Beneficial effects of endophytic fungi colonization on plants

Endophytic entomopathogenic fungi as biological control agents of insect pests

Entomopathogenic fungi capable of establishing mutualistic endophytic relationships with plants have a tremendous potential as biocontrol agents of insect pests. While fungi have long played an important and highly effective role in pest suppression, the utility of endophytic entomopathogenic fungi in pest management is a relatively new and emerging topic of biocontrol. Here we discuss the relevance of endophytic fungi to plant health in general, synthesize the current knowledge of the effectiveness of endophytic entomopathogenic fungi against diverse insect pests, discuss the indirect plant-mediated effects of endophytic entomopathogenic fungi on arthropods, and describe the diverse benefits of endophytic fungi to plants that are likely to affect herbivores and plant pathogens as well. Lastly, we consider major challenges to incorporating endophytic entomopathogenic fungi in biocontrol, such as their non-target effects and field efficacy, which can be variable and influenced by environmental factors. Continued research on endophyte-insect-plant-environment interactions is critical to advancing our knowledge of these fungi as a sustainable pest management tactic. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Morphological, Metabolomic and Genomic Evidences on Drought Stress Protective Functioning of the Endophyte Bacillus safensis Ni7

The metabolomic and genomic characterization of an endophytic Bacillus safensis Ni7 was carried out in this study. This strain has previously been isolated from the xerophytic plant Nerium indicum L. and reported to enhance the drought tolerance in Capsicum annuum L. seedlings. The effects of drought stress on the morphology, biofilm production, and metabolite production of B. safensis Ni7 are analyzed in the current study. From the results obtained, the organism was found to have multiple strategies such as aggregation and clumping, robust biofilm production, and increased production of surfactin homologues under the drought induced condition when compared to non-stressed condition. Further the whole genome sequencing (WGS) based analysis has demonstrated B. safensis Ni7 to have a genome size of 3,671,999 bp, N50 value of 3,527,239, and a mean G+C content of 41.58%. Interestingly the organism was observed to have the presence of various stress-responsive genes (13, 20U, 16U,160, 39, 17M, 18, 26, and ctc) and genes responsible for surfactin production (srfAA, srfAB, srfAC, and srfAD), biofilm production (epsD, epsE, epsF, epsG, epsH, epsI, epsK, epsL, epsM, epsN, and pel), chemotaxis (cheB_1, cheB_2, cheB_3, cheW_1, cheW_2 cheR, cheD, cheC, cheA, cheY, cheV, and cheB_4), flagella synthesis (flgG_1, flgG_2, flgG_3, flgC, and flgB) as supportive to the drought tolerance. Besides these, the genes responsible for plant growth promotion (PGP), including the genes for nitrogen (nasA, nasB, nasC, nasD, and nasE) and sulfur assimilation (cysL_1&L_2, cysI) and genes for phosphate solubilization (phoA, phoP_1& phoP_2, and phoR) could also be predicted. Along with the same, the genes for catalase, superoxide dismutase, protein homeostasis, cellular fitness, osmoprotectants production, and protein folding could also be predicted from its WGS data. Further pan-genome analysis with plant associated B. safensis strains available in the public databases revealed B. safensis Ni7 to have the presence of a total of 5391 gene clusters. Among these, 3207 genes were identified as core genes, 954 as shell genes and 1230 as cloud genes. This variation in gene content could be taken as an indication of evolution of strains of Bacillus safensis as per specific conditions and hence in the case of B. safensis Ni7 its role in habitat adaptation of plant is well expected. This diversity in endophytic bacterial genes may attribute its role to support the plant system to cope up with stress conditions. Overall, the study provides genomic evidence on Bacillus safensis Ni7 as a stress alleviating microbial partner in plants.

A new Schizophyllum commune strain as a potential biocontrol agent against blueberry root rot

In recent years, blueberry root rot has been caused mainly by Fusarium commune, and there is an urgent need for a green and efficient method to control this disease. To date, research on Schizophyllum commune has focused on antioxidant mechanisms, reactive dye degradation, etc., but the mechanism underlying the inhibition of pathogenic microorganisms is still unclear. Here, the control effects of S. commune on F. commune and blueberry root rot were studied using adversarial culture, tissue culture, and greenhouse pot experiments. The results showed that S. commune can dissolve insoluble phosphorus and secrete various extracellular hydrolases. The results of hyphal confrontation and fermentation broth antagonism experiments showed that S. commune had a significant inhibitory effect on F. commune, with inhibition rates of 70.30% and 22.86%, respectively. Microscopy results showed distortion of F. commune hyphae, indicating that S. commune is strongly parasitic. S. commune had a significant growth-promoting effect on blueberry tissue-cultured seedlings. After inoculation with S. commune, inoculation with the pathogenic fungus, or inoculation at a later time, the strain significantly reduced the root rot disease index in the potted blueberry seedlings, with relative control effects of 79.14% and 62.57%, respectively. In addition, S. commune G18 significantly increased the antioxidant enzyme contents in the aboveground and underground parts of potted blueberry seedlings. We can conclude that S. commune is a potential biocontrol agent that can be used to effectively control blueberry root rot caused by F. commune in the field.

Exploring the potential of endophyte-plant interactions for improving crop sustainable yields in a changing climate

Climate change poses a major threat to global food security, significantly reducing crop yields as cause of abiotic stresses, and for boosting the spread of new and old pathogens and pests. Sustainable crop management as a route to mitigation poses the challenge of recruiting an array of solutions and tools for the new aims. Among these, the deployment of positive interactions between the micro-biotic components of agroecosystems and plants can play a highly significant role, as part of the agro-ecological revolution. Endophytic microorganisms have emerged as a promising solution to tackle this challenge. Among these, Arbuscular Mycorrhizal Fungi (AMF) and endophytic bacteria and fungi have demonstrated their potential to alleviate abiotic stresses such as drought and heat stress, as well as the impacts of biotic stresses. They can enhance crop yields in a sustainable way also by other mechanisms, such as improving the nutrient uptake, or by direct effects on plant physiology. In this review we summarize and update on the main types of endophytes, we highlight several studies that demonstrate their efficacy in improving sustainable yields and explore possible avenues for implementing crop-microbiota interactions. The mechanisms underlying these interactions are highly complex and require a comprehensive understanding. For this reason, omic technologies such as genomics, transcriptomics, proteomics, and metabolomics have been employed to unravel, by a higher level of information, the complex network of interactions between plants and microorganisms. Therefore, we also discuss the various omic approaches and techniques that have been used so far to study plant-endophyte interactions.

Dynamic changes in fungal communities and functions in different air-curing stages of cigar tobacco leaves

Introduction

Air curing (AC) plays a crucial role in cigar tobacco leaf production. The AC environment is relatively mild, contributing to a diverse microbiome. Fungi are important components of the tobacco and environmental microbiota. However, our understanding of the composition and function of fungal communities in AC remains limited.

Methods

In this study, changes in the chemical constituents and fungal community composition of cigar tobacco leaves during AC were evaluated using flow analysis and high-throughput sequencing.

Results

The moisture, water-soluble sugar, starch, total nitrogen, and protein contents of tobacco leaves exhibited decreasing trends, whereas nicotine showed an initial increase, followed by a decline. As determined by high-throughput sequencing, fungal taxa differed among all stages of AC. Functional prediction showed that saprophytic fungi were the most prevalent type during the AC process and that the chemical composition of tobacco leaves is significantly correlated with saprophytic fungi.

Conclusion

This study provides a deeper understanding of the dynamic changes in fungal communities during the AC process in cigar tobacco leaves and offers theoretical guidance for the application of microorganisms during the AC process.

The diversity of endophytic fungi in Tartary buckwheat (Fagopyrum tataricum) and its correlation with flavonoids and phenotypic traits

Tartary buckwheat (Fagopyrum tataricum) is a significant medicinal crop, with flavonoids serving as a crucial measure of its quality. Presently, the artificial cultivation of Tartary buckwheat yields low results, and the quality varies across different origins. Therefore, it is imperative to identify an effective method to enhance the yield and quality of buckwheat. Endophytic fungi reside within plants and form a mutually beneficial symbiotic relationship, aiding plants in nutrient absorption, promoting host growth, and improving secondary metabolites akin to the host. In this study, high-throughput sequencing technology was employed to assess the diversity of endophytic fungi in Tartary buckwheat. Subsequently, a correlation analysis was performed between fungi and metabolites, revealing potential increases in flavonoid content due to endophytic fungi such as Bipolaris, Hymenula, and Colletotrichum. Additionally, a correlation analysis between fungi and phenotypic traits unveiled the potential influence of endophytic fungi such as Bipolaris, Buckleyzyma, and Trichosporon on the phenotypic traits of Tartary buckwheat. Notably, the endophytic fungi of the Bipolaris genus exhibited the potential to elevate the content of Tartary buckwheat metabolites and enhance crop growth. Consequently, this study successfully identified the resources of endophytic fungi in Tartary buckwheat, explored potential functional endophytic fungi, and laid a scientific foundation for future implementation of biological fertilizers in improving the quality and growth of Tartary buckwheat.

