Soil arthropod mesofauna takes the stage: Advances from whole-community haplotype-level metabarcoding
dr. paula arribas
Island Ecology and Evolution Group, IPNA-CSIC, Spain
dr. carmelo andújar
Island Ecology and Evolution Group, IPNA-CSIC, Spain
Our understanding of the spatial structure and the underlying processes of community assembly of soil biodiversity have increased dramatically in the last years. However, this knowledge is still strongly unbalanced across taxonomic groups, a situation which hampers the development of an integrative framework for soil biodiversity. In particular, there is a pronounced shortage for soil arthropods, in part because the implementation of high-throughput sequencing to this soil biodiversity fraction has seen comparative little and delayed progress in adapting and exploiting these tools.
Figure 1. Flotation–Berlese–flotation (FBF) protocol for the extraction of soil arthropod mesofauna and subsequent molecular and bioinformatic steps for the multi hierarchical study of community assembly (Arribas et al., 2020).
New approaches using whole-community metabarcoding with the mitochondrial COI gene are now speeding up the exploration of the diversity, distribution and community assembly of this soil fauna. The flotation–Berlese–flotation protocol (FBF, Figure 1 A, B) for example, takes advance of the soil flotation method (homologous to elutriation of nematodes), that has been traditionally used by entomologists for the isolation of endogean specimens from large volumes of soil. This approach allows drastically increasing sample size respect to direct Berlese extraction, but also respect to the few grams of soil usually used for soil DNA extraction. Concerning the second, the FBF protocol also has the advantage to substantially reduce the bacterial component in the DNA extractions, which has traditionally impeded the use of the standard COI animal barcode fragment for the metabarcoding of soil fauna. The use of the COI metabarcoding has multiple advantages for characterising animal assemblages, including the availability of larger reference databases and the potential to approximate community profiles at the species but also intraspecific levels of genetic diversity.
Figure 2. Bulk arthropod sample obtained by the implementation of the FBF protocol to a soil sample from a Quercus forest (northern France).
In our last study, we take profit of all the recent advances in the COI metabarcoding of soil arthropods to generate comparative data of whole communities at three hierarchical levels: genetic, species and supra-specific lineages. This multi hierarchical framework (Figure 1 C-E) applied to entire assemblages of mites, springtails and beetles from three geographically distinct mountain regions in southern Europe allows exploring the spatial scale at which dispersal constraints are effective in determining species distributions and community assembly, a still open question in soil biodiversity research. High levels of spatial structure, distance decay and endemicity were found within habitat patches at the scale of a few kilometres. Local spatial patterns were self-similar for the haplotypes and higher hierarchical entities, and this fractal structure was similar in all regions, suggesting that uniform processes of limited dispersal determine local-scale community assembly. Our results from whole-community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. And if generalised across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod diversity and reinforcing the importance to catalogue this fraction of soil biodiversity on Earth.
Publication: Arribas P, Andújar C, Salces-Castellano A, Emerson BC, Vogler AP (2020) The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding. Molecular Ecology (in press). https://doi.org/10.1111/mec.15591