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Temperature is a key factor that influences chemical biotransformation potential and rates, on which exposure and fate models rely to predict the environmental (micro)pollutant fate. Arrhenius-based models are currently implemented in environmental exposure assessment to adapt biotransformation rates to actual temperatures, assuming validity in the 0-30 °C range. However, evidence on how temperature shifts affect the physicochemical and microbial features in biological systems is scarce, questioning the validity of the existing modeling approaches. In this work, laboratory-scale batch assays were designed to investigate how a mixed microbial community responds to short-term temperature shifts, and how this impacts its ability to biotransform a range of structurally diverse micropollutants. Our results revealed three distinct kinetic responses at temperatures above 20 °C, mostly deviating from the classic Arrhenius-type behavior. Micropollutants with similar temperature responses appeared to undergo mostly similar initial biotransformation reactions, with substitution-type reactions maintaining Arrhenius-type behavior up to higher temperatures than oxidation-type reactions. Above 20 °C, the microbial community also showed marked shifts in both composition and activity, which mostly correlated with the observed deviations from Arrhenius-type behavior, with compositional changes becoming a more relevant factor in biotransformations catalyzed by more specific enzymes (e.g., oxidation reactions). Our findings underline the need to re-examine and further develop current environmental fate models by integrating biological aspects, to improve accuracy in predicting the environmental fate of micropollutants.

Rhodococcus equi ATCC13557 was selected as a model organism to study oestrogen degradation based on its previous ability to degrade 17α-ethinylestradiol (EE2). Biodegradation experiments revealed that R. equi ATCC13557 was unable to metabolise EE2. However, it was able to metabolise E2 with the major metabolite being E1 with no further degradation of E1. However, the conversion of E2 into E1 was incomplete, with 11.2 and 50.6% of E2 degraded in mixed (E1-E2-EE2) and E2-only conditions, respectively. Therefore, the metabolic pathway of E2 degradation by R. equi ATCC13557 may have two possible pathways. The genome of R. equi ATCC13557 was sequenced, assembled, and mapped for the first time. The genome analysis allowed the identification of genes possibly responsible for the observed biodegradation characteristics of R. equi ATCC13557. Several genes within R. equi ATCC13557 are similar, but not identical in sequence, to those identified within the genomes of other oestrogen degrading bacteria, including Pseudomonas putida strain SJTE-1 and Sphingomonas strain KC8. Homologous gene sequences coding for enzymes potentially involved in oestrogen degradation, most commonly a cytochrome P450 monooxygenase (oecB), extradiol dioxygenase (oecC), and 17β-hydroxysteroid dehydrogenase (oecA), were identified within the genome of R. equi ATCC13557. These searches also revealed a gene cluster potentially coding for enzymes involved in steroid/oestrogen degradation; 3-carboxyethylcatechol 2,3-dioxygenase, 2-hydroxymuconic semialdehyde hydrolase, 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase, 3-(3-hydroxy-phenyl)propionate hydroxylase, cytochrome P450 monooxygenase, and 3-oxosteroid 1-dehydrogenase. Further, the searches revealed steroid hormone metabolism gene clusters from the 9, 10-seco pathway, therefore R. equi ATCC13557 also has the potential to metabolise other steroid hormones such as cholesterol.