Identification and distribution of a fungal endosymbiotic Alternaria species (Alternaria section Undifilum sp.) in Astragalus garbancillo tissues

Plants belonging to the genera Astragalus, Oxytropis, Ipomoea, Sida, and Swainsona often contain the toxin swainsonine (SW) produced by an associated fungal symbiont. Consumption of SW-containing plants causes a serious neurological disorder in livestock, which can be fatal. In this study, a fungal endophyte, Alternaria section Undifilum, was identified in Astragalus garbancillo seeds, using polymerase chain reaction (PCR) followed by direct sequencing. In seeds, the SW concentrations were about 4 times higher than in other parts of the plant. Furthermore, microscopic examination demonstrated that the fungus mycelium grows inside the petioles and stems, on the outer surface and inside the mesocarp of the fruit, in the mesotesta and endotesta layers of the seed coat, and inside the endosperm of the seeds. Our results support the notion that the SW-producing fungus is vertically transmitted in the host plant A. garbancillo.

A review on endophytic fungi: a potent reservoir of bioactive metabolites with special emphasis on blight disease management

Phytopathogenic microorganisms have caused blight diseases that present significant challenges to global agriculture. These diseases result in substantial crop losses and have a significant economic impact. Due to the limitations of conventional chemical treatments in effectively and sustainably managing these diseases, there is an increasing interest in exploring alternative and environmentally friendly approaches for disease control. Using endophytic fungi as biocontrol agents has become a promising strategy in recent years. Endophytic fungi live inside plant tissues, forming mutually beneficial relationships, and have been discovered to produce a wide range of bioactive metabolites. These metabolites demonstrate significant potential for fighting blight diseases and provide a plentiful source of new biopesticides. In this review, we delve into the potential of endophytic fungi as a means of biocontrol against blight diseases. We specifically highlight their significance as a source of biologically active compounds. The review explores different mechanisms used by endophytic fungi to suppress phytopathogens. These mechanisms include competing for nutrients, producing antifungal compounds, and triggering plant defense responses. Furthermore, this review discusses the challenges of using endophytic fungi as biocontrol agents in commercial applications. It emphasizes the importance of conducting thorough research to enhance their effectiveness and stability in real-world environments. Therefore, bioactive metabolites from endophytic fungi have considerable potential for sustainable and eco-friendly blight disease control. Additional research on endophytes and their metabolites will promote biotechnology solutions.

Beneficial endophytic fungi improve the yield and quality of Salvia miltiorrhiza by performing different ecological functions

Background

Endophytic fungi can enhance the growth and synthesis of secondary metabolites in medicinal plants. Salvia miltiorrhiza Bunge is frequently employed for treating cardiovascular and cerebrovascular ailments, with the primary bioactive components being salvianolic acid and tanshinone. However, their levels in cultivated S. miltiorrhiza are inferior to that of the wild herbs, so the production of high-quality medicinal herbs is sharply declining. Consequently, the utilization of beneficial endophytic fungi to improve the yield and quality of S. miltiorrhiza holds great significance for the cultivation of medicinal plants.

Methods

In this study, nine non-pathogenic, endophytic fungal strains were introduced into sterile S. miltiorrhiza seedlings and cultivated both in vitro and in situ (the greenhouse). The effects of these strains on the growth indices, C and N metabolism, antioxidant activity, photosynthesis, and content of bioactive ingredients in S. miltiorrhiza were then evaluated.

Results

The results showed that the different genera, species, or strains of endophytic fungi regulated the growth and metabolism of S. miltiorrhiza in unique ways. These endophytic fungi primarily exerted their growth-promoting effects by increasing the net photosynthetic rate, intercellular CO2 concentration, and the activities of sucrose synthase, sucrose phosphate synthase, nitrate reductase, and glutamine synthetase. They also enhanced the adaptability and resistance to environmental stresses by improving the synthesis of osmoregulatory compounds and the activity of antioxidant enzymes. However, their regulatory effects on the growth and development of S. miltiorrhiza were affected by environmental changes. Moreover, the strains that significantly promoted the synthesis and accumulation of phenolic acids inhibited the accumulation of tanshinones components, and vice versa. The endophytic fungal strains Penicillium meloforme DS8, Berkeleyomyces basicola DS10, and Acremonium sclerotigenum DS12 enhanced the bioaccumulation of tanshinones. Fusarium solani DS16 elevated the rosmarinic acid content and yields in S. miltiorrhiza. The strain Penicillium javanicum DS5 improved the contents of dihydrotanshinone, salvianolic acid B, and rosmarinic acid. The strains P. meloforme DS8 and B. basicola DS10 improved resistance.

Conclusion

Various endophytic fungi affected the quality and yield of S. miltiorrhiza by regulating different physiological and metabolic pathways. This study also provides a novel and effective method to maximize the effects of beneficial endophytic fungi by selecting specific strains to design microbial communities based on the different ecological functions of endophytic fungi under varying environments and for specific production goals.

Insight of endophytic fungi promoting the growth and development of woody plants

Microorganisms play an important role in plant growth and development. In particular, endophytic fungi is one of the important kinds of microorganisms and has a mutually beneficial symbiotic relationship with host plants. Endophytic fungi have many substantial benefits to host plants, especially for woody plants, such as accelerating plant growth, enhancing stress resistance, promoting nutrient absorption, resisting pathogens and etc. However, the effects of endophytic fungi on the growth and development of woody plants have not been systematically summarized. In this review, the functions of endophytic fungi for the growth and development of woody plants have been mainly reviewed, including regulating plant growth (e.g., flowering, root elongation, etc.) by producing nutrients and plant hormones, and improving plant disease, insect resistance and heavy metal resistance by producing secondary metabolites. In addition, the diversity of endophytic fungi could improve the ability of woody plants to adapt to adverse environment. The components produced by endophytic fungi have excellent potential for the growth and development of woody plants. This review has systematically discussed the potential regulation mechanism of endophytic fungi regulating the growth and development of woody plants, it would be of great significance for the development and utilization of endophytic fungi resource from woody plants for the protection of forest resources.

Multiomics Reveals Mechanisms of Alternaria oxytropis Inhibiting Pathogenic Fungi in Oxytropis ochrocephala

Endophytic fungi can benefit the host plant and increase the plant resistance. Now, there is no in-depth study of how Alternaria oxytropis (A. oxytropis) is enhancing the ability of inhibiting pathogenic fungi in Oxytropis ochrocephala (O. ochrocephala). In this study, the fungal community and metabolites associated with endophyte-infected (EI) and endophyte-free (EF) O. ochrocephala were compared by multiomics. The fungal community indicated that there was more A. oxytropis, less phylum Ascomycota, and less genera Leptosphaeria, Colletotrichum, and Comoclathris in the EI group. As metabolic biomarkers, the levels of swainsonine and apigenin-7-O-glucoside-4-O-rutinoside were significantly increased in the EI group. Through in vitro validation experiments, swainsonine and apigenin-7-O-glucoside-4-O-rutinoside can dramatically suppress the growth of pathogenic fungi Leptosphaeria sclerotioides and Colletotrichum americae-borealis by increasing the level of oxidative stress. This work suggested that O. ochrocephala containing A. oxytropis could increase the resistance to fungal diseases by markedly enhancing the content of metabolites inhibiting pathogenic fungi.

Interaction with the entomopathogenic fungus Beauveria bassiana influences tomato phenome and promotes resistance to Botrytis cinerea infection

Plants are central to complex networks of multitrophic interactions. Increasing evidence suggests that beneficial microorganisms (BMs) may be used as plant biostimulants and pest biocontrol agents. We investigated whether tomato (Solanum lycopersicum) plants are thoroughly colonized by the endophytic and entomopathogenic fungus Beauveria bassiana, and how such colonization affects physiological parameters and the phenotype of plants grown under unstressed conditions or exposed to the pathogenic fungus Botrytis cinerea. As a positive control, a strain of the well-known biocontrol agent and growth inducer Trichoderma afroharzianum was used. As multitrophic interactions are often driven by (or have consequences on) volatile organic compounds (VOCs) released by plants constitutively or after induction by abiotic or biotic stresses, VOC emissions were also studied. Both B. bassiana and T. afroharzianum induced a significant but transient (one to two-day-long) reduction of stomatal conductance, which may indicate rapid activation of defensive (rejection) responses, but also limited photosynthesis. At later stages, our results demonstrated a successful and complete plant colonization by B. bassiana, which induced higher photosynthesis and lower respiration rates, improved growth of roots, stems, leaves, earlier flowering, higher number of fruits and yield in tomato plants. Beauveria bassiana also helped tomato plants fight B. cinerea, whose symptoms in leaves were almost entirely relieved with respect to control plants. Less VOCs were emitted when plants were colonized by B. bassiana or infected by B. cinerea, alone or in combination, suggesting no activation of VOC-dependent defensive mechanisms in response to both fungi.

