Описание
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/).
Записи данных
Данные этого occurrence ресурса были опубликованы в виде Darwin Core Archive (DwC-A), который является стандартным форматом для обмена данными о биоразнообразии в виде набора из одной или нескольких таблиц. Основная таблица данных содержит 1 117 записей.
Также в наличии 2 таблиц с данными расширений. Записи расширений содержат дополнительную информацию об основной записи. Число записей в каждой таблице данных расширения показано ниже.
Данный экземпляр IPT архивирует данные и таким образом служит хранилищем данных. Данные и метаданные ресурсов доступны для скачивания в разделе Загрузки. В таблице версий перечислены другие версии ресурса, которые были доступны публично, что позволяет отслеживать изменения, внесенные в ресурс с течением времени.
Версии
В таблице ниже указаны только опубликованные версии ресурса, которые доступны для свободного скачивания.
Как оформить ссылку
Исследователи должны дать ссылку на эту работу следующим образом:
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
Права
Исследователи должны соблюдать следующие права:
Публикующей организацией и владельцем прав на данную работу является Biology Section, Uppsala University. Насколько это возможно по закону, издатель отказался от всех прав на эти данные и посвятил их Public Domain (CC0 1.0). Пользователи могут без ограничений копировать, изменять, распространять и использовать работу, в том числе в коммерческих целях.
Регистрация в GBIF
Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: d850eb3d-d7e2-48f9-b6c1-cf1136a50bbb. Biology Section, Uppsala University отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке GBIF Sweden.
Ключевые слова
Occurrence
Контакты
- Metadata Provider ●
- Originator ●
- Point Of Contact
- Associate Professor
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- +46184716444
http://orcid.org/0000-0002-7003-5941
- Metadata Provider
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- Originator
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- Originator
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- Originator
- Associate Professor
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- Metadata Provider
- Associate Professor
- Evolutionsbiologiskt centrum, Norbyvägen 18D
Географический охват
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.
| Ограничивающие координаты | Юг Запад [59,836, 17,661], Север Восток [59,837, 17,663] |
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Временной охват
| Дата начала | 2016-06-07 |
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Данные проекта
Описание отсутсвует
| Название | Kungsängen soil microbial communities |
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Исполнители проекта:
- Principal Investigator
Методы сбора
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.
| Охват исследования | 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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Описание этапа методики:
- 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)
Дополнительные метаданные
| Альтернативные идентификаторы | d850eb3d-d7e2-48f9-b6c1-cf1136a50bbb |
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| https://www.gbif.se/ipt/resource?r=pb363_kungsangen_otu_a |