Community Assembly of Endophytic Fungi in Ectomycorrhizae of Betulaceae Plants at a Regional Scale

Artificial Cultivation Changes Foliar Endophytic Fungal Community of the Ornamental Plant Lirianthe delavayi

Many wild ornamental plant species have been introduced to improve the landscape of cities; however, until now, no study has been performed to explore the composition and function of foliar endophytes associated with cultivated rare plants in cities after their introduction. In this study, we collected the leaves of the healthy ornamental plant Lirianthe delavayi from wild and artificially cultivated habitats in Yunnan and compared their diversity, species composition, and functional predictions of their foliar endophytic fungal community based on high-throughput sequencing technology. In total, 3125 ASVs of fungi were obtained. The alpha diversity indices of wild L. delavayi populations are similar to those of cultivated samples; however, the species compositions of endophytic fungal ASVs were significantly varied in the two habitats. The dominant phylum is Ascomycota, accounting for more than 90% of foliar endophytes in both populations; relatively, artificial cultivation trends to increase the frequency of common phytopathogens of L. delavayi, such as Alternaria, Erysiphe. The relative abundance of 55 functional predictions is different between wild and cultivated L. delavayi leaves (p < 0.05); in particular, chromosome, purine metabolism, and peptidases are significantly increased in wild samples, while flagellar assembly, bacterial chemotaxis, and fatty acid metabolism are significantly enhanced in cultivated samples. Our results indicated that artificial cultivation can greatly change the foliar endophytic fungal community of L. delavayi, which is valuable for understanding the influence of the domestication process on the foliar fungal community associated with rare ornamental plants in urban environments.

The cultivable endophytic fungal community of Scutellaria baicalensis: diversity and relevance to flavonoid production by the host

Scutellaria baicalensis (SB), a traditional Chinese medicinal plant, is widely used because of its important pharmacological activities. However, the endophytic fungi that promote flavonoid accumulation in SB remain unclear. Therefore, we analyzed the endophytic fungal community of SB and screened the endophytic fungi that might promote flavonoid synthesis in SB. ITS1/ITS4Blast was used to identify the endophytic fungi in SB. In total, 687 strains were identified in 57 genera. The dominant genus in the leaves and stems was Alternaria and that in the roots was Fusarium. Alternaria was the dominant genus in SB collected from all sites and in wild and cultivated SB. Alpha diversity indexes indicated more abundant endophytic fungi in samples from Chengde, the genuine producing area of SB, than in those from other sites. Beta diversity index analysis indicated that SB plants with closer geographical relationships showed more similar endophytic fungal community profiles. Spearman correlation analysis revealed that baicalin, wogonoside, wogonin, and oroxylin A contents were significantly correlated with the relative abundance of Alternaria. Overall, the results indicate the importance of geographical factors in influencing the endophytic fungal community of SB and suggest that the presence of Alternaria spp. might contribute to flavonoid synthesis in SB.

Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland

Distinct plant associated microbiomes live in rhizosphere soil, roots, and leaves. However, the differences in community assembly of fungi and bacteria along soil-plant continuum are less documented in ecosystems. We examined fungal and bacterial communities associated with leaves, roots, and rhizosphere soil of the dominant arbuscular mycorrhizal (AM) plants Taraxacum mongolicum and Elymus nutans and non-AM plant Carex enervis in the Zoige Wetland by using high throughput sequencing techniques. The operational taxonomic unit (OTU) richness of fungi and bacteria was significantly higher in rhizosphere soil than in roots and leaves, and their community compositions were significantly different in the rhizosphere soil, roots, and leaves in each plant species. The co-occurrence network analysis revealed that the sensitive fungal and bacterial OTUs with various taxonomic positions were mainly clustered into different modules according to rhizosphere soil, roots, and leaves in each plant species. Along the soil-plant continuum, the rhizosphere soil pool contributed more source on bacterial than on fungal communities in roots and leaves of the three plant species, and more source on bacterial and fungal communities in leaves of T. mongolicum and E. nutans compared with C. enervis. Furthermore, the root pool contributed more source on bacterial than on fungal communities in leaves of T. mongolicum and E. nutans but not that of C. enervis. This study highlights that the host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities along the soil-plant continuum in AM plants T. mongolicum and E. nutans and non-AM plant C. enervis in the Zoige Wetland. IMPORTANCE Elucidating the community microbiome assemblage alone the soil-plant continuum will help to better understand the biodiversity maintenance and ecosystem functioning. Here, we examined the fungal and bacterial communities in rhizosphere soil, roots, and leaves of two dominant AM plants and a non-AM plant in Zoige Wetland. We found that along the soil - plant continuum, host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities in the AM- and non-AM plants. This is the first report provides evidence of different assembly patterns of fungal and bacterial communities along the soil-plant continuum in the AM- and non-AM plants in the Zoige Wetland.

