An overview on polyurethane-degrading enzymes.

Polyurethanes (PUR) are durable synthetic polymers widely used in various industries, contributing significantly to global plastic consumption. PUR pose unique challenges in terms of degradability and recyclability, as they are characterised by intricate compositions and diverse formulations. Additives and proprietary structures used in commercial PUR formulations further complicate recycling efforts, making the effective management of PUR waste a daunting task. In this review, we delve into the complex challenge of enzymatic degradation of PUR, focusing on the structural and functional attributes of both enzymes and PUR. We also present documented native enzymes with reported efficacy in hydrolysing specific bonds within PUR, analysis of these enzyme structures, reaction mechanisms, substrate specificity, and binding site architecture. Furthermore, we propose essential features for the future redesign of enzymes to optimise PUR biodegradation efficiency. By outlining prospective research directions aimed at advancing the field of enzymatic biodegradation of PUR, we aim to contribute to the development of sustainable solutions for managing PUR waste and reducing environmental pollution.

Increasing resistance of lawn grasses to zinc and copper pollution.

Coppe and zinc are priority pollutants in city soils. Copper and zinc are the limiting factors for lawn grasses. Cell selection can increase the resistance of lawn grasses to zinc and copper. The effect of zinc on the morphogenic ability of the callus was determined. The results of this study showed that zinc is less toxic to calli than copper. The method of obtaining lawn grass resistant to zinc has been developed. The results were used to develop the cell selection technology for obtaining plants resistant to the complex effect of zinc and copper. Concentrations of Copper (75 mg/l) and zinc (150 mg/L) were selected as selective. The author developed the cell selection scheme for obtaining plants resistant to the complex effect of Cu and Zn. The regenerants showed increased resistance to copper and zinc.

The bioinformatics landscape in environmental omics: Lessons from a national ELIXIR survey.

As a research infrastructure with a mission to provide services for bioinformatics, ELIXIR aims to identify and inform its target audiences. Here, we present a survey on a community of researchers studying the environment with omics approaches in Greece, one of the youngest member countries of ELIXIR. Personal interviews followed by quantitative and qualitative analysis were employed to document interactions and practices of the community and to perform a gap analysis for the transition toward multiomics and systems biology. Environmental omics in Greece mostly concerns production of data, in large majority on microbes and non-model organisms. Our survey highlighted (1) the popularity and suitability of targeted hands-on training events; (2) data quality and management issues as important elements for the transition to multiomics, and (3) lack of knowledge and misconceptions regarding interoperability, metadata standards, and pre-registration. The publicly available collected answers represent a valuable resource in view of future strategic planning.

Building blocks toward sustainable biofertilizers: variation in arbuscular mycorrhizal spore germination when immobilized with diazotrophic bacteria in biodegradable hydrogel beads.

AIM: We investigated whether there was interspecies and intraspecies variation in spore germination of 12 strains of arbuscular mycorrhizal fungi when co-entrapped with the diazotrophic plant growth-promoting bacteria, Azospirillum brasilense Sp7 in alginate hydrogel beads. METHODS AND RESULTS: Twelve Rhizophagus irregularis, Rhizophagus intraradices, and Funneliformis mosseae strains were separately combined with a live culture of Azospirillum brasilense Sp7. Each fungal-bacterial consortia was supplemented with sodium alginate to a 2% concentration (v/v) and cross-linked in calcium chloride (2% w/v) to form biodegradable hydrogel beads. One hundred beads from each combination (total of 1200) were fixed in solidified modified Strullu and Romand media. Beads were observed for successful spore germination and bacterial growth over 14 days. In all cases, successful growth of A. brasilense was observed. For arbuscular mycorrhizal fungi, interspecies variation in spore germination was observed, with R. intraradices having the highest germination rate (64.3%), followed by R. irregularis (45.5%) and F. mosseae (40.3%). However, a difference in intraspecies germination was only observed among strains of R. irregularis and F. mosseae. Despite having varying levels of germination, even the strains with the lowest potential were still able to establish with the plant host Brachypodium distachyon in a model system. CONCLUSIONS: Arbuscular mycorrhizal spore germination varied across strains when co-entrapped with a diazotrophic plant growth-promoting bacteria. This demonstrates that hydrogel beads containing a mixed consortium hold potential as a sustainable biofertilizer and that compatibility tests remain an important building block when aiming to create a hydrogel biofertilizer that encases a diversity of bacteria and fungi. Moving forward, further studies should be conducted to test the efficacy of these hydrogel biofertilizers on different crops across varying climatic conditions in order to optimize their potential.

