Exploring multifaceted roles of bambusicolous Apiospora in Phyllostachys sp.

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Sun Lul Kwon, Chang Wan Seo, Haeun Kwon, Minseo Cho, Yeonjae Yoo, and 10 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6757679/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 05 Nov, 2025 Read the published version in Microbial Ecology → Version 1 posted 10 You are reading this latest preprint version Abstract Bamboo plays a crucial role in mitigating climate change. Among various microorganisms inhabiting bamboo, Apiospora is a common bambusicolous fungus that induces black spots, functioning either as a saprobe or a plant pathogen. However, the diversity and ecological roles of Apiospora as an endophyte in bamboo remain poorly understood. This study explored the diversity and ecological functions of bambusicolous Apiospora in Phyllostachys forests. Bamboo samples representing different stages—young (one-year-old, without black spots), mature (aged three years, few black spots), and dead (with many black spots)—were collected. Microbiome analyses across different tissues (culm, leaf, root) and environmental samples (forest soil) revealed diverse Apiospora species throughout the bamboo lifecycle. Notably, Ap. hysterina emerged as a prevalent endophyte, inhabiting not only mature but also younger, healthier bamboo stages. Biological activity assays, including antioxidant, antifungal, and plant hormone tests, indicated that Ap. hysterina exhibits mutualistic interactions beneficial to bamboo. Conversely, genomic analyses of carbohydrate-active enzyme profiles and biosynthetic gene clusters suggested a pathogenic potential driven by secondary metabolites. These findings reveal the widespread presence of Apiospora species as endophytes from the early to senescent bamboo stages, highlighting Ap. hysterina ’s dual capacity as a pathogen and symbiont. Our study underscores the complexity of bambusicolous Apiospora ’s ecological roles, emphasizing the need for further investigation into its interactions with bamboo ecosystems. amplicon analysis Apiospora hysterina bamboo culm endophytic fungi plant hormone plant pathogen Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Introduction Bamboo (family Poaceae, subfamily Bambusoideae) is a valuable grass plant renowned for diverse ecological roles, including biodiversity conservation [ 1 ], carbon fixation [ 2 ], soil and water conservation [ 3 ], and economic activities [ 4 ]. Phyllostachys , known as running bamboo, is one of the largest bamboo genera, consisting of approximately 50 species, predominantly found in Asia (China and Japan). In Korea, bamboo forests cover an area of approximately 22,000 ha, mainly consisting of Phyllostachys species ( P. bambusoides , P. nigra var. henonis , and P. edulis ), with 96% located in the southern region [ 5 ]. Bambusicolous fungi live on various bamboo substrates, including culms, leaves, branches, rhizomes, and roots, and play a crucial role in bamboo diversity conservation and ecosystem maintenance [ 6 ]. Over 1,100 species within 228 genera have been identified as bambusicolous fungi, primarily including Ascomycetes (630 species), Basidiomycetes (150 species), and anamorphic fungi (330 species) [ 7 , 8 ]. These fungi significantly influence bamboo ecosystems by functioning as endophytes, pathogens, and saprobes. Endophyte-plant symbiosis provides valuable insights into plant-microbe interactions with potential applications in agriculture and environmental sustainability [ 9 , 10 ]. For instance, fungal endophytes can produce growth hormones, such as gibberellins and auxins, promoting plant growth, enhancing root development, and improving overall plant health [ 9 ]. Bambusicolous endophytic fungi are known to synthesize bioactive compounds with antioxidant, antimicrobial, antitumor, and plant growth-promoting activities [ 11 ]. Currently, Index Fungorum (2024) lists 175 epithets of Apiospora , with 42 species recorded as bambusicolous fungi. Many Apiospora species are saprobes, causing black spot formation on dead or decaying bamboo [ 12 , 13 ], and some are pathogenic [ 15 – 16 ]. Additionally, Apiospora species are prevalent as endophytes in running bamboo ( Phyllostachys spp.) and dwarf bamboo ( Sasa spp.) in Japan [ 17 ], offering competitive advantages to their hosts through hormone synthesis, seed germination promotion, and antimicrobial and antioxidant activities [ 18 ]. These findings underscore the ecological versatility of Apiospora as saprobes, pathogens, and endophytes [ 8 , 17 , 19 ]. Thus, we hypothesize that bambusicolous Apiospora species significantly influence the bamboo lifecycle, serving as symbionts during growth stages, pathogens during maturation, and saprobes in dead bamboo tissues. However, the diversity, ecological traits, and symbiotic interactions of endophytic Apiospora in bamboo hosts remain unclear. This study aimed to explore the diversity of bamboo endophytic fungi, focusing on Apiospora , across various bamboo tissues (culm, leaf, root) and soil, as well as different bamboo stages (young, mature, dead). We investigated the ecological preferences (niches) of these endophytes and analyze the biological activities and genetic characteristics of bambusicolous Apiospora to elucidate their multifaceted ecological roles in Korean Phyllostachys forests. Methods Detailed descriptions are provided in the Supplementary Text. Sampling collection and treatment Bamboo materials ( Phyllostachys sp .) from Juknokwon, Damyang−gun, Korea, were collected in December 2021 and categorized into “Young” (5 years) based on appearance. Samples (culm, leaf, root, soil) were stored at –80°C. Surface sterilization was performed following the methodology outlined by Barra et al. [20], and samples were crushed in liquid nitrogen using a Freeze Mill (SPEX 6875D). Bambusicolous fungal community analysis DNA was extracted using DNeasy Powerlyzer PowerSoil Kit (Qiagen). Polymerase chain reaction amplified ITS2 regions with primers ITS3 and ITS4. Libraries were sequenced on Illumina MiSeq (2×300 bp, paired end). ITS2 sequences were analyzed using QIIME2. DADA2 plugin filtered low−quality, short, and chimeric sequences. Operational taxonomic units (OTUs) were clustered at 99% similarity using VSEARCH, excluding OTUs <10 sequences. Taxonomy assignments utilized modified UNITE v8.3 and enhanced GenBank sequences. Phylogenetic analysis used MAFFT and RAxML with reference sequences of Apiospora and related genera from the GenBank database (Additional file 1: Table S1). Alpha and beta diversity analyses ("vegan" package) assessed community variation. PERMANOVA with Bray−Curtis distances identified significant factors. Principal coordinate analysis (PCoA), Venn diagrams, linear discriminant analysis (LefSe), and heat maps ("pheatmap") were used to visualize data. Indicator species were analyzed with the "Indicspecies" package. Biological activity and metabolite analysis Nine strains from the Korea University Culture Collection, representing three species ( Ap. arundinis, Ap. camelliae−sinensis, Ap. hysterina ), were analyzed based on microbiome findings. Extracts were prepared from strains cultured on potato dextrose agar, extracted with methanol and ethyl acetate. Radical scavenging activities were measured using 2,2'−Azino−bis (3−ethylbenzothiazoline−6−sulfonic acid (ABTS) and 2,2−Diphenyl−1−picrylhydrazyl (DPPH) assays with standard controls (Trolox and L−Ascorbic acid, respectively). Antifungal activity against Botrytis cinerea , Colletotrichum gloeosporioides , and Fusarium oxysporum was assessed via disk diffusion assay. Indole−3−acetic acid (IAA), Abscisic acid ABA, and Gibberellic acid (GA) production by strains was evaluated using liquid chromatography with tandem mass spectrometry (LC−MS/MS) with an Orbitrap Exploris 120 mass spectrometer. Molecular networks were generated using GNPS and visualized in Cytoscape. Whole genome analysis Genomic DNA from selected Apiospora was sequenced with the PacBio Sequel and NovaSeq6000 platforms. Assembly involved Flye, Racon, and Hapo−G. Genomes were annotated with RepeatModeler, RepeatMasker, BRAKER2, GeMoMa, tRNAscan−SE, Rfam, and MMseqs2. CAZyme−related genes identified via dbCAN3, with trophic lifestyles classified by CATAStrophy. Secondary metabolite clusters identified using antiSMASH. Genome−scale modeling and BLAST analyses identified hormone synthesis pathways, visualized using ChemDraw. Results Fungal microbiome analysis Fungal microbiomes of bamboo and soil samples A total of 89 bamboo forest samples (26 culms, 27 leaves, 27 roots, and 9 soil types) were collected for fungal microbiome analysis. For ITS2 amplicon analysis, 14,439,126 paired sequences were obtained, and 9,205,658 merged paired reads (average length 319 bp) were retained after quality filtering. Rarefaction curves confirmed sufficient sequencing depth (Additional file 1: Fig. S1 ). After clustering and discarding low coverage mOTUs, 4,303 mOTUs were retained. Among these, 31 mOTUs were assigned to the candidate Apiospora species. Phylogenetic analysis for precise species identification (Additional file 1: Fig. S2 and Additional file 2: Table S2 ) revealed 31 mOTUs as seven known Apiospora species ( Ap. arundinis , Ap. hysterina , Ap. camelliae-sinensis, Ap. minutispora , Ap. pseudohyphopodii , Ap. rasikravindrae , and Ar. phaeospermum ), as well as a new candidate species ( Apiospora sp. 1) and four indistinct species (ITS_Apio_01, ITS_Apio_12, ITS_Apio_13, and ITS_Apio_29). These 12 Apiospora species were used for ALC analysis. For GLC analysis, the 21 most abundant fungal genera (> 0.5% of the total reads) were selected, with the exception of unidentified genera. Among them, Apiospora was the most dominant genus in the culms and leaves with mean relative abundances of 46.56% and 13.25%, respectively (Fig. 1 A; Additional file 2: Table S3 ). Moreover, Apiospora was the most dominant genus across the bamboo stages with high mean relative abundances (Young, 22.21%; Mature, 23.39%; and Dead, 16.33%), but the proportion of Apiospora decreased in the dead samples and was minimized in the soil samples (0.37%). In bamboo roots and soils, Mycena (12.65%) and Mortierella (Mortierellaceae) (12.96%) were the most abundant genera, respectively (Fig. 1 A; Additional file 2: Table S3 ). Among the 21 major genera, 14 were detected in all bamboo compartments (culms, leaves, roots, and soil) (Fig. 1 C). In contrast, no unique genera were detected in each bamboo compartment. Across the bamboo tissue stages, 14/19, 12/19, and 9/20 genera were shared between the culm, leaf, and root stages, respectively. The genera detected at all stages in all bamboo tissues were Apiospora , Mycena , Fusarium , Colletotrichum , Neptunomyces , and Trichoderma (Additional file 2: Table S4). In ALC analysis, four species were commonly detected throughout the life of bamboo tissues: Ap. arundinis , Ap. camelliae-sinensis, Ap. hysterina , and Ap. rasikravindrae (Fig. 1 D, E; Additional file 