Expression of endogenous UDP-glucosyltransferase in endophyte Phomopsis liquidambaris reduces deoxynivalenol contamination in wheat.

Fusarium head blight is a devastating disease that causes severe yield loses and mycotoxin contamination in wheat grain. Additionally, balancing the trade-off between wheat production and disease resistance has proved challenging. This study aimed to expand the genetic tools of the endophyte Phomopsis liquidambaris against Fusarium graminearum. Specifically, we engineered a UDP-glucosyltransferase-expressing P. liquidambaris strain (PL-UGT) using ADE1 as a selection marker and obtained a deletion mutant using an inducible promoter that drives Cas9 expression. Our PL-UGT strain converted deoxynivalenol (DON) into DON-3-G in vitro at a rate of 71.4 % after 36 h. DON inactivation can be used to confer tolerance in planta. Wheat seedlings inoculated with endophytic strain PL-UGT showed improved growth compared with those inoculated with wildtype P. liquidambaris. Strain PL-UGT inhibited the growth of Fusarium graminearum and reduced infection rate to 15.7 %. Consistent with this finding, DON levels in wheat grains decreased from 14.25 to 0.56 µg/g when the flowers were pre-inoculated with PL-UGT and then infected with F. graminearum. The expression of UGT in P. liquidambaris was nontoxic and did not inhibit plant growth. Endophytes do not enter the seeds nor induce plant disease, thereby representing a novel approach to fungal disease control.

Depletion of protective microbiota promotes the incidence of fruit disease.

Plant-associated microbiomes play important roles in plant health and productivity. However, despite fruits being directly linked to plant productivity, little is known about the microbiomes of fruits and their potential association with fruit health. Here, by integrating 16S rRNA gene, ITS high-throughput sequencing data, and microbiological culturable approaches, we reported that roots and fruits (pods) of peanut, a typical plant that bears fruits underground, recruit different bacterial and fungal communities independently of cropping conditions and that the incidence of pod disease under monocropping conditions is attributed to the depletion of Bacillus genus and enrichment of Aspergillus genus in geocarposphere. On this basis, we constructed a synthetic community (SynCom) consisting of three Bacillus strains from geocarposphere soil under rotation conditions with high culturable abundance. Comparative transcriptome, microbiome profiling, and plant phytohormone signaling analysis reveal that the SynCom exhibited more effective Aspergillus growth inhibition and pod disease control than individual strain, which was underpinned by a combination of molecular mechanisms related to fungal cell proliferation interference, mycotoxins biosynthesis impairment, and jasmonic acid-mediated plant immunity activation. Overall, our results reveal the filter effect of plant organs on the microbiome and that depletion of key protective microbial community promotes the fruit disease incidence.

Legume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification.

Biological nitrogen fixation by free-living bacteria and rhizobial symbiosis with legumes plays a key role in sustainable crop production. Here, we study how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota via metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Based on a long-term (8 year) diversified cropping field experiment, we find that peanut co-cultured with maize and oilseed rape lead to specific changes in peanut rhizosphere metabolite profiles and bacterial functions and nodulation. Flavonoids and coumarins accumulate due to the activation of phenylpropanoid biosynthesis pathways in peanuts. These changes enhance the growth and nitrogen fixation activity of free-living bacterial isolates, and root nodulation by symbiotic Bradyrhizobium isolates. Peanut plant root metabolites interact with Bradyrhizobium isolates contributing to initiate nodulation. Our findings demonstrate that tailored intercropping could be used to improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions.

Seed-borne bacterial synthetic community resists seed pathogenic fungi and promotes plant growth.

AIMS: In this study, the control effects of synthetic microbial communities composed of peanut seed bacteria against seed aflatoxin contamination caused by Aspergillus flavus and root rot by Fusarium oxysporum were evaluated. METHODS AND RESULTS: Potentially conserved microbial synthetic communities (C), growth-promoting synthetic communities (S), and combined synthetic communities (CS) of peanut seeds were constructed after 16S rRNA Illumina sequencing, strain isolation, and measurement of plant growth promotion indicators. Three synthetic communities showed resistance to root rot and CS had the best effect after inoculating into peanut seedlings. This was achieved by increased defense enzyme activity and activated salicylic acid (SA)-related, systematically induced resistance in peanuts. In addition, CS also inhibited the reproduction of A. flavus on peanut seeds and the production of aflatoxin. These effects are related to bacterial degradation of toxins and destruction of mycelia. CONCLUSIONS: Inoculation with a synthetic community composed of seed bacteria can help host peanuts resist the invasion of seeds by A. flavus and seedlings by F. oxysporum and promote the growth of peanut seedlings.

