Role of microbiome and biofilm in environmental plastic degradation

Genomic and phenotypic characterization of Chryseomicrobium imtechense from canine pyometra

Chryseomicrobium imtechense is a bacterium primarily isolated in environment samples. Here we demonstrated the virulent and antimicrobial resistant profile of the C. imtechense LBV029/19 strain, which was isolated in a pyometra infection in canines, being related as causal agent of that disease. The bacterium was recovered from purulent content of a uterus with pyometra and the identity was confirmed by both, biochemical tests followed MALDI-TOF MS and 16S-rDNA gene sequencing. Antimicrobial susceptibility test, biofilm formation assessment, genomic sequencing with Illumina MiSeq platform followed by the genome characterization and phylogenetic relationships were conducted with C. imtechense LBV029/19 strain. The phylogenetic analysis revealed a close evolutionary relationship between the C. imtechense LBV029/19 and the others publicly available 16S-rDNA genes of C. imtechense. The in vitro assays shown that C. imtechense LBV029/19 has a strong ability for biofilm formation. Additionally, the antimicrobial susceptibility tests revealed a smaller inhibition zone for novobiocin, cefuroxime, and erythromycin. To the best of our knowledge the C. imtechense LBV029/19 genome is the first genome sequenced and available of C. imtechense. Regarding the genotypic profile, resistance genes to tetracyclines, fluoroquinolones, beta-lactams, and multidrug resistance were present in this genome. Additionally, genes encoded to virulence factors, including biofilm formation, motility, and sporulation were identified. The phenotypic profile associated with the genotypic description indicates the potential of C. imtechense LBV029/19 as a primary agent of animal infectious diseases. The genomic description will contribute to the understanding of the biology of the bacterium and the pathogenesis process involved in the disease.

Plastic-mediated transformation: A new route to navigate plasmid-borne antibiotic resistance genes

Among the anthropogenic sources of pollution, accumulation of plastic polymers in aquatic ecosystems is scaling at unprecedented rates and emerging as a new niche for bacterial colonization and horizontal gene transfer (HGT). The current study focuses on determining the ability of bacteria to acquire plasmid DNA from the extracellular environment under exposure to different treatments (soil, CaCl2 salt solution, soil plus CaCl2, Escherichia coli cell-free extract, and plastic debris) that simulate possible conditions experienced by microorganisms in natural environments. The transformation frequency of two plasmids (pACYC:Hyg and pBAV-1k) was tested following two experimental approaches: single species microcosm of E. coli cells (SSM) and bacterial consortium microcosm (BCM) of strains isolated from freshwater ecosystems. Plastic fragments (with consistent results obtained using polypropylene) proved to be remarkably efficient in increasing the bacterial competence towards plasmid DNA uptake as compared to the other conditions. Moreover, the effects of different plastic polymers and four incubation conditions on bacterial DNA transformation were analyzed to gain deeper insight into the exchange of genetic material. Our findings from both experimental approaches demonstrate that simultaneous incubation of microorganisms, plasmids, and plastic fragments enhances the bacterial ability to uptake plasmids and to express genes required for survival under stress conditions. The two microcosm models prove to be promising tools to mimic natural transformation events leading to the dissemination of antibiotic-resistant genes via HGT in the environment.

On the role of bacterial gut microbiota from supralittoral amphipod Talitrus saltator (Montagu, 1808) in bioplastic degradation

