OSD Pilot Event on December 19th 2013 at Venice Acqua Alta Platform (OSD63)

OSD Site 63 Venice Acqua Alta Platform (North Western Adriatic Sea)

The sampling site is the Acqua Alta oceanographic platform, a site for long term ecological research (LTER) operated by the Institute of Marine Science of the National Research Council of Italy. The tower, built in 1970, is located at about 10 nautical miles off the city of Venice, at the water depth of 16 meters. Acqua Alta currently serves as a multi-disciplinary station for a wide variety of marine researches, and is equipped with a meteo-oceanographic station (providing measurements of temperature, wind, humidity, solar radiation, rain, waves and tides), sensors for the main hydrological parameters, and underwater webcams. Instruments can be controlled remotely, and real time data are available. It is part of the LTER network and decadal time series are available at ISMAR-CNR about the trophic state of the area, the ecology and biodiversity of plankton, and the biogeochemistry.

Due to the adverse meteorological conditions forecasted for the 20^th, the OSD sampling was carried out on the 19^th December. We left from the pier in front of the Institute around 9:00 onboard the boat Litus. Water sampling was performed at 2:00 pm. The sea conditions were calm and the weather was sunny. In addition to collecting samples to be filtered onto Sterivex for bacterial diversity analyses, we performed CTD casts for measuring the main physical-chemical variables and collected water samples for phytoplankton/zooplankton abundance, and the determination of total suspended matter and chlorophyll.

The OSD team of the ISMAR–CNR in Venice before departure. From left to right: Mauro Bastianini, Gian Marco Luna, Grazia Marina Quero and Lucia Bongiorni.

The OSD sampling site 63: the oceanographic tower Acqua Alta operated by the ISMAR-CNR.

A view on the Northern Adriatic Sea from the upper floors of the tower.

Live phytoplankton cells observed in the water samples collected during the pilot event.

We are looking forward to the OSD sampling day in 2014!

Gian Marco Luna (OSD Site 63 coordinator), Grazia Marina Quero, Lucia Bongiorni, Mauro Bastianini – Institute of Marine Science, National Research Council of Italy, Venice (Italy)

OSD Open Call For Data Generation Partners

All of the work of the Ocean Sampling Day effort has been based on tremendous in kind contributions of the community co-ordinated by the Micro B3 project.  Now, based on the successful engagement of 60+ sites, in close collaboration with the Genomic Observatories (GOs) Network, preliminary sequencing results, generated by Argonne National Lab and a growing legal framework, including the option for bioarchiving through the Smithsonian’s GGI initiative, we are making an open call for participation in the main OSD event on the summer solstice June 2014.

In addition to expressions of interest from expert sampling sites, we are looking forward to add additional data generation activities, specifically DNA extraction, PCR and sequencing support, to OSD.

We expect to have around 500 samples and are particularly interested in the following types of data, but are open to additional uses of OSD samples:

OSD PRIORITY DATA SETS

Foundational dataset:

Community profiling of bacteria & archea - 16S (V3, V4) (already started by ANL)

Plus any or all:

- Metagenomes (shotgun sequencing)

- 18S

- ITS

- Viral sequencing

- Use of other primers for bacterial communities profiling (other regions of 16S, other loci, etc)

- Targeted deep sequencing of specific samples

- Metatranscriptomes

Further wish list:

- Cell densities

- Environmental parameters

- Microarrays

To express formal interest in participating in OSD as a data generation partner please fill in this brief form:

https://www.surveymonkey.com/s/PQ8YMP5

The OSD Team will follow up if we have further questions.  For further information or to discuss ideas please contact the OSD Team via osd-contact<at>microb3<dot>eu.

EXPRESSION OF INTEREST:

- Main contact and affiliation

- Short summary of your offered contribution to OSD

- Type of data you would like to generate and Why

- Scientific Contributions/Hypotheses to be tested

- How much DNA is required from each sample

- How many samples you are willing to analyze

- A costing for the contribution (in kind costs)

- Any further comments

Funding to Support OSD June 2014 Data Generation Activities

As part of ramping up OSD for 2014 we will be making available a limited budget of roughly 50k Euros for data generation activities under an open competition.  We would like to be able to fund the engagement of as many groups as possible and will be seeking further funding so we welcome ideas for partnerships.