Root endophyte-mediated alteration in plant H2O2 homeostasis regulates symbiosis outcome and reshapes the rhizosphere microbiota.

Endophytic symbioses between plants and fungi are a dominant feature of many terrestrial ecosystems, yet little is known about the signaling that defines these symbiotic associations. Hydrogen peroxide (H2O2) is recognized as a key signal mediating the plant adaptive response to both biotic and abiotic stresses. However, the role of H2O2 in plant-fungal symbiosis remains elusive. Using a combination of physiological analysis, plant and fungal deletion mutants, and comparative transcriptomics, we reported that various environmental conditions differentially affect the interaction between Arabidopsis and the root endophyte Phomopsis liquidambaris, and link this process to alterations in H2O2 levels and H2O2 fluxes across root tips. We found that enhanced H2O2 efflux leading to a moderate increase in H2O2 levels at the plant-fungal interface is required for maintaining plant-fungal symbiosis. Disturbance of plant H2O2 homeostasis compromises the symbiotic ability of plant roots. Moreover, the fungus-regulated H2O2 dynamics modulate the rhizosphere microbiome by selectively enriching for the phylum Cyanobacteria, with strong antioxidant defenses. Our results demonstrated that the regulation of H2O2 dynamics at the plant-fungal interface affects the symbiotic outcome in response to external conditions and highlight the importance of the root endophyte in reshaping the rhizosphere microbiota.

Endofungal bacteria and ectomycorrhizal fungi synergistically promote the absorption of organic phosphorus in Pinus massoniana.

Ectomycorrhizal fungi (ECMFs) that are involved in phosphorus mobilisation and turnover have limited ability to mineralise phytate alone. The endofungal bacteria in the ectomycorrhizal fruiting body may contribute to achieving this ecological function of ECMFs. We investigated the synergistic effect and mechanisms of endofungal bacteria and ECMF Suillus grevillea on phytate mineralisation. The results showed that soluble phosphorus content in the combined system of endofungal bacterium Cedecea lapagei and S. grevillea was 1.8 times higher than the sum of C. lapagei and S. grevillea alone treatment under the phytate mineralisation experiment. The S. grevillea could first chemotactically assist C. lapagei in adhering to the surface of S. grevillea. Then, the mineralisation of phytate was synergistically promoted by increasing the biomass of C. lapagei and the phosphatase and phytase activities of S. grevillea. The expression of genes related to chemotaxis, colonisation, and proliferation of C. lapagei and genes related to phosphatase and phytase activity of S. grevillea was also significantly upregulated. Furthermore, in the pot experiment, we verified that there might exist a ternary symbiotic system in the natural forest in which endofungal bacteria and ECMFs could synergistically promote phytate uptake in the plant Pinus massoniana via the ectomycorrhizal system.

Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease.

It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.

The loss of microbial autotoxin degradation functions is associated with the decline of beneficial bacterial agents induced by phenolic acids.

