Antarctic Circumnavigation Bacterial Collection (ACBC).

***** Dataset abstract *****

We collected natural bacterial communities from the Southern Ocean during the Antarctic Circumnavigation Expedition (ACE) from December 2016 to March 2017. The expedition travelled 33,565 kilometres around Antarctica, allowing us to bring back unprecedented live samples from the Southern Ocean for isolation and identification purposes.

***** Original data collection *****

Water samples were collected at 15 different sites at the surface (0), 15, 100 and at 1000 m depth. Two additional samples were collected: one in the Ross Sea at 3800 m to get the signature of the Antarctic Bottom Water, and another at 700 m on the seabed underneath the Mertz glacier. 

Briefly, 500 mL of seawater was filtered through 0.2 µm pore-size at low pressure (<0.2 Hg) until 1 mL was left on the top. Bacterial cells deposited on the filter were gently resuspended and collected in the seawater and then deposited on two marine growth media in triplicates. Bacteria colonies were first grown in nutrient rich (Marine Broth) and poor (R2A) agar media at 4°C directly on board the R/V Akademik Tryoshnikov. Each colony was subsequently isolated a first time at sea, followed by additional isolation steps in the laboratory in Geneva, Switzerland until we got pure cultures. A total of 314 isolates were recovered, documented and archived at -80°C. DNA was extracted from the pure culture of the bacterial isolate directly from marine agar plates and using the DNeasy blood and tissue kit (Qiagen). The 16S rRNA gene was amplified using the universal primers* 27f and 1492r. The two sequences obtained with primers P0 (=27f) and P6 (=1492r) were trimmed with Chromas Lite (free Chromas version), then manually aligned using BioEdit software. Contigs were built using BioEdit software from forward and reverse sequences on 3’ and 5’. Finally, Contigs larger than 50bp were used to search homologous sequences against 16S rRNA sequences in the EZBioCloud database (Yoon et al., 2017). Using 16S RNA Sanger sequencing, we have so far characterized the bacterial diversity of 186 of these isolates. 

*Universal Primer 27f and 1492r from Fasteris Company 
P0 5'-AGAGTTTGATCCTGGCTCAG-3'
P6 5'-GTACGGCTACCTTGTTACGA-3'

Sample processing steps – 16S protocol:
1. Initial Quality Control;
2. Washing the cells;
In general, 10 uL of the concentrated culture is mixed with 200 uL H2O and centrifuged;
3. PCR-ready DNA;
The pellet is re-suspended in 50 uL Prepman Ultra (Applied Biosystems).
The lysate is heated at 99°C for 10 minutes;
4. Direct PCR; Ribosomal 16S DNA is amplified from 1 uL of PCR-ready DNA using the high-fidelity polymerase PrimeSTAR (Takara) and the standard primers P0 and P6 in presence of betaine:
3’ at 95°C; 30 cycles of 30” at 95°C, 30” at 56°C, 2’ at 72°C; 5’ at 72°C.
5. PCR products purification;
6. Capillary Sequencing

***** Dataset contents *****

- antarctic_circumnaviation_bacterial_collection.csv, data file, comma-separated values
- README.txt, metadata, text
- data_file_header.txt, metadata, text

***** Dataset contact *****
Marion Fourquez, Aix Marseille University. ORCID: 0000-0001-5395-4877. Email: marion.fourquez@gmail.com

***** Data license *****

This Antarctic Circumnavigation Bacterial Collection (ACBC) is made available under the Creative Commons Attribution 4.0 International License (CC BY 4.0) whose full text can be found at https://creativecommons.org/licenses/by/4.0/

***** Dataset citation *****

This dataset can be cited as: 
Fourquez, M. and Hassler, C. (2021). Antarctic Circumnavigation Bacterial Collection (ACBC). (1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5763724