Chiang Mai Journal of Science

First Report of Bioluminescence in Omphalotus flagelliformis (Omphalotaceae, Basidiomycota) Revealed Through Photographic Evidence

1. INTRODUCTION

     The discovery of new fungal species has rapidly increased with the development of molecular techniques, drawing attention to the enormous fungal diversity on Earth. These advances have greatly accelerated species identification and highlighted the vast number of fungi that remain unexplored [1–5]. In addition to their taxonomic richness, fungi are prolific producers of secondary metabolites with ecological and pharmaceutical relevance [6,7]. They also play crucial roles in agriculture by inducing host resistance and serving as biocontrol agents against plant pathogens [8–12]. However, compared to the growing body of research on fungal diversity, secondary metabolism, and biocontrol, the taxonomy and ecological roles of bioluminescent fungi remain poorly understood.
     Bioluminescence in fungi refers to the emission of visible light through a chemical reaction in which luciferase catalyzes the oxidation of fungal luciferin, producing oxyluciferin and emitting visible green light [13]. Though rare, this trait is ecologically significant, as it may attract phototropic insects that facilitate spore dispersal, deter fungivorous organisms, or recruit predators of those fungivores [13]. In Basidiomycota, bioluminescence has been reported in over 130 species across several genera, including Armillaria, Mycena, and Omphalotus, which are grouped into five distinct lineages: Armillaria, Eoscyphella, Lucentipes, Mycenoid, and Omphalotus [14–16].
     Omphalotus is one of the bioluminescent genera, first introduced by Fayod [17] and typified by O. olearius. It is widely distributed from temperate to subtropical regions, with species found in Australia, Belgium, China, Croatia, France, Greece, Guatemala, Hungary, Italy, Japan, Mexico, South Africa, and the United States [18]. Historically, this genus was placed in the family Paxillaceae under order Boletales due to pigment similarities with Boletes [19,20]. However, Kämmerer et al. [21] established the family Omphalotaceae to accommodate Omphalotus, citing physiological differences from Paxillaceae. Members of Omphalotaceae exhibit saprotrophic or parasitic lifestyles and have a wide geographic distribution [22,23]. Three genera in this family, Neonothopanus, Nothopanus, and Omphalotus, exhibit bioluminescence [15]. Recently, phylogenetic studies have confirmed Omphalotus as a monophyletic group within the suborder Marasmiineae (Agaricales), although several species were previously described under broader genera such as Agaricus, Lampteromyces, Monodelphus, and Pleurotus [24–26]. For instance, Omphalotus atraetopus, one transferred from Paxillus to Omphalotus, is now considered a synonym [27]. According to Index Fungorum (https://www.indexfungorum.org/), 16 epithets of Omphalotus have been recorded to date, of which seven (O. guepiniiformis, O. illudens, O. mangensis, O. nidiformis, O. olearius, O. olivascens, and O. subilludens) are recognized as bioluminescent species [15]. However, confirmed evidence of bioluminescence has not been documented for several species within the genus, including O. flagelliformis.
     In this study, we report the first confirmed case of bioluminescence in O. flagelliformis, collected from Yunnan Province, China. This discovery is based on both in situ and culture-based observations, supported by photographic evidence, morphological descriptions, and phylogenetic analyses. This finding has important implications for the phylogenetic and functional understanding of fungal bioluminescence, suggesting that light-emitting capability may be more widespread within Omphalotus than previously recognized.

