Determinants of endophytic and pathogenic lifestyle in root colonizing fungi

Cell wall bricks of defence: the case study of oligogalacturonides

The plant cell wall (CW) is more than a structural barrier; it serves as the first line of defence against pathogens and environmental stresses. During pathogen attacks or physical damage, fragments of the CW, known as CW-derived Damage-Associated Molecular Patterns (CW-DAMPs), are released. These molecular signals play a critical role in activating the plant's immune responses. Among CW-DAMPs, oligogalacturonides (OGs), fragments derived from the breakdown of pectin, are some of the most well-studied. This review highlights recent advances in understanding the functional and signalling roles of OGs, beginning with their formation through enzymatic CW degradation during pathogen invasion or mechanical injury. We discuss how OGs perception triggers intracellular signalling pathways that enhance plant defence and regulate interactions with microbes. Given that excessive OG levels can negatively impact growth and development, we also examine the regulatory mechanisms plants use to fine-tune their responses, avoiding immune overactivation or hyper- immunity. As natural immune modulators, OGs (and more generally CW-DAMPs), offer a promising, sustainable alternative to chemical pesticides by enhancing crop resilience without harming the environment. By strengthening plant defences and supporting eco-friendly agricultural practices, OGs hold great potential for advancing resilient and sustainable farming systems.

A fusarioid fungus forms mutualistic interactions with poplar trees that resemble ectomycorrhizal symbiosis

Fusarium species, recognised as global priority pathogens, frequently induce severe diseases in crops; however, certain species exhibit alternative symbiotic lifestyles and are either non-pathogenic or endophytic. In this study, we characterised the mutualistic relationship between the eFp isolate of F.pseudograminearum and five poplar species, resulting in formation root structures reminiscent of ectomycorrhizal (ECM) symbiosis. This functional symbiosis is evidenced by enhanced plant growth, reciprocal nutrient exchange, improved nitrogen and phosphorus uptake and upregulation of root sugar transporter gene expression (PtSweet1). Comparative and population genomics confirmed that eFp maintains a structurally similar genome, but exhibits significant divergence from ten conspecific pathogenic isolates. Notably, eFp enhanced the growth of diverse plant lineages (Oryza, Arabidopsis, Pinus and non-vascular liverworts), indicating a near-complete loss of virulence. Although this specialised symbiosis has only been established in vitro, it holds significant value in elucidating the evolutionary track from endophytic to mycorrhizal associations.

Composition and Biodiversity of Culturable Endophytic Fungi in the Roots of Alpine Medicinal Plants in Xinjiang, China

(1) Background: Endophytic fungi play an important role in plant growth and stress resistance. The presence of a special fungal taxon such as the dark septate endophytic (DSE) fungi in alpine environments is particularly important for plant resistance to environmental stresses. However, the composition of root endophytic fungi in different environments and between different host plants has not been well studied. (2) Results: A total of 408 culturable endophytic fungi were isolated from the roots of Saussurea involucrata and Rhodiola crenulata which were collected in 5 plots from the Tianshan and Karakoram Mountains of the Xinjiang region, belonging to 91 species, 54 genera, 31 families, and 3 phyla based on the morphological characteristics and molecular sequence. Among them, DSE fungi were the dominant group, accounting for 52.94%, and Leptodontidium orchidicola was the dominant species. In addition, we also compared the composition and diversity of root endophytic fungi from different plants and different sites, with emphasis on special fungal taxa such as DSE. (3) Conclusions: The composition and diversity of cultural endophytic fungi are significantly different in the two alpine medicinal plant species and across various locations. Some fungi showed the preferences of the host or environment. The endophytic fungal resources, especially DSE, were very rich in the two alpine medicinal plants, indicating that these fungi may play a crucial role in the ecological adaptation of host plants in harsh environments.

Endophytic strategies decoded by genome and transcriptome analysis of Fusarium nematophilum strain NQ8GII4

Introduction

Fusarium nematophilum strain NQ8GII4 is an endophytic fungus with significant potential for improving growth and disease resistance of alfalfa. However, the molecular mechanisms underlying the symbiotic relationship between NQ8GII4 and alfalfa roots remain poorly understood.

Methods

In this study, we conducted (1) a comparative genomic analysis of selected saprophytic, pathogenic, and endophytic fungi, including molecular phylogeny analysis, whole-genome alignment, and divergence date estimation positioning, and (2) transcriptomic profiling of alfalfa roots infected with NQ8GII4.

