Isolation and Characterization of Plant Growth-Promoting Endophytic Fungi from the Roots of Dendrobium moniliforme

Plant Growth-Promoting Potential of Colletotrichum sp. Isolated from Ocimum basilicum L. Leaves: A Broad-Spectrum Evaluation

The primary objective of this study was to assess the growth-promoting potential of Colletotrichum sp. as a broad-spectrum plant inoculant and to investigate its applicability beyond its natural host range. Out of ten endophytes isolated from Ocimum basilicum, only four were reported for IAA production and among them, Colletotrichum sp. was chosen for further investigation due to its higher IAA production. Highest production of IAA was observed by providing Czapek dox broth with dextrose as carbon source, ammonium sulphate as nitrogen source at pH 7 and 32 °C. The crude fungal extract from Colletotrichum sp. was tested for its impact on rice plants under different application methods (soil drenching, foliar spraying, and seed immersion). Seed immersion treatment showed a notable effect on the growth of rice seedlings in contrast to soil drenching and foliar spraying. Plant growth assay with fungal elicitor treatment of plantlets produced by shoot culture, supplementing with 0.04 mL of culture filtrate per 30 mL media has significant impact on induction of rooting and overall biomass in Ocimum tenuiflorum as compared to untreated control plants. High-resolution liquid chromatography mass spectrometry (HR-LCMS) analysis of the fungal extract revealed the production of 3-indoleacetic acid and related intermediates.

Transcriptome analysis reveals potential medicinal ingredient synthesis in ornamental Dendrobium

Dendrobium is divided into ornamental and medicinal varieties due to ornamental and medicinal values. However, current research mainly focuses on medicinal Dendrobium, with less study on the medicinal value of ornamental Dendrobium. We analyzed the microstructures, active components of the stems from twelve ornamental Dendrobium, and explored the biosynthetic networks of these active components based on transcriptome sequencing. This study found the Dendrobium with the highest content of polysaccharide, alkaloid, and flavonoid was Dendrobium aphyllum (53.89 %), Dendrobium thyrsiflorum (2.11 %) and Dendrobium loddigesii (7.21 %). Further research revealed 9 DEGs associated with polysaccharide biosynthesis were highly expressed in D. aphyllum; 4 DEGs related to alkaloid biosynthesis were highly expressed in D. thyrsiflorum; 8 DEGs associated with flavonoid biosynthesis were highly expressed in D. loddigesii. This study revealed the potential medicinal value of ornamental Dendrobium and the synthetic mechanisms of its medicinal components, providing a foundation for the medical applications of ornamental Dendrobium.

The Role of Mycorrhizal Fungi in Orchids

BACKGROUND

In nature, orchid plants are obligate myco-heterotrophs, and rely on mycorrhizal nutrient resources to grow and sustain in the wild, until they become physiologically active photosynthetic plants. Their seeds lack nutrient reserves and receive the necessary carbon from symbiotic fungi during germination. A mycorrhizal fungus provides nutrients, especially sugars, as well as water to the corresponding host plant. The range and distribution of orchid mycorrhizal fungi influence the survivability of orchid populations in their natural habitats. Mycorrhizae form symbiotic connections with the parenchymatous tissues of the roots of orchid plants. That the symbiotic orchid mycorrhiza can invade through roots of orchid seedling, raised in vitro, has been patented.

OBJECTIVE

The objective of this study was to examine the presence of mycorrhiza in the roots of Aerides multiflora during the vegetative phase.

METHODS

Fresh roots were hand-sectioned, and thin sections were observed under the microscope to locate the presence of mycorrhiza. Simultaneously, to observe the expansion of mycorrhiza in the cortical region.

RESULTS

During the vegetative phase of plant growth, a peloton-like structure forms within the cortical region of the orchid roots. Mycorrhizae was observed to be distributed throughout the cortical layer of the root.

CONCLUSION

This communication reviews the role of mycorrhiza in orchid plants.

Extract from endophytic Fusarium isolates stimulates seed germination of the host and protocorm development of non-host orchids

We isolated endophytic Fusarium strains from the healthy roots, stems, and leaves of Dendrobium moschatum to investigate their plant growth-promoting activities in vitro. Subsequently, Indole acetic acid (IAA) was quantified and the IaaM gene (responsible for IAA synthesis in fungi) was amplified and sequenced. Finally, a germination assay was performed with seeds of D. moschatum and a plant growth assay with protocorms of Dendrobium longicornu to test their plant growth-promoting activities. Five Fusarium isolates (CDS11, PDL1, PDL3, PDR6, PDR7) were identified in this study. The highest amount (60µgml-1) of indole acetic acid was recorded in the PDR7 extract, whereas it was not detected in PDR6 and CDS11. The fungal extracts of isolates PDR6 and PDR7 were highly effective for seed germination by approximately 80% and 90% (respectively) of the host plant. The fungal extract of PDR7 showed a high IAA content and promoted in vitro seed germination of the host (D. moschatum) and protocorm development of the non-host (D. longicornu). In contrast, IAA content in the fungal extract of PDR6 remained undetected but was effective in both seed germination and protocorm development. Our results demonstrated the potential beneficial application of endophytic Fusarium in orchid mass propagation.

Mass Spectrometry-Based Molecular Networks Applied to Study the Molecular Interaction Between Two Endophytic Fungi Isolated From Tibouchina granulosa (Vell.) Cogn (Melastomataceae)

Establishing a microorganism as an endophyte involves complex molecular interactions with its host plant and a broader microbial community. Precise detection methods and comprehensive metabolite annotation are essential to study these interactions. This study focused on characterizing the chemical composition of metabolites produced by two endophytic fungi, Colletotrichum siamense and Xylaria berteroi, isolated from Tibouchina granulosa leaves in axenic conditions and coculture. We examined the fungal metabolites using ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HR-MS/MS) and analysis tools like Cytoscape and Global Natural Products Social Molecular Networking. Co-cultivation revealed unique compounds not produced in isolation, including N-acetyltryptamine. A total of 32 compounds were identified, many with biotechnological potential due to their bioactivities. The untargeted metabolomics approach demonstrated that interactions among these T. granulosa endophytes can activate inactive metabolic pathways under axenic conditions, potentially producing novel bioactive molecules. This study is the first study of the chemical profile and interaction between endophytes isolated from T. granulosa.

Culture-dependent methods reveal the diversity of endophytic fungi of Psidium cattleianum leaves (Myrtales: Myrtaceae)

Endophytic fungi are a diverse group of microorganisms that reside within plant tissues and play a crucial ecological role in the development of their hosts. Psidium cattleianum (Myrtales: Myrtaceae: 'Cattley guava') is a Brazilian native species with economic potential due to the diverse applications of its fruits, wood, and essential oils. Despite their significance, the diversity of endophytic fungi associated with P. cattleianum remains unexplored. Here, we investigated the diversity of endophytic fungi in the leaves of this plant using cultivation-dependent isolation methods, analysis of the macroscopic characters of the isolates, and phylogenetic analyses employing the ITS barcode marker. A total of 396 isolates, classified into 25 fungal taxa, were obtained, namely, Alternaria, Aspergillus, Cladosporium, Colletotrichum, Coprinellus, Coriolopsis, Diaporthe, Induratia, Mycosphaerella, Muyocoprom, Myrmecridium, Neofusicoccum, Pantospora, Paracamarosporium, Parapallidocercospora, Paraphaeosphaeria, Penicillium, Perenniporia, Phaeophleospora, Phyllosticta, Pseudofusicoccum, Talaromyces, Xylaria, Sordariomycetes, and Xylariomycetes. Our findings reveal a significant diversity of fungi associated with P. cattleianum leaves; however, our study suggests an even greater diversity of fungi associated with this plant species. Interestingly, although P. cattleianum shares endophytic fungi with other plants in the Myrtaceae family, this plant species harbors a unique fungal community. This distinction is evidenced by certain fungal genera and seven potentially new phylogenetic species, isolated in this study.

