Rhizoscyphus ericae

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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].

NCBI: Genome [1] Species [2]

Description and significance

Rhizoscyphus ericae is a part of the ericoid mycorrhizal fungi group. Fungi that form ericoid mycorrhizae come from many different lineages. Ericoid mycorrhizae are responsible for forming symbiotic relationships with the roots of plants in the plant family Ericaceae[3]. This plant-fungus mutualistic relationship is usually found in temperate climates, such as boreal forests, bogs, and heathlands, where acidic soils are nutrient-poor[4]. Rhizoscyphus ericae are plants’ key to survival in acidic environments – combatting the low soil organic matter availability in temperate ecosystems by mobilizing nutrients to their host plant[5]. The full capacity of how humans can use R. ericae to protect plant life and the environment is still unknown. Recent studies on the functioning, composition, and relationships of Rhizoscyphus ericae detail its effect on plant diversification[6], growth rates[7], and degradation of complex organic compounds[7][8].

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 c[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[[[#References|[6]]], or carbohydrate-active enzymes, involved in the metabolism and recognition of complex carbohydrates, which contribute to their symbiosis.

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].

Metabolic processes

Rhizoscyphus ericae can act as saprotrophs, gaining nutrition from the decomposed material within soil organic matter[6]. 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 compounds[10]. 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].

Ecology

Rhizoscyphus ericae can be found widely in the Northern Hemisphere and is able to withstand colder temperatures at high altitudes[4]. It was recently discovered that R. ericae could be found in the Southern Hemisphere, mainly in locations of higher altitudes that have a more favorable temperature and environment for the fungi to thrive in[4], as well as soil conditions in which ericoid mycorrhizal fungi need for plants to obtain nutrients.

R. ericae demonstrates mutually beneficial relationships with plants of the Ericaceae family, a group of plants that produce flowers with over 4,000 different species[16]. The types of plants that R. ericae has been observed to form a symbiotic relationship with are typically herbaceous and hardwood plants[4]. R. ericae was first isolated in the hair roots of the Calluna vulgaris plant, which demonstrated a symbiotic relationship that includes an exchange of nitrogen and phosphorus from the fungi to the roots of the plant in exchange for energy from [16]. A new discovery of R. ericae fungus-plant relationships described as “sheathed ericoid mycorrhiza” shows a type of symbiotic relationship with Vaccinium spp plants[17], which is the general name of the type of plants blueberries grow from. In this mutualistic connection between plant and fungi, the R. ericae produce 1-to-3 layer sheaths around the plant roots of Vaccinium spp. This action protects and provides nutrients to the roots, promoting further growth and plant diversification[17]. R. ericae is known to protect its host plant roots against toxic compounds in soil by breaking down the heavy metals around them and feeding off of the nutrients provided by them[10]. In the roots of cranberry plants specifically, R. ericae allows sufficient absorption of NO3– in low pH soil environments, which otherwise would interfere with nutrient uptake and inhibit plant growth[13].

R. ericae demonstrates its importance in the plant community as it provides a habitable environment for its host plant that is living in an otherwise uninhabitable environment due to the slow decomposition and soil organic matter turnover in acidic soils[6]. R. ericae has also shown the ability to break down compounds that contaminate water in waste treatment plants[7]. R. ericae and other ericoid mycorrhizae also help host plants in low substrate pH deal with low nutrient conditions and elevated heavy metal toxicity[9]. Fungal-mediated remediation using R. ericae has the potential to change our understanding and treatment of chemical hazards in our water sources[10].

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].

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 sources [10]. In future applications, R. ericae could serve as a natural alternative for water waste treatment plants to reduce antibiotic resistance in the human population.

References

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

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]