2. MATERIALS AND METHODS

2.1 Sample Collection, Isolation, and Photograph
     Fresh specimens were collected on the premises of Qujing Normal University (QJNU), China, a region characterized by a subtropical monsoon climate, during the rainy seasons of 2022 and 2025. Photographs were captured in the field or laboratory during daylight conditions, and bioluminescent photographs were taken either in the field or in the laboratory in complete darkness using a long exposure on a smartphone (Beijing, China). Specimens were collected from the trunk base of Camphora officinarum and from the adjacent root-zone soil of Buxus megistophylla. The sample collection data were recorded as described in Rathnayaka et al. [28]. Fresh basidiomata were described in situ for their macroscopic characteristics, using color terms and codes from Kornerup & Wanscher [29]. The specimens were then brought to the mycology laboratory at QJNU. One fresh specimen was selected for tissue isolation, while the remaining specimens were dried at 40 °C using an electric food dryer [30]. Small tissue fragments taken aseptically from the inner context of the basidiome were placed on potato dextrose agar (PDA) plates and incubated at 28 °C, where hyphal growth became evident within 2 days. Emerging mycelium was then subcultured onto fresh PDA with a sterile inoculating needle and maintained under the same temperature conditions to establish pure cultures. Following isolation and drying, the dried specimens and living cultures were deposited in the Guizhou Medical University Herbarium (GMB) and the Guizhou Medical University Culture Collection (GMBCC), respectively.

2.2 Morphological Study
     Morphological characteristics of basidiomata were described following the methodology of Lu et al. [1]. Dried materials were sectioned freehand, mounted in 5% KOH solution and Congo red, and then examined and photographed under an Olympus optical microscope (Japan) equipped with an Olympus DP74 digital camera. In the descriptions of basidiospores, the abbreviation [n/m/p] is used to indicate the number of measured basidiospores, where n basidiospores measured from m basidiomata of p collections; Measurements are presented in the format (a–) b–c (–d), where b–c represents a minimum of 90% of measured valves, while “a” and “d” denote the extreme values. Q is used to mean “length/width ratio” of a spore; Qm means the average Q of all basidiospores ± sample standard deviation. Detailed illustrations of microstructures were drawn freehand using rehydrated materials and subsequently refined using Adobe Illustrator 2019.

2.3 DNA Extraction, PCR Amplification, and Sequencing
     Genomic DNAs were extracted from both dry basidiomata tissue (gills) and pure culture using the Biospin Fungus Genomic DNA Extraction Kit-BSC14S1 (BioFlux, China) according to the instructions with slight modifications. PCR Amplification was performed in a 25 μL reaction volume, containing 12.5 μL of 2x Master Mix (mixture of Easy Taq TM DNA Polymerase, dNTPs, and optimized buffer (Beijing Trans Gen Biotech Co., Chaoyang District, Beijing, China), 8.5 μL distilled water, 2 μL DNA template, and 1 μL each of forward and reverse primers. The primer pair (ITS5/ITS4) of Internal Transcribed Spacer (ITS) used for PCR amplification was as described by Yang and Feng [31]. The cycle parameters were as follows: an initial denaturation at 94 °C for 5 min; denaturation at 94 °C for 30s, annealing at 54 °C for 40s, and extension at 72 °C for 1 min, repeated for 35 cycles; followed by a final extension at 72 °C for 10 min. Sequencing work was done by Sangon Biotech Co., Ltd. (Kunming, China). The newly generated sequences were deposited in GenBank (https://www.ncbi.nlm.nih.gov/genbank, accessed on September 5, 2025), and the accession numbers are listed in Table 1.
 

2.4 Phylogenetic Analyses
     BioEdit version 7.2.5 was used to check sequence quality [32]. A BLASTn search on NCBI (http://http://www.ncbi.nlm.nih.gov) was performed to identify closely related taxa. Related sequences used in the phylogenetic analyses were obtained based on previous publications [31]. Reverse and pairwise alignment of individual strain sequences was performed using Sequencher version 5.4.6 (https://www.genecodes.com/). Sequences alignment was carried out using MAFFT v. 7 (http://mafft.cbrc.jp/alignment/server) [33], and manual editing was done in BioEdit v. 7.2.5 when necessary [32]. FASTA files were converted to PHYLIP and NEXUS format using the Alignment Transformation Environment (ALTER) online tool (https://www.sing-group.org/ALTER/) [34].
     Phylogenetic analyses were conducted using maximum likelihood (ML) and Bayesian inference (BI) methods via the CIPRES Science Gateway (https://www.phylo.org/portal2/home.action) [35]. ML analyses were conducted using RAxML-HPC2 on ACCESS (version 8.2.12) with 1,000 non-parametric bootstrap replicates, employing the GTR+GAMMA model of nucleotide evolution. For Bayesian analysis, the best-fit model (K2P+R2) was estimated using MrModeltest version 2.2 [36]. The BI analyses were conducted on XSEDE version 3.2.7a, using the same web portal as ML, with six simultaneous Markov chains run for 2,000,000 generations. Trees were sampled every 100th generation, resulting in 20,000 trees. The first 25% of the trees were discarded as burn-in. The resulting phylogram was visualized in FigTree version 1.4.4 [37] and edited in Microsoft PowerPoint.

