Polyethylene (PE) is the most produced synthetic polymer and as a result, a major source of microplastic waste accumulating globally. Exposure to photo- and thermo-oxidative conditions in the environment can cause PE to degrade into carbonyl-containing compounds, hydrocarbons, and low molecular weight PE (LMWPE). In both marine and freshwater ecosystems, fish, including Atlantic salmon, can ingest PE and its derivatives, creating opportunities for interactions with their gut microbes. Here, we investigated the ability of a bacterial isolate from the gut of salmon, Rhodococcus sp002259485 strain ASF-10, to grow on an LMWPE model substrate for partially depolymerized and oxidized PE. Comparative genomic analyses showed that ASF-10 has a smaller genome than other Rhodococcus species yet retaining conserved functions including those related to utilization of medium- and long-chain hydrocarbons. In-depth characterization of the substrate following growth with ASF-10 confirmed depletion of alkanes and 2-ketones deriving from LMWPE, while the polymeric component remained unchanged. Proteomic analysis identified multiple enzymes that were likely to be involved in the degradation of LMWPE-derivatives, including an alkane 1-monooxygenase, cytochrome P450 hydroxylases and Baeyer-Villiger monooxygenases, as well as proteins for production of biofilm and a surfactant that may enhance accessibility to the substrate. Collectively, our findings advance the understanding of the ecology and enzymatic mechanisms underlying utilization of medium- to long-chain alkanes and oxidized variants thereof, that resemble molecules that can occur from abiotic PE degradation, by a fish gut-associated microbe. This metabolic capacity could be harnessed to develop sustainable strategies for bioremediation of oxidized, LMWPE-derivatives. Importance: The widespread presence of plastics in marine and freshwater environments has raised concerns due to their toxicity when ingested by fish. Microbial mechanisms driving breakdown of microplastic components, such as LMWPE and derivatives, in gut systems remain poorly understood. This study reveals how a bacterium isolated from the gut of salmon, Rhodococcus sp002259485 strain ASF-10, metabolizes alkanes and oxidized variants thereof, that can result from abiotic PE decomposition. We identified key enzymes that are potentially involved in this process as well as in the production of biofilm and surfactants that may facilitate access to the substrate. Besides extending the knowledge of the enzymatic basis for degradation of PE-derivatives in gut-associated microbes from aquatic organisms, our results provide a framework that couples advanced compositional characterization of the substrate with omics techniques, offering valuable insight to support future studies aimed at unequivocally identifying microbes and their enzymes implicated in transformation of PE-derivatives.

Polyethylene (PE) is the most produced synthetic polymer and, consequently, a major source of microplastic waste accumulating globally. Exposure to photo- and thermo-oxidative conditions in the environment can promote PE degradation into carbonyl-containing compounds, hydrocarbons, and low-molecular-weight PE (LMWPE). In both marine and freshwater ecosystems, fish, including Atlantic salmon, can ingest PE and its derivatives, creating opportunities for interactions with their gut microbes. Here, we investigated the capacity of a bacterial isolate from the salmon gut, Rhodococcus sp002259485 strain ASF-10, to grow on an LMWPE model substrate for partially depolymerized and oxidized PE. Comparative genomic analyses showed that ASF-10 has a smaller genome than other Rhodococcus species yet retains conserved functions, including those related to utilization of medium- and long-chain hydrocarbons. In-depth characterization of the substrate following growth with ASF-10 confirmed depletion of alkanes and 2-ketones deriving from LMWPE, whereas the polymeric component remained unchanged. Proteomic analysis identified multiple enzymes likely involved in the degradation of LMWPE derivatives, including an alkane 1-monooxygenase and cytochrome P450 hydroxylases, as well as proteins for the production of biofilm and a surfactant that may enhance accessibility to the substrate. The bacterium was detected as metabolically active in a metatranscriptomic data set derived from freshwater-reared salmon. Collectively, our findings advance the