Journal of Hazardous Materials

The facultative methylotroph model organism Methylorubrum extorquens AM1 is a known lanthanide user, which has shed light on the role of rare-earth metals in biochemistry. The characterization of a methanol dehydrogenase (MDH) protein which requires lanthanides as an enzymatic cofactor outlined the question of how these metals are acquired from the environment. It has been proposed that mesophilic organisms as M. extorquens AM1 can produce siderophore-like molecules, which chelate, transport and traffic rare-earth elements into the microbial cell. Therefore, we performed the bioinformatic and chemical investigation of M. extorquens AM1 by using genome mining, the CAS and arsenazo assay, molecular networking and chemical analytical techniques. Our results showed that indeed Methylorubrum extorquens AM1 harbored a gene cluster to produce metal chelators. The chemical analysis confirmed the production of the known hybrid hydroxamate-citrate siderophores schizokinen A and N-deoxyschizokinen A, which are very likely the side products of the transformation of schizokinen and N-deoxyschizokinen. The determination of the lanthanide chelation activity of the schizokinen siderophores series against three different lanthanides (La, Eu and Lu) showed no coordination activity, thus ruling out the involvement of schizokinen siderophores in rare-earth metal transport.

Microbial ammonia oxidation, the first and rate-limiting step of nitrification, plays a central role in soil nitrogen cycling. It is most relevant in agricultural soils as nitrifiers compete with crops for ammonia-based fertilizers. Therefore, synthetic nitrification inhibitors are widely used alongside fertilizers to reduce the activities of dominant drivers of this process, i.e. ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the physiological responses of ammonia oxidizers remain poorly resolved. Here the response of the AOA Nitrososphaera viennensis to the nitrification inhibitors 3,4-dimethylpyrazole phosphate (DMPP) and allylthiourea (ATU) were investigated using a combination of functional genomics, physiological assays, and relief experiments. The results overturn earlier assumptions that DMPP and ATU act by chelating free copper. Both compounds affected ammonia oxidation and triggered broader shifts in energy metabolism and stress-response pathways, which diverged markedly between the two inhibitors. We propose a competitive inhibition of the ammonia monooxygenase complex with DMPP as it can be alleviated by additional ammonia and elicits activation of urea acquisition, while ATU acted as a non-competitive inhibitor generally inducing quiescence. Both modes of inhibition were associated with clear transcriptomic and proteomic signals that will be advantageous for the identification of mechanisms of other nitrification inhibitors in the future. Key word: Ammonia-oxidizing archaea, nitrification, nitrification inhibitors, archaea, nitrogen cycle

In recent years, the synergistic role of endocrine-disrupting chemicals (EDCs) and gut microbiota in the development of diabetes has been increasingly documented in rodent models. However, most studies have focused on one or two EDCs with varying doses and exposure durations, limiting the identification of a shared microbial signature associated with EDC-induced glucose dysregulation. This meta-analysis aimed to identify a common gut microbiome pattern across rodent studies involving diverse EDC exposures linked to glucose dyshomeostasis. A systematic search yielded 3,748 studies, of which ten met the inclusion criteria, comprising sequence data from 189 samples. These studies evaluated gut microbiota alterations in diabetes induced by various EDCs, including pesticides, food additives, and heavy metals, across different exposure conditions. Meta-analysis revealed a consistent reduction in microbial diversity and an increased Firmicutes/Bacteroidetes ratio following EDC exposure. At the phylum level, Firmicutes, Proteobacteria, Desulfobacterota, and Patescibacteria were significantly enriched. Although beneficial genera such as Lactobacillus, Bifidobacterium, and Akkermansia showed a decreasing trend, these changes were not statistically significant. In contrast, xenobiotic-associated genera including Desulfovibrio, Pseudomonas, Parasutterella, and Candidatus Saccharimonas were significantly increased. Notably, sulfate-reducing bacteria were the only inflammation-associated group consistently elevated. These microbial alterations were distinct from those observed in high-fat diet-induced diabetic models. This study identifies a distinct gut microbiome signature associated with EDC exposure in rodent models of glucose imbalance. These findings suggest unique microbiome-mediated pathways in EDC-induced diabetes and highlight potential microbial targets for early intervention in environmentally driven metabolic disorders.

