Description
Bacterial and fungal ASVs (Amplicon Sequence Variant) that inhabit the rhizosphere soil and root endosphere of Pinus sylvestris trees affected by forest decline and asymptomatic individuals. Trees are located in the National Park of Sierra Nevada, Natural Park of Sierra de Baza, and Natural Park of Sierras de Almijara, Tejeda y Alhama (Granada, Southeast Spain). Furthermore, the physico-chemical properties of the soil close to the roots of each tree are included.
Data Records
The data in this sampling event resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 192 records.
2 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.
This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.
Versions
The table below shows only published versions of the resource that are publicly accessible.
How to cite
Researchers should cite this work as follows:
Lasa A V, Pérez-Luque A J, Fernández López M (2024). Root-associated microbiota of decline-affected and asymptomatic Pinus sylvestris trees. Version 2.0. Estación Experimental del Zaidín (CSIC). Samplingevent dataset. https://doi.org/10.15470/dardca
Rights
Researchers should respect the following rights statement:
The publisher and rights holder of this work is Estación Experimental del Zaidín (CSIC). This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY-NC 4.0) License.
GBIF Registration
This resource has been registered with GBIF, and assigned the following GBIF UUID: 1826d3c2-9e33-43e8-afaa-450b7d6e2b9b. Estación Experimental del Zaidín (CSIC) publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF Spain.
Keywords
Samplingevent; Pinus sylvestris; drought; bacteria; fungi; genotype; bacterial ecology
Contacts
- Originator ●
- User ●
- Point Of Contact
- Postdoctoral Researcher
- Profesor Albareda 1
https://orcid.org/0000-0003-3783-7157
- Originator ●
- Point Of Contact
- Postdoctoral Researcher
- Ctra. de la Coruña, 7.5
- Originator ●
- Point Of Contact
- Tenured Scientist
- Profesor Albareda 1
Geographic Coverage
Three mountainous protected areas in Andalusia (southeast Spain): Sierras de Tejeda, Almijara y Alhama; Sierra de Baza, and Sierra Nevada. Several Pinus sylvestris stands (asymptomatic and decline affected pines) were selected.
| Bounding Coordinates | South West [36.875, -3.924], North East [37.287, -2.706] |
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Taxonomic Coverage
All bacterial and fungal ASV were classified at Kingdom, Phylum, Class, Order, Family and Genus level where possible.
Temporal Coverage
| Start Date / End Date | 2022-04-20 / 2022-05-11 |
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Project Data
The project SUMHAL aims at implementing a strategy for biodiversity conservation in the Mediterranean area by setting a technologically efficient and scientifically robust system. The project combines fieldwork and virtual research environments for the recording, storing, analysis, and dissemination of the conservation status and threats of biodiversity in Andalusia (Southern Spain)
| Title | Sustainability for Mediterranean Hotspots in Andalusia integrating LifeWatch ERIC (SUMHAL). Working package 7: Improving sustainability of Mediterranean forests and silvopastoral agrosystems under climate change |
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| Identifier | LIFEWATCH-2019-09-CSIC-4, POPE 2014-2020 |
| Funding | This study was funded by MICINN through European Regional Development Fund [SUMHAL, LIFEWATCH-2019-09-CSIC-4, POPE 2014-2020] and by the Spanish Ministry of Economy, Industry and Competitiveness [AGL2015-66048-C2-1-R; RTI2018-098015-B-I00]. To be referred from 2023 onwards as SUMHAL, LIFEWATCH-2019-09-CSIC-4, POPE 2014-2020. |
| Study Area Description | Three mountainous areas were studied in this work, where Pinus sylvestris stands were located, in Andalusia (Spain). Sierra Nevada, where Pinus sylvestris stands affected by forest decline were located (Collado del Pino, Solana de Benabre, municipal district of Lanteira, 1949 meters above sea level) and also non-affected forest (Puerto de la Ragua, municipal district of Aldeire, 1852 meters above sea level). Sierra de Alhama, Tejeda y Almijara, were just asymptomatic individuals were found (municipal district of Alhama de Granada, 1545 meters above sea level), and Sierra de Baza, where just decline-affected P. sylvestris trees were found (municipal district of Caniles, 1587 meters above sea level) |