2: Table S4). Ap. arundinis , Ap. camelliae-sinensis , and Ap. rasikravindrae were also detected in soil samples, but Ap. hysterina was not detected in soil samples exhibiting an obligatory association with bamboo. Ap. hysterina was the most abundant species in young culms (25.9%), mature culms (39.1%), and mature leaves (15.2%) (Fig. 1 B). Ap. arundinis was highly abundant in young culms (12.5%) and leaves (8.1%) but was present at a considerably lower proportion in the mature and dead stages. Ap. camelliae-sinensis and Ap. pseudohyphopodii were highly abundant in bamboo culms, followed by Ap. hysterina (Fig. 1 B); however, they were only abundant in young and dead culms, respectively (Fig. 1 B). Apiospora sp. 1 was uniquely detected in mature culm tissues, whereas ITS_Apio_01 was detected at all stages of bamboo leaves growth. Ap. minutispora and ITS_Apio_29 were only detected in dead bamboo tissues (Fig. 1 D, E; Additional file 2: Table S4). Variation in endophytic fungal community and its ecological niche α- and β-diversity analyses indicated significant differences in endophytic communities across bamboo tissue types (Figs. 1 A, 1 B, 2 B, 2 C; Additional file 2: Tables S5, S6). Variation among bamboo growth stages was significant only in β-diversity analyses (ALC, Fig. 2 C). Community variation by stage within each tissue showed significant α-diversity differences only in leaf ALC (Fig. 1 B). β-diversity differences were observed in culm and root ALC and leaf GLC analyses. PERMANOVA confirmed tissue type as the most influential factor on fungal community structure, followed by the interaction of tissue type and stage, and stage alone (Fig. 2 A). Representative fungal taxa were identified via LEfSe (Fig. 3 A, B). Major genera such as Apiospora (young culms), Didymella (mature culms), Colletotrichum (young leaves), Neptunomyces (dead leaves), Fusarium and Mycena (mature roots), and Trichoderma (soil) exhibited significant associations (LDA > 2.0, p < 0.05). Apiospora species ( Ap. arundinis, Ap. camelliae-sinensis , young culms; Ap. hysterina , mature culms) also showed significant preferences. Heat map clustering (Spearman correlation) confirmed taxa associations, dividing representative fungi into aboveground and underground clusters (Fig. 3 C). High positive correlations were noted for Mycena, Trichoderma, Colletotrichum, Neptunomyces, Didymella, Apiospora, Ap. hysterina, Ap. arundinis , and Ap. camelliae-sinensis , supporting LEfSe findings. Major Apiospora species were significantly associated with living bamboo culms. Biological activities The biological activity analysis was conducted examining three bambusicolous Apiospora species using microbiome analysis. Ap. arundinis (KUC21601 and KUC21792), Ap. camelliae-sinensis KUC21546, and Ap. hysterina (KUC21437 and KUC21435) exhibited high antioxidant activity in both the ABTS and DPPH assays (Additional file 2: Table S7). In the antifungal activity assay, Ap. camelliae-sinensis KUC21538 and Ap. hysterina (KUC21437 and KUC21435) inhibited the growth of Botrytis cinerea KUC21265. The extracts of Ap. hysterina (KUC21437 and KUC21435) inhibited the growth of Colletotrichum gloeosporioides KUC21266. However, the Ap. arundinis strains did not exhibit antifungal activity against phytopathogenic fungi. The plant hormone ABA was detected in the fungal extracts of Ap. hysterina (KUC21437 and KUC21435) and Ap. camelliae-sinensis (KUC21536 and KUC21538) using MS/MS spectral matching with authentic standard compounds (Additional file 1: Fig. S3 ). GA derivatives (nodes 7451 and 7445) clustered with the node of GA (78103) were detected in the extracts of the strains of Ap. hysterina (KUC21435, KUC21437, and KUC21438) (Additional file 1: Fig. S4). However, the LC-MS analysis of the standard and extract did not detect IAA. Genomic analysis Genome sequencing, assembly, and annotation Genomic analysis was conducted on the most dominant bambusicolous endophyte Apiospora species in this study, Ap. hysterina (Fig. 1 A). The strain Ap. hysterina KUC21437 was selected due to its various biological activities and plant hormone production ability (ABA and GA). We obtained a 48.0 Mbp genome (GC content: 48.6%) with eight contigs (max. length and N50: 5.7 Mbp) excluding the mitochondrial genome. The genome assembly completeness in terms of gene content ranged from 97.7% ( Ascomycota ) and 99.2% ( Fungi ) with BUSCO 5.4.6 [ 21 ] and OrthoDB 10 [ 22 ]. A total of 14,433 protein-coding genes were identified via structural genome annotation. Trophic lifestyle prediction The CAZyme analysis of the KUC21437 genome revealed 692 genes across 133 CAZyme families. Glycoside hydrolases (GH; 302 genes) dominated, with GH18 (chitinase; 21 genes) and AA7 (oxidase; 71 genes) being prevalent (Additional file 1: Fig. S5). CATAStrophy analysis predicted the lifestyle of Ap. hysterina KUC21437 as a “necrotroph”, representing the major trophic class under common trophic terms (Nomenclature 1) (Table 1 ). Principal component analysis revealed that the fungus was located close to the necrotrophs and hemibiotrophs and was significantly distinguished from the symbionts and biotrophs (Fig. 4 A). According to the trophic mode classification (Nomenclature 2) of Hane et al. [ 23 ], the fungus was predicted to be a “vasculartroph (major trophic class)” based on the RCD score (Fig. 4 B; Table 1 ). Moreover, it can be classified as “mesotroph_intracellular (major trophic class)” in novel trophic sub-classes (Nomenclature 3) based on the RCD score (Fig. 4 C; Table 1 ). “Vasculotrophs” refers to fungal species commonly associated with diseases such as wilts, rots, or anthracnoses. “Mesotroph_intracellular” describes typical hemibiotrophic fungi that produce specialized structures, such as appressoria, to facilitate intracellular colonization. Table 1 Summary of CATAStrophy classifications of Apiospora hysterina KUC21437 with relative centroid distance (RCD) scores ranging from 0 to 1 Apiospora hysterina KUC21437 Nomenclature 1 Necrotroph Hemibiotroph Saprotroph Symbiont Biotroph 1 0.90 0.39 0.26 0.0 Nomenclature 2 Vasculartroph Mesotroph Polymertroph Saprotroph Monomertroph 1 0.89 0.88 0.31 0.0 Nomenclature 3 Mesotroph_intracellular Polymertroph_narrow Vasculartroph Polymertroph_broad Mesotroph_extracellular 1 0.91 0.89 0.67 0.55 RCD score of 1 (bold and underlined) indicates memberships in a major trophic class, and score ≥ 0.95 (bold) predicts affinity for one or more trophic sub−classes. SM BGCs of Apiospora hysterina A total of 81 secondary metabolite biosynthetic gene clusters (SM BGCs) were identified, including 25 type 1 polyketide synthases (T1PKS), 1 type 3 polyketide synthase (T3PKS), 18 terpenes, 12 non-ribosomal peptide synthetases (NRPS), 11 NRPS-like, and 14 hybrid genes (Additional file 1: Fig. S6). Among these, 25 BGCs matched 22 known clusters, with 7 clusters characterized as 5 known SM BGCs at 100% AntiSMASH similarity (Additional file 2: Table S8). Notably, identified clusters included ACR toxin I, dimethyl coprogen, (R)-mellein, ACT toxin II, and AbT1. Plant hormone synthesis pathways Genome analysis predicted complete biosynthetic pathways for ABA and GA (Fig. 5 ). The ABA biosynthesis gene cluster, homologous to Botrytis cinerea , was identified on chromosome 2 (1,571,658–1,592,948), containing homologs of bcABA1, bcABA2 , and bcABA3 (VJ940_3286, VJ940_3285, VJ940_3287), and bcABA4 was located in an unannotated region (1,592,151–1,592,948) (Fig. 5 A, B). Genes involved in GA biosynthesis from farnesyl diphosphate to GA14 were also detected. A gene cluster encoding enzymes from geranylgeranyl diphosphate to ent-kaurenoate was identified on chromosome 2 (6,063,250–6,076,058). Additional genes for GA derivative conversions (GA4 to GA1 and GA7 to GA3) were detected outside this cluster (VJ940_13065) (Fig. 5 B). Discussion Endophytic fungi play critical roles as mutualists or pathogens in plant ecosystems, influencing health, stress tolerance, and overall fitness through diverse interactions. Using microbiome analysis, this study examined the diversity of bambusicolous endophytic fungi across bamboo tissues and stages, focusing on the genus Apiospora . The microbiome analysis revealed that some Apiospora species are significant components of bambusicolous endophytic fungi, inhabiting bamboo culms and leaves from the young developmental stage to the dead state. To further explore the ecological roles of Apiospora , we employed a multidisciplinary approach integrating microbiome, biological activity tests (antioxidant, antifungal, and plant hormones production), and genomic analyses (CAZyme and SM BGCs) to identify their intricate ecological roles in the bamboo environment and provide new insights into their multifaceted roles. In this study, we mainly focused on Ap. hysterina to explore its ecological roles in bamboo. Through microbiome analysis, it was identified as the dominant endophytic fungi living in healthy culms and leaves but was absent from the soil. This distribution pattern indicates a strong ecological specificity to the host plant of this fungus compared to other fungi. Furthermore, its ability to produce two plant hormones (ABA and GA) and antioxidant and antifungal activities highlights its potential as a key player in the bamboo ecosystem as a mutualist. Therefore, Ap. hysterina was selected for further comprehensive investigations, including genomic analyses, to better understand its ecological roles. Putative pathogenic characteristics of Ap. hysterina Some Apiospora species have been historically identified as plant pathogens that cause diseases such as culm blight ( Ap. kogelbergensis ) [ 19 ], culm base rot ( Ar. phaeospermum ) [ 24 ], culm staining ( Apiospora indica ) [ 24 ], and dieback ( Apiospora sp.) [ 24 ] in bamboo. In addition to bamboo, Apiospora species have also been reported as plant pathogens in other crops, such as reddish-brown discoloration in sugarcane flesh [ 25 ]. Our genomic analyses of Ap. hysterina support its pathogenic potential, consistent with previous studies. Specifically, the CAZyme content of Ap. hysterina KUC21437 suggests a trophic lifestyle consistent with a “necrotroph” (Nomenclature 1), “vasculartroph” (Nomenclature 2), and “mesotroph_intracellular” (Nomenclature 3) with high RCD scores (RCD score > 0.95) (Table 1 ). These classifications imply that the CAZyme content of Ap. hysterina is well-suited for plant infections, including vascular invasion and intracellular penetration via appressorial structure formation [ 23 ]. However, appressorial structures have been observed in phylogenetically close species, such as Ap. pseudohyphopodii and Ap. yunnana [ 26 ]. Direct evidence for such structures in Ap. hysterina has not yet been obtained. Nonetheless, its phylogenetic proximity suggests the potential for similar capabilities, requiring further research. BGC analysis using antiSMASH detected several secondary metabolite BGCs associated with plant pathogenicity in Ap. hysterina KUC21437 (Additional file 2: Table S8). Previously