Continuous cultivation of medicinal plants can disrupt the rhizosphere's microbial community. There is still a need to know about the beneficial bacterial community, their putative drivers, and the potential functions they may have. This study used different growth years of Sanqi ginseng (Panax notoginseng) with root rot to look at the beneficial microbial community structure, the function of microbial carbon source utilization, and the function of rhizosphere soil metabolism. The beneficial bacterial community changed and the relative abundance of beneficial agents was suppressed significantly with the successive Sanqi ginseng plantings. The carbon source utilization capacity and diversity increased significantly, whereas three autotoxin degradation-related pathways (biosynthesis of other secondary metabolites, metabolism of terpenoids and polyketides, and xenobiotics biodegradation and metabolism) were downregulated considerably with planting year extended. The changes in the beneficial agents were driven by the shifts in phenolic acid profiles, and the decline of beneficial microbes led to the loss of microbial autotoxin degradation functions. Overall, these results provide insight into beneficial microbes, microbial functions, phenolic acids, and their interactions, and these findings are essential for maintaining healthy and sustainable cultivation of Sanqi ginseng. IMPORTANCE Sanqi ginseng is a valuable perennial Chinese herb with various benefits for human health. However, continuous cultivation causes a high incidence of root rot disease, which leads to decreased yield and serious economic losses and ultimately impedes the sustainable development of Chinese medicine production. The significance of this study is to reveal the pattern of changes in beneficial bacteria and their related functions in root rot diseased rhizosphere with the successive planting years of Sanqi ginseng. This study found that the decline of beneficial bacterial agents mediated by phenolic acid profiles appears to be associated with the loss of microbial autotoxin degradation functions. This result may have new implications for deciphering the causes of Sanqi ginseng's continuous cropping obstacles.

Fungal endophyte promotes plant growth and disease resistance of Arachis hypogaea L. by reshaping the core root microbiome under monocropping conditions.

Fungal endophytes play critical roles in helping plants adapt to adverse environmental conditions. The root endophyte Phomopsis liquidambaris can promote the growth and disease control of peanut plants grown under monocropping systems; however, how such beneficial traits are produced is largely unknown. Since the plant endophytic microbiome is directly linked to plant growth and health, and the composition of which has been found to be potentially influenced by microbial inoculants, this study aims to clarify the roles of root endophytic bacterial communities in P. liquidambaris-mediated plant fitness enhancement under monocropping conditions. Here, we found that P. liquidambaris inoculation induced significant changes in the root bacterial community: enriching some beneficial bacteria such as Bradyrhizobium sp. and Streptomyces sp. in the roots, and improving the core microbial-based interaction network. Next, we assembled and simplified a synthetic community (SynII) based on P. liquidambaris-derived key taxa, including Bacillus sp. HB1, Bacillus sp. HB9, Burkholderia sp. MB7, Pseudomonas sp. MB2, Streptomyces sp. MB6, and Bradyrhizobium sp. MB15. Furthermore, the application of the simplified synthetic community suppressed root rot caused by Fusarium oxysporum, promoted plant growth, and increased peanut yields under continuous monocropping conditions. The resistance of synII to F. oxysporum is related to the increased activity of defense enzymes. In addition, synII application significantly increased shoot and root biomass, and yield by 35.56%, 81.19%, and 34.31%, respectively. Collectively, our results suggest that the reshaping of root core microbiota plays an important role in the probiotic-mediated adaptability of plants under adverse environments.

Endophytic Fungus Reshapes Spikelet Microbiome to Reduce Mycotoxin Produced by Fusarium proliferatum through Altering Rice Metabolites.

Rice spikelet rot disease (RSRD) caused by Fusarium proliferatum seriously reduces rice yield and produces mycotoxins that threaten human health. The root symbiotic endophytic fungus Phomopsis liquidambaris reduces RSRD incidence and fumonisins accumulation in grain by 21.5 and 9.3%, respectively, while the mechanism of disease resistance remains largely elusive. Here, we found that B3 significantly reduced the abundance of pathogen from 79.91 to 2.84% and considerably enriched resistant microbes Pseudomonas and Proteobacteria in the spikelet microbial community. Further study revealed that B3 altered the metabolites of spikelets, especially hordenine and l-aspartic acid, which played a key role in reshaping the microbiome and supporting the growth of the functional core microbe Pseudomonas, and inhibited the pathogen growth and mycotoxin production. This study provided a feasibility of regulating the function of aboveground microbial communities by manipulating plant subsurface tissues to control disease and mycotoxin pollutants in agricultural production.

Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil.

