Fungal and plant gene expression during the colonization of cacao seedlings by endophytic isolates of four Trichoderma species

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.

Endophytic colonization of five Trichoderma species and their effects on growth of a Eucalyptus hybrid

The study aimed to evaluate the effectiveness of endophytic colonization via leaf and root inoculation of five Trichoderma species in a Eucalyptus hybrid, as well as the effects of inoculation on plant growth. The experimental design was completely randomized in a 6 × 2 factorial scheme. Plant growth was evaluated during the experimental period at three different times: 20 days after inoculation (d.a.i), 40 d.a.i., and 60 d.a.i. A statistical difference was observed between the inoculation methods during each period and between the Trichoderma species. Plants inoculated with T. asperellum showed the greatest growth among the treatments. Root-inoculated plants produced the greatest growth response. This showed that the presence of Trichoderma in the roots assisted in nutrient assimilation, promoted greater plant growth, when compared with leaf-inoculated plants. Evaluation of the effectiveness of endophytic colonization was performed at each sampling period by collecting leaf samples, and at 60 d.a.i., by collecting leaf, stem, and root samples. T. longibrachiatum and T. harzianum were isolated from leaves at 20 d.a.i., with an increase in the number of colonized plants throughout the evaluation of leaf-inoculated plants. In root-inoculated plants, treatment with T. longibrachiatum, T. harzianum, and T. asperellum presented the highest endophytic colonization in the stem and root samples (at 60 d.a.i.).

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.

Endophytic fungi: hidden treasure chest of antimicrobial metabolites interrelationship of endophytes and metabolites

Endophytic fungi comprise host-associated fungal communities which thrive within the tissues of host plants and produce a diverse range of secondary metabolites with various bioactive attributes. The metabolites such as phenols, polyketides, saponins, alkaloids help to mitigate biotic and abiotic stresses, fight against pathogen attacks and enhance the plant immune system. We present an overview of the association of endophytic fungal communities with a plant host and discuss molecular mechanisms induced during their symbiotic interaction. The overview focuses on the secondary metabolites (especially those of terpenoid nature) secreted by endophytic fungi and their respective function. The recent advancement in multi-omics approaches paved the way for identification of these metabolites and their characterization via comparative analysis of extensive omics datasets. This study also elaborates on the role of diverse endophytic fungi associated with key agricultural crops and hence important for sustainability of agriculture.

Trichoderma: a multipurpose, plant-beneficial microorganism for eco-sustainable agriculture

Trichoderma is a cosmopolitan and opportunistic ascomycete fungal genus including species that are of interest to agriculture as direct biological control agents of phytopathogens. Trichoderma utilizes direct antagonism and competition, particularly in the rhizosphere, where it modulates the composition of and interactions with other microorganisms. In its colonization of plants, on the roots or as an endophyte, Trichoderma has evolved the capacity to communicate with the plant and produce numerous multifaceted benefits to its host. The intricacy of this plant-microorganism association has stimulated a marked interest in research on Trichoderma, ranging from its capacity as a plant growth promoter to its ability to prime local and systemic defence responses against biotic and abiotic stresses and to activate transcriptional memory affecting plant responses to future stresses. This Review discusses the ecophysiology and diversity of Trichoderma and the complexity of its relationships in the agroecosystem, highlighting its potential as a direct and indirect biological control agent, biostimulant and biofertilizer, which are useful multipurpose properties for agricultural applications. We also highlight how the present legislative framework might accommodate the demonstrated evidence of Trichoderma proficiency as a plant-beneficial microorganism contributing towards eco-sustainable agriculture.

Trichoderma asperellum empowers tomato plants and suppresses Fusarium oxysporum through priming responses

Plant-associated microbes play crucial roles in plant health and promote growth under stress. Tomato (Solanum lycopersicum) is one of the strategic crops grown throughout Egypt and is a widely grown vegetable worldwide. However, plant disease severely affects tomato production. The post-harvest disease (Fusarium wilt disease) affects food security globally, especially in the tomato fields. Thus, an alternative effective and economical biological treatment to the disease was recently established using Trichoderma asperellum. However, the role of rhizosphere microbiota in the resistance of tomato plants against soil-borne Fusarium wilt disease (FWD) remains unclear. In the current study, a dual culture assay of T. asperellum against various phytopathogens (e.g., Fusarium oxysporum, F. solani, Alternaria alternata, Rhizoctonia solani, and F. graminerarum) was performed in vitro. Interestingly, T. asperellum exhibited the highest mycelial inhibition rate (53.24%) against F. oxysporum. In addition, 30% free cell filtrate of T. asperellum inhibited F. oxysporum by 59.39%. Various underlying mechanisms were studied to explore the antifungal activity against F. oxysporum, such as chitinase activity, analysis of bioactive compounds by gas chromatography–mass spectrometry (GC–MS), and assessment of fungal secondary metabolites against F. oxysporum mycotoxins in tomato fruits. Additionally, the plant growth-promoting traits of T. asperellum were studied (e.g., IAA production, Phosphate solubilization), and the impact on tomato seeds germination. Scanning electron microscopy, plant root sections, and confocal microscopy were used to show the mobility of the fungal endophyte activity to promote tomato root growth compared with untreated tomato root. T. asperellum enhanced the growth of tomato seeds and controlled the wilt disease caused by the phytopathogen F. oxysporum by enhancing the number of leaves as well as shoot and root length (cm) and fresh and dry weights (g). Furthermore, Trichoderma extract protects tomato fruits from post-harvest infection by F. oxysporum. Taking together, T. asperellum represents a safe and effective controlling agent against Fusarium infection of tomato plants.

