Evidence for biotrophic lifestyle and biocontrol potential of dark septate endophyte Harpophora oryzae to rice blast disease

Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696)

The draft genome sequence of an agriculturally important actinobacterial species Amycolatopsis sp. BCA-696 was developed and characterized in this study. Amycolatopsis BCA-696 is known for its biocontrol properties against charcoal rot and also for plant growth-promotion (PGP) in several crop species. The next-generation sequencing (NGS)-based draft genome of Amycolatopsis sp. BCA-696 comprised of ~ 9.05 Mb linear chromosome with 68.75% GC content. In total, 8716 protein-coding sequences and 61 RNA-coding sequences were predicted in the genome. This newly developed genome sequence has been also characterized for biosynthetic gene clusters (BGCs) and biosynthetic pathways. Furthermore, we have also reported that the Amycolatopsis sp. BCA-696 produces the glycopeptide antibiotic vancomycin that inhibits the growth of pathogenic gram-positive bacteria. A comparative analysis of the BCA-696 genome with publicly available closely related genomes of 14 strains of Amycolatopsis has also been conducted. The comparative analysis has identified a total of 4733 core and 466 unique orthologous genes present in the BCA-696 genome The unique genes present in BCA-696 was enriched with antibiotic biosynthesis and resistance functions. Genome assembly of the BCA-696 has also provided genes involved in key pathways related to PGP and biocontrol traits such as siderophores, chitinase, and cellulase production.

Genome-Wide Identification and Characterization of Effector Candidates with Conserved Motif in Falciphora oryzae

Microbes employ effectors to disrupt immune responses and promote host colonization. Conserved motifs including RXLR, LFLAK-HVLVxxP (CRN), Y/F/WxC, CFEM, LysM, Chitin-bind, DPBB_1 (PNPi), and Cutinase have been discovered to play crucial roles in the functioning of effectors in filamentous fungi. Nevertheless, little is known about effectors with conserved motifs in endophytes. This research aims to discover the effector genes with conserved motifs in the genome of rice endophyte Falciphora oryzae. SignalP identified a total of 622 secreted proteins, out of which 227 were predicted as effector candidates by EffectorP. By utilizing HMM features, we discovered a total of 169 effector candidates with conserved motifs and three novel motifs. Effector candidates containing LysM, CFEM, DPBB_1, Cutinase, and Chitin_bind domains were conserved across species. In the transient expression assay, it was observed that one CFEM and one LysM activated cell death in tobacco leaves. Moreover, two CFEM and one Chitin_bind inhibited cell death induced by Bax protein. At various points during the infection, the genes' expression levels were increased. These results will help to identify functional effector proteins involving omics methods using new bioinformatics tools, thus providing a basis for the study of symbiosis mechanisms.

Endophytic fungus Falciphora oryzae enhances salt tolerance by modulating ion homeostasis and antioxidant defense systems in pepper

Endophytic fungi play an important role in the induction of plant tolerance to abiotic and biotic stresses. However, the role of endophytic fungi in the response of horticultural plants to plant stress remains largely unknown. Here, we addressed the role of the endophytic fungus Falciphora oryzae in enhancing salt tolerance in pepper (Capsicum annuum L.) by inoculation with the endophyte in the rhizosphere. F. oryzae could indeed colonize the roots of pepper and significantly improved the tolerance of pepper to salt stress. This resulted in increased plant growth and photosynthetic performance compared with control plants, which was accompanied by increases in indole acetic acid and abscisic acid biosynthesis and signaling. Furthermore, inoculation with F. oryzae significantly upregulated a subset of transcripts involved in Na+ homeostasis (NHX3, NHX6, NHX8, HKT2-1, and SOS1) and the high-affinity K+ transporter protein-related gene HAK1 in the leaves to maintain Na+ /K+ homeostasis. Moreover, the activity of antioxidant enzymes (catalase, peroxidase, glutathione, and ascorbate peroxidase), the content of glutathione, the transcript level of genes related to antioxidants (catalase, ascorbate peroxidase, glutathione reductase, peroxidase, glutamate-cysteine ligase, and glutamine synthetase) in the leaves were significantly upregulated after inoculation with F. oryzae, which led to decreased levels of lipid peroxidation (malondialdehyde) and reactive oxygen species. These results indicate that inoculation with F. oryzae can enhance the salt tolerance of pepper by promoting ion homeostasis and upregulating antioxidant defense systems.

Growth of alfalfa in the presence of metabolites from a dark septate endophyte strain Alternaria sp. 17463 cultured with a nonionic surfactant and emulsifier

AIM

Dark septate endophytes (DSE) were widely used in the agriculture and ecological restoration. The objective of this work was to assess the effect of culture media nonionic surfactant and emulsifier on the biomass and metabolites of DSE strain Alternaria sp. 17463.

METHODS AND RESULTS

Changes in the composition of DSE metabolites following the addition of Tween 80 during liquid culture of a DSE fungus were analyzed and used in growth tests of alfalfa.Shaking flask fermentation was carried out and the surfactant was fed to the fungus during the fermentation. The residual sugar content and pH declined significantly in the medium and the biomass of DSE increased by 7.27% over controls with no surfactant. Metabolomic analysis showed that adding the surfactant significantly increased the content of 63 metabolites (P < 0.05). These include lipids and lipid-like molecules, organooxygen compounds, amino acids and organic acids, and flavonoids. Enrichment analysis of metabolic pathways indicates that surfactant addition promoted carbohydrate metabolism and amino acid synthesis. A plant hydroponic experiment indicated that these changes in metabolites altered the root structure of alfalfa seedlings. They also promoted significant increases in root length and root surface area, and increased alfalfa total biomass by 50.2%.

CONCLUSIONS

The addition of the surfactant promoted sugar utilization by the DSE fungus and increased the synthesis of lipids and amino acids, resulting in the ability of the fungal metabolites to change root structure and promote plant growth.

Induction of systemic resistance in Solanum lycopersicum and Capsicum annum seedlings against Fusarium wilt by Streptomyces bioformulations

Plant diseases induced by various phytopathogens pose a significant threat to contemporary agricultural systems around the world. In modern agriculture, the use of pesticides is still a valuable and effective method to control plant diseases. However, agrochemicals are becoming less popular because of the accretion of toxic compounds perilous and potentially hazardous to humans and the environment. Taking into consideration these aspects, the present study was conducted to explore the biocontrol potential of an endophytic Streptomyces sp. SP5 bioformulations against Fusarium wilt. Three bioformulations were prepared using cell biomass and different carriers, i.e., B1 (talc-kaolin), B2 (MgSO4/glycerol/Na-alginate/talc/Ca-lignosulfonate), and B3 (calcium carbonate/CMC/talc). Apart from antagonistic action against Fusarium wilt, the influence of bioformulations on plant growth and systemic resistance was investigated by analyzing morphological parameters (root length, shoot length, root weight, shoot weight), biochemical parameters (photosynthetic pigments, non-enzymatic antioxidants), and induction of antioxidative enzymes, e.g., catalase (CAT), ascorbate peroxidase (APX), guaiacol peroxidase (GPX), and superoxide dismutase (SOD), in S. lycopersicum and C. annum seedlings. The results revealed that Streptomyces bioformulations effectively controlled Fusarium wilt in S. lycopersicum and C. annum (82.6-83.4% and 81.8-100%, respectively). Besides reducing disease prevalence, bioformulations significantly increased all the morphological parameters and increased the activity of antioxidative enzymes, i.e., CAT, APX, GPX, and SOD, in plants. The current findings display that bioformulations can be utilized as environment-friendly biocontrol agents against Fusarium wilt and also as plant growth promoters.