Anthropogenic nitrogen inputs lead to a high ammonium (NH4+)/nitrate (NO3-) ratio in the soil, which restricts hyphal spreading of soil fungi. Access of symbiotic fungi to roots is a prerequisite for plant-fungal interactions. Hyphosphere bacteria protect fungi from environmental stress, yet the impact of hyphosphere bacteria on adaptation of host fungi to NH4+-enriched conditions remains unclear. By developing soil microcosm assays, we report that a plant-symbiotic fungus, Phomopsis liquidambaris, harbors specific hyphosphere bacteria that facilitate hyphal spreading and assist in the root colonization in NH4+-enriched soil. Genetic manipulation, 16S rRNA gene analysis and coinoculation assays revealed that the genus Enterobacter was enriched in the hyphosphere of NH4+-sensitive wild-type compared to NH4+-preferring nitrite reductase-deficient strain. The representative Enterobacter sp. SZ2-promoted hyphal spreading is only evident in nonsterilized soil. We further identified an increased abundance and diversity of ammonia-oxidizing archaea (AOA) and a synchronously decreased NH4+:NO3- ratio following SZ2 inoculation. Microbial supplementation and inhibitor assays showed that AOA-mediated reduction in NH4+:NO3- ratio is responsible for SZ2-enhanced fungal adaptation to NH4+-enriched conditions. The Ph. liquidambaris-Enterobacter-AOA triple interaction promoted rice growth in NH4+-enriched soil. Our study reveals the essential role of hyphosphere microorganism-based hyphal spreading in plant-fungal symbiosis establishment within nitrogen-affected agroecosystems.

Endofungal Bacterial Microbiota Promotes the Absorption of Chelated Inorganic Phosphorus by Host Pine through the Ectomycorrhizal System.

Ectomycorrhizal fungi play an irreplaceable role in phosphorus cycling. However, ectomycorrhizal fungi have a limited ability to dissolve chelated inorganic phosphorus, which is the main component of soil phosphorus. Endofungal bacteria in ectomycorrhizal fruiting bodies are always closely related to the ecological function of ectomycorrhizal fungi. In this study, we explore endofungal bacteria in the fruiting body of Tylopilus neofelleus and their function during the absorption of chelated inorganic phosphorus by host pine through the ectomycorrhizal system. The results showed that the endofungal bacterial microbiota in the fruiting body of T. neofelleus might be related to the dissolution of chelated inorganic phosphorus in soil. The soluble phosphorus content in the combined system of T. neofelleus and endofungal bacteria Bacillus sp. strain B5 was five times higher than the sum of T. neofelleus-only treatment and Bacillus sp. strain B5-only treatment in the dissolution experiment of chelated inorganic phosphorus. The results showed that T. neofelleus not only promoted the proliferation of Bacillus sp. strain B5 in the combined system but also improved the expression of genes related to organic acid metabolism, as assesed by transcriptomic analysis. Lactic acid content was five times higher in the combined system than the sum of T. neofelleus-only treatment and Bacillus sp. strain B5-only treatment. Two essential genes related to lactate metabolism of Bacillus sp. strain B5, gapA and pckA, were significantly upregulated. Finally, in a pot experiment, we verified that T. neofelleus and Bacillus sp. strain B5 could synergistically promote the absorption of chelated inorganic phosphorus by Pinus sylvestris in a ternary symbiotic system. IMPORTANCE Ectomycorrhizal fungi (ECMF) have a limited ability to dissolve chelated inorganic phosphorus, which is the main component of soil phosphorus. In the natural environment, the extraradical hyphae of ECMF alone may not satisfy the phosphorus demand of the plant ectomycorrhizal system. In this study, our results innovatively show that the ectomycorrhizal system might be a ternary symbiont in which ectomycorrhizal fungi might recruit endofungal bacteria that could synergistically promote the mineralization of chelated inorganic phosphorus, which ultimately promotes plant phosphorus absorption by the ectomycorrhizal system.

Engineered Phomopsis liquidambaris with Fhb1 and Fhb7 Enhances Resistance to Fusarium graminearum in Wheat.

