Wasser, S. P. Reishi or ling zhi (Ganoderma lucidum). Encyclopedia of dietary supplements 1, 603–622 (2005).
Boh, B., Berovic, M., Zhang, J. & Zhi-Bin, L. Ganoderma lucidum and its pharmaceutically active compounds. Biotechnol. Annu. Rev. 13, 265–301 (2007).
Qin, L. H., Wang, C., Qin, L. W., Liang, Y. F. & Wang, G. H. Spore powder of Ganoderma lucidum for Alzheimer’s disease: A protocol for systematic review. Medicine 98, e14382 (2019).
Hua, M. Current situation and development countermeasures of Ganoderma lucidum industry in China. Northern Economy Trade 10, 82–83 (2010). (in Chinese).
Buckley, D. H. & Schmidt, T. M. The structure of microbial communities in soil and the lasting impact of cultivation. Microb. Ecol. 42, 11–21 (2001).
Wasof, S. et al. Linkages between aboveground and belowground community compositions in grasslands along a historical land-use intensity gradient. Plant Soil 434, 289–304 (2019).
Clermont-Dauphin, C., Cabidoche, Y. M. & Meynard, J. M. Effects of intensive monocropping of bananas on properties of volcanic soils in the uplands of the French West Indies. Soil Use Manage 20, 105–113 (2010).
Wang, T. et al. Characterizing differences in microbial community composition and function between Fusarium wilt diseased and healthy soils under watermelon cultivation. Plant Soil 438, 1–13 (2019).
Fierer, N., Jackson, J. A., Vilgalys, R. & Jackson, R. B. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl. Environ. Microbiol. 71, 4117–4120 (2005).
He, J. Z., Zheng, Y., Chen, C. R., He, Y. Q. & Zhang, L. M. Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches. J. Soil Sediment 8, 349–358 (2008).
Muller, D. B., Vogel, C., Bai, Y. & Vorholt, J. A. The plant microbiota: systems-level insights and perspectives. Annu. Rev. Genet. 50, 211–234 (2016).
Hong, C., Si, Y., Xing, Y. & Li, Y. Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas. Environ. Sci. Pollut. Res. 22, 10788–10799 (2015).
Frindte, K., Pape, R., Werner, K., Löffler, J. & Knief, C. Temperature and soil moisture control microbial community composition in an arctic–alpine ecosystem along elevational and micro-topographic gradients. ISME J. 13, 2031–2043 (2019).
Black, C. A., Evans, D. D. & Dinauer, R. C. Methods of soil analysis. American Society of Agronomy: Madison, USA, 1–1178 (1965).
Chang, S., Puryear, J. & Cairney, J. A simple and efficient method for isolating RNA from pine trees. Plant. Mol. Biol. Rep. 11, 113–116 (1993).
White, T. J., Bruns, T., Lee, S. & Taylor, J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR protocols: A guide to methods and applications; Innis, M. A., Gelfand, D. H., Sninsky, J. J., White, T. J. Eds.; Academic Press: New York, USA, 315–322 (1990).
Ai, C. et al. Distinct responses of soil bacterial and fungal communities to changes in fertilization regime and crop rotation. Geoderma 319, 156–166 (2018).
Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Schloss, P. D., Gevers, D. & Westcott, S. L. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA–based studies. PloS One 6, e27310 (2011).
UNITE Community. UNITE mothur release. Version 01.12.2017. UNITE Community, https://doi.org/10.15156/BIO/587478 (2017).
Quast, C., et al The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41 (Database), D590–D596 (2013).
Mothur Calculators. Available online: https://www.mothur.org/wiki/Calculators (04-26-2019).
R Core Team. R: A language and environment for statistical computing. R foundation for Statistical Computing: Vienna, Austria (2013).
Plassart, P. et al. Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect. Sci. Rep. 9, e605 (2019).
Lienhard, P. et al. Pyrosequencing evidences the impact of cropping on soil bacterial and fungal diversity in Laos tropical grassland. Agron. Sustain. Dev. 34, 525–533 (2014).
Constancias, F. et al. Mapping and determinism of soil microbial community distribution across an agricultural landscape. MicrobiologyOpen 4, 505–517 (2015).
Terrat, S. et al. Mapping and predictive variations of soil bacterial richness across France. PloS One 12, e0190128 (2017).
Brinkmann, N. et al. Intensive tropical land use massively shifts soil fungal communities. Sci. Rep. 9, e3403 (2019).
Lauber, C. L., Ramirez, K. S., Aanderud, Z., Lennon, J. & Fierer, N. Temporal variability in soil microbial communities across land-use types. ISME J. 7, 1641–1650 (2013).
Delgado-Baquerizo, M. et al. A global atlas of the dominant bacteria found in soil. Science 359, 320–325 (2018).