Effects of Flubeneteram on Inhibiting the Development of Puccinia striiformis f. sp. tritici in Wheat Leaves

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a serious threat to wheat production, and the application of fungicides is one of the most important means for controlling the disease. The purpose of this study is to determine the effects of a new succinate dehydrogenase inhibitor (SDHI) fungicide, flubeneteram, on reducing stripe rust. The baseline sensitivity of 173 Pst isolates from 13 provinces of China to flubeneteram was determined. Flubeneteram displayed significant effects on inhibiting SDH enzymes of Pst. Histological observations showed that after flubeneteram application, the formation and development of Pst hyphae and haustoria were significantly inhibited, and the structures were destroyed. Flubeneteram primed wheat for salicylic acid-induced defenses via upregulating pathogenesis-related genes (PR1 and PR2). Altogether, our study is the first to provide evidence that flubeneteram induces wheat defense against Pst infection. The findings indicate that flubeneteram could be an effective fungicide for managing stripe rust.

Polydomus karssenii gen. nov. sp. nov. is a dark septate endophyte with a bifunctional lifestyle parasitising eggs of plant parasitic cyst nematodes (Heterodera spp.)

In this study fungal strains were investigated, which had been isolated from eggs of the cereal cyst nematode Heterodera filipjevi, and roots of Microthlaspi perfoliatum (Brassicaceae). The morphology, the interaction with nematodes and plants and the phylogenetic relationships of these strains originating from a broad geographic range covering Western Europe to Asia Minor were studied. Phylogenetic analyses using five genomic loci including ITSrDNA, LSUrDNA, SSUrDNA, rpb2 and tef1-α were carried out. The strains were found to represent a distinct phylogenetic lineage most closely related to Equiseticola and Ophiosphaerella, and Polydomus karssenii (Phaeosphaeriaceae, Pleosporales) is introduced here as a new species representing a monotypic genus. The pathogenicity tests against nematode eggs fulfilled Koch's postulates using in vitro nematode bioassays and showed that the fungus could parasitise its original nematode host H. filipjevi as well as the sugar beet cyst nematode H. schachtii, and colonise cysts and eggs of its hosts by forming highly melanised moniliform hyphae. Light microscopic observations on fungus-root interactions in an axenic system revealed the capacity of the same fungal strain to colonise the roots of wheat and produce melanised hyphae and microsclerotia-like structure typical for dark septate endophytes. Confocal laser scanning microscopy further demonstrated that the fungus colonised the root cells by predominant intercellular growth of hyphae, and frequent formation of appressorium-like as well as penetration peg-like structures through internal cell walls surrounded by callosic papilla-like structures. Different strains of the new fungus produced a nearly identical set of secondary metabolites with various biological activities including nematicidal effects irrespective of their origin from plants or nematodes.

Endophytes and their potential in biotic stress management and crop production

Biotic stress is caused by harmful microbes that prevent plants from growing normally and also having numerous negative effects on agriculture crops globally. Many biotic factors such as bacteria, fungi, virus, weeds, insects, and nematodes are the major constrains of stress that tends to increase the reactive oxygen species that affect the physiological and molecular functioning of plants and also led to the decrease in crop productivity. Bacterial and fungal endophytes are the solution to overcome the tasks faced with conventional farming, and these are environment friendly microbial commodities that colonize in plant tissues without causing any damage. Endophytes play an important role in host fitness, uptake of nutrients, synthesis of phytohormone and diminish the injury triggered by pathogens via antibiosis, production of lytic enzymes, secondary metabolites, and hormone activation. They are also reported to help plants in coping with biotic stress, improving crops and soil health, respectively. Therefore, usage of endophytes as biofertilizers and biocontrol agent have developed an eco-friendly substitute to destructive chemicals for plant development and also in mitigation of biotic stress. Thus, this review highlighted the potential role of endophytes as biofertilizers, biocontrol agent, and in mitigation of biotic stress for maintenance of plant development and soil health for sustainable agriculture.

Plantago lagopus extract as a green fungicide induces systemic resistance against Rhizoctonia root rot disease in tomato plants

Extensive use of chemical control agents and fungicides typically leads to numerous risks to human health and the environment. Using plant extracts as natural substances represents a dual key for the environment and sustainable food production, as it reduces the input of synthetic pesticides into the environment and/or controls plant pathogens. For the first time, a Plantago lagopus ethanolic extract has been characterized and evaluated for its protective and curative effects against Rhizoctonia solani in tomato plants. The results showed that P. lagopus extract (10 μg/ml) completely inhibited R. solani mycelial growth in vitro. At 20 days of post fungal inoculation, the results demonstrated that using P. lagopus extract (100 μg/ml) in vivo enhanced tomato plant growth by significantly increasing shoot and root parameters in protective and curative treatments. Furthermore, the protective and curative treatments significantly reduced the disease index by 18.66 and 38.66%, respectively. Induction of systemic resistance with upregulation of PR-1 and PR-2 and a significant increase in the transcriptional levels of PR-3 and CHS in all P. lagopus extract-treated tomato plants were reported compared to untreated plants. HPLC analysis showed that the most common polyphenolic components detected in P. lagopus extract were rutin (74206.3 mg/kg), naringenin (2388.74 mg/kg), quercetin (1249.13 mg/kg), and p-hydroxybenzoic acid (1035.87 mg/kg). In addition, the ellagic acid (798.47 mg/kg), vanillic acid (752.55 mg/kg), catechol (648.89 mg/kg), cinnamic acid (332.51 mg/kg), ferulic acid (296.32 mg/kg), benzoic acid (295.95 mg/kg), and chlorogenic acid (116.63 mg/kg) were also reported. Our study is the first to show that P. lagopus extract can help plants fight off R. solani fungal infection. Furthermore, the findings imply that using the P. lagopus extract as a natural biocontrol agent could be a sustainable strategy to manage plant fungal diseases.

The influence of endophytes on rice fitness under environmental stresses

KEY MESSAGE

Endophytes are crucial for the promotion of rice growth and stress tolerance and can be used to increase rice crop yield. Endophytes can thus be exploited in biotechnology and genetic engineering as eco-friendly and cost-effective means for the development of high-yielding and stress-tolerant rice plants. Rice (Oryza sativa) crop is continuously subjected to biotic and abiotic stresses, compromising growth and consequently yield. The situation is exacerbated by climate change impacting on ecosystems and biodiversity. Genetic engineering has been used to develop stress-tolerant rice, alongside physical and chemical methods to mitigate the effect of these stresses. However, the success of these strategies has been hindered by short-lived field success and public concern on adverse effects associated. The limited success in the field of stress-tolerant cultivars developed through breeding or transgenic approaches is due to the complex nature of stress tolerance as well as to the resistance breakdown caused by accelerated evolution of pathogens. It is therefore necessary to develop novel and acceptable strategies to enhance rice stress tolerance and durable resistance and consequently improve yield. In the last decade, plant growth promoting (PGP) microbes, especially endophytes, have drawn the attention of agricultural scientists worldwide, due to their ability to mitigate environmental stresses in crops, without causing adverse effects. Increasing evidence indicates that endophytes effectively confer fitness benefits also to rice under biotic and abiotic stress conditions. Endophyte-produced metabolites can control the expression of stress-responsive genes and improve the physiological performance and growth of rice plants. This review highlights the current evidence available for PGP microbe-promoted tolerance of rice to abiotic stresses such as salinity and drought and to biotic ones, with special emphasis on endophytes. Associated molecular mechanisms are illustrated, and prospects for sustainable rice production also in the light of the impending climate change, discussed.

