Antimicrobial secondary metabolites from agriculturally important fungi as next biocontrol agents

First Investigation of Secondary Metabolites from Aspergillus xerophilus Reveals Compounds with Inhibitive Effects against Three Phytopathogenic Fungi of Agrarian Crops

Fungal secondary metabolites play a highly significant role in crop protection, which is related to their antifungal activity against agriculturally important phytopathogens. In fact, plant diseases caused by fungi including species belonging to the genera of Alternaria, Botrytis, and Fusarium have become increasingly serious affecting crop yield and quality. Hence, there is increasing awareness by the scientific community of the importance of exploiting fungal products for finding new compounds able to inhibit phytopathogens. In this study several drimane-type sesquiterpenes have been detected for the first time as products of Aspergillus xerophilus by GC-MS analysis of the organic extracts obtained from the mycelia and culture filtrates of the fungus grown on two different substrates. Seven pure drimane-type sesquiterpenes were also isolated and identified by spectroscopic methods. The inhibitory effects of the pure compounds have been investigated against three phytopathogenic fungi of agrarian crops (i.e., Botrytis cinerea, Alternaria alternata, and Fusarium oxysporum f. sp. pisi). Among the drimane-type sesquiterpenes isolated in this study, 9,11-dihydroxy-6-oxodrim-7-ene is the most active against the three phytopathogens. Our findings also reveal the high sensitivity of A. alternata to the isolated compounds. These results pave the way for future applications in agriculture of both A. xerophilus and its metabolites.

Cytospotones A-D, four new polyketones from the endophytic fungus Cytospora sp. A879

Three new α-pyrone derivatives cytospotones A-C (1-3) and a new cyclohexenone derivative cytospotone D (4) together with four known α-pyrones were isolated from the endophytic fungus Cytospora sp. A879 of Pogostemon cablin (Blanco) Benth. The structures of 1-4 were elucidated primarily by spectroscopic methods (1D, 2D NMR and HRESIMS), ECD spectra analyses, and ECD calculations. Furthermore, the four new compounds (1-4) were evaluated for their anti-inflammatory and α-glucosidase inhibitory activities. The results showed that compound 1 had moderate inhibitory effect on LPS-induced NO production in RAW 264.7 macrophages.

Pathological consequences, metabolism and toxic effects of trichothecene T-2 toxin in poultry

Contamination of feed with mycotoxins has become a severe issue worldwide. Among the most prevalent trichothecene mycotoxins, T-2 toxin is of particular importance for livestock production, including poultry posing a significant threat to animal health and productivity. This review article aims to comprehensively analyze the pathological consequences, metabolism, and toxic effects of T-2 toxin in poultry. Trichothecene mycotoxins, primarily produced by Fusarium species, are notorious for their potent toxicity. T-2 toxin exhibits a broad spectrum of negative effects on poultry species, leading to substantial economic losses as well as concerns about animal welfare and food safety in modern agriculture. T-2 toxin exposure easily results in negative pathological consequences in the gastrointestinal tract, as well as in parenchymal tissues like the liver (as the key organ for its metabolism), kidneys, or reproductive organs. In addition, it also intensely damages immune system-related tissues such as the spleen, the bursa of Fabricius, or the thymus causing immunosuppression and increasing the susceptibility of the animals to infectious diseases, as well as making immunization programs less effective. The toxin also damages cellular processes on the transcriptional and translational levels and induces apoptosis through the activation of numerous cellular signaling cascades. Furthermore, according to recent studies, besides the direct effects on the abovementioned processes, T-2 toxin induces the production of reactive molecules and free radicals resulting in oxidative distress and concomitantly occurring cellular damage. In conclusion, this review article provides a complex and detailed overview of the metabolism, pathological consequences, mechanism of action as well as the immunomodulatory and oxidative stress-related effects of T-2 toxin. Understanding these effects in poultry is crucial for developing strategies to mitigate the impact of the T-2 toxin on avian health and food safety in the future.

Streptomyces as a promising biological control agents for plant pathogens

Plant diseases caused by pathogenic microorganisms in agriculture present a considerable obstacle, resulting in approximately 30-40% crop damage. The use of conventional techniques to manage these microorganisms, i.e., applying chemical pesticides and antimicrobials, has been discovered to have adverse effects on human health and the environment. Furthermore, these methods have contributed to the emergence of resistance among phytopathogens. Consequently, it has become imperative to investigate natural alternatives to address this issue. The Streptomyces genus of gram-positive bacteria is a potentially viable natural alternative that has been extensively researched due to its capacity to generate diverse antimicrobial compounds, such as metabolites and organic compounds. Scientists globally use diverse approaches and methodologies to extract new bioactive compounds from these bacteria. The efficacy of bioactive compounds in mitigating various phytopathogens that pose a significant threat to crops and plants has been demonstrated. Hence, the Streptomyces genus exhibits potential as a biological control agent for combating plant pathogens. This review article aims to provide further insight into the Streptomyces genus as a source of antimicrobial compounds that can potentially be a biological control against plant pathogens. The investigation of various bioactive compounds synthesized by this genus can enhance our comprehension of their prospective utilization in agriculture.

