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Biotic and abiotic degradation of PHAs: mechanisms, environments, and potential applications of degradation products.

This review seeks to compile Polyhydroxyalkanoates (PHAs) degradation studies published over the past 20 years. It highlights the effect of physical properties, such as crystallinity and molecular weight, on the decomposition rate of these molecules. Both biotic processes, mediated by bacteria, fungi, and enzymes, as well as abiotic processes, such as hydrolysis and thermal degradation, are analyzed. A repertoire of diverse microorganisms, including their metabolic pathways and enzymes for PHA breakdown, is presented. Furthermore, this review presents the decomposition of PHAs in various environments, such as soil and seawater, highlighting their potential as a sustainable alternative. Finally, the resulting degradation products are described, emphasizing their potential applications in medicine and industry. Although degradation of PHAs has been extensively studied through these years, several knowledge gaps remain undisclosed, including the degradation of diverse polyester monomers. PHAs comprise numerous monomer compositions with variable properties, which present opportunities for different applications but pose a challenge in their degradation. The reader of this review can extract useful information for both the production of PHAs and their potential applications.

Biodegradation

Effects of a novel Paraburkholderia phage IPK on the phenanthrene degradation efficiency of the PAH-degrading strain Paraburkholderia caledonica Bk.

Phages are a major cause of bacterial mortality, affecting bacterial diversity and ecosystem functioning. However, the impact of phage-host interactions in contaminated environments and their role in pollutant biodegradation have largely been overlooked. We isolated and characterized a novel phage that infects the PAH-degrading bacterium Paraburkholderia caledonica Bk from a polycyclic aromatic hydrocarbon (PAH)-contaminated soil and investigated the effect of different multiplicity of infection (MOI) ratios on the degradation efficiency of phenanthrene. The phage IPK is a temperate phage with a wide pH and temperature tolerance and a burst size of 80  PFU ml⁻1. The phage was classified as a member of the Caudoviricetes and is related to Pseudomonas and Burkholderia phages. However, its low intergenomic similarity indicates that it is a new species. Three auxiliary metabolic genes (AMGs) related to amino acid metabolism and to bacterial growth regulation were identified in the phage genome. The highest multiplicity of infection (MOI 10) showed a rapid recovery of the host density and greater phenanthrene degradation than MOIs ranging from 0.01 to 1. This work highlights the important role of phage-host interactions in modulating the efficiency of pollutant degradation, which could be a key for improving the establishment of inoculants in bioremediation processes.

Phenanthrenes

The mhqPOD gene cluster in lignin-degrading Paenibacillus sp. B2 encodes a pathway for the degradation of lignin-derived 5,5'-di(dehydrovanillic acid) (DDVA).

Lignin-degrading bacteria Paenibacillus sp. B2, Agrobacterium sp. B1, and Ochrobactrum sp. each contain mhqO genes encoding ring cleavage dioxygenase enzymes whose biochemical function is unknown. Each of these strains was found to degrade the biphenyl-containing lignin fragment 5,5'-di(dehydrovanillic acid) (DDVA) on solid media. An operon of five mhq genes in Paenibacillus sp. B2 was analysed via gene expression using quantitative PCR, and all five genes were highly induced (400-1000-fold overexpression) by the presence of DDVA. Recombinant azoreductase MhqP was found to demethylate DDVA to its monodemethylated derivative. Hence, these genes are proposed to be responsible for DDVA degradation, via a pathway involving the same biochemical steps as that studied in Sphingobium lignivorans SYK-6, but using several unrelated genes. Decarboxylation of later pathway intermediate 5-carboxyvanillic acid in Paenibacillus sp. B2 is proposed to be catalysed by decarboxylase UbiD, whose gene is also upregulated in the presence of DDVA. Degradation of the other fragment 4-carboxy-2-hydroxypentadienoic acid is proposed to occur via hydratase UxuA, whose gene is also upregulated by DDVA, and 4-hydroxy-4-methyl-2-oxoglutarate aldolase.

Paenibacillus

Comparative genomic analysis and functional investigations for MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria in ecology.