Despite the promise of a reduced environmental impact, bioplastics are subjected to dispersion and accumulation similarly to traditional plastics, especially in marine and coastal environments. The environmental impact of bioplastics is attracting increasing attention due to the growing market demand. The ability of the supralittoral amphipod Talitrus saltator to ingest and survive on pristine starch-based bioplastic has already been assessed. However, the involvement of the gut microbiota of this key coastal species in making bioplastics a dietary supplement, remains unknown. In this study, we investigated the modification of T. saltator gut microbiota following bioplastic ingestion and the effect of this change on the modification of their chemical composition. Groups of adult amphipods were fed with: 1 - two different kinds of starch-based bioplastic; 2 - a 50 %/50 % chitosan-starch mixture; and 3 - paper and dry-fish-food. Freshly collected, unfed individuals were used as control group. Faecal pellets from the amphipods were collected and characterized using ATR-FTIR spectroscopy. DNA was extracted from gut samples for metagenomic analysis. Spectroscopic investigation suggested a partial digestion of polysaccharide components in the experimental polymeric materials. The analysis of the gut microbiota revealed that bioplastic feeding induced modification of sandhopper's gut microbial communities, shifting the abundance of specific microbial genera already present in the gut, towards bacterial genera associated with plastic/bioplastic degradation, especially in groups fed with starch-based bioplastics. Overall, our results highlight the involvement of T. saltator's gut microbiota in bioplastic modification, providing new insights into the potential role of microbial consortia associated to sandhoppers in bioplastic management.

Bacteria isolated from soil degrade low-density polyethylene for growth and polyhydroxyalkanoate synthesis

The low-density polyethylene (LDPE) used in food packaging contributes significantly to the environmental accumulation of microplastics and plastic waste. The aim of this study was to identify and characterize bacteria from plastic waste-contaminated soils that degrade LDPEs. After 16 weeks of degradation, the greatest percentage of LDPE weight loss were achieved with the bacterial consortium and Chitinophaga oryzae NT1-2 (21.97 ± 8.81 % and 16.14 ± 0.46 %, respectively). After bacteria were exposed to LDPE, numerous new functional groups, including aldehydes, ketones, and carboxylic acids, were identified by Fourier transform infrared spectroscopy (FTIR) analysis, while field emission scanning electron microscopy showed that the treated LDPE film surface had more grooves and cracks and was rougher than the control LDPE film surface. The highest total (1781.20 ± 42 U/min/mL) and specific (2.53 ± 0.06 U/min/mg protein) activities of alkane hydroxylase were detected in Bothriochloa intermedia MK2-8, whereas the total and specific alcohol dehydrogenase activities of the MK2-8 strain were 95.57 ± 4.16 U/min/mL and 0.14 ± 0.01 U/min/mg protein, respectively. In Pseudomonas aeruginosa CB1-2, the highest total and specific lipase activities were 10.00 ± 0.20 U/min/mL and 0.10 ± 0.03 U/min/mg protein, respectively. These LDPE-degrading bacteria produced polyhydroxyalkanoate (PHA), with C. oryzae NT1-2 giving the highest yield of 26.27 ± 8.40 mg PHA/g-glucose. Thus, bacteria isolated from plastic contaminated soil possess the capability to enzymatically degrade LDPE and convert it into the PHA biopolymer, thereby contributing to environmental sustainability and resource efficiency.

From biofilms to biocatalysts: Innovations in plastic biodegradation for environmental sustainability

The increase in plastic waste has evolved into a severe environmental crisis, which requires innovative recycling technologies to repurpose used plastic with adequate environmental protection. This review highlights the urgent need for innovative approaches to the treatment and degradation of post-use plastics. It investigates the promising role of biofilms in the biodegradation of polymers, especially for polymers such as polyethylene terephthalate (PET), polyurethane (PU), and polyethylene (PE). By examining biofilms, researchers can determine key enzymes involved in polymer degradation and improve their efficiency through genetic engineering. In addition, the review explores in detail the structure and development of biofilms on polymeric surfaces, elucidating the role of specific microbial strains necessary for biofilm formation and maintenance. Techniques for identifying enzymes within biofilms and improving their degradation ability are also discussed. The review concludes with recent discoveries in enzyme isolation and the key role of biofilms in the degradation and recycling of major plastic pollutants such as PET, PU, and PE. These findings highlight the potential of biofilm-derived enzymes to promote sustainable polymer recycling.

