Endophytic Trichoderma isolates from tropical environments delay disease onset and induce resistance against Phytophthora capsici in hot pepper using multiple mechanisms

Endophytic Trichoderma: Potential and Prospects for Plant Health Management

The fungus Trichoderma is widely regarded as the most common fungal biocontrol agent for plant health management. More than 25 Trichoderma species have been extensively studied and have demonstrated significant potential in inhibiting not only phytopathogen growth but also insect pest infestations. In addition to their use as biopesticides, there is increasing evidence that several Trichoderma species can function as fungal endophytes by colonizing the tissues of specific plants. This colonization enhances a plant's growth and improves its tolerance to abiotic and biotic stresses. In recent decades, there has been a proliferation of literature on the role of Trichoderma endophytes in crop protection. Although the mechanisms underlying plant-fungal endophyte interactions are not yet fully understood, several studies have suggested their potential application in agriculture, particularly in the mitigation of plant pests and diseases. This review focuses on the diversity of Trichoderma endophytic strains and their potential use in controlling specific diseases and pests of crop plants. Trichoderma endophytes are considered a potential solution to reduce production costs and environmental impact by decreasing reliance on agrochemicals.

Mechanisms for plant growth promotion activated by Trichoderma in natural and managed terrestrial ecosystems

Trichoderma spp. are free-living fungi present in virtually all terrestrial ecosystems. These soil fungi can stimulate plant growth and increase plant nutrient acquisition of macro- and micronutrients and water uptake. Generally, plant growth promotion by Trichoderma is a consequence of the activity of potent fungal signaling metabolites diffused in soil with hormone-like activity, including indolic compounds as indole-3-acetic acid (IAA) produced at concentrations ranging from 14 to 234 μg l-1, and volatile organic compounds such as sesquiterpene isoprenoids (C15), 6-pentyl-2H-pyran-2-one (6-PP) and ethylene (ET) produced at levels from 10 to 120 ng over a period of six days, which in turn, might impact plant endogenous signaling mechanisms orchestrated by plant hormones. Plant growth stimulation occurs without the need of physical contact between both organisms and/or during root colonization. When associated with plants Trichoderma may cause significant biochemical changes in plant content of carbohydrates, amino acids, organic acids and lipids, as detected in Arabidopsis thaliana, maize (Zea mays), tomato (Lycopersicon esculentum) and barley (Hordeum vulgare), which may improve the plant health status during the complete life cycle. Trichoderma-induced plant beneficial effects such as mechanisms of defense and growth are likely to be inherited to the next generations. Depending on the environmental conditions perceived by the fungus during its interaction with plants, Trichoderma can reprogram and/or activate molecular mechanisms commonly modulated by IAA, ET and abscisic acid (ABA) to induce an adaptative physiological response to abiotic stress, including drought, salinity, or environmental pollution. This review, provides a state of the art overview focused on the canonical mechanisms of these beneficial fungi involved in plant growth promotion traits under different environmental scenarios and shows new insights on Trichoderma metabolites from different chemical classes that can modulate specific plant growth aspects. Also, we suggest new research directions on Trichoderma spp. and their secondary metabolites with biological activity on plant growth.

Biochemical changes, antioxidative profile, and efficacy of the bio-stimulant in plant defense response against Sclerotinia sclerotiorum in common bean (Phasaeolus vulgaris L.)

Sclerotinia sclerotiorum, is a highly destructive pathogen with widespread impact on common bean (Phasaeolus vulgaris L.) worldwide. In this work, we investigated the efficacy of microbial consortia in bolstering host defense against sclerotinia rot. Specifically, we evaluated the performance of a microbial consortia comprising of Trichoderma erinaceum (T51) and Trichoderma viride (T52) (referred to as the T4 treatment) in terms of biochemical parameters, alleviation of the ROS induced cellular toxicity, membrane integrity (measured as MDA content), nutrient profiling, and the host defense-related antioxidative enzyme activities. Our findings demonstrate a notable enhancement in thiamine content, exhibiting 1.887 and 1.513-fold higher in the T4 compared to the un-inoculated control and the T1 treatment (only S. sclerotiorum treated). Similarly, the total proline content exhibited 3.46 and 1.24-fold higher and the total phenol content was 4.083 and 2.625-fold higher in the T4 compared to the un-inoculated control and the T1 treatment, respectively. Likewise, a general trend was found for other antioxidative and non-oxidative enzyme activities. However, results found were approximately similar in T2 treatment (bioprimed with T51) or T3 treatments (bioprimed with T52). Further, host defense attribute (survival rate) under the pathogen challenged condition was maximum in the T4 (15.55 % disease incidence) compared to others. Therefore, bio priming with consortia could be useful in reducing the economic losses incited by S. sclerotiorum in common beans.

Transcriptomic characterization of Trichoderma harzianum T34 primed tomato plants: assessment of biocontrol agent induced host specific gene expression and plant growth promotion

In this study, we investigated the intricate interplay between Trichoderma and the tomato genome, focusing on the transcriptional and metabolic changes triggered during the late colonization event. Microarray probe set (GSE76332) was utilized to analyze the gene expression profiles changes of the un-inoculated control (tomato) and Trichoderma-tomato interactions for identification of the differentially expressed significant genes. Based on principal component analysis and R-based correlation, we observed a positive correlation between the two cross-comaparable groups, corroborating the existence of transcriptional responses in the host triggered by Trichoderma priming. The statistically significant genes based on different p-value cut-off scores [(padj-values or q-value); padj-value < 0.05], [(pcal-values); pcal-value < 0.05; pcal < 0.01; pcal < 0.001)] were cross compared. Through cross-comparison, we identified 156 common genes that were consistently significant across all probability thresholds, and showing a strong positive corelation between p-value and q-value in the selected probe sets. We reported TD2, CPT1, pectin synthase, EXT-3 (extensin-3), Lox C, and pyruvate kinase (PK), which exhibited upregulated expression, and Glb1 and nitrate reductase (nii), which demonstrated downregulated expression during Trichoderma-tomato interaction. In addition, microbial priming with Trichoderma resulted into differential expression of transcription factors related to systemic defense and flowering including MYB13, MYB78, ERF2, ERF3, ERF5, ERF-1B, NAC, MADS box, ZF3, ZAT10, A20/AN1, polyol sugar transporter like zinc finger proteins, and a novel plant defensin protein. The potential bottleneck and hub genes involved in this dynamic response were also identified. The protein-protein interaction (PPI) network analysis based on 25 topmost DEGS (pcal-value < 0.05) and the Weighted Correlation Gene Network Analysis (WGCNA) of the 1786 significant DEGs (pcal-value < 0.05) we reported the hits associated with carbohydrate metabolism, secondary metabolite biosynthesis, and the nitrogen metabolism. We conclude that the Trichoderma-induced microbial priming re-programmed the host genome for transcriptional response during the late colonization event and were characterized by metabolic shifting and biochemical changes specific to plant growth and development. The work also highlights the relevance of statistical parameters in understanding the gene regulatory dynamics and complex regulatory networks based on differential expression, co-expression, and protein interaction networks orchestrating the host responses to beneficial microbial interactions.

Phytophthora capsici, 100 Years Later: Research Mile Markers from 1922 to 2022

In 1922, Phytophthora capsici was described by Leon Hatching Leonian as a new pathogen infecting pepper (Capsicum annuum), with disease symptoms of root rot, stem and fruit blight, seed rot, and plant wilting and death. Extensive research has been conducted on P. capsici over the last 100 years. This review succinctly describes the salient mile markers of research on P. capsici with current perspectives on the pathogen's distribution, economic importance, epidemiology, genetics and genomics, fungicide resistance, host susceptibility, pathogenicity mechanisms, and management.