Antifungal activity of cyclopaldic acid from Antarctic Penicillium against phytopathogenic fungi

Plant pathogens cause great economic losses in agriculture. To reduce damage, chemical pesticides have been frequently used, but these compounds in addition to causing risks to the environment and health, its continuous use has given rise to resistant phytopathogens, threatening the efficiency of control methods. One alternative for such a problem is the use of natural products with high antifungal activity and low toxicity. Here, we present the production, isolation, and identification of cyclopaldic acid, a bioactive compound produced by Penicillium sp. CRM 1540, a fungal strain isolated from Antarctic marine sediment. The crude extract was fractionated by reversed-phase chromatography and yielded 40 fractions, from which fraction F17 was selected. We used 1D and 2D Nuclear Magnetic Resonance analysis in DMSO-d6 and CDCl3, together with mass spectrometry, to identify the compound as cyclopaldic acid C11H10O6 (238 Da). The pure compound was evaluated for antimicrobial activity against phytopathogenic fungi of global agricultural importance, namely: Macrophomina phaseolina, Rhizoctonia solani, and Sclerotinia sclerotiorum. The antifungal assay revealed the potential of cyclopaldic acid, produced by Penicillium sp. CRM 1540, as a leading molecule against M. phaseolina and R. solani, with more than 90% of growth inhibition after 96h of contact with the fungal cells using 100 µg mL-1, and more than 70% using 50 µg mL-1.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03792-9.

Genomic Based Analysis of the Biocontrol Species Trichoderma harzianum: A Model Resource of Structurally Diverse Pharmaceuticals and Biopesticides

Fungi represents a rich repository of taxonomically restricted, yet chemically diverse, secondary metabolites that are synthesised via specific metabolic pathways. An enzyme's specificity and biosynthetic gene clustering are the bottleneck of secondary metabolite evolution. Trichoderma harzianum M10 v1.0 produces many pharmaceutically important molecules; however, their specific biosynthetic pathways remain uncharacterised. Our genomic-based analysis of this species reveals the biosynthetic diversity of its specialised secondary metabolites, where over 50 BGCs were predicted, most of which were listed as polyketide-like compounds associated clusters. Gene annotation of the biosynthetic candidate genes predicted the production of many medically/industrially important compounds including enterobactin, gramicidin, lovastatin, HC-toxin, tyrocidine, equisetin, erythronolide, strobilurin, asperfuranone, cirtinine, protoilludene, germacrene, and epi-isozizaene. Revealing the biogenetic background of these natural molecules is a step forward towards the expansion of their chemical diversification via engineering their biosynthetic genes heterologously, and the identification of their role in the interaction between this fungus and its biotic/abiotic conditions as well as its role as bio-fungicide.

Vineyard Management and Physicochemical Parameters of Soil Affect Native Trichoderma Populations, Sources of Biocontrol Agents against Phaeoacremonium minimum

Native strains of Trichoderma in vineyard soil represent an opportunity for reducing the incidence of grapevine trunk diseases (GTDs) in vineyards. Moreover, its relationship with the environment (physicochemical soil characteristics and farming management practices) remains unclear. In the current study, a survey was carried out on farming management used by viticulturists, and soil samples were studied to analyze their physicochemical properties and to isolate Trichoderma strains. Later, statistical analyses were performed to identify possible correlations between Trichoderma populations, soil management and soil characteristics. In addition, in vitro tests, including antibiosis and mycoparasitism, were performed to select those Trichoderma strains able to antagonize Phaeoacremonium minimum. In this study a positive correlation was found between the iron content and pH in the soil, and a lower pH increases Trichoderma populations in soils. Vineyard management also affects Trichoderma populations in the soil, negatively in the case of fertilization and tillage and positively in the case of herbicide spraying. Two Trichoderma native strains were selected as potential biocontrol agents (Trichoderma gamsii T065 and Trichoderma harzianum T087) using antibiosis and mycoparasitism as mechanisms of action. These results led to the conclusion that native Trichoderma strains hold great potential as biological control agents and as producers of secondary metabolites.

Biosurfactants' multifarious functional potential for sustainable agricultural practices

Increasing food demand by the ever-growing population imposes an extra burden on the agricultural and food industries. Chemical-based pesticides, fungicides, fertilizers, and high-breeding crop varieties are typically employed to enhance crop productivity. Overexploitation of chemicals and their persistence in the environment, however, has detrimental effects on soil, water, and air which consequently disturb the food chain and the ecosystem. The lower aqueous solubility and higher hydrophobicity of agrochemicals, pesticides, metals, and hydrocarbons allow them to adhere to soil particles and, therefore, continue in the environment. Chemical pesticides, viz., organophosphate, organochlorine, and carbamate, are used regularly to protect agriculture produce. Hydrophobic pollutants strongly adhered to soil particles can be solubilized or desorbed through the usage of biosurfactant/s (BSs) or BS-producing and pesticide-degrading microorganisms. Among different types of BSs, rhamnolipids (RL), surfactin, mannosylerythritol lipids (MELs), and sophorolipids (SL) have been explored extensively due to their broad-spectrum antimicrobial activities against several phytopathogens. Different isoforms of lipopeptide, viz., iturin, fengycin, and surfactin, have also been reported against phytopathogens. The key role of BSs in designing and developing biopesticide formulations is to protect crops and our environment. Various functional properties such as wetting, spreading, penetration ability, and retention period are improved in surfactant-based formulations. This review emphasizes the use of diverse types of BSs and their source microorganisms to challenge phytopathogens. Extensive efforts seem to be focused on discovering the innovative antimicrobial potential of BSs to combat phytopathogens. We discussed the effectiveness of BSs in solubilizing pesticides to reduce their toxicity and contamination effects in the soil environment. Thus, we have shed some light on the use of BSs as an alternative to chemical pesticides and other agrochemicals as sparse literature discusses their interactions with pesticides. Life cycle assessment (LCA) and life cycle sustainability analysis (LCSA) quantifying their impact on human activities/interventions are also included. Nanoencapsulation of pesticide formulations is an innovative approach in minimizing pesticide doses and ultimately reducing their direct exposures to humans and animals. Some of the established big players and new entrants in the global BS market are providing promising solutions for agricultural practices. In conclusion, a better understanding of the role of BSs in pesticide solubilization and/or degradation by microorganisms represents a valuable approach to reducing their negative impact and maintaining sustainable agricultural practices.