Omic-driven strategies to unveil microbiome potential for biodegradation of plastics: a review

Plastic waste accumulation has lately been identified as the leading and pervasive environmental concern, harming all living beings, natural habitats, and the global market. Given this issue, developing ecologically friendly solutions, such as biodegradation instead of standard disposal, is critical. To effectively address and develop better strategies, it is critical to understand the inter-relationship between microorganisms and plastic, the role of genes and enzymes involved in this process. However, the complex nature of microbial communities and the diverse mechanisms involved in plastic biodegradation have hindered the development of efficient plastic waste degradation strategies. Omics-driven approaches, encompassing genomics, transcriptomics and proteomics have revolutionized our understanding of microbial ecology and biotechnology. Therefore, this review explores the application of omics technologies in plastic degradation studies and discusses the key findings, challenges, and future prospects of omics-based approaches in identifying novel plastic-degrading microorganisms, enzymes, and metabolic pathways. The integration of omics technologies with advanced molecular technologies such as the recombinant DNA technology and synthetic biology would guide in the optimization of microbial consortia and engineering the microbial systems for enhanced plastic biodegradation under various environmental conditions.

An integrated approach for plastic polymer degradation by the gut bacterial resident of superworm, Zophobas morio (Coleoptera:Tenebrionidae)

The potential of superworm to remove certain plastic polymers has recently been noted. In this study, aerobic bacterial strains were isolated from the gut of Zophobas morio larvae which were fed with polyethylene (PE), polyethylene terephthalate (PET), polypropylene (PP), and polystyrene (PS) polymers. Strains P2 (Leminorella), P6 (Bacillus), P9 (Bacillus), and P5 (Citrobacter) were associated with the highest PS (2.7%), PP (1.3%), PET (1.1%), and PE (0.42%) weight loss after 28 days, respectively. Pretreatments including thermal treatment (80 °C for 10 days), weathering (4 months in the free environment), and nitric and sulfuric acids (1 N, 10 days) improved the degradation of PE (1.3%), PET (1.9%), PP (5.2%), and PS (8.3%) by the same strains, respectively. Further analyses on the PS degradation by Leminorella sp. P2 revealed acid pretreatment promoted the formation of the C = C, C = O, and O-H functional groups. Surface irregularities, as well as a 3.6-fold increase in surface roughness, were observed in the PS film subjected to biodegradation. The contact angle dropped from 98.4° to 42.2° following the biodegradation. Bacterial depolymerization was confirmed by the 8.7% and 3.4% reduction of Mn and Mw and the change in polydispersity from 1.65 to 1.75. The results suggest that Zophobas morio microbiota in combination with abiotic pretreatment can be considered for plastic waste management.

Studying microbially induced corrosion on glass using ToF-SIMS

Microbially induced corrosion (MIC) is an emerging topic that has huge environmental impacts, such as long-term evaluation of microbial interactions with radioactive waste glass, environmental cleanup and disposal of radioactive material, and weathering effects of microbes. Time-of-flight secondary ion mass spectrometry (ToF-SIMS), a powerful mass spectral imaging technique with high surface sensitivity, mass resolution, and mass accuracy, can be used to study biofilm effects on different substrates. Understanding how to prepare biofilms on MIC susceptible substrates is critical for proper analysis via ToF-SIMS. We present here a step-by-step protocol for preparing bacterial biofilms for ToF-SIMS analysis, comparing three biofilm preparation techniques: no desalination, centrifugal spinning (CS), and water submersion (WS). Comparisons of two desalinating methods, CS and WS, show a decrease in the media peaks up to 99% using CS and 55% using WS, respectively. Proper desalination methods also can increase biological signals by over four times for fatty acids using WS, for example. ToF-SIMS spectral results show chemical compositional changes of the glass exposed in a Paenibacillus polymyxa SCE2 biofilm, indicating its capability to probe microbiologically induced corrosion of solid surfaces. This represents the proper desalination technique to use without significantly altering biofilm structure and substrate for ToF-SIMS analysis. ToF-SIMS spectral results showed chemical compositional changes of the glass exposed by a Paenibacillus bacterial biofilm over 3-month inoculation. Possible MIC products include various phosphate phase molecules not observed in any control samples with the highest percent increases when experimental samples were compared with biofilm control samples.