Effects of the dual inoculation of dark septate endophytes and Trichoderma koningiopsis on blueberry growth and rhizosphere soil microorganisms

Blueberry is a shallow root plant in which the absorption of nutrients is inefficient, resulting in slow growth under artificial cultivation conditions. Endophytes play an important role in promoting plant growth; however, the effects of Trichoderma spp. and dark septate endophytes (DSEs) on host plant growth and soil microorganisms are still debatable. We isolated two endophytic fungal species, Trichoderma koningiopsis (TK) and a DSE (Amesia nigricolor; AN), from blueberry roots, which can solubilize insoluble phosphorus and produce amylase and cellulase to promote plant growth. We found that under dual inoculation, the colonization rate and colonization intensity of TK were higher than they were under single inoculation with TK, while the colonization rate and colonization intensity of AN were lower under dual inoculation than under single inoculation with AN. The plant nutrients, root activity, available potassium, and parts of soil phosphatase activities were highest under dual inoculation. TK inoculation resulted in the highest diversity and richness in the soil fungi and bacteria, followed by dual inoculation. The abundance of Ascomycota, Acidobacteriae, Firmicutes, and Actinobacteriota increased significantly, resulting in Trichoderma and Vicinamibacteria inoculated with TK, Chaetomium and Alicyclobacillales inoculated with AN, and Hypocreales and Burkholderiaceae with dual inoculation enriched in the soil.

Application of Trichoderma Hz36 and Hk37 as Biocontrol Agents against Clubroot Caused by Plasmodiophora brassicae

Clubroot, a soil-infective disease caused by Plasmodiophora brassicae, is a serious disease affecting cruciferous plants around the world. There is no effective control measure to completely remove this pathogen from fields after infection. Here, we screened and identified two strains (Hz36, Trichoderma guizhouense; Hk37, Trichoderma koningiopsis) of Trichoderma from the gall of clubroot in rapeseed fields with biocontrol potential for clubroot. The fermentation broth of Hz36 could significantly inhibit the germination of resting spores of P. brassicae, and promote the seed germination and root growth of rapeseed. The biocontrol efficiency of Hz36 strain on clubroot for rapeseed and Arabidopsis thaliana was 44.29% and 52.18%, respectively. The qPCR results revealed that strain Hz36 treatment could significantly reduce the content of P. brassicae in root cells, and paraffin section analysis revealed that it could delay the development of P. brassicae. Strain Hk37 showed similar effects to strain Hz36, whose biocontrol efficiency of clubroot could reach 57.30% in rapeseed and 68.01% in A. thaliana. These results indicate that strains Hz36 and Hk37 have the potential for the biocontrol of clubroot.

Isolation, Identification, and Biocontrol Potential of Root Fungal Endophytes Associated with Solanaceous Plants against Potato Late Blight (Phytophthora infestans)

Late blight of potato caused by Phytophthora infestans is one of the most damaging diseases affecting potato production worldwide. We screened 357 root fungal endophytes isolated from four solanaceous plant species obtained from Kenya regarding their in vitro antagonistic activity against the potato late blight pathogen and evaluated their performance in planta. Preliminary in vitro tests revealed that 46 of these isolates showed potential activity against the pathogen. Based on their ITS-sequences, 37 out of 46 endophytes were identified to species level, three isolates were connected to higher taxa (phylum or genus), while two remained unidentified. Confrontation assays, as well as assays for volatile or diffusible organic compounds, resulted in the selection of three endophytes (KB1S1-4, KA2S1-42, and KB2S2-15) with a pronounced inhibitory activity against P. infestans. All three isolates produce volatile organic compounds that inhibit mycelial growth of P. infestans by up to 48.9%. The addition of 5% extracts obtained from KB2S2-15 or KA2S1-42 to P. infestans sporangia entirely suppressed their germination. A slightly lower inhibition (69%) was achieved using extract from KB1S1-4. Moreover, late blight symptoms and the mycelial growth of P. infestans were completely suppressed when leaflets were pre-treated with a 5% extract from these endophytes. This might suggest the implementation of such biocontrol candidates or their fungicidal compounds in late blight control strategies.

The Interactions between Arbuscular Mycorrhizal Fungi and Trichoderma longibrachiatum Enhance Maize Growth and Modulate Root Metabolome under Increasing Soil Salinity

Trichoderma longibrachiatum sp. are free-living filamentous fungi which are common in agro-ecosystems. However, few studies thus far have examined the interaction between Trichoderma longibrachiatum and arbuscular mycorrhizal (AM) fungi in saline soil and their potential for improving plant stress tolerance. Here, single, dual-inoculated (T. longibrachiatum MF, AM fungal community or Glomus sp.), and non-inoculated maize (Zea may L.) were subjected to different salinity levels (0, 75, 150, and 225 mM NaCl) to test the synergistic effects of dual inoculants on maize plants in different salt stress conditions. Plant performance and metabolic profiles were compared to find the molecular mechanisms underlying plant protection against salt stress. The first experiment revealed that dual inoculation of an AM fungal community and T. longibrachiatum MF improved the biomass and K⁺/Na⁺ ratio in maize under non-saline conditions, and generally enhanced AM fungal growth in root and soil under all but the 225 mM NaCl conditions. However, MF inoculant did not influence the structure of AM fungal communities in maize roots. In the second experiment, dual inoculation of Glomus sp. and T. longibrachiatum MF increased maize plant biomass, K⁺/Na⁺ ratio, and AM fungal growth in root and soil significantly at both 0 and 75 mM NaCl conditions. We identified metabolic compounds differentially accumulated in dual-inoculated maize that may underline their enhanced maize plant tolerance to increasing soil salinity. Our data suggested that the combination of Glomus sp. and T.longibrachiatum leads to interactions, which may play a potential role in alleviating the stress and improve crop productivity in salt-affected soils.

Compatible interaction of Brachypodium distachyon and endophytic fungus Microdochium bolleyi

Brachypodium distachyon is a useful model organism for studying interaction of cereals with phytopathogenic fungi. The present study tested the possibility of a compatible interaction of B. distachyon with the endophytic fungus Microdochium bolleyi originated from wheat roots. There was evaluated the effect of this endophytic fungus on the intensity of the attack by pathogen Fusarium culmorum in B. distachyon and wheat, and also changes in expression of genes (in B. distachyon: BdChitinase1, BdPR1-5, BdLOX3, BdPAL, BdEIN3, and BdAOS; and in wheat: TaB2H2(chitinase), TaPR1.1, TaLOX, TaPAL, TaEIN2, and TaAOS) involved in defence against pathogens. Using light microscopy and newly developed specific primers was found to be root colonization of B. distachyon by the endophyte M. bolleyi. B. distachyon plants, as well as wheat inoculated with M. bolleyi showed significantly weaker symptoms on leaves from infection by fungus F. culmorum than did plants without the endophyte. Expression of genes BdPR1-5, BdChitinase1, and BdLOX3 in B. distachyon and of TaPR1.1 and TaB2H2 in wheat was upregulated after infection with F. culmorum. M. bolleyi-mediated resistance in B. distachyon was independent of the expression of the most tested genes. Taken together, the results of the present study show that B. distachyon can be used as a model host system for endophytic fungus M. bolleyi.

A novel salt-tolerant strain Trichoderma atroviride HN082102.1 isolated from marine habitat alleviates salt stress and diminishes cucumber root rot caused by Fusarium oxysporum

Background

Salt stress threaten the growth of plants, and even aggravate plant disease. In this article, salt-tolerant Trichoderma strain was isolated, and its potential to alleviate salt stress and diminish cucumber root rot caused by Fusarium oxysporum was evaluated.