Microcystins (MCs) significantly threaten the ecosystem and public health. Biodegradation has emerged as a promising technology for removing MCs. Many MCs-degrading bacteria have been identified, including an indigenous bacterium Sphingopyxis sp. YF1 that could degrade MC-LR and Adda completely. Herein, we gained insight into the MCs biodegradation mechanisms and evolutionary dynamics of MCs-degrading bacteria, and revealed the toxic risks of the MCs degradation products. The biochemical characteristics and genetic repertoires of strain YF1 were explored. A comparative genomic analysis was performed on strain YF1 and six other MCs-degrading bacteria to investigate their functions. The degradation products were investigated, and the toxicity of the intermediates was analyzed through rigorous theoretical calculation. Strain YF1 might be a novel species that exhibited versatile substrate utilization capabilities. Many common genes and metabolic pathways were identified, shedding light on shared functions and catabolism in the MCs-degrading bacteria. The crucial genes involved in MCs catabolism mechanisms, including mlr and paa gene clusters, were identified successfully. These functional genes might experience horizontal gene transfer events, suggesting the evolutionary dynamics of these MCs-degrading bacteria in ecology. Moreover, the degradation products for MCs and Adda were summarized, and we found most of the intermediates exhibited lower toxicity to different organisms than the parent compound. These findings systematically revealed the MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria. Consequently, this research contributed to the advancement of green biodegradation technology in aquatic ecology, which might protect human health from MCs.

Humans

Multi-omics association study of hexadecane degradation in haloarchaeal strain Halogranum rubrum RO2-11.

Haloarchaea with the capacity to degrade alkanes is promising to deal with petroleum pollution in hypersaline environments. However, only a limited number of haloarchaeal species are investigated, and their pathway and mechanism for alkane degradation remain unclear. In this study, Halogranum rubrum RO2-11, a haloarchaeal strain, verified the ability to degrade kerosene and hexadecane in 184 g/L NaCl, with 53% and 52% degradation rates after 9 and 4 days, respectively. Genome sequencing and gene annotation indicated that strain RO2-11 possesses a complete potential alkane-degrading pathway, of which alkane hydroxylases may include CYP450, AlmA, and LadA. Transcriptome and metabolome analyses revealed that the upregulation of related genes in TCA cycle, lysine biosynthesis, and acetylation may help improve hexadecane degradation. Additionally, an alternative degrading pathway of hexadecane based on dual-terminal β-oxidation may occur in strain RO2-11. It is likely to be the first report of alkane degradation by the genus Halogranum, which may be helpful for applications of oil-pollution bioremediation under high-salt conditions.

Alkanes

Near-Infrared Fluorescent PROTAC Enables Theranostic Imaging and Selective Tau Degradation in Alzheimer's Disease.

The hyperphosphorylated Tau (p-Tau) protein plays a central role in the pathogenesis of Alzheimer's disease (AD) by driving neurofibrillary tangle formation and neuronal dysfunction. While proteolysis targeting chimeras (PROTACs) offer a promising approach for directly eliminating pathogenic proteins, their real-time visualization in living systems remains challenging. Here, we report the rational design and synthesis of a series of near-infrared (NIR) fluorescent Tau-targeting degraders that integrate theranostic imaging with targeted protein degradation. Among them, compound D9 emerges as a dual-functional degrader capable of both high-contrast fluorescence tracking and potent Tau clearance at 10 nM. Mechanistic investigations indicate that D9 induces Tau degradation through activation of the ubiquitin-proteasome system (UPS), as confirmed by inhibitor assays. Beyond Tau degradation, D9 also downregulates amyloid precursor protein (APP) and β-amyloid (Aβ) expression, suggesting broader neuroprotective effects. In in vivo studies, D9 significantly promotes p-Tau clearance and alleviates cognitive deficits in 3 ×Tg-AD mice. These findings demonstrate that D9 represents a first-in-class NIR fluorescent PROTAC for theranostic imaging and targeted degradation of Tau, providing a powerful platform for visualizing degradation dynamics and developing next-generation AD therapeutics.

Alzheimer's disease

DOT1L-mediated H3K79me3 of ITCH promotes AURKA ubiquitination to suppress ECM degradation in osteoarthritis.

