The dark septate endophytic fungus Phialocephala fortinii is a potential decomposer of soil organic compounds and a promoter of Asparagus officinalis growth

Enhancing drought resistance in Pinus tabuliformis seedlings through root symbiotic fungi inoculation

Background

Drought constitutes a major abiotic stress factor adversely affecting plant growth and productivity. Plant-microbe symbiotic associations have evolved regulatory mechanisms to adapt to environmental stress conditions. However, the interactive effects of different fungi on host growth and stress tolerance under drought conditions remain unclear.

Objective

This study explored the effects of varying polyethylene glycol (PEG-6000) concentrations (0%, 15%, 25%, and 35%) on the growth and physiological responses of two ectomycorrhizal fungi (Suillus granulatus (Sg) and Pisolithus tinctorius (Pt)) and two dark septate endophytes (Pleotrichocladium opacum (Po) and Pseudopyrenochaeta sp. (Ps)) isolated from the root system of Pinus tabuliformis. Specifically, the study aimed to evaluate six inoculation treatments, including no inoculation (CK), single inoculations with Sg, Pt, Po, Ps, and a mixed inoculation (Sg: Pt : Po: Ps = 1:1:1:1), on the growth and physiological characteristics of P. tabuliformis seedlings under different water regimes: well-watered at 70% ± 5%, light drought at 50% ± 5%, and severe drought at 30% ± 5% of the maximum field water holding capacity.

Results

All four fungi exhibited the capacity to cope with drought stress by enhancing antioxidant activities and regulating osmotic balance. Upon successful root colonization, they increased plant height, shoot biomass, root biomass, total biomass, and mycorrhizal growth response in P. tabuliformis seedlings. Under drought stress conditions, fungal inoculation improved seedling drought resistance by increasing superoxide dismutase and catalase activities, free proline and soluble protein contents, and promoting nitrogen and phosphorus uptake. Notably, mixed inoculation treatments significantly enhanced antioxidant capacity, osmotic adjustment, and nutrient acquisition abilities, leading to superior growth promotion effects under drought stress compared to single inoculation treatments.

Conclusion

All four fungi tolerated PEG-induced drought stress, with increased antioxidant enzyme activities and osmotic adjustment substances and they promoted the growth and enhanced drought resistance of P. tabuliformis seedlings.

Enhancing boreal forest resilience: A four-year impact of biochar on soil quality and fungal communities

Boreal forests commonly suffer from nutrient deficiency due to restricted biological activity and decomposition. Biochar has been used as a promising strategy to improve soil quality, yet its impacts on forest soil microbes, particularly in cold environment, remains poorly understood. In this study, we investigated the effects of biochar, produced at different pyrolysis temperatures (500 °C and 650 °C) and applied at different amounts (0.5 kg·m-2 and 1.0 kg·m-2), on soil property, soil enzyme activity, and fungal community dynamics in a boreal forest over a span of two to four years. Our results showed that, four-year post-application of biochar produced at 650 °C and applied at 1.0 kg·m-2, significantly increased the relative abundance of Mortierellomycota and enhanced fungal species richness, α-diversity and evenness compared to the control (CK) (P < 0.05). Notably, the abundance of Phialocephala fortinii increased with the application of biochar produced at 500 °C and applied at 0.5 kg·m-2, exhibiting a positively correlation with the carbon cycling-related enzyme β-cellobiosidase. Functionally, distinct fungal gene structures were formed between different biochar pyrolysis temperatures, and between application amounts in four-year post-biochar application (P < 0.05). Additionally, correlation analyses revealed the significance of the duration post-biochar application on the soil properties, soil extracellular enzymes, soil fungal dominant phyla, fungal community and gene structures (P < 0.01). The interaction between biochar pyrolysis temperature and application amount significantly influenced fungal α-diversity (P < 0.01). Overall, these findings provide theoretical insights and practical application for biochar as soil amendment in boreal forest ecosystems.

Importance of Dark Septate Endophytes in Agriculture in the Face of Climate Change

Climate change is a notable challenge for agriculture as it affects crop productivity and yield. Increases in droughts, salinity, and soil degradation are some of the major consequences of climate change. The use of microorganisms has emerged as an alternative to mitigate the effects of climate change. Among these microorganisms, dark septate endophytes (DSEs) have garnered increasing attention in recent years. Dark septate endophytes have shown a capacity for mitigating and reducing the harmful effects of climate change in agriculture, such as salinity, drought, and the reduced nutrient availability in the soil. Various studies show that their association with plants helps to reduce the harmful effects of abiotic stresses and increases the nutrient availability, enabling the plants to thrive under adverse conditions. In this study, the effect of DSEs and the underlying mechanisms that help plants to develop a higher tolerance to climate change were reviewed.

Isolation, structural elucidation, and biological activity of a novel isocoumarin from the dark septate endophytic fungus Phialocephala fortinii

A novel isocoumarin was isolated from the mycelia of the dark septate endophytic fungus Phialocephala fortinii. The chemical structure was determined to be 8-hydroxy-6-methoxy-3,7-dimethyl-1H-2-benzopyran-1-one based on mass spectrometry, 1H-nuclear magnetic resonance (NMR), and 13C-NMR spectroscopic analyses, including 2D-NMR experiments. The isolated compound inhibited root growth of Arabidopsis thaliana, suggesting its potential as a plant growth regulator.

©Relationship between endophytic fungal diversity and colonization and soil factors of cultured blueberry roots in Guizhou Province, Southwest China

Dark septate endophytes (DSEs) inhabit plant roots and soil in ecosystems and host plants worldwide. DSE colonization is influenced by cultivars, soil factors, and specific habitat conditions. The regular diversity of DSEs in blueberries in Guizhou, China, is still unclear. In this study, four cultivars (Gardenblue, Powderblue, O'Neal, and Legacy) in three areas (Gaopo, Majiang, and Fenggang) in Guizhou were used to identify DSEs by morphological and molecular biological methods and to clarify the relationship between DSE diversity and DSE colonization and soil factors of cultivated blueberries in Guizhou. The DSEs isolated from cultivated blueberry roots in 3 areas in Guizhou Province were different, belonging to 17 genera, and the dominant genera were Penicillium, Phialocephala, and Thozetella. DSEs isolated from Majiang belonged to 12 genera and 16 species, those from Gaopo belonged to 7 genera and 15 species, and those from Fenggang belonged to 5 genera and 7 species. Among the different blueberry varieties, 11 genera were isolated from O'Neal, 12 genera were isolated from Powderblue, 11 genera were isolated from Legacy and 13 genera were isolated from Gardenblue. Coniochaeta is endemic to O'Neal, Chaetomium and Curvularia are endemic to Powderblue, and Thielavia is endemic to Legacy. Correlation analysis showed that DSE diversity was significantly correlated with DSE colonization and soil factors.

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Trees interact with a multitude of microbes through their roots and root symbionts such as mycorrhizal fungi and root endophytes. Here, we explore the role of fungal root symbionts as predictors of the soil and root-associated microbiomes of widespread broad-leaved trees across a European latitudinal gradient. Our results suggest that, alongside factors such as climate, soil, and vegetation properties, root colonization by ectomycorrhizal, arbuscular mycorrhizal, and dark septate endophytic fungi also shapes tree-associated microbiomes. Notably, the structure of root and soil microbiomes across our sites is more strongly and consistently associated with dark septate endophyte colonization than with mycorrhizal colonization and many abiotic factors. Root colonization by dark septate endophytes also has a consistent negative association with the relative abundance and diversity of nutrient cycling genes. Our study not only indicates that root-symbiotic interactions are an important factor structuring soil communities and functions in forest ecosystems, but also that the hitherto less studied dark septate endophytes are likely to be central players in these interactions.