Application of antimicrobial, potential hazard and mitigation plans

The tremendous rise in the consumption of antimicrobial products had aroused global concerns, especially in the midst of pandemic COVID-19. Antimicrobial resistance has been accelerated by widespread usage of antimicrobial products in response to the COVID-19 pandemic. Furthermore, the widespread use of antimicrobial products releases biohazardous substances into the environment, endangering the ecology and ecosystem. Therefore, several strategies or measurements are needed to tackle this problem. In this review, types of antimicrobial available, emerging nanotechnology in antimicrobial production and their advanced application have been discussed. The problem of antimicrobial resistance (AMR) due to antibiotic-resistant bacteria (ARB)and antimicrobial resistance genes (AMG) had become the biggest threat to public health. To deal with this problem, an in-depth discussion of the challenges faced in antimicrobial mitigations and potential alternatives was reviewed.

Peptaibol Production and Characterization from Trichoderma asperellum and Their Action as Biofungicide

Peptaibols (Paib), are a class of biologically active peptides isolated from soil, fungi and molds, which have interesting properties as antimicrobial agents. Paib production was optimized in flasks by adding sucrose as a carbon source, 2-aminoisobutyric acid (Aib) as an additive amino acid, and F. oxysporum cell debris as an elicitor. Paib were purified, sequenced and identified by High-performance liquid chromatography (HPLC)coupled to mass spectrometry. Afterward, a Paib extract was obtained from the optimized fermentations. The biological activity of these extracts was evaluated using in vitro and in vivo methods. The extract inhibited the growth of specific plant pathogens, and it showed inhibition rates similar to those from commercially available fungicides. Growth inhibition rates were 92.2, 74.2, 58.4 and 36.2% against Colletotrichum gloeosporioides, Botrytis cinerea, Alternaria alternata and Fusarium oxysporum, respectively. Furthermore, the antifungal activity was tested in tomatoes inoculated with A. alternata, the incidence of the disease in tomatoes treated with the extract was 0%, while the untreated fruit showed a 92.5% incidence of infection Scanning electron microscopy images showed structural differences between the fungi treated with or without Paib. The most visual alterations were sunk and shriveled morphology in spores, while the hyphae appeared to be fractured, rough and dehydrated.

Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes

Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because the original microbiomes quickly re-establish. Since the complex biological networks involved are little understood, progress through conventional means is time-consuming. Synthetic biology, with its practical successes in multiple industries, could speed up this research considerably. Some fascinating candidates for production by synthetic microbiomes are organic nitrogen metabolites and related pyridoxal-5'-phosphate-dependent enzymes, which have pivotal roles in microbe-microbe and plant-microbe interactions. This review summarizes recent studies of these metabolites and enzymes and discusses prospective synthetic biology platforms for sustainable agriculture.

Phytotoxicity Optimization of Fungal Metabolites Produced by Solid and Submerged Fermentation and its Ecotoxicological Effects

Research and commercial production of bioherbicides occur to a lesser extent compared to bioinsecticides and biofungicides. In order to contribute to developing new bioherbicides with low environmental impact, this study aimed to increase the phytotoxicity of metabolites of the fungus Mycoleptodiscus indicus UFSM 54 by optimizing solid and submerged fermentation and evaluate the ecotoxicological effects on earthworms (Eisenia andrei). The Plackett-Burman and central composite rotatable designs were used to optimize metabolite phytotoxicity. The variables optimized in the fermentation were temperature, agitation, pH, water volume in the culture medium, glucose concentration, and yeast extract. The fungus was grown on sugarcane bagasse substrate, and its metabolites were applied to detached Cucumis sativus, Conyza sp., and Sorghum bicolor leaves and used in an avoidance test and acute exposure to earthworms. Metabolite phytotoxicity in submerged fermentation was optimized at 35 °C, 50 rpm, and 1.5 g l^-1 of glucose and in solid fermentation at 30-37 °C and in 14-32 ml of water. The metabolites severely damaged germination, initial growth, and leaves of the three plants, and at the doses tested (maximum of 113.92 ml kg^-1), the metabolites of M. indicus UFSM 54 were not toxic to earthworms.