As a prevalent chronic joint disorder, osteoarthritis (OA) is characterized by degenerative changes, primarily driven by the pathological degradation of the chondrocyte extracellular matrix (ECM). Current therapies lack efficacy in halting ECM degradation, making elucidation of its regulatory mechanisms crucial for developing novel OA treatments. This study investigated the role of the DOT1L/ITCH/AURKA axis in ECM degradation during OA development. An in vitro OA model was established by treating rat chondrocytes with 10 ng/mL IL-1β for 24 h. TNF-α and IL-6 secretion was measured by ELISA. ECM content was assessed via alcian blue staining. RT-qPCR, western blot, and immunofluorescence staining analyzed associated molecule expression. Co-IP verified ITCH-AURKA interaction and AURKA ubiquitination. ChIP detected DOT1L and H3K79me3 enrichment at the ITCH promoter. An anterior cruciate ligament transection (ACL-T)-induced OA rat model with intra-articular injection of DOT1L-overexpressing lentivirus was further established, followed by HE staining, safranin O-fast green staining, and IHC analysis. IL-1β stimulation upregulated AURKA but downregulated DOT1L and ITCH expression in rat chondrocytes. ITCH promoted AURKA ubiquitination and degradation, thereby attenuating IL-1β-stimulated degradation of ECM in rat chondrocytes. DOT1L upregulated ITCH expression by mediating H3K79me3 modification at its promoter. DOT1L-dependent H3K79me3 enrichment at the ITCH promoter downregulated AURKA, ultimately inhibiting IL-1β-induced ECM degradation in rat chondrocytes. In vivo, DOT1L overexpression alleviated ACL-T-induced cartilage degeneration and reversed the ACL-T-induced downregulation of ITCH and upregulation of AURKA and ADAMTS5. Collectively, our findings identify the DOT1L/ITCH/AURKA axis as a key epigenetic and post-translational regulatory mechanism that protects against ECM degradation in OA.

Animals

Contaminant-degrading bacteria are super carriers of antibiotic resistance genes in municipal landfills: A metagenomics-based study.

Municipal landfills are hotspot sources of antimicrobial resistance (AMR) and are also important habitats of contaminant-degrading bacteria. However, high diversity of antibiotic resistance genes (ARGs) in landfills hinders assessing AMR risks in the affected environment. More concerned, whether there is co-selection or enrichment of antibiotic-resistant bacteria and contaminant-degrading bacteria in these extremely polluted environments is far less understood. Here, we collected metagenomic datasets of 32 raw leachate and 45 solid waste samples in 22 municipal landfills of China. The antibiotic resistome, antibiotic-resistant bacteria and contaminant-degrading bacteria were explored, and were then compared with other environmental types. Results showed that the antibiotic resistome in landfills contained 1,403 ARG subtypes, with the total abundance over the levels in natural environments and reaching the levels in human feces and sewage. Therein, 49 subtypes were listed as top priority ARGs for future surveillance based on the criteria of enrichment in landfills, mobilizable and present in pathogens. By comparing to those in less contaminated river environments, we elucidated an enrichment of antibiotic-resistant bacteria with contaminant-degrading potentials in landfills. Bacteria in Pseudomonadaceae, Moraxellaceae, Xanthomonadaceae and Enterobacteriaceae deserved the most concerns since 72.2 % of ARG hosts were classified to them. Klebsiella pneumoniae, Acinetobacter nosocomialis and Escherichia coli were abundant multidrug-resistant pathogenic species in raw leachate (∼10.2 % of total microbiomes), but they rarely carried contaminant-degradation genes. Notably, several bacterial genera belonging to Pseudomonadaceae had the most antibiotic-resistant, pathogenic, and contaminant-degrading potentials than other bacteria. Overall, the findings highlight environmental selection for contaminant-degrading antibiotic-resistant pathogens, and provide significant insights into AMR risks in municipal landfills.

Metagenomics

Unlocking microbial potential: advances in omics and bioinformatics for aromatic hydrocarbon degradation.