Degradation of polyethylene terephthalate (PET) plastics by wastewater bacteria engineered via conjugation

Wastewater treatment plants are one of the major pathways for microplastics to enter the environment. In general, microplastics are contaminants of global concern that pose risks to ecosystems and human health. Here, we present a proof-of-concept for reduction of microplastic pollution emitted from wastewater treatment plants: delivery of recombinant DNA to bacteria in wastewater to enable degradation of polyethylene terephthalate (PET). Using a broad-host-range conjugative plasmid, we enabled various bacterial species from a municipal wastewater sample to express FAST-PETase, which was released into the extracellular environment. We found that FAST-PETase purified from some transconjugant isolates could degrade about 40% of a 0.25 mm thick commercial PET film within 4 days at 50°C. We then demonstrated partial degradation of a post-consumer PET product over 5-7 days by exposure to conditioned media from isolates. These results have broad implications for addressing the global plastic pollution problem by enabling environmental bacteria to degrade PET.

Towards environmentally sustainable management: A review on the generation, degradation, and recycling of polypropylene face mask waste

There has been a considerable increase in the use of face masks in the past years. Managing face mask waste has become a global concern, as the current waste management system is insufficient to deal with such a large quantity of solid waste. The drastic increase in quantity, along with the material's inability to degrade plastic components such as polypropylene, has led to a large accumulation of plastic waste, causing a series of environmental and ecological challenges. In addition, the growing use also imposes pressure on waste management methods such as landfill and incineration, raising concerns about high energy consumption, low value-added utilization, and the release of additional pollutants during the process. This article initially reviews the impact of mask-related plastic waste generation and degradation behavior in the natural environment. It then provides an overview of various recently developed methods for recycling face mask plastic waste. The article also offers forward-looking strategies and recommendations on face mask plastic waste management. The review aims to provide guidance on harnessing the complexities of mask waste and other medical plastic pollution issues, as well as improving the current waste management system's deficiencies and inefficiencies in tackling the growing plastic waste problem.

Exploring Microorganisms from Plastic-Polluted Sites: Unveiling Plastic Degradation and PHA Production Potential

The exposure of microorganisms to conventional plastics is a relatively recent occurrence, affording limited time for evolutionary adaptation. As part of the EU-funded project BioICEP, this study delves into the plastic degradation potential of microorganisms isolated from sites with prolonged plastic pollution, such as plastic-polluted forests, biopolymer-contaminated soil, oil-contaminated soil, municipal landfill, but also a distinctive soil sample with plastic pieces buried three decades ago. Additionally, samples from Arthropoda species were investigated. In total, 150 strains were isolated and screened for the ability to use plastic-related substrates (Impranil dispersions, polyethylene terephthalate, terephthalic acid, and bis(2-hydroxyethyl) terephthalate). Twenty isolates selected based on their ability to grow on various substrates were identified as Streptomyces, Bacillus, Enterococcus, and Pseudomonas spp. Morphological features were recorded, and the 16S rRNA sequence was employed to construct a phylogenetic tree. Subsequent assessments unveiled that 5 out of the 20 strains displayed the capability to produce polyhydroxyalkanoates, utilizing pre-treated post-consumer PET samples. With Priestia sp. DG69 and Neobacillus sp. DG40 emerging as the most successful producers (4.14% and 3.34% of PHA, respectively), these strains are poised for further utilization in upcycling purposes, laying the foundation for the development of sustainable strategies for plastic waste management.