Results

Our findings reveal that NQ8GII4 is genetically closely related to F. solani, suggesting it diverged from Fusarium phytopathogens. During the early stages of symbiosis establishment, genes encoding glycosyltransferases (GTs), fungal cell wall-degrading enzymes (FCWDEs), and steroid-14α-demethylase (CYP51) were significantly downregulated, potentially suppressing hyphal growth of the fungus. Once symbiosis was established, NQ8GII4 secreted effectors that activated plant immunity, which in turn could slow growth of the fungus. Moreover, genes involved in secondary metabolite biosynthesis, such as type I polyketide synthases (T1PKS) and non-ribosomal peptide synthetases (NRPSs), were significantly downregulated. Homologs of autophagy-related genes, including ATG1, ATG2, ATG11, and others, were also downregulated, suggesting that reduced phytotoxin production and autophagy inhibition is a consequence of NQ8GII4's symbiosis.

Discussion

This study investigated the comprehensive molecular and genetic mechanisms governing the interaction between NQ8GII4 and alfalfa roots. Beyond the NQ8GII4-alfalfa system, these findings also provide a valuable molecular framework for understanding the mechanism of interactions between endophytic fungi and their host plants.

Microbial inheritance through seed: a clouded area needs to be enlightened

Seed endophytes are actively used by the mother plant as both reservoir and vector of beneficial microbes. During seed dormancy endophytes experience significant physiochemical changes and only competent endophytes could colonise successfully in seeds and some of them act as obligate endophyte that are transmitted vertically across generations. The adaptive nature of endophytes allows them to switch lifestyles depending on environment and host conditions. In this review, instead of providing broad discussion on applicability of endophytes in plant growth improvement, the fundamental nature of endophytes, their survival strategies under stress conditions, transmittance, etc. have been broadly highlighted by collaborating recent discoveries and theories. We have also tried to differentiate endophyte with their pathogenic counterpart and their survival mechanism during seed dormancy stages. Critical analyses of physio-biochemical changes in seeds during maturation and parallel modifications of life styles of seed endophytes along with pathogens will enlighten the shaded part of seed-microbiome interactions. The mutualistic interrelations as well as their shipment towards pathogenic behaviour under stress are being discussed acutely. Finally, importances of conservation of seed microbiome to maintain seed quality and vigour have been pointed out. Throughout the manuscript, the knowledge gap on seed-microbiota have been mentioned, thus, in future, studies on these areas could help us to understand properly the actual role of endophytes for the betterment of maintaining seed quality and vigour.

Extract from endophytic Fusarium isolates stimulates seed germination of the host and protocorm development of non-host orchids

We isolated endophytic Fusarium strains from the healthy roots, stems, and leaves of Dendrobium moschatum to investigate their plant growth-promoting activities in vitro. Subsequently, Indole acetic acid (IAA) was quantified and the IaaM gene (responsible for IAA synthesis in fungi) was amplified and sequenced. Finally, a germination assay was performed with seeds of D. moschatum and a plant growth assay with protocorms of Dendrobium longicornu to test their plant growth-promoting activities. Five Fusarium isolates (CDS11, PDL1, PDL3, PDR6, PDR7) were identified in this study. The highest amount (60µgml-1) of indole acetic acid was recorded in the PDR7 extract, whereas it was not detected in PDR6 and CDS11. The fungal extracts of isolates PDR6 and PDR7 were highly effective for seed germination by approximately 80% and 90% (respectively) of the host plant. The fungal extract of PDR7 showed a high IAA content and promoted in vitro seed germination of the host (D. moschatum) and protocorm development of the non-host (D. longicornu). In contrast, IAA content in the fungal extract of PDR6 remained undetected but was effective in both seed germination and protocorm development. Our results demonstrated the potential beneficial application of endophytic Fusarium in orchid mass propagation.

Comparative Genomics of Different Lifestyle Fungi in Helotiales (Leotiomycetes) Reveals Temperature and Ecosystem Adaptations

Helotiales, a diverse fungal order within Leotiomycetes (Ascomycota), comprises over 6000 species occupying varied ecological niches, from plant pathogens to saprobes and symbionts. Despite their importance, their genetic adaptations to temperature and environmental conditions are understudied. This study investigates temperature adaptations in infection genes and substrate degradation genes through a comparative genomics analysis of 129 Helotiales species, using the newly sequenced genomes of Gyoerffyella rotula and Anguillospora crassa. Key gene families such as cytochrome P450 enzymes, virulence factors, effector proteins, and carbohydrate-active enzymes (CAZymes) were analyzed to understand their roles in temperature and lifestyle adaptations, uncovering possible alternative lifestyle mechanisms. Our findings reveal that Helotiales fungi possess genes associated with nutrient acquisition, pathogenicity, and symbiotic relationships strongly adapted to cold environments that might be impacted by global warming. On the other hand, some species demonstrate potential for adaptation to warmer climates, suggesting increased activity in response to global warming. This study reveals the adaptive mechanisms enabling Helotiales fungi to thrive in both cold and warm environments. These findings provide valuable insights into their ecological success and evolutionary resilience, which may facilitate their ability to transition between pathogenic, symbiotic, and saprobic phases in response to changing environmental conditions.

