More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers?

High throughput sequencing has revolutionizedmicrobial ecology. We now have the ability to characterize both prokaryotic and eukaryotic microbial communities more thoroughly and disentangle relationships among broad organismal groups (B€odeker et al., 2016; Morri€en et al., 2017; Toju et al., 2017). Arbuscular mycorrhizal fungi (AMF; subphylum Glomeromycotina, Spatafora et al., 2016) are no exception, and high throughput sequencing has revealed greater richness within communities compared with Sanger sequencing ( € Opik et al., 2009), as well as an increased understanding about global distribution patterns and their potential underlying drivers (Davison et al., 2015). AMF are apparently asexual (but see Corradi & Brachmann, 2017), obligate symbionts that exchange nutrients and other services for plant carbon (Smith & Read, 2008). There are c. 300 morphologicallydefined ( € Opik & Davison, 2016) and 1000 or more molecularlydefined species of AMF (Kivlin et al., 2011; € Opik et al., 2014). This is low compared to other mycorrhizal fungi, and surprising given the prevalence and potential ability by AMF to colonize > 200 000 plant species (Brundrett, 2009). As molecular techniques have evolved, different marker regions have been used to characterize AMF communities, each with their strengths and weaknesses (Hart et al., 2015). The small subunit rRNA (SSU rRNA) gene is the region most often targeted because primer pairs exist that amplify most known AMF families. Also, sequences can be aligned against virtual taxa (VTs) using the curated database MaarjAM ( € Opik et al., 2010), which facilitates comparisons across studies. The internal transcribed spacer (ITS) region is the universal barcode for fungi (Schoch et al., 2012) and AMF specific primers exist for ITS (Kr€ uger et al., 2009), but this region is less frequently used inAMFcommunity surveys. Thismay be due to poor amplification of AMF with general fungal ITS primers (Tedersoo et al., 2015, 2018), or high variation within species and even individuals that hampers clade recognition (Thi ery et al., 2016). Yet with the exponential increase in sequencing output with high throughput sequencing, AMF sequences are now detected and discussed in studies using general fungal primers that target all soil fungi. For example,Tedersoo et al. (2014) used ITS to show that AMF sequences make up a small proportion of the total fungal abundance and that AMF richness is positively correlatedwith soil pH and potential evapotranspiration. Likewise, Leff et al. (2015) used a shift in total number of AMF sequences relative to other fungal groups to discuss potential changes in AMF abundance with fertilizer additions. Targeting the ITS rather than the SSU is appealing as it allows fungal ecologists to make broad comparisons that include all fungi. It is unclear, however, if general fungal ITS primers detect similar AMF communities and show comparable responses to shifts in environmental conditions as AMF-specific SSU primers do. If they do, targeting the ITS rather than the SSU will provide broader comparisons using the same effort and resources without the loss of precision in detecting shifts in AMF communities.