1. Achievements2. Data in IDP20173. Success, challenges, moving forward4. Linking genomic with Geotraces IDP data5. Expected data in IDP2021 Maite Maldonado input from Ben Twining, Mak Saito, Julie LaRoche, and Paul Berube (P. Chisholm’s lab) Hobart, Australia, Sept. 7, 2019

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BioGEOTRACES achievements

1. Completed 5 intercalibration protocols for: a) single cell trace metals; b) metagenomics; c) metalloproteomicsd) HPLC pigments; e) FRRF protocols

2. Created naming conventions for BioGeotraces parameters3. New BioGeotraces members for the S&I committee (Alyson Santoro)4. Various data sets submitted

Data in IDP20171. Mak Saito (prokaryotic proteomics) DATA in the IDP2017

a) submitted metalloproteomic data for Metzyme (now onto GA03)b) challenges with parameters naming: length of peptide sequences

PEP_VAAEAVLSMTK_NiSOD_ProSyn_BOTTLE

2. Moffett/Bob Bidigare's (HPLC pigment data) DATA in the IDP2017 a) submitted HPLC pigment data for GP16 & GA10

3. Ben Twining (single cell trace metals) DATA in the IDP2017v2a) submitted single cell trace metals data for GA03 & GP16

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4. Maite Maldonado DATA not in the IDP2017 or v2, (not a priority)a) submitted HPLC pigment data for Canadian Arctic 2015, Leg 2

5. LaRoche lab (16s, 18s diversity and abundance, gene abundance) GA03:DATA not in the IDP2017 or v2a) submitted data for IDP2017 (nif gene for GA03)b) her intercalibration report to the S&I committee was sent too late

Data not in IDP2017 Bio

Data not in IDP20176. Chisholm lab (Paul Berube, Sara Collins, Shane Hogle) (Prochlorococcus/Synechococcus ) DATA not in the IDP2017 or v2

analyzed 3 types of BioGEOTRACES data:

1) relative taxonomic counts for all stations & depths sampled2) 630 metagenomics & 3) 623 single cell genomics

These data are dynamic and too complex for GEOTRACES IDPSubmitted genomic data to NCBI & JGI

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Problem: # will change depending on ever-growing genome reference databasesSolution: dynamic output; generate # depending on database

DATA Type 1: depth profile of relative taxonomic counts

DATA Type 2: Single cell genomics & 3: Metagenomics

SOLUTION: Create special portal for these data in IMG within Department of Energy Joint Genome Institute (JGI)

.

https://gold.jgi.doe.gov/study?id=Gs0127550

IMG for BioGEOTRACES Single cell genome inJGI GOLD: Project Gs0127550

NOW…..

NOW…..IMG for BioGEOTRACES Single cell genomes inJGI GOLD: Project Gs0127550

ADD GEOTRACES as an External Project link?

See Reiner’s presentation

NCBI Single Cell Genomics(raw genomic data) Accession # Project ID

NCBI Single Cell Genomics

NCBI Single Cell Genomics

NCBI Single Cell Genomics

NCBI Metagenomes.... Accession # Project ID

Each Single Cell Genome

IMG & IMG/ProPortal

ProjectGold Study

0127550

Each metagenome

IMG & IMG/ProPortal

NCBI

NCBI project385854

Each metagenomeAccession #

& extra info :

GEOTRACES cruise, section, bottle #, …

NCBI project445865

Each genomeAccession # extra info :

GEOTRACES cruise, section,

bottle #, …

IMG accession #

IMG accession #NCBI project #

and/or accession #NCBI project #

and/or accession #

Working on…Chisholm1. Incorporating GEOTRACES data into these genomic data portalsa) Now the genomic data in NCBI and JGI is publicb) Working with Reiner to extract TEI data from GEOTRACES to

incorporate into NCBI and JGI data portals....

2. Incorporating links to genomic data portals in GEOTRACES IDPa) Paul Berube: table where to find the BioGeotraces genomic data b) Can we incorporate project /accession # in IDP2021? HOW? FOR EACH BOTTLE ID: 1 METAGENOME & 50 SINGLE CELL GENOMEs; indicate ONLY Bioproject ID in ncbi

(ID 385854 for metagenome & ID 445865 for single cell genomes)OR Simply highlight stations with genomic data?

.

Chisholm’s papers published

Chisholm’s papers published or almost submitted

3. Hogle et al. Siderophore-mediated iron acquisition by marine picocyanobacteria: Evidence for adaptation across ocean basins. (includes Geotraces chemical data) (In preparation).4. Satinsky et al. Examine relationships/patterns between the metabolic capabilities of Prochlorococcus communities and macro- & micro-nutrient distributions (In preparation).

Working on...1. Ben Twining (single-cell metals):

a) analyzed single-cell metals for US Arctic GEOTRACESb) pulled together all SXRF quota data into a harmonized database (~ 80 stations globally), not all GEOTRACES projects & not all published, but analyzed following GEOTRACES compliant manner.

