Elucidating the impact of microbial community biodiversity on pharmaceutical biotransformation during wastewater treatment

Biological degradation of organic micropollutants in GAC filters-temporal development and spatial variations

The capacity for organic micropollutant removal in granular activated carbon (GAC) filters for wastewater treatment changes over time. These changes are in general attributed to changes in adsorption, but may in some cases also be affected by biological degradation. Knowledge on the degradation of organic micropollutants, however, is scarce. In this work, the degradation of micropollutants in several full-scale GAC and sand filters was investigated through incubation experiments over a period of three years, using 14C-labeled organic micropollutants with different susceptibilities to biological degradation (ibuprofen, diclofenac, and carbamazepine), with parallel 16S rRNA gene sequencing. The results showed that the degradation of diclofenac and ibuprofen in GAC filters increased with increasing numbers of bed volumes when free oxygen was available in the filter, while variations over filter depth were limited. Despite relatively large differences in bacterial composition between filters, a degradation of diclofenac was consistently observed for the GAC filters that had been operated with high influent oxygen concentration (DO >8 mg/L). The results of this comprehensive experimental work provide an increased understanding of the interactions between microbial composition, filter material, and oxygen availability in the biological degradation of organic micropollutants in GAC filters.

Exploring long-term retention and reactivation of micropollutant biodegradation capacity

The factors limiting micropollutant biodegradation in the environment and how to stimulate this process have often been investigated. However, little information is available on the capacity of microbial communities to retain micropollutant biodegradation capacity in the absence of micropollutants or to reactivate micropollutant biodegradation in systems with fluctuating micropollutant concentrations. This study investigated how a period of 2 months without the addition of micropollutants and other organic carbon affected micropollutant biodegradation by a micropollutant-degrading microbial community. Stimulation of micropollutant biodegradation was performed by adding different types of dissolved organic carbon (DOC)-extracted from natural sources and acetate-increasing 10 × the micropollutant concentration, and inoculating with activated sludge. The results show that the capacity to biodegrade 3 micropollutants was permanently lost. However, the biodegradation activity of 2,4-D, antipyrine, chloridazon, and its metabolites restarted when these micropollutants were re-added to the community. Threshold concentrations similar to those obtained before the period of no substrate addition were achieved, but biodegradation rates were lower for some compounds. Through the addition of high acetate concentrations (108 mg-C/L), gabapentin biodegradation activity was regained, but 2,4-D biodegradation capacity was lost. An increase of bentazon concentration from 50 to 500 µg/L was necessary for biodegradation to be reactivated. These results provide initial insights into the longevity of micropollutant biodegradation capacity in the absence of the substance and strategies for reactivating micropollutant biodegrading communities.

Biostimulation with oxygen and electron donors supports micropollutant biodegradation in an experimentally simulated nitrate-reducing aquifer

The availability of suitable electron donors and acceptors limits micropollutant natural attenuation in oligotrophic groundwater. This study investigated how electron donors with different biodegradability (humics, dextran, acetate, and ammonium), and different oxygen concentrations affect the biodegradation of 15 micropollutants (initial concentration of each micropollutant = 50 μg/L) in simulated nitrate reducing aquifers. Tests mimicking nitrate reducing field conditions showed no micropollutant biodegradation, even with electron donor amendment. However, 2,4-dichlorophenoxyacetic acid and mecoprop were biodegraded under (micro)aerobic conditions with and without electron donor addition. The highest 2,4-dichlorophenoxyacetic acid and mecoprop biodegradation rates and removal efficiencies were obtained under fully aerobic conditions with amendment of an easily biodegradable electron donor. Under microaerobic conditions, however, amendment with easily biodegradable dissolved organic carbon (DOC) inhibited micropollutant biodegradation due to competition between micropollutants and DOC for the limited oxygen available. Microbial community composition was dictated by electron acceptor availability and electron donor amendment, not by micropollutant biodegradation. Low microbial community richness and diversity led to the absence of biodegradation of the other 13 micropollutants (such as bentazon, chloridazon, and carbamazepine). Finally, adaptation and potential growth of biofilms interactively determined the location of the micropollutant removal zone relative to the point of amendment. This study provides new insight on how to stimulate in situ micropollutant biodegradation to remediate oligotrophic groundwaters as well as possible limitations of this process.

Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater

Organic contaminants enter aquatic ecosystems from various sources, including wastewater treatment plant effluent. Freshwater biofilms play a major role in the removal of organic contaminants from receiving water bodies, but knowledge of the molecular mechanisms driving contaminant biotransformations in complex stream biofilm (periphyton) communities remains limited. Previously, we demonstrated that biofilms in experimental flume systems grown at higher ratios of treated wastewater (WW) to stream water displayed an increased biotransformation potential for a number of organic contaminants. We identified a positive correlation between WW percentage and biofilm biotransformation rates for the widely-used insect repellent, N,N-diethyl-meta-toluamide (DEET) and a number of other wastewater-borne contaminants with hydrolyzable moieties. Here, we conducted deep shotgun sequencing of flume biofilms and identified a positive correlation between WW percentage and metagenomic read abundances of DEET hydrolase (DH) homologs. To test the causality of this association, we constructed a targeted metagenomic library of DH homologs from flume biofilms. We screened our complete metagenomic library for activity with four different substrates, including DEET, and a subset thereof with 183 WW-related organic compounds. The majority of active hydrolases in the metagenomic library preferred aliphatic and aromatic ester substrates while, remarkably, only a single reference enzyme was capable of DEET hydrolysis. Of the 626 total enzyme-substrate combinations tested, approximately 5% were active enzyme-substrate pairs. Metagenomic DH family homologs revealed a broad substrate promiscuity spanning 22 different compounds when summed across all enzymes tested. We biochemically characterized the most promiscuous and active enzymes identified based on metagenomic analysis from uncultivated Rhodospirillaceae and Planctomycetaceae. In addition to characterizing new DH family enzymes, we exemplified a framework for linking metagenome-guided hypothesis generation with experimental validation. Overall, this study expands the scope of known enzymatic contaminant biotransformations for metagenomic hydrolases from WW-receiving stream biofilm communities.