Insights into the beneficial roles of dark septate endophytes in plants under challenging environment: resilience to biotic and abiotic stresses

Dark septate endophytes (DSE) exert a plethora of effects in regulating plant growth, signalling and stress tolerance. The advent of metagenomics has led to the identification of various species of DSE to be associated with plant organs. They are known to modulate growth, nutrient uptake, phytohormone biosynthesis and production of active bioconstituents in several plants. The interactions between the DSE and host plants are mostly mutualistic but they can also be neutral or exhibit negative interactions. The DSE has beneficial role in removal/sequestration of toxic heavy metals from various environmental sites. Here, we discuss the beneficial role of DSE in enhancing plant tolerance to heavy metal stress, drought conditions, high salinity and protection from various plant pathogens. Furthermore, the underlying mechanism of stress resilience facilitated by DSE-plant interaction has also been discussed. The article also provides insights to some important future perspectives associated with DSE-mediated phytoremediation and reclamation of polluted land worldwide thus facilitating sustainable agriculture.

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 New Species in Pseudophialophora From Wild Rice and Beneficial Potential

Wild rice (Oryza granulata) is a natural resource pool containing abundant unknown endophytic fungi species. There are few reports on the endophytic fungi in wild rice. Here, one isolate recovered from wild rice roots was identified as a new species Pseudophialophora oryzae sp. nov based on the molecular phylogeny and morphological characteristics. Fluorescent protein-expressing P. oryzae was used to monitor the fungal colonization pattern. Hyphae invaded the epidermis to the inner cortex but not into the root stele. The inoculation of P. oryzae promoted the rice growth, with the growth parameters of chlorophyll content, shoot height, root length, fresh shoot weight, fresh root weight and dry weight increasing by 24.10, 35.32, 19.35, 90.00, 33.3, and 79.17%, respectively. P. oryzae induced up-regulation of nitrate transporter OsPTR9 and potassium transporter OsHAK16 by 7.28 ± 0.84 and 2.57 ± 0.80 folds, promoting nitrogen and potassium elements absorption. In addition, P. oryzae also conferred a systemic resistance against rice blast, showing a 72.65 and 75.63% control rate in sterile plates and potting conditions. This systemic resistance was mediated by the strongly up-regulated expression of resistance-related genes NAC, OsSAUR2, OsWRKY71, EL5, and PR1α. Since P. oryzae can promote rice growth, biomass and induce systemic disease resistance, it can be further developed as a new biogenic agent for agricultural production, providing a new approach for biocontrol of rice blast.

Novel Genetic Dysregulations and Oxidative Damage in Fusarium graminearum Induced by Plant Defense Eliciting Psychrophilic Bacillus atrophaeus TS1

This study elaborates inter-kingdom signaling mechanisms, presenting a sustainable and eco-friendly approach to combat biotic as well as abiotic stress in wheat. Fusarium graminearum is a devastating pathogen causing head and seedling blight in wheat, leading to huge yield and economic losses. Psychrophilic Bacillus atrophaeus strain TS1 was found as a potential biocontrol agent for suppression of F. graminearum under low temperature by carrying out extensive biochemical and molecular studies in comparison with a temperate biocontrol model strain Bacillus amyloliquefaciens FZB42 at 15 and 25 °C. TS1 was able to produce hydrolytic extracellular enzymes as well as antimicrobial lipopeptides, i.e., surfactin, bacillomycin, and fengycin, efficiently at low temperatures. The Bacillus strain-induced oxidative cellular damage, ultrastructural deformities, and novel genetic dysregulations in the fungal pathogen as the bacterial treatment at low temperature were able to downregulate the expression of newly predicted novel fungal genes potentially belonging to necrosis inducing protein families (fgHCE and fgNPP1). The wheat pot experiments conducted at 15 and 25 °C revealed the potential of TS1 to elicit sudden induction of plant defense, namely, H₂O₂ and callose enhanced activity of plant defense-related enzymes and induced over-expression of defense-related genes which accumulatively lead to the suppression of F. graminearum and decreased diseased leaf area.

Paediatric Antimicrobial Stewardship for Respiratory Infections in the Emergency Setting: A Systematic Review

Antimicrobial resistance occurs due to the propensity of microbial pathogens to develop resistance to antibiotics over time. Antimicrobial stewardship programs (ASPs) have been developed in response to this growing crisis, to limit unnecessary antibiotic prescription through initiatives such as education-based seminars, prescribing guidelines, and rapid respiratory pathogen (RRP) testing. Paediatric patients who present to the emergency setting with respiratory symptoms are a particularly high-risk population susceptible to inappropriate antibiotic prescribing behaviours and are therefore an ideal cohort for focused ASPs. The purpose of this systematic review was to assess the efficacy and safety of ASPs in this clinical context. A systematic search of PubMed, Medline, EMBASE and the Cochrane Database of Systematic Reviews was conducted to review the current evidence. Thirteen studies were included in the review and these studies assessed a range of stewardship interventions and outcome measures. Overall, ASPs reduced the rates of antibiotic prescription, increased the prescription of narrow-spectrum antibiotics, and shortened the duration of antibiotic therapy. Multimodal interventions that were education-based and those that used RRP testing were found to be the most effective. Whilst we found strong evidence that ASPs are effective in reducing antibiotic prescribing, further studies are required to assess whether they translate to equivalent clinical outcomes.

Advances in the Role of Dark Septate Endophytes in the Plant Resistance to Abiotic and Biotic Stresses

Endophytic fungi have been studied in recent decades to understand how they interact with their hosts, the types of relationships they establish, and the potential effects of this interaction. Dark septate endophytes (DSE) are isolated from healthy plants and form melanised structures in the roots, including inter- and intracellular hyphae and microsclerotia, causing low host specificity and covering a wide geographic range. Many studies have revealed beneficial relationships between DSE and their hosts, such as enhanced plant growth, nutrient uptake, and resistance to biotic and abiotic stress. Furthermore, in recent decades, studies have revealed the ability of DSE to mitigate the negative effects of crop diseases, thereby highlighting DSE as potential biocontrol agents of plant diseases (BCAs). Given the importance of these fungi in nature, this article is a review of the role of DSE as BCAs. The findings of increasing numbers of studies on these fungi and their relationships with their plant hosts are also discussed to enable their use as a tool for the integrated management of crop diseases and pests.

Dark septate endophyte Falciphora oryzae-assisted alleviation of cadmium in rice

Dark septate endophytes (DSEs) are the typical representatives of root endophytic fungi in heavy metal (HM)-contaminated environments. However, little is known about their roles in the HMs tolerance of hosts and the underlying mechanism. Here, we investigated the biological roles and molecular mechanisms of a DSE strain Falciphora oryzae in alleviating cadmium (Cd) toxicities in rice. It was found that F. oryzae possessed a capacity of accumulating Cd in its vacuoles and chlamydospores. During symbiosis, F. oryzae conferred improved Cd tolerance to rice, decreasing Cd accumulation in roots and translocation to shoots. F. oryzae alleviated Cd toxicity to rice by sequestering Cd in its vacuoles. Further application of F. oryzae as fertilizer in the field could reduce Cd content in rice grains. We identified a SNARE Syntaxin 1 gene through proteomics, which participated in Cd tolerance of F. oryzae by regulating chlamydospore formation and vacuole enlargement. This study provided novel insights into how the DSEs and their host plants combat Cd stress.

