Ibuprofen-enhanced biodegradation in solution and sewage sludge by a mineralizing microbial consortium. Shift in associated bacterial communities

Description of Labrys sedimenti sp. nov., isolated from a diclofenac-degrading enrichment culture, and genome-based reclassification of Labrys portucalensis as a later heterotypic synonym of Labrys neptuniae

A Gram-stain-negative strain, designated as Zidic-5T, was isolated from diclofenac-degrading enrichment culture and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene sequence analysis revealed that strain Zidic-5T belongs to the genus Labrys, with the highest 16S rRNA gene similarity to Labrys neptuniae LMG 23578T (99.13%), followed by Labrys portucalensis F11T (99.06%), Labrys methylaminiphilus JLW10T (98.58%) and Labrys okinawensis DSM 18385T (98.32%). The draft genome sequence of strain Zidic-5T is 7.64 Mb long, and the G+C content of the genome is 63.5 mol%. The orthologous average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain Zidic-5T and its closest relatives were below the threshold values for species demarcation, confirming that strain Zidic-5T is distinctly separated from its closest relatives. Additionally, comparative whole-genome analysis of type strains of L. neptuniae and L. portucalensis indicated that they belong to the same genomic species, suggesting that L. portucalensis is a later heterotypic synonym of L. neptuniae. Cells of strain Zidic-5T were strictly aerobic, coccoid-shaped and non-motile. The predominant fatty acids (>10% of the total) of strain Zidic-5T were C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω7c. The major ubiquinone of strain Zidic-5T was Q-10, while the major polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. Based on the polyphasic study, it is concluded that strain Zidic-5T represents a novel species of the genus Labrys; thus, the name of Labrys sedimenti sp. nov. is proposed. The type strain of the species is strain Zidic-5T (=LMG 33565T=NCAIM B.02686T).

The overlooked interaction of emerging contaminants and microbial communities: a threat to ecosystems and public health

CONTEXT AND AIMS

Emerging contaminants (ECs) and microbial communities should not be viewed in isolation, but through the One Health perspective. Both ECs and microorganisms lie at the core of this interconnected framework, as they directly influence the health of humans, animals, and the environment.The interactions between ECs and microbial communities can have profound implications for public health, affecting all three domains. However, these ECs-microorganism interactions remain underexplored, potentially leaving significant public health and ecological risks unrecognized. Therefore, this article seeks to alert the scientific community to the overlooked interactions between ECs and microbial communities, emphasizing the pivotal role these interactions may play in the management of 'One Health.'

RESULTS

The most extensively studied interaction between ECs and microbial communities is biodegradation. However, other more complex and concerning interactions demand attention, such as the impact of ECs on microbial ecology (disruptions in ecosystem balance affecting nutrient and energy cycles) and the rise and spread of antimicrobial resistance (a growing global health crisis). Although these ECs-microbial interactions had not been extensively studied, there are scientific evidence that ECs impact on microbial communities may be concerning for public health and ecosystem balance.

CONCLUSIONS

So, this perspective summarizes the impact of ECs through a One Health lens and underscores the urgent need to understand their influence on microbial communities, while highlighting the key challenges researchers must overcome. Tackling these challenges is vital to mitigate potential long-term consequences for both ecosystems and public health.

Profiling trace organic chemical biotransformation genes, enzymes and associated bacteria in microbial model communities

Microbial biotransformation of trace organic chemicals (TOrCs) is an essential process in wastewater treatment to eliminate environmental pollution. Understanding TOrC biotransformation mechanisms, especially at their original concentrations, is important to optimize treatment performance, whereas our current knowledge is limited. Here, we investigated the biotransformation of seven TOrCs by 24 model communities. The genome-centric analyses unraveled potential biotransformation drivers concerning functional genes, enzymes, and responsible bacteria. We obtained efficient model communities for completely removing ibuprofen, caffeine, and atenolol, with transformation efficiencies between 0 % and 45 % for sulfamethoxazole, carbamazepine, trimethoprim, and gabapentin. Biotransformation performance was not fully reflected by the presence of known biotransformation genes and enzymes in the metagenomes of the communities. Functional similar homologs to existing biotransformation genes and enzymes (e.g., long-chain-fatty-acid-CoA ligase encoded by fadD and fadD13 gene) could play critical roles in TOrC metabolism. Finally, we identified previously undescribed degrading strains, e.g., Rhodococcus qingshengii for caffeine, carbamazepine, sulfamethoxazole, and ibuprofen biotransformation, and potential transformation enzymes, e.g., SDR family oxidoreductase targeting sulfamethoxazole and putative hypothetical proteins for caffeine, atenolol and gabapentin biotransformation. This study provides fundamental insights into naturally assembled low-complexity degrader communities that can help to identify and tackle the current research gaps on biotransformation.

