Description
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.
Enregistrements de données
Les données de cette ressource données d'échantillonnage 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 19 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:
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
Droits
Les chercheurs doivent respecter la déclaration de droits suivante:
L’éditeur et détenteur des droits de cette ressource est Institute of physicochemical and biological problems in soil science of the Russian Academy of Sciences. Ce travail est sous licence Creative Commons Attribution Non Commercial (CC-BY-NC) 4.0.
Enregistrement GBIF
Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : e11d99cb-4a96-4e9d-847e-d078cfd59f6c. Institute of physicochemical and biological problems in soil science of the Russian Academy of Sciences publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du Participant Node Managers Committee.
Mots-clé
Samplingevent; permafrost; protists; drilling and coring; carbon-14 analysis; DNA sequencing; microbiology
Contacts
- Fournisseur Des Métadonnées ●
- Auteur ●
- Créateur ●
- Personne De Contact
- Researcher
- Institutskaya 2
- +79167091696
http://orcid.org/0000-0003-0470-9378
- Auteur
- Senior Researcher
- Institutskaya 2
- +79851476903
- Auteur
- Researcher
- Institutskaya 2
- Chercheur Principal
- Laboratory Head
- Institutskaya 2
Couverture géographique
Permafrost samples for the strain isolation were obtained in North-Eastern Eurasia, from Yamal Peninsula to Chukotka.
| Enveloppe géographique | Sud Ouest [65, 65], Nord Est [75, 180] |
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Couverture temporelle
| Epoque de formation | 2000-ongoing |
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Données sur le projet
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.
| Titre | Biodiversity and evolution of heterotrophic protists and giant viruses from Holocene and Pleistocene Arctic permafrost |
|---|---|
| Identifiant | RFBR-CNRS-a-17-54-150003 |
| Financement | Russian Foundation for Basic Research (RFBR), grant 17-54-150003 |
| Description du domaine d'étude / de recherche | Northern Siberia, from Yamal Peninsula to Chukotka |
| Description du design | 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). |
Les personnes impliquées dans le projet:
- Processeur
Méthodes d'échantillonnage
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.
| Etendue de l'étude | 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. |
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| Contrôle qualité | 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. |
Description des étapes de la méthode:
- 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).
Données de collection
| Nom de la collection | Коллекция образцов вечной мерзлоты лаборатории криологии почв ИФХиБПП РАН |
|---|---|
| Identifiant de collection | SCL |
| Nom de la collection | Коллекция амебоидных протистов лаборатории криологии почв ИФХиБПП РАН |
|---|---|
| Identifiant de collection | SCL-Prot |
| Méthode de conservation des spécimens | No treatment, Microscopic preparation, Deep frozen |
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Citations bibliographiques
- 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.
Métadonnées additionnelles
Empty cells represent "no data" N/A: "not applicable"
| Identifiants alternatifs | e11d99cb-4a96-4e9d-847e-d078cfd59f6c |
|---|---|
| http://gbif.ru:8080/ipt/resource?r=ancientpermafrostamoeboidprotists |