identified plant pathogenicity-related BGCs in Apiospora species, including ACR toxin I, dimethyl coprogen, and (R)-Mellein BGCs, were also detected. Notably, ACT toxin II BGC, an essential host-selective toxin responsible for the pathogenesis of Alternaria alternata [ 27 ], was identified for the first time in Ap. hysterina KUC21437. ACT toxin II is known to cause alternaria brown spots in tangerines ( Citrus reticulate Blanco), grapefruits ( Ci. paradise Macfad.), and their hybrids [ 28 ]. Additionally, Ap. hysterina has been reported as the causal agent of severe leaf spots in faba bean ( Vicia faba ), leading to symptoms that eventually result in leaf abscission [ 29 ]. Despite genomic evidence, no reports to date have linked Ap. hysterina to disease symptoms in bamboo. Therefore, further research on secondary metabolites and pathogenicity bioassays is necessary to fully understand the role of bamboo pathogens. Mutualistic role of Ap. hysterina Plant-fungal interactions must consider not only genetic traits but also biological activities. Thus, investigating the biological activities associated with symbiotic interactions is a fundamental approach for elucidating the critical role of endophytic fungi in the health and resilience of their hosts [ 30 ]. Through biological activity analyses, we identified mutualistic traits in Ap. hysterina that may benefit bamboo in addition to its pathogenic potential. The antioxidant production capability of Apiospora species, as demonstrated in this study, highlights their ability to reduce reactive oxygen species (ROS). ROS reduction can enhance plant tolerance by mitigating multiple stresses, including drought [ 31 ], metals [ 32 ], pathogens [ 33 ], and salinity [ 31 ]. Moreover, antioxidants play a critical role in stress signaling [ 34 ], facilitating chemical communication between the host and an asymptomatic endophyte (including an avirulent pathogen). This enables the host to rapidly respond to pathogenesis and differentiate between mutualistic and pathogenic interactions [ 35 ]. The antifungal activity of Ap. hysterina KUC21437 against plant pathogens further supports its role as a mutualistic endophyte. BGC analysis revealed the presence of antibiotic-related BGCs, including AbT1, a precursor for synthesizing Aureobasidin A (AbA) in Aureobasidium pullulans [ 36 ]. AbA is a cyclic depsipeptide antibiotic with potent antifungal activity against various plant fungal pathogens, including Aspergillus fumigates , As. nidulans , As. niger , and As. oryzae , Blastomyces dermatitidis , Candida albicans , Cryptococcus neoformans , Histoplasma capsulatum , and Schizosaccharomyces pombe [ 36 – 38 ]. These findings suggest that Apiospora contribute to the microbiome’s protective functions against external threats. Multifaceted roles and trophic mode switching The dual roles of Apiospora as mutualists and pathogens suggest a complex ecological strategy. In this study, Ap. hysterina was unexpectedly dominant in bamboo tissues at all stages, including the early young stages, without visible black spots. This observation, combined with the absence of Apiospora in the surrounding soil, suggests that Apiospora establishes itself as an endophyte before pathogenic symptoms manifest. The ability of Apiospora to produce plant hormones further underscores its multifaceted roles. In this study, GA derivatives and ABA were detected in Ap. hysterina , but IAA was not detected. While IAA is strongly associated with symbiosis in host plants, both GA and ABA have roles linked to pathogenicity and mutualism [ 39 , 40 ]. GA regulates various plant processes, such as seed development [ 41 ], pollen tube growth [ 41 ], plant development [ 42 ], and internode elongation. Fungal GA production has been reported to enhance seed germination under salt stress and may facilitate plant carbon sink activity in infected cells [ 43 ]. We report that Apiospora species produce ABA. Fungal ABA has been identified as a virulence factor that suppresses plant immune responses [ 44 , 45 ] and is associated with the establishment of symbiosis with the host plant [ 46 ]. Although the specific role of ABA in Apiospora remains unclear, it may help infect bamboo species by reducing plant resistance. Collectively, we propose that Apiospora initially functions as a mutualistic endophyte that promotes bamboo growth and stress tolerance. However, it may transition to a pathogenic state under specific environmental or host conditions. Such trophic mode switching has been well-documented in other fungal endophytes, such as dark septate endophytes, whose interactions shift from mutualism to parasitism based on nutrient availability or host performance [ 47 ]. This dynamic aligns with the “balanced antagonism” theory, which posits that fungal-host interactions are shaped by biochemical communication and environmental factors [ 48 ]. Similar examples in bamboo-endophyte systems underscore this multifaceted role. For instance, Shiraia sp. isolated from bamboo seeds ( Phyllostachys edulis ) act as antimicrobial endophytes but are also significant bamboo pathogens [ 49 ]. Similarly, Aciculosporium take , an endophytic bambusicolous fungus, promotes shoot growth via auxin production but causes witch’s broom disease [ 50 ]. These cases highlight the potential of endophytes to navigate complex ecological roles within their hosts. Genomic evidence of pathogenic Apiospora traits suggests transcriptional regulation controls trophic mode shifts. Future gene expression studies during the infection stages could reveal these transitions. Conclusion This study highlights the multifaceted roles of Apiospora hysterina in bamboo ecosystems as endophytes, demonstrating their potential as mutualists and pathogens. The coexistence of these roles underscores the complexity of plant-fungal interactions, emphasizing the necessity of exploring fungal behavior across different ecological contexts. Understanding these dynamics could have broader implications for managing bamboo health and leveraging endophytes for sustainable bamboo cultivation. Furthermore, this research highlights the significance of adopting a holistic approach (microbiome, chemical, and genomic analysis) in studying plant-fungal relationships involving bamboo- Apiospora and the need for further research in this field. Declarations Acknowledgments We are grateful to Seonju Marincowitz (FABI, University of Pretoria) for critical advice that improved the manuscript and thank Editage (www.editage.co.kr) for English language editing and review. This work was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) [2021R1A2C1011894, RS-2024-00343166], the Korea University Grant, and the Korea Polar Research Institute (PN24120). Funding This project received funding from National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) [2021R1A2C1011894]. This study was also supported by the Korea University Grant, Korea Polar Research Institute (PN24120), and the NRF grant funded by the Korea government (RS-2024-00343166). Competing interests Y.M. Heo is employed by COSMAX BTI. The rest of the authors declare that the research was conducted in the absence of any commercial or financial relationship that could be construed as a potential conflict of interest. Author Contributions Conceptualization, S.L.K., C.W.S., H.L., G.H.K., and J.K.; data collection, S.L.K. and C.W.S; methodology, S.L.K., C.W.S., H.K., D.L., S.L., and D.Y.K.; data analysis, S.L.K., C.W.S., and Y.W.L.; resources, S.L.K, M.C., Y.Y., S.L., Y.M.H., and J.K.; writing, S.L.K., C.W.S., Y.C., and H.L.; visualization, S.L.K. and C.W.S.; supervision, J.K. Data Availability The whole genome sequence of Ap. hysterina KUC21437 generated and analyzed during the current study are available in the NCBI repository, NCBI BioProject PRJNA1060443 with accession number JAYMYE000000000. The amplicon sequencing data are available in the NCBI SRA repository, BioProject PRJNA1065571. 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Plant Biol (Stuttg) 8:281–290. https://doi.org/10.1055/s-2006-923882 Iqbal N, Nazar R, Khan MIR, Masood A, Khan NA (2011) Role of gibberellins in regulation of source–sink relations under optimal and limiting environmental conditions. Curr Sci 100:998–1007 Finkelstein R (2013) Abscisic acid synthesis and response. Arabidopsis Book 11:e0166. https://doi.org/10.1199/tab.0166 Lievens L, Pollier J, Goossens A, Beyaert R, Staal J (2017) Abscisic acid as pathogen effector and immune regulator. Front Plant Sci 8:587. https://doi.org/10.3389/fpls.2017.00587 Hill RA, Wong‐Bajracharya J, Anwar S, Coles D, Wang M, Lipzen A, Ng V, Grigoriev IV, Martin F, Anderson IC, Cazzonelli CI, Jeffries T, Plett KL, Plett JM (2022) Abscisic acid supports colonization of Eucalyptus grandis roots by the mutualistic ectomycorrhizal fungus Pisolithus microcarpus . New Phytol 233:966–982. https://doi.org/10.1111/nph.17825 Jumpponen A (2001) Dark septate endophytes–are they mycorrhizal? Mycorrhiza 11:207–211. https://doi.org/10.1007/s005720100112 Schulz B, Boyle C (2005) The endophytic continuum. Mycol Res 109:661–686. https://doi.org/10.1017/s095375620500273x Cabello MA, Platas G, Collado J, Díez MT, Martín I, Vicente F, Meinz M, Onishi JC, Douglas C, Thompson J, Kurtz MB, Schwartz RE, Bills GF, Giacobbe RA, Abruzzo GK, Flattery AM, Kong L, Peláez F (2001) Arundifungin, a novel antifungal compound produced by fungi: biological activity and taxonomy of the producing organisms. Int Microbiol 4:93–102. https://doi.org/10.1007/s101230100020 Tanaka E (2009) Specific in situ visualization of the pathogenic endophytic fungus Aciculosporium take , the cause of witches’ broom in bamboo. Appl Environ Microbiol 75:4829–4834. https://doi.org/10.1128/AEM.00635-09 Additional Declarations Competing interest reported. Y.M. Heo is employed by COSMAX BTI. The rest of the authors declare that the research was conducted in the absence of any commercial or financial relationship that could be construed as a potential conflict of interest. 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09:23:05","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6757679/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6757679/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s00248-025-02631-z","type":"published","date":"2025-11-05T15:56:56+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":83666763,"identity":"d6e47ede-d48c-4806-bd07-481dda852f6e","added_by":"auto","created_at":"2025-05-30 11:55:09","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":960862,"visible":true,"origin":"","legend":"\u003cp\u003eBambusicolous endophytic fungal community structures. Fungal community structures at the \u003cstrong\u003eA\u003c/strong\u003e genus level and \u003cstrong\u003eB \u003c/strong\u003eAnalysis of \u003cem\u003eApiospora \u003c/em\u003especies communities according to factors based on mean relative abundance. Shannon diversity of the communities was compared between the bamboo compartment and each tissue stage. Venn diagram of the genus- and species-level community in C and D, respectively, showing the overlap frequency between bamboo compartments and between the bamboo tissue stages. \u003cstrong\u003eE \u003c/strong\u003eDetected or undetected \u003cem\u003eApiospora\u003c/em\u003especies across the bamboo compartments and stages are shown in the table. The detected \u003cem\u003eApiospora\u003c/em\u003e species are highlighted in blue boxes.