Results

Twenty-seven Trichoderma isolates were isolated from samples of sea muds and algae collected from the South Sea of China. Among these, the isolate HN082102.1 showed the most excellent salt tolerance and antagonistic activity against F. oxysporum causing root rot in cucumber and was identified as T. atroviride. Its antagonism ability may be due to mycoparasitism and inhibition effect of volatile substances. The application of Trichoderma mitigated the adverse effects of salt stress and promoted the growth of cucumber under 100 mM and 200 mM NaCl, especially for the root. When T. atroviride HN082102.1 was applied, root fresh weights increased by 92.55 and 84.86%, respectively, and root dry weights increased by 75.71 and 53.31%, respectively. Meanwhile, the application of HN082102.1 reduced the disease index of cucumber root rot by 63.64 and 71.01% under 100- and 0-mM saline conditions, respectively, indicating that this isolate could inhibit cucumber root rot under salt stress.

Conclusions

This is the first report of salt-tolerant T. atroviride isolated from marine habitat showing antagonistic activity to F. oxysporum, and the results provide evidence for the novel strain T. atroviride HN082102.1 in alleviating salt stress and diminishing cucumber root rot, indicating that T. atroviride strain HN082102.1 can be used as biological control agent in saline alkali land.

The Role of Plant Growth Promoting Rhizosphere Microbiome as Alternative Biofertilizer in Boosting Solanum melongena L. Adaptation to Salinity Stress

Recent ecological perturbations are presumed to be minimized by the application of biofertilizers as a safe alternative to chemical fertilizers. The current study aims to use bioinoculum (I) as an alternative biofertilizer and to alleviate salinity stress in the cultivar Solanum melongena L. Baldi. The salinity drench was 200 mM NaCl (S), which was used with different treatments (0; I; S; S + I) in pots prefilled with clay and sand (1:2). Results showed that salinity stress inhibited both plant fresh and dry weights, water content, and photosynthetic pigments. The content of root spermine (Spm), spermidine (Spd), and puterscine (Put) decreased. However, addition of the bioinoculum to salt-treated plants increased pigment content (80.35, 39.25, and 82.44% for chl a, chl b, and carotenoids, respectively). Similarly, K+, K+/Na+, Ca2+, P, and N contents were significantly enhanced. Increases were recorded for Spm + Spd and Put in root and shoot (8.4-F, 1.6-F and 2.04-F, 2.13-F, respectively). RAPD PCR showed gene expression upregulation of photosystem II D2 protein, glutathione reductase, glutathione-S-transferase, protease I, and protease II. The current work recommends application of the selected bioinoculum as a green biofertilizer and biopesticide. Additionally, the studied eggplant cultivar can be regarded as a source of salt tolerance genes in agricultural fields.

How plants recruit their microbiome? New insights into beneficial interactions

•

Plant-microbiome interaction occurs at the rhizosphere, endosphere, and phyllosphere.

•

Root exudates can favor the recruitment of a beneficial microbiome in the rhizosphere.

•

Plant topology and phytochemistry influence the recruitment of the phyllosphere microbiome.

•

Diverse plant strategies selectively recruit beneficial microbiomes.

•

Multiple plant mechanisms displace potential pathogens from the rhizosphere.

•

The beneficial microbiome helps plants to recruit other beneficial microbiota.

Background

Research on beneficial mechanisms by plant-associated microbiomes, such as plant growth stimulation and protection from plant pathogens, has gained considerable attention over the past decades; however, the mechanisms used by plants to recruit their microbiome is largely unknown.

Aim of Review

Here, we review the latest studies that have begun to reveal plant strategies in selectively recruiting beneficial microbiomes, and how they manage to exclude potential pathogens.

Key Scientific concepts of Review: We examine how plants attract beneficial microbiota from the main areas of interaction, such as the rhizosphere, endosphere, and phyllosphere, and demonstrate that such process occurs by producing root exudates, and recognizing molecules produced by the beneficial microbiota or distinguishing pathogens using specific receptors, or by triggering signals that support plant-microbiome homeostasis. Second, we analyzed the main environmental or biotic factors that modulate the structure and successional dynamics of microbial communities. Finally, we review how the associated microbiome is capable of engaging with other synergistic microbes, hence providing an additional element of selection. Collectively, this study reveals the importance of understanding the complex network of plant interactions, which will improve the understanding of bioinoculant application in agriculture, based on a microbiome that interacts efficiently with plant organs under different environmental conditions.

The Threat of Pests and Pathogens and the Potential for Biological Control in Forest Ecosystems

Forests are an essential component of the natural environment, as they support biodiversity, sequester carbon, and play a crucial role in biogeochemical cycles—in addition to producing organic matter that is necessary for the function of terrestrial organisms. Forests today are subject to threats ranging from natural occurrences, such as lightning-ignited fires, storms, and some forms of pollution, to those caused by human beings, such as land-use conversion (deforestation or intensive agriculture). In recent years, threats from pests and pathogens, particularly non-native species, have intensified in forests. The damage, decline, and mortality caused by insects, fungi, pathogens, and combinations of pests can lead to sizable ecological, economic, and social losses. To combat forest pests and pathogens, biocontrol may be an effective alternative to chemical pesticides and fertilizers. This review of forest pests and potential adversaries in the natural world highlights microbial inoculants, as well as research efforts to further develop biological control agents against forest pests and pathogens. Recent studies have shown promising results for the application of microbial inoculants as preventive measures. Other studies suggest that these species have potential as fertilizers.

Diversity of Endophytic and Pathogenic Fungi of Saffron (Crocus sativus) Plants from Cultivation Sites in Italy

Crocus sativus is an important crop for the production of saffron and bioactive compounds. Plant endophytic fungi are a source of secondary metabolites additional to those produced by the plant itself. We analysed the biodiversity of endophytic fungi present in corms, stems, leaves, tepals, and stigmas of C. sativus from ten Italian sites; furthermore, we isolated putative pathogenic fungi from rotten plants. We used an in vitro isolation approach followed by molecular analysis of the internal transcribed spacer (ITS rDNA) region. We obtained 165 strains belonging to 39 OTUs, spreading over 26 genera and 29 species. Dark septate endophytes of the genus Cadophora and the species Talaromyces pinophilus dominated in corms, while Alternaria alternata, Epicoccum spp., T. pinophilus, Mucor fragilis, and Stemphylium vesicarium dominated in other tissues. The most frequently isolated pathogens were Fusarium oxysporum and Rhizopus oryzae. Endophytic communities significantly differed among tissues and life stages, whereas differences among cultivation sites were not statistically supported. Several endophytes were hypothesized to have changing trophic modes and/or to be latent pathogens in C. sativus. All strains were conserved ex-situ for future bioactivity tests and production of metabolites.

Effect of co-application of Trichoderma spp. with organic composts on plant growth enhancement, soil enzymes and fungal community in soil

The application of Trichoderma spp. has the potential to reduce not only mineral fertilizer use in agriculture but also improve soil health through increased soil biological activity. Trichoderma spp. have shown potential as bio-control agents and plant growth promoting ability, but little attention has been paid to the effect of Trichoderma spp. inoculation on nutrient availability and the soil microbiome. In this study, we evaluated the effect of Trichoderma spp. inoculation on nitrogen mineralization and quantified soil enzymatic activities along with plant growth promotion potential. The influence of Trichoderma spp. and organic amendments on the soil fungal community was also investigated. For this purpose, pots and incubation experiment was carried out, and seven treatments were set as follows; poultry compost (PC), poultry compost + RW309 (PCT), cattle compost (CC), cattle compost + RW309 (CCT), rapeseed oil cake (OC), inorganic fertilizer (N) and only soil (S) were set as control. We evaluated that Trichoderma sp. RW309 produced indole-3-acetic acid, which suggested that it could contribute to plant growth enhancement during early plant growth. Inoculation of RW309 with organic materials stimulated nitrogen mineralization and increased soil phosphatase activity. Furthermore, RW309 altered the fungal community in rhizosphere soil. However, cattle compost was a more suitable culture medium for RW309 than poultry compost in terms of nitrogen mineralization, soil enzyme activity, and growth of RW309. In conclusion, Trichoderma sp. RW309 could be considered for use as a bioorganic fertilizer in combination with organic compost to minimize the use of mineral fertilizers.

