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 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.

2. OSD Sampling Protocol: An updated protocol will be posted soon. Click to find out about the sampling protocol used for June & December 2012 Solstice OSD-Pilot Events.

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

4. OSD 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 June 2013 OSD Pilot Samples: Click to register samples & metadata for June 2012 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. How to Join OSD: Click to register your interest to take part in OSD officially.

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

OSD Core Team visits the OSD BioArchiving Facility at the Smithsonian Institute's Natural History Museum!

Left to right: Anna Klindworth (OSD Coordinator), Mesude Bicak (OSD Coordinator/Bioinformatician), Katja Lehmann (RSD Coordinator) and The Smithsonian Goose!

The Smithsonian Institute's BioRepository (Museum Support Center (MSC)), also serves as OSD's BioArchiving Facility! It is a collections storage and conservation facility which houses Smithsonian collections which are not on display in the museums. BioRepository also houses material for projects in biodiversity, phylogenetics, population genetics, toxicology, environmental monitoring, etc. since the early 1970s. It is a state-of-the-art storage and conservation facility and its climate-control system maintains the desired environmental conditions in all areas of the building year-round. (See the MSC webpage for further details.) 

OSD samples will be stored at the -80°C mechanical freezers of the lab!

Mechanical freezers (-80°C)

All freezers and refrigerators in the Biorepository are continuously monitored by an electronic system that calls responders during an outage or other emergency. This monitoring system is also accessible via a secure web application, so freezer temperatures can be checked remotely at will. In addition, state-of-the-art tracking and barcodes systems allow you to easily find and track your samples. So we can be sure that our OSD samples stored at the MSC are safe and trackable :) 

Monitoring system

As part of the tour, BioRepository Coordinator Chris Huddleston also introduced as to the Sampling Robot, which is used to position and label sampling tubes with the barcodes/vouchers that are used for identification. 

Sorting Robot

Barcodes!

Sampling tubes

As part of OSD Pilot, two samples from the OSD Sites Helgoland & Belgium were sent to the BioRepository. We were very excited to find them enjoying their new home at the BioRepository freezers! Special thanks to Antje Wichels (OSD Helgoland Site Coordinator) and Simon Claus & Klaas Deneudt (OSD Belgium Team) for their magnificent efforts and making the pilot pipeline a success!

                

OSD Belgium Sample from June 2012 Solstice   OSD Helgoland Sample from June 2012 Solstice

BioRepository also contains large liquid nitrogen freezers which allow storage at -196°C (-321°F). We had a great time exploring them! 

OSD Core Team would like to thank Katharine Barker (Smithsonian's Global Genome Initiative Coordinator) for organizing and Chris Huddleston (BioRepository Coordinator) for giving us a great tour!

Photos: Courtesy of Anna Klindworth & Katja Lehmann.

How to Contact us

The OSD Core Team consists of Professor Dawn Field (OSD Lead Coordinator), Dr. Mesude Bicak (OSD Coordinator/Bioinformatician) and Dr. Anna Klindworth (OSD Coordinator). 

For any questions or to obtain info/assistance, you can contact us by sending an email to: osd-contact<at>microb3<dot>eu.

Further to OSD Core Team, OSD Network also contains many other OSD Coordinators, which are listed here.

From Left to Right: Frank Oliver Glöckner (Micro B3 Coordinator), Anna Klindworth (OSD Core Team), Mesude Bicak (OSD Core Team), Katja Lehmann (River Sampling Day Coordinator) and Dawn Field (OSD Lead Coordinator).

OSD Sites

Below is the current list of all OSD sites. This list is growing very quickly!

As part of OSD, Micro B3 we are working towards an OSD Sites Registry. As a first step for this goal, we have put together a list of sites in OSD this far! Many thanks to all Site Co-ordinators for their help and contributions! 

For now, we just picked “short names” as site names, with an aim of making "unique ID" name generation easier for corresponding site samples.

Existing OSD Sites: 
If there are any changes/additions you'd like to make, please tell us via osd-contact<at>microb3<dot>eu.

New Potential OSD Sites: 
If you would like to register your site in OSD, please check our blog on "Joining OSD" - link can be found on the top-right of this page.

List of OSD Sites:

