Skip to main content

Advertisement

SpringerLink
Log in

Association of Bacterial Communities with Psychedelic Mushroom and Soil as Revealed in 16S rRNA Gene Sequencing

  • Original Article
  • Published:
Applied Biochemistry and Biotechnology Aims and scope Submit manuscript

Abstract

Microbial communities’ resident in the mushroom fruiting body and the soil around it play critical roles in the growth and propagation of the mushroom. Among the microbial communities associated with psychedelic mushrooms and the rhizosphere soil, bacterial communities are considered vital since their presence greatly influences the health of the mushrooms. The present study aimed at finding the microbiota present in the psychedelic mushroom Psilocybe cubensis and the soil the mushroom inhabits. The study was conducted at two different locations in Kodaikanal, Tamil Nadu, India. The composition and structure of microbial communities in the mushroom fruiting body and the soil were deciphered. The genomes of the microbial communities were directly assessed. High-throughput amplicon sequencing revealed distinct microbial diversity in the mushroom and the related soil. The interaction of environmental and anthropogenic factors appeared to have a significant impact on the mushroom and soil microbiome. The most abundant bacterial genera were Ochrobactrum, Stenotrophomonas, Achromobacter, and Brevundimonas. Thus, the study advances the knowledge of the composition of the microbiome and microbial ecology of a psychedelic mushroom, and paves the way for in-depth investigation of the influence of microbiota on the mushroom, with special emphasis on the impact of bacterial communities on mushroom growth. Further studies are required for a deeper understanding of the microbial communities that influence the growth of P. cubensis mushroom.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

Data Availability

Metagenomics sequence data from psychedelic mushroom fruiting bodies and soil have been deposited in the NCBI submission portal with the accession number PRJNA744345.

The GenBank accession numbers for the sequence of Psilocybecubensisis are ON415277 and ON415278.

References

  1. Chisholm, S. T., Coaker, G., Day, B., & Staskawicz, B. J. (2006). Host-microbe interactions: Shaping the evolution of the plant immune response. Cell, 124, 803–814.

    Article  CAS  PubMed  Google Scholar 

  2. Pent, M., Põldmaa, K., & Bahram, M. (2017). Bacterial communities in boreal forest mushrooms are shaped both by soil parameters and host identity. Frontiers in Microbiology, 8, 836.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Ruan, R., Jiang, Z., Wu, Y., Xu, M., & Ni, J. (2019). High-throughput sequence analysis reveals variation in the relative abundance of components of the bacterial and fungal microbiota in the rhizosphere of Ginkgo biloba. Peer J7, 7, e8051.

    Article  Google Scholar 

  4. Berg, G., Rybakova, D., Fischer, D., Cernava, T., Vergès, M. C. C., Charles, T., Chen, X., Cocolin, L., Eversole, K., Corral, G. H., & Kazou, M. (2020). Microbiome definition re-visited: Old concepts and new challenges. Microbiome, 8, 1–22.

    Google Scholar 

  5. Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007). The human microbiome project. Nature, 449(7164), 804–810.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Proctor, L. (2019). Priorities for the next 10 years of human microbiome research. Nature, 569(7758), 623–625.

    Article  CAS  PubMed  Google Scholar 

  7. Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J. R., Prifti, E., Nielsen, T., & Juncker, A. S. (2014). An integrated catalog of reference genes in the human gut microbiome. Nature Biotechnology, 32(8), 834–841.

    Article  CAS  PubMed  Google Scholar 

  8. Shi, W., Qi, H., Sun, Q., Fan, G., Liu, S., Wang, J., Zhu, B., Liu, H., Zhao, F., Wang, X., & Hu, X. (2019). gcMeta: A Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data. Nucleic Acids Research, 47(D1), D637–D648.