Endophytic fungi: a tool for plant growth promotion and sustainable agriculture

Endophytic fungi are found in most, if not all, plant species on the planet. They colonise inner plant tissues without causing symptoms of disease, thus providing benefits to the host plant while also benefiting from this interaction. The global concern for the development of more sustainable agriculture has increased in recent years, and research has been performed to decipher ecology and explore the potential of endophytic interactions in plant growth. To date, many studies point to the positive aspects of endophytic colonisation, and in this review, such research is summarised based on the direct (acquisition of nutrients and phytohormone production) and indirect (induced resistance, production of antibiotics and secondary metabolites, production of siderophores and protection for abiotic and biotic stresses) benefits of endophytic colonisation. An in-depth discussion of the mechanisms is also presented.

Endophytic fungi: a tool for plant growth promotion and sustainable agriculture

Endophytic fungi are found in most, if not all, plant species on the planet. They colonise inner plant tissues without causing symptoms of disease, thus providing benefits to the host plant while also benefiting from this interaction. The global concern for the development of more sustainable agriculture has increased in recent years, and research has been performed to decipher ecology and explore the potential of endophytic interactions in plant growth. To date, many studies point to the positive aspects of endophytic colonisation, and in this review, such research is summarised based on the direct (acquisition of nutrients and phytohormone production) and indirect (induced resistance, production of antibiotics and secondary metabolites, production of siderophores and protection for abiotic and biotic stresses) benefits of endophytic colonisation. An in-depth discussion of the mechanisms is also presented.

Effects of Trichoderma strigosellum in Eucalyptus urophylla Development and Leaf-Cutting Ant Behavior

Fungal endophytes can protect plants against herbivory and be used to control leaf-cutting ants. In this study, we aimed to evaluate the potential of endophytic colonization of Eucalyptus urophylla by three filamentous fungal species and their influence on the plant development and foraging behavior of Atta sexdens. The study design was completely randomized and comprised a factorial scheme of 4 × 3, three antagonistic fungal species (Escovopsis sp., Metarhizium anisopliae, and Trichoderma strigosellum) of the leaf-cutting ant, and one control and three inoculation methods (conidial suspension via foliar spray [FS] and soil drench [SD] inoculation, and seedlings inoculated with mycelium [SWM]). The SWM method allowed T. strigosellum to colonize all plant organs, and these plants exhibited higher height, leaf number, shoot dry mass, and total dry mass than the ones subjected to the other inoculation methods. The SWM method increased the plant height than the control plants and those inoculated with Escovopsis sp. and M. anisopliae. Trichoderma strigosellum, previously isolated from soil, colonized E. urophylla plants and positively influenced their development, as demonstrated by the SWM method. Trichoderma strigosellum promoted the increase in E. urophylla height compared with when the FS and SD methods were used (by 19.62% and 18.52%, respectively). Our results reveal that A. sexdens workers preferentially began cutting the leaves from plants not previously colonized by T. strigosellum. This behavior can be explained by modifications in the phenotypic traits of the eucalyptus leaves.

Why Is the Correct Selection of Trichoderma Strains Important? The Case of Wheat Endophytic Strains of T. harzianum and T. simmonsii

The search for endophytic fungi in the roots of healthy wheat plants from a non-irrigation field trial allowed us to select 4 out of a total of 54 cultivable isolates belonging to the genus Trichoderma, identified as T. harzianum T136 and T139, T. simmonsii T137, and T. afroharzianum T138. In vitro assays against the phytopathogenic fungus Fusarium graminearum showed that the T. harzianum strains had the highest biocontrol potential and that T136 exhibited the highest cellulase and chitinase activities. Production patterns of eight phytohormones varied among the Trichoderma strains. All four, when applied alone or in combination, colonized roots of other wheat cultivars and promoted seed germination, tillering, and plant growth under optimal irrigation conditions in the greenhouse. Apart from T136, the endophytic Trichoderma strains showed plant protection capacity against drought as they activated the antioxidant enzyme machinery of the wheat plants. However, T. simmonsii T137 gave the best plant size and spike weight performance in water-stressed plants at the end of the crop. This trait correlated with significantly increased production of indole acetic acid and abscisic acid and increased 1-aminocyclopropane-1-carboxylic acid deaminase activity by T137. This study shows the potential of Trichoderma endophytes and that their success in agricultural systems requires careful selection of suitable strains.

Characterization of Endophytic Fungi, Acremonium sp., from Lilium davidii and Analysis of Its Antifungal and Plant Growth-Promoting Effects

The present study was aimed at isolating endophytic fungi from the Asian culinary and medicinal plant Lilium davidii and analyzing its antifungal and plant growth-promoting effects. In this study, the fungal endophyte Acremonium sp. Ld-03 was isolated from the bulbs of L. davidii and identified through morphological and molecular analysis. The molecular and morphological analysis confirmed the endophytic fungal strain as Acremonium sp. Ld-03. Antifungal effects of Ld-03 were observed against Fusarium oxysporum, Botrytis cinerea, Botryosphaeria dothidea, and Fusarium fujikuroi. The highest growth inhibition, i.e., 78.39 ± 4.21%, was observed for B. dothidea followed by 56.68 ± 4.38%, 43.62 ± 3.81%, and 20.12 ± 2.45% for B. cinerea, F. fujikuroi, and F. oxysporum, respectively. Analysis of the ethyl acetate fraction through UHPLC-LTQ-IT-MS/MS revealed putative secondary metabolites which included xanthurenic acid, valyl aspartic acid, gancidin W, peptides, and cyclic dipeptides such as valylarginine, cyclo-[L-(4-hydroxy-Pro)-L-leu], cyclo(Pro-Phe), and (3S,6S)-3-benzyl-6-(4-hydroxybenzyl)piperazine-2,5-dione. Other metabolites included (S)-3-(4-hydroxyphenyl)-2-((S)-pyrrolidine-2-carboxamido)propanoic acid, dibutyl phthalate (DBP), 9-octadecenamide, D-erythro-C18-Sphingosine, N-palmitoyl sphinganine, and hydroxypalmitoyl sphinganine. The strain Ld-03 showed indole acetic acid (IAA) production with or without the application of exogenous tryptophan. The IAA ranged from 53.12 ± 3.20 μg ml⁻¹ to 167.71 ± 7.12 μg ml⁻¹ under different tryptophan concentrations. The strain was able to produce siderophore, and its production was significantly decreased with increasing Fe(III) citrate concentrations in the medium. The endophytic fungal strain also showed production of organic acids and phosphate solubilization activity. Plant growth-promoting effects of the strain were evaluated on in vitro seedling growth of Allium tuberosum. Application of 40% culture dilution resulted in a significant increase in root and shoot length, i.e., 24.03 ± 2.71 mm and 37.27 ± 1.86 mm, respectively, compared to nontreated control plants. The fungal endophyte Ld-03 demonstrated the potential of conferring disease resistance and plant growth promotion. Therefore, we conclude that the isolated Acremonium sp. Ld-03 should be further investigated before utilization as a biocontrol agent and plant growth stimulator.

