MicroRespire - review of existing and required parameter codes for respiration rate measurements in aquatic environments using different methods

[gwemon]

To start the review of semantic requirements, the following list of respiration methods was compiled by Carol Robinson with additions from Isabel Seguro Requejo and Gwen Moncoiffé:

1. In vitro incubations – water samples incubated in bottles kept as close as possible to in situ temperature and in the dark Four main combinations: Oxygen consumption during shipboard dark incubations measured with optodes Oxygen consumption during shipboard dark incubations measured with Winkler titrations Oxygen consumption during shipboard dark incubations measured with membrane inlet mass spectrometry Carbon dioxide production during shipboard dark incubations measured as 14CO2 production

Considerations:

• we will also need to distinguish between "on-deck" vs "in-situ" in-vitro incubations (beware of distinction between manipulation-free "in-situ" incubations (see below) and "in-situ" in-vitro incubations)
• all of these could be on size classes within the community
• with pre-incubation size fractionation through gravity fed filtration unit for example or from water and particles separated within a marine snow catcher – so need some indication of the ‘type’ of water sample. With optodes probably need a field detailing which type of optode. For winkler titrations probably need a field detailing how the endpoint is determined e.g. photometrically, spectrophotometrically, potentiometrically, amperometrically

2. In situ incubations – water sample enclosed in manipulation-free enclosures for a set period of time – measured in hours – in surface waters this would be over night time darkness (usually incubation is for full 24h to measure net community production so data used to derive respiration would be that collected during the period of darkness) - in mesopelagic waters you could measure over 24h darkness - incubators often deployed for days to months on moorings Two main combinations: Oxygen consumption measured within in situ incubators using optodes Oxygen consumption during in situ incubations as the difference between 18O-GOP and net O2/Ar changes

3. In situ incubations – water sample enclosed in some way for a set period of time – particles in the water separated from the bulk water sample Oxygen consumption of particle attached microbes measured within in situ incubators using optodes

4. In situ measurements using optodes on a variety of platforms – CTD, gliders, floats etc. Oxygen consumption derived from diel changes in in situ oxygen measured with optodes on gliders Oxygen consumption derived from diel changes in in situ oxygen measured with optodes on CTDs Seasonal oxygen consumption measured with optodes on BGC-Argo floats Seasonal consumption of particulate organic carbon based on BGC-Argo data

Considerations: – need to mention type of optode and time scale of measurement – daily, seasonal, annual – usually recorded as AOU, TOU etc.

5. Respiration derived from proxies of the activity of the electron transport system ‘Classical ETS’ Potential activity of the electron transport system (Vmax) of plankton cells captured on different sized filters

This requires indication of the type (usually GFF) and pore size of the filters used. Also the equation by which the activity is converted into oxygen consumption – this equation has changed over the years so the ideal would be to have the uncorrected ETS to be able to use the latest correction equation – also important is the volume filtered as this has some bearing on the effective pore size of the filter

Recent development is to size fractionate the water sample to assess the respiration of size classes of plankton – then need to use polycarbonate filters

In vivo activity of the electron transport system of plankton cells captured on different sized filters estimated from an enzyme kinetic model (EKM)

This is the latest suggested way to ‘correct’ the classical ETS to respiration – by measuring the activity of the enzymes on the actual sample – first used on AMT – so this is one o the ways of ‘correcting’ the ETS measurements but involved several more measurements so should be a ‘method’ in itself

In vivo activity of the electron transport system derived from the reduction of the tetrazolium salt INT during shipboard incubations of plankton cells captured on different sized filters

INT is a proxy for respiration – should record the raw formazan production data, the correction equation used, the filter size and type – the correction equation has changed over the years so ideally with the formazan we could back correct all the data with the same correction equation

6. Respiration derived from fluorescence of the dye Redox Sensor Green (RSG)

7. Respiration of zooplankton – these can either be mixed samples which have been size fractionated or individual zooplankton which have been picked out – need to record the size and method of separating, the type of net used to collect them, depth range

Zooplankton respiration derived from electron transport system activity (classical ETS technique)

This is a proxy of respiration, needs to be converted to oxygen consumption so ideally record formazan production and the conversion equation used as well as size, taxonomy etc of the zooplankton – usually collected on GFF filters

In vitro incubations of individual or mixed community of size class of zooplankton, incubated in a bottle for a set period of time at simulated in situ temperature and usually darkness – respiration derived from oxygen consumption – oxygen concentration measured with either optodes or winkler titrations – optodes need to record which type, winkler titrations need to record method of determining endpoint as above Zooplankton respiration derived from dissolved oxygen consumption measured with optodes Zooplankton respiration derived from dissolved oxygen consumption measured with Winkler titrations

[gwemon]

Decision (confirmed in meeting of 20/11/2023) is to create in a first instance, a set of detailed P01 parameter codes that contain key elements of methodology. We are proposing the following combinations for bulk water samples:

• [ ] Consumption rate of oxygen per unit time per unit volume of the water body by shipboard in-vitro incubations in the dark and Winkler titration

• [ ] Consumption rate of oxygen per unit time per unit volume of the water body by shipboard in-vitro incubations in the dark and optode

• [ ] Consumption rate of oxygen per unit time per unit volume of the water body by shipboard in-vitro incubations in the dark and membrane inlet mass spectrometry (MIMS)

• [ ] Consumption rate of oxygen per unit time per unit volume of the water body by in-situ in-vitro incubations and Winkler titration

• [ ] Consumption rate of oxygen per unit time per unit volume of the water body by in-situ incubator and optode

• [ ] Consumption rate of oxygen per unit time per unit volume of the water body by in-situ incubator and difference between 18O-GOP and net O2/Ar changes

• [ ] Production rate of carbon dioxide per unit time per unit volume of the water body

• [ ] Consumption rate of oxygen per unit time per unit area of the water body

• [ ] Production rate of carbon per unit time per unit area of the water body

• [ ] Production rate of formazan per unit time per unit volume of the water body [particulate >GF/F] -- this is for uncorrected ETS--

• [ ] Consumption rate of oxygen per unit time per unit protein biomass of biota {zooplankton}