Aromatic hydrocarbons (AHs) are persistent environmental pollutants with high toxicity. Bacterial degradation of AHs provides a sustainable and cost-effective approach for the remediation of sites contaminated with both mono- and polycyclic aromatic hydrocarbons. Aerobic degradation of AHs typically involves oxygenases-mediated hydroxylation followed by aromatic ring cleavage. In contrast, anaerobic degradation relies on diverse activation mechanisms that ultimately converge on the central intermediate benzoyl-CoA. Over the past decades, research on bacterial degradation of AHs has grown steadily, supported by advances in omics and bioinformatics. In this review, we summarize the current knowledge on the pathways, enzymes, and microbial diversity involved in AH degradation, highlighting how omics and bioinformatic approaches are advancing our understanding of this process. However, to improve our knowledge of microbial AHs catabolism, it is crucial to prioritize the characterization of novel enzymes and pathways, especially those mediating anaerobic and hybrid degradation strategies. Addressing this gap requires the development of specialized resources that incorporate a broader taxonomic diversity and an expanded inventory of anaerobic genes and enzymes supported by experimental evidence. Equally important is the integration of multi-omics technologies, artificial intelligence, and ecological modeling into unified analytical pipelines. These efforts will be key to fully unlocking microbial metabolic potential and guiding more effective bioremediation and monitoring strategies for AHs.

Biodegradation, Environmental

Nitrilase-mediated degradation of insecticides flonicamid and thiacloprid by immobilized engineered Escherichia coli with a novel pathway.

The nitrile‑containing insecticides flonicamid (FLO) and thiacloprid (THI) are widely used in agriculture, posing risks to the environment and animal health. Nitrilase is a key catalyst for the degradation of nitrile compounds, and immobilized engineered bacteria are preferred in wastewater treatment. However, immobilized engineered bacteria expressing nitrilase have never been investigated for pollutant degradation. Here, engineered Escherichia coli pET28a‑VbNitA harboring the nitrilase gene VbNitA was immobilized by calcium alginate encapsulation. FLO was degraded into N-(4-trifluoromethylnicotinoyl)glycinamide and 4-(trifluoromethyl)nicotinol glycine by the immobilized cells via VbNitA. THI was converted to THI‑amide and THI‑imine using the same system. Notably, this is the first report of a nitrilase converting THI to THI‑amide and of THI‑imine as a biodegradation intermediate. Compared with free cells, the immobilized E. coli pET28a‑VbNitA showed higher tolerance to high temperature, alkaline, and acidic environments, and better long-term storage stability. The substrate inhibition model showed that the optimal initial concentrations of FLO and THI for degradation by immobilized E. coli pET28a‑VbNitA were 45.13 and 127.50 μmol/L, respectively. FLO was degraded more rapidly than THI by the immobilized cells. Molecular docking revealed that both FLO and THI formed stable interactions with VbNitA, with FLO positioned closer to Cys165 of the catalytic triad. This study presents a novel THI degradation pathway and provides a new, efficient immobilized biocatalyst for the remediation of wastewater with nitrile‑containing insecticides.

Escherichia coli

Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities.

BACKGROUND: The rumen functions as an anaerobic fermentation chamber, housing microorganisms with cellulolytic and proteolytic capabilities that facilitate feed utilization. Fiber-degrading bacteria possess the capability to enhance the productivity of cellulolytic feed. The application of omics technologies has greatly improved our understanding of the rumen microbiome. Determining microbial composition and functional patterns in the rumen does not equate to a comprehensive exploration of rumen microbial resources and their mechanisms of action. This study seeks to integrate high throughput 16S rRNA data with information on culturomics, cellulolytic activities, nutrition, and synthetic microbial communities (SynCom) engineering. The objective is to evaluate the relationship between rumen microbial activity and fiber utilization efficiency in cattle, ultimately aiming to develop a more powerful intervention strategy for the ruminant industry. RESULTS: The enrichment culture with various carbon sources led to significant alterations in the composition and structure of rumen microbiota, particularly enhancing those associated with carbohydrate metabolism. Employing the culturomics methodology, 896 strains from 78 species (including 8 novel species) were isolated, resulting in a 10.1% isolation rate relative to the rumen bacterial community. Among them, 35 strains demonstrated boosted cellulose-degrading capability on plates, while 25 exhibited the ability to degrade hemicellulose as well. SynComs of these candidates were prepared based on the ratio observed in rumen microbiota exhibiting high cellulolytic performance. SynCom 3 improved the neutral detergent fiber degradation (NDFD) by 20.39% averagely. Additionally, both in vitro and in situ assessments indicated that the optimization of dose/strain in SynCom 3 significantly improved the in vitro NDFD by 20.56% and increased the in situ NDFD by 7.81%, along with the acidic detergent fiber (ADF, + 11.47%). Genomic analysis revealed that the SynCom 3 functioned well in fiber degradation through the synergistic action of key carbohydrate-active enzymes. CONCLUSIONS: This study strengthens rumen microbiome research by integrating omics and SynCom engineering within a microbiota-bacteria-enzymes-genes framework, revealing the significance of enzymatic synergy in carbohydrate metabolism. The findings establish a framework for utilizing low-abundance microbes and engineering functional consortia, which are crucial for improving ruminant feed utilization and biomass conversion. Future research should investigate the transcriptomic profiles and the metabolic cross-feeding mechanisms of fiber-degrading strains in the rumen. Video Abstract.

