Endophytic colonization of barley (Hordeum vulgare) roots by the nematophagous fungus Pochonia chlamydosporia reveals plant growth promotion and a general defense and stress transcriptomic response

Biological control of the native endophytic fungus Pochonia chlamydosporia from the root nodule of Dolichos lablab on Fusarium wilt of banana TR4

Fusarium wilt of banana caused by Fusarium oxysporum f. sp. cubense, Tropical Race 4 (TR4) is a soil-borne disease, and it is devastating. At present, the biological control using antagonistic microorganisms to mitigate TR4 is one of the best strategies as a safe and green way. Yunnan has abundant and diverse microbial resources. Using the dual-culture method, the antagonistic endophytic fungi against TR4 were isolated and screened from the root nodule of Dolichos lablab. The effect of the highest antagonistic activity strain on the morphology of the TR4 mycelium was observed using the scanning electron microscope. According to morphological characteristics and sequence analysis, the strain was identified. The biocontrol effect and plant growth promotion were investigated by greenhouse pot experiment. Using the confocal laser scanning microscope and the real-time fluorescence quantitative PCR, the dynamics of TR4 infestation and the TR4 content in banana plant roots and corms would also be detected. In this study, 18 native endophytic fungi were isolated from a root nodule sample of Dolichos lablab in the mulch for banana fields in Yuxi, Yunnan Province, China. The YNF2217 strain showed a high antagonistic activity against TR4 in plate confrontation experiments, and the inhibition rate of YNF2217 is 77.63%. After TR4 culture with YNF2217 for 7 days in plate confrontation experiments, the morphology of the TR4 mycelium appeared deformed and swollen when observed under a scanning electron microscope. According to morphological characteristics and sequence analysis, the strain YNF2217 was identified as Pochonia chlamydosporia. In the greenhouse pot experiment, the biocontrol effect of YNF2217 fermentation solution on TR4 was 70.97% and 96.87% on banana plant leaves and corms, respectively. Furthermore, YNF2217 significantly promoted the growth of banana plants, such as plant height, leaf length, leaf width, leaf number, pseudostem girth, and both the aboveground and underground fresh weight. Observations of TR4 infestation dynamics in banana roots and corms, along with real-time fluorescence quantitative PCR, verified that YNF2217 inoculation could significantly reduce the TR4 content. Therefore, YNF2217 as P. chlamydosporia, which was found first time in China and reported here, is expected to be an important new fungal resource for the green control of Fusarium wilt of banana in the future.

EMNPD: a comprehensive endophytic microorganism natural products database for prompt the discovery of new bioactive substances

The discovery and utilization of natural products derived from endophytic microorganisms have garnered significant attention in pharmaceutical research. While remarkable progress has been made in this field each year, the absence of dedicated open-access databases for endophytic microorganism natural products research is evident. To address the increasing demand for mining and sharing of data resources related to endophytic microorganism natural products, this study introduces EMNPD, a comprehensive endophytic microorganism natural products database comprising manually curated data. Currently, EMNPD offers 6632 natural products from 1017 endophytic microorganisms, targeting 1286 entities (including 94 proteins, 282 cell lines, and 910 species) with 91 diverse bioactivities. It encompasses the physico-chemical properties of natural products, ADMET information, quantitative activity data with their potency, natural products contents with diverse fermentation conditions, systematic taxonomy, and links to various well-established databases. EMNPD aims to function as an open-access knowledge repository for the study of endophytic microorganisms and their natural products, thereby facilitating drug discovery research and exploration of bioactive substances. The database can be accessed at http://emnpd.idrblab.cn/ without the need for registration, enabling researchers to freely download the data. EMNPD is expected to become a valuable resource in the field of endophytic microorganism natural products and contribute to future drug development endeavors.

An insight into endophytic antimicrobial compounds: an updated analysis

Resistance in micro-organisms against antimicrobial compounds is an emerging phenomenon in the modern era as compared to the traditional world which brings new challenges to discover novel antimicrobial compounds from different available sources, such as, medicinal plants, various micro-organisms, like, bacteria, fungi, algae, actinomycetes, and endophytes. Endophytes reside inside the plants without exerting any harmful impact on the host plant along with providing ample of benefits. In addition, they are capable of producing diverse antimicrobial compounds similar to their host, allowing them to serve as useful micro-organism for a range of therapeutic purposes. In recent years, a large number of studies on the antimicrobial properties of endophytic fungi have been carried out globally. These antimicrobials have been used to treat various bacterial, fungal, and viral infections in humans. In this review, the potential of fungal endophytes to produce diverse antimicrobial compounds along with their various benefits to their host have been focused on. In addition, classification systems of endophytic fungi as well as the need for antimicrobial production with genetic involvement and some of the vital novel antimicrobial compounds of endophytic origin can further be utilized in the pharmaceutical industries for various formulations along with the role of nanoparticles as antimicrobial agents have been highlighted.

Effect of Pochonia chlamydosporia Endophytism and Meloidogyne incognita Parasitism on WRKYs and Defense Gene Expression in Tomato Roots

The expression of WRKY transcription factors and plant defense-related genes was studied in the roots of Apulian tomato (Solanum lycopersicum) cv Regina di Fasano (accessions MRT and PLZ) endophytically colonized by Pochonia chlamydosporia and parasitized or not by the root-knot nematode (RKN) Meloidogyne incognita. The effect on plant growth, nematode parasitism and histological aspect of the interaction were considered. The association of P. chlamydosporia with RKN-parasitized MRT plants increased the total biomass and shoot fresh weight in comparison with healthy plants and with those only parasitized by RKN, without the endophyte. However, the PLZ accession showed no significant difference in the observed biometric parameters. The number of RKN-induced galls per plant was not affected by endophytism eight days after inoculation. No histological changes were observed in the nematode feeding sites in the presence of the fungus. Gene expression analysis showed an accession-specific response to P. chlamydosporia with differential activation of WRKY-related genes. No significant change was found for WRKY76 expression in nematode-parasitized plants compared with control roots, confirming cultivar susceptibility. Data indicate genotype-specific responses of the WRKY genes to parasitism examined in roots with nematodes and/or endophytic P. chlamydosporia. At 25 days post-inoculation with P. chlamydosporia, no significant difference was observed in the expression of defense-related genes in both accessions, suggesting that salicylic acid (SA) (PAL and PR1) and jasmonate (JA) related genes (Pin II) are not active during endophytism.

