Evaluation of antifungal, phosphate solubilisation, and siderophore and chitinase release activities of endophytic fungi from Pistacia vera

Species diversity and major host/substrate associations of the genus Akanthomyces (Hypocreales, Cordycipitaceae)

Akanthomyces, a group of fungi with rich morphological and ecological diversity in Cordycipitaceae (Ascomycota, Hypocreales), has a wide distribution amongst diverse habitats. By surveying arthropod-pathogenic fungi in China and Southeast Asia over the last six years, nine Akanthomyces spp. were found and identified. Five of these were shown to represent four known species and an undetermined species of Akanthomyces. Four of these were new species and they were named A.kunmingensis and A.subaraneicola from China, A.laosensis from Laos and A.pseudonoctuidarum from Thailand. The new species were described and illustrated according to the morphological characteristics and molecular data. Akanthomycesaraneogenus, which was isolated from spiders from different regions in China, Thailand and Vietnam, was described as a newly-recorded species from Thailand and Vietnam. The phylogenetic positions of the nine species were evaluated, based on phylogenetic inferences according to five loci, namely, ITS, nrLSU, TEF, RPB1 and RPB2. In this study, we reviewed the research progress achieved for Akanthomyces regarding its taxonomy, species diversity, geographic distribution and major host/substrate associations. The morphological characteristics of 35 species in Akanthomyces, including four novel species and 31 known taxa, were also compared.

Characterization of three new plant growth-promoting microbes and effects of the interkingdom interactions on plant growth and disease prevention

KEY MESSAGE

The novel interkingdom PGPM consortia enhanced the ability of plant growth promotion and disease resistance, which would be beneficial to improve plant growth in sustainable agriculture through engineering microbiome. Plant growth-promoting microbes (PGPMs) play important roles in promoting plant growth and bio-controlling of pathogens. Much information reveals that the plant growth-promoting ability of individual PGPM affects plant growth. However, the effects of the PGPM consortia properties on plant growth remain largely unexplored. Here, we characterized three new PGPM strains including Rhodotorula graminis JJ10.1 (termed as J), Pseudomonas psychrotolerans YY7 (termed as Y) and P. chlororaphis T8 (termed as T), and assessed their effects in combination with Bacillus amyloliquefaciens FZB42 (termed as F) on plant growth promotion and disease prevention in Arabidopsis thaliana and tomato (Solanum lycopersicum) plants by investigating morphological changes, whole-genome sequencing and plant growth promoting (PGP) characterization. Results revealed that the three new strains R. graminis JJ10.1, P. psychrotolerans YY7 and P. chlororaphis T8 had the potential for being combined with B. amyloliquefaciens FZB42 to form interkingdom PGPM consortia. The combinations of R. graminis JJ10.1, B. amyloliquefaciens FZB42, and P. psychrotolerans YY7, i. e. JF and JYF, exhibited the strongest ability of synergetic biofilm production. Furthermore, the growth-promotion abilities of the consortia were significantly enhanced compared with those of individual strains under both inoculation and volatile organic compounds (VOCs) treatment. Importantly, the consortia showed stronger abilities of in planta disease prevention than individual strains. Findings of our study may provide future guidance for engineering the minimal microbiome communities to improve plant growth and/or disease resistance in sustainable agriculture.

Plant-Associated Neoscytalidium dimidiatum-Taxonomy, Host Range, Epidemiology, Virulence, and Management Strategies: A Comprehensive Review

Neoscytalidium dimidiatum, a plant- and human-associated fungus, has emerged as a substantial global ecological and agricultural threat aggravated by global warming. It inflicts various diseases, including canker, blight, dieback, leaf spot, root rot, and fruit rot, across a wide spectrum of fruit trees, field crops, shrubs, and arboreal species, with a host range spanning 46 plant families, 84 genera, and 126 species, primarily affecting eudicot angiosperms. Six genera are asymptomatic hosts. Neoscytalidium dimidiatum exhibits worldwide distribution, with the highest prevalence observed in Asia and North America, notably in Iran, Turkey, and California. Rising disease prevalence and severity, aggravated by climate change, particularly impact tropical arid places across 37 countries spanning all 7 continents. This comprehensive review encapsulates recent advancements in the understanding of N. dimidiatum, encompassing alterations in its taxonomic classification, host range, symptoms, geographic distribution, epidemiology, virulence, and strategies for effective management. This study also concentrates on comprehending the taxonomic relationships and intraspecific variations within N. dimidiatum, with a particular emphasis on N. oculus and N. hylocereum, proposing to consider these two species as synonymous with N. dimidiatum. Furthermore, this review identifies prospective research directions aimed at augmenting our fundamental understanding of host-N. dimidiatum interaction.

