Calculating the energy budget of an ecosystem requires measuring biomass at each trophic level, then measuring the production of new biomass per unit biomass. Respiration must be measured to distinguish between net and gross productivity. All these measurements involve samples, extrapolation, and a good bit of reasonable estimation to fill in blanks. Sometimes it's not clear who is eating whom and at what rate. Stable isotope analysis sometimes helps clarify feeding relationships.
Isotopes are atoms with the same number of protons but different neutrons.
Stable isotopes are isotopes that don't undergo radioactive decay. Many elements used by living organisms have naturally occurring stable isotopes. Living organisms, however, often contain different proportions of heavy and light isotopes because of differences in uptake or different food sources. For example, the carbon fixed during photosynthesis by C4 plants has proportionately more heavy isotopes than the carbon fixed by C3 plants. The differences in fixation of isotopes of C, N, and S by phytoplankton, upland C3 plants, and the C4 estuarine grass Spartina , were used to determine the source of food for the dominant mussel in New England salt marshes.