説明
Permafrost, frozen ground cemented with ice, occupies about a quarter of the Earth’s hard surface and reaches up to a thousand meters depth. Due to constant negative temperatures, permafrost sediments represent a unique record of past epochs, whenever it comes to accumulated methane, oxygen isotope ratio, or stored mummies of animals. Permafrost is also a unique environment where cryptobiotic stages of different microorganisms are trapped and stored alive for up to hundreds of thousands of years. Several strains isolated from permafrost cores have been already described.
Here described is the collection of strains of clonal amoeboid protists of the Soil Cryology Lab, Pushchino, as well as permafrost samples from which the strains were isolated. The dataset presented contains different core characteristics and the taxonomy of isolated strains. Specimens of the collection are available from the Soil Cryology Lab upon request. The cores are stored frozen at −18 °C and may be used for further detailed studies and isolation attempts.
データ レコード
この sampling event 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、19 レコードが含まれています。
拡張データ テーブルは2 件存在しています。拡張レコードは、コアのレコードについての追加情報を提供するものです。 各拡張データ テーブル内のレコード数を以下に示します。
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。:
Malavin S, Shmakova L (2020): Amoeboid protists isolated from ancient Siberian permafrost. v1.4. Institute of physicochemical and biological problems in soil science of the Russian Academy of Sciences. Dataset/Samplingevent. http://gbif.ru:8080/ipt/resource?r=ancientpermafrostamoeboidprotists&v=1.4
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 Institute of physicochemical and biological problems in soil science of the Russian Academy of Sciences。 This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY-NC 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: e11d99cb-4a96-4e9d-847e-d078cfd59f6cが割り当てられています。 Participant Node Managers Committee 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Institute of physicochemical and biological problems in soil science of the Russian Academy of Sciences が、このリソースをパブリッシュしました。
キーワード
Samplingevent; permafrost; protists; drilling and coring; carbon-14 analysis; DNA sequencing; microbiology
連絡先
- メタデータ提供者 ●
- 論文著者 ●
- 最初のデータ採集者 ●
- 連絡先
- Researcher
- Institutskaya 2
- +79167091696
http://orcid.org/0000-0003-0470-9378
- 論文著者
- Senior Researcher
- Institutskaya 2
- +79851476903
- 論文著者
- Researcher
- Institutskaya 2
- 研究代表者
- Laboratory Head
- Institutskaya 2
地理的範囲
Permafrost samples for the strain isolation were obtained in North-Eastern Eurasia, from Yamal Peninsula to Chukotka.
| 座標（緯度経度） | 南 西 [65, 65], 北 東 [75, 180] |
|---|
時間的範囲
| 生成(収集）期間 | 2000-ongoing |
|---|
プロジェクトデータ
The project aims at expanding the view on the diversity of protists and their viruses that could be found in ancient (Pliocene to Holocene) Arctic permafrost.
