The grapevine flagellin receptor VvFLS2 differentially recognizes flagellin-derived epitopes from the endophytic growth-promoting bacterium Burkholderia phytofirmans and plant pathogenic bacteria

• The role of flagellin perception in the context of plant beneficial bacteria still remains unclear. Here, we characterized the flagellin sensing system flg22-FLAGELLIN SENSING 2 (FLS2) in grapevine, and analyzed the flagellin perception in the interaction with the endophytic plant growth-promoting rhizobacterium (PGPR) Burkholderia phytofirmans. • The functionality of the grapevine FLS2 receptor, VvFLS2, was demonstrated by complementation assays in the Arabidopsis thaliana fls2 mutant, which restored flg22-induced H₂O₂ production and growth inhibition. Using synthetic flg22 peptides from different bacterial origins, we compared recognition specificities between VvFLS2 and AtFLS2. • In grapevine, flg22-triggered immune responses are conserved and led to partial resistance against Botrytis cinerea. Unlike flg22 peptides derived from Pseudomonas aeruginosa or Xanthomonas campestris, flg22 peptide derived from B. phytofirmans triggered only a small oxidative burst, weak and transient defense gene induction and no growth inhibition in grapevine. Although, in Arabidopsis, all the flg22 epitopes exhibited similar biological activities, the expression of VvFLS2 into the fls2 background conferred differential flg22 responses characteristic for grapevine. • These results demonstrate that VvFLS2 differentially recognizes flg22 from different bacteria, and suggest that flagellin from the beneficial PGPR B. phytofirmans has evolved to evade this grapevine immune recognition system.

Indole derivative production by the root endophyte Piriformospora indica is not required for growth promotion but for biotrophic colonization of barley roots

Beneficial effects elicited by the root endophyte Piriformospora indica are widely known, but the mechanism by which these are achieved is still unclear. It is proposed that phytohormones produced by the fungal symbiont play a crucial role in the interaction with the plant roots. Biochemical analyses of the underlying biosynthetic pathways for auxin production have shown that, on tryptophan feeding, P. indica can produce the phytohormones indole-3-acetic acid (IAA) and indole-3-lactate (ILA) through the intermediate indole-3-pyruvic acid (IPA). Time course transcriptional analyses after exposure to tryptophan designated the piTam1 gene as a key player. A green fluorescence protein (GFP) reporter study and transcriptional analysis of colonized barley roots showed that piTam1 is induced during the biotrophic phase. Piriformospora indica strains in which the piTam1 gene was silenced via an RNA interference (RNAi) approach were compromised in IAA and ILA production and displayed reduced colonization of barley (Hordeum vulgare) roots in the biotrophic phase, but the elicitation of growth promotion was not affected compared with the wild-type situation. Our results suggest that IAA is involved in the establishment of biotrophy in P. indica-barley symbiosis and might represent a compatibility factor in this system.

Mutualistic root endophytism is not associated with the reduction of saprotrophic traits and requires a noncompromised plant innate immunity

During a compatible interaction, the sebacinoid root-associated fungi Piriformospora indica and Sebacina vermifera induce modification of root morphology and enhance shoot growth in Arabidopsis thaliana. The genomic traits common in these two fungi were investigated and compared with those of other root-associated fungi and saprotrophs. The transcriptional responses of the two sebacinoid fungi and of Arabidopsis roots to colonization at three different symbiotic stages were analyzed by custom-designed microarrays. We identified key genomic features characteristic of sebacinoid fungi, such as expansions for gene families involved in hydrolytic activities, carbohydrate-binding and protein-protein interaction. Additionally, we show that colonization of Arabidopsis correlates with the induction of salicylic acid catabolism and accumulation of jasmonate and glucosinolates (GSLs). Genes involved in root developmental processes were specifically induced by S. vermifera at later stages during interaction. Using different Arabidopsis indole-GSLs mutants and measurement of secondary metabolites, we demonstrate the importance of the indolic glucosinolate pathway in the growth restriction of P. indica and S. vermifera and we identify indole-phytoalexins and specifically indole-carboxylic acids derivatives as potential key players in the maintenance of a mutualistic interaction with root endophytes.

Effect of endophyte-infection on growth parameters and Cd-induced phytotoxicity of Cd-hyperaccumulator Solanum nigrum L

The aim of this work was to evaluate effects of endophytic bacterium inoculation on plant growth and assess the possible mechanism of endophyte in heavy metal phytoremediation. Seeds of Solanum nigrum L. were inoculated with endophyte Serratia nematodiphila LRE07 and were subjected to Cd in the growing medium. Cd produced a significant inhibition on plant growth and a reduction in the content of photosynthetic pigments. The inoculation of endophytic bacterium alleviated the Cd-induced changes, resulting in more biomass production and higher photosynthetic pigments content of leaves compared with non-symbiotic ones. The beneficial effect was more obvious at relatively low Cd concentration (10 μM). Based on the alteration of nutrient uptake and activated oxygen metabolism in infected plants, the possible mechanisms of endophytic bacterium in Cd phytotoxicity reduction can be concluded as uptake enhancement of essential mineral nutrition and improvement in the antioxidative enzymes activities in infected plant.