Transcriptomics reveal a mechanism of niche defense: two beneficial root endophytes deploy an antimicrobial GH18-CBM5 chitinase to protect their hosts

Effector secretion is crucial for root endophytes to establish and protect their ecological niche. We used time-resolved transcriptomics to monitor effector gene expression dynamics in two closely related Sebacinales, Serendipita indica and Serendipita vermifera, during symbiosis with three plant species, competition with the phytopathogenic fungus Bipolaris sorokiniana, and cooperation with root-associated bacteria. We observed increased effector gene expression in response to biotic interactions, particularly with plants, indicating their importance in host colonization. Some effectors responded to both plants and microbes, suggesting dual roles in intermicrobial competition and plant-microbe interactions. A subset of putative antimicrobial effectors, including a GH18-CBM5 chitinase, was induced exclusively by microbes. Functional analyses of this chitinase revealed its antimicrobial and plant-protective properties. We conclude that dynamic effector gene expression underpins the ability of Sebacinales to thrive in diverse ecological niches with a single fungal chitinase contributing substantially to niche defense.

Molecular Dialogue During Host Manipulation by the Vascular Wilt Fungus Fusarium oxysporum

Vascular wilt fungi are a group of hemibiotrophic phytopathogens that infect diverse crop plants. These pathogens have adapted to thrive in the nutrient-deprived niche of the plant xylem. Identification and functional characterization of effectors and their role in the establishment of compatibility across multiple hosts, suppression of plant defense, host reprogramming, and interaction with surrounding microbes have been studied mainly in model vascular wilt pathogens Fusarium oxysporum and Verticillium dahliae. Comparative analysis of genomes from fungal isolates has accelerated our understanding of genome compartmentalization and its role in effector evolution. Also, advances in recent years have shed light on the cross talk of root-infecting fungi across multiple scales from the cellular to the ecosystem level, covering their interaction with the plant microbiome as well as their interkingdom signaling. This review elaborates on our current understanding of the cross talk between vascular wilt fungi and the host plant, which eventually leads to a specialized lifestyle in the xylem. We particularly focus on recent findings in F. oxysporum, including multihost associations, and how they have contributed to understanding the biology of fungal adaptation to the xylem. In addition, we discuss emerging research areas and highlight open questions and future challenges.

New insights into decoding the lifestyle of endophytic Fusarium lateritium Fl617 via comparing genomes

Fungal-plant interactions have persisted for 460 million years, and almost all terrestrial plants on Earth have endophytic fungi. However, the mechanism of symbiosis between endophytic fungi and host plants has been inconclusive. In this dissertation, we used a strain of endophytic Fusarium lateritium (Fl617), which was found in the previous stage to promote disease resistance in tomato, and selected the pathogenic Fusarium oxysporum Fo4287 and endophytic Fusarium oxysporum Fo47, which are in the same host and the closest relatives of Fl617, to carry out a comparative genomics analysis of the three systems and to provide a new perspective for the elucidation of the special lifestyle of the fungal endophytes. We found that endophytic F. lateritium has a smaller genome, fewer clusters and genes associated with pathogenicity, and fewer plant cell wall degrading enzymes (PCWDEs). There were also relatively fewer secondary metabolisms and typical Fusarium spp. toxins, and a lack of the key Fusarium spp. pathogenicity factor, secreted in xylem (SIX), but the endophytic fungi may be more sophisticated in their regulation of the colonization process. It is hypothesized that the endophytic fungi may have maintained their symbiosis with plants due to the relatively homogeneous microenvironment in plants for a long period of time, considering only plant interactions and discarding the relevant pathogenicity factors, and that their endophytic evolutionary tendency may tend to be genome streamlining and to enhance the fineness of the regulation of plant interactions, thus maintaining their symbiotic status with plants.