Endophytic Isaria javanica pf185 Persists after Spraying and Controls Myzus persicae (Hemiptera: Aphididae) and Colletotrichum acutatum (Glomerellales: Glomerellaceae) in Pepper

Simple Summary

The green peach aphid (Myzus persicae) and the phytopathogenic fungus Colletotrichum acutatum cause significant losses in a wide variety of crops. To efficiently protect their crops, farmers use chemical pesticides, but this kind of practice is not sustainable because of its negative effects on the environment. This study suggests an environmentally friendly method such as the use of the endophytic Isaria javanica pf185 in pepper plants. Suspension of the endophytic fungus (EF) was sprayed on plants under cage while those same leaves were sampled and assessed under laboratory conditions. The EF can both penetrate inside the leaf tissues and survive on the surface of the leaf after five weeks. The suspension showed an evident insecticidal efficiency against M. persicae and a lower one against C. acutatum. Therefore, its antifungal efficiency against C. acutatum was not correlated with weather patterns. Authors recommend I. javanica pf185 as a potential biocontrol agent against M. persicae and C. acutatum.

Abstract

This study endeavored to sustainably control aphids and anthracnose after spraying endophytic Isaria javanica pf185 under field conditions. Under two different tents; one batch of seedlings was sprayed with a 10⁷ conidia/mL I. javanica pf185 suspension; while another was sprayed with 0.05% Tween 80^® in distilled water. Six leaf discs from the top; middle; and bottom part of the plant canopy were weekly collected and placed on moistened filter paper in a Petri dish for insecticidal and antifungal bioassays against Myzus persicae and Colletotrichum acutatum. Differences were noticed from the 18th day after spraying with mortality (86.67 ± 0.57% versus 36.67 ± 0.64%) and leaf damage (13.45 ± 0.03% versus 41.18 ± 0.06%) on fungus-treated and controlled, respectively. The corrected insecticidal efficacy was 20.43, 39.82, 72.32, 66.43 and 70.04%, while the corrected fungicidal efficacy was 26.07, 38.01, 53.35, 29.08 and 41.81% during five successive weeks. A positive correlation was evident between insecticidal efficacy and relative humidity (r² = 0.620) and temperature (r² = 0.424), respectively. No correlation was found between antifungal activity and relative humidity (r² = 0.061) and temperature (r² = 0), respectively. The entomopathogenic fungus survived on leaf surface area and in tissues after spraying.

Exploring endophytes for in vitro synthesis of bioactive compounds similar to metabolites produced in vivo by host plants

Endophytes represent microorganisms residing within plant tissues without typically causing any adverse effect to the plants for considerable part of their life cycle and are primarily known for their beneficial role to their host-plant. These microorganisms can in vitro synthesize secondary metabolites similar to metabolites produced in vivo by their host plants. If microorganisms are isolated from certain plants, there is undoubtedly a strong possibility of obtaining beneficial endophytes strains producing host-specific secondary metabolites for their potential applications in sustainable agriculture, pharmaceuticals and other industrial sectors. Few products derived from endophytes are being used for cultivating resilient crops and developing non-toxic feeds for livestock. Our better understanding of the complex relationship between endophytes and their host will immensely improve the possibility to explore their unlimited functionalities. Successful production of host-secondary metabolites by endophytes at commercial scale might progressively eliminate our direct dependence on high-valued vulnerable plants, thus paving a viable way for utilizing plant resources in a sustainable way.

Endophytic Fungi: From Symbiosis to Secondary Metabolite Communications or Vice Versa?

Endophytic fungi (EF) are a group of fascinating host-associated fungal communities that colonize the intercellular or intracellular spaces of host tissues, providing beneficial effects to their hosts while gaining advantages. In recent decades, accumulated research on endophytic fungi has revealed their biodiversity, wide-ranging ecological distribution, and multidimensional interactions with host plants and other microbiomes in the symbiotic continuum. In this review, we highlight the role of secondary metabolites (SMs) as effectors in these multidimensional interactions, and the biosynthesis of SMs in symbiosis via complex gene expression regulation mechanisms in the symbiotic continuum and via the mimicry or alteration of phytochemical production in host plants. Alternative biological applications of SMs in modern medicine, agriculture, and industry and their major classes are also discussed. This review recapitulates an introduction to the research background, progress, and prospects of endophytic biology, and discusses problems and substantive challenges that need further study.