Unveiling combined ecotoxicity: Interactions and impacts of engineered nanoparticles and PPCPs

Emerging contaminants such as engineered nanoparticles (ENPs), pharmaceuticals and personal care products (PPCPs) are of great concern because of their wide distribution and incomplete removal in conventional wastewater and soil treatment processes. The production and usage of ENPs and PPCPs inevitably result in their coexistence in different environmental media, thus posing various risks to organisms in aquatic and terrestrial ecosystems. However, the existing literature on the physicochemical interactions between ENPs and PPCPs and their effects on organisms is rather limited. Therefore, this paper summarized the ecotoxicity of combined ENPs and PPCPs by discussing: (1) the interactions between ENPs and PPCPs, including processes such as aggregation, adsorption, transformation, and desorption, considering the influence of environmental factors like pH, ionic strength, dissolved organic matter, and temperature; (2) the effects of these interactions on bioaccumulation, bioavailability and biotoxicity in organisms at different trophic levels; (3) the impacted of ENPs and PPCPs on cellular-level biological process. This review elucidated the potential ecological hazards associated with the interaction of ENPs and PPCPs, and serves as a foundation for future investigations into the ecotoxicity and mode of action of ENPs, PPCPs, and their co-occurring metabolites.

Effect of dissolved organic carbon on micropollutant biodegradation by aquifer and soil microbial communities

Groundwater, a major source of drinking water worldwide, is often contaminated with micropollutants. Although microbial communities in aquifers and soils have the capability to biodegrade some micropollutants, this process is limited in situ. Biostimulation with dissolved organic carbon (DOC) is known to promote micropollutant biodegradation, but the role of DOC biodegradability is still poorly understood. This study investigated how three DOC types with different biodegradability (humics, dextran and acetate) affect the biodegradation of 15 micropollutants by aquifer and soil microbial communities under aerobic and nitrate reducing conditions. Although originating from different environments, both communities were able to biodegrade the same 4 micropollutants under aerobic conditions - 2,4-D, MCPP, chloridazon (CLZ) and chloridazon-desphenyl. However, DOC addition only affected MCPP biodegradation, promoting MCPP biodegradation regardless of DOC biodegradability. Biodegradation of 2,4-D, MCPP and CLZ under aerobic conditions was observed after a lag phase, whose duration differed per compound. 2,4-D was biodegraded first and fully. Aquifer community was able to degrade about half of the initial MCPP concentration (removal efficiency of 49.3 ± 11.7%). CLZ was fully biodegraded by the aquifer community, but not by the soil community, possibly due to substrate competition with organics originating from the inoculum. Therefore, the natural organic carbon present in the inocula and in environmental systems can influence micropollutant biodegradation. Under nitrate reducing conditions micropollutant biodegradation was not observed nor biostimulated by DOC addition. The results also highlight the importance of sufficient exposure time to trigger in situ micropollutant biodegradation.

Dietary exposure to sulfamethazine alters fish intestinal homeostasis and promotes resistance gene transfer

The present study was undertaken to explore the effects of sulfamethazine (SMZ) dietary exposure on the enrichment of the intestine microbial structure, and antibiotic resistance gene (ARGs) transmission in marine medaka, with respect to antibiotic dose, duration, and sex. In male fish, a dietary exposure of 10 μg/L SMZ led to a heightened SMZ enrichment in the intestine, whereas metabolite (N-SMZ) levels were elevated at a higher exposure concentration (100 μg/L). Conversely, female fish exhibited stable levels of accumulation and metabolic rates across the exposure period. The composition of intestinal microorganisms revealed that exposure duration exerted a greater impact on the abundance and diversity of gut microbes, and microbial responses to SMZ varied across exposure time points. The expansion of Bacteroidetes and Ruegeria likely stimulated SMZ metabolism and contributed to the more balanced level of SMZ and N-SMZ observed in females. In males, short-term SMZ stress resulted in a disruption of intestinal homeostasis, while the rise in the abundance of the Fusobacteria and Propionigeniuma suggested a potential enhancement in intestinal anti-inflammatory capacity over time. Overall, female medaka exhibited greater adaptability to SMZ, and males appear to experience prolonged effects due to SMZ. A total of 11 ARGs and 5 mobile genetic elements (MGEs) were identified. Ruegeria is the main carrier of two types of MGEs (IS1247, ISSm2-Xanthob), and may serve as an indicator of ARG transmission. Therefore, it is rational to consider some fish breeding areas in natural waters as potential "reservoirs" of antibiotic resistance. This research will provide a valuable reference for the transmission of drug resistance along the food chain.