Epicoccum nigrum P16, a sugarcane endophyte, produces antifungal compounds and induces root growth

BACKGROUND

Sugarcane is one of the most important crops in Brazil, mainly because of its use in biofuel production. Recent studies have sought to determine the role of sugarcane endophytic microbial diversity in microorganism-plant interactions, and their biotechnological potential. Epicoccum nigrum is an important sugarcane endophytic fungus that has been associated with the biological control of phytopathogens, and the production of secondary metabolites. In spite of several studies carried out to define the better conditions to use E. nigrum in different crops, little is known about the establishment of an endophytic interaction, and its potential effects on plant physiology.

METHODOLOGY/PRINCIPAL FINDINGS

We report an approach based on inoculation followed by re-isolation, molecular monitoring, microscopic analysis, plant growth responses to fungal colonization, and antimicrobial activity tests to study the basic aspects of the E. nigrum endophytic interaction with sugarcane, and the effects of colonization on plant physiology. The results indicate that E. nigrum was capable of increasing the root system biomass and producing compounds that inhibit the in vitro growth of sugarcane pathogens Fusarium verticillioides, Colletotrichum falcatum, Ceratocystis paradoxa, and Xanthomomas albilineans. In addition, E. nigrum preferentially colonizes the sugarcane surface and, occasionally, the endophytic environment.

CONCLUSIONS/SIGNIFICANCE

Our work demonstrates that E. nigrum has great potential for sugarcane crop application because it is capable of increasing the root system biomass and controlling pathogens. The study of the basic aspects of the interaction of E. nigrum with sugarcane demonstrated the facultative endophytism of E. nigrum and its preference for the phylloplane environment, which should be considered in future studies of biocontrol using this species. In addition, this work contributes to the knowledge of the interaction of this ubiquitous endophyte with the host plant, and also to a better use of microbial endophytes in agriculture.

The effects of root endophyte and arbuscular mycorrhizal fungi on growth and cadmium accumulation in wheat under cadmium toxicity

The effects of Piriformospora indica and Glomus mosseae on some growth and physiological parameters, and cadmium (Cd) amounts in Triticum aestivum cv. Sardari39 plants under the toxic levels of Cd were investigated. The experiment was carried out including four treatments (P. indica inoculation, G. mosseae inoculation, co-inoculation of G. mosseae and P. indica, and non-inoculation), each having four Cd concentrations (0, 0.3, 0.6 and 0.9 mM Cd). In non-inoculated plants, by increasing Cd concentration in the soil, growth parameters, chlorophyll content, performance index (PI) and Fv/Fm were reduced, whereas root and shoot Cd accumulation were increased. The colonized plants with P. indica and G. mosseae (in solitary or together) had higher growth, chlorophyll content and PI compared to control. In the presence of P. indica, the Cd concentration was increased in roots, whereas it was decreased in shoots under higher soil Cd concentrations. The presence of G. mosseae decreased root Cd concentration under lower Cd concentration in the soil. Results from this study indicate that P. indica inoculation yielded greater readings of growth parameters, chlorophyll content, PI, root colonization and also reduced shoot Cd content compared to G. mosseae inoculation.

The response of dark septate endophytes (DSE) to heavy metals in pure culture

Dark septate endophytes (DSE) occur widely in association with plants exposed to heavy metal stress. However, little is known about the response of DSE exposed to heavy metals. In this study, five DSE were isolated from the roots of Astragalus adsurgens Pall. seedlings growing on lead-zinc mine tailings in China. Based on morphological characteristics and DNA sequence analyses, the isolates were identified as Gaeumannomyces cylindrosporus, Paraphoma chrysanthemicola, Phialophora mustea, Exophiala salmonis, and Cladosporium cladosporioides. G. cylindrosporus was selected to explore responses to Pb stress. Scanning electron microscopic observations of G. cylindrosporus grown on solid medium revealed curling of hyphae and formation of hyphal coils in response to Pb. In contrast, in liquid medium, hyphae became thick and swollen with an increase in Pb (II) concentration. We interpret that these changes are related to the variation in cell wall components. We also demonstrated that fungal melanin content increased with the addition of Pb(II). Melanin, as an important component in the cell wall, is known to be an essential antioxidant responsible for decreasing heavy metal toxicity. We also measured the total soluble protein content and glutathione (GSH) concentrations in G. cylindrosporus and found that they initially increased and then decreased with the increase of Pb(II) concentrations. The antioxidant enzyme activities were also examined, and the results showed that superoxide dismutase (SOD) activity was significantly positively correlated with Pb(II) concentrations (r = 0.957, P<0.001). Collectively, our observations indicate that the intracellular antioxidant systems, especially fungal melanin, play an important role in abating the hazards of heavy metals.