3. RESULTS AND DISCUSSION

3.1 Phylogenetic Analyses
     The best-scoring ML tree was generated from ITS sequence data comprising 51 Omphalotaceae sequences and three Mycetinis species as outgroup taxa, for a total alignment of 613 characters (Figure 1). The best-scoring RAxML tree had a final ML optimization likelihood value of -2941.515395. The alignment matrix included 230 distinct patterns, with 0.72% of the characters undetermined or representing gaps. Estimated base frequencies were as follows; A = 0.221453, C = 0.219601, G = 0.224433, T = 0.334512; substitution rates AC = 1.251775, AG = 5.959715, AT = 1.901680, CG = 0.915906, CT = 5.998614, GT = 1.000000. The gamma distribution shape parameter α = 0.356186, and the total tree-length was 0.933118. The topologies of the phylogenetic trees generated in this study were consistent with those reported in a previous study [31]. The ML and BI tree topologies were highly similar, and the ML phylogenetic tree is presented in Figure 1. In our phylogenetic analyses, two strains from collections (GMB-W1214 and GMBCC1149) clustered with O. flagelliformis (HKAS 76645, holotype) with strong support, 97% BS, and PP 0.95. Additionally, three other strains (GMB-W1464, GMB-W1215, and GMBCC1152) formed a basal clade within this group, with strong support (BS 100% and PP 1.00). All of our strains were nested within the same lineage as O. flagelliformis (HKAS 76645) and not in a distinct lineage, clearly separated from all other species in Omphalotus (Figure 1). This strongly supports the identification of our collections as O. flagelliformis.