Successive accumulation of biotic assemblages at a fine spatial scale along glacier-fed waters.

Glacier-fed waters create strong environmental filtering for biota, whereby different organisms may assume distinct distribution patterns. By using environmental DNA-based metabarcoding, we investigated the multi-group biodiversity distribution patterns of the Parlung No. 4 Glacier, on the Tibetan Plateau. Altogether, 642 taxa were identified from the meltwater stream and the downstream Ranwu Lake, including 125 cyanobacteria, 316 diatom, 183 invertebrate, and 18 vertebrate taxa. As the distance increased from the glacier terminus, community complexity increased via sequential occurrences of cyanobacteria, diatoms, invertebrates, and vertebrates, as well as increasing taxa numbers. The stream and lake showed different community compositions and distinct taxa. Furthermore, the correlations with environmental factors and community assembly mechanisms showed group- and habitat-specific patterns. Our results reveal the rapid spatial succession and increasing community complexity along glacial flowpaths and highlight the varying adaptivity of different organisms, while also providing insight into the ecosystem responses to global change.

Harnessing photosynthetic microorganisms for enhanced bioremediation of microplastics: A comprehensive review.

Mismanaged plastics, upon entering the environment, undergo degradation through physicochemical and/or biological processes. This process often results in the formation of microplastics (MPs), the most prevalent form of plastic debris (<1 mm). MPs pose severe threats to aquatic and terrestrial ecosystems, necessitating innovative strategies for effective remediation. Some photosynthetic microorganisms can degrade MPs but there lacks a comprehensive review. Here we examine the specific role of photoautotrophic microorganisms in water and soil environments for the biodegradation of plastics, focussing on their unique ability to grow persistently on diverse polymers under sunlight. Notably, these cells utilise light and CO2 to produce valuable compounds such as carbohydrates, lipids, and proteins, showcasing their multifaceted environmental benefits. We address key scientific questions surrounding the utilisation of photosynthetic microorganisms for MPs and nanoplastics (NPs) bioremediation, discussing potential engineering strategies for enhanced efficacy. Our review highlights the significance of alternative biomaterials and the exploration of strains expressing enzymes, such as polyethylene terephthalate (PET) hydrolases, in conjunction with microalgal and/or cyanobacterial metabolisms. Furthermore, we delve into the promising potential of photo-biocatalytic approaches, emphasising the coupling of plastic debris degradation with sunlight exposure. The integration of microalgal-bacterial consortia is explored for biotechnological applications against MPs and NPs pollution, showcasing the synergistic effects in wastewater treatment through the absorption of nitrogen, heavy metals, phosphorous, and carbon. In conclusion, this review provides a comprehensive overview of the current state of research on the use of photoautotrophic cells for plastic bioremediation. It underscores the need for continued investigation into the engineering of these microorganisms and the development of innovative approaches to tackle the global issue of plastic pollution in aquatic and terrestrial ecosystems.

Cultivation and sequencing-free protocol for Serratia marcescens detection and typing.

Serratia marcescens is an opportunistic pathogen that survives in inhospitable environments causing large outbreaks, particularly in neonatal intensive care units (NICUs). Genomic studies revealed that most S. marcescens nosocomial infections are caused by a specific clone (here "Infectious clone"). Whole genome sequencing (WGS) is the only portable method able to identify this clone, but it requires days to obtain results. We present a cultivation-free hypervariable-locus melting typing (HLMT) protocol for the fast detection and typing of S. marcescens, with 100% detection capability on mixed samples and a limit of detection that can reach the 10 genome copies. The protocol was able to identify the S. marcescens infectious clone with 97% specificity and 96% sensitivity when compared to WGS, yielding typing results portable among laboratories. The protocol is a cost and time saving method for S. marcescens detection and typing for large environmental/clinical surveillance screenings, also in low-middle income countries.