Animals

Intestinal content accelerates muscle protein degradation in red shrimp (Solenocera crassicornis) during refrigeration: Insights from metagenomics and metabolomics.

This study systematically explored the effects of intestinal components on muscle quality deterioration and protein degradation of red shrimp during refrigerated storage. The results demonstrated that refrigeration induced continuous quality degradation and muscle protein breakdown in red shrimp, whereas eliminating intestinal tissues effectively retarded muscle spoilage and protein degradation, and optimized muscle texture. The intestinal microorganisms could secrete extracellular proteases to promote muscle protein degradation were primarily Vibrio, Bacillus, Pseudomonas, Photobacterium, and Shewanella. These microorganisms promote protein degradation by secreting zinc proteases, serine proteases, and aspartyl proteases. This study elucidates the molecular mechanisms of intestinal microbial metabolism influences the muscle protein degradation of red shrimp during refrigeration. The findings provide a theoretical foundation for precise regulation of intestinal-targeted microorganisms, thereby maintaining optimal quality of shrimps during refrigeration.

Animals

Multiomic insights into fungal polylactic acid degradation: Metabolic adaptation and hydrolytic mechanisms of Sporobolomyces pararoseus.

Polylactic acid (PLA), a biodegradable polyester from renewable resources, is a sustainable alternative to petrochemical plastics. However, its environmental degradation is inefficient naturally, requiring specific microbial activities. While bacterial PLA-degrading mechanisms are well documented, fungal degrading systems-particularly their molecular mechanisms-are underexplored.We isolated Sporobolomyces pararoseus ZRQ01 from the gut microbiota of PLA-fed mealworms. This fungal strain noticeably degraded PLA in PLA-containing medium supplemented with 2% glucose. Biodegradation assays revealed 22.8% loss of the PLA film weight after 35 days of incubation, and scanning electron microscopy confirmed extensive surface erosion and pore formation. Integrated transcriptomic and proteomic analyses, together with the reference genome of S. pararoseus ZRQ01, revealed that S. pararoseus ZRQ01 upregulates hydrolytic enzymes at both transcript and protein levels to cleave PLA into lactic acid. After lactic acid is transferred into S. pararoseus ZRQ01 cells by monocarboxylate transporters with increased abundance, it is assimilated by pathways of pyruvate metabolism and the TCA cycle with increased protein abundance. Intriguingly, upregulation of genes in autophagy-related and MAPK signaling pathways underscores an adaptive stress response potentially supporting cellular homeostasis and degradation-related gene expression. Our results highlight S. pararoseus ZRQ01's metabolic potential for bioremediation and offer insights into fungal bioplastic degradation pathways.

Polyesters

Amino acid reprogramming and biofilm-specific tricarboxylate transporters in PET-degrading Piscinibacter sakaiensis.

