Periodic Reporting for period 1 - SOILBIODIV (Beyond the limits of scale: a novel pipeline for the measurement of soil arthropod biodiversity)
Periodo di rendicontazione: 2016-07-01 al 2018-06-30
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.
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. Resources and results generated in SOILBIODIV will be very relevant for (i) the European Initiative BEST (Biodiversity and Ecosystem Services in Territories), (ii) the new International Platform IPBE (Intergovernmental Platform on Biodiversity & Ecosystem Services), (iii) the Strategic Objective C of the Strategic Plan for the Biological Diversity 2011-2020 (Aichi Targets www.cbd.int) and for (iv) the quantification and control of biodiversity loss under climate change on Special Territories of the European Union (ORs and OCTs) as highlighted by the recent International Conference on Biodiversity and Climate Change (October 2014, see www.cbd.int).
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.
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. Resources and results generated in SOILBIODIV will be very relevant for (i) the European Initiative BEST (Biodiversity and Ecosystem Services in Territories), (ii) the new International Platform IPBE (Intergovernmental Platform on Biodiversity & Ecosystem Services), (iii) the Strategic Objective C of the Strategic Plan for the Biological Diversity 2011-2020 (Aichi Targets www.cbd.int) and for (iv) the quantification and control of biodiversity loss under climate change on Special Territories of the European Union (ORs and OCTs) as highlighted by the recent International Conference on Biodiversity and Climate Change (October 2014, see www.cbd.int).
We have achieved all the objectives planned for the period of 7.5 months covered by the final report. These include the phase of data acquisition and the initial work on the preparation of manuscripts for publications. The new position of CA (Spanish government funded research fellowship) within the host institute (IPNA-CSIC) ensure that the obtained data and results will be fully exploited in the context of the aims of SOILBIODIV and publications achieved. We have achieved the three milestones planned for the first 9 months of the project.
WP1.1. Sampling: Preparation of Berlesse Lab (equipped with a battery of Berlesse apparatus), collecting soil samples in Tenerife, and soil fauna extraction and preservation. Months 1-3. Sampling in La Palma in month 6. Specimen sorting: Sample processing and fauna classification. Months-2-4 and 6. (Milestones WP1.1 " Finishing sampling and specimen sorting" achieved)
WP1.2. Generation of reference mitogenomes: Assemble and annotation of complete mitochondrial genomes for Coleoptera, Acari and Collembola (300 mitogenomes) and generation of reference phylogenetic tree. Months 4-7. (Milestones WP1.1 "Mitochondrial genomes and trees generated" achieved)
WP1.3. Metabarcode sequencing: Molecular lab work for the metabarcode sequencing of 96 samples in the IlluminaMiSeqplatform. Month 7. (Milestones WP1.3. "Metabarcode sequences generated" Achieved after the early grant termination (month 7.5) as planned to be finished in month 9).
Together these results will be part of a minimum of two publications in top scientific journals. The first paper is in an advanced phase of writing, and deals with the phylogenetic tree of soil mites based on the more than 100 mitogenomes generated (where a single one was previously available for the main group of soil mites, Oribatida). The second paper will be based on the generated metabarcodes, where we are currently in the analytical phase. Note that the early termination was due to the 3-year research position gained by CA that is associated with a new project to study soil biodiversity that will build up on the SOILBIODIV project.
WP1.1. Sampling: Preparation of Berlesse Lab (equipped with a battery of Berlesse apparatus), collecting soil samples in Tenerife, and soil fauna extraction and preservation. Months 1-3. Sampling in La Palma in month 6. Specimen sorting: Sample processing and fauna classification. Months-2-4 and 6. (Milestones WP1.1 " Finishing sampling and specimen sorting" achieved)
WP1.2. Generation of reference mitogenomes: Assemble and annotation of complete mitochondrial genomes for Coleoptera, Acari and Collembola (300 mitogenomes) and generation of reference phylogenetic tree. Months 4-7. (Milestones WP1.1 "Mitochondrial genomes and trees generated" achieved)
WP1.3. Metabarcode sequencing: Molecular lab work for the metabarcode sequencing of 96 samples in the IlluminaMiSeqplatform. Month 7. (Milestones WP1.3. "Metabarcode sequences generated" Achieved after the early grant termination (month 7.5) as planned to be finished in month 9).
Together these results will be part of a minimum of two publications in top scientific journals. The first paper is in an advanced phase of writing, and deals with the phylogenetic tree of soil mites based on the more than 100 mitogenomes generated (where a single one was previously available for the main group of soil mites, Oribatida). The second paper will be based on the generated metabarcodes, where we are currently in the analytical phase. Note that the early termination was due to the 3-year research position gained by CA that is associated with a new project to study soil biodiversity that will build up on the SOILBIODIV project.
In the 7.5 months of the project life, prior to its termination, we have gained important knowledge that fulfills the objectives of SOILBIODIV for that period. 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. 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.