Bar-Coded Pyrosequencing Reveals the Responses of PBDE-Degrading Microbial Communities to Electron Donor Amendments

Polybrominated diphenyl ethers (PBDEs) can be reductively degraded by microorganisms under anaerobic conditions. However, little is known about the effect of electron donors on microbial communities involved in PBDEs degradation. Here we employed 454 Titanium pyrosequencing to examine the phylogenetic diversity, composition, structure and dynamics of microbial communities from microcosms under the conditions of different electron donor amendments. The community structures in each of the five alternate electron donor enrichments were significantly shifted in comparison with those of the control microcosm. Commonly existing OTUs between the treatment and control consortia increased from 5 to 17 and more than 50% of OTUs increased around 13.7 to 186 times at least in one of the microcosms after 90-days enrichment. Although the microbial communities at different taxonomic levels were significantly changed by different environmental variable groups in redundancy analysis, significant correlations were observed between the microbial communities and PBDE congener profiles. The lesser-brominated PBDE congeners, tri-BDE congener (BDE-32) and hexa-BDE, were identified as the key factors shaping the microbial community structures at OTU level. Some rare populations, including the known dechlorinating bacterium, Dehalobacter, showed significant positive-correlation with the amounts of PBDE congeners in the consortia. The same results were also observed on some unclassified bacteria. These results suggest that PBDEs-degrading microbial communities can be successfully enriched, and their structures and compositions can be manipulated through adjusting the environmental parameters

Isotopic techniques to measure N2O, N2 and their sources

GHG emissions are usually the result of several simultaneous processes. Furthermore, some gases such as N2 are very difficult to quantify and require special techniques. Therefore, in this chapter, the focus is on stable isotope methods. Both natural abundance techniques and enrichment techniques are used. Especially in the last decade, a number of methodological advances have been made. Thus, this chapter provides an overview and description of a number of current state-of-theart techniques, especially techniques using the stable isotope 15N. Basic principles and recent advances of the 15N gas flux method are presented to quantify N2 fluxes, but also the latest isotopologue and isotopomer methods to identify pathways for N2O production. The second part of the chapter is devoted to 15N tracing techniques, the theoretical background and recent methodological advances. A range of different methods is presented from analytical to numerical tools to identify and quantify pathway-specific N2O emissions. While this chapter is chiefly concerned with gaseous N emissions, a lot of the techniques can also be applied to other gases such as methane (CH4), as outlined in Sect. 5.3

Impact of elevated nitrate on sulfate-reducing bacteria: A comparative study of Desulfovibrio vulgaris

Sulfate-reducing bacteria have been extensively studied for their potential in heavy-metal bioremediation. However, the occurrence of elevated nitrate in contaminated environments has been shown to inhibit sulfate reduction activity. Although the inhibition has been suggested to result from the competition with nitrate-reducing bacteria, the possibility of direct inhibition of sulfate reducers by elevated nitrate needs to be explored. Using Desulfovibrio vulgaris as a model sulfate-reducing bacterium, functional genomics analysis reveals that osmotic stress contributed to growth inhibition by nitrate as shown by the upregulation of the glycine/betaine transporter genes and the relief of nitrate inhibition by osmoprotectants. The observation that significant growth inhibition was effected by 70 mM NaNO{sub 3} but not by 70 mM NaCl suggests the presence of inhibitory mechanisms in addition to osmotic stress. The differential expression of genes characteristic of nitrite stress responses, such as the hybrid cluster protein gene, under nitrate stress condition further indicates that nitrate stress response by D. vulgaris was linked to components of both osmotic and nitrite stress responses. The involvement of the oxidative stress response pathway, however, might be the result of a more general stress response. Given the low similarities between the response profiles to nitrate and other stresses, less-defined stress response pathways could also be important in nitrate stress, which might involve the shift in energy metabolism. The involvement of nitrite stress response upon exposure to nitrate may provide detoxification mechanisms for nitrite, which is inhibitory to sulfate-reducing bacteria, produced by microbial nitrate reduction as a metabolic intermediate and may enhance the survival of sulfate-reducing bacteria in environments with elevated nitrate level

Push-pull tests for estimating effective porosity: expanded analytical solution and in situ application

The analytical solution describing the one-dimensional displacement of the center of mass of a tracer during an injection, drift, and extraction test (push-pull test) was expanded to account for displacement during the injection phase. The solution was expanded to improve the in situ estimation of effective porosity. The truncated equation assumed displacement during the injection phase was negligible, which may theoretically lead to an underestimation of the true value of effective porosity. To experimentally compare the expanded and truncated equations, single-well push-pull tests were conducted across six test wells located in a shallow, unconfined aquifer comprised of unconsolidated and heterogeneous silty and clayey fill materials. The push-pull tests were conducted by injection of bromide tracer, followed by a non-pumping period, and subsequent extraction of groundwater. The values of effective porosity from the expanded equation (0.6–5.0%) were substantially greater than from the truncated equation (0.1–1.3%). The expanded and truncated equations were compared to data from previous push-pull studies in the literature and demonstrated that displacement during the injection phase may or may not be negligible, depending on the aquifer properties and the push-pull test parameters. The results presented here also demonstrated the spatial variability of effective porosity within a relatively small study site can be substantial, and the error-propagated uncertainty of effective porosity can be mitigated to a reasonable level (< ± 0.5%). The tests presented here are also the first that the authors are aware of that estimate, in situ, the effective porosity of fine-grained fill material

Correction to: Push-pull tests for estimating effective porosity: expanded analytical solution and in situ application (Hydrogeology Journal, (2018), 26, 2, (381-393), 10.1007/s10040-017-1672-3)

In the recent article by Paradis et al. (2018), an error was made when developing a conceptual model and an analytical solution to describe the one-dimensional displacement of the center of mass of a non-reactive tracer during a single-well injection, drift, and extraction test (push-pull test)

Quantification of In Situ Denitrification Rates in Groundwater Below an Arable and a Grassland System

peer-reviewedUnderstanding denitrification rates in groundwater ecosystems can help predict where agricultural reactive nitrogen (N) contributes to environmental degradation. In situ groundwater denitrification rates were determined in subsoil, at the bedrock-interface and in bedrock at two sites, grassland and arable, using an in situ ‘push-pull’ method with 15N labelled nitrate (NO3--N). Measured groundwater denitrification rates ranged from 1.3 to 469.5 µg N kg-1d-1. Exceptionally high denitrification rates observed at the bedrock-interface at grassland site (470±152µg N kg-1d-1; SE, standard error) suggest that deep groundwater can serve as substantial hotspots for NO3--N removal. However, denitrification rates at the other locations were low and may not substantially reduce NO3--N delivery to surface waters. Denitrification rates were negatively correlated with ambient dissolved oxygen (DO), redox potential (Eh), ks and NO3- (all p-values p<0.01) and positively correlated with SO42- (p<0.05). Higher mean N2O/(N2O+N2) ratios at arable (0.28) site than the grassland (0.10) revealed that arable site has higher potential to indirect N2O emissions. Identification of areas with high and low denitrification and related site parameters can be a tool to manage agricultural N to safeguard the environment.Department of Agriculture and Food, Ireland - Research Stimulus Fund Programme (Grant RSF 06383