Continuous UV-C/H2O2 and UV-C/Chlorine applied to municipal secondary effluent and nanofiltration retentate: removal of contaminants of emerging concern, ecotoxicity, and reuse potential

As global effects of water scarcity raise concerns and environmental regulations evolve, contemporary wastewater treatment plants (WWTPs) face the challenge of effectively removing a diverse range of contaminants of emerging concern (CECs) from municipal effluents. This study focuses on the assessment of advanced oxidation processes (AOPs), specifically UV-C/H2O2 and UV-C/Chlorine, for the removal of 14 target CECs in municipal secondary effluent (MSE, spiked with 10 μg L-1 of each CEC) or in the subsequent MSE nanofiltration retentate (NFR, no spiking). Phototreatments were carried out in continuous mode operation, with a hydraulic retention time of 3.4 min, using a tube-in-tube membrane photoreactor. For both wastewater matrices, UV-C photolysis (3.3 kJ L-1) exhibited high efficacy in removing CECs susceptible to photolysis, although lower treatment performance was observed for NFR. In MSE, adding 10 mg L-1 of H2O2 or Cl2 enhanced treatment efficiency, with UV-C/H2O2 outperforming UV-C/Chlorine. Both UV-C/AOPs eliminated the chronic toxicity of MSE toward Chlorella vulgaris. In the NFR, not only was the degradation of target CECs diminished, but chronic toxicity to C. vulgaris persisted after both UV-C/AOPs, with UV-C/Chlorine increasing toxicity due to potential toxic by-products. Nanofiltration permeate (NFP) exhibited low CECs and microbial content. A single chlorine addition effectively controlled Escherichia coli regrowth for 3 days, proving NFP potential for safe reuse in crop irrigation (< 1 CFU/100 mL for E. coli; < 1 mg L-1 for free chlorine). These findings provide valuable insights into the applications and limitations of UV-C/H2O2 and UV-C/Chlorine for distinct wastewater treatment scenarios.

Carbon-based materials for water disinfection and heavy metals removal

The presence of heavy metals and/or harmful bacteria in drinking water represents significant risks to human health. This study aimed to develop a low-cost water treatment technology using synthesized nanocomposites with metal nanoparticles supported on activated carbon (AC) for bacteria and heavy metal removal. In addition, the performance of the developed nanomaterials was compared with that of commercial materials - carbon fibers of three different typologies. The chemical and textural properties of all tested materials were characterized. To simulate a technology to be applied in a water outlet point, removal tests were carried out in a continuous system using suspensions of Escherichia coli and/or Staphylococcus aureus, wherein the contact time with the two phases was minimal (1 min). The obtained results revealed that iron and copper oxides supported on AC with a calcination treatment (CuFeO/AC-C) was the nanocomposite with the best performance, achieving a 6 log reduction for both bacteria in the same suspension up to 9 h operation. A mix of bacteria and heavy metals, simulating a real water, was treated with CuFeO/AC-C obtaining a 6 log reduction of bacteria, a Pb2+ removal >99.9% and Cd2+ removal between 97 and 98% over 180 passage times.

The Complex Interplay Between Antibiotic Resistance and Pharmaceutical and Personal Care Products in the Environment

Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are important environmental contaminants. Nonetheless, what drives the evolution, spread, and transmission of antibiotic resistance dissemination is still poorly understood. The abundance of ARB and ARGs is often elevated in human-impacted areas, especially in environments receiving fecal wastes, or in the presence of complex mixtures of chemical contaminants, such as pharmaceuticals and personal care products. Self-replication, mutation, horizontal gene transfer, and adaptation to different environmental conditions contribute to the persistence and proliferation of ARB in habitats under strong anthropogenic influence. Our review discusses the interplay between chemical contaminants and ARB and their respective genes, specifically in reference to co-occurrence, potential biostimulation, and selective pressure effects, and gives an overview of mitigation by existing man-made and natural barriers. Evidence and strategies to improve the assessment of human health risks due to environmental antibiotic resistance are also discussed. Environ Toxicol Chem 2024;43:637-652. © 2022 SETAC.

Catalyst-free persulfate activation by UV/visible radiation for secondary urban wastewater disinfection

This study focuses on the treatment of secondary urban wastewater (W) to improve the effluent quality aiming at the reduction of pathogenic microorganisms for the safe reuse of the treated wastewater (TW). Catalyst-free persulfate activation by radiation-based oxidation was applied as a treatment technology. A parametric study was carried out to select the best operating conditions. Total enterobacteria inactivation (quantified by the log reduction (CFU/100 mL)) was achieved when using [S2O82-] = 1 mM, pH = 8.5 (natural pH of W), T = 25 °C, and I = 500 W/m2. However, storing TW for 3 days promoted the regrowth of bacteria, risking its reutilization. Therefore, in this study, and for the first time, the potential beneficial role of inoculation of wastewater treated by the radiation-activated persulfate process with a diverse bacterial community was evaluated in order to control the regrowth of potentially harmful microorganisms through bacterial competition. For this, TW was diluted with river water (R) in the volume percentages of 5, 25, and 50 (percentages refer to R content), and enterobacteria and total heterotrophs were enumerated before and after storage for 72 h. The results showed total heterotrophs and enterobacteria regrowth for TW and R + TW diluted 5 and 25% after storage. However, for R + TW diluted 50%, only the total heterotrophs regrew. Hence, the treated wastewater generated by the oxidative process diluted with 50% river water complies with the legislated limits for reuse in urban uses or irrigation.

Survival of clinical and environmental carbapenem-resistant Klebsiella pneumoniae ST147 in surface water

Carbapenem-resistant Klebsiella pneumoniae represents a healthcare threat, already disseminated in the environment. This study aimed to compare the behaviour of a clinical and an environmental K. pneumoniae strain (multilocus sequence type ST147) harbouring the gene blaKPC-3 in water. The abundance of the genes phoE (specific for K. pneumoniae) and blaKPC-3 was monitored by quantitative PCR in urban runoff water and sterile ultra-pure water microcosms, aiming to assess survival, blaKPC-3 persistence, and the effect of the native water microbiota. In sterile ultra-pure water, the abundance of cultivable K. pneumoniae and blaKPC-3 gene did not change over the incubation period (8 days). In contrast, in urban runoff, the K. pneumoniae and the genes phoE and blaKPC genes decreased by up to 3 log-units. These results suggest that K. pneumoniae were outcompeted by the native microbiota of the urban runoff water and that the decay of blaKPC-3 gene was due to host death, rather than to gene loss. The study highlights that although native microbiota is essential to hamper the persistence of non-native bacteria, carbapenemase producing K. pneumoniae can survive in urban runoff water for at least one week.

Novel photoelectrochemical 3D-system for water disinfection by deposition of modified carbon nitride on vitreous carbon foam

Graphitic carbon nitride (GCN) is an optical semiconductor with excellent photoactivity under visible light irradiation. It has been widely applied for organic micropollutant removal from contaminated water, and less investigated for microorganisms' inactivation. The photocatalytic degradation mechanism using GCN is attributed to a series of reactions with reactive oxygen species and photogenerated holes that can be boosted by modifying its physical-chemical structure. This work reports a successful improvement of the overall photocatalytic and electrocatalytic activities of the pristine material by thermal and chemical modification by a copolymerisation synthesis method. The copolymerisation of dicyandiamide as a precursor with barbituric acid strongly reduced photoluminescence due to the enhanced charge separation thus improving the catalyst efficiency under visible light irradiation. The material with 1.6 wt% of barbituric acid showed the best photocatalytic performance and electrochemical properties. This photocatalyst was selected for immobilisation on a conductive carbon foam, which promotes a higher electrochemical active surface area and enhanced mass transfer. This three-dimensional metal-free electrode was employed for the photoelectrochemical inactivation of two different microorganisms, Escherichia coli, and Enterococcus faecalis, obtaining removals below the detection limit after 30 min in simulated faecal-contaminated waters. This photoelectrochemical reactor was also applied to treat polluted river and urban waste waters, and the faecal contamination indicators were vastly reduced to values below the detection limit in 60 min in both cases, showing the wide applicability of this innovative photoelectrode for different types of polluted aqueous matrices.

