Ash-free-dry-weight determinations for a representative range of living brachiopod genera have revealed that a consistently high proportion of total organic mass is contained within the shell, partly as the organic matrix for biomineralisation and partly as minute extensions of the mantle tissues (caeca) housed within hollow endopunctae permeating the shell. On average 40% to 50% of the total organic mass of both articulate and inarticulate brachiopods is situated within the shell. This is true even for a rhynchonellid brachiopod which does not possess endopunctae, but which has a more dense protein matrix in its shell. The effectively hidden constituent of brachiopod tissue mass which is included in this component has often been overlooked, and as a result total metabolic tissue mass has been underestimated. This throws into question some previous interpretations of brachiopod respiratory and metabolic data.
The oxygen consumption rates of several living brachiopods have been measured, and when respiring tissue in caeca in the shell is taken into consideration, it is clear that brachiopod metabolic rates are low when compared with other marine invertebrates (e.g. between 10% and 50% of the oxygen uptake of comparable gastropods and bivalve molluscs held in similar conditions). This low rate cannot be attributed to a slower pumping rate by the brachiopod lophophore, as has been suggested, because the rate of water movement is comparable to that across the bivalve gill.
Nitrogen excretion rates have also been measured for a few living brachiopods, allowing a comparison with rates of oxygen consumption and providing an indication of the metabolic substrates used. These data on oxygen: nitrogen ratios suggest that one Antarctic brachiopod utilises exclusively protein as a metabolic substrate, while a temperate latitude species uses mainly protein during winter but lipids and carbohydrates during summer months. Histological observations, particularly of Terebratulina retusa from temperate waters, show that a specialised tissue layer in the brachiopod outer mantle epithelium proximal to the shell may be the site of storage of the protein that is metabolised during winter, and of carbohydrate mobilised during gonadal development in summer. The caeca have also been suggested as sites of storage of metabolites, and the possible relationships between these areas of mantle are discussed. It seems that the ability to store nutrients in the mantle, combined with flexibility of substrate utilisation and an inherently low metabolic rate, have been important factors in brachiopod evolution.