Archaea from the ANDEEP3 expedition

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Description

This dataset describes a 16S ribosomal DNA clone library analysis, performed to assess archaeal diversity within three surficial sediment samples obtained from the bathypelagic zone (depth : 2,165 -3,406 m) of the Weddell Sea, Antarctica. The nearly complete 16S rDNA gene (1440 bp) was obtained for 146 clones and 46 phylotypes were defined. The majority of the sequences (> 99%) formed three clusters within the Marine Group I Crenarchaeota. The most important cluster, with 78.8% of the clones, included Candidatus Nitrosopumilus maritimus, a mesophilic archaeon able to oxidize ammonia. The most important subgroup in that cluster was the APA4-0cm subgroup (with 62.3% of the clones). This subgroup might represent important Crenarchaeota in the functioning of the bathypelagic sedimentary ecosystems of the Weddell Sea because it dominated the clone libraries in all sampling stations, and was found in sediments separated by very large geographic distances. Only one clone grouped within the Euryarchaeota. This euryarchaeal clone could not be affiliated with any of the previously defined clusters and might represent a novel Euryarchaeal lineage

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Gillan, David C., and Bruno Danis. 2007. The archaebacterial communities in Antarctic bathypelagic sediments. Deep Sea Research Part II: Topical Studies in Oceanography 54 (16-17) (August): 1682-1690.

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est Antarctic Biodiversity Information Facility (ANTABIF). Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

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Mots-clé

EARTH SCIENCE; BIOLOGICAL CLASSIFICATION; BACTERIA/ARCHAEA

Contacts

Bruno Danis

Fournisseur Des Métadonnées ●
Créateur ●
Utilisateur ●
Personne De Contact

Antarctic Biodiversity Information Facility

29, rue Vautier

1000 Brussels

bruno.danis@gmail.com

http://www.biodiversity.aq

David Gillan

Auteur

Laboratoire de Biologie Marine

50, av FD Roosevelt

Brussels

Couverture géographique

ANDEEP 3 cruise track, from Cape Town (SA) to Punta Arenas (CH). Four study regions were selected, but the main focus was on the Powell Basin and the Weddell Basin of the Weddell Sea, and their slopes. Two comparative samples were taken further north in the adjacent Agulhas and southern Cape Basins, which are separated from each other by the Agulhas Ridge. Four study regions were selected, but the main focus was on the Powell Basin and the Weddell Basin of the Weddell Sea, and their slopes. The major South Atlantic deep-sea basins started forming during Jurassic and Cretaceous times in connection with the Gondwana break-up and seafloor spreading (Brandt et al., 2004a, 2007; Lawver and Gahagan, 2003). The Weddell Basin is separated from the northerly basins by the South- west India Ridge (LaBrecque, 1986). The Powell Basin on the western side of the Weddell Sea was formed in the Tertiary by geological processes opening the Drake Passage and tectonic movements in the Scotia Sea (Lawver and Gahagan, 2003; Mitchell et al., 2000). The oceanography of the deep South Atlantic seafloor is defined by its prominent water mass, the Antarctic Bottom Water (Tomczak and Godfrey, 2001). The Antarctic Bottom Water expands north- wards into the Atlantic basins east and west of the Mid-Atlantic Ridge, like the Agulhas Basin, but can only enter the basins north of the Walvis Ridge (e.g., Cape Basin) via the northerly Romanche Fracture Zone. The Weddell Sea Bottom Water (WSBW), defined by a temperature of 0.7 1C and a salinity of 34.64 ppt (Orsi et al., 1993), is the main water mass above the Weddell Sea benthos (Fahrbach et al., 2001). The WSBW flows from the western Weddell Sea into the Scotia Sea and South Sandwich Forearc, and its circulation is driven by the Weddell Sea gyre. The sediments in the bathyal and abyssal Weddell and Powell Basins are dominated by silt and clay.

Enveloppe géographique	Sud Ouest [-71,31, 0], Nord Est [-61,5, 64,64]

Couverture taxonomique

Pas de description disponible

Domain	Archaea

Couverture temporelle

Date de début	2005-02-21

Date de début	2005-03-14

Date de début	2005-03-18

Données sur le projet

Pas de description disponible

Titre	ANDEEP: Antarctic Deep Sea Biodiversity
Description du domaine d'étude / de recherche	The study area of this dataset was set in the Southern Ocean and focused on deep sea stations distributed on the continental slopes of the eastern Weddell Sea (off Kapp Norvegia) and western Weddell Sea and the South Orkney Islands, and deep Cape, Agulhas, Weddell and Powell BasinsSouthern Ocean. The Southern Ocean deep-sea is a very under sampled area, according to a recent gap analysis carried out by Griffiths et al (2011).