Rhizosphere 16S-ITS Metabarcoding Profiles in Banana Crops Are Affected by Nematodes, Cultivation, and Local Climatic Variations

Agriculture affects soil and root microbial communities. However, detailed knowledge is needed on the effects of cropping on rhizosphere, including biological control agents (BCA) of nematodes. A metabarcoding study was carried out on the microbiota associated with plant parasitic and other nematode functional groups present in banana farms in Tenerife (Canary Islands, Spain). Samples included rhizosphere soil from cv Pequeña Enana or Gruesa and controls collected from adjacent sites, with the same agroecological conditions, without banana roots. To characterize the bacterial communities, the V3 and V4 variable regions of the 16S rRNA ribosomal gene were amplified, whereas the internal transcribed spacer (ITS) region was used for the fungi present in the same samples. Libraries were sequenced with an Illumina MiSeq™ in paired ends with a 300-bp read length. For each sample, plant parasitic nematodes (PPN) and other nematodes were extracted from the soil, counted, and identified. Phytoparasitic nematodes were mostly found in banana rhizosphere. They included Pratylenchus goodeyi, present in northern farms, and Helicotylenchus spp., including H. multicinctus, found in both northern and southern farms. Metabarcoding data showed a direct effect of cropping on microbial communities, and latitude-related factors that separated northern and southern controls from banana rizosphere samples. Several fungal taxa known as nematode BCA were identified, with endophytes, mycorrhizal species, and obligate Rozellomycota endoparasites, almost only present in the banana samples. The dominant bacterial phyla were Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, and Acidobacteria. The ITS data showed several operational taxonomic units (OTUs) belonging to Sordariomycetes, including biocontrol agents, such as Beauveria spp., Arthrobotrys spp., Pochonia chlamydosporia, and Metarhizium anisopliae. Other taxa included Trichoderma harzianum, Trichoderma longibrachiatum, Trichoderma virens, and Fusarium spp., together with mycoparasites such as Acrostalagmus luteoalbus. However, only one Dactylella spp. showed a correlation with predatory nematodes. Differences among the nematode guilds were found, as phytoparasitic, free-living, and predatory nematode groups were correlated with specific subsets of other bacteria and fungi. Crop cultivation method and soil texture showed differences in taxa representations when considering other farm and soil variables. The data showed changes in the rhizosphere and soil microbiota related to trophic specialization and specific adaptations, affecting decomposers, beneficial endophytes, mycorrhizae, or BCA, and plant pathogens.

Production of Purpureocillium lilacinum and Pochonia chlamydosporia by Submerged Liquid Fermentation and Bioactivity against Tetranychus urticae and Heterodera glycines through Seed Inoculation

Pochoniachlamydosporia and Purpureocilliumlilacinum are fungal bioagents used for the sustainable management of plant parasitic nematodes. However, their production through submerged liquid fermentation and their use in seed treatment have been underexplored. Therefore, our goal was to assess the effect of different liquid media on the growth of 40 isolates of P. lilacinum and two of P. chlamydosporia. The most promising isolates tested were assessed for plant growth promotion and the control of the two-spotted spider mite (Tetranychus urticae) and the soybean cyst nematode (Heterodera glycines). Most isolates produced > 108 blastospores mL−1 and some isolates produced more than 104 microsclerotia mL−1. Microsclerotia of selected isolates were used to inoculate common bean (Phaseolus vulgaris L.) seeds in greenhouse trials. All fungal isolates reduced the T. urticae fecundity in inoculated plants through seed treatment, while P. chlamydosporia ESALQ5406 and P. lilacinum ESALQ2593 decreased cyst nematode population. Purpureocillium lilacinum was more frequently detected in soil, whereas P. chlamydosporia colonized all plant parts. Pochonia chlamydosporia ESALQ5406 improved the root development of bean plants. These findings demonstrate the possibility of producing submerged propagules of P. chlamydosporia and P. lilacinum by liquid culture, and greenhouse trials support the applicability of fungal microsclerotia in seed treatment to control P. vulgaris pests.

Attraction and toxicity: Ways volatile organic compounds released by Pochonia chlamydosporia affect Meloidogyne incognita

The production of volatile organic compounds (VOCs) acting against plant-parasitic nematodes has been characterized in different fungi; however, the role of VOCs emitted by Pochonia chlamydosporia in its trophic interaction with Meloidogyne incognita is still unknown. The aim of this study was to determine the effects of VOCs emitted by P. chlamydosporia strain Pc-10 on different stages (eggs, juveniles and female) of the M. incognita life cycle. Exposure of M. incognita eggs to VOCs released by Pc-10 resulted in a reduction up to 88 % in the nematode egg hatching, when compared to the control treatments. The VOCs emitted by Pc-10 also attracted M. incognita second-stage juveniles (J2). Through gas chromatography-mass spectrometry (GC-MS), three molecules were identified from the volatiles of the strain Pc-10, with 1,4-dimethoxybenzene being the major compound. In tests performed in vitro, 1,4-dimethoxybenzene at a concentration of 1050 μg mL-1 inhibited M. incognita egg hatching by up to 78.7 % compared to the control (0 μg mL-1) and attracted M. incognita J2 in all concentrations evaluated (1, 10, 100, 1000, and 10000 μg mL-1). The 1,4-dimethoxybenzene also showed fumigant and non-fumigant nematicidal activity against M. incognita. This compound presented lethal concentration for 50 % (LC50) of M. incognita J2 ranged from 132 to 136 μg mL-1. Fumigation with 1,4-dimethoxybenzene (100 mg) reduced egg hatching by up to 89 % and killed up to 86 % of M. incognita J2 compared to the control (0 μg mL-1). In vivo, the VOCs produced by Pc-10, 1,4-dimethoxybenzene, and the combination of both (Pc-10 + 1,4-dimethoxybenzene) attracted the M. incognita J2, compared to the respective controls. To the best of our knowledge, this is the first report on the attraction of M. incognita J2 and the toxicity to eggs and J2 by VOCs from P. chlamydosporia in which 1,4-dimethoxybenzene is the main toxin and attractant.

