[Exports_project_office] EXPORTS and AtlantECO

Thu Sep 10 07:27:36 PDT 2020

Hi Uta

We have been sampling for metagenomics from MSC deployments at both SOTS
and Atlantic Southern Ocean in spring and summer as part of SCALE
programme. We have some data back from the SOTS cruise that our PhD student
is currently working up with co-supervisor Thulani Makhalanyani.

It would be great to share our respective sampling strategies as well as
participate in the proposed workshop on protocols to ensure that we adopt
possible improvements and best practices going forward.

I would be happy to send you (perhaps not everyone cc'd unless you are
particularly interested then please let me know) a methodology summary that
we have followed thus far and we can compare approaches and devise a best
practices approach for MSC sampling going forward?

Kind regards
Sandy

Dr Sandy Thomalla
Principal Scientist
Southern Ocean Carbon and Climate Observatory
CSIR

Tel: +27 (0)21 658 2764

*** Visit our new website: http://socco.org.za <http://socco.org.za/>***

On Wed, 9 Sep 2020 at 15:19, Passow, Uta <uta.passow at lifesci.ucsb.edu>
wrote:

> Hi,
>
> Yes some MSC samples went to "omics" (Alyson and Tatjana), but we have not
> seen results (they are being processed currently, due to delays due to
> obvious reasons). We'd be very interested in omic work on MSC samples in
> the Atlantic, but learned during our last cruise that we were severely
> volume limited for such sampling (and all the other samples we needed). I'm
> hoping that the situation will be better during 'spring" in the Atlantic
> (higher concentrations of "stuff"), but we do need to be careful not to
> spread ourselves too thin.
>
> I've cc Elisa Romanelli, my and Dave's student who is developing a
> sampling plan for the Atlantic, as it will be an important part of her
> thesis.
>
>
> Let's keep the discussion open!
>
> Cheers
>
> uta
>
>
> Let's keep communications open - and hopefully we get some results from
> the Pacific soon to guide us.
> On 2020-09-09 8:19 a.m., Stéphane PESANT wrote:
>
> Hi Dave,
>
> Thanks for the enthusiastic response. I will let you know as soon as we
> get confirmation that Tara could join EXPORTS, and then happy to join the
> planning team to coordinate with you.
>
> We are organising a workshop on AtlantECO standard protocols in late
> October, early November. I will forward you the invitation in case someone
> from your 'Omics team can join. In any case, let's plan an
> AtlnatECO/EXPORTS meeting after the workshop.
>
> Re. the Marine Snow Catcher, great that this was already in the planning.
> I will let Sandy pick up the discussion with Uta, Colleen and Alyson.
>
> Cheers,
> Stéphane
>
> Le 08/09/2020 à 19:49, David Siegel a écrit :
>
> 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
> URL: people.eri.ucsb.edu/~davey
>
> On Sep 3, 2020, at 10:32 AM, Stéphane PESANT <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
> [image: ORCID iD icon]https://orcid.org/0000-0002-4936-5209
> <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
>
>
>
> --
> Stéphane PESANT
> [image: ORCID iD icon]https://orcid.org/0000-0002-4936-5209
> <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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