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Proteomics in environmental pollution research: Advances, challenges, and future directions.

Environmental proteomics has emerged as a powerful approach for elucidating the molecular mechanisms underlying pollutant-induced biological effects. Although this field has developed rapidly, the systematic review of recent proteomics applications in environmental pollution research remains limited. This review explored the emerging roles of toxicoproteomics in biomarker discovery and mechanistic elucidation, as well as ecotoxicoproteomics in ecological risk assessment and bioremediation strategies. Here, we review the field, highlighting recent trends such as the integration of proteomics with genomics, transcriptomics, and metabolomics to provide a comprehensive view of biological responses to environmental stressors. We further discuss the growing application of artificial intelligence in improving proteomics data interpretation and accelerating biomarker discovery. In addition, recent technological advances in environmental proteomics are highlighted, including next-generation tissue microarray proteomics, nanoscale proteomics, single-cell proteomics, and spatial proteomics. Despite its potential, proteomics faces challenges, such as high operational costs, computational complexity in analysis, and technical limitations in low-abundance protein detection. We propose that the convergence of proteomics with artificial intelligence and multi-omics approaches offers promising solutions to these challenges, enhancing the practical application of proteomics in environmental monitoring and risk assessment.

Proteomics

The regulative role of food consumption in the induction of rat liver cell proliferation by drugs and environmental pollutants.

alpha-hexachlorocyclohexane (alpha-HCH) was used to stimulate cell proliferation in rat liver. Food consumption at two different stages of the replicative cycle was found to be required for the enhancement of DNA synthesis by this agent: (1) Before or at the time of alpha-HCH administration (G0), (2) 12--15 hours later, i.e. 5--8 hours before initiation of DNA synthesis ("R"-point). Other alpha-HCH mediated changes in the liver i.e. organ enlargement and the induction of drug-metabolising enzymes, remained unaffected by the absence of food. This suggests that the nutritional control is specific for induction of DNA synthesis. It is concluded that food consumption, in addition to specific stimuli of liver growth, is an exogenous regulator of liver cell proliferation.

Animals

Environmental pollutants and the epidemiology of cancer.

Cancer etiology involves the interplay of genetic and environmental factors. Striking geographic differences and changes in cancer incidence over time have led epidemiologists to infer that probably the major etiologic component is environmental. Recent experiences with vinyl chloride, kepone, and polybrominated biphenyl illustrate the problems involved in epidemiologic studies of proven or suspected environmental carcinogens. While epidemiologic studies will continue to be an essential means for monitoring potential human risks, the long latent periods involved in human carcinogenesis severely limit the usefulness of such approaches for disease prevention. While in vitro and animal test systems can never fully supplant human studies, they represent our only means for detecting potential carcinogenicity before human exposure has become widespread or long established.

Animals

A cross-sectional study of oxidative stress pathway genotypes and their interactions with environmental pollutant levels identifies associations with gene expression and lung function.

BACKGROUND: Asthma is a heterogeneous disease influenced by genetic and environmental factors. Fine particulate matter (PM2.5) exacerbates asthma, likely through oxidative stress pathways, but whether genetic variation modifies this effect remains unclear. METHODS: We analysed data on 948 adults with asthma from the Severe Asthma Research Program (SARP), linking ZIP-code-level PM2.5 exposure with whole-genome sequencing data. We tested 4337 single nucleotide polymorphisms (SNPs) in 120 oxidative stress pathway genes for gene-environment (GxE) interactions with PM2.5 on lung function (forced expiratory volume in 1 s [FEV1] % predicted) using weighted linear regression. Gene expression data from bronchial epithelial cells (n = 170) were used to assess cis-expression quantitative trait loci (eQTLs). FINDINGS: Higher PM2.5 exposure was associated with lower FEV1% predicted (β per μg/m3 = -0.7, p = 0.01). We identified 20 SNPs across seven genes (OXSR1, PXDN, TPO, LRRK2, APP, MSRA, MSRB2) with significant GxE interactions after multiple-testing correction. Five SNPs were also eQTLs, linking PM2.5-modified gene expression to lung function. Minor alleles in OXSR1 and PXDN were associated with reduced gene expression and worsened FEV1% under high PM2.5 exposure. Conversely, TPO variants were associated with higher baseline expression and lower lung function, but under increasing PM2.5 exposure, minor allele carriers showed suppressed TPO expression and improved FEV1%. INTERPRETATION: This study identified 20 SNPs in oxidative stress pathway genes that modify the effect of PM2.5 on lung function in asthma. These findings highlight the importance of integrating environmental context in genetic studies and suggest potential therapeutic targets for pollution-sensitive asthma phenotypes. FUNDING: Supported by NIH grants.