Pochonia chlamydosporia Isolate PC-170-Induced Expression of Marker Genes for Defense Pathways in Tomatoes Challenged by Different Pathogens

Pochonia chlamydosporia is a fungal parasite of nematode eggs. Studies have shown that some strains of Pochonia chlamydosporia can promote plant growth and induce plants’ systemic resistance to root-knot nematodes by colonizing in their roots. This study aimed to verify the effect of the PC-170 strain on tomato growth and systemic resistance. Split-root experiments were conducted to observe the systemic resistance induced by PC-170. To explore the defense pathway that was excited due to the colonization by PC-170, we tested the expression of marker genes for defense pathways, and used mutant lines to verify the role of plant defense pathways. Our results showed that PC-170 can colonize roots, and promotes growth. We found a role for jasmonic acid (JA) in modulating tomato colonization by PC-170. PC-170 can activate tomato defense responses to reduce susceptibility to infection by the root-knot nematode Meloidogyne incognita, and induced resistance to some pathogens in tomatoes. The marker genes of the defense pathway were significantly induced after PC-170 colonization. However, salicylic acid (SA)- and jasmonic acid (JA)-dependent defenses in roots were variable with the invasion of different pathogens. Defense pathways play different roles at different points in time. SA- and JA-dependent defense pathways were shown to cross-communicate. Different phytohormones have been involved in tomato plants’ responses against different pathogens. Our study confirmed that adaptive JA signaling is necessary to regulate PC-170 colonization and induce systemic resistance in tomatoes.

Root Endophytism by Pochonia chlamydosporia Affects Defense-Gene Expression in Leaves of Monocot and Dicot Hosts under Multiple Biotic Interactions

A study was carried out on the effect of the root endophytic fungus Pochonia chlamydosporia on plant systemic signal of defense related genes during fungal or nematode parasitism. Different biotic stress factors were examined, inoculating roots of dicot and monocot hosts with the endophyte, and measuring the expression of defense genes in leaves. A first greenhouse assay was carried out on expression of PAL, PIN II, PR1 and LOX D in leaves of tomato cv Tondino inoculated with Phytophthora infestans (CBS 120920), inoculating or not the roots of infected plants with P. chlamydosporia DSM 26985. In a second assay, plants of banana (Musa acuminata cv Grand Naine) were artificially infected with Fusarium oxysporum f. sp. cubense Tropical race 4 (TR4) and inoculated or not with DSM 26985. In a further experiment, banana plants were inoculated or not with P. chlamydosporia plus juveniles of the root knot nematode (RKN) Meloidogyne incognita. A similar assay was also carried out in vitro with adults and juveniles of the lesion nematode Pratylenchus goodeyi. Differential expression of the defense genes examined was observed for all plant-stress associations, indicative of early, upward systemic signals induced by the endophyte. Changes in expression profiles included a 5-fold down-regulation of PIN II at 2 dai in leaves of tomato plants treated with P. infestans and/or P. chlamydosporia, and the up-regulation of PAL by the endophyte alone, at 2 and 7 dai. In the TR4 assay, PR1 was significantly up-regulated at 7 dai in banana leaves, but only in the P. chlamydosporia treated plants. At 10 dai, PIN II expression was significantly higher in leaves of plants inoculated only with TR4. The banana-RKN assay showed a PR1 expression significantly higher than controls at 4 and 7 dai in plants inoculated with P. chlamydosporia alone, and a down-regulation at 4 dai in leaves of plants also inoculated with RKN, with a PR1 differential up-regulation at 10 dai. Pratylenchus goodeyi down-regulated PIN at 21 dai, with or without the endophyte, as well as PAL but only in presence of P. chlamydosporia. When inoculated alone, the endophyte up-regulated PR1 and LOX. The gene expression patterns observed in leaves suggest specific and time-dependent relationships linking host plants and P. chlamydosporia in presence of biotic stress factors, functional to a systemic, although complex, activation of defense genes.

Putative LysM Effectors Contribute to Fungal Lifestyle

Fungal LysM effector proteins can dampen plant host–defence responses, protecting hyphae from plant chitinases, but little is known on these effectors from nonpathogenic fungal endophytes. We found four putative LysM effectors in the genome of the endophytic nematophagous fungus Pochonia chlamydosporia (Pc123). All four genes encoding putative LysM effectors are expressed constitutively by the fungus. Additionally, the gene encoding Lys1—the smallest one—is the most expressed in banana roots colonised by the fungus. Pc123 Lys1, 2 and 4 display high homology with those of other strains of the fungus and phylogenetically close entomopathogenic fungi. However, Pc123 Lys3 displays low homology with other fungi, but some similarities are found in saprophytes. This suggests evolutionary divergence in Pc123 LysM effectors. Additionally, molecular docking shows that the NAcGl binding sites of Pc123 Lys 2, 3 and 4 are adjacent to an alpha helix. Putative LysM effectors from fungal endophytes, such as Pc123, differ from those of plant pathogenic fungi. LysM motifs from endophytic fungi show clear conservation of cysteines in Positions 13, 51 and 63, unlike those of plant pathogens. LysM effectors could therefore be associated with the lifestyle of a fungus and give us a clue of how organisms could behave in different environments.