Bioactive compounds guided diversity of endophytic fungi from Baliospermum montanum and their potential extracellular enzymes

Baliospermum montanum (Willd.) Muell. Arg, a medicinal plant distributed throughout India from Kashmir to peninsular-Indian region is extensively used to treat jaundice, asthma, and constipation. In the current study, 203 endophytic fungi representing twenty-nine species were isolated from tissues of B. montanum. The colonization and isolation rate of endophytes were higher in stem followed by seed, root, leaf and flower. The phytochemical analysis revealed 70% endophytic isolates showed alkaloids and flavonoids, 13% were positive for phenols, saponins and terpenoids. Further, these endophytes produced remarkable extracellular enzymes such as amylase, cellulase, phosphates, protease and lipase. The most promisive three endophytic fungi were identified by ITS region and secreted metabolites were identified by gas chromatography-mass spectrometry (GC-MS/MS). The GC-MS profile detected twenty-five bioactive compounds from ethyl acetate extracts. Among endophytic fungi, Trichoderma reesei isolated from flower exhibited nine bioactive compounds namely, 2-Cyclopentenone, 2-(4-chloroanilino)-4-piperidino, Oxime-methoxy-Phenyl, Methanamine N-hydroxy-N-methyl, Strychane, Cyclotetrasiloxane, Octamethyl and 1-Acetyl-20a-hydroxy-16-methylene. The endophyte, Aspergillus brasiliensis isolated from root and Fusarium oxysporum isolated from seed produced nine and seven bioactive compounds, respectively. Overall, a significant contribution of bioactive compounds was noticed from the diverse endophytic fungi associated with B. montanum and could be explored for development of novel drug with commercial values.

Studies on fungal communities and functional guilds shift in tea continuous cropping soils by high-throughput sequencing

Purpose

Although soil fungal communities are considered important in tea orchard ecosystems, experimental research on their responses to the long-term continuous ratooning cultivation of tea plants are limited.

Methods

In this study, Illumina high-throughput sequencing technology was employed to investigate soil fungal communities in tea orchards with continuous cropping histories of 0, 1, 10, and 20 years.

Results

Results indicated that the predominant phyla were Ascomycota and Basidiomycota in all tea soil samples. Plant pathogen fungi Alternaria was the most predominant genus in the 10- and 20-year soils and significantly higher than that in the 0- and 1-year soils. FUNGuild revealed that the symbiotrophs in the 1-year soil (8.00%) was markedly higher than those in the 0-, 10-, and 20-year soils (1.43%~2.47%). The saprotrophs in the 20-year soils was approximately two-fold higher than those identified in the 0-, 1-, and 10-year soils. The pathotroph–saprotroph–symbiotroph fungi were higher in the 10- and 20-year soils in comparison to the 0- and 1-year soils as expected. Diversity analysis showed that the indices of Shannon and Simpson in the 1-year soils were higher than those in other treatments. Redundancy analysis suggested that fungal community structure and function were evidently interrelated to pH and exchangeable aluminum in the soils, respectively.

Conclusion

In summary, the long-term continuous ratooning cultivation of tea plants changed the fungal communities in the rhizosphere, enriched saprotrophs and plant pathogens (Alternaria spp.), and reduced beneficial fungi (symbiotrophs). Results of this work can be used to explore reasonable management measures, such as microbial fertilizer application, and eventually relieve the long-term monoculture problems of tea plants.

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.

Evaluation of the Biocontrol Potential of Endophytic Fungus Fusarium solani CEF559 against Verticillium dahliae in Cotton Plant

Verticillium wilt of cotton, caused by the soilborne pathogen Verticillium dahliae, is one of the most serious diseases of cotton worldwide. Increased concerns about the side effects of synthetic pesticides have resulted in greater interest in developing biocontrol strategies against Verticillium wilt. We evaluated a Fusarium solani CEF559 isolate, obtained from the endosphere of healthy cotton plants, for its biocontrol potential against V. dahliae in vitro and in vivo. In addition to disease assessment, three key genes in the lignin metabolism pathway and four pathogenesis-related (PR) genes were monitored using qRT-PCR. In the laboratory tests, F. solani CEF559 inhibited V. dahliae colony growth by 75% and sporulation by nearly 80% and completely suppressed conidial production. However, volatile metabolites from CEF559 did not affect V. dahliae colony growth. In the greenhouse study, CEF559 significantly reduced wilt development, with a control efficacy greater than 60% when assessed 25 days postinoculation. In a field experiment, CEF559 reduced wilt development, with the efficacy ranting from 30.1% to 56.3%. PR genes and those key genes in the lignin metabolism pathway were transiently upregulated in the cotton roots pretreated with CEF559 when subsequently inoculated with V. dahliae, compared with those plants inoculated with V. dahliae only. Moreover, CEF559 inhibited V. dahliae colonisation of both the roots and hypocotyls. The present results suggest that this cotton endophytic fungal strain, F. solani CEF559, confers protection against V. dahliae.

Genome and transcriptome analysis of the latent pathogen Lasiodiplodia theobromae, an emerging threat to the cacao industry

Lasiodiplodia theobromae (Pat.) Griffon & Maubl., a member of the family Botryosphaeriaceae, is becoming a significant threat to crops and woody plants in many parts of the world, including the major cacao growing areas. While attempting to isolate Ceratobasidium theobromae, a causal agent of vascular streak dieback (VSD), from symptomatic cacao stems, 74% of isolated fungi were Lasiodiplodia spp. Sequence-based identification of 52 putative isolates of L. theobromae indicated that diverse species of Lasiodiplodia were associated with cacao in the studied areas, and the isolates showed variation in aggressiveness when assayed using cacao leaf discs. The present study reports a 43.75 Mb de novo assembled genome of an isolate of L. theobromae from cacao. Ab initio gene prediction generated 13 061 protein-coding genes, of which 2862 are unique to L. theobromae, when compared with other closely related Botryosphaeriaceae. Transcriptome analysis revealed that 11 860 predicted genes were transcriptionally active and 1255 were more highly expressed in planta compared with cultured mycelia. The predicted genes differentially expressed during infection were mainly those involved in carbohydrate, pectin, and lignin catabolism, cytochrome P450, necrosis-inducing proteins, and putative effectors. These findings significantly expand our knowledge of the genome of L. theobromae and the genes involved in virulence and pathogenicity.

Potential of Yeasts as Biocontrol Agents of the Phytopathogen Causing Cacao Witches' Broom Disease: Is Microbial Warfare a Solution?

