Pollutant profile complexity governs wastewater removal of recalcitrant pharmaceuticals.

Organic pollutants are an increasing threat for wildlife and humans. Managing their removal is however complicated by the difficulties in predicting degradation rates. In this work, we demonstrate that the complexity of the pollutant profile, the set of co-existing contaminants, is a major driver of biodegradation in wastewater. We built representative assemblages out of one to five common pharmaceuticals (caffeine, atenolol, paracetamol, ibuprofen, and enalapril) selected along a gradient of biodegradability. We followed their individual removal by wastewater microbial communities. The presence of multichemical background pollution was essential for the removal of recalcitrant molecules such as ibuprofen. High-order interactions between multiple pollutants drove removal efficiency. We explain these interactions by shifts in the microbiome, with degradable molecules such as paracetamol enriching species and pathways involved in the removal of several organic pollutants. We conclude that pollutants should be treated as part of a complex system, with emerging pollutants potentially showing cascading effects and offering leverage to promote bioremediation.

Direct ammonium oxidation to nitrogen gas (Dirammox) in Alcaligenes strain HO-1: The electrode role.

It has been recently suggested that Alcaligenes use a previously unknown pathway to convert ammonium into dinitrogen gas (Dirammox) via hydroxylamine (NH2OH). This fact alone already implies a significant decrease in the aeration requirements for the process, but the process would still be dependent on external aeration. This work studied the potential use of a polarised electrode as an electron acceptor for ammonium oxidation using the recently described Alcaligenes strain HO-1 as a model heterotrophic nitrifier. Results indicated that Alcaligenes strain HO-1 requires aeration for metabolism, a requirement that cannot be replaced for a polarised electrode alone. However, concomitant elimination of succinate and ammonium was observed when operating a previously grown Alcaligenes strain HO-1 culture in the presence of a polarised electrode and without aeration. The usage of a polarised electrode together with aeration did not increase the succinate nor the nitrogen removal rates observed with aeration alone. However, current density generation was observed along a feeding batch test representing an electron share of 3% of the ammonium removed in the presence of aeration and 16% without aeration. Additional tests suggested that hydroxylamine oxidation to dinitrogen gas could have a relevant role in the electron discharge onto the anode. Therefore, the presence of a polarised electrode supported the metabolic functions of Alcaligenes strain HO-1 on the simultaneous oxidation of succinate and ammonium.

Soil microbiomes divergently respond to heavy metals and polycyclic aromatic hydrocarbons in contaminated industrial sites.

Contaminated sites from electronic waste (e-waste) dismantling and coking plants feature high concentrations of heavy metals (HMs) and/or polycyclic aromatic hydrocarbons (PAHs) in soil. Mixed contamination (HMs + PAHs) hinders land reclamation and affects the microbial diversity and function of soil microbiomes. In this study, we analyzed HM and PAH contamination from an e-waste dismantling plant and a coking plant and evaluated the influences of HM and PAH contamination on soil microbiomes. It was noticed that HMs and PAHs were found in all sites, although the major contaminants of the e-waste dismantling plant site were HMs (such as Cu at 5,947.58 ± 433.44 mg kg-1, Zn at 4,961.38 ± 436.51 mg kg-1, and Mn at 2,379.07 ± 227.46 mg kg-1), and the major contaminants of the coking plant site were PAHs (such as fluorene at 11,740.06 ± 620.1 mg kg-1, acenaphthylene at 211.69 ± 7.04 mg kg-1, and pyrene at 183.14 ± 18.89 mg kg-1). The microbiomes (diversity and abundance) of all sites were determined via high-throughput sequencing of 16S rRNA genes, and redundancy analysis was conducted to investigate the relations between soil microbiomes and contaminants. The results showed that the microbiomes of the contaminated sites divergently responded to HMs and PAHs. The abundances of the bacterial genera Sulfuritalea, Pseudomonas, and Sphingobium were positively related to PAHs, while the abundances of the bacterial genera Bryobacter, Nitrospira, and Steroidobacter were positively related to HMs. This study promotes an understanding of how soil microbiomes respond to single and mixed contamination with HMs and PAHs.

Immobilisation and stabilisation of glycosylated enzymes on boronic acid-functionalised silica nanoparticles.

We report a method of glycosylated enzymes' surface immobilisation and stabilisation. The enzyme is immobilised at the surface of silica nanoparticles through the reversible covalent binding of vicinal diols of the enzyme glycans with a surface-attached boronate derivative. A soft organosilica layer of controlled thickness is grown at the silica surface, entrapping the enzyme and thus avoiding enzyme leaching. We demonstrate that this approach results not only in high and durable activity retention but also enzyme stabilisation.