Chitosan modulates Pochonia chlamydosporia gene expression during nematode egg parasitism

Climate change makes plant‐parasitic nematodes (PPN) an increasing threat to commercial crops. PPN can be managed sustainably by the biocontrol fungus Pochonia chlamydosporia (Pc). Chitosan generated from chitin deacetylation enhances PPN parasitism by Pc. In this work, we investigate the molecular mechanisms of Pc for chitosan resistance and root‐knot nematode (RKN) parasitism, using transcriptomics. Chitosan and RKN modify the expression of Pc genes, mainly those involved in oxidation–reduction processes. Both agents significantly modify the expression of genes associated to 113 GO terms and 180 Pc genes. Genes encoding putative glycoproteins (Pc adhesives) to nematode eggshell, as well as genes involved in redox, carbohydrate and lipid metabolism trigger the response to chitosan. We identify genes expressed in both the parasitic and endophytic phases of the Pc lifecycle; these include proteases, chitosanases and transcription factors. Using the Pathogen—Host Interaction database (PHI‐base), our previous RNA‐seq data and RT‐PCR of Pc colonizing banana we have investigated genes expressed both in the parasitic and endophytic phases of Pc lifecycle.

Metarhizium: jack of all trades, master of many

The genus Metarhizium and Pochonia chlamydosporia comprise a monophyletic clade of highly abundant globally distributed fungi that can transition between long-term beneficial associations with plants to transitory pathogenic associations with frequently encountered protozoans, nematodes or insects. Some very common 'specialist generalist' species are adapted to particular soil and plant ecologies, but can overpower a wide spectrum of insects with numerous enzymes and toxins that result from extensive gene duplications made possible by loss of meiosis and associated genome defence mechanisms. These species use parasexuality instead of sex to combine beneficial mutations from separate clonal individuals into one genome (Vicar of Bray dynamics). More weakly endophytic species which kill a narrow range of insects retain sexuality to facilitate host-pathogen coevolution (Red Queen dynamics). Metarhizium species can fit into numerous environments because they are very flexible at the genetic, physiological and ecological levels, providing tractable models to address how new mechanisms for econutritional heterogeneity, host switching and virulence are acquired and relate to diverse sexual life histories and speciation. Many new molecules and functions have been discovered that underpin Metarhizium associations, and have furthered our understanding of the crucial ecology of these fungi in multiple habitats.

Fungi-Nematode Interactions: Diversity, Ecology, and Biocontrol Prospects in Agriculture

Fungi and nematodes are among the most abundant organisms in soil habitats. They provide essential ecosystem services and play crucial roles for maintaining the stability of food-webs and for facilitating nutrient cycling. As two of the very abundant groups of organisms, fungi and nematodes interact with each other in multiple ways. Here in this review, we provide a broad framework of interactions between fungi and nematodes with an emphasis on those that impact crops and agriculture ecosystems. We describe the diversity and evolution of fungi that closely interact with nematodes, including food fungi for nematodes as well as fungi that feed on nematodes. Among the nematophagous fungi, those that produce specialized nematode-trapping devices are especially interesting, and a great deal is known about their diversity, evolution, and molecular mechanisms of interactions with nematodes. Some of the fungi and nematodes are significant pathogens and pests to crops. We summarize the ecological and molecular mechanisms identified so far that impact, either directly or indirectly, the interactions among phytopathogenic fungi, phytopathogenic nematodes, and crop plants. The potential applications of our understanding to controlling phytophagous nematodes and soilborne fungal pathogens in agricultural fields are discussed.

Isolates of the Nematophagous Fungus Pochonia chlamydosporia Are Endophytic in Banana Roots and Promote Plant Growth

The biocontrol fungus Pochonia chlamydosporia colonizes banana roots endophytically. Root hairs and root surface were colonized by a stable GFP (green fluorescent protein) transformant of the fungus. Hyphal penetration in root cells was also observed. Spores of P. chlamydosporia 123, significantly increase root and leaf length and weight in banana plantlets (Musa acuminata cv. ‘Dwarf Cavendish’) in growth chamber experiments 30 days post-inoculation. In greenhouse 8-L pot experiments, P. chlamydosporia 123 spore inoculation significantly increases root, corm and leaf length, and leaf weight in banana plants (75 days post-inoculation). Spore inoculation of P. chlamydosporia strains from diverse origin (Pc21, Pc123, Pc399, and Pccat), significantly increase root, corm and leaf length and weight in banana plantlets. Pc21 from Italy was the best colonizer of banana roots. Consequently, this strain significantly increases banana root and leaf length most. Root colonization by P. chlamydosporia was also detected using cultural techniques and qPCR.

Biological Control of Plant-Parasitic Nematodes by Filamentous Fungi Inducers of Resistance: Trichoderma, Mycorrhizal and Endophytic Fungi

Plant-parasitic-nematodes represent a major threat to the agricultural production of different crops worldwide. Due to the high toxicity of chemical nematicides, it is necessary to develop new control strategies against nematodes. In this respect, filamentous fungi can be an interesting biocontrol alternative. The genus Trichoderma, mycorrhizal and endophytic fungi are the main groups of filamentous fungi studied and used as biological control agents (BCAs) against nematodes as resistance inducers. They are able to reduce the damage caused by plant-parasitic nematodes directly by parasitism, antibiosis, paralysis and by the production of lytic enzymes. But they also minimize harm by space and resource-competition, by providing higher nutrient and water uptake to the plant, or by modifying the root morphology, and/or rhizosphere interactions, that constitutes an advantage for the plant-growth. Besides, filamentous fungi are able to induce resistance against nematodes by activating hormone-mediated (salicylic and jasmonic acid, strigolactones among others) plant-defense mechanisms. Additionally, the alteration of the transport of chemical defense components through the plant or the synthesis of plant secondary metabolites and different enzymes can also contribute to enhancing plant defenses. Therefore, the use of filamentous fungi of the mentioned groups as BCAs is a promising durable biocontrol strategy in agriculture against plant-parasitic nematodes.

