Continent-wide DNA analysis of soil eukaryotes

Soil eukaryotes play a crucial role in maintaining ecosystem functions and services, yet the factors driving their diversity and distribution remain poorly understood. While many studies focus on some eukaryotic groups (mostly fungi), they are limited in their spatial scale. Here, we analyzed an unprecedented amount of observational data of soil eukaryomes at continental scale (787 sites across Europe) to gain further insights into the impact of a wide range of environmental conditions (climatic and edaphic) on their community composition and structure. We found that the diversity of fungi, protists, rotifers, tardigrades, nematodes, arthropods, and annelids was predominantly shaped by ecosystem type (annual and permanent croplands, managed and unmanaged grasslands, coniferous and broadleaved woodlands), and higher diversity of fungi, protists, nematodes, arthropods, and annelids was observed in croplands than in less intensively managed systems, such as coniferous and broadleaved woodlands. Also in croplands, we found more specialized eukaryotes, while the composition between croplands was more homogeneous compared to the composition of other ecosystems. The observed high proportion of overlapping taxa between ecosystems also indicates that DNA has accumulated from previous land uses, hence mimicking the land transformations occurring in Europe in the last decades. This strong ecosystem-type influence was linked to soil properties, and particularly, soil pH was driving the richness of fungi, rotifers, and annelids, while plant-available phosphorus drove the richness of protists, tardigrades, and nematodes. Furthermore, the soil organic carbon to total nitrogen ratio crucially explained the richness of fungi, protists, nematodes, and arthropods, possibly linked to decades of agricultural inputs. Our results highlighted the importance of long-term environmental variables rather than variables measured at the time of the sampling in shaping soil eukaryotic communities, which reinforces the need to include those variables in addition to ecosystem type in future monitoring programs and conservation efforts.

Soil the foundation of terrestrial life

There has been a growing recognition of the crucial role played by soil biodiversity in maintaining the ecosystem services. Prokaryotes (bacteria and archaea) and eukaryotes (fungi, protists, rotifers, tardigrades, nematodes, arthropods and earthworms) form a complex and dynamic network. They provide crucial ecosystem services, building the foundation for terrestrial life. For example, they decompose organic material, provide antibiotics, and allow soils to filter and store water. They play a particularly critical role in agriculture. Soil organisms provide nutrients to plants and enhance the plants' resilience to stressors.  For example, they suppress soil-borne pathogens and pests. Despite their importance, knowledge on soil life remains limited.

Taxonomical assignment and proportion of shared taxa between ecosystem type

We found 97% of the 79,383 ASVs to be assigned to eukaryotes. We further classified the 97 eukaryotic phyla into three kingdoms: protists (57%), fungi (33%), and animals (10%). Within the latter group, 52.2% of reads belonged to nematodes, 32.9% to arthropods, 10.6% to rotifers, 3.4% to tardigrades, and 0.8% to annelids (Figure 2). For fungi, the dominant groups were two phyla belonging to the Dikaria subkingdom, namely Ascomycota (approximately 50%) and Basidiomycota (>35%), followed by the subphylum Mucoromycotina (>10%; Figure S1). The highest relative abundance for protists was found for two phyla, namely Cercozoa (>50%) and Ciliophora (20%), and the superphylum Heterokonta (>10%).

Missing taxonomic information was particularly high for protists and arthropods on order level (72% and 48.5% of the total number of ASVs, respectively; Figure S1). This lack of information increased further at lower taxonomic levels. For example, at the species level, 86.7% of rotifers, 85% of protists species, 79.3% of arthropod species, 87.8% of tardigrade species, and 69.9% of nematode species could not be assigned to any known sequence (unknown).

Fig. 1. 18S-rDNA sequencing read results. (a) Proportion of ASVs assigned to different domains, with the majority of sequence reads found to belong to eukaryotes. (b) Proportion of taxa assigned to the different eukaryotic kingdoms. (c) Proportion of taxa assigned to the different phyla.

Eukaryotic diversity increases with the intensity gradient

The α-diversity values for fungi, protists, nematodes, arthropods, and annelids were significantly different between ecosystem types (Kruskal–Wallis p < 0.05). The highest richness (number of ASVs) was measured for fungi (495), followed by protists (484), nematodes (77), and arthropods (59). . In contrast, the lowest values were observed for rotifers (19), annelids (15), and tardigrades (12) across all ecosystem types. Furthermore, α-diversity declined toward the less intensely managed ecosystems, with the highest values being observed in annual croplands and the lowest ones in coniferous woodlands.  Despite both metrics (ASV richness and Shannon index) showing similar patterns, we found fewer significant differences when comparing the Shannon index between ecosystems. For example, no significant differences in the Shannon diversity of rotifers between different ecosystem types were found.

Fig. 2. α-diversity of eukaryotic groups in different ecosystem types. Observed ASV richness for (a) fungi and protists and for (b) animals (rotifers, tardigrades, nematodes, arthropods, and annelids). Shannon index for (c) fungi and protists, and for (d) animals. The number of sampled sites was reduced after statistical filtering to 787 sites for fungi, 785 protists, 315 rotifers, 589 tardigrades, 587 nematodes, 583 arthropods, and 666 annelids.

Greatest diversity in croplands as a legacy effect of past land uses

Surprisingly, croplands exhibited greater biodiversity despite intensive land use. Croplands were also more homogeneous compared to the composition of other ecosystems. High numbers of taxa of eukaryotic groups overlapped in croplands, grasslands and woodlands. For the majority of the groups, croplands hosted the most unique taxa. The study proposes a possible explanation for the greater diversity detected in agricultural areas. In recent decades, many grasslands and woodlands across the European were converted into croplands. The high diversity observed in croplands and the great proportion of overlapping taxa between ecosystems might reflect DNA accumulation from previous land uses. The higher soil biodiversity in croplands could be a legacy effect from the DNA of dormant or dead organisms. This might also explain why long-term variables for land use and climate were more relevant compared to monthly variables.

Download the data: Soil biodiversity - DNA eukaryotes

Reference: Köninger, J. Ballabio, C., Panagos, P., Jones, A., Schmid, M.W., Orgiazzi, A, Briones, M.J.I. 2023. Ecosystem type drives soil eukaryotic diversity and composition in Europe. Global Change Biology. 29(19): 5706-5719. DOI: 10.1111/gcb.16871