Venice Gulf & Venice Lagoon, Adriatic Sea - OSD Pilot June 21st 2013 Study

Mini report from University of Padova, Italy (OSD Site 47 and Site 48) 
Tuesday, 9 July 2013

This OSD sampling was the first one for the Department of Biology here at the University of Padova. Having as a logistic base our hydrobiological station in Chioggia, in the southern part of the Venice Lagoon, we decided to sample two different sites. The first one was “Palude della Rosa” (OSD site 47), in the northern part of the lagoon, a shallow eutrophic salt marsh pond which is considered one of the best preserved remnant of the ancient lagoon ecosystem. The second one (OSD site 48) was located around 2 miles away from the coast in the Gulf of Venice.

We moved from the hydrobiological station at around 8:30 am (local time) in a sunny day and all the expedition took place in a quiet and pleasant sea. Since the dimension of our boat, all the filtering steps, both for sampling and chlorophyll measurement, were done by hand. As previously supposed, we were able to filter only a small volume of water for each site, ranging from 360 ml per filter in the lagoon to 600 ml per filter in the open sea. We are anyway confident that Jack at the Argonne National Laboratory will be able to extract enough DNA from the filters!

In less than 5 hours we were back to Chioggia, where Vito and Andrea, technicians of the hydrobiological station, took care of some metadata and, of course, of the boat. Instead, Fabio, Riccardo and myself, with the filters and the water for nutrient measurement preserved in dry ice, moved to Padova. It has to be noticed that nutrient and chlorophyll measurement will be performed by Dr. Chiara Facca from the Department of Environmental Sciences, University of Venezia, which collaborates with us for metadata production.

See you at the next Ocean Sampling Day!!

Alessandro Vezzi, Coordinator of OSD Sites 47 and 48.

Palude della Rosa, OSD sampling site 47. Picture was taken from the boat while filtering, and shows a fishnet and behind it the Isle of Torcello.

Fabio (on the left) and Riccardo (on the right) while filtering water for chlorophyll and nutrients measurement.

The hydrobiological station of the Department of Biology, located in Chioggia.

Helgoland, North Sea - OSD Pilot June 21st 2013 Study

OSD sampling was performed for the third time at Helgoland in the North Sea, about 60 km off the estuaries of the Elbe and Weser rivers. Orginally, I (Anna Klindworth, OSD Coordinator, MPI-Bremen) was supposed to join the sampling campaign but due to challenging weather conditions it was impossible for me to reach the island in time. Luckily the crew and scientists from the Biologische Anstalt Helgoland (BAH) have a lot of experience with the rough sea and they were still able to sample despite the weather. In the meantime heavy rain caused a “flash flood” in the basement of the institute. This incident severely hampered the sampling effort as the necessary filtration equipment is stored downstairs. For a short while it was unsure whether they would be able take OSD samples at all, but Team Helgoland successfully overcome this problem as well. With combined team power they were able to pump the water out in time!

Despite the whole stress, OSD Site Coordinator Dr. Antje Wichels managed to filter the OSD samples and took the opportunity to test their new filtration construction for the first time. It has  been designed by  Dr. Gunnar Gerdts and built by in-house technicians for future large scale sampling campaigns using Sterivex filters. The construction worked well and it was possible to filter up to 6 samples at the same time, but it also revealed room for improvement. This clearly shows the benefit of a pilot study which gives us enough time to prepare and optimize protocols for the main OSD event.

I would like to take the opportunity to thank Antje, Gunnar and Team Helgoland for their sampling effort despite all incidents. And also thanks to all other OSD participants for reporting and exchanging experience. Every habitat has its own conditions and your observations help us a lot to optimize the protocols.

Anna Klindworth

Samples from OSD pilot study summer 2013

Sampling Boat "Aade" from the Biologische Anstalt Helgoland. Photo has been taken when the sun was shining :)

Dr. Antje Wichels is testing the new construction for simultaneous Sterivex filtration

Towards an OSD Data Policy

Draft OSD Data Policy

The OSD data policy applies to everyone in the OSD Consortium (to date this means everyone who has constructively contributed to OSD sampling events). The draft policy describes the tenets of data sharing in OSD, release of the data, and the membership in and authorship with the OSD Consortium. The current draft of the OSD Data Policy is here along with the members of the OSD Data Policy Working group:

https://docs.google.com/document/d/1qOliwqSnreJUKZqSK1Yjmok8onM_pwsEf4IghKksH3Y/edit

Status to date

This first draft data policy covering the collection, dissemination, analysis and publication of OSD data has been developed in 2012/13 during the pilot events of OSD. Within Micro B3, WP8 is responsible for the Micro B3 data policy.  The OSD policy will be based on this policy.  We welcome input from all OSD participants on shaping of the OSD data policy. Please send comments to osd-contact@microb3.eu.