Effect of Different Basal Media and Organic Supplements on In Vitro Seedling Development of the Endangered Orchid Species Dendrobium moniliforme (L.) Swartz

The orchid Dendrobium moniliforme faces endangerment due to habitat loss and illegal harvesting, necessitating the development of an optimized artificial propagation system to aid conservation and reintroduction efforts. This study evaluated the effects of three plant growth media, namely Murashige and Skoog (MS), Hyponex, and Orchid Maintenance Medium (OMM) (P668), and various organic additives (apple homogenate, banana homogenate, and coconut water) on the in vitro seedling growth of D. moniliforme. The results reveal that, in early postgermination stages, seedlings achieve maximum growth in the Hyponex medium, with a fresh weight (92 mg) and root length (2.7 cm) approximately 20-fold greater than those in the MS medium and OMM. After 6 months, for seedlings grown in MS medium and OMM with banana (50 g·L-1), the mean fresh weights were 29 and 107 mg, respectively; however, the highest biomass was observed in seedlings grown in the Hyponex medium with coconut water (50 mL·L-1), exhibiting a mean fresh weight of 201 mg. This study highlights Hyponex medium with coconut water as the most effective combination for promoting D. moniliforme growth and identifies suitable organic supplements for the in vitro cultivation of seedlings from asymbiotic seed culture. This propagation system offers valuable technical support for the mass production and conservation of this epiphytic orchid.

Aromatic components and endophytic fungi during the formation of agarwood in Aquilaria sinensis were induced by exogenous substances

The process of formation of aromatic components for agarwood in Aquilaria sinensis is closely related to endophytic fungi and the result of complex multiple long-term joint interactions with them. However, the interactions between the aromatic components and endophytic fungi remain unclear during the formation of agarwood. In this study, precise mixed solution of hormones, inorganic salts, and fungi was used to induce its formation in A. sinensis, and sample blocks of wood were collected at different times after inoculation. This study showed that the aromatic compounds found in the three treatments of A. sinensis were primarily chromones (31.70-33.65%), terpenes (16.68-27.10%), alkanes (15.99-23.83%), and aromatics (3.13-5.07%). Chromones and terpenes were the primary components that characterized the aroma. The different sampling times had a more pronounced impact on the richness and diversity of endophytic fungal communities in the A. sinensis xylem than the induction treatments. The species annotation of the operational taxonomic units (OTUs) demonstrated that the endophytic fungi were primarily composed of 18 dominant families and 20 dominant genera. A linear regression analysis of the network topology properties with induction time showed that the interactions among the fungal species continued to strengthen, and the network structure tended to become more complex. The terpenes significantly negatively correlated with the Pielou evenness index (p < 0.05), while the chromones significantly positively correlated with the OTUs and Shannon indices.

Diversity of unique, nonmycorrhizal endophytic fungi in cultivated Phalaenopsis orchids: A pilot study

Orchids comprise one of the largest, most diverse, and most broadly distributed families of flowering plants and contribute significantly to habitat biodiversity. One key aspect of orchid growth and development is the formation of mycorrhizal symbioses with compatible endophytic fungi, which are maintained throughout the life of the plant. Substantial efforts to identify the fungi that form mycorrhizal symbioses across a range of orchid species have often also uncovered numerous nonmycorrhizal, endophytic fungi. These fungi could also have significant effects on orchid growth and development and are beginning to be analyzed more closely, particularly in wild species. The role of endophytic fungi in the production, distribution, and continued growth by the hobbyist of orchids is not known. As an initial step toward characterizing nonmycorrhizal endophytic fungi associated with cultivated orchids, we undertook a survey of fungi residing within roots of Phalaenopsis plants growing in home environments. Sequence analysis of ITS regions amplified from total DNA isolated from roots allowed rapid identification of endophytic fungi to the class level and may offer a useful initial screening method for beneficial species, for example, in horticultural settings. ITS-PCR sequences subsequently obtained from individual fungi cultured from surface-sterilized orchid roots corroborated the findings of the initial screen, while also providing a more complete characterization of the array of fungal taxa that were present. Although lower in diversity than has been reported for orchids growing in the wild, these endophytes have the potential to substantially enhance the growth and disease resistance of horticultural orchids.

Bioprospecting of endophytic fungi from medicinal plant Anisomeles indica L. for their diverse role in agricultural and industrial sectors

Endophytes are microorganisms that inhabit various plant parts and cause no damage to the host plants. During the last few years, a number of novel endophytic fungi have been isolated and identified from medicinal plants and were found to be utilized as bio-stimulants and bio fertilizers. In lieu of this, the present study aims to isolate and identify endophytic fungi associated with the leaves of Anisomeles indica L. an important medicinal plant of the Terai-Duars region of West Bengal. A total of ten endophytic fungi were isolated from the leaves of A. indica and five were identified using ITS1/ITS4 sequencing based on their ability for plant growth promotion, secondary metabolite production, and extracellular enzyme production. Endophytic fungal isolates were identified as Colletotrichum yulongense Ai1, Colletotrichum cobbittiense Ai2, Colletotrichum alienum Ai2.1, Colletotrichum cobbittiense Ai3, and Fusarium equiseti. Five isolates tested positive for their plant growth promotion potential, while isolates Ai4. Ai1, Ai2, and Ai2.1 showed significant production of secondary metabolites viz. alkaloids, phenolics, flavonoids, saponins, etc. Isolate Ai2 showed maximum total phenolic concentration (25.98 mg g-1), while isolate Ai4 showed maximum total flavonoid concentration (20.10 mg g-1). Significant results were observed for the production of extracellular enzymes such as cellulases, amylases, laccases, lipases, etc. The isolates significantly influenced the seed germination percentage of tomato seedlings and augmented their growth and development under in vitro assay. The present work comprehensively tested these isolates and ascertained their huge application for the commercial utilization of these isolates both in the agricultural and industrial sectors.

Endophytic fungi: Unravelling plant-endophyte interaction and the multifaceted role of fungal endophytes in stress amelioration

Endophytic fungi colonize interior plant tissue and mostly form mutualistic associations with their host plant. Plant-endophyte interaction is a complex mechanism and is currently a focus of research to understand the underlying mechanism of endophyte asymptomatic colonization, the process of evading plant immune response, modulation of gene expression, and establishment of a balanced mutualistic relationship. Fungal endophytes rely on plant hosts for nutrients, shelter, and transmission and improve the host plant's tolerance against biotic stresses, including -herbivores, nematodes, bacterial, fungal, viral, nematode, and other phytopathogens. Endophytic fungi have been reported to improve plant health by reducing and eradicating the harmful effect of phytopathogens through competition for space or nutrients, mycoparasitism, and through direct or indirect defense systems by producing secondary metabolites as well as by induced systemic resistance (ISR). Additionally, for efficient crop improvement, practicing them would be a fruitful step for a sustainable approach. This review article summarizes the current research progress in plant-endophyte interaction and the fungal endophyte mechanism to overcome host defense responses, their subsequent colonization, and the establishment of a balanced mutualistic interaction with host plants. This review also highlighted the potential of fungal endophytes in the amelioration of biotic stress. We have also discussed the relevance of various bioactive compounds possessing antimicrobial potential against a variety of agricultural pathogens. Furthermore, endophyte-mediated ISR is also emphasized.

Antitumor and antibacterial activity of metabolites of endophytic Colletotrichum siamense isolated from coffee (Coffea arabica L. cv IAPAR-59)

Endophytic fungi produce a range of known metabolites and several others, not yet explored, which present important biological activities from the pharmaceutical and industrial perspective. Several studies have reported the diversity of endophytes in Coffea arabica plants, although few have been described in organic cultures. In the current paper, we describe the chemical profile of specialized metabolites in the ethyl acetate phase in a strain of the endophytic fungus Colletotrichum siamense associated with coffee (Coffea arabica L.) (Rubiaceae) and its potential against tumor cells and bacteria of medical and food importance. Cytotoxicity assays in tumor cells MCF-7 and HepG2/C3A were performed by MTT and microdilution in broth to evaluate the antibacterial action of metabolic extract. The antiproliferative assay showed promising results after 24 h of treatment, with 50% injunction concentrations for the two cell types. UHPLC-MS/MS analyses with an electrospray ionization source were used to analyze the extracts and identify compounds of species Colletotrichum siamense, which is still little explored as a source of active metabolites. Many of these compounds observed in the endophytic need to be chemically synthesized in industry, at high costs, while production by the fungus becomes a chemically and economically more viable alternative. Pyrocatechol, gentisyl alcohol, and alpha-linolenic acid, associated with different mechanisms of action against tumor cells, were detected among the main compounds. The extract of the endophytic fungus Colletotrichum siamense presented several compounds with pharmacological potential and antibacterial activity, corroborating its potential in biotechnological applications.