Morphogenesis and metabolomics reveal the compatible relationship among Suillus bovinus, Phialocephala fortinii, and their co-host, Pinus massoniana

Ectomycorrhizal (ECM) fungi and dark septate endophytes (DSEs) can both form a symbiotic relationship with the same host plant. However, the interactions that occur among these two types of fungi and their co-hosts are largely unknown. Here, we investigated interactions that occur among the ECM fungus Suillus bovinus, the DSE Phialocephala fortinii, and their co-host Pinus massoniana. We used both scanning electron microscopy and optical microscopy to characterize the morphogenesis of the two symbionts and employed the ultra-high-performance liquid chromatography-tandem mass spectrometry technique to assess the effects of fungal inoculation on the root metabolome. Under pure culture conditions, no synergistic or antagonistic effects were observed between Phi. fortinii and S. bovinus. Generally, S. bovinus and Phi. fortinii can simultaneously colonize P. massoniana roots without affecting each other's symbiotic processes. S. bovinus can colonize the root locus where Phi. fortinii has already invaded but not vice versa, which may be due to the physical barrier effect of the mantle. Both fungi can significantly promote the growth of P. massoniana, and they have a synergistic effect on host N and K uptake. Metabolite accumulation patterns in roots inoculated with Phi. fortinii and/or S. bovinus were greatly altered, especially with respect to organic acids, flavonoids, lipids, and phenolic acids. S. bovinus inoculation significantly enhanced root flavonoid biosynthesis, whereas Phi. fortinii and dual-inoculation treatments mainly induced phenylpropanoid biosynthesis. These findings reveal compatible relationships among P. massoniana, S. bovinus, and Phi. fortinii, and suggest a theoretical basis for ECM fungi and DSE co-application when cultivating seedlings. IMPORTANCE The prevalence of both ectomycorrhizal fungi and dark septate endophytes in the roots of a wide spectrum of tree species is well recognized. In this study, we investigated the interactions that occur among the ECM fungus S. bovinus, the DSE Phi. fortinii, and their co-host, P. massoniana. The two fungi can simultaneously colonize P. massoniana roots without affecting each other's symbiotic processes. S. bovinus appears to be superior to Phi. fortinii in microniche competition, which may be due to the physical barrier effect of the mantle. The two fungi have different effects on root metabolite accumulation patterns. S. bovinus inoculation significantly enhanced root flavonoid biosynthesis, whereas Phi. fortinii and dual-inoculation treatments mainly induced phenylpropanoid biosynthesis. This is the first study revealing the morphological and metabolic mechanisms that contribute to the compatible relationship among ECM fungi, DSEs, and their co-host.

Effects of Phosphorus-dissolving Dark Septate Endophytes on the Growth of Blueberry

Dark septate endophytes (DSEs) are widely distributed and improve plant growth. DSEs secrete large amounts of enzymes to mineralize insoluble phosphorus in soil and convert it into soluble phosphorus, promoting plant uptake of phosphorus. However, the effects of DSEs with phosphate-solubilizing ability on host plants need further study. In this study, phosphorus-dissolving DSEs were screened for growth-promoting effects. We isolated, identified and characterized three DSE species (Thozetella neonivea, Pezicula ericae and Hyaloscyphaceae sp.) showing phosphate-solubilizing ability. The impact of single, dual or triple inoculation of DSEs on blueberry plant characteristics was studied. Their effects on colonization intensity, seedling biomass, nutrients in plants and soil, and activities of plant resistance enzymes and soil enzymes were markedly upregulated relative to the control (P < 0.05). The available phosphorus and acid phosphatase levels in different combinations were significantly increased. These findings indicate that the application of the three DSEs may be valuable in facilitating the cultivation of blueberry with a higher biomass and improved plant quality.

Endophytic fungi mediates production of bioactive secondary metabolites via modulation of genes involved in key metabolic pathways and their contribution in different biotechnological sector

Endophytic fungi stimulate the production of an enormous number of bioactive metabolites in medicinal plants and affect the different steps of biosynthetic pathways of these secondary metabolites. Endophytic fungi possess a number of biosynthetic gene clusters that possess genes for various enzymes, transcription factors, etc., in their genome responsible for the production of secondary metabolites. Additionally, endophytic fungi also modulate the expression of various genes responsible for the synthesis of key enzymes involved in metabolic pathways of such as HMGR, DXR, etc. involved in the production of a large number of phenolic compounds as well as regulate the expression of genes involved in the production of alkaloids and terpenoids in different plants. This review aims to provide a comprehensive overview of gene expression related to endophytes and their impact on metabolic pathways. Additionally, this review will emphasize the studies done to isolate these secondary metabolites from endophytic fungi in large quantities and assess their bioactivity. Due to ease in synthesis of secondary metabolites and their huge application in the medical industry, these bioactive metabolites are now being extracted from strains of these endophytic fungi commercially. Apart from their application in the pharmaceutical industry, most of these metabolites extracted from endophytic fungi also possess plant growth-promoting ability, bioremediation potential, novel bio control agents, sources of anti-oxidants, etc. The review will comprehensively shed a light on the biotechnological application of these fungal metabolites at the industrial level.

Contribution of Arbuscular Mycorrhizal and Endophytic Fungi to Drought Tolerance in Araucaria araucana Seedlings

In its natural distribution, Araucaria araucana is a plant species usually exposed to extreme environmental constraints such as wind, volcanism, fires, and low rainfall. This plant is subjected to long periods of drought, accentuated by the current climate emergency, causing plant death, especially in its early growth stages. Understanding the benefits that both arbuscular mycorrhizal fungi (AMF) and endophytic fungi (EF) could provide plants under different water regimes would generate inputs to address the above-mentioned issues. Here, the effect of AMF and EF inoculation (individually and combined) on the morphophysiological variables of A. araucana seedlings subjected to different water regimes was evaluated. Both the AMF and EF inocula were obtained from A. araucana roots growing in natural conditions. The inoculated seedlings were kept for 5 months under standard greenhouse conditions and subsequently subjected to three different irrigation levels for 2 months: 100, 75, and 25% of field capacity (FC). Morphophysiological variables were evaluated over time. Applying AMF and EF + AMF yielded a noticeable survival rate in the most extreme drought conditions (25% FC). Moreover, both the AMF and the EF + AMF treatments promoted an increase in height growth between 6.1 and 16.1%, in the production of aerial biomass between 54.3 and 62.6%, and in root biomass between 42.5 and 65.4%. These treatments also kept the maximum quantum efficiency of PSII (Fv/Fm 0.71 for AMF and 0.64 for EF + AMF) stable, as well as high foliar water content (>60%) and stable CO₂ assimilation under drought stress. In addition, the EF + AMF treatment at 25% FC increased the total chlorophyll content. In conclusion, using indigenous strains of AMF, alone or in combination with EF, is a beneficial strategy to produce A. araucana seedlings with an enhanced ability to tolerate prolonged drought periods, which could be of great relevance for the survival of these native species under the current climate change.