An Integrative Volatile Terpenoid Profiling and Transcriptomics Analysis in Hoya cagayanensis, Hoya lacunosa and Hoya coriacea (Apocynaceae, Marsdenieae)

Hoya’s R.Br. attractive flower shapes and unique scents make it suitable to be exploited as a new source of tropical fragrance. Therefore, this study aims to elucidate the biosynthesis of secondary metabolites using phytochemical and transcriptomic approaches to understand the mechanisms of scents biosynthesis, especially terpenoid in Hoya. Three Hoya flower species were selected in this study: Hoya cagayanensis, Hoya lacunosa, and Hoya coriacea. The secondary metabolite profiles characterizing scents on flowers were performed using head space solid phase microextraction (HS-SPME). Gas chromatography-mass spectrometry (GC-MS) revealed 23 compounds from H. cagayanensis, 14 from H. lacunose, and 36 from H. coriacea. Volatiles from the three species had different fragrance profiles, with β-ocimene and methyl salicylate compounds dominating the odor in H. cagayanensis. The 1-octane-3-ol was found highest in H. lacunosa, and (Z)-acid butyric, 3-hexenyl ester was found highest in H. coriacea. Subsequent studies were conducted to identify the biosynthesis pathway of secondary metabolites responsible for the aroma profile released by Hoya flowers through transcriptome sequencing using the Illumina Hiseq 4000 platform. A total of 109,240 (75.84%) unigenes in H. cagayanensis, 42,479 (69.00%) in H. lacunosa and 72,610 (70.55%) in H. coriacea of the total unigenes were successfully annotated using public databases such as NCBI-Nr, KEGG, InterPro, and Gene Ontology (GO). In conclusion, this study successfully identified the complete outline of terpenoid biosynthesis pathways for the first time in Hoya. This discovery could lead to the exploitation of new knowledge in producing high-value compounds using the synthetic biology approach.

Bioprotection strategies in winemaking

Worldwide the interest for biological control of food spoilage microorganisms has significantly increased over the last decade. Wine makes no exception to this trend, as consumer demands for wines free of preservatives that are considered negative for human health, increase. Biological control during wine fermentation aims at producing high quality wines, while minimizing, or even eliminating, the use of chemical additives. Its success lies in the inoculation of microorganisms to prevent, inhibit or kill undesired microbes, therefore maintaining wine spoilage at the lowest level. The food industry already makes use of this practice, with dedicated commercial microbes already on the market. In winemaking, there are commercial microbes currently under investigation, particularly with the aim to reduce or replace the use of sulphur dioxide. In this review, the potential of wine yeasts and lactic acid bacteria as bioprotection agents and their mechanisms of action during wine fermentation are presented.

Desert soil fungi isolated from Saudi Arabia: cultivable fungal community and biochemical production

Desert soils harbor fungi that have survived under highly stressed conditions of high temperature and little available moisture. This study was designed to survey the communities of cultivable fungi in the desert soils of the Arabian Peninsula and to screen the fungi for the potentially valuable antioxidants (flavonoids, phenols, saponins, steroids, tannins, terpenoids, and alkaloids) and enzymes (cellulase, laccase, lipase, protease, amylase, and chitinase). Desert soil was sampled at 30 localities representing different areas of Saudi Arabia and studied for physico-chemical soil properties. Five types of soil texture (sand, loamy sand, sandy loam, silty loam, and sandy clay loam) were observed. A total of 25 saprotrophic species was identified molecularly from 68 isolates. Our survey revealed 13 culturable fungal species that have not been reported previously from Arabian desert soils and six more species not reported from Saudi Arabian desert soils. The most commonly recorded genera were Aspergillus (isolated from 20 localities) and Penicillium (6 localities). The measurements of biochemicals revealed that antioxidants were produced by 49 and enzymes by 52 isolates; only six isolates did not produce any biochemicals. The highest biochemical activity was observed for the isolates Fusarium brachygibbosum and A. phoenicis. Other active isolates were A. proliferans and P. chrysogenum. The same species, for instance, A. niger had isolates of both high and low biochemical activities. Principal component analysis gave a tentative indication of a relationship between the biochemical activity of fungi isolated from soil and soil texture variables namely the content of silt, clay and sand. However, any generalizable relation between soil properties and fungal biochemical activities cannot be suggested. Each fungal isolate is probable to produce several antioxidants and enzymes, as shown by the correlation within the compound groups. Desert soil warrants further research as a promising source of biochemicals.

Trichoderma spp. mediated induction of systemic defense response in brinjal against Sclerotinia sclerotiorum

Induction of resistance to pathogen is associated with the colonization of root by Trichoderma spp. has been attributed as one of the major mechanisms contributing to pathogenic invasion. The present study sheds light on the defense network of brinjal plant bioprimed with Trichoderma spp. challenged with Sclerotinia sclerotiorum. Plants treated with dual inoculation of Trichoderma harzianum and Trichoderma asperellum triggered further synthesis of TPC under S. sclerotiorum challenge with maximum increment recorded at 72 hours. In consortium treated and pathogen challenged plants, a higher amount of shikimic acid was observed at 72 hours, whereas other phenolics showed little differences among the treatments. The consortium treatment showed significantly higher defense related enzymes (Phenylalanine Ammonia Lyase, Peroxidase and Polyphenol Oxidase) activity than other treatments. The study signifies how Trichoderma spp. reprograms the host's defense network to provide robust protection against S. sclerotiorum. In the present case, overall protection was provided to the brinjal plants against the attack of S. sclerotiorum.