A novel endophytic fungus strain of Cladosporium: its identification, genomic analysis, and effects on plant growth

INTRODUCTION

Endophytic microorganisms are bacteria or fungi that inhabit plant internal tissues contributing to various biological processes of plants. Some endophytic microbes can promote plant growth, which are known as plant growth-promoting endophytes (PGPEs). There has been an increasing interest in isolation and identification of PGPEs for sustainable production of crops. This study was undertaken to isolate PGPEs from roots of a halophytic species Sesuvium portulacastrum L. and elucidate potential mechanisms underlying the plant growth promoting effect.

METHODS

Surface-disinfected seeds of S. portulacastrum were germinated on an in vitro culture medium, and roots of some germinated seedlings were contaminated by bacteria and fungi. From the contamination, an endophytic fungus called BF-F (a fungal strain isolated from bacterial and fungal contamination) was isolated and identified. The genome of BF-F strain was sequenced, its genome structure and function were analyzed using various bioinformatics software. Additionally, the effect of BF-F on plant growth promotion were investigated by gene cluster analyses.

RESULTS

Based on the sequence homology (99%) and phylogenetic analysis, BF-F is likely a new Cladosporium angulosum strain or possibly a new Cladosporium species that is most homologous to C. angulosum. The BF-F significantly promoted the growth of dicot S. portulacastrum and Arabidopsis as well as monocot rice. Whole genome analysis revealed that the BF-F genome has 29,444,740 bp in size with 6,426 annotated genes, including gene clusters associated with the tryptophan synthesis and metabolism pathway, sterol synthesis pathway, and nitrogen metabolism pathway. BF-F produced indole-3-acetic acid (IAA) and also induced the expression of plant N uptake related genes.

DISCUSSION

Our results suggest that BF-F is a novel strain of Cladosporium and has potential to be a microbial fertilizer for sustainable production of crop plants. The resulting genomic information will facilitate further investigation of its genetic evolution and its function, particularly mechanisms underlying plant growth promotion.

Towards further understanding the applications of endophytes: enriched source of bioactive compounds and bio factories for nanoparticles

The most significant issues that humans face today include a growing population, an altering climate, an growing reliance on pesticides, the appearance of novel infectious agents, and an accumulation of industrial waste. The production of agricultural goods has also been subject to a great number of significant shifts, often known as agricultural revolutions, which have been influenced by the progression of civilization, technology, and general human advancement. Sustainable measures that can be applied in agriculture, the environment, medicine, and industry are needed to lessen the harmful effects of the aforementioned problems. Endophytes, which might be bacterial or fungal, could be a successful solution. They protect plants and promote growth by producing phytohormones and by providing biotic and abiotic stress tolerance. Endophytes produce the diverse type of bioactive compounds such as alkaloids, saponins, flavonoids, tannins, terpenoids, quinones, chinones, phenolic acids etc. and are known for various therapeutic advantages such as anticancer, antitumor, antidiabetic, antifungal, antiviral, antimicrobial, antimalarial, antioxidant activity. Proteases, pectinases, amylases, cellulases, xylanases, laccases, lipases, and other types of enzymes that are vital for many different industries can also be produced by endophytes. Due to the presence of all these bioactive compounds in endophytes, they have preferred sources for the green synthesis of nanoparticles. This review aims to comprehend the contributions and uses of endophytes in agriculture, medicinal, industrial sectors and bio-nanotechnology with their mechanism of action.

Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria

This review evaluates oilseed crop soybean endophytic bacteria, their prospects, and challenges for sustainable agriculture. Soybean is one of the most important oilseed crops with about 20-25% protein content and 20% edible oil production. The ability of soybean root-associated microbes to restore soil nutrients enhances crop yield. Naturally, the soybean root endosphere harbors root nodule bacteria, and endophytic bacteria, which help increase the nitrogen pool and reclamation of another nutrient loss in the soil for plant nutrition. Endophytic bacteria can sustain plant growth and health by exhibiting antibiosis against phytopathogens, production of enzymes, phytohormone biosynthesis, organic acids, and secondary metabolite secretions. Considerable effort in the agricultural industry is focused on multifunctional concepts and bioprospecting on the use of bioinput from endophytic microbes to ensure a stable ecosystem. Bioprospecting in the case of this review is a systemic overview of the biorational approach to harness beneficial plant-associated microbes to ensure food security in the future. Progress in this endeavor is limited by available techniques. The use of molecular techniques in unraveling the functions of soybean endophytic bacteria can explore their use in integrated organic farming. Our review brings to light the endophytic microbial dynamics of soybeans and current status of plant microbiome research for sustainable agriculture.

Complete Genome Sequence of Dyella sp. Strain GSA-30, a Predominant Endophytic Bacterium of Dendrobium Plants

We report a complete genome sequence of Dyella sp. strain GSA-30, a predominant endophytic bacterium of Dendrobium plants. The genome consists of a circular 5,501,810-bp chromosome with a G+C content of 61.4%. The genome was predicted to harbor 6 rRNA genes, 51 tRNA genes, and 4,713 coding sequences.

Improved Cultivation and Isolation of Diverse Endophytic Bacteria Inhabiting Dendrobium Roots by Using Simply Modified Agar Media

Dendrobium plants are members of the family Orchidaceae, many of which are endangered orchids with ornamental and medicinal values. Dendrobium endophytic microbes have attracted attention for the development of strategies for plant protection and utilization of medicinal principles. However, the role of endophytic bacteria is poorly elucidated due to the lack of their successful cultivation. This study obtained a total of 749 endophytic isolates from Dendrobium roots using solid media prepared by simply modified methods (separate sterilization of phosphate and agar [PS] and use of gellan gum as a gelling reagent [GG]) and by a conventional method of autoclaving the phosphate and agar together (PT method). Notably, based on a comparison of 16S rRNA gene sequences between the isolates and the Dendrobium root endophyte community, we successfully retrieved more than 50% (17 out of 30) of the predominant endophytic bacterial operational taxonomic units (OTUs) using PS and GG media, which is a much higher recovery rate than that of PT medium (16.7%). We further found that a number of recalcitrant bacteria, including phylogenetically novel isolates and members of even the rarely cultivated phyla Acidobacteriota and Verrucomicrobiota, were obtained only when using PS and/or GG medium. Intriguingly, the majority of these recalcitrant bacteria formed colonies faster on PS or GG medium than on PT medium, which may have contributed to their successful isolation. Taken together, this study succeeded in isolating a wide variety of Dendrobium endophytic bacteria, including predominant ones using PS and GG media, and enables performance of future studies to clarify their unknown roles associated with the growth of Dendrobium plants. IMPORTANCE Dendrobium endophytic bacteria are of great interest since their functions may contribute to the protection of endangered orchids with ornamental and medicinal values. To understand and reveal the "true roles" of the endophytes, obtaining those axenic cultures is necessary even in the metagenomic era. However, no effective methods for isolating a variety of endophytic bacteria have been established. This study first demonstrated that the use of simply modified medium is quite effective and indeed allows the isolation of more than half of the predominant endophytic bacteria inhabiting Dendrobium roots. Besides, even phylogenetically novel and/or recalcitrant endophytic bacteria were successfully obtained by the same strategy. The obtained endophytic bacteria could serve as "living material" for elucidating their unprecedented functions related to the conservation of endangered orchid plants. Furthermore, the culture method used in this study may enable the isolation of various endophytic bacteria dominating not only in orchid plants but also in other useful plants.