Many agricultural soils are deficient in key macronutrients needed for healthy plant development. Relying on highly water-soluble commercial fertilizers for long durations can be costly and environmentally harmful. This study investigates a phosphorus-loaded Mg/Fe layered double hydroxide (LDH) dispersed on Douglas fir biochar (Mg/Fe-LDH biochar) as a controlled-release fertilizer and evaluates its impact on bush bean (Phaseolus vulgaris L.) growth. Emphasizing sustainability, the work integrates controlled-release fertilizers, biochar, and LDH modification to enhance nutrient use efficiency and mitigate environmental runoff. Mg/Fe-LDH was directly synthesized on biochar via a co-precipitation approach, loaded the composite with phosphate by anion exchange, and characterized the material using elemental analysis, N2 Brunauer-Emmett-Teller (BET) determinations surface area analysis, and x-ray photoelectron spectroscopy to confirm successful LDH modification on Douglas fir biochar, and high surface area with accessible active sites. The synthesis yielded a stable P-Mg/Fe-LDH biochar with enhanced dispersibility and phosphate-buffering capacity, enabling controlled-release fertilization. In greenhouse experiments, bush beans grown with the P-Mg/Fe-LDH biochar exhibited improved growth metrics, including increased yield (beans fresh weight of 31.7 g), biomass (plant dry weight of 6.3 g), plant height (32.8 cm), and improved nutrient uptakes (1.88 mg (P) g-1) at 100.88 kg (P2O5) ha-1 compared with unfertilized controls and conventional P fertilizers, indicating efficient, controlled-release phosphate delivery and sustained nutrient availability. The results demonstrate that integrating LDH-modified biochar can enhance P uptake and plant growth while reducing leaching losses. Overall, this study highlights the strategic significance of combining biochar, layered double hydroxides, and controlled-release formulations to advance sustainable nutrient management and improve crop performance in agroecosystems. The findings offer a promising pathway for environmentally conscious fertilizer design and soil amendment strategies that align with global goals for resource efficiency and food security. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/727001v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@316444org.highwire.dtl.DTLVardef@adcd48org.highwire.dtl.DTLVardef@8068aforg.highwire.dtl.DTLVardef@58d623_HPS_FORMAT_FIGEXP M_FIG C_FIG

Gold is widely distributed in the biosphere, and higher plants growing on geochemically anomalous substrates can accumulate significant amounts of gold. This study reports, for the first time from Goa, the detection, spectroscopic characterisation, and X-ray diffraction analysis of phytoformic gold -- biologically sequestered crystalline gold -- in the above-ground dry litter ash of six tree species (Acacia auriculiformis, Alstonia scholaris, Anacardium occidentale, Artocarpus heterophyllus, Ficus benghalensis, Syzygium cumini) growing on mining dumps within the North Goa Banded Iron Formation (BIF) Belt of the Western Dharwad Craton. Microgravimetric analysis of aqua regia-extracted heavy ash fractions revealed gold concentrations of 275-1100 ppm, two to five orders of magnitude above the crustal background ([~]0.004 ppm). Fourier Transform Infrared (FTIR) spectroscopy of 0.22{square}m membrane-filtered crude extracts confirmed the tetrachloroaurate(III) complex [AuCl{square}]{square} as the dominant dissolved gold species, with the diagnostic 1400-1700{square}cm{square}1 absorption envelope present in all six species. UV-Visible spectrophotometry confirmed chloroauric acid formation with a universal {lambda}max at 372.5{square}nm across all species. Powder X-ray diffraction (XRD) of heavy ash fractions yielded the characteristic FCC metallic gold reflections Au(111), Au(200), and Au(220) in all five species analysed. Application of the Debye-Scherrer equation to the Au(111) reflection (2{theta} = 38.2{degrees}, Cu K) established crystallite sizes of 17.7-31.8{square}nm, confirming that phytoformic gold exists as nanoscale crystalline particles in all species. Ficus benghalensis produced the largest and most crystalline gold nanoparticles (31.8{square}nm) and uniquely exhibited strawberry-shaped isomorphic auriferous siliceous biominerals designated phytoauroliths. The described low-cost protocol -- ashing, aqua regia extraction, membrane filtration, and multi-technique spectroscopic and diffraction confirmation -- constitutes a validated method for rapid biogeochemical gold anomaly detection. Applications in gold phytoextraction and mining waste phytoremediation are discussed.