Exploring indoor and outdoor dust as a potential tool for detection and monitoring of COVID-19 transmission.

This study investigated the potential of using SARS-CoV-2 viral concentrations in dust as an additional surveillance tool for early detection and monitoring of COVID-19 transmission. Dust samples were collected from 8 public locations in 16 districts of Bangkok, Thailand, from June to August 2021. SARS-CoV-2 RNA concentrations in dust were quantified, and their correlation with community case incidence was assessed. Our findings revealed a positive correlation between viral concentrations detected in dust and the relative risk of COVID-19. The highest risk was observed with no delay (0-day lag), and this risk gradually decreased as the lag time increased. We observed an overall decline in viral concentrations in public places during lockdown, closely associated with reduced human mobility. The effective reproduction number for COVID-19 transmission remained above one throughout the study period, suggesting that transmission may persist in locations beyond public areas even after the lockdown measures were in place.

Green synthesized cobalt nanoparticles from Trianthema portulacastrum L. as a novel antimicrobials and antioxidants.

Trianthema portulacastrum is a dietary and medicinal plant that has gained substantial importance due to its pharmacological properties. This plant was used for its various healing properties since the ancient period in ayurvedic system of medicine. The green synthesis technique is an eco-friendly as well as cost effective technique which can produce more biocompatible nanoparticles when compared with those fabricated by physio-chemical methods. Therefore, nanoparticles produced by green synthesis are credible alternatives to those which are produced by conventional synthesis techniques. This research mainly aims to produce nanoparticles with the methanolic leaf extract of T. portulacastrum. The optimized nanoparticles were further analyzed for anti-fungal, anti-bacterial and antioxidant properties. Disk diffusion assay was used for the determination of the antimicrobial property and on the other hand, DPPH radical scavenging assay as well as hydrogen peroxide scavenging activity proved the antioxidant property of the formulation. The study revealed that Escherichia coli (gram negative strain) shows greater zone of inhibition when compared with Bacillus subtilis (gram positive bacteria). The nanoparticles have also been reported to show significant anti-fungal activity against the strains of Aspergillus niger and Fusarium oxysporum which proves its desirability for its further use against both bacterial as well as fungal infections. The novel formulation can be explored dually as antimicrobial and antioxidant agent.

Environmental biotechnology and the involving biological process using graphene-based biocompatible material.

Biotechnology is a promising approach to environmental remediation but requires improvement in efficiency and convenience. The improvement of biotechnology has been illustrated with the help of biocompatible materials as biocarrier for environmental remediations. Recently, graphene-based materials (GBMs) have become promising materials in environmental biotechnology. To better illustrate the principle and mechanisms of GBM application in biotechnology, the comprehension of the biological response of microorganisms and enzymes when facing the GBMs is needed. The review illustrated distinct GBM-microbe/enzyme composites by providing the GBM-microbe/enzyme interaction and the determining factors. There are diverse GBM modifications for distinct biotechnology applications. Each of these methods and applications depends on the physicochemical properties of GBMs. The applications of these composites were mainly categorized as pollutant adsorption, anaerobic digestion, microbial fuel cells, and organics degradation. Where information was available, the strategies and mechanisms of GBMs in improving application efficacies were also demonstrated. In addition, the biological response, from microbial community changes, extracellular polymeric substances changes to biological pathway alteration, may become important in the application of these composites. Furthermore, we also discuss challenges facing the environmental application of GBMs, considering their fate and toxicity in the ecosystem, and offer potential solutions. This research significantly enhances our comprehension of the fundamental principles, underlying mechanisms, and biological pathways for the in-situ utilization of GBMs.

Mode of action of antifouling compound albofungin in inhibiting barnacle larval settlement.