Age-dependent dendrobine biosynthesis in Dendrobium nobile: insights into endophytic fungal interactions

Introduction

Dendrobium nobile (D. nobile), a valued Chinese herb known for its diverse pharmacological effects, owes much of its potency to the bioactive compound dendrobine. However, dendrobine content varies significantly with plant age, and the mechanisms governing this variation remain unclear. This study delves into the potential role of endophytic fungi in shaping host-microbe interactions and influencing plant metabolism.

Methods

Using RNA-seq, we examined the transcriptomes of 1-year-old, 2-year-old, and 3-year-old D. nobile samples and through a comprehensive analysis of endophytic fungal communities and host gene expression in D. nobile stems of varying ages, we aim to identify associations between specific fungal taxa and host genes.

Results

The results revealing 192 differentially expressed host genes. These genes exhibited a gradual decrease in expression levels as the plants aged, mirroring dendrobine content changes. They were enriched in 32 biological pathways, including phagosome, fatty acid degradation, alpha-linolenic acid metabolism, and plant hormone signal transduction. Furthermore, a significant shift in the composition of the fungal community within D. nobile stems was observed along the age gradient. Olipidium, Hannaella, and Plectospherella dominated in 1-year-old plants, while Strelitziana and Trichomerium prevailed in 2-year-old plants. Conversely, 3-year-old plants exhibited additional enrichment of endophytic fungi, including the genus Rhizopus. Two gene expression modules (mediumpurple3 and darkorange) correlated significantly with dominant endophytic fungi abundance and dendrobine accumulation. Key genes involved in dendrobine synthesis were found associated with plant hormone synthesis.

Discussion

This study suggests that the interplay between different endophytic fungi and the hormone signaling system in D. nobile likely regulates dendrobine biosynthesis, with specific endophytes potentially triggering hormone signaling cascades that ultimately influence dendrobine synthesis.

The Potential of Endophytes in Improving Salt-Alkali Tolerance and Salinity Resistance in Plants

Ensuring food security for the global population is a ceaseless and critical issue. However, high-salinity and high-alkalinity levels can harm agricultural yields throughout large areas, even in largely agricultural countries, such as China. Various physical and chemical treatments have been employed in different locations to mitigate high salinity and alkalinity but their effects have been minimal. Numerous researchers have recently focused on developing effective and environmentally friendly biological treatments. Endophytes, which are naturally occurring and abundant in plants, retain many of the same characteristics of plants owing to their simultaneous evolution. Therefore, extraction of endophytes from salt-tolerant plants for managing plant growth in saline-alkali soils has become an important research topic. This extraction indicates that the soil environment can be fundamentally improved, and the signaling pathways of plants can be altered to increase their defense capacity, and can even be inherited to ensure lasting efficacy. This study discusses the direct and indirect means by which plant endophytes mitigate the effects of plant salinity stress that have been observed in recent years.

How do root fungi of Alnus nepalensis and Schima wallichii recover during succession of abandoned land?

Alnus nepalensis and Schima wallichii are native tree species accompanying succession in abandoned agricultural land in the middle mountainous region of central Nepal. To understand how root fungi recover during spontaneous succession, we analyzed the diversity and composition of arbuscular mycorrhizal (AM), ectomycorrhizal (ECM), and total fungi in tree fine roots from three land use types, short-term abandoned land (SA), long-term abandoned land (LA), and regenerated forest (RF) as a reference. Additionally, ECM morphotypes were examined. The results showed different speeds of succession in the studied fungal groups. While the change in the AM fungal community appears to be rapid and LA resembles the composition of RF, the total fungi in the abandoned land types are similar to each other but differed significantly from RF. Interestingly, the relative abundance of Archaeosporaceae followed a trend differing between the tree species (SA < LA in A. nepalensis, but SA > LA in S. wallichii). Unlike AM and total fungi, there was no significant difference in the ECM community of A. nepalensis between land use types, probably due to their low species diversity (9 ECM morphotypes, 31 ECM operational taxonomic units). However, Cortinarius sp. was significantly more abundant in RF than in the other land use types, whereas Alnicola, Tomentella, and Russula preferred young stages. Our results suggest that for both studied tree species the AM fungal succession could reach the stage of regenerated forest relatively fast. In the case of total fungi, because of hyperdiversity and composed of species specialized to a variety of environments and substrates, the transition was expected to be delayed in abandoned land where the vegetation was still developing and the ecosystem was not as complex as that found in mature forests.

Biocontrol of bacterial wilt disease in tomato using Bacillus subtilis strain R31

Bacterial wilt disease caused by Ralstonia solanacearum is a widespread, severe plant disease. Tomato (Solanum lycopersicum), one of the most important vegetable crops worldwide, is particularly susceptible to this disease. Biological control offers numerous advantages, making it a highly favorable approach for managing bacterial wilt. In this study, the results demonstrate that treatment with the biological control strain Bacillus subtilis R31 significantly reduced the incidence of tomato bacterial wilt. In addition, R31 directly inhibits the growth of R. solanacearum, and lipopeptides play an important role in this effect. The results also show that R31 can stably colonize the rhizosphere soil and root tissues of tomato plants for a long time, reduce the R. solanacearum population in the rhizosphere soil, and alter the microbial community that interacts with R. solanacearum. This study provides an important theoretical basis for elucidating the mechanism of B. subtilis as a biological control agent against bacterial wilt and lays the foundation for the optimization and promotion of other agents such as R31.

Contribution of endophytes towards improving plant bioactive metabolites: a rescue option against red-taping of medicinal plants

Medicinal plants remain a valuable source for natural drug bioprospecting owing to their multi-target spectrum. However, their use as raw materials for novel drug synthesis has been greatly limited by unsustainable harvesting leading to decimation of their wild populations coupled with inherent low concentrations of constituent secondary metabolites per unit mass. Thus, adding value to the medicinal plants research dynamics calls for adequate attention. In light of this, medicinal plants harbour endophytes which are believed to be contributing towards the host plant survival and bioactive metabolites through series of physiological interference. Stimulating secondary metabolite production in medicinal plants by using endophytes as plant growth regulators has been demonstrated to be one of the most effective methods for increasing metabolite syntheses. Use of endophytes as plant growth promotors could help to ensure continuous supply of medicinal plants, and mitigate issues with fear of extinction. Endophytes minimize heavy metal toxicity in medicinal plants. It has been hypothesized that when medicinal plants are exposed to harsh conditions, associated endophytes are the primary signalling channels that induce defensive reactions. Endophytes go through different biochemical processes which lead to activation of defence mechanisms in the host plants. Thus, through signal transduction pathways, endophytic microorganisms influence genes involved in the generation of secondary metabolites by plant cells. Additionally, elucidating the role of gene clusters in production of secondary metabolites could expose factors associated with low secondary metabolites by medicinal plants. Promising endophyte strains can be manipulated for enhanced production of metabolites, hence, better probability of novel bioactive metabolites through strain improvement, mutagenesis, co-cultivation, and media adjustment.

Diversity of Fungal Communities on Diseased and Healthy Cinnamomum burmannii Fruits and Antibacterial Activity of Secondary Metabolites

The composition and structure of fungal communities on healthy and diseased fruits of Cinnamomum burmannii (Nees and Nees) Blume were characterized, with evaluation of the antibacterial activity of secondary metabolites from culturable fungi following the first identification of secondary metabolites in the fungus Medicopsis romeroi (Esf-14; GenBank accession number OK242756). These results are significant for understanding the functional variation in bioactivity in fungal communities and developing a broader range of bioactive resources. High-throughput sequencing results indicated that the fungal community in diseased fruit differed from that in healthy fruit at the phylum, class, order, or genus level, with significant differences in the species and relative abundance of the dominant flora. A total of 49 (healthy fruit) and 122 (diseased fruit) artificially cultivable endophytic fungi were isolated, and 41 different strains (11 from healthy fruit and 30 from diseased fruit) were successfully identified by morphological and molecular biological analyses, which were classified into 8 groups and 23 genera by phylogenetic tree analysis, with Pleosporales, Glomerellales, and Hypocreales being the dominant groups at the order level and Colletotrichum being the dominant group at the genus level. The results of the antibacterial assay demonstrated that the secondary metabolites of all strains had different degrees of antibacterial activity, while the secondary metabolites of endophytic fungi from diseased fruit were generally stronger than those of fungi from healthy fruit, with the active secondary metabolites dominated by small and moderately polar compounds. Combined analysis of fungal communities, phylogenetic tree analysis, and bioactivity analysis of culturable strains revealed strong antibacterial activity of both upregulated and downregulated flora in diseased fruit. Five compounds, including two new (5,6-dimethoxy-[1',1:4,1″-terphenyl]-2-ol [compound 1] and 5-(methoxycarbonyl)-2-methylbenzo[d][1,3]dioxole-2-carboxylic acid [compound 2]) and three known compounds (3,7-dihydroxy-1,9-dimethyldibenzofuran [compound 3], methyl 3-hydroxybenzoate [compound 4], and uracil [compound 5]), were isolated and identified for the first time from the endophytic fungus Medicopsis romeroi. In general, the diversity of fungal communities on diseased fruit was lower than that on healthy fruits, while the antibacterial activity of artificially cultured endophytic fungi on diseased fruits was generally stronger than that on healthy fruits, suggesting excellent promise for the development of secondary metabolites from active strains on diseased fruit as antibacterial agents. IMPORTANCE Powdery fruit disease is a notorious disease of Cinnamomum burmannii that causes severe loss in fruit production. Studies on the function of endophytic fungal communities in healthy plant tissues are not new, while little is known about the functional changes of fungal communities in disease-causing plant tissues. Our results demonstrate that fungal communities in diseased fruits differ from those in healthy fruits at the level of phylum, class, order, or genus, with significant differences in the species and relative abundance of dominant groups. Endophytic fungi in diseased fruits appeared to produce secondary metabolites with stronger antibacterial properties, although the community diversity was not as varied as that in healthy fruits. In addition, secondary metabolites of the Medicopsis romeroi strain from diseased fruits were identified for the first time. These results have important implications for understanding the functional variation of bioactivity in fungal communities and for developing a broader resource of bioactivity.