Pochonia chlamydosporia Induces Plant-Dependent Systemic Resistance to Meloidogyne incognita

Meloidogyne spp. are the most damaging plant parasitic nematodes for horticultural crops worldwide. Pochonia chlamydosporia is a fungal egg parasite of root-knot and cyst nematodes able to colonize the roots of several plant species and shown to induce plant defense mechanisms in fungal-plant interaction studies, and local resistance in fungal-nematode-plant interactions. This work demonstrates the differential ability of two out of five P. chlamydosporia isolates, M10.43.21 and M10.55.6, to induce systemic resistance against M. incognita in tomato but not in cucumber in split-root experiments. The M10.43.21 isolate reduced infection (32-43%), reproduction (44-59%), and female fecundity (14.7-27.6%), while the isolate M10.55.6 only reduced consistently nematode reproduction (35-47.5%) in the two experiments carried out. The isolate M10.43.21 induced the expression of the salicylic acid pathway (PR-1 gene) in tomato roots 7 days after being inoculated with the fungal isolate and just after nematode inoculation, and at 7 and 42 days after nematode inoculation too. The jasmonate signaling pathway (Lox D gene) was also upregulated at 7 days after nematode inoculation. Thus, some isolates of P. chlamydosporia can induce systemic resistance against root-knot nematodes but this is plant species dependent.

Time-dependent effects of Pochonia chlamydosporia endophytism on gene expression profiles of colonized tomato roots

A transcriptome analysis was produced from tomato roots inoculated with the hyphomycete Pochonia chlamydosporia at three different times. Gene expression data were also yielded from fungus grown in vitro or endophytic. A next-generation sequencing (NGS) and network analysis approach were applied. We identified 3.676 differentially expressed tomato genes (DEG), highlighting a core of 93 transcripts commonly down- or upregulated at every time point, shedding light on endophytism process. Functional categories related to plant information-processing system, which recognizes, percepts, and transmits signals, were associated with gene upregulated early in time, with higher representations in processes such as plant defense regulation later in time. Network analysis of a DEG subset showed dominance of MAP kinase hubs in the uninoculated control samples, replaced by an increased centrality of WRKY transcription factor and ETR-ethylene response factor genes in the colonized roots. Fungus genes expressed during progression of plant colonization, therefore related to the host colonization process or endophytism persistence, were also identified. Data provided a high-resolution insight on tomato transcriptome changes as induced by endophytism, highlighting a specific modulation of stress-responsive transcripts, related to a selective activation of defense pathways, likely required by the fungus to establish a persistent endophytic lifestyle.

Comparative analyses of albumin/globulin grain proteome fraction in differentially salt-tolerant Tunisian barley landraces reveals genotype-specific and defined abundant proteins

Salinity is one of the major abiotic stresses threatening crop production and yield worldwide. Breeding programmes are therefore needed to improve yield under cultivation in soil. Traits from locally adopted landraces provide a resource to assist breeding of novel elite genotypes. Here, we examine differentially expressed proteins by performing comparative proteomic profiling of the albumin/globulin grain fraction of Tunisian barley genotype landraces with contrasting salinity tolerance. Tunisian barley Boulifa (B, tolerant) and Testour (T, sensitive) mature grains were assessed in 2-DE profiles. Differentially expressed spots, with an abundance enhanced 1.5-fold in the grain, were subjected to MALDI TOF/TOF MS for identification. Distinctiveness between tolerant and sensitive genotypes was proved in the albumin/globulin fraction using PCA; 64 spots showed significant differential abundance. Increased accumulation of 40 spots was confirmed in Boulifa with, interestingly, four genotype-specific spots. Two of these four spots were sHSP. Proteins with highest abundance were serpin Z7, 16.9 KDa Class I HSP and phosphogluconolactonase 2. Proteins such as expansin, kiwellin, kinesin and succinyl-CoA ligase were identified for the first time in barley grain. Moreover, ß-amylase, LEA family and others were identified as abundant in Boulifa. On the other hand, proteins more accumulated in Testour are implicated mainly in ROS scavenging and protease inhibition. Our results clearly indicate proteomic contrast between the two selected genotypes. With identification of specific HSP, high abundant stress-protective and other defined proteins, we provide biochemical traits that will support breeding programmes to address the threat of salinity in agricultural production.

Infection of Plasmodiophora brassicae changes the fungal endophyte community of tumourous stem mustard roots as revealed by high-throughput sequencing and culture-dependent methods

Diverse fungal endophytes live in plants and are shaped by some abiotic and biotic stresses. Plant disease as particular biotic stress possibly gives an impact on the communities of fungal endophytes. In this study, clubroot disease caused by an obligate biotroph protist, Plasmodiophora brassicae, was considered to analyze its influence on the fungal endophyte community using an internal transcribed spacer (ITS) through high-throughput sequencing and culture-dependent methods. The results showed that the diversity of the endophyte community in the healthy roots was much higher than the clubroots. Ascomycota was the dominant group of endophytes (Phoma, Mortierella, Penicillium, etc.) in the healthy roots while P. brassicae was the dominant taxon in the clubroots. Hierarchical clustering, principal component analysis (PCA), principal coordinates analysis (PCoA) and analysis of similarities (ANOSIM) indicated significant differences between the endophyte communities in the healthy roots and clubroots. Linear discriminant analysis effect size (LefSe) analysis showed that the dominant genera could be regarded as potential biomarkers. The endophyte community in the healthy roots had a more complex network compared with the clubroots. Also, many plant pathogenic Fusarium were isolated from the clubroots by the culture-dependent method. The outcome of this study illustrates that P. brassicae infection may change the fungal endophyte community associated with the roots of tumourous stem mustard and facilitates the entry of soil pathogen into the roots.

