Does large-scale turnover in soil biodiversity mirror what we see aboveground?
John Davison
Associate Professor, Institute of Ecology and Earth Sciences, University of Tartu, Estonia
Figure 1. Microbial eukaryotic (a) and prokaryotic (b) microbiomes and the temperature (MAT), precipitation (MAP) and pH conditions recorded in each (c - microbial eukaryotic microbiomes; d – prokaryotic microbiomes). Figure reproduced from Vasar et al. (2022).
Plants are foundational primary producers and form the great majority of biomass in terrestrial ecosystems. So, it is not unreasonable that we use vegetation characteristics, along with macro-climatic correlates and a dose of expert opinion, to classify large-scale variation in biodiversity (i.e. biomes). Yet, we know surprisingly little about how well these classifications represent structure in the diversity of different organismal groups. Studying large-scale patterns of biodiversity is always a challenge, but sequencing and identifying environmental DNA (metabarcoding) offers a feasible way to study small, relatively sessile organisms, such as microbes, over large areas.
In our recently study (Vasar et al 2022), we used 345 soil samples and a metabarcoding approach to identify large-scale variation in eukaryotic and prokaryotic soil microbial communities worldwide. We also recorded a number of soil chemical variables in situ in order to understand what drives variation in belowground microbial diversity. Several interesting findings emerged. We found that variation in most organism groups – including bacteria, archaea and different fungal guilds – was best explained by the combination of air temperature and soil pH; with eukaryotic groups responding more to temperature and prokaryotic groups more to pH. Different groups formed patterns of clustering across the globe (microbiomes) that were distinguished to varying degrees by different temperature and pH conditions (Fig 1). The microbiomes, especially the prokaryotic microbiomes, did not closely match the biomes of existing global classifications. For example, in both eukaryotic and prokaryotic classifications, the microbiome occurring in cool, low pH conditions largely coincides with two biome types - tundra and boreal forest; similarly, the biome types tundra and boreal forest each overlap with multiple microbiomes occurring in different soil conditions. A notable characteristic of many microbiomes is that they cut across biome types with fundamentally different vegetation structure. This means that microbiomes can span adjacent grassland, scrub and forest biomes as long as they experience relatively similar temperature and pH conditions.
The results of our study tell us that turnover in the unseen diversity beneath our feet cannot be directly extrapolated from what we see aboveground. Given the tremendous diversity of soil microbes, this suggests that we need to go beyond current global biome classifications to summarise diversity in the biosphere as a whole. Our results also provide information that can be harnessed for applied purposes. For example, at present, studies investigating different ecosystem functions routinely target different biomes; while global ecosystem models rely heavily on plant-based habitat characteristics. Microbiome-level data can inform empirical study design and improve our ability to predict how microbially-mediated ecosystem processes respond to environmental change.
Publication: Vasar, M., Davison, J., Sepp, S.-K., Mucina, L., Oja, J., Al-Quraishy, S., Anslan, S., Bahram, M., Bueno, C. G., Cantero, J. J., Decocq, G., Fraser, L., Hiiesalu, I., Hozzein, W. N., Koorem, K., Meng, Y., Moora, M., Onipchenko, V., Öpik, M., Pärtel, M., Vahter, Y., Zobel, M. (2022). Global soil microbiomes: A new frontline of biome-ecology research. Global Ecology and Biogeography, DOI: https://doi.org/10.1111/geb.13487