Antibiotic residues exceeding selective concentrations for antibiotic-resistant bacteria have been detected in various environments, including manure, wastewater, and effluents from wastewater treatment plants. When these residues come into contact with soils, for instance, due to wastewater irrigation or fertilization with manure, they interact with soil constituents. Soil colloids (1-1000 nm), such as montmorillonite, have been observed to adsorb pharmaceuticals, including antibiotics. We investigated the effect of colloids on the bioavailability of ciprofloxacin and found, that added to bacterial growth medium, montmorillonite reduces, but does not completely prevent, the growth-inhibitory effect of the antibiotic. The bacteria were able to grow at up to roughly double the concentration of ciprofloxacin in the presence of montmorillonite. We show that the incomplete deactivation of ciprofloxacin was most probably caused by medium components that decreased the adsorption of ciprofloxacin to montmorillonite. We conclude that a selective potential of this highly active antibiotic in contaminated soils, which also contain nutrients enabling bacterial growth, cannot be ruled out. Environmental implicationAntibiotics such as ciprofloxacin are frequently detected in water bodies and soils due to wastewater irrigation or manure application. These residues raise concerns about environmental toxicity and antibiotic resistance. This study demonstrates that montmorillonite, a common clay mineral in soils, significantly reduces the antimicrobial efficacy of environmental ciprofloxacin concentrations by sorption. The findings reveal a natural attenuation mechanism that may influence the environmental fate and bioavailability of antibiotics. Understanding such interactions is critical for predicting antibiotic behavior in terrestrial systems and for designing more accurate environmental risk assessments.

Riverine ecosystems particularly in industrialized environment are subjected to chronic press disturbances, resulting from the decadal release of synthetic organic compounds and other xenobiotics. While indigenous microbial communities are highly sensitive to such stressors, the resulting metabolic restructuring and functional reshaping of the microbiome, driven by these long-term anthropogenic pressures remains poorly characterized. In this study, a microbial ecology of Bhadar River flowing across the Jetpur Industrial Estate, (Jetpur) were studied. Using a cross-sectional comparative approach, soil/sediment samples were collected from the diverse polluted and non-polluted sites from the estate. The taxonomic profiling using 16S rRNA gene amplicon sequencing, taxo-phenomic shifts (through metaphenomics) was studied, while the functional potential of metabolic pathways was validated using high-resolution shot-gun metagenomic study. Due to prolong pollution, the samples were rich in sulphur (9809 to 12391 mg/L), where polluted samples were having elevated COD (2432 to 4150 mg/L) as well as BOD (1000 to 1420 mg/L) values, along with the presence of heavy metals (e.g., Fe, Mg). Results revealed a distinct taxonomic shift at both the bacterial and archaeal levels. In non-polluted sites Proteobacteria (33 to 57%) dominated along with Acidobacteria and Actinobacteria, with diverse genera like Alcaligenes and Serratia. Whereas, polluted sites exhibited marked increase in Bacteroidetes (13 to 29%), Firmicutes, and Synergistetes and genera like Alkalitalea, Mesotoga and Desulfomicrobium, reflecting anaerobic, fermentative, and sulfate-reducing phenotypes. The archaeal communities at polluted sites were dominated by Euryarchaeota (78 to 99%), specifically methanogenic genera of Methanosaeta and Methanocalculus, contrasting with the Methanomassiliicoccus dominance in non-polluted areas. The alpha-diversity was marginally higher in polluted sites (Shannon: 4.11 to 4.81 vs. 3.81 to 5.39 (non-polluted)), but beta-diversity underscored clear separation (94% variance explained by pollution). The shot-gun metagenomic analysis indicated a substantial enhancement in anaerobic metabolic capacities within the polluted microbiome, primarily in sulphur respiration (dissimilatory sulfate reduction), methanogenesis (elucidating biogenic pathways), along with nitrogen cycling (identifying key denitrification and ammonification genes). The polluted microbiome have developed the potential to metabolise/degrade complex aromatic compounds (pcaK for benzoate/protocatechuate transport) and heavy metal resistance. The strong positive co-occurrences among anaerobic phyla (Thermotogae, Synergistetes, Bacteroidetes) in polluted sites was established, indicating syntrophic interactions for xenobiotic metabolism. These findings provide a theoretical ecological model for perturbed industrial ecosystems, emphasizing the role of habitat selection in shaping microbial functional diversity and demonstrate the remarkable adaptation of autochthonous communities to persistent press disturbances.