Consortium of five fungal isolates conditioning root growth and arbuscular mycorrhiza in soybean, corn, and sugarcane

Plant growth and arbuscular mycorrhizal colonization were studied in sugarcane, corn and soybean by applying five plant growth promoting fungi: Beauveria bassiana, Metarhizium anisopliae, Pochonia chlamydosporia, Purpureocillium lilacinum, and Trichoderma asperella. Sugarcane, corn and soybean were grown in pots under two treatments: (1) inoculation with the fungal consortium and (2) control without inoculation. In the inoculated treatment, fungal spore suspension were applied to the seeds and shoots were sprayed every 28 days. Means were analyzed by analysis of variance and Tukey's test at 5% probability level. The experiment was arranged in a completely randomized design, with six replications. Fungi consortium mediate root growth in soybean and corn, and arbuscular mycorrhizal colonization in soybean and sugarcane. These findings are probably caused by the fungi producing phytohormones and inducing the plants to synthesize phytohormones: auxins for root growth; and jasmonic, abscisic, and salicylic acids with a role in the regulation of mycorrhizal colonization. These effects are important when seeking conservation strategies in agriculture and livestock production, since Fungi consortium can better mediate soil resource acquisition, promoting greater absorption of nutrients and water.

Colonization and destruction of ants of the genus Camponotus sp. (Hymenoptera: Formicidae) in vitro by the fungus Pochonia chlamydosporia in the southeast region of Brazil

The objective of this study was to evaluate, in vitro, the colonization and destruction of ants of the genus Camponotus sp. by the ovicidal fungus Pochonia chlamydosporia (VC4 isolate), in the southeast region of Brazil. The insects used in the experiment were worker ants of the genus Camponotus sp., collected periodically in the environment and immediately transported to the laboratory in test tubes. Then, VC4 growth was promoted in 2% chitin agar medium (2% WQ) to obtain a fungal solution containing conidia and/or chlamydospores. Two experimental groups were formed. Treated group consisted of Petri dishes containing 2% agar-water culture medium (2% WA) with nine live insects and 20 µL of fungal solution at the concentration of 15,000 conidia/chlamydospores. Control group consisted of Petri dishes containing 2% WA culture medium and nine live insects. The dishes in the treated and control groups were incubated in BOD at 25 ± 1 °C and 80 ± 10% relative humidity for 4 days. After 4 days, it was observed that the VC4 had grown, colonized, and caused the destruction of the ants. The fungus P. chlamydosporia was efficient at colonizing and destroying the urban ants collected on an experimental basis. Thus, it could open up new ways to reduce the use of chemical compounds in the future, decreasing health and environmental problems.

The 'PhenoBox', a flexible, automated, open-source plant phenotyping solution

There is a need for flexible and affordable plant phenotyping solutions for basic research and plant breeding. We demonstrate our open source plant imaging and processing solution ('PhenoBox'/'PhenoPipe') and provide construction plans, source code and documentation to rebuild the system. Use of the PhenoBox is exemplified by studying infection of the model grass Brachypodium distachyon by the head smut fungus Ustilago bromivora, comparing phenotypic responses of maize to infection with a solopathogenic Ustilago maydis (corn smut) strain and effector deletion strains, and studying salt stress response in Nicotiana benthamiana. In U. bromivora-infected grass, phenotypic differences between infected and uninfected plants were detectable weeks before qualitative head smut symptoms. Based on this, we could predict the infection outcome for individual plants with high accuracy. Using a PhenoPipe module for calculation of multi-dimensional distances from phenotyping data, we observe a time after infection-dependent impact of U. maydis effector deletion strains on phenotypic response in maize. The PhenoBox/PhenoPipe system is able to detect established salt stress responses in N. benthamiana. We have developed an affordable, automated, open source imaging and data processing solution that can be adapted to various phenotyping applications in plant biology and beyond.

Belowground Microbiota and the Health of Tree Crops

Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.

Genome and secretome analysis of Pochonia chlamydosporia provide new insight into egg-parasitic mechanisms

Pochonia chlamydosporia infects eggs and females of economically important plant-parasitic nematodes. The fungal isolates parasitizing different nematodes are genetically distinct. To understand their intraspecific genetic differentiation, parasitic mechanisms, and adaptive evolution, we assembled seven putative chromosomes of P. chlamydosporia strain 170 isolated from root-knot nematode eggs (~44 Mb, including 7.19% of transposable elements) and compared them with the genome of the strain 123 (~41 Mb) isolated from cereal cyst nematode. We focus on secretomes of the fungus, which play important roles in pathogenicity and fungus-host/environment interactions, and identified 1,750 secreted proteins, with a high proportion of carboxypeptidases, subtilisins, and chitinases. We analyzed the phylogenies of these genes and predicted new pathogenic molecules. By comparative transcriptome analysis, we found that secreted proteins involved in responses to nutrient stress are mainly comprised of proteases and glycoside hydrolases. Moreover, 32 secreted proteins undergoing positive selection and 71 duplicated gene pairs encoding secreted proteins are identified. Two duplicated pairs encoding secreted glycosyl hydrolases (GH30), which may be related to fungal endophytic process and lost in many insect-pathogenic fungi but exist in nematophagous fungi, are putatively acquired from bacteria by horizontal gene transfer. The results help understanding genetic origins and evolution of parasitism-related genes.