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-6757679/v1/67a4c416578e8bc493be3908.png"},{"id":83666264,"identity":"4b46c63f-c217-455c-8bd8-a2ac0b1846dc","added_by":"auto","created_at":"2025-05-30 11:47:09","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":365116,"visible":true,"origin":"","legend":"\u003cp\u003eBeta diversity of bambusicolous endophytic fungi. \u003cstrong\u003eA \u003c/strong\u003ePERMANOVA test was used to determine the effect size of the factors on fungal communities, displaying the percent variation explained by the factors of bamboo “tissue type” (culm, leaf, and root), “stages” (young, mature, and dead), and “combination of both factors.” The undefined effects are summarized under “other.” Principal coordinate analysis ordination plot based on Bray–Curtis distance was used to explore variations in bambusicolous fungal diversity according to the factors. The ellipses indicate clusters of fungal communities according to tissue type. The red arrows indicate significant vectors. The first two principal coordinates explain \u003cstrong\u003eB\u003c/strong\u003e 35% of the total variance of the genus scale community and \u003cstrong\u003eC\u003c/strong\u003e47% of the total variance of the \u003cem\u003eApiospora\u003c/em\u003ecommunity. Significance levels are indicated by asterisks (*\u003cem\u003ep \u0026lt; \u003c/em\u003e0.05; **\u003cem\u003ep \u0026lt; \u003c/em\u003e0.01; ***\u003cem\u003ep \u0026lt; \u003c/em\u003e0.001; ns: Not significant).\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-6757679/v1/2696ef17b48feff2a5c4fc47.png"},{"id":83666270,"identity":"b905398a-87f9-4783-96c0-ca1bfed10210","added_by":"auto","created_at":"2025-05-30 11:47:09","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":641323,"visible":true,"origin":"","legend":"\u003cp\u003eEcological niches of bambusicolous endophytic fungi.\u003cstrong\u003e \u003c/strong\u003eRepresentative bambusicolous fungal taxa are shown in the linear discriminant analysis effect size (LEfSe) analysis between the stages of bamboo tissue and soil (LDA score \u0026gt; 2.0, \u003cem\u003ep \u0026lt; \u003c/em\u003e0.05). \u003cstrong\u003eA\u003c/strong\u003e Histogram represents the significantly representative taxa based on LDA effect sizes at taxonomic levels from phylum to species. \u003cstrong\u003eB\u003c/strong\u003e The cladogram shows the phylogenetic biomarkers of fungal lineages at different bamboo tissue stages and in soils. Significant biomarkers are highlighted and marked.\u003cstrong\u003e C\u003c/strong\u003e Heatmap clustering between relative abundances of representative bambusicolous taxa and stages of bamboo tissue and soil based on Spearman correlation. Ten representative taxa were selected for the LDA. The matrix values were normalized by row-wise Z-score normalization. The horizontal row shows the stages of bamboo tissue and soil growth, the vertical row represents the abundance of the bambusicolous fungal community, and the legend indicates the Z-score. The ecological preferences of the representative fungal species were calculated and presented as statistical correlation indices with \u003cem\u003ep\u003c/em\u003e-values. Significance levels are indicated by asterisks (*\u003cem\u003ep \u0026lt; \u003c/em\u003e0.05; **\u003cem\u003ep \u0026lt; \u003c/em\u003e0.01; ***\u003cem\u003ep \u0026lt; \u003c/em\u003e0.001; ns: Not significant).\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-6757679/v1/8133b4264c3833dc45ad406e.png"},{"id":83666271,"identity":"8b079b0c-29e3-4d8a-89f6-bddc03899d27","added_by":"auto","created_at":"2025-05-30 11:47:09","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":351183,"visible":true,"origin":"","legend":"\u003cp\u003eCarbohydrate-active enzyme (CAZyme) gene contents were compared across species to predict trophic lifestyle using principal component analysis (PCA) plots. PC1: Principal component 1, PC2: Principal component 2. The plot shows the CAZyme-inferred phenotypic trophism of 109 reference species of fungi and \u003cem\u003eoomycetes\u003c/em\u003e with different lifestyles. The red arrows indicate \u003cem\u003eApiospora hysterina\u003c/em\u003eKUC21437. Three plots are indicated with \u003cstrong\u003eA \u003c/strong\u003ecommon trophic terms (Nomenclature 1), \u003cstrong\u003eB \u003c/strong\u003efive major trophic classes (Nomenclature 2), and \u003cstrong\u003eC\u003c/strong\u003e nine sub-classes (Nomenclature 3). The novel trophic classes were proposed based on Hane et al. [23].\u003c/p\u003e","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-6757679/v1/0ce20eddcce6d59bcbb46772.png"},{"id":83666273,"identity":"72c9884a-d7cb-48f9-a104-85899683cde1","added_by":"auto","created_at":"2025-05-30 11:47:09","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":519678,"visible":true,"origin":"","legend":"\u003cp\u003eScheme of the plant hormone biosynthetic pathways. \u003cstrong\u003eA\u003c/strong\u003e ABA and \u003cstrong\u003eB\u003c/strong\u003e GA in \u003cem\u003eAp. hysterina\u003c/em\u003e KUC21437 based on genome analysis. The predicted compounds in the pathway are linked by arrows, and the genome (red italics) and enzymes (blue) are denoted next to the arrow. The arrow with the dotted line indicates an unannotated pathway.\u003c/p\u003e","description":"","filename":"5.png","url":"https://assets-eu.researchsquare.com/files/rs-6757679/v1/8706f0adf77f0ae7623081e5.png"},{"id":95563900,"identity":"0b1f5239-6188-4200-981d-2f5057a2c397","added_by":"auto","created_at":"2025-11-10 16:01:51","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3461063,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6757679/v1/989a5957-f6ba-45cb-86a7-0a8ba0970300.pdf"},{"id":83666272,"identity":"2d5f1e9e-a40d-40d2-bbba-30e57ccb2df2","added_by":"auto","created_at":"2025-05-30 11:47:09","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":2337381,"visible":true,"origin":"","legend":"","description":"","filename":"Additionalfile1ME.docx","url":"https://assets-eu.researchsquare.com/files/rs-6757679/v1/a93b41b968f34042152a902a.docx"},{"id":83666267,"identity":"63097ea9-cf56-4a2e-abf1-90f8f169b11e","added_by":"auto","created_at":"2025-05-30 11:47:09","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":73191,"visible":true,"origin":"","legend":"","description":"","filename":"Additionalfile2ME.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-6757679/v1/a81234f27564160c2476990f.xlsx"},{"id":83666269,"identity":"3fd2a5b1-9a84-4a3b-8f61-7a071f4e49ab","added_by":"auto","created_at":"2025-05-30 11:47:09","extension":"docx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":39957,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryText.docx","url":"https://assets-eu.researchsquare.com/files/rs-6757679/v1/fec036ecba191f4933bc529d.docx"}],"financialInterests":"Competing interest reported. Y.M. Heo is employed by COSMAX BTI. The rest of the authors declare that the research was conducted in the absence of any commercial or financial relationship that could be construed as a potential conflict of interest.","formattedTitle":"\u003cp\u003eExploring multifaceted roles of bambusicolous \u003cem\u003eApiospora \u003c/em\u003ein\u003cem\u003e Phyllostachys\u003c/em\u003e sp.\u003c/p\u003e","fulltext":[{"header":"Introduction","content":"\u003cp\u003eBamboo (family Poaceae, subfamily Bambusoideae) is a valuable grass plant renowned for diverse ecological roles, including biodiversity conservation [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e], carbon fixation [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e], soil and water conservation [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e], and economic activities [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. \u003cem\u003ePhyllostachys\u003c/em\u003e, known as running bamboo, is one of the largest bamboo genera, consisting of approximately 50 species, predominantly found in Asia (China and Japan). In Korea, bamboo forests cover an area of approximately 22,000 ha, mainly consisting of \u003cem\u003ePhyllostachys\u003c/em\u003e species (\u003cem\u003eP. bambusoides\u003c/em\u003e, \u003cem\u003eP. nigra var. henonis\u003c/em\u003e, and \u003cem\u003eP. edulis\u003c/em\u003e), with 96% located in the southern region [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eBambusicolous fungi live on various bamboo substrates, including culms, leaves, branches, rhizomes, and roots, and play a crucial role in bamboo diversity conservation and ecosystem maintenance [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. Over 1,100 species within 228 genera have been identified as bambusicolous fungi, primarily including Ascomycetes (630 species), Basidiomycetes (150 species), and anamorphic fungi (330 species) [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e, \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. These fungi significantly influence bamboo ecosystems by functioning as endophytes, pathogens, and saprobes. Endophyte-plant symbiosis provides valuable insights into plant-microbe interactions with potential applications in agriculture and environmental sustainability [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. For instance, fungal endophytes can produce growth hormones, such as gibberellins and auxins, promoting plant growth, enhancing root development, and improving overall plant health [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. Bambusicolous endophytic fungi are known to synthesize bioactive compounds with antioxidant, antimicrobial, antitumor, and plant growth-promoting activities [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eCurrently, Index Fungorum (2024) lists 175 epithets of \u003cem\u003eApiospora\u003c/em\u003e, with 42 species recorded as bambusicolous fungi. Many \u003cem\u003eApiospora\u003c/em\u003e species are saprobes, causing black spot formation on dead or decaying bamboo [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e, \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e], and some are pathogenic [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e–\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. Additionally, \u003cem\u003eApiospora\u003c/em\u003e species are prevalent as endophytes in running bamboo (\u003cem\u003ePhyllostachys\u003c/em\u003e spp.) and dwarf bamboo (\u003cem\u003eSasa\u003c/em\u003e spp.) in Japan [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e], offering competitive advantages to their hosts through hormone synthesis, seed germination promotion, and antimicrobial and antioxidant activities [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. These findings underscore the ecological versatility of \u003cem\u003eApiospora\u003c/em\u003e as saprobes, pathogens, and endophytes [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e, \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e, \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eThus, we hypothesize that bambusicolous \u003cem\u003eApiospora\u003c/em\u003e species significantly influence the bamboo lifecycle, serving as symbionts during growth stages, pathogens during maturation, and saprobes in dead bamboo tissues. However, the diversity, ecological traits, and symbiotic interactions of endophytic \u003cem\u003eApiospora\u003c/em\u003e in bamboo hosts remain unclear. This study aimed to explore the diversity of bamboo endophytic fungi, focusing on \u003cem\u003eApiospora\u003c/em\u003e, across various bamboo tissues (culm, leaf, root) and soil, as well as different bamboo stages (young, mature, dead). We investigated the ecological preferences (niches) of these endophytes and analyze the biological activities and genetic characteristics of bambusicolous \u003cem\u003eApiospora\u003c/em\u003e to elucidate their multifaceted ecological roles in Korean \u003cem\u003ePhyllostachys\u003c/em\u003e forests.