[Environmental scientists & microbiologists from China & EU: take the responsibility to cherish the Earth homeland].

Humanity shares the common interest to protect the environment and to maintain a healthy global ecosystem. International collaboration is key in this context, to advance the necessary science and technology. The National Science Foundation of China (NSFC) and European Commission (EC) have agreed to collaborate in innovative knowledge and technology in the field of bioremediation of polluted environments and biodegradation of plastics. In this context, projects on bioremediation of soils, wastewater and sediment matrices and on microbial degradation of plastics were supported. This special issue aimed to introduce these projects and their progresses in the related fields. In total, 23 papers have been collected in this issue, covering both fundamental and applied researches.

[ELECTRA: electricity-driven low energy and chemical input technology for accelerated bioremediation].

The international cooperation project "electricity-driven low energy and chemical input technology for accelerated bioremediation" (abridged as "ELECTRA") is jointly supported by National Nature Science Foundation of China (NSFC) and European Commission (EC). The ELECTRA consortium consists of 5 research institutions and universities from China and 17 European research institutions and universities, as well as high-tech companies of EC countries. ELECTRA focuses on researches of biodegradation of emerging organic compounds (EOCs) and novel environmental biotechnologies of low-energy and low-chemical inputs. The project has been successfully operated for 2 years, and has made important progresses in obtaining EOCs-degrading microbes, developing weak-electricity-accelerated bioremediation, and 3D-printing techniques for microbial consortium. The ELECTRA has promoted collaborations among the Chinese and European scientists. In the future, ELECTRA will overcome the negative impact of the COVID-19 pandemic and fulfill the scientific objectives through strengthening the international collaboration.

[Insights into the applications of 3D bioprinting for bioremediation technologies].

A plethora of organic pollutants such as pesticides, polycyclic and halogenated aromatic hydrocarbons, and emerging pollutants, such as flame retardants, is continuously being released into the environment. This poses a huge threat to the society in terms of environmental pollution, agricultural product quality, and general safety. Therefore, effective removal of organic pollutants from the environment has become an important challenge to be addressed. As a consequence of the recent and rapid developments in additive manufacturing, 3D bioprinting technology is playing an important role in the pharmaceutical industry. At the same time, an increasing number of microorganisms suitable for the production of biomaterials with complex structures and functions using 3D bioprinting technology, have been identified. This article briefly discusses the principles, advantages, and disadvantages of different 3D bioprinting technologies for pollutant removal. Furthermore, the feasibility and challenges of developing bioremediation technologies based on 3D bioprinting have also been discussed.

Microbial Interactions Drive the Complete Catabolism of the Antibiotic Sulfamethoxazole in Activated Sludge Microbiomes.

Microbial communities are believed to outperform monocultures in the complete catabolism of organic pollutants via reduced metabolic burden and increased robustness to environmental challenges; however, the interaction mechanism in functional microbiomes remains poorly understood. Here, three functionally differentiated activated sludge microbiomes (S1: complete catabolism of sulfamethoxazole (SMX); S2: complete catabolism of the phenyl part of SMX ([phenyl]-SMX) with stable accumulation of its heterocyclic product 3-amino-5-methylisoxazole (3A5MI); A: complete catabolism of 3A5MI rather than [phenyl]-SMX) were enriched. Combining time-series cultivation-independent microbial community analysis, DNA-stable isotope probing, molecular ecological network analysis, and cultivation-dependent function verification, we identified key players involved in the SMX degradation process. Paenarthrobacter and Nocardioides were primary degraders for the initial cleavage of the sulfonamide functional group (-C-S-N- bond) and 3A5MI degradation, respectively. Complete catabolism of SMX was achieved by their cross-feeding. The co-culture of Nocardioides, Acidovorax, and Sphingobium demonstrated that the nondegraders Acidovorax and Sphingobium were involved in the enhancement of 3A5MI degradation. Moreover, we unraveled the internal labor division patterns and connections among the active members centered on the two primary degraders. Overall, the proposed methodology is promisingly applicable and would help generate mechanistic, predictive, and operational understanding of the collaborative biodegradation of various contaminants. This study provides useful information for synthetic activated sludge microbiomes with optimized environmental functions.

Tuning the Properties of Natural Promiscuous Enzymes by Engineering Their Nano-environment.