Cross-Sectional Studies

Microorganisms as indices of environmental pollution by smelting industry.

The aim of the study was to prove suitability of some microbiological tests for determination of the degree of soil pollution by copper industry. The microbiological tests reveal sensitivity to metal compounds present in dusts emitted by smelters. The sensitivity of the selected strains to the dust present in the agar medium and soil has been determined and 30 strains, of which 50% reacted to the presence of 1--2 g of the dust in medium, were recommended for the tests. The tests showed accumulation of heavy metals contained in the dust mainly in the upper soil horizons and the highest pollution with the dust approximately 800 m away from the emitor in northeastern direction, which is the direction of prevailing winds of that area. The results obtained are in accordance with theoretical assumption as well as with the literature based on chemical analyses of polluted soil.

Bacteria

Bioprospecting Chromobacterium violaceum for bioremediation: an alternative to environmental lead pollution.

Lead pollution is a major environmental concern, but current decontamination technologies remain limited due to high costs. Therefore, alternative biotechnological processes have been successfully developed and applied due to their reduced cost and lower aggressiveness in the environment. The remarkable adaptive versatility of Chromobacterium violaceum in metal-contaminated environments makes this bacterium a promising candidate for Pb bioremediation. Therefore, the reference strain C. violaceum ATCC 12,472 and the environmental isolate C. violaceum SCV1, the first strain of this species isolated from a Brazilian area with natural Pb occurrence, were evaluated for Pb resistance under different Pb concentrations and exposure times. Pb biosorption was assessed by scanning electron microscopy, while strain-specific protein profiles were characterized using tandem mass spectrometry-based proteomic analysis. The results obtained revealed the potential of C. violaceum to perform lead bioremediation. Scanning electron microscopy analysis confirmed the biosorption of lead by C. violaceum strains. C. violaceum SCV1 was able to remove up to 40% more lead concentration when compared to ATCC 12,472 which suggested adaptation through natural selection process of C. violaceum SCV1. Proteome analysis revealed 1531 proteins, of which several are candidates for lead bioremediation. This is the first study on the resistance proteomics of C. violaceum against lead. The acclimatization of the bacteria linked to the identification of several proteins related to: biosorption; efflux and ionic uptake (bioaccumulation); biomolecule transport; and biomethylation, point out to this organism as a potential lead bioremediation agent.

Chromobacterium

Epigenetic alterations in bioaccumulators of cadmium: Lessons from mammalian kidneys and plants.

Faced with unpredictable changes in global weather patterns, release and redistribution of metals through land erosion and water movements add to the increasing use of metals in industrial activities causing high levels of environmental pollution and concern to the health of all living organisms. Cadmium is released into the environment by smelting and mining, entering the food chain via contaminated soils, water, and phosphate fertilizers. Bioaccumulation of cadmium in plants represents the first major step into the human food chain and contributes to toxicity of several organs, especially the kidneys, where biomagnification of cadmium occurs over decades of exposure. Even in small amounts, cadmium brings about alterations at the molecular and cellular levels in eukaryotes through mutagenicity, molecular mimicry at metal binding sites and oxidative stress. The epigenome dictates expression of a gene's output through a number of regulatory steps involving chromatin remodeling, nucleosome unwinding, DNA accessibility, or nucleic acid modifications that ultimately impact the transcriptional and translational machinery. Several epigenetic enzymes exhibit zinc-dependence as zinc metalloenzymes and zinc finger proteins thus making them susceptible to deregulation through displacement by cadmium. In this review, we summarize the literature on cadmium-induced epigenetic mechanisms in mammalian kidneys and plants, compare similarities in the epigenetic defense between these bioaccumulators, and explore how future studies could advance our understanding of the cadmium-induced stress response and disruption to biological health.

Cadmium

Measurement of the responses of individuals to environmental stress and pollution: studies with bivalve molluscs.