The Endophytic Fungus Piriformospora Indica-Assisted Alleviation of Cadmium in Tobacco

Increasing evidence suggests that the endophytic fungus Piriformospora indica helps plants overcome various abiotic stresses, especially heavy metals. However, the mechanism of heavy metal tolerance has not yet been elucidated. Here, the role of P. indica in alleviating cadmium (Cd) toxicities in tobacco was investigated. It was found that P. indica improved Cd tolerance to tobacco, increasing Cd accumulation in roots but decreasing Cd accumulation in leaves. The colonization of P. indica altered the subcellular repartition of Cd, increasing the Cd proportion in cell walls while reducing the Cd proportion in membrane/organelle and soluble fractions. During Cd stress, P. indica significantly enhanced the peroxidase (POD) activity and glutathione (GSH) content in tobacco. The spatial distribution of GSH was further visualized by Raman spectroscopy, showing that GSH was distributed in the cortex of P. indica-inoculated roots while in the epidermis of the control roots. A LC-MS/MS-based label-free quantitative technique evaluated the differential proteomics of P. indica treatment vs. control plants under Cd stress. The expressions of peroxidase, glutathione synthase, and photosynthesis-related proteins were significantly upregulated. This study provided extensive evidence for how P. indica enhances Cd tolerance in tobacco at physiological, cytological, and protein levels.

An efficient genetic manipulation protocol for dark septate endophyte Falciphora oryzae

OBJECTIVE

To investigate the protoplast preparation and transformation system of endophytic fungus Falciphora oryzae.

RESULTS

F. oryzae strain obtained higher protoplast yield and effective transformation when treated with enzyme digestion solution containing 0.9 M KCl solution and 10 mg mL^-1 glucanase at 30 °C with shaking at 80 rpm for 2-3 h. When the protoplasts were plated on a regenerations-agar medium containing 1 M sucrose, the re-growth rate of protoplasts was the highest. We successfully acquired green fluorescent protein-expressing transformants by transforming the pKD6-GFP vector into protoplasts. Further, the GFP expression in fungal hyphae possessed good stability and intensity during symbiosis in rice roots.

CONCLUSIONS

This study provided a protoplast transformation system of F. oryzae, creating opportunities for future genetic research in other endophytic fungi.

Effects of Dark Septate Endophytes Strain A024 on Damping-off Biocontrol, Plant Growth and the Rhizosphere Soil Enviroment of Pinus sylvestris var. mongolica Annual Seedlings

Dark septate endophytes (DSEs) exert a vital role in promoting plant growth, improving mineral absorption, biological disease control, and enhancing plant stress resistance. The effects of dark septate endophyte strain, Phialocephala bamuru A024 on damping-off biocontrol, plant development, nutrients within the rhizosphere soil, as well as bacterial communities in the annual seedlings of P. sylvestris var. Mongolica were studied. According to our findings, following P. bamuru A024 inoculation, the damping-off disease morbidity decreased significantly compared with control, some physiological indices such as β-1,3-glucanase, chitinase enzyme activity as well as a soluble protein and proline content in P. sylvestris var. mongolica were elevated under R. solani stress. After inoculation with P. bamuru A024, the biomass in seedlings, nutrients in soil, root structure index, together with activities of soil enzymes were remarkably up-regulated relative to control (p < 0.05). As suggested by the results of high-throughput sequencing, the microbial structure in the rhizosphere soil of the P. sylvestris var. mongolica showed significant differences (p < 0.05) after P. bamuru A024 inoculation compared to control treatment and the rhizosphere soil bacterial community structure after DSE A024 inoculation was positively correlated to the main soil nutrition indices.

Plant performance of enhancing licorice with dual inoculating dark septate endophytes and Trichoderma viride mediated via effects on root development

BACKGROUND

This study aimed to assess whether licorice (Glycyrrhiza uralensis) can benefit from dual inoculation by Trichoderma viride and dark septate endophytes (DSE) isolated from other medicinal plants.

METHODS

First, we isolated and identified three DSE (Paraboeremia putaminum, Scytalidium lignicola, and Phoma herbarum) and Trichoderma viride from medicinal plants growing in farmland of China. Second, we investigated the influences of these three DSE on the performance of licorice at different T. viride densities (1 × 106, 1 × 107, and 1 × 108 CFU/mL) under sterilised condition in a growth chamber.

RESULTS

Three DSE strains could colonize the roots of licorice, and they established a positive symbiosis with host plants depending on DSE species and T. viride densities. Inoculation of P. putaminum increased the root biomass, length, surface area, and root:shoot ratio. S. lignicola increased the root length, diameter and surface area and decreased the root:shoot ratio. P. herbarum increased the root biomass and surface area. T. viride increased the root biomass, length, and surface area. Structural equation model (SEM) analysis showed that DSE associated with T. viride augmented plant biomass and height, shoot branching, and root surface area. Variations in root morphology and biomass were attributed to differences in DSE species and T. viride density among treatments. P. putaminum or P. herbarum with low- or medium T. viride density and S. lignicola with low- or high T. viride density improved licorice root morphology and biomass.

CONCLUSIONS

DSE isolated from other medicinal plants enhanced the root growth of licorice plants under different densities T. viride conditions and may also be used to promote the cultivation of medicinal plants.

Dimethyl disulfide exerts antifungal activity against Sclerotinia minor by damaging its membrane and induces systemic resistance in host plants

Microbial volatile compounds (MVCs) significantly influence the growth of plants and phytopathogens. However, the practical application of MVCs at the field level is limited by the fact that the concentrations at which these compounds antagonize the pathogens are often toxic for the plants. In this study, we investigated the effect of dimethyl disulfide (DMDS), one of the MVCs produced by microorganisms, on the fitness of tomato plants and its fungicidal potential against a fungal phytopathogen, Sclerotinia minor. DMDS showed strong fungicidal and plant growth promoting activities with regard to the inhibition of mycelial growth, sclerotia formation, and germination, and reduction of disease symptoms in tomato plants infected with S. minor. DMDS exposure significantly upregulated the expression of genes related to growth and defense against the pathogen in tomato. Especially, the overexpression of PR1 and PR5 suggested the involvement of the salicylic acid pathway in the induction of systemic resistance. Several morphological and ultrastructural changes were observed in the cell membrane of S. minor and the expression of ergosterol biosynthesis gene was significantly downregulated, suggesting that DMDS damaged the membrane, thereby affecting the growth and pathogenicity of the fungus. In conclusion, the tripartite interaction studies among pathogenic fungus, DMDS, and tomato revealed that DMDS played roles in antagonizing pathogen as well as improving the growth and disease resistance of tomato. Our findings provide new insights into the potential of volatile DMDS as an effective tool against sclerotial rot disease.

The Effectiveness of a Dark Septate Endophytic Fungus, Cladophialophora chaetospira SK51, to Mitigate Strawberry Fusarium Wilt Disease and With Growth Promotion Activities

Strawberry Fusarium wilt, caused by the virulent fungus Fusarium oxysporum formae speciales fragariae (Fof) is a devastating soil-borne disease that causes severe production losses worldwide, including Japan. Fof is one of the top 10 fungal pathogens that threaten global crop security, and a method to effectively control this pathogen has yet to be found. This study aimed to investigate the effectiveness of dark septate endophytic (DSE) fungi against Fof to develop an efficient, effective, and environmentally friendly approach to improve plant health and fitness. A total of 19 fungal isolates were assessed, out of which three (SK47, SK48, and SK51) were selected based on their effectiveness in disease suppression in controlled growth chamber conditions using a soil system. Isolates SK47, SK48, and SK51 suppressed disease severity by 85.71, 61.90, and 90.48%, respectively. Molecular identification based on highly conserved small subunit (SSU), internal transcribed spacer (ITS), and large subunit (LSU) nrRNA regions identified these isolates as DSE Exophiala sp., Exophiala pisciphila, and Cladophialophora chaetospira, respectively. The sequences were deposited under accession numbers MN811693-MN811695 in the GenBank database. Notably, our results revealed that isolate C. chaetospira SK51 possessed superior growth promotion activities as well as disease suppression by significantly increased plant growth parameters (shoot and root dry mass, chlorophyll content, flower bud initiation, and number of fruit) in comparison to control plants and other two fungal candidates. Root colonization by C. chaetospira SK51 was visualized, and it was confirmed that the symbiosis with strawberry plants occurred successfully. Our results provide new insights in the application of DSE fungus C. chaetospira SK51 as a biocontrol agent on strawberry plants could promote plant growth, flower bud initiation, and fruit formation. C. chaetospira SK51 exhibited remarkable beneficial traits for the host plant, and it can potentially be applied in the development of new, safe, and effective treatments as an alternative to chemical fertilizers and fungicides for sustainable crop protection.