Effect of Coal Mining on Soil Microorganisms from Stipa krylovii Rhizosphere in Typical Grassland

The environmental changes caused by coal mining activities caused disturbances to the plant, soil, and microbial health in the mining area. Arbuscular mycorrhizal fungi (AMF) play an important role in the ecological restoration of mining areas. However, it is less understood how soil fungal communities with multiple functional groups respond to coal mining, and the quantitative impact and risk of mining disturbance. Therefore, in this study, the effect of coal mining on soil microorganisms' composition and diversity were analyzed near the edge of an opencast coal-mine dump in the Shengli mining area, Xilingol League, Inner Mongolia. The response strategy of soil fungi to coal mining and the stability of arbuscular mycorrhizal fungi (AMF) in the soil fungal community were determined. Our results showed that coal mining affected AMF and soil fungi in areas within 900 m from the coal mine. The abundance of endophytes increased with the distance between sampling sites and the mine dump, whereas the abundance of saprotroph decreased with the distance between sampling sites and the mine dump. Saprotroph was the dominant functional flora near the mining area. The nodes percentage of Septoglomus and Claroideoglomus and AMF phylogenetic diversity near the mining area were highest. AMF responded to the mining disturbance via the variety and evolution strategy of flora. Furthermore, AMF and soil fungal communities were significantly correlated with edaphic properties and parameters. Soil available phosphorus (AP) was the main influencer of soil AMF and fungal communities. These findings evaluated the risk range of coal mining on AMF and soil fungal communities and elucidated the microbial response strategy to mining disturbance.

The dark septate endophyte Phialocephala sphaeroides suppresses conifer pathogen transcripts and promotes root growth of Norway spruce

Plant-associated microbes including dark septate endophytes (DSEs) of forest trees play diverse functional roles in host fitness including growth promotion and increased defence. However, little is known about the impact on the fungal transcriptome and metabolites during tripartite interaction involving plant host, endophyte and pathogen. To understand the transcriptional regulation of endophyte and pathogen during co-infection, Norway spruce (Picea abies) seedlings were infected with DSE Phialocephala sphaeroides, or conifer root-rot pathogen Heterobasidion parviporum, or both. Phialocephala sphaeroides showed low but stable transcripts abundance (a decrease of 40%) during interaction with Norway spruce and conifer pathogen. By contrast, H. parviporum transcripts were significantly reduced (92%) during co-infection. With RNA sequencing analysis, P. sphaeroides experienced a shift from cell growth to anti-stress and antagonistic responses, while it repressed the ability of H. parviporum to access carbohydrate nutrients by suppressing its carbohydrate/polysaccharide-degrading enzyme machinery. The pathogen on the other hand secreted cysteine peptidase to restrict free growth of P. sphaeroides. The expression of both DSE P. sphaeroides and pathogen H. parviporum genes encoding plant growth promotion products were equally detected in both dual and tripartite interaction systems. This was further supported by the presence of tryptophan-dependent indolic compound in liquid culture of P. sphaeroides. Norway spruce and Arabidopsis seedlings treated with P. sphaeroides culture filtrate exhibited auxin-like phenotypes, such as enhanced root hairs, and primary root elongation at low concentration but shortened primary root at high concentration. The results suggested that the presence of the endophyte had strong repressive or suppressive effect on H. parviporum transcripts encoding genes involved in nutrient acquisition.

The Role of Phialocephala fortinii in Improving Plants' Phosphorus Nutrition: New Puzzle Pieces

Plants' mineral nutrition in acidic soils can be facilitated by phosphate solubilizing fungi inhabiting the root systems of these plants. We attempt to find dark septate endophyte (DSE) isolates in the roots of wild-heather plants, which are capable of improving plants' phosphorus nutrition levels. Bright-field and confocal laser scanning microscopy were used for the visualization of endophytes. A model system of co-cultivation with Vaccinium macrocarpon Ait. was used to study a fungal isolate's ability to supply plants with phosphorus. Fungal phytase activity and phosphorus content in plants were estimated spectrophotometrically. In V. vitis-idaea L. roots, we obtained a Phialocephala fortinii Wang, Wilcox DSE2 isolate with acid phytase activity (maximum 6.91 ± 0.17 U on 21st day of cultivation on potato-dextrose broth medium) and the ability to accumulate polyphosphates in hyphae cells. The ability of the isolate to increase both phosphorus accumulation and biomass in V. macrocarpon is also shown. The data obtained for the same isolate, as puzzle pieces put together, indicate the possible mediation of P. fortinii DSE2 isolate in the process of phosphorus intake from inorganic soil reserves to plants.

Effects of nitrogen addition and root fungal inoculation on the seedling growth and rhizosphere soil microbial community of Pinus tabulaeformis

Nitrogen (N) availability is significant in different ecosystems, but the response of forest plant-microbial symbionts to global N deposition remains largely unexplored. In this study, the effects of different N concentration levels on four types of fungi, Suillus granulatus (Sg), Pisolithus tinctorius (Pt), Pleotrichocladium opacum (Po), and Pseudopyrenochaeta sp. (Ps), isolated from the roots of Pinus tabulaeformis were investigated in vitro. Then, the effects of the fungi on the growth performance, nutrient uptake, and rhizosphere soil microbial community structure of P. tabulaeformis under different N addition conditions (0, 40, and 80 kg hm⁻² year⁻¹) were examined. The biomass and phytohormone contents of the Sg, Pt and Po strains increased with increasing N concentration, while those of the Ps strain first increased and then decreased. All four fungal strains could effectively colonize the plant roots and form a strain-dependent symbiosis with P. tabulaeformis. Although the effects depended on the fungal species, the growth and root development of inoculated seedlings were higher than those of uninoculated seedlings under N deficiency and normal N supply conditions. However, these positive effects disappeared and even became negative under high N supply conditions. The inoculation of the four fungal strains also showed significant positive effects on the shoot and root nutrient contents of P. tabulaeformis. Fungal inoculation significantly increased different microbial groups and the total soil microorganisms but decreased the microbial diversity under N deficiency stress. In summary, exogenous symbiotic fungal inoculations could increase the growth performance of P. tabulaeformis under N deficiency and normal N supply conditions, but the effects were negative under excessive N addition.

Plant association with dark septate endophytes: When the going gets tough (and stressful), the tough fungi get going

Dark septate endophytes (DSEs) comprise a diverse and ubiquitous group of fungal generalists with broad habitat niches that robustly colonize the roots of plants in stressful environments. DSEs possess adaptation strategies that determine their high tolerance to heavy metal (HM) contamination, drought, and salinity. Most DSEs developed efficient melanin-dependent and melanin-independent mechanisms of HM detoxification and osmoprotection, including intracellular immobilization and extracellular efflux of HMs and excess ions, and the scavenging of reactive oxygen species. DSEs form mutualistic relationship with plants according to the hypothesis of "habitat-adapted associations", supporting the survival of their hosts under stressful conditions. As saprophytes, DSEs mineralize a complex soil substrate improving plants' nutrition and physiological parameters. They can protect the host plant from HMs by limiting HM accumulation in plant tissues and causing their sequestration in root cell walls as insoluble compounds, preventing further HM translocation to shoots. The presence of DSE in drought-affected plants can substantially ameliorate the physiology and architecture of root systems, improving their hydraulic properties. Plant growth-promoting features, supported by the versatility and easy culturing of DSEs, determine their high potential to enhance phytoremediation and revegetation projects for HM-contaminated, saline, and desertic lands reclamation.

Effects of Dark Septate Endophytes on the Performance and Soil Microbia of Lycium ruthenicum Under Drought Stress

In the current study, we explored the effects of dark septate endophytes (DSE) (Neocamarosporium phragmitis, Alternaria chlamydospore, and Microascus alveolaris) on the performance and rhizosphere soil microbial composition of Lycium ruthenicum Murr under drought stress. Differences in plant growth and physiological indexes, soil parameters, and microbial composition under different treatments were studied. Three DSE species could form good symbiotic relationships with L. ruthenicum plants, and the symbionts depended on DSE species and water availability. Inoculation of DSE had the greatest benefit on host plants under drought conditions. In particular, N. phragmitis and A. chlamydospore had a significant positive influence on the biomass, morphological and physiological indexes of host plants. Additionally, the content of arbuscular mycorrhiza (AM) fungi, gram-negative bacteria, and actinomycetes in the soil was significantly elevated after DSE inoculation in the absence of water. Based on a variance decomposition analysis, DSE was the most important factor affecting the growth and physiological parameters of host plants, and DSE inoculation combined with water conditions significantly affected the contents of soil microbial communities. Structural equation model (SEM) analysis showed that the positive effects of DSE on L. ruthenicum varied with DSE species and plant parameters under different water conditions. These results are helpful to understand the ecological function of DSE and its potential application in the cultivation of L. ruthenicum plants in drylands.