Interplay of biotic and abiotic factors shapes tree seedling growth and root-associated microbial communities

Root-associated microbes can alleviate plant abiotic stresses, thus potentially supporting adaptation to a changing climate or to novel environments during range expansion. While climate change is extending plant species fundamental niches northward, the distribution and colonization of mutualists (e.g., arbuscular mycorrhizal fungi) and pathogens may constrain plant growth and regeneration. Yet, the degree to which biotic and abiotic factors impact plant performance and associated microbial communities at the edge of their distribution remains unclear. Here, we use root microscopy, coupled with amplicon sequencing, to study bacterial, fungal, and mycorrhizal root-associated microbial communities from sugar maple seedlings distributed across two temperate-to-boreal elevational gradients in southern Québec, Canada. Our findings demonstrate that soil pH, soil Ca, and distance to sugar maple trees are key drivers of root-associated microbial communities, overshadowing the influence of elevation. Interestingly, changes in root fungal community composition mediate an indirect effect of soil pH on seedling growth, a pattern consistent at both sites. Overall, our findings highlight a complex role of biotic and abiotic factors in shaping tree-microbe interactions, which are in turn correlated with seedling growth. These findings have important ramifications for tree range expansion in response to shifting climatic niches.

Wheat fungal endophyte communities are inseparable from the host and influence plant development

Plants harbor complex and highly diverse fungal endophyte communities (FECs), making it difficult to evaluate the functional role of individual taxa, subsets of the community, or the FEC as a whole. To reduce the complexity of this system, we aimed to produce fungi-null wheat (Triticum aestivum) plants. To this end, we treated seeds with heat and fungicides and generated plants from rescued embryos and callus tissue. A culture-based approach and reverse transcription PCR analysis were negative, indicating that all treatments produced plants apparently free of fungi. However, the analysis of DNA using digital droplet PCR and next-generation sequencing revealed that tissues from all treatments retained low levels but diversity-rich FECs. While the FECs varied in composition across treatments and tissues, they all included core taxa of the mycobiome. The reduced fungal biomass, along with the changes in FEC composition, negatively affected plant development, supporting a FEC contribution to proper plant development and fitness. Our discovery that a large part of the FEC cannot be separated from plants and can be transmitted through seeds and tissue culture calls for reevaluation of particular microbiome paradigms, such as core taxa concepts, transmission modes, and functional species.IMPORTANCEThe native microbiome in a given plant must be considered when evaluating the effect of a single taxon or synthetic community. The pre-existing microbiome can interact with artificially added microbial cargo, which affects the final outcome. Such issues can be at least partially solved by the use of endophyte-free plants, which provide a clean background that should be useful in determining the effect of a single taxon, taxa combinations, or the entire microbiome on plant performance. Previous reports regarded plants as endophyte-free or axenic by the lack of fungal growth on culture media or the generation of plants from tissue cultures. We showed here that while fungi could not be isolated from fungicide-treated or tissue culture-regenerated plants, nevertheless, all plants contained rich fungal endophyte communities; namely, it was impossible to create fungi-free wheat plants. Our results call for rethinking fundamental microbiome-related concepts, such as core taxa, transmission mode, and functional species.

The antifungal metabolites from coculture of Aspergillus fumigatus and Alternaria alternata associated with Coffea arabica

One new cyclohexenone derivative, asperfumtone A (1) along with six known compounds were obtained from the coculture of Aspergillus fumigatus and Alternaria alternata associated with Coffea arabica. The configuration of 2 was first reported in the research. The structures were determined by extensive spectroscopic analyses, and ECD calculation. Compounds 3, 4 and 7 showed significant antifungal activities against coffee phytopathogens A. alternata and Fusarium incarnatum with MICs of 1 μg/mL. Compounds 1 and 2 showed weak antifungal activities against A. alternata and F. incarnatum with MICs of 32-64 μg/mL.

Genome sequencing and molecular networking analysis of the wild fungus Anthostomella pinea reveal its ability to produce a diverse range of secondary metabolites

BACKGROUND

Filamentous fungi are prolific producers of bioactive molecules and enzymes with important applications in industry. Yet, the vast majority of fungal species remain undiscovered or uncharacterized. Here we focus our attention to a wild fungal isolate that we identified as Anthostomella pinea. The fungus belongs to a complex polyphyletic genus in the family of Xylariaceae, which is known to comprise endophytic and pathogenic fungi that produce a plethora of interesting secondary metabolites. Despite that, Anthostomella is largely understudied and only two species have been fully sequenced and characterized at a genomic level.