    Article  CAS  PubMed  Google Scholar 

  9. Girish, G., & Prakash, V. (2015). A checklist of gilled mushrooms (Basidiomycota: Agaricomycetes) with diversity analysis in Hollong apar Gibbon Wildlife Sanctuary, Assam, India. Journal of Threatened Taxa, 7, 8272–8287.

    Article  Google Scholar 

  10. Griffiths, R. R., Johnson, M. W., Carducci, M. A., Umbricht, A., Richards, W. A., Richards, B. D., Cosimano, M. P., & Klinedinst, M. A. (2016). Psilocybin produces substantial and sustained decreases in depression and anxiety in patients with life-threatening cancer: A randomized double-blind trial. Journal of Psychopharmacology, 30, 1181–1197.

    Article  CAS  PubMed  Google Scholar 

  11. Kowalczyk, M., Mleczko, P., Olszowy, Z., Zubek, S., & Kupiec, T. (2015). Practical aspects of genetic identification of hallucinogenic and other poisonous mushrooms for clinical and forensic purposes. Forensic Sciences, 56, 32–40.

    CAS  Google Scholar 

  12. Dhanasekaran, D., Latha, S., Suganya, P., Panneerselvam, A., Senthilkumar, T., Alharbi, N. S., Arunachalam, C., Alharbi, S. A., & Thajuddin, N. (2020). Taxonomic identification and bioactive compounds characterization of Psilocybe cubensis DPT1 to probe its antibacterial and mosquito larvicidal competency. Microbial Pathogenesis, 143, 104138.

    Article  CAS  PubMed  Google Scholar 

  13. Tonge, D. P., Pashley, C. H., & Gant, T. W. (2014). Amplicon-based metagenomic analysis of mixed fungal samples using proton release amplicon sequencing. PloS One, 9, e93849.

    Article  PubMed  PubMed Central  Google Scholar 

  14. Kemp, P. F., & Aller, J. Y. (2004). Bacterial diversity in aquatic and other environments: What 16S rDNA libraries can tell us. FEMS Microbiology Ecology, 47, 161–177.

    Article  CAS  PubMed  Google Scholar 

  15. Cole, J. R., Ross, R. P., & O’Toole, P. W. (2010). Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Research, 38, e200.

    Article  PubMed  PubMed Central  Google Scholar 

  16. Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., & Huttley, G. A. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335–336.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., & Mende, D. R. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59–56.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Abdel-Wahab, M., Bahkali, A. H., El-Gorban, A. M., & Jones, G. (2021). Metagenomics study of fungi and fungi-like organisms associated with the seagrass Halophilastipulacea (Forssk.) Asch. from Al-Leith Mangroves, Saudi Arabia. Microbial Pathogenesis, 10(2), 1–19.

    CAS  Google Scholar 

  19. Silva, L. J., Crevelin, E. J., Souza, W. R., Moraes, L. A., Melo, I. S., & Zucchi, T. D. (2014). Streptomyces araujoniae produces a multiantibiotic complex with ionophoric properties to control Botrytis cinerea. Phytopathology, 104, 1298–1305.

    Article  CAS  PubMed  Google Scholar 

  20. Hassan, M., Essam, T., & Megahed, S. (2018). Illumina sequencing and assessment of new cost-efficient protocol for metagenomic-DNA extraction from environmental water samples. Brazilian Journal of Microbiology, 49, 1–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Zhang, Y., Ding, L., Yan, Z., Zhou, D., Jiang, J., Qiu, J., & Xin, Z. (2021). Identification and characterization of a novel carboxylesterase belonging to family VIII with promiscuous acyltransferase activity toward cyanidin-3-o-glucoside from a soil metagenomic library. Applied Biochemistry and Biotechnology, 13, 1–9. https://doi.org/10.1007/s12010-021-03614-9

    Article  CAS  Google Scholar 

  22. Srinivasan, M., Dhanasekaran, D., & Archunan, G. (2019). Vaginal microbiome analysis of buffalo (Bubalusbubalis) during estrous cycle using high-throughput amplicon sequence of 16S rRNA gene. Symbiosis, 78, 97–106.

