DNA metabarcoding of the prey and microbiome of museum specimen Antarctic trematomid fishes

データ レコード

この オカレンス（観察データと標本) リソース内のデータは、1 つまたは複数のデータ テーブルとして生物多様性データを共有するための標準化された形式であるダーウィン コア アーカイブ (DwC-A) として公開されています。 コア データ テーブルには、239 レコードが含まれています。

この IPT はデータをアーカイブし、データ リポジトリとして機能します。データとリソースのメタデータは、 ダウンロード セクションからダウンロードできます。 バージョン テーブルから公開可能な他のバージョンを閲覧でき、リソースに加えられた変更を知ることができます。

バージョン

次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。

引用方法

研究者はこの研究内容を以下のように引用する必要があります。:

Heindler F, Christiansen H, Frédérich B, Dettaï A, Lepoint G, Van de Putte A, Volckaert F (2020): DNA metabarcoding of the prey and microbiome of museum specimen Antarctic trematomid fishes. v1.3. SCAR - Microbial Antarctic Resource System. Dataset/Occurrence. https://ipt.biodiversity.aq/resource?r=historic_antarctic_fish_dataset_2019&v=1.3

権利

研究者は権利に関する下記ステートメントを尊重する必要があります。:

パブリッシャーとライセンス保持者権利者は SCAR - Microbial Antarctic Resource System。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF登録

このリソースをはGBIF と登録されており GBIF UUID: ccba820a-bc62-4cf4-85f2-e0a991efcc6cが割り当てられています。   Scientific Committee on Antarctic Research によって承認されたデータ パブリッシャーとして GBIF に登録されているSCAR - Microbial Antarctic Resource System が、このリソースをパブリッシュしました。

キーワード

Samplingevent

連絡先

地理的範囲

Various places in the Souther Ocean and the coastal waters of the Antarctic continent. Geographic coordinates not available for all the museum specimen.

生物分類学的範囲

Fish specimen of the genus Trematomus, with DNA samples of the stomach and gut for prey composition and micro biome.

Bacterial and Archaeal microbiome in the stomach and gut of the fish was profiled with the 16S ssu rRNA gene

Prey (eukaryotes) of the fish were investigated with the COI marker gene

時間的範囲

プロジェクトデータ

説明がありません

プロジェクトに携わる要員:

収集方法

Fish were carefully dissected: stomachs were opened to remove stomach content and a small portion of the hindgut (1 cm) was removed. Stomach content and hindgut were stored separately in 70% ethanol.

Method step description:

1. A large piece of stomach content (0.5 × 0.5 cm) or the entire piece of hindgut (1 cm) was placed into screwcap microtubes with 500 μl of Phosphate Buffered Saline (PBS) at pH 9. Tissue was fragmented thoroughly in each tube to ameliorate efficiency. Samples were heated to 100°C for 10 min, left to cool on ice for 5 min and then spun down with 20,000 × g for 5 min. PBS was carefully removed without taking any tissue and replaced by 500 μl of PBS at pH 7.2 and again heated to 100°C for 10 min. PBS was again carefully removed and further purification steps were conducted using the commercial Nucleospin® Tissue (Macherey-Nagel, Accession number: 740952) DNA extraction kit following the manufacturer's protocol.
2. For prey identification a 313 bp region of the COI gene was amplified from the stomach content using the tailed primers NGSmlCOIint and NGSjgHCO2198. The V3 and V4 region (460 bp) of the 16S rRNA gene was amplified using the tailed primers 16s-IllumTS-F and 16s-IllumTS-R to assess the microbiome composition. The reaction mix for the amplicon PCR for COI contained 12.5 μl of MytaqTM 2x Mix (Bioline, Accession number: BIO-25041), 0.5 μl of each primer (20 μM), 10.5 μl of molecular grade water and 1 μl of DNA template with a PCR profile of 10 s of denaturation at 95°C, 30 s of annealing at 62°C and 60 s elongation at 72°C for 16 cycles with the annealing temperature dropping every cycle by 1°C, followed by 25 cycles with an annealing temperature at 46°C. The reaction mix for the amplicon PCR for 16S contained 12.5 μl of MytaqTM 2x Mix, 2.5 μl of each primer (1 μM), 2.5 μl of DNA template (5 ng ul−1) and 5 μl of molecular grade water with a PCR profile of 60 s of initial denaturation at 95°C followed by 25 cycles of 15 s denaturation at 95°C, 15 s of annealing at 55°C and 10 s elongation at 72°C, finishing with a final extension of 72°C for 300 s. PCR products were cleaned up using Agencourt AMPure XP beads (Beckman Coulter, Accession number: A63882) following the manufacturer's instructions with a bead to template ratio of 0.8 to 1. Thereafter followed an indexing PCR, which binds a unique primer barcode to each respective sample following Lange et al. (2014) with a PCR mix of 10 μl of MytaqTM 2x Mix, 0.5 μl of each forward and reverse indexing-primer (to form a unique identifiable primer combination for each sample; 20 μM) and 9 μl of DNA template with a PCR profile of an initial denaturation of 1 min at 95°C followed by 15 cycles of denaturation for 15 s at 95°C, 15 s of annealing at 51°C and 10 s of extension at 72°C finishing with a final extension of 5 min at 72°C. The PCR product was cleaned up again, then quantified using the commercial Quant-iTTM Picogreen® kit (Thermo Fisher) and pooled, if sufficient template (20 ng) was available. Sequencing took place on an Illumina MiSeq PE 3000 (Genomics Core, KU Leuven, Belgium).

コレクションデータ

書誌情報の引用

1. Heindler F.M., Christiansen H., Frédérich B., et al. (2018) ‘Historical DNA Metabarcoding of the Prey and Microbiome of Trematomid Fishes Using Museum Samples’. Frontiers in Ecology and Evolution 6: 151, https://doi.org/10.3389/fevo.2018.00151. https://doi.org/10.3389/fevo.2018.00151.

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