Metabolite Chemical Composition of the Bletilla striata (Thunb.) Reichb. f. Endophyte Penicillium oxalicum

Penicillium oxalicum strain can be isolated from the Bletilla striata (Thunb.) Reichb. f. tubers. Its solid-state fermentation products are concentrated by percolation extraction. Separation and purification have been conducted to the ethyl acetate extracts by preparative HPLC. Based on the use of spectrometry, we have determined 17 known compounds, 12,13-dihydroxy-fumitremorgin C (1), pseurotin A (2), tyrosol (3), cyclo-(L-Pro-L-Val) (4), cis-4-hydroxy-8-O-methylmellein (5), uracil (6), cyclo-(L-Pro-L-Ala) (7), 1,2,3,4-tetrahydro-4-hydroxy-4-quinolin carboxylic acid (8), cyclo-(Gly-L-Pro) (9), 2'-deoxyuridine (10), 1-(β-D-ribofuranosyl)thymine (11), cyclo-(L-Val-Gly) (12), 2'-deoxythymidine (13), cyclo-(Gly-D-Phe) (14), cyclo-L-(4-hydroxyprolinyl)-D-leucine (15), cyclo-(L)-4-hydroxy-Pro-(L)-Phe (16), uridine (17). Here, we report compounds 1-3, 5, 7-8, 11-12, 14-17 are first found and isolated from this endophyte.

Positive effects of Cordyceps cateniannulata colonization in tobacco: Growth promotion and resistance to abiotic stress

Background

Entomopathogenic fungi can live in insects to cause disease and death and are the largest group of entomopathogenic microorganisms. Therefore, these fungi are best known for their microbial control potential. Importantly, they also have other beneficial effects, including promoting plant growth and development by colonizing plant. Here, the study sought to identify specific strains of the entomopathogenic fungus, Cordyceps cateniannulata that would form endophytic associations with tobacco, thus benefiting plant growth and resistance to abiotic stresses, thereby highlighting the application of entomopathogenic fungi in tobacco.

Methods

The C. cateniannulata-tobacco symbiont was constructed by root irrigation. The effects of C. cateniannulata on tobacco growth were evaluated by measuring the maximum leaf length, maximum leaf width, number of leaves, plant height, stem thickness, stem circumference, dry and fresh shoot weight 7, 14, 21, and 28 days after colonization. The peroxidase, catalase, superoxide dismutase, and malondialdehyde were measured to observe the impact of C. cateniannulata on tobacco defense enzyme activity. Finally, high-throughput sequencing was used to access microbial communities in the rhizosphere, with data subsequently linked to growth indicators.

Results

After tobacco was inoculated with C. cateniannulata X8, which significantly promoted growth and related enzyme activity, malondialdehyde was decreased. The most significant impact was on peroxidase, with its activity being upregulated by 98.20, 154.42, 180.65, and 170.38% in the four time periods, respectively. The high throughput sequencing results indicated that C. cateniannulata had changed the rhizosphere microbial relative abundances, such as increasing Acidobacteria and Ascomycetes, and decreasing Actinomycetes and Basidiomycetes. The redundancy analysis showed that C. cateniannulata significantly boosted tobacco growth by reducing the abundance of specific dominant genera such as Stachybotrys, Cephalotrichum, Streptomyces, Isoptericola, and Microbacterium.

Conclusion

Specific strains of C. cateniannulata can be introduced into host plants as endophytes, resulting in promotion of host plant growth and increased resistance to abiotic stress and microbial pathogens. The study provides a foundation for future studies of C. cateniannulata as an ecological agent.

Brassicaceae Fungi and Chromista Diseases: Molecular Detection and Host–Plant Interaction

Brassicaceae plants cover a large number of species with great economic and nutritional importance around the world. The production of Brassica spp. is limited due to phytopathogenic fungal species causing enormous yield losses. In this scenario, precise and rapid detection and identification of plant-infecting fungi are essential to facilitate the effective management of diseases. DNA-based molecular methods have become popular methods for accurate plant disease diagnostics and have been used to detect Brassicaceae fungal pathogens. Polymerase chain reaction (PCR) assays including nested, multiplex, quantitative post, and isothermal amplification methods represent a powerful weapon for early detection of fungal pathogens and preventively counteract diseases on brassicas with the aim to drastically reduce the fungicides as inputs. It is noteworthy also that Brassicaceae plants can establish a wide variety of relationships with fungi, ranging from harmful interactions with pathogens to beneficial associations with endophytic fungi. Thus, understanding host and pathogen interaction in brassica crops prompts better disease management. The present review reports the main fungal diseases of Brassicaceae, molecular methods used for their detection, review studies on the interaction between fungi and brassicas plants, and the various mechanisms involved including the application of omics technologies.

Astragalicola ephedrae sp. nov., isolated from the stem of Ephedra gerardiana in Ladakh, India

An endophytic fungus designated as EIT4^T (MCC 9756^T) was isolated from the asymptomatic stem tissue of Ephedra gerardiana collected from the Kargil district of Ladakh Union territory, India. Phylogenetic analysis based on concatenated nuclear ribosomal ITS (internal transcribed spacer) and LSU (large ribosomal subunit) sequence datasets revealed its placement within the genus Astragalicola. However, it formed a separate clade exhibiting strong bootstrap support value (80%). The highest nrITS sequence similarity between EIT4^T and species of Astragalicola was 95.19% (A. vasilyevae) and 94.26% (A. amorpha), while nrLSU sequence similarity was 99.27% (A. amorpha). Morphologically, EIT4^T differs from the other species of Astragalicola in having larger sub-globose to pyriform conidiomata, smaller and mostly unbranched conidiophores, and polymorphic translucent conidia with two terminal guttules. Based on combined cultural, micromorphological, molecular, and phylogenetic analyses, EIT4^T represents a novel species in the genus Astragalicola proposed here as Astragalicola ephedrae sp. nov. Detailed description and illustrations of the novel species are provided. The type strain is EIT4^T (= MCC 9756 ^T = MN29^T).

Diversity of Culturable Endophytic Fungi in Crocus sativus and Their Correlation with Crocin Content

The presence and diversity of endophytic fungi associated with host plants are important not just for host plant growth and defense, but also impact the production of medicinal secondary metabolites. However, the correlation between endophytic fungi and crocin production in Crocus sativus (CS) remains underexplored. Here, we explore the relationship between endophytic fungal diversity and crocin content among different CS tissues and field sites. Specifically, we isolated endophytic fungi from five different field sites (Shanghai, Jiande, Huzhou, Anhui, and Hebei) and five different tissues (corm, scape, leaf, petal, and stigma) and analyzed fungal community diversity, richness, and evenness. We identified a total of 32 endophytic fungal taxa, assigned to 7 orders within 4 classes (Eurotiomycetes, Agaricomycetes, Dothideomycetes, and Sordariomycetes). The most dominant order was Eurotiales, and the most dominant genera were Penicillium and Talaromyces. Species richness tended to be highest in belowgrown tissues, such as corm and scape. Additionally, several fungal taxa were found to be either site- or tissue-specific. Three genera in particular were correlated with crocin content: Penicillium, Sistotrema, and Bjerkandera. Given the fact that endophytic microorganisms can both promote the production of secondary metabolites in host plants and potentially produce secondary metabolites themselves, further study is required to understand the mechanistic relationship between these and other fungal genera and crocin production.

Comparison of the diversity and structure of the rhizosphere microbial community between the straight and twisted trunk types of Pinus yunnanensis

Background

Pinus yunnanensis is a major silvicultural species in Southwest China. Currently, large areas of twisted-trunk Pinus yunnanensis stands severely restrict its productivity. Different categories of rhizosphere microbes evolve alongside plants and environments and play an important role in the growth and ecological fitness of their host plant. However, the diversity and structure of the rhizosphere microbial communities between P. yunnanensis with two different trunk types-straight and twisted-remain unclear.

Methods

We collected the rhizosphere soil of 5 trees with the straight and 5 trees with the twisted trunk type in each of three sites in Yunnan province. We assessed and compared the diversity and structure of the rhizosphere microbial communities between P. yunnanensis with two different trunk types by Illumina sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions.