Quantitative Structure Biodegradation Relationships (QSBRs) are a tool to predict the biodegradability of chemicals. The objective of this work was to generate reliable biodegradation data for mono-aromatic chemicals in order to evaluate and verify previously developed QSBRs models. A robust biodegradation test method was developed to estimate specific substrate utilization rates, which were used as a proxy for biodegradation rates of chemicals in pure culture. Five representative mono-aromatic chemicals were selected that spanned a wide range of biodegradability. Aerobic biodegradation experiments were performed for each chemical in batch reactors seeded with known degraders. Chemical removal, degrader growth and CO2 production were monitored over time. Experimental data were interpreted using a full carbon mass balance model, and Monod kinetic parameters (Y, Ks, qmax and μmax) for each chemical were determined. In addition, stoichiometric equations for aerobic mineralization of the test chemicals were developed. The theoretically estimated biomass and CO2 yields were similar to those experimentally observed; 35% (s.d ± 8%) of the recovered substrate carbon was converted to biomass, and 65% (s.d ± 8%) was mineralised to CO2. Significant correlations were observed between the experimentally determined specific substrate utilization rates, as represented by qmax and qmax/Ks, at high and low substrate concentrations, respectively, and the first order biodegradation rate constants predicted by a previous QSBR study. Similarly, the correlation between qmax and selected molecular descriptors characterizing the chemicals structure in a previous QSBR study was also significant. These results suggest that QSBR models can be reliable and robust in prioritising chemical half-lives for regulatory screening purposes.

The use of activated carbon (AC) amendments to reduce exposure risks for hydrophobic contaminants like polycyclic aromatic hydrocarbons (PAHs) by adsorption is an innovative soil remediation approach. However, AC amendment side-effects on the pollution biodegradation are poorly understood. This study assessed for optimized nutrient ratio conditions, effects of 5% soil wet weight AC amendments, if added from the beginning or after five months, on the outcomes of one year of crude oil polluted soil bioremediation. CO2, residual hydrocarbon concentrations and microbial community structure analysis revealed how AC amendment hindered crude oil biodegradation much more, if added from the start, as compared to after 5 months, i.e. after the initial phase of biodegradation. Putative crude oil degrading microorganisms from the genera Marinobacter, Parvibaculum, Salinibacterium, Muricauda, and Alcanivorax were more sensitive to the AC amendment than those from the genus Rhodococcus. Rhodococci possess hydrophobic cell walls which may enable them to accumulate hydrocarbons in the AC amended soil, despite of their reduced availability. AC amendment from the start had the highest alkane and total US EPA PAH residues, but was more effective than one year of bioremediation, with or without AC amendment after 5 months, in reducing PAH availability in the soil.

This study evaluated the microbiological safety of the water distribution system of a city in the state of Minas Gerais (Brazil), population 120,000 inhabitants. During the study, the city suffered a severe drought that had a significant impact on water availability and quality in the river that supplies water to the city. Samples (2 liters) were collected from the distribution system over a period of six months, which included wet and dry months, from three points: the point with the lowest altitude in the distribution network, the farthest point from the water treatment works, and an intermediate point. Free chlorine was measured in situ using a Hach kit. DNA was extracted using a FastDNA Spin Kit Soil (Qbiogene). Advanced sequencing techniques (Ion Torrent) were used to identify and quantify the relative abundance of potentially pathogenic bacteria present in the samples. Coliforms and Escherichia coli, indicators currently used worldwide to assess microbiological safety of drinking water, were measured on all samples using an enzyme substrate method (ONPG-MUG Colilert®). Next generation sequencing results retrieved 16SrRNA sequences of E. coli and some potentially pathogenic bacteria, even in the presence of free chlorine. Operational taxonomic units related to pathogenic bacteria were present in all samples from the drinking water distribution system (DWS) and, in general, at high relative abundance (up to 5%). A total of 19 species related to bacterial pathogens were detected. Inadequate operational practices that could affect the microbiological safety of the DWS were identified and discussed. The current paper is the first to evaluate the community of potentially pathogenic bacteria in a real DWS.

