Fungi
Fungi made it possible for plants to live on land. Fungi participate in decomposition of organic matter and deliver nutrients for plant growth. Besides specific groups such as entomopathogens (pathogenic fungi to insects like Cordyceps), nematophagous fungi (feeding on nematodes) and fungal endophytes (living inside plants) central groups are saprotrophic fungi (decomposers), arbuscular mycorrhizal fungi (AMF) (paramount in herbaceous systems such as grasslands) and ectomycorrhizal fungi that facilitate the communication between trees as the wood wide web. Mycorrhiza provide plants with mainly phosphorous and receive carbohydrates and other building blocks in return. Endophytes can fight-off rusts but also boost plant growth promotion, production of secondary plant metabolites and other bioactive compounds which boosts disease resistance in plants [1],[2].
Fungi range from being microscopically small to being the largest organisms on earth. They are present in almost all soils[3],[4]. Although their biomass in temperate zones is only a small fraction of the total microbial biomass in most ecosystems they are highly active. Even in mostly bacterial dominated agricultural systems fungi handle most of the plant derived carbon[5],[6]. Some crops suffer from fungal- and oomycete diseases such as rusts, Potato Blight disease (Oomycete), Take-all fungus on wheat and Fusarium infections. However, most fungi are beneficial for nutrient cycling, elongating the root system and fighting of bacterial pathogens. Fungi, are due to their central functional role in the soil food web serve as important indicators for soil quality[7]. Fungi play an important role in all four of the soil functions considered on the BIOSIS platform: Nutrient Cycling, Carbon and Climate Regulation, Water Regulation and Purification and Disease and Pest Management.
Fungi can be extracted from soil and analyzed using molecular tools such as Illumina sequencing platform (among others) targeting the ITS region. The UNITE database and FUNguild provide the information to not only classify them into taxa but also into functional guilds[8],[9]. Quantitative analyses using qPCR work well on some groups while on other groups containing multiple nuclei (such as mycorrhiza) this is a larger challenge[10]. More classical techniques such as plating and quantifying root infections after hyphal staining work well for some groups.
Text by Dr. Elly Morriën, Faculty of Science, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam
[1] Terhonen E et al. 2019. Forest Tree Microbiomes and Associated Fungal Endophytes: Functional Roles and Impact on Forest Health. Forest 10: 42.
[2] Fadiji AE & Babalola OO. 2020. Elucidating Mechanisms of Endophytes Used in Plant Protection and Other Bioactivities With Multifunctional Prospects. Frontiers in Bioengeneering & Biotechnology 8:467.
[3] Baldrian P et al. 2012. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME Journal 6: 248–258.
[4] Davison J. 2015. Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism. Science 349: 970-973.
[5] Hannula SE et al. 2012. 13C pulse-labeling assessment of the community structure of active fungi in the rhizosphere of a genetically starch-modified potato (Solanum tuberosum) cultivar and its parental isoline. New Phytologist 194: 784–799.
[6] Frąc M et al. 2018. Fungal Biodiversity and Their Role in Soil Health. Frontier in Microbiology 9:707.
[7] Jones DL et al. 2014. Plant and mycorrhizal regulation of rhizodeposition. New Phytologist 163 : 459–48.
[8] Nilsson RH. 2019. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research 47: D259–D264.
[9] Nguyen NH et al. 2016. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecoogy 2016: 241–248.
[10] Bodenhausen N. 2021. Relative qPCR to quantify colonization of plant roots by arbuscular mycorrhizal fungi. Mycorrhiza 31: 137–148.