Abstract

Abstract This study uses dual‐labeled ( 13 C and 15 N) stable isotope applications to examine microbial uptake and short‐term processing of carbon (C) and nitrogen (N) from organic and inorganic compounds in subtropical intertidal sediment. Four treatment applications were applied: (1) algal dissolved organic matter (DOM), (2) amino acid mixture, (3) glucose and , and (4) NaHCO 3 and to assess bioavailability effects on processing (1 vs. 2) and short‐term processing for OM fixed via microphytobenthos only (pennate diatom dominated) (4) vs. material taken up by the entire microbial community (3) across 24 h. 13 C from algal‐DOM was preferentially used by the microbial community vs. 15 N. At 24 h more 13 C from algal‐DOM remained in microbial biomass indicating use of labeled precursor molecules to form biomass. Conversely, 13 C from the amino acid treatment was not incorporated into biomass and was either rapidly respired to DIC or discarded as the in situ microbial community preferentially used and retained 15 N from amino acids. Short‐term export of 13 C as CO 2 from glucose was lower than from microphytobenthos‐C, while retention of 15 N from was similar between treatments (3 and 4) despite doubling the application N concentration, suggesting potentially higher glucose‐stimulated 15 N export via nitrification–denitrification that was not confirmed via flux measurements in this study. Despite careful site selection for similar tidal exposure and sediment types among the three estuaries, the uptake and processing of labeled substrate varied substantially between replicates and sites which challenged traditional statistical analysis. Disproportionate processing of substrates occurring in sediment hotspots of microbial activity can cause variability spanning orders of magnitude which was found to be widespread through comparison of our results against 19 previous studies in intertidal settings. Development of robust analytical techniques to handle variability from abiotic and biotic factors will allow greater clarity surrounding in situ biogeochemical processing in intertidal environments.