Plant diseases caused by fungal pathogens are responsible for major crop losses worldwide, with a significant socio-economic impact on the life of millions of people who depend on agriculture-exclusive economy. This is the case of the Witches’ Broom Disease (WBD) affecting cacao plant and fruit in South and Central America. The severity and extent of this disease is prospected to impact the growing global chocolate market in a few decades. WBD is caused by the basidiomycete fungus Moniliophthora perniciosa. The methods used to contain the fungus mainly rely on chemical fungicides, such as copper-based compounds or azoles. Not only are these highly ineffective, but also their utilization is increasingly restricted by the cacao industry, in part because it promotes fungal resistance, in part related to consumers’ health concerns and environmental awareness. Therefore, the disease is being currently tentatively controlled through phytosanitary pruning, although the full removal of infected plant material is impossible and the fungus maintains persistent inoculum in the soil, or using an endophytic fungal parasite of Moniliophthora perniciosa which production is not sustainable. The growth of Moniliophthora perniciosa was reported as being antagonized in vitro by some yeasts, which suggests that they could be used as biological control agents, suppressing the fungus multiplication and containing its spread. Concurrently, some yeast-based products are used in the protection of fruits from postharvest fungal spoilage, and the extension of diverse food products shelf-life. These successful applications suggest that yeasts can be regarded a serious alternative also in the pre-harvest management of WBD and other fungal plant diseases. Yeasts’ GRAS (Generally Recognized as Safe) nature adds to their appropriateness for field application, not raising major ecological concerns as do the present more aggressive approaches. Importantly, mitigating WBD, in a sustainable manner, would predictably have a high socioeconomic impact, contributing to diminish poverty in the cacao-producing rural communities severely affected by the disease. This review discusses the importance/advantages and the challenges that such a strategy would have for WBD containment, and presents the available information on the molecular and cellular mechanisms underlying fungi antagonism by yeasts.

Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots

Background

Trichoderma spp. are majorly composed of plant-beneficial symbionts widely used in agriculture as bio-control agents. Studying the mechanisms behind Trichoderma-derived plant benefits has yielded tangible bio-industrial products. To better take advantage of this fungal-plant symbiosis it is necessary to obtain detailed knowledge of which genes Trichoderma utilizes during interaction with its plant host. In this study, we explored the transcriptional activity undergone by T. virens during two phases of symbiosis with maize; recognition of roots and after ingress into the root cortex.

Results

We present a model of T. virens – maize interaction wherein T. virens experiences global repression of transcription upon recognition of maize roots and then induces expression of a broad spectrum of genes during colonization of maize roots. The genes expressed indicate that, during colonization of maize roots, T. virens modulates biosynthesis of phytohormone-like compounds, secretes a plant-environment specific array of cell wall degrading enzymes and secondary metabolites, remodels both actin-based and cell membrane structures, and shifts metabolic activity. We also highlight transcription factors and signal transduction genes important in future research seeking to unravel the molecular mechanisms of T. virens activity in maize roots.

Conclusions

T. virens displays distinctly different transcriptional profiles between recognizing the presence of maize roots and active colonization of these roots. A though understanding of these processes will allow development of T. virens as a bio-control agent. Further, the publication of these datasets will target future research endeavors specifically to genes of interest when considering T. virens – maize symbiosis.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5651-z) contains supplementary material, which is available to authorized users.

Rhizoremediation prospects of Polyaromatic hydrocarbon degrading rhizobacteria, that facilitate glutathione and glutathione-S-transferase mediated stress response, and enhance growth of rice plants in pyrene contaminated soil

Rhizoremediation is a strategy where pollutant degrading bacteria are augmented through plant roots using plant-microbe interaction. Therefore, for effective rhizoremediation of pyrene contaminated soil, bacterial strains were experimented for amelioration of stress response in host plant along with biodegradation ability. A total of 28 bacteria, having ability to degrade polycyclic aromatic hydrocarbons were isolated from contaminated sites and checked for their plant growth promoting attributes, such as indole acetic acid (IAA) production, phosphate solubilization, atmospheric nitrogen fixation and siderophore release. Among these isolates, Klebsiella pneumoniae AWD5 was found to degrade 60% of pyrene. While other isolates, i.e. Alcaligenes faecalis BDB4, Pseudomonas fragi DBC, Pseudomonas aeruginosa PDB1, Acinetobactor sp. PDB4 degraded 48.5%, 50.29%, 31.3% and 36% of pyrene, respectively, after 6 days of incubation. K. pneumoniae AWD5 produced 94.2 μg/ml IAA and 3.1 mM/mg/h unit of ACC deaminase, which was best among eighteen indole acetic acid producers and five of the 1-aminocyclopropane-1-carboxylate (ACC) deaminase producing isolates. P. aeruginosa PDB1 resulted in highest phosphate solubilization activity of 875.26 ng/ml of soluble phosphate among seven phosphate solubilizers. The isolates AWD5 and PDB1 both have shown a good amount of siderophore release (56.3% and 84.3% unit). There was 19.1% increase in shoot length of rice seedlings treated with PDB1 in presence of pyrene. Similarly, 26.5% increase in the root length of AWD5 treated rice was recorded in pyrene contaminated soil. Bacterial inoculation also induced and improved the stress response in host plant, in presence of pyrene, as suggested by the superoxide dismutase, glutathione and glutathione-S-transferase activities in rice.

