Descripción
Since Linnaeus's time, the Kungsängen Nature Reserve has drawn frequent visitors because of its vegetation including the largest population of Fritillaria meleagris L. in Sweden. The reserve is a meadow with an abrupt moisture transition, where the wetter part has a Carex acuta dominated plant community with low species richness, visually distinct from the drier part, which has a species rich plant community including a high density of Fritillaria meleagris. To investigate the link between plant and below-ground micro-eukaryotic communities, we amplified and sequenced the ITS and LSU regions of the rDNA operon (1500 bp) from soil using PacBio SMRT sequencing, and evaluated three different methods for generation of operational taxonomic units. We found distinct communities associated with wet and mesic-dry soil conditions but estimated richness was not so different. Both soil conditions host communities dominated by protists, a large fraction of which were taxonomically assigned to Ciliphora (Alveolata), while 30-40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of the read clustering method used. However, different clustering methods affect the taxonomic and phylogenetic resolution of community characterization with implications for how well members of the micro-eukaryotic communities can be recognized in the data. This data resource contain amplicon sequence variant (ASV) sequences generated with DADA2 using the Ampliseq pipeline (https://nf-co.re/ampliseq). This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/).
Registros
Los datos en este recurso de registros biológicos han sido publicados como Archivo Darwin Core(DwC-A), el cual es un formato estándar para compartir datos de biodiversidad como un conjunto de una o más tablas de datos. La tabla de datos del core contiene 1.117 registros.
también existen 2 tablas de datos de extensiones. Un registro en una extensión provee información adicional sobre un registro en el core. El número de registros en cada tabla de datos de la extensión se ilustra a continuación.
Este IPT archiva los datos y, por lo tanto, sirve como repositorio de datos. Los datos y los metadatos del recurso están disponibles para su descarga en la sección descargas. La tabla versiones enumera otras versiones del recurso que se han puesto a disposición del público y permite seguir los cambios realizados en el recurso a lo largo del tiempo.
Versiones
La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.
¿Cómo referenciar?
Los usuarios deben citar este trabajo de la siguiente manera:
Rosling A, Eshghi Sahraei S, Furneaux B, Kluting K, Zakieh M (2024). Kungsängen soil microbial communities. Version 1.7. Biology Section, Uppsala University. Occurrence dataset. https://www.gbif.se/ipt/resource?r=pb363_kungsangen_otu_a&v=1.7
Derechos
Los usuarios deben respetar los siguientes derechos de uso:
El publicador y propietario de los derechos de este trabajo es Biology Section, Uppsala University. En la medida de lo posible según la ley, el publicador ha renunciado a todos los derechos sobre estos datos y los ha dedicado al Dominio público (CC0 1.0). Los usuarios pueden copiar, modificar, distribuir y utilizar la obra, incluso con fines comerciales, sin restricciones.
Registro GBIF
Este recurso ha sido registrado en GBIF con el siguiente UUID: d850eb3d-d7e2-48f9-b6c1-cf1136a50bbb. Biology Section, Uppsala University publica este recurso y está registrado en GBIF como un publicador de datos avalado por GBIF Sweden.
Palabras clave
Occurrence
Contactos
- Proveedor De Los Metadatos ●
- Originador ●
- Punto De Contacto
- Associate Professor
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- +46184716444
http://orcid.org/0000-0002-7003-5941
- Proveedor De Los Metadatos
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- Originador
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- Originador
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- Originador
- Associate Professor
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- Proveedor De Los Metadatos
- Associate Professor
- Evolutionsbiologiskt centrum, Norbyvägen 18D
Cobertura geográfica
Kungsängen Nature Reserve (N59°50’, E17°40’) is a 12.5-hectare reserve in a larger meadow located in the south of Uppsala, Sweden, along the east shore of the Fyris River. Soil samples were taken across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic-dry part that has a species rich grass-dominated plant community including a high frequency of F. meleagris.
| Coordenadas límite | Latitud Mínima Longitud Mínima [59,836, 17,661], Latitud Máxima Longitud Máxima [59,837, 17,663] |
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Cobertura temporal
| Fecha Inicial | 2016-06-07 |
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Datos del proyecto
No hay descripción disponible
| Título | Kungsängen soil microbial communities |
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Personas asociadas al proyecto:
- Investigador Principal
Métodos de muestreo
Soil samples were taken with a soil corer when possible (5cm diameter x 10 cm depth), or with a hand shovel when soil was to wet (sampling depth and volume estimated to correspond to that of the soil cores). Soil samples were individually placed in plastic bags and kept on ice during sampling before storage at 4degC over night. The day after, soils were homogenized in the plastic bags and subsamples were transferred to 15ml conical centrifuge tubes and frozen at -20degC prior to freeze drying. Approximately 250 to 500 mg of freeze-dried soil was used for total DNA extraction. The entire ITS and partial LSU regions of rDNA, approximately 1500 bp, was amplified using a modified ITS1 primer and the LR5 primer. Both primers were indexed for multiplexing to allow pooling of the samples during sequencing. The pooled library was sequenced at SciLifeLab/NGI (Uppsala, Sweden) on the PacBio RSII sequencing platform.
| Área de Estudio | Soil samples were collected on June 7th, 2016, at Kungsängen Nature Reserve (N59°50’, E17°40’). Samples were taken from five locations 30 m apart on each side of the soil moisture transition border separated by 30 m across the transition border. |
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Descripción de la metodología paso a paso:
- Sequence denoising and ASV creation was performed with DADA2 using the nfcore/ampliseq pipeline (https://nf-co.re/ampliseq), commit 5adaf23d7f. Taxonomy assignment was based on the ITS2 region and performed according to https://docs.biodiversitydata.se/analyse-data/molecular-tools/#taxonomy-annotation, using nf-core/ampliseq commit e1bdbfb623 and the database unite-alleuk=8.3 (UNITE general FASTA release for Eukaryotes - Version 8.3, https://doi.org/10.15156/BIO/1280127)
Metadatos adicionales
| Identificadores alternativos | d850eb3d-d7e2-48f9-b6c1-cf1136a50bbb |
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| https://www.gbif.se/ipt/resource?r=pb363_kungsangen_otu_a |