Owing to their outstanding catalytic properties, enzymes represent powerful tools for carrying out a wide range of (bio)chemical transformations with high proficiency. In this context, enzymes with high biocatalytic promiscuity are somewhat neglected. Here, we demonstrate that a meticulous modification of a synthetic shell that surrounds an immobilized enzyme possessing broad substrate specificity allows the resulting nanobiocatalyst to be endowed with enantioselective properties while maintaining a high level of substrate promiscuity. Our results show that control of the enzyme nano-environment enables tuning of both substrate specificity and enantioselectivity. Further, we demonstrate that our strategy of enzyme supramolecular engineering allows the enzyme to be endowed with markedly enhanced stability in an organic solvent (i.e., acetonitrile). The versatility of the method was assessed with two additional substrate-promiscuous and structurally different enzymes, for which improvements in enantioselectivity and stability were confirmed. We expect this method to promote the use of supramolecularly engineered promiscuous enzymes in industrially relevant biocatalytic processes.

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.

Subsistence and complexity of antimicrobial resistance on a community-wide level.

There are a multitude of resistance strategies that microbes can apply to avoid inhibition by antimicrobials. One of these strategies is the enzymatic modification of the antibiotic, in a process generally termed inactivation. Furthermore, some microorganisms may not be limited to the mere inactivation of the antimicrobial compounds. They can continue by further enzymatic degradation of the compounds' carbon backbone, taking nutritional and energetic advantage of the former antibiotic. This driving force to harness an additional food source in a complex environment adds another level of complexity to the reasonably well-understood process of antibiotic resistance proliferation on a single cell level: It brings bioprotection into play at the level of microbial community. Despite the possible implications of a resistant community in a host and a lurking antibiotic failure, knowledge of degradation pathways of antibiotics and their connections is scarce. Currently, it is limited to only a few families of antibiotics (e.g. ß-lactams and sulfonamides). In this article, we discuss the fluctuating nature of the relationship between antibiotic resistance and the biodegradation of antibiotics. This distinction mainly depends on the genetic background of the microbe, as general resistance genes can be recruited to function in a biodegradation pathway.

Transformation of catechol coupled to redox alteration of humic acids and the effects of Cu and Fe cations.

Humic substances are reactive during redox alteration. However, the role of this reactivity in the transformation of organic compounds and in carbon cycling in the environment is still unclear. Here, we used 14C-radioactive tracer to study abiotic transformation and humification of catechol, a representative of naturally occurring monomeric phenols and phenolic pollutants, in suspensions of humic acids (HAs) at original and H2/Pd-reduced redox states with flux of air (HAorg-Air and HAred-Air, respectively) or N2 (HAorg-N2 and HAred-N2, respectively) for 20 min in absence and presence of Cu(II) and Fe(II). Both HAorg and HAred can transform catechol in the absence of O2 to 19% and 25% of the initially applied amount, respectively. The transformation of catechol strongly increased when air was introduced, amounting to 75% in HAred-Air treatment and 43% in HAorg-Air treatment, owing to the generation of reactive oxygen species. Considerable amounts of catecholic carbons were incorporated into HAs (26% for HAred-Air and 19% for HAorg-Air), constituting humification of catechol. The presence of Cu(II) strongly inhibited the overall transformation and humification of catechol, although it significantly increased humification at the start of incubation. The presence of Fe(II) overall enhanced both the transformation and humification. The results provide first insights into the impacts of redox alteration of humic substances together with the presence of metal ions with variable valences on the fate of phenolic compounds in the environment. This study points out that redox alteration-induced abiotic transformation may be one important process for dissipation of phenolic pollutants and humification of phenolic carbons in environments rich in HAs and subject to redox fluctuation.

Partially shielded enzymes capable of processing large protein substrates.

We report the first method of enzyme protection enabling the production of partially shielded enzymes capable of processing substrates as large as proteins. We show that partially shielded sortase retains its transpeptidase activity and can perform bioconjugation reactions on antibodies. Moreover, a partially shielded trypsin is shown to outperform its soluble counterpart in terms of proteolytic kinetics. Remarkably, partial enzyme shielding results in a drastic increase in temporal stability of the enzyme.

Accumulation and Transformation of 2,2',4,4'-Tetrabrominated Diphenyl Ether (BDE47) by the Earthworm Metaphire vulgaris in Soil.