Benefits to Plant Health and Productivity From Enhancing Plant Microbial Symbionts

Plants exist in close association with uncountable numbers of microorganisms around, on, and within them. Some of these endophytically colonize plant roots. The colonization of roots by certain symbiotic strains of plant-associated bacteria and fungi results in these plants performing better than plants whose roots are colonized by only the wild populations of microbes. We consider here crop plants whose roots are inhabited by introduced organisms, referring to them as Enhanced Plant Holobionts (EPHs). EPHs frequently exhibit resistance to specific plant diseases and pests (biotic stresses); resistance to abiotic stresses such as drought, cold, salinity, and flooding; enhanced nutrient acquisition and nutrient use efficiency; increased photosynthetic capability; and enhanced ability to maintain efficient internal cellular functioning. The microbes described here generate effects in part through their production of Symbiont-Associated Molecular Patterns (SAMPs) that interact with receptors in plant cell membranes. Such interaction results in the transduction of systemic signals that cause plant-wide changes in the plants' gene expression and physiology. EPH effects arise not only from plant-microbe interactions, but also from microbe-microbe interactions like competition, mycoparasitism, and antibiotic production. When root and shoot growth are enhanced as a consequence of these root endophytes, this increases the yield from EPH plants. An additional benefit from growing larger root systems and having greater photosynthetic capability is greater sequestration of atmospheric CO2. This is transferred to roots where sequestered C, through exudation or root decomposition, becomes part of the total soil carbon, which reduces global warming potential in the atmosphere. Forming EPHs requires selection and introduction of appropriate strains of microorganisms, with EPH performance affected also by the delivery and management practices.

New species and records of Trichoderma isolated as mycoparasites and endophytes from cultivated and wild coffee in Africa

A survey for species of the genus Trichoderma occurring as endophytes of Coffea, and as mycoparasites of coffee rusts (Hemileia), was undertaken in Africa; concentrating on Cameroon and Ethiopia. Ninety-four isolates of Trichoderma were obtained during this study: 76 as endophytes of healthy leaves, stems and berries and, 18 directly from colonized rust pustules. A phylogenetic analysis of all isolates used a combination of three genes: translation elongation factor-1α (tef1), rpb2 and cal for selected isolates. GCPSR criteria were used for the recognition of species; supported by morphological and cultural characters. The results reveal a previously unrecorded diversity of Trichoderma species endophytic in both wild and cultivated Coffea, and mycoparasitic on Hemileia rusts. Sixteen species were delimited, including four novel taxa which are described herein: T. botryosum, T. caeruloviride, T. lentissimum and T. pseudopyramidale. Two of these new species, T. botryosum and T. pseudopyramidale, constituted over 60% of the total isolations, predominantly from wild C. arabica in Ethiopian cloud forest. In sharp contrast, not a single isolate of Trichoderma was obtained using the same isolation protocol during a survey of coffee in four Brazilian states, suggesting the existence of a 'Trichoderma void' in the endophyte mycobiota of coffee outside of Africa. The potential use of these African Trichoderma isolates in classical biological control, either as endophytic bodyguards-to protect coffee plants from Hemileia vastatrix, the fungus causing coffee leaf rust (CLR)-or to reduce its impact through mycoparasitism, is discussed, with reference to the on-going CLR crisis in Central America.

Applications of endophytic microbes in agriculture, biotechnology, medicine, and beyond

Endophytes are emerging as integral components of plant microbiomes. Some of them play pivotal roles in plant development and plant responses to pathogens and abiotic stresses, whereas others produce useful and/or interesting secondary metabolites. The appreciation of their abilities to affect plant phenotypes and produce useful compounds via genetic and molecular interactions has paved the way for these abilities to be exploited for health and welfare of plants, humans and ecosystems. Here we comprehensively review current and potential applications of endophytes in the agricultural, pharmaceutical, and industrial sectors. In addition, we briefly discuss the research objectives that should be focused upon in the coming years in order for endophytes and their metabolites to be fully harnessed for potential use in diverse areas.

Screening of Endophytic Fungal Isolates Against Raffaelea quercus-mongolicae Causing Oak Wilt Disease in Korea

Oak wilt disease caused by Raffaelea quercus-mongolicae has emerged obviously in Korea. We selected antifungal isolates against R. quercus-mongolicae among 368 endophytic fungal isolates from different parts of oak and pine trees. The experiment was conducted in the primary and secondary screenings by dual culture test. The antifungal activity of the selected isolates was assessed in culture filtrate test based on the inhibition rates in mycelial growth, sporulation, and spore germination of oak wilt fungus. Five isolates, E089, E199, E282, E409 and E415, showed strong antifungal activity in culture filtrate test, and their antifungal activity decreased on the culture media supplemented with heated culture filtrate. Higher mycelial growth inhibitions on the unheated media were recorded in E409 (Colletotrichum acutatum), E089 (Daldinia childiae), E415 (Alternaria alternata) and E199 (Daldinia childiae) with the inhibition rates of 79.0%, 70.1%, 68.9% and 64.5%, respectively. These isolates also had the higher sporulation inhibitions on unheated media with the rates of 96.8%, 84.2%, 82.8% and 80.5%, respectively. The spore germination of the oak wilt fungus was completely inhibited by E282 (Nectria balsamea) on both unheated and heated media. These results showed that a higher number of potent antifungal isolates against oak wilt fungus was isolated from the petiole compared to the other parts. This study could contribute to the development of biological control approaches for the management of oak wilt disease caused by R. quercus-mongolicae.

Metagenomics Reveal Correlations Between Microbial Organisms in Soils and the Health of Populus euphratica

Biological diversity plays an important role in the stability of ecosystems. The Mu Us Desert (MUD), located in Northern China, is an aeolian desert. Although it has been governed by a series of ecological restoration programs, the MUD still has limited biological diversity. Populus euphratica (P. euphratica), a xerophytic plant, has great potential to improve the biological diversity of the MUD. However, the survival rate of P. euphratica in the MUD has been very low. The current study tried to explore the mechanism of the high death rate of P. euphratica in the microbiome perspective. The correlation study between soil community composition and soil properties showed that water-filled pore space (WFPS), pH, EC, AP, NO₃ ^-, and NH₄ ⁺ possess higher potential to change the bacterial community (18%) than the fungal community (9%). Principal coordinate analysis indicated that the composition of both bacteria (Proteobacteria and Bacteroidetes) and fungi (Ascomycota) in the root soil can be increased by P. euphratica. By systematically comparing between the fungal diversity in the root soil around P. euphratica and the pathogenic fungus extract from the pathogenic site of P. euphratica, we found that the high death rate of P. euphratica was associated with specific pathogenic fungus Alternaria alternate and Didymella glomerata. In addition, the microbiome composition analysis indicated that P. euphratica planting could also influence the portions of bacteria community, which also has great potential to lead to future infection. However, as the extraction and separation of bacteria from plants is challenging, the correlation between pathogenic bacteria and the high death rate of P. euphratica was not studied here and could be explored in future work.

Endophytes: Colonization, Behaviour, and Their Role in Defense Mechanism

Biotic and abiotic factors cause an enormous amount of yield and economical loss. However, endophytes can play a significant role in enhancing the tolerance of plants. Endophytes systematically colonize different parts of the host, but plants use a variety of defense mechanisms towards microbial infection. However, they have to survive the oxidative environments, and endophytes like Enterobacter sp. encode superoxide dismutases, catalases, and hydroperoxide reductases to cope up the oxidative stress during colonization. On the contrary, others produce subtilomycin which binds with flagella to affect flg22-induced plant defense. The behavior of endophytes can be affected by different genes in hydrolase activity when they come into contact with the host plant. The lifestyle of endophytes is influenced by environmental factors, the host, and microbial genotypes, as well as an imbalance in nutrient exchange between the microbe and the host. For instance, induction of PiAMT1 in root endophyte Piriformospora indica indicates depletion of nitrogen which plays as a triggering factor for activation of the saprotrophic program. Microbes enhance disease resistance through induced systemic resistance (ISR), and Bacillus cereus triggers ISR against Botrytis cinerea through an accumulation of the PR1 protein and activates MAPK signaling and WRKY53 gene expression by the JA/ET signaling pathway. Similarly, Trichoderma arundinaceum produces trichodiene that affects Botrytis cinerea through induction of defense-related genes encoding salicylic acid (SA) and jasmonate (JA). Overall, endophytes can play a vital role in disease management.