Development of Plant-Fungal Endophyte Associations to Suppress Phoma Stem Canker in Brassica

Endophytic microorganisms are found within the tissues of many plants species, with some conferring several benefits to the host plant including resistance to plant diseases. In this study, two putative endophytic fungi that were previously isolated from wild seeds of Brassica, identified as Beauveria bassiana and Pseudogymnoascus pannorum, were inoculated into cultivars of three Brassica species—Brassica napus, Br. rapa and Br. oleracea. Both fungal endophytes were reisolated from above- and below-ground tissues of inoculated plants at four different plant-growth stages, including cotyledon, one-leaf, two-leaf, and four-leaf stages. None of the plants colonised by these fungi exhibited any obvious disease symptoms, indicating the formation of novel mutualistic associations. These novel plant–endophyte associations formed between Brassica plants and Be. bassiana significantly inhibited phoma stem canker, a devastating disease of Brassica crops worldwide, caused by the fungal pathogen Leptosphaeria maculans. The novel association formed with P. pannorum significantly suppressed the amount of disease caused by L. maculans in one out of two experiments. Although biological control is not a new strategy, endophytic fungi with both antiinsect and antifungal activity are a highly conceivable, sustainable option to manage pests and diseases of economically important crops.

Biosynthesis and beneficial effects of microbial gibberellins on crops for sustainable agriculture

Soil microbes promote plant growth through several mechanisms such as secretion of chemical compounds including plant growth hormones. Among the phytohormones, auxins, ethylene, cytokinins, abscisic acid and gibberellins are the best understood compounds. Gibberellins were first isolated in 1935 from the fungus Gibberella fujikuroi and are synthesized by several soil microbes. The effect of gibberellins on plant growth and development has been studied, as has the biosynthesis pathways, enzymes, genes and their regulation. This review revisits the history of gibberellin research highlighting microbial gibberellins and their effects on plant health with an emphasis on the early discoveries and current advances that can find vital applications in agricultural practices.

Genomic Features and Molecular Function of a Novel Stress-Tolerant Bacillus halotolerans Strain Isolated from an Extreme Environment

Simple Summary

The Qinghai–Tibet Plateau is known as the “third pole of the world”. Due to the extreme geographical location, Qinghai–Tibet Plateau has unique ecosystems characterized by oxygen deficiency, low temperature, high salinity and alkalinity. We carried out the current study to explore the excellent extremophilic Bacillus strains via potential stress resistance as well as biocontrol properties in the Qinghai–Tibet Plateau. We found a Bacillus halotolerans strain with a promising ability to withstand harsh environments and which also exhibits an optimistic biocontrol activity against plant pathogens. We revealed the whole genome sequencing and its taxonomic position and elucidated its molecular functions that were responsible for enhancing stress tolerance as well as suppressing plant pathogens at the genetic level. Lastly, we identified this strain harbored the specific genes associated with stresses resistance, biocontrol function, and can be used as a biological agent in the agriculture field.

Abstract

Due to its topographical position and climatic conditions, the Qinghai–Tibet Plateau possesses abundant microorganism resources. The extremophilic strain KKD1 isolated from Hoh Xil possesses strong stress tolerance, enabling it to propagate under high salinity (13%) and alkalinity (pH 10.0) conditions. In addition, KKD1 exhibits promising biocontrol activity against plant pathogens. To further explore these traits at the genomic level, we performed whole-genome sequencing and analysis. The taxonomic identification according to the average nucleotide identity based on BLAST revealed that KKD1 belongs to Bacillus halotolerans. Genetic screening of KKD1 revealed that its stress resistance mechanism depends on osmotic equilibrium, membrane transportation, and the regulation of ion balance under salt and alkaline stress. The expression of genes involved in these pathways was analyzed using real-time quantitative PCR. The presence of different gene clusters encoding antimicrobial secondary metabolites indicated the various pathways by which KKD1 suppresses phytopathogenic growth. Moreover, the lipopeptides surfactin and fengycin were identified as being significant antifungal components of KKD1. Through comparative genomics analysis, we noticed that KKD1 harbored specific genes involved in stress resistance and biocontrol, thus providing a new perspective on the genomic features of the extremophilic Bacillus species.

Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications

Natural products derived from microbes are crucial innovations that would help in reaching sustainability development goals worldwide while achieving bioeconomic growth. Trichoderma species are well-studied model fungal organisms used for their biocontrol properties with great potential to alleviate the use of agrochemicals in agriculture. However, identifying and characterizing effective natural products in novel species or strains as biological control products remains a meticulous process with many known challenges to be navigated. Integration of recent advancements in various "omics" technologies, next generation biodesign, machine learning, and artificial intelligence approaches could greatly advance bioprospecting goals. Herein, we propose a roadmap for assessing the potential impact of already known or newly discovered Trichoderma species for biocontrol applications. By screening publicly available Trichoderma genome sequences, we first highlight the prevalence of putative biosynthetic gene clusters and antimicrobial peptides among genomes as an initial step toward predicting which organisms could increase the diversity of natural products. Next, we discuss high-throughput methods for screening organisms to discover and characterize natural products and how these findings impact both fundamental and applied research fields.