Endophytic Bacillus and Pseudomonas spp. Modulate Apple Shoot Growth, Cellular Redox Balance, and Protein Expression Under in Vitro Conditions

Interactions between host plants and endophytic microorganisms play an important role in plant responses to pathogens and environmental stresses and have potential applications for plant stress management under in vitro conditions. We assessed the effect of endophytic bacteria on the growth and proliferation of domestic apple cv. Gala shoots in vitro. Further, a model apple cell suspension system was used to examine molecular events and protein expression patterns at an early stage of plant-endophyte interaction. Among the seven strains used in the study, Bacillus spp. strains Da_1, Da_4, and Da_5 and the Pseudomonas fluorescens strain Ga_1 promoted shoot growth and auxiliary shoot proliferation. In contrast, Bacillus sp. strain Oa_4, P. fluorescens strain Ga_3 and P. orientalis strain G_12 inhibited shoot development. In the cell suspension, the effects of the association between endophytic bacteria and plant cells were specific to each strain. Modulation of the cellular redox balance was monitored in the apple cells using a 2',7'-dichlorodihydrofluorescein diacetate (H₂DCFDA) probe, and strain-specific effects were observed that correlated with the in vitro shoot development results. Proteomic analysis revealed differences in protein expressions in apple cells co-cultivated with different Bacillus spp. strains that had contrasting effects on cellular redox balance and shoot development. The Bacillus sp. strain Da_4, which enhanced shoot development and oxidation of H₂DCFDA, induced differential expression of proteins that are mainly involved in the defense response and regulation of oxidative stress. Meanwhile, treatment with Bacillus sp. strain Oa_4 led to strong upregulation of PLAT1, HSC70-1 and several other proteins involved in protein metabolism and cell development. Taken together, the results suggest that different cell signaling and response events at the early stage of the plant-endophyte interaction may be important for strain-dependent regulation of cellular redox balance and development of shoot phenotype.

Identification of tomato miRNAs responsive to root colonization by endophytic Pochonia chlamydosporia

The molecular mechanisms active during the endophytic phase of the fungus Pochonia chlamydosporia are still poorly understood. In particular, few data are available on the links between the endophyte and the root response, as modulated by noncoding small RNAs. In this study, we describe the microRNAs (miRNAs) that are differentially expressed (DE) in the roots of tomato, colonized by P. chlamydosporia. A genome-wide NGS expression profiling of small RNAs in roots, either colonized or not by the fungus, showed 26 miRNAs upregulated in inoculated roots. Their predicted target genes are involved in the plant information processing system, which recognizes, percepts, and transmits signals, with higher representations in processes such as apoptosis and plant defense regulation. RNAseq data showed that predicted miRNA target genes were downregulated in tomato roots after 4, 7, 10, and 21 days post P. chlamydosporia inoculation. The differential expression of four miRNAs was further validated using qPCR analysis. The P. chlamydosporia endophytic lifestyle in tomato roots included an intricate network of miRNAs and targets. Data provide a first platform of DE tomato miRNAs after P. chlamydosporia colonization. They indicated that several miRNAs are involved in the host response to the fungus, playing important roles for its recognition as a symbiotic microorganism, allowing endophytism by modulating the host defense reaction. Data also indicated that endophytism affects tRNA fragmentation. This is the first study on miRNAs induced by P. chlamydosporia endophytism and related development regulation effects in Solanum lycopersicum.

Chitosan Increases Tomato Root Colonization by Pochonia chlamydosporia and Their Combination Reduces Root-Knot Nematode Damage

The use of biological control agents could be a non-chemical alternative for management of Meloidogyne spp. [root-knot nematodes (RKN)], the most damaging plant-parasitic nematodes for horticultural crops worldwide. Pochonia chlamydosporia is a fungal parasite of RKN eggs that can colonize endophytically roots of several cultivated plant species, but in field applications the fungus shows a low persistence and efficiency in RKN management. The combined use of P. chlamydosporia with an enhancer could help its ability to develop in soil and colonize roots, thereby increasing its efficiency against nematodes. Previous work has shown that chitosan enhances P. chlamydosporia sporulation and production of extracellular enzymes, as well as nematode egg parasitism in laboratory bioassays. This work shows that chitosan at low concentrations (up to 0.1 mg ml-1) do not affect the viability and germination of P. chlamydosporia chlamydospores and improves mycelial growth respect to treatments without chitosan. Tomato plants irrigated with chitosan (same dose limit) increased root weight and length after 30 days. Chitosan irrigation increased dry shoot and fresh root weight of tomato plants inoculated with Meloidogyne javanica, root length when they were inoculated with P. chlamydosporia, and dry shoot weight of plants inoculated with both P. chlamydosporia and M. javanica. Chitosan irrigation significantly enhanced root colonization by P. chlamydosporia, but neither nematode infection per plant nor fungal egg parasitism was affected. Tomato plants cultivated in a mid-suppressive (29.3 ± 4.7% RKN egg infection) non-sterilized clay loam soil and irrigated with chitosan had enhanced shoot growth, reduced RKN multiplication, and disease severity. Chitosan irrigation in a highly suppressive (73.7 ± 2.6% RKN egg infection) sterilized-sandy loam soil reduced RKN multiplication in tomato. However, chitosan did not affect disease severity or plant growth irrespective of soil sterilization. Chitosan, at an adequate dose, can be a potential tool for sustainable management of RKN.

Managing the plant microbiome for biocontrol fungi: examples from Hypocreales

Feeding an increasing global population requires continued improvements in agricultural efficiency and productivity. Meeting estimated future production levels requires the adoption of practices that increase output without environmental degradation associated with external inputs to supplement nutrition or control pests. Enriching the community of microbes associated with plants in agricultural systems for those providing ecosystem services such as pest control is one possible component towards achieving sustainable productivity increases. In this review we explore the current state of knowledge for Hypocreales fungi used in biological control. Advances in understanding the field ecology, diversity and genetic determinants of host range and virulence of hypocrealean fungi provide the means to improve their efficacy.