Plastic-degrading bacteria predominantly colonize polymer surfaces as biofilms, yet it remains unclear whether the biofilm phenotype contributes to metabolism beyond retaining extracellular enzymes. Here, we combine population-level RNA-sequencing across three conditions-biofilm cells on polyethylene terephthalate (PET), planktonic cells incubated with PET, and planktonic cells on maltose-with single-cell Raman spectroscopy to characterize the PET response of Piscinibacter sakaiensis (formerly Ideonella sakaiensis). This integrated approach reveals two metabolically distinct response layers. A carbon-source-driven response shared by all PET-exposed cells is dominated by a broad amino acid reprogramming, led by upregulation of branched-chain amino acid transport genes, enhanced serine biosynthesis, and reduced chemotaxis. A biofilm-specific layer selectively induces tripartite tricarboxylate transporter genes from three distinct genomic loci. This transcriptional feature is accompanied by a single-cell phenotype consistent with a protein-rich and saturated membrane. These results suggest that biofilm formation is not limited to enzyme retention but is associated with selective activation of transport systems, consistent with a putative role in capturing PET-derived intermediates at the polymer interface. This two-layer model separates general metabolic adaptation to PET from biofilm-specific functions and provides a framework for understanding how surface-associated bacterial physiology contributes to plastic degradation.IMPORTANCEPolyethylene terephthalate (PET) degradation in natural and engineered environments is largely mediated by surface-attached microbial communities, yet the physiological role of biofilm state during plastic degradation remains poorly understood. Using the model PET degrader Piscinibacter sakaiensis, we show that biofilm-associated cells are not simply retained near the polymer surface but exhibit a distinct metabolic program characterized by selective induction of tripartite tricarboxylate transporters. In contrast, extensive amino acid reprogramming occurs in both biofilm and planktonic PET-exposed cells, indicating that it is driven by carbon source rather than surface attachment. These findings reveal that PET degradation involves two separable physiological layers: a general metabolic response to PET-derived carbon shared across cell phenotypes, and a biofilm-specific transport response potentially linked to substrate capture at the plastic interface. This work advances our understanding of how microbial physiology is organized during plastic biodegradation and identifies transport processes as previously unrecognized components of PET-degrading biofilms.

PET biodegradation

BRD9 Degraders Unleash GBAF Chromatin Remodeling Activity in Synovial Sarcoma.

UNLABELLED: Synovial sarcoma incorporates the SS18::SSX fusion oncoprotein into GLTSCR1-containing BRG1/BRM and associated factors (GBAF) complexes, which confers a dependency on the GBAF subunit BRD9. However, synovial sarcoma clinical trials with multiple BRD9 degraders failed to achieve clinically impactful remissions. In this study, we identified a mechanistic framework to explain these results. BRD9 depletion served to blunt proliferation in synovial sarcoma harboring minimal genomic alterations, rare in trial participants. In cultured cells, xenografts, and recombinant-purified complexes, BRD9 loss did not affect GBAF assembly. Although BRD9 degradation in synovial sarcoma reduced GBAF enrichment at target loci, BRD9-less complexes maintained or increased chromatin accessibility and associated gene transcription. Biochemical assays with purified recombinant GBAF demonstrated increased nucleosome sliding in the absence of BRD9. Together, these findings show that BRD9 restrains GBAF activity, with BRD9 degradation increasing enzymatic remodeling and target gene expression by fusion oncoprotein-distributed GBAFs in synovial sarcoma. This subtle epigenetic disturbance creates a low hurdle for synovial sarcoma to surpass, limiting the therapeutic efficacy of BRD9 degraders. SIGNIFICANCE: BRD9 represses the GBAF chromatin remodeling complex, which causes enhanced rather than disrupted SS18::SSX complex activity following BRD9 degradation and explains the lack of efficacy of pharmacological BRD9 degraders in synovial sarcoma.

Sarcoma, Synovial

Searching for new plastic-degrading enzymes from the plastisphere of alpine soils using a metagenomic mining approach.