RESULTS

In this work, we used long-read sequencing to obtain the complete 53.7 Mb genome sequence including the full mitochondrial DNA. We performed extensive structural and functional annotation of coding sequences, including genes encoding enzymes with potential applications in biotechnology. Among others, we found that the genome of A. pinea encodes 91 biosynthetic gene clusters, more than 600 CAZymes, and 164 P450s. Furthermore, untargeted metabolomics and molecular networking analysis of the cultivation extracts revealed a rich secondary metabolism, and in particular an abundance of sesquiterpenoids and sesquiterpene lactones. We also identified the polyketide antibiotic xanthoepocin, to which we attribute the anti-Gram-positive effect of the extracts that we observed in antibacterial plate assays.

CONCLUSIONS

Taken together, our results provide a first glimpse into the potential of Anthstomella pinea to provide new bioactive molecules and biocatalysts and will facilitate future research into these valuable metabolites.

Novel Endophytic Pseudescherichia sp. GSE25 Strain Significantly Controls Fusarium graminearum and Reduces Deoxynivalenol in Wheat

Fusarium heading blight (FHB) is a devastating disease in wheat, primarily caused by field invasion of Fusarium graminearum. Due to the scarcity of resistant wheat varieties, the agricultural sector resorts to chemical fungicides to control FHB incidence. On the other hand, biocontrol represents a promising, eco-friendly approach aligned with sustainable and green agriculture concepts. In the present study, a bacterial endophyte, Pseudescherichia sp. (GSE25), was isolated from wheat seeds and identified through complete genome sequencing and phylogenetic analysis. In vitro testing of this endophytic strain demonstrated strong antifungal activity against F. graminearum PH-1 by inhibiting spore germination, suppressing germ tube growth, and causing cell membrane damage. Under field conditions, the strain GSE25 significantly reduced the FHB incidence and the associated deoxynivalenol mycotoxin accumulation by over 60% and 80%, respectively. These findings highlight the potential of the isolated bacterial endophyte Pseudescherichia sp. GSE25 strain as a biocontrol agent in protecting wheat from FHB-caused F. graminearum. This is the first report showing a biocontrol effect of Pseudescherichia sp. a strain against phytopathogens.

Transcriptional plasticity of schizotrophic Sclerotinia sclerotiorum responds to symptomatic rapeseed and endophytic wheat hosts

IMPORTANCE

The broad host range of fungi with differential fungal responses leads to either a pathogenic or an endophytic lifestyle in various host plants. Yet, the molecular basis of schizotrophic fungal responses to different plant hosts remains unexplored. Here, we observed a general increase in the gene expression of S. sclerotiorum associated with pathogenicity in symptomatic rapeseed, including small protein secretion, appressorial formation, and oxalic acid toxin production. Conversely, in wheat, many carbohydrate metabolism and transport-associated genes were induced, indicating a general increase in processes associated with carbohydrate acquisition. Appressorium is required for S. sclerotiorum during colonization in symptomatic hosts but not in endophytic wheat. These findings provide new clues for understanding schizotrophic fungi, fungal evolution, and the emergence pathways of new plant diseases.

Microbial diversity in soils suppressive to Fusarium diseases

Fusarium species are cosmopolitan soil phytopathogens from the division Ascomycota, which produce mycotoxins and cause significant economic losses of crop plants. However, soils suppressive to Fusarium diseases are known to occur, and recent knowledge on microbial diversity in these soils has shed new lights on phytoprotection effects. In this review, we synthesize current knowledge on soils suppressive to Fusarium diseases and the role of their rhizosphere microbiota in phytoprotection. This is an important issue, as disease does not develop significantly in suppressive soils even though pathogenic Fusarium and susceptible host plant are present, and weather conditions are suitable for disease. Soils suppressive to Fusarium diseases are documented in different regions of the world. They contain biocontrol microorganisms, which act by inducing plants' resistance to the pathogen, competing with or inhibiting the pathogen, or parasitizing the pathogen. In particular, some of the Bacillus, Pseudomonas, Paenibacillus and Streptomyces species are involved in plant protection from Fusarium diseases. Besides specific bacterial populations involved in disease suppression, next-generation sequencing and ecological networks have largely contributed to the understanding of microbial communities in soils suppressive or not to Fusarium diseases, revealing different microbial community patterns and differences for a notable number of taxa, according to the Fusarium pathosystem, the host plant and the origin of the soil. Agricultural practices can significantly influence soil suppressiveness to Fusarium diseases by influencing soil microbiota ecology. Research on microbial modes of action and diversity in suppressive soils should help guide the development of effective farming practices for Fusarium disease management in sustainable agriculture.