Trichoderma asperellum xylanases promote growth and induce resistance in poplar

Xylanase secreted by Trichoderma asperellum ACCC30536 can stimulate the systemic resistance of host plants against pathogenic fungi. Following T. asperellum conidia co-culture with Populus davidiana × P. alba var. pyramidalis Louche (PdPap) seedlings, the expression of xylanases TasXyn29.4 and TasXyn24.2 in T. asperellum were upregulated, peaking at 12 h, by 106 (2^6.74) and 10.1 (2^3.34)-fold compared with the control, respectively. However, the expression of TasXyn24.4 and TasXyn24.0 was not detected. When recombinant xylanases rTasXyn29.4 and rTasXyn24.2 were heterologously expressed in Pichia pastoris GS115, their activities reached 18.9 IU/mL and 20.4 IU/mL, respectively. In PdPap seedlings induced by rTasXyn29.4 and rTasXyn24.2, the auxin and jasmonic acid signaling pathways were activated to promote growth and enhance resistance against pathogens. PdPap seedlings treated with both xylanases showed increased methyl jasmonate contents at 12 hpi, reaching 122 % (127 μg/g) compared with the control. However, neither of the xylanases could induce the salicylic acid signaling pathway in PdPap seedlings. Meanwhile, both xylanases could enhance the antioxidant ability of PdPap seedlings by improving their catalase activity. Both xylanases significantly induced systemic resistance of PdPap seedlings against Alternaria alternata, Rhizoctonia solani, and Fusarium oxysporum. However, the xylanases could only be sensed by the roots of the PdPap seedlings, not the leaves. In summary, rTasXyn29.4 and rTasXyn24.2 from T. asperellum ACCC30536 promoted growth and induced systemic resistance of PdPap seedlings, which endowed the PdPap seedlings broad-spectrum resistance to phytopathogens.

Molecular methods unravel the biosynthetic potential of Trichoderma species

Members of the genus Trichoderma are a well-established and studied group of fungi, mainly due to their efficient protein production capabilities and their biocontrol activities. Despite the immense interest in the use of different members of this species as biopesticides and biofertilizers, the study of their active metabolites and their biosynthetic gene clusters has not gained significant attention until recently. Here we review the challenges and opportunities in exploiting the full potential of Trichoderma spp. for the production of natural products and new metabolic engineering strategies used to overcome some of these challenges.

Recent advancements for microorganisms and their natural compounds useful in agriculture

During the past years, microorganisms have been the cause of many problems for human's health. However, today with the development of many techniques of microbiology, the researchers have studied several roles of microorganisms which may help the society. Microbial-based products are expected to play important role in agriculture-enhancing plant production and therefore increasing crop's yieldeswani et al. . Microorganisms can act by several action mechanisms including antibiosis or mechanisms in plant-microbe interactions underlining the dual function of microbial strains toward plant nutrition and protection. The market has increased with the development of microbial-based products. Currently, it is normal to think that microorganisms help us in agriculture by applying them as biological control. In this mini review, we collect the last findings about this topic including very recent literature. KEY POINTS: • Microorganisms play a beneficial role in agriculture by different mechanisms. • One of these mechanisms is the secretion of chemical compounds with different activities.

Role and function of Chondrostereum purpureum in biocontrol of trees

Abstract

A decay fungus, Chondrostereum purpureum (Pers. Ex Fr.) Pouzar, has been investigated in Europe, Northern America and New Zealand for its ability to decay hardwood stumps and thus prevent sprouting. The aim of these investigations has been to find an alternative to mechanical (cutting only) and chemical sprout control (cutting and applying chemicals to stumps in order to prevent sprouting). Mechanical sprout control is not an efficient option due to hardwood tree species’ ability to re-sprout efficiently after cutting, and therefore management costs are high. Chemicals would be efficient but due to their harmful effects on the environment, alternatives are needed. The fungal treatment, i.e., cutting accompanied with C. purpureum inoculum is an environmentally friendly and efficient option for sprout control. This mini-review comprises the role and function of C. purpureum in biocontrol of trees: the ecology of C. purpureum, its sprout control efficacy, factors affecting sprout control efficacy, devices in biological sprout control, potential risks, and the future perspectives of biological sprout control.

Key points

• A fungus Chondrostereum purpureum is efficient in preventing sprouting of hardwoods

• C. purpureum is not sensitive to environmental conditions

• Devices should be developed for cost-efficient biological sprout control

Secondary Metabolites with Agricultural Antagonistic Potentials from Beauveria felina, a Marine-Derived Entomopathogenic Fungus

Soil-borne pathogens and weeds could synergistically affect vegetable growth and result in serious losses. The investigation of antagonistic metabolites from a marine-derived entomopathogenic fungus, Beauveria felina, obtained polyhydroxy steroid (1), tricyclic diterpenoid (2), isaridin (3), and destruxin cyclodepsipeptides (4-6). The structures and absolute configurations of new 1-3 were elucidated by extensive spectroscopic and X-ray crystallographic analyses, as well as electronic circular dichroism (ECD) calculations. Compounds 1 and 2 showed antifungal activities against carbendazim-resistant strains of Botrytis cinerea, with the minimum inhibitory concentration (MIC) values ranging from 16 to 32 μg/mL, which were significantly better than those of carbendazim (MIC = 256 μg/mL). Compound 5 exhibited significant antagonistic activity against the radicle growth of Amaranthus retroflexus seedlings, which was almost identical to that of the positive control (2,4-dichlorophenoxyacetic acid). The structure-activity differences of 4-6 suggested that the Cl atom in HMPA¹ and β-Me in Pro² should be the key factors to their herbicidal activities. Besides, compounds 3-6 showed moderate nematicidal activities against Meloidogyne incognita. These antagonistic effects of 1-6 were first reported and further revealed the synergistically antagonistic potential of B. felina to be developed into the biopesticide.