The dark septate endophyte Phialocephala sphaeroides confers growth fitness benefits and mitigates pathogenic effects of Heterobasidion on Norway spruce

Forest trees frequently interact with a diverse range of microorganisms including dark septate endophytes (DSEs) and fungal pathogens. Plant defense responses to either individual pathogens or endophytes have been widely studied, but very little is known on the effect of coinfection on host defenses. To study the impact of coinfection or tripartite interaction on plant growth and host defenses, Norway spruce (Picea abies (L.) Karst) seedlings were inoculated with a DSE Phialocephala sphaeroides or with a root pathogen Heterobasidion parviporum Niemela & Korhonen or coinfected with both fungi. The results showed that the DSE promoted the root growth of spruce seedlings. Control seedlings without any inoculum were subjected to sequencing and used as a baseline for identification of differentially expressed genes (DEGs). RNA-seq analysis of seedlings inoculated with P. sphaeroides, infected with H. parviporum or coinfected with both fungi resulted in a total of 5269 DEGs. The majority of DEGs were found in P. sphaeroides-inoculated seedlings. Lignin biosynthesis pathways were generally activated during fungal infections. The pattern was distinct with endophyte inoculation. The majority of the genes in the flavonoid biosynthesis pathway were generally suppressed during fungal infections. A specific transcriptional response to P. sphaeroides inoculation was the increased transcripts of genes involved in jasmonic acid biosynthesis, mitogen-activated protein kinases signaling pathway, plant hormone signal transduction and calcium-mediated signaling. This may have potentially contributed to promoting the root growth of seedlings. Although the coinfection suppressed the induction of numerous genes, no negative effect on the growth of the spruce seedlings occurred. We conclude that the subsequent H. parviporum infection triggered reprogramming of host metabolism. Conversely, the endophyte (P. sphaeroides), on the other hand, counteracted the negative effects of H. parviporum on the growth of the spruce seedlings.

Dark septate endophytes: mutualism from by-products?

Plant roots are abundantly colonized by dark septate endophytic (DSE) fungi in virtually all ecosystems. DSE fungi are functionally heterogeneous and their relationships with plants range from antagonistic to mutualistic. Here, we consider the role of by-product benefits in DSE and other root-fungal symbioses. We compared host investments against symbiont-derived benefits for the host plant and categorized these benefits as by-products or benefits requiring reciprocal investment from the host. By-product benefits may provide the variability required for the evolution of invested mutualisms between the host and symbiont. We suggest that DSE could be considered as 'a by-product mutualist transitional phase' in the evolution of cooperative mycorrhizal symbionts from saprotrophic fungi.

Dual inoculation of dark septate endophytes and Trichoderma viride drives plant performance and rhizosphere microbiome adaptations of Astragalus mongholicus to drought

Rhizosphere microbiome adapts their structural compositions to water scarcity and have the potential to mitigate drought stress of plants. To unlock this potential, it is crucial to understand community responses to drought in the interplay between soil properties, water management and exogenous microbes interference. Inoculation with dark septate endophytes (DSE) (Acrocalymma vagum, Paraboeremia putaminum) and Trichoderma viride on Astragalus mongholicus grown in the non-sterile soil was exposed to drought. Rhizosphere microbiome were assessed by Illumina MiSeq sequencing of the 16S and ITS2 rRNA genes. Inoculation positively affected plant growth depending on DSE species and water regime. Ascomycota, Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes were the dominant phyla. The effects of dual inoculation on bacterial community were greater than those on fungal community, and combination of P. putaminum and T. viride exerted a stronger impact on the microbiome under drought stress. The observed changes in soil factors caused by inoculation could be explained by the variations in microbiome composition. Rhizosphere microbiome mediated by inoculation exhibited distinct preferences for various growth parameters. These findings suggest that dual inoculation of DSE and T. viride enriched beneficial microbiota, altered soil nutrient status and might contribute to enhance the cultivation of medicinal plants in dryland agriculture.

Fungal Endophyte: An Interactive Endosymbiont With the Capability of Modulating Host Physiology in Myriad Ways

Endophytic fungi ubiquitously dwell inside the tissue-spaces of plants, mostly asymptomatically. They grow either intercellularly or intracellularly in a particular host plant to complete the whole or part of their life cycle. They have been found to be associated with almost all the plants occurring in a natural ecosystem. Due to their important role in the survival of plants (modulate photosynthesis, increase nutrient uptake, alleviate the effect of various stresses) they have been selected to co-evolve with their hosts through the course of evolution. Many years of intense research have discovered their tremendous roles in increasing the fitness of the plants in both normal and stressed conditions. There are numerous literature regarding the involvement of various endophytic fungi in enhancing plant growth, nutrient uptake, stress tolerance, etc. But, there are scant reports documenting the specific mechanisms employed by fungal endophytes to manipulate plant physiology and exert their effects. In this review, we aim to document the probable ways undertaken by endophytic fungi to alter different physiological parameters of their host plants. Our objective is to present an in-depth elucidation about the impact of fungal endophytes on plant physiology to make this evolutionarily conserved symbiotic interaction understandable from a broader perspective.

Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network

Permafrost-affected soil stores a significant amount of organic carbon. Identifying the biological constraints of soil organic matter transformation, e.g., the interaction of major soil microbial soil organic matter decomposers, is crucial for predicting carbon vulnerability in permafrost-affected soil. Fungi are important players in the decomposition of soil organic matter and often interact in various mutualistic relationships during this process. We investigated four different soil horizon types (including specific horizons of cryoturbated soil organic matter (cryoOM)) across different types of permafrost-affected soil in the Western Canadian Arctic, determined the composition of fungal communities by sequencing (Illumina MPS) the fungal internal transcribed spacer region, assigned fungal lifestyles, and by determining the co-occurrence of fungal network properties, identified the topological role of keystone fungal taxa. Compositional analysis revealed a significantly higher relative proportion of the litter saprotroph Lachnum and root-associated saprotroph Phialocephala in the topsoil and the ectomycorrhizal close-contact exploring Russula in cryoOM, whereas Sites 1 and 2 had a significantly higher mean proportion of plant pathogens and lichenized trophic modes. Co-occurrence network analysis revealed the lowest modularity and average path length, and highest clustering coefficient in cryoOM, which suggested a lower network resistance to environmental perturbation. Zi-Pi plot analysis suggested that some keystone taxa changed their role from generalist to specialist, depending on the specific horizon concerned, Cladophialophora in topsoil, saprotrophic Mortierella in cryoOM, and Penicillium in subsoil were classified as generalists for the respective horizons but specialists elsewhere. The litter saprotrophic taxon Cadophora finlandica played a role as a generalist in Site 1 and specialist in the rest of the sites. Overall, these results suggested that fungal communities within cryoOM were more susceptible to environmental change and some taxa may shift their role, which may lead to changes in carbon storage in permafrost-affected soil.

