupA content. The correlation index of Derxomyces with HupA contents displayed the highest value (CI = 0.92), whereas Trichomerium showed the lowest value (CI = 0.02). Through electrospray ionization mass spectrometry (ESI-MS), it was confirmed that the HS7-1 strain could produce HupA and the total alkaloid concentration was 3.7 ug/g. This study will enable us to screen and isolate the strain that can produce HupA and to figure out the correlation between endophytic fungal diversity with HupA content in different plant organs. This can provide new insights into the screening of strains that can produce HupA more effectively.