Marine biofouling causes huge economic losses to the marine industry every year. Albofungin is a potential antifoulant showing strong anti-macrofouling activities against larval settlement of major fouling organisms. In the present study, directed RNA-seq and proteomic analyses were used to investigate changes in the transcriptome and proteome of a major fouling barnacle Amphibalanus amphitrite cyprids in response to albofungin treatment. Results showed that albofungin treatment remarkably upregulated the metabolism of xenobiotics by the cytochrome P450 pathway to discharge the compound and downregulated energy metabolic processes. Intriguingly, immunostaining and whole-mount in situ hybridization (WISH) revealed the spatial expression patterns of selected differentially expressed genes (glutathione S-transferase [GST], nitric oxide synthase [NOS], and calmodulin [CaM]) distributed in the thorax and antennule of A. amphitrite. Our study provides new insights into the mechanism of albofungin in interrupting the larval settlement of A. amphitrite and suggests its potential application as an antifouling agent in marine environments.

Emerging contaminants bioremediation by enzyme and nanozyme-based processes - A review.

Due to their widespread occurrence and the inadequate removal efficiencies by conventional wastewater treatment plants, emerging contaminants (ECs) have recently become an issue of great concern. Current ongoing studies have focused on different physical, chemical, and biological methods as strategies to avoid exposing ecosystems to significant long-term risks. Among the different proposed technologies, the enzyme-based processes rise as green biocatalysts with higher efficiency yields and lower generation of toxic by-products. Oxidoreductases and hydrolases are among the most prominent enzymes applied for bioremediation processes. The present work overviews the state of the art of recent advances in enzymatic processes during wastewater treatment of EC, focusing on recent innovations in terms of applied immobilization techniques, genetic engineering tools, and the advent of nanozymes. Future trends in the enzymes immobilization techniques for EC removal were highlighted. Research gaps and recommendations on methods and utility of enzymatic treatment incorporation in conventional wastewater treatment plants were also discussed.

Toward the future of OECD/ISO biodegradability testing-new approaches and developments.

In the past decades, industrial and scientific communities have developed a complex standardized system (e.g., OECD, ISO, CEN) to evaluate the biodegradability of chemical substances. This system includes for OECD three levels of testing (ready and inherent biodegradability tests, simulation tests). It was adopted by many countries and is completely integrated into European legislation (registration, evaluation, authorization, and restriction of chemicals, REACH). Nevertheless, the different tests have certain deficiencies, and the question arises of how accurately these tests display the situation in the real environment and how the results can be used for predictions. This review will focus on the technical advantages and weaknesses of current tests concerning the technical setup, the inoculum characterization, and its biodegradation potential as well as the use of adequate reference compounds. A special focus of the article will be on combined test systems offering enhanced possibilities to predict biodegradation. The properties of microbial inocula are critically discussed, and a new concept concerning the biodegradation adaptation potential (BAP) of inocula is proposed. Furthermore, a probability model and different in silico QSAR (quantitative structure-activity relationships) models to predict biodegradation from chemical structures are reviewed. Another focus lies on the biodegradation of difficult single compounds and mixtures of chemicals like UVCBs (unknown or variable composition, complex reaction products, or biological materials) which will be an important challenge for the forthcoming decades. KEY POINTS: • There are many technical points to be improved in OECD/ISO biodegradation tests • The proper characterization of inocula is a crucial point in biodegradation tests • Combined biodegradation test systems offer extended possibilities for biodegradation tests.

Degradation of Antibiotic Resistance Genes by VADER with CRISPR-Cas Immunity.