| タイトル | Biodiversity and evolution of heterotrophic protists and giant viruses from Holocene and Pleistocene Arctic permafrost |
|---|---|
| 識別子 | RFBR-CNRS-a-17-54-150003 |
| ファンデイング | Russian Foundation for Basic Research (RFBR), grant 17-54-150003 |
| Study Area Description | Northern Siberia, from Yamal Peninsula to Chukotka |
| 研究の意図、目的、背景など（デザイン） | Protists and viruses are aseptically isolated from permafrost samples, borehole cores and outcrop samples, taken using specially developed technique (Gilichinskiy, D.A., Khlebnikova, G.M., Zvyagintsev, D.G., Fedorov-Davydov, D.G., Kudryavtseva, N.N., 1989. Microbiology of sedimentary materials in the permafrost zone. International Geology Review 31, 847–858. https://doi.org/10.1080/00206818909465938. Shi, T., Reeves, R.H., Gilichinsky, D.A., Friedmann, E.I., 1997. Characterization of viable bacteria from Siberian permafrost by 16S rDNA sequencing. Microbial Ecology 33, 169–179. https://doi.org/10.1007/s002489900019). Isolated strains are studied using general microbiological techniques (cloning, axenization, DNA isolation and characterization, microscopy observations, physiological essays, taxonomic identification and description). |
プロジェクトに携わる要員:
- データ処理者
収集方法
The drilling was performed using a mobile drilling rig (core-drilling machine) UKB-12/25 (V.V. Vorovsky Machine-Building Plant, Moscow, Russia) operated without flushing and blowing. Flushing and blowing were shown to cause contamination of the cores by modern soil microorganisms. Cores were removed each 30—70 cm of the drilling. The core diameters were 115 to 75 mm, depending on the well depth (the deeper the well the smaller). A removed core was enveloped in a one-centimeter-thick coat of half-melted cuttings. This coat was removed with a knife, showing a completely frozen inner part. After a short lithological and glaciological description of the sediments, the core was passed to a clean field lab organized in a tent. Operations in the lab were conducted behind a gas-fired burner using disposable materials and gloves, following general microbiological practice. In the lab, the core was shaved with a sterile scalpel so that an approximately five mm outermost layer was removed. This remaining core was four to six cm in diameter, depending on the initial value. Immediately after shaving, the core was put into a sterile plastic bag and placed in a portable freezer, a cave dug into an ice wedge, or an empty borehole used as a freezer. In total, the “outdoor” stage of the process lasted five to ten minutes, depending on the current well depth. The “indoor” lab stage generally took around five minutes. All collected cores were kept at negative temperatures during the whole period of transportation to the stationary lab. Outcrops are natural exposures of ancient permafrost sediments formed at sea and river banks. The advantage of sampling from the outcrop wall is the possibility of visual inspection and description of the whole sediment layer. Samples from outcrops were taken from the frozen surface of the outcrop wall after the removal of melted material. In the wall, a hole of about 40 cm deep was made with either a hand-held drill, a chisel, or a knife. A cylinder sample of about 5 cm in diameter was carefully carved or drilled out from the bottom of the hole, treated with 95% ethanol, and immediately placed into a sterile plastic bag. As with the cores, all collected outcrop samples were kept frozen during the whole period of transportation. Buried terminal nesting chambers of the ground squirrel (Citellus) burrows are unique paleontological objects of Pleistocene Ice Complex sediments. They usually contain animal supplies made of seeds of surrounding grasses. Usually frozen in the living state, they are very well preserved. From the tissue of a Silene stenophylla seed, a viable flowering plant was grown (Yashina et al. 2012). Chambers also contain a diverse community of protists and fungi. Chambers were cut from the outcrop wall in one or several pieces ten or more cm in each dimension, put immediately in sterile plastic bags, and kept frozen until processing in the lab.
| Study Extent | The samples were collected in the field and stored constantly frozen during all periods of transportation and processing. In the lab, a part of each sample was used to isolate protist strains. The remaining part has never been melted and is stored at −18 °C. The isolation was done in sterile conditions. Obtained samples were cloned and maintained as bacterized or axenic cultures on plastic or agar with liquid overlay. |
|---|---|