Titre

ANDEEP: Antarctic Deep Sea Biodiversity

Description du domaine d'étude / de recherche

The study area of this dataset was set in the Southern Ocean and focused on deep sea stations distributed on the continental slopes of the eastern Weddell Sea (off Kapp Norvegia) and western Weddell Sea and the South Orkney Islands, and deep Cape, Agulhas, Weddell and Powell BasinsSouthern Ocean. The Southern Ocean deep-sea is a very under sampled area, according to a recent gap analysis carried out by Griffiths et al (2011).

Les personnes impliquées dans le projet:

Angelika Brandt

Chercheur Principal

Méthodes d'échantillonnage

Archaeal communities were analyzed in sediments in three bathypelagic stations (2200-3400m) sampled during the ANTXXII-3 cruise of RV Polarstern (ANDEEP3). Sediments were sampled using a box-corer. The sediments were immediately and aseptically sampled using 3 ml polyethylene (PET) cryovials (top 2 cm of the sediments). The cryovials were immediately frozen in liquid nitrogen and the samples were then stored at -20°C. Six replicate samples of the same core were collected at each site.

Etendue de l'étude	Bathypelagic sediment samples were taken from 3 stations during the ANDEEP3 expedition to the Weddell Sea.
Contrôle qualité	PCR-generated chimeric sequences were first detected and eliminated using three different softwares : CHIMERA_CHECK version 2.7 of the Ribosomal Database Project II (Cole et al., 2003), Bellerophon (Huber et al., 2004), and Pintail version 0.33 (Ashelford et al., 2005). Sequences were then submitted to BLAST version 2.2.12 to identify the closest relatives and download their 16S rDNA sequence (Madden et al., 1996). All sequences were manually aligned and analyzed using Se-Al version 2.0a11 (Rambaut, 1996). Alignments and similarity calculations were also performed using the EMBOSS-Align tool of the EMBL-EBI (http://www.ebi.ac.uk). Distance and maximum-likelihood trees were generated with the Phylip program package, version 3.6 (Felsenstein, 2002). Distance trees were generated with "Dnadist" using Jukes-Cantor distances and Neighbour-Joining. Maximum-likelihood trees were generated with "Dnaml" (Ti/Tv=2.0; empirical base frequencies, one category of sites with a constant rate of variation). The statistical significance of the phylogenetic groups within the trees was tested by using bootstrap analysis with the Phylip programs "Seqboot" and "Consense" (100 bootstrap replicates, using using Jukes-Cantor distances and Neighbour-Joining). Trees were created using the program Treeview (version 1.6.6.).

Etendue de l'étude

Bathypelagic sediment samples were taken from 3 stations during the ANDEEP3 expedition to the Weddell Sea.

Contrôle qualité

PCR-generated chimeric sequences were first detected and eliminated using three different softwares : CHIMERA_CHECK version 2.7 of the Ribosomal Database Project II (Cole et al., 2003), Bellerophon (Huber et al., 2004), and Pintail version 0.33 (Ashelford et al., 2005). Sequences were then submitted to BLAST version 2.2.12 to identify the closest relatives and download their 16S rDNA sequence (Madden et al., 1996). All sequences were manually aligned and analyzed using Se-Al version 2.0a11 (Rambaut, 1996). Alignments and similarity calculations were also performed using the EMBOSS-Align tool of the EMBL-EBI (http://www.ebi.ac.uk). Distance and maximum-likelihood trees were generated with the Phylip program package, version 3.6 (Felsenstein, 2002). Distance trees were generated with "Dnadist" using Jukes-Cantor distances and Neighbour-Joining. Maximum-likelihood trees were generated with "Dnaml" (Ti/Tv=2.0; empirical base frequencies, one category of sites with a constant rate of variation). The statistical significance of the phylogenetic groups within the trees was tested by using bootstrap analysis with the Phylip programs "Seqboot" and "Consense" (100 bootstrap replicates, using using Jukes-Cantor distances and Neighbour-Joining). Trees were created using the program Treeview (version 1.6.6.).

Description des étapes de la méthode:

A MICROBIAL_SEQUENCE_SET Description file describing 3 data sets was uploaded to the ANTABIF IPT instance (http://ipt.biodiversity.aq).

Citations bibliographiques

Brandt A, Gooday AJ, Brandao SN, Brix S, Brökeland W, Cedhagen T, Choudhury M, Cornelius N, Danis B, De Mesel I, Diaz RJ, Gillan DC, Ebbe B, Howe JA, Janussen D, Kaiser S, Linse K, Malyutina M, Pawlowski J, Raupach M, Vanreusel A, 2007. First insights into the biodiversity and biogeography of the Southern Ocean deep sea. Nature 447:307-311. http://dx.doi.org/10.1038/nature05827

Métadonnées additionnelles

marine, harvested by iOBIS

Identifiants alternatifs	https://ipt.biodiversity.aq/resource?r=andeep3_archaebacterial_communities