Описание
Записи данных
Данные этого событие отбора проб 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 330 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:
Chenuil A, Meglecz E, Bouchereau E, Legrand T, Calvert V, Chemin C, Chenesseau S, Guillemain D, Gutiérrez Ortega J M, Haguenauer A, Leduc M, Marschal F, Marschal C, Mirleau F, Selva M, Vanbostal L, Zuberer F, Mirleau P, Plaisance L, Rossi V, Ruitton S, Dubut V (2026). Separating faces in ARMS metabarcoding improves marine biodiversity monitoring. Version 1.0. OSU Pytheas. Samplingevent dataset. https://ipt.data-terra.org/resource?r=metabarcoding_faces&v=1.0
Права
Исследователи должны соблюдать следующие права:
Публикующей организацией и владельцем прав на данную работу является OSU Pytheas. Эта работа находится под лицензией Creative Commons Attribution (CC-BY 4.0).
Регистрация в GBIF
Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: 17930d18-ba23-4954-95b0-c919b743086d. OSU Pytheas отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке GBIF France.
Ключевые слова
Samplingevent; Occurrence; Observation
Контакты
- Originator ●
- Point Of Contact
https://orcid.org/0000-0001-8141-7147
- Originator ●
- Point Of Contact
- Originator
- Originator
- Originator
- Originator
- Originator
- Originator
Географический охват
Mediterranean Sea - Western Basin http://marineregions.org/mrgid/4279
| Ограничивающие координаты | Юг Запад [42,443, 3,111], Север Восток [43,689, 7,335] |
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Временной охват
| Дата начала / Дата окончания | 2018-03-05 / 2019-04-19 |
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Данные проекта
Spatial structure and connectivity of marine populations for ecosystem management Innovative and standardized monitoring of marine biodiversity Biodiversity protection: a critical planetary challenge
| Название | SEAMOBB - Monitoring protocol for benthic marine biodiversity of rocky habitats |
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Исполнители проекта:
Методы сбора
Autonomous Reef Monitoring Structures (ARMS) were deployed by scuba divers at 12 sites distributed across three regions of the French Mediterranean coast (Figure 1) at depths of 16–22 m (Table 1). Units were immersed between 27 February and 7 April 2017 and retrieved between 5 March and 9 May 2018 (Table 1). Before dismantling and photographic documentation, each ARMS was kept in aerated seawater for 1 h to overnight. To remove vagile fauna, each plate was gently shaken prior to photography. After imaging, the sessile benthos was scraped from each face, preserved in 96 % ethanol, and stored in at +4°C until DNA extraction. Each ARMS consisted of nine superimposed plates (Figure 1), with an upper face (oriented upward) and a lower face (oriented toward the seafloor). In alternating inter-plate spaces, crossbars subdivided the gap into four compartments (see Pearman et al., 2020). Plate faces were designated by plate number and orientation (e.g. 1T, 2B, 2T … 9T, where “T” denotes the upward-facing surface and “B” the downward-facing surface). For subsequent statistical analyses, we grouped the 17 faces into five structural categories: • 9T, the uppermost face; • BC (bottom closed): faces 2B, 4B, 6B, 8B; • BO (bottom open): faces 3B, 5B, 7B, 9B; • TC (top closed): faces 1T, 3T, 5T, 7T; • TO (top open): faces 2T, 4T, 6T, 8T. This hierarchical face-type classification was used to test how fine-scale microhabitat influences community composition, and to evaluate whether grouping faces by structural categories before DNA extraction is an efficient approach for metabarcoding-based monitoring.
| Охват исследования | North-western Mediterranean Sea; 2028-19 |
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| Контроль качества | Sessile material scraped from ARMS plate faces was homogenized (~15 sec. in a blender), briefly rinsed, and transferred to clean 50 mL Falcon tubes filled with fresh 96 % ethanol. For DNA extraction, 1.5 mL of homogenate was used. To minimize cross-contamination, extractions were performed in individual tubes rather than in the 96-well plate format of the extraction kit (see Corse et al. 2017). DNA extractions and COI metabarcoding followed the protocol described by Thomasdotter et al. (2023), with the following key steps: (i) DNA was extracted using the NucleoSpin® Soil kit (Macherey-Nagel, Germany); (ii) the cytochrome c oxidase subunit I (COI) gene was amplified in triplicate PCRs with primers IIICRrevN (3′-GGNTGAACNGTNTAYCCNCC-5′) and HBR2d (5′-TAWACTTCDGGRTGNCCRAARAAYCA-3′), which include a heterogeneity spacer and 11–13 nucleotide sample-identifying tags, and target a broad spectrum of eukaryotic and algal phyla; (iii) a two-step tailed PCR generated paired-end, ready-to-load libraries; (iv) libraries were sequenced on an Illumina MiSeq using v2 chemistry (2 × 250 bp); and (v) a full series of negative and positive controls (two distinct mock communities) was incorporated. |
Описание этапа методики:
- For bioinformatic processing we used VTAM v0.2.0 (Validation and Taxonomic Assignment of Metabarcoding data; González et al., 2023), a pipeline specifically designed to leverage the presence of technical replicates and control samples (including negative controls and mock communities). The core principle of VTAM is to optimize parameter values across multiple filtering steps to maximize the removal of false-positive occurrences in control samples while retaining all expected variants (i.e., no false negatives in mock samples and the minimal possible number of false positives). Once optimized, these parameters are applied uniformly to all samples within the same sequencing library and run, under the rationale that parameter values validated on control samples are also appropriate for the corresponding experimental samples. The detailed protocol is availbale at : https://github.com/meglecz/seamobb_metabarcoding_pipeline
Дополнительные метаданные
| Благодарности |
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