Microalgae systems - environmental agents for wastewater treatment and further potential biomass valorisation

Water is the most valuable resource on the planet. However, massive anthropogenic activities generate threatening levels of biological, organic, and inorganic pollutants that are not efficiently removed in conventional wastewater treatment systems. High levels of conventional pollutants (carbon, nitrogen, and phosphorus), emerging chemical contaminants such as antibiotics, and pathogens (namely antibiotic-resistant ones and related genes) jeopardize ecosystems and human health. Conventional wastewater treatment systems entail several environmental issues: (i) high energy consumption; (ii) high CO₂ emissions; and (iii) the use of chemicals or the generation of harmful by-products. Hence, the use of microalgal systems (entailing one or several microalgae species, and in consortium with bacteria) as environmental agents towards wastewater treatment has been seen as an environmentally friendly solution to remove conventional pollutants, antibiotics, coliforms and antibiotic resistance genes. In recent years, several authors have evaluated the use of microalgal systems for the treatment of different types of wastewater, such as agricultural, municipal, and industrial. Generally, microalgal systems can provide high removal efficiencies of: (i) conventional pollutants, up to 99%, 99%, and 90% of total nitrogen, total phosphorus, and/or organic carbon, respectively, through uptake mechanisms, and (ii) antibiotics frequently found in wastewaters, such as sulfamethoxazole, ciprofloxacin, trimethoprim and azithromycin at 86%, 65%, 42% and 93%, respectively, through the most desirable microalgal mechanism, biodegradation. Although pathogens removal by microalgal species is complex and very strain-specific, it is also possible to attain total coliform and Escherichia coli removal of 99.4% and 98.6%, respectively. However, microalgal systems' effectiveness strongly relies on biotic and abiotic conditions, thus the selection of operational conditions is critical. While the combination of selected species (microalgae and bacteria), ratios and inoculum concentration allow the efficient removal of conventional pollutants and generation of high amounts of biomass (that can be further converted into valuable products such as biofuels and biofertilisers), abiotic factors such as pH, hydraulic retention time, light intensity and CO₂/O₂ supply also have a crucial role in conventional pollutants and antibiotics removal, and wastewater disinfection. However, some rationale must be considered according to the purpose. While alkaline pH induces the hydrolysis of some antibiotics and the removal of faecal coliforms, it also decreases phosphates solubility and induces the formation of ammonium from ammonia. Also, while CO₂ supply increases the removal of E. coli and Pseudomonas aeruginosa, as well as the microalgal growth (and thus the conventional pollutants uptake), it decreases Enterococcus faecalis removal. Therefore, this review aims to provide a critical review of recent studies towards the application of microalgal systems for the efficient removal of conventional pollutants, antibiotics, and pathogens; discussing the feasibility, highlighting the advantages and challenges of the implementation of such process, and presenting current case-studies of different applications of microalgal systems.

Ozone membrane contactor for tertiary treatment of urban wastewater: Chemical, microbial and toxicological assessment

A membrane ozone contactor, operated under continuous mode, was applied to promote the tertiary treatment of urban wastewater (UWW), targeting the removal of contaminants of emerging concern (CECs), bacterial disinfection, and toxicity reduction. This system relies on the homogeneous radial distribution of ozone (O₃) in the reaction zone by "titration" through a microfiltration borosilicate tubular membrane, while the UWW swirls around the membrane and drags the O₃ microbubbles generated in the membrane shell-side. The membrane is coated with titanium dioxide (TiO₂-P25) and radiation can be externally supplied via four UV lamps. The ozonation tests were carried out with secondary-treated UWW collected in different seasons (winter and summer) and spiked with a mix of 19 CECs (10 μg L^-1 each). For an O₃ dose of 18 g m^-3, the best performance was obtained by increasing the O₃ concentration (maximum [O₃]_G,inlet of 200 g Nm^-3) and decreasing the gas flow rate (minimum Q_G of 0.15 Ndm³ min^-1), providing the highest ozone transfer yield (88 %) and, thus higher specific ozone dose (g O₃ per g dissolved organic carbon). Under these conditions, removals >80 % or concentrations below the limit of quantification were obtained for up to 13 of the 19 CECs and reductions up to 5 log units for total heterotrophs and below the limit of detection for enterobacteria and enterococci. Tests including a UVC dose of 0.10 kJ L^-1 enhanced disinfection ability but had no impact on CECs oxidation. After ozonation, the abundance of antibiotic resistant bacteria was reduced but not eliminated, and microbial regrowth after 3-day storage was observed. No toxic effect was detected on zebrafish embryos using a dilution factor of 4 for the ozonized UWW and when granular activated carbon adsorption was subsequently applied the dilution factor decreased to 2.

Disinfection of treated urban effluents for reuse by combination of coagulation/flocculation and Fenton processes

In this study, a combination of coagulation/flocculation and Fenton processes was studied as tertiary treatment in order to generate treated water susceptible to reuse. The combination of both processes has never been applied in disinfection of real urban wastewater. The best removals of turbidity and enterobacteria were achieved when applying a coagulant (FeCl₃) dosage of 120 mg/L and the natural pH of the effluent (7.14). The following Fenton reaction presented the maximal enterobacteria inactivation after 120 min at 25 °C, when using hydrogen peroxide and added iron concentrations of 100 mg/L and 7 mg/L, respectively. The abundance of antibiotic resistant (amoxicillin and sulfamethoxazole) enterobacteria and total enterobacteria, enterococci, and heterotrophs, and antibiotic resistance genes - ARG - (sul1, bla_TEM and qnrS) was evaluated before and after each step of the treatment. Values below 10 CFU/100 mL were achieved for total and resistant cultivable enterobacteria immediately after treatment and after storage for 72 h, therefore meeting the strictest limit imposed for E. coli. Physico-chemical parameters also met the established limits for water reuse. Despite harbouring a rich and diverse bacterial community, the final stored disinfected wastewater contained high relative abundance of potentially hazardous bacteria. Such results point out the need of a deep microbiological characterization of treated wastewater to evaluate the risk of its reuse in irrigation.

Application of iron-activated persulfate for municipal wastewater disinfection

To address the increasing contamination of aquatic environments and incidence of waterborne diseases, advanced oxidation processes with activated persulfate have emerged as tools to inactivate wastewater microorganisms and contaminants. In this work, the disinfection of a secondary effluent from a wastewater treatment plant by iron-based persulfate activation was studied. Experiments in a batch stirred tank reactor were carried out to evaluate the performance along reaction time and the effect of operational parameters in the oxidative process efficiency (oxidant and iron concentration, pH and temperature). After 60 min of reaction, persulfate and iron concentrations of 3 mM and 0.75 mM, respectively, combined with a neutral initial pH (7.5) and a temperature of 40 °C, allowed to reach values below the detection limit (<10 CFU/100 mL) of enterococci and enterobacteria with and without ciprofloxacin resistance, as well as a 91% inactivation of total heterotrophic organisms and a 70% removal of total organic carbon. Regrowth of microorganisms was evaluated 72 h after treatment and it was only noticed a slight increase in total heterotrophs. Evaluation of physico-chemical characteristics of the treated water showed that it meets the requirements imposed by European and Portuguese legislation for its reuse in irrigation and most urban utilities.

Overgrowth control of potentially hazardous bacteria during storage of ozone treated wastewater through natural competition

Improving the chemical and biological quality of treated wastewater is particularly important in world regions under water stress. In these regions, reutilization of wastewater is seen as an alternative to reduce water demand, particularly for agriculture irrigation. In a reuse scenario, the treated wastewater must have enough quality to avoid chemical and biological contamination of the receiving environment. Ozonation is among the technologies available to efficiently remove organic micropollutants and disinfect secondary effluents, being implemented in full-scale urban wastewater treatment plants worldwide. However, previous studies demonstrated that storage of ozone treated wastewater promoted the overgrowth of potentially harmful bacteria, putting at risk its reutilization, given for instance the possibility of contaminating the food-chain. Therefore, this study was designed to assess the potential beneficial role of inoculation of ozone treated wastewater with a diverse bacterial community during storage, for the control of the overgrowth of potentially hazardous bacteria, through bacterial competition. To achieve this goal, ozone treated wastewater (TWW) was diluted with river water (RW) in the same proportion, and the resulting bacterial community (RW+TWW) was compared to that of undiluted TWW over 7 days storage. As hypothesized, in contrast to TWW, where dominance of Beta- and Gammaproteobacteria, namely Pseudomonas spp. and Acinetobacter spp., was observed upon storage for 7 days, the bacterial communities of the diluted samples (RW+TWW) were diverse, resembling those of RW. Moreover, given the high abundance of antibiotic resistance genes in RW, the concentration of these genes in RW+TWW did not differ from that of the non-ozonated controls (WW, RW and RW+WW) over the storage period. These results highlight the necessity of finding a suitable pristine diverse bacterial community to be used in the future to compete with bacteria surviving ozonation, to prevent reactivation of undesirable bacteria during storage of treated wastewater.