Next steps

This draft data policy is undergoing OSD community consultation until the end of 2013 and will be finalized and voted upon in the Micro B3 General Assembly (GA) planned for April 2014 and then adopted.  It will remain the responsibility of the OSD Data Policy working group to make sure the policy is fit for purpose and all are aware of it when submitting and using data of the OSD Consortium.  If you would like to join the group please contact osd-contact@microb3.eu.

Background:

We are developing the OSD Data Policy by drawing on existing policies (See Biosharing: http://biosharing.org/policies), current best practice in genomics and the needs of Micro B3 and the OSD community.  We are developing the policy according to the “12 steps to a data policy” outlined in Field et al (2009) Science:

12 Step Path to a Data Policy: 

http://blog.biosharing.org/2010/02/12-steps-to-creating-data-sharing.html

OSD is teaming up with Summer Sailstice

OSD is partnering with Summer Sailstice who is currently asking sailors to volunteer for testing the Sampling Kits and Smartphone App. The latter are required for our planned citizen science and crowdfunding project starting on October 1^st until November 10^th (UNESCO World Science Day), 2013. We are really grateful for the support of the Summer Sailstice Team and we are looking forward to a successful citizen science campaign.

Fair winds to all sailors!

River Sampling Day Call

Background to River Sampling Day (RSD)
RSD is a sister initiative to Ocean Sampling Day, the global marine sampling campaign which is part of the EU-funded Micro B3.
Microbial communities in rivers are greatly under-researched, even though they play important roles in the biogeochemical cycling of nutrients and carbon, and the clean-up of freshwater pollution. To help address this gap in knowledge, we are launching River Sampling Day (RSD), a simultaneous sampling campaign of the world’s rivers. The RSD pilot study will take place in 2013 on the solstices (June 21st and December 21st). The Samples collected on these days will be contextualized by the same environmental parameters and will be processed together in the same way. As one dataset, they will provide insights into fundamental rules of riverine microbial diversity and function, and will provide a snapshot of the microbial seed bank in participating rivers and river catchments. We hope that RSD 2013 will be the starting point of a coordinated long-term sampling campaign that will create a reference data set for other freshwater experiments in years to come. We also hope that sites participating in RSD will form the core of an international freshwater Genomic Observatories Network.


RSD pilot study
We have received pump-priming funds from the Centre for Ecology and Hydrology (CEH) to sequence 300 16S community profiles and 8 to 10 shotgun metagenomes from selected, well-contextualized sites. The aims of the pilot study are to build a network of future collaborators, to use the collected metagenomes to predict community metabolic potential and compare it to flux data (PRMT method, Larsen et al, 2011)
 and to develop an index of ‘indigenous’ to ‘transient’ riverine microbiota as a potential predictor of the levels of inputs and river health. Lastly we will use the data to develop an Ecological Niche Modelling approach in collaboration with BioVEL.

Call for participation in River Sampling Day
We would like to invite external researchers to join RSD. If you are associated with a river research site or other regular river research activity and would like to participate in the RSD pilot study please register using this link:
http://www.surveymonkey.com/s/W6T9HJZ

Ocean Sampling Day - Iceland - December 2012

Ocean Sampling Day‐ Winter solstice 2012‐12‐21 at Faxaflói, Iceland – Matis

Viggó Thór Marteinsson, Eyjólfur Reynisson and Kristinn Guðmundsson

Sampling was performed for the second 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) in a ruff sea and a strong wind (wind speed 20 m/sec) but the air temperature was unusually warm (8°C). Despite of heavy rolling and unstable conditions on board the small boat, we manage to collect three replicate samples from the sampling station from a depth of 0.2 meter using acid cleaned bucket. The sampling was at 12:30 o´clock on the winter solstice 2012‐12‐21.The water samples (1 L) were filtrated instantly on site through four 0.22 μm Sterivex filters (Millipore). Filtering time was around 50 min. Filters were sealed and immediately frozen at ‐196 °C in individual plastic tubes.