Please make your expression of interest by December 15th for consideration by the OSD Committee in January 2014.

All proposals will be judged first on scientific merit and activities that will be prioritized for contributed funding will include those that:

• offer significant in kind contributions to OSD
• align well with the existing efforts and priorities of OSD
• extend the breadth of taxonomic coverage of OSD
• extend the breadth of loci examined in OSD
• enable the comparison of OSD data to existing datasets
• help to build the OSD Consortium

River Sampling Day‐ Summer solstice 2013‐06‐21 at the River Ellidaá, Iceland – Matis

Sampling was performed for the first time in the salmon river Ellidaá, a river located in Reykjavik in Iceland (Lat: 64°05,848’ N, Long: 21° 47,925’ V). We collected three replicate samples about 3 meters from the river bank using an acid cleaned bucket. The sampling was at 14:46 o´clock on the summer solstice 2012‐13‐21 and the weather was exceptionally good that day. The water samples (1 L) were filtrated (after 30 minutes) through four 0.22 μm Sterivex filters (Millipore). Filtering time was around 30 min. Filters were sealed and immediately frozen at ‐80 °C in individual plastic tubes.

Map of the RSD sampling 

Additional site information:

Air temperature: 20.3°C 

Water temperature surface: 16.1 ̊C

Water conductivity 100uS/cm

pH 9.59

RSD sampling

Viggó Thór Marteinsson, Alexandra M. Klonowski

OSD ‐ Summer solstice 2013‐06‐21 at Faxaflói, Iceland – Matis

Sampling was performed for the third time in Faxaflói, a bay in Southwest-Iceland between the peninsulas of Reykjanes and Snæfellsnes. A small boat was used to go to the OSD sampling station (Lat: 64° 12,50’ N, Long: 22° 00,90’ V). We collected three replicate samples from the sampling station from a depth of 0.2 meter using acid cleaned bucket. The sampling was at 12:04 o´clock on the summer solstice 2012‐13‐21 and the weather was exceptionally good. The water samples (1 L) were filtrated (after 1 hour) through four 0.22 μm Sterivex filters (Millipore). Filtering time was around 30 min. Filters were sealed and immediately frozen at ‐80 °C in individual plastic tubes.

Map of the OSD sampling site 

Additional site information:

Air temperature: 17°C ?

Water temperature surface: 10.4 ̊C

Salinity 3,5

View from the boat to the shore of Reykjavík

Viggó Thór Marteinsson, Alexandra M. Klonowski

OSD sampling at Western Channel Observatory - L4 site

View from L4 cam on 18.12.2012

The Western Channel Observatory (WCO), Science Leader – Tim Smyth, is an oceanographic time-series and marine biodiversity reference site in the Western English Channel. In situ measurements are undertaken weekly at coastal station L4 and fortnightly at open shelf station E1 using the research vessels of the Plymouth Marine Laboratory (PML) and the Marine Biological Association (MBA).  WCO has contributed three samples towards the Ocean Sampling Day activities – June 2012, December 2012 & June 2013.  Surface water is collected near the L4 mooring (50.150 N, 4.130 W) using Plymouth Quest, brought back to PML where Denise passes 5L volumes through the 0.22 μm Sterivex filters (Millipore) and subsequent DNA extractions from these filters were carried out by Cecilia and Declan at the molecular suite at the MBA.  Replica filters are archived at -80C. Samples were sent to Argonne for next-generation sequencing.

Site and Sample Information:

Western Channel Observatory sampling stations

Declan Schroeder (Marine Biological Association), Tim Smyth (Plymouth Marine Laboratory), Cecilia Balestreri (Marine Biological Association) & Denise Cummings (Plymouth Marine Laboratory).

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