Re-vitalizing of endophytic microbes for soil health management and plant protection

Soil health management and increase crop productivity are challenging issues for researchers and scientists. Many research publications have given multiple technological solutions for improving soil health and crop productivity but main problem is sustainability of those technologies under field condition and different agro-climatic zone. Due to the random industrialization, deforestation, mining and other environmental factor reduce soil fertility and human health. Many alternative options e.g., crop rotation, green manuring, integrated farming, biofertilizer (plant-growth-promoting microorganism, microbial consortium of rhizosphere soils), and vermicomposting are available for adapting and improving the soil heath and crop productivity by farmers. Recent trends of new research dimension for sustainable agriculture, endophytic microbes and its consortium is one of the better alternative for increasing crop productivity, soil health and fertility management. However, current trends are focuses on the endophytic microbes, which are present mostly in all plant species. Endophytic microbes are isolated from plant parts-root, shoot, leaf, flower and seeds which have very potential ability of plant growth promotion and bio-controlling agent for enhancing plant growth and development. Mostly plant endophytes showed multi-dimensional (synergistic, mutualistic, symbiotic etc.) interactions within the host plants. It promotes the plant growth, protects from pathogen, and induces resistance against biotic and abiotic environmental stresses, and improves the soil fertility. Till date, most of the scientific research has been done on assuming that interaction of plant endophytes with the host is similar like the plant-growth-promoting microorganism (PGPM). It would be very interesting to explore the functional properties of plant endophytes to modulate the essential gene expression during biotic and abiotic stresses. Endophytes have the ability to induce the soil fertility by improving soil essential nutrient, enzymatic activity and influence the other physiochemical property. In this study, we have discussed details about functional properties of plant endophytes and their mechanism for enhancing plant productivity and soil health and fertility management under climate-resilient agricultural practices. Our main objective is to promote and explore the beneficial plant endophytes for enhancing sustainable agricultural productivity.

Response of ectomycorrhizal and other Pinus sylvestris root-associated fungi to the load of allochthonous material from a great cormorant colony

Colonies of piscivorous birds nesting in forests bring in loads of allochthonous material in amounts significantly exceeding atmospheric depositions, eventually causing major ecosystem changes. We studied the effect of increasing ornithogenic impact on ectomycorrhizal (EMF) and other root-associated fungi in a Scots pine forest affected by a colony of great cormorants. We evaluated quantitative data of ectomycorrhiza (numbers of root tips and morphotypes) and identified fungal species from pine root tips and from sporocarps collected in three designated study zones: D (zone of active nesting), E (colony margin), and G (pristine forest). Species-bearing sporocarps were absent in zone D, and their number steadily decreased in zone E and was significantly lower than in zone G. Species communities and occurrence frequencies of individual species differed significantly between the zones. Environmental factors, both directly (nutrient addition) and indirectly (changes in vegetation cover), associated with bird activity have significantly influenced fungal communities. We hypothesize that the first signs of increased avian impact on root-associated fungi are the reduced diversity of sporocarps and the low presence and diversity of boletoid fungi in root tips.

Dark Septate Endophytes Isolated From Wild Licorice Roots Grown in the Desert Regions of Northwest China Enhance the Growth of Host Plants Under Water Deficit Stress

This study aimed to explore dark septate endophytes (DSE) that may improve the cultivation of medicinal plants in arid ecosystems. We isolated and identified eight DSE species (Acremonium nepalense, Acrocalymma vagum, Alternaria chartarum, Alternaria chlamydospora, Alternaria longissima, Darksidea alpha, Paraphoma chrysanthemicola, and Preussia terricola) colonizing the roots of wild licorice (Glycyrrhiza uralensis) in the desert areas of northwest China. Moreover, we investigated the osmotic stress tolerance of the DSE using pure culture, along with the performance of licorice plants inoculated with the DSE under drought stress in a growth chamber, respectively. Here, five species were first reported in desert habitats. The osmotic-stress tolerance of DSE species was highly variable, A. chlamydospora and P. terricola increased the total biomass and root biomass of the host plant. All DSE except A. vagum and P. chrysanthemicola increased the glycyrrhizic acid content; all DSE except A. chartarum increased the glycyrrhizin content under drought stress. DSE × watering regimen improved the glycyrrhizic acid content, soil organic matter, and available nitrogen. Structural equation model analysis showed that DSE × watering regimen positively affected soil organic matter, and total biomass, root length, glycyrrhizic acid, and glycyrrhizin (Shapotou site); and positively affected soil organic matter, available phosphorus, and glycyrrhizin (Minqin site); and positively affected the root length (Anxi site). DSE from the Shapotou site accounted for 8.0, 13.0, and 11.3% of the variations in total biomass, root biomass, and active ingredient content; DSE from the Minqin site accounted for 6.6 and 8.3% of the variations in total biomass and root biomass; DSE from the Anxi site accounted for 4.2 and 10.7% of the variations in total biomass and root biomass. DSE × watering regimen displayed a general synergistic effect on plant growth and active ingredient contents. These findings suggested that the DSE-plant interactions were affected by both DSE species and DSE originating habitats. As A. chlamydospora and P. terricola positively affected the total biomass, root biomass, and active ingredient content of host plants under drought stress, they may have important uses as promoters for the cultivation of licorice in dryland agriculture.

Dark septate endophytes isolated from non-hyperaccumulator plants can increase phytoextraction of Cd and Zn by the hyperaccumulator Noccaea caerulescens

Dark septate endophytes (DSEs) can improve plant stress tolerance by promoting growth and affecting element accumulation. Due to its ability to accumulate high Cd, Zn, and Ni concentrations in its shoots, Noccaea caerulescens is considered a promising candidate for phytoextraction in the field. However, the ability of DSEs to improve trace element (TE) phytoextraction with N. caerulescens has not yet been studied. The aim of this study was therefore to determine the ability of five DSE strains, previously isolated from poplar roots collected at different TE-contaminated sites, to improve plant development, mineral nutrient status, and metal accumulation by N. caerulescens during a pot experiment using two soils differing in their level of TE contamination. Microscopic observations revealed that the tested DSE strains effectively colonised the roots of N. caerulescens. In the highly contaminated (HC) soil, a threefold increase in root biomass was found in plants inoculated with the Leptodontidium sp. Pr30 strain compared to that in the non-inoculated condition; however, the plant nutrient status was not affected. In contrast, the two strains Phialophora mustea Pr27 and Leptodontidium sp. Me07 had positive effects on the mineral nutrient status of plants without significantly modifying their biomass. Compared to non-inoculated plants cultivated on HC soil, Pr27- and Pr30-inoculated plants extracted more Zn (+ 30%) and Cd (+ 90%), respectively. In conclusion, we demonstrated that the responses of N. caerulescens to DSE inoculation ranged from neutral to beneficial and we identified two strains (i.e. Leptodontidium sp. (Pr30) and Phialophora mustea (Pr27)) isolated from poplar that appeared promising as they increased the amounts of Zn and Cd extracted by improving plant growth and/or TE accumulation by N. caerulescens. These results generate interest in further characterising the DSEs that naturally colonise N. caerulescens and testing their ability to improve phytoextraction.