\u003c/p\u003e "},{"header":"Methods","content":"\u003cp\u003eDetailed descriptions are provided in the Supplementary Text.\u003c/p\u003e\n\u003cp\u003e\u0026nbsp;\u003cstrong\u003eSampling collection and treatment\u003c/strong\u003e\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eBamboo materials (\u003cem\u003ePhyllostachys sp\u003c/em\u003e.) from Juknokwon, Damyang−gun, Korea, were collected in December 2021 and categorized into “Young” (\u0026lt;1 year), “Mature” (3 years), and “Dead” (\u0026gt;5 years) based on appearance. Samples (culm, leaf, root, soil) were stored at –80°C. Surface sterilization was performed following the methodology outlined by Barra et al. [20], and samples were crushed in liquid nitrogen using a Freeze Mill (SPEX 6875D).\u003c/p\u003e\n\u003cp\u003e\u0026nbsp;\u003cstrong\u003eBambusicolous fungal community analysis\u003c/strong\u003e\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eDNA was extracted using DNeasy Powerlyzer PowerSoil Kit (Qiagen). Polymerase chain reaction amplified ITS2 regions with primers ITS3 and ITS4. Libraries were sequenced on Illumina MiSeq (2×300 bp, paired end). ITS2 sequences were analyzed using QIIME2. DADA2 plugin filtered low−quality, short, and chimeric sequences. Operational taxonomic units (OTUs) were clustered at 99% similarity using VSEARCH, excluding OTUs \u0026lt;10 sequences. Taxonomy assignments utilized modified UNITE v8.3 and enhanced GenBank sequences. Phylogenetic analysis used MAFFT and RAxML with reference sequences of Apiospora and related genera from the GenBank database (Additional file 1: Table S1). Alpha and beta diversity analyses (\"vegan\" package) assessed community variation. PERMANOVA with Bray−Curtis distances identified significant factors. Principal coordinate analysis (PCoA), Venn diagrams, linear discriminant analysis (LefSe), and heat maps (\"pheatmap\") were used to visualize data. Indicator species were analyzed with the \"Indicspecies\" package.\u003c/p\u003e\n\u003cp\u003e\u0026nbsp;\u003cstrong\u003eBiological activity and metabolite analysis\u003c/strong\u003e\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eNine strains from the Korea University Culture Collection, representing three species (\u003cem\u003eAp. arundinis, Ap. camelliae−sinensis, Ap. hysterina\u003c/em\u003e), were analyzed based on microbiome findings. Extracts were prepared from strains cultured on potato dextrose agar, extracted with methanol and ethyl acetate. Radical scavenging activities were measured using 2,2'−Azino−bis (3−ethylbenzothiazoline−6−sulfonic acid (ABTS) and 2,2−Diphenyl−1−picrylhydrazyl (DPPH) assays with standard controls (Trolox and L−Ascorbic acid, respectively). Antifungal activity against \u003cem\u003eBotrytis cinerea\u003c/em\u003e, \u003cem\u003eColletotrichum gloeosporioides\u003c/em\u003e, and \u003cem\u003eFusarium oxysporum\u003c/em\u003e was assessed via disk diffusion assay. Indole−3−acetic acid (IAA), Abscisic acid ABA, and Gibberellic acid (GA) production by strains was evaluated using liquid chromatography with tandem mass spectrometry (LC−MS/MS) with an Orbitrap Exploris 120 mass spectrometer. Molecular networks were generated using GNPS and visualized in Cytoscape.\u003c/p\u003e\n\u003cp\u003e\u0026nbsp;\u003cstrong\u003eWhole genome analysis\u003c/strong\u003e\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eGenomic DNA from selected \u003cem\u003eApiospora\u003c/em\u003e was sequenced with the PacBio Sequel and NovaSeq6000 platforms. Assembly involved Flye, Racon, and Hapo−G. Genomes were annotated with RepeatModeler, RepeatMasker, BRAKER2, GeMoMa, tRNAscan−SE, Rfam, and MMseqs2. CAZyme−related genes identified via dbCAN3, with trophic lifestyles classified by CATAStrophy. Secondary metabolite clusters identified using antiSMASH. Genome−scale modeling and BLAST analyses identified hormone synthesis pathways, visualized using ChemDraw.\u003c/p\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eFungal microbiome analysis\u003c/h2\u003e \u003cdiv id=\"Sec4\" class=\"Section3\"\u003e \u003ch2\u003eFungal microbiomes of bamboo and soil samples\u003c/h2\u003e \u003cp\u003eA total of 89 bamboo forest samples (26 culms, 27 leaves, 27 roots, and 9 soil types) were collected for fungal microbiome analysis. For ITS2 amplicon analysis, 14,439,126 paired sequences were obtained, and 9,205,658 merged paired reads (average length 319 bp) were retained after quality filtering. Rarefaction curves confirmed sufficient sequencing depth (Additional file 1: Fig. \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e). After clustering and discarding low coverage mOTUs, 4,303 mOTUs were retained. Among these, 31 mOTUs were assigned to the candidate \u003cem\u003eApiospora\u003c/em\u003e species. Phylogenetic analysis for precise species identification (Additional file 1: Fig. \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e and Additional file 2: Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e) revealed 31 mOTUs as seven known \u003cem\u003eApiospora\u003c/em\u003e species (\u003cem\u003eAp. arundinis\u003c/em\u003e, \u003cem\u003eAp. hysterina\u003c/em\u003e, \u003cem\u003eAp. camelliae-sinensis, Ap. minutispora\u003c/em\u003e, \u003cem\u003eAp. pseudohyphopodii\u003c/em\u003e, \u003cem\u003eAp. rasikravindrae\u003c/em\u003e, and \u003cem\u003eAr. phaeospermum\u003c/em\u003e), as well as a new candidate species (\u003cem\u003eApiospora\u003c/em\u003e sp. 1) and four indistinct species (ITS_Apio_01, ITS_Apio_12, ITS_Apio_13, and ITS_Apio_29). These 12 \u003cem\u003eApiospora\u003c/em\u003e species were used for ALC analysis.\u003c/p\u003e \u003cp\u003eFor GLC analysis, the 21 most abundant fungal genera (\u0026gt;\u0026thinsp;0.5% of the total reads) were selected, with the exception of unidentified genera. Among them, \u003cem\u003eApiospora\u003c/em\u003e was the most dominant genus in the culms and leaves with mean relative abundances of 46.56% and 13.25%, respectively (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA; Additional file 2: Table \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e). Moreover, \u003cem\u003eApiospora\u003c/em\u003e was the most dominant genus across the bamboo stages with high mean relative abundances (Young, 22.21%; Mature, 23.39%; and Dead, 16.33%), but the proportion of \u003cem\u003eApiospora\u003c/em\u003e decreased in the dead samples and was minimized in the soil samples (0.37%). In bamboo roots and soils, \u003cem\u003eMycena\u003c/em\u003e (12.65%) and \u003cem\u003eMortierella\u003c/em\u003e (Mortierellaceae) (12.96%) were the most abundant genera, respectively (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA; Additional file 2: Table \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e). Among the 21 major genera, 14 were detected in all bamboo compartments (culms, leaves, roots, and soil) (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eC). In contrast, no unique genera were detected in each bamboo compartment. Across the bamboo tissue stages, 14/19, 12/19, and 9/20 genera were shared between the culm, leaf, and root stages, respectively. The genera detected at all stages in all bamboo tissues were \u003cem\u003eApiospora\u003c/em\u003e, \u003cem\u003eMycena\u003c/em\u003e, \u003cem\u003eFusarium\u003c/em\u003e, \u003cem\u003eColletotrichum\u003c/em\u003e, \u003cem\u003eNeptunomyces\u003c/em\u003e, and \u003cem\u003eTrichoderma\u003c/em\u003e (Additional file 2: Table S4).\u003c/p\u003e \u003cp\u003eIn ALC analysis, four species were commonly detected throughout the life of bamboo tissues: \u003cem\u003eAp. arundinis\u003c/em\u003e, \u003cem\u003eAp. camelliae-sinensis, Ap. hysterina\u003c/em\u003e, and \u003cem\u003eAp. rasikravindrae\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eD, E; Additional file 2: Table S4). \u003cem\u003eAp. arundinis\u003c/em\u003e, \u003cem\u003eAp. camelliae-sinensis\u003c/em\u003e, and \u003cem\u003eAp. rasikravindrae\u003c/em\u003e were also detected in soil samples, but \u003cem\u003eAp. hysterina\u003c/em\u003e was not detected in soil samples exhibiting an obligatory association with bamboo.\u003c/p\u003e \u003cp\u003e \u003cem\u003eAp. hysterina\u003c/em\u003e was the most abundant species in young culms (25.9%), mature culms (39.1%), and mature leaves (15.2%) (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB). \u003cem\u003eAp. arundinis\u003c/em\u003e was highly abundant in young culms (12.5%) and leaves (8.1%) but was present at a considerably lower proportion in the mature and dead stages. \u003cem\u003eAp. camelliae-sinensis\u003c/em\u003e and \u003cem\u003eAp. pseudohyphopodii\u003c/em\u003e were highly abundant in bamboo culms, followed by \u003cem\u003eAp. hysterina\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB); however, they were only abundant in young and dead culms, respectively (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB). \u003cem\u003eApiospora\u003c/em\u003e sp. 1 was uniquely detected in mature culm tissues, whereas ITS_Apio_01 was detected at all stages of bamboo leaves growth. \u003cem\u003eAp. minutispora\u003c/em\u003e and ITS_Apio_29 were only detected in dead bamboo tissues (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eD, E; Additional file 2: Table S4).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003c/div\u003e\n\u003ch3\u003eVariation in endophytic fungal community and its ecological niche\u003c/h3\u003e\n\u003cp\u003eα- and β-diversity analyses indicated significant differences in endophytic communities across bamboo tissue types (Figs.