Root Fungal Endophytes Enhance Heavy-Metal Stress Tolerance of Clethra barbinervis Growing Naturally at Mining Sites via Growth Enhancement, Promotion of Nutrient Uptake and Decrease of Heavy-Metal Concentration

Clethra barbinervis Sieb. et Zucc. is a tree species that grows naturally at several mine sites and seems to be tolerant of high concentrations of heavy metals, such as Cu, Zn, and Pb. The purpose of this study is to clarify the mechanism(s) underlying this species' ability to tolerate the sites' severe heavy-metal pollution by considering C. barbinervis interaction with root fungal endophytes. We measured the heavy metal concentrations of root-zone soil, leaves, branches, and fine roots collected from mature C. barbinervis at Hitachi mine. We isolated fungal endophytes from surface-sterilized root segments, and we examined the growth, and heavy metal and nutrient absorption of C. barbinervis seedlings growing in sterilized mine soil with or without root fungal endophytes. Field analyses showed that C. barbinervis contained considerably high amounts of Cu, Zn, and Pb in fine roots and Zn in leaves. The fungi, Phialocephala fortinii, Rhizodermea veluwensis, and Rhizoscyphus sp. were frequently isolated as dominant fungal endophyte species. Inoculation of these root fungal endophytes to C. barbinervis seedlings growing in sterilized mine soil indicated that these fungi significantly enhanced the growth of C. barbinervis seedlings, increased K uptake in shoots and reduced the concentrations of Cu, Ni, Zn, Cd, and Pb in roots. Without root fungal endophytes, C. barbinervis could hardly grow under the heavy-metal contaminated condition, showing chlorosis, a symptom of heavy-metal toxicity. Our results indicate that the tree C. barbinervis can tolerate high heavy-metal concentrations due to the support of root fungal endophytes including P. fortinii, R. veluwensis, and Rhizoscyphus sp. via growth enhancement, K uptake promotion and decrease of heavy metal concentrations.

Antimicrobial potential of endophytic fungi derived from three seagrass species: Cymodocea serrulata, Halophila ovalis and Thalassia hemprichii

Endophytic fungi from three commonly found seagrasses in southern Thailand were explored for their ability to produce antimicrobial metabolites. One hundred and sixty endophytic fungi derived from Cymodoceaserrulata (Family Cymodoceaceae), Halophilaovalis and Thalassiahemprichii (Family Hydrocharitaceae) were screened for production of antimicrobial compounds by a colorimetric broth microdilution test against ten human pathogenic microorganisms including Staphylococcus aureus ATCC 25923, a clinical isolate of methicillin-resistant S. aureus, Escherichia coli ATCC 25923, Pseudomonas aeruginosa ATCC 27853, Candida albicans ATCC 90028 and NCPF 3153, Cryptococcus neoformans ATCC 90112 and ATCC 90113 and clinical isolates of Microsporumgypseum and Penicilliummarneffei. Sixty-nine percent of the isolates exhibited antimicrobial activity against at least one test strain. Antifungal activity was more pronounced than antibacterial activity. Among the active fungi, seven isolates including Hypocreales sp. PSU-ES26 from C. serrulata, Trichoderma spp. PSU-ES8 and PSU-ES38 from H. ovalis, and Penicillium sp. PSU-ES43, Fusarium sp. PSU-ES73, Stephanonectria sp. PSU-ES172 and an unidentified endophyte PSU-ES190 from T. hemprichii exhibited strong antimicrobial activity against human pathogens with minimum inhibitory concentrations (MIC) of less than 10 µg/ml. The inhibitory extracts at concentrations of 4 times their MIC destroyed the targeted cells as observed by scanning electron microscopy. These results showed the antimicrobial potential of extracts from endophytic fungi from seagrasses.

Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation

All plants form symbioses with endophytic fungi, which affect host plant health and function. Most endophytic fungi are horizontally transmitted, and consequently, local environment and geographic location greatly influence endophyte community composition. Growing evidence also suggests that identity of the plant host (e.g., species, genotype) can be important in shaping endophyte communities. However, little is known about how disturbances to plants affect their fungal symbiont communities. The goal of this study was to test if disturbances, from both natural and anthropogenic sources, can alter endophyte communities independent of geographic location or plant host identity. Using the plant species white snakeroot (Ageratina altissima; Asteraceae), we conducted two experiments that tested the effect of perturbation on endophyte communities. First, we examined endophyte response to leaf mining insect activity, a natural perturbation, in three replicate populations. Second, for one population, we applied fungicide to plant leaves to test endophyte community response to an anthropogenic perturbation. Using culture-based methods and Sanger sequencing of fungal isolates, we then examined abundance, diversity, and community structure of endophytic fungi in leaves subjected to perturbations by leaf mining and fungicide application. Our results show that plant host individual and geographic location are the major determinants of endophyte community composition even in the face of perturbations. Unexpectedly, we found that leaf mining did not impact endophyte communities in white snakeroot, but fungicide treatment resulted in small but significant changes in endophyte community structure. Together, our results suggest that endophyte communities are highly resistant to biotic and anthropogenic disturbances.