The evolution and dissemination of antibiotic resistance genes (ARGs) are prompting severe health and environmental issues. While environmental processes, e.g., biological wastewater treatment, are key barriers to prevent the spread of ARGs, they are often sources of ARGs at the same time, requiring upgraded biotechnology. Here, we present VADER, a synthetic biology system for the degradation of ARGs based on CRISPR-Cas immunity, an archaeal and bacterial immune system for eliminating invading foreign DNAs, to be implemented for wastewater treatment processes. Navigated by programmable guide RNAs, VADER targets and degrades ARGs depending on their DNA sequences, and by employing an artificial conjugation machinery, IncP, it can be delivered via conjugation. The system was evaluated by degrading plasmid-borne ARGs in Escherichia coli and further demonstrated via the elimination of ARGs on the environmentally relevant RP4 plasmid in Pseudomonas aeruginosa. Next, a prototype conjugation reactor at a 10-mL scale was devised, and 100% of the target ARG was eliminated in the transconjugants receiving VADER, giving a proof of principle for the implementation of VADER in bioprocesses. By generating a nexus of synthetic biology and environmental biotechnology, we believe that our work is not only an enterprise for tackling ARG problems but also a potential solution for managing undesired genetic materials in general in the future. IMPORTANCE Antibiotic resistance has been causing severe health problems and has led to millions of deaths in recent years. Environmental processes, especially those of the wastewater treatment sector, are an important barrier to the spread of antibiotic resistance from the pharmaceutical industry, hospitals, or civil sewage. However, they have been identified as a nonnegligible source of antibiotic resistance at the same time, as antibiotic resistance with its main cause, antibiotic resistance genes (ARGs), may accumulate in biological treatment units. Here, we transplanted the CRISPR-Cas system, an immune system via programmable DNA cleavage, to tackle the antibiotic resistance problem raised in wastewater treatment processes, and we propose a new sector specialized in ARG removal with a conjugation reactor to implement the CRISPR-Cas system. Our study provides a new angle for resolving public health issues via the implementation of synthetic biology in environmental contexts at the process level.

Direct and indirect impacts of synthetic biology on biodiversity conservation.

The world's biodiversity is in crisis. Synthetic biology has the potential to transform biodiversity conservation, both directly and indirectly, in ways that are negative and positive. However, applying these biotechnology tools to environmental questions is fraught with uncertainty and could harm cultures, rights, livelihoods, and nature. Decisions about whether or not to use synthetic biology for conservation should be understood alongside the reality of ongoing biodiversity loss. In 2022, the 196 Parties to the United Nations Convention on Biological Diversity are negotiating the post-2020 Global Biodiversity Framework that will guide action by governments and other stakeholders for the next decade to conserve the worlds' biodiversity. To date, synthetic biologists, conservationists, and policy makers have operated in isolation. At this critical time, this review brings these diverse perspectives together and emerges out of the need for a balanced and inclusive examination of the potential application of these technologies to biodiversity conservation.

Use of whole-cell bioreporters to assess bioavailability of contaminants in aquatic systems.

Water contamination has become increasingly a critical global environmental issue that threatens human and ecosystems' health. Monitoring and risk assessment of toxic pollutants in water bodies is essential to identifying water pollution treatment needs. Compared with the traditional monitoring approaches, environmental biosensing via whole-cell bioreporters (WCBs) has exhibited excellent capabilities for detecting bioavailability of multiple pollutants by providing a fast, simple, versatile and economical way for environmental risk assessment. The performance of WCBs is determined by its elements of construction, such as host strain, regulatory and reporter genes, as well as experimental conditions. Previously, numerous studies have focused on the design and construction of WCB rather than improving the detection process and commercialization of this technology. For investigators working in the environmental field, WCB can be used to detect pollutants is more important than how they are constructed. This work provides a review of the development of WCBs and a brief introduction to genetic construction strategies and aims to summarize key studies on the application of WCB technology in detection of water contaminants, including organic pollutants and heavy metals. In addition, the current status of commercialization of WCBs is highlighted.

Different mechanisms driving increasing abundance of microbial phosphorus cycling gene groups along an elevational gradient.

Microbes play an integral role in forest soil phosphorus (P) cycling. However, the variation of microbial P-cycling functional genes and their controlling factors in forest soils is unclearly. We used metagenomics to investigate changes in the abundance of genes involved in P-starvation response regulation, P-uptake and transport, and P-solubilization and mineralization along the five elevational gradients. Our results showed the abundance of three P cycling gene groups increasing along the elevational gradient. Acidobacteria and Proteobacteria were the dominant microbial phyla determining the turnover of soil P-solubilization and immobilization. Along the elevational gradient, soil substrates are the major factor explaining variation in P-starvation response regulation genes. Soil environment is the main driver of P-uptake and transport and P-solubilization and mineralization genes. This study provided insights into the regulation of P-cycling from a microbial functional profile perspective, highlighting the importance of substrate and environmental factors for P-cycling genes in forest soils.

Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.

Species composition in high-alpine ecosystems is a useful indicator for monitoring climatic and environmental changes at the upper limits of habitable environments. We used environmental DNA (eDNA) analysis to document the breadth of high-alpine biodiversity present on Earth's highest mountain, Mt. Everest (8,849 m a.s.l.) in Nepal's Khumbu region. In April-May 2019, we collected eDNA from ten ponds and streams between 4,500 m and 5,500 m. Using multiple sequencing and bioinformatic approaches, we identified taxa from 36 phyla and 187 potential orders across the Tree of Life in Mt. Everest's high-alpine and aeolian ecosystem. These organisms, all recorded above 4,500 m-an elevational belt comprising <3% of Earth's land surface-represents ∼16% of global taxonomic order estimates. Our eDNA inventory will aid future high-Himalayan biomonitoring and retrospective molecular studies to assess changes over time as climate-driven warming, glacial melt, and anthropogenic influences reshape this rapidly transforming world-renowned ecosystem.

Bacterial cellulose biopolymers: The sustainable solution to water-polluting microplastics.

Microplastics (MPs) pollution has become one of our time's most consequential issue. These micropolymeric particles are ubiquitously distributed across all natural and urban ecosystems. Current filtration systems in wastewater treatment plants (WWTPs) rely on non-biodegradable fossil-based polymeric filters whose maintenance procedures are environmentally damaging and unsustainable. Following the need to develop sustainable filtration frameworks for MPs water removal, years of R&D lead to the conception of bacterial cellulose (BC) biopolymers. These bacterial-based naturally secreted polymers display unique features for biotechnological applications, such as straightforward production, large surface areas, nanoporous structures, biodegradability, and utilitarian circularity. Diligently, techniques such as flow cytometry, scanning electron microscopy and fluorescence microscopy were used to evaluate the feasibility and characterise the removal dynamics of highly concentrated MPs-polluted water by BC biopolymers. Results show that BC biopolymers display removal efficiencies of MPs of up to 99%, maintaining high performance for several continuous cycles. The polymer's characterisation showed that MPs were both adsorbed and incorporated in the 3D nanofibrillar network. The use of more economically- and logistics-favourable dried BC biopolymers preserves their physicochemical properties while maintaining high efficiency (93-96%). These polymers exhibited exceptional structural preservation, conserving a high water uptake capacity which drives microparticle retention. In sum, this study provides clear evidence that BC biopolymers are high performing, multifaceted and genuinely sustainable/circular alternatives to synthetic water treatment MPs-removal technologies.

Peroxidases-based enticing biotechnological platforms for biodegradation and biotransformation of emerging contaminants.

Rampant industrial boom, urbanization, and exponential population growth resulted in widespread environmental pollution, with water being one of the leading affected resources. All kinds of pollutants, including phenols, industrial dyes, antibiotics, pharmaceutically active residues, and persistent/volatile organic compounds, have a paramount effect, either directly or indirectly, on human health and aquatic entities. Strategies for affordable and efficient decontamination of these emerging pollutants have become the prime focus of academic researchers, industry, and government to constitute a sustainable human society. Classical treatment techniques for environmental contaminants are associated with several limitations, such as inefficiency, complex pretreatments, overall high process cost, high sludge generation, and highly toxic side-products formation. Enzymatic remediation is considered a green and ecologically friendlier method that holds considerable potential to mitigate any kinds of contaminating agents. Exploiting the potential of various peroxidases for pollution abatement is an emerging research area and has considerable advantages, such as efficiency and ease of handling, over other methods. This work is designed to provide recent progress in deploying peroxidases as green and versatile biocatalytic tools for the degradation and transformation of a spectrum of potentially hazardous environmental pollutants to broaden their scope for biotechnological and environmental purposes. More studies are required to explicate the degradation mechanisms, assess the toxicology levels of bio-transformed metabolites, and standardize the treatment strategies for economic viability.