Unraveling the Role of Repurposed Drugs in the Treatment of Acne: Success so Far and the Road Ahead

Acne is a skin disease that impacts 9.4% of the world's population. Available treatments for managing acne include retinoid-like drugs, antibiotics, corticosteroids, photo, and radiotherapy. Howevere, the aforementioned treatments have certain limitations such as possibility of developing skin cancer from tetracycline, doxycycline, and corticosteroids, microbial resistance to antibiotics, and deadly side effects, and so forth. Repurposing of existing therapeutics having excellent safety profile can be promising way to treat acne efficiently. The repurposed drugs and phytoceuticals from diverse classes have demonstrated promising effects in treating acne. These repurposed drugs have displayed antiacne effectiveness by targeting single or multiple signaling pathways. Various repurposed therapeutics undergoing clinical trials at different phases demonstrated their safety and efficacy in treating acne. Despite being a very good, safe, and less time-consuming strategy, drug repurposing (DR) faces multiple challenges such as lack of regulatory guidelines, preservation of intellectual property, and clinical validation of claimed therapeutic indication. DR appears to be a viable approach and is likely to offer effective treatment at a reasonable cost in alleviating acne.

Optimizing Bioaugmentation for Pharmaceutical Stabilization of Sewage Sludge: A Study on Short-Term Composting Under Real Conditions

A significant concentration of pharmaceuticals has been detected within composted sewage sludge. Their uncomplete removal and lack of monitoring during composting neglects their potentially toxic effects when used as a soil organic amendment. Previously, we successfully implemented a bioaugmentation-composting system focused on toxicity and pharmaceuticals' concentration reduction. This method, however, comprised a long inoculant-acclimatization period, making it an unprofitable technology. Hence, this work aimed to explore a shorter and yet effective composting process by simultaneously implementing the inoculation of a native microbial consortium and the fungus Penicillium oxalicum XD 3.1 in composting piles of sewage sludge and olive prunings. All the piles were subjected to frequent inoculation, windrow turning, and monitoring of the physicochemical and biological parameters. Additionally, both the bioaugmentation stability and pharmaceuticals degradation were evaluated through different analysis and removal rates calculations. One hundred days earlier than previous attempts, both bioaugmentation treatments achieved adequate composting conditions, maintained core native populations while improving the degrading microbial diversity, and achieved around 70-72% of pharmaceutical remotion. Nevertheless, only Penicillium inoculation produced favorable toxicity results ideal for organic amendments (acute microtoxicity and phytotoxicity). Thus, a shorter but equally stable and effective degrading bioaugmentation-composting with P. oxalicum was achieved here.

Genetic and species rearrangements in microbial consortia impact biodegradation potential

Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the re-organisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.

Microbes as Resources to Remove PPCPs and Improve Water Quality

The inadequate removal of pharmaceuticals and personal care products (PPCPs) by traditional wastewater treatment plants (WWTPs) poses a significant environmental and public health challenge. Residual PPCPs find their way into aquatic ecosystems, leading to bioaccumulation in aquatic biota, the dissemination of antibiotic resistance genes (ARGs), and contamination of both water sources and vegetables. These persistent pollutants can have negative effects on human health, ranging from antibiotic resistance development to endocrine disruption. To mitigate these risks, there is a growing interest in exploiting microorganisms and their enzymes for bioremediation purposes. By harnessing the metabolic capabilities of microbial communities, PPCPs can be efficiently degraded, transformed, or sequestered in water systems. Additionally, microbial communities exhibit remarkable adaptability and resilience to diverse PPCP contaminants, further underscoring their potential as sustainable and cost-effective solutions for water treatment. This review explores the promise of microbial bioremediation as an approach to addressing the complex challenges posed by persistent PPCP contamination, emphasising its potential to safeguard both environmental integrity and human well-being.