Biochar-bacteria-plant partnerships: Eco-solutions for tackling heavy metal pollution

Over the past 30 years, the ever-rising demands of the modern and growing population have led to the rapid development of agricultural and industrial sectors worldwide. However, this expansion has exposed the environment to various pollutants including heavy metal (HM)s. Almost all HMs are serious toxicants and can pose serious health risks to living organisms in addition to their bioaccumulative and non-biodegradable nature. Different techniques have been developed to restore the ecological functions of the HM-contaminated soil (HMCS). However, the major downfalls of the commonly used remediation technologies are the generation of secondary wastes, high operating costs, and high energy consumption. Phytoremediation is a prominent approach that is more innocuous than the existing remediation approaches. Some microbes-plant interactions enhance the bioremediation process, with heavy metal resistant-plant growth promoting bacteria (HMRPGPB) being widely used to assist phytoremediation of HMs. However, the most common of all major microbial assisted-phytoremediation disturbances is that the HM-contaminated soil is generally deficient in nutrients and cannot sustain the rapid growth of the applied HMRPGPB. In this case, biochar has recently been approved as a potential carrier of microbial agents. The biochar-HMRPGPB-plant association could provide a promising green approach to remediate HM-polluted sites. Therefore, this review addresses the mechanisms through which biochar and HMRPGPB can enhance phytoremediation. This knowledge of biochar-HMRPGPB-plant interactions is significant with respect to sustainable management of the HM-polluted environment in terms of both ecology and economy, and it offers the possibility of further development of new green technologies.

A Strong Antifungal Activity of 7-O-Succinyl Macrolactin A vs Macrolactin A from Bacillus amyloliquefaciens ELI149

Chemical analysis of the crude extract of bacterial strain Bacillus amyloliquefaciens ELI149, which had been previously isolated from soil, resulted in the isolation and characterization of two known macrolactin derivatives, macrolactin A (1) and 7-O-succinyl macrolactin A (2). The structures of two compounds were assigned by 1D/2D NMR techniques. The two compounds were demonstrated antifungal activity against some important phytopathogens. However, the presence of the succinyl moiety at C-7 gives to the molecule more activity being the second compound more active than the first, showing for the first time, a structure/activity relationship. The cellular damage was also studied in two important phytopathogen fungi.

In Vitro Antagonistic Activity of Trichoderma harzianum against Fusarium sudanense Causing Seedling Blight and Seed Rot on Wheat

Fusarium sudanense is a novel fungus recently isolated from asymptomatic samples of wheat grains in Argentina. The fungus caused symptoms of seedling blight and seed rot on wheat after artificial inoculations. It is known that the production of mycotoxins by pathogens belonging to the Fusarium genus is harmful to human and animal health. Moreover, the warm and humid conditions that are favorable for growth and mycotoxin production of these species put the Argentinian wheat production area at a high risk of mycotoxin contamination with this novel pathogen. The aim of this work was to evaluate the antagonistic effect of Trichoderma harzianum against F. sudanense under in vitro tests at different environmental conditions. Fungi were screened in dual culture at different water activities (α_w) (0.995, 0.98, 0.95, and 0.90) and temperatures (25 and 15 °C). The growth rate of the fungi, interaction types, and dominance index were evaluated. Also, the interaction between T. harzianum and F. sudanense was examined by light and cryo-scanning microscopy. T. harzianum suppressed the growth of F. sudanense at 0.995, 0.98, and 0.95 α_w at 25 °C and 0.995 and 0.98 α_w at 15 °C. Macroscopic study revealed different interaction types between F. sudanense and T. harzianum on dual culture. Dominance on contact where the colonies of T. harzianum overgrew the pathogen was the most common interaction type determined. The competitive capacity of T. harzianum was diminished by decreasing the temperature and α_w. At 0.95 α_w and 15 °C, both fungi grew slowly, and interaction type "A" was assigned. Microscopic analysis from the interaction zone of dual cultures revealed an attachment of T. harzianum to the F. sudanense hyphae, penetration with or without formation of appressorium-like structures, coiling, plasmolysis, and a veil formation. According to our results, T. harzianum demonstrated capability to antagonize F. sudanense and could be a promising biocontrol agent.

Auxins of microbial origin and their use in agriculture

To maintain the world population demand, a sustainable agriculture is needed. Since current global vision is more friendly with the environment, eco-friendly alternatives are desirable. In this sense, plant growth-promoting rhizobacteria could be the choice for the management of soil-borne diseases of crop plants. These rhizobacteria secrete chemical compounds which act as phytohormones. Indole-3-acetic acid (IAA) is the most common plant hormone of the auxin class which regulates various processes of plant growth. IAA compound, in which structure can be found a carboxylic acid attached through a methylene group to the C-3 position of an indole ring, is produced both by plants and microorganisms. Plant growth-promoting rhizobacteria and fungi secrete IAA to promote the plant growth. In this review, IAA production and mechanisms of action by bacteria and fungi along with the metabolic pathways evolved in the IAA secretion and commercial prospects are revised.Key points• Many microorganisms produce auxins which help the plant growth promotion.• These auxins improve the plant growth by several mechanisms.• The auxins are produced through different mechanisms.