Endophytic biocatalysts with enoate reductase activity isolated from Mentha pulegium

The biotransformation of (4R)-(-)-carvone by Mentha pulegium (pennyroyal) leaves and its endophytic bacteria was performed in order to search for novel biocatalysts with enoate reductase activity. The obtained results clearly indicated that endophytes play an important role in the biotransformation of (4R)-(-)-carvone with pennyroyal plant tissues. The best activity was associated to the endophytic bacteria Pseudomonas proteolytica FM18Mci1 and Bacillus sp. FM18civ1. Enoate reductase activity for the reduction of (4R)-(-)-carvone and (4S)-(+)-carvone as model substrates was evaluated for each strain. Finally, both isolated strains were evaluated for the kinetic resolution of racemic carvone. The two bacteria gave (1R, 4R) or (1R, 4S)-dihydrocarvone as major products. P. proteolytica FM18Mci1 had preference for the 4S-(-)-carvone, reaching a conversion 95% in 24 h. In contrast, Bacillus sp. FM18civ1 had preference for (4R)-(-)-carvone. The results obtained in the kinetic resolution of carvone indicated that the Bacillus strain could be useful for resolving a racemic mixture of carvone.

Induction of abiotic stress tolerance in plants by endophytic microbes

Endophytes are micro-organisms including bacteria and fungi that survive within healthy plant tissues and promote plant growth under stress. This review focuses on the potential of endophytic microbes that induce abiotic stress tolerance in plants. How endophytes promote plant growth under stressful conditions, like drought and heat, high salinity and poor nutrient availability will be discussed. The molecular mechanisms for increasing stress tolerance in plants by endophytes include induction of plant stress genes as well as biomolecules like reactive oxygen species scavengers. This review may help in the development of biotechnological applications of endophytic microbes in plant growth promotion and crop improvement under abiotic stress conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

Increasing human populations demand more crop yield for food security while crop production is adversely affected by abiotic stresses like drought, salinity and high temperature. Development of stress tolerance in plants is a strategy to cope with the negative effects of adverse environmental conditions. Endophytes are well recognized for plant growth promotion and production of natural compounds. The property of endophytes to induce stress tolerance in plants can be applied to increase crop yields. With this review, we intend to promote application of endophytes in biotechnology and genetic engineering for the development of stress-tolerant plants.

Mortierella alpina CS10E4, an oleaginous fungal endophyte of Crocus sativus L. enhances apocarotenoid biosynthesis and stress tolerance in the host plant

Crocus sativus is the only plant species which produces apocarotenoids like crocin, picrocrocin and safranal in significant amounts. These compounds impart organoleptic properties to saffron (dried stigmas of Crocus flower) making it world’s costliest spice. Crocus apocarotenoids have tremendous medicinal properties as well. Effect of endophytes on Crocus apocarotenoid production and the molecular mechanism involved has not been reported so far. Here we studied the effect of an oleaginous fungal endophyte, Mortierella alpina CS10E4 on Crocus growth, apocarotenoid metabolism and tolerance to corm rot disease. The results demonstrated that there was a significant improvement in many morphological and physiological traits in endophyte treated Crocus plants including total biomass and size of corms, stigma biomass, number of apical sprouting buds, and number of adventitious roots. The endophyte also shifted metabolic flux towards enhanced production of apocarotenoids by modulating the expression of key pathway genes. Further, M. alpina CS10E4 enhanced tolerance to corm rot disease by releasing arachidonic acid which acts as conserved defense signal and induces jasmonic acid production in endophyte treated Crocus corms. This is first report on effect of a fungal endophyte on Crocus apocarotenoid metabolism and stress tolerance.

Involvement of Trichoderma harzianum Epl-1 Protein in the Regulation of Botrytis Virulence- and Tomato Defense-Related Genes

Several Trichoderma spp. are well known for their ability to: (i) act as important biocontrol agents against phytopathogenic fungi; (ii) function as biofertilizers; (iii) increase the tolerance of plants to biotic and abiotic stresses; and (iv) induce plant defense responses via the production and secretion of elicitor molecules. In this study, we analyzed the gene-regulation effects of Trichoderma harzianum Epl-1 protein during the interactions of mutant Δepl-1 or wild-type T. harzianum strains with: (a) the phytopathogen Botrytis cinerea and (b) with tomato plants, on short (24 h hydroponic cultures) and long periods (4-weeks old plants) after Trichoderma inoculation. Our results indicate that T. harzianum Epl-1 protein affects the in vitro expression of B. cinerea virulence genes, especially those involved in the botrydial biosynthesis (BcBOT genes), during the mycoparasitism interaction. The tomato defense-related genes were also affected, indicating that Epl-1 is involved in the elicitation of the salicylic acid pathway. Moreover, Epl-1 also regulates the priming effect in host tomato plants and contributes to enhance the interaction with the host tomato plant during the early stage of root colonization.

Recognition of endophytic Trichoderma species by leaf-cutting ants and their potential in a Trojan-horse management strategy

Interactions between leaf-cutting ants, their fungal symbiont (Leucoagaricus) and the endophytic fungi within the vegetation they carry into their colonies are still poorly understood. If endophytes antagonistic to Leucoagaricus were found in plant material being carried by these ants, then this might indicate a potential mechanism for plants to defend themselves from leaf-cutter attack. In addition, it could offer possibilities for the management of these important Neotropical pests. Here, we show that, for Atta sexdens rubropilosa, there was a significantly greater incidence of Trichoderma species in the vegetation removed from the nests-and deposited around the entrances-than in that being transported into the nests. In a no-choice test, Trichoderma-infested rice was taken into the nest, with deleterious effects on both the fungal gardens and ant survival. The endophytic ability of selected strains of Trichoderma was also confirmed, following their inoculation and subsequent reisolation from seedlings of eucalyptus. These results indicate that endophytic fungi which pose a threat to ant fungal gardens through their antagonistic traits, such as Trichoderma, have the potential to act as bodyguards of their plant hosts and thus might be employed in a Trojan-horse strategy to mitigate the negative impact of leaf-cutting ants in both agriculture and silviculture in the Neotropics. We posit that the ants would detect and evict such 'malign' endophytes-artificially inoculated into vulnerable crops-during the quality-control process within the nest, and, moreover, that the foraging ants may then be deterred from further harvesting of 'Trichoderma-enriched' plants.