Influence of redox condition and inoculum on micropollutant biodegradation by soil and activated sludge communities

Micropollutant biodegradation is selected by the interplay among environmental conditions and microbial community composition. This study investigated how different electron acceptors, and different inocula with varying microbial diversity, pre-exposed to distinct redox conditions and micropollutants, affect micropollutant biodegradation. Four tested inocula comprised of agricultural soil (Soil), sediment from a ditch in an agricultural field (Ditch), activated sludge from a municipal WWTP (Mun AS), and activated sludge from an industrial WWTP (Ind AS). Removal of 16 micropollutants was investigated for each inoculum under aerobic, nitrate reducing, iron reducing, sulfate reducing, and methanogenic conditions. Micropollutant biodegradation was highest under aerobic conditions with removal of 12 micropollutants. Most micropollutants were biodegraded by Soil (n = 11) and Mun AS inocula (n = 10). A positive correlation was observed between inoculum community richness and the number of different micropollutants a microbial community initially degraded. The redox conditions to which a microbial community had been exposed appeared to positively affect micropollutant biodegradation performance more than pre-exposure to micropollutants. Additionally, depletion of the organic carbon present in the inocula resulted in lower micropollutant biodegradation and overall microbial activities, suggesting that i) an additional carbon source is needed to promote micropollutant biodegradation; and ii) overall microbial activity can be a good indirect indicator for micropollutant biodegradation activity. These results could help to develop novel micropollutant removal strategies.

Ketoprofen as an emerging contaminant: occurrence, ecotoxicity and (bio)removal

Ketoprofen, a bicyclic non-steroidal anti-inflammatory drug commonly used in human and veterinary medicine, has recently been cited as an environmental contaminant that raises concerns for ecological well-being. It poses a growing threat due to its racemic mixture, enantiomers, and transformation products, which have ecotoxicological effects on various organisms, including invertebrates, vertebrates, plants, and microorganisms. Furthermore, ketoprofen is bioaccumulated and biomagnified throughout the food chain, threatening the ecosystem function. Surprisingly, despite these concerns, ketoprofen is not currently considered a priority substance. While targeted eco-pharmacovigilance for ketoprofen has been proposed, data on ketoprofen as a pharmaceutical contaminant are limited and incomplete. This review aims to provide a comprehensive summary of the most recent findings (from 2017 to March 2023) regarding the global distribution of ketoprofen in the environment, its ecotoxicity towards aquatic animals and plants, and available removal methods. Special emphasis is placed on understanding how ketoprofen affects microorganisms that play a pivotal role in Earth's ecosystems. The review broadly covers various approaches to ketoprofen biodegradation, including whole-cell fungal and bacterial systems as well as enzyme biocatalysts. Additionally, it explores the potential of adsorption by algae and phytoremediation for removing ketoprofen. This review will be of interest to a wide range of readers, including ecologists, microbiologists, policymakers, and those concerned about pharmaceutical pollution.

Chemical and biological tracers to identify source and transport pathways of septic system contamination to streams in areas with low permeability soils

Septic systems are widely used in rural areas that lack centralized sewage treatment systems. Incomplete removal of domestic wastewater contaminants in septic systems can lead to leaching of nutrients (P and N), bacteria/viruses, and trace contaminants to surrounding groundwater and surface water. This study focuses on delineating the fate of wastewater contaminants in localities where septic systems are installed in moderate to fine-grained overburden materials to assess potential impacts on groundwater and surface water quality in these settings. Nutrients and a suite of anthropogenic tracers, including host-specific fecal indicator bacteria (bovine- and human-specific Bacteroides), pharmaceutical compounds (caffeine, carbamazepine, gemfibrozil, ibuprofen, naproxen, and sulfamethoxazole), and an artificial sweetener (acesulfame-K), were selected to evaluate differences in transport properties. Surface water samples (n = 103) were collected from streams upstream (US) and downstream (DS) of three rural hamlets up to two times monthly over one year. Results indicate the presence of wastewater indicators in the streams, with DS locations showing significantly elevated concentrations of both chemical and biological anthropogenic tracers. Human-specific Bacteroides, caffeine, and acesulfame-K were consistently observed at elevated concentrations at all DS sites. Nutrients exhibited varied concentrations between US and DS locations at three study sites. The occurrence of human-specific Bacteroides in the surface water samples suggests the presence of preferential flow pathways within the silt/clay overburden. These results demonstrate the advantages of using a combined tracer approach, involving a conservative tracer such as acesulfame-K coupled with the human-specific biological indicator Bacteroides (BacHum), to understand not only impacting sources but also potential transport pathways of septic system contamination to nearby streams. Septic systems may be an underappreciated contaminant source in rural hamlets located in fine-grained overburden materials; although, a distinction of specific nutrient sources (septic systems vs. agriculture) remains challenging.

