Beyond the limits of scale: a novel pipeline for the measurement of soil arthropod biodiversity

MARIE SKŁODOWSKA-CURIE ACTIONS (Individual Fellowships-IF-Call: H2020-MSCA-IF-2015


Knowledge of the magnitude, distribution and structure of biological communities is essential for our understanding of ecosystem processes and their response to impacts, and is thus critical for the development of effective management strategies. Soil fauna, composed of abundant minute and wingless species characterised by generalised low dispersal capacity and strict niche requirements, are a functionally important but vulnerable component of biodiversity. Despite the known importance of soil biodiversity, our knowledge is extremely poor, and at the community level almost non-existent. Soil biodiversity is considered one of the last ‘biotic frontiers’ together with rainforest canopy biodiversity, and the biodiversity of deep seas. Three of the most abundant and diverse groups of arthropods in the soil – beetles, springtails and mites, are essential for functional soil processes, such as the decomposition and mineralisation of organic matter and nutrient cycling. To preserve and maintain fundamental soil ecosystem processes, it is essential to first understand the vulnerability of soil communities under ongoing global change, something that first requires the characterisation of community composition and structure.

Logistical difficulties for the identification and quantification of soil arthropods from a single standard soil sample arise from the very high numbers of individuals (up to 100,000 per m2 of soil), and the typically cryptic nature of species boundaries. However, recent technical advances provide a tool to bridge this knowledge gap. In recent years high throughput DNA sequencing (HTS) has been harnessed to quantify the microbial diversity of ecosystems and is now revolutionizing the study of complex and hyperdiverse macroscopic communities. Now, for the first time, we can obtain quantitative measures of the mesofaunal biodiversity of soil, and its spatial structure and functional dimension, through the application of tailored ‘metabarcoding’ and ‘mitochondrial metagenomics’ protocols. SOILBIODIV applied these novel HTS techniques to develop new molecular protocols within a multidisciplinary project for the characterization of soil arthropod communities (beetles, springtails and mites) in an insular setting of the Canary Islands.

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The main objectives of SOILBIODIV were (1) Develop and validate an interdisciplinary metabarcoding and mitochondrial metagenomics pipeline for robust measures of invertebrate soil biodiversity, applicable across all spatial scales; and (2) characterize soil arthropod mesofauna richness, community structure and turnover within and among ecosystems and islands, identify introduced species and associated biodiversity risks.

Data generated within SOILBIODIV allows for the estimation of community responses and vulnerability of soil invertebrate biodiversity to (i) climate change and (ii) invasive species, two important drivers of global change. In the 7.5 months of the project life we have gained important knowledge that fulfills the objectives of SOILBIODIV.

-We have analysed more than 300 mitogenomes of Coleoptera, Collembola and Acari, where it is particularly worth highlighting the latter group. We have duplicated the available number of mitogenomes for mites species (from 69 to about 150), providing approximately 50 complete mitogenomes for the highly diverse order Oribatida where only one was available before SOILBIODIV.

-We have collected 120 soil samples in the Tenerife and La Palma islands covering the main terrestrial zonal ecosystems: (1) xerophilous scrub (“Tabaibal”), (2) thermophilous forest, (3) wet forest (“Laurisilva”), (4) pine forest and. Each sample includes (i) all leaf litter and humus layer for 1 m2 surface area and (ii) 20 litres of soil from cores of up 40 cm in depth. Samples have been processed following the Flotation-Berlese-Flotation method (Arribas et al. 2016). These samples are now being sequenced to produce metabarcode data in order to characterise soil mesofaunal communities.

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Figure 2. Laurisilva forest in the Anaga region and associated mesofaunal community collected with the Flotation-Berlese-Flotation method (Arribas et al. 2016).

The mitogenome data, together with the metabarcodes generated from samples collected in the Canary Islands, and the knowledge gained about the distribution of soil fauna related to the main natural habitats in the Canaries (laurisilva forest, pine forest, tabaibal and thermophilic vegetation) has established the background needed to conduct further studies on soil biodiversity. These include the characterization of environmental risk due to invasive species and global change, and the integrative study of soil communities and its effects on the main crops of the Canary Islands. These objectives that were beyond the termination date of the project SOILBIODIV will now be developed within the Spanish government funded fellowship that CA has been awarded