Functional Characterization of Endophytic Fungal Community Associated with Oryza sativa L. and Zea mays L

In a natural ecosystem, the plant is in a symbiotic relationship with beneficial endophytes contributing huge impact on its host plant. Therefore, exploring beneficial endophytes and understanding its interaction is a prospective area of research. The present work aims to characterize the fungal endophytic communities associated with healthy maize and rice plants and to study the deterministic factors influencing plant growth and biocontrol properties against phytopathogens, viz, Pythium ultimum, Sclerotium oryzae, Rhizoctonia solani, and Pyricularia oryzae. A total of 123 endophytic fungi was isolated using the culture-dependent approach from different tissue parts of the plant. Most dominating fungal endophyte associated with both the crops belong to genus Fusarium, Sarocladium, Aspergillus, and Penicillium and their occurrence was not tissue specific. The isolates were screened for in vitro plant growth promotion, stress tolerance, disease suppressive mechanisms and based on the results, each culture from both the cereal crops was selected for further study. Acremonium sp. (ENF 31) and Penicillium simplicisssum (ENF22), isolated from maize and rice respectively could potentially inhibit the growth of all the tested pathogens with 46.47 ± 0.16 mm to 60.09 ± 0.04 mm range zone of inhibition for ENF31 and 35.48 ± 0.14 to 62.29 ± 0.15 mm for ENF22. Both significantly produce the defensive enzymes, ENF31 could tolerate a wide range of pH from 2 to 12, very important criteria, for studying plant growth in different soil types, especially acidic as it is widely prevalent here, making more land unsuitable for cultivation. ENF22 grows in pH range 3–12, with 10% salt tolerating ability, another factor of consideration. Study of root colonization during 7th to 30th days of growth phase reveals that ENF31 could colonize pleasantly in rice, though a maize origin, ranging from 1.02 to 1.21 log10 CFU/g root and in maize, it steadily colonizes ranging from 0.95 to 1.18 log10 CFU, while ENF22 could colonize from 0.98 to 1.24 Log10CFU/g root in rice and 1.01 to 1.24Log10CFU/g root in maize, just the reverse observed in Acremonium sp. Therefore, both the organism has the potency of a promising Bio-resource agent, that we must definitely explore to fill the gap in the agriculture industry.

Phytophthora megakarya and P. palmivora, Causal Agents of Black Pod Rot, Induce Similar Plant Defense Responses Late during Infection of Susceptible Cacao Pods

Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) cause black pod rot of Theobroma cacao L. (cacao). Of these two clade 4 species, Pmeg is more virulent and is displacing Ppal in many cacao production areas in Africa. Symptoms and species specific sporangia production were compared when the two species were co-inoculated onto pod pieces in staggered 24 h time intervals. Pmeg sporangia were predominantly recovered from pod pieces with unwounded surfaces even when inoculated 24 h after Ppal. On wounded surfaces, sporangia of Ppal were predominantly recovered if the two species were simultaneously applied or Ppal was applied first but not if Pmeg was applied first. Pmeg demonstrated an advantage over Ppal when infecting un-wounded surfaces while Ppal had the advantage when infecting wounded surfaces. RNA-Seq was carried out on RNA isolated from control and Pmeg and Ppal infected pod pieces 3 days post inoculation to assess their abilities to alter/suppress cacao defense. Expression of 4,482 and 5,264 cacao genes was altered after Pmeg and Ppal infection, respectively, with most genes responding to both species. Neural network self-organizing map analyses separated the cacao RNA-Seq gene expression profiles into 24 classes, 6 of which were largely induced in response to infection. Using KEGG analysis, subsets of genes composing interrelated pathways leading to phenylpropanoid biosynthesis, ethylene and jasmonic acid biosynthesis and action, plant defense signal transduction, and endocytosis showed induction in response to infection. A large subset of genes encoding putative Pr-proteins also showed differential expression in response to infection. A subset of 36 cacao genes was used to validate the RNA-Seq expression data and compare infection induced gene expression patterns in leaves and wounded and unwounded pod husks. Expression patterns between RNA-Seq and RT-qPCR were generally reproducible. The level and timing of altered gene expression was influenced by the tissues studied and by wounding. Although, in these susceptible interactions gene expression patterns were similar, some genes did show differential expression in a Phytophthora species dependent manner. The biggest difference was the more intense changes in expression in Ppal inoculated wounded pod pieces further demonstrating its rapid progression when penetrating through wounds.

Desorption electrospray ionization mass spectrometry imaging reveals chemical defense of Burkholderia seminalis against cacao pathogens

DESI-MSI of metabolites identified inB. seminalis.

Application of Plant-Growth-Promoting Fungi Trichoderma longibrachiatum T6 Enhances Tolerance of Wheat to Salt Stress through Improvement of Antioxidative Defense System and Gene Expression

Soil salinity is a serious problem worldwide that reduces agricultural productivity. Trichoderma longibrachiatum T6 (T6) has been shown to promote wheat growth and induce plant resistance to parasitic nematodes, but whether the plant-growth-promoting fungi T6 can enhance plant tolerance to salt stress is unknown. Here, we determined the effect of plant-growth-promoting fungi T6 on wheat seedlings' growth and development under salt stress, and investigated the role of T6 in inducing the resistance to NaCl stress at physiological, biochemical, and molecular levels. Wheat seedlings were inoculated with the strain of T6 and then compared with non-inoculated controls. Shoot height, root length, and shoot and root weights were measured on 15 days old wheat seedlings grown either under 150 mM NaCl or in a controlled setting without any NaCl. A number of colonies were re-isolated from the roots of wheat seedlings under salt stress. The relative water content in the leaves and roots, chlorophyll content, and root activity were significantly increased, and the accumulation of proline content in leaves was markedly accelerated with the plant growth parameters, but the content of leaf malondialdehyde under saline condition was significantly decreased. The antioxidant enzymes-superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in wheat seedlings were increased by 29, 39, and 19%, respectively, with the application of the strain of T6 under salt stress; the relative expression of SOD, POD, and CAT genes in these wheat seedlings were significantly up-regulated. Our results indicated that the strain of T6 ameliorated the adverse effects significantly, protecting the seedlings from salt stress during their growth period. The possible mechanisms by which T6 suppresses the negative effect of NaCl stress on wheat seedling growth may be due to the improvement of the antioxidative defense system and gene expression in the stressed wheat plants.