1 L4 Institution: Western Observatory Channel, Plymouth Marine Laboratory Country: UK Site Lat,Lon: 50.25, -4.22 Institution Lat, Lon: 50.150, -4.131 2 Roscoff Institution: Station Biologique de Roscoff, France Country: France Site Lat,Lon: 48.778, -3.938 Institution Lat, Lon: 48.719, -3.990 3 Helgoland Institution: Biologische Anstalt Helgoland (BAH) - Alfred Wegner Institute (AWI) Country: Germany Site Lat,Lon: 54.18194, 7.9 Institution Lat, Lon: 54.183, 7.88861 4 Naples Institution: Stazione Zoologica Anton Dohrn Country: Italy Site Lat,Lon: 40.808, 14.25 Institution Lat, Lon: 40.8312, 14.226 5 Crete Institution: Hellenic Centre for Marine Research Country: Greece Site Lat,Lon: 35.78, 24.92 (when bad weather, samples collected from 35.66N 24.99E) Institution Lat, Lon: 35.33, 25.28 6 Blanes Institution: Institut de Ciències del Mar (CSIC) Country: Barcelona, Spain Site Lat,Lon: 41.666667, 2.8 Institution Lat, Lon: 41.385, 2.197 7 Moorea 
 Institution: Moorea EcoStation (UC Berkeley Gump Station and CRIOBE CNRS-EPHE USR3278) Country: Tahiti, French Polynesia Site Lat,Lon: -17.50, -149.83 Institution Lat, Lon: -17.4907, -149,8261 8 BATS Institution: The Bermuda Biological Station for Research, Inc. (BBSR) Country: USA Site Lat,Lon: ? Institution Lat, Lon: 32.166667, -64.5 9 SPOTS Institution: San Pedro Ocean Time Series, USC Microbial Observatory, University of Southern California Country: California, USA Site Lat,Lon: 33.58, -118.38 Institution Lat, Lon: 32.87, -117.23 10 HOT Institution: ? Country: USA Site Lat,Lon: ? Institution Lat, Lon: ? 11 Rothera Institution: Rothera Research Station / NERC British Antarctic Survey Country: Antarctica / UK Site Lat,Lon: -67.57, -68.13 Institution Lat, Lon: -67.5667, -68.1333 12 Churchill Institution: Churchill Northern Studies, University of Guelph Country: Canada Site Lat,Lon: 58.73, -94.07 Institution Lat, Lon: 58.73, -94.07 13 Thames Institution: Centre for Ecology and Hydrology Country: UK Site Lat,Lon: Multiple Institution Lat, Lon: 51.6015, -1.11 14 Banyuls Institution: Oceanology Observatory of Banyuls Country: France Site Lat,Lon: 42.49, 3.14 Institution Lat, Lon: 42.4803, 3.1336 15 Villefranche Institution: Observatoire Oceanologique de Villefranche sur mer Country: France Site Lat,Lon: 43.685, 7.326 Institution Lat, Lon: 43.6963, 7.3068 16 Kristineberg Institution: Sven Loven Centrum fur marina vetenskaper Country: Gullmarsfiord, Sweden Site Lat,Lon: ? Institution Lat, Lon: 58.876, 11.148 17 VLIZ Institution: Flanders Marine Institute Country: Oostende, Belgium Site Lat,Lon: 51.43333333, 2.80833333 Institution Lat, Lon: 51.233, 2.931 18 Nauset Marsh Institution: Woods Hole Oceanographic Institution Country: USA Site Lat,Lon: 41.83608333, -69.97183333 Institution Lat, Lon: 41.5245, -70.6710
19 North Cyprus Kyrenia Institution: Near East University Country: North Cyprus Site Lat,Lon: 35.36, 33.29 Institution Lat, Lon: 35.2290, 33.3248 20 North Cyprus Famagusta Institution: Eastern Mediterranean University Country: North Cyprus Site Lat,Lon: 35.198548, 33.919753 Institution Lat, Lon: 35.1436, 33.9096 21 Iceland Institution: MATIS Country: Faxafloi, Iceland Site Lat,Lon: 64.08, -22.13 Institution Lat, Lon: 64.128, -21.773 22 Croatia Institution: Institut Ruđer Bošković Rovinj Country: Croatia Site Lat,Lon: 45.08, 13.61 Institution Lat, Lon: 45.8294, 15.9869 23 Red Sea Institution: KAUST Country: Saudi Arabia Site Lat,Lon:  22.26711, 38.77321 Institution Lat, Lon: 22.3036098480225, 39.09812927246094

Ocean Sampling Day - Helgoland

In the German Bight, about 60 km off the estuaries of the Elbe and Weser rivers, lies the small rocky island Helgoland. Due to its highly diverse marine life and many different easily accessible intertidal and subtidal habitats, this location has attracted many scientists for more than 150 years. In 1873, the Helgoland Roads Data Series started with daily measurements of temperature and salinity which was extended to cover microbiology in 1963. This long-term series of daily measurements and water sampling is under the supervision of the Biologische Anstalt Helgoland (BAH - http://www.awi.de/en/institute/sites/helgoland/) and takes place at the ‘Kabeltonne’ on Helgoland Roads (54°11.3’N, 07°54.0’E).

Lange Anna ("Long Anna" or "Tall Anna") on Helgoland

The sample collection was carried out by the BAH. Although the North Sea can be rough in winter, the institute has a lot of experience to allow sampling almost every day throughout the year. The filtering process was carried out by Hilke Döpke in the lab. This time it was possible to filter 2 x 2L of water through a Sterivex Filter without a prior pre-filtration step. Due to the upcoming Christmas holiday we decided to postpone the shipping and rather store the samples at the BAH until January 2013.

A local airline offers regular flights from Helgoland to Bremerhaven

A couple of weeks ago we started to prepare shipping of the samples to Argonne National Lab in Chicago, USA. If you live on Helgoland it is sometimes challenging to plan for international shipping especially during winter season. Dry ice is mandatory for international shipping and the cold chain is often interrupted when the airplane or the ship cannot reach the island due to heavy weather conditions. Moreover, dry ice needs to be shipped from the mainland first and often it is sublimated when the ship finally reaches the island. Therefore we decided to do the shipping via the Max Planck Institute for Marine Microbiology (MPIMM) in Bremen. This means first of all we had to transport the samples to the mainland. This was done by airplane to avoid long transport time without proper cooling. In the next step, samples were picked up at the airport and transported to the MPIMM for further processing. Finally, with the samples stored at the MPIMM it was easy for us order dry ice and ship them to the US. Although shipping samples from Helgoland is challenging we think that the OSD is definitely worth the effort. Along with the contextual data provided by the Helgoland Roads Data Series we further believe that our samples can contribute to determine a baseline of marine biodiversity and functions on the molecular level.

Antje Wichels, Hilke Döpke, Gunnar Gerdts und Anna Klindworth