Rhizoscyphus ericae

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1. Classification

a. Higher order taxa

Eukaryota; Fungi; Ascomycota; Leotiomycetes; Helotiales; Hyaloscyphaceae; Hyaloscypha; Hyaloscypha hepaticiola/Rhizoscyphus ericae species complex

b. Species

Rhizoscyphus ericae

Some consider it a species complex, known as the Rhizoscyphus ericae species complex/aggregate (REA). This complex includes several fungal taxa isolated from ericoid mycorrhizal roots that are phylogenetically close to R. ericae[1].

2. Description and significance

Describe the appearance, habitat, etc. of the organism, and why you think it is important.

• Include as many headings as are relevant to your microbe. Consider using the headings below, as they will allow readers to quickly locate specific information of major interest*

3. Genome structure

The Rhizoscyphus ericae genome is a single set of chromosomes and has a genome assembly containing 57,410,000 base pairs[2]. The genome contains 16,843 genes, 16,783 of which are protein-coding genes[2]. Additionally, the genome has 267 scaffolds, which are portions of the sequenced genome where the order of bases is known to a high confidence level[2]. The sequenced strain UAMH 7357 has only been assembled to the scaffold level, but there is not enough mapping information for the chromosome level yet[2]. The small and large subunit ribosomal RNA genes have been partially sequenced[11].

Comparing nuclear ribosomal DNA genotypes between R. ericae and Hyaloscypha hepaticicola showed that R. ericae represents sexual and asexual forms of the same organism[12]. Further analysis of genetic sequences between R. ericae[4] and H. Hepaticola revealed nearly identical similarity, which indicated the two aggregates are closely related and are most likely members of the same species[12]. The genome sequence of R. ericae shows genes linked to melanin biosynthesis are enriched compared to fungi with different ecological strategies, which helps fungi survive unfavorable environmental conditions[6]. R. ericae genes coding for polysaccharide-degrading enzymes and proteases for secondary metabolism are more closely related to saprotrophs and pathogens[6].

R. ericae produces specific enzymes, such as proteases and chitinases, that allow R. ericae to use complex compounds as nutrient sources. These enzymes allow R. ericae to use peptides, proteins, chitin, and other molecules that are not accessible to non-mycorrhizal plants[13]. The R. ericae genome has a significant presence of genes involved in self/non-self recognition, nutrient uptake and exchange (sugar transporters), and responses to environmental pollutants and stresses (cytochrome P450, ankyrin repeats, and carboxylesterases)[6]. The R. ericae genome has 1,173 transporter genes, a majority being driven by electrochemical potential[14]. R. ericae exhibit specific enzymes, including histidine triad domain-containing proteins and isochorismate synthase, for resistance to environmental stresses[6]. Isochorismate is a precursor to primary and secondary metabolites, like salicylic acid, that are involved in plants’ responses to stress[6]. R. ericae and other ericoid mycorrhizae genomes contain 560 CAZyme genes[6], or carbohydrate-active enzymes, involved in the metabolism and recognition of complex carbohydrates, which contribute to their symbiosis.

4. Cell structure

Rhizoscyphus ericae range in colors, generally appearing white to a gray-brown, and sometimes yellow [12]. They are distinguishable by their dense intracellular hyphal coils they form in Ericaceae plants, used for nutrient exchange. Sometimes, the hyphae are able to branch outward and enter neighboring hair root cells, as well as the one that the coils were originally formed in. R. ericae have been found to have both asexual and sexual morphotypes [12]. They produce apothecia, a cup-shaped structure containing the hymenium, which is a layer of tissue containing and releasing spores used for sexual reproduction [12].

5. Metabolic processes

"Rhizoscyphus ericae" can act as saprotrophs, gaining nutrition from the decomposed material within soil organic matter6. However, "R. ericae" can also engage in nutrient exchange in symbiotic ericoid mycorrhizal relationships [13]. "R. ericae" utilizes carbohydrate-active enzymes, lipases, and proteases to digest complex, recalcitrant compounds10. Plant carbohydrates act as the primary carbon sources for "R. ericae", which degrades cellulose, tannic acid, pectin, and chitin [13]. In addition to carbohydrates, "R. ericae" degrades cell wall polymers, like proteins and nucleic acids, found in the organic nitrogen component of soil matter [13]. Moreover, from that soil organic matter, ericoid mycorrhizal fungi metabolize organic nitrogen and organic phosphorus to help support the nutrient needs of their host plants [13].

6. Ecology

Habitat; symbiosis; contributions to the environment.

7. Pathology

Ericoid mycorrhizal fungal genes coding for polysaccharide-degrading enzymes and proteases for secondary metabolism are more closely related to saprotrophs and pathogens than ectomycorrhizal fungi. While Rhizoscyphus ericae are saprotrophic, the R. ericae genome has similar protease-, lipase-, and enzyme-coding genes to those of pathogens [6]. There are no known instances of R. ericae being pathogenic to plants or animals. As ericoid mycorrhizal fungi are draining sugars from the host, they counter this by improving the mineral nutrition of the plant [6].

8. Current Research

a. Toxin Removal

Currently, the effectiveness of Rhizoscyphus ericae -mediated wastewater treatments are under investigation. Rhizoscyphus ericae exhibits a potential capability to eliminate ground and wastewater contaminants [7]. R. ericae is able to use substrates with amine and amide groups, many of which are toxic and carcinogenic to humans, as nutrients [7]. Therefore, R. ericae could provide a possible eco-friendly method of breaking down harmful chemicals and removing toxins from the ground and wastewaters. This has not yet been applied to real wastewater treatment, as more in-depth studies are needed to supplement this introductory one.

b. Pharmaceutical Biodegradation

Rhizoscyphus ericae decomposition of the antibiotic neomycin has been of recent interest. While most neomycin is excreted into wastewater, the antibiotic has a complex chemical structure that cannot be broken down by traditional treatments and causes a level of antibiotic resistance [10]. Unique to R. ericae, biodegradation of neomycin is possible in the presence and absence of other nutrient sources10. In future applications, R. ericae could serve as a natural alternative for water waste treatment plants to reduce antibiotic resistance in the human population.