| Design Description | Our main goal was to gain more insights into the diversity, structure and taxonomic composition of the microbiota (fungi and bacteria) associated to the roots of decline-affected and asymptomatic Pinus sylvestris trees in three different mountainous areas of Andalusia, Spain. We hypothesized that the structure and taxonomical profiles of root-associated microbiota depended on the status of the trees. |
Sampling Methods
In each experimental area, rhizosphere soil samples and young roots were collected from the same tree, and processed in parallel as described below. Thus, after sample processing, for each of the 12 replicates rhizosphere and root endosphere microbial communities came from the same tree, obtaining 96 bacterial and 96 fungal samples (12 x ASH, 12 x BSD, 12 x NSH, 12 x NSD x 2 plant compartments). After the sequencing data processing, four samples were removed from the analysis due to the low quality of the sequencing reads or due to the inadequate number of quality reads.
| Study Extent | Three mountainous regions were selected for sample collection: Sierra de Almijara, Sierra Nevada and Sierra the Baza, all of them located in Granada (Andalusia, southeast Spain). In Sierra de Almijara, 12 unaffected P. sylvestris trees were chosen and marked (ASH01-12), while just decline-affected Scots pines were found in Sierra de Baza, and 12 individuals were also selected (BSD01-12). In contrast, 12 asymptomatic and 12 affected P. sylvestris trees were considered for the analyses in Sierra Nevada, which were named NSH and NSD, respectively. Those trees showing stunted growth, yellowing of the crown and/or defoliation were classified as symptomatic. All the samplings were performed in spring of 2022. |
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Method step description:
- At a distance of less than 50 cm from the trunk of the trees, the topsoil (25-50 cm) was removed by digging. Then, the main roots of the selected tree were followed until young poorly suberized roots were found. The soil closely adhered to these roots was collected by rubbing them manually (rhizosphere soil samples). Furthermore, the roots were also collected and kept at 4ºC along with rhizosphere samples until they were processed in the laboratory. It should be marked that two samples of rhizosphere soil and roots were taken from two different parts of the same root system of each tree (2 x 48 trees). Roots were surface esterilized as described Lasa and co-workers (2024; https://doi.org/10.1016/j.scitotenv.2024.171858). Then, total DNA from rhizosphere soil and sterilized roots was extracted by using the DNeasy® PowerSoil® Pro and DNeasy® Plant Pro Kits (Qiagen; Hilden, Germany), respectively, following the manufacturer's instructions.The hypervariable regions V3-V4 of the bacterial 16 rRNA gene and the fungal ITS2 were sequenced following a 2 × 275 PE strategy at the genomics service of the Institute of Parasitology and Biomedicine López-Neyra (CSIC; Granada, Spain). Sequencing reads were processed in R by using the packages and functions, and the methods described in Lasa et al., (2024). Lasa, A.V., et al. (2024) Mediterranean pine forest decline: A matter of root-associated microbiota and climate change. Science of the Total Environment 926, 171858. https://doi.org/10.1016/j.scitotenv.2024.171858
Bibliographic Citations
- Lasa, A.V.; Fernández-González, A.J.; Villadas, P.J.; Mercado-Blanco, J.; Pérez-Luque, A.J.; Fernández-López, M. Mediterranean pine forest decline: a matter of root-associated microbiota and climate change. Science of The Total Environment 926: 171858 https://doi.org/10.1016/j.scitotenv.2024.171858
Additional Metadata
| Alternative Identifiers | 10.15470/dardca |
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| https://ipt.gbif.es/resource?r=psylvestris_microbiota |