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA, \u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB, \u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eB, \u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eC; Additional file 2: Tables S5, S6). Variation among bamboo growth stages was significant only in β-diversity analyses (ALC, Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eC). Community variation by stage within each tissue showed significant α-diversity differences only in leaf ALC (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB). β-diversity differences were observed in culm and root ALC and leaf GLC analyses. PERMANOVA confirmed tissue type as the most influential factor on fungal community structure, followed by the interaction of tissue type and stage, and stage alone (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eA).\u003c/p\u003e \u003cp\u003eRepresentative fungal taxa were identified via LEfSe (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eA, B). Major genera such as \u003cem\u003eApiospora\u003c/em\u003e (young culms), \u003cem\u003eDidymella\u003c/em\u003e (mature culms), \u003cem\u003eColletotrichum\u003c/em\u003e (young leaves), \u003cem\u003eNeptunomyces\u003c/em\u003e (dead leaves), \u003cem\u003eFusarium\u003c/em\u003e and \u003cem\u003eMycena\u003c/em\u003e (mature roots), and \u003cem\u003eTrichoderma\u003c/em\u003e (soil) exhibited significant associations (LDA\u0026thinsp;\u0026gt;\u0026thinsp;2.0, p\u0026thinsp;\u0026lt;\u0026thinsp;0.05). \u003cem\u003eApiospora\u003c/em\u003e species (\u003cem\u003eAp. arundinis, Ap. camelliae-sinensis\u003c/em\u003e, young culms; \u003cem\u003eAp. hysterina\u003c/em\u003e, mature culms) also showed significant preferences.\u003c/p\u003e \u003cp\u003eHeat map clustering (Spearman correlation) confirmed taxa associations, dividing representative fungi into aboveground and underground clusters (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eC). High positive correlations were noted for \u003cem\u003eMycena, Trichoderma, Colletotrichum, Neptunomyces, Didymella, Apiospora, Ap. hysterina, Ap. arundinis\u003c/em\u003e, and \u003cem\u003eAp. camelliae-sinensis\u003c/em\u003e, supporting LEfSe findings. Major Apiospora species were significantly associated with living bamboo culms.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003c/p\u003e\n\u003ch3\u003eBiological activities\u003c/h3\u003e\n\u003cp\u003eThe biological activity analysis was conducted examining three bambusicolous \u003cem\u003eApiospora\u003c/em\u003e species using microbiome analysis. \u003cem\u003eAp. arundinis\u003c/em\u003e (KUC21601 and KUC21792), \u003cem\u003eAp. camelliae-sinensis\u003c/em\u003e KUC21546, and \u003cem\u003eAp. hysterina\u003c/em\u003e (KUC21437 and KUC21435) exhibited high antioxidant activity in both the ABTS and DPPH assays (Additional file 2: Table S7). In the antifungal activity assay, \u003cem\u003eAp. camelliae-sinensis\u003c/em\u003e KUC21538 and \u003cem\u003eAp. hysterina\u003c/em\u003e (KUC21437 and KUC21435) inhibited the growth of \u003cem\u003eBotrytis cinerea\u003c/em\u003e KUC21265. The extracts of \u003cem\u003eAp. hysterina\u003c/em\u003e (KUC21437 and KUC21435) inhibited the growth of \u003cem\u003eColletotrichum gloeosporioides\u003c/em\u003e KUC21266. However, the \u003cem\u003eAp. arundinis\u003c/em\u003e strains did not exhibit antifungal activity against phytopathogenic fungi.\u003c/p\u003e \u003cp\u003eThe plant hormone ABA was detected in the fungal extracts of \u003cem\u003eAp. hysterina\u003c/em\u003e (KUC21437 and KUC21435) and \u003cem\u003eAp. camelliae-sinensis\u003c/em\u003e (KUC21536 and KUC21538) using MS/MS spectral matching with authentic standard compounds (Additional file 1: Fig. \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e). GA derivatives (nodes 7451 and 7445) clustered with the node of GA (78103) were detected in the extracts of the strains of \u003cem\u003eAp. hysterina\u003c/em\u003e (KUC21435, KUC21437, and KUC21438) (Additional file 1: Fig. S4). However, the LC-MS analysis of the standard and extract did not detect IAA.\u003c/p\u003e\n\u003ch3\u003eGenomic analysis\u003c/h3\u003e\n\u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eGenome sequencing, assembly, and annotation\u003c/h2\u003e \u003cp\u003eGenomic analysis was conducted on the most dominant bambusicolous endophyte \u003cem\u003eApiospora\u003c/em\u003e species in this study, \u003cem\u003eAp. hysterina\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA). The strain \u003cem\u003eAp. hysterina\u003c/em\u003e KUC21437 was selected due to its various biological activities and plant hormone production ability (ABA and GA). We obtained a 48.0 Mbp genome (GC content: 48.6%) with eight contigs (max. length and N50: 5.7 Mbp) excluding the mitochondrial genome. The genome assembly completeness in terms of gene content ranged from 97.7% (\u003cem\u003eAscomycota\u003c/em\u003e) and 99.2% (\u003cem\u003eFungi\u003c/em\u003e) with BUSCO 5.4.6 [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e] and OrthoDB 10 [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e]. A total of 14,433 protein-coding genes were identified via structural genome annotation.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eTrophic lifestyle prediction\u003c/h3\u003e\n\u003cp\u003eThe CAZyme analysis of the KUC21437 genome revealed 692 genes across 133 CAZyme families. Glycoside hydrolases (GH; 302 genes) dominated, with GH18 (chitinase; 21 genes) and AA7 (oxidase; 71 genes) being prevalent (Additional file 1: Fig. S5). CATAStrophy analysis predicted the lifestyle of \u003cem\u003eAp. hysterina\u003c/em\u003e KUC21437 as a \u0026ldquo;necrotroph\u0026rdquo;, representing the major trophic class under common trophic terms (Nomenclature 1) (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Principal component analysis revealed that the fungus was located close to the necrotrophs and hemibiotrophs and was significantly distinguished from the symbionts and biotrophs (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eA). According to the trophic mode classification (Nomenclature 2) of Hane et al. [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e], the fungus was predicted to be a \u0026ldquo;vasculartroph (major trophic class)\u0026rdquo; based on the RCD score (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eB; Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Moreover, it can be classified as \u0026ldquo;mesotroph_intracellular (major trophic class)\u0026rdquo; in novel trophic sub-classes (Nomenclature 3) based on the RCD score (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eC; Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). \u0026ldquo;Vasculotrophs\u0026rdquo; refers to fungal species commonly associated with diseases such as wilts, rots, or anthracnoses. \u0026ldquo;Mesotroph_intracellular\u0026rdquo; describes typical hemibiotrophic fungi that produce specialized structures, such as appressoria, to facilitate intracellular colonization.\u003c/p\u003e\u003ctable id=\"Tab1\" border=\"1\" class=\"fr-table-selection-hover\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eSummary of CATAStrophy classifications of \u003cem\u003eApiospora hysterina\u003c/em\u003e KUC21437 with relative centroid distance (RCD) scores ranging from 0 to 1\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\" rowspan=\"9\"\u003e\n \u003cp\u003e\u003cem\u003eApiospora hysterina\u003c/em\u003e KUC21437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" colspan=\"2\"\u003e\n \u003cp\u003eNomenclature 1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNecrotroph\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eHemibiotroph\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSaprotroph\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSymbiont\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eBiotroph\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cspan type=\"BoldUnderline\" class=\"BoldUnderline\" name=\"Emphasis\"\u003e1\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0.90\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0.39\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0.26\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0.0\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\" colspan=\"2\"\u003e\n \u003cp\u003e\u003cstrong\u003eNomenclature 2\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eVasculartroph\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eMesotroph\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003ePolymertroph\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eSaprotroph\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eMonomertroph\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cspan type=\"BoldUnderline\" class=\"BoldUnderline\" name=\"Emphasis\"\u003e1\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0.89\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0.88\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0.31\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0.0\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\" colspan=\"2\"\u003e\n \u003cp\u003e\u003cstrong\u003eNomenclature 3\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eMesotroph_intracellular\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003ePolymertroph_narrow\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eVasculartroph\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003ePolymertroph_broad\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eMesotroph_extracellular\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cspan type=\"BoldUnderline\" class=\"BoldUnderline\" name=\"Emphasis\"\u003e1\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0.91\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0.89\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0.67\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e0.55\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\n\u003cp\u003eRCD score of 1 (bold and underlined) indicates memberships in a major trophic class, and score \u0026ge; 0.95 (bold) predicts affinity for one or more trophic sub\u0026minus;classes.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eSM BGCs of\u003c/strong\u003e \u003cstrong\u003eApiospora hysterina\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eA total of 81 secondary metabolite biosynthetic gene clusters (SM BGCs) were identified, including 25 type 1 polyketide synthases (T1PKS), 1 type 3 polyketide synthase (T3PKS), 18 terpenes, 12 non-ribosomal peptide synthetases (NRPS), 11 NRPS-like, and 14 hybrid genes (Additional file 1: Fig. S6). Among these, 25 BGCs matched 22 known clusters, with 7 clusters characterized as 5 known SM BGCs at 100% AntiSMASH similarity (Additional file 2: Table S8). Notably, identified clusters included ACR toxin I, dimethyl coprogen, (R)-mellein, ACT toxin II, and AbT1.