Effects of co-selection of antibiotic-resistance and metal-resistance genes on antibiotic-resistance potency of environmental bacteria and related ecological risk factors

The inadequate elimination of micropollutants in wastewater treatment plants (WWTP), cause to increase in the incidence of antibiotic resistant bacterial strains. Growth of microbial pathogens in WWTP is one of the serious public health problems. The widespread and simultaneous emergence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment with heavy metals create persistent and selective pressure for co-selection of both genes on environmental microorganisms. Co-localization of ARGs and HMRGs on the same horizontal mobile genetic elements (MGEs) allows the spreading of numerous antibiotic-resistant strains of bacteria in aquatic and terrestrial environment. The biofilm formation and colonization potential of environmental bacteria leads to the co-selection of multi-antibiotic resistance and multi-metal tolerance. Horizontal gene transfer (HGT), co-localization of both ARGs and HMRGs on the same MGEs, and the shared resistomes are important bacteria-associated ecological risks factors, which reduce the effectiveness of antibiotics against bacterial infections.

Influence of metabolism and microbiology on organic micropollutants biotransformation in anoxic heterotrophic reactors

There is scarce information about the biotransformation of organic micropollutants (OMPs) under anoxic conditions. In this study, a heterotrophic denitrifying bioreactor was set up to study the fate of several OMPs from metabolic and microbiological points of view. Primary metabolic activity was increased by adding progressively higher nitrogen loading rates during the operation (from 0.075 to 0.4 g N-NO₃^- L^-1 d^-1), which resulted in an important shift in the microbial population from a specialized biomass to a more diverse community. Such a change provoked a significant increase in the removal efficiency of erythromycin (ERY), roxithromycin (ROX) and bisphenol-A (BPA), and some bacterial taxa, such as Rhodoplanes, were identified as possible indicators related to the biodegradation of these compounds. The increasing primary metabolic activity in the reactor did not enhance the OMP-specific removal rates, suggesting that the bacterial composition is more influential than cometabolism.

Pharmaceutical Biotransformation is Influenced by Photosynthesis and Microbial Nitrogen Cycling in a Benthic Wetland Biomat

In shallow, open-water engineered wetlands, design parameters select for a photosynthetic microbial biomat capable of robust pharmaceutical biotransformation, yet the contributions of specific microbial processes remain unclear. Here, we combined genome-resolved metatranscriptomics and oxygen profiling of a field-scale biomat to inform laboratory inhibition microcosms amended with a suite of pharmaceuticals. Our analyses revealed a dynamic surficial layer harboring oxic-anoxic cycling and simultaneous photosynthetic, nitrifying, and denitrifying microbial transcription spanning nine bacterial phyla, with unbinned eukaryotic scaffolds suggesting a dominance of diatoms. In the laboratory, photosynthesis, nitrification, and denitrification were broadly decoupled by incubating oxic and anoxic microcosms in the presence and absence of light and nitrogen cycling enzyme inhibitors. Through combining microcosm inhibition data with field-scale metagenomics, we inferred microbial clades responsible for biotransformation associated with membrane-bound nitrate reductase activity (emtricitabine, trimethoprim, and atenolol), nitrous oxide reduction (trimethoprim), ammonium oxidation (trimethoprim and emtricitabine), and photosynthesis (metoprolol). Monitoring of transformation products of atenolol and emtricitabine confirmed that inhibition was specific to biotransformation and highlighted the value of oscillating redox environments for the further transformation of atenolol acid. Our findings shed light on microbial processes contributing to pharmaceutical biotransformation in open-water wetlands with implications for similar nature-based treatment systems.

Removal of organic micropollutants from municipal wastewater by aerobic granular sludge and conventional activated sludge

Removal performances of organic micropollutants by conventional activated sludge (CAS) and aerobic granular sludge (AGS) were investigated at a full-scale wastewater treatment plant. Lab-scale kinetic experiments were performed to assess the micropollutant transformation rates under oxic and anoxic conditions. Transformation rates were used to model the micropollutant removal in the full-scale processes. Metagenomic sequencing was used to compare the microbial communities and antimicrobial resistance genes of the CAS and AGS systems. Higher transformation ability was observed for CAS compared to AGS for most compounds, both at the full-scale plant and in the complementary batch experiments. Oxic conditions supported the transformation of several micropollutants with faster and/or comparable rates compared to anoxic conditions. The estimated transformation rates from batch experiments adequately predicted the removal for most micropollutants in the full-scale processes. While the compositions in microbial communities differed between AGS and CAS, the full-scale biological reactors shared similar resistome profiles. Even though granular biomass showed lower potential for micropollutant transformation, AGS systems had somewhat higher gene cluster diversity compared to CAS, which could be related to a higher functional diversity. Micropollutant exposure to biomass or mass transfer limitations, therefore played more important roles in the observed differences in OMP removal.

Enzymatic cometabolic biotransformation of organic micropollutants in wastewater treatment plants: A review

Biotransformation of trace-level organic micropollutants (OMPs) by complex microbial communities in wastewater treatment facilities is a key process for their detoxification and environmental impact reduction. Therefore, understanding the metabolic activities and mechanisms that contribute to their biotransformation is essential when developing approaches aiming to minimize their discharge. This review addresses the relevance of cometabolic processes and discusses the main enzymatic activities currently known to take part in OMPs removal under different redox environments in the compartments of wastewater treatment plants. Furthermore, the most common methodologies to decipher such enzymes are discussed, including the use of in vitro enzyme assays, enzymatic inhibitors, the analysis of transformation products and the application of several -omic techniques. Finally, perspectives on major challenges and future research requirements to improve OMPs biotransformation are proposed.

