Connecting organic to mineral: How the physiological state of an ecosystem-engineer is linked to its habitat structure

•Biochemical markers can be informative for monitoring bioengineered habitats.•Management measures should cover multiple bioconstruction types and phases.•Physiological distress is not correlated with retrograding bioconstructions.•Worms in retrograding bioconstructions have a higher quantity of available food.•Three biochemical markers stand out as relevant physiological state descriptors.