Removal of Ibuprofen in Water by Bioaugmentation with Labrys neptuniae CSW11 Isolated from Sewage Sludge-Assessment of Biodegradation Pathway Based on Metabolite Formation and Genomic Analysis

Ibuprofen (IBP) is one of the most consumed drugs in the world. It is only partially removed in wastewater treatment plants (WWTPs), being present in effluent wastewater and sewage sludge, causing the widespread introduction of IBP as an emergent xenobiotic in different environmental compartments. This study describes the use of Labrys neptuniae CSW11, recently described as an IBP degrader, through bioaugmentation processes for the removal of IBP from water under different conditions (additional carbon sources, various concentrations of glucose and IBP). L. neptuniae CSW11 showed very good results in a wide range of IBP concentrations, with 100% removal in only 4 days for 1 and 5 mg L-1 IBP and 7 days for 10 mg L-1, and up to 48.4% removal in 28 days for IBP 100 mg L-1 when using glucose 3 g L-1 as an additional carbon source. Three IBP metabolites were identified during the biotransformation process: 1-hydroxyibuprofen (1-OH-IBP), 2-hydroxyibuprofen (2-OH-IBP), and carboxyibuprofen (CBX-IBP), whose concentrations declined drastically in the presence of glucose. IBP metabolites maintained a certain degree of toxicity in solution, even when IBP was completely removed. The results indicate that L. neptuniae CSW11 can be quite effective in degrading IBP in water, but the bioaugmentation method should be improved using CSW11 in consortia with other bacterial strains able to degrade the toxic metabolites produced. A genome-based analysis of L. neptuniae CSW11 revealed different enzymes that could be involved in IBP biodegradation, and a potential metabolic pathway was proposed based on the metabolites observed and genome analysis.

Occurrence and dissipation mechanisms of organic contaminants during sewage sludge anaerobic digestion: A critical review

Sewage sludge, a complex mixture of contaminants and pathogenic agents, necessitates treatment or stabilization like anaerobic digestion (AD) before safe disposal. AD-derived products (solid digestate and liquid fraction) can be used as fertilizers. During AD, biogas is also produced, and used for energy purposes. All these fractions can be contaminated with various compounds, whose amount depends on the feedstocks used in AD (and their mutual proportions). This paper reviews studies on the distribution of organic contaminants across AD fractions (solid digestate, liquid fraction, and biogas), delving into the mechanisms behind contaminant dissipation and proposing future research directions. AD proves to be a relatively effective method for removing polychlorinated biphenyls, polycyclic aromatic hydrocarbons, pharmaceuticals, antibiotic resistance genes and hydrocarbons. Contaminants are predominantly removed through biodegradation, but many compounds, especially hydrophobic (e.g. per- and polyfluoroalkyl substances), are also sorbed onto digestate particles. The process of sorption is suggested to reduce the bioavailability of contaminants. As a result of sorption, contaminants accumulate in the largest amount in the solid digestate, whereas in smaller amounts in the other AD products. Polar pharmaceuticals (e.g. metformin) are particularly leached, while volatile methylsiloxanes and polycyclic aromatic hydrocarbons, characterized by a high Henry's law constant, are volatilized into the biogas. The removal of compounds can be affected by AD operational parameters, the type of sludge, physicochemical properties of contaminants, and the sludge pretreatment used.

New bacterial strains for ibuprofen biodegradation: Drug removal, transformation, and potential catabolic genes