Effect of concentration and hydraulic reaction time on the removal of pharmaceutical compounds in a membrane bioreactor inoculated with activated sludge

Pharmaceuticals are often not fully removed in wastewater treatment plants (WWTPs) and are thus being detected at trace levels in water bodies all over the world posing a risk to numerous organisms. These organic micropollutants (OMPs) reach WWTPs at concentrations sometimes too low to serve as growth substrate for microorganisms; thus, co-metabolism is thought to be the main conversion mechanism. In this study, the microbial removal of six pharmaceuticals was investigated in a membrane bioreactor at increasing concentrations (4-800 nM) of the compounds and using three different hydraulic retention times (HRT; 1, 3.5 and 5 days). The bioreactor was inoculated with activated sludge from a municipal WWTP and fed with ammonium, acetate and methanol as main growth substrates to mimic co-metabolism. Each pharmaceutical had a different average removal efficiency: acetaminophen (100%) > fluoxetine (50%) > metoprolol (25%) > diclofenac (20%) > metformin (15%) > carbamazepine (10%). Higher pharmaceutical influent concentrations proportionally increased the removal rate of each compound, but surprisingly not the removal percentage. Furthermore, only metformin removal improved to 80-100% when HRT or biomass concentration was increased. Microbial community changes were followed with 16S rRNA gene amplicon sequencing in response to the increment of pharmaceutical concentration: Nitrospirae and Planctomycetes 16S rRNA relative gene abundance decreased, whereas Acidobacteria and Bacteroidetes increased. Remarkably, the Dokdonella genus, previously implicated in acetaminophen metabolism, showed a 30-fold increase in abundance at the highest concentration of pharmaceuticals applied. Taken together, these results suggest that the incomplete removal of most pharmaceutical compounds in WWTPs is dependent on neither concentration nor reaction time. Accordingly, we propose a chemical equilibrium or a growth substrate limitation as the responsible mechanisms of the incomplete removal. Finally, Dokdonella could be the main acetaminophen degrader under activated sludge conditions, and non-antibiotic pharmaceuticals might still be toxic to relevant WWTP bacteria.

Increased expression of antibiotic-resistance genes in biofilm communities upon exposure to cetyltrimethylammonium bromide (CTAB) and other stress conditions

Quaternary ammonium compounds (QAC, e.g., cetyltrimethylammonium bromide, (CTAB)) are widely used as surfactants and disinfectants. QAC already are commonly found in wastewaters, and their concentration could increase, since QAC are recommended to inactivate the SARS-CoV-2 (COVID-19) virus. Exposure of bacteria to QAC can lead to proliferation of antibiotic resistance genes (ARG). In particular, O₂-based membrane biofilm reactors (O₂-MBfRs) achieved excellent CTAB biodegradation, but ARG increased in their biofilms. Here, we applied meta-transcriptomic analyses to assess the impacts of CTAB exposure and operating conditions on microbial community's composition and ARG expression in the O₂-MBfRs. Two opportunistic pathogens, Pseudomonas aeruginosa and Stenotrophomonas maltophilia, dominated the microbial communities and were associated with the presence of ARG. Operating conditions that imposed stress on the biofilms, i.e., limited supplies of O₂ and nitrogen or a high loading of CTAB, led to large increases in ARG expression, particularly for genes conferring antibiotic-target protection. Important within the efflux pumps was the Resistance-Nodulation-Division (RND) family, which may have been active in exporting CTAB from cells. Oxidative stress appeared to be the key factor that triggered ARG proliferation by selecting intrinsically resistant species and accentuating the expression of ARG. Our findings suggest that means to mitigate the spread of ARG, such as shown here in a O₂-based membrane biofilm reactor, need to consider the impacts of stressors, including QAC exposure and stressful operating conditions.

Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium

The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.

The engineering of complex communities can be a successful path to understand the ecology of microbial systems and improve biotechnological processes. Here, we developed a strategy to assemble a minimal and effective lignocellulolytic microbial consortium (MELMC) using a sequential combination of dilution-to-stimulation and dilution-to-extinction approaches. The consortium was retrieved from Andean forest soil and selected through incubation in liquid medium with a mixture of three types of agricultural plant residues. After the dilution-to-stimulation phase, approximately 50 bacterial sequence types, mostly belonging to the Sphingobacteriaceae, Enterobacteriaceae, Pseudomonadaceae, and Paenibacillaceae, were significantly enriched. The dilution-to-extinction method demonstrated that only eight of the bacterial sequence types were necessary to maintain microbial growth and plant biomass consumption. After subsequent stabilization, only two bacterial species (Pseudomonas sp. and Paenibacillus sp.) became highly abundant (>99%) within the MELMC, indicating that these are the key players in degradation. Differences in the composition of bacterial communities between biological replicates indicated that selection, sampling, and/or priority effects could shape the consortium structure. The MELMC can degrade up to ∼13% of corn stover, consuming mostly its (hemi)cellulosic fraction. Tests with chromogenic substrates showed that the MELMC secretes an array of endoenzymes able to degrade xylan, arabinoxylan, carboxymethyl cellulose, and wheat straw. Additionally, the metagenomic profile inferred from the phylogenetic composition along with an analysis of carbohydrate-active enzymes of 20 bacterial genomes support the potential of the MELMC to deconstruct plant polysaccharides. This capacity was mainly attributed to the presence of Paenibacillus sp.