Results

The available phosphorus in soil differed significantly between P. yunnanensis with straight and twisted trunks. Available potassium had a significant effect on fungi. Chloroflexi dominated the rhizosphere soils of the straight trunk type, while Proteobacteria was predominant in the rhizosphere soils of the twisted trunk type. Trunk types significantly explained 6.79% of the variance in bacterial communities.

Conclusion

This study revealed the composition and diversity of bacterial and fungal groups in the rhizosphere soil of P. yunnanensis with straight and twisted trunk types, providing proper microbial information for different plant phenotypes.

Comparative analysis of fungal communities between herbicide-resistant and -susceptible Alopecurus aequalis

Introduction

Alopecurus aequalis is a grass species invading Chinese canola and wheat fields. An A. aequalis KMN-R population surviving mesosulfuron-methyl treatment with recommended rates was acquired from wheatland. Here, we aimed to confirm the resistance profiles of KMN-R to acetolactate synthetase (ALS) inhibiting herbicides and explore the possible resistance mechanisms to mesosulfuron-methyl in this weed population.

Methods

The dose-response tests performed in our study were used to test the toxicity of A. aequalis to ALS-inhibiting herbicides. Sanger sequencing was used to analyze the ALS gene of mesosulfuron-methyl -resistant and -susceptible A. aequalis. RNA sequencing analysis was used to find candidate genes that may confer metabolic resistance to the mesosulfuron-methyl in resistant A. aequalis population. Mesosulfuron-methyl -resistant and -susceptible A. aequalis populations fungal composition was measured via Illumina MiSeq Sequencing.

Results

Dose-response results indicated that KMN-R population evolved resistance to mesosulfuron-methyl and other tested ALS-inhibiting herbicides. Known resistance-conferring Trp-574-Leu gene mutation in A. aequalis ALS was detected in the KMN-R population. Pretreatment with 4-chloro-7-nitrobenzoxadiazole reversed mesosulfuron-methyl resistance in KMN-R. Glutathione S-transferases (GST) gene GSTZ2 and GSTT3 were highly expressed in KMN-R population. In addition, we evaluated the alpha diversity in A. aequalis, centering on OTU abundance, equality, and multiplicity, and found that the fungal community composition had more unexplained variance between KMN-R and KMN-S A. aequalis. We also observed higher abundances of specific fungi in KMN-R A. aequalis.

Discussion

The results proved that resistance to mesosulfuron-methyl in A. aequalis KMN-R population is probably caused by target site- and non-target site-based relating GST and provided the basis for further research between fungal interaction and herbicide resistance.

Biostimulation of tomato growth and biocontrol of Fusarium wilt disease using certain endophytic fungi

BACKGROUND

Tomato plant (Solanum lycopersicum L.) suffers from numerous fungal pathogens that cause damage to yeild production qualitatively and quantitatively. One of the most destructive disease of tomato is Fusarium wilt that caused by soil borne fungus called F. oxysporum.

METHODS

In this study, the anti-Fusarium capabilities of the foliar application of fungal endophytes extracts have been investigated on tomato under Fusarium challenges. Antifungal assay, inhibition of conidial germination, disease severity, photosynthetic pigments, osmolytes, secondary metabolites, oxidative stress, peroxidase (POD) and polyphenol oxidases (PPO) isozymes were tested for potential resistance of tomato growing under Fusarium infection.

RESULTS

Ethyl acetate extracts of A. flavus MZ045563, A. fumigatus MZ045562 and A. nidulans MZ045561 exhibited antifungal activity toward F. oxysporum where inhibition zone diameters were 15, 12 and 20 mm, respectively. Moreover, extracts of all fungal isolates at concentration 7.5 mg/mL reduced conidia germination from 94.4 to 100%. Fusarium infection caused a destructive effects on tomato plant, high severity desiese index 84.37%, reduction in growth parameters, photosynthetic pigments, and soluble protein. However, contents of proline, total phenol, malondialdehyde (MDA), hydrogen peroxide (H₂O₂) and antioxidant enzymes activity were increased in tomato plants grown under Fusarium wilt. Treatment of healthy or infected tomato plants by ethyl acetate fungal extracts showed improvements in morphological traits, photosynthetic pigments, osmolytes, total phenol and antioxidant enzymes activity. Besides, the harmful impacts of Fusarium wilt disease on tomato plants have also been reduced by lowering MDA and H₂O₂ levels. Also, treated tomato plants showed different responses in number and density of POD and PPO isozymes.

CONCLUSION

It could be suggested that application of ethyl acetate extracts of tested fungal endophytes especially combination of A. flavus, A. nidulans and A. fumigatus could be commercially used as safe biostimulation of tomato plants as well as biofungicide against tomato Fusarium wilt disease.

Anti-Epstein-Barr Viral Agents from the Medicinal Herb-Derived Fungus Alternaria alstroemeriae Km2286

Chromatographic separation on the liquid-state fermented products produced by the fungal strain Alternaria alstroemeriae Km2286 isolated from the littoral medicinal herb Atriplex maximowicziana Makino resulted in the isolation of compounds 1-9. Structures were determined by spectroscopic analysis as four undescribed perylenequinones, altertromins A-D (1-4), along with altertoxin IV (5), altertoxin VIII (6), stemphyperylenol (7), tenuazonic acid (8), and allo-tenuazonic acid (9). Compounds 1-6 exhibited antiviral activities against Epstein-Barr virus (EBV) with EC₅₀ values ranging from 0.17 ± 0.07 to 3.13 ± 0.31 μM and selectivity indices higher than 10. In an anti-neuroinflammatory assay, compounds 1-4, 6, and 7 showed inhibitory activity of nitric oxide production in lipopolysaccharide-induced microglial BV-2 cells, with IC₅₀ values ranging from 0.33 ± 0.04 to 4.08 ± 0.53 μM without significant cytotoxicity. This is the first report to describe perylenequinone-type compounds with potent anti-EBV and anti-neuroinflammatory activities.

Chemical elicitation as an avenue for discovery of bioactive compounds from fungal endophytes

The present study investigated the molecular phylogeny, antimicrobial and cytotoxic activities of fungal endophytes obtained from the A*STAR Natural Organism Library (NOL) and previously isolated from Sungei Buloh Wetland Reserve, Singapore. Phylogenetic analysis based on ITS2 gene suggests that these isolates belong to 46 morphotypes and are affiliated to 23 different taxa in 17 genera of the Ascomycota phylum. Colletotrichum was the most dominant fungal genus accounting for 37% of all the isolates, followed by Diaporthe (13%), Phyllosticta (10.9%) and Diplodia (8.7%). Chemical elicitation using 5-azacytidine, a DNA methyltransferase inhibitor and suberoylanilide hydroxamic acid, a histone deacetylase inhibitor resulted in an increase in the number of active strains. Bioassay-guided isolation and structural elucidation yielded pestahivin and two new analogues from Bartalinia sp. F9447. Pestahivin and its related analogues did not exhibit antibacterial activity against Staphylococcus aureus but displayed strong antifungal activities against Candida albicans and Aspergillus brasiliensis, with IC₅₀ values ranging from 0.46 ± 0.06 to 144 ± 18 µM. Pestahivin and its two analogues furthermore exhibited cytotoxic activity against A549 and MIA PACA-2 cancer cell lines with IC₅₀ values in the range of 0.65 ± 0.12 to 42 ± 5.2 µM. The finding from this study reinforces that chemical epigenetic induction is a promising approach for the discovery of bioactive fungal secondary metabolites encoded by cryptic gene clusters.

Novel RNA Viruses Discovered in Weeds in Rice Fields

Weeds often grow alongside crop plants. In addition to competing with crops for nutrients, water and space, weeds host insect vectors or act as reservoirs for viral diversity. However, little is known about viruses infecting rice weeds. In this work, we used metatranscriptomic deep sequencing to identify RNA viruses from 29 weed samples representing 23 weed species. A total of 224 RNA viruses were identified: 39 newly identified viruses are sufficiently divergent to comprise new families and genera. The newly identified RNA viruses clustered within 18 viral families. Of the identified viruses, 196 are positive-sense single-stranded RNA viruses, 24 are negative-sense single-stranded RNA viruses and 4 are double-stranded RNA viruses. We found that some novel RNA viruses clustered within the families or genera of several plant virus species and have the potential to infect plants. Collectively, these results expand our understanding of viral diversity in rice weeds. Our work will contribute to developing effective strategies with which to manage the spread and epidemiology of plant viruses.