Diversity of endophytic bacteria in Lolium perenne and their potential to degrade petroleum hydrocarbons and promote plant growth

The aim of this study was to assess the ability of twenty-nine endophytic bacteria isolated from the tissues of ryegrass (Lolium perenne L.) to promote plant growth and the degradation of hydrocarbon. Most of the isolates belonged to the genus Pseudomonas and showed multiple plant growth-promoting abilities. All of the bacteria that were tested exhibited the ability to produce indole-3-acetic acid and were sensitive to streptomycin. These strains were capable of phosphate solubilization (62%), cellulolytic enzyme production (62%), a capacity for motility (55%) as well as for the production of siderophore (45%), ammonium (41%) and hydrogen cyanide (38%). Only five endophytes had the emulsification ability that results from the production of biosurfactants. The 1-aminocyclopropane-1-carboxylate deaminase (ACCD) gene (acdS) was found in ten strains. These bacteria exhibited ACCD activities in the range from 1.8 to 56.6 μmol of α-ketobutyrate mg(-1)h(-1), which suggests that these strains may be able to modulate ethylene levels and enhance plant growth. The potential for hydrocarbon degradation was assessed by PCR amplification on the following genes: alkH, alkB, C23O, P450 and pah. The thirteen strains that were tested had the P450 gene but the alkH and pah genes were found only in the Rhodococcus fascians strain (L11). Four endophytic bacteria belonging to Microbacterium sp. and Rhodococcus sp. (L7, S12, S23, S25) showed positive results for the alkB gene.

Identification of arsenic resistant endophytic bacteria from Pteris vittata roots and characterization for arsenic remediation application

Mitigation of arsenic (As) pollution is a topical environmental issue of high R&D priority. The present investigation was carried out to isolate As resistant endophytes from the roots of Indian ecotype Pteris vittata and characterize their As transformation and tolerance ability, plant growth promoting characteristics and their role to facilitate As uptake by the plant. A total of 8 root endophytes were isolated from plants grown in As amended soil (25 mg As kg(-1)). These isolates were studied for minimum inhibitory concentration (MIC), arsenite As(III) - arsenate As(V) transformation ability, plant growth promoting (PGP) characteristics through siderophore, indole acetic acid (IAA) production, phosphatase, ACC deaminase activity, and presence of arsenite oxidase (aox) and arsenite transporter (arsB) genes. On the basis of 16S rDNA sequence analysis, these isolates belong to Proteobacteria, Firmicutes and Bacteroidetes families under the genera Bacillus, Enterobacter, Stenotrophomonas and Rhizobium. All isolates were found As tolerant, of which one isolates showed highest tolerance up to 1000 mg L(-1) concentration in SLP medium. Five isolates were IAA positive with highest IAA production up to 60 mg/L and two isolates exhibited siderophore activity. Phosphatase activity was shown by only one isolate while ACC deaminase activity was absent in all the isolates. The As transformation study by silver nitrate test showed that only two strains had dual characteristics of As(III) oxidation and As (V) reduction, four strains exhibited either of the characteristics while other two didn't confirmed any of the two characteristics. Presence of aox gene was detected in two strains and arsB gene in six isolates. The strain with highest As tolerance also showed highest IAA production and occurrence of arsB gene. Present investigation may open up further scope of utilizing these endophytes for up gradation of phytoextraction process.

Bacterial communities of three plant species from Pb-Zn contaminated sites and plant-growth promotional benefits of endophytic Microbacterium sp. (strain BXGe71)

The endophytic bacterial community of two hyperaccumulators (Arabis alpine, Dysphania ambrosioides) and Veronica ciliate was investigated by Illumina sequencing technology. In addition, the culturable endophytic bacteria (EB) were isolated and their plant-growth promotion capabilities were studied. A dataset consisting of 221,075 filtered high-quality and classifiable unique 16S rDNA gene tags, and an average of 36,846 tags with a mean length of 464-bp for each sample was generated. In total, 10801 different operational taxonomic units (OTUs) were detected, belonging to 18 bacterial phyla, 41 classes, 91 orders, 135 families, and 215 genera. Pseudomonas was the most dominant genus in both shoots and roots of the two hyperaccumulators, making up 81.56% and 81.13%, 41.60% and 77.06% of the total number of OTUs, respectively. However, both Chao 1 and Shannon indices of EB of the two hyperaccumulators were significantly lower than those of V. ciliate (P <. 05), except the Shannon index of D. ambrosioides shoots. The endophytic bacterial community of roots and shoots of A. alpine showed greater similarity with that of D. ambrosioides roots (12 km away), and clustered to one group in dendrogram, in clear contrast to that of V. ciliate, which grew closer to A. alpine (60 m away). Combining results of soil and plant analyses, we suggest that the soil properties, especially heavy metal concentration, may influence the plants endophytic bacterial community composition. Pot experiments showed that the strain BXGe71 (Microbacterium sp.) from A. alpine significantly enhanced host plants' growth under multi-heavy metal (HM) stress (P < .05, t-test).