understanding of the ecology and enzymatic mechanisms underlying the utilization of medium- to long-chain alkanes and oxidized variants thereof, that resemble molecules that can occur from abiotic PE degradation, by a fish gut-associated microbe. This metabolic capacity could be harnessed to develop sustainable strategies for bioremediation of LMWPE derivatives. IMPORTANCE: The widespread presence of plastics in marine and freshwater environments has raised concerns due to their toxicity when ingested by fish. Microbial mechanisms driving the breakdown of microplastic components, such as low-molecular-weight polyethylene (LMWPE) and derivatives, in gut systems remain poorly understood. This study reveals how a bacterium isolated from the gut of salmon, Rhodococcus sp002259485 strain ASF-10, metabolizes alkanes and oxidized variants thereof that can result from abiotic PE decomposition. We identified key enzymes that are potentially involved in this process, as well as in the production of biofilm and surfactants that may facilitate access to the substrate. Besides extending the knowledge of the enzymatic basis for the degradation of PE derivatives in gut-associated microbes from aquatic organisms, our results provide a framework that couples advanced compositional characterization of the substrate with omics techniques, offering valuable insight to support future studies aimed at unequivocally identifying microbes and their enzymes implicated in the transformation of PE derivatives.

Crude oil, primarily consisting of alkanes, and plastic derivatives are integral to modern society, yet their widespread use has led to persistent pollution that devastates ecosystems worldwide. Enzymatic and microbial biodegradation are highly desirable to become alternatives to conventional methods for the control of these pollutants in terrestrial and aquatic environments. Consequently, investigating the enzymatic machinery of specialized microbes that thrive in contaminated areas and possess the catabolic potential to degrade alkanes and plastics is of considerable interest. In this study, we present a genomic and proteomic analysis of Acinetobacter towneri RMS-02 that was isolated from sludge obtained from mixed food waste and sewage. Consistent with its ability to grow and persist in this environment, the genome of A. towneri RMS-02 encodes enzymes to catabolize different types of polyphenols and aromatic compounds, including trans -cinnamic acid, o -cresol, toluene, benzene, and benzoate. In addition, it encodes serine proteases, metallopeptidase, and transporters facilitating the uptake of amino acids and possibly small peptides, as well as enzymes potentially involved in the depolymerization of alkanes and 2-ketones. Proteomics analysis of A. towneri RMS-02 revealed an extensive repertoire of enzymes involved in terminal and subterminal oxidation of medium- and long-chain alkanes and ketones, which were specifically more abundant during growth on a product that consists of a mixture of these compounds and an oxidized low-molecular-weight polyethylene (LMWPE). Substrate characterization following bacterial growth confirmed the selective utilization of alkanes with chain lengths of C10–C25 and 2-ketones of C13–C26, while the polymeric fraction of the substrate remained unaltered. IMPORTANCE: Crude oil and plastic pollution threaten ecosystems worldwide, creating an urgent need for sustainable remediation strategies. Microbial and enzymatic degradation provides a sustainable alternative to physical, chemical, and thermal treatments by biologically breaking down hydrocarbons into harmless products or recyclable monomers. Here, we describe a detailed genomic characterization of A. towneri RMS-02, identifying core metabolic functions underlying its potential to utilize phenols, aromatic compounds, proteins, and small-chain hydrocarbons. Using proteomics, we show that a diverse enzymatic arsenal is deployed when growing on an oxidized LMWPE product that includes a mixture of alkanes and 2-ketones. Remarkably, the proteomics results were corroborated by advanced analysis of the spent substrate, confirming that A. towneri RMS-02 metabolizes alkanes and 2-ketones but is unable to interact with the polymeric LMWPE component. Our results expand the understanding of the metabolic repertoire supporting Acinetobacter towneri ’s survival and identify candidate enzymes with potential for the bioremediation of alkanes and 2-ketones.

