How diverse is the soil life across Europe? A first continent-wide DNA analysis sheds light on the biodiversity below our feet

by julia Köninger, universidade de vigo, Spain

Much more than just a brown mass - soils are full of life. However, we still don't fully understand how this life is distributed. Large-scale studies are especially rare. This is where DNA analysis comes in handy because it allows us to quickly identify many different groups of organisms fairly easily. In our Europe-wide study, we analyzed soil DNA through the LUCAS framework of the European Commission. We used metabarcoding to screen the 18S gene providing information on soil eukaryotes (which include fungi, animals, and protists) to understand who lives where and why. We looked at 787 sites and examined how soil properties and climate affect the diversity of these organisms. The ecosystems we studied included croplands (both annual and permanent), managed and unmanaged grasslands, and broadleaved and coniferous woodlands.

We found 97 different groups (phyla) of eukaryotes belonging to three main categories: protists (57%), fungi (33%), and animals (10%). Among the animals, 52% were nematodes, 33% were arthropods, 11% were rotifers, 3% were tardigrades, and 0.8% were annelids.

The results showed that the type of ecosystem is the most important factor influencing soil eukaryotic diversity. Soil properties have a greater impact than climatic, although long-term climate and land-use also play significant roles. Specifically, soil pH affects the richness of fungi, rotifers, and annelids, while plant-available phosphorus influenced the richness of protists, tardigrades, and nematodes.

Surprisingly, croplands had the highest diversity of fungi, protists, nematodes, arthropods, and annelids among the ecosystems considered. However, those sites were also more homogeneous in species composition compared to other ecosystems. Taxa between croplands, grasslands, and woodlands often overlapped, with croplands hosting the most specialized taxa for many groups. The high diversity in croplands might be due to previous land uses, with DNA from dormant or dead organisms adding to the diversity we observed. While the study showed factors that should be considered in future monitoring and conservation efforts, it also points to some limitations in often applied DNA analysis methods. These methods do not distinguish between DNA from living organisms and dead material (necromass), which can skew biodiversity assessments. Moreover, the soil samples we used were too small to capture the diversity of larger soil animals, like arthropods and earthworms.

Our study on soil eukaryotes is complemented by a parallel study on bacteria (16S gene) and fungi (ITS gene), helping us get a better grasp of the overall soil biodiversity. Our results are just a few of many to come as more funding has been allocated to soil biodiversity research reflecting a growing awareness of its importance. The new knowledge should be translated into soil biodiversity indicators for different ecosystems and climatic zones. Including target values and baselines in legislations is crucial, as it allows to detect alarming changes and to respond appropriately.