The interactions of Trichoderma at multiple trophic levels: inter-kingdom communication

Trichoderma spp. are universal saprotrophic fungi in terrestrial ecosystems, and as rhizosphere inhabitants, they mediate interactions with other soil microorganisms, plants, and arthropods at multiple trophic levels. In the rhizosphere, Trichoderma can reduce the abundance of phytopathogenic microorganisms, which involves the action of potent inhibitory molecules, such as gliovirin and siderophores, whereas endophytic associations between Trichoderma and the seeds and roots of host plants can result in enhanced plant growth and crop productivity, as well as the alleviation of abiotic stress. Such beneficial effects are mediated via the activation of endogenous mechanisms controlled by phytohormones such as auxins and abscisic acid, as well as by alterations in host plant metabolism. During either root colonization or in the absence of physical contact, Trichoderma can trigger early defense responses mediated by Ca²⁺ and reactive oxygen species, and subsequently stimulate plant immunity by enhancing resistance mechanisms regulated by the phytohormones salicylic acid, jasmonic acid, and ethylene. In addition, Trichoderma release volatile organic compounds and nitrogen or oxygen heterocyclic compounds that serve as signaling molecules, which have effects on plant growth, phytopathogen levels, herbivorous insects, and at the third trophic level, play roles in attracting the natural enemies (predators and parasitoids) of herbivores. In this paper, we review some of the most recent advances in our understanding of the environmental influences of Trichoderma spp., with particular emphasis on their multiple interactions at different trophic levels.

Trichoderma Isolates Inhibit Fusarium virguliforme Growth, Reduce Root Rot, and Induce Defense-Related Genes on Soybean Seedlings

Sudden death syndrome (SDS) caused by Fusarium virguliforme is among the most important diseases affecting soybean in the United States. The use of biological control agents (BCAs) such as Trichoderma spp. can be a valuable resource to suppress F. virguliforme populations. Therefore, this research focused on screening possible BCAs against F. virguliforme and evaluating mycoparasitism and the induction of systemic resistance as mechanisms underlying the antagonistic activity of selected BCAs against F. virguliforme. In total, 47 potential BCAs, including 41 Trichoderma isolates and 6 Mortierella isolates, were screened in a dual-plate assay. The most effective isolates belonged to the Trichoderma harzianum species and were able to inhibit F. virguliforme radial growth by up to 92%. Selected Trichoderma isolates were tested in the greenhouse and in a microplot study. They reduced root rot caused by F. virguliforme when the plants were coinoculated with the pathogen and the BCA. The tested BCA's ability to reduce F. virguliforme growth may be related to several mechanisms of action, including mycoparasitism and induction of defense-related genes in plants, as revealed by monitoring the expression of defense-related genes in soybean. Our results highlight the potential of native Trichoderma isolates to inhibit F. virguliforme growth and reduce SDS severity, providing the basis for future implementation of biological control in soybean production. More efforts are needed to implement the use of these approaches in production fields, and to deepen the current knowledge on the biology of these highly antagonistic isolates.

A Compost Treatment Acts as a Suppressive Agent in Phytophthora capsici - Cucurbita pepo Pathosystem by Modifying the Rhizosphere Microbiota

Phytophthora capsici Leonian (PHC) is a filamentous pathogen oomycete that causes root, fruit, foliar and crown rot over a wide host range, including the economically and nutritionally important summer squash (Cucurbita pepo var. cylindrica L.) crop. PHC chemical control strategies are difficult to adopt, due to the limited number of registered chemicals that are permitted and the scalar harvest system. For these reasons, other strategies, such as the use of waste-based composts that can act as suppressive agents against several soilborne pathogens, have been studied intensively. It is well known that compost's microbiota plays an important role to confer its suppressive ability. In this study, four different composts were analyzed with both 16S rRNA gene and 18S rRNA gene real-time PCR amplification and with 26S gene amplicon-based sequencing; the total abundance of the bacterial and fungal communities was found to be higher compared to literature, thus confirming that the four composts were a good inoculum source for agricultural applications. The core mycobiota was mainly composed of 31 genera; nevertheless, it was possible to observe a clear predominance of the same few taxa in all the composts. The four composts were then tested, at different concentrations (1-10-20% v/v), to establish their ability to confer suppressiveness to the Phytophthora capsici (PHC) - Cucurbita pepo pathosystem in controlled greenhouse pot trials. A total of 12 compost mixtures were considered, and of these, one (Trichoderma-enriched compost at 10% v/v) was able to statistically reduce the disease incidence caused by PHC (by 50% compared to the untreated control). Hence, the microbiota composition of the most effective compost treatment was investigated and compared with untreated and chemical (metalaxyl) controls. Mycobiota sequencing showed genera differences between the three treatments, with relative abundances of several fungal genera that were significantly different among the samples. Moreover, PCA analyses clustered the compost treatment differently from the chemical and the untreated controls. These findings suggest that suppressive activity of a compost is strictly influenced by its microbiota and the applied dosage, but the ability to induce a shaping in the rhizosphere microbial composition is also required.

Plant-Microbe Symbiosis: What Has Proteomics Taught Us?

Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based "omic" approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.

Apple endophyte community is shaped by tissue type, cultivar and site and has members with biocontrol potential against Neonectria ditissima

AIMS

This research aimed to identify factors influencing endophyte community structure in apple shoots and the bioactivity of cultured representatives against the fungal pathogen Neonectria ditissima.

METHODS AND RESULTS

The endophyte community in leaves and stems of the apple cultivars 'Royal Gala' and 'Braeburn' were analysed by a cultivation-independent method (PCR-DGGE) which showed that tissue type, cultivar and site were determinant factors, with the endophyte taxa in 'Royal Gala' more variable than that in 'Braeburn', with leaf endophyte communities typically differing from stems in both cultivars. Seasonal (spring vs autumn) and regional (Nelson vs Hawke's Bay) variations were not obvious in woody stems. A collection of 783 bacterial and 87 fungal endophytes were recovered from leaves and stems of 'Royal Gala', 'Braeburn', 'Scilate' and/or 'Scifresh' from Nelson (nine sites) and Hawke's Bay (five sites) in spring and from Nelson (three sites) in autumn. A dual culture plating assay was used to test their ability to inhibit the mycelial growth of N. ditissima. Thirteen bacterial (mean of percent inhibition ≥20%) and 17 fungal isolates were antagonistic towards N. ditissima. These isolates belonged to the bacterial genera Bacillus and Pseudomonas, and fungal genera Chaetomium, Epicoccum, Biscogniauxia, Penicillium, Diaporthe, Phlyctema and two unidentified fungal isolates.

CONCLUSIONS

Endophyte communities in apple shoots were determined by tissue type, cultivar and site. Endophytic bacterial and fungal isolates inhibiting N. ditissima growth in vitro were found.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results provided new evidence of factors influencing apple endophyte community in New Zealand. Endophytes with potential to reduce N. ditissima infection were identified, with the potential to be developed into a biocontrol strategy for European canker.