Gibberellins Producing Endophytic Fungus Porostereum spadiceum AGH786 Rescues Growth of Salt Affected Soybean

In the pursuit of sustainable agriculture through environment and human health friendly practices, we evaluated the potential of a novel gibberellins (GAs) producing basidiomycetous endophytic fungus Porostereum spadiceum AGH786, for alleviating salt stress and promoting health benefits of soybean. Soybean seedlings exposed to different levels of NaCl stress (70 and 140 mM) under greenhouse conditions, were inoculated with the AGH786 strain. Levels of phytohormones including GAs, JA and ABA, and isoflavones were compared in control and the inoculated seedlings to understand the mechanism through which the stress is alleviated. Gibberellins producing endophytic fungi have been vital for promoting plant growth under normal and stress conditions. We report P. spadiceum AGH786 as the ever first GAs producing basidiomycetous fungus capable of producing six types of GAs. In comparison to the so for most efficient GAs producing Gibberella fujikuroi, AGH786 produced significantly higher amount of the bioactive GA3. Salt-stressed phenotype of soybean seedlings was characterized by low content of GAs and high amount of ABA and JA with reduced shoot length, biomass, leaf area, chlorophyll contents, and rate of photosynthesis. Mitigation of salt stress by AGH786 was always accompanied by high GAs, and low ABA and JA, suggesting that this endophytic fungus reduces the effect of salinity by modulating endogenous phytohormones of the seedlings. Additionally, this strain also enhanced the endogenous level of two isoflavones including daidzen and genistein in soybean seedlings under normal as well as salt stress conditions as compared to their respective controls. P. spadiceum AGH786 boosted the NaCl stress tolerance and growth in soybean, by modulating seedlings endogenous phytohormones and isoflavones suggesting a valuable contribution of this potent fungal biofertilizer in sustainable agriculture in salt affected soils.

Endophytic fungal diversity of Fragaria vesca, a crop wild relative of strawberry, along environmental gradients within a small geographical area

BACKGROUND

Fungal endophytes are highly diverse ubiquitous asymptomatic microorganisms, some of which appear to be symbiotic. Depending on abiotic conditions and genotype of the plant, the diversity of endophytes may confer fitness benefits to plant communities.

METHODS

We studied a crop wild relative (CWR) of strawberry, along environmental gradients with a view to understand the cultivable root-derived endophytic fungi that can be evaluated for promoting growth and tolerating stress in selected plant groups. The main objectives were to understand whether: (a) suboptimal soil types are drivers for fungal distribution and diversity; (b) high pH and poor nutrient availability lead to fungal-plant associations that help deliver fitness benefits; and (c) novel fungi can be identified for their use in improving plant growth, and alleviate stress in diverse crops.

RESULTS

The study revealed that habitats with high pH and low nutrient availability have higher fungal diversity, with more rare fungi isolated from locations with chalky soil. Plants from location G were the healthiest even though soil from this location was the poorest in nutrients. Study of environmental gradients, especially extreme habitat types, may help understand the root zone fungal diversity of different functional classes. Two small in vitro pilot studies conducted with two isolates showed that endophytic fungi from suboptimal habitats can promote plant growth and fitness benefits in selected plant groups.

DISCUSSION

Targeting native plants and crop wild relatives for research offers opportunities to unearth diverse functional groups of root-derived endophytic fungi that are beneficial for crops.

Arabidopsis thaliana root colonization by the nematophagous fungus Pochonia chlamydosporia is modulated by jasmonate signaling and leads to accelerated flowering and improved yield

Pochonia chlamydosporia has been intensively studied in nematode control of different crops. We have investigated the interaction between P. chlamydosporia and the model system Arabidopsis thaliana under laboratory conditions in the absence of nematodes. This study demonstrates that P. chlamydosporia colonizes A. thaliana. Root colonization monitored with green fluorescent protein-tagged P. chlamydosporia and quantitative PCR (qPCR) quantitation methods revealed root cell invasion. Fungal inoculation reduced flowering time and stimulated plant growth, as determined by total FW increase, faster development of inflorescences and siliques, and a higher yield in terms of seed production per plant. Precocious flowering was associated with significant expression changes in key flowering-time genes. In addition, we also provided molecular and genetic evidence that point towards jasmonate signaling as an important factor to modulate progression of plant colonization by the fungus. Our results indicate that P. chlamydosporia provides benefits to the plant in addition to its nematophagous activity. This report highlights the potential of P. chlamydosporia to improve yield in economically important crops.

CAZyme content of Pochonia chlamydosporia reflects that chitin and chitosan modification are involved in nematode parasitism

Pochonia chlamydosporia is a soil fungus with a multitrophic lifestyle combining endophytic and saprophytic behaviors, in addition to a nematophagous activity directed against eggs of root-knot and other plant parasitic nematodes. The carbohydrate-active enzymes encoded by the genome of P. chlamydosporia suggest that the endophytic and saprophytic lifestyles make use of a plant cell wall polysaccharide degradation machinery that can target cellulose, xylan and, to a lesser extent, pectin. This enzymatic machinery is completed by a chitin breakdown system that involves not only chitinases, but also chitin deacetylases and a large number of chitosanases. P. chlamydosporia can degrade and grow on chitin and is particularly efficient on chitosan. The relevance of chitosan breakdown during nematode egg infection is supported by the immunolocalization of chitosan in Meloidogyne javanica eggs infected by P. chlamydosporia and by the fact that the fungus expresses chitosanase and chitin deacetylase genes during egg infection. This suggests that these enzymes are important for the nematophagous activity of the fungus and they are targets for improving the capabilities of P. chlamydosporia as a biocontrol agent in agriculture.

Mechanisms Involved in Nematode Control by Endophytic Fungi

Colonization of plants by particular endophytic fungi can provide plants with improved defenses toward nematodes. Evidently, such endophytes can be important in developing more sustainable agricultural practices. The mechanisms playing a role in this quantitative antagonism are poorly understood but most likely multifactorial. This knowledge gap obstructs the progress regarding the development of endophytes or endophyte-derived constituents into biocontrol agents. In part, this may be caused by the fact that endophytic fungi form a rather heterogeneous group. By combining the knowledge of the currently characterized antagonistic endophytic fungi and their effects on nematode behavior and biology with the knowledge of microbial competition and induced plant defenses, the various mechanisms by which this nematode antagonism operates or may operate are discussed. Now that new technologies are becoming available and more accessible, the currently unresolved mechanisms can be studied in greater detail than ever before.