Fusarium head blight is one of the most serious diseases caused by Fusarium graminearum in wheat. Here, we developed a new way to prevent and control Fusarium head blight by introducing the resistance genes Fhb1 and Fhb7 into the endophytic fungus Phomopsis liquidambaris, named PL-Fhb1 and PL-Fhb7, respectively, which could colonize wheat. The wheat seedlings were preinoculated with PL-Fhb1 and PL-Fhb7 to enhance the resistance against deoxynivalenol (DON) and PL-Fhb1 and PL-Fhb7 inhibited the growth of F. graminearum by 73% and 49%, respectively. The incidence rate of diseased spikes decreased to 35.2% and 45.4%, and the corresponding DON levels for wheat grains decreased from 13.2 to 1.79 µg/g and from 13.2 µg/g to 0.39 µg/g when the leaves were preinoculated with PL-Fhb1 and PL-Fhb7 after overwintering, respectively. The incidence rates of diseased spikes decreased to 25.7% and 34.7%, and the DON levels for wheat grains decreased from 17.48 µg/g to 1.23 µg/g and from 17.48 µg/g to 0 µg/g when the wheat flowers were inoculated with PL-Fhb1 and PL-Fhb7, and the wheat flowers were subsequently infected with F. graminearum, respectively. It was confirmed that DON was transformed into DON-glutathione (GSH) by PL-Fhb7 using high-performance liquid chromatography-mass spectrometry (HPLC-MS). However, PL-Fhb1 may have increased plant immunity and enhanced the resistance to F. graminearum. This study indicates that engineered endophytes can improve the resistance to Fusarium head blight and presents a new method for the biological control of Fusarium head blight.

Plant and fungal species interactions differ between aboveground and belowground habitats in mountain forests of eastern China.

Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody plant species across more than 2,000-km span of mountain forests in eastern China. The relative contributions of plant, climate, soil and space to the variation of fungal communities were assessed, and the plant-fungus network topologies were inferred. Plant phylogeny was the strongest predictor for fungal community composition in leaves, accounting for 19.1% of the variation. In soils, plant phylogeny, climatic factors and soil properties explained 9.2%, 9.0% and 8.7% of the variation in soil fungal community, respectively. The plant-fungus networks in leaves exhibited significantly higher specialization, modularity and robustness (resistance to node loss), but less complicated topology (e.g., significantly lower linkage density and mean number of links) than those in soils. In addition, host/fungus preference combinations and key species, such as hubs and connectors, in bipartite networks differed strikingly between aboveground and belowground samples. The findings provide novel insights into cross-kingdom (plant-fungus) species co-occurrence at large spatial scales. The data further suggest that community shifts of trees due to climate change or human activities will impair aboveground and belowground forest fungal diversity in different ways.

Alteration of plant immunity in the interaction of roots with the endophytic fungus Phomopsis liquidambaris in response to external nitrogen conditions.

The complex environments of plants force them to prioritize their immune responses to stimuli occurring simultaneously, including colonization by microbes or nutrient availability. Little is known about how the interplay between endophytes and nutrient status affects the immune responses of both plants and fungi. We primarily monitored immune responses in rice following inoculation with the endophytic fungus Phomopsis liquidambaris under different nitrogen (N) conditions. Ph. liquidambaris promoted plant growth under low N (LN) conditions, concomitant with higher root colonization. Plant production of oxidative signals, including hydrogen peroxide and nitric oxide, was activated by Ph. liquidambaris colonization under LN conditions, while salicylic acid (SA) was maintained at high levels and was involved in controlling rice-fungal interactions. High N (HN) conditions enhanced the ability of Ph. liquidambaris in suppressing plant cell death and the ability of roots to degrade Ph. liquidambaris cell walls. Furthermore, under both LN and HN conditions, the activity of plant defence-associated enzymes and fungal antioxidases was not affected in the interactive association. Our data reveal the alteration of plant immunity, including oxidative signalling and plant cell death, by fungal colonization in response to external N conditions and identify SA signalling as a potential controller for rice-Ph. liquidambaris interaction.

Towards biomass production and wastewater treatment by enhancing the microalgae-based nutrients recovery from liquid digestate in an innovative photobioreactor integrated with dialysis bag.

