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We investigated the effects of wastewater treatment plant (WWTP) discharge on the ecology of bacterial communities in the sediment of a small, low-gradient stream in South Australia. The quantification of genes involved in the biogeochemical cycling of carbon and nitrogen was used to assess potential impacts on ecosystem functions. The effects of disturbance on bacterial community structure were assessed by PCRdenaturing gradient gel electrophoresis of 16S rRNA genes, and clone library analysis was used to phylogenetically characterize significant shifts. Significant (P < 0.05) shifts in bacterial community structures were associated with alteration of the sediment's physicochemical properties, particularly nutrient loading from the WWTP discharge. The effects were greatest at the sampling location 400 m downstream of the outfall where the stream flow is reduced. This highly affected stretch of sediment contained representatives of the gammaproteobacteria that were absent from less-disturbed sites, including Oceanospirillales and Methylococcaceae. 16S rRNA gene sequences from less-disturbed sites had representatives of the Caulobacteraceae, Sphingomonadaceae, and Nitrospirae which were not represented in samples from disturbed sediment. The diversity was lowest at the reference site; it increased with proximity to the WWTP outfall and declined toward highly disturbed (400 m downstream) sites (P < 0.05). The potential for biological transformations of N varied significantly with the stream sediment location (P < 0.05). The abundance of amoA, narG, and nifH genes increased with the distance downstream of the outfall. These processes are driven by N and C availability, as well as redox conditions. Together these data suggest cause and effect between nutrient loading into the creek, shift in bacterial communities through habitat change, and alteration of capacity for biogeochemical cycling of N.

Biofi lms living on gold (Au) grains play a key role in the biogeochemical cycle of Au by promoting the dispersion of Au via the formation of Au nanoparticles as well as the formation of secondary biomorphic Au. Gold grains from Queensland, Australia, are covered by a polymorphic, organic-inorganic layer that is up to 40 µm thick. It consists of a bacterial biofi lm containing Au nanoparticles associated with extracellular polymeric substances as well as bacterioform Au. Focused ion beam (FIB) sectioning through the biofi lm revealed that aggregates of nanoparticulate Au line open spaces beneath the active biofi lm layer. These aggregates (bacterioform Au type 1) resulted from the reprecipitation of dissolved Au, and their internal growth structures provide direct evidence for coarsening of the Au grains. At the contact between the polymorphic layer and the primary Au, bacterioform Au type 2 is present. It consists of solid rounded forms into which crystal boundaries of underlying primary Au extend, and is the result of dealloying and Ag dissolution from the primary Au. This study demonstrates that (1) microbially driven dissolution, precipitation, and aggregation lead to the formation of bacterioform Au and contribute to the growth of Au grains under supergene conditions, and (2) the microbially driven mobilization of coarse Au into nanoparticles plays a key role in mediating the mobility of Au in surface environments, because the release of nanoparticulate Au upon biofi lm disintegration greatly enhances environmental mobility compared to Au complexes only.

Biological ammonia oxidation had long been thought to be mediated solely by discrete clades of b-and c-proteobacteria (ammonia-oxidizing bacteria; AOB). However, ammonia-oxidizing Crenarchaeota (ammonia-oxidizing archaea; AOA) have recently been identified and proposed to be the dominant agents of ammonia oxidation in soils. Nevertheless, the dynamics of AOB versus AOA, and their relative contribution to soil ammonia oxidation and ecosystem functioning on stress and environmental perturbation, remain unknown. Using a 3-year longitudinal field study and the amoA gene as a molecular marker, we demonstrate that AOB, but not AOA, mediate recovery of nitrification after zinc (Zn) contamination. Pristine soils showed approximately equal amoA gene copy numbers and transcript levels for AOB and AOA. At an intermediate Zn dose (33.7 mmol Zn per kg), ammonia oxidation was completely inhibited, and the numbers of AOB and AOA amoA gene copies and gene transcripts were reduced. After 2 years, ammonia oxidation in the field soils was fully restored to preexposure levels, and this restoration of function was concomitant with an increase of AOB amoA gene copy and gene transcript numbers. Analysis of the restored community revealed domination by a phylogenetically distinct Zn-tolerant Nitrosospira sp. community. In contrast, the numbers of AOA amoA gene copies and gene transcripts remained 3-and 10 4 -fold lower than recovered AOB values, respectively. Thus, although recent findings have emphasized a dominant role of archaea in soil-borne ammonia oxidation, we demonstrate that a phylogenetic shift within the AOB community drives recovery of nitrification from Zn contamination in this soil.