9. References

1. Hyaloscypha hepaticicola [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2004 – [cited 2023 Oct 13]. Available from: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2082293&lvl=3&lin=f&keep=1&srchmode=1&unlock 2. Genome assembly Rhier1 [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2004 – [cited 2023 Oct 13]. Available from: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_002865625.1/ 3. Ericoid mycorrhiza. (2023, August 16). In Wikipedia. https://en.wikipedia.org/wiki/Ericoid_mycorrhiza 4. Bruzone, M.C., Fehrer, J., Fontenla, S.B., & Vohník, M. (2017). First record of Rhizoscyphus ericae in Southern Hemisphere’s Ericaceae. Mycorrhiza, 27, 147–163. https://doi-org.ezproxy.bu.edu/10.1007/s00572-016-0738-8 5. Perotto, S., Martino, E., Abbà, S., & Vallino, M. (2012). 14 Genetic Diversity and Functional Aspects of Ericoid Mycorrhizal Fungi. In: Hock, B. (Eds.), The Mycota, vol 9: Fungal Associations (pp. 255-285). Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30826-0_14 6. Martino, E., Morin, E., Grelet, G.-A., Kuo, A., Kohler, A., Daghino, S., Barry, K.W., Cichocki, N., Clum, A., Dockter, R.B., Hainaut, M., Kuo, R.C., LaButti, K., Lindahl, B.D., Lindquist, E.A., Lipzen, A., Khouja, H.-R., Magnuson, J., Murat, C., Ohm, R.A., Singer, S.W., Spatafora, J.W., Wang, M., Veneault-Fourrey, C., Henrissat, B., Grigoriev, I.V., Martin, F.M., & Perotto, S. (2018). Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists. New Phytologist, 217(3): 1213-1229. https://doi.org/10.1111/nph.14974 7. Stenholm, Å., Backlund, A., Holmström, S., Backlund, M., Hedeland, M., & Fransson, P. (2021). Survival and growth of saprotrophic and mycorrhizal fungi in recalcitrant amine, amide and ammonium containing media. PloS One, 16(9), e0244910. https://doi.org/10.1371/journal.pone.0244910 8. Martino, E., Turnau, K., Girlanda, M., Bonfante, P., & Perotto, S. (2000). Ericoid mycorrhizal fungi from heavy metal polluted soils: Their identification and growth in the presence of zinc ions. Mycological Research, 104(3), 338-344. https://doi.org/10.1017/S0953756299001252 9. Cairney, J.W.G., & Meharg, A.A. (2003). Ericoid mycorrhiza: A partnership that exploits harsh edaphic conditions. European Journal of Soil Science, 54(4), 735-740. https://doi.org/10.1046/j.1351-0754.2003.0555.x 10. Stenholm, Å., Hedeland, M. & Pettersson, C.E. (2022). Investigation of neomycin biodegradation conditions using ericoid mycorrhizal and white rot fungal species. BMC Biotechnology, 22(1), 29. https://doi.org/10.1186/s12896-022-00759-1 11. ​​Hyaloscypha hepaticicola strain UAMH 7357 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2004 – [cited 2023 Oct 20]. Available from: https://www.ncbi.nlm.nih.gov/nuccore/OM238143.1 12. Fehrer, J., Réblová, M., Bambasová, V., & Vohník, M. (2019). The root-symbiotic Rhizoscyphus ericae aggregate and Hyaloscypha (Leotiomycetes) are congeneric: Phylogenetic and experimental evidence. Studies in Mycology, 92, 195-225. https://doi.org/10.1016/j.simyco.2018.10.004 13. Wei, X., Zhang, W., Zulfiqar, F., Zhang, C., & Chen, J. (2022). Ericoid mycorrhizal fungi as biostimulants for improving propagation and production of ericaceous plants. Frontiers in Plant Science, 13. https://doi.org/10.3389/fpls.2022.1027390 14. Nordberg, H., Cantor, M., Dusheyko, S., Hua, S., Poliakov, A., Shabalov, I., Smirnova, T., Grigoriev IV, & Dubchak, I. (2018). Rhizoscyphus ericae UAMH 7357 v1.0, Joint Genome Institute. https://mycocosm.jgi.doe.gov/Rhier1/Rhier1.home.html 15. Drula, E., Garron, M.L., Dogan, S., Lombard, V., Henrissat, B., & Terrapon, N. (2022) The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res, 50(D1):D571-D577. https://doi:10.1093/nar/gkab1045 16. Kariman, K., Barker, S. J., & Tibbett, M. (2018). Structural plasticity in root-fungal symbioses: diverse interactions lead to improved plant fitness. PeerJ, 6, e6030. https://doi.org/10.7717/peerj.6030 17. Vohník, M., Sadowsky, J.J., Kohout, P., Lhotáková, Z., Nestby, R., & Kolařík, M. (2012). Novel root-fungus symbiosis in Ericaceae: sheathed ericoid mycorrhiza formed by a hitherto undescribed basidiomycete with affinities to Trechisporales. PloS One, 7(6), e39524. https://doi.org/10.1371/journal.pone.0039524