Micro- and nanoplastics (MNPs) are now recognized as ubiquitous dietary and environmental contaminants, yet practical strategies to reduce gastrointestinal exposure remain limited. This study evaluated whether Qi601, a heat-inactivated Limosilactobacillus fermentum biofilm-derived postbiotic, could bind plastic particles and reduce intestinal epithelial plastic burden. Prior probiotic studies have demonstrated live bacterial adsorption of MNPs and mitigation of MNP-associated toxicity in vivo; here, we evaluate whether a nonviable postbiotic preparation can produce analogous MNP-binding and epithelial-protective effects. Qi601 durably bound polystyrene nanoplastics under in vitro simulated digestion conditions. In Caco-2 intestinal epithelial monolayers, Qi601 reduced surface-associated and intracellular nanoplastic burden in both protection and rescue models, indicating decreased epithelial particle interaction both before and after established nanoplastic exposure. Multimodal imaging, including confocal microscopy, atomic force microscopy, and scanning electron microscopy, confirmed close physical association between Qi601 and nanoplastics. Finally, a first-in-human proof-of-concept chewing-gum study showed Qi601 binding in the human mouth to heterogeneous gum-derived microplastic fragments released during mastication. Together, these findings support the concept of postbiotic intervention for gastrointestinal epithelial protection against ingested MNPs.

Glyphosate, the worlds most widely used herbicide, targets the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which is conserved across plants and many bacteria. While its environmental effects are increasingly recognized, its role on antimicrobial resistance (AMR) remains incompletely understood. In particular, the link between intrinsic glyphosate sensitivity and AMR gene content or evolutionary dynamics has not been systematically explored. We examined the relationship between bacterial sensitivity to glyphosate, AMR profiles, and the evolution of AMR genes. We analyzed genome datasets from the human gut microbiota and the Alignable Tight Genomic Clusters (ATGC). EPSPS sequences were identified via BLAST and annotations and classified based on the intrinsic sensitivity to glyphosate using the EPSPSClass webserver. AMR genes, including associated drug classes and resistance mechanisms, were annotated using the Comprehensive Antibiotic Resistance Database (CARD). Across datasets, glyphosate-sensitive bacteria carried a greater diversity of AMR genes and mechanisms. In contrast, probabilistic modeling revealed that glyphosate-resistant bacteria accumulate AMR genes at significantly higher rates. Phylogenetic birth-and-death analyses and stochastic mapping further revealed elevated AMR gene gain, loss, expansion, and reduction in resistant strains. These results indicate a decoupling between AMR gene diversity and evolutionary dynamics: sensitive bacteria maintain more resistance genes, whereas resistant bacteria display accelerated AMR gene turnover. This suggests that glyphosate resistance is linked to increased genome dynamics, potentially enhancing bacterias adaptability under combined herbicide and antimicrobial pressures. Given glyphosates extensive agricultural use and potential human exposure, these findings highlight an underappreciated link between herbicide resistance and the evolution of AMR in bacterial populations.

Black Soldier Fly larvae (BSFL, Hermetia illucens) are highly effective for the bioconversion of food waste. However, their rearing process often produces substantial ammonia emissions, which are malodorous and environmentally concerning. We investigated the co-cultivation of BSFL with the sulfur-oxidizing bacterium Thiobacillus thioparus as a strategy to mitigate ammonia release. Importantly, under conditions where ammonia emissions were significantly reduced, neither larval growth nor bacterial viability was negatively affected. Furthermore, even when the initial bacterial inoculum was reduced to 3.3*105 CFU/g-food wastes, the bacterium rapidly recovered to functional levels and effectively controlled ammonia emissions. This indicates the absence of harmful interaction or nutrient competition between BSFL and T. thioparus. These findings suggest an efficient method for controlling ammonia in large-scale BSFL waste treatment. By reducing the required bacterial inoculum, this approach enables scalable microbial co-culturing with environmental and production benefits.