Dark septate endophytic fungi mitigate the effects of salt stress on cowpea plants

The association of plant with microorganisms, such as dark septate endophytic fungi, has mitigated the harmful effects of chemical, physical, and biological agents on the host. The objective of this work was to evaluate the interaction of the dark septate endophytic fungi with cowpea plants under salt stress. Endophytic fungi were isolated from Vochysia divergens root system, and molecular identification of fungi was performed by sequencing the ITS region. We selected and identified Sordariomycetes sp1-B'2 and Melanconiella elegans-21W2 for their ability to infect V. divergens root in vitro with development of typical dark septate fungi structures. Cowpea plants-inoculated or not inoculated with Sordariomycetes sp1-B'2 and M. elegans 21W2-were cultivated in 5-L pots under greenhouse conditions and submitted to four different electrical conductivities of irrigation water (1.2, 2.2, 3.6, and 5.0 dS m-1). The salinity caused decrease in leaf concentration of K and increased leaf concentration of calcium, sodium, and chlorine; and no influence of dark septate endophytic fungi was observed in these responses. On the other hand, root colonization with Sordariomycetes sp1-B'2 and M. elegans 21W2 resulted in improved nutrition with N and P in cowpea under salt stress, favoring the growth and rate of liquid photosynthesis. However, such positive responses were evident only at moderate levels of salinity.

Biocontrol by Fusarium oxysporum Using Endophyte-Mediated Resistance

Interactions between plants and the root-colonizing fungus Fusarium oxysporum (Fo) can be neutral, beneficial, or detrimental for the host. Fo is infamous for its ability to cause wilt, root-, and foot-rot in many plant species, including many agronomically important crops. However, Fo also has another face; as a root endophyte, it can reduce disease caused by vascular pathogens such as Verticillium dahliae and pathogenic Fo strains. Fo also confers protection to root pathogens like Pythium ultimum, but typically not to pathogens attacking above-ground tissues such as Botrytis cinerea or Phytophthora capsici. Endophytes confer biocontrol either directly by interacting with pathogens via mycoparasitism, antibiosis, or by competition for nutrients or root niches, or indirectly by inducing resistance mechanisms in the host. Fo endophytes such as Fo47 and CS-20 differ from Fo pathogens in their effector gene content, host colonization mechanism, location in the plant, and induced host-responses. Whereas endophytic strains trigger localized cell death in the root cortex, and transiently induce immune signaling and papilla formation, these responses are largely suppressed by pathogenic Fo strains. The ability of pathogenic strains to compromise immune signaling and cell death is likely attributable to their host-specific effector repertoire. The lower number of effector genes in endophytes as compared to pathogens provides a means to distinguish them from each other. Co-inoculation of a biocontrol-conferring Fo and a pathogenic Fo strain on tomato reduces disease, and although the pathogen still colonizes the xylem vessels this has surprisingly little effect on the xylem sap proteome composition. In this tripartite interaction the accumulation of just two PR proteins, NP24 (a PR-5) and a β-glucanase, was affected. The Fo-induced resistance response in tomato appears to be distinct from induced systemic resistance (ISR) or systemic acquired resistance (SAR), as the phytohormones jasmonate, ethylene, and salicylic acid are not required. In this review, we summarize our molecular understanding of Fo-induced resistance in a model and identify caveats in our knowledge.

Endophytic fungus Falciphora oryzae promotes lateral root growth by producing indole derivatives after sensing plant signals

The endophytic fungus Falciphora oryzae was initially isolated from wild rice (Oryza granulata) and colonizes many crop species and promotes plant growth. However, the molecular mechanisms underlying F. oryzae-mediated growth promotion are still unknown. We found that F. oryzae was able to colonize Arabidopsis thaliana. The most dramatic change after F. oryzae inoculation was observed in the root architecture, as evidenced by increased lateral root growth but reduced primary root length, similar to the effect of auxin, a significant plant growth hormone. The expression of genes responsible for auxin biosynthesis, transport, and signalling was regulated in Arabidopsis roots after F. oryzae cocultivation. Indole derivatives were detected at significantly higher levels in liquid media after cocultivation compared with separate cultivation of Arabidopsis and F. oryzae. Consistently, the expression of indole biosynthetic genes was highly upregulated in F. oryzae upon treatment with Arabidopsis exudates. Global analysis of Arabidopsis gene expression at the early stage after F. oryzae cocultivation suggested that signals were exchanged to initiate Arabidopsis-F. oryzae interactions. All these results suggest that signalling molecules from Arabidopsis roots are perceived by F. oryzae and induce the biosynthesis of indole derivatives in F. oryzae, consequently stimulating Arabidopsis lateral root growth.

Tolerance of dark septate endophytic fungi (DSE) to agrochemicals in vitro

Dark septate endophytes (DSE) are a heterogeneous group of fungi, mostly belonging to the Phylum Ascomycota, that are involved in a mutualistic symbiosis with plant roots. The aim of this study is to evaluate the behavior of two strains of DSE isolated from wheat roots of two cropping areas in the province of Buenos Aires, Argentina, against some agrochemicals. Of all the isolates obtained, two strains were identified as Alternaria alternata and Cochliobolus sp. These DSE were found to be tolerant to glyphosate, carbendazim and cypermethrin when evaluated at the recommended agronomic dose (AD), 2 AD and, in some cases, 10 AD. This work contributes to the study of the biology of this group of fungi and their tolerance in the presence of xenobiotics widely used in agriculture.

Secondary Metabolites of The Endophytic Fungus Alternaria alternata JS0515 Isolated from Vitex rotundifolia and Their Effects on Pyruvate Dehydrogenase Activity

The fungal strain Alternaria alternata JS0515 was isolated from Vitex rotundifolia (beach vitex). Twelve secondary metabolites, including one new altenusin derivative (1), were isolated. The isolated metabolites included seven known altenusin derivatives (2–8), two isochromanones (9, 10), one perylenequinone (11), and one benzocycloalkanone (12). Their structures were determined via 1D and 2D nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and computational electronic circular dichroism (ECD) analysis. Compounds 3 and 11 increased pyruvate dehydrogenase (PDH) activity in AD-293 human embryonic kidney cells and significantly inhibited PDH phosphorylation. The IC₅₀ values of 3 and 11 were 32.58 and 27.82 μM, respectively.

Differential interaction of the dark septate endophyte Cadophora sp. and fungal pathogens in vitro and in planta

Dark septate endophytes (DSEs) present a group of widespread root-colonizing fungi. The role of these endophytes in ecosystems and their interactions with plant pathogens are not well understood. In the current study, we assessed the antagonistic potential of the model DSE Cadophora sp. against the tomato soilborne pathogens Rhizoctonia solani, Pythium aphanidermatum and Verticillium dahliae. To investigate their interactions, we conducted in vitro assays followed by a greenhouse experiments in which tomato plants were inoculated with different combinations of the DSE and pathogens. RNA accumulation of selected tomato pathogenesis-related genes and of Cadophora sp. genes with putative antifungal function was analyzed. Cadophora sp. inhibited the growth of the fungal pathogens in vitro and vice versa; a negative impact of the pathogens on the growth of the DSE was also detected. In roots, however, this mutual negative interaction could not be observed. Expression analyses of plant genes could not explain this differential effect, but among the Cadophora sp. genes analyzed, a gene coding for a chalcone synthase was downregulated in planta. The data indicate that plants can change the interaction between fungi and, therefore, in vitro detected antagonism does not necessarily reflect the situation inside the plant.