Parthenium hysterophorus's Endophytes: The Second Layer of Defense against Biotic and Abiotic Stresses

Parthenium hysterophorus L. is considered an obnoxious weed due to its rapid dispersal, fast multiplications, and agricultural and health hazards. In addition to its physio-molecular and phytotoxic allelochemical usage, this weed most probably uses endophytic flora as an additional line of defense to deal with stressful conditions and tolerate both biotic and abiotic stresses. The aim of this article is to report the diversity of endophytic flora (fungi and bacteria) in P. hysterophorus and their role in the stress mitigation (biotic and abiotic) of other important crops. Various endophytes were reported from P.&nbsp;hysterophorus and their roles in crops evaluated under biotic and abiotic stressed conditions. These endophytes have the potential to alleviate different stresses by improving crops/plants growth, development, biomass, and photosynthetic and other physiological traits. The beneficial role of the endophytes may be attributed to stress-modulating enzymes such as the antioxidants SOD, POD and APX and ACC deaminases. Additionally, the higher production of different classes of bioactive secondary metabolites, i.e., flavonoids, proline, and glutathione may also overcome tissue damage to plants under stressed conditions. Interestingly, a number of medicinally important phytochemicals such as anhydropseudo-phlegmcin-9, 10-quinone-3-amino-8-O methyl ether 'anhydropseudophlegmacin-9, 10-quinone-3-amino-8-Omethyl ether were reported from the endophytic flora of P. hysterophorus. Moreover, various reports revealed that fungal and bacterial endophytes of P. hysterophorus enhance plant growth-promoting attributes and could be added to the consortium of biofertilizers.

Synergistic Effects of Trichoderma harzianum, 1,3 Dichloropropene and Organic Matter in Controlling the Root-Knot Nematode Meloidogyne incognita on Tomato

Environmental concerns raised by synthetic nematicides are encouraging integrated management strategies based on their combination with non-chemical control tools, such as biocontrol agents and/or organic amendments. In this study, the combination of the fumigant 1,3-dichloropropene (1,3-D) with a commercial formulation of the biocontrol agent Trichoderma harzianum (TH) and an organic fertilizer (OF) was investigated in two consecutive tomato crops for its effect on the root-knot nematode Meloidogyne incognita and plant growth and yield. The application of 1,3-D was only performed on the first crop, while TH and OF were provided to both crops. Almost all treatments significantly reduced nematode infestation in both crops, though the greatest nematicidal effect was caused by a combination of the three products. The treatment with 1,3-D limited its nematicidal efficacy to the first crop only. Fumigant integration with TH and OF also resulted in the greatest increases of plant growth and yield. Therefore, the integrated management of root-knot nematodes with a soil fumigant, a bionematicide as T. harzianum and a source of organic matter demonstrated effective nematode suppression though limiting the number of chemical applications.

The Diversity of Fungal Endophytes from Wild Grape Vitis amurensis Rupr

Grapevine endophytic fungi have great potential for application in agriculture and represent an important source of various compounds with valuable biological activities. Wild grapevine is known to host a great number of rare and unidentified endophytes and may represent a rich repository of potential vineyard biocontrol agents. This investigation aimed to study the fungal endophytic community of wild grape Vitis amurensis Rupr. using a cultivation-dependent (fungi sowing) and a cultivation-independent (next-generation sequencing, NGS) approach. A comprehensive analysis of the endophytic fungal community in different organs of V. amurensis and under different environmental conditions has been performed. According to the NGS analysis, 12 taxa of class level were presented in different grapevine organs (stem, leaf, berry, seed). Among the 12 taxa, sequences of two fungal classes were the most represented: Dothideomycetes-60% and Tremellomycetes-33%. The top five taxa included Vishniacozyma, Aureobasidiaceae, Cladosporium, Septoria and Papiliotrema. The highest number of fungal isolates and sequences were detected in the grape leaves. The present data also revealed that lower temperatures and increased precipitation favored the number and diversity of endophytic fungi in the wild Amur grape. The number of fungi recovered from grape tissues in autumn was two times higher than in summer. Thus, this study is the first to describe and analyze the biodiversity of the endophytic fungal community in wild grapevine V. amurensis.

Perspectives and potential applications of endophytic microorganisms in cultivation of medicinal and aromatic plants

Ensuring food and nutritional security, it is crucial to use chemicals in agriculture to boost yields and protect the crops against biotic and abiotic perturbations. Conversely, excessive use of chemicals has led to many deleterious effects on the environment like pollution of soil, water, and air; loss of soil fertility; and development of pest resistance, and is now posing serious threats to biodiversity. Therefore, farming systems need to be upgraded towards the use of biological agents to retain agricultural and environmental sustainability. Plants exhibit a huge and varied niche for endophytic microorganisms inside the planta, resulting in a closer association between them. Endophytic microorganisms play pivotal roles in plant physiological and morphological characteristics, including growth promotion, survival, and fitness. Their mechanism of action includes both direct and indirect, such as mineral phosphate solubilization, fixating nitrogen, synthesis of auxins, production of siderophore, and various phytohormones. Medicinal and aromatic plants (MAPs) hold a crucial position worldwide for their valued essential oils and several phytopharmaceutically important bioactive compounds since ancient times; conversely, owing to the high demand for natural products, commercial cultivation of MAPs is on the upswing. Furthermore, the vulnerability to various pests and diseases enforces noteworthy production restraints that affect both crop yield and quality. Efforts have been made towards enhancing yields of plant crude drugs by improving crop varieties, cell cultures, transgenic plants, etc., but these are highly cost-demanding and time-consuming measures. Thus, it is essential to evolve efficient, eco-friendly, cost-effective simpler approaches for improvement in the yield and health of the plants. Harnessing endophytic microorganisms as biostimulants can be an effective and alternative step. This review summarizes the concept of endophytes, their multidimensional interaction inside the host plant, and the salient benefits associated with endophytic microorganisms in MAPs.

Advancement in the molecular perspective of plant-endophytic interaction to mitigate drought stress in plants

Change in global climate has started to show its effect in the form of extremes of temperatures and water scarcity which is bound to impact adversely the global food security in near future. In the current review we discuss the impact of drought on plants and highlight the ability of endophytes, microbes that inhabit the plants asymptomatically, to confer stress tolerance to their host. For this we first describe the symbiotic association between plant and the endophytes and then focus on the molecular and physiological strategies/mechanisms adopted by these endophytes to confer stress tolerance. These include root alteration, osmotic adjustment, ROS scavenging, detoxification, production of phytohormones, and promoting plant growth under adverse conditions. The review further elaborates on how omics-based techniques have advanced our understanding of molecular basis of endophyte mediated drought tolerance of host plant. Detailed analysis of whole genome sequences of endophytes followed by comparative genomics facilitates in identification of genes involved in endophyte-host interaction while functional genomics further unveils the microbial targets that can be exploited for enhancing the stress tolerance of the host. Thus, an amalgamation of endophytes with other sustainable agricultural practices seems to be an appeasing approach to produce climate-resilient crops.

Phytostimulants in sustainable agriculture

The consistent use of synthetic fertilizers and chemicals in traditional agriculture has not only compromised the fragile agroecosystems but has also adversely affected human, aquatic, and terrestrial life. The use of phytostimulants is an alternative eco-friendly approach that eliminates ecosystem disruption while maintaining agricultural productivity. Phytostimulants include living entities and materials, such as microorganisms and nanomaterials, which when applied to plants or to the rhizosphere, stimulate plant growth and induce tolerance to plants against biotic and abiotic stresses. In this review, we focus on plant growth-promoting rhizobacteria (PGPR), beneficial fungi, such as arbuscular mycorrhizal fungi (AMF) and plant growth-promoting fungi (PGPF), actinomycetes, cyanobacteria, azolla, and lichens, and their potential benefits in the crop improvement, and mitigation of abiotic and biotic stresses either alone or in combination. PGPR, AMF, and PGPF are plant beneficial microbes that can release phytohormones, such as indole acetic acid (IAA), gibberellic acid (GA), and cytokinins, promoting plant growth and improving soil health, and in addition, they also produce many secondary metabolites, antibiotics, and antioxidant compounds and help to combat biotic and abiotic stresses. Their ability to act as phytostimulator and a supplement of inorganic fertilizers is considered promising in practicing sustainable agriculture and organic farming. Glomalin is a proteinaceous product, produced by AMF, involved in soil aggregation and elevation of soil water holding capacity under stressed and unstressed conditions. The negative effects of continuous cropping can be mitigated by AMF biofertilization. The synergistic effects of PGPR and PGPF may be more effective. The mechanisms of control exercised by PGPF either direct or indirect to suppress plant diseases viz. by competing for space and nutrients, mycoparasitism, antibiosis, mycovirus-mediated cross-protection, and induced systemic resistance (ISR) have been discussed. The emerging role of cyanobacterial metabolites and the implication of nanofertilizers have been highlighted in sustainable agriculture.

Hairy roots: An untapped potential for production of plant products

While plants are an abundant source of valuable natural products, it is often challenging to produce those products for commercial application. Often organic synthesis is too expensive for a viable commercial product and the biosynthetic pathways are often so complex that transferring them to a microorganism is not trivial or feasible. For plants not suited to agricultural production of natural products, hairy root cultures offer an attractive option for a production platform which offers genetic and biochemical stability, fast growth, and a hormone free culture media. Advances in metabolic engineering and synthetic biology tools to engineer hairy roots along with bioreactor technology is to a point where commercial application of the technology will soon be realized. We discuss different applications of hairy roots. We also use a case study of the advancements in understanding of the terpenoid indole alkaloid pathway in Catharanthus roseus hairy roots to illustrate the advancements and challenges in pathway discovery and in pathway engineering.