Fungal Endophyte-Mediated Crop Improvement: The Way Ahead

Endophytes are non-disease causing microbes (bacteria and fungi) surviving in living tissues of plants. Their intimate association and possible coevolution with their plant partners have resulted in them contributing to an array of plant growth benefits ranging from enhanced growth and biomass accumulation, tolerance to abiotic and biotic stresses and in nutrient acquisition. The last couple of decades have witnessed a burgeoning literature on the role of endophytes (Class 3 type) in regulating plant growth and development and their adaptation to abiotic and biotic stresses. Though the underlying mechanisms of plant-endophyte interactions are far from clear, several studies have raised the hope of their potential application in agriculture, especially in mitigating abiotic and biotic stresses. The use of endophytes is envisaged as a route to reduce the production cost and burden on the environment by lessening the dependence on breeding for crop improvement and agrochemicals. Unfortunately, save a few well documented examples of their use, a little of these insights has been translated into actual agricultural applications. Here, we reflect on this paucity and elaborate on some of the important bottlenecks that might stand in way of fully realizing the potential that endophytes hold for crop improvement. We stress the need to study various facets of the endophyte-plant association for their gainful application in agriculture.

Molecular Mechanisms of the 1-Aminocyclopropane-1-Carboxylic Acid (ACC) Deaminase Producing Trichoderma asperellum MAP1 in Enhancing Wheat Tolerance to Waterlogging Stress

Waterlogging stress (WS) induces ethylene (ET) and polyamine (spermine, putrescine, and spermidine) production in plants, but their reprogramming is a decisive element for determining the fate of the plant upon waterlogging-induced stress. WS can be challenged by exploring symbiotic microbes that improve the plant's ability to grow better and resist WS. The present study deals with identification and application of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing fungal endophyte Trichoderma asperellum (strain MAP1), isolated from the roots of Canna indica L., on wheat growth under WS. MAP1 positively affected wheat growth by secreting phytohormones/secondary metabolites, strengthening the plant's antioxidant system and influencing the physiology through polyamine production and modulating gene expression. MAP1 inoculation promoted yield in comparison to non-endophyte inoculated waterlogged seedlings. Exogenously applied ethephon (ET synthesis inducer) and 1-aminocyclopropane carboxylic acid (ACC; ET precursor) showed a reduction in growth, compared to MAP1-inoculated waterlogged seedlings, while amino-oxyacetic acid (AOA; ET inhibitor) application reversed the negative effect imposed by ET and ACC, upon waterlogging treatment. A significant reduction in plant growth rate, chlorophyll content, and stomatal conductance was noticed, while H₂O₂, MDA production, and electrolyte leakage were increased in non-inoculated waterlogged seedlings. Moreover, in comparison to non-inoculated waterlogged wheat seedlings, MAP1-inoculated waterlogged wheat exhibited antioxidant-enzyme activities. In agreement with the physiological results, genes associated with the free polyamine (PA) biosynthesis were highly induced and PA content was abundant in MAP1-inoculated seedlings. Furthermore, ET biosynthesis/signaling gene expression was reduced upon MAP1 inoculation under WS. Briefly, MAP1 mitigated the adverse effect of WS in wheat, by reprogramming the PAs and ET biosynthesis, which leads to optimal stomatal conductance, increased photosynthesis, and membrane stability as well as reduced ET-induced leaf senescence.

Endophytes from Wild Rubber Trees as Antagonists of the Pathogen Corynespora cassiicola

The Corynespora leaf fall disease of rubber trees, caused by the necrotrophic fungus Corynespora cassiicola, is responsible for important yield losses in Asian and African plantations, whereas its impact is negligible in South America. The objective of this study was to identify potential antagonists of C. cassiicola among fungal endophytes (i.e., Pestalotiopsis, Colletotrichum, and Trichoderma spp.) isolated from wild and cultivated rubber trees distributed in the Peruvian Amazon. We first tested the endophytes in dual in vitro confrontation assays against a virulent C. cassiicola isolate (CCP) obtained from diseased rubber trees in the Philippines. All Trichoderma isolates overran the CCP colony, suggesting some antagonistic mechanism, while species from the other genera behaved as mutual antagonists. Trichoderma isolates were then tested through antibiosis assays for their capacity to produce growth-inhibiting molecules. One isolate (LA279), recovered as an endophyte from a wild Hevea guianensis specimen and identified as Trichoderma koningiopsis, showed significant antibiosis capacity. We demonstrated that LA279 was also able to endophytically colonize the cultivated rubber tree species (H. brasiliensis). Under controlled laboratory conditions, rubber plants were inoculated with three Trichoderma strains, including LA279, in combination with the pathogenic CCP. Results showed that 1 week preinoculation with the endophytes differentially reduced CCP mycelial development and symptoms. In conclusion, this study suggests that T. koningiopsis isolate LA279-and derivate compounds-could be a promising candidate for the biological control of the important rubber tree pathogen C. cassiicola.

Trichoderma as a Model to Study Effector-Like Molecules

Plants are capable of perceiving microorganisms by coordinating processes to establish different forms of plant–microbe relationships. Plant colonization is governed in fungal and bacterial systems by secreted effector molecules, suppressing plant defense responses and modulating plant physiology to promote either virulence or compatibility. Proteins, secondary metabolites, and small RNAs have been described as effector molecules that use different mechanisms to establish the interaction. Effector molecules have been studied in more detail due to their involvement in harmful interactions, leading to a negative impact on agriculture. Recently, research groups have started to study the effectors in symbiotic interactions. Interestingly, most symbiotic effectors are members of the same families present in phytopathogens. Nevertheless, the quantity and ratio of secreted effectors depends on the microorganism and the host, suggesting a complex mechanism of recognition between the plant and their associated microorganisms. Fungi belonging to Trichoderma genus interact with plants by inducing their defense system and promoting plant growth. Research suggests that some of these effects are associated with effector molecules that Trichoderma delivers during the association with the plant. In this review, we will focus on the main findings concerning the effector molecules reported in Trichoderma spp. and their role during the interaction with plants, mainly in the molecular dialogue that takes place between them.

Symbiotic Root-Endophytic Soil Microbes Improve Crop Productivity and Provide Environmental Benefits

Plants should not be regarded as entities unto themselves, but as the visible part of plant-microbe complexes which are best understood as "holobiomes." Some microorganisms when given the opportunity to inhabit plant roots become root symbionts. Such root colonization by symbiotic microbes can raise crop yields by promoting the growth of both shoots and roots, by enhancing uptake, fixation, and/or more efficient use of nutrients, by improving plants' resistance to pests, diseases, and abiotic stresses that include drought, salt, and other environmental conditions, and by enhancing plants' capacity for photosynthesis. We refer plant-microbe associations with these capabilities that have been purposefully established as enhanced plant holobiomes (EPHs). Here, we consider four groups of phylogenetically distinct and distant symbiotic endophytes: (1) Rhizobiaceae bacteria; (2) plant-obligate arbuscular mycorrhizal fungi (AMF); (3) selected endophytic strains of fungi in the genus Trichoderma; and (4) fungi in the Sebicales order, specifically Piriformospora indica. Although these exhibit quite different "lifestyles" when inhabiting plants, all induce beneficial systemic changes in plants' gene expression that are surprisingly similar. For example, all induce gene expression that produces proteins which detoxify reactive oxygen species (ROS). ROS are increased by environmental stresses on plants or by overexcitation of photosynthetic pigments. Gene overexpression results in a cellular environment where ROS levels are controlled and made more compatible with plants' metabolic processes. EPHs also frequently exhibit increased rates of photosynthesis that contribute to greater plant growth and other capabilities. Soil organic matter (SOM) is augmented when plant root growth is increased and roots remain in the soil. The combination of enhanced photosynthesis, increasing sequestration of CO2 from the air, and elevation of SOM removes C from the atmosphere and stores it in the soil. Reductions in global greenhouse gas levels can be accelerated by incentives for carbon farming and carbon cap-and-trade programs that reward such climate-friendly agriculture. The development and spread of EPHs as part of such initiatives has potential both to enhance farm productivity and incomes and to decelerate global warming.