Plant and microbial features governing an endophytic lifestyle

Beneficial microorganisms colonizing internal plant tissues, the endophytes, support their host through plant growth promotion, pathogen protection, and abiotic stress alleviation. Their efficient application in agriculture requires the understanding of the molecular mechanisms and environmental conditions that facilitate in planta accommodation. Accumulating evidence reveals that commensal microorganisms employ similar colonization strategies as their pathogenic counterparts. Fine-tuning of immune response, motility, and metabolic crosstalk accounts for their differentiation. For a holistic perspective, in planta experiments with microbial collections and comprehensive genome data exploration are crucial. This review describes the most recent findings on factors involved in endophytic colonization processes, focusing on bacteria and fungi, and discusses required methodological approaches to unravel their relevance within a community context.

Interkingdom ecological networks between plants and fungi drive soil multifunctionality across arid inland river basin

Despite the known collective contribution of above- (plants) and below-ground (soil fungi) biodiversity on multiple soil functions, how the associations among plant and fungal communities regulate soil multifunctionality (SMF) differentially remains unknown. Here, plant communities were investigated at 81 plots across a typical arid inland river basin, within which associated soil fungal communities and seven soil functions (nutrients storage and biological activity) were measured in surface (0-15 cm) and subsurface soil (15-30 cm). We evaluated the relative importance of species richness and biotic associations (reflected by network complexity) on SMF. Our results demonstrated that plant species richness and plant-fungus network complexity promoted SMF in surface and subsurface soil. SMF in two soil layers was mainly determined by plant-fungus network complexity, mean groundwater depth and soil variables, among which plant-fungus network complexity played a crucial role. Plant-fungus network complexity had stronger effects on SMF in surface soil than in subsurface soil. We present evidence that plant-fungus network complexity surpassed plant-fungal species richness in determining SMF in surface and subsurface soil. Moreover, plant-fungal species richness could not directly affect SMF. Greater plant-fungal species richness indirectly promoted SMF since they ensured greater plant-fungal associations. Collectively, we concluded that interkingdom networks between plants and fungi drive SMF even in different soil layers. Our findings enhanced our knowledge of the underlying mechanisms that above- and below-ground associations promote SMF in arid inland river basins. Future study should place more emphasis on the associations among plant and microbial communities in protecting soil functions under global changes.

Global Change Factors Influence Plant-Epichloë Associations

There is an increasing interest in determining the influence of global change on plant-microorganism interactions. We review the results of experiments that evaluated the effects of the global change factors carbon dioxide, ozone, temperature, drought, flooding, and salinity on plant symbioses with beneficial Epichloë endophytes. The factors affected the performance of both plants and endophytes as well as the frequency of plants symbiotic with the fungus. Elevated carbon dioxide levels and low temperatures differentially influenced the growth of plants and endophytes, which could compromise the symbioses. Furthermore, we summarise the plant stage in which the effects of the factors were quantified (vegetative, reproductive, or progeny). The factors ozone and drought were studied at all plant stages, but flooding and carbon dioxide were studied in just a few of them. While only studied in response to ozone and drought, evidence showed that the effects of these factors on symbiotic plants persisted trans-generationally. We also identified the putative mechanisms that would explain the effects of the factors on plant-endophyte associations. These mechanisms included the increased contents of reactive oxygen species and defence-related phytohormones, reduced photosynthesis, and altered levels of plant primary metabolites. Finally, we describe the counteracting mechanisms by which endophytes would mitigate the detrimental effects of the factors on plants. In presence of the factors, endophytes increased the contents of antioxidants, reduced the levels of defence-related phytohormones, and enhanced the plant uptake of nutrients and photosynthesis levels. Knowledge gaps regarding the effects of global change on plant-endophyte associations were identified and discussed.

Environmental interference of plant-microbe interactions

Environmental stresses can compromise the interactions of plants with beneficial microbes. In the present review, experimental results showing that stresses negatively affect the abundance and/or functionality of plant beneficial microbes are summarized. It is proposed that the environmental interference of these plant-microbe interactions is explained by the stress-mediated induction of plant signalling pathways associated with defence hormones and reactive oxygen species. These plant responses are recognized to regulate beneficial microbes within plants. The direct negative effect of stresses on microbes may also contribute to the environmental regulation of these plant mutualisms. It is also posited that, in stress situations, beneficial microbes harbour mechanisms that contribute to maintain the mutualistic associations. Beneficial microbes produce effector proteins and increase the antioxidant levels in plants that counteract the detrimental effects of plant stress responses on them. In addition, they deliver specific stress-protective mechanisms that assist to their plant hosts to mitigate the negative effects of stresses. Our study contributes to understanding how environmental stresses affect plant-microbe interactions and highlights why beneficial microbes can still deliver benefits to plants in stressful environments.