Fungal endophytes of Brassicaceae: Molecular interactions and crop benefits

Brassicaceae family includes an important group of plants of great scientific interest, e.g., the model plant Arabidopsis thaliana, and of economic interest, such as crops of the genus Brassica (Brassica oleracea, Brassica napus, Brassica rapa, etc.). This group of plants is characterized by the synthesis and accumulation in their tissues of secondary metabolites called glucosinolates (GSLs), sulfur-containing compounds mainly involved in plant defense against pathogens and pests. Brassicaceae plants are among the 30% of plant species that cannot establish optimal associations with mycorrhizal hosts (together with other plant families such as Proteaceae, Chenopodiaceae, and Caryophyllaceae), and GSLs could be involved in this evolutionary process of non-interaction. However, this group of plants can establish beneficial interactions with endophytic fungi, which requires a reduction of defensive responses by the host plant and/or an evasion, tolerance, or suppression of plant defenses by the fungus. Although much remains to be known about the mechanisms involved in the Brassicaceae-endophyte fungal interaction, several cases have been described, in which the fungi need to interfere with the GSL synthesis and hydrolysis in the host plant, or even directly degrade GSLs before they are hydrolyzed to antifungal isothiocyanates. Once the Brassicaceae-endophyte fungus symbiosis is formed, the host plant can obtain important benefits from an agricultural point of view, such as plant growth promotion and increase in yield and quality, increased tolerance to abiotic stresses, and direct and indirect control of plant pests and diseases. This review compiles the studies on the interaction between endophytic fungi and Brassicaceae plants, discussing the mechanisms involved in the success of the symbiosis, together with the benefits obtained by these plants. Due to their unique characteristics, the family Brassicaceae can be seen as a fruitful source of novel beneficial endophytes with applications to crops, as well as to generate new models of study that allow us to better understand the interactions of these amazing fungi with plants.

Zanthoxylum bungeanum root-rot associated shifts in microbiomes of root endosphere, rhizosphere, and soil

Root-rot disease has lead to serious reduction in yields and jeopardized the survival of the economically and ecologically important Zanthoxylum bungeanum trees cultured in Sichuan Province. In order to investigate the interaction between the microbiome and the root-rot disease, a metagenomic analysis was performed to characterize the microbial communities and functions in Z. bungeanum root endosphere, rhizosphere and bulk soil with/without root-rot disease. Soil physicochemical properties, microbial population size and enzyme activities were also analyzed for finding their interactions with the root-rot disease. As results, lower total nitrogen (TN) and available phosphorus (AP) contents but higher pH in rhizosphere and bulk soil, as well as lower substrate-induced respiration (SIR) and higher protease activity in bulk soil of diseased trees were found, in comparison with that of healthy trees. Microbial diversity and community composition were changed by root-rot disease in the endosphere, but not in rhizosphere and bulk soils. The endophytic microbiome of diseased trees presented higher Proteobacteria abundance and lower abundances of Bacteroidetes, Firmicutes and dominant fungal phyla. The relative abundances of nitrogen cycle- and carbon cycle-related genes in endophytic microbiomes were different between the diseased and healthy trees. Based on ANOSIM and PCoA, functional profiles (KEGG and CAZy) of microbiomes in rhizosphere and bulk soil shifted significantly between the diseased and healthy trees. In addition, soil pH, TN, AP, SIR, invertase and protease were estimated as the main factors influencing the shifts of taxonomic and functional groups in microbiomes of rhizosphere and bulk soil. Conclusively, the imbalance of root and soil microbial function groups might lead to shifts in the root endosphere-rhizosphere microenvironment, which in turn resulted in Z. bungeanum root-rot.

Diversity of endophytic fungi in Coptis chinensis Franch. and their activity against methicillin-resistant Staphylococcus aureus

This study aimed at investigating the diversity of endophytic fungi from Coptis chinensis and their activity against methicillin-resistant Staphylococcus aureus (MRSA). Seventy-nine fungal isolates obtained from C. chinensis were identified to belong to 27 species based on morphological features and internal transcript spacer (ITS) gene sequencing analysis. Comparing relative frequency values, the most frequent genera were Colletotrichum and Fusarium, while most frequent species were C. gloeosporioides and F. avenaceum. Analysis of diversity indices indicated that C. chinensis harbored abundant fungal resources. Methanol extracts of fungal endophyte cultures were evaluated for antibacterial activity against S. aureus ATCC 25923 and two other MRSA clinical strains. Nine of 27 endophytic fungi exhibited inhibitory activities against S. aureus ATCC 25923. Among them, Paraboeremia litseae HL-17, Fusarium sp. HL-23, and Fusarium sp. HL-27 exhibited obvious inhibition against the three S. aureus strains. Our findings suggest that the endophytic fungi in C. chinensis have a high diversity and an obvious tissue specificity, and could be of potential interest in screening anti-MRSA agents. To the best of our knowledge, this is the first report on the diversity and anti-MRSA activity of fungal endophytes from C. chinensis.

Metabolites characterisation of endophytic Phyllosticta fallopiae L67 isolated from Aloe vera with antimicrobial activity on diabetic wound microorganisms

This study aimed to assess the antimicrobial activity of endophytic Phyllosticta fallopiae L67 isolated from Aloe vera against diabetic wound microorganisms and characterise their active fraction for biologically important metabolites. The dichloromethane (DCM) extract exhibited the most significant activity with inhibition zones ranging from 11.33 to 38.33 mm. The minimal inhibitory and lethality concentrations of DCM extract ranged from 78.13 to 2500.00 µg/ml and 625.00 to 5000.00 µg/ml, respectively. The extract showed teratogenicity and lethality in the zebrafish model, where peritoneal and hepatic oedema occurred at 62.50 µg/ml, and no abnormality appeared at 31.25 µg/ml. The extract also inhibited more than 82% biofilm formation. Bioassay-guided fractionation on DCM extract yielded 18 fractions and the most active fraction was subjected to UPLC-QTOF-MS/MS analysis. Flavones, stilbenes, flavanonols, isoflavonoids, phenolic glycosides and phenol derivatives were detected. In conclusion, endophytic P. fallopiae possessed bioactive metabolites with significant antimicrobial activity against diabetic wound microorganisms.

Biosynthetic Mechanisms of Secondary Metabolites Promoted by the Interaction Between Endophytes and Plant Hosts

Endophytes is a kind of microorganism resource with great potential medicinal value. The interactions between endophytes and host not only promote the growth and development of each other but also drive the biosynthesis of many new medicinal active substances. In this review, we summarized recent reports related to the interactions between endophytes and hosts, mainly regarding the research progress of endophytes affecting the growth and development of host plants, physiological stress and the synthesis of new compounds. Then, we also discussed the positive effects of multiomics analysis on the interactions between endophytes and their hosts, as well as the application and development prospects of metabolites synthesized by symbiotic interactions. This review may provide a reference for the further development and utilization of endophytes and the study of their interactions with their hosts.

Fungal Endophytes to Combat Biotic and Abiotic Stresses for Climate-Smart and Sustainable Agriculture

The agricultural sustainability concept considers higher food production combating biotic and abiotic stresses, socio-economic well-being, and environmental conservation. On the contrary, global warming-led climatic changes have appalling consequences on agriculture, generating shifting rainfall patterns, high temperature, CO2, drought, etc., prompting abiotic stress conditions for plants. Such stresses abandon the plants to thrive, demoting food productivity and ultimately hampering food security. Though environmental issues are natural and cannot be regulated, plants can still be enabled to endure these abnormal abiotic conditions, reinforcing the stress resilience in an eco-friendly fashion by incorporating fungal endophytes. Endophytic fungi are a group of subtle, non-pathogenic microorganisms establishing a mutualistic association with diverse plant species. Their varied association with the host plant under dynamic environments boosts the endogenic tolerance mechanism of the host plant against various stresses via overall modulations of local and systemic mechanisms accompanied by higher antioxidants secretion, ample enough to scavenge Reactive Oxygen Species (ROS) hence, coping over-expression of defensive redox regulatory system of host plant as an aversion to stressed condition. They are also reported to ameliorate plants toward biotic stress mitigation and elevate phytohormone levels forging them worthy enough to be used as biocontrol agents and as biofertilizers against various pathogens, promoting crop improvement and soil improvement, respectively. This review summarizes the present-day conception of the endophytic fungi, their diversity in various crops, and the molecular mechanism behind abiotic and biotic resistance prompting climate-resilient aided sustainable agriculture.