Effect of copper and zinc as sulfate or nitrate salts on soil microbiome dynamics and blaVIM-positive Pseudomonas aeruginosa survival

The exposure of soil to metals and to antibiotic resistant bacteria may lead to the progressive deterioration of soil quality. The persistence of antibiotic resistant bacteria or antibiotic resistance genes in soil can be influenced by the microbial community or by soil amendments with metal salts. This work assessed the effect of soil amendment with copper and zinc, as sulfate or nitrate salts, on the fate of a carbapenem-resistant (bla_VIM⁺) hospital effluent isolate of Pseudomonas aeruginosa (strain H1FC49) and on the variations of the microbial community composition. Microcosms with soil aged or not with copper and zinc salts (20 mM), and inoculated with P. aeruginosa H1FC49 were monitored at 0, 7, 14 and/or 30 days, for community composition (16S rRNA gene amplicon) and strain H1FC49 persistence. Data on culturable P. aeruginosa, quantitative PCR of the housekeeping gene ecf, and the presumably acquired genes bla_VIM⁺ and integrase (intI1), and community composition were interpreted based on descriptive statistics and multivariate analysis. P. aeruginosa and the presumably acquired genes, were quantifiable in soil for up to one month, in both metal-amended and non-amended soil. Metal amendments were associated with a significant decrease of bacterial community diversity and richness. The persistence of P. aeruginosa and acquired genes in soils, combined with the adverse effect of metals on the bacterial community, highlight the vulnerability of soil to both types of exogenous contamination.

Rethinking water treatment targets: Bacteria regrowth under unprovable conditions

Ozonation is among the currently used technologies to remove chemical and biological contaminants from secondary treated urban wastewater (UWW). Despite its effectiveness on the abatement of organic micropollutants (OMPs) and disinfection, previous studies have shown that regrow of bacteria may occur upon storage of the ozonated UWW. This reactivation has been attributed to the high content of assimilable organic carbon after treatment. In order to investigate if ozonation by-products are the main biological regrowth drivers in stored ozonated UWW, the ozonation surviving cells were resuspended in sterile bottled mineral water (MW), simulating a pristine oligotrophic environment. After 7 days storage, organisms such as Acinetobacter, Methylobacterium, Cupriavidus, Massilia, Acidovorax and Pseudomonas were dominant in both ozonated UWW and pristine MW, demonstrating that bacterial regrowth is not strictly related to the eventual presence of ozonation by-products, but instead with the ability of the surviving cells to cope with nutrient-poor environments. The resistome of UWW before and after ozonation was analysed by metagenomic techniques. Draft metagenome assembled genomes (dMAGs), recovered from both ozonated UWW and after cell resuspension in MW, harboured genes conferring resistance to diverse antibiotics classes. Some of these antibiotic resistance genes (ARGs) were located in the vicinity of mobile genetic elements, suggesting their potential to be mobilized. Among these, dMAGs affiliated to taxa with high relative abundance in stored water, such as P. aeruginosa and Acinetobacter spp., harboured ARGs conferring resistance to 12 and 4 families of antibiotics, respectively, including those encoding carbapenem hydrolysing oxacillinases. The results herein obtained point out that the design and development of new wastewater treatment technologies should include measures to attenuate the imbalance of the bacterial communities promoted by storage of the final treated wastewater, even when applying processes with high mineralization rates.

Feasibility of using magnetic nanoparticles in water disinfection

Disinfection is a crucial step during the water treatment process due to the significant risks of water contamination with human and animal excreta. The development of innovative disinfection technologies that can be applied at water point of use, avoiding contamination problems in water distribution systems and reservoirs, are needed. Thus, the present work aimed at assessing the disinfection efficiency of iron oxide magnetic nanoparticles (MNPs) modified with different compounds, such as carbon nanotubes, copper and silver, in water solutions contaminated with bacteria. Kinetic and influence of nanoparticles concentration experiments, performed with Escherichia coli, allowed to define the optimal reaction conditions to apply in batch experiments (1 min of contact time and 50 mg/mL of MNPs). During these experiments, CuFeO/CNT, C-FeO@CVD750 and 5% Ag/FeO were selected as the most efficient presenting log reduction values of 2.99, 1.50 and 2.11, respectively; however, experiments performed with Staphylococcus aureus suspension and a mixed bacterial suspension (E. coli + S. aureus) allowed to observe a slight decrease in nanomaterials efficiency, which was more evident for C-FeO@CVD750 and 5% Ag/FeO materials achieving efficiencies of 94 and 83% (corresponding log reductions of 1.26 and 0.77, respectively). CuFeO/CNT nanoparticles proved to be the most efficient material for both bacteria removal presenting an efficiency of 99% (corresponding log reduction of 1.99) for the mixed bacterial suspension. These nanoparticles proved to have great stability over successive experiments, and the low leaching values of the metals present in their composition after reaction proved the resistance and efficiency of these magnetic nanoparticles.

Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene

Carbapenem-resistant Klebsiella pneumoniae are a major global threat in healthcare facilities. The propagation of carbapenem resistance determinants can occur through vertical transmission, with genetic elements being transmitted by the host bacterium, or by horizontal transmission, with the same genetic elements being transferred among distinct bacterial hosts. This work aimed to track carbapenem resistance transmission by K. pneumoniae in a healthcare facility. The study involved a polyphasic approach based on conjugation assays, resistance phenotype and genotype analyses, whole genome sequencing, and plasmid characterization by pulsed field gel electrophoresis and optical DNA mapping. Out of 40 K. pneumoniae clinical isolates recovered over two years, five were carbapenem- and multidrug-resistant and belonged to multilocus sequence type ST147. These isolates harboured the carbapenemase encoding blaKPC-3 gene, integrated in conjugative plasmids of 140 kbp or 55 kbp, belonging to replicon types incFIA/incFIIK or incN/incFIIK, respectively. The two distinct plasmids encoding the blaKPC-3 gene were associated with distinct genetic lineages, as confirmed by optical DNA mapping and whole genome sequence analyses. These results suggested vertical (bacterial strain-based) transmission of the carbapenem-resistance genetic elements. Determination of the mode of transmission of antibiotic resistance in healthcare facilities, only possible based on polyphasic approaches as described here, is essential to control resistance propagation.

The challenge of removing waste from wastewater: let technology use nature!

Tertiary treatments capable of removing chemical and biological contaminants of emerging concern have been successfully developed and implemented at full scale, opening the possibility of using wastewater treatment plants as recycling units, capable of producing wastewater that can be reused in various activities, such as agriculture irrigation; However, tertiary treatments remove only part of the wastewater microbiota, leaving the opportunity for regrowth and/or reactivation of potentially hazardous microorganisms, facilitated by the poor competition among the surviving microorganisms; Under the motto 'added by technology, lead by nature', the treatment and storage of treated wastewater must find the balance to develop a protection shield against the impoverishment the microbial quality and the development of potentially hazardous bacteria.

Living with sulfonamides: a diverse range of mechanisms observed in bacteria

Sulfonamides are the oldest class of synthetic antibiotics still in use in clinical and veterinary settings. The intensive utilization of sulfonamides has been leading to the widespread contamination of the environment with these xenobiotic compounds. Consequently, in addition to pathogens and commensals, also bacteria inhabiting a wide diversity of environmental compartments have been in contact with sulfonamides for almost 90 years. This review aims at giving an overview of the effect of sulfonamides on bacterial cells, including the strategies used by bacteria to cope with these bacteriostatic agents. These include mechanisms of antibiotic resistance, co-metabolic transformation, and partial or total mineralization of sulfonamides. Possible implications of these mechanisms on the ecosystems and dissemination of antibiotic resistance are also discussed. KEY POINTS: • Sulfonamides are widespread xenobiotic pollutants; • Target alteration is the main sulfonamide resistance mechanism observed in bacteria; • Sulfonamides can be modified, degraded, or used as nutrients by some bacteria.

Re-thinking the main goals of biological sciences: is it possible to build new knowledge without fundamental research?

Relationships between collective scientific knowledge and country's economic prosperity and competitiveness have been described. Hence, interaction between industry and academic institutions is seen as a way to valorize this knowledge at social and economic levels. The ability to translate scientific knowledge in social and economic benefits is now receiving most of the funding for public research. However, and despite the evident long-term benefits of funding applied science, drastic reduction of budget for fundamental research may eventually lead to the opposite outcome.