Flowering-mediated root-fungus symbiosis loss is related to jasmonate-dependent root soluble sugar deprivation

The role of flowering in root-fungal symbiosis is not well understood. Because flowering and fungal symbionts are supported by carbohydrates, we hypothesized that flowering modulates root-beneficial fungal associations through alterations in carbohydrate metabolism and transport. We monitored fungal colonization and soluble sugars in the roots of Arabidopsis thaliana following inoculation with a mutualistic fungus Phomopsis liquidambari across different plant developmental stages. Jasmonate signalling of wild-type plants, sugar transport, and root invertase of wild-type and jasmonate-insensitive plants were exploited to assess whether and how jasmonate-dependent sugar dynamics are involved in flowering-mediated fungal colonization alterations. We found that flowering restricts root-fungal colonization and activates root jasmonate signalling upon fungal inoculation. Jasmonates reduce the constitutive and fungus-induced accumulation of root glucose and fructose at the flowering stage. Further experiments with sugar transport and metabolism mutant lines revealed that root glucose and fructose positively influence fungal colonization. Diurnal, jasmonate-dependent inhibitions of sugar transport and soluble invertase activity were identified as likely mechanisms for flowering-mediated root sugar depletion upon fungal inoculation. Collectively, our results reveal that flowering drives root-fungus cooperation loss, which is related to jasmonate-dependent root soluble sugar depletion. Limiting the spread of root-fungal colonization may direct more resources to flower development.

Function of miR825 and miR825* as Negative Regulators in Bacillus cereus AR156-elicited Systemic Resistance to Botrytis cinerea in Arabidopsis thaliana

Small RNAs function to regulate plant defense responses to pathogens. We previously showed that miR825 and miR825* downregulate Bacillus cereus AR156 (AR156)-triggered systemic resistance to Pseudomonassyringae pv. tomato DC3000 in Arabidopsis thaliana (Arabidopsis). Here, Northern blotting revealed that miR825 and miR825* were more strongly downregulated in wild type Arabidopsis Col-0 (Col-0) plants pretreated with AR156 than in nontreated plants upon Botrytis cinerea (B. cinerea) B1301 infection. Furthermore, compared with Col-0, transgenic plants with attenuated miR825 and miR825* expression were more resistant to B. cinerea B1301, yet miR825- and miR825*-overexpressing (OE) plants were more susceptible to the pathogen. With AR156 pretreatment, the transcription of four defense-related genes (PR1, PR2, PR5, and PDF1.2) and cellular defense responses (hydrogen peroxide production and callose deposition) were faster and stronger in miR825 and miR825* knockdown lines but weaker in their OE plants than in Col-0 plants upon pathogen attack. Also, AR156 pretreatment caused stronger phosphorylation of MPK3 and MPK6 and expression of FRK1 and WRKY53 genes upon B. cinerea B1301 inoculation in miR825 and miR825* knockdown plants than in Col-0 plants. Additionally, the assay of agrobacterium-mediated transient co-expression in Nicotiana benthamiana confirmed that AT5G40910, AT5G38850, AT3G04220, and AT5G44940 are target genes of miR825 or miR825*. Compared with Col-0, the target mutant lines showed higher susceptibility to B. cinerea B1301, while still expressing AR156-triggered induced systemic resistance (ISR). The two-way analysis of variance (ANOVA) revealed a significant (P < 0.01) interactive effect of treatment and genotype on the defense responses. Hence, miR825 and miR825*act as negative regulators of AR156-mediated systemic resistance to B. cinerea B1301 in Arabidopsis.

Effects of Dark Septate Endophytes on the Performance of Hedysarum scoparium Under Water Deficit Stress

Hedysarum scoparium, a species characterized by rapid growth and high drought resistance, has been used widely for vegetative restoration of arid regions in Northwest China that are prone to desertification. Desert soil is typically deficient in available water and the alleviation of drought stress to host plants by endophytes could be an efficient strategy to increase the success of desert restoration. With the objective to seek more beneficial symbionts that can be used in the revegetation strategies, we addressed the question whether H. scoparium can benefit from inoculation by dark septate endophytes (DSEs) isolated from other desert plants. We investigated the influences of four non-host DSE strains (Phialophora sp., Knufia sp., Leptosphaeria sp., and Embellisia chlamydospora) isolated from other desert plants on the performance of H. scoparium under different soil water conditions. Differences in plant performance, such as plant growth, antioxidant enzyme activities, carbon, nitrogen, and phosphorous concentration under all the treatments, were examined. Four DSE strains could colonize the roots of H. scoparium successfully, and they established a positive symbiosis with the host plants depending on DSE species and water availability. The greatest benefits of DSE inoculation occurred in water stress treatment. Specifically, Phialophora sp. and Leptosphaeria sp. improved the root biomass, total biomass, nutrient concentration, and antioxidant enzyme activities of host plants under water deficit conditions. These data contribute to the understanding of the ecological function of DSE fungi in drylands.

Re-evaluation of Mycoleptodiscus species and morphologically similar fungi

Mycoleptodiscus includes plant pathogens, animal opportunists, saprobic and endophytic fungi. The present study presents the first molecular phylogeny and revision of the genus based on four loci, including ITS, LSU, rpb2, and tef1. An extensive collection of Mycoleptodiscus cultures, including ex-type strains from the CBS, IMI, MUCL, BRIP, clinical isolates from the USA, and fresh isolates from Brazil and Spain, was studied morphologically and phylogenetically to resolve their taxonomy. The study showed that Mycoleptodiscus sensu lato is polyphyletic. Phylogenetic analysis places Mycoleptodiscus in Muyocopronales (Dothideomycetes), together with Arxiella, Leptodiscella, Muyocopron, Neocochlearomyces, and Paramycoleptodiscus. Mycoleptodiscus terrestris, the type species, and M. sphaericus are reduced to synonyms, and one new species is introduced, M. suttonii. Mycoleptodiscus atromaculans, M. coloratus, M. freycinetiae, M. geniculatus, M. indicus, M. lateralis (including M. unilateralis and M. variabilis as its synonyms) and M. taiwanensis belong to Muyocopron (Muyocopronales, Dothideomycetes), and M. affinis, and M. lunatus to Omnidemptus (Magnaporthales, Sordariomycetes). Based on phylogenetic analyses we propose Muyocopron alcornii sp. nov., a fungus associated with leaf spots on Epidendrum sp. (Orchidaceae) in Australia, Muyocopron zamiae sp. nov. associated with leaf spots on Zamia (Zamiaceae) in the USA, and Omnidemptus graminis sp. nov. isolated from a grass (Poaceae) in Spain. Furthermore, Neomycoleptodiscus venezuelense gen. & sp. nov. is introduced for a genus similar to Mycoleptodiscus in Muyocopronaceae.

A metabolite of endophytic fungus Cadophora orchidicola from Kalimeris indica serves as a potential fungicide and TLR4 agonist

AIM

To investigate the bioactive metabolite of endophytic fungus from Kalimeris indica.