Hibbett, D. S. et al. 14 Agaricomycetes, In Systematics and Evolution. The Mycota (A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research), vol. 7A; McLaughlin D., Spatafora J. Eds.; Springer: Berlin, Germany, 373–429 (2014).
Wang, Z. et al. Impact of long-term grazing exclusion on soil microbial community composition and nutrient availability. Biol. Fert. Soils 55, 121–134 (2019).
Zhang, N. & Wang. Z. 3 Pezizomycotina: Sordariomycetes and Leotiomycetes. In Systematics and Evolution. The Mycota (A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research), vol 7B; McLaughlin D., Spatafora J. Eds.; Springer: Berlin, Germany, 57–88 (2015).
Trujillo, M. E. Actinobacteria. eLS, 1–16, https://doi.org/10.1002/9780470015902.a0020366.pub2 (2001).
Shinmen, Y., Shimizu, S., Akimoto, K., Kawashima, H. & Yamada, H. Production of arachidonic acid by Mortierella fungi. Appl. Biochem. Biotech. 31, 11–16 (1989).
Papanikolaou, S., Komaitis, M. & Aggelis, G. Single cell oil (SCO) production by Mortierella isabellina grown on high-sugar content media. Bioresource Technol. 95, 287–291 (2004).
Bari, E. et al. Ecology of wood‐inhabiting fungi in northern forests of Iran. Forest Pathol. 49, e12501 (2019).
Cho, M. A. et al. Streptomyces Cytochrome P450 Enzymes and Their Roles in the Biosynthesis of Macrolide Therapeutic Agents. Biomol. Ther. 27, 127 (2019).
Prudence, S. et al. Root-associated archaea: investigating the niche occupied by ammonia oxidising archaea within the wheat root microbiome. Access Microbiol. 1A, https://doi.org/10.1099/acmi.ac2019.po0112 (2019).
He, W. et al. Effect of paraquat on soil bacteria diversity in a young eucalypt plantation. Acta Scientiae Circumstantiae 32, 2857–2864 (2012).
Lee, J. et al. Comparative microbiome analysis of Dermatophagoides farinae, Dermatophagoides pteronyssinus, and Tyrophagus putrescentiae. J. Allergy Clin. Immun 143, 1620–1623 (2019).
Huq, M. A., Akter, S. & Lee, S. Y. Mucilaginibacter formosus sp. nov., a bacterium isolated from road-side soil. Antonie van Leeuwenhoek 112, 513–521 (2019).
Gadkari, P., Haggblom, M., Barkay, T., Kerkhof, L. & Mannisto, M. Ecology and physiological potential of tundra soil bacteria. Detail 2020, 01–31 (2019).
Feng, Y. et al. Effect of Sphingomonas sp. strain on degradation of polyphenols in redried tobacco leaves. Acta Tabacaria Sinica 25, 19–24 (2019).
Liu, J., Lin, H., Dong, Y. & Li, B. Elucidating the biodegradation mechanism of tributyl phosphate (TBP) by Sphingomonas sp. isolated from TBP-contaminated mine tailings. Environmental Pollution 250, 284–291 (2019).
Zhang, Y., Li, Q., Chen, Y., Dai, Q. & Hu, J. Mudflat reclamation causes changes of gene abundance in nitrogen cycle under long‐term rice cultivation. J. basic microbiol, https://doi.org/10.1002/jobm.201800660 (2019).
Liuting, Z. et al. Variation in soil fungal community structure during successive rotations of Casuarina equisetifolia plantations as determined by high-throughput sequencing analysis. Plant Growth Regulation 87, 445–453 (2019).
Lasota, S., Stephan, I., Horn, M. A., Otto, W. & Noll, M. Copper in wood preservatives delayed wood decomposition and shifted soil fungal but not bacterial community composition. Appl. Environ. Microbiol. 85, e02391–18 (2019).
Fischer, C. et al. Plant species richness and functional groups have different effects on soil water content in a decade‐long grassland experiment. J. Ecol. 107, 127–141 (2019).
Colin, Y. et al. Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence. Sci. Rep. 7, e9604 (2017).
Ren, F., Dong, W., Sun, H. & Yan, D. H. Endophytic Mycobiota of Jingbai Pear Trees in North China. Forests 10((3)), 260 (2019).
Li, X. et al. Legacy of land use history determines reprogramming of plant physiology by soil microbiome. ISME J. 13((3)), 738 (2019).
Khan, I. et al. Mushroom polysaccharides from Ganoderma lucidum and Poria cocos reveal prebiotic functions. J. Funct. Food. 41, 191–201 (2018).
Chang, C. J. et al. Ganoderma lucidum reduces obesity in mice by modulating the composition of the gut microbiota. Nature Commun. 6, 7489 (2015).
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