Biosurfactants in Plant Protection Against Diseases: Rhamnolipids and Lipopeptides Case Study

Biosurfactants are amphiphilic surface-active molecules that are produced by a variety of microorganisms including fungi and bacteria. Pseudomonas, Burkholderia, and Bacillus species are known to secrete rhamnolipids and lipopeptides that are used in a wide range of industrial applications. Recently, these compounds have been studied in a context of plant-microbe interactions. This mini-review describes the direct antimicrobial activities of these compounds against plant pathogens. We also provide the current knowledge on how rhamnolipids and lipopeptides stimulate the plant immune system leading to plant resistance to phytopathogens. Given their low toxicity, high biodegradability and ecological acceptance, we discuss the possible role of these biosurfactants as alternative strategies to reduce or even replace pesticide use in agriculture.

Symbiosis disruption in the olive fruit fly, Bactrocera oleae (Rossi), as a potential tool for sustainable control

BACKGROUND

The olive fruit fly Bactrocera oleae (Rossi) (OLF) is a major agricultural pest, whose control primarily relies on the use of chemical insecticides. Therefore, development of sustainable control strategies is highly desirable. The primary endosymbiotic bacterium of OLF, 'Candidatus Erwinia dacicola', is essential for successful larval development in unripe olive fruits. Therefore, targeting this endosymbiont with antimicrobial compounds may result in OLF fitness reduction and may exert control on natural populations of OLF.

RESULTS

Here, we evaluate the impact of compounds with antimicrobial activity on the OLF endosymbiont. Copper oxychloride (CO) and the fungal metabolite viridiol (Vi), produced by Trichoderma spp., were used. Laboratory bioassays were carried out to assess the effect of oral administration of these compounds on OLF fitness and molecular analyses (quantitative polymerase chain reaction) were conducted to measure the load of OLF-associated microorganisms in treated flies. CO and Vi were both able to disrupt the symbiotic association between OLF and its symbiotic bacteria, determining a significant reduction in the endosymbiont and gut microbiota load as well as a decrease in OLF fitness. CO had a direct negative effect on OLF adults. Conversely, exposure to Vi significantly undermined larval development of the treated female's progeny but did not show any toxicity in OLF adults.

CONCLUSIONS

These results provide new insights into the symbiotic control of OLF and pave the way for the development of more sustainable strategies of pest control based on the use of natural compounds with antimicrobial activity. © 2020 Society of Chemical Industry.

Bioactive Secondary Metabolites from Trichoderma spp. against Phytopathogenic Fungi

Phytopathogenic fungi, causing significant economic and production losses, are becoming a serious threat to global food security. Due to an increase in fungal resistance and the hazardous effects of chemical fungicides to human and environmental health, scientists are now engaged to explore alternate non-chemical and ecofriendly management strategies. The use of biocontrol agents and their secondary metabolites (SMs) is one of the potential approaches used today. Trichoderma spp. are well known biocontrol agents used globally. Many Trichoderma species are the most prominent producers of SMs with antimicrobial activity against phytopathogenic fungi. Detailed information about these secondary metabolites, when grouped together, enhances the understanding of their efficient utilization and further exploration of new bioactive compounds for the management of plant pathogenic fungi. The current literature provides the information about SMs of Trichoderma spp. in a different context. In this review, we summarize and group different antifungal SMs of Trichoderma spp. against phytopathogenic fungi along with a comprehensive overview of some aspects related to their chemistry and biosynthesis. Moreover, a brief overview of the biosynthesis pathway, action mechanism, and different approaches for the analysis of SMs and the factors affecting the regulation of SMs in Trichoderma is also discussed.

New Strategies in the Cultivation of Olive Trees and Repercussions on the Nutritional Value of the Extra Virgin Olive Oil

The health advantages of extra-virgin olive oil (EVOO) are ascribed mainly to the antioxidant ability of the phenolic compounds. Secoiridoids, hydroxytyrosol, tyrosol, phenolic acid, and flavones, are the main nutraceutical substances of EVOO. Applications of beneficial microbes and/or their metabolites impact the plant metabolome. In this study the effects of application of selected Trichoderma strains or their effectors (secondary metabolites) on the phenolic compounds content and antioxidant potential of the EVOOs have been evaluated. For this purpose, Trichoderma virens (strain GV41) and Trichoderma harzianum (strain T22), well-known biocontrol agents, and two their metabolites harzianic acid (HA) and 6-pentyl-α-pyrone (6PP) were been used to treat plants of Olea europaea var. Leccino and var. Carolea. Then the nutraceutical potential of EVOO was evaluated. Total phenolic content was estimated by Folin–Ciocalteau’s assay, metabolic profile by High-Resolution Mass spectroscopy (HRMS-Orbitrap), and antioxidant activity by DPPH and ABTS assays. Our results showed that in the cultivation of the olive tree, T22 and its metabolites improve the nutraceutical value of the EVOOs modulating the phenolic profile and improving antioxidants activity.