Aquaculture is a rapidly growing industry, with Atlantic salmon being one of the most intensively farmed food-producing fish in the world. While the gut microbiota is recognized to play an important role in the health and performance of various fish, knowledge of its functional capacities in salmon is gradually expanding, facilitating a better understanding of host–microbiome interactions. Nevertheless, data on the gut microbiota of juvenile salmon remain limited. Here, we isolated and genotypically characterized 11 bacteria obtained from the gut content of Atlantic salmon fry. Whole-genome sequencing using long-read Nanopore technology and functional annotation revealed their extensive metabolic versatility, including a broad array of carbohydrate-active enzymes, proteases, lipases, and (poly)phenol-degrading enzymes potentially contributing to the metabolism of feed-derived components. Additionally, all isolates possessed genomic potential for producing beneficial metabolites, including the short-chain fatty acids acetate and propionate, as well as several B vitamins and vitamin K2. Genes encoding bacteriocins and other secondary metabolites were identified, suggesting niche competitiveness against intestinal pathogens. Among the isolates, we further show that Lactococcus raffinolactis ASF-5 has the potential to selectively remove indigestible oligosaccharides from plant-based feeds. Indeed, this isolate grew on raffinose, an oligosaccharide associated with anti-nutritional effects in salmon. Using AlphaFold 3 models, we show that this capability is supported by a GH36 α-galactosidase and two GH32 sucrases, which can act cooperatively in the complete hydrolysis of raffinose. Finally, L. raffinolactis ASF-5 had a favorable safety profile for use as a feed supplement, showing susceptibility to all tested antibiotics and lacking hemolytic activity. IMPORTANCE: Although metataxonomy studies have enhanced our knowledge of the salmon gut microbiota, the functional potential of bacteria from this ecosystem remains underexplored. Well-characterized bacterial isolates are crucial to advance the growing salmon aquaculture field, allowing insights into nutrient metabolism, informing the development of beneficial interventions, and helping in identifying enzymes to improve feed digestibility. This study highlights the functional capacity of 11 bacteria isolated from the gut of salmon fry in contributing to the metabolism of carbohydrates, proteins, lipids, fatty acids, and (poly)phenols from feed, potentially increasing nutrient availability for the host or providing beneficial metabolites, including short-chain fatty acids, vitamins, and bacteriocins. Importantly, Lactococcus raffinolactis ASF-5 could be used to remove indigestible sugars like raffinose from plant meals. Identifying such beneficial, host-specific bacteria opens new opportunities for developing customized feed supplements or enzymes that enhance feed digestibility, to promote the health and welfare of Atlantic salmon, and enhance the economic sustainability of aquaculture.

PSA testing plays an important role in the diagnostic workup of prostate cancer; despite this, its cancer specificity is a well-recognised limitation. Consequently, more reliable, non-invasive diagnostic tools that are capable of improving specificity while maintaining sensitivity are needed, thereby enabling better risk stratification, personalised patient management, and reduction in unnecessary invasive procedures. In this study, we characterised the small RNA profile—including miRNAs and tsRNAs—in seminal small extracellular vesicles (sEVs) using high-throughput sequencing to expand biomarker discovery for distinguishing benign from malignant prostate conditions in patients with moderately elevated PSA levels, a setting where non-invasive biomarkers are critically needed. Our analysis confirms a small number of differentially represented sncRNA transcripts contained in seminal sEVs between benign and malignant prostate disease, most of which are of low abundance. This result suggests that shared underlying molecular mechanisms are likely to occur between both prostate disease conditions, especially in patients with moderate PSA levels. Subsequent RT-qPCR analysis revealed differences in expression in PCa compared with healthy controls but not when compared with benign prostatic disease. Given the complexity of the underlying pathophysiological process and the heterogeneity in clinical phenotypes, this limitation was addressed through the application of multivariate approaches (including isomiRs or tRFs), which are proposed as fluid-based biomarkers for prostate cancer, collectively offering improved accuracy and enhancing the negative predictive value of PSA used in clinical settings.