Visualizing the invisible: class excursions to ignite children's enthusiasm for microbes

We have recently argued that, because microbes have pervasive - often vital - influences on our lives, and that therefore their roles must be taken into account in many of the decisions we face, society must become microbiology-literate, through the introduction of relevant microbiology topics in school curricula (Timmis et al. 2019. Environ Microbiol 21: 1513-1528). The current coronavirus pandemic is a stark example of why microbiology literacy is such a crucial enabler of informed policy decisions, particularly those involving preparedness of public-health systems for disease outbreaks and pandemics. However, a significant barrier to attaining widespread appreciation of microbial contributions to our well-being and that of the planet is the fact that microbes are seldom visible: most people are only peripherally aware of them, except when they fall ill with an infection. And it is disease, rather than all of the positive activities mediated by microbes, that colours public perception of 'germs' and endows them with their poor image. It is imperative to render microbes visible, to give them life and form for children (and adults), and to counter prevalent misconceptions, through exposure to imagination-capturing images of microbes and examples of their beneficial outputs, accompanied by a balanced narrative. This will engender automatic mental associations between everyday information inputs, as well as visual, olfactory and tactile experiences, on the one hand, and the responsible microbes/microbial communities, on the other hand. Such associations, in turn, will promote awareness of microbes and of the many positive and vital consequences of their actions, and facilitate and encourage incorporation of such consequences into relevant decision-making processes. While teaching microbiology topics in primary and secondary school is key to this objective, a strategic programme to expose children directly and personally to natural and managed microbial processes, and the results of their actions, through carefully planned class excursions to local venues, can be instrumental in bringing microbes to life for children and, collaterally, their families. In order to encourage the embedding of microbiology-centric class excursions in current curricula, we suggest and illustrate here some possibilities relating to the topics of food (a favourite pre-occupation of most children), agriculture (together with horticulture and aquaculture), health and medicine, the environment and biotechnology. And, although not all of the microbially relevant infrastructure will be within reach of schools, there is usually access to a market, local food store, wastewater treatment plant, farm, surface water body, etc., all of which can provide opportunities to explore microbiology in action. If children sometimes consider the present to be mundane, even boring, they are usually excited with both the past and the future so, where possible, visits to local museums (the past) and research institutions advancing knowledge frontiers (the future) are strongly recommended, as is a tapping into the natural enthusiasm of local researchers to leverage the educational value of excursions and virtual excursions. Children are also fascinated by the unknown, so, paradoxically, the invisibility of microbes makes them especially fascinating objects for visualization and exploration. In outlining some of the options for microbiology excursions, providing suggestions for discussion topics and considering their educational value, we strive to extend the vistas of current class excursions and to: (i) inspire teachers and school managers to incorporate more microbiology excursions into curricula; (ii) encourage microbiologists to support school excursions and generally get involved in bringing microbes to life for children; (iii) urge leaders of organizations (biopharma, food industries, universities, etc.) to give school outreach activities a more prominent place in their mission portfolios, and (iv) convey to policymakers the benefits of providing schools with funds, materials and flexibility for educational endeavours beyond the classroom.

Removal of microorganisms and antibiotic resistance genes from treated urban wastewater: A comparison between aluminium sulphate and tannin coagulants

The presence of antibiotic resistant-bacteria (ARB) and antibiotic resistance genes (ARG) in treated effluents of urban wastewater treatment plants (WWTP) may represent a threat to the environment and public health. Therefore, cost-effective technologies contributing to minimize loads of these contaminants in the final effluents of WWTP are required. This study aimed at assessing the capacity of coagulation to reduce the ARB&ARG load in secondary treated urban wastewater (STWW), as well as the impact of the process on the structure and diversity of the bacterial community. Coagulation performance using aluminium sulphate, a synthetic substance, and tannins, a biowaste, was compared. Samples were analysed immediately before (STWW) and after the coagulation treatment (Alu, Tan), as well as after 3-days storage in the dark at room temperature (RSTWW, RAlu, RTan), to assess possible reactivation events. Both coagulants decreased the turbidity and colour and reduced the bacterial load (16S rRNA gene copy number, total heterotrophs (HET), and ARB (faecal coliforms resistant to amoxicillin (FC/AMX) or ciprofloxacin (FC/CIP) up to 1-2 log immediately after the treatment. Both coagulants reduced the load of intl1, but in average, aluminium sulphate was able to decrease the content of the analysed ARGs (bla_TEM and qnrS) to lower levels than tannin. Reactivation after storage was observed mainly in RTan. In these samples the load of the culturable populations and qnrS gene prevalence increased, sometimes to values higher than those found in the initial wastewater. Reactivation was also characterized by an increment in Gammaproteobacteria relative abundance in the bacterial community, although with distinct patterns for RTan and RAlu. Curvibacter, Undibacterium and Aquaspirillum were among the most abundant genera in RAlu and Aeromonas, Pseudomonas and Stenotrophomonas in RTan. These bacterial community shifts were in agreement with the variations in the culturable bacterial counts of HET for RTan and FC/CIP for RAlu. In summary, the overall performance of aluminium sulphate was better than that of tannins in the treatment of treated urban wastewater.

Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP

Background

Microbial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified.

Results

Previous studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements.

Conclusions

Comparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.

Continuous ozonation of urban wastewater: Removal of antibiotics, antibiotic-resistant Escherichia coli and antibiotic resistance genes and phytotoxicity

This work evaluated the removal of a mixture of eight antibiotics (i.e. ampicillin (AMP), azithromycin (AZM), erythromycin (ERY), clarithromycin (CLA), ofloxacin (OFL), sulfamethoxazole (SMX), trimethoprim (TMP) and tetracycline (TC)) from urban wastewater, by ozonation operated in continuous mode at different hydraulic retention times (HRTs) (i.e. 10, 20, 40 and 60 min) and specific ozone doses (i.e. 0.125, 0.25, 0.50 and 0.75 gO₃ gDOC^{- 1}). As expected, the efficiency of ozonation was highly ozone dose- and contact time-dependent. The removal of the parent compounds of the selected antibiotics to levels below their detection limits was achieved with HRT of 40 min and specific ozone dose of 0.125 gO₃ gDOC^{- 1}. The effect of ozonation was also investigated at a microbiological and genomic level, by studying the efficiency of the process with respect to the inactivation of Escherichia coli and antibiotic-resistant E. coli, as well as to the reduction of the abundance of selected antibiotic resistance genes (ARGs). The inactivation of total cultivable E. coli was achieved under the experimental conditions of HRT 40 min and 0.25 gO₃ gDOC^-1, at which all antibiotic compounds were already degraded. The regrowth examinations revealed that higher ozone concentrations were required for the permanent inactivation of E. coli below the Limit of Quantification (<LOQ = 0.01 CFU mL^{- 1}). Also, the abundance of the examined ARGs (intl1, aadA1, dfrA1, qacEΔ1 and sul1) was found to decrease with increasing HRT and ozone dose. Despite the fact that the mildest operating parameters were able to eliminate the parent compounds of the tested antibiotics in wastewater effluents, it was clearly demonstrated in this study that higher ozone doses were required in order to confer permanent damage and/or death and prevent potential post-treatment re-growth of both total bacteria and ARB, and to reduce the abundance of ARGs below the LOQ. Interestingly, the mineralization of wastewater, in terms of Dissolved Organic Carbon (DOC) removal, was found to be significantly low even when the higher ozone doses were applied, leading to an increased phytotoxicity towards various plant species. The findings of this study clearly underline the importance of properly optimising the ozonation process (e.g. specific ozone dose and contact time) taking into consideration both the bacterial species and associated ARGs, as well as the wastewater physicochemical properties (e.g. DOC), in order to mitigate the spread of ARB&ARGs, as well as to reduce the potential phytotoxicity.

Genetic variation in the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain

Bacteria harboring conjugative plasmids have the potential for spreading antibiotic resistance through horizontal gene transfer. It is described that the selection and dissemination of antibiotic resistance is enhanced by stressors, like metals or antibiotics, which can occur as environmental contaminants. This study aimed at unveiling the composition of the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain (H1FC54) under different mating conditions. To meet this objective, plasmid pulsed field gel electrophoresis, optical mapping analyses and DNA sequencing were used in combination with phenotype analysis. Strain H1FC54 was observed to harbor five plasmids, three of which were conjugative and two of these, pH1FC54_330 and pH1FC54_140, contained metal and antibiotic resistance genes. Transconjugants obtained in the absence or presence of tellurite (0.5 μM or 5 μM), arsenite (0.5 μM, 5 μM or 15 μM) or ceftazidime (10 mg/L) and selected in the presence of sodium azide (100 mg/L) and tetracycline (16 mg/L) presented distinct phenotypes, associated with the acquisition of different plasmid combinations, including two co-integrate plasmids, of 310 kbp and 517 kbp. The variable composition of the conjugative plasmidome, the formation of co-integrates during conjugation, as well as the transfer of non-transferable plasmids via co-integration, and the possible association between antibiotic, arsenite and tellurite tolerance was demonstrated. These evidences bring interesting insights into the comprehension of the molecular and physiological mechanisms that underlie antibiotic resistance propagation in the environment.

