DOI: 10.20350/digitalcsic/15101
title: Morfospecies and zOTUs interacting with each host plant from the PERDIVER project

description: [Description of methods used for collection/generation of data] For Morphospecies_abundance.csv: Aerial sampling, Berlese sampling, cafeteria experiments, vacuuming sampling, shake sampling. For zOTU_Abundance.csv: DNA extraction was carried out with 0.05-0.1 grams of root material using a Mobio PowerSoil DNA Isolation Kit (Mobio Laboratories). PCR and sequencing of the 16 rRNA gene was done with Illumina MiSeq (NGS) following the methods from the central genomic services of RTSF-MSU (Michigan State University, USA) (https://rtsf.natsci.msu.edu/). We analyzed the V4 variable region of the 16S rRNA gene (250 nucleotides) using primers F515 (5'-GTGCCAGCMGCCGCGGTAA-3') and R806 (5'-GGACTACHVGGGTWTCTAAT-3'). Raw rRNA gene sequences were processed using the UPARSE pipeline (Edgar, 2013) to identify zOTUS (zero-radius operational taxonomic units). Taxonomic assignment used the naive Bayes scikit-learn classifier implemented in QIIME2 (Caporaso et al., 2010) and the SILVA 132 database (Quast et al., 2012). Chloroplast, mitochondrial, and unclassified sequences were excluded from further analyses. For PERDIVER_Alpha_diversity.csv: Multiple diversity metrics using R. For each community associated with each plant species: Species richnes, Shannon and Simpson diversity indices and standard effect size of the phylogenetic mean pairwise distance between species in the community (mpd.obs.z). Above ground phylogenetic distances come from Chesters, D. (2020), The phylogeny of insects in the data-driven era. Syst Entomol, 45: 540-551. Belowground distances from QIIME2 (Caporaso, J., Kuczynski, J., Stombaugh, J. et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335–336 (2010).) and the SILVA 128 reference database (Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012). The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Research, 41(D1), D590–D596.)
description: Data from the PERDIVER and INTERACTOMA projects. The goal of the projects was to characterize the communities of species that interact with seven rare or endangered plants in Aragón and if those communities changed between isolated and non-isolated plant populations. The aboveground was surveyed in 2016, 2017, and 2018 during the flowering season of the host plant. All individual animals, visiting any part of flowering and non-flowering plants over an area covered visually by the observer were either visually identified or sampled, if needed to confirm identification. All animals trapped by the sticky leaves of pinlon were also identified. Sampling area and length of surveys varied among plant species, depending on size of plants and frequency of interactions, but ≥ 20 surveys were performed at each site, resulting in a total of &gt; 9,000 minutes and 638 surveys. Sampling investment varied among plant species, because they differed in interaction detectability. However, sampling effort was always similar among patches of the same plant species. Other methods like Berlese funnnel traps, fruit sampling or cafeteria experiments were used to unveil interactions that are not easily visible, like those by small or camouflaged animals. Below ground microbial communities were characterized for each plant population with three samples composed of root material from different individuals.
description: Morphospecies_abundance.csv zOTU_Abundance.csv PERDIVER_Alpha_diversity.csv