[Exports_project_office] EXPORTS and AtlantECO

Thu Sep 10 07:47:22 PDT 2020

Hi Stéphane

Thanks for opening up these ‘omics discussions. A couple of us on the EXPORTS team are also involved in developing an omics intercalibration and standardization effort for oceanographic field programs. We are specifically focused on developing standards for the collection, sampling, and processing of nucleic acid samples. We held a workshop to develop these ideas this past January.

https://www.us-ocb.org/ocean-nucleic-acids-omics-workshop/

It would be great to see how our two groups can collaborate. I’ve filled out the doodle poll and hope to make some of the upcoming AtlantECO workshops depending on when they are schedule. Echoing Tatiana’s statements, we are glad to discuss more or help out with sample collections on EXPORTS.

Scott

____________________________________

Scott Gifford
Assistant Professor
Sewell Family Foundation Fellow
Department of Marine Sciences
University of North Carolina at Chapel Hill
(919) 962-0269

From: Stéphane PESANT <pesant at ebi.ac.uk>
Sent: Wednesday, September 09, 2020 6:50 AM
To: T. Rynearson <rynearson at uri.edu>; David Siegel <david.siegel at ucsb.edu>
Cc: Laura Lorenzoni <laura.lorenzoni at nasa.gov>; Dave Siegel <davey at eri.ucsb.edu>; Ivona Cetinic <icetinic at gmail.com>; Sandy Thomalla <sandy.thomalla at gmail.com>; Lampitt, Richard S. <r.lampitt at noc.ac.uk>; exports_project_office at espo.nasa.gov; Giering, Sarah L.C. <s.giering at noc.ac.uk>; Uta Passow <passow at lifesci.ucsb.edu>; Emmanuel Boss <emmanuel.boss at maine.edu>; Lee Karp-Boss <lee.karp-boss at maine.edu>; Gifford, Scott Michael <sgifford at email.unc.edu>; Marchetti, Adrian <amarchet at email.unc.edu>; Nicolas Nicolas <nicolas.cassar at duke.edu>; Alyson Santoro <asantoro at ucsb.edu>; Colleen Durkin <cdurkin at mlml.calstate.edu>; Bethany Jenkins <bdjenkins at uri.edu>
Subject: Re: EXPORTS and AtlantECO

Hi Tatiana,

I pasted the email invitation below. Please fill in the Doodle.
Our protocols for Mission Microbiomes will be based on the ones developed for Tara Oceans, but we will streamline and make some improvements. We envision the following two strategies:

Discrete depth (e.g. surface or 400m)
*5x 20L-or-15min pre-filtered on 20µm and filtered in series on 3µm and 0.22µm 142mm membranes (each replicate is extracted individually but combined as needed for sequencing)
3x 10L of filtrate from the 0.22µm incubated/flocculated with FeCl3 and filtered on 1µm 142mm membranes
1x 10,000L (or more) concentrated either with a 20µm mesh net (horizontal tow) or with a McLane in situ pump, and prefiltered/sieved on 200µm
1x 100,000L (or more) concentrated with a 200µm mesh net (horizontal tow), and sieved on 2000µm
*we use to do 20L-or-15min for prok & euk MetaT, and 100L for euk MetaG, but now wish to do a single protocol 20L-or-15min with 5 replicates that can be combined bioinformatically in order to reach 100L for the euk.

Integrated layer (e.g. 10-120m)
**9 depths x 20L-or-15min pre-filtered on 20µm and filtered in series on 3µm and 0.22µm 142mm membranes (each replicate is extracted individually but combined as needed for sequencing)
3x10L of filtrate from the 0.22µm incubated/flocculated with FeCl3 and filtered on 1µm 142mm membranes
10,000L (or more) concentrated either with a 20µm mesh net (vertical tow) or with a McLane in situ pump, and prefiltered/sieved on 200µm
100,000L (or more) concentrated with a 200µm mesh net (vertical tow), and sieved on 2000µm
**the 9 depths would be sequenced separately so one can do MetaB/G/T on each depth, and can also combine bioinformatically the results to describe the entire layer, which is more comparable to the large size fractions collected with a vertical net tow over the same depth range.