Biodegradation of phenanthrene by endophytic fungus Phomopsis liquidambari in vitro and in vivo

Phenanthrene, as a widespread polycyclic aromatic hydrocarbons (PAHs) contaminant in vitro and in vivo of plant, has the characteristics of carcinogenicity, teratogenicity and mutagenicity. This work aimed to explore the phenanthrene metabolic mechanism by Phomopsis liquidambari in vitro, as well as the bioremediation ability through P. liquidambari-rice combination. This strain was able to use phenanthrene as source of carbon and energy to grow, more than 77% of added 50 mg L^-1 phenanthrene was removed after 10 d in MSM. We identified the metabolic products via HPLC-MS and proposed two possible degradation pathways. Phenanthrene was firstly combined with oxygen to become phenanthrene 9,10-oxide, and then degraded to 9-phenanthrol, followed by oxidization to 9,10-dihydroxyphenanthrene. In addition, that epoxide (phenanthrene 9,10-oxide) was also hydrolyzed to phenanthrene trans-9,10-dihydrodiol, and then dehydrogenized to 9,10-dihydroxyphenanthrene, which was further degraded to 9,10-phenanthrenequinone; during this metabolic pathway, the changes of P450 monooxygenase, epoxide hydrolase, dehydrogenase and catechol 2,3-dioxygenase activities and their corresponding gene transcription levels were closely related. What's more, P. liquidambari could combine with rice to eliminate phenanthrene accumulated in vivo of rice seedlings, and the removal rate in inoculation treatment represented a significant difference (increased 25.68%) compared with uninoculation treatment after cultivation 30 d. Therefore, we concluded that P. liquidambari could not only respond to phenanthrene pollution stress in vitro but also exert a mitigation effect on plants accumulated phenanthrene. This work provides a foundation for applying endophytic fungi to PAHs bioremediation in vitro and in vivo.

Diversity, molecular phylogeny, and bioactive potential of fungal endophytes associated with the Himalayan blue pine (Pinus wallichiana)

In this study, we investigated the diversity of fungal endophytes associated with Pinus wallichiana from the Western Himalayas, with emphasis on comparison of endophytic communities harbored by the stem and needle tissues of the host and their antimicrobial potential. A total number of 130 isolates, comprising of 38 different genera, were recovered from 210 fragments of the plant. Among the isolated fungi, only a single isolate, Tritirachium oryzae, belonged to the Phylum Basidiomycota whereas the rest belonged to Ascomycota. Dothideomycetes was the dominant class with the highest isolation frequency of 49.2 %. The most frequent colonizers of the host were Alternaria spp., Pestalotiopsis spp., Preussia spp., and Sclerostagonospora spp. The diversity and species richness were higher in needle tissues than in the stems. Antimicrobial activities were displayed by extracts from a total number of 22 endophytes against one or more pathogens. Endophytes designated as P1N13 (Coniothyrium carteri), P2N8 (Thielavia subthermophila), P4S6b (Truncatella betulae), P7N10 (Cochliobolus australiensis), and P8S4 (Tritirachium oryzae) were highly active against Candida albicans. Broad spectrum antimicrobial activities were obtained with the extracts of P8-S4 (Tritirachium oryzae) and P5-N26 (Coniochaeta gigantospora) that were potentially active against the Gram-positive and Gram-negative bacteria as well as the fungal pathogen, Candida albicans. The most prominent antagonistic activity against fungal pathogens was shown by P8-S4 (Tritirachium oryzae), P5-N31a (Truncatella spadicea), and P5-N20 (Fusarium larvarum). Our findings indicate that Pinus wallichiana harbors a rich endophytic fungal community with potential antimicrobial activities. Further studies are needed to understand the ecology and evolutionary context of the associations between the Himalayan pine and its endophytes.