Azospirillum brasilense and Zinc Rates Effect on Fungal Root Colonization and Yield of Wheat-Maize in Tropical Savannah Conditions

A successful microbial inoculant can increase root colonization and establish a positive interaction with native microorganisms to promote growth and productivity of cereal crops. Zinc (Zn) is an intensively reported deficient nutrient for maize and wheat production in Brazilian Cerrado. It can be sustainably managed by inoculation with plant growth-promoting bacteria and their symbiotic association with other microorganisms such as arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE). The objective of this study was to evaluate the effect of Azospirillum brasilense inoculation and residual Zn rates on root colonization and grain yield of maize and wheat in succession under the tropical conditions of Brazil. These experiments were conducted in a randomized block design with four replications and arranged in a 5 × 2 factorial scheme. The treatments consisted of five Zn rates (0, 2, 4, 6 and 8 kg ha-1) applied from zinc sulfate in maize and residual on wheat and without and with seed inoculation of A. brasilense. The results indicated that root colonization by AMF and DSE in maize-wheat cropping system were significantly increased with interaction of Zn rates and inoculation treatments. Inoculation with A. brasilense at residual Zn rates of 4 kg ha-1 increased root colonization by AMF under maize cultivation. Similarly, inoculation with A. brasilense at residual Zn rates of 2 and 4 kg ha-1 reduced root colonization by DSE under wheat in succession. The leaf chlorophyll index and leaf Zn concentration were increased with inoculation of the A. brasilense and residual Zn rates. The inoculation did not influence AMF spore production and CO2-C in both crops. The grain yield and yield components of maize-wheat were increased with the inoculation of A. brasilense under residual Zn rates of 3 to 4 kg ha-1 in tropical savannah conditions. Inoculation with A. brasilense under residual Zn rates up to 4 kg ha-1 promoted root colonization by AMF and DSE in the maize cropping season. While the inoculation with A. brasilense under 2 and 4 kg ha-1 residual Zn rates reduced root colonization by AMF and DSE in the wheat cropping season. Therefore, inoculation with A. brasilense in combination with Zn fertilization could consider a sustainable approach to increase the yield and performance of the maize-wheat cropping system in the tropical savannah conditions of Brazil.

Fungal Effectoromics: A World in Constant Evolution

Effectors are small, secreted molecules that mediate the establishment of interactions in nature. While some concepts of effector biology have stood the test of time, this area of study is ever-evolving as new effectors and associated characteristics are being revealed. In the present review, the different characteristics that underly effector classifications are discussed, contrasting past and present knowledge regarding these molecules to foster a more comprehensive understanding of effectors for the reader. Research gaps in effector identification and perspectives for effector application in plant disease management are also presented, with a focus on fungal effectors in the plant-microbe interaction and interactions beyond the plant host. In summary, the review provides an amenable yet thorough introduction to fungal effector biology, presenting noteworthy examples of effectors and effector studies that have shaped our present understanding of the field.

Investigations of specialised metabolites of endophyte Diaporthe destruens hosted in Illigera orbiculata C. Y. Wu

A chemical investigation of the endophytic fungus Diaporthe destruens from the Hernandiaceae plant Illigera orbiculata C. Y. Wu collected from southern Yunnan Province, China, led to the isolation of six undescribed compounds, including two azaphilone analogs, which are a pair of epimers (13R-hydroxy-chermesinone A and 13S-hydroxy-chermesinone A); a pyrrole derivative (1-(4-(methoxymethyl)-1H-pyrrol-3-yl)ethan-1-one); an isoindolone derivative (4-hydroxy-6-methoxyisoindolin-1-one); a benzylbenzene derivative (destruensine A) and a conjectural fragment of polyketide ((2R,4R)-2-(methoxymethyl)pentane-1,4-diol) along with nine known compounds. Their structures were elucidated by spectroscopic methods and HRESIMS, and the absolute configurations were further confirmed by electronic circular dichroism (ECD) and chemical derivatization. The antimicrobial activities, anti-acetylcholinesterase activities, antiproliferation, and NO production inhibitory effects of compounds 1-15 were evaluated.

