One of most essential equipment is CTD (conductivity, temperature, depth). Maybe 1st generation of CTD mainly measure the properties but nowadays scientists use for measuring lots of properties such as oxygen, light, particle concentration, etc. depending on extra sensors you attach on CTD. Also, CTD is equipped with bottles called Niskin that allow collecting water at any depth.
The bottles and all other equipment are controlled on deck.
CTD is best friend!
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