A typical station where two discrete depths and an integrated layer are sampled (bgc+omics+imaging+plastics) would last about 24h.

Let's keep in touch. I am happy to join your team discussions if that helps.

... and follow/share with us on Twitter @EU_AtlantECO :)

Best,
Stéphane

===============
AtlantECO - First workshop on sampling and analysis protocols

Dear microbiome and microplastics enthusiasts,

I would like to invited you to participate to the first edition of the AtlantECO workshop on sampling and analysis protocols, planned for October/November this year.

AtlantECO will hold a standards & best practice workshop every year over the next four years to recommend sampling, biobanking and analysis protocols for the study of microbiomes, plastics and the plastisphere in marine, estuarine, sediment and atmospheric environments. Although our recommendations will be relevant to a wide range of applications (e.g. genomic observatories), our prime objective is to provide a coherent set of selected protocols that are adapted to the activities of AtlantECO, including dedicated cruises on oceanographic vessels and research sail boats, opportunistic cruises, the all-Atlantic Ocean Sampling Day, and the citizen sail-4-science. Every year, we will update an online handbook. AtlantECO project description: https://doi.org/10.5281/zenodo.3741972

The format of the workshop will be five VIRTUAL sessions from Monday to Friday:
Mon 15h-17h CET - Overview (speakers tbd)
Tue 14h-18h CET - Session 1. Microbiomes protocols (chair tbd)
Wed 15h-17h CET - Session 2. Plastics protocols (chair tbd)
Thu 15h-17h CET - Session 3. Plastic microbiome protocols, including experiments (chair tbd)
Fri 15h-17h CET - Sessions reporting & synthesis

In order to select a week with maximum participation, please indicate your availability in this Doodle: https://doodle.com/poll/qhmfwfr92k36rxd6
It is up to you to join one or many sessions. The handbook will also be open for review/comments during the following months.

Finally, I would like to draw your attention to this new Research Topic in Frontiers in Microbiology where we could aim to publish a few manuscripts in 2021 as an outcome of the first workshop: https://www.frontiersin.org/research-topics/15877/marine-microbiomes-towards-standard-methods-and-best-practices

Best regards,
Stéphane
==============

Le 08/09/2020 à 21:22, T. Rynearson a écrit :

Hi all, particularly Stephane,

Thanks for reaching out about the next EXPORTS cruise.  It would be great to collaborate as it sounds like we have synergistic goals. I think it makes sense for the exports 'omics group and your group to have a mtg sometime this fall.  As Dave mentioned, we're working on revising our plans at the moment.  I suggest that after our 'omics subgroup has written up a revised plan, we'll reach out to you so that we can see where where the most fruitful collaborations/additional samples lie.

In the meantime, if you have any documentation re. goals you'd like to accomplish as part of the EXPORTS collaboration, please feel free to send those along.  There could very well be bases that you'd like to cover that we simply don't have the bandwidth to touch.  Information on volumes needed may also help as we tackle the water budgets.

In terms of sampling, I or someone from my lab will be happy to help collect samples for you on the upcoming cruise.

All the best-

Tatiana
On 9/8/20 1:49 PM, David Siegel wrote:
Hi Stéphane,

Thanx for the email. The plan of the moment is for EXPORTS to charter the RRS Discovery and RRS James Cook. We would be sailing late May through end of June 2021 fromSouthampton UK, targeting a site near the PAP Observatory for 28 days of sampling. We are on the NOC and NERC schedules but are awaiting final approval and schedule in Oct. It also looks like the WHOI OTZ group will join us for 10 days on site on the R/V Sarmiento De Gamboa. The EXPORTS team is working on revising our plans from this year over the next couple of months. We have some challenges ahead (COVID ??'s, 6 fewer berths than our planned deployment for this year, working on UK vs. US ships, etc.). But we’ll get there.

We remain very interested in collaborating with AtlantECO and I have cc:ed here the ‘omics folks involved in EXPORTS. I severely doubt we will have available berths on either ship for additional participants.  Sorry.  However, I see no reason why samples cannot be collected for you, given proper preparation, etc.  If this comes to pass it would be great to have serious conversations amongst our teams so the details are worked through (sampling protocols, filters and primers used, etc.).