Plastic materials, including microplastics, accumulate in all types of ecosystems, even in remote and cold environments such as the European Alps. This pollution poses a risk for the environment and humans and needs to be addressed. Using shotgun DNA metagenomics of soils collected in the eastern Swiss Alps at about 3,000 m a.s.l., we identified genes and their proteins that potentially can degrade plastics. We screened the metagenomes of the plastisphere and the bulk soil with a differential abundance analysis, conducted similarity-based screening with specific databases dedicated to putative plastic-degrading genes, and selected those genes with a high probability of signal peptides for extracellular export and a high confidence for functional domains. This procedure resulted in a final list of nine candidate genes. The lengths of the predicted proteins were between 425 and 845 amino acids, and the predicted genera producing these proteins belonged mainly to Caballeronia and Bradyrhizobium. We applied functional validation, using heterologous expression followed by enzymatic assays of the supernatant. Five of the nine proteins tested showed significantly increased activities when we used an esterase assay, and one of these five proteins from candidate genes, a hydrolase-type esterase, clearly had the highest activity, by more than double. We performed the fluorescence assays for plastic degradation of the plastic types BI-OPL and ecovio® only with proteins from the five candidate genes that were positively active in the esterase assay, but like the negative controls, these did not show any significantly increased activity. In contrast, the activity of the positive control, which contained a PLA-degrading gene insert known from the literature, was more than 20 times higher than that of the negative controls. These findings suggest that in silico screening followed by functional validation is suitable for finding new plastic-degrading enzymes. Although we only found one new esterase enzyme, our approach has the potential to be applied to any type of soil and to plastics in various ecosystems to search rapidly and efficiently for new plastic-degrading enzymes.

Humans

A comparative genomic study of a hydrocarbon-degrading marine bacterial consortium.

Ocean oil pollution has a large impact on the environment and the health of living organisms. Bioremediation cleaning strategies are promising eco-friendly alternatives for tackling this problem. Previously, we designed and reported a hydrocarbon (HC) degrading microbial consortium of four marine strains belonging to the species Alloalcanivorax xenomutans, Halopseudomonas aestusnigri, Paenarthrobacter sp., and Pseudomonas aeruginosa. However, the knowledge about the metabolic potential of this bacterial consortium for HC bioremediation is not yet well understood. Here, we analyzed the complete genomes of these marine bacterial strains accompanied by a phylogenetic reconstruction along with 138 bacterial strains. Synteny between complete genomes of the same species or genus, revealed high conservation among strains of the same species, covering over 91% of their genomic sequences. Functional predictions highlighted a high abundance of genes related to HC degradation, which may result in functional redundancy within the consortium; however, unique and complete gene clusters linked to aromatic degradation were found in the four genomes, suggesting substrate specialization. Pangenome gain and loss analysis of genes involved in HC degradation provided insights into the evolutionary history of these capabilities, shedding light on the acquisition and loss of relevant genes related to alkane and aromatic degradation. Our work, including comparative genomic analyses, identification of secondary metabolites, and prediction of HC-degrading genes, enhances our understanding of the functional diversity and ecological roles of these marine bacteria in crude oil-contaminated marine environments and contributes to the applied knowledge of bioremediation.

Biodegradation, Environmental

Investigating the degradation potential of microbial consortia for perfluorooctane sulfonate through a functional "top-down" screening approach.

Perfluorooctane sulfonate (PFOS) is a prominent perfluorinated compound commonly found in the environment, known to pose various risks to human health. However, the removal of PFOS presents significant challenges, primarily due to the limited discovery of bacteria capable of effectively degrading PFOS. Moreover, single degradation bacteria often encounter obstacles in individual cultivation and the breakdown of complex pollutants. In contrast, microbial consortia have shown promise in pollutant degradation. This study employed a continuous enrichment method, combined with multiple co-metabolic substrates, to investigate a microbial consortium with the potential for PFOS degradation. By employing this methodology, we effectively identified a microbial consortium that demonstrated the capacity to reduce PFOS when exposed to an optimal concentration of methanol. The consortium predominantly comprised of Hyphomicrobium species (46.7%) along with unclassified microorganisms (53.0%). Over a duration of 20 days, the PFOS concentration exhibited a notable decrease of 56.7% in comparison to the initial level, while considering the exclusion of adsorption effects. Furthermore, by comparing the predicted metabolic pathways of the microbial consortium with the genome of a known chloromethane-degrading bacterium, Hyphomicrobium sp. MC1, using the KEGG database, we observed distinct variations in the metabolic pathways, suggesting the potential role of the unclassified microorganisms. These findings underscore the potential effectiveness of a "top-down" functional microbial screening approach in the degradation of stubborn pollutants.

Fluorocarbons