Sarcodon aspratus (Berk.) S. Ito is a Japanese local dish with unique aroma and is effective against allergic diseases. However, its cultivation was still difficult. Recently, coexisting bacteria were regarded as an important factor for mycelium growth and fruiting body formation. Therefore, we performed 16S rRNA amplicon sequencing in the fruiting body of S. aspratus and its adhered soil to understand the bacterial communities in the fruiting body of S. aspratus. The fruiting body group showed lower alpha diversities and a significant difference in the structure of bacterial communities compared to the soil group. In addition, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium had the highest relative abundance in the fruiting body group, and it was also a potential coexisting bacterium in the fruiting body of S. aspratus by linear discriminant analysis effect size (LEfSe) analysis. This highest relative abundance phenomenon in Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade was also found in the fruiting body of Cantharellus cibarius. These findings suggested that Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium plays a key role in the bacterial communities in the fruiting body of S. aspratus. Bacteria in the fruit bodies of S. aspratus and C. cibarius probably present a similar coexistence model.

Institute of Wood Technology Akita Prefectural University Akita Japan

Interdisciplinary Graduate School of Agriculture and Engineering University of Miyazaki Miyazaki Japan

Jin Sing Chen's Mushroom Farm No 31 Donghu Road Dali District Taichung City Taiwan ROC

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Benucci GMN, Bonito GM (2016) The truffle microbiome: species and geography effects on bacteria associated with fruiting bodies of Hypogeous Pezizales. Microb Ecol 72:4–8. https://doi.org/10.1007/s00248-016-0755-3 PubMed DOI

Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J (2018) Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6:90 PubMed DOI PMC

Chao A (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11:265–270. Retrieved January 2024. http://www.jstor.org/stable/4615964

Chen FC, Motoda T, Kamei I, Kijidani Y (2023) Characterization of microbial communities during Grifola frondosa (maitake) wood log cultivation. J Wood Sci 69:39. https://doi.org/10.1186/s10086-023-02111-3 DOI

Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Cons 61:1–10 DOI

Ge W, Zhang ZY, Dong CB, Han YF, Deshmukh SK, Liang ZQ (2021) Bacterial community analysis and potential functions of core taxa in different parts of the fungus Cantharellus cibarius. Pol J Microbiol 70:373–385. https://doi.org/10.33073/pjm-2021-035

Ge W, Ren Y, Dong C, Shao Q, Bai Y, He Z, Yao T, Zhang Y, Zhu G, Deshmukh SK, Han Y (2023) New perspective: symbiotic pattern and assembly mechanism of Cantharellus cibarius-associated bacteria. Front Microbiol 14:1074468. https://doi.org/10.3389/fmicb.2023.1074468 PubMed DOI PMC

Gehlenborg N (2019) UpSetR: a more scalable alternative to Venn and Euler diagrams for visualizing intersecting sets. Retrieved January 2024. https://CRAN.R-project.org/package=UpSetR

Gohar D, Pent M, Põldmaa K, Bahram M (2020) Bacterial community dynamics across developmental stages of fungal fruiting bodies. FEMS Microbiol Ecol 96:fiaa175. https://doi.org/10.1093/femsec/fiaa175 PubMed DOI

Kiyoto M, Suzuki H, Hara T, Yagi Y, Cho NS, Aoyama M (2005) Moderate angiotensin-converting enzyme (ACE) inhibitor from the fruit body of Sarcodon aspratus. Mushroom Sci Biotechnol 13:189–194

Kolde R (2019) pheatmap: pretty heatmaps. Retrieved January 2024. https://CRAN.R-project.org/package=pheatmap

Liu Y, Sun Q, Li J, Lian B (2018) Bacterial diversity among the fruit bodies of ectomycorrhizal and saprophytic fungi and their corresponding hyphosphere soils. Sci Rep 8:11672. https://doi.org/10.1038/s41598-018-30120-6 PubMed DOI PMC

Liu D, Perez-Moreno J, He X, Garibay-Orijel R, Yu F (2021a) Truffle microbiome is driven by fruit body compartmentalization rather than soils conditioned by different host trees. mSphere 6:e0003921. https://doi.org/10.1128/mSphere.00039-21 PubMed DOI

Liu D, Perez-Moreno J, Zhang P, Wang R, Chater CCC, Yu F (2021b) Distinct compartmentalization of microbial community and potential metabolic function in the fruiting body of Tricholoma matsutake. J Fungi 7:586. https://doi.org/10.3390/jof7080586 DOI

Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235 PubMed DOI PMC

Lozupone CA, Hamady M, Kelley ST, Knight R (2007) Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73:1576–1585 PubMed DOI PMC

Napitupulu TP, Ayudhya SPN, Aimi T, Shimomura N (2022) Mycelial growth-promoting potential of extracellular metabolites of Paraburkholderia spp. isolated from Rhizopogon roseolus Sporocarp. J Pure Appl Microbiol 16:1154–1166. https://doi.org/10.22207/JPAM.16.2.43 DOI

Oh SY, Kim M, Eimes JA, Lim YW (2018) Effect of fruiting body bacteria on the growth of Tricholoma matsutake and its related molds. PLoS ONE 13:e0190948. https://doi.org/10.1371/journal.pone.0190948 PubMed DOI PMC

Parks DH, Tyson GW, Hugenholtz P, Beiko RG (2014) STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30:3123–3124 PubMed DOI PMC

Pent M, Põldmaa K, Bahram M (2017) Bacterial communities in boreal forest mushrooms are shaped both by soil parameters and host identity. Front Microbiol 8:836. https://doi.org/10.3389/fmicb.2017.00836 PubMed DOI PMC

Pent M, Bahram M, Põldmaa K (2020) Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups. ISME J 14:2131–2141. https://doi.org/10.1038/s41396-020-0674-7 PubMed DOI PMC

Pielou E (1966) The measurement of diversity in different types of biological collections. J Theor Biol 13:131–144 DOI

Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12:R60. https://doi.org/10.1186/gb-2011-12-6-r60 PubMed DOI PMC

Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois

Splivallo R, Deveau A, Valdez N, Kirchhoff N, Frey-Klett P, Karlovsky P (2015) Bacteria associated with truffle-fruiting bodies contribute to truffle aroma. Environ Microbiol 17:2647–2660. https://doi.org/10.1111/1462-2920.12521 PubMed DOI

Tateishi K, Hosono T, Shimazu S, Fujimoto M (2000) Anti-allergenic properties of the fruiting bodies of Sarcodon aspratus. Nippon Shokuhin Kagaku Kogaku Kaishi 47:281–286 DOI

Xia Y, He R, Xu W, Zhang J (2023) The Zoige pioneer plant Leymus secalinus has different endophytic bacterial community structures to adapt to environmental conditions. PeerJ 11:e15363. https://doi.org/10.7717/peerj.15363 PubMed DOI PMC

Yamada A, Furukawa F, Yamanaka T (2017) Cultivation of edible ectomycorrhizal mushrooms in Japan. Rev Fitotec Mex 40:379–389

Yu FM, Jayawardena RS, Thongklang N, Lv ML, Zhu XT, Zhao Q (2022) Morel production associated with soil nitrogen-fixing and nitrifying microorganisms. J Fungi 8:299. https://doi.org/10.3390/jof8030299 DOI