The accumulation and transformation of 2,2',4,4'-tetrabrominated diphenyl ether (BDE47), one congener of the flame retardants polybrominated diphenyl ethers (PBDEs), in soil-feeding fauna are still unknown. Using radioactivity tracer, we incubated 14C-labelled BDE47 in soil for 21 days in the presence and absence of the geophagous earthworm Metaphire vulgaris. BDE47 accumulated in the earthworm predominantly via oral ingestion of soil, giving a biota-soil accumulation factor (BSAF) value of 1.3 for radioactivity at the end of incubation, and was mostly located in intestine, followed by clitellum (organs region) and skin of earthworms. Accumulation was accompanied by significant decrease of BDE47 concentration in soil porewater and BDE47 mineralization in soil. BDE47 was transformed in the earthworm gut into two metabolites with higher polarities than BDE47. The results provide for the first time insights into accumulation and transformation of lower-brominated congeners of PBDEs in geophagous earthworms, being helpful for environmental risk assessment of PBDEs.

Fate of lower-brominated diphenyl ethers (LBDEs) in a red soil - Application of 14C-labelling.

Lower-brominated diphenyl ethers (LBDEs) occur ubiquitously in soil, however their fate there has not been well evaluated, mainly owing to that the unavailability of commercial radioactively labelled LBDE congeners hampers the investigation on fate of LBDEs in the environment with complex matrixes, such as soil and sediment. Here, we successfully synthesized three congeners of LBDEs, i.e., 4-bromodiphenyl ether (BDE3), 4,4'-dibromodiphenyl ether (BDE15), and 2,2',4,4'-tetrabromodiphenyl ether (BDE47), with 14C-labelling on one aromatic ring, starting from commercially available 14C-labelled phenol in two steps with high yields and high radiochemical purities. Using the 14C-labelled congeners, we studied the fate of LBDEs in a red soil under oxic conditions, where LBDEs have been frequently detected in high levels. The major fate of the LBDE congeners in the soil was formation of NERs, followed by mineralization to CO2, while no transformation product was detected in the soil after incubation for 105 days. The mineralization strongly decreased with increasing number of the bromine atom on the congener molecule, amounting to 10.4 ± 0.3%, 2.45 ± 0.04%, and 0.51 ± 0.05% for BDE3, BDE15, and BDE47, respectively, at the end of incubation, while mineralization rate constant was independent of the molecular structure, suggesting that solubility of LBDEs is the limit factor for their persistence in soil. The mineralization was positively linearly correlated with the formation of NERs (22.5 ± 1.9%, 11.0 ± 3.6%, and 6.7 ± 2.7% for BDE3, BDE15, and BDE47, respectively), which was mainly located in humin fraction and formed also in sterilized soil, suggesting a binding of transformation intermediates to soil humic substances and a physico-chemical entrapment of LBDEs in soil. The results provide new insights into fate of LBDE congeners in soil, and suggest a need to elucidate nature of the NERs of LBDEs, especially the stability of NERs in the environment.

Fate of 2,4,6-Tribromophenol in Soil Under Different Redox Conditions.

Fate of 2,4,6-tribromophenol (TBP) in environmental matrices is obscure. We used 14C-tracer to investigated mineralization, transformation, and non-extractable residue (NER)-formation of TBP in a soil under continuously oxic, continuously anoxic, and anoxic-oxic alteration conditions. In all cases, TBP rapidly dissipated, mineralized to CO2, and formed NERs in the soil. Considerable amounts of transformation products (2-12%) were detected during the incubation. Marked mineralization (13-26%) indicated that soil microorganisms used TBP as their energy source. About 62-70% of the initial radioactivity was transformed into NERs, being mainly attributed to binding to humic and fulvic acid fractions. TBP transformation was significantly faster under oxic conditions than under anoxic conditions, and was boosted when the soil redox changed from anoxic to oxic state. The results provide new insights into fate of TBP in soil and suggest the importance to evaluate the stability of NERs for risk assessment of TBP in soil.

Degradation and transformation of nitrated nonylphenol isomers in activated sludge under nitrifying and heterotrophic conditions.

Nitrated nonylphenols (2-nitro-nonylphenols, NNPs) are metabolites of the endocrine-disrupter nonylphenols (NPs). While they have been detected in the environment, their fate in activated sludge has yet to be determined. In this study, we used synthesized NNP isomers and a 14C-tracer technique to study the degradation and transformation of four NNP isomers (NNP111, NNP112, NNP38, and NNP65) in nitrifying activated sludge (NAS) and heterotrophic bacteria-enhanced activated sludge (HAS). Our results showed that the degradation of NNPs in both NAS and HAS was isomer-specific. The half-lives of the NNPs decreased in the order: NNP111 > NNP112 > NNP38 > NNP65. After 36 days of incubation, 9.48 % and 4.01 % of the 14C-NNP111 was mineralized in NAS and HAS, respectively. In addition to mineralization, five metabolites of NNPs containing hydroxyl, carbonyl, and carboxyl substituents on the alkyl chains were formed in NAS but not in HAS. The transformation of NNPs differed in NAS and HAS, mainly due to the differences in their microbial communities and the activities thereof in NAS and HAS. This is the first study of the isomer-specific fate of NNP isomers in activated sludge. Future studies should assess the toxicity, stability and potential risks of NNP metabolites in the environment.

