Coupling microbial incubations and Fourier transform infrared analysis shows differences in persistence among organic compounds in salt marsh soils

Salt marshes have a high capacity to stabilize organic carbon in their soils due to their high primary production and the prevailing anoxic conditions. However, halophytes transport oxygen to their rhizosphere, creating a heterogeneous environment where oxic, microoxic and anoxic micro-niches coexist. Understanding which mechanisms, beyond anoxia, protect organic matter (OM) from microbial consumption is crucial for explaining its persistence in the soil. We assessed the potential of soil microbial communities to consume carbon sources and to identify compounds that are preserved by mechanisms other than anoxia. Soil samples were collected at several depths, up to 89 cm, in 3 distinct halophyte communities and bare sediments in the Ria de Aveiro (Portugal). EcoPlates TM microbial incubations and Fourier-transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR) were successfully applied to explore OM microbial mineralization (38 samples). The soil samples showed a high spatial homogeneity in microbial potential consumption, regarding both depth and halophyte species. The high potential aerobic consumption of all samples showed that, in the case of soil erosion, aerobic degradation of the accumulated soil OM may begin with the existent microbial community. Two of the carbon sources that were not consumed were likely embedded within larger molecules—d-galacturonic acids in hemicellulose and 4-hydroxybenzoic acids in phenolic compounds. The latter may have been accumulated, thereby contributing to the role of salt marshes as carbon sinks. Our study shows the potential of microbial incubations coupled with FTIR to greatly increase our understanding of OM dynamics in salt marsh soils by exploring the accumulation of specific compounds.