2. LaRoche lab (16s, 18s diversity and abundance, gene abundance): a) more data to submit….

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nifH qPCR assay specific for the novel isolate BB40, a gammaproteobacterium

French GEOVIDE (GA01)(Geotraces) Summer 2014

LaRoche Lab

N2

fixat

ion

(µm

olN

m-2

d-1)

Dr. Debany Fonseca P. Batista (OFI international Postdoc)

BB40 nifH copies/L

Log nifHcopies/L

N2 fixation rates

2. LaRoche• GA03 (USA) Southern North Atlantic transect

– DNA samples/nifH qPCR– Published (Ratten et al. 2015 Deep-Sea Research special issue)

• GA01 (France) Geovide cruise Northern North Atlantic transect/Labrador Sea– DNA samples/glyTE samples for single cell analysis – Partly published

• Fonseca Batista et al 2019, Biogeoscience nifH and N2 fixation• Louropoulou et al. 2019, Frontiers in Aquatic Microbiology Heme distribution and phytoplankton(metabarcoding of chloroplast 16S rRNA genes)

• GN01 (Canada) Canadian Arctic cruise– DNA samples/flow cytometry/16S and 18S rRNA gene – Manuscripts in prep

• Microbial community structure in the particulate Mn maximum• Diazotrophs and phytoplankton community structure in the Canadian Arctic Ocean

• GI07 (Germany) Southern Indian Ocean cruise 2020– In planning: DNA samples, amplicon sequencing, metagenomics, flow cytometry, N2 fixation

Diagnosing Nutrient Stresses of Eukaryotic Phytoplankton: Dinoflagellates on the METZYME Geotraces-compliant section, Cohen et al., submitted

dFe[nM]

NO3 + NO2 [µM]

Urease [TPM counts]Iron starvation induced 2A [TPM counts]

𝑈𝑈𝑈𝑈𝑈𝑈𝑈𝑈 + 3 𝐻𝐻2𝑂𝑂 → 𝐶𝐶𝑂𝑂2 + 2𝑁𝑁𝐻𝐻4𝑂𝑂𝐻𝐻

Offshore dinos upregulate NO3 and Fe transporter and/or other proteins depending on nutrient levels

3. Mak Saito (prokaryotic proteomics)a) More Metzyme Pacific data submitted to BCO-DMO

b) Led Ocean Metaproteomics Data Sharing & Best Practices Workshop, Saito et al. 2019 Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. J. Proteome Res.

c) Metaproteomic intercalibration funded by OCB, led by Saito and McIlvin

d) Ocean Protein Portal funded by NSF EarthCube, launched

e) METZYME compliant raw spectra loaded PRIDE repository (16000 proteins)

d) Clio: a vehicle for BioGeotraces sampling

Ocean Protein Portalhttps://proteinportal.whoi.edu/

Clio (by Chip Breier &WHOI)

• A vehicle for BioGEOTRACES• Particulate sampling occurring off-wire during

TM/CTD rosette casts • Allows particulate metal & omics samples (with

preservation) to be collected simultaneously at each depth

• Trace metal clean & Deployed vertically

CLIO Example Operations:Full Depth Particulate Off-Wire Sampling during other

deck operations (CTD and Trace Metal Rosette Sampling)

Enable ship-based, full depth, high-throughput acquisition of filtered biochemical,genomics, transcriptomics, and chemical samples on ocean sections and time series

Clio Update• Completed Bermuda– WHOI Transect: June of 2019

• 9 Dives comprising an upper 1000m section

• 18 samples per dive, glass & membrane filters for (POC, pTE), 9-18 depths over ~14 hours (could be increased, only 2 of 4 payload bays utilized)

• Successfully tested adaptive sampling of the Chlorophyll maximum using sensors (Clio identifies the max and selects depths in real time)

• Over 20,000L filtered on the section and over 2000 discrete samples from Clio (dissolved, particulate phases, omics, metals, POC, nutrients etc).

• Funded work for the Pacific OMZ in 2021

Moving forward• Keep supporting submissions from the BioGeotraces labs for

IDP2021

• Come up with ways to integrate/cite complex (dynamic) BioGeotraces data sets in the Geotraces IDP (Paul Berube, MakSaito, Reiner)

• AND viceversa

Identified national BioGeotraces representatives…Sweden: Angela Wulff, angela.wulff@bioenv.gu.se; Helle Ploug, helle.ploug@marine.gu.seAnna Godhe, anna.godhe@marine.gu.seSouth America (Chile) Rodrigo Torres, rtorres@ciep.clRussia Mikhail Flint, m_flint@ocean.ru, m_flint@orc.ruS. Africa Susanne Fietz, sfietz@sun.ac.zaFrance Ingrid Obernosterer, obernosterer@obs-banyuls.frGermany Anja Engel, aengel@geomar.de; include Sebastian Rokitta, sebastian.rokitta@awi.deJapan Kohji Suzuki, kojis@ees.hokudai.ac.jpThe Netherlands Corina Brussaard, Corina.Brussaard@nioz.nl; Rob Middag, rob.middag@nioz.nlTaiwan Tung-Yuan Ho, tyho@gate.sinica.edu.twUK Mark Moore, cmm297@noc.soton.ac.ukUSA Mak Saito, msaito@whoi.eduSpain Patricia Ziveri, patrizia.ziveri@uab.catAustralia/New Zealand Phil Boyd, philip.boyd@utas.edu.auIndia no bioGeotraces activitiesChina Dalin SHI (Xiamen Univ.), dshi@xmu.edu.cnIsrael: Ilana Berman-frank <Ilana.Berman-Frank@biu.ac.il>