It would be awesome if Tara Ocean could join us and we are super happy to help facilitate operational logistics, collaborations, etc. Emmanuel Boss and Lee Karp-Boss are EXPORTS PI’s and can help make sure we Tara Ocean could extend the remote sensing capabilities of the deployment as well - furthering NASA’s mission.

The plan of the moment is to have marine snow catchers on the EXPORTS process ship. Uta Passow is the PI uncharge of the MSC collections, but she is not planning on sailing (we will work this out somehow…).  I know Colleen Durkin and Alyson Santoro have been working on ‘omics on collected aggregates from our North Pacific cruise and it would be great for them and Sandy to talk more.  So, the long answer is yes.

Hope this helps and it would be good for us all to talk over the next couple of months.

Best, Dave, Ivona and Laura

************************
David A. Siegel
Chair, Interdepartmental Graduate Program in Marine Science, and
Professor, Department of Geography and Earth Research Institute
UC Santa Barbara
Santa Barbara, CA 93106-3060, USA
Ph: 01-805-893-4547
Em: david.siegel at ucsb.edu<mailto:david.siegel at ucsb.edu>
URL: people.eri.ucsb.edu/~davey<https://urldefense.proofpoint.com/v2/url?u=http-3A__people.eri.ucsb.edu_-7Edavey&d=DwMFaQ&c=dWz0sRZOjEnYSN4E4J0dug&r=9-A3IUCipbuYyp1xathec2M2HhLHL0pWHIkoI4IiYd4&m=9VzBgwbSyRArW56U6a7MQNi-llsx2VXxwxBAtWFOsto&s=WwWfZdh4sXyvhx4xninTUxxGOpOlyqbw5g5bolNANmI&e=>

On Sep 3, 2020, at 10:32 AM, Stéphane PESANT <pesant at ebi.ac.uk<mailto:pesant at ebi.ac.uk>> wrote:

Dear Dave and Laura,

AtlantECO is kicking-off this month and I wanted to get back to you regarding our participation to EXPORTS next spring. We are still very much interested to come on board and contribute to the microbiome genomics programme, using AtlantECO's standard protocols based on Tara Oceans protocols.

Alternatively, there is a chance that our Mission Microbiomes on board Tara cannot leave for the South Atlantic this winter as planned. If that was the case, could Tara join EXPORTS to conduct targeted 'omics sampling in coordination with you before heading South?

Finally, Sandy Thomalla (cc'd) will do genomics on aggregates collected with a marine snow catcher in the Southern Ocean as part of AtlantECO, and we were wondering if something similar could be done as part of EXPORTS. Did you already plan to use a marine snow catcher, and did anyone plan to do 'omics on aggregates?

We look forward to getting your feedback on these ideas, and building synergies between EXPORTS and AtlantECO.

Best wishes,
Stéphane

AtlantECO project: https://doi.org/10.5281/zenodo.3741972
--
Stéphane PESANT
[cid:~WRD0000.jpg]https://orcid.org/0000-0002-4936-5209<https://urldefense.proofpoint.com/v2/url?u=https-3A__orcid.org_0000-2D0002-2D4936-2D5209&d=DwMFaQ&c=dWz0sRZOjEnYSN4E4J0dug&r=9-A3IUCipbuYyp1xathec2M2HhLHL0pWHIkoI4IiYd4&m=9VzBgwbSyRArW56U6a7MQNi-llsx2VXxwxBAtWFOsto&s=FWRBKz2DYFsYVKbVHChlkBye4eNYC19NK61_Drnbd8M&e=>

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

--

----------------------

Tatiana Rynearson

Professor

Graduate School of Oceanography

University of Rhode Island, Bay Campus

South Ferry Road

Narragansett, RI 02882-1197

Phone (401)874-6022

https://web.uri.edu/rynearson-lab/

--
Stéphane PESANT
[cid:~WRD0000.jpg]https://orcid.org/0000-0002-4936-5209

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
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