\u003c/p\u003e\n\u003ch3\u003ePlant hormone synthesis pathways\u003c/h3\u003e\n\u003cp\u003eGenome analysis predicted complete biosynthetic pathways for ABA and GA (Fig. \u003cspan class=\"InternalRef\"\u003e5\u003c/span\u003e). The ABA biosynthesis gene cluster, homologous to \u003cem\u003eBotrytis cinerea\u003c/em\u003e, was identified on chromosome 2 (1,571,658\u0026ndash;1,592,948), containing homologs of \u003cem\u003ebcABA1, bcABA2\u003c/em\u003e, and \u003cem\u003ebcABA3\u003c/em\u003e (VJ940_3286, VJ940_3285, VJ940_3287), and \u003cem\u003ebcABA4\u003c/em\u003e was located in an unannotated region (1,592,151\u0026ndash;1,592,948) (Fig. \u003cspan class=\"InternalRef\"\u003e5\u003c/span\u003eA, B). Genes involved in GA biosynthesis from farnesyl diphosphate to GA14 were also detected. A gene cluster encoding enzymes from geranylgeranyl diphosphate to ent-kaurenoate was identified on chromosome 2 (6,063,250\u0026ndash;6,076,058). Additional genes for GA derivative conversions (GA4 to GA1 and GA7 to GA3) were detected outside this cluster (VJ940_13065) (Fig. \u003cspan class=\"InternalRef\"\u003e5\u003c/span\u003eB).\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eEndophytic fungi play critical roles as mutualists or pathogens in plant ecosystems, influencing health, stress tolerance, and overall fitness through diverse interactions. Using microbiome analysis, this study examined the diversity of bambusicolous endophytic fungi across bamboo tissues and stages, focusing on the genus \u003cem\u003eApiospora\u003c/em\u003e. The microbiome analysis revealed that some \u003cem\u003eApiospora\u003c/em\u003e species are significant components of bambusicolous endophytic fungi, inhabiting bamboo culms and leaves from the young developmental stage to the dead state. To further explore the ecological roles of \u003cem\u003eApiospora\u003c/em\u003e, we employed a multidisciplinary approach integrating microbiome, biological activity tests (antioxidant, antifungal, and plant hormones production), and genomic analyses (CAZyme and SM BGCs) to identify their intricate ecological roles in the bamboo environment and provide new insights into their multifaceted roles.\u003c/p\u003e \u003cp\u003eIn this study, we mainly focused on \u003cem\u003eAp. hysterina\u003c/em\u003e to explore its ecological roles in bamboo. Through microbiome analysis, it was identified as the dominant endophytic fungi living in healthy culms and leaves but was absent from the soil. This distribution pattern indicates a strong ecological specificity to the host plant of this fungus compared to other fungi. Furthermore, its ability to produce two plant hormones (ABA and GA) and antioxidant and antifungal activities highlights its potential as a key player in the bamboo ecosystem as a mutualist. Therefore, \u003cem\u003eAp. hysterina\u003c/em\u003e was selected for further comprehensive investigations, including genomic analyses, to better understand its ecological roles.\u003c/p\u003e \u003cp\u003e \u003cb\u003ePutative pathogenic characteristics of\u003c/b\u003e \u003cb\u003eAp. hysterina\u003c/b\u003e\u003c/p\u003e \u003cp\u003eSome \u003cem\u003eApiospora\u003c/em\u003e species have been historically identified as plant pathogens that cause diseases such as culm blight (\u003cem\u003eAp. kogelbergensis\u003c/em\u003e) [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e], culm base rot (\u003cem\u003eAr. phaeospermum\u003c/em\u003e) [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e], culm staining (\u003cem\u003eApiospora indica\u003c/em\u003e) [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e], and dieback (\u003cem\u003eApiospora\u003c/em\u003e sp.) [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e] in bamboo. In addition to bamboo, \u003cem\u003eApiospora\u003c/em\u003e species have also been reported as plant pathogens in other crops, such as reddish-brown discoloration in sugarcane flesh [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eOur genomic analyses of \u003cem\u003eAp. hysterina\u003c/em\u003e support its pathogenic potential, consistent with previous studies. Specifically, the CAZyme content of \u003cem\u003eAp. hysterina\u003c/em\u003e KUC21437 suggests a trophic lifestyle consistent with a \u0026ldquo;necrotroph\u0026rdquo; (Nomenclature 1), \u0026ldquo;vasculartroph\u0026rdquo; (Nomenclature 2), and \u0026ldquo;mesotroph_intracellular\u0026rdquo; (Nomenclature 3) with high RCD scores (RCD score\u0026thinsp;\u0026gt;\u0026thinsp;0.95) (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). These classifications imply that the CAZyme content of \u003cem\u003eAp. hysterina\u003c/em\u003e is well-suited for plant infections, including vascular invasion and intracellular penetration via appressorial structure formation [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e]. However, appressorial structures have been observed in phylogenetically close species, such as \u003cem\u003eAp. pseudohyphopodii\u003c/em\u003e and \u003cem\u003eAp. yunnana\u003c/em\u003e [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. Direct evidence for such structures in \u003cem\u003eAp. hysterina\u003c/em\u003e has not yet been obtained. Nonetheless, its phylogenetic proximity suggests the potential for similar capabilities, requiring further research. BGC analysis using antiSMASH detected several secondary metabolite BGCs associated with plant pathogenicity in \u003cem\u003eAp. hysterina\u003c/em\u003e KUC21437 (Additional file 2: Table S8). Previously identified plant pathogenicity-related BGCs in \u003cem\u003eApiospora\u003c/em\u003e species, including ACR toxin I, dimethyl coprogen, and (R)-Mellein BGCs, were also detected. Notably, ACT toxin II BGC, an essential host-selective toxin responsible for the pathogenesis of \u003cem\u003eAlternaria alternata\u003c/em\u003e [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e], was identified for the first time in \u003cem\u003eAp. hysterina\u003c/em\u003e KUC21437. ACT toxin II is known to cause alternaria brown spots in tangerines (\u003cem\u003eCitrus reticulate\u003c/em\u003e Blanco), grapefruits (\u003cem\u003eCi. paradise\u003c/em\u003e Macfad.), and their hybrids [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e]. Additionally, \u003cem\u003eAp. hysterina\u003c/em\u003e has been reported as the causal agent of severe leaf spots in faba bean (\u003cem\u003eVicia faba\u003c/em\u003e), leading to symptoms that eventually result in leaf abscission [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eDespite genomic evidence, no reports to date have linked \u003cem\u003eAp. hysterina\u003c/em\u003e to disease symptoms in bamboo. Therefore, further research on secondary metabolites and pathogenicity bioassays is necessary to fully understand the role of bamboo pathogens.\u003c/p\u003e \u003cp\u003e \u003cb\u003eMutualistic role of\u003c/b\u003e \u003cb\u003eAp. hysterina\u003c/b\u003e\u003c/p\u003e \u003cp\u003ePlant-fungal interactions must consider not only genetic traits but also biological activities. Thus, investigating the biological activities associated with symbiotic interactions is a fundamental approach for elucidating the critical role of endophytic fungi in the health and resilience of their hosts [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]. Through biological activity analyses, we identified mutualistic traits in \u003cem\u003eAp. hysterina\u003c/em\u003e that may benefit bamboo in addition to its pathogenic potential.\u003c/p\u003e \u003cp\u003eThe antioxidant production capability of \u003cem\u003eApiospora\u003c/em\u003e species, as demonstrated in this study, highlights their ability to reduce reactive oxygen species (ROS). ROS reduction can enhance plant tolerance by mitigating multiple stresses, including drought [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e], metals [\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e], pathogens [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e], and salinity [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e]. Moreover, antioxidants play a critical role in stress signaling [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e], facilitating chemical communication between the host and an asymptomatic endophyte (including an avirulent pathogen). This enables the host to rapidly respond to pathogenesis and differentiate between mutualistic and pathogenic interactions [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eThe antifungal activity of \u003cem\u003eAp. hysterina\u003c/em\u003e KUC21437 against plant pathogens further supports its role as a mutualistic endophyte. BGC analysis revealed the presence of antibiotic-related BGCs, including AbT1, a precursor for synthesizing Aureobasidin A (AbA) in \u003cem\u003eAureobasidium pullulans\u003c/em\u003e [\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e]. AbA is a cyclic depsipeptide antibiotic with potent antifungal activity against various plant fungal pathogens, including \u003cem\u003eAspergillus fumigates\u003c/em\u003e, \u003cem\u003eAs. nidulans\u003c/em\u003e, \u003cem\u003eAs. niger\u003c/em\u003e, and \u003cem\u003eAs. oryzae\u003c/em\u003e, \u003cem\u003eBlastomyces dermatitidis\u003c/em\u003e, \u003cem\u003eCandida albicans\u003c/em\u003e, \u003cem\u003eCryptococcus neoformans\u003c/em\u003e, \u003cem\u003eHistoplasma capsulatum\u003c/em\u003e, and \u003cem\u003eSchizosaccharomyces pombe\u003c/em\u003e [\u003cspan additionalcitationids=\"CR37\" citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]. These findings suggest that \u003cem\u003eApiospora\u003c/em\u003e contribute to the microbiome\u0026rsquo;s protective functions against external threats.\u003c/p\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003eMultifaceted roles and trophic mode switching\u003c/h2\u003e \u003cp\u003eThe dual roles of \u003cem\u003eApiospora\u003c/em\u003e as mutualists and pathogens suggest a complex ecological strategy. In this study, \u003cem\u003eAp. hysterina\u003c/em\u003e was unexpectedly dominant in bamboo tissues at all stages, including the early young stages, without visible black spots. This observation, combined with the absence of \u003cem\u003eApiospora\u003c/em\u003e in the surrounding soil, suggests that \u003cem\u003eApiospora\u003c/em\u003e establishes itself as an endophyte before pathogenic symptoms manifest.\u003c/p\u003e \u003cp\u003eThe ability of \u003cem\u003eApiospora\u003c/em\u003e to produce plant hormones further underscores its multifaceted roles. In this study, GA derivatives and ABA were detected in \u003cem\u003eAp. hysterina\u003c/em\u003e, but IAA was not detected. While IAA is strongly associated with symbiosis in host plants, both GA and ABA have roles linked to pathogenicity and mutualism [\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e, \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e]. GA regulates various plant processes, such as seed development [\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e], pollen tube growth [\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e], plant development [\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e], and internode elongation. Fungal GA production has been reported to enhance seed germination under salt stress and may facilitate plant carbon sink activity in infected cells [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eWe report that \u003cem\u003eApiospora\u003c/em\u003e species produce ABA. Fungal ABA has been identified as a virulence factor that suppresses plant immune responses [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e, \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e] and is associated with the establishment of symbiosis with the host plant [\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e]. Although the specific role of ABA in \u003cem\u003eApiospora\u003c/em\u003e remains unclear, it may help infect bamboo species by reducing plant resistance.