Bioaugmentation of membrane bioreactor with Achromobacter denitrificans strain PR1 for enhanced sulfamethoxazole removal in wastewater

Achromobacter denitrificans strain PR1, previously found to harbour specific degradation pathways with high sulfamethoxazole (SMX) degradation rates, was bioaugmented into laboratory-scale membrane bioreactors (MBRs) operated under aerobic conditions to treat SMX-containing real domestic wastewater. Different hydraulic retention times (HRTs), which is related to reaction time and loading rates, were considered and found to affect the SMX removal efficiency. The availability of primary substrates was important in both bioaugmented and non-bioaugmented activated sludge (AS) for cometabolism of SMX. High HRT (24 h) resulted in low food to microorganism ratio (F/M) and low SMX removal, due to substrate limitation. Decrease in HRT from 24 h to 12 h, 6 h and finally 4 h led to gradual increases in primary substrates availability, e.g. organic compounds and ammonia, resulted in increased SMX removal efficiency and degradation rate, and is more favorable for high-rate wastewater treatment processes. After inoculation into the MBRs, the bioaugmentation strain was sustained in the reactor for a maximum of 31 days even though a significant decrease in abundance was observed. The bioaugmented MBRs showed enhanced SMX removal, especially under SMX shock loads compared to the control MBRs. The results of this study indicate that re-inoculation is required regularly after a period of time to maintain the removal efficiency of the target compound.

A rationale for the high limits of quantification of antibiotic resistance genes in soil

The determination of values of abundance of antibiotic resistance genes (ARGs) per mass of soil is extremely useful to assess the potential impacts of relevant sources of antibiotic resistance, such as irrigation with treated wastewater or manure application. Culture-independent methods and, in particular, quantitative PCR (qPCR), have been regarded as suitable approaches for such a purpose. However, it is arguable if these methods are sensitive enough to measure ARGs abundance at levels that may represent a risk for environmental and human health. This study aimed at demonstrating the range of values of ARGs quantification that can be expected based on currently used procedures of DNA extraction and qPCR analyses. The demonstration was based on the use of soil samples spiked with known amounts of wastewater antibiotic resistant bacteria (ARB) (Enterococcus faecalis, Escherichia coli, Acinetobacter johnsonii, or Pseudomonas aeruginosa), harbouring known ARGs, and also on the calculation of expected values determined based on qPCR. The limits of quantification (LOQ) of the ARGs (vanA, qnrS, bla_TEM, bla_OXA, bla_IMP, bla_VIM) were observed to be approximately 4 log-units per gram of soil dry weight, irrespective of the type of soil tested. These values were close to the theoretical LOQ values calculated based on currently used DNA extraction methods and qPCR procedures. The observed LOQ values can be considered extremely high to perform an accurate assessment of the impacts of ARGs discharges in soils. A key message is that ARGs accumulation will be noticeable only at very high doses. The assessment of the impacts of ARGs discharges in soils, of associated risks of propagation and potential transmission to humans, must take into consideration this type of evidence, and avoid the simplistic assumption that no detection corresponds to risk absence.

Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP

In the last decade, biological degradation and mineralization of antibiotics have been increasingly reported feats of environmental bacteria. The most extensively described example is that of sulfonamides that can be degraded by several members of Actinobacteria and Proteobacteria. Previously, we reported sulfamethoxazole (SMX) degradation and partial mineralization by Achromobacter denitrificans strain PR1, isolated from activated sludge. However, further studies revealed an apparent instability of this metabolic trait in this strain. Here, we investigated this instability and describe the finding of a low-abundance and slow-growing actinobacterium, thriving only in co-culture with strain PR1. This organism, named GP, shared highest 16S rRNA gene sequence similarity (94.6-96.9%) with the type strains of validly described species of the genus Leucobacter. This microbial consortium was found to harbor a homolog to the sulfonamide monooxygenase gene (sadA) also found in other sulfonamide-degrading bacteria. This gene is overexpressed in the presence of the antibiotic, and evidence suggests that it codes for a group D flavin monooxygenase responsible for the ipso-hydroxylation of SMX. Additional side reactions were also detected comprising an NIH shift and a Baeyer-Villiger rearrangement, which indicate an inefficient biological transformation of these antibiotics in the environment. This work contributes to further our knowledge in the degradation of this ubiquitous micropollutant by environmental bacteria.

Insights on sulfamethoxazole bio-transformation by environmental Proteobacteria isolates

Although sulfonamide residues are frequently reported as freshwaters contaminants, information on the ability of native bacteria to modify these synthetic antibiotics is scarce. Our purpose was to investigate the potential of bacteria from different aquatic environments to cleave or transform sulfamethoxazole (SMX) and infer on their ability to reduce the toxicity of this antibiotic. From a collection of about 100 Proteobacteria, 47 strains previously isolated from drinking water, surface water, and wastewater grew in the presence of 200 μM_SMX, and were further studied. Out of these, 14 strains, mostly from mineral drinking water, transformed SMX into equimolar amounts of the lesser toxic derivative N⁴-acetyl-sulfamethoxazole. The highest percentage of SMX transformation was recorded for two strains affiliated to Pseudomonas mandelii. For P. mandelii McBPA4 higher SMX transformation rate and extent were observed in fed-batch (∼8 μM_SMX/h, 81%) than in batch conditions (∼5 μM_SMX/h, 25%), but similar specific transformation rates were found in both cultivation modes (∼20 μmol_SMX/g_{cell dry weight}/h), indicating the dependence of the process on the microbial load. These results evidence that the capacity to transform synthetic antibiotics may be common among bacteria and highlight the potential of environmental bacteria in attenuating the potential adverse effects of pollution with sulfonamides.

Antibiotic resistance in wastewater treatment plants: Tackling the black box

Wastewater is among the most important reservoirs of antibiotic resistance in urban environments. The abundance of carbon sources and other nutrients, a variety of possible electron acceptors such as oxygen or nitrate, the presence of particles onto which bacteria can adsorb, or a fairly stable pH and temperature are examples of conditions favouring the remarkable diversity of microorganisms in this peculiar habitat. The wastewater microbiome brings together bacteria of environmental, human and animal origins, many harbouring antibiotic resistance genes (ARGs). Although numerous factors contribute, mostly in a complex interplay, for shaping this microbiome, the effect of specific potential selective pressures such as antimicrobial residues or metals, is supposedly determinant to dictate the fate of antibiotic resistant bacteria (ARB) and ARGs during wastewater treatment. This paper aims to enrich the discussion on the ecology of ARB&ARGs in urban wastewater treatment plants (UWTPs), intending to serve as a guide for wastewater engineers or other professionals, who may be interested in studying or optimizing the wastewater treatment for the removal of ARB&ARGs. Fitting this aim, the paper overviews and discusses: i) aspects of the complexity of the wastewater system and/or treatment that may affect the fate of ARB&ARGs; ii) methods that can be used to explore the resistome, meaning the whole ARB&ARGs, in wastewater habitats; and iii) some frequently asked questions for which are proposed addressing modes. The paper aims at contributing to explore how ARB&ARGs behave in UWTPs having in mind that each plant is a unique system that will probably need a specific procedure to maximize ARB&ARGs removal.

Solar treatment (H2O2, TiO2-P25 and GO-TiO2 photocatalysis, photo-Fenton) of organic micropollutants, human pathogen indicators, antibiotic resistant bacteria and related genes in urban wastewater

Solar-driven advanced oxidation processes were studied in a pilot-scale photoreactor, as tertiary treatments of effluents from an urban wastewater treatment plant. Solar-H₂O₂, heterogeneous photocatalysis (with and/or without the addition of H₂O₂ and employing three different photocatalysts) and the photo-Fenton process were investigated. Chemical (sulfamethoxazole, carbamazepine, and diclofenac) and biological contaminants (faecal contamination indicators, their antibiotic resistant counterparts, 16S rRNA and antibiotic resistance genes), as well as the whole bacterial community, were characterized. Heterogeneous photocatalysis using TiO₂-P25 and assisted with H₂O₂ (P25/H₂O₂) was the most efficient process on the degradation of the chemical organic micropollutants, attaining levels below the limits of quantification in less than 4 h of treatment (corresponding to Q_UV < 40 kJ L^-1). This performance was followed by the same process without H₂O₂, using TiO₂-P25 or a composite material based on graphene oxide and TiO₂. Regarding the biological indicators, total faecal coliforms and enterococci and their antibiotic resistant (tetracycline and ciprofloxacin) counterparts were reduced to values close, or beneath, the detection limit (1 CFU 100 mL^-1) for all treatments employing H₂O₂, even upon storage of the treated wastewater for 3-days. Moreover, P25/H₂O₂ and solar-H₂O₂ were the most efficient processes in the reduction of the abundance (gene copy number per volume of wastewater) of the analysed genes. However, this reduction was transient for 16S rRNA, intI1 and sul1 genes, since after 3-days storage of the treated wastewater their abundance increased to values close to pre-treatment levels. Similar behaviour was observed for the genes qnrS (using TiO₂-P25), bla_CTX-M and bla_TEM (using TiO₂-P25 and TiO₂-P25/H₂O₂). Interestingly, higher proportions of sequence reads affiliated to the phylum Proteobacteria (Beta- and Gammaproteobacteria) were found after 3-days storage of treated wastewater than before its treatment. Members of the genera Pseudomonas, Rheinheimera and Methylotenera were among those with overgrowth.