Improved seed germination and plant growth mediated by compounds synthesized by endophytic Aspergillus niger (isolate 29) isolated from Albizia lebbeck (L.) Benth

Plant-microbe interactions are remarkably diverse and dynamic. These interactions can be in the form of endophytic association. Colonization of endophytic microflora in crop plants improves crop health leading to crop enhancement. They stimulate the overall growth of plants by facilitating nutrient uptake and regulating various hormones. This eventually improves the plant biomass and grain yield. Owing to the assistance of the endophytes to the host plants, augmentation of crop plants with potential fungal endophytes or their extracted bioactive compound can upsurge the overall crop production and provide promising solutions for environmentally sustainable agriculture. In this light, the present study deals with the prospects of bioactive metabolites produced by endophytic fungi in Albizia lebbeck (L.) Benth, a medicinal native plant of Rajasthan. The metabolomic analysis of a partially purified extract of Aspergillus niger (isolate 29) showed the presence of a total of 919 compounds using UHPLC-MS/MS. The metabolic pathway analysis revealed that these compounds were influencing super pathway of gibberellin and isoflavonoid biosynthesis. Significant increase in seed germination percentage (73-93%), seed vigour index (834.44-1498.21) and germination index (2.54-3.67 seeds/day) was found in treated seeds compared to untreated. There was a significant improvement in root (45-185%) and shoot length (215-295%) of wheat, barley and millet and a significant increase in root number (38-97%) in wheat and barley. Positive correlation was observed in the growth parameters of all the crops upon treatment. Overall, the results indicated that the partially purified fraction of A. niger (isolate 29) improved seed germination and promoted plant growth in cash crops. The results emphasize towards the importance of secondary metabolites in seed germination and enhancement of plant growth. These results also suggest a probable mutualistic role of endophyte with the host plant.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03332-x.

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.

Analysis of the different growth years accumulation of flavonoids in Dendrobium moniliforme (L.) Sw. by the integration of metabolomic and transcriptomic approaches

Dendrobium moniliforme (L.) Sw. is a valuable herbal crop, and flavonoids are primarily distributed as active ingredients in the stem, but the composition and synthesis mechanisms of flavonoids in different growth years are not clear. The accumulation of flavonoids in D. moniliforme from four different years was investigated, using a combined metabolomics and transcriptomics approach in this study. The phenylpropanoid and flavonoid biosynthetic pathways were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). The widely targeted metabolomics technique revealed a total of 173 kinds of flavonoid metabolites. The metabolomics data confirmed the trend of total flavonoids (TF) content in stems of D. moniliforme, with chalcone, naringenin, eriodictyol, dihydroquercetin, and other flavonoids considerably up-accumulating in the third year. Twenty DEGs were detected that regulate flavonoid synthesis and the expression of these genes in different growth years was verified using real-time quantitative PCR (qRT-PCR). Furthermore, a comprehensive regulatory network was built for flavonoid biosynthesis and it was discovered that there is one FLS gene, one CCR gene and two MYB transcription factors (TFs) with a high connection with flavonoid biosynthesis by weighted gene co-expression network analysis (WGCNA). In this study, the correlation between genes involved in flavonoid biosynthesis and metabolites was revealed, and a new regulatory mechanism related to flavonoid biosynthesis in D. moniliforme was proposed. These results provide an important reference for the farmers involved in the cultivation of D. moniliforme.

Roles of plant-associated microorganisms in regulating the fate of Hg in croplands: A perspective on potential pathways in maintaining sustainable agriculture

In heavy metal-contaminated croplands, plant-associated microorganisms play important roles in the adaptation of crops to heavy metals. Plant-associated microbes can interact with Hg and stimulate plant resistance to Hg toxicity, which is crucial for impeding Hg accumulation along the food chain. The roles of rhizosphere microorganisms for the improvement of plant growth and Hg resistance have drawn great research attention. However, the interactions among plant-endophyte-Hg have been neglected although they might be important for in vivo Hg detoxification. In this study, we systematically summarized 1) the roles of plant-associated microorganisms in Hg detoxification and plant growth, 2) Hg methylation and demethylation driven by plant-associated microbes, 3) the relationships between plant-associated microbes and Hg biogeochemical cycling. The possible mechanisms underlying crop-endophyte-Hg interactions were discussed, although limited studies on this aspect are available to date. The challenges and perspectives of plant-endophytes in dampening Hg phytotoxicity and controlling Hg accumulation in croplands were proposed on the basis of the present knowledge. Taken together, this work provides evidence for further understanding the interactions between soil-plant-endophyte-Hg systems and as well as new interpretations and perspectives into regulating the fate of Hg in croplands.

Microbial endophytes: application towards sustainable agriculture and food security

Microbial endophytes are ubiquitous and exist in each recognised plant species reported till date. Within the host plant, the entire community of microbes lives non-invasively within the active internal tissues without causing any harm to the plant. Endophytes interact with their host plant via metabolic communication enables them to generate signal molecules. In addition, the host plant's genetic recombination with endophytes helps them to imitate the host's physicochemical functions and develop identical active molecules. Therefore, when cultured separately, they begin producing the host plant phytochemicals. The fungal species Penicillium chrysogenum has portrayed the glory days of antibiotics with the invention of the antibiotic penicillin. Therefore, fungi have substantially supported social health by developing many bioactive molecules utilised as antioxidant, antibacterial, antiviral, immunomodulatory and anticancerous agents. But plant-related microbes have emanated as fountainheads of biologically functional compounds with higher levels of medicinal perspective in recent years. Researchers have been motivated by the endless need for potent drugs to investigate alternate ways to find new endophytes and bioactive molecules, which tend to be a probable aim for drug discovery. The current research trends with these promising endophytic organisms are reviewed in this review paper. KEY POINTS: • Identified 54 important bioactive compounds as agricultural relevance • Role of genome mining of endophytes and "Multi-Omics" tools in sustainable agriculture • A thorough description and graphical presentation of agricultural significance of plant endophytes.

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.

Developmental Characteristics and Auxin Response of Epiphytic Root in Dendrobium catenatum

Dendrobium catenatum, a traditional precious Chinese herbal medicine, belongs to epiphytic orchids. Its special life mode leads to the specialization of roots, but there is a lack of systematic research. The aerial root in D. catenatum displays diverse unique biological characteristics, and it initially originates from the opposite pole of the shoot meristem within the protocorm. The root development of D. catenatum is not only regulated by internal cues but also adjusts accordingly with the change in growth environments. D. catenatum root is highly tolerant to auxin, which may be closely related to its epiphytic life. Exogenous auxin treatment has dual effects on D. catenatum roots: relatively low concentration promotes root elongation, which is related to the induced expression of cell wall synthesis genes; excessive concentration inhibits the differentiation of velamen and exodermis and promotes the overproliferation of cortical cells, which is related to the significant upregulation of WOX11-WOX5 regeneration pathway genes and cell division regulatory genes. Overexpression of D. catenatum WOX12 (DcWOX12) in Arabidopsis inhibits cell and organ differentiation, but induces cell dedifferentiation and callus production. Therefore, DcWOX12 not only retains the characteristics of ancestors as stem cell regulators, but also obtains stronger cell fate transformation ability than homologous genes of other species. These findings suggest that the aerial root of D. catenatum evolves special structure and developmental characteristics to adapt to epiphytic life, providing insight into ideal root structure breeding of simulated natural cultivation in D. catenatum and a novel target gene for improving the efficiency of monocot plant transformation.

Colonization with non-mycorrhizal culturable endophytic fungi enhances orchid growth and indole acetic acid production

BACKGROUND

Symbiotic associations of endophytic fungi have been proved by possessing an ability to produce hormones and metabolites for their host plant. Members of the Orchidaceae are obligate mycorrhizal species but a non-mycorrhizal association needs more investigation for their ability to promote plant growth and produce plant growth hormones. In the present study, endophytic fungi were isolated from the roots of Dendrobium longicornu Lindl., to investigate the root colonizing activity and role in plant growth and development.

RESULTS

Among 23 fungal isolates were identified both by morphological and molecular technique as Penicillium sp., Fusarium sp., Coniochaeta sp., Alternaria sp., and Cladosporium sp. The dominate species were Coniochaeta sp. and Cladosporium sp. The dominant species as per the isolation was Coniochaeta sp. These fungal strains were screened for growth-promoting activity of Cymbidium aloifolium (plantlet) consider as cross genus interaction and Dendrobium longicornu (protocorms) as a host plant in in-vitro condition. Importantly, Cladosporium sp., and Coniochaeta sp. showed successful colonization and peloton formation with roots of C. aloifolium. Moreover, it also enhanced acclimatization of plantlets. Fungal elicitors from nine fungal isolates enhanced the growth of the in vitro grown protocorms of D. longicornu. Key bioactive compounds detected in the fungal colonized plant extract were 2H-pyran-2-one, Cyclopropanecarboxylic acid, Oleic Acid and d-Mannitol, which may have a potential role in plant-microbe interaction. All fungal endophytes were able to synthesize the indole acetic acid (IAA) in presence of tryptophan. Moreover, fungal extract DLCCR7 treated with DL-tryptophan yielded a greater IAA concentration of 43 μg per ml than the other extracts. The iaaM gene involved in IAA synthesis pathway was amplified using iaaM gene primers successfully from Alternaria sp., Cladosporium sp., and Coniochaeta sp.

