Jennifer W. Edmonds

Denitrification in a large river: consideration of geomorphic controls on microbial activity and community structure

Ecological theory argues that the controls over ecosystem processes are structured hierarchically, with broader-scale drivers acting as constraints over the interactions and dynamics at nested levels of organization. In river ecosystems, these interactions may arise from broadscale variation in channel form that directly shapes benthic habitat structure and indirectly constrains resource supply and biological activity within individual reaches. To evaluate these interactions, we identified sediment characteristics, water chemistry, and denitrifier community structure as factors influencing benthic denitrification rates in a sixth-order river that flows through two physiographic provinces and the transitional zone between them, each with distinct geomorphological properties. We found that denitrification rates tracked spatial changes in sediment characteristics and varied seasonally with expected trends in stream primary production. Highest rates were observed during the spring and summer seasons in the physiographic province dominated by fine-grained sediments, illustrating how large-scale changes in river structure can constrain the location of denitrification hotspots. In addition, nirS and nirK community structure each responded differently to variation in channel form, possibly due to changes in dissolved oxygen and organic matter supply. This shift in denitrifier community structure coincident with higher rates of N removal via denitrification suggests that microbial community structure may influence biogeochemical processes.

The Diverse Bacterial Community in Intertidal, Anaerobic Sediments at Sapelo Island, Georgia

The phylogenetic diversity and composition of the bacterial community in anaerobic sediments from Sapelo Island, GA, USA were examined using 16S rRNA gene libraries. The diversity of this community was comparable to that of soil, and 1,186 clones formed 817 OTUs at 99% sequence similarity. Chao1 estimators for the total richness were also high, at 3,290 OTUs at 99% sequence similarity. The program RDPquery was developed to assign clones to taxonomic groups based upon comparisons to the RDP database. While most clones could be assigned to describe phyla, fewer than 30% of the clones could be assigned to a described order. Similarly, nearly 25% of the clones were only distantly related (<90% sequence similarity) to other environmental clones, illustrating the unique composition of this community. One quarter of the clones were related to one or more undescribed orders within the γ-Proteobacteria. Other abundant groups included the δ-Proteobacteria, Bacteroidetes, and Cyanobacteria. While these phyla were abundant in other estuarine sediments, the specific members at Sapelo Island appeared to be different from those previously described in other locations, suggesting that great diversity exists between as well as within estuarine intertidal sediments. In spite of the large differences in pore water chemistry with season and depth, differences in the bacterial community were modest over the temporal and spatial scales examined and generally restricted to only certain taxa.

Variation in Prokaryotic Community Composition as a Function of Resource Availability in Tidal Creek Sediments

ABSTRACT In anaerobic coastal sediments, hydrolytic and/or fermentative bacteria degrade polymeric material and produce labile intermediates, which are used by terminal metabolizers to complete the conversion of organic material to CO2. We used molecular approaches to evaluate the response of two bacterial terminal metabolizer groups from a coastal tidal creek sediments, sulfate reducers and methanogens, to controlled changes in carbon resource supply. Tidal creek sediment bioreactors were established in April and August 2004. For each date, intact sediment sections were continuously supplied with flowthrough seawater that was either unamended or amended with the high-molecular-weight polysaccharide dextran. Biogeochemical data indicate that the activity of fermenting bacteria and the terminal metabolizers was limited by organic carbon supply during both experiments, with a significant increase in net volatile fatty acid (VFA) production and rates of sulfate reduction and methanogenesis following dextran addition. Community composition (measured by using terminal restriction fragment length polymorphism analysis, and functional gene [dsrA, mcrA] clone libraries) changed from April to August. However, community composition was not different between amended and unamended cores within each month, despite the change in resource level. Moreover, there was no relationship between community richness and evenness with resource level. This lack of variation in community composition with C addition could be attributed to the dynamic environment these sediment communities experience in situ. Fluctuations in VFA concentrations are most likely very high, so that the dominant bacterial species must be able to outcompete other species at both high and low resource levels.