Mycorrhizal fungi
Arbuscular mycorrhizal fungi (AMF) occur in almost all ecosystems and perform critical functions for plant health and soil quality. Their main effects are the enhancement of uptake of nutrients with limited mobility, like P, Zn or Cu, higher seed quality, improved drought tolerance (both through increased access to soil water and increased photosynthetic efficiency during drought as a consequence of hormonal changes), improved tolerance of biotic attack by both above-ground and below-ground pests and diseases, enhanced plant tolerance of high salinity and high levels of available heavy metals, and improvement of soil structure. Arbuscular mycorrhizal fungi exhibit dual niches, both inside plant roots and in the soil. For both dimensions of the fungal niche methods for assessment are available.
Quantifying AMF abundance in roots is still often done by staining these fungi inside roots. Protocols for this are well-established [1]. Quantifying AMF abundance in soil is currently done by using a specific fatty acid (the neutral lipid and phospholipid fatty acids, NLFA and PLFA, 16:1ω5) [2]. Formerly microscopic assessments of hyphal length density were applied, but such methods are time-consuming and require a level of expertise.
Estimates of global species richness are variable. Based on classical taxonomic traits (especially spore morphology) global species number has been estimated as a few hundred species, implying little endemism and little dispersal limitation. However, molecular methods have suggested that the number of species is at least one order of magnitude larger, and there is debate whether the most commonly used molecular marker (the ribosomal subunit, SSU) underestimates species richness, implying that other molecular markers (ITS) would further inflate estimates of global species richness. Current assessments of species richness are based on metabarcoding root or soil samples, using AMF-specific primers. The use of SSU primers has the benefit that the data can be easily integrated in a global database (MaarjAM) [3]. There is a usually reasonable match between root and soil assessments of species richness and composition.
The use of functional genes has also been suggested but is not yet operational. However, molecular methods do not allow for quantification, although read numbers derived from sequencing are often used as surrogate for quantitative estimates of abundance of individual species. Quantitative PCR would be needed for assessment of the abundance of individual species, yet only for a few species there are specific primers available [4]. Most methods for quantification therefore assess all AMF together, a practice that is justified by the limited host selectivity of these AMF. The use of functional genes (e.g., expression of phosphate transporters) has been suggested but is not yet operational for soil quality assessments.
A specific glycoprotein, called glomalin, to measure legacy effects of AMF has previously been applied as a proxy indicator for soil quality as it is linked to the longer term storage of soil organic matter. However, it has become evident that this operational pool consists of much more than AMF necromass, and therefore glomalin-related soil protein (GRSP) measure is no longer advisable to apply in this context.
Text by Prof. dr. Thom Kuijper, Soil Biology Group, Wageningen University and Research
[1] http://mycorrhizas.info/method.html
[2] Ruess & Chamberlain. 2010. The fat that matters: Soil food web analysis using fatty acids and their carbon stable isotope signature. Soil Biology and Biochemistry 42: 1898-1910.
[3] Öpik et al. 2010. The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytologist 188: 223-241; https://maarjam.botany.ut.ee/
[4] Voříšková et al. 2017. Real-time PCR quantification of arbuscular mycorrhizal fungi: does the use of nuclear or mitochondrial markers make a difference? Mycorrhiza 27: 577-585.