| Quality Control | During the development of the permafrost microbiological sampling technique, several tests for contamination of the core interior have been established at different phases of sampling and storage. Gilichinskiy et al. (2010) and Shi et al. (1997) used Serratia marcescens cultures (Bacteria) producing easy-to-notice red colonies. A drilling barrel was covered with a culture suspension 2 h prior to drilling. In a parallel experiment, frozen samples were seeded with the same suspension already in the lab and left intact at negative temperature for several hours to several months. In both experiments, the distribution of S. marcescens cells in a core has been investigated during the sample processing. In all tests, bacteria have been found exclusively in the outer layer and never inside the core. Later, Juck et al. (2005) used fluorescent latex beads (microspheres) 0.5 μm in diameter and a transformed Pseudomonas strain expressing the green fluorescent protein (GFP). Both beads and transformed bacteria were applied to the drilling equipment before drilling, similar way as described above for S. marcescens suspension. Fluorescence microscopy showed that neither beads nor bacteria penetrate into a sample to a depth exceeding one cm from the surface. Additionally, PCR revealed no amplification of the GFP gene from the inner part of the cores. Based on the negative results obtained for bacteria and fluorescent beads, i.e. particles around two μm in diameter or less, we consider it proven that resting protist cysts, which are at least five times bigger, can’t move inside the frozen ground and thus could not penetrate the sediments considerably later than they were deposited. Same way, the contamination of the inner part of the samples during sampling and laboratory processing is not possible either. |
Method step description:
- Field sampling (see above)
- Isolation of protists in the lab For the isolation of protists, 1—5 grams of the sediment from the inner part of the frozen sample were placed in 90 mm Petri dishes filled with autoclaved mineral Prescott and James (PJ) medium (Prescott and James 1955). Negative controls (same procedures without sample inoculation) were performed simultaneously. The isolation was performed in a laminar flow hood using disposal or sterilized equipment. After 7—10 days of incubation, samples were examined using a Nikon TMF100 inverted microscope. Detected cells were transferred to the fresh medium by a glass capillary. Strains were cloned and further cultured in 60 mm Petri dishes using 0.01% Cerophyl infusion made on PJ medium (Smirnov and Brown 2004).
コレクションデータ
| コレクション名 | Коллекция образцов вечной мерзлоты лаборатории криологии почв ИФХиБПП РАН |
|---|---|
| コレクション識別子 | SCL |
| コレクション名 | Коллекция амебоидных протистов лаборатории криологии почв ИФХиБПП РАН |
|---|---|
| コレクション識別子 | SCL-Prot |
| 標本保存方法 | No treatment, Microscopic preparation, Deep frozen |
|---|
書誌情報の引用
- Malavin, S., Shmakova, L., 2020. Isolates from ancient permafrost help to elucidate species boundaries in Acanthamoeba castellanii complex (Amoebozoa: Discosea). European Journal of Protistology 73, 125671. https://doi.org/10.1016/j.ejop.2020.125671
- Shatilovich, A.V., Shmakova, L.A., Mylnikov, A.P., Gilichinsky, D.A., 2009. Ancient Protozoa isolated from permafrost, in: Margesin, R. (Ed.), Permafrost Soils. Springer Berlin Heidelberg, Berlin, Heidelberg, pp. 97–115. https://doi.org/10.1007/978-3-540-69371-0_8
- Shmakova, L., Bondarenko, N., Smirnov, A., 2016. Viable species of Flamella (Amoebozoa: Variosea) isolated from ancient Arctic permafrost sediments. Protist 167, 13–30. https://doi.org/10.1016/j.protis.2015.11.001
- Shmakova, L.A., Karpov, S.A., Malavin, S.A., Smirnov, A.V., 2018. Morphology, biology and phylogeny of Phalansterium arcticum sp. n. (Amoebozoa, Variosea), isolated from ancient Arctic permafrost. European Journal of Protistology 63, 117–129. https://doi.org/10.1016/j.ejop.2018.02.002
- Shmakova, L.A., Rivkina, E.M., 2015. Viable eukaryotes of the phylum Amoebozoa from the Arctic permafrost. Paleontological Journal 49, 572–577. https://doi.org/10.1134/S003103011506012X
- Демидов, Н.Э., Баранская, А.В., Дурденко, Е.В., Занина, О.Г., Караевская, Е.С., Пушина, З.В., Ривкина, Е.М., Спирина, Е., Спенсер, Р., 2016. Биогеохимия мерзлых толщ арктического побережья полуострова Гыдан. Проблемы Арктики и Антарктики 3, 34–49.
追加のメタデータ
Empty cells represent "no data" N/A: "not applicable"
| 代替識別子 | e11d99cb-4a96-4e9d-847e-d078cfd59f6c |
|---|---|
| http://gbif.ru:8080/ipt/resource?r=ancientpermafrostamoeboidprotists |