A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

All sequence data from this study were deposited at the European Bioinformatics Institute under the accession numbers ERS1670018 to ERS1670023. Further, all assigned genes, taxonomy, function, sequences of contigs, genes and proteins can be found in Table S3.In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (2136% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.This study was supported by a grant of BE-Basic-FES funds from the Dutch Ministry of Economic Affairs. The research of A.J.M. Stams is supported by an ERC grant (project 323009) and the gravitation grant “Microbes for Health and Environment” (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science. F. Hugenholtz was supported by the same gravitation grant (project 024.002.002). B. Hornung is supported by Wageningen University and the Wageningen Institute for Environment and Climate Research (WIMEK) through the IP/OP program Systems Biology (project KB-17-003.02-023).info:eu-repo/semantics/publishedVersio

Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes

Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated

The abundance of nitrogen cycle genes and potential greenhouse gas fluxes depends on land use type and little on soil aggregate size

Soil structure is known to influence microbial communities in soil and soil aggregates are the fundamental ecological unit of organisation that support soil functions. However, still little is known about the distribution of microbial communities and functions between soil aggregate size fractions in relation to land use. Thus, the objective of this study was to determine the gene abundance of microbial communities related to the nitrogen cycle and potential greenhouse gas (GHG) fluxes in six soil aggregate sizes (0–0.25, 0.25–0.5, 0.5–1.0, 1–2, 2–5, 5–10 mm) in four land uses (i.e. grassland, cropland, forest, young forest). Quantitative-PCR (Q-PCR) was used to investigate the abundance of bacteria, archaea and fungi, and functional guilds involved in N-fixation (nifH gene), nitrification (bacterial and archaeal amoA genes) and denitrification (narG, nirS, and nosZ genes). Land use leads to significantly different abundances for all genes analysed, with the cropland site showing the lowest abundance for all genes except amoA bacteria and archaea. In contrast, not a single land use consistently showed the highest gene abundance for all the genes investigated. Variation in gene abundance between aggregate size classes was also found, but the patterns were gene specific and without common trends across land uses. However, aggregates within the size class of 0.5–1.0 mm showed high bacterial 16S, nifH, amoA bacteria, narG, nirS and nosZ gene abundance for the two forest sites but not for fungal ITS and archaeal 16S. The potential GHG fluxes were affected by land use but the effects were far less pronounced than for microbial gene abundance, inconsistent across land use and soil aggregates. However, few differences in GHG fluxes were found between soil aggregate sizes. From this study, land use emerges as the dominant factor that explains the distribution of N functional communities and potential GHG fluxes in soils, with less pronounced and less generalized effects of aggregate size

Fate of antibiotics and antibiotic resistance genes during conventional and additional treatment technologies in wastewater treatment plants

Information on the removal of antibiotics and ARGs in full-scale WWTPs (with or without additional treatment technology) is limited. However, it is important to understand the efficiency of full-scale treatment technologies in removing antibiotics and ARGs under a variety of conditions relevant for practice to reduce their environmental spreading. Therefore, this study was performed to evaluate the removal of antibiotics and ARGs in a conventional wastewater treatment plant (WWTP A) and two full-scale combined with additional treatment technologies. WWTP B, a conventional activated sludge treatment followed by an activated carbon filtration step (1-STEP® filter) as a final treatment step. WWTP C, a treatment plant using aerobic granular sludge (NEREDA®) as an alternative to activated sludge treatment. Water and sludge were collected and analysed for 52 antibiotics from four target antibiotic groups (macrolides, sulfonamides, quinolones, tetracyclines) and four target ARGs (ermB, sul 1, sul 2 and tetW) and integrase gene class 1 (intI1). Despite the high removal percentages (79–88%) of the total load of antibiotics in all WWTPs, some antibiotics were detected in the various effluents. Additional treatment technology (WWTP C) showed antibiotics removal up to 99% (tetracyclines). For ARGs, WWTP C reduced 2.3 log followed by WWTP A with 2.0 log, and WWTP B with 1.3 log. This shows that full-scale WWTP with an additional treatment technology are promising solutions for reducing emissions of antibiotics and ARGs from wastewater treatment plants. However, total removal of the antibiotics and ARGS cannot be achieved for all types of antibiotics and ARGs. In addition, the ARGs were more abundant in the sludge compared to the wastewater effluent suggesting that sludge is an important reservoir representing a source for later ARG emissions upon reuse, i.e. as fertilizer in agriculture or as resource for bioplastics or bioflocculants. These aspects require further research

Mobility, turnover and storage of pollutants in soils, sediments and waters : achievements and results of the EU project AquaTerra : a review.

