Despite desert ecosystem being crucial to our understanding of natural geography, species evolution and global climate change, there is limited information on the dynamics of their composition and the diversity of endophytic fungi communities driven by plant identity and organ differentiation. Here, an extensive investigation of endophytic fungal microbiome in root, stem, and leaf organs associated with five xerophyte shrubs in an extremely arid desert, Northwest China, were examined. The fungal community dominated by Dothideomycetes and Pleosporales. Shrub species strongly drive the niche-based processes of endophytic fungi across the root, stem and leaf compartments. The diversity and composition of endophytic fungi in stem showed higher variability among plant species than leaf and root. The fungal communities in root libraries were more diverse and exhibited a remarkable differentiation of community composition. We further demonstrated the significant host preferences and tissue specificity of desert endophytic fungi, and unique specific taxa were also observed. The co-occurrence network revealed the coexistence of fungal endophytes in arid desert, and the root fungal network harbored the highest interspecies connectivity. Members of Pleosporales were the most common keystone species in the root fungal network. This is the first report of mycobiota in both plant species and organ differentiation in an extremely arid desert ecosystem.

Dark septate endophytes (DSEs) usually colonize plant roots, especially in stress environments. However, their relationship with plants ranges from beneficial to harmful and has remained largely uncharacterized. In the present study, 14 DSE species grouped into 11 genera were isolated from the roots of a desert plant, Artemisia ordosica, which is widely distributed in northwest China. Three dominant DSE species—Paraphoma chrysanthemicola (Pc), Alternaria chartarum (Ac), and Acrocalymma vagum (Av)—were selected and tested for their resistance to drought in vitro. Furthermore, we characterized the responses of A. ordosica under drought conditions in relation to the presence of these DSEs following inoculation. The results showed that all three strains grew well under in vitro drought stress, and the biomass of Ac and Av was significantly higher than that of the unstressed control. The effects of DSE inoculation on the growth of A. ordosica under drought stress varied according to the different DSE species but were generally beneficial. Under drought stress, Av and Pc promoted plant growth, antioxidant enzyme activity, and root development of the hosts. The Ac strain conferred obvious positive effects on the antioxidant enzyme activity of the hosts. In general, Av and Pc demonstrated better application potential for improving the drought resistance of A. ordosica.

To evaluate the applicability of desert dark septate endophytes (DSEs) in crop cultivation, Alternaria alternata (Fr.) Keissl. (Aa), Paraphoma pye Moslemi & P.W.J. Taylor (Pp), and Paraphoma radicina (McAlpine) Morgan-Jones & J.F. White (Pr) were inoculated into nonhost wheat growing under three water conditions. The plants’ biomass, vegetative growth, and physiological parameters were investigated. At harvest, all DSE strains were effective colonizers under all treatments. These DSEs generally positively affected wheat growth but varied among different DSE species, and this promoting effect was more obvious under drought conditions. Under mild drought (MD) treatments, Aa and Pr increased the leaf number and plant height of hosts. Pr showed a significant beneficial influence on the wheat’s total biomass under all treatments, while Aa and Pp showed benefits only under the well-watered or MD treatment. The response mechanisms of DSE-inoculated wheat under stress may be due to the enhanced photosynthetic efficiency and antioxidant system. Generally, Pr had a stronger beneficial effect. The improved growth and fitness of the inoculated hosts under drought stress may reduce their water supply requirements during seedling growth. We speculate that inoculating wheat with this strain could be a promising approach for water-saving cultivation in arid environments.

Dark septate endophytes (DSE) commonly inhabit the root systems of plants that flourish in heavy metal-contaminated soils. Nevertheless, there is limited understanding regarding the overall response of medicinal plants to DSE under heavy metal stress. The present study utilized a non-sterile pot experiment to evaluate the beneficial impacts of DSE (Paraphoma chlamydocopiosa, Paraboeremia selaginellae, and Paraphoma radicina) inoculation on Astragalus mongholicus under cadmium (Cd) stress. At 0 mg Cd/kg soil, inoculation with DSE led to a significant increase in the total biomass of the host plant by up to 34.0%. Although plant biomass decreased at 5 mg Cd/kg soil and 10 mg Cd/kg soil, the total biomass of the host plant increased by up to 72.3% after DSE inoculation. The plant height, branch number, soil and plant analyzer development (SPAD) value, and biomass were not affected by Cd concentration after inoculation with P. chlamydocopiosa and P. selaginellae. DSE emerged as the most prominent explanatory variable (44.2%) for plant growth at 10 mg Cd/kg soil. Inoculation with P. chlamydocopiosa increased root length by 47.9% and root biomass by 74.1%, and inoculation with P. chlamydocopiosa and P. selaginellae increased the indole-3-acetic acid (IAA) content by 103.6% and 105.8%, respectively, at 10 mg Cd/kg soil. Additionally, P. radicina inoculation was preferred to increase the content of calycosin-7-O-glucoside, while P. chlamydocopiosa increased the content of formononetin. DSE enhanced the accumulation of Cd in the shoot, whereas P. radicina exhibited an inhibitory effect on Cd accumulation in the root system. P. chlamydocopiosa decreased the Cd translocation factor, while P. radicina increased the Cd translocation factor, which exceeded one. The interaction between DSE and soil factors significantly contributed to the host plant growth. DSE inoculation improved soil organic carbon content and inoculation with P. chlamydocopiosa, and P. selaginellae reduced available nitrogen content, regardless of the Cd stress. DSE inoculation reduced available phosphorus content at 10 mg Cd/kg soil. Importantly, P. radicina promote the performance and calycosin-7-O-glucoside accumulation of the host plant, and reduced Cd content in the roots at 5 mg Cd/kg soil. These data enhanced comprehension of the ecological function of DSE in heavy metal-contaminated soils and demonstrated the potential utility of DSE strains for cultivating medicinal plants.

Introduction: Exploring the interactions between dark septate endophytes (DSE) in plant roots across diverse heavy metal habitats—considering host plants, site characteristics, and microbial communities—provides insights into the distribution patterns of DSE in metal-rich environments and their mechanisms for developing heavy metal resistance.Methods: This study collected samples of three common plant species (Phragmites australis, PA, Setaria viridis, SV, and Artemisia annua, AA) and their corresponding soil samples from three heavy metal-contaminated sites: Baiyang Lake, BY, Fengfeng mining area, FF, and Huangdao, HD. Utilizing high-throughput sequencing and physicochemical analysis methods, the biological and abiotic factors affecting DSE colonization and distribution in the roots were investigated.Results: Twenty-two DSE species were isolated and identified with 11 species found in BY, 8 species in FF, and 11 species in HD. The screening for heavy metal resistance discovered 10 heavy metal-tolerant DSE species. Soil available phosphate, available nitrogen, and Cd contents, as well as the composition of different root fungal communities, influence the resistance and distribution of heavy metal-tolerant DSE. Notably, 12 DSE species, including Paraphoma radicina and Paraphoma chrysanthemicola, were reported for the first time in heavy metal habitats. The colonization rates of DSE in the roots of PA (96%) and AA (76%) were highest in BY, while the highest colonization rate in the roots of SV was observed in HD (94%). Site-specific soil parameters, such as available K, organic contents, Zn, and Cd contents from different sites are the main determinants affecting DSE colonization. Meanwhile, the diversity and richness of other root-associated endophytic fungi, which varied considerably across sites, served as significant biological factors influencing DSE distribution and colonization.Discussion: The results of this study provide a strong theoretical framework for the effective utilization of DSE fungi to mitigate soil heavy metal pollution.