IMPORTANCE The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.

Fate of Trace Organic Compounds in Hyporheic Zone Sediments of Contrasting Organic Carbon Content and Impact on the Microbiome

The organic carbon in streambed sediments drives multiple biogeochemical reactions, including the attenuation of organic micropollutants. An attenuation assay using sediment microcosms differing in the initial total organic carbon (TOC) revealed higher microbiome and sorption associated removal efficiencies of trace organic compounds (TrOCs) in the high-TOC compared to the low-TOC sediments. Overall, the combined microbial and sorption associated removal efficiencies of the micropollutants were generally higher than by sorption alone for all compounds tested except propranolol whose removal efficiency was similar via both mechanisms. Quantitative real-time PCR and time-resolved 16S rRNA gene amplicon sequencing revealed that higher bacterial abundance and diversity in the high-TOC sediments correlated with higher microbial removal efficiencies of most TrOCs. The bacterial community in the high-TOC sediment samples remained relatively stable against the stressor effects of TrOC amendment compared to the low-TOC sediment community that was characterized by a decline in the relative abundance of most phyla except Proteobacteria. Bacterial genera that were significantly more abundant in amended relative to unamended sediment samples and thus associated with biodegradation of the TrOCs included Xanthobacter, Hyphomicrobium, Novosphingobium, Reyranella and Terrimonas. The collective results indicated that the TOC content influences the microbial community dynamics and associated biotransformation of TrOCs as well as the sorption potential of the hyporheic zone sediments.

Association between Aquatic Micropollutant Dissipation and River Sediment Bacterial Communities

Assessment of micropollutant biodegradation is essential to determine the persistence of potentially hazardous chemicals in aquatic ecosystems. We studied the dissipation half-lives of 10 micropollutants in sediment-water incubations (based on the OECD 308 standard) with sediment from two European rivers sampled upstream and downstream of wastewater treatment plant (WWTP) discharge. Dissipation half-lives (DT50s) were highly variable between the tested compounds, ranging from 1.5 to 772 days. Sediment from one river sampled downstream from the WWTP showed the fastest dissipation of all micropollutants after sediment RNA normalization. By characterizing sediment bacteria using 16S rRNA sequences, bacterial community composition of a sediment was associated with its capacity for dissipating micropollutants. Bacterial amplicon sequence variants of the genera Ralstonia, Pseudomonas, Hyphomicrobium, and Novosphingobium, which are known degraders of contaminants, were significantly more abundant in the sediment incubations where fast dissipation was observed. Our study illuminates the limitations of the OECD 308 standard to account for variation of dissipation rates of micropollutants due to differences in bacterial community composition. This limitation is problematic particularly for those compounds with DT50s close to regulatory persistence criteria. Thus, it is essential to consider bacterial community composition as a source of variability in regulatory biodegradation and persistence assessments.

Ibuprofen Degradation and Associated Bacterial Communities in Hyporheic Zone Sediments

Ibuprofen, a non-steroidal anti-inflammatory pain reliever, is among pharmaceutical residues of environmental concern ubiquitously detected in wastewater effluents and receiving rivers. Thus, ibuprofen removal potentials and associated bacteria in the hyporheic zone sediments of an impacted river were investigated. Microbially mediated ibuprofen degradation was determined in oxic sediment microcosms amended with ibuprofen (5, 40, 200, and 400 µM), or ibuprofen and acetate, relative to an un-amended control. Ibuprofen was removed by the original sediment microbial community as well as in ibuprofen-enrichments obtained by re-feeding of ibuprofen. Here, 1-, 2-, 3-hydroxy- and carboxy-ibuprofen were the primary transformation products. Quantitative real-time PCR analysis revealed a significantly higher 16S rRNA abundance in ibuprofen-amended relative to un-amended incubations. Time-resolved microbial community dynamics evaluated by 16S rRNA gene and 16S rRNA analyses revealed many new ibuprofen responsive taxa of the Acidobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Latescibacteria, and Proteobacteria. Two ibuprofen-degrading strains belonging to the genera Novosphingobium and Pseudomonas were isolated from the ibuprofen-enriched sediments, consuming 400 and 300 µM ibuprofen within three and eight days, respectively. The collective results indicated that the hyporheic zone sediments sustain an efficient biotic (micro-)pollutant degradation potential, and hitherto unknown microbial diversity associated with such (micro)pollutant removal.