CONCLUSIONS

Hence, this study confirms the production of IAA by endophytes and demonstrated their host as well as cross-genus plant growth-promoting potential by producing metabolites required for the growth of the plant.

Fungal Endophytes and Their Role in Agricultural Plant Protection against Pests and Pathogens

Virtually all examined plant species harbour fungal endophytes which asymptomatically infect or colonize living plant tissues, including leaves, branches, stems and roots. Endophyte-host interactions are complex and span the mutualist-pathogen continuum. Notably, mutualist endophytes can confer increased fitness to their host plants compared with uncolonized plants, which has attracted interest in their potential application in integrated plant health management strategies. In this review, we report on the many benefits that fungal endophytes provide to agricultural plants against common non-insect pests such as fungi, bacteria, nematodes, viruses, and mites. We report endophytic modes of action against the aforementioned pests and describe why this broad group of fungi is vitally important to current and future agricultural practices. We also list an extensive number of plant-friendly endophytes and detail where they are most commonly found or applied in different studies. This review acts as a general resource for understanding endophytes as they relate to potential large-scale agricultural applications.

Weeds harbor an impressive diversity of fungi, which offers possibilities for biocontrol

The use of herbicides for weed control is very common, but some of them represent a threat to human health, are environmentally detrimental and stimulate herbicide resistance. Therefore, using microorganisms as natural herbicides appears as a promising alternative. The mycoflorae colonizing different species of symptomatic and asymptomatic weeds were compared to characterize the possible mycoherbicidal candidates associated with symptomatic weeds. A collection of 475 symptomatic and asymptomatic plants belonging to 23 weed species was established. A metabarcoding approach based on amplification of the internal transcribed spacer (ITS) region combined with high-throughput amplicon sequencing revealed the diversity of fungal communities hosted by these weeds: 542 fungal genera were identified. The variability of the composition of fungal communities revealed a dispersed distribution of taxa governed neither by geographical location nor by the botanical species, suggesting a common core displaying non-specific interactions with host plants. Beyond this core, specific taxa were more particularly associated with symptomatic plants. Some of these, such as Alternaria, Blumeria, Cercospora, Puccinia, are known pathogens, while others such as Sphaerellopsis, Vishniacozyma and Filobasidium are not, at least on crops, and constitute new tracks to be followed in the search for mycoherbicidal candidates. IMPORTANCE: This approach is original because the diversity of weed-colonizing fungi has rarely been studied before. Furthermore, targeting both the ITS1 and ITS2 regions to characterize the fungal communities i) highlighted the complementarity of these two regions, ii) revealed a great diversity of weed-colonizing fungi, and iii) allowed for the identification of potential mycoherbicides, among which unexpected genera.

Diversity, Chemical Constituents, and Biological Activities of Endophytic Fungi Isolated From Ligusticum chuanxiong Hort

The objective of this study was to evaluate the diversity of endophytic fungi of different parts of Ligusticum chuanxiong Hort (CX) and further characterize their biological activities and identify chemical compounds produced by these endophytic fungi. A total of 21 endophytic fungi were isolated and identified from CX. Penicillium oxalicum, Simplicillium sp., and Colletotrichum sp. were identified as promising strains by the color reaction. Comparing different organic extracts of the three strains, it was observed that the ethyl acetate extract of Penicillium oxalicum and Simplicillium sp. and the n-butanol extract of Colletotrichum sp. showed significant antioxidant and antibacterial activities. The ethyl acetate extracts of Penicillium oxalicum had outstanding antioxidant and antibacterial effects, and its radical scavenging rates for ABTS and DPPH were 98.43 ± 0.006% and 90.11 ± 0.032%, respectively. At the same time, their IC₅₀ values were only 0.18 ± 0.02 mg/mL and 0.04 ± 0.003 mg/mL. The ethyl acetate extract of Penicillium oxalicum showed MIC value of only 0.5 mg/mL against Escherichia coli and Staphylococcus aureus. By liquid chromatography-mass spectrometry (LC-MS), we found that Penicillium oxalicum could produce many high-value polyphenols, such as hesperidin (36.06 μmol/g), ferulic acid (1.17 μmol/g), and alternariol (12.64 μmol/g), which can be a potential resource for the pharmaceutical industry. In conclusion, these results increase the diversity of CX endophytic fungi and the antioxidant and antibacterial activities of their secondary metabolites.

The plant endosphere-hidden treasures: a review of fungal endophytes

The endosphere represents intracellular regions within plant tissues colonize by microbial endophytes without causing disease symptoms to host plants. Plants harbor one or two endophytic microbes capable of synthesizing metabolite compounds. Environmental factors determine the plant growth and survival as well as the kind of microorganisms associated with them. Some fungal endophytes that symbiotically colonize the endosphere of medicinal plants with the potential of producing biological products have been employed in traditional and modern medicine. The bioactive resources from endophytic fungi are promising; biotechnologically to produce cheap and affordable commercial bioactive products as alternatives to chemical drugs and other compounds. The exploration of bioactive metabolites from fungal endophytes has been found applicable in agriculture, pharmaceutical, and industries. Thus, fungal endophytes can be engineered to produce a substantive quantity of pharmacological drugs through the biotransformation process. Hence, this review shall provide an overview of fungal endophytes, ecology, their bioactive compounds, and exploration with the biosystematics approach.

Multifarious functional traits of free-living rhizospheric fungi, with special reference to Aspergillus spp. isolated from North Indian soil, and their inoculation effect on plant growth

Purpose

Rhizospheric soil fungi are critical for plant and soil health. However, their multiple functional traits and impact on plant growth have not been systematically explored.

Methods

During this study, biochemical traits of 73 indigenous soil fungal isolates and 15 unidentified isolates related to plant growth promotion and production of extracellular enzymes were studied.

Results

Forty four (65.67%) of the total isolates produced indole acetic acid (IAA) followed by siderophore (52.23%), phosphate solubilization (37.31%), and antibiotic (11.93%). 91.04% of the studied isolates produced ammonia whereas 28.35% produced organic acid. Extracellular enzyme activities of lipase, amylase, chitinase, and cellulase were detected among 95.52%, 61.11%, 35.82%, and 41.79% isolates, respectively. Based on these activities, 73 fungal isolates were categorized into different biotypes. Quantitative analysis of IAA production and phosphate solubilization was carried out for Aspergillus, Penicillium, and Rhizopus isolates. Aspergillus isolates exhibited varying activities of IAA production and phosphate solubilization. Most of the Aspergillus isolates and some other fungi demonstrated multiple activities. Based on the multiple traits of selected fungal isolates, Aspergillus sp-07, Penicillium sp-03, and Rhizopus sp-02 were further evaluated in different combinations for their inoculation effect on the growth and yield of wheat under field conditions.

Conclusions

The results indicated that these isolates could be developed into bio-inoculants to enhance plant growth. The consortium of these three isolates was also found to be compatible and beneficial for plant growth.

Evaluating the Endophytic Activities of Beauveria bassiana on the Physiology, Growth, and Antioxidant Activities of Extracts of Lettuce (Lactuca sativa L.)