An insight into endophytic antimicrobial compounds: an updated analysis

Resistance in micro-organisms against antimicrobial compounds is an emerging phenomenon in the modern era as compared to the traditional world which brings new challenges to discover novel antimicrobial compounds from different available sources, such as, medicinal plants, various micro-organisms, like, bacteria, fungi, algae, actinomycetes, and endophytes. Endophytes reside inside the plants without exerting any harmful impact on the host plant along with providing ample of benefits. In addition, they are capable of producing diverse antimicrobial compounds similar to their host, allowing them to serve as useful micro-organism for a range of therapeutic purposes. In recent years, a large number of studies on the antimicrobial properties of endophytic fungi have been carried out globally. These antimicrobials have been used to treat various bacterial, fungal, and viral infections in humans. In this review, the potential of fungal endophytes to produce diverse antimicrobial compounds along with their various benefits to their host have been focused on. In addition, classification systems of endophytic fungi as well as the need for antimicrobial production with genetic involvement and some of the vital novel antimicrobial compounds of endophytic origin can further be utilized in the pharmaceutical industries for various formulations along with the role of nanoparticles as antimicrobial agents have been highlighted.

Ilex paraguariensis Hosts Root-Trichoderma spp. with Plant-Growth-Promoting Traits: Characterization as Biological Control Agents and Biofertilizers

In this study, the effect of native plant-growth-promoting microorganisms (PGPM) as bio-inoculants was assessed as an alternative to improve Ilex paraguariensis Saint Hilaire growth in the nursery. Fourteen Trichoderma strains isolated from yerba mate roots were evaluated in vitro for their potential as biological control agents (BCA) and PGPM. The PGPM properties were evaluated through the strain's antagonistic activity against three fungal pathogens (Alternaria sp., F. oxysporum, and F. solani) plus the production of extracellular cell-wall-degrading enzymes such as chitinase, β-1,3-glucanase, and cellulase. These results were used to calculate different PGPM indices to select the strains with the optimal properties. Four Trichoderma strains: T. asperelloides LBM193, LBM204, LBM206, and Trichoderma sp. LBM202, were selected based on their indirect and direct PGPM properties used in an inoculation assay on yerba mate plants in greenhouse conditions. A highly significant positive effect of bio-inoculation with these Trichoderma strains was observed in one-year-old yerba mate seedlings. Inoculated plants exhibited a greater height, chlorophyll content, and dry weight than un-inoculated plants; those treated with LBM193 manifested the best results. Yerba mate plants treated with LBM202 exhibited a healthy appearance and were more vigorous, showing potential for biocontrol agent. In conclusion, yerba mate seedlings in the Misiones region were found to have a reservoir of Trichoderma species that increases the yield of this crop in the nursery and protects them from adverse biotic and abiotic agents.

Plant associated endophytic fungi as potential bio-factories for extracellular enzymes: Progress, Challenges and Strain improvement with precision approaches

There is an intricate network of relations between endophytic fungi and their hosts that affects the production of various bioactive compounds. Plant-associated endophytic contain industrially important enzymes and have the potential to fulfill their rapid demand in the international market to boost business in technology. Being safe and metabolically active, they have replaced the usage of toxic and harmful chemicals and hold a credible application in biotransformation, bioremediation, and industrial processes. Despite these, there are limited reports on fungal endophytes that can directly cater to the demand and supply of industrially stable enzymes. The underlying reasons include low endogenous production and secretion of enzymes from fungal endophytes which have raised concern for widely accepted applications. Hence it is imperative to augment the biosynthetic and secretory potential of fungal endophytes. Modern state-of-the-art biotechnological technologies aiming at strain improvement using cell factory engineering as well as precise gene editing like Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its Associated proteins (Cas) systems which can provide a boost in fungal endophyte enzyme production. Additionally, it is vital to characterize optimum conditions to grow one strain with multiple enzymes (OSME). The present review encompasses various plants-derived endophytic fungal enzymes and their applications in various sectors. Further, we postulate the feasibility of new precision approaches with an aim for strain improvement and enhanced enzyme production.

