On grasping soil biodiversity through DNA analysis or a little discourse into my PhD work (the struggle is real putting three years of research into a little blog article).
The Diversity of Life Beneath Our Feet
Soils are so much more than a brown mass – they are full of life. But how diverse is this life? Across 787 sites in Europe, together with my team, we analysed soil DNA to answer this question. So far, it is still not fully clear how soil life is distributed. This is partly because not many large-scale studies have been done using the same methods. Here, DNA analysis comes in handy because it allows us to quickly identify many different groups of organisms. This is why we aimed to understand how diverse soil life is in different European ecosystems ranging from croplands, to grasslands and woodlands (the photos below show a small selection of studied sites). Soil samples were collected through the LUCAS framework of the European Commission. In the next step, we used a method allowing us to screen the genes of life in soil, called metabarcoding. We went for one gene in particular, the 18S gene, giving hints to forms of life with a nucleus, the eukaryotes. They include fungi, animals, and one-celled protists. To understand why soil organisms live in specific sites, we correlated the DNA data with soil properties and climate to see how those variables affect the diversity of soil organisms. Surprisingly, we found croplands to host the highest diversity among various ecosystems. However, species composition was also most homogeneous there compared to other ecosystems (the diversity between sites refers to the beta diversity). In the following, I want to share some insights on our results, how soil properties and climate influence this underground world, but also on the implications for future soil biodiversity monitoring and conservation efforts.
Many samples (see photos below) produced a lot of data. The samples were taken by eurostat and then sent out to various contracted laboratories across Europe for the analysis. The next task was up to the bioinformatic, allowing to “read” DNA sequences and translate them into organisms’ taxonomy which means that we can identify in some cases even their species and in others at least their genera, family, group or class. Luckily, I got some help here, because bioinformatics is a very complex and fastly evolving field. Many questions are still open here and for a PhD student doing all steps of the analysis from sampling to result publication for this amount of data, would have clearly been a bit too much (not to forget a pandemic and some Spansish bureaucracy in between that did not necessarily facilitated the matters). Nevertheless, I had to learn how to program for the analysis to handle the large datasets most effectively. After countless error messages in “R” and some desperate shout-outs to my dear colleague/R-goodess, it worked out, and there were some results (these were times before AI provided its kind assistance in programming).
For example, 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 (e.g. earthworms and podworms).
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.
Also, we found that taxa between croplands, grasslands, and woodlands often overlapped. In croplands we found the most specialized taxa for many groups with highest taxa overlapping with the other ecosystems.
The higher diversity in croplands made me wonder. Apart from the higher overlaps in croplands, interestingly, we also found historic variables (such as long-term climatic variables) to better represent the diversity in those fields. When I went to the GSBI conference in Dublin and the Global Soil Science conference in Glasgow the year before, I heard presentations on necromass and the accumulation of DNA in the soil. Those together with some previously published articles on the matter and countless conversations with different ecologists all over the world, made us wonder if the high diversity in croplands might not stem from previous land uses. DNA from dormant or dead organisms (necromass) might add to the diversity we observed that can skew biodiversity assessments. This is an important aspect that should be considered in future research since there are some methods now available that prevent filtering for the dead biomass (e.g. through the washing of extracellular DNA).
Our study identified factors that should be taken into account when setting up monitoring and conservation schemes. Apart from the potential problems with dead DNA accumulating in the soil, another limitation of our research was likely caused by the volume of soil samples taken. Only very small volumes (0.7g) were considered. Previous studies found that at least 10g of soil should be used when studying ‘larger’ organisms, ranging from mesofauna to macrofauna, including insects, nematodes, and earthworms.
Overall, this study taught me a lot how science works. How important collaboration and exchanges are and feedback from all sides. Not only the own supervisors, colleagues but also the feedback from a person just met a poster session on conferences or over a loud pub screaming over the music. This constant feeding back is what makes science.
Some other colleagues worked on other genes for bacteria (16S gene) and fungi (ITS gene) that were sampled for the same sites, 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 assessments so the awareness of the importance of the biodiversity of our soils is luckily raising. What we need in a next step is to translate this knowledge into soil biodiversity indicators for different ecosystems and climatic zones. Currently, there are no target values included in European soil or agricultural legislations which makes it hard to monitor and detect changes of soil biodiversity that could be reacted upon. Knowing a kind of baseline allows in a next step to see variation and thus to detect alarming changes and to respond appropriately.