Endophytic entomopathogens have growth promoting, nutrient fortifying, and anti-insect properties that could improve the yield and quality of lettuce (Lactuca sativa L.). Lactuca sativa is a vegetable crop with high demand; however, it is susceptible to aphid infestations. This study's objectives were to assess the pathogenicity of Beauveria bassiana (strain: SM3) (Bals.) Vuil. (Hypocreales) against Myzus persicae Sulzer, tissue colonization of lettuce by conidia of B. bassiana, as well as the effects of fungal inoculation on growth, tissue nutrient content, and proximate composition of the lettuce plants. Furthermore, the involvement of tissue nutrients in mediating the influence of endophytic fungus on the plant traits was examined. Insects and plants were exposed to four fungal conidial concentrations: 0, 1 × 10⁶, 1 × 10⁷ and 1 × 10⁸ conidia mL^-1 in an anti-insect bioassay and a greenhouse experiment, respectively. The B. bassiana strain was pathogenic against M. persicae, inducing mean insect mortality of 78% at the highest concentration (1 × 10⁸ conidia mL^-1). The B. bassiana endophytically colonized up to 76% of plants exposed to 1 × 10⁸ conidia mL^-1. Crown size and plant height varied significantly among treatments. However, the plant fresh and dry weights and nutrient elements N, P, K, Ca, and Mg did not vary significantly among treatments. Among the plant macronutrients assessed, only tissue carbon content was significantly (p < 0.01) affected by conidial treatments. The tissue C and Cu contents significantly correlated with the antioxidant capacity of the lettuce plants. Most of the micronutrients, viz. Mn, Fe, Cu, and B were remarkably higher (p < 0.05) in the fungus-treated plants than in the control plants. The antioxidant capacity (FRAP and TEAC) of plant extracts varied significantly (p < 0.001) among treatments, with the highest conidial treatment yielding the most increased antioxidant activity. In conclusion, the B. bassiana strain was endophytic to lettuce, pathogenic against M. persicae, and induced increased micro-nutrient tissue contents and antioxidant activities. This study demonstrated that B. bassiana could be potentially used in the biofortification of nutritive and medicinal qualities of plants.

Progress and Prospects of Mycorrhizal Fungal Diversity in Orchids

Orchids form mycorrhizal symbioses with fungi in natural habitats that affect their seed germination, protocorm growth, and adult nutrition. An increasing number of studies indicates how orchids gain mineral nutrients and sometime even organic compounds from interactions with orchid mycorrhizal fungi (OMF). Thus, OMF exhibit a high diversity and play a key role in the life cycle of orchids. In recent years, the high-throughput molecular identification of fungi has broadly extended our understanding of OMF diversity, revealing it to be a dynamic outcome co-regulated by environmental filtering, dispersal restrictions, spatiotemporal scales, biogeographic history, as well as the distribution, selection, and phylogenetic spectrum width of host orchids. Most of the results show congruent emerging patterns. Although it is still difficult to extend them to all orchid species or geographical areas, to a certain extent they follow the "everything is everywhere, but the environment selects" rule. This review provides an extensive understanding of the diversity and ecological dynamics of orchid-fungal association. Moreover, it promotes the conservation of resources and the regeneration of rare or endangered orchids. We provide a comprehensive overview, systematically describing six fields of research on orchid-fungal diversity: the research methods of orchid-fungal interactions, the primer selection in high-throughput sequencing, the fungal diversity and specificity in orchids, the difference and adaptability of OMF in different habitats, the comparison of OMF in orchid roots and soil, and the spatiotemporal variation patterns of OMF. Further, we highlight certain shortcomings of current research methodologies and propose perspectives for future studies. This review emphasizes the need for more information on the four main ecological processes: dispersal, selection, ecological drift, and diversification, as well as their interactions, in the study of orchid-fungal interactions and OMF community structure.

Harnessing the Rhizosphere of the Halophyte Grass Aeluropus littoralis for Halophilic Plant-Growth-Promoting Fungi and Evaluation of Their Biostimulant Activities

Hydroponic systems have gained interest and are increasingly used in hot and dry desert areas. Numbers of benefits are offered by hydroponic systems such as the ability to save water, enhance nutrients use efficiency, easy environmental control, and prevention of soil-borne diseases. However, the high consumption of chemical fertilizers for nutrient solution and the sensitivity of closed hydroponic systems to salinity are issues that need solutions. Thus, the main goal of our research activities is to isolate plant growth promoting fungi in order to develop sustainable hydroponic systems. We are working on isolating and testing the possibility to incorporate the cell-free filtrate (CFF) of plant growth promoting fungi (PGPF) in the composition of the nutrient solution. In this work, we isolated six strains of PGPF from the rhizosphere of the halophyte grass Aeluropus littoralis. Phylogenetic analyses of DNA sequences amplified by ITS1 and ITS4 primers identified the isolated fungi as: Byssochlamys spectabilis, Chaetomium globosum, Cephalotheca foveolata, Penicillium melinii, Alternaria tenuissima, and Nigrospora chinensis. The promoting of vigor in tobacco seedlings was used as criteria to evaluate the biostimulant activity of these fungi by adding either their mycelia (DE: direct effect) or their cell-free filtrates (CFF: indirect effect) to the plant-growth media. The best significant growth stimulation was obtained with plants treated by B. spectabilis. However, only the CFFs of Byssochlamys spectabilis (A5.1) and Penicillium melinii (A8) when added at a dilution factor of 1/50 to half-strength nutritive solution (0.5NS) resulted in significant improvement of all assessed growth parameters. Indeed, the A5.1CFF and A8CFF in 0.5NS induced a significant better increase in the biomass production when compared to NS or 0.5NS alone. All fungi produced indole acetic acid in the CFFs, which could be one of the key factors explaining their biostimulant activities. Furthermore, six genes involved in nitrogen-metabolism (NR1 and NRT1), auxin biosynthesis (Tryp1 and YUCCA6-like), and brassinosteroid biosynthesis (DET2 and DWF4) were shown to be induced in roots or leaves following treatment of plants with the all CFFs. This work opens up a prospect to study in deep the biostimulant activity of PGPFs and their applications to decrease the requirement of chemical fertilizers in the hydroponic growing systems.

A prospectus of plant growth promoting endophytic bacterium from orchid (Vanda cristata)

Background

A plant growth-promoting endophytic bacterium PVL1 isolated from the leaf of Vanda cristata has the ability to colonize with roots of plants and protect the plant. PVL1 was isolated using laboratory synthetic media. 16S rRNA gene sequencing method has been employed for identification before and after root colonization ability.

Results

Original isolated and remunerated strain from colonized roots were identified as Bacillus spp. as per EzBiocloud database. The presence of bacteria in the root section of the plantlet was confirmed through Epifluorescence microscopy of colonized roots. The in-vitro plantlet colonized by PVL1 as well as DLMB attained higher growth than the control. PVL1 capable of producing plant beneficial phytohormone under in vitro cultivation. HPLC and GC-MS analysis suggest that colonized plants contain Indole Acetic Acid (IAA). The methanol extract of Bacillus spp., contains 0.015 μg in 1 μl concentration of IAA. PVL1 has the ability to produce antimicrobial compounds such as ethyl iso-allocholate, which exhibits immune restoring property. One-way ANOVA shows that results were statistically significant at P ≤ 0.05 level.

Conclusions

Hence, it has been concluded that Bacillus spp. PVL1 can promote plant growth through secretion of IAA during root colonization and ethyl iso-allocholate to protect plants from foreign infections. Thus, this study supports to support Koch’s postulates of bacteria establishment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12896-021-00676-9.

Comparative Cytotoxic Activity of Wild Harvested Stems and In Vitro-Raised Protocorms of Dendrobium chryseum Rolfe in Human Cervical Carcinoma and Glioblastoma Cell Lines

From the medicinal orchid Dendrobium chryseum Rolfe, which is used in traditional and folk Chinese medicine, the protocorms were raised in Murashige and Skoog (MS) media in three strengths, full strength (FMS), half strength (1/2 MS), and quarter strength (1/4 MS), with or without the phytohormones 6-benzylaminopurine (BAP) and 1-naphthaleneacetic acid (NAA) and coconut water (CW). The comparative cytotoxic activities of the wild and in vitro-raised protocorms were evaluated in human cervical carcinoma (HeLa) and human glioblastoma (U251) cell lines by MTT assay. In in vivo and in vitro, the methanol extracts of D. chryseum showed significant cytotoxic activities. Significant growth inhibition (%) and potent IC₅₀ values were demonstrated in HeLa cell lines (49.79% (210.5 μg/mL) for in vitro-raised Dendrobium chryseum (DCT) versus 46.97% (226.5 μg/mL) for wild Dendrobium chryseum (DCW)). Similarly, activities against U251 cell lines exhibited also significant inhibition (28.76% (612.54 μg/mL) for DCW and 17.15% (1059.92 μg/mL) for DCT). The cytotoxic activities of both, wild and tissue-cultured samples, were superior in HeLa cells. In U251 cells, the wild sample was more active than the tissue-cultured one with a moderate cytotoxic effect. Hence, protocorm culture may therefore be a promising future tool for producing pharmacologically bioactive compounds in medicinal orchids. Such sustainable technology approach will minimize the pressure on the natural population of threatened but commercially important medicinal orchids.