Certain physiological differences between individuals in different populations of the mussel, Mytilus edulis, are described. In particular, the scope for growth differs in space and time and may be used to assess the animals' physiological condition. When the required measurements are made in the field, the rates of growth predicted from the physiological data agree well with observed rates of growth. An alternative approach utilizes mussels transplanted to various waters, with indices of condition then measured in then measured in the laboratory under standard conditions; an example of this approach is illustrated. Laboratory experiments are used to equate various levels of physiological condition with fecundity, in an attempt to equate physiological effects on the individual with likely population damage. A cytochemical index of stress is described, based on the latency of lysosomal enzymes; spatial variability in this index, and its relation with the scope for growth, are discussed. Finally, the results of some experiments on the effects of petroleum hydrocarbons on mussels are described and the presence of inducible activity of NADPH-dependent tetrazolium reductase in the blood cells is demonstrated. Certain considerations that apply in adopting similar measurements of biological effects of pollution in environmental monitoring programmes are discussed.

Animals

Antimony species-dependent enrichment and transcriptional activity of antibiotic and metal resistance genes in the gut microbiome of male mice.

The gut microbiome is a reservoir for antibiotic resistance genes (ARGs) and is sensitive to environmental pollutants. ARGs in environmental and host-associated microbiomes can be enriched by metal(loid)s through co-selection with metal resistance genes (MRGs). However, as a ubiquitous toxic metalloid, antimony (Sb) induced alterations of ARGs in the gut microbiome and the underlying mechanisms remain unclear. Here, by integrating genome-resolved metagenomics and metatranscriptomics, we characterized the genomic potential and transcriptional activity of ARGs and MRGs in the gut microbiome of mice exposed to Sb(III)- and Sb(V)-contaminated drinking water. We found that both Sb(III) and Sb(V) significantly increased ARGs abundance, whereas only Sb(III) enhanced ARGs transcription (288.40&#x202f;&#xb1;&#x202f;41.67 TPM, P&#x202f;<&#x202f;0.05). Co-selection of ARGs and MRGs was observed through metagenome-assembled genomes (MAGs) analysis, and key taxa driving this process were identified (e.g., Eubacterium_J and Lachnospiraceae_COE1). Sb(III), but not Sb(V), induced co-regulation of macrolide-lincosamide-streptogramin resistance genes and arsRABC operon. A potentially higher risk of ARG dissemination under Sb(III) stress was suggested by the increased abundance and transcription of mobile genetic elements (MGEs). This study advances our understanding of the interactions between Sb and ARGs in the gut microbiome and highlights the potential chemical species-dependent enrichment and transcriptional activation of ARGs.

Antibiotic resistance gene

Exploring perceptions and willingness to recycle wastes among small businesses in selected townships of the Gauteng province in South Africa.

Although small businesses play an important role in generating employment opportunities and local economic development, their involvement in recycling programs has not been characterized in greater detail. This study explored the perceptions and willingness of selected small businesses in Gauteng province townships to reuse or recycle some of their waste materials. This study used a quantitative research approach to explore the perceptions and willingness of selected small businesses to reuse or recycle some of the waste they generate. The results showed that the perceptions about the contribution of recycling to environmental pollution reduction among small businesses in the study differed significantly across the townships (&#x3c7;2&#x2009;=&#x2009;6.892, p&#x2009;=&#x2009;0.003). On the other hand, most formal businesses significantly agreed with the potential benefits of waste recycling on environmental pollution reduction (&#x3c7;2&#x2009;=&#x2009;16.118, p&#x2009;=&#x2009;0.003), saving landfill space (&#x3c7;2&#x2009;=&#x2009;11.610, p&#x2009;=&#x2009;0.003), improving environmental quality (&#x3c7;2&#x2009;=&#x2009;10.443, p&#x2009;=&#x2009;0.005), and providing job opportunities (&#x3c7;2&#x2009;=&#x2009;10.263, p&#x2009;=&#x2009;0.036). However, regardless of their formality (&#x3c7;2&#x2009;=&#x2009;2.957, p&#x2009;=&#x2009;0.228) or location (&#x3c7;2&#x2009;=&#x2009;9.463, p&#x2009;=&#x2009;0.051), there was no statistically significant variation in the recycling practices of the small businesses in this study. Moreover, businesses' willingness to use recycling facilities if they were located nearby differed across townships (0.05 > p&#x2009;=&#x2009;0.010) but was similar despite the formality of the enterprises. In conclusion, recycling perceptions and willingness of small businesses can vary significantly depending on whether they are formal or informal and across townships. As a result, relevant educational interventions should be uniquely developed to raise awareness about the need for waste minimization through recovery, re-use, and recycling among small businesses in the Gauteng province.Implications: Small, Medium, and Micro enterprises (SMMEs) play a crucial role in local economic development in South Africa. However, research on their environmental sustainability is scarce, despite their significant impacts on natural resources and contributions to pollution. Most waste management studies have focused on households and municipalities, leaving a gap in understanding SMMEs' waste management behaviors, particularly in townships.