Diversity and Ginsenoside Biotransformation Potential of Cultivable Endophytic Fungi Associated With Panax bipinnatifidus var. bipinnatifidus in Qinling Mountains, China

To obtain novel fungi with potent β-glucosidase for minor ginsenoside production, Panax bipinnatifidus var. bipinnatifidus, which is a traditional medicinal plant containing various ginsenosides, was first employed to isolate endophytic fungi in this study. A total of 93 representative morphotype strains were isolated and identified according to ITS rDNA sequence analyses, and they were grouped into three phyla (Ascomycota, Basidiomycota, and Mucoromycota), five classes (Dothideomycetes, Sordariomycetes, Eurotiomycetes, Agaricomycetes, and Mucoromycetes), and 24 genera. Plectosphaerella (RA, 19.35%) was the most abundant genus, followed by Paraphoma (RA, 11.83%) and Fusarium (RA, 9.70%). The species richness index (S, 34) and the Shannon–Wiener index (H’, 3.004) indicated that P. bipinnatifidus harbored abundant fungal resources. A total of 26 endophytic fungal ethyl acetate extracts exhibited inhibitory activities against at least one pathogenic bacterium or fungus. In total, 11 strains showed strong β-glucosidase activities and also presented with the ability of ginsenoside biotransformation with varied glycoside-hydrolyzing pathways. Excitingly, three genera, namely, Ilyonectria, Sarocladium, and Lecanicillium, and all 11 taxa were first found to have the ability to transform ginsenosides in our study. The results indicated that P. bipinnatifidus could be a new fungi resource with potential novel natural compounds with antimicrobial activity and potent β-glucosidase for varied minor ginsenoside production.

Plant-microbial interaction: The mechanism and the application of microbial elicitor induced secondary metabolites biosynthesis in medicinal plants

Plants and microbes interact with each other via different chemical signaling pathways. At the risophere level, the microbes can secrete molecules, called elicitors, which act on their receptors located in plant cells. The so-called elicitor molecules as well as their actions differ according to the mcirobes and induce different bilogical responses in plants such as the synthesis of secondary metabolites. Microbial compounds induced phenotype changes in plants are known as elicitors and signaling pathways which integrate elicitor's signals in plants are called elicitation. In this review, the impact of microbial elicitors on the synthesis and the secretion of secondary metabolites in plants was highlighted. Moreover, biological properties of these bioactive compounds were also highlighted and discussed. Indeed, several bacteria, fungi, and viruses release elicitors which bind to plant cell receptors and mediate signaling pathways involved in secondary metabolites synthesis. Different phytochemical classes such as terpenoids, phenolic acids and flavonoids were synthesized and/or increased in medicinal plants via the action of microbial elicitors. Moreover, these compounds compounds exhibit numerous biological activities and can therefore be explored in drugs discovery.

Identifying the Specific Root Microbiome of the Hyperaccumulator Noccaea brachypetala Growing in Non-metalliferous Soils

Noccaea brachypetala is a close relative of Noccaea caerulescens, a model plant species used in metal hyperaccumulation studies. In a previous survey in the Catalan Pyrenees, we found two occidental and two oriental N. brachypetala populations growing on non-metalliferous soils, with accumulated high concentrations of Cd and Zn. Our hypothesis was that the microbiome companion of the plant roots may influence the ability of these plants to absorb metals. We performed high-throughput sequencing of the bacterial and fungal communities in the rhizosphere soil and rhizoplane fractions. The rhizobiomes and shoot ionomes of N. brachypetala plants were analyzed along with those from other non-hyperaccumulator Brassicaceae species found at the same sampling locations. The analyses revealed that microbiome richness and relative abundance tended to increase in N. brachypetala plants compared to non-hyperaccumulator species, regardless of plant location. We confirmed that the root compartment is a key factor in describing the community composition linked to the cohabiting Brassicaceae species, and the rhizoplane fraction contained the specific and rare taxa associated with each species. N. brachypetala plants harbored a similar relative abundance of fungi compared to the other plant hosts, but there was a notable reduction in some specific taxa. Additionally, we observed an enrichment in the hyperaccumulator rhizoplane of previously described metal-tolerant bacteria and bacteria involved in nitrogen cycling. The bacteria involved in the nitrogen cycle could contribute indirectly to the hyperaccumulator phenotype by improving soil quality and fertility. Our results indicate that N. brachypetala captures a particular prokaryotic community from the soil. This particular prokaryotic community may benefit the extraction of metal ions and/or improve plant nutrition. Our research identified satellite groups associated with the root niche of a hyperaccumulator plant that may assist in improving biological strategies in heavy metal remediation.

Influence of Peanut, Sorghum, and Soil Salinity on Microbial Community Composition in Interspecific Interaction Zone

Soil microorganisms play important roles in crop production and sustainable agricultural management. However, soil conditions and crop selection are key determining factors for soil microbial communities. This study investigated the effect of plant types and soil salinity on the microbial community of interspecific interaction zone (II) based on the sorghum/peanut intercropping system. Microbial community diversity and composition were determined through PacBio single molecule, real-time sequencing of 16S rDNA and internal transcribed spacer (ITS) genes. Results showed Proteobacteria, Bacteroidota, and Acidobacteriota to be the dominant bacterial phyla in IP, II, and IS, whereas Ascomycota, Basidiomycota, and Mucoromycota were the dominant fungal phyla. Under salt-treated soil conditions, the plants-specific response altered the composition of the microbial community (diversity and abundance). Additionally, the interspecific interactions were also helpful for maintaining the stability and ecological functions of microbial communities by restructuring the otherwise stable core microbiome. The phylogenetic structure of the bacterial community was greatly similar between IP and II while that of the fungal community was greatly similar between IP and IS; however, the phylogenetic distance between IP and IS increased remarkably upon salinity stress. Overall, salinity was a dominant factor shaping the microbial community structure, although plants could also shape the rhizosphere microenvironment by host specificity when subjected to environmental stresses. In particular, peanut still exerted a greater influence on the microbial community of the interaction zone than sorghum.