BackgroundBenzene, toluene, ethylbenzene, and xylene (BTEX) are volatile aromatic hydrocarbons that are widespread environmental pollutants arising from petroleum processing, fuel combustion, and other industrial activities. Persistent BTEX contamination poses substantial risks to human health and ecosystems, underscoring the need for effective long term remediation strategies. Microbial bioremediation is a promising and sustainable approach for BTEX removal, but development of these approaches requires accurate detection of the genes and pathways responsible for substrate specific degradation. Although profile hidden Markov model (HMM) databases are widely used for functional annotation, existing annotation resources lack the substrate-specific resolution needed to distinguish between closely-related BTEX-degrading enzymes with different catalytic specificities. ResultsWe developed BTEXgenie as a sensitive annotation tool that uses custom HMMs built from alignments of experimentally validated BTEX degradation proteins to identify genes involved in the initial steps of aerobic and anaerobic BTEX degradation. BTEXgenie improved detection of anaerobic BTEX degradation genes that were absent from KOfam annotations. In benchmarking against the KEGG KOfam HMM database, BTEXgenie achieved 17.73%higher overall sensitivity while maintaining comparable specificity at 97.02%across genes involved in BTEX degradation pathways. When applied to environmental metagenomes, BTEXgenie recovered pathway patterns consistent with reported site characteristics and known degradation potential. In addition to gene annotation, BTEXgenie supports downstream interpretation through KEGG pathway-based visualization of detected functions and Circos-based visualization of genomic hit distributions. ConclusionsBTEXgenie is a substrate-specific annotation tool built from custom HMMs for detecting genes involved in BTEX degradation. By integrating gene annotation with pathway and genome-level visualizations, BTEXgenie facilitates characterization of microbial BTEX degradation potential in environmental and comparative genomic studies.

Pregnant women are frequently exposed to various endocrine-disrupting chemicals (EDCs), such as bisphenol A (BPA), causing harm to both the developing placenta and fetus. BPA can promote placental dysfunction by altering key cellular processes such as differentiation, invasion, and migration in trophoblast cells. These cellular processes are also tightly managed by the ubiquitin proteasomal system via maintenance of the ubiquitinated protein pool. However, the BPA-mediated dysregulation of this ubiquitin proteasomal homeostasis is poorly understood. Therefore, we identified 19 deubiquitinases (DUBs) and a dynamic ubiquitinome profile of extravillous trophoblast cells (HTR8/SVneo), which reduced trophoblast cell migration post-BPA exposure. Further investigation using an integrated substrate-ligase-deubiquitinase network shows that BPA binding to PPAR-alpha or indirect regulation of its E3 Ligase MuRF1 and DUB USP5 via BPA resulted in hyper-ubiquitination of PPAR-alpha, triggering its nuclear localization. In the nucleus, the ubiquitinated PPAR-alpha can deregulate its migration-associated target gene expression, causing a reduction in the migration of HTR8/SVneo cells. This physiological alteration of extravillous trophoblast cells (EVTs) through BPA can disrupt placental homeostasis. Hence, we assumed that BPA-induced cellular alteration in EVTs can promote placental defects, which might contribute to adverse pregnancy outcomes.