Microbial Effectors: Key Determinants in Plant Health and Disease

Effectors are small, secreted molecules that alter host cell structure and function, thereby facilitating infection or triggering a defense response. Effectoromics studies have focused on effectors in plant-pathogen interactions, where their contributions to virulence are determined in the plant host, i.e., whether the effector induces resistance or susceptibility to plant disease. Effector molecules from plant pathogenic microorganisms such as fungi, oomycetes and bacteria are major disease determinants. Interestingly, the effectors of non-pathogenic plant organisms such as endophytes display similar functions but have different outcomes for plant health. Endophyte effectors commonly aid in the establishment of mutualistic interactions with the plant and contribute to plant health through the induction of systemic resistance against pathogens, while pathogenic effectors mainly debilitate the plant's immune response, resulting in the establishment of disease. Effectors of plant pathogens as well as plant endophytes are tools to be considered in effectoromics for the development of novel strategies for disease management. This review aims to present effectors in their roles as promotors of health or disease for the plant host.

Conserved secreted effectors contribute to endophytic growth and multihost plant compatibility in a vascular wilt fungus

Fungal interactions with plant roots, either beneficial or detrimental, have a crucial impact on agriculture and ecosystems. The cosmopolitan plant pathogen Fusarium oxysporum (Fo) provokes vascular wilts in more than a hundred different crops. Isolates of this fungus exhibit host-specific pathogenicity, which is conferred by lineage-specific Secreted In Xylem (SIX) effectors encoded on accessory genomic regions. However, such isolates also can colonize the roots of other plants asymptomatically as endophytes or even protect them against pathogenic strains. The molecular determinants of endophytic multihost compatibility are largely unknown. Here, we characterized a set of Fo candidate effectors from tomato (Solanum lycopersicum) root apoplastic fluid; these early root colonization (ERC) effectors are secreted during early biotrophic growth on main and alternative plant hosts. In contrast to SIX effectors, ERCs have homologs across the entire Fo species complex as well as in other plant-interacting fungi, suggesting a conserved role in fungus-plant associations. Targeted deletion of ERC genes in a pathogenic Fo isolate resulted in reduced virulence and rapid activation of plant immune responses, while ERC deletion in a nonpathogenic isolate led to impaired root colonization and biocontrol ability. Strikingly, some ERCs contribute to Fo infection on the nonvascular land plant Marchantia polymorpha, revealing an evolutionarily conserved mechanism for multihost colonization by root infecting fungi.

The primary function of Six5 of Fusarium oxysporum is to facilitate Avr2 activity by together manipulating the size exclusion limit of plasmodesmata

Pathogens produce effector proteins to manipulate their hosts. While most effectors act autonomously, some fungal effectors act in pairs and rely on each other for function. During the colonization of the plant vasculature, the root-infecting fungus Fusarium oxysporum (Fo) produces 14 so-called Secreted in Xylem (SIX) effectors. Two of these effector genes, Avr2 (Six3) and Six5, form a gene pair on the pathogenicity chromosome of the tomato-infecting Fo strain. Avr2 has been shown to suppress plant defense responses and is required for full pathogenicity. Although Six5 and Avr2 together manipulate the size exclusion limit of plasmodesmata to facilitate cell-to-cell movement of Avr2, it is unclear whether Six5 has additional functions as well. To investigate the role of Six5, we generated transgenic Arabidopsis lines expressing Six5. Notably, increased susceptibility during the early stages of infection was observed in these Six5 lines, but only to Fo strains expressing Avr2 and not to wild-type Arabidopsis-infecting Fo strains lacking this effector gene. Furthermore, neither PAMP-triggered defense responses, such as ROS accumulation and callose deposition upon treatment with Flg22, necrosis and ethylene-inducing peptide 1-like protein (NLP), or chitosan, nor susceptibility to other plant pathogens, such as the bacterium Pseudomonas syringae or the fungus Verticilium dahlia, were affected by Six5 expression. Further investigation of the ability of the Avr2/Six5 effector pair to manipulate plasmodesmata (PD) revealed that it not only permits cell-to-cell movement of Avr2, but also facilitates the movement of two additional effectors, Six6 and Six8. Moreover, although Avr2/Six5 expands the size exclusion limit of plasmodesmata (i.e., gating) to permit the movement of a 2xFP fusion protein (53 kDa), a larger variant, 3xFP protein (80 kDa), did not move to the neighboring cells. The PD manipulation mechanism employed by Avr2/Six5 did not involve alteration of callose homeostasis in these structures. In conclusion, the primary function of Six5 appears to function together with Avr2 to increase the size exclusion limit of plasmodesmata by an unknown mechanism to facilitate cell-to-cell movement of Fo effectors.