We studied the effects of two percent by weight activated carbon versus biochar amendments in 93 cm long sand columns on the biofiltration of petroleum vapours released by a non-aqueous phase liquid (NAPL) source. Activated carbon greatly enhanced, whereas biochar slightly reduced, the biofiltration of volatile petroleum hydrocarbons (VPHs) over 430 days. Sorbent amendment benefitted the VPH biofiltration by retarding breakthrough during the biodegradation lag phase. Subsequently, sorbent amendment briefly reduced the mineralization of petroleum hydrocarbons by limiting their bioavailability. During the last and longest study period, when conditions became less supportive of microbial growth, because of inorganic nutrient scarcity, the sorbents again improved the pollution attenuation by preventing the degrading microorganisms from being overloaded with VPHs. A 16S rRNA gene based analysis showed sorbent amendment effects on soil microbial communities. Nocardioidaceae benefitted the most from petroleum hydrocarbons in activated carbon amended soil, whereas Pseudomonadacea predominated in unamended soil. Whilst the degrading microorganisms were overloaded with VPHs in the unamended soil, the reduced mobility and bioavailability of VPHs in the activated carbon amended soil led to the emergence of communities with higher specific substrate affinity, which removed bioavailable VPHs effectively at low concentrations. A numerical pollutant fate model reproduced these experimental observations by considering sorption effects on the pollutant migration and bioavailability for growth of VPH degrading biomass, which is limited by a maximum soil biomass carrying capacity. Activated carbon was a much stronger sorbent for VPHs than biochar, which explained the diverging effects of the two sorbents in this study.

Volatile Petroleum Hydrocarbon (VPH) class effects on soil microbial composition were investigated using two next-generation sequencing (NGS) techniques - 454 pyrosequencing and ion torrent sequencing. Microbial activity was stimulated by adding different VPH compound classes to the sandy soil in comparison with live controls without VPH addition. Microbial community structure was significantly affected by the various VPH classes. At the genus level, Rhodococcus, Desulfosporosinus, Polaromonas, Mesorhizobium and Methylibium had the highest relative abundances in the straight-chain alkane (str-alk) treated soil as compared to the control (p 0.05, 2 sample t-tests) while Pseudomonas was more dominant in the cyclic alkane (cyc-alk) contaminated soil. Pseudonocardia was significantly higher in relative abundance in the aromatic hydrocarbon (aro-H) treated batches as compared to the control (p 0.05, 2 sample t-tests). A non-metric multidimensional scaling (NMDS) of the Bray Curtis similarity between microbial communities in the batches revealed at least 60% similarity for each treatment and also showed that VPH class was a statistically significant factor in shaping the bacterial communities in the soil treatments (Global R = 0.861, p 0.01). The NGS platforms (454 GS Junior and Ion torrent) compared in this study did not appear to affect the outcomes of the microbial community structure and composition analysis.

The objective of this work was to develop a QSBR model for the prioritization of organic pollutants based on biodegradation rates from a database containing globally harmonized biodegradation tests using relevant molecular descriptors. To do this, we first categorized the chemicals into three groups (Group 1: simple aromatic chemicals with a single ring, Group 2: aromatic chemicals with multiple rings and Group3: Group 1 plus Group 2) based on molecular descriptors, estimated the first order biodegradation rate of the chemicals using rating values derived from the BIOWIN3 model, and finally developed, validated and defined the applicability domain of models for each group using a multiple linear regression approach. All the developed QSBR models complied with OECD principles for QSAR validation. The biodegradation rate in the models for the two groups (Group 2 and 3 chemicals) are associated with abstract molecular descriptors that provide little relevant practical information towards understanding the relationship between chemical structure and biodegradation rates. However, molecular descriptors associated with the QSBR model for Group 1 chemicals (R