Brown rot wood-degrading fungi release carbon (C) from deadwood but leave behind a large fraction of C sequestered in lignin residues or as fungal metabolites. The strength of sequestration in these C residuals remains unclear, but proteobacteria-dominated bacterial communities have been implicated in metabolizing C from decay residues, possibly erasing the C sequestration potential assumed for brown rot. Here, we paired a model brown rot fungus (Rhodonia placenta) with a model Alphaproteobacterium (Rhodopseudomonas palustris) to track fungal release and bacterial utilization of C derived from decaying wood. We found that fungal decay products generated by R. placenta could be used by R. palustris for growth, and later decay stages contained more usable substrates than early stages. High performance liquid chromatography with mass spectrometry identified a range of aromatic and non-aromatic compounds in the fungal-decayed wood, but after 95 days of bacterial growth, R. palustris preferentially consumed non-aromatic acids over aromatic lignin monomers. Genes involved with aromatic compound degradation were unimportant for bacterial growth, and RNA sequencing revealed that aromatic compound degradation genes were repressed on decayed wood extract. Randomly barcoded transposon sequencing failed to identify a solitary catabolic pathway used by R. palustris, suggestive of substrate co-utilization, and surprisingly, showed that genes involved with copper toxicity were essential. Finally, we found that genes involved with biosynthesis of certain cofactors and amino acids were no longer essential on decayed wood extract, suggesting these nutrients were readily accessible. This study helps lay the foundation to understand potential bacterial-fungal interactions in decayed wood. Graphical abstractTo explore how brown rot fungi support and compete with bacterial partners in the wood decay environment, the model brown rot fungus Rhodonia placenta was used to degrade aspen wafers which were then infused into bacterial growth medium. By leveraging the range of molecular biology tools available for the model Alphaproteobacterium Rhodopseudomonas palustris, we discovered that R. palustris preferentially consumes short organic acids instead of aromatic lignin monomers which it would otherwise consume if provided in isolation. Additionally, R. palustris scavenged certain amino acids (AAs) and enzyme cofactors including methionine, biotin, and PLP from the decayed wood extract, highlighting these as key shared resources for bacterial-fungal partnerships. We found that R. placenta increased the concentration of certain metals (Cu and Al) inducing a metal stress response in R. palustris, indicating that metal toxicity could be an important mode of competition between fungi and bacteria in the wood decay environment. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/723453v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@16f31fcorg.highwire.dtl.DTLVardef@13a9b34org.highwire.dtl.DTLVardef@a37dcforg.highwire.dtl.DTLVardef@198bf1c_HPS_FORMAT_FIGEXP M_FIG C_FIG

Benzo[a]pyrene (BaP), a representative polycyclic aromatic hydrocarbon (PAH), is a widespread environmental toxicant and potent ligand of the aryl hydrocarbon receptor (AHR). Yet, how early developmental exposure to BaP influences human neurodevelopment remains poorly understood. We first examined AHR expression dynamics during human embryonic stem cell (ESC)-derived cerebral organoid development and found that AHR expression was highest at the ESC stage and declined during subsequent differentiation, suggesting a potential window of heightened susceptibility to AHR-mediated environmental perturbations. Based on this observation, ESCs were exposed to BaP (0.1, 1 M) for 7 days prior to organoid generation. BaP exposure did not alter proliferation, cell death, or global transcription of ESCs but increased expression of a subset of AHR target genes. Remarkably, however, organoids derived from BaP-exposed ESCs exhibited profound morphological defects resulting from premature neurogenesis, characterized by disrupted neural rosette organization, reduced EOMES intermediate progenitors, and increased BCL11B neurons. Pharmacological inhibition of AHR with CH-223191 attenuated AHR activation and rescued the progenitor-neuron imbalance. These findings identify AHR signaling as a critical upstream mediator of BaP-induced developmental neurotoxicity and highlight the vulnerability of early pluripotent stages to environmental insults.

Until now, there has been no animal-free alternative method for predicting chronic inflammation and delivering the associated dose responses, the timing of onset, and the duration of inflammation, as required by regulatory agencies. We present the results of pre-validation of an in-vitro-learned digital twin (InFiniteLungDT) capable of predicting chronic neutrophilic lung inflammation for regulatory use. The method is based on measuring the dynamics of early biological effects in vitro induced by respirable materials or their mixtures, without the need to know their intrinsic properties. We constructed the digital twin(s) for each of the material, for which we have in vivo exposure data. The instillation data set, comprising 49 different nanomaterials, was used as the primary anchor to calibrate the model. Inhalation data set, comprising 7 different nanomaterials, compliant with OECD TG 412, was used to show the general applicability of the method across species and for different exposure scenaria. In total, about 3094 single mouse exposures and 364 rat exposures (and approx. 775/225 non-exposed mouse/rat controls) were used to predict concentration-dependent time-evolved neutrophil influx into the lung. The accuracy (predictive capacity) of LOAEL determination is 93% for instillation and 84% for inhalation exposure. Taking into account the time-to-deliver-result being less than 1 week, this proves that the effect of inhaled material from acute to chronic conditions can be assessed orders of magnitude faster and cheaper than in a reference animal study.