Combined use of Enterobacter sp. MN17 and zeolite reverts the adverse effects of cadmium on growth, physiology and antioxidant activity of Brassica napus

The objective of the study was to evaluate role of zeolite and Enterobacter sp. MN17 on Cd uptake, growth, physiological and biochemical responses of Brassica napus on Cd-contaminated soil. A sandy clay loam soil in plastic pots was spiked with Cd (0 and 80 mg kg-1) and amended with zeolite (0 and 10 g kg-1). Seeds of B. napus were inoculated with Enterobacter sp. MN17. Both inoculated and non-inoculated seeds of B. napus were sown and plants were harvested after 60 days of growth and data were collected. Although sole application of zeolite and seed inoculation reverted adverse effects of Cd in B. napus plants, the combined use resulted in even higher growth and physiological responses compared to control plants. The combined use under Cd stress increased plant height, root length, dry biomass of shoot and root up to 32%, 57%, 42% and 64%, respectively compared to control. The different physiological attributes (photosynthetic rate, chlorophyll content, transpiration rate, stomatal conductance) of B. napus were improved from 6% to 137%. Moreover, combined use of zeolite and seed inoculation on Cd-contaminated soil reduced the stress to plants as antioxidant activities decreased up to 25-64%, however enzyme activities were still higher than plants grown on normal soil. Root and shoot analysis of B. napus for Cd content depicted that zeolite and bacterium decreased Cd uptake from soil. It is concluded that combined use of zeolite and strain MN17 reduces Cd uptake from soil and improves physiological and biochemical responses of B. napus which is helpful to alleviate Cd toxicity to plants.

An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host

Endophytes, both of bacterial and fungal origin, are ubiquitously present in all plants. While their origin and evolution are enigmatic, there is burgeoning literature on their role in promoting growth and stress responses in their hosts. We demonstrate that a salt-tolerant endophyte isolated from salt-adapted Pokkali rice, a Fusarium sp., colonizes the salt-sensitive rice variety IR-64, promotes its growth under salt stress and confers salinity stress tolerance to its host. Physiological parameters, such as assimilation rate and chlorophyll stability index were higher in the colonized plants. Comparative transcriptome analysis revealed 1348 up-regulated and 1078 down-regulated genes in plants colonized by the endophyte. Analysis of the regulated genes by MapMan and interaction network programs showed that they are involved in both abiotic and biotic stress tolerance, and code for proteins involved in signal perception (leucine-rich repeat proteins, receptor-like kinases) and transduction (Ca2+ and calmodulin-binding proteins), transcription factors, secondary metabolism and oxidative stress scavenging. For nine genes, the data were validated by qPCR analysis in both roots and shoots. Taken together, these results show that salt-adapted Pokkali rice varieties are powerful sources for the identification of novel endophytes, which can be used to confer salinity tolerance to agriculturally important, but salt-sensitive rice varieties.

Effect of endophytic Bacillus cereus ERBP inoculation into non-native host: Potentials and challenges for airborne formaldehyde removal

Phytoremediation could be a cost-effective, environmentally friendly approach for the treatment of indoor air. However, some drawbacks still dispute the expediency of phytotechnology. Our objectives were to investigate the competency of plant growth-promoting (PGP) endophytic Bacillus cereus ERBP (endophyte root blue pea), isolated from the root of Clitoria ternatea, to colonize and stabilize within Zamioculcas zamiifolia and Euphorbia milii as non-native hosts without causing any disease or stress symptoms. Moreover, the impact of B. cereus ERBP on the natural shoot endophytic community and for the airborne formaldehyde removal capability of non-native hosts was assessed. Non-native Z. zamiifolia was effectively inoculated with B. cereus ERBP through soil as the most efficient method of endophyte inoculation. Denaturing gradient gel electrophoresis profiling of the shoot endophytic community verified the colonization and stability of B. cereus ERBP within its non-native host during a 20-d fumigation period without interfering with the natural shoot endophytic diversity of Z. zamiifolia. B. cereus ERBP conferred full protection to its non-native host against formaldehyde phytotoxicity and enhanced airborne formaldehyde removal of Z. zamiifolia whereas non-inoculated plants suffered from formaldehyde phytotoxicity because their natural shoot endophytic community was detrimentally affected by formaldehyde. In contrast, B. cereus ERBP inoculation into non-native E. milii deteriorated airborne formaldehyde removal of the non-native host (compared to a non-inoculated one) as B. cereus ERBP interfered with natural shoot endophytic community of E. milii, which caused stress symptoms and stimulated ethylene biosynthesis. Non-native host inoculation with PGP B. cereus ERBP could bear potentials and challenges for airborne formaldehyde removal.

Impact of salicylic acid- and jasmonic acid-regulated defences on root colonization by Trichoderma harzianum T-78

We recently found that the beneficial fungus Trichoderma harzianum T-78 primes tomato plants for salicylic acid (SA)- and jasmonic acid (JA)-regulated defenses, resulting in enhanced resistance against the root knot nematode Meloidogyne incognita. By using SA- and JA-impaired mutant lines and exogenous hormonal application, here we investigated whether the SA- and JA-pathways also have a role in T-78 root colonization of Arabidopsis thaliana. Endophytic colonization by T-78 was faster in the SA-impaired mutant sid2 than in the wild type. Moreover, elicitation of SA-dependent defenses by SA application reduced T-78 colonization, indicating that the SA-pathway affects T-78 endophytism. In contrast, elicitation of the JA-pathway, which antagonized SA-dependent defenses, resulted in enhanced endophytic colonization by T-78. These findings are in line with our previous observation that SA-dependent defenses are repressed by T-78, which likely aids colonization by the endophytic fungus.

