Sedimentary microbial communities play a critical ecological role in lotic ecosystems and are responsible for numerous biogeochemical transformations, including dissolved organic matter (DOM) uptake, degradation, and mineralization. The goals of this study were to elucidate the benthic microbes responsible for utilization of humic DOM in streams and to assess overall variability in microbial biomass and community structure over time and across multiple spatial scales in stream networks, as DOM quality and quantity will likely change with stream order. In Chapter 2, multiple spatial patterns of microbial biomass and community structure were examined in stream sediments from two watersheds; the Neversink River watershed (NY; 1st, 3rd and 5th order streams sampled) and the White Clay Creek watershed (PA; 1st through 3rd order streams sampled). Microbial biomass and community structure were estimated by phospholipid phosphate and phospholipid fatty acids (PLFA) analyses. Multivariate analysis showed that sedimentary C:N ratios, percent carbon, sediment surface area and percent water content explained 68% of the variations in total microbial biomass. Overall, the magnitude of within stream variation in microbial biomass was small compared to the variability noted among streams and between watersheds. Principal component analysis (PCA) of PLFA profiles showed that microbial community structure displayed a distinct watershed-level biogeography, as well as variation along a stream order gradient. Chapter 3 demonstrated that benthic microbial biomass was seasonally dynamic and significantly correlated to a combination of high and low flood pulse counts, variability in daily flow and DOC concentration in the White Clay Creek. Additionally, the seasonal pattern of variation observed in microbial community structure was as a result of shift between the ratios of prokaryotic to eukaryotic component of the community. This shift was significantly correlated with seasonal changes in median daily flow, high and low flood pulse counts, DOC concentrations and water temperature. Compound-specific 13C analysis of PLFA showed that both bacterial and microeukaryotic stable carbon isotope ratios were heaviest in the spring and lightest in autumn or winter. Bacterial lipids were isotopically depleted on average by 2 - 5 / relative to δ13C of total organic carbon suggesting bacterial consumption of allochthonous organic matter, and enriched relative to δ13C algae-derived carbon source. In Chapter 4, heterotrophic microbes that metabolize humic DOM in a third-order stream were identified through trace-additions of 13C-labeled tree tissue leachate (13C-DOC) into stream sediment mesocosms. Microbial community structure was assessed using PLFA biomarkers, and metabolically active members were identified through 13C-PLFA analysis (PLFA-SIP). Comparison by PCA of the microbial communities in stream sediments and stream sediments incubated in both the presence and absence of 13C-DOC showed our mesocosm-based experimental design as sufficiently robust to investigate the utilization of 13C-DOC by sediment microbial communities. After 48 hours of incubation, PLFA-SIP identified heterotrophic α, β, and γ- proteobacteria and facultative anaerobic bacteria as the organisms primarily responsible for humic DOC consumption in streams and heterotrophic microeucaryotes as their predators. The evidence presented in this study shows a complex relationship between microbial community structure, environmental heterogeneity and utilization of humic DOC, indicating that humic DOC quality and quantity along with other hydro-ecological variables should be considered among the important factors that structure benthic microbial communities in lotic ecosystems.

Fluvial systems have been estimated to transform, transport, or store 2.75 petagrams (Pg) of Organic Carbon (OC) per year. Although approximately 1Pg per year of terrestrial carbon is fluxed to the atmosphere through inland waters, little is known about the factors regulating its eventual ecological fate. 28 day lability incubations were conducted concurrent with the measurement of several environmental parameters including discharge, nutrient concentration, DO13C, and DOC:DON at several sites along Bigelow Brook and the East Branch of the Swift River, Massachusetts. Temporal and spatial variation of DOC, DOC:DON and DO13C were explored. Two distinct DOC consumption rates, short and long term, as well as overall consumption rate (k), were evaluated to determine the interactions with source, quality, and nutrients. Dissolved organic nutrient concentrations significantly increased long term consumption rates but had little effect on short term rates suggesting that short term rate may be tightly coupled to local, in stream, processes. The short term rate was significantly correlated to k. Interestingly, few significant relationships were found between various rate metrics and the source or quality of the DOC. A large recalcitrant DOC pool persisted after the 28 day period suggestive of downstream export of a large fraction of initial DOC pool.

Drier and hotter conditions linked with anthropogenic climate change increase wildfire activity which can influence terrestrial and aquatic carbon cycles at broad spatial and temporal scales. Other aspects of environmental change such as climate warming enhance soil decomposition leading to accelerated rates of sedimentation and leaching from soils into aquatic systems, a phenomenon known as "browning." Large-scale ecological disturbances like wildfire can increase the occurrence of browning from post-fire erosion. I tested the effects of fire-treatment (burned vs. unburned plant material) and its interaction with terrestrial loading on dissolved organic carbon (DOC) composition, concentration, and degradation (biological vs. photochemical) in freshwater mesocosms. DOC concentration increased nonlinearly with added plant material in both burning treatments and degraded most rapidly at intermediate concentrations, indicating that decomposition at intermediate concentrations removes DOC at a faster rate than at higher concentrations. Excitation-Emission Matrix (EEM) fluorescence spectroscopy showed that the effect of fire and browning changed chemical signatures apparent in the EEMs, and that both mainly affected the humification index and the specific ultraviolet absorbance at 254 nm over time. Incubations showed that biodegradation contributed more to DOC decomposition than photodegradation, and that DOC decomposition was most rapid at intermediate loading levels likely because anoxia at high terrestrial input inhibited microbial activity. My thesis shows that fire and browning elicit non-linear responses in the dynamics and composition of DOC in aquatic systems, and that fire alters the chemistry of organic detritus in ways that impact its processing and role in aquatic environments.