METHODS AND RESULTS

A strain ZJLQ336 was separated from the leaves of K. indica. It was identified as Cadophora orchidicola based on the phylogenetic analysis of ITS-rDNA sequences. From the fermentation broth a metabolite cercosporamide (compound 1) was isolated, and its structure was determined by spectroscopic analysis. Additionally, this compound was subjected to bioactivity assays, including antifungal activity against seven plant pathogenic fungi, as well as its potential immunoregulatory effects on HEK-BLUE™-hTLR4 cells, splenocytes and macrophages. The results showed that cercosporamide had strong growth inhibition against five common plant pathogenic fungi, including Pestalotia diospyri, Botrytis cinerea, Fusarium oxysporum, Sclerotium rolfsii and Penicillum digitatum with EC₅₀ values of 5·29 × 10^-3 , 0·61, 0·93, 2·89 and 6·7 μg ml^-1 respectively. Among which S. rolfsii was one of the main pathogens in K. indica. Moreover, cercosporamide not only significantly stimulated TLR4 activation, splenocyte proliferation and production of cytokines, IFN-γ and TNF-α, but also up-regulated the production of TNF-α and NO in RAW264.7 macrophages clearly.

CONCLUSIONS

This is the first report of endophytic C. orchidicola from K. indica and its metabolite cercosporamide. The results of pharmacological tests highlight the potential fungicide and TLR4 agonist of cercosporamide.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study indicates endophytic fungi are good resources for natural bioactive metabolites. It also suggests that cercosporamide is a potential fungicide and TLR4 agonist.

The Dark Septate Endophytes and Ectomycorrhizal Fungi Effect on Pinus tabulaeformis Carr. Seedling Growth and their Potential Effects to Pine Wilt Disease Resistance

Pine wilt disease (PWD), a worldwide threat to pine forests, has caused tremendous damage to conifer forest in the world. However, little research has been conducted on the relationship between symbiosis functions of root associated fungi and pine wilt disease. In this study, we assessed the influence of seven ectomycorrhizal fungi (ECMF) and five dark septate endophytic fungi (DSE) on the growth traits and root morphology as well as the correlation of these parameters to the cumulative mortality and the morbidity rates in Pinus tabulaeformis Carr.showed the lowest cumulative mortality rates. We propose that the ECMF/DSE symbiosis enhanced the resistance of pine wilt disease via mitigation the dysfunction of water caused by PWN infection. Our research provided evidence that inoculation of ECMF/DSE could be a potential way for pine wilt disease prevention. To find highly efficient fungi for pine wilt disease management, more ECMF and DSE species should be tested.

The Role of Iron Competition in the Antagonistic Action of the Rice Endophyte Streptomyces sporocinereus OsiSh-2 Against the Pathogen Magnaporthe oryzae

Rice blast caused by Magnaporthe oryzae severely impacts global rice yield stability. The rice endophyte Streptomyces sporocinereus OsiSh-2, with strong antagonistic activity towards M. oryzae, has been reported in our previous study. To decipher the model of the antagonistic action of OsiSh-2 towards M. oryzae, we compared the iron-capturing abilities of these two strains. The cultivation of OsiSh-2 and a M. oryzae strain under iron-rich and iron-starved conditions showed that M. oryzae depended more on iron supplementation for growth and development than did OsiSh-2. Genomic analysis of the S. sporocinereus and M. oryzae species strains revealed that they might possess different iron acquisition strategies. The actinobacterium OsiSh-2 is likely to favor siderophore utilization compared to the fungus M. oryzae. In addition, protein annotations found that OsiSh-2 contains the highest number of the siderophore biosynthetic gene clusters among the 13 endophytic actinomycete strains and 13 antifungal actinomycete strains that we compared, indicating the prominent siderophore production potential of OsiSh-2. Additionally, we verified that OsiSh-2 could excrete considerably more siderophores than Guy11 under iron-restricted conditions and displayed greater Fe³⁺-reducing activity during iron-supplemental conditions. Measurements of the iron mobilization between the antagonistic OsiSh-2 and Guy11 showed that the iron concentration is higher around OsiSh-2 than around Guy11. In addition, adding iron near OsiSh-2 could decrease the antagonism of OsiSh-2 towards Guy11. Our study revealed that the antagonistic capacity displayed by OsiSh-2 towards M. oryzae was related to the competition for iron. The highly efficient iron acquisition system of OsiSh-2 may offer valuable insight for the biocontrol of rice blast.

Dark septate endophytes isolated from a xerophyte plant promote the growth of Ammopiptanthus mongolicus under drought condition

Dark septate endophytes (DSE) may facilitate plant growth and stress tolerance in stressful ecosystems. However, little is known about the response of plants to non-host DSE fungi isolated from other plants, especially under drought condition. This study aimed to seek and apply non-host DSE to evaluate their growth promoting effects in a desert species, Ammopiptanthus mongolicus, under drought condition. Nine DSE strains isolated from a super-xerophytic shrub, Gymnocarpos przewalskii, were identified and used as the non-host DSE. And DSE colonization rate (30–35%) and species composition in the roots of G. przewalskii were first reported. The inoculation results showed that all DSE strains were effective colonizers and formed a strain-dependent symbiosis with A. mongolicus. Specifically, one Darksidea strain, Knufia sp., and Leptosphaeria sp. increased the total biomass of A. mongolicus compared to non-inoculated plants. Two Paraconiothyrium strains, Phialophora sp., and Embellisia chlamydospora exhibited significantly positive effects on plant branch number, potassium and calcium content. Two Paraconiothyrium and Darksidea strains particularly decreased plant biomass or element content. As A. mongolicus plays important roles in fixing moving sand and delay desertification, the ability of certain DSE strains to promote desert plant growth indicates their potential use for vegetation recovery in arid environments.

Co-inoculation of Lolium perenne with Funneliformis mosseae and the dark septate endophyte Cadophora sp. in a trace element-polluted soil

The presence of dark septate endophytes (DSEs) or arbuscular mycorrhizal fungi (AMF) in plant roots and their effects on plant fitness have been extensively described. However, little is known about their interactions when they are simultaneously colonizing a plant root, especially in trace element (TE)-polluted soils. We therefore investigated the effects of Cadophora sp. and Funneliformis mosseae on ryegrass (Lolium perenne) growth and element uptake in a Cd/Zn/Pb-polluted soil. The experiment included four treatments, i.e., inoculation with Cadophora sp., inoculation with F. mosseae, co-inoculation with Cadophora sp. and F. mosseae, and no inoculation. Ryegrass biomass and shoot Na, P, K, and Mg concentrations significantly increased following AMF inoculation as compared to non-inoculated controls. Similarly, DSE inoculation increased shoot Na concentration, whereas dual inoculation significantly decreased shoot Cd concentration. Moreover, oxidative stress determined by ryegrass leaf malondialdehyde concentration was alleviated both in the AMF and dual inoculation treatments. We used quantitative PCR and microscope observations to quantify colonization rates. They demonstrated that DSEs had no effect on AMF colonization, while AMF colonization slightly decreased DSE frequency. We also monitored fluorescein diacetate (FDA) hydrolysis and alkaline phosphatase (AP) activity in the rhizosphere soils. FDA hydrolysis remained unchanged in the three inoculated treatments, but AMF colonization increased AP activity and P mobility in the soil whereas DSE colonization did not alter AP activity. In this experiment, we unveiled the interactions between two ecologically important fungal groups likely to occur in roots which involved a decrease of oxidative stress and Cd accumulation in shoots. These results open promising perspectives on the fungal-based phytomanagement of TE-contaminated sites by the production of uncontaminated and marketable plant biomass.

Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed

Barnyardgrass (Echinochloa crus-galli) is a pernicious weed in agricultural fields worldwide. The molecular mechanisms underlying its success in the absence of human intervention are presently unknown. Here we report a draft genome sequence of the hexaploid species E. crus-galli, i.e., a 1.27 Gb assembly representing 90.7% of the predicted genome size. An extremely large repertoire of genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with detoxification are found. Two gene clusters involved in the biosynthesis of an allelochemical 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and a phytoalexin momilactone A are found in the E. crus-galli genome, respectively. The allelochemical DIMBOA gene cluster is activated in response to co-cultivation with rice, while the phytoalexin momilactone A gene cluster specifically to infection by pathogenic Pyricularia oryzae. Our results provide a new understanding of the molecular mechanisms underlying the extreme adaptation of the weed.