A novel function of N-signaling in plants with special reference to Trichoderma interaction influencing plant growth, nitrogen use efficiency, and cross talk with plant hormones

Trichoderma spp. is considered as a plant growth promoter and biocontrol fungal agents. They colonize on the surface of root in most of the agriculture crops. They secrete different secondary metabolites and enzymes which promote different physiological processes as well as protect plants from various environmental stresses. This is part of their vital functions. They are widely exploited as a biocontrol agent and plant growth promoter in agricultural fields. Colonization of Trichoderma with roots can enhance nutrient acquisition from surrounding soil to root and can substantially increase nitrogen use efficiency (NUE) in crops and linked with activation of plant signaling cascade. Among Trichoderma species, only some Trichoderma species were well characterized which help in the uptake of nitrogen-containing compound (especially nitrate form) and induced nitric oxide (NO) in plants. Both nitrate and NO are known as a signaling agent, involved in plant growth and development and disease resistance. Activation of these signaling molecules may crosstalk with other signaling molecule (Ca²⁺) and phytohormone (auxin, gibberellins, cytokinin and ethylene). This ability of Trichoderma is important to agriculture not only for increased plant growth but also to control plant diseases. Recently, Trichoderma strains have been shown to encompass the ability to regulate transcripts level of high-affinity nitrate transporters and probably it was positively regulated by NO. This review aims to focus the usage of Trichoderma strains on crops by their abilities to regulate transcript levels, probably through activation of plant N signaling transduction that improve plant health.

Trichoderma as a Model to Study Effector-Like Molecules

Plants are capable of perceiving microorganisms by coordinating processes to establish different forms of plant-microbe relationships. Plant colonization is governed in fungal and bacterial systems by secreted effector molecules, suppressing plant defense responses and modulating plant physiology to promote either virulence or compatibility. Proteins, secondary metabolites, and small RNAs have been described as effector molecules that use different mechanisms to establish the interaction. Effector molecules have been studied in more detail due to their involvement in harmful interactions, leading to a negative impact on agriculture. Recently, research groups have started to study the effectors in symbiotic interactions. Interestingly, most symbiotic effectors are members of the same families present in phytopathogens. Nevertheless, the quantity and ratio of secreted effectors depends on the microorganism and the host, suggesting a complex mechanism of recognition between the plant and their associated microorganisms. Fungi belonging to Trichoderma genus interact with plants by inducing their defense system and promoting plant growth. Research suggests that some of these effects are associated with effector molecules that Trichoderma delivers during the association with the plant. In this review, we will focus on the main findings concerning the effector molecules reported in Trichoderma spp. and their role during the interaction with plants, mainly in the molecular dialogue that takes place between them.

Defense responses of wheat plants (Triticum aestivum L.) against brown spot as a result of possible elicitors application

ABSTRACT: The objective of this research was to evaluate the response of wheat plants to the application of possible elicitor compounds against Bipolaris sorokiniana pathogen. This response was measured through the quantification of antioxidant enzymes, malondialdehyde and flavonoids, evaluation of the severity of brown spot disease and productivity in wheat, greenhouse and field crops. The treatments consisted of suspensions of endophytic fungi Aspergillus japonicus and Trichoderma tomentosum, salicylic acid, acibenzolar-S-methyl and fungicide. In the field trials, in 2015 and 2016, the development of the disease was lower and productivity was higher in all treatments, with emphasis on the fungicide. However, endophytic fungi suspensions demonstrated potential as growth promoters, disease severity reducers and protective antioxidant response activators, as they promoted significant increase in superoxide dismutase, catalase, glutathione and flavonoid enzymes.

Screening of bacterial endophytes as potential biocontrol agents against soybean diseases

AIMS

This research was aimed at identifying and characterizing endophytic micro-organisms associated with soybean that have antimicrobial activity towards soybean pathogens.

METHODS AND RESULTS

Soybean plants were collected from field trials in four locations of southern Brazil that were cultivated with conventional (C) and transgenic glyphosate-resistant (GR) soybeans. Endophytic bacteria isolated from roots, stems and leaves of soybeans were evaluated for their capacity to inhibit fungal and bacterial plant pathogens and 13 micro-organisms were identified with antagonistic activity. Approximately 230 bacteria were isolated and identified based on the 16S rRNA and rpoN gene sequences. Bacteria isolated from conventional and transgenic soybeans were significantly different not only in population diversity but also in their antagonistic capacity. Thirteen isolates showed in vitro antagonism against Sclerotinia sclerotiorum, Phomopsis sojae and Rhizoctonia solani. Bacillus sp. and Burkholderia sp. were the most effective isolates in controlling bacterial and fungal pathogens in vitro. Extracts and precipitates from culture supernatants of isolates showed different patterns of inhibitory activity on growth of fungal and bacterial pathogens.

CONCLUSIONS

Bacillus sp. and Burkholderia sp. were the most effective isolates in controlling fungal pathogens in vitro, and the activity is mainly due to peptides. However, most of the studied bacteria showed the presence of antimicrobial compounds in the culture supernatant, either peptides, bacteriocins or secondary metabolites.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results could be significant to develop tools for the biological control of soybean diseases. The work brought to the identification of micro-organisms such as Bacillus sp. and Burkholderia sp. that have the potential to protect crops in order to enhance a sustainable management system of crops. Furthermore, the study provides the first evidences of the influence of management as well as the genetics of glyphosate-resistant soybean on the diversity of bacterial endophytes of soybean phytobiome.

Network hubs in root-associated fungal metacommunities

BACKGROUND

Although a number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges. In this respect, network analytical methods have provided a basis for exploring "hub" microbial species, which potentially organize community-scale processes of plant-microbe interactions.

METHODS

By compiling Illumina sequencing data of root-associated fungi in eight forest ecosystems across the Japanese Archipelago, we explored hubs within "metacommunity-scale" networks of plant-fungus associations. In total, the metadata included 8080 fungal operational taxonomic units (OTUs) detected from 227 local populations of 150 plant species/taxa.

RESULTS

Few fungal OTUs were common across all the eight forests. However, in each of the metacommunity-scale networks representing northern four localities or southern four localities, diverse mycorrhizal, endophytic, and pathogenic fungi were classified as "metacommunity hubs," which were detected from diverse host plant taxa throughout a climatic region. Specifically, Mortierella (Mortierellales), Cladophialophora (Chaetothyriales), Ilyonectria (Hypocreales), Pezicula (Helotiales), and Cadophora (incertae sedis) had broad geographic and host ranges across the northern (cool-temperate) region, while Saitozyma/Cryptococcus (Tremellales/Trichosporonales) and Mortierella as well as some arbuscular mycorrhizal fungi were placed at the central positions of the metacommunity-scale network representing warm-temperate and subtropical forests in southern Japan.

CONCLUSIONS

The network theoretical framework presented in this study will help us explore prospective fungi and bacteria, which have high potentials for agricultural application to diverse plant species within each climatic region. As some of those fungal taxa with broad geographic and host ranges have been known to promote the survival and growth of host plants, further studies elucidating their functional roles are awaited.

Endophytic Trichoderma citrinoviride isolated from mountain-cultivated ginseng (Panax ginseng) has great potential as a biocontrol agent against ginseng pathogens

Background

Ginseng (Panax ginseng Meyer) is an invaluable medicinal plant containing various bioactive metabolites (e.g., ginsenosides). Owing to its long cultivation period, ginseng is vulnerable to various biotic constraints. Biological control using endophytes is an important alternative to chemical control.

Methods

In this study, endophytic Trichoderma citrinoviride PG87, isolated from mountain-cultivated ginseng, was evaluated for biocontrol activity against six major ginseng pathogens. T. citrinoviride exhibited antagonistic activity with mycoparasitism against all ginseng pathogens, with high endo-1,4-β-D-glucanase activity.