3.2 Taxonomy
Omphalotus flagelliformis Zhu L. Yang & B. Feng, Mycosystema 32(3): 547 (2013). Figures 2,3
Index Fungorum number: 802884
     Basidiomata medium-sized to large, with centrally attached stipes. Pileus 20–90 mm in diam., initially broadly convex to depressed, flattened and then infundibuliform (funnel-shaped), sometimes flabelliform, umbonate, laterally crowded arrangement; surface dry, radially fibrillose to somewhat velvety, dark brown to reddish-brown (7D5–6, 7E5–6), paler toward the margin, smooth, fibrillose; margin uplifted and wavy at age; context orange-yellow, firm, fibrous, thin. Lamellae decurrent, moderately close, narrow, yellow to orange-yellow (5A6–8, 6A6–8), contrasting with the darker pileus; lamellulae 2–3 tiers. Stipe 2–7 × 0.8–2 cm, cylindrical to slightly attenuate upwards and downwards, somewhat compressed, short and often curved or twisted, eccentric due to dense clustering, surface yellowish to orange to brownish, sometimes slightly darker brown toward the base, context pale yellow to pale orange-yellow. Odor and taste undetermined.
     Basidiospores [60/1/3] 3.5–5(–5.5) × 3–4.5 µm, Q = 0.92–1.17 (Qm=1.07±0.09), predominantly subglobose, varying from nearly globose to broadly ellipsoid, hyaline, occasionally with brownish-yellow inclusions, thin-walled (up to 0.5 µm thick), smooth, sometimes with a small apical protrusion, inamyloid and indextrinoid. Basidia 20–30 × 5–7 µm, narrowly clavate to cylindric, 4-sterigmate, with basal clamp connections, hyaline, thin-walled, sterigmata up to 3.5 µm long, basidioles similar in shape of basidia but smaller in size. Cheilocystidia 15–25 × 5–8 µm (without apical outgrowths), mainly clavate, lageniform to subfusiform, or with irregularly branched to coralloid apical outgrowths, hyaline, with yellowish to brownish pigments visible in KOH, thin-walled. Pleurocystidia absent. Lamellar trama comprises filamentous hyphae, 3–12 µm in width, thin-walled, and arranged in a more or less regular configuration. Pileipellis a cutis composed of repent cylindrical hyphae 4–6 μm wide, with terminal cells erect to suberect, clavate, fusiform to irregular, with brown to yellow-brown pigments, and turn to olivaceous green in KOH, thin-walled, with clamp connections. Stipitipellis composed of parallel hyphae 4–8 μm wide, with clamp connections. Caulocystidia 20–45 × 2–7 µm, variable in shape, clavate, lanceolate, subcylindrical to irregularly branched, thin-walled, hyaline.
     Culture characteristics: Colonies on PDA reached 5–6.5 cm in diameter after 7 days at 28°C, circular, cottony to floccose, dense, with a slightly raised center and entire margins. Front view was initially white, becoming yellowish to brown after 7 days, and finally dark brown with age. Brown pigmented exudates were produced on the colony surface, reverse pale yellow. Mycelia exhibited stable bioluminescence in darkness (Figure 2D2).
     Ecology and distribution: Gregarious, caespitose to clustered, on the trunk of Fagaceous, China [29], Camphora officinarum (this study), and on soil near Buxus megistophylla (this study) from southwestern China.
     Specimens examined: CHINA, Yunnan Province, Qujing City, QJNU, elev. 1880m, 25°31′29.43″N 103°44′51.26″E, on soil near Buxus megistophylla, 15 June 2022, W.H. Lu (QJ169 = GMB-W1464). Ibid., on the trunk of Camphora officinarum, 24 June 2025, W.H. Lu (LWH300 = GMB-W1215). Ibid., 25° 31′ 22.16″ N, 103° 44′ 40.22″ E, on the trunk of Camphora officinarum, 3 July 2025, W.H. Lu (QJNU25-25 = GMB-W1214), living cultures GMBCC1149, GMBCC1150, GMBCC1151, GMBCC1152, GMBCC1153, GMBCC1156, GMBCC1161, GMBCC1162, GMBCC1163.
     Notes: Omphalotus flagelliformis is recorded to exhibit bioluminescence for the first time. The specimens collected in this study match the holotype of Omphalotus flagelliformis from Yunnan, China, as originally described by Yang and Feng [31], in terms of basidiomata morphology, decurrent lamellae, flagelliform to rostrate appendages on cheilocystidia, and other micromorphological characteristics. Minor differences were observed in basidiomata size (stipe 2–7 × 0.8–2 cm in our specimens vs. 5–12 × 1–2.5 cm in the holotype) and slight variation in pileus coloration. However, these differences fall within the range of intraspecific variation described in the protologue. Molecular analysis based on ITS sequences further supports the identification of our specimens as O. flagelliformis, as they cluster closely with reference sequences from the holotype [31]. Ecologically, our specimens were found growing on the trunk of Camphora officinarum (Lauraceae) and in soil around Buxus megistophylla (Buxaceae), whereas previous records reported the species primarily from Fagaceous hosts. This indicates an expansion of the known substrate preferences of the species. Morphologically, O. flagelliformis is similar to O. illudens, O. mexicanus, and O. olearius, having an umbonate pileus with yellowish-orange coloration. However, O. illudens differs in having larger basidiospores, a pileipellis composed of refractive hyphae, and the absence of cheilocystidia [38,39]. Omphalotus mexicanus can be distinguished by its bluish-black to blackish basidiomata, comparatively larger basidiospores, and the presence of violet incrusting pigments in the pileipellis [40,41]. Omphalotus olearius is distinguished by the absence of cheilocystidia and caulocystidium, along with larger basidiospores [42,43]. In the phylogenetic analysis, O. flagelliformis forms a well-supported clade with O. illudens and O. mexicanus, yet each species is clearly distinct. The clade received strong support values of 93% BS/0.99 BI for O. illudens, and 100% BS/1.0 PP for O. mexicanus (Figure 1).