Genomic and Physiological Investigation of Heavy Metal Resistance from Plant Endophytic Methylobacterium radiotolerans MAMP 4754, Isolated from Combretum erythrophyllum

Combretum erythrophyllum is an indigenous southern African tree species, a metal hyperaccumulator that has been used as a phytoextraction option for tailing dams in Johannesburg, South Africa. In hyperaccumulators, metal detoxification has also been linked or attributed to the activities of endophytes, and, in this regard, metal detoxification can be considered a form of endophytic behavior. Therefore, we report herein on the identification of proteins that confer heavy metal resistance, the in vitro characterization of heavy metal resistance, and the production of plant growth-promoting (PGP) volatiles by Methylobacterium radiotolerans MAMP 4754. Multigenome comparative analyses of M. radiotolerans MAMP 4754 against eight other endophytic strains led to the identification of zinc, copper, and nickel resistance proteins in the genome of this endophyte. The maximum tolerance concentration (MTC) of this strain towards these metals was also investigated. The metal-exposed cells were analyzed by transmission electron microscopy (TEM). The ethyl acetate and chloroform extracts (1:1 v/v) of heavy metal untreated M. radiotolerans MAMP 4754 were also screened for the production of PGP compounds by Gas Chromatography–Mass Spectroscopy (GC/MS). The MTC was recorded at 15 mM, 4 mM, and 12 mM for zinc, copper, and nickel, respectively. The TEM analysis showed the accumulation of metals in the intracellular environment of M. radiotolerans MAMP 4754, while the GC/MS analysis revealed several plant growth-promoting compounds, including alcohols, phthalate esters, alkenes, ketones, sulfide derivatives, phenols, and thiazoles. Our findings suggest that the genetic makeup of M. radiotolerans MAMP 4754 encodes heavy metal resistant proteins that indicate hyperaccumulator-specific endophytic behavior and the potential for application in bioremediation. The production of plant growth-promoting volatiles in pure culture by M. raditotolerans MAMP 4754 is a characteristic feature for plant growth-promoting bacteria.

Isolation and screening of stress-resistant endophytic fungus strains from wild and cultivated soybeans in cold region of China

In this study, we firstly reported the large-scale screening and isolation of endophytic fungi from nine wild and six cultivated soybeans in the cold regions of China. We totally isolated 302 endophytic fungal strains, of which 215 strains are isolated from the wild soybeans and 87 are identified from cultivated soybeans. Among these endophytic fungal strains, in the roots, stems, and leaves, 24.17% were isolated from roots, 28.8% were isolated from stems, and 47.01% were isolated from leaves, respectively. Most endophytic fungal strains isolated from the wild soybean roots were the species of Fusarium genus, and the fungal strains in the stems were the species of ascomycetes and Fusarium fungi, whereas most strains in the leaves were Alternaria fungi. To analyze the taxonomy of the obtained samples, we sequenced and compared their rDNA internal transcribed spacer (ITS) sequences. The data showed that 6 strains are putatively novel strains exhibiting ≤ 97% homology with the known strains. We next measured the secondary metabolites produced by the different strains and we found 11 strains exhibited high-performance synthesis of triterpenoids, phenols, and polysaccharides. Furthermore, we characterized their tolerance to abiotic stresses. The results indicated that 4 strains exhibited high tolerance to cadmium, and some strains exhibited resistance to acid, and alkali. The results of the study could facilitate the further exploration of the diversity of plant endophytic fungi and the potential applications of the fungi to practical agriculture and medicine industries. KEY POINTS: • 302 endophytic fungal strains isolated from wild soybean and cultivated soybean • 11 strains had high contents of triterpenoids, phenols, and polysaccharides • 4 strains exhibited high Cd tolerance, and a few strains with strong tolerance to acid and alkali solution.

Antioxidant, anticancer and antimicrobial effects of In vitro developed protocorms of Dendrobium longicornu

In vitro seed germination and protocorms formation were successfully established in traditionally used Dendrobium longicornu. Fresh protocorms (178.34 g - 183.90 g) were produced on the elicitor of Alternaria sp, Bacillus subtilis and Fusarium solani supplemented MS-medium. Methanol extract of D. longicornu protocorms has scavenged 94.31 % of DPPH radicals at 1000 μg/mL. Its 117.56 μg/mL concentration has scavenged 50 % DPPH radical (IC50). Similarly, it inhibits 25.39 % and 27.80 % HeLa and U251 cells at 500 μg/mL. The IC50 was found as 350.06 μg/mL and 507.22 μg/mL for HeLa and U251 cells respectively. Further, it inhibited the growth of E. coli, K. pneumoniae and E. cloacae with the zone of inhibition 4, 2 and 2 mm respectively. In conclusion, protocorms developed through in vitro seeds culture have accumulated and synthesized bioactive secondary metabolites. Therefore, protocorms could be utilized to the isolation of compounds for formulation of herbal drugs without damaging natural populations.

Škrbić B, Jigjiddorj EA, Vágvölgyi C, Szekeres A. Characterization of the Plant Growth-Promoting Activities of Endophytic Fungi Isolated from Sophora flavescens

Endophytic fungi in symbiotic association with their host plant are well known to improve plant growth and reduce the adverse effects of both biotic and abiotic stresses. Therefore, fungal endophytes are beginning to receive increased attention in an effort to find growth-promoting strains that could be applied to enhance crop yield and quality. In our study, the plant growth-promoting activities of endophytic fungi isolated from various parts of Sophora flavescens (a medicinally important plant in Mongolia and China) have been revealed and investigated. Fungal isolates were identified using molecular taxonomical methods, while their plant growth-promoting abilities were evaluated in plate assays. Altogether, 15 strains were isolated, representing the genera Alternaria, Didymella, Fusarium and Xylogone. Five of the isolates possessed phosphate solubilization activities and twelve secreted siderophores, while all of them were able to produce indoleacetic acid (IAA) in the presence or absence of tryptophan. The endogenous and exogenous accumulation of IAA were also monitored in liquid cultures using the HPLC-MS/MS technique to refine the plate assay results. Furthermore, for the highest IAA producer fungi, the effects of their extracts were also examined in plant bioassays. In these tests, the primary root lengths of the model Arabidopsis thaliana were increased in several cases, while the biomasses were significantly lower than the control IAA treatment. Significant alterations have also been detected in the photosynthetic pigment (chlorophyll-a, -b and carotenoids) content due to the fungal extract treatments, but these changes did not show any specific trends.

Isolation, characterization, and plant growth-promoting activities of endophytic fungi from a wild orchid Vanda cristata

Endophytism is one of the widely explored phenomena related to orchids and fungi. Endophytic fungi assist plants by supplementing nutrient acquisition, and synthesis of plant growth regulators. Vanda cristata is an epiphytic orchid that has a great diversity of endophytic fungi. Endophytic fungi were isolated from roots, stems, and leaves of V.cristata and identified by both morphological and molecular study. Furthermore, the isolated endophytic fungi were subjected to auxin synthesis, phosphate solubilization, ammonia synthesis, and elicitor growth test for understanding their growth-promoting effect in a qualitative and quantitative manner. Altogether, 12 different endophytic fungi were isolated from roots, stems, and leaves of V. cristata of which most species belonged to Ascomycota. Unidentified II fungi were found to be most effective for auxin synthesis and phosphate solubilization while Agaricus bisporous and Mycolepto discus were most effective for ammonia synthesis. We have tested the plant growth-promoting activity of the twelve isolated endophytic fungi on Cymbidium aloifolium protocorms (12 weeks old). All the endophytic fungi showed growth-promoting activity. Plant growth of Cymbidium aloifolium was found higher on the MS medium supplemented with all fungal elicitors. Fungal elicitor CVS4, however, showed the highest plant growth-promoting activity toward C. aloifolium.