Microencapsulation of Gulosibacter molinativorax ON4T cells by a spray-drying process using different biopolymers

Molinate is a thiocarbamate herbicide used in rice crop protection. As other pesticides, molinate is a recognized environmental pollutant and bio-accumulated by some wildlife forms. Gulosibacter molinativorax ON4^T is able to hydrolyse molinate into metabolites which are further degraded by other un-related bacteria. Hence, it can be used in molinate bioremediation processes. The aim of this work was to investigate the possibility of producing G. molinativorax ON4^T microparticles, using different non-toxic biopolymers (arabic gum, modified chitosan, calcium alginate and sodium alginate) as encapsulating agents by a spray-drying process. Several formulations of microparticles were prepared, and their physicochemical structures were analyzed by scanning electron microscopy (SEM), laser granulometry analysis and zeta potential analysis. The obtained microparticles were evaluated considering their ability to degrade molinate, the metabolic activity (by colour development of the tetrazolium violet redox), and also the survival rate and shelf-life/storage stability of microparticles. Based on their molinate degrading activity, the biopolymers calcium alginate and modified chitosan cross-linked with tripolyphosphate appear to be the best options for the microencapsulation of the G. molinativorax ON4^T. However, the microparticles produced with modified chitosan cross-linked with tripolyphosphate present the best combination of physical properties and activity degradation of molinate.

Oryzisolibacter propanilivorax gen. nov., sp. nov., a propanil-degrading bacterium

Strain EPL6^T, a Gram-negative, motile, short rod was isolated from a propanil and 3,4-dichloroaniline enrichment culture produced from rice paddy soil. Based on the analyses of the 16S rRNA gene sequence, strain EPL6^T was observed to be a member of the family Comamonadaceae, sharing the highest pairwise identity with type strains of the species Alicycliphilus denitrificans K601^T (96.8 %) and Melaminivora alkalimesophila CY1^T (96.8 %). Strain EPL6^T was able to grow in a temperature range of 15-37 °C, pH 6-9 and in the presence of up to 4 % (w/v) NaCl and tested positive for catalase and oxidase reactions. The major respiratory quinone was Q8. The genomic DNA had a G+C content of 69.4±0.9 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol, and the major fatty acid methyl esters comprised C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH). Comparison of the genome sequence of strain EPL6^T and of its closest neighbours, Melaminivora alkalimesophila CY1^T and Alicycliphilus denitrificans K601^T, yielded values of ANI ≤84.1 % and of AAI ≤80.3 %. Therefore, the genetic, phylogenetic, phenotypic and chemotaxonomic characteristics support the classification of this organism into a new taxon. Considering the genetic divergence of strain EPL6^T from the type strains of the closest species, which belong to distinct genera, we propose a new genus within the family Comamonadaceae, named Oryzisolibacter propanilivorax gen. nov., sp. nov., represented by the isolate EPL6^T as the type strain of the species (=LMG 28427^T=CECT 8927^T).

Ubiquitous and persistent Proteobacteria and other Gram-negative bacteria in drinking water

Drinking water comprises a complex microbiota, in part shaped by the disinfection and distribution systems. Gram-negative bacteria, mainly members of the phylum Proteobacteria, represent the most frequent bacteria in drinking water, and their ubiquity and physiological versatility raises questions about possible implications in human health. The first step to address this concern is the identification and characterization of such bacteria that is the first objective of this study, aiming at identifying ubiquitous or persistent Gram-negative bacteria, Proteobacteria or members of other phyla, isolated from tap water or from its source. >1000 bacterial isolates were characterized and identified, and a selected group (n=68) was further analyzed for the minimum inhibitory concentrations (MIC) to antibiotics (amoxicillin and gentamicin) and metals (copper and arsenite). Total DNA extracts of tap water were examined for the presence of putatively acquired antibiotic resistance or related genes (intI1, bla_TEM, qnrS and sul1). The ubiquitous tap water genera comprised Proteobacteria of the class Alpha- (Blastomonas, Brevundimonas, Methylobacterium, Sphingobium, Sphingomonas), Beta- (Acidovorax, Ralstonia) and Gamma- (Acinetobacter and Pseudomonas). Persistent species were members of genera such as Aeromonas, Enterobacter or Dechloromonas. Ralstonia spp. showed the highest MIC values to gentamicin and Acinetobacter spp. to arsenite. The genes intI1, bla_TEM or sul1 were detected, at densities lower than 2.3×10⁵copies/L, 2.4×10⁴copies/L and 4.6×10²copies/L, respectively, in most tap water samples. The presence of some bacterial groups, in particular of Beta- or Gammaproteobacteria (e.g. Ralstonia, Acinetobacter, Pseudomonas) in drinking water may deserve attention given their potential as reservoirs or carriers of resistance or as opportunistic pathogens.

Ozonation and UV254nm radiation for the removal of microorganisms and antibiotic resistance genes from urban wastewater

Conventional wastewater treatment has a limited capacity to reduce antibiotic resistant bacteria and genes (ARB&ARG). Tertiary treatment processes are promising solutions, although the transitory inactivation of bacteria may select ARB&ARG. This study aimed at assessing the potential of ozonation and UV_254nm radiation to inactivate cultivable fungal and bacterial populations, and the selected genes 16S rRNA (common to all bacteria), intI1 (common in Gram-negative bacteria) and the ARG vanA, bla_TEM, sul1 and qnrS. The abundance of the different microbiological parameters per volume of wastewater was reduced by ∼2 log units for cultivable fungi and 16S rRNA and intI1 genes, by∼3-4 log units, for total heterotrophs, enterobacteria and enterococci, and to values close or below the limits of quantification for ARG, for both processes, after a contact time of 30min. Yet, most of the cultivable populations, the 16S rRNA and intI1 genes as well as the ARG, except qnrS after ozonation, reached pre-treatment levels after 3days storage, suggesting a transitory rather than permanent microbial inactivation. Noticeably, normalization per 16S rRNA gene evidenced an increase of the ARG and intI1 prevalence, mainly after UV_254nm treatment. The results suggest that these tertiary treatments may be selecting for ARB&ARG populations.

Proteobacteria become predominant during regrowth after water disinfection

Disinfection processes aim at reducing the number of viable cells through the generation of damages in different cellular structures and molecules. Since disinfection involves unspecific mechanisms, some microbial populations may be selected due to resilience to treatment and/or to high post-treatment fitness. In this study, the bacterial community composition of secondarily treated urban wastewater and of surface water collected in the intake area of a drinking water treatment plant was compared before and 3-days after disinfection with ultraviolet radiation, ozonation or photocatalytic ozonation. The aim was to assess the dynamics of the bacterial communities during regrowth after disinfection. In all the freshly collected samples, Proteobacteria and Bacteroidetes were the predominant phyla (40-50% and 20-30% of the reads, respectively). Surface water differed from wastewater mainly in the relative abundance of Actinobacteria (17% and <5% of the reads, respectively). After 3-days storage at light and room temperature, disinfected samples presented a shift of Gammaproteobacteria (from 8 to 10% to 33-65% of the reads) and Betaproteobacteria (from 14 to 20% to 31-37% of the reads), irrespective of the type of water and disinfection process used. Genera such as Pseudomonas, Acinetobacter or Rheinheimera presented a selective advantage after water disinfection. These variations were not observed in the non-disinfected controls. Given the ubiquity and genome plasticity of these bacteria, the results obtained suggest that disinfection processes may have implications on the microbiological quality of the disinfected water.

Production of microparticles of molinate degrading biocatalysts using the spray drying technique

Previous studies demonstrated the capability of mixed culture DC1 to mineralize the thiocarbamate herbicide molinate through the activity of molinate hydrolase (MolA). Because liquid suspensions are not compatible with long-term storage and are not easy to handle when bioremediation strategies are envisaged, in this study spray drying was evaluated as a cost-effective method to store and transport these molinate biocatalysts. Microparticles of mixed culture DC1 (DC1) and of cell free crude extracts containing MolA (MA) were obtained without any carrier polymer, and with calcium alginate (CA) or modified chitosan (MCt) as immobilizing agents. All the DC1 microparticles showed high molinate degrading activity upon storage for 6 months, or after 9 additions of ∼0.4 mM molinate over 1 month. The DC1-MCt microparticles were those with the highest survival rate and lowest heterogeneity. For MA microparticles, only MA-MCt degraded molinate. However, its Vmax was only 1.4% of that of the fresh cell free extract (non spray dried). The feasibility of using the DC1-MCt and MA-MCt microparticles in bioaugmentation processes was assessed in river water microcosms, using mass (g):volume (L) ratios of 1:13 and 1:0.25, respectively. Both type of microparticles removed ∼65-75% of the initial 1.5 mg L(-1) molinate, after 7 days of incubation. However, only DC1-MCt microparticles were able to degrade this environmental concentration of molinate without disturbing the native bacterial community. These results suggest that spray drying can be successfully used to produce DC1-MCt microparticles to remediate molinate polluted sites through a bioaugmentation strategy.

