| Summary: | The aims of this thesis were to characterize the molecular ecology of the hyporheic zone – between dissolved organic matter (DOM) and microbes – and to test whether seasonal and spatial patterns existed in correlation with seasonal ecosystem processes. The hyporheic zone is an area of vertical integration between groundwater and surface water, and lateral integration between terrestrial and stream ecosystems. Colonization corers were used to collect in situ DOM and bacterial communities from the hyporheic sediments of two streams that varied in hydroperiod (i.e., permanent vs. intermittent). DOM was collected using passive samplers and analyzed using 1H NMR and fluorescence spectroscopy; bacteria were characterized using terminal-restriction fragment length polymorphism. At the permanent site, bacteria correlated significantly with seasonal environmental factors including: fall communities with DOM concentration; spring and winter communities with nitrate concentrations; and summer communities with temperature. Bacterial communities at the intermittent site were significantly correlated with flooding as a function of hydrologic connectivity. Sediment communities were discriminated between hyporheic sediments and interstitial porewaters, and shared several operational taxonomic units (OTUs). Sediment communities were more distinct when hydrologic connectivity was low, and porewater communities changed dramatically upon flooding. Fifteen out of 259 OTUs were shared across aquatic sediments, interstitial porewater and watershed soil samples. DOM was spatially and seasonally dynamic in both sites. Five key DOM groups described using 1H NMR spectroscopy revealed spatial differences between the permanent and intermittent sites. EEM-PARAFAC models confirmed that despite significantly different molecular components, the relative sources of DOM at both sites were similar, including humic-like terrestrial sources and tyrosine (microbial) sources. This study provides new knowledge on both organic matter dynamics and bacterial communities in a dynamic aquatic ecotone, and also confirmed the hypothesis that bacterial communities correlated significantly with ecosystem processes within a watershed.
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