Screening fungal endophytes from a wild grass for growth promotion in tritordeum, an agricultural cereal

Celtica gigantea(= Stipa gigantea) is a large perennial grass which grows in nutrient-poor sandy soils in semiarid zones of the western Iberian Peninsula. The purpose of this work was to find out if culturable fungal symbionts isolated from roots of this wild grass could have growth promoting activity in tritordeum, a hybrid cereal for human consumption. A survey of fungi from the root endosphere of C. gigantea produced an isolate collection consisting of 60 different taxa, mostly ascomycetes. Fungal strains were inoculated into tritordeum plants in order to evaluate their effect in leaf and root biomass, nutrient content, and total antioxidant capacity. Two consecutive screening processes were made to test endophyte effects in plants. In the first screening, 66 strains were inoculated into seedlings by dipping roots in a liquid suspension of inoculum. In the second screening, 13 strains selected from the first screening were inoculated by sowing seeds in a substrate containing inoculum. The inoculation method used in the second screening involved less labor and plant manipulation and improved the quantity and quality of the inoculum, making it more appropriate for big scale experimental inoculation procedures. Several fungal strains promoted leaf or root growth. In particular, a strain belonging to the genus Diaporthe caused an increase in leaf and root biomass in both screening processes, suggesting that this endophyte might have a good potential for field application in tritordeum.

Fungal Symbionts Enhance N-Uptake for Antarctic Plants Even in Non-N Limited Soils

Plant-fungi interactions have been identified as fundamental drivers of the plant host performance, particularly in cold environments where organic matter degradation rates are slow, precisely for the capacity of the fungal symbiont to enhance the availability of labile nitrogen (N) in the plant rhizosphere. Nevertheless, these positive effects appear to be modulated by the composition and amount of the N pool in the soil, being greater when plant hosts are growing where N is scarce as is the case of Antarctic soils. Nevertheless, in some coastal areas of this continent, seabirds and marine mammal colonies exert, through their accumulated feces and urine a strong influence on the edaphic N content surrounding their aggregation points. To evaluate if the fungal symbionts (root endophytes), associated to the only two Antarctic vascular plants Colobanthus quitensis and Deschampsia antarctica, act as N-uptake enhancers, even in such N-rich conditions as those found around animal influence, we assessed, under controlled conditions, the process of N mineralization in soil by the accumulation of NH4 + in the rizhosphere and the biomass accumulation of plants with (E+) and without (E-) fungal symbionts. Complementarily, taking advantage of the isotopic N-fractionation that root-fungal symbionts exert on organic N molecules during its acquisition process, we also determined if endophytes actively participate in the Antarctic plants N-uptake, when inorganic N is not a limiting factor, by estimating the δ15N isotopic signatures in leaves. Overall, symbiotic interaction increased the availability of NH4 + in the rhizosphere of both species. As expected, the enhanced availability of inorganic N resulted in a higher final biomass in E + compared with E- plants of both species. In addition, we found that the positive role of fungal symbionts was also actively linked to the process of N-uptake in both species, evidenced by the contrasting δ15N signatures present in E+ (-0.4 to -2.3‰) relative to E- plants (2.7-3.1‰). In conclusion, despite being grown under rich N soils, the two Antarctic vascular plants showed that the presence of root-fungal endophytes, furthermore enhanced the availability of inorganic N sources in the rhizosphere, has a positive impact in their biomass, remarking the active participation of these endophytes in the N-uptake process for plants inhabiting the Antarctic continent.

Dark Septate Endophytic Fungi Associated with Sugarcane Plants Cultivated in São Paulo, Brazil

Dark septate endophytes (DSEs) constitute a polyphyletic group within the Ascomycota, with global distribution and a wide range of host plant species. The present study evaluated the diversity of DSE in sugarcane roots of the varieties RB867515, RB966928, and RB92579, and four varieties of not commercialized energy cane. A total of 16 DSE strains were isolated, mostly from the varieties RB966928 and RB867515, with six and five isolates, respectively. Just one of the four energy cane varieties had fungi with DSE appearance. The analyses of the DNA sequences from the internal transcribed spacer (ITS) and the large subunit (LSU), in association with the micromorphology of the isolates, allowed the differentiation of the 16 isolates in at least five species, within the families Periconiaceae, Pleosporaceae, Lentitheciaceae, Vibrisseaceae, and Apiosporaceae and the orders Pleosporales, Helotiales, and Xylariales. The order Pleosporales represented 80% of the isolates, and the species Periconia macrospinosa, with six isolates, accounted for the highest isolation frequency. The results confirm the natural occurrence of the DSE symbiosis in sugarcane varieties and the generalist character of these fungi as some of the detected species have already been reported associated with other host plants, ecosystems, and regions of the world.

Effects of Dark Septate Endophytes Strain A024 on Damping-off Biocontrol, Plant Growth and the Rhizosphere Soil Enviroment of Pinus sylvestris var. mongolica Annual Seedlings

Dark septate endophytes (DSEs) exert a vital role in promoting plant growth, improving mineral absorption, biological disease control, and enhancing plant stress resistance. The effects of dark septate endophyte strain, Phialocephala bamuru A024 on damping-off biocontrol, plant development, nutrients within the rhizosphere soil, as well as bacterial communities in the annual seedlings of P. sylvestris var. Mongolica were studied. According to our findings, following P. bamuru A024 inoculation, the damping-off disease morbidity decreased significantly compared with control, some physiological indices such as β-1,3-glucanase, chitinase enzyme activity as well as a soluble protein and proline content in P. sylvestris var. mongolica were elevated under R. solani stress. After inoculation with P. bamuru A024, the biomass in seedlings, nutrients in soil, root structure index, together with activities of soil enzymes were remarkably up-regulated relative to control (p < 0.05). As suggested by the results of high-throughput sequencing, the microbial structure in the rhizosphere soil of the P. sylvestris var. mongolica showed significant differences (p < 0.05) after P. bamuru A024 inoculation compared to control treatment and the rhizosphere soil bacterial community structure after DSE A024 inoculation was positively correlated to the main soil nutrition indices.

Plant performance of enhancing licorice with dual inoculating dark septate endophytes and Trichoderma viride mediated via effects on root development

BACKGROUND

This study aimed to assess whether licorice (Glycyrrhiza uralensis) can benefit from dual inoculation by Trichoderma viride and dark septate endophytes (DSE) isolated from other medicinal plants.

METHODS

First, we isolated and identified three DSE (Paraboeremia putaminum, Scytalidium lignicola, and Phoma herbarum) and Trichoderma viride from medicinal plants growing in farmland of China. Second, we investigated the influences of these three DSE on the performance of licorice at different T. viride densities (1 × 106, 1 × 107, and 1 × 108 CFU/mL) under sterilised condition in a growth chamber.

RESULTS

Three DSE strains could colonize the roots of licorice, and they established a positive symbiosis with host plants depending on DSE species and T. viride densities. Inoculation of P. putaminum increased the root biomass, length, surface area, and root:shoot ratio. S. lignicola increased the root length, diameter and surface area and decreased the root:shoot ratio. P. herbarum increased the root biomass and surface area. T. viride increased the root biomass, length, and surface area. Structural equation model (SEM) analysis showed that DSE associated with T. viride augmented plant biomass and height, shoot branching, and root surface area. Variations in root morphology and biomass were attributed to differences in DSE species and T. viride density among treatments. P. putaminum or P. herbarum with low- or medium T. viride density and S. lignicola with low- or high T. viride density improved licorice root morphology and biomass.

CONCLUSIONS

DSE isolated from other medicinal plants enhanced the root growth of licorice plants under different densities T. viride conditions and may also be used to promote the cultivation of medicinal plants.