Induced Systemic Resistance against Botrytis cinerea by Bacillus cereus AR156 through a JA/ET- and NPR1-Dependent Signaling Pathway and Activates PAMP-Triggered Immunity in Arabidopsis

Induced resistance response is a potent and cost effective plant defense against pathogen attack. The effectiveness and underlying mechanisms of the suppressive ability by Bacillus cereus AR156 to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) in Arabidopsis has been investigated previously; however, the strength of induced systemic resistance (ISR) activity against Botrytis cinerea remains unknown. Here, we show that root-drench application of AR156 significantly reduces disease incidence through activation of ISR. This protection is accompanied with multilayered ISR defense response activated via enhanced accumulation of PR1 protein expression in a timely manner, hydrogen peroxide accumulation and callose deposition, which is significantly more intense in plants with both AR156 pretreatment and B. cinerea inoculation than that in plants with pathogen inoculation only. Moreover, AR156 can trigger ISR in sid2-2 and NahG mutants, but not in jar1, ein2 and npr1 mutant plants. Our results indicate that AR156-induced ISR depends on JA/ET-signaling pathway and NPR1, but not SA. Also, AR156-treated plants are able to rapidly activate MAPK signaling and FRK1/WRKY53 gene expression, both of which are involved in pathogen associated molecular pattern (PAMP)-triggered immunity (PTI). The results indicate that AR156 can induce ISR by the JA/ET-signaling pathways in an NPR1-dependent manner and involves multiple PTI components.

De novo Transcriptome Assembly of Phomopsis liquidambari Provides Insights into Genes Associated with Different Lifestyles in Rice (Oryza sativa L.)

The mechanisms that trigger the switch from endophytic fungi to saprophytic fungi are largely unexplored. Broad host range Phomopsis liquidambari is established in endophytic and saprophytic systems with rice (Oryza sativa L.). Endophytic P. liquidambari promotes rice growth, increasing rice yield and improving the efficiency of nitrogen fertilizer. This species's saprophytic counterpart can decompose rice litterfall, promoting litter organic matter cycling and the release of nutrients and improving the soil microbial environment. Fluorescence microscopy, confocal laser scanning microscopy and quantitative PCR investigated the colonization dynamics and biomass of P. liquidambari in rice in vivo. P. liquidambari formed infection structures similar to phytopathogens with infected vascular tissues that systematically spread to acrial parts. However, different from pathogenic infection, P. liquidambari colonization exhibits space restriction and quantity restriction. Direct comparison of a fungal transcriptome under three different habitats provided a better understanding of lifestyle conversion during plant-fungi interactions. The isolated total RNA of Ck (pure culture), EP (endophytic culture) and FP (saprophytic culture) was subjected to Illumina transcriptome sequencing. To the best of our knowledge, this study is the first to investigate Phomopsis sp. using RNA-seq technology to obtain whole transcriptome information. A total of 27,401,258 raw reads were generated and 22,700 unigenes were annotated. Functional annotation indicated that carbohydrate metabolism and biosynthesis of secondary metabolites played important roles. There were 2522 differentially expressed genes (DEGs) between the saprophytic and endophytic lifestyles. Quantitative PCR analysis validated the DEGs of RNA-seq. Analysis of DEGs between saprophytic and endophytic lifestyles revealed that most genes from amino acids metabolism, carbohydrate metabolism, fatty acid biosynthesis, secondary metabolism and terpenoid and steroid biosynthesis were up-regulated in EP. Secondary metabolites of these pathways may affect fungal growth and development and contribute to signaling communication with the host. Most pathways of xenobiotic biodegradation and metabolism were upregulated in FP. Cytochrome P450s play diverse vital roles in endophytism and saprophytism, as their highly specialized functions are evolutionarily adapted to various ecological niches. These results help to characterize the relationship between fungi and plants, the diversity of fungi for ecological adaptations and the application prospects for fungi in sustainable agriculture.

Differential Communications between Fungi and Host Plants Revealed by Secretome Analysis of Phylogenetically Related Endophytic and Pathogenic Fungi

During infection, both phytopathogenic and endophytic fungi form intimate contact with living plant cells, and need to resist or disable host defences and modify host metabolism to adapt to their host. Fungi can achieve these changes by secreting proteins and enzymes. A comprehensive comparison of the secretomes of both endophytic and pathogenic fungi can improve our understanding of the interactions between plants and fungi. Although Magnaporthe oryzae, Gaeumannomyces graminis, and M. poae are economically important fungal pathogens, and the related species Harpophora oryzae is an endophyte, they evolved from a common pathogenic ancestor. We used a pipeline analysis to predict the H. oryzae, M. oryzae, G. graminis, and M. poae secretomes and identified 1142, 1370, 1001, and 974 proteins, respectively. Orthologue gene analyses demonstrated that the M. oryzae secretome evolved more rapidly than those of the other three related species, resulting in many species-specific secreted protein-encoding genes, such as avirulence genes. Functional analyses highlighted the abundance of proteins involved in the breakdown of host plant cell walls and oxidation-reduction processes. We identified three novel motifs in the H. and M. oryzae secretomes, which may play key roles in the interaction between rice and H. oryzae. Furthermore, we found that expression of the H. oryzae secretome involved in plant cell wall degradation was downregulated, but the M. oryzae secretome was upregulated with many more upregulated genes involved in oxidation-reduction processes. The divergent in planta expression patterns of the H. and M. oryzae secretomes reveal differences that are associated with mutualistic and pathogenic interactions, respectively.

Interspecific metabolic diversity of root-colonizing endophytic fungi revealed by enzyme activity tests

Although dark septate endophytes (DSE) represent a worldwide dispersed form group of root-colonizing endophytic fungi, our knowledge on their role in ecosystem functioning is far limited. In this study, we aimed to test if functional diversity exists among DSE fungi representing different lineages of root endophytic fungal community of semiarid sandy grasslands. To address this question and to gain general information on function of DSE fungi, we adopted api-ZYM and BioLog FF assays to study those non-sporulating filamentous fungi and characterized the metabolic activity of 15 different DSE species. Although there were striking differences among the species, all of the substrates tested were utilized by the DSE fungi. When endophytes characteristic to grasses and non-grass host plants were separately considered, we found that the whole substrate repertoire was used by both groups. This might illustrate the complementary functional diversity of the communities root endophytic plant-associated fungi. The broad spectra of substrates utilized by these root endophytes illustrate the functional importance of their diversity, which can play role not only in nutrient mobilization and uptake of plants from with nutrient poor soils, but also in general plant performance and ecosystem functioning.

An autophagy gene, HoATG5, is involved in sporulation, cell wall integrity and infection of wounded barley leaves

The endophytic fungus Harpophora oryzae is a beneficial endosymbiont isolated from wild rice. H. oryzae can not only promote rice growth and biomass accumulation but also protect rice roots from invasion by its close relative Magnaporthe oryzae. Autophagy is a highly evolutionary conserved process from lower to higher eukaryotic organisms, and is involved in the maintenance of normal cell differentiation and development. In this study, we isolated a gene (HoATG5) which encodes an essential protein required for autophagy from the beneficial endophyte fungus H. oryzae. Using targeted gene replacement, a ΔHoATG5 mutant was generated and used to investigate the biological functions of autophagy in H. oryzae. We found that the autophagic process was blocked in the HoATG5 deletion mutant. The mutant showed increased vegetative growth and sporulation, and was sensitive to nutrient starvation. The ΔHoATG5 mutant lost its ability to penetrate and infect the wounded barley leaves. These results provide new knowledge to elaborate the molecular machinery of autophagy in endophytic fungi.