Little is known about the forces that determine the assembly of diverse bacterial communities inhabiting drinking water treatment filters and how this affects drinking water quality. Two contrasting ecological theories can help to understand how natural microbial communities assemble; niche theory and neutral theory, where environmental deterministic factors or stochastic factors predominate respectively. This study investigates the development of the microbial community on two common contrasting filter materials (quartz sand and granular activated carbon-GAC), to elucidate the main factors governing their assembly, through the evaluation of environmental (i.e. filter medium type) and stochastic forces (random deaths, births and immigration). Laboratory-scale filter columns were used to mimic a rapid gravity filter; the microbiome of the filter materials, and of the filter influent and effluent, was characterised using next generation 16S rRNA gene amplicon sequencing and flow-cytometry. Chemical parameters (i.e. dissolved organic carbon, trihalomethanes formation) were also monitored to assess the final effluent quality. The filter communities seemed to be strongly assembled by selection rather than neutral processes, with only 28% of those OTUs shared with the source water detected on the filter medium following predictions using a neutral community model. GAC hosted a phylogenetically more diverse community than sand. The two filter media communities seeded the effluent water, triggering differences in both water quality and community composition of the effluents. Overall, GAC proved to be better than sand in controlling microbial growth, by promoting higher bacterial decay rates and hosting less bacterial cells, and showed better performance for putative pathogen control by leaking less Legionella cells into the effluent water.

Rieske non-heme iron oxygenases enzymes have been widely studied, as they catalyse essential reactions initiating the bacterial degradation of organic compounds, for instance aromatic hydrocarbons. The genes encoding these enzymes offer a potential target for studying aromatic hydrocarbon-degrading organisms in the environment. However, previously reported primer sets that target dioxygenase gene sequences or the common conserved Rieske centre of aromatics dioxygenases have limited specificity and/or target non-dioxygenase genes. In this work, an extensive database of dioxygenase α-subunit gene sequences was constructed, and primer sets targeting the conserved Rieske centre were developed. The high specificity of the primers was confirmed by polymerase chain reaction analysis, agarose gel electrophoresis and sequencing. Quantitative polymerase chain reaction (qPCR) assays were also developed and optimized, following MIQE guidelines (Minimum Information for Publication of Quantitative Real-Time PCR Experiments). Comparison of the qPCR quantification of dioxygenases in spiked sediment samples and in pure cultures demonstrated an underestimation of the Ct value, and the requirement for a correction factor at gene abundances below 108 gene copies per g of sediment. Externally validated qPCR provides a valuable tool to monitor aromatic hydrocarbon degrader population abundances at contaminated sites., Our study aimed to re-evaluate the phylogeny of Rieske non-heme iron dioxygenases using only retrieved primary nucleic acid sequences for the development of quantitative real-time PCR primers., Graphical Abstract Figure. Our study aimed to re-evaluate the phylogeny of Rieske non-heme iron dioxygenases using only retrieved primary nucleic acid sequences for the development of quantitative real-time PCR primers.

We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of available pollutants by biodegradation was most notable in unamended soil.

Bioremediation and activated carbon (AC) amendment were compared as remediation strategies for sediment from the River Tyne containing 16.4 +/- 7.3 microg/g polycyclic aromatic hydrocarbons (PAHs) and approximately 5% coal particles by total dry sediment weight. Unamended, nutrient amended (biostimulated) and nutrient and Pseudomonas putida amended (bioaugmented) sediment microcosms failed to show a significant decrease in total sediment PAH concentrations over a one month period. Polyethylene passive (PE) samplers were embedded for 21 days in these sediment microcosms in order to measure the available portion of PAHs and accumulated 4.70 +/- 0.25, 12.43 +/- 1.78, and 23.49 +/- 2.73 microg PAHs/g PE from the unamended, biostimulated, and bioaugmented microcosms, respectively. Higher PAH uptake by PE samplers in biostimulated and bioaugmented microcosms coincided with slower degradation of spiked phenanthrene in sediment-free filtrate from these microcosms compared to filtrate from the unamended microcosms. Microbial community analysis revealed changes in the bacterial community directly following the addition of nutrients, but the added P. putida community failed to establish itself. Addition of 2% by dry sediment weight activated carbon reduced PAH uptake by PE samplers to 0.28 +/- 0.01 microg PAHs/g PE, a greater than 90% reduction compared to the unamended microcosms.

This paper describes a novel, composite device, based not on optical excitation but on the transfer of holes from Si to the TiO(2)/air or TiO(2)/water interface, for the disinfection and detoxification of fluid streams.