The Effectiveness of a Dark Septate Endophytic Fungus, Cladophialophora chaetospira SK51, to Mitigate Strawberry Fusarium Wilt Disease and With Growth Promotion Activities

Strawberry Fusarium wilt, caused by the virulent fungus Fusarium oxysporum formae speciales fragariae (Fof) is a devastating soil-borne disease that causes severe production losses worldwide, including Japan. Fof is one of the top 10 fungal pathogens that threaten global crop security, and a method to effectively control this pathogen has yet to be found. This study aimed to investigate the effectiveness of dark septate endophytic (DSE) fungi against Fof to develop an efficient, effective, and environmentally friendly approach to improve plant health and fitness. A total of 19 fungal isolates were assessed, out of which three (SK47, SK48, and SK51) were selected based on their effectiveness in disease suppression in controlled growth chamber conditions using a soil system. Isolates SK47, SK48, and SK51 suppressed disease severity by 85.71, 61.90, and 90.48%, respectively. Molecular identification based on highly conserved small subunit (SSU), internal transcribed spacer (ITS), and large subunit (LSU) nrRNA regions identified these isolates as DSE Exophiala sp., Exophiala pisciphila, and Cladophialophora chaetospira, respectively. The sequences were deposited under accession numbers MN811693-MN811695 in the GenBank database. Notably, our results revealed that isolate C. chaetospira SK51 possessed superior growth promotion activities as well as disease suppression by significantly increased plant growth parameters (shoot and root dry mass, chlorophyll content, flower bud initiation, and number of fruit) in comparison to control plants and other two fungal candidates. Root colonization by C. chaetospira SK51 was visualized, and it was confirmed that the symbiosis with strawberry plants occurred successfully. Our results provide new insights in the application of DSE fungus C. chaetospira SK51 as a biocontrol agent on strawberry plants could promote plant growth, flower bud initiation, and fruit formation. C. chaetospira SK51 exhibited remarkable beneficial traits for the host plant, and it can potentially be applied in the development of new, safe, and effective treatments as an alternative to chemical fertilizers and fungicides for sustainable crop protection.

Plant Growth and Soil Microbial Impacts of Enhancing Licorice With Inoculating Dark Septate Endophytes Under Drought Stress

This study mainly aimed to investigate the effects of dark septate endophytes (DSE) (Acrocalymma vagum, Paraboeremia putaminum, and Fusarium acuminatum) on the growth and microbial community composition in the rhizosphere soil of a medicinal plant, licorice (Glycyrrhiza uralensis), grown in the non-sterile soil under drought stress. The results showed that three DSE strains could effectively colonize the plant roots and form a strain-dependent symbiosis with licorice. Although drought stress declined the growth of licorice plants, these decreases were partly recovered by DSE inoculation. Specifically, the inoculation of A. vagum and P. putaminum significantly increased the biomass and glycyrrhizin content, whereas A. vagum and F. acuminatum increased glycyrrhizic acid content of host plants under drought stress. However, the inoculation of F. acuminatum showed significant negative effects on the shoot, root, and total biomass of licorice plants. In addition, the effects of DSE inoculation on the morphological, photosynthetic, and antioxidant parameters of licorice plants, and mineral nutrient and microbial community composition in the rhizosphere soil were dependent on the DSE species as well as water regime. Interestingly, DSE inoculation significantly increased AM fungi content under drought stress. In addition, DSE associated with water had a significant positive influence on soil organic matter, available phosphorus (P), AM fungi, leaf number, soluble protein, SOD activity, total root length, root branch, and glycyrrhizic acid content. Based on the results of variance partitioning analysis, 17.0, 34.0, 14.9, 40.1, 28.2, and 18.0% variations in shoot morphology, root morphology, plant biomass, active ingredient, photosynthetic parameters, and antioxidant parameters, respectively, were attributable to the presence of certain soil microorganisms. These findings suggest the possibility that DSE inoculation improved the root development and nutrient absorption of host plants, altered the soil microbiota, and might also contribute to plant growth and survival under drought conditions. As A. vagum exhibited positive effects on the plant biomass, morphological and physiological parameters, and active ingredient content in licorice plants under drought stress, it was considered to be the best fungus for licorice cultivation. These results contribute to the understanding of the ecological function of DSE fungi in dryland agriculture.

Effects of Dark Septate Endophytes on the Performance of Hedysarum scoparium Under Water Deficit Stress

Hedysarum scoparium, a species characterized by rapid growth and high drought resistance, has been used widely for vegetative restoration of arid regions in Northwest China that are prone to desertification. Desert soil is typically deficient in available water and the alleviation of drought stress to host plants by endophytes could be an efficient strategy to increase the success of desert restoration. With the objective to seek more beneficial symbionts that can be used in the revegetation strategies, we addressed the question whether H. scoparium can benefit from inoculation by dark septate endophytes (DSEs) isolated from other desert plants. We investigated the influences of four non-host DSE strains (Phialophora sp., Knufia sp., Leptosphaeria sp., and Embellisia chlamydospora) isolated from other desert plants on the performance of H. scoparium under different soil water conditions. Differences in plant performance, such as plant growth, antioxidant enzyme activities, carbon, nitrogen, and phosphorous concentration under all the treatments, were examined. Four DSE strains could colonize the roots of H. scoparium successfully, and they established a positive symbiosis with the host plants depending on DSE species and water availability. The greatest benefits of DSE inoculation occurred in water stress treatment. Specifically, Phialophora sp. and Leptosphaeria sp. improved the root biomass, total biomass, nutrient concentration, and antioxidant enzyme activities of host plants under water deficit conditions. These data contribute to the understanding of the ecological function of DSE fungi in drylands.

Characterization of Dark Septate Endophytic Fungi and Improve the Performance of Liquorice Under Organic Residue Treatment

Dark septate endophytic (DSE) fungi is a diverse group of Ascomycetes fungi that colonize the plants roots, and may facilitate plant growth and fitness, however, their ecological roles need further clarification. This study aimed to evaluate the growth promoting effects of DSE fungi in a medicinal plant, liquorice (Glycyrrhiza uralensis), under additional organic residues. First, we isolated, identified and characterized, two DSE fungal species (Acrocalymma vagum and Paraboeremia putaminum) harboring inside the roots of liquorice growing in arid areas of China. Second, we examined the performance and rhizosphere soil parameters of liquorice plants inoculated with these fungi under additional sterilized organic residues and unsterilized organic residue (containing Trichoderma viride population) in a growth chamber. The results showed that two DSE strains could effectively colonize plant roots and formed a strain-dependent symbiosis with liquorice. DSE inoculation alone increased the plant biomass, and glycyrrhizic acid and glycyrrhizin content. It also improved the root system and N and P absorption by plants, consequently depleting these macronutrients in the soil. Residues alone increased soil organic matter, available phosphorus (P), and available nitrogen (N) content, and plant biomass, N, P, glycyrrhizic acid, and glycyrrhizin content. Mantel test and structural equation model (SEM) analysis demonstrated that DSE associated with residues significantly positively influenced soil organic matter, available P and available N, and plant biomass, glycyrrhizin, N, P, and root surface area. Variation in plant growth and glycyrrhizic acid and glycyrrhizin accumulation can be attributed to the effects of DSE inoculation. DSE associated with residues exhibited a general synergistic effect on the growth and accumulation of glycyrrhizic acid and glycyrrhizin of liquorice. We demonstrate for the first time, two DSE fungi in the liquorice roots that have potential use as promoter for the cultivation of medicinal plant.

