Text by Maarja Öpik
How to measure things? How to measure biodiversity? For organisms which are visible to human eye, detecting them is not an issue, though identifying the species might be. The situation is fully different for organisms we cannot see with our detector (human eye) or in cases when we wish to use other detection systems, such as sequencing DNA obtained from the organisms, and subsequent identification of the sequences.
The way how it most commonly works in the DNA-based detection and identification of organisms, be they microbial or macroscopic, is first getting their DNA in a small volume of a liquid (we call it DNA extraction, from, e.g., soil). Next, the amount of DNA of interest is increased (amplified) via PCR so that it is easier to work with it, such as to sequence the DNA and match the DNA sequences against others we already know. The result of this step is dependent on the specificity of primers, short DNA fragments, which selectively bind to the DNA in the sample only if they are of the same sequence. This is like fishing in the dark and only knowing which fish was out there once we check the hook. But is our fishing hook the right one? Could we use the same hook for different kinds of fish, or do we need separate hooks for all fishes?
In our new paper, led by Ylva Lekberg (MPG Ranch, Missoula, Montana, USA; University of Montana, Missoula, Montana, USA), we asked analogous question about soil fungi: can we use general fungal primers to characterise diversity of arbuscular mycorrhizal (AM) fungi sufficiently well, or do we need to use separate primers for these fungi? There has been a lab lore around for some time that the commonly used general fungal primers do not catch AM fungi sufficiently well, and thus would underestimate their diversity. This is a problem if we want to understand both the diversity patterns of all fungi in our system, and to zoom in to specific groups, such as fungi forming arbuscular mycorrhiza.
In this paper we made use of DNA sequence data obtained by using the two kinds of “fishing hooks” in parallel: sequencing AM fungi separately, by using AM fungal specific primers, and sequencing all fungi from the same samples with general fungal primers. What was our answer? As all too often, we learned that it depends… First, we detected higher diversity of AM fungi in our samples when using AM fungal specific primers. However, when we looked at how the AM fungal diversity responded to the experimental manipulations of soil moisture, or changed during the growing seasons in nature, our two detection systems revealed the same shifts in AM fungal diversity. Thus, the inaccuracy of AM fungal detection with the general fungal primers did not change the ecological conclusions regarding the responses of AM fungi to climate manipulations. However, using the higher accuracy of detection with the AM fungal specific system we can learn better which AM fungi respond in which ways, and in particular, we are better equipped to find fungi with differential behaviour.
This result is important. It means that we can learn about AM fungal responses to environmental changes in large datasets addressing big spatiotemporal scales and broad groups of organisms. It also means that there is no longer any reason to neglect AM fungi in these big datasets, and better so, because AM fungi carry important functions for all of us. Think of fresh air – the lungs of the planet, tropical rainforests, need AM fungi, and not just any, but the right ones. Or your next cup of coffee, slice of bread or an apple – all the same. Or your garden, organic farm or urban landscape. Still the same.
Citation: Lekberg, Y., Vasar, M., Bullington, L. S., Sepp, S. K., Antunes, P. M., Bunn, R., Larkin, B. G. & Öpik, M. (2018). More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers?. New Phytologist, DOI: link to full text). (