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.

Deciphering endophyte behaviour: the link between endophyte biology and efficacious biological control agents

Endophytes associate with the majority of plant species found in natural and managed ecosystems. They are regarded as extremely important plant partners that provide improved stress tolerance to the host compared with plants that lack this symbiosis. Fossil records of endophytes date back more than 400 million years, implicating these microorganisms in host plant adaptation to habitat transitions. However, it is only recently that endophytes, and their bioactive products, have received meaningful attention from the scientific community. The benefits some endophytes can confer on their hosts include plant growth promotion and survival through the inhibition of pathogenic microorganisms and invertebrate pests, the removal of soil contaminants, improved tolerance of low fertility soils, and increased tolerance of extreme temperatures and low water availability. Endophytes are extremely diverse and can exhibit many different biological behaviours. Not all endophyte technologies have been successfully commercialised. Of interest in the development of the next generation of plant protection products is how much of this is due to the biology of the particular endophytic microorganism. In this review, we highlight selected case studies of endophytes and discuss their lifestyles and behavioural traits, and discuss how these factors contribute towards their effectiveness as biological control agents.

Dose-dependent response of Trichoderma harzianum in improving drought tolerance in rice genotypes

This study demonstrates a dose-dependent response of Trichoderma harzianum Th-56 in improving drought tolerance in rice by modulating proline, SOD, lipid peroxidation product and DHN / AQU transcript level, and the growth attributes. In the present study, the effect of colonization of different doses of T. harzianum Th-56 strain in rice genotypes were evaluated under drought stress. The rice genotypes treated with increasing dose of T. harzianum strain Th-56 showed better drought tolerance as compared with untreated control plant. There was significant change in malondialdehyde, proline, higher superoxide dismutase level, plant height, total dry matter, relative chlorophyll content, leaf rolling, leaf tip burn, and the number of scorched/senesced leaves in T. harzianum Th-56 treated rice genotypes under drought stress. This was corroborated with altered expression of aquaporin and dehydrin genes in T. harzianum Th-56 treated rice genotypes. The present findings suggest that a dose of 30 g/L was the most effective in improving drought tolerance in rice, and its potential exploitation will contribute to the advancement of rice genotypes to sustain crop productivity under drought stress. Interaction studies of T. harzianum with three aromatic rice genotypes suggested that PSD-17 was highly benefitted from T. harzianum colonization under drought stress.

Morphological, Physiological, and Taxonomic Characterization of Actinobacterial Isolates Living as Endophytes of Cacao Pods and Cacao Seeds

Vascular plants are commonly colonized by endophytic actinobacteria. However, very little is known about the relationship between these microorganisms and cacao fruits. In order to determine the physiological and taxonomic relationships between the members of this community, actinobacteria were isolated from cacao fruits and seeds. Among the 49 isolates recovered, 11 morphologically distinct isolates were selected for further characterization. Sequencing of the 16S rRNA gene allowed the partition of the selected isolates into three phylogenetic clades. Most of the selected endophytic isolates belonged to the Streptomyces violaceusniger clade. Physiological characterization was carried out and a similarity index was used to cluster the isolates. However, clustering based on physiological properties did not match phylogenetic lineages. Isolates were also characterized for traits commonly associated with plant growth-promoting bacteria, including antibiosis and auxin biosynthesis. All isolates exhibited resistance to geldanamycin, whereas only two isolates were shown to produce this antibiotic. Endophytes were inoculated on radish seedlings and most isolates were found to possess plant growth-promoting abilities. These endophytic actinobacteria inhibited the growth of various plant pathogenic fungi and/or bacteria. The present study showed that S. violaceusniger clade members represent a significant part of the actinobacterial community living as endophytes in cacao fruits and seeds. While several members of this clade are known to be geldanamycin producers and efficient biocontrol agents of plant diseases, we herein established the endophytic lifestyle of some of these microorganisms, demonstrating their potential as plant health agents.

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.

Exploring plant growth-promotion actinomycetes from vermicompost and rhizosphere soil for yield enhancement in chickpea

The main objective of the present study was to isolate and characterize actinomycetes for their plant growth-promotion in chickpea. A total of 89 actinomycetes were screened for their antagonism against fungal pathogens of chickpea by dual culture and metabolite production assays. Four most promising actinomycetes were evaluated for their physiological and plant growth-promotion properties under in vitro and in vivo conditions. All the isolates exhibited good growth at temperatures from 20 °C to 40 °C, pH range of 7–11 and NaCl concentrations up to 8%. These were also found highly tolerant to Bavistin, slightly tolerant to Thiram and Captan (except VAI-7 and VAI-40) but susceptible to Benlate and Ridomil at field application levels and were found to produce siderophore, cellulase, lipase, protease, chitinase (except VAI-40), hydrocyanic acid (except VAI-7 and VAI-40), indole acetic acid and β-1,3-glucanase. When the four actinomycetes were evaluated for their plant growth-promotion properties under field conditions on chickpea, all exhibited increase in nodule number, shoot weight and yield. The actinomycetes treated plots enhanced total N, available P and organic C over the un-inoculated control. The scanning electron microscope studies exhibited extensive colonization by actinomycetes on the root surface of chickpea. The expression profiles for indole acetic acid, siderophore and β-1,3-glucanase genes exhibited up-regulation for all three traits and in all four isolates. The actinomycetes were identified as Streptomyces but different species in the 16S rDNA analysis. It was concluded that the selected actinomycetes have good plant growth-promotion and biocontrol potentials on chickpea.