Suppose the energy at the second trophic level as given in an energy pyramid is 100 kcal per square metre. It could mean either of the two following things:
- 100 kcal is the energy this primary consumer has stored in its flesh - that is, the energy left over from the amount consumed, after assimilation and respiration. This would be the net productivity of that consumer, or the energy available to the secondary consumer which feeds on this.
- 100 kcal is the energy this primary consumer consumes. It will utilise a part of this in respiration, lose some amount in assimilation, so that a small amount is left over which is then stored in it as mass, or flesh - which would be its net productivity.
Similarly, the first trophic level, the autotrophs' energy could represent either the total amount of food they make (the GPP), that is, the energy akin to the second case above, or the energy stored in them and available to the next trophic level (the NPP), like in the case 1 above. So which of these is correct - what do we represent as the energy of a trophic level in an energy pyramid? I think it should be the first case, the stored energies, since after all these are what you will measure as the energy of any trophic level - the stored energy at that level.