    Article  Google Scholar 

  23. Edgar, R. C. (2016). UNOISE2: Improved error correction for Illumina 16S and ITS amplicon sequencing. BioRxiv, 15, 081257. https://doi.org/10.1101/081257

    Article  Google Scholar 

  24. Li, X., Duan, J., Xiao, H., Li, Y., Liu, H., Guan, F., & Zhai, X. (2017). Analysis of bacterial community composition of corroded steel immersed in Sanya and Xiamen seawaters in China via method of Illumina MiSeq sequencing. Frontiers in Microbiology, 8, 1737.

    Article  PubMed  PubMed Central  Google Scholar 

  25. Narayanasamy, M., Dhanasekaran, D., & Thajuddin, N. (2021). Root nodule microbiome from actinorhizal Casuarina plant. In D. Dhanasekaran, D. Paul, N. Amaresan, A. Sankaranarayanan, & Y. S. Shouche (Eds.), Microbiome-host interactions (1st ed., pp. 295–305). CRC Press.

    Google Scholar 

  26. Qiao, Y. Q., Cai, C. W., & Ran, Z. H. (2016). Therapeutic modulation of the gut microbiota in IBD — More questions to be answered. Journal of Diagnostic Disease, 17, 800–810.

    Article  Google Scholar 

  27. O’Brien, H. E., Parrent, J. L., Jackson, J. A., Moncalvo, J., & Vilgalys, R. (2005). Fungal community analysis by large-scale sequencing of environmental samples. Applied Environment and Microbiology, 71, 5544–5550.

    Article  Google Scholar 

  28. Wang, W., Zhai, Y., Cao, L., Tan, H., & Zhang, R. (2016). Illumina-based analysis of core actinobacteriome in roots, stems, and grains of rice. Microbiology Research, 190, 12–18.

    Article  Google Scholar 

  29. Liu, Y., Sun, Q., Li, J., & Lian, B. (2018). Bacterial diversity among the fruit bodies of ectomycorrhizal and saprophytic fungi and their corresponding hypersphere soils. Scientific Report, 8, 11672.

    Article  Google Scholar 

  30. Aparna, C. R., Nishi, S., Kumar, A., Maushumi, D., Tony, G., Suma, A., Vijay, P., & Ilora, G. (2021). Exploring prevalence of potential pathogens and fecal indicators in geographically distinct river systems through comparative metagenomics. Environmental Pollution, 282, 117003.

    Article  Google Scholar 

  31. Osimani, A., Milanovic, V., Roncolini, A., Riolo, P., Ruschioni, S., Isidoro, N., Loreto, N., Franciosi, E., Tuohy, K., Olivotto, I., & Zarantoniello, M. (2019). Hermetia illucens in diets for zebrafish (Daniorerio): A study of bacterial diversity by using PCR-DGGE and metagenomic sequencing. PloS One, 14, e0225956.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Zheng, J., Zhang, J., Lin, G., Kong, F., Shen, G., Rui, W., & Gao, J. (2020). The effects of tetracycline residues on the microbial community structure of tobacco soil in pot experiment. Scientific Reports, 10, 8804.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Qiang, W., Xuan, H., Yu, S., Hailun, P., Yueli, Z., Zhiguo, P., & Lei, S. (2021). Impact of the gut microbiota on heatstroke rat mediated by Xuebijing metabolism. Microbial Pathogenesis, 155, 104861.

    Article  CAS  PubMed  Google Scholar 

  34. Zheng, J., Xiao, X., Zhang, Q., Mao, L., Yu, M., & Xu, J. (2015). The placental microbiome varies in association with low birth weight in full-term neonates. Nutrients, 7, 6924–6937.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Travanty, N. V., Ponnusamy, L., & Apperson, C. S. (2019). Diversity and structure of the bacterial microbiome of the American dog tick, Dermacentor variabilis, is dominated by the endosymbiont Francisella. Symbiosis, 79, 239–250.