Fluorinated chemicals are increasingly prevalent in pharmaceuticals and agrochemicals, yet their influence on the human gut microbiome and the potential for microbial biotransformation to alter therapeutic and toxicological profiles remain poorly understood. Here, we investigated the bidirectional relationship between 15 structurally diverse fluorinated chemicals and the gut microbiota by using an ex vivo high-throughput fermentation system. Screening revealed that flutamide, fluazinam, and pretomanid were consistently biotransformed across the donor microbiomes, while other compounds showed substantial inter-individual variability in degradation. Furthermore, exposure to fluorinated chemicals induced compound-specific shifts in microbial diversity and community composition, demonstrating their capacity to alter gut microbial ecology. Using a computational workflow combining in silico biotransformation predictions with untargeted LC-MS/MS analysis, we identified nitroreduction as the primary gut microbial transformation across all three compounds. Single-strain experiments confirmed that the nitroreduction of flutamide to flu-6, previously attributed only to hepatic metabolism, is a widespread capacity among gut bacterial strains. Finally, in vitro cytotoxicity assays and in silico modelling further revealed flu-6 to be a less hepatotoxic derivative than the parent compound, suggesting a potential detoxifying role for the gut microbiota. Together, these findings establish an integrated ex vivo, in vitro, and in silico approach for assessing the bidirectional interactions between fluorinated chemicals and the gut microbiome.

Plant growth promoting microbes enhance developmental progression of the host by influencing its nutrient availability or by deploying secondary metabolites responsible for manipulating the hormonal crosstalk. Microbacterium bengalense sp. nov. GB16_1_BI (Accession number: SRX9280401), a newly identified ammonium releasing Actinomycetota, could enhance plant growth by manipulating rhizosphere bacteria. Amplicon sequencing of the 16S rRNA V3-V4 region from the rhizosphere of the black rice (Chakhao Poireiton) showed that GB16_1_BI could inhibit most bacteria. However, GB16_1_BI inoculation encouraged the growth of rare bacteria specific to waterlogged rice rhizosphere. Analysis of the OTUs using PICRUSt2 (Phylogenetic investigation of communities by reconstruction of unobserved states) showed increased abundance in the marker genes for nitrogen cycling (nifH, nrfA and nrt) but not for nifD or nifK which was also reflected in the ANOSIM analysis in the OTUs of the N-fixing bacteria. Marker genes for methane metabolism (comA, comB, cofG and cofH) were also more abundant in the inoculated plants than the control; however, ANOSIM studies did not support this observation in the OTUs of methane cycling bacteria. Both Methylosinus and Methylocystis, the two most abundant methanotrophic OTUs, are also known to be nitrogen fixers. Hence, GB16_1_BI could influence plant growth predominantly by manipulating nitrogen cycling microbes. The genome sequence as well as untargeted metabolome analyses of GB16_1_BI showed abundance of secondary metabolites with probable antimicrobial activity. GB16_1_BI could utilize varied carbohydrates and amino acid as energy source and form persister-like cells may help it to survive in the soil in absence of the host plant.