Photocatalytic ozonation of urban wastewater and surface water using immobilized TiO2 with LEDs: Micropollutants, antibiotic resistance genes and estrogenic activity

Photocatalytic ozonation was employed for the first time in continuous mode with TiO2-coated glass Raschig rings and light emitting diodes (LEDs) to treat urban wastewater as well as surface water collected from the supply area of a drinking water treatment plant (DWTP). Different levels of contamination and types of contaminants were considered in this work, including chemical priority substances (PSs) and contaminants of emerging concern (CECs), as well as potential human opportunistic antibiotic resistant bacteria and their genes (ARB&ARG). Photocatalytic ozonation was more effective than single ozonation (or even than TiO2 catalytic ozonation) in the degradation of typical reaction by-products (such as oxalic acid), and more effective than photocatalysis to remove the parent micropollutants determined in urban wastewater. In fact, only fluoxetine, clarithromycin, erythromycin and 17-alpha-ethinylestradiol (EE2) were detected after photocatalytic ozonation, by using solid-phase extraction (SPE) pre-concentration and LC-MS/MS analysis. In surface water, this treatment allowed the removal of all determined micropollutants to levels below the limit of detection (0.01-0.20 ng L(-1)). The efficiency of this process was then assessed based on the capacity to remove different groups of cultivable microorganisms and housekeeping (16S rRNA) and antibiotic resistance or related genes (intI1, blaTEM, qnrS, sul1). Photocatalytic ozonation was observed to efficiently remove microorganisms and ARGs. Although after storage total heterotrophic and ARB (to ciprofloxacin, gentamicin, meropenem), fungi, and the genes 16S rRNA and intI1, increased to values close to the pre-treatment levels, the ARGs (blaTEM, qnrS and sul1) were reduced to levels below/close to the quantification limit even after 3-days storage of treated surface water or wastewater. Yeast estrogen screen (YES), thiazolyl blue tetrazolium reduction (MTT) and lactate dehydrogenase (LDH) assays were also performed before and after photocatalytic ozonation to evaluate the potential estrogenic activity, the cellular metabolic activity and the cell viability. Compounds with estrogenic effects and significant differences concerning cell viability were not observed in any case. A slight cytotoxicity was only detected for Caco-2 and hCMEC/D3 cell lines after treatment of the urban wastewater, but not for L929 fibroblasts.

Bordetella bronchialis sp. nov., Bordetella flabilis sp. nov. and Bordetella sputigena sp. nov., isolated from human respiratory specimens, and reclassification of Achromobacter sediminum Zhang et al. 2014 as Verticia sediminum gen. nov., comb. nov

The phenotypic and genotypic characteristics of four Bordetella hinzii-like strains from human respiratory specimens and representing nrdA gene sequence based genogroups 3, 14 and 15 were examined. In a 16S rRNA gene sequence based phylogenetic tree, the four strains consistently formed a single coherent lineage but their assignment to the genus Bordetella was equivocal. The respiratory quinone, polar lipid and fatty acid profiles generally conformed to those of species of the genus Bordetella and were characterized by the presence of ubiquinone 8, of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several aminolipids, and of high percentages of C16 : 0, cyclo-C17 : 0 and summed feature 2, as major chemotaxonomic marker molecules, respectively. The DNA G+C content was about 66 mol%, which corresponded with that of the high-percentage DNA G+C content genera of the family Alcaligenaceae including the genus Bordetella. DNA–DNA hybridization experiments revealed the presence of three distinct genomospecies and thus confirmed phenotypic differences as revealed by means of extensive biochemical characterization. We therefore propose to formally classify Bordetella genogroups 3, 14 and 15 as Bordetella bronchialis sp. nov. (type strain LMG 28640T = AU3182T = CCUG 56828T), Bordetella sputigena sp. nov. (type strain LMG 28641T = CCUG 56478T) and Bordetella flabilis sp. nov. (type strain LMG 28642T = AU10664T = CCUG 56827T). In addition, we propose to reclassify Achromobacter sediminum into the novel genus Verticia, as Verticia sediminum, gen. nov., comb. nov., on the basis of its unique phylogenetic position, its marine origin and its distinctive phenotypic, fatty acid and polar lipid profile.

Comparison of the bacterial composition of two commercial composts with different physicochemical, stability and maturity properties

Previously, two municipal solid waste commercial composts (MSW1 and MSW2) were characterized. Although sharing the same type of raw material, most of their physicochemical, stability and maturity properties differed. The present study aimed to characterize them at a microbiological level, and to infer on possible relationships between the composts properties and the structure of their bacterial communities. Both the 16S rRNA gene-based PCR-DGGE profiling and 454-pyrosequencing technology showed that the structure of the bacterial communities of these composts was distinct. The bacterial community of MSW1 was more diverse than that of MSW2. Multivariate analyses revealed that the high electrical conductivity, Cu content as well as the low phytotoxity of compost MSW1, when compared to MSW2, contributed most to shape its bacterial community structure. Indeed, high abundance of halophilic (Halomonadaceae and Brevibacteriaceae) and metal resistant organisms (Brevibacteriaceae and Bacillaceae) were found in MSW1. In addition, Pseudonocardiaceae, Streptomycetaceae, Bacillaceae, and Brevibacteriaceae may have contributed to the high humic-like acids content and low phytotoxicity of MSW1. In contrast, the high organic matter content and the high density of the cultivable fungi population were the parameters most correlated with the structure of the bacterial community of compost MSW2, dominated by Corynebacteriaceae and mainly Aerococcaceae, taxonomic groups not commonly found in composts.

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

Quinolone resistant Aeromonas spp. as carriers and potential tracers of acquired antibiotic resistance in hospital and municipal wastewater

Members of the genus Aeromonas are recognized carriers of antibiotic resistance in aquatic environments. However, their importance on the spread of resistance from hospital effluents to the environment is poorly understood. Quinolone resistant Aeromonas spp. (n = 112) isolated from hospital effluent (HE) and from raw (RWW) and treated wastewater (TWW) of the receiving urban wastewater treatment plant (UWTP) were characterized. Species identification and genetic intraspecies diversity were assessed based on the 16S rRNA, cpn60 and gyrB genes sequence analysis. The antibiotic resistance phenotypes and genotypes (qnrA, qnrB, qnrC, qnrD, qnrS, qnrVC; qepA; oqxAB; aac(6′)-Ib-cr; blaOXA; incU) were analyzed in function of the origin and taxonomic group. Most isolates belonged to the species Aeromonas caviae and Aeromonas hydrophila (50% and 41%, respectively). The quinolone and the beta-lactamase resistance genes aac(6′)-Ib-cr and blaOXA, including gene blaOXA-101, identified for the first time in Aeromonas spp., were detected in 58% and 56% of the isolates, respectively, with identical prevalence in HE and UWTP wastewater. In contrast, the gene qnrS2 was observed mainly in isolates from the UWTP (51%) and rarely in HE isolates (3%), suggesting that its origin is not the clinical setting. Bacterial groups and genes that allow the identification of major routes of antibiotic resistance dissemination are valuable tools to control this problem. In this study, it was concluded that members of the genus Aeromonas harboring the genes aac(6′)-Ib-cr and blaOXA are relevant tracers of antibiotic resistance dissemination in wastewater habitats, while those yielding the gene qnrS2 allow the traceability from non-clinical sources.

Fast mineralization and detoxification of amoxicillin and diclofenac by photocatalytic ozonation and application to an urban wastewater

The degradation of two organic pollutants (amoxicillin and diclofenac) in 0.1 mM aqueous solutions was studied by using advanced oxidation processes, namely ozonation, photolysis, photolytic ozonation, photocatalysis and photocatalytic ozonation. Diclofenac was degraded quickly under direct photolysis by artificial light (medium-pressure vapor arc, λ(exc) > 300 nm), while amoxicillin remained very stable. In the presence of ozone, regardless of the type of process, complete degradation of both organic pollutants was observed in less than 20 min. Photolysis or ozonation on their own led to modest values of total organic carbon (TOC) removal (<6% or 41%, respectively in 180 min), while for photocatalysis (no ozone present) a significant fraction of nonoxidizable compounds remained in the treated water (∼15% after 180 min). In the case of photolytic ozonation, the kinetics of TOC removal was slow. In contrast, a relatively fast and complete mineralization of amoxicillin and diclofenac (30 and 120 min, respectively) was achieved when applying the photocatalytic ozonation process. The absence of toxicity of the treated waters was confirmed by growth inhibition assays using two different microorganisms, Escherichia coli and Staphylococcus aureus. Photocatalytic ozonation was also applied to an urban wastewater spiked with both amoxicillin and diclofenac. The parent pollutants were easily oxidized, but the TOC removal was only as much as 68%, mainly due to the persistent presence of oxamic acid in the treated sample. The same treatment allowed the effective degradation of a wide group of micropollutants (pesticides, pharmaceuticals, hormones and an industrial compound) detected in non-spiked urban wastewater.