Bacterial Diversity Controls Transformation of Wastewater-Derived Organic Contaminants in River-Simulating Flumes

Hyporheic zones are the water-saturated flow-through subsurfaces of rivers which are characterized by the simultaneous occurrence of multiple physical, biological, and chemical processes. Two factors playing a role in the hyporheic attenuation of organic contaminants are sediment bedforms (a major driver of hyporheic exchange) and the composition of the sediment microbial community. How these factors act on the diverse range of organic contaminants encountered downstream from wastewater treatment plants is not well understood. To address this knowledge gap, we investigated dissipation half-lives (DT50s) of 31 substances (mainly pharmaceuticals) under different combinations of bacterial diversity and bedform-induced hyporheic flow using 20 recirculating flumes in a central composite face factorial design. By combining small-volume pore water sampling, targeted analysis, and suspect screening, along with quantitative real-time PCR and time-resolved amplicon Illumina MiSeq sequencing, we determined a comprehensive set of DT50s, associated bacterial communities, and microbial transformation products. The resulting DT50s of parent compounds ranged from 0.5 (fluoxetine) to 306 days (carbamazepine), with 20 substances responding significantly to bacterial diversity and four to both diversity and hyporheic flow. Bacterial taxa that were associated with biodegradation included Acidobacteria (groups 6, 17, and 22), Actinobacteria (Nocardioides and Illumatobacter), Bacteroidetes (Terrimonas and Flavobacterium) and diverse Proteobacteria (Pseudomonadaceae, Sphingomonadaceae, and Xanthomonadaceae). Notable were the formation of valsartan acid from irbesartan and valsartan, the persistence of N-desmethylvenlafaxine across all treatments, and the identification of biuret as a novel transformation product of metformin. Twelve additional target transformation products were identified, which were persistent in either pore or surface water of at least one treatment, indicating their environmental relevance.

Environmental Risk and Risk of Resistance Selection Due to Antimicrobials' Occurrence in Two Polish Wastewater Treatment Plants and Receiving Surface Water

In this study, a screening of 26 selected antimicrobials using liquid chromatography coupled to a tandem mass spectrometry method in two Polish wastewater treatment plants and their receiving surface waters was provided. The highest average concentrations of metronidazole (7400 ng/L), ciprofloxacin (4300 ng/L), vancomycin (3200 ng/L), and sulfamethoxazole (3000 ng/L) were observed in influent of WWTP2. Ciprofloxacin and sulfamethoxazole were the most dominant antimicrobials in influent and effluent of both WWTPs. In the sludge samples the highest mean concentrations were found for ciprofloxacin (up to 28 μg/g) and norfloxacin (up to 5.3 μg/g). The removal efficiency of tested antimicrobials was found to be more than 50% for both WWTPs. However, the presence of antimicrobials influenced their concentrations in the receiving waters. The highest antimicrobial resistance risk was estimated in influent of WWTPs for azithromycin, ciprofloxacin, clarithromycin, metronidazole, and trimethoprim and in the sludge samples for the following antimicrobials: azithromycin, ciprofloxacin, clarithromycin, norfloxacin, trimethoprim, ofloxacin, and tetracycline. The high environmental risk for exposure to azithromycin, clarithromycin, and sulfamethoxazole to both cyanobacteria and eukaryotic species in effluents and/or receiving water was noted. Following the obtained results, we suggest extending the watch list of the Water Framework Directive for Union-wide monitoring with sulfamethoxazole.

Distribution and Removal of Pharmaceuticals in Liquid and Solid Phases in the Unit Processes of Sewage Treatment Plants

In this study, we analyzed 27 pharmaceuticals in liquid and solid phase samples collected from the unit processes of four different sewage treatment plants (STPs) to evaluate their distribution and behavior of the pharmaceuticals. The examination of the relative distributions of various categories of pharmaceuticals in the influent showed that non-steroidal anti-inflammatory drugs (NSAIDs) were the most dominant. While the relative distribution of antibiotics in the influent was not high (i.e., 3%–5%), it increased to 14%–30% in the effluent. In the four STPs, the mass load of the target pharmaceuticals was reduced by 88%–95% mainly in the biological treatment process, whereas the ratio of pharmaceuticals in waste sludge to those in the influent (w/w) was only 2%. In all the STPs, the removal efficiencies for the stimulant caffeine, NSAIDs (acetaminophen, naproxen, and acetylsalicylic acid), and the antibiotic cefradine were high; they were removed mainly by biological processes. Certain compounds, such as the NSAID ketoprofen, contrast agent iopromide, lipid regulator gemfibrozil, and antibiotic sulfamethoxazole, showed varying removal efficiencies depending on the contribution of biodegradation and sludge sorption. In addition, a quantitative meta-analysis was performed to compare the pharmaceutical removal efficiencies of the biological treatment processes in the four STPs, which were a membrane bioreactor (MBR) process, sequencing batch reactor (SBR) process, anaerobic–anoxic–oxic (A2O) process, and moving-bed biofilm reactor (MBBR) process. Among the biological processes, the removal efficiency was in the order of MBR > SBR > A2O > MBBR. Among the tertiary treatment processes investigated, powdered activated carbon showed the highest removal efficiency of 18%–63% for gemfibrozil, ibuprofen, ketoprofen, atenolol, cimetidine, and trimethoprim.

Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures

The capacity of microbes to degrade recalcitrant materials has been extensively explored for environmental remediation and industrial production. Significant achievements have been made with single strains, but focus is now going toward the use of microbial consortia owning to their functional stability and efficiency. However, assembly of simplified microbial consortia (SMC) from complex environmental communities is still far from trivial due to large diversity and the effect of biotic interactions. Here we propose a strategy, based on enrichment and dilution-to-extinction cultures, to construct SMC with reduced diversity for degradation of keratinous materials. Serial dilutions were performed on a keratinolytic microbial consortium pre-enriched from a soil sample, monitoring the dilution effect on community growth and enzymatic activities. An appropriate dilution regime (10-9) was selected to construct a SMC library from the enriched microbial consortium. Further sequencing analysis and keratinolytic activity assays demonstrated that obtained SMC displayed actual reduced microbial diversity, together with various taxonomic composition, and biodegradation capabilities. More importantly, several SMC possessed equivalent levels of keratinolytic efficiency compared to the initial consortium, showing that simplification can be achieved without loss of function and efficiency. This methodology is also applicable to other types of recalcitrant material degradation involving microbial consortia, thus considerably broadening its application scope.

Relating Metatranscriptomic Profiles to the Micropollutant Biotransformation Potential of Complex Microbial Communities

Biotransformation of chemical contaminants is of importance in various natural and engineered systems. However, in complex microbial communities and with chemical contaminants at low concentrations, our current understanding of biotransformation at the level of enzyme-chemical interactions is limited. Here, we explored an approach to identify associations between micropollutant biotransformation and specific gene products in complex microbial communities, using association mining between chemical and metatranscriptomic data obtained from experiments with activated sludge grown at different solid retention times. We successfully demonstrate proportional relationships between the measured rate constants and associated gene transcripts for nitrification as a major community function, but also for the biotransformation of two nitrile-containing micropollutants (bromoxynil and acetamiprid) and transcripts of nitrile hydratases, a class of enzymes that we experimentally confirmed to produce the detected amide transformation products. As these results suggest that metatranscriptomic information can indeed be quantitatively correlated with low abundant community functions such as micropollutant biotransformation in complex microbial communities, we proceeded to explore the potential of association mining to highlight enzymes likely involved in catalyzing less well-understood micropollutant biotransformation reactions. Specifically, we use the cases of nitrile hydration and oxidative biotransformation reactions to show that the consideration of additional experimental evidence (such as information on biotransformation pathways) increases the likelihood of detecting plausible novel enzyme-chemical relationships. Finally, we identify a cluster of mono- and dioxygenase fourth-level enzyme classes that most strongly correlate with oxidative micropollutant biotransformation reactions in activated sludge.

Using recirculating flumes and a response surface model to investigate the role of hyporheic exchange and bacterial diversity on micropollutant half-lives

Enhancing the understanding of the fate of wastewater-derived organic micropollutants in rivers is crucial to improve risk assessment, regulatory decision making and river management. Hyporheic exchange and sediment bacterial diversity are two factors gaining increasing importance as drivers for micropollutant degradation, but are complex to study in field experiments and usually ignored in laboratory tests aimed to estimate environmental half-lives. Flume mesocosms are useful to investigate micropollutant degradation processes, bridging the gap between the field and batch experiments. However, few studies have used flumes in this context. We present a novel experimental setup using 20 recirculating flumes and a response surface model to study the influence of hyporheic exchange and sediment bacterial diversity on half-lives of the anti-epileptic drug carbamazepine (CBZ) and the artificial sweetener acesulfame (ACS). The effect of bedform-induced hyporheic exchange was tested by three treatment levels differing in number of bedforms (0, 3 and 6). Three levels of sediment bacterial diversity were obtained by diluting sediment from the River Erpe in Berlin, Germany, with sand (1 : 10, 1 : 1000 and 1 : 100 000). Our results show that ACS half-lives were significantly influenced by sediment dilution and number of bedforms. Half-lives of CBZ were higher than ACS, and were significantly affected only by the sediment dilution variable, and thus by bacterial diversity. Our results show that (1) the flume-setup is a useful tool to study the fate of micropollutants in rivers, and that (2) higher hyporheic exchange and bacterial diversity in the sediment can increase the degradation of micropollutants in rivers.

Oxygen Half-Saturation Constants for Pharmaceuticals in Activated Sludge and Microbial Community Activity under Varied Oxygen Levels

Aeration accounts for the largest energy demand in conventional activated sludge wastewater treatment. Emerging aeration control strategies for energy conservation have significantly reduced operational bulk liquid dissolved oxygen (DO) from above 2 mg/L to at or below 0.5 mg/L. As we move toward low DO treatment processes, there is a need to understand how low DO impacts the kinetics of micropollutant biotransformation. The objective of this study was to characterize the impact of DO concentration on pharmaceutical biotransformation rates via two approaches: (1) Determine oxygen half saturation constants that describe the community-wide impact of DO on biotransformation rates. (2) Evaluate shifts in the microbial community 16S rRNA pool due to DO concentration. Batch experiments were performed at several DO concentrations using biomass from a full-scale wastewater treatment plant. Results reveal that substantial reductions in bulk liquid DO concentrations to 0.5 mg-O₂/L are possible without compromising pharmaceutical biotransformation rates. Sequencing of cDNA generated from community rRNA revealed that diverse, low abundance community members may play important roles in pharmaceutical transformation. The results of this work advance our ability to predict and model the impact of DO on pharmaceutical biotransformations during wastewater treatment and identify taxonomic groups associated with those biotransformations.