Microplastics in the soil environment: Focusing on the sources, its transformation and change in morphology

Microplastics (MPs) are small plastic pieces less than 5 mm in size. Previous studies have focused on the sources, transports, and fates of MPs in marine or sediment environments. However, limited attention has been given to the role of land as the primary source of MPs, and how plastic polymers are transformed into MPs through biological or abiotic effects during the transport process remains unclear. Here, we focus on the exploration of the main sources of MPs in the soil, highlighting that MP generation is not solely a byproduct of plastic production but can also result from the impact of biological and abiotic factors during the process of MPs transport. This review presents a new perspective on understanding the degradation of MPs in soil, considering soil as a distinct fluid and suggesting that the main transformation and change mediated by abiotic factors occur on the soil surface, while the main biodegradation occurs in the soil interior. This viewpoint is suggested because the role of some abiotic factors becomes less obvious in the soil interior, and MPs, whose surface is expected to colonize microorganisms, are gradually considered a carbon source independent of photosynthesis and net primary production. This review emphasizes the need to understand basic MPs information in soil for a rational evaluation of its environmental toxicity. Such understanding enables better control of MPs pollution in affected areas and prevents contamination in unaffected regions. Finally, knowledge gaps and future research directions necessary for advancements in this field are provided.

Toxic effect of chronic exposure to polyethylene nano/microplastics on oxidative stress, neurotoxicity and gut microbiota of adult zebrafish (Danio rerio)

The rapid development of aquaculture industry has provided a large amount of high-quality animal protein, while the food safety caused by microplastics and nanoplastics (MP/NPs) has become a major concern. In addition, recent evidence has shown the potential toxic effect of PE-MP/NPs, highlighting the need for further research into their environmental and health impacts. Chronic exposure of polyethylene microplastics (PE-MPs) and nanoplastics (PE-NPs) on adult zebrafish were conducted in the present study for 21 d. Organ-dependent oxidative damage induced by MP/NPs was observed. Insignificant differences in neurotoxicity and dysbiosis of gut microbiota were found between MPs and NPs. Changes in glutathione S-transferase (GST), glutathione (GSH), catalase (CAT), lipid peroxidation (LPO), and superoxide dismutase (SOD) showed that MP/NPs induced oxidative damage in gill and intestinal cells of zebrafish. The inhibited AChE activity suggested the potential neurotoxicity of microplastics and nanoplastics (MP/NPs). In addition, chronic exposure increased the alpha-diversity of intestinal microbiota. At the phylum level, the average relative abundance of Proteobacteria increased from 29.73% (control group) to 66.10% (microplastics), 54.84% (nanoplastics) and 60.03% (combined exposure), respectively. Tenericutes decreased from 55.43% (control group) to 20.02% (microplastics), 22.44% (nanoplastics) and 31.77% (combined exposure), respectively. Overall, this study provides new insights and objective evidence for the toxicity assessment of PE-MPs.

Discovering untapped microbial communities through metagenomics for microplastic remediation: recent advances, challenges, and way forward

Microplastics (MPs) are ubiquitous pollutants persisting almost everywhere in the environment. With the increase in anthropogenic activities, MP accumulation is increasing enormously in aquatic, marine, and terrestrial ecosystems. Owing to the slow degradation of plastics, MPs show an increased biomagnification probability of persistent, bioaccumulative, and toxic substances thereby creating a threat to environmental biota. Thus, remediation of MP-pollutants requires efficient strategies to circumvent the mobilization of contaminants leaching into the water, soil, and ultimately to human beings. Over the years, several microorganisms have been characterized by the potential to degrade different plastic polymers through enzymatic actions. Metagenomics (MGs) is an effective way to discover novel microbial communities and access their functional genetics for the exploration and characterization of plastic-degrading microbial consortia and enzymes. MGs in combination with metatranscriptomics and metabolomics approaches are a powerful tool to identify and select remediation-efficient microbes in situ. Advancement in bioinformatics and sequencing tools allows rapid screening, mining, and prediction of genes that are capable of polymer degradation. This review comprehensively summarizes the growing threat of microplastics around the world and highlights the role of MGs and computational biology in building effective response strategies for MP remediation.

