Description
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/).
Enregistrements de données
Les données de cette ressource occurrence ont été publiées sous forme d'une Archive Darwin Core (Darwin Core Archive ou DwC-A), le format standard pour partager des données de biodiversité en tant qu'ensemble d'un ou plusieurs tableurs de données. Le tableur de données du cœur de standard (core) contient 1 117 enregistrements.
2 tableurs de données d'extension existent également. Un enregistrement d'extension fournit des informations supplémentaires sur un enregistrement du cœur de standard (core). Le nombre d'enregistrements dans chaque tableur de données d'extension est illustré ci-dessous.
Cet IPT archive les données et sert donc de dépôt de données. Les données et métadonnées de la ressource sont disponibles pour téléchargement dans la section téléchargements. Le tableau des versions liste les autres versions de chaque ressource rendues disponibles de façon publique et permet de tracer les modifications apportées à la ressource au fil du temps.
Versions
Le tableau ci-dessous n'affiche que les versions publiées de la ressource accessibles publiquement.
Comment citer
Les chercheurs doivent citer cette ressource comme suit:
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
Droits
Les chercheurs doivent respecter la déclaration de droits suivante:
L’éditeur et détenteur des droits de cette ressource est Biology Section, Uppsala University. En vertu de la loi, l'éditeur a abandonné ses droits par rapport à ces données et les a dédié au Domaine Public (CC0 1.0). Les utilisateurs peuvent copier, modifier, distribuer et utiliser ces travaux, incluant des utilisations commerciales, sans aucune restriction.
Enregistrement GBIF
Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : d850eb3d-d7e2-48f9-b6c1-cf1136a50bbb. Biology Section, Uppsala University publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du GBIF Sweden.
Mots-clé
Occurrence
Contacts
- Fournisseur Des Métadonnées ●
- Créateur ●
- Personne De Contact
- Associate Professor
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- +46184716444
http://orcid.org/0000-0002-7003-5941
- Fournisseur Des Métadonnées
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- Créateur
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- Créateur
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- Créateur
- Associate Professor
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- Fournisseur Des Métadonnées
- Associate Professor
- Evolutionsbiologiskt centrum, Norbyvägen 18D
Couverture géographique
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.
| Enveloppe géographique | Sud Ouest [59,836, 17,661], Nord Est [59,837, 17,663] |
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Couverture temporelle
| Date de début | 2016-06-07 |
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Données sur le projet
Pas de description disponible
| Titre | Kungsängen soil microbial communities |
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Les personnes impliquées dans le projet:
- Chercheur Principal
Méthodes d'échantillonnage
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.
| Etendue de l'étude | 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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Description des étapes de la méthode:
- 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)
Métadonnées additionnelles
| Identifiants alternatifs | d850eb3d-d7e2-48f9-b6c1-cf1136a50bbb |
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| https://www.gbif.se/ipt/resource?r=pb363_kungsangen_otu_a |