Two crew members (Eyjó and Kristinn) working on deck

A map of the OSD sampling site

View to the shore from the sampling site

Additional site information:

Air temperature: 8°C

Water temperature surface: 3,5 ̊C

Salinity 3,5

Wind speed 20 m/sec

All the best from Viggó and Eyjó

All About Ocean Sampling Day & How to Participate

Ocean Sampling Day (OSD) is a highly collaborative project contributed to by many.  It has a complex workflow that covers the capturing of samples from a global network of sites through data generation, analysis and publication.  As the OSD Consortium, we are working towards making information about OSD as public as possible. Consequently, we have collated information from our internal collaborative documents (OSD Collection Googledocs) and this blog post will serve to guide you through all OSD documentation. If you do not have access to any of the documents via the below links, please contact the OSD Core Team on osd-contact<at>microb3<dot>eu.

This list of documents is also for the benefit of the OSD Coordinators, as among formal documentation, all OSD activities are also documented.

1. OSD 2014 Pipeline:
We are pleased to introduced the official OSD 2014 Pipeline, which shows the workflow from sampling to shipping, and analysis to submission. This pipeline is now the official pipeline for the Main OSD Event to be held on June 21st, 2014, Saturday. It is based on in-kind contributions from OSD Partners, as well as agreements made around OSD Committee decisions on OSD Budget allocation, which was awarded from EU just to be allocated for the Main OSD Event in 2014.

2. OSD Sampling Protocol: Click to view the sampling protocol used for OSD Pilot Events.

3. OSD Shipping Protocol: Click to find out about how to ship your OSD-Pilot samples.


4. OSD Pilot Samples & Metadata Registration:
It is of ultimate importance to have supporting in-situ contextual data for your samples, hence we highly encourage all our participants to collect such metadata during sampling.

• Metadata for December 2013 OSD Pilot Samples: Click to register samples & metadata for December 2013 OSD Pilot samples. Read the first sheet for instructions.

• Metadata for June 2013 OSD Pilot Samples: Click to register samples & metadata for June 2013 OSD-Pilot samples. Read the first sheet for instructions.


• Metadata for December 2012 OSD Pilot Samples: Click to register samples & metadata for December 2012 OSD-Pilot samples. Read the first sheet for instructions.
  


• Metadata for June 2012 OSD Pilot Samples: Click to register samples & metadata for June 2012 OSD-Pilot samples. Read the first sheet for instructions.

5. OSD Pilot Pipeline: Below is the OSD Pilot pipeline, which shows the current workflow from sampling to shipping, and analysis to submission. Please note that this pipeline is not the official pipeline - it is all set up to serve the Pilot OSD project based on in-kind contributions from OSD Partners - therefore it may change as the project proceeds. Such changes will be reflected/updated in this blog.

5. How to Join OSD: Click to find out how to formally register your interest to take part in OSD.

6. OSD Weekly Telecons: Click to find out more on four telecons per week.

7. OSD Coordinators Network: Click to find out about OSD Coordinators and their areas of expertise.

8. OSD Sites: Click to view the list of OSD Sites who signed up for participation.

9. Status of OSD Sites: Click here to view the matrix of OSD Sites summarising their progress.  

10. OSD Analysis Report: Coming Soon
Contents will include:
OSD Analysis Rationale and Template, as well as results from June & December 2012 OSD pilots.

11. OSD Crowdsourcing Campaign: Click to read on related plans on citizen science engagement.

12. OSD Data Policy: Click to view the latest draft of the OSD Data Policy.

13. Additional Links for Co-ordinators:
All of the OSD internal documents are kept here.  Once you formally become part of OSD you will be given access. There are many documents. Please consult the OSD Core Team if you need help navigating or need to start a new document.

The master list of members of the consortium is here.

The master document for all of OSD is here.

14. How to contact the OSD Core Team: Click to find out how to contact us.

15. Documentation In Progress:

• Scientific rationale: Coming soon
• Sequencing and DNA prep: Coming soon
• Integration with environmental data: Coming soon
• Biotechnology applications: To be developed