Forest Tree Microbiomes and Associated Fungal Endophytes: Functional Roles and Impact on Forest Health

Terrestrial plants including forest trees are generally known to live in close association with microbial organisms. The inherent features of this close association can be commensalism, parasitism or mutualism. The term “microbiota” has been used to describe this ecological community of plant-associated pathogenic, mutualistic, endophytic and commensal microorganisms. Many of these microbiota inhabiting forest trees could have a potential impact on the health of, and disease progression in, forest biomes. Comparatively, studies on forest tree microbiomes and their roles in mutualism and disease lag far behind parallel work on crop and human microbiome projects. Very recently, our understanding of plant and tree microbiomes has been enriched due to novel technological advances using metabarcoding, metagenomics, metatranscriptomics and metaproteomics approaches. In addition, the availability of massive DNA databases (e.g., NCBI (USA), EMBL (Europe), DDBJ (Japan), UNITE (Estonia)) as well as powerful computational and bioinformatics tools has helped to facilitate data mining by researchers across diverse disciplines. Available data demonstrate that plant phyllosphere bacterial communities are dominated by members of only a few phyla (Proteobacteria, Actinobacteria, Bacteroidetes). In bulk forest soil, the dominant fungal group is Basidiomycota, whereas Ascomycota is the most prevalent group within plant tissues. The current challenge, however, is how to harness and link the acquired knowledge on microbiomes for translational forest management. Among tree-associated microorganisms, endophytic fungal biota are attracting a lot of attention for their beneficial health- and growth-promoting effects, and were preferentially discussed in this review.

Investigating the Role of Endophytic Fungi in Gentiana scabra bge. by Cross-Growth Period Inoculation

Gentiana scabra Bge. (gentian) is a Chinese medicinal plant. Endophytic fungi from the roots of gentian were isolated and cross-growth period inoculation was performed to study the roles of three Trichoderma spp. strains (F1, F2, and F9) in their original host plant. In treatments inoculated with F1, F2, and F9, gentiopicroside content increased 33.6, 23.7 and 13% than that in the control. Strains F1, F2, and F9 could also improve polysaccharide content by more than 6.6, 18.7 and 30% compared to the control. The incidence of spot blight in gentian inoculated with F1, F2, and F9 decreased by 31.2, 26.7 and 8.5%. Inconsistent changes in the activity of the three enzymes (superoxide dismutase, catalase and peroxidase) were observed when the plants were attacked by pathogens or inoculated with fungi. High enzymatic activity did not reflect mild disease. Cross-growth period inoculation, which takes into account the original living environment (gentian plant as "substrate" and different microorganisms as symbionts) of endophytic fungi, provides a new idea for studying effects of endophytes on their original hosts. This is the first research about the role of endophytic fungi in Gentiana scabra bge. in vivo.

Production of bioproducts by endophytic fungi: chemical ecology, biotechnological applications, bottlenecks, and solutions

Endophytes are microorganisms that colonize the interior of host plants without causing apparent disease. They have been widely studied for their ability to modulate relationships between plants and biotic/abiotic stresses, often producing valuable secondary metabolites that can affect host physiology. Owing to the advantages of microbial fermentation over plant/cell cultivation and chemical synthesis, endophytic fungi have received significant attention as a mean for secondary metabolite production. This article summarizes currently reported results on plant-endophyte interaction hypotheses and highlights the biotechnological applications of endophytic fungi and their metabolites in agriculture, environment, biomedicine, energy, and biocatalysts. Current bottlenecks in industrial development and commercial applications as well as possible solutions are also discussed.

Dark Septate Endophytic Fungi Increase Green Manure-15N Recovery Efficiency, N Contents, and Micronutrients in Rice Grains

An understanding of the interaction between rice and dark septate endophytic (DSE) fungi, under green fertilization, may lead to sustainable agricultural practices. Nevertheless, this interaction is still poorly understood. Therefore, in this study, we aimed to evaluate the accumulation of macro- and micronutrients, dry matter, and protein and N recovery efficiency from Canavalia ensiformis (L.)-¹⁵N in rice inoculated with DSE fungi. An experiment under greenhouse conditions was conducted in a randomized complete block design comprising split-plots, with five replicates of rice plants potted in non-sterilized soil. Rice (Piauí variety) seedlings were inoculated with DSE fungi, A101 and A103, or left uninoculated (control) and transplanted into pots containing 12 kg of soil, which had previously been supplemented with dry, finely ground shoot biomass of C. ensiformis enriched with 2.15 atom % ¹⁵N. Two collections were performed in the experiment: one at 54 days after transplanting (DAT) and one at 130 DAT (at maturation). Growth indicators (at 54 DAT), grain yield, nutrient content, recovery efficiency, and the amount of N derived from C. ensiformis were quantified. At 54 DAT, the N content, chlorophyll content, and plant height of inoculated plants had increased significantly compared with the control, and these plants were more proficient in the use of N derived from C. ensiformis. At maturation, plants inoculated with A103 were distinguished by the recovery efficiency and amount of N derived from C. ensiformis and N content in the grain and shoot being equal to that in A101 inoculation and higher than that in the control, resulting in a higher accumulation of crude protein and dry matter in the full grain and panicle of DSE-rice interaction. In addition, Fe and Ni contents in the grains of rice inoculated with these fungi doubled with respect to the control, and in A103 inoculation, we observed Mn accumulation that was three times higher than in the other treatments. Our results suggest that the inoculation of rice with DSE fungi represents a strategy to improve green manure-N recovery, grain yield per plant, and grain quality in terms of micronutrients contents in cropping systems with a low N input.

Effects of Rhizobium Species Living with the Dark Septate Endophytic Fungus Veronaeopsis simplex on Organic Substrate Utilization by the Host

Bacteria harbored in/on the hyphae of the dark septate endophyte, Veronaeopsis simplex Y34, were identified as a single Rhizobium species by molecular analyses of bacterial 16S rRNA genes, and were successfully isolated from the endophyte. The Rhizobium-cured fungus was prepared thoroughly by an antibiotic treatment, thereby allowing an examination of their effects on organic substrate utilization. Assays with Biolog® FF microplates revealed that the respiration potential for 52.6% of the tested compounds were significantly different between Rhizobium-harboring and -cured fungal hosts, indicating that organic substrate utilization by V. simplex Y34 was significantly influenced by the presence of the associated Rhizobium sp. VsBac-Y9.

Dark Septate Endophytic Fungi Help Tomato to Acquire Nutrients from Ground Plant Material

Dark septate endophytic (DSE) fungi are facultative biotrophs that associate with hundreds of plant species, contributing to their growth. These fungi may therefore aid in the search for sustainable agricultural practices. However, several ecological functions of DSE fungi need further clarification. The present study investigated the effects of DSE fungi inoculation on nutrient recovery efficiency, nutrient accumulation, and growth of tomato plants fertilized with organic and inorganic N sources. Two experiments were carried out under greenhouse conditions in a randomized blocks design, with five replicates of tomato seedlings grown in pots filled with non-sterile sandy soil. Tomato seedlings (cv. Santa Clara I-5300) inoculated with DSE fungi (isolates A101, A104, and A105) and without DSE fungi (control) were transplanted to pots filled with 12 kg of soil which had previously received finely ground plant material [Canavalia ensiformis (L.)] that was shoot enriched with 0.7 atom % 15N (organic N source experiment) or ammonium sulfate-15N enriched with 1 atom % 15N (mineral N source experiment). Growth indicators, nutrient content, amount of nitrogen (N) in the plant derived from ammonium sulfate-15N or C. ensiformis-15N, and recovery efficiency of 15N, P, and K by plants were quantified 50 days after transplanting. The treatment inoculated with DSE fungi and supplied with an organic N source showed significantly higher recovery efficiency of 15N, P, and K. In addition, the 15N, N, P, K, Ca, Mg, Fe, Mn, and Zn content, plant height, leaf number, leaf area (only for the A104 inoculation), and shoot dry matter increased. In contrast, the only positive effects observed in the presence of an inorganic N source were fertilizer-K recovery efficiency, content of K, and leaf area when inoculated with the fungus A104. Inoculation with A101, A104, and A105 promoted the growth of tomato using organic N source (finely ground C. ensiformis-15N plant material).