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).

The OSD Crowdfunding has Started - Participate NOW!

Support the biggest crowdfunding for the oceans. Let's take marine research to the next level and support the OSD crowdfunding project. 

The ocean needs you! Participate now!

Open Ship "Maria S. Merian" & OSD Citizen Science

The state-of-the-art research vessel Maria S. Merian was designed to perform research at the ice boarders of the arctic sea as well as the open sea worldwide. Named after Maria Sibylla Merian  this multidisciplinary research platform is equipped with outstanding facilities which allow the use of all modern methods of investigation of the sea-bottom, the water and the atmosphere.  

On 21./22. September 2013, the Maria S. Merian anchored in Bremen and was open to the public. Around 3000 young and old visitors enjoyed a diverse program of guided tours of the ship, activities for children, movies and lectures, exhibitions and much more. Scientists from the Center for Marine Environmental Sciences (MARUM), Environmental Physics (IUP), the Max Planck Institute for Marine Microbiology (MPIMM), the Alfred Wegener Institute of Polar and Marine Research (AWI) and Jacobs University Bremen were present and explained how samples are taken and examined, how underwater robots work and how bacteria can survive in the ocean. 

The Micro B3 prject and the Ocean Sampling Day (OSD) were represented by Frank Oliver Glöckner, Julia Schnetzer, Michael Richter and Anna Klindworth. It was a great opportunity to introduce the OSD citizen science project and raise awareness for the importance of marine microorganisms in times of climate change. We enjoyed fruitful dialogues with many interested citizens and were stunned by childrens creative drawings of marine microbes.  

  

Kids drawings of marine microbes from the Open Ship Day can be found at 

www.my-osd.org

OSD Citizen Science Project: Crowdfunding Campaign starts on Oct 1st!

The Micro B3 Consortium has teamed up with the multimedia company Mediomix to initiate a Crowdfunding Campaign to support Ocean Sampling Day and to produce a movie about this important and unique event. Scientists and citizens will collaborate on OSD in a completely new way. Everyone can join the OSD Citizen Science Project and support the scientists by recording water parameters such as temperature and phosphate and send their results directly to a central database with a Mobile Phone App. This way all supporters can not only help finance the event and raise awareness, but also have the opportunity to actively participate in the project! The OSD Crowdfunding Campaign starts on October 1st and runs until November 10th (UNESCO World Science Day), 2013.

Our oceans have made life on this Earth possible, and we believe that the time for us to pay back is now. Be part of science! Be part of something amazing! Be a citizen scientist!

To find out more information about the OSD Citizen Science Project and how to participate, please check the following link:

www.my-osd.org

Help us to spread the word. The official hashtag is #OSD2014

Check out our promotional teaser produced by Mediomix:
http://www.youtube.com/watch?feature=player_embedded&v=FEw5AS1qo-o

Ocean Sampling Day at Rothera, Antarctic Peninsula

Ocean Sampling Day – Rothera’s (OSD11) delayed contribution!

Picture 1 North Cove is still 

covered in ice. 

(Photo: Sabrina Heiser)

Rothera is the British Antarctic Survey research station, located on Adelaide Island on the Antarctic Peninsula at 67° South (http://www.antarctica.ac.uk/living_and_working/
research_stations/rothera). Like last year, we were planning to get out on the actual Ocean Sampling Day but were stopped by the weather and ice conditions. We had fast ice in Ryder Bay which prevented us from getting a boat in the water. However, as the ice was staying longer and longer, we were getting very excited about the possibility of doing a CTD and water sampling through the ice! When it was finally signed off, we were ready to go but the wind once more was in our way. Luckily, we were able to dive through the ice as it is closer to the shore and less dangerous. Then, we experienced why Antarctica is called the windiest continent on the planet. After a weekend of around 40-50 knots winds, half the sea ice in Ryder Bay had been blown out. Luckily, this meant we were able to get a boat into the water on the first calm day (just before the sea started freezing again).

Picture 3 Map of Ryder Bay showing the 

three CTD sites (open circles): 

1 is the main site (CTD1), 2 the secondary site (CTD2), 

and 3 is the fall-back site at Biscoe Wharf (WS3).  

Picture 2 Icycles we saw on one of our ice dives. 

(Photo: Sabrina Heiser)

We got out to Site 2 (67°34.850 S, 68°09.340 W) on the 22^nd of July. Site 2 is one of three sites commonly used for the RaTS (Rothera Biological and Oceanographic Time Series) sampling (see Picture 3). We sampled just on the edge of the fast ice. The day started off very calm, but winds were picking up later on and finished just in time before we would have had to abort the sampling. The air temperature was only around -5°C. The water temperature was similar to last year -1.52°C. We deployed the CTD to 300m and winched it back up again by hand. Afterwards we collected water samples from 15m with our Niskin bottles.

Same as last year, we filtered 2l for each filter. However, on the ship last summer we finally got some Sterivex filters in which we used (4 replicates). They were frozen immediately with liquid nitrogen and are being stored in the -80°C freezer until the ship next March picks them up together with the samples from our Ocean Sampling Day in the summer.

Picture 4 Myself and Amber taking water samples. 

Picture 5 Sampling by the ice edge with 

crabeater seals paying a visit. 

(Photo: Sabrina Heiser)

The RaTS program includes various aspects of sampling. With our CTD we measure depth, salinity, temperature, PAR and fluorescence and the water samples we take back are mostly bottled up for analysis back in the UK by a number of different institutes. We analyse chlorophyll and ammonia in our lab here at Rothera. Whereas analyses for HPLC, nutrients, CO₂, salts, isotopes, DOC, viruses, Barium and metagenomics is conducted elsewhere.

Sabrina Heiser, Rothera Marine Assistant

Crew: Amber Annett (Marine Assistant for the Dutch collaboration), Peter Webster (Diving Officer)