Microplastics and their interactions with microbiota

As a new pollutant, Microplastics (MPs) are globally known for their negative impacts on different ecosystems and living organisms. MPs are easily taken up by the ecosystem in a variety of organisms due to their small size, and cause immunological, neurological, and respiratory diseases in the impacted organism. Moreover, in the impacted environments, MPs can release toxic additives and act as a vector and scaffold for colonization and transportation of specific microbes and lead to imbalances in microbiota and the biogeochemical and nutrients dynamic. To address the concerns on controlling the MPs pollution on the microbiota and ecosystem, the microbial biodegradation of MPs can be potentially considered as an effective environment friendly approach. The objectives of the presented paper are to provide information on the toxicological effects of MPs on microbiota, to discuss the negative impacts of microbial colonization of MPs, and to introduce the microbes with biodegradation ability of MPs.

The Relationship between Brachionus calyciflorus-Associated Bacterial and Bacterioplankton Communities in a Subtropical Freshwater Lake

Zooplankton bodies are organic-rich micro-environments that support fast bacterial growth. Therefore, the abundance of zooplankton-associated bacteria is much higher than that of free-living bacteria, which has profound effects on the nutrient cycling of freshwater ecosystems. However, a detailed analysis of associated bacteria is still less known, especially the relationship between those bacteria and bacterioplankton. In this study, we analyzed the relationships between Brachionus calyciflorus-associated bacterial and bacterioplankton communities in freshwater using high-throughput sequencing. The results indicated that there were significant differences between the two bacterial communities, with only 29.47% sharing OTUs. The alpha diversity of the bacterioplankton community was significantly higher than that of B. calyciflorus-associated bacteria. PCoA analysis showed that the bacterioplankton community gathered deeply, while the B. calyciflorus-associated bacterial community was far away from the whole bacterioplankton community, and the distribution was relatively discrete. CCA analysis suggested that many environmental factors (T, DO, pH, TP, PO₄^3-, NH₄⁺, and NO₃^-) regulated the community composition of B. calyciflorus-associated bacteria, but the explanatory degree of variability was only 37.80%. High-throughput sequencing revealed that Raoultella and Delftia in Proteobacteria were the dominant genus in the B. calyciflorus-associated bacterial community, and closely related to the biodegradation function. Moreover, several abundant bacterial members participating in carbon and nitrogen cycles were found in the associated bacterial community by network analysis. Predictive results from FAPROTAX showed that the predominant biogeochemical cycle functions of the B. calyciflorus-associated bacterial community were plastic degradation, chemoheterotrophy, and aerobic chemoheterotrophy. Overall, our study expands the current understanding of zooplankton-bacteria interaction and promotes the combination of two different research fields.

Ecotoxicological and health implications of microplastic-associated biofilms: a recent review and prospect for turning the hazards into benefits

Microplastics (MPs), over the years, have been regarded as a severe environmental nuisance with adverse effects on our ecosystem as well as human health globally. In recent times, microplastics have been reported to support biofouling by genetically diverse organisms resulting in the formation of biofilms. Biofilms, however, could result in changes in the physicochemical properties of microplastics, such as their buoyancy and roughness. Many scholars perceived the microplastic-biofilm association as having more severe consequences, providing evidence of its effects on the environment, aquatic life, and nutrient cycles. Furthermore, other researchers have shown that microplastic-associated biofilms have severe consequences on human health as they serve as vectors of heavy metals, toxic chemicals, and antibiotic resistance genes. Despite what is already known about their adverse effects, other interesting avenues are yet to be fully explored or developed to turn the perceived negative microplastic-biofilm association to our advantage. The major inclusion criteria for relevant literature were that it must focus on microplastic association biofilms, while we excluded papers solely on biofilms or microplastics. A total of 242 scientific records were obtained. More than 90% focused on explaining the environmental and health impacts of microplastic-biofilm association, whereas only very few studies have reported the possibilities and opportunities in turning the microplastic biofilms association into benefits. In summary, this paper concisely reviews the current knowledge of microplastic-associated biofilms and their adverse consequences and further proposes some approaches that can be developed to turn the negative association into positive.