Analysis of Secondary Metabolites from Plant Endophytic Fungi

Filamentous fungi produce a wide variety of secondary metabolites, which are recognized as a rich source of biomolecules with potential medicinal applications. According to chemical structures and biosynthetic pathways, secondary metabolites are mainly divided into four groups, including polyketide, nonribosomal peptides, alkaloids, and terpenes. Owing to their special living environment, plant endophytic fungi potentially produce many bioactive metabolites with diverse structural features. Some of these metabolites have been demonstrated to hold pharmaceutical and ecological significance. In order to identify bioactive compounds, different methods have been developed to isolate secondary metabolites from plant endophytic fungi. In this chapter, we describe the procedures for fungal fermentation, metabolite extraction, and analysis using high-performance liquid chromatography (HPLC). The endophytic fungus Pestalotiopsis fici, which was isolated from the healthy branches of Camellia sinensis (Theaceae), produces 88 secondary metabolites including 70 new natural products. Combining 74 secondary metabolite clusters revealed by genome sequencing analysis, P. fici is used as an example for analysis of secondary metabolites. The procedures could also be adopted for other fungi after small modifications.

Ethanol and methanol can improve huperzine A production from endophytic Colletotrichum gloeosporioides ES026

Huperzine A (HupA) is a plant alkaloid that is of great interest as a therapeutic candidate for the treatment of Alzheimer's disease. However, the current production of HupA from plants in large quantity is unsustainable because the plant resource is scarce and the content of HupA in plants is extremely low. Surprisingly, this compound was recently found to be produced by various endophytic fungi, which are much more controllable than the plants due to simpler genetics and ease of manipulation. However, it might be due to the innate properties of endophytic symbiosis, that production of this chemical in large quantity from endophytes has not yet been put into practice. Endophytic Colletotrichum gloeosporioides ES026 was previously isolated from a HupA producing plant and the fungi also proved to produce HupA. In this study, various fermentation conditions were tried to optimize the production of HupA from C. gloeosporioides ES026. Optimization of these parameters resulted in a 25.58% increase in HupA yield. Potato extracts supplemented with glucose or sucrose but not maltose facilitated HupA producing from the fungi. A final concentration of 0.5–2% ethanol stimulated the growth of fungi while methanol with the same treatment slightly inhibited the growth. However, both methanol and ethanol greatly increased the HupA production with the highest yield of HupA (51.89% increment) coming from ethanol treatment. Further analysis showed that both ethanol and methanol were strong inducers of HupA production, while ethanol was partially used as a carbon source during fermentation. It was noticed that the color of that ethanol treated mycelia gradually became dark while methanol treated ones stayed grey during fermentation. The present study sheds light on the importance of optimizing the fermentation process, which, combined with effective inducers, maximizes production of chemicals of important economic interest from endophytic fungi.

Endophyte-mediated effects on the growth and physiology of Achnatherum sibiricum are conditional on both N and P availability

The interaction of endophyte-grass associations are conditional on nitrogen (N) availability, but the reported responses of these associations to N are inconsistent. We hypothesized that this inconsistency is caused, at least in part, by phosphorus (P) availability. In this experiment, we compared the performance of endophyte-infected (EI) and endophyte-free (EF) Achnatherum sibiricum subjected to four treatments comprising a factorial combination of two levels of N (N+ vs. N-, i.e. N supply vs. N deficiency) and two levels of P (P+ vs. P-, i.e. P supply vs. P deficiency) availability. The results showed that A. sibiricum-Neotyphodium associations were conditional on both N and P availability, but more conditional on N than P. Under N+P- conditions, endophyte infection significantly improved acid phosphatase activity of EI plants, such that the biomass of EI plants was not affected by P deficiency (i.e. similar growth to N+P+ conditions), and resulted in more biomass in EI than EF plants. Under N-P+ conditions, biomass of both EI and EF decreased compared with N+P+; however, EI biomass decreased slowly by decreasing leaf N concentration more rapidly but allocating higher fractions of N to photosynthetic machinery compared with EF plants. This change of N allocation not only improved photosynthetic ability of EI plants but also significantly increased their biomass. Under N-P- conditions, EI plants allocated higher fractions of N to photosynthesis and had greater P concentrations in roots, but there was no significant difference in biomass between EI and EF plants. Our results support the hypothesis that endophyte-grass interactions are dependent on both N and P availability. However, we did not find a clear cost of endophyte infection in A. sibiricum.