Results

T. citrinoviride inoculation significantly reduced the disease symptoms caused by Botrytis cinerea and Cylindrocarpon destructans and induced ginsenoside biosynthesis in ginseng plants. T. citrinoviride was formulated as dustable powder and granules. The formulated agents also exhibited significant biocontrol activity and induced ginsenosides production in the controlled environment and mountain area.

Conclusion

Our results revealed that T. citrinoviride has great potential as a biological control agent and elicitor of ginsenoside production.

Host Specificity of Endophytic Mycobiota of Wild Nicotiana Plants from Arid Regions of Northern Australia

In arid regions of northern Australia, plants survive under water deficit, high temperatures, intense solar radiation and nutrient-impoverished soils. They employ various morpho-physiological and biochemical adaptations including interaction with microbial symbionts. We evaluated identity, host and tissue association with geographical distribution of fungal endophytes isolated from above- and below-ground tissues of plants of three indigenous Australian Nicotiana species. Isolation frequency and α-diversity were significantly higher for root endophyte assemblages than those of stem and leaf tissues. We recorded no differences in endophyte species richness or diversity as a function of sampling location, but did detect differences among different host genotypes and plant tissues. There was a significant pattern of community similarity associated with host genotypes but no consistent pattern of fungal community structuring associated with sampling location and tissue type, regardless of the community similarity measurements used.

A morel improved growth and suppressed Fusarium infection in sweet corn

A post-fire morel collected from Populus simonii stands in Mt. Qingling was identified as Morchella crassipes Mes-20 by using nuclear ribosomal DNA internal transcribed spacer phylogeny. It was inoculated into sweet corn to observe colonized roots in purified culture and in greenhouse experiments. The elongation and maturation zones of sweet corn were remarkably colonized at the cortex intercellular and intracellular cells, vessel cells, and around the Casparian strip, forming ectendomycorrhiza-like structures. Colonization was also observed in the zone of cell division proximal to the root cap. Greenhouse assays with sweet corn showed that this morel stimulated the development of the root system and significantly increased the dry root biomass. M. crassipes also significantly reduced the incidence of Fusarium verticillioides in the kernels of mature ears when inoculated into young ears before Fusarium inoculation and prevented Fusarium infection in corn ears compared with that of the control in the greenhouse. When grown under axenic conditions, M. crassipes produced the phytohormones abscisic acid, indole-3-acetic acid, and salicylic acid. The benefits to plants elicited by M. crassipes may result from these phytohormones which may improve the drought resistance, biomass growth and resistance to Fusarium.

Chilli Anthracnose: The Epidemiology and Management

Indian cuisine is renowned and celebrated throughout the world for its spicy treat to the tongue. The flavor and aroma of the food generated due to the use of spices creates an indelible experience. Among the commonly utilized spices to stimulate the taste buds in Indian food, whole or powdered chilli constitutes an inevitable position. Besides being a vital ingredient of of Indian food, chilli occupy an important position as an economic commodity, a major share in Indian economy. Chilli also has uncountable benefits to human health. Fresh green chilli fruits contain more Vitamin C than found in citrus fruits, while red chilli fruits have more Vitamin A content than as found in carrots. The active component of the spice, Capsaicin possesses the antioxidant, anti-mutagenic, anti-carcinogenic and immunosuppressive activities having ability to inhibit bacterial growth and platelet aggregation. Though introduced by the Portuguese in the Seventeenth century, India has been one of the major producers and exporters of this crop. During 2010-2011, India was the leading exporter and producer of chilli in the world, but recently due to a decline in chilli production, it stands at third position in terms of its production. The decline in chilli production has been attributed to the diseases linked with crop like anthracnose or fruit rot causing the major share of crop loss. The disease causes severe damage to both mature fruits in the field as well as during their storage under favorable conditions, which amplifies the loss in yield and overall production of the crop. This review gives an account of the loss in production and yield procured in chili cultivation due to anthracnose disease in Indian sub-continent, with emphasis given to the sustainable management strategies against the conventionally recommended control for the disease. Also, the review highlights the various pathogenic species of Colletotrichum spp, the causal agent of the disease, associated with the host crop in the country. The information in the review will prove of immense importance for the groups targeting the problem, for giving a collective information on various aspects of the epidemiology and management of the disease.

Nitrogen Metabolism and Growth Enhancement in Tomato Plants Challenged with Trichoderma harzianum Expressing the Aspergillus nidulans Acetamidase amdS Gene

Trichoderma is a fungal genus that includes species that are currently being used as biological control agents and/or as biofertilizers. In addition to the direct application of Trichoderma spp. as biocontrol agents in plant protection, recent studies have focused on the beneficial responses exerted on plants, stimulating the growth, activating the defenses, and/or improving nutrient uptake. The amdS gene, encoding an acetamidase of Aspergillus, has been used as a selectable marker for the transformation of filamentous fungi, including Trichoderma spp., but the physiological effects of the introduction of this gene into the genome of these microorganisms still remains unexplored. No evidence of amdS orthologous genes has been detected within the Trichoderma spp. genomes and the amdS heterologous expression in Trichoderma harzianum T34 did not affect the growth of this fungus in media lacking acetamide. However, it did confer the ability for the fungus to use this amide as a nitrogen source. Although a similar antagonistic behavior was observed for T34 and amdS transformants in dual cultures against Rhizoctonia solani, Botrytis cinerea, and Fusarium oxysporum, a significantly higher antifungal activity was detected in amdS transformants against F. oxysporum, compared to that of T34, in membrane assays on media lacking acetamide. In Trichoderma-tomato interaction assays, amdS transformants were able to promote plant growth to a greater extent than the wild-type T34, although compared with this strain the transformants showed similar capability to colonize tomato roots. Gene expression patterns from aerial parts of 3-week-old tomato plants treated with T34 and the amdS transformants have also been investigated using GeneChip Tomato Genome Arrays. The downregulation of defense genes and the upregulation of carbon and nitrogen metabolism genes observed in the microarrays were accompanied by (i) enhanced growth, (ii) increased carbon and nitrogen levels, and (iii) a higher sensitivity to B. cinerea infections in plants treated with amdS transformants as detected in greenhouse assays. These observations suggest that the increased plant development promoted by the amdS transformants was at expense of defenses.

Phenotypic evaluation and genetic dissection of resistance to Phytophthora sojae in the Chinese soybean mini core collection

BACKGROUND

Phytophthora root and stem rot (PRR) caused by Phytophthora sojae is one of the most serious diseases affecting soybean (Glycine max (L.) Merr.) production all over the world. The most economical and environmentally-friendly way to control the disease is the exploration and utilization of resistant varieties.

RESULTS

We screened a soybean mini core collection composed of 224 germplasm accessions for resistance against eleven P. sojae isolates. Soybean accessions from the Southern and Huanghuai regions, especially the Hubei, Jiangsu, Sichuan and Fujian provinces, had the most varied and broadest spectrum of resistance. Based on gene postulation, Rps1b, Rps1c, Rps4, Rps7 and novel resistance genes were identified in resistant accessions. Consequently, association mapping of resistance to each isolate was performed with 1,645 single nucleotide polymorphism (SNP) markers. A total of 14 marker-trait associations for Phytophthora resistance were identified. Among them, four were located in known PRR resistance loci intervals, five were located in other disease resistance quantitative trait locus (QTL) regions, and five associations unmasked novel loci for PRR resistance. In addition, we also identified candidate genes related to resistance.

CONCLUSION

This is the first P. sojae resistance evaluation conducted using the Chinese soybean mini core collection, which is a representative sample of Chinese soybean cultivars. The resistance reaction analyses provided an excellent database of resistant resources and genetic variations for future breeding programs. The SNP markers associated with resistance will facilitate marker-assisted selection (MAS) in breeding programs for resistance to PRR, and the candidate genes may be useful for exploring the mechanism underlying P. sojae resistance.