Bacterial members of the rhizosphere microbiota of Quercus ilex subsp. ballota

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Gómez Aparicio L, Zamora Ballesteros C, Gil Martinez M, García Garrido S (2023). Bacterial members of the rhizosphere microbiota of Quercus ilex subsp. ballota. Version 2.0. Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC). Samplingevent dataset. https://doi.org/10.15470/e6gnqd

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC). Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

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Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 0f162245-914b-4726-91d5-c11d3f556eba.  Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC) publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du GBIF Spain.

Mots-clé

Samplingevent; Biodiversity; Edafic Biodiversity

Contacts

Couverture géographique

Huelva (Spain), Sevilla (Spain) and Córdoba (Spain)

Données sur le projet

The general objective of thE WP7 is to advance our understanding of the impacts of global change drivers - mainly climate change and exotic pathogens - on the above- and below-ground biodiversity of Mediterranean forests and silvopastoral agrosystems, and to use the resulting information to propose management tools aim to improve the resistance and resilience of these forests in scenarios of increasing abiotic and biotic stress.

Les personnes impliquées dans le projet:

Méthodes d'échantillonnage

The Illumina paired-end raw sequences were processed using the freely available bioinformatics software QIIME 2 version 2022.2.0 (Bolyen et al., 2019). The sequences from each target (bacteria, fungi or Phytophthora spp.) and each sequencing run were processed equally but separately throughout the analysis. The sequences were trimmed by implementing cutadapt (Martin, 2011) in QIIME 2 with q2-cutadapt plugin and trim-paired command. Chimeric sequences were identified and deleted after quality filtering and de-noising using the Divisive Amplicon Denoising Algorithm 2 (DADA2) pipeline implemented in QIIME 2 with q2-dada2 plugin and denoise-paired command (Callahan et al., 2016). The resulting amplicon sequence variants (ASVs) identified were curated using mumu by removing taxonomically redundant and erroneous ASVs. This involved constructing a database of the ASV sequences using makeblastdb application from the BLAST v.2.9.0 software suite, from which match lists were created using the blastn algorithm (query coverage: 80; percent identity cutoff: 84). These match lists and the ASV feature tables were input into the mumu algorithm to produce curated ASV tables. Singletons were excluded from the analysis.

Description des étapes de la méthode:

1. The taxonomic assignment to the ASVs identified in the analysis of Phytohthora species was performed by generating a reference database from a combination of sequences from five different sources: the UNITE dynamic database v.8.3 (consisting of 58,440 eukaryotic sequences), reference sequences from phytophthoradb (http://www.phytophthoradb.org/; 340 sequences), reference sequences from Phytopthora-id (http://Phytophthora-id.org; 270 sequences), 174 sequences of Phytophthora spp. from the database generated in Riddell et al. (2019), and 39,701 sequences from Genbank matching the search "oomycota 'internal transcribed spacer'". In the latter case, the taxonomy for the Genbank accessions was obtained using the taxonomizr package (v 0.10.2) in R v 4.2.2. Finally, the reference sequence database, namely the combined fasta file (98,925 sequences), and the associated taxonomy description file were imported into QIIME 2 and used together with the qiime feature-classifier plugin and the classify-consensus-blast command. As a first step, the sequences of the potential Phytophthora ASVs were aligned against the custom reference database using strict homology parameters (query coverage: 90; percent identity cutoff: 99) to ensure that successful matches belong to a Phytophthora species. The unaligned ASVs were submitted to a second step with relaxed parameters (query coverage: 75; percent identity cutoff: 65). The third step consisted of comparing the unassigned ASVs from the second step to the entire NCBI non-redundant protein database (release-255) using default parameters. In the fourth step, the low confidence ASVs assigned in the second and third steps were concatenated, aligned with MAFFT, and used to construct a maximum likelihood (ML) phylogenetic tree using RAxML (v 8.2.12; Stamatakis, 2014). The tree was inferred employed a general time reversible substitution model with a computational work–around (GTRCAT) without rate heterogeneity with a correction for ascertainment bias. Statistical support was calculated by applying bootstrap runs in an automated approach (autoMRE), where RaxML executes a maximum of 1000 BS replicate searches, although convergence may occur earlier. The best-scoring ML tree of the search analysis was then visualized using the software FIGTREE version 1.4.4 (Rambaut, 2018).

Citations bibliographiques

1. Abarenkov, K., Zirk, A., Piirmann, T., Pöhönen, R., Ivanov, F., Nilsson, R.H., Kõljalg, U., 2021. UNITE QIIME release for Fungi. Version 10.05.2021. [WWW Document]. UNITE Community. URL https://doi.plutof.ut.ee/doi/10.15156/BIO/1264708 (accessed 1.17.23)
2. Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C.C., Al-Ghalith, G.A., Alexander, H., Alm, E.J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J.E., Bittinger, K., Brejnrod, A., Brislawn, C.J., Brown, C.T., Callahan, B.J., Caraballo-Rodríguez, A.M., Chase, J., Cope, E.K., Da Silva, R., Diener, C., Dorrestein, P.C., Douglas, G.M., Durall, D.M., Duvallet, C., Edwardson, C.F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J.M., Gibbons, S.M., Gibson, D.L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G.A., Janssen, S., Jarmusch, A.K., Jiang, L., Kaehler, B.D., Kang, K.B., Keefe, C.R., Keim, P., Kelley, S.T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M.G.I., Lee, J., Ley, R., Liu, Y.-X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B.D., McDonald, D., McIver, L.J., Melnik, A.V., Metcalf, J.L., Morgan, S.C., Morton, J.T., Naimey, A.T., Navas-Molina, J.A., Nothias, L.F., Orchanian, S.B., Pearson, T., Peoples, S.L., Petras, D., Preuss, M.L., Pruesse, E., Rasmussen, L.B., Rivers, A., Robeson, M.S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S.J., Spear, J.R., Swafford, A.D., Thompson, L.R., Torres, P.J., Trinh, P., Tripathi, A., Turnbaugh, P.J., Ul-Hasan, S., van der Hooft, J.J.J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K.C., Williamson, C.H.D., Willis, A.D., Xu, Z.Z., Zaneveld, J.R., Zhang, Y., Zhu, Q., Knight, R., Caporaso, J.G., 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37, 852–857. https://doi.org/10.1038/s41587-019-0209-9
3. Callahan, B.J., McMurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A., Holmes, S.P., 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581–583. https://doi.org/10.1038/nmeth.3869
4. Martin, M., 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12. https://doi.org/10.14806/ej.17.1.200
5. Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., Glöckner, F.O., 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41, D590–D596. https://doi.org/10.1093/nar/gks1219
6. Rambaut, A., 2018. FigTree.
7. Riddell, C.E., Frederickson-Matika, D., Armstrong, A.C., Elliot, M., Forster, J., Hedley, P.E., Morris, J., Thorpe, P., Cooke, D.E.L., Pritchard, L., Sharp, P.M., Green, S., 2019. Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. In soils at public gardens and amenity woodlands in Britain. PeerJ 7, e6931. https://doi.org/10.7717/PEERJ.6931/SUPP-3
8. Stamatakis, A., 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313. https://doi.org/10.1093/bioinformatics/btu033

Métadonnées additionnelles