Ibuprofen (IBU) is a significant contaminant frequently found in wastewater treatment plants due to its widespread use and limited removal during treatment processes. This leads to its discharge into the environment, causing considerable environmental concerns. The use of microorganisms has recently been recognized as a sustainable method for mitigating IBU contamination in wastewater. In this study, new bacteria capable of growing in a solid medium with IBU as the only carbon source and removing IBU from a liquid medium were isolated from environmental samples, including soil, marine, mine, and olive mill wastewater. Four bacterial strains, namely Klebsiella pneumoniae TIBU2.1, Klebsiella variicola LOIBU1.1, Pseudomonas aeruginosa LOIBU1.2, and Mycolicibacterium aubagnense HPB1.1, were identified through 16S rRNA gene sequencing. These strains demonstrated significant IBU removal efficiencies, ranging from 60 to 100% within 14 days, starting from an initial IBU concentration of 5 mg per litre. These bacteria have not been previously reported in the literature as IBU degraders, making this work a valuable contribution to further studies in the field of bioremediation in environments contaminated by IBU. Based on the IBU removal results, the most promising bacteria, K. pneumoniae TIBU2.1 and M. aubagnense HPB1.1, were selected for an in silico analysis to identify genes potentially involved in IBU biodegradation. Interestingly, in the tests with TIBU2.1, a peak of IBU transformation product(s) was detected by high-performance liquid chromatography, while in the tests with HPB1.1, it was not detected. The emerging peak was analysed by liquid chromatography-mass spectrometry, indicating the presence of possible conjugates between intermediates of IBU biodegradation. The proteins encoded on their whole-genome sequences were aligned with proteins involved in an IBU-degrading pathway reported in bacteria with respective catabolic genes. The analysis indicated that strain HPB1.1 possesses genes encoding proteins similar to most enzymes reported associated with the IBU metabolic pathways used as reference bacteria, while strain TIBU2.1 has genes encoding proteins similar to enzymes involved in both the upper and the lower part of that pathway. Notably, in the tests with the strain having more candidate genes encoding IBU-catabolic enzymes, no IBU transformation products were detected, while in the tests with the strain having fewer of these genes, detection occurred.

Stress responses of the seagrass Cymodocea nodosa to environmentally relevant concentrations of pharmaceutical ibuprofen: Ecological implications

Pharmaceuticals like ibuprofen (IBU) entering marine environments are of great concern due to their increasing consumption and impact on wildlife. No information on IBU toxicity to seagrasses is yet available. Seagrasses form key habitats and are threatened worldwide by multiple stressors. Here, the responses of the seagrass Cymodocea nodosa to a short-term exposure (12 days) to environmentally realistic IBU concentrations (0.25-2.5-25 µg L-1), both at organism (plant growth) and sub-organism level (oxidative status, photosynthetic efficiency, and specialized metabolites production), were assessed in mesocosm. Chemical analyses to detect the presence of IBU and its metabolites in seawater and plants were also performed. IBU did not affect plant growth but caused physiological alterations which varied in severity depending on its concentration. Concentrations of 0.25 and 2.5 µg L-1 resulted in oxidative stress, but an increased antioxidant enzyme activity enabled plants to tolerate stress. A concentration of 25 µg L-1 caused greater oxidative stress, reduced antioxidant enzyme activity and specialized metabolites production, and impaired photosynthetic machinery functioning (particularly PSII). IBU was detected in seawater but not in plants suggesting no bioaccumulation. These findings indicate that C. nodosa could not withstand high IBU stress, and this could reduce its resilience to additional environmental stressors.

Polyethyleneimine-functionalized magnetic sugarcane bagasse cellulose film for the efficient adsorption of ibuprofen

Polyethyleneimine-modified magnetic sugarcane bagasse cellulose film (P-SBC/Fe3O4 film) was simply fabricated for the removal of ibuprofen (IBP), a typical emerging organic contaminant. The P-SBC/Fe3O4 film exhibited an equilibrium adsorption amount of 370.52 mg/g for IBP and a corresponding removal efficiency of 92.63 % under following adsorption conditions: 318 K, pH 4, and 0.25 mg/mL dosage. Thermodynamic studies indicated that adsorption of IBP on the P-SBC/Fe3O4 film was spontaneous (∆G < 0) and endothermic (∆H > 0). The adsorption data conformed to the Freundlich isotherm model and multilayer adsorption model (two layers), and an average of 3-4 active sites on the P-SBC/Fe3O4 film share an IBP molecule. Both the EDR-IDR and AOAS models vividly described the dynamic characteristics of adsorption process. Model fitting results, theoretical calculations, and comprehensive characterization revealed that adsorption is driven by electrostatic interactions between the primary amine of P-SBC/Fe3O4 film and the carboxyl group of IBP molecule, while other weak interactions are also non-ignorable. Furthermore, quantitative calculations based on density functional theory (DFT) underscored the importance of PEI functionalization. In conclusion, P-SBC/Fe3O4 film is an environmentally friendly and cost-effective adsorbent with significant potential for effectively removing IBP, while maintaining its efficacy over multiple cycles.