Antibiotic resistance in urban aquatic environments: can it be controlled?

Over the last decade, numerous evidences have contributed to establish a link between the natural and human-impacted environments and the growing public health threat that is the antimicrobial resistance. In the environment, in particular in areas subjected to strong anthropogenic pressures, water plays a major role on the transformation and transport of contaminants including antibiotic residues, antibiotic-resistant bacteria, and antibiotic resistance genes. Therefore, the urban water cycle, comprising water abstraction, disinfection, and distribution for human consumption, and the collection, treatment, and delivery of wastewater to the environment, is a particularly interesting loop to track the fate of antibiotic resistance in the environment and to assess the risks of its transmission back to humans. In this article, the relevance of different transepts of the urban water cycle on the potential enrichment and spread of antibiotic resistance is reviewed. According to this analysis, some gaps of knowledge, research needs, and control measures are suggested. The critical rationale behind the measures suggested and the desirable involvement of some key action players is also discussed.

Development of an automatic identification algorithm for antibiogram analysis

Routinely, diagnostic and microbiology laboratories perform antibiogram analysis which can present some difficulties leading to misreadings and intra and inter-reader deviations. An Automatic Identification Algorithm (AIA) has been proposed as a solution to overcome some issues associated with the disc diffusion method, which is the main goal of this work. AIA allows automatic scanning of inhibition zones obtained by antibiograms. More than 60 environmental isolates were tested using susceptibility tests which were performed for 12 different antibiotics for a total of 756 readings. Plate images were acquired and classified as standard or oddity. The inhibition zones were measured using the AIA and results were compared with reference method (human reading), using weighted kappa index and statistical analysis to evaluate, respectively, inter-reader agreement and correlation between AIA-based and human-based reading. Agreements were observed in 88% cases and 89% of the tests showed no difference or a <4mm difference between AIA and human analysis, exhibiting a correlation index of 0.85 for all images, 0.90 for standards and 0.80 for oddities with no significant difference between automatic and manual method. AIA resolved some reading problems such as overlapping inhibition zones, imperfect microorganism seeding, non-homogeneity of the circumference, partial action of the antimicrobial, and formation of a second halo of inhibition. Furthermore, AIA proved to overcome some of the limitations observed in other automatic methods. Therefore, AIA may be a practical tool for automated reading of antibiograms in diagnostic and microbiology laboratories.

Hydromonas duriensis gen. nov., sp. nov., isolated from freshwater

An aerobic, Gram-stain-negative rod, designated strain A2P5T, was isolated from the Douro river, in Porto, Portugal. Cells were catalase- and oxidase-positive. Growth occurred at 15–30 °C, at pH 6–8 and in the presence of 1 % (w/v) NaCl. The major respiratory quinone was Q8, the genomic DNA had a G+C content of 47 ± 1 mol%, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, strain A2P5T was observed to be a member of the family Burkholderiaceae, but could not be identified as a member of any validly named genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa ( < 91 %), together with the comparative analysis of phenotypic and chemotaxonomic characteristics, supported the proposal of a novel species of a new genus within the family Burkholderiaceae. The name Hydromonas duriensis gen. nov., sp. nov. is proposed. The type strain of Hydromonas duriensis is A2P5T ( = LMG 28428T = CCUG 66137T).

Inactivation of Geobacillus stearothermophilus spores by alkaline hydrolysis applied to medical waste treatment

Although alkaline hydrolysis treatment emerges as an alternative disinfection/sterilization method for medical waste, information on its effects on the inactivation of biological indicators is scarce. The effects of alkaline treatment on the resistance of Geobacillus stearothermophilus spores were investigated and the influence of temperature (80 °C, 100 °C and 110 °C) and NaOH concentration was evaluated. In addition, spore inactivation in the presence of animal tissues and discarded medical components, used as surrogate of medical waste, was also assessed. The effectiveness of the alkaline treatment was carried out by determination of survival curves and D-values. No significant differences were seen in D-values obtained at 80 °C and 100 °C for NaOH concentrations of 0.5 M and 0.75 M. The D-values obtained at 110 °C (2.3-0.5 min) were approximately 3 times lower than those at 100 °C (8.8-1.6 min). Independent of the presence of animal tissues and discarded medical components, 6 log10 reduction times varied between 66 and 5 min at 100 °C-0.1 M NaOH and 110 °C-1 M NaOH, respectively. The alkaline treatment may be used in future as a disinfection or sterilization alternative method for contaminated waste.

Relationships among bulk soil physicochemical, biochemical, and microbiological parameters in an organic alfalfa-rice rotation system

The microbial communities of bulk soil of rice paddy fields under an ancient organic agriculture regimen, consisting on an alfalfa-rice rotation system, were characterized. The drained soil of two adjacent paddies at different stages of the rotation was compared before rice seeding and after harvesting. The relationships among the soil microbial, physicochemical, and biochemical parameters were investigated using multivariate analyses. In the first year of rice cropping, aerobic cultivable heterotrophic populations correlated with lineages of presumably aerobic bacteria (e.g., Sphingobacteriales, Sphingomonadales). In the second year of rice cropping, the total C content correlated with presumable anaerobic bacteria (e.g., Anaerolineae). Independently of the year of rice cropping, before rice seeding, proteolytic activity correlated positively with the cultivable aerobic heterotrophic and ammonifier populations, the soil catabolic profile and with presumable aerobes (e.g., Sphingobacteriales, Rhizobiales) and anaerobes (e.g., Bacteroidales, Anaerolineae). After harvesting, strongest correlations were observed between cultivable diazotrophic populations and bacterial groups described as comprising N2 fixing members (e.g., Chloroflexi-Ellin6529, Betaproteobacteria, Alphaproteobacteria). It was demonstrated that chemical parameters and microbial functions were correlated with variations on the total bacterial community composition and structure occurring during rice cropping. A better understanding of these correlations and of their implications on soil productivity may be valid contributors for sustainable agriculture practices, based on ancient processes.

Structure-guided engineering of molinate hydrolase for the degradation of thiocarbamate pesticides

Molinate is a recalcitrant thiocarbamate used to control grass weeds in rice fields. The recently described molinate hydrolase, from Gulosibacter molinativorax ON4T, plays a key role in the only known molinate degradation pathway ending in the formation of innocuous compounds. Here we report the crystal structure of recombinant molinate hydrolase at 2.27 Å. The structure reveals a homotetramer with a single mononuclear metal-dependent active site per monomer. The active site architecture shows similarities with other amidohydrolases and enables us to propose a general acid-base catalysis mechanism for molinate hydrolysis. Molinate hydrolase is unable to degrade bulkier thiocarbamate pesticides such as thiobencarb which is used mostly in rice crops. Using a structural-based approach, we were able to generate a mutant (Arg187Ala) that efficiently degrades thiobencarb. The engineered enzyme is suitable for the development of a broader thiocarbamate bioremediation system.

Genetic characterization of fluoroquinolone resistant Escherichia coli from urban streams and municipal and hospital effluents

Escherichia coli with reduced susceptibility to ciprofloxacin, isolated from urban streams, wastewater treatment plants and hospital effluent between 2004 and 2012, were compared based on multilocus sequence typing (MLST), quinolone and beta-lactam resistance determinants and plasmid replicon type. Isolates from the different types of water and isolation dates clustered together, suggesting the persistence and capacity to propagate across distinct aquatic environments. The most prevalent MLST groups were ST10 complex and ST131. Almost all isolates (98%) carried mutations in the chromosomal genes gyrA and/or parC, and 10% possessed the genes qepA, aac(6('))-Ib-cr and/or qnrS1. Over 80% of the isolates were resistant to three or more classes of antibiotics (MDR ≥ 3). The most prevalent beta-lactamase encoding gene was blaTEM, followed by blaCTX-M-15, co-existing with plasmid mediated quinolone resistance. The plasmid replicon types of the group IncF were the most prevalent and distributed by different MLST groups. The genes aac(6('))-Ib-cr and/or qnrS1 could be transferred by conjugation in combination with the genes blaTEM,blaSHV-12 or blaOXA-1 and the plasmid replicon types I1-Iγ, K, HI2 and/or B/O. The potential of multidrug resistant E. coli with reduced susceptibility to ciprofloxacin, harboring mobile genetic elements and with ability to conjugate and transfer resistance genes, to spread and persist across different aquatic environments was demonstrated.