Current Perspectives on Chitinolytic Enzymes and Their Agro-Industrial Applications

Chitinases are a large and diversified category of enzymes that break down chitin, the world's second most prevalent polymer after cellulose. GH18 is the most studied family of chitinases, even though chitinolytic enzymes come from a variety of glycosyl hydrolase (GH) families. Most of the distinct GH families, as well as the unique structural and catalytic features of various chitinolytic enzymes, have been thoroughly explored to demonstrate their use in the development of tailor-made chitinases by protein engineering. Although chitin-degrading enzymes may be found in plants and other organisms, such as arthropods, mollusks, protozoans, and nematodes, microbial chitinases are a promising and sustainable option for industrial production. Despite this, the inducible nature, low titer, high production expenses, and susceptibility to severe environments are barriers to upscaling microbial chitinase production. The goal of this study is to address all of the elements that influence microbial fermentation for chitinase production, as well as the purifying procedures for attaining high-quality yield and purity.

Isolation and characterization of endophytic fungi having plant growth promotion traits that biosynthesizes bacosides and withanolides under in vitro conditions

Endophytes are regarded with immense potentials in terms of plant growth promoting (PGP) elicitors and mimicking secondary metabolites of medicinal importance. Here in the present study, we explored Bacopa monnieri plants to isolate, identify fungal endophytes with PGP elicitation potentials, and investigate secretion of secondary metabolites such as bacoside and withanolide content under in vitro conditions. Three fungal endophytes isolated (out of 40 saponin producing isolates) from leaves of B. monnieri were examined for in vitro biosynthesis of bacosides. On morphological, biochemical, and molecular identification (ITS gene sequencing), the isolated strains SUBL33, SUBL51, and SUBL206 were identified as Nigrospora oryzae (MH071153), Alternaria alternata (MH071155), and Aspergillus terreus (MH071154) respectively. Among these strains, SUBL33 produced highest quantity of Bacoside A3 (4093 μg mL-1), Jujubogenin isomer of Bacopasaponin C (65,339 μg mL-1), and Bacopasaponin C (1325 μg mL-1) while Bacopaside II (13,030 μg mL-1) was produced by SUBL51 maximally. Moreover, these aforementioned strains also produced detectable concentration of withanolides-Withaferrin A, Withanolide A (480 μg mL-1), and Withanolide B (1024 μg mL-1) respectively. However, Withanolide A was not detected in the secondary metabolites of strain SUBL51. To best of our knowledge, the present study is first reports of Nigrospora oryzae as an endophyte in B. monnieri with potentials of biosynthesis of economically important phytomolecules under in vitro conditions.

Aptitude of endophytic microbes for production of novel biocontrol agents and industrial enzymes towards agro-industrial sustainability

Background

Endophytes have continued to receive increased attention worldwide, probably, due to the enormous biotechnological potentials spanning through various industrial sectors. This paper outlines the biotechnological potentials of endophytes in biocontrol and industrial enzyme production, and the possible contribution towards achieving agro-industrial sustainability using published articles on endophytes in both Web of Science and Scopus (1990–2020).

Main body of the abstract

This review discusses the potential of endophytes to produce novel secondary metabolites with effective biocontrol activity against insect pests and plant pathogens. More so, the aptitude of endophytes for production of a wide range of enzymes with potential applications in agriculture, energy and health is discussed in this review. Furthermore, this review highlights the emerging potentials of endophytes in the production of exopolysaccharide and fatty acids. This paper also advocates the need for bioprospecting endophytes for novel biocontrol agents against termites, which are known for causing significant damage to forest and stored products.

Short conclusion

Exploration of endophytes for biocontrol and production of biomolecules of industrial significance could contribute significantly towards agricultural and industrial sustainability.

