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The assessment of organic matter (OM) sources in sediments and soils is a key to better understand the biogeochemical cycling of carbon in aquatic environments. While traditional molecular marker-based methods have provided such information for typical two end member (allochthonous/terrestrial vs. autochthonous/microbial)-dominated systems, more detailed, biomass-specific assessments are needed for ecosystems with complex OM inputs such as tropical and sub-tropical wetlands and estuaries where aquatic macrophytes and macroalgae may play an important role as OM sources. The aim of this study was to assess the utility of a combined approach using compound specific stable carbon isotope analysis and an
n-alkane based proxy (P
aq) to differentiate submerged and emergent/terrestrial vegetation OM inputs to soils/sediments from a sub-tropical wetland and estuarine system, the Florida Coastal Everglades.
Results show that P
aq values (0.13–0.51) for the emergent/terrestrial plants were generally lower than those for freshwater/marine submerged vegetation (0.45–1.00) and that compound specific
δ
13C values for the
n-alkanes (C
23 to C
31) were distinctively different for terrestrial/emergent and freshwater/marine submerged plants. While crossplots of the P
aq and
n-alkane stable isotope values for the C
23
n-alkane suggest that OM inputs are controlled by vegetation changes along the freshwater to marine transect, further resolution regarding OM input changes along this landscape was obtained through principal component analysis (PCA), successfully grouping the study sites according to the OM source strengths. The data show the potential for this
n-alkane based multi-proxy approach as a means of assessing OM inputs to complex ecosystems.