    Article  CAS  Google Scholar 

  36. Ke, L., Li, P., Xu, J., Wang, Q., & Wang, L. (2019). Microbial communities and soil chemical features associated with commercial production of the medicinal mushroom Ganodermalingzhi in soil. Scientific Reports, 9, 15839.

    Article  PubMed  PubMed Central  Google Scholar 

  37. Prehn-kristensen, A., Zimmermann, A., Tittmann, L., Lieb, W., Schreiber, S., Baving, L., & Fischer, A. (2018). Reduced microbiome alpha diversity in young patients with ADHD. PLoS One, 1(3), 1–19.

    Google Scholar 

  38. Wang, B., Deng, B., Yong, F., Zhou, H., Qu, C., & Zhou, Z. (2020). Comparison of the fecal microbiomes of healthy and diarrheic captive wild boar. Microbial Pathogenesis, 147, 104377.

    Article  CAS  PubMed  Google Scholar 

  39. Ghosh, S., Sarkar Paria, D., & Chatterjee, S. (2022). Comparative study on bacterial population dynamics of foregut, midgut, and hindgut content of Perionyxexcavatus (Perrier) isolated from eco-friendly, non-hazardous vermicompost. Applied Biochemistry and Biotechnology, 194, 6126–6139.

    Article  CAS  PubMed  Google Scholar 

  40. Liu, Y.-X., Quin, Y., Chen, T., Lu, M., Qian, X., Guo, X., & Bai, Y. (2021). A practical guide to amplicon and metagenomic analysis of microbiome data. Protein Cell, 12(5), 315–330.

    Article  PubMed  Google Scholar 

  41. Singha, K. M., Singh, B., & Pandey, P. (2021). Host-specific endophytic microbiome diversity and associated functions in three varieties of scented black rice are dependent on growth stage. Scientific Reports, 11, 1–17.

    Article  Google Scholar 

  42. Dhariwal, A., Chong, J., Habib, S., King, I. L., Agellon, L. B., & Xia, J. (2017). Microbiome analyst: A web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Research, 45(W1), W180–W188.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Edgar, R. C. (2013). UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10, 996.

    Article  CAS  PubMed  Google Scholar 

  44. Lv, X. M., Shao, M. F., Li, J., & Li, C.-L. (2015). Metagenomic analysis of the sludge microbial community in a lab-scale denitrifying phosphorus removal reactor. Applied Biochemistry and Biotechnology, 175, 3258–3270.

    Article  CAS  PubMed  Google Scholar 

  45. Lee, K. C.-Y., Dunfield, P. F., Morgan, X. C., Crowe, M. A., Houghton, K. M., Vyssotski, M., Jason, L. J. R., Kirill, L., Ian, R. M., & Matthew, B. S. (2011). Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10. International Journal of Systematic and Evolutionary Microbiology, 61, 2482–2490.

    Article  CAS  PubMed  Google Scholar 

  46. Maarastawi Sarah, A., Katharina, F., Marius, L., & Claudia, K. (2018). Crop rotation and straw application impact microbial communities in Italian and Philippine soils and the rhizosphere of Zeamays. Frontiers in Microbiology, 9, 1295.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Hirsch, P. R., & Mauchline, T. H. (2012). Who’s who in the plant root microbiome. Nature Biotechnology, 30, 961–962.

    Article  CAS  PubMed  Google Scholar 

  48. Lewin, G. R., Carlos, C., Chevrette, M. G., Horn, H. A., McDonald, B. R., Stankey, R. J., Fox, B. G., & Currie, C. R. (2016). Evolution and ecology of Actinobacteria and their bioenergy applications. Annual Review of Microbiology, 70, 235.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Yu, S., Bai, X., Liang, J., Wei, Y., Huang, S., Li, Y., Dong, L., Liu, X., Qu, J., & Yan, L. (2019). Inoculation of Pseudomonas sp. GHD-4 and mushroom residue carrier increased the soil enzyme activities and microbial community diversity in Pb-contaminated soils. Journal of Soils Sediments, 19, 1064–1076.