Potential of microbial endophytes to enhance the resistance to postharvest diseases of fruit and vegetables

Food loss of fruit and vegetables caused by postharvest diseases is a major issue worldwide. The method used to prevent and control postharvest diseases is usually to use chemical fungicides, but long-term and large-scale use will make the pathogens resistant and potentially have a negative impact on human health and the ecological environment. Therefore, finding a safe and effective biological control method instead of chemical control is a hot research topic in recent years. Endophytes, colonizing plants asymptomatically, can promote the growth of the hosts and enhance their resistance. The use of endophytes as biological control agents for postharvest diseases of fruit and vegetables has attracted increasing attention in the last 20 years. Compared with chemical control, endophytes have the advantages of being more environmentally friendly, sustainable, and safer. However, there are relatively few relevant studies, so herein we summarize the available literature. This review focuses mainly on the recent progress of using endophytes to enhance the resistance of postharvest fruit and vegetables to diseases, with the emphasis on the possible mechanisms and the potential applications. Furthermore, this article suggests future areas for study using antagonistic endophytes to prevent and control fruit and vegetable postharvest diseases: (i) screening more potential broad-spectrum anti-pathogen endophytes and their metabolic active substances by the method of macrogenomics; (ii) elucidating the underlining molecular mechanism among endophytes, harvested vegetables and fruit, pathogens, and microbial communities; (iii) needing more application research to overcome the difficulties of commercialization practice. © 2020 Society of Chemical Industry.

The Fungal Endophyte Epicoccum dendrobii as a Potential Biocontrol Agent Against Colletotrichum gloeosporioides

Anthracnose caused by Colletotrichum gloeosporioides is one of most serious fungal diseases on Chinese fir (Cunninghamia lanceolata). Eight fungal endophytes were isolated from a young heathy branch of Chinese fir and screened against the pathogen in vitro. One isolate, designated as SMEL1 and subsequently identified as Epicoccum dendrobii based on morphological and phylogenetic analyses, suppressed mycelial growth of Colletotrichum gloeosporioides on dual-culture plates. Additionally, E. dendrobii metabolites significantly decreased the biomass of Colletotrichum gloeosporioides. E. dendrobii was able to enter the internal tissues of the host plant via stomatal cells. Metabolites of E. dendrobii significantly inhibited conidial germination and appressorium formation, which at least partly explained why the endophyte significantly inhibited lesion development caused by Colletotrichum gloeosporioides on various host plants. We further confirmed that some components with antifungal activity could be extracted from E. dendrobii using ethyl acetate as an organic solvent. To our knowledge, this is the first report of E. dendrobii as a potential biocontrol agent against a fungal phytopathogen.

Sarocladium and Lecanicillium Associated with Maize Seeds and Their Potential to Form Selected Secondary Metabolites

The occurrence and diversity of Lecanicillium and Sarocladium in maize seeds and their role in this cereal are poorly understood. Therefore, the present study aimed to investigate Sarocladium and Lecanicillium communities found in endosphere of maize seeds collected from fields in Poland and their potential to form selected bioactive substances. The sequencing of the internally transcribed spacer regions 1 (ITS 1) and 2 (ITS2) and the large-subunit (LSU, 28S) of the rRNA gene cluster resulted in the identification of 17 Sarocladium zeae strains, three Sarocladium strictum and five Lecanicillium lecanii isolates. The assay on solid substrate showed that S. zeae and S. strictum can synthesize bassianolide, vertilecanin A, vertilecanin A methyl ester, 2-decenedioic acid and 10-hydroxy-8-decenoic acid. This is also the first study revealing the ability of these two species to produce beauvericin and enniatin B1, respectively. Moreover, for the first time in the present investigation, pyrrocidine A and/or B have been annotated as metabolites of S. strictum and L. lecanii. The production of toxic, insecticidal and antibacterial compounds in cultures of S. strictum, S. zeae and L. lecanii suggests the requirement to revise the approach to study the biological role of fungi inhabiting maize seeds.

Paecilomyces and Its Importance in the Biological Control of Agricultural Pests and Diseases

Incorporating beneficial microorganisms in crop production is the most promising strategy for maintaining agricultural productivity and reducing the use of inorganic fertilizers, herbicides, and pesticides. Numerous microorganisms have been described in the literature as biological control agents for pests and diseases, although some have not yet been commercialised due to their lack of viability or efficacy in different crops. Paecilomyces is a cosmopolitan fungus that is mainly known for its nematophagous capacity, but it has also been reported as an insect parasite and biological control agent of several fungi and phytopathogenic bacteria through different mechanisms of action. In addition, species of this genus have recently been described as biostimulants of plant growth and crop yield. This review includes all the information on the genus Paecilomyces as a biological control agent for pests and diseases. Its growth rate and high spore production rate in numerous substrates ensures the production of viable, affordable, and efficient commercial formulations for agricultural use.