4. DISCUSSION

     In this study, we report a bioluminescent fungal species previously unrecorded in the literature, thereby expanding the known diversity of bioluminescent fungi in China. Morphological characteristics and molecular phylogenetic analyses support its O. flagelliformis. Some species of Omphalotus have been reported as non-bioluminescent; however, such reports may reflect limited observations rather than a true absence of the trait. Bioluminescence in fungi can vary with developmental stage (e.g., mycelium vs. basidiomata), tissue type (e.g., pileus, lamellae, stipe, spore), and environmental conditions (e.g., substrate, temperature, pH), raising the possibility that “non-luminescent” designations may be premature [15]. Our study provides the first clear documentation of bioluminescence in O. flagelliformis, a taxon for which luminescence had not previously been reported, and highlights the need to re-evaluate other species within the genus currently regarded as non-bioluminescent.
     Bioluminescent fungi, predominantly basidiomycetes within the order Agaricales, exhibit remarkable diversity, with over 130 species documented across five main lineages [14,16,44]. Their yellowish-green light emission (520–530 nm), regulated by a luciferase-luciferin enzymatic system, exhibits circadian rhythms and is believed to have originated once within the Agaricales, with multiple independent losses accounting for its absence in related taxa [16]. These fungi are globally distributed, with diversity hotspots in subtropical and tropical forests, particularly in Japan, China, Southeast Asia, and South and Central America [31,38–43]. In China, Yunnan Province is a significant center of diversity for Omphalotus species, accounting for approximately 45% of known taxa [31] and encompassing both widespread species [e.g., O. guepiniformis (synonym: O. japonicus) and O. olearius] and locally endemic or undescribed taxa (e.g., O. flagelliformis, O. mangensis, and Omphalotus sp.) [31,45]. The region’s complex topography, rich biodiversity, and biogeographical location within the transitional zone between temperate and subtropical floristic regions likely create ecological and evolutionary conditions favorable for diversification within the genus. Ecologically, bioluminescent fungi make significant contributions to nutrient cycling by decomposing woody and leafy substrates, and may also enhance spore dispersal by attracting insects. Their high sensitivity to environmental factors, combined with their unique biochemical properties, underpins emerging applications in environmental monitoring, biotechnology, and sustainable lighting technologies [15]. Despite recent advances, substantial gaps remain in our understanding of their distribution, ecological roles, and evolutionary trajectories of bioluminescent fungi. Integrative studies that combine molecular, ecological, and conservation approaches are therefore essential to fully characterize their diversity, evolutionary history, and biotechnological potential.

ACKNOWLEDGEMENTS

     SCK and ST thank the National Natural Science Foundation of China (No. 32260004), Yunnan Revitalization Talents Support Plan (High-End Foreign Experts and Young Talents Programs), and the Key Laboratory of Yunnan Provincial Department of Education of the Deep-Time Evolution on Biodiversity from the Origin of the Pearl River, for their support. The authors extend their appreciation to the Ongoing Research Funding Program (ORF-Ctr-2025-6), King Saud University, Riyadh, Saudi Arabia. WL, NS, and JK were partially supported by Chiang Mai University, Thailand.

AUTHOR CONTRIBUTIONS

Wenhua Lu: Writing - Original draft preparation, Methodology, Resources. Saowaluck Tibpromma: Data curation, Writing- Reviewing and Editing. Nakarin Suwannarach: Visualization, Investigation, Writing- Reviewing and Editing, Supervision. Jaturong Kumla: Methodology, Writing- Reviewing and Editing. Abdallah M. Elgorban: Software, Validation. Dong-Qin Dai: Formal analysis, Writing- Reviewing and Editing. Fuqiang Yu: Writing- Reviewing and Editing. Samantha C. Karunarathna: Conceptualization, Writing- Reviewing and Editing, Supervision, Project administration.

CONFLICT OF INTEREST STATEMENT

     The authors declare no conflict of interest.

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