Bio-optics

The establishment of a national bio-optical research competency that will allow multi-ecosystem observations. SOCCO have recently set up a CapEx funded world-class bio-optical research facility under the leadership of Dr Sandy Thomalla. To date SOCCO have put in place new IOP sensors on the CTD’s, a multi-spectral profiling radiometre (C-OPS) and a Beckman Multisizer 4 for characterising the size distribution of the phytoplankton community. In Addition, SOCCO have developed an underway IOP system that can be set up to run in both underway mode (using the ships underway water supply) and bench top mode (using discreet water samples from CTD’s, bio-assay incubation experiments and cultures. The observational objectives of the underway IOP system are as follows: 1) Calibration‐independent hyperspectral measurements of particulate absorption ap(λ) and attenuation cp(λ) via periodic measurements of total (unfiltered) and 0.2 m filtered absorption at(λ) – aCDOM(λ), and attenuation ct(λ) – cCDOM(λ) 1,2 [WET Labs AC-S], 2) Supporting hyperspectral measurements of filtered absorption aCDOM(λ) using long pathlength (integrating cavity) absorption meter [TriOS OSCAR], 3) Multi-λ measurements of particulate backscattering bbp(λ) [WET Labs BB-9], 4) In‐line acidification of seawater for bbbp(λ), supporting PIC estimates, 5) simultaneous feeds of de-bubbled flow-through seawater to other flow-through instruments [e.g., Fast repetition rate fluorometry, Multi-λ excitation fluorometry]. The new bio-optics facility also includes autonomous platforms such as Gliders (with fluorescence and backscattering at two wavelengths) and specialised bio-optics floats with florescence, backscattering and beam attenuation sensors with the additional capability of measuring carbon export.

  • The underway IOP system on the SA Agulhas that measures Hyperspectral particulate and dissolved absorption a(λ) and attenuation c(λ), supporting hyperspectral measurements of dissolved absorption aCDOM(λ), multi-λ measurements of particulate backscattering bbp(λ), in‐line acidification of seawater for bbp(λ) supporting PIC estimates, simultaneous feeds of de-bubbled flow-through seawater for Fast Repetition Rate Fluorometry and Multi-λ excitation fluorescence
  • Two bio-optics floats with sensors for measuring temperature, salinity, dissolved oxygen, fluorescence, backscattering and beam attenuation at two wavelengths (red and blue).
  • The dry laboratory on the SA Agulhas II showing the Beckmann Coulter counter for characterising the size distribution and the SHIMADZU spectrophotometre for measuring spectral absorption.
  • The underway IOP system and accessory instruments in the wet laboratory on the SA Agulhas II.
  • Deploying the profiling radiometer C-OPS from Biospherical
  • The profiling radiometer C-OPS from Biospherical gets deployed over the side of the SA Agulhas
Related News and Publications

The establishment of a national bio-optical research competency that will allow multi-ecosystem observations. SOCCO have recently set up a CapEx funded world-class bio-optical research facility under the leadership of Dr Sandy Thomalla. To date SOCCO have put in place new IOP sensors on the CTD’s, a multi-spectral profiling radiometre (C-OPS) and a Beckman Multisizer 4 for characterising the size distribution of the phytoplankton community. In Addition, SOCCO have developed an underway IOP system that can be set up to run in both underway mode (using the ships underway water supply) and bench top mode (using discreet water samples from CTD’s, bio-assay incubation experiments and cultures. The observational objectives of the underway IOP system are as follows: 1) Calibration‐independent hyperspectral measurements of particulate absorption ap(λ) and attenuation cp(λ) via periodic measurements of total (unfiltered) and 0.2 m filtered absorption at(λ) – aCDOM(λ), and attenuation ct(λ) – cCDOM(λ) 1,2 [WET Labs AC-S], 2) Supporting hyperspectral measurements of filtered absorption aCDOM(λ) using long pathlength (integrating cavity) absorption meter [TriOS OSCAR], 3) Multi-λ measurements of particulate backscattering bbp(λ) [WET Labs BB-9], 4) In‐line acidification of seawater for bbbp(λ), supporting PIC estimates, 5) simultaneous feeds of de-bubbled flow-through seawater to other flow-through instruments [e.g., Fast repetition rate fluorometry, Multi-λ excitation fluorometry]. The new bio-optics facility also includes autonomous platforms such as Gliders (with fluorescence and backscattering at two wavelengths) and specialised bio-optics floats with florescence, backscattering and beam attenuation sensors with the additional capability of measuring carbon export.

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