AquaTerra is one of the first environmental projects within the 6th Framework program by the European Commission. It began in June 2004 with a multidisciplinary team of 45 partner organizations from 13 EU countries, Switzerland, Serbia, Romania and Montenegro. Results from sampling and modeling in 4 large river basins (Ebro, Danube, Elbe and Meuse) and one catchment of the Brévilles Spring in France led to new evaluations of diffuse and hotspot input of persistent organic and metal pollutants including dynamics of pesticides and polycyclic aromatic hydrocarbons, as well as metal turnover and accumulation. While degradation of selected organic compounds could be demonstrated under controlled conditions in the laboratory, turnover of most persistent pollutants in the field seems to range from decades to centuries. First investigations of long-term cumulative and degradation effects, particularly in the context of climate change, have shown that it is also necessary to consider the predictions of more than one climate model when trying to assess future impacts. This is largely controlled by uncertainties in climate model responses. It is becoming evident, however, that changes to the climate will have important impacts on the diffusion and degradation of pollutants in space and time that are just at the start of their exploration

Fate of antibiotics and antibiotic resistance genes during conventional and additional treatment technologies in wastewater treatment plants

Information on the removal of antibiotics and ARGs in full-scale WWTPs (with or without additional treatment technology) is limited. However, it is important to understand the efficiency of full-scale treatment technologies in removing antibiotics and ARGs under a variety of conditions relevant for practice to reduce their environmental spreading. Therefore, this study was performed to evaluate the removal of antibiotics and ARGs in a conventional wastewater treatment plant (WWTP A) and two full-scale combined with additional treatment technologies. WWTP B, a conventional activated sludge treatment followed by an activated carbon filtration step (1-STEP® filter) as a final treatment step. WWTP C, a treatment plant using aerobic granular sludge (NEREDA®) as an alternative to activated sludge treatment. Water and sludge were collected and analysed for 52 antibiotics from four target antibiotic groups (macrolides, sulfonamides, quinolones, tetracyclines) and four target ARGs (ermB, sul 1, sul 2 and tetW) and integrase gene class 1 (intI1). Despite the high removal percentages (79–88%) of the total load of antibiotics in all WWTPs, some antibiotics were detected in the various effluents. Additional treatment technology (WWTP C) showed antibiotics removal up to 99% (tetracyclines). For ARGs, WWTP C reduced 2.3 log followed by WWTP A with 2.0 log, and WWTP B with 1.3 log. This shows that full-scale WWTP with an additional treatment technology are promising solutions for reducing emissions of antibiotics and ARGs from wastewater treatment plants. However, total removal of the antibiotics and ARGS cannot be achieved for all types of antibiotics and ARGs. In addition, the ARGs were more abundant in the sludge compared to the wastewater effluent suggesting that sludge is an important reservoir representing a source for later ARG emissions upon reuse, i.e. as fertilizer in agriculture or as resource for bioplastics or bioflocculants. These aspects require further research.</p

Fate of antibiotics and antibiotic resistance genes during conventional and additional treatment technologies in wastewater treatment plants

Information on the removal of antibiotics and ARGs in full-scale WWTPs (with or without additional treatment technology) is limited. However, it is important to understand the efficiency of full-scale treatment technologies in removing antibiotics and ARGs under a variety of conditions relevant for practice to reduce their environmental spreading. Therefore, this study was performed to evaluate the removal of antibiotics and ARGs in a conventional wastewater treatment plant (WWTP A) and two full-scale combined with additional treatment technologies. WWTP B, a conventional activated sludge treatment followed by an activated carbon filtration step (1-STEP® filter) as a final treatment step. WWTP C, a treatment plant using aerobic granular sludge (NEREDA®) as an alternative to activated sludge treatment. Water and sludge were collected and analysed for 52 antibiotics from four target antibiotic groups (macrolides, sulfonamides, quinolones, tetracyclines) and four target ARGs (ermB, sul 1, sul 2 and tetW) and integrase gene class 1 (intI1). Despite the high removal percentages (79–88%) of the total load of antibiotics in all WWTPs, some antibiotics were detected in the various effluents. Additional treatment technology (WWTP C) showed antibiotics removal up to 99% (tetracyclines). For ARGs, WWTP C reduced 2.3 log followed by WWTP A with 2.0 log, and WWTP B with 1.3 log. This shows that full-scale WWTP with an additional treatment technology are promising solutions for reducing emissions of antibiotics and ARGs from wastewater treatment plants. However, total removal of the antibiotics and ARGS cannot be achieved for all types of antibiotics and ARGs. In addition, the ARGs were more abundant in the sludge compared to the wastewater effluent suggesting that sludge is an important reservoir representing a source for later ARG emissions upon reuse, i.e. as fertilizer in agriculture or as resource for bioplastics or bioflocculants. These aspects require further research

Biodegradation of Fipronil:Transformation Products, Microbial Characterisation and Toxicity Assessment

Fipronil is a highly active, broad spectrum insecticide with increasing and wide use. The degradation of fipronil was studied in Brazilian soil under oxic and anoxic conditions. Under oxic conditions, the half-life of fipronil was 16.9 days, with fipronil sulfone as the main metabolite, and no further degradation during 30 days of incubation. This degradation was accompanied by an increase of bacterial and archaeal ammonia oxidizers, as well as denitrifiers, and microorganisms related to Sphingomonas. Under anoxic conditions, a half-life of 15.7 days for fipronil was obtained, with fipronil sulphide as the primary metabolite, and fipronil sulfone at lower concentrations, with no further degradation of these metabolites during 90 days of incubation. In these conditions, complete degradation of fipronil was accompanied by an increase of denitrifiers, iron-reducers and ammonia oxidizers and selection of microorganisms that are related to uncultured Clostridiales (family VIII). Sulphate reducers and methanogens and most of the microbial community were not affected by fipronil and its metabolites. Toxicity evaluation, using in vitro effect-based CALUX assays confirmed that the metabolites have a similar toxic potency as compared to the parent compound fipronil. Therefore, the potential (eco)toxicity of fipronil does not seem to decrease upon microbial degradation.</p