The effect of long-term Cd and Ni exposure on seed endophytes of Agrostis capillaris and their potential application in phytoremediation of metal-contaminated soils

We examined whether long-term Cd exposure leads to beneficial changes in the cultivable endophytic bacteria present in the seeds of Agrostis capillaris. Therefore the cultivable seed endophytes of Agrostis capillaris growing on a long-term Cd/Ni-contaminated plot (Cd/Ni seeds) were compared with those originating from a non-contaminated plot (control seeds). We observed plant- and contaminant-dependent effects on the population composition between control and Cd/Ni seeds. Also differences in phenotypic characteristics were found: endophytes from Cd/Ni seeds exhibited more ACC deaminase activity and production of siderophores and IAA, while endophytes from control seeds, very surprisingly, showed more metal tolerance. Finally, the 3 most promising seed endophytes were selected based on their metal tolerance and plant growth promoting potential, and inoculated in Agrostis capillaris seedlings. In case of non-exposed plants, inoculation resulted in a significantly improved plant growth; after inoculation of Cd-exposed plants an increased Cd uptake was achieved without affecting plant growth. This indicates that inoculation of Agrostis with its seed endophytes might be beneficial for its establishment during phytoextraction and phytostabilisation of Cd-contaminated soils.

Does co-inoculation of Lactuca serriola with endophytic and arbuscular mycorrhizal fungi improve plant growth in a polluted environment?

Phytoremediation of polluted sites can be improved by co-inoculation with mycorrhizal and endophytic fungi. In this study, the effects of single- and co-inoculation of Lactuca serriola with an arbuscular mycorrhizal (AM) fungus, Rhizoglomus intraradices, and endophytic fungi, Mucor sp. or Trichoderma asperellum, on plant growth, vitality, toxic metal accumulation, sesquiterpene lactone production and flavonoid concentration in the presence of toxic metals were evaluated. Inoculation with the AM fungus increased biomass yield of the plants grown on non-polluted and polluted substrate. Co-inoculation with the AM fungus and Mucor sp. resulted in increased biomass yield of plants cultivated on the polluted substrate, whereas co-inoculation with T. asperellum and the AM fungus increased plant biomass on the non-polluted substrate. In the presence of Mucor sp., mycorrhizal colonization and arbuscule richness were increased in the non-polluted substrate. Co-inoculation with the AM fungus and Mucor sp. increased Zn concentration in leaves and roots. The concentration of sesquiterpene lactones in plant leaves was decreased by AM fungus inoculation in both substrates. Despite enhanced host plant costs caused by maintaining symbiosis with numerous microorganisms, interaction of wild lettuce with both mycorrhizal and endophytic fungi was more beneficial than that with a single fungus. The study shows the potential of double inoculation in unfavourable environments, including agricultural areas and toxic metal-polluted areas.

Distribution of endophytic bacteria in Alopecurus aequalis Sobol and Oxalis corniculata L. from soils contaminated by polycyclic aromatic hydrocarbons

The distributions of endophytic bacteria in Alopecurus aequalis Sobol and Oxalis corniculata L. grown in soils contaminated with different levels of polycyclic aromatic hydrocarbons (PAHs) were investigated with polymerase chain reaction followed by denaturing gradient gel electrophoresis technology (PCR-DGGE) and cultivation methods. Twelve types of PAHs, at concentrations varying from 0.16 to 180 mg·kg⁻¹, were observed in the roots and shoots of the two plants. The total PAH concentrations in Alopecurus aequalis Sobol obtained from three different PAH-contaminated stations were 184, 197, and 304 mg·kg⁻¹, and the total PAH concentrations in Oxalis corniculata L. were 251, 346, and 600 mg·kg⁻¹, respectively. The PCR-DGGE results showed that the endophytic bacterial communities in the roots and shoots of the two plants were quite different, although most bacteria belonged to Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. A total of 68 endophytic bacterial strains were isolated from different tissues of the two plants and classified into three phyla: Firmicutes, Proteobacteria and Bacteroidetes. In both plants, Bacillus spp. and Pseudomonas spp. were the dominant cultivable populations. With an increase in the PAH pollution level, the diversity and distribution of endophytic bacteria in the two plants changed correspondingly, and the number of cultivable endophytic bacterial strains decreased rapidly. Testing of the isolated endophytic bacteria for tolerance to each type of PAH showed that most isolates could grow well on Luria-Bertani media in the presence of different PAHs, and some isolates were able to grow rapidly on a mineral salt medium with a single PAH as the sole carbon and energy source, indicating that these strains may have the potential to degrade PAHs in plants. This research provides the first insight into the characteristics of endophytic bacterial populations under different PAH pollution levels and provides a species resource for the isolation of PAH-degrading endophytic bacteria.