Pesticides are ubiquitous in agroecosystems and pose substantial risks to non-target organisms. Traditional ecotoxicological assessments focus on survival, reproduction, or overt behavior, yet these endpoints may fail to detect subtle, molecular-level stress. Here, we investigated the effects of sublethal deltamethrin exposure on the head proteome of field-collected European earwig (Forficula auricularia) females, sampled at two life stages (pre-oviposition and post-family life) to account for physiological context. Our results reveal that deltamethrin induces a robust proteomic response shared across developmental stages, including the regulation of key detoxification enzymes (NADPH- cytochrome P450 reductase, arginine kinase). In parallel, stage-specific responses were observed, involving proteins related to metabolism, stress response, and cellular organization. Strikingly, these molecular perturbations occurred without detectable changes in reproductive traits, highlighting a disconnect between cellular stress and organismal phenotypes. Several uncharacterized proteins were consistently regulated, representing promising targets for future studies on pesticide adaptation and potential detoxification pathways. Overall, these findings suggest that classical phenotypic assays may underestimate sublethal pesticide effects, and that proteomic profiling provides a sensitive framework to uncover underlying molecular responses. By integrating natural variability, realistic exposure, and reproductive physiology, our study emphasizes the need for molecular approaches in environmental risk assessment and offers a new perspective on the subtle, cryptic effects of agrochemicals.

INTRODUCTIONMounting evidence support exposome influences on brain function and health, complementing genome influences. Understanding the molecular imprint of exposome on brain metabolism and the biochemical communication between the body and brain can impact our fundamental understanding and treatment of neuropsychiatric diseases. METHODSLeveraging two complementary metabolomics platforms, we classified 1400 features in 514 brains from the ROSMAP collection. We evaluated the origin of these compounds using literature and databases. We correlated those metabolites with cognitive function using linear models. RESULTSWe identified over 230 non-endogenous compounds in the brain, including 103 drugs and metabolites, 120 dietary and microbial products and possibly 15 compounds from environmental exposures. Over 20 dietary and gut microbial compounds showed associations with cognition. DISCUSSIONComprehensive profiling of chemicals in the brain and the link to cognitive function provides foundational work to connect body and brain in the study of AD and related dementias.

Quaternary ammonium compounds (QACs) are high production volume biocidal compounds increasingly scrutinized for their potential to promote antimicrobial resistance spread. This study compared the release of QACs, QAC resistance indicator genes (qacE/qacE{Delta}1), and QAC tolerant bacteria from livestock and human waste streams into the environment. Five livestock farms with on-farm biogas plants (BGPs), a rural and an urban municipal wastewater treatment plant (WWTP) were studied in parallel. In WWTPs, <1% of incoming QACs were discharged with treated wastewater but 10-20% were transferred to sewage sludge. QAC concentrations in sewage sludge far exceeded those in raw and digested manure. The qacE/qacE{Delta}1 genes were detected in all samples with a higher relative abundance in solid than liquid samples. Relative abundances of QAC tolerant fast growing heterotrophic bacteria cultivated under high nutrient conditions at 37{degrees}C were higher in human than livestock waste streams. Providencia and Pseudomonas dominated the cultivated QAC tolerant bacteria in both systems but showed higher QAC tolerance when originating from human waste streams. Additionally, Enterobacteriaceae with higher QAC tolerance were cultivated from human waste streams. Most QAC tolerant strains carried antibiotic resistances without strong system differences. Only few strains carried the qacE/qacE{Delta}1 gene indicating that other mechanisms must be responsible for the increased QAC tolerance. In conclusion, QACs, qacE/qacE{Delta}1, and viable QAC tolerant bacteria including potential pathogenic bacteria were released from livestock and human waste streams into the environment with highest abundances in a post-pandemic sewage sludge sample. Highlights- QACs most abundant in human waste streams, especially biosolids - Higher relative abundance of QAC tolerant bacteria in human waste streams - Pseudomonas and Providencia dominated QAC tolerant bacteria in both waste streams - Enterobacteriaceae with higher QAC tolerance abundant in human waste streams - Most QAC tolerant strains carried additional antibiotic resistances Environmental implicationMunicipal wastewater treatment plants (WWTPs) and livestock farms are hotspots for antimicrobial resistance (AMR) propagation. We compared the simultaneous occurrence of quaternary ammonium compounds (QACs), resistance genes (RGs), QAC-tolerant bacteria, and their multidrug-resistance status in livestock and human waste streams. QACs, indicators of QAC tolerance and AMR occurred in both systems but were higher in WWTPs, especially sewage sludge. Our findings highlight the need for prudent disinfectant use and enhanced waste treatments to reduce the risks of spreading micropollutants, pathogens, and AMR via organic fertilizers or treated wastewater recycled in circular agricultural practice.