Inhibition of quorum sensing-associated virulence factors and biofilm formation in Pseudomonas aeruginosa PAO1 by Mycoleptodiscus indicus PUTY1

Pseudomonas aeruginosa is the second most emerging multidrug-resistant, opportunistic pathogen after Acinetobacter baumannii that poses a threat in nursing homes, hospitals, and patients who need devices such as ventilators and blood catheters. Its ability to form quorum sensing-regulated virulence factors and biofilm makes it more resistant to top most therapeutic agents such as carbapenems and next-generation antibiotics. In the current study, we studied the quorum quenching potential of secondary metabolites of Mycoleptodiscus indicus PUTY1 strain. In vitro observation showed a mitigation in virulence factors such as rhamnolipids, protease, elastase pyocyanin, exopolysaccharides, and hydrogen cyanide gas. Furthermore, a significant reduction in the motility such as swimming, swarming, twitching, and inhibition in biofilm formation by Pseudomonas aeruginosa PAO1 was observed. Results of in vitro studies were further confirmed by in silico studies through docking and molecular dynamic simulation of GC-MS-detected compounds of Mycoleptodiscus indicus employing LasR and RhlR proteins. Both in vitro and in silico observations indicate a new alternative approach for combating virulence of Pseudomonas aeruginosa by targeting its protein receptors LasR and RhlR. Graphical abstract.

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

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

Aspergillus ochraceopetaliformis SSP13 modulates quorum sensing regulated virulence and biofilm formation in Pseudomonas aeruginosa PAO1

Pseudomonas aeruginosa is an opportunistic nosocomial pathogen causing the majority of acute and persistent infections in human beings. The ability to form biofilm adds a new dimension to its resistance to conventional therapeutic agents. In the present study, down-regulation of quorum sensing regulated virulence and biofilm development resulting from exposure to Aspergillus ochraceopetaliformis SSP13 extract was investigated. The in vitro results inferred impairment in the production of LasA protease, LasB elastase, chitinase, pyocyanin, exopolysaccharides and rhamnolipids. In addition, motility and biofilm formation by P. aeruginosa PAO1 was significantly altered. The in vitro results were further supported by molecular docking studies of the metabolites obtained from GC-MS analysis depicting the quorum sensing attenuation by targeting the receptor proteins LasR and RhlR. The in vitro and in silico studies suggested new avenues for the development of bioactive metabolites from A. ochraceopetaliformis SSP13 extract as potential anti-infective agents.

Attenuation of quorum sensing regulated virulence and biofilm development in Pseudomonas aeruginosa PAO1 by Diaporthe phaseolorum SSP12

In recent years, Pseudomonas aeruginosa PAO1 emerged as the significant pathogenic microorganism in majority of the hospital-acquired infections due to its resistance to the conventional antibiotics by virtue of its highly organized quorum sensing and associated biofilm formation. In the present study, quorum sensing attenuation potential of Diaporthe phaseolorum SSP12 extract was investigated against P. aeruginosa PAO1 amply supported by molecular docking studies. D. phaseolorum SSP12 extract significantly inhibited the production of LasI/R mediated LasA protease, LasB elastase and chitinase with 66.52 ± 5.41, 71.26 ± 4.58 and 61.16 ± 4.28% of inhibition respectively at a concentration of 750 μg mL^-1. In addition, RhlI/R mediated production of pyocyanin, exopolysaccharides and rhamnolipids were also down-regulated by 74.71 ± 3.97, 66.41 ± 3.62 and 63.75 ± 3.76% respectively on treatment with sub-MIC concentration of D. phaseolorum SSP12. The light, fluorescence and confocal laser scanning microscopic (CLSM) analysis confirmed the significant disruption in biofilm formation. The presence of bioactive constituents such as phenyl ethylalcohol, 2, 4-di-tert-butylphenol, fenaclon, 1, 4-phenylenediacetic acid, and benzyl hydrazine in D. phaseolorum SSP12 extract was evident from Gas chromatography-mass spectrophotometric (GC-MS) analysis. From the in silico molecular docking studies, fenaclon and 2, 4-di-tert-butylphenol competitively binds to QS receptors LasR and RhlR and alters the binding of its cognate ligands and modulates the expression of virulence phenotypes. The promising anti quorum sensing efficacy of D. phaseolorum SSP12 extract suggested new avenues for development of anti-infective drugs from fungal derived metabolites to counteract the problems associated with conventional antibiotic therapies.