Cytotoxic effect of selected wild orchids on two different human cancer cell lines

Majority of the orchid species are used in the traditional medicines for the treatment of several diseases. They are the sources of polysaccharides, phenanthrenes, bibenzyl derivatives, revesteral, stilbenoids and polyphenol compounds. This study explored the cytotoxic activity of seven wild orchid species and identification of medicinally active compounds. The extracts of orchid species were screened for cytotoxic effect on the human cervical cancer cells (HeLa) and human glioblastoma cells (U251) using an MTT assay. The medicinally active compounds of high cytotoxic extracts were identified by GC-MS resulting in many stilbenoids and phenolic derivatives. The extract of Dendrobium transparens (DTs) and Vanda cristata (VCw) showed high cytotoxic effect towards the HeLa and U251 cell lines (IC50 of DTs: 382.14 μg/ml and 75.84 μg/ml respectively and IC50 of VCw: 317.23 μg/ml and 163.66 μg/ml respectively). This study concludes that they could be used as cancer therapeutics.

Orchids and their mycorrhizal fungi: an insufficiently explored relationship

Orchids are associated with diverse fungal taxa, including nonmycorrhizal endophytic fungi as well as mycorrhizal fungi. The orchid mycorrhizal (OM) symbiosis is an excellent model for investigating the biological interactions between plants and fungi due to their high dependency on these symbionts for growth and survival. To capture the complexity of OM interactions, significant genomic, numerous transcriptomic, and proteomic studies have been performed, unraveling partly the role of each partner. On the other hand, several papers studied the bioactive metabolites from each partner but rarely interpreted their significance in this symbiotic relationship. In this review, we focus from a biochemical viewpoint on the OM dynamics and its molecular interactions. The ecological functions of OM in plant development and stress resistance are described first, summarizing recent literature. Secondly, because only few studies have specifically looked on OM molecular interactions, the signaling pathways and compounds allowing the establishment/maintenance of mycorrhizal association involved in arbuscular mycorrhiza (AM) are discussed in parallel with OM. Based on mechanistic similarities between OM and AM, and recent findings on orchids' endophytes, a putative model representing the different molecular strategies that OM fungi might employ to establish this association is proposed. It is hypothesized here that (i) orchids would excrete plant molecule signals such as strigolactones and flavonoids but also other secondary metabolites; (ii) in response, OM fungi would secrete mycorrhizal factors (Myc factors) or similar compounds to activate the common symbiosis genes (CSGs); (iii) overcome the defense mechanism by evasion of the pathogen-associated molecular patterns (PAMPs)-triggered immunity and by secretion of effectors such as small inhibitor proteins; and (iv) finally, secrete phytohormones to help the colonization or disrupt the crosstalk of plant defense phytohormones. To challenge this putative model, targeted and untargeted metabolomics studies with special attention to each partner's contribution are finally encouraged and some technical approaches are proposed.

Bacterial and Fungal Endophytes: Tiny Giants with Immense Beneficial Potential for Plant Growth and Sustainable Agricultural Productivity

The conventional means of achieving enhanced agricultural productivity are not ecologically balanced and sustainable. The excessive use of synthetic agrochemicals, declining soil nutrients, and water-use issues, amongst others, are threats to the ecosystem. Additionally, environmental degradation and an increasing global population that will reach 9 billion by 2030 are further considerations. These issues mean a decline in the volume of food resources available to feed the world. Therefore, sustainably increasing agricultural productivity is a necessity for restoring soil fertility, feeding the populace, and improving the ecosystem. A way to achieve this is by using eco-friendly microbial inoculants. Endophytes inhabit the tissues of plants asymptomatically without causing adverse effects. Bacterial and fungal endophytes benefit plants by promoting growth, suppressing pathogens, and improving the stress tolerance and immunity of plants. Despite this vital role played by endophytes in their interactions with host plants, there is still a paucity of relevant review data. More importantly, the prospective use of endophytes as an alternative to synthetic agrochemicals to ensure agro-ecological crop productivity has not been well reviewed in the literature. Therefore, this review sought to highlight the potential use of endophytic microbial resources to achieve enhancements in agro-food system crops in a sustainable manner.

A comprehensive review on fungal endophytes and its dynamics on Orchidaceae plants: current research, challenges, and future possibilities

In the development of medicinally important Orchidaceae, the extent of fungal endophytes specificity is not presently very clear. Limited study has been available on natural products formed and its role on plant growth, defence mechanism by endophytes, and to characterize the chief treasure of bioactive molecules. Therefore, this review article presents an evaluation of the endophytes associated with Orchidaceae for physiology, metabolism, and genomics which have prominently contributed to the resurgence of novel metabolite research increasing our considerate of multifaceted mechanisms regulatory appearance of biosynthetic gene groups encoding diverse metabolites. Additionally, we presented the comprehensive recent development of bio-strategies for the cultivation of endophytes from Orchidaceae and integration of bioengineered ‘Genomics with metabolism’ approaches with emphases collective omics as powerful approach to discover novel metabolite compounds. The Orchidaceae-fungal endophytes' biodynamics for sustainable development of bioproducts and its applications are supported in large-scale biosynthesis of industrially and pharmaceutical important biomolecules.

Bioprospecting endophytic fungi from Fusarium genus as sources of bioactive metabolites

Endophytic fungi became an attractive source for the discovery of new leads, because of the complexity and the structural diversity of their secondary metabolites. The genus Fusarium comprising about 70 species is extremely variable in terms of genetics, biology, ecology, and consequently, secondary metabolism and have been isolated from countless plants genera from diverse habitats. These endophytic microbes may provide protection and survival strategies in their host plants with production of a repertoire of chemically diverse and structurally unprecedented secondary metabolites reported to exhibit an incredible array of biological activities including antimicrobial, anticancer, antiviral, antioxidants, antiparasitics, immunosuppressants, immunomodulatory, antithrombotic, and biocontrol ability against plants pathogens and nematodes. This review comprehensively highlights over the period 1981-2019, the bioactive potential of metabolites produced by endophytes from Fusarium genus. Abbreviations: AIDS: Acquired immune deficiency syndrome; BAPT: C-13 phenylpropanoid side chain-CoA acyltransferase; CaBr2: Calcium bromide; DBAT: 10-deacetylbaccatin III-10-O-acetyl transferase; DNA: Deoxyribonucleic acid; EI-MS: Electron ionization mass spectrometer; EN: Enniatin; ERK: Extracellular regulated protein kinase; EtOAc: Ethyl acetate; FDA: Food and Drug Administration; GAE/g: Gallic acid equivalent per gram; GC-MS: Gas chromatography-mass spectrometry; HA: Hyperactivation; HCV: Hepatitis C Virus; HCVPR: Hepatitis C Virus protease; HeLa: Human cervical cancer cell line; HIV: Human immunodeficiency viruses; HPLC: High Performance Liquid Chromatography; IAA: Indole-3-acetic acid; IARC: International Agency for Research on Cancer; IC50: Half maximal inhibitory concentration; LC50: Concentration of the compound that is lethal for 50% of exposed population; LC-MS: Liquid chromatography-mass spectrometry; MCF-7: Human breast cancer cell line; MDR: Multidrug-resistant; MDRSA: Multidrug-resistant S. aureus; MFC: Minimum fungicidal concentration; MIC: Minimum inhibitory concentration; MRSA: Multidrug-resistant S. aureus; MTCC: Microbial type culture collection; PBMCs: Peripheral blood mononuclear cells; PCR: Polymerase chain reaction; TB: Tuberculosis; TLC: Thin layer chromatography; TNF: Tumor necrosis factor; WHO: World Health Organization http://www.zoobank.org/urn:lsid:zoobank.org:pub:D0A7B2D8-5952-436D-85C8-C79EAAD1013C.

Piriformospora indica promotes the growth of the in-vitro-raised Cymbidium aloifolium plantlet and their acclimatization

Cymbidium aloifolium is known for its ornamental and medicinal values. It has been listed as threatened orchid species. In this study, in vitro propagated C. aloifolium plantlets were interacted with the Piriformospora indica. The growth assay was performed for 45 days; the plant growth pattern such as number and length of roots and shoots were measured. Microscopic study of the root section stained by trypan blue was done to detect the peloton formation. The methanol extracts of the fungal colonized plant as well as uncolonized (control) plant were prepared and various metabolites were identified by gas chromatography mass spectroscopy. Acclimatization was done in a substrate composition of coco peat: gravel: charcoal in ratio 2:2:1. P. indica-colonized plantlet showed the highest growth with the formation of clamdospore in the root section. The growth regulator such as auxin, ascorbic acid, andrographolide, hexadecanoic acid, and DL-proline were identified. After three months of field transfer, plantlet colonized by P. indica survived and remained healthy as compared to uncolonized control plantlet.