    Article  CAS  Google Scholar 

  50. Carrasco, J., & Preston, G. M. (2020). Growing edible mushrooms: A conversation between bacteria and fungi. Environmental Microbiology, 22(3), 858–872.

    Article  PubMed  Google Scholar 

  51. McgeeCF, B. H., Irvine, A., & Wilson, J. (2017). Diversity and dynamics of the DNA and cDNA-derived bacterial compost communities throughout the Agaricus bisporus mushroom cropping process. Annals of Microbiology, 67, 751–761.

    Article  Google Scholar 

  52. Boubekri, K., Soumare, A., Mardad, I., Lyamlouli, K., Ouhdouch, Y., Hafidi, M., & Kouisni, L. (2022). Multifunctional role of Actinobacteria in agricultural production sustainability: A review. Microbiological Research, 261, 127059.

    Article  CAS  PubMed  Google Scholar 

  53. Tank, M., & Bryant, D. A. (2015). Nutrient requirements and growth physiology of the photoheterotrophic Acidobacterium Chloracidobacterium thermophilum. Frontiers in Microbiology, 6, 226.

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We record our gratitude to Dr. R. Thirumurugan, Coordinator of the National Centre for Alternatives to Animal Experiments (NCAAE), for being of support during the course of the research. The financial assistance of the Department of Science and Technology, Government of India, under the DST-Promotion of University Research and Scientific Excellence (PURSE) Scheme-Phase II, Rashtriya Uchchatar Shiksha Abhiyan (RUSA)-2.0, and the National Centre for Alternatives to Animal Experiments (NCAAE) project, under the University Grants Commission’s Centre with Potential for Excellence in Particular Area (UGC-CPEPA), is also gratefully acknowledged. The help in sample collection by Dr. Senthil Kumar and Mrs. Antony Samy is heartily acknowledged.

Author information

Authors and Affiliations

  1. Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India

    Karthiyayini Balakrishnan, Dheebhashriee Krishnaa & Dhanasekaran Dharumadurai

  2. National Centre for alternatives to Animal Experiments, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India

    Karthiyayini Balakrishnan & Gowdhami Balakrishnan

  3. Department of Animal Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India

    Gowdhami Balakrishnan

  4. Department of Biotechnology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India

    Muthuselvam Manickam

  5. Mahatma Gandhi-Dorenkamp Centre, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India

    Akbarsha Mohammad Abdulkader

  6. Department of Biotechnology & Research Coordinator, National College (Autonomous), Tiruchirappalli, Tamil Nadu, India

    Akbarsha Mohammad Abdulkader

Authors
  1. Karthiyayini Balakrishnan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dheebhashriee Krishnaa
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gowdhami Balakrishnan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Muthuselvam Manickam
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Akbarsha Mohammad Abdulkader
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Dhanasekaran Dharumadurai
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

DD and KB conceived the idea and designed the research. KB, DK, and GB conducted the experiments. KB wrote the paper. DD, GB, MM, and MAA contributed to materials characterization and data analysis. All authors take part in the result and discussion. DD and MAA did the correction and language editing.

Corresponding author

Correspondence to Dhanasekaran Dharumadurai.

Ethics declarations

Ethics Approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Conflict of Interest

The authors declare no competing interests.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Balakrishnan, K., Krishnaa, D., Balakrishnan, G. et al. Association of Bacterial Communities with Psychedelic Mushroom and Soil as Revealed in 16S rRNA Gene Sequencing. Appl Biochem Biotechnol (2023). https://doi.org/10.1007/s12010-023-04527-5

Download citation

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12010-023-04527-5

Keywords

Search

Navigation