South Africa

Laboratory model ecosystem evaluation of the chemical and biological behavior of radiolabeled micropollutants.

A standardized laboratory model ecosystem has been used to evaluate the comparative behavior of radiolabeled micropollutants including organochlorine, organophosphorus, carbamate, and hormone-mimic insecticides; herbicides; important industrial organic compounds including phthalate esters and PCB's; and specific pollutants such as TCBD and hexachlorobenzene. The compounds have been studies for ecological effects over a terrestrial-aquatic interface and through several food chains, especially with regard to the development of quantitative information on ecological magnification and biodegradability index. The pathways of chemical degradation in the various organisms have been evaluated and the ecological effects of degradation products investigated. Illustrations are given of the use of the model ecosystem technology for screening new candidate pesticides for effects on environmental quality; for evaluating the hazards of environmental pollution by industrial waste effluents; and for fundamental studies of the principles fo biodegradability of organic chemicals in a variety of organisms.

Animals

Small noncoding RNAs and sperm nuclear basic proteins reflect the environmental impact on germ cells.

BACKGROUND: Molecular techniques can complement conventional spermiogram analyses to provide new information on the fertilizing potential of spermatozoa and to identify early alterations due to environmental pollution. METHODS: Here, we present a multilevel molecular profiling by small RNA sequencing and sperm nuclear basic protein analysis of male germ cells from 33 healthy young subjects residing in low and high-polluted areas. RESULTS: Although sperm motility and sperm concentration were comparable between samples from the two sites, those from the high-pollution area had a higher concentration of immature/immune cells, a lower protamine/histone ratio, a reduced ability of sperm nuclear basic proteins to protect DNA from oxidative damage, and an altered copper/zinc ratio in sperm. Sperm levels of 32 microRNAs involved in intraflagellar transport, oxidative stress response, and spermatogenesis were different between the two areas. In parallel, a decrease of Piwi-interacting RNA levels was observed in samples from the high-polluted area. CONCLUSIONS: This comprehensive analysis provides new insights into pollution-driven epigenetic alterations in sperm not detectable by spermiogram.

Male

Longitudinal dynamics of gene expression and metabolomics in an aging population cohort.

Multiomic profiling provides a comprehensive physiological overview at the molecular level, but understanding of its spatiotemporal dynamics remains limited in human populations. We profiled longitudinal whole-blood gene expression and metabolite levels in 335 females over 8 years. Levels of 5061 genes and 181 metabolites changed over time, with individual trajectories often diverging from population-level trends. Longitudinally variable genes showed cell type specificity and enrichment for aging-relevant pathways, including cardiometabolic and neurodegenerative disorders. Longitudinal trajectories were further shaped by genetics, circadian rhythm, seasonality, and environmental pollutant exposures. Integrative analyses revealed extensive static and time-variable cross-omic connectivity. Longitudinal profiling offers insight into the temporal evolution of age-related conditions at the molecular level, and understanding individual variation within these longitudinal patterns will be essential for future precision medicine approaches.

Female

Deodorization of pig feces by actinomycetes.

Peg feces, a malodorous substance causing environmental pollution, were completely deodorized within 2 days by Streptomyces. The optimum conditions for deodorization were as follows: pH, 8.6 to 10; temperature, 35 to 40 degrees C; moisture content, 42 to 63%; and minimum amount of inoculum, 2 g of seed culture per 10 g of fresh feces. Many kinds of microorganisms were isolated from the deodorized feces, of which only actinomycetes were found to have the ability to deodorize. Two strains with strong deodorizing activity were identified as Streptomyces griseus and Streptomyces antibioticus. The low-molecular-weight fatty acids, which are the specific malodorous agents of pig feces, scarcely could be found in feces deodorized by the isolated strains. Chemical analysis showed that the deodorized feces are useful as manure.

Animals

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