Comparative Genomics of Three Aspergillus Strains Reveals Insights into Endophytic Lifestyle and Endophyte-Induced Plant Growth Promotion

Aspergillus includes both plant pathogenic and beneficial fungi. Although endophytes beneficial to plants have high potential for plant growth promotion and improving stress tolerance, studies on endophytic lifestyles and endophyte-plant interactions are still limited. Here, three endophytes belonging to Aspergillus, AS31, AS33, and AS42, were isolated. They could successfully colonize rice roots and significantly improved rice growth. The genomes of strains AS31, AS33, and AS42 were sequenced and compared with other Aspergillus species covering both pathogens and endophytes. The genomes of AS31, AS33, and AS42 were 36.8, 34.8, and 35.3 Mb, respectively. The endophytic genomes had more genes encoding carbohydrate-active enzymes (CAZymes) and small secreted proteins (SSPs) and secondary metabolism gene clusters involved in indole metabolism than the pathogens. In addition, these endophytes were able to improve Pi (phosphorus) accumulation and transport in rice by inducing the expression of Pi transport genes in rice. Specifically, inoculation with endophytes significantly increased Pi contents in roots at the early stage, while the Pi contents in inoculated shoots were significantly increased at the late stage. Our results not only provide important insights into endophyte-plant interactions but also provide strain and genome resources, paving the way for the agricultural application of Aspergillus endophytes.

Strategies to Enhance the Use of Endophytes as Bioinoculants in Agriculture

The findings on the strategies employed by endophytic microbes have provided salient information to the researchers on the need to maximally explore them as bio-input in agricultural biotechnology. Biotic and abiotic factors are known to influence microbial recruitments from external plant environments into plant tissues. Endophytic microbes exhibit mutualism or antagonism association with host plants. The beneficial types contribute to plant growth and soil health, directly or indirectly. Strategies to enhance the use of endophytic microbes are desirable in modern agriculture, such that these microbes can be applied individually or combined as bioinoculants with bioprospecting in crop breeding systems. Scant information is available on the strategies for shaping the endophytic microbiome; hence, the need to unravel microbial strategies for yield enhancement and pathogen suppressiveness have become imperative. Therefore, this review focuses on the endophytic microbiome, mechanisms, factors influencing endophyte recruitment, and strategies for possible exploration as bioinoculants.

The Multifunctions and Future Prospects of Endophytes and Their Metabolites in Plant Disease Management

Endophytes represent a ubiquitous and magical world in plants. Almost all plant species studied by different researchers have been found to harbor one or more endophytes, which protect host plants from pathogen invasion and from adverse environmental conditions. They produce various metabolites that can directly inhibit the growth of pathogens and even promote the growth and development of the host plants. In this review, we focus on the biological control of plant diseases, aiming to elucidate the contribution and key roles of endophytes and their metabolites in this field with the latest research information. Metabolites synthesized by endophytes are part of plant disease management, and the application of endophyte metabolites to induce plant resistance is very promising. Furthermore, multi-omics should be more fully utilized in plant–microbe research, especially in mining novel bioactive metabolites. We believe that the utilization of endophytes and their metabolites for plant disease management is a meaningful and promising research direction that can lead to new breakthroughs in the development of more effective and ecosystem-friendly insecticides and fungicides in modern agriculture.

Endophytic Fungus Phomopsis liquidambaris Enhances Fe Absorption in Peanuts by Reducing Hydrogen Peroxide

Iron (Fe) deficiency in alkaline calcium soil is a problem that needs to be solved urgently as Fe is an essential and commonly limiting nutrient for plants. Endophytic fungus, Phomopsis liquidambaris (P. liquidambaris), has been reported to promote Fe absorption in peanuts (Arachis hypogaea L.), however, the mechanisms remain unclear. Under prolonged Fe deficiency, an increase in hydrogen peroxide (H₂O₂) often triggers a series of signaling events and leads to the inhibition of Fe acquisition. The main purpose of this study was to explore whether and how the endophytic fungus P. liquidambaris promote Fe absorption in peanut through regulating H₂O₂ and assisting in resisting oxidative stress. In this study, we detected the Fe deficiency-induced transcription factor (FIT), Fe²⁺ transporter (IRT1), and ferric reduction oxidase 2 (FRO2) of peanuts, and confirmed that they were negatively related to Fe concentration. Similarly, FIT, IRT1, and FRO2 were also inhibited by H₂O₂. The addition of P. liquidambaris reduces H₂O₂ under Fe-deficiency with an increase in Fe content, while the exogenous addition of H₂O₂ further decreases it, and the addition of catalase (CAT) under Fe-deficiency reverses this phenomenon. Through transcriptome analysis, we proved that the expression of FIT, IRT1, FRO2 and CAT are consistent with our hypothesis, and P. liquidambaris has a stress-mitigating effect on peanuts mainly via CAT, glutathione peroxidase, and malondialdehyde. Our study proved the Fe-absorption promoting effect and stress mitigation effect of P. liquidambaris under Fe-deficiency in peanuts, and their combined usage may help peanuts grow better.

Prospecting potential of endophytes for modulation of biosynthesis of therapeutic bioactive secondary metabolites and plant growth promotion of medicinal and aromatic plants

Medicinal and aromatic plants possess pharmacological properties (antidiabetes, anticancer, antihypertension, anticardiovascular, antileprosy, etc.) because of their potential to synthesize a wide range of therapeutic bioactive secondary metabolites. The concentration of bioactive secondry metabolites depends on plant species, local environment, soil type and internal microbiome. The internal microbiome of medicinal plants plays the crucial role in the production of bioactive secondary metabolites, namely alkaloids, steroids, terpenoids, peptides, polyketones, flavonoids, quinols and phenols. In this review, the host specific secondry metabolites produced by endophytes, their therapeutic properties and host-endophytes interaction in relation to production of bioactive secondry metaboloites and the role of endophytes in enhancing the production of bioactive secondry metabolites is discussed. How biological nitrogen fixation, phosphorus solubilization, micronutrient uptake, phytohormone production, disease suppression, etc. can play a vital role in enhacing the plant growth and development.The role of endophytes in enhancing the plant growth and content of bioactive secondary metabolites in medicinal and aromatic plants in a sustainable mode is highlighted.

Isolation of Potato Endophytes and Screening of Chaetomium globosum Antimicrobial Genes

Antimicrobial peptides (AMPs) have natural antibacterial activities that pathogens find difficult to overcome. As a result of this occurrence, AMPs can act as an important substitute against the microbial resistance. In this study, we used plate confrontation tests to screen out 20 potential endophytes from potato tubers. Among them, endophyte F5 was found to significantly inhibit the growth of five different pathogenic fungi. Following that, phylogenetic analysis revealed that the internal transcribed spacer (ITS) sequences were 99% identical to Chaetomium globosum corresponding sequences. Thereafter, the Bacillus subtilis expression system was used to create a C. globosum cDNA library in order to isolate the resistance genes. Using this approach, the resistance gene screening technology in the indicator bacteria built-in library was used to identify two antimicrobial peptides, CgR2150 and CgR3101, with broad-spectrum antibacterial activities. Furthermore, the results showed that CgR2150 and CgR3101 have excellent UV, thermal, and enzyme stabilities. Also, these two peptides can significantly inhibit the growth of various bacteria (Xanthomonas oryzae pv. oryzae, Xanthomonas oryzae pv. oryzicola, Clavibacter michiganensis, and Clavibacter fangii) and fungi (Fusarium graminearum, Rhizoctonia solani, and Botrytis cinerea). Scanning electron microscopy (SEM) observations revealed that CgR2150 and CgR3101 peptides act against bacteria by disrupting bacterial cell membranes. Moreover, hemolytic activity assay showed that neither of the two peptides exhibited significant hemolytic activity. To conclude, the antimicrobial peptides CgR2150 and CgR3101 are promising in the development of a new antibacterial agent and for application in plant production.

Comprehensive Review of Fungi on Coffee

Coffee is grown in more than 80 countries as a cash crop and consumed worldwide as a beverage and food additive. It is susceptible to fungal infection during growth, processing and storage. Fungal infections, in particular, can seriously affect the quality of coffee and threaten human health. The data for this comprehensive review were collected from the United States Department of Agriculture, Agricultural Research Service (USDA ARS) website and published papers. This review lists the fungal species reported on coffee based on taxonomy, life mode, host, affected plant part and region. Five major fungal diseases and mycotoxin-producing species (post-harvest diseases of coffee) are also discussed. Furthermore, we address why coffee yield and quality are affected by fungi and propose methods to control fungal infections to increase coffee yield and improve quality. Endophytic fungi and their potential as biological control agents of coffee disease are also discussed.

Is the rhizosphere a source of applicable multi-beneficial microorganisms for plant enhancement?

The plant faces different pedological and climatic challenges that influence its growth and enhancement. While, plant-microbes interactions throught the rhizosphere offer several privileges to this hotspot in the service of plant, by attracting multi-beneficial mutualistic and symbiotic microorganisms as plant growth-promoting bacteria (PGPB), archaea, mycorrhizal fungi, endophytic fungi, and others…). Currently, numerous investigations showed the beneficial effects of these microbes on growth and plant health. Indeed, rhizospheric microorganisms offer to host plants the essential assimilable nutrients, stimulate the growth and development of host plants, and induce antibiotics production. They also attributed to host plants numerous phenotypes involved in the increase the resistance to abiotic and biotic stresses. The investigations and the studies on the rhizosphere can offer a way to find a biological and sustainable solution to confront these environmental problems. Therefore, the interactions between microbes and plants may lead to interesting biotechnological applications on plant improvement and the adaptation in different climates to obtain a biological sustainable agricultures without the use of chemical fertilizers.