Fate of 4-bromodiphenyl ether (BDE3) in soil and the effects of co-existed copper.

The quantitative fate of polybrominated diphenyl ethers (PBDEs) in soil is unknown. Furthermore, the effects of co-contamination by toxic copper on the behavior of PBDEs have not been investigated. Using a 14C-tracer, we studied mineralization, metabolism, and formation of non-extractable residues (NERs) of one PBDE congener, i.e., the 4-bromodiphenyl ether (BDE3) in oxic soil for 50 days, without and with amendment of Cu (400 mg kg-1 soil dw). BDE3 rapidly dissipated with a half-life of 5.5 days and large amounts of CO2 (38.8 ± 0.3% of initial applied amount at the end of incubation) and NERs (42.5 ± 0.4%) were rapidly produced. One hydroxylated metabolite (4'-HO-BDE3) was formed (8.1 ± 0.6%) at the beginning of the incubation, but then decreased to 2.2 ± 0.4%. Only BDE3 occurred in physico-chemically entrapped NERs, amounting to 9.2 ± 0.7%, while only 4'-HO-BDE3 in ester-linked NERs (10.9 ± 0.7%). The addition of Cu strongly reduced the kinetics constants of the transformations (including dissipation, mineralization, and NER-formation), the predicted maximal amounts of mineralization, as well as covalent binding of 4'-HO-BDE3 to soil. The results provide first quantitative insights into the fate of low-brominated congeners of PBDEs in soil and indicate that co-contamination by Cu may increase the environmental risks of biodegradable PBDEs in soil by increasing their persistence.

State-of-the-Art Production Chains for Peas, Beans and Chickpeas-Valorization of Agro-Industrial Residues and Applications of Derived Extracts.

The world is confronted with the depletion of natural resources due to their unsustainable use and the increasing size of populations. In this context, the efficient use of by-products, residues and wastes generated from agro-industrial and food processing opens the perspective for a wide range of benefits. In particular, legume residues are produced yearly in very large amounts and may represent an interesting source of plant proteins that contribute to satisfying the steadily increasing global protein demand. Innovative biorefinery extraction cascades may also enable the recovery of further bioactive molecules and fibers from these insufficiently tapped biomass streams. This review article gives a summary of the potential for the valorization of legume residual streams resulting from agro-industrial processing and more particularly for pea, green bean and chickpea by-products/wastes. Valuable information on the annual production volumes, geographical origin and state-of-the-art technologies for the extraction of proteins, fibers and other bioactive molecules from this source of biomass, is exhaustively listed and discussed. Finally, promising applications, already using the recovered fractions from pea, bean and chickpea residues for the formulation of feed, food, cosmetic and packaging products, are listed and discussed.

Biodegradation of Polyethylene and Polystyrene by Greater Wax Moth Larvae (Galleria mellonella L.) and the Effect of Co-diet Supplementation on the Core Gut Microbiome.

Plastics waste and microplastics including polyethylene (PE) and polystyrene (PS) have been an environmental concern for years. Recent research has revealed that larvae of Galleria mellonella are capable of biodegrading low density PE film. In this study, we tested the feasibility of enhancing larval survival and the effect of supplementing the co-diet on plastic degradation by feeding the larvae beeswax or wheat bran as a co-diet. Significant mass loss of plastic was observed over a 21-day period, i.e., with respective consumption of 0.88 and 1.95 g by 150 larvae fed only either PS or PE. The formation of C═O and C-O containing functional groups and long chain fatty acids as the metabolic intermediates of plastics in the residual polymers indicated depolymerization and biodegradation. Supplementing beeswax and bran increased the survival rates but decreased the consumption of plastic. The changes in the gut microbiome revealed that Bacillus and Serratia were significantly associated with the PS and PE diets. Beeswax and bran showed different shaping effects on the core gut microbiome of larvae fed the PE and PS. These results suggest that supplementing the co-diet affected the physiological properties of the larvae and plastic biodegradation and shaped the core gut microbiome.