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The subsystem is where work is processed on the system.

Atmosphere:

Plants on land release oxygen during photosynthesis and the subsystem will be atmosphere because oxygen is finally processed on the atmosphere.

Geosphere:

Bacteria living underground converts ammonia to nitrates and the waste from livestock add nitrogen to the soil have geosphere as the subsystem  because both the process finally occur under the soil.

Hydrosphere:

Marine life adds carbon-dioxide to ocean water during respiration have hydrosphere as a subsystem because carbon-dioxide is finnaly processed in the water medium.