SEUS-MBON-cruise

This repo is the entry point for learning about the South-East US Marine Biodiversity Observation Network (SEUS-MBON) research cruise.

Quick links:

• ./pipeline : an overview of how collected data flows through processing steps and into data endpoints
• Data
  • USF Cruise data is in box.com/imars_mbon_cruises
• USF's Cruise Protocol
  • cruise scripts
• Specific Processing Efforts
  • BB3 : Sebastian's processing and matchup
  • Taxa occurrence data:
    • Zooplankton microscopy
      • ref 1
      • ref 2
    • eDNA processed by Anni Djurhuus and Enrique Montes
    • Sebastian's phytoplankton from Pigments
      • TODO: put this data into OBIS
  • CTD:
    • Mostafa's CTD Processing & Reports
    • Mostafa's additional data proceessin scripts

Background

MBON cruises taken in S FL starting in the 2016 and collections ongoing as of 2023. 2015 was a trial run, but funding began for the cruises in 2016. Chris Kelble has data from before 2015. Surface & CTD going back to 1998.

Digna has manually created a master spreadsheet to track this data that is stored in USF's box.com under mbon_imars_cruises. Sebastian created an R script to generate a spreadsheet that focuses in on a subset of the data. Ian Smith maintains this spreadsheet.

Data

Much of this data is hosted on box.com; the effort of putting things there was done by Sebastian. That data is here.

"Raw" data will soon be available in ERDDAP.

Data collected includes :

• CDOM
• a_ph, a_nap, and chlorophyll
  • all parameters come from the same sample
• HPLC
  • phytoplankton pigment data, extracted and QA/QC by NASA, further processesing by Sebastian and Anna
• eDNA
  • moved to NOAA AOML August 2022 and further crusies will also stay at NOAA.
• zooplankton microscopy
  • changed between Jaime (pre-2018) and Natalia (2018 - 2020)
    • Natalia's method is published. The published DwC data will have the protocol links.
    • Jaime's processed data:
      • published to OBIS
        • the dates are wrong as of 2023-01. See this issue.
• vessel flowthrough information
  • NOAA AOML submits to NCEI
  • Parameters: pCO2, temperature, salinity, etc.
• GER data (i.e. Rrs)
  • Enrique will have info
• BB3
  • raw count data
  • contact Herardo if he wants to process
• CAS data is processed through collab w/ GCOOS.
• CTD data available https://gcoos5.geos.tamu.edu/erddap/index.html
• TODO: add missing data mentioned by Chris Kelble and Kelly Montenero here

For more information you can contact:

• Sebastian
• Enrique : especially for eDNA and GER/SVC
• Digna
• Jenn : for instrument details

Ship Info

Most cruises are done on the R/V Walton Smith, two cruises used R/V Savannah, and one cruise used the R/V Weatherbird II.

• R/V Walton Smith (WS)
  • U Miami RASMES, Miami, FL
  • Most cruises
• R/V Savannah (SV)
  • Was docked in Miami for cruise
  • Skidaway Insititute of Oceanography, GA
  • Two cruises in early 2018
• R/V Weatherbird II (WB)
  • Florida Institute of Oceanography, St. Pete, FL
  • August 2022

Submission Locations

Data from this cruise is being submitted to

• SEABASS
  • a_ph
  • a_nap
  • a_CDOM
  • HPLC
  • GER
  • BB3
• OBIS
  • zooplankton

CDOM

The labwork of CDOM data analysis may be transitioning to be done in Miami and managed by Enrique & AOML in 2023. About 20 duplicate samples have been taken to verify that the results are the same when compared with existing methods. Some of these smaples were near-shore and others were offshore.

CDOM (wavelengths 200 to 800 nm) includes: abs_ag = gelbstoff (or CDOM) absorbance coefficient (averaged raw duplicate scans); ag = gelbstoff (or CDOM) absorption coefficient (null point corrected).

Absorption Pads

Absorption Spectra (wavelengths 400 to 800 nm) includes: abs_ap = Optical density spectra of total particulates (unitless); abs_ad = Optical density spectra of detritus (unitless); ap = Absorption spectra of total particulates (units: 1/m); ad = Absorption spectra of detritus (units: 1/m).

eDNA

Carolina and Anni in process of submitting eDNA occurrence data to OBIS (2023-03). Luke Thompson and Enrique in Miami watching over the project. Processed using OTU-based methods. DwC data will be submitted using occurrence core with the DNA extension. Carolina + Anni will be meeting weekly to push it forward.

HPLC

status (updated 2023-03)

HPLC sampled since 2015. We have HPLC data for many cruises. HPLC data has been sent to NASA SEABASS only from one cruise to 2016.

Sebastian found issues in HPLC metadata; Digna is working to clean it up and send to NASA SEABASS. Sebastian has the data almost read to submit

Phytoplankton

MBON phytoplankton pigment data was corrected using R.

Spectral

We submit the radience, irradience, and reflectance to SEABASS.

AOML is starting to collect spectral data in 2023. IMaRS's GER was last calibrated in 2012 and is owned by NOAA. The overlap of RRS is fairly similar. Magnitudes of raw radiance are different. Might be calibration errors, a units issue, or the program not taking into account integration time. The SVC software does show the same units when comparing. The GER is about 8x less than the measurement from the new SVC. David (Dave) English is the expert at AOML to figure it all out, the plan is to test the instrument.

Sebastian gives the data to Enrique and he puts it in a google drive. So long as AOML is taking scans then IMaRS does not need to.

chlorophyll

In the box.com cruise main folder with name like {year}_{month}_WS_abs.xlsx.

Protocols

Data Collection Protocols

In USF box.com.

TODO: add links?

Data Processing Protocols

Data processing for each cruise is done using R and organized here.