Bacterial community profiles from sediments of the Anacostia River using metabolic and molecular analyses.

UNLABELLED: BACKGROUND AIM AND SCOPE: Though the tidal Anacostia River, a highly polluted riverine system, has been well characterized with regard to contaminants, its overall resident bacterial populations have remained largely unknown. Improving the health of this system will rely upon enhanced understanding of the diversity and functions of these communities. Bacterial DNA was extracted from archived (AR, year 2000) and fresh sediments (RE, year 2006) collected from various locations within the Anacostia River. Using a combination of metabolic and molecular techniques, community snapshots of sediment bacterial diversity and activity were produced. RESULTS: Employing Biolog EcoPlates, metabolic analysis of RE sediments from July revealed similar utilization of amines, amino acids, carbohydrates, carboxylic acids, and polymers at all sites. Normalized optical density measurements demonstrated that for most compounds, utilizations were similar though when differences did occur, the downstream site was enhanced compared to one or both of the upstream sites. Using denaturing gradient gel electrophoresis, bacterial diversity fingerprints of operational taxonomic units (OTUs) were obtained. Dendograms of the banding patterns revealed qualitative relationships as well as differences between replicate samples from similar sites. Replicates from the AR sites shared several common OTUs, while RE sites were more varied. Species richness and Shannon diversity indices generally increased with increasingly downstream locations, and were significant for the AR sediments (analysis of variance, P < 0.0001). Carbon and nitrogen content and concentration of fine grain sediment (<63 µm) were positively correlated with OTU richness (r (2) = 0.37, P = 0.0008; r (2) = 0.45, P < 0.0001; r (2) = 0.48, P = 0.001, respectively). CONCLUSIONS: This study demonstrated that the bacterial communities from all regions sampled were not only metabolically active with the capacity to utilize several different compounds as energy sources but also were genetically diverse. This study is the first to focus on the overall bacterial community, providing insight into this vital component of stream ecosystems. Understanding the bacterial components of aquatic systems such as the Anacostia River will increase our knowledge of the overall structure and function of the ecological communities in polluted systems, subsequently enhancing our ability to improve the health of this important tidal river.

Nutrients, oxygen dynamics, stable isotopes and fatty acid concentrations of a freshwater tidal system, Washington, D.C.

The Anacostia River in Washington, D.C., USA is an urban waterway contaminated with PAHs, PCBs, metals and sewage. Although several studies have examined the heavy metal geochemistry within the river, no studies have examined basic biogeochemical processes within the Anacostia river system. This study examines nutrients, bacterial biomarkers, organic material, and carbon, nitrogen and sulfur sources in the system. High biological oxygen demand and low nitrogen (0.33-0.56 mg L(-1)) and phosphorus (0.014-0.021 mg L(-1)) concentrations were observed in three areas of the river. Downstream sites had higher nutrient concentrations and dissolved organic matter (up to 13.7 mg L(-1)). Odd-chain length and branched fatty acids (FAs) in the sediments indicated bacterial sources, but long chain FAs indicative of terrestrial primary production were also abundant in some sediments. Sediment carbon stable isotope analyses showed a mix of autochthonous and allochthonous derived materials, but most carbon was derived from terrestrial sources (-23.3 to -31.7 per thousand). Sediment nitrogen stable isotopes ranged from -5.4 to 5.6 per thousand, showing nitrate uptake by plants and also recycling of nitrogen within the river. Sulfur sources were generally between 3 and -5 per thousand, reflecting local sulfate sources and anaerobic sulfate reduction.

Nitrifier and denitrifier molecular operational taxonomic unit compositions from sites of a freshwater estuary of Chesapeake Bay.

Temporal and spatial changes in the molecular operational taxonomic unit (OTU) compositions of bacteria harboring genes for nitrification and denitrification were assessed using denaturing gradient gel electrophoresis (DGGE), clone-based DNA sequencing of selected PCR products, and analyses of ammonium and organic matter concentrations. Sediment, overlying water, and pore-water samples were taken from different vegetated sites of Jug Bay National Estuarine Research Reserve, Maryland, during spring, summer, and fall 2006. OTU richness and the diversities of nitrifiers and denitrifiers were assessed by the presence of bands on DGGE gels, both ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were seasonally dependent. AOB OTU richness was highest in the summer when NOB richness was decreased, whereas NOB richness was highest in the spring when AOB richness was decreased. The OTU diversities of nitrifiers did not correlate with ammonium concentrations, organic matter concentrations, or the presence of vegetation. The OTU diversities of denitrifiers possessing either the nirK or nosZ genes were not seasonally dependent but were positively correlated with organic matter content (p = 0.0015, r2 = 0.27; p < 0.0001, r2 = 0.39, respectively). Additionally, the presence of vegetation significantly enhanced nosZ species richness (Wilcoxon/Kruskal-Wallis test, p < 0.008), but this trend was not seen for nirK OTU richness. Banding patterns for nirK OTUs were more similar within sites for each season compared with any of the other genes. Over all seasons, nirK OTU richness was highest and AOB and nosZ OTU richness were lowest (Wilcoxon/Kruskal-Wallis test, p < 0.0001). High levels of sequence divergence among cloned nirK PCR products indicate a broad diversity of nirK homologs in this freshwater estuary.