\u003c/p\u003e \u003cp\u003eCollectively, we propose that \u003cem\u003eApiospora\u003c/em\u003e initially functions as a mutualistic endophyte that promotes bamboo growth and stress tolerance. However, it may transition to a pathogenic state under specific environmental or host conditions. Such trophic mode switching has been well-documented in other fungal endophytes, such as dark septate endophytes, whose interactions shift from mutualism to parasitism based on nutrient availability or host performance [\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e]. This dynamic aligns with the \u0026ldquo;balanced antagonism\u0026rdquo; theory, which posits that fungal-host interactions are shaped by biochemical communication and environmental factors [\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eSimilar examples in bamboo-endophyte systems underscore this multifaceted role. For instance, \u003cem\u003eShiraia\u003c/em\u003e sp. isolated from bamboo seeds (\u003cem\u003ePhyllostachys edulis\u003c/em\u003e) act as antimicrobial endophytes but are also significant bamboo pathogens [\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e]. Similarly, \u003cem\u003eAciculosporium take\u003c/em\u003e, an endophytic bambusicolous fungus, promotes shoot growth via auxin production but causes witch\u0026rsquo;s broom disease [\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]. These cases highlight the potential of endophytes to navigate complex ecological roles within their hosts.\u003c/p\u003e \u003cp\u003eGenomic evidence of pathogenic \u003cem\u003eApiospora\u003c/em\u003e traits suggests transcriptional regulation controls trophic mode shifts. Future gene expression studies during the infection stages could reveal these transitions.\u003c/p\u003e \u003c/div\u003e"},{"header":"Conclusion","content":"\u003cp\u003eThis study highlights the multifaceted roles of \u003cem\u003eApiospora hysterina\u003c/em\u003e in bamboo ecosystems as endophytes, demonstrating their potential as mutualists and pathogens. The coexistence of these roles underscores the complexity of plant-fungal interactions, emphasizing the necessity of exploring fungal behavior across different ecological contexts. Understanding these dynamics could have broader implications for managing bamboo health and leveraging endophytes for sustainable bamboo cultivation. Furthermore, this research highlights the significance of adopting a holistic approach (microbiome, chemical, and genomic analysis) in studying plant-fungal relationships involving bamboo-\u003cem\u003eApiospora\u003c/em\u003e and the need for further research in this field.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe are grateful to Seonju Marincowitz (FABI, University of Pretoria) for critical advice that improved the manuscript and thank Editage (www.editage.co.kr) for English language editing and review. This work was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) [2021R1A2C1011894, RS-2024-00343166], the Korea University Grant, and the Korea Polar Research Institute (PN24120).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis project received funding from National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) [2021R1A2C1011894]. This study was also supported by the Korea University Grant, Korea Polar Research Institute (PN24120), and the NRF grant funded by the Korea government (RS-2024-00343166).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003eCompeting interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eY.M. Heo is employed by COSMAX BTI. The rest of the authors declare that the research was conducted in the absence of any commercial or financial relationship that could be construed as a potential conflict of interest.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003eAuthor Contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eConceptualization, S.L.K., C.W.S., H.L., G.H.K., and J.K.; data collection, S.L.K. and C.W.S; methodology, S.L.K., C.W.S., H.K., D.L., S.L., and D.Y.K.; data analysis, S.L.K., C.W.S., and Y.W.L.; resources, S.L.K, M.C., Y.Y., S.L., Y.M.H., and J.K.; writing, S.L.K., C.W.S.,\u0026nbsp;Y.C.,\u0026nbsp;and H.L.; visualization, S.L.K. and C.W.S.; supervision, J.K.\u003c/p\u003e\n\u003cp\u003e\u0026nbsp;\u003cstrong\u003eData Availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe whole genome sequence of \u003cem\u003eAp. hysterina\u003c/em\u003e KUC21437 generated and analyzed during the current study are available in the NCBI repository, NCBI BioProject PRJNA1060443 with accession number JAYMYE000000000. The amplicon sequencing data are available in the NCBI SRA repository, BioProject PRJNA1065571.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003ePaudyal K, Li Y, Trinh T, Adhikari S, Lama S, Prasad Bhatta K (2022) Ecosystem services from bamboo forests: key findings, lessons learnt and call for actions from global synthesis, INBAR working paper. https://hdl.handle.net/10568/118098\u003c/li\u003e\n\u003cli\u003eNfornkah BN, Rene K, Louis Z, Martin T, Cedric CD (2020) Bamboo diversity and carbon stocks of dominant species in different agro-ecological zones in Cameroon. Afr J Environ Sci Technol 14:290\u0026ndash;300. https://doi.org/10.5897/AJEST2020.2871\u003c/li\u003e\n\u003cli\u003eBorisade TV, Odiwe AI (2018) Nutrient input in litters and soil of \u003cem\u003eBambusa vulgaris\u003c/em\u003e stands in a secondary rainforest, Ile-Ife, Nigeria. 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Appl Environ Microbiol 75:4829\u0026ndash;4834. https://doi.org/10.1128/AEM.00635-09\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"microbial-ecology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"meco","sideBox":"Learn more about [Microbial Ecology](https://www.springer.com/journal/248)","snPcode":"248","submissionUrl":"https://submission.nature.com/new-submission/248/3","title":"Microbial Ecology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"amplicon analysis, Apiospora hysterina, bamboo culm, endophytic fungi, plant hormone, plant pathogen","lastPublishedDoi":"10.21203/rs.3.rs-6757679/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6757679/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eBamboo plays a crucial role in mitigating climate change. Among various microorganisms inhabiting bamboo, \u003cem\u003eApiospora\u003c/em\u003e is a common bambusicolous fungus that induces black spots, functioning either as a saprobe or a plant pathogen. However, the diversity and ecological roles of \u003cem\u003eApiospora\u003c/em\u003e as an endophyte in bamboo remain poorly understood. This study explored the diversity and ecological functions of bambusicolous \u003cem\u003eApiospora\u003c/em\u003e in \u003cem\u003ePhyllostachys\u003c/em\u003e forests. Bamboo samples representing different stages\u0026mdash;young (one-year-old, without black spots), mature (aged three years, few black spots), and dead (with many black spots)\u0026mdash;were collected. Microbiome analyses across different tissues (culm, leaf, root) and environmental samples (forest soil) revealed diverse \u003cem\u003eApiospora\u003c/em\u003e species throughout the bamboo lifecycle. Notably, \u003cem\u003eAp. hysterina\u003c/em\u003e emerged as a prevalent endophyte, inhabiting not only mature but also younger, healthier bamboo stages. Biological activity assays, including antioxidant, antifungal, and plant hormone tests, indicated that \u003cem\u003eAp. hysterina\u003c/em\u003e exhibits mutualistic interactions beneficial to bamboo. Conversely, genomic analyses of carbohydrate-active enzyme profiles and biosynthetic gene clusters suggested a pathogenic potential driven by secondary metabolites. These findings reveal the widespread presence of \u003cem\u003eApiospora\u003c/em\u003e species as endophytes from the early to senescent bamboo stages, highlighting \u003cem\u003eAp. hysterina\u003c/em\u003e\u0026rsquo;s dual capacity as a pathogen and symbiont. Our study underscores the complexity of bambusicolous \u003cem\u003eApiospora\u003c/em\u003e\u0026rsquo;s ecological roles, emphasizing the need for further investigation into its interactions with bamboo ecosystems.\u003c/p\u003e","manuscriptTitle":"Exploring multifaceted roles of bambusicolous Apiospora in Phyllostachys sp.","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-05-30 11:47:04","doi":"10.21203/rs.3.rs-6757679/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-07-24T18:36:26+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-07-10T15:14:27+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-06-27T13:21:28+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"300362313537153044902308256630678882533","date":"2025-06-15T00:01:14+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"301217120526586893732318543321677755499","date":"2025-06-11T18:15:53+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"214431972162057006491743364021823364765","date":"2025-06-09T18:58:36+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-05-28T16:20:53+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-05-28T14:01:48+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-05-28T14:00:21+00:00","index":"","fulltext":""},{"type":"submitted","content":"Microbial Ecology","date":"2025-05-27T09:00:10+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"microbial-ecology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"meco","sideBox":"Learn more about [Microbial Ecology](https://www.springer.com/journal/248)","snPcode":"248","submissionUrl":"https://submission.nature.com/new-submission/248/3","title":"Microbial Ecology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"b97acccf-6ff3-47ac-bdfd-1cfc9305dbfc","owner":[],"postedDate":"May 30th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-11-10T15:58:44+00:00","versionOfRecord":{"articleIdentity":"rs-6757679","link":"https://doi.org/10.1007/s00248-025-02631-z","journal":{"identity":"microbial-ecology","isVorOnly":false,"title":"Microbial Ecology"},"publishedOn":"2025-11-05 15:56:56","publishedOnDateReadable":"November 5th, 2025"},"versionCreatedAt":"2025-05-30 11:47:04","video":"","vorDoi":"10.1007/s00248-025-02631-z","vorDoiUrl":"https://doi.org/10.1007/s00248-025-02631-z","workflowStages":[]},"version":"v1","identity":"rs-6757679","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6757679","identity":"rs-6757679","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}