Microalgae-based nutrients recovery from liquid anaerobic digestate of swine manure has been a hotspot in recent decades. Nevertheless, in consideration of the high NH4+-N content and poor light penetrability exhibited by the original liquid digestate, uneconomical pretreatment on liquid digestate including centrifugation and dilution are indispensable before microalgae cells inoculation. Herein, aiming at eliminating the energy-intensive and freshwater-consuming pretreatment on liquid digestate and enhancing microalgae growth, the dialysis bag which permits nutrients transferring across its wall surface whereas retains almost all matters characterized by impeding light transmission within the raw liquid digestate was integrated into a column photobioreactor (DB-PBR). Consequently, light availability of microalgae cells in DB-PBR was elevated remarkably and thus contributed to a 357.58% improvement on microalgae biomass concentration in DB-PBR than the conventional PBR under 80 µmol m-2 s-1. Likewise, superior nutrients removal efficiencies from liquid digestate were obtained in DB-PBR (NH4+-N: 74.84%, TP: 63.75%) over the conventional PBR (NH4+-N: 30.27%, TP: 16.86%). Furthermore, higher microalgae biomass concentration (1.87 g L-1) and nutrients removal efficiencies (NH4+-N: 95.12%, TP: 76.87%) were achieved in the DB-PBR by increasing the light intensity to 140 µmol m-2 s-1. More importantly, the DB-PBR may provide a simple and greener solution to purify other kinds of wastewater.

Preinoculation with Endophytic fungus Phomopsis liquidambaris reduced rice bakanae disease caused by Fusarium proliferatum via enhanced plant resistance.

AIMS: This study evaluated the control effect of the endophytic fungus Phomopsis liquidambaris B3 against rice bakanae disease (RBD) caused by Fusarium proliferatum and the disease control result of different inoculation times of beneficial micro-organisms. METHODS AND RESULTS: Rice seedlings preinoculated, coinoculated and noninoculated with B3 were exposed to F. proliferatum stress and grown under controlled conditions. Greenhouse experimental results showed that rice preinoculation with B3 significantly reduced rice bakanae disease by 21.45%, inhibited the colonization of F. proliferatum, increased defence-related enzyme activities, upregulated the expression of defence genes and promoted plant photosynthesis. However, bakanae disease in rice coinoculation with B3 increased by 11.45%, resulted in excessive reactive oxygen species (ROS) bursts and plant cell death. CONCLUSIONS: Preinoculation with the endophytic fungus P. liquidambaris B3 significantly reduced rice bakanae disease by triggering the SA-dependent defence pathways of plants, and promoted plant growth. However, coinoculatiton with P. liquidambaris B3 activated excessive defence responses, resulting in plants cell death and aggravation of bakanae disease. SIGNIFICANCE AND IMPACT OF THE STUDY: This study indicated that P. liquidambaris B3 was an effective method for agricultural control against rice bakanae disease caused by F. proliferatum, and provides an experimental basis for the development of sustainable endophytic fungal resources to effectively control plant diseases caused by pathogenic fungi, and suggests that precise application of beneficial micro-organisms may be become a key factor in farmland crop disease management.

Generalist endophyte Phomopsis liquidambaris colonization of Oryza sativa L. promotes plant growth under nitrogen starvation.

Fungal endophytes establish symbiotic relationships with host plants, which results in a mutual growth benefit. However, little is known about the plant genetic response underpinning endophyte colonization. Phomopsis liquidambaris usually lives as an endophyte in a wide range of asymptomatic hosts and promotes biotic and abiotic stress resistance. In this study, we show that under low nitrogen conditions P. liquidambaris promotes rice growth in a hydroponic system, which is free of other microorganisms. In order to gain insights into the mechanisms of plant colonization by P. liquidambaris under low nitrogen conditions, we compared root and shoot transcriptome profiles of root-inoculated rice at different colonization stages. We determined that genes related to plant growth promotion, such as gibberellin and auxin related genes, were up-regulated at all developmental stages both locally and systemically. The largest group of up-regulated genes (in both roots and shoots) were related to flavonoid biosynthesis, which is involved in plant growth as well as antimicrobial compounds. Furthermore, genes encoding plant defense-related endopeptidase inhibitors were strongly up-regulated at the early stage of colonization. Together, these results provide new insights into the molecular mechanisms of plant-microbe mutualism and the promotion of plant growth by a fungal endophyte under nitrogen-deficient conditions.