Accurate Prediction of Rat Acute Oral Toxicity and Reference Dose for Thousands of Polycyclic Aromatic Hydrocarbon Derivatives Based on Chemometric QSAR and Machine Learning.

Acute oral toxicity is currently not available for most polycyclic aromatic hydrocarbons (PAHs), especially their derivatives, because it is cost-prohibitive to experimentally determine all of them. Here, quantitative structure-activity relationship (QSAR) models using machine learning (ML) for predicting the toxicity of PAH derivatives were developed, based on oral toxicity data points of 788 individual substances of rats. Both the individual ML algorithm gradient boosting regression trees (GBRT) and the stacking ML algorithm (extreme gradient boosting + GBRT + random forest regression) provided the best prediction results with satisfactory determination coefficients for both cross-validation and the test set. It was found that those PAH derivatives with fewer polar hydrogens, more large-sized atoms, more branches, and lower polarizability have higher toxicity. Software based on the optimal ML-QSAR model was successfully developed to expand the application potential of the developed model, obtaining reliable prediction of pLD50 values and reference doses for 6893 external PAH derivatives. Among these chemicals, 472 were identified as moderately or highly toxic; 10 out of them had clear environment detection or use records. The findings provide valuable insights into the toxicity of PAHs and their derivatives, offering a standard platform for effectively evaluating chemical toxicity using ML-QSAR models.

High-throughput single-molecule long-read RNA sequencing analysis of tissue-specific genes and isoforms in lettuce (Lactuca sativa L.).

Lettuce is one of the most widely cultivated and consumed dicotyledonous vegetables globally. Despite the availability of its reference genome sequence, lettuce gene annotation remains incomplete, impeding comprehensive research and the broad application of genomic resources. Long-read RNA isoform sequencing (Iso-Seq) offers substantial advantages for analyzing RNA alternative splicing and aiding gene annotation, yet it faces throughput limitations. We present the HIT-ISOseq method tailored for bulk sample analysis, significantly enhancing RNA sequencing throughput on the PacBio platform by concatenating cDNA. Here we show, HIT-ISOseq generates 3-4 cDNA molecules per CCS read in lettuce, yielding 15.7 million long reads per PacBio Sequel II SMRT Cell 8 M. We validate its effectiveness in analyzing six lettuce tissue samples, including roots, stems, and leaves, revealing tissue-specific gene expression patterns and RNA isoforms. Leveraging diverse tissue long-read RNA sequencing, we refine the transcript annotation of the lettuce reference genome, expanding its GO and KEGG annotation repertoire. Collectively, this study serves as a foundational reference for genome annotation and the analysis of multi-sample isoform expression, utilizing high-throughput long-read transcriptome sequencing.

Simultaneous biodegradation of polycyclic aromatic hydrocarbons and phthalates by bacterial consortium and its bioremediation for complex polluted soil and sewage sludge.

Simultaneous biodegradation of multiple micropollutantslike polycyclic aromatic hydrocarbons (PAHs) and phthalates (PAEs) by microbial consortia remain unclear. Here, four distinct bacterial consortia capable of degrading PAHs and PAEs were domesticated from sludge and its composts. PAH-degrading consortium HS and PAE-degrading consortium EC2 displayed the highest degradation efficiencies for PAHs (37 %-99 %) and PAEs (98 %-99 %), respectively, being significantly higher than those of individual member strains. Consortia HS and EC2 could simultaneously degrade both PAHs and PAEs. Remarkably, a synthetic consortium Syn by co-culturing consortia HS and EC2 demonstrated proficient simultaneous biodegradation for both PAHs (65 %-98 %) and PAEs (91 %-97 %). These consortia changed their community structure with enriching pollutant-degrading genera and extracellular polymeric substance contents to promote simultaneous biodegradation of multiple pollutants. Moreover, consortium Syn significantly enhanced degradation of both PAHs and PAEs in soil and sludge. This study provides strong candidates for simultaneous bioremediation of complex polluted environments by PAHs and PAEs.

Improving key gene expression and di-n-butyl phthalate (DBP) degrading ability in a novel Pseudochrobactrum sp. XF203 by ribosome engineering.

Di-n-butyl phthalate (DBP) is one of the important phthalates detected commonly in soils and crops, posing serious threat to human health. Pseudochrobactrum sp. XF203 (XF203), a new strain related with DBP biodegradation, was first identified from a natural habitat lacking human disturbance. Genomic analysis coupled with gene expression comparison assay revealed this strain harbors the key aromatic ring-cleaving gene catE203 (encoding catechol 2,3-dioxygenase/C23O) involved DBP biodegradation. Following intermediates identification and enzymatic analysis also indicated a C23O dependent DBP lysis pathway in XF203. The gene directed ribosome engineering was operated and to generate a desirable mutant strain XF203R with highest catE203 gene expression level and strong DBP degrading ability. The X203R removed DBP in soil jointly by reassembling bacterial community. These results demonstrate a great value of XF203R for the practical DBP bioremediation application, highlighting the important role of the key gene-directed ribosome engineering in mining multi-pollutants degrading bacteria from natural habitats where various functional genes are well conserved.

Mining flotation reagents: Quantitative and robust analysis of metal-xanthate complexes in water.

Xanthates, common mining flotation reagents, strongly bind thiophilic metals such as copper (Cu), lead (Pb), cadmium (Cd), and zinc (Zn) and consequentially change their bioavailability and mobility upon their discharge into the environment. However, accurate quantification of the metal-xanthate complexes has remained elusive. This study develops a novel and robust method that realizes the accurate quantification of the metal-xanthate complexes resulted from single and multiple reactions of three typical xanthates (ethyl, isopropyl, and butyl xanthates) and four thiophilic metals (Cu, Pb, Cd, and Zn) in water samples. This method uses sulfur (S2-) dissociation, followed by tandem solid phase extraction of C18 + PWAX and subsequent LC-MS/MS analysis. It has a wide linearity range (1-1000 µg/L, R2 ≥ 0.995), low method detection limits (0.002-0.036 µg/L), and good recoveries (70.6-107.0 %) at 0.01-10 mg/L of xanthates. Applications of this method showed ubiquitous occurrence of the metal-xanthate complexes as the primary species in flotation wastewaters, which the concentrations were 4.6-28.9-fold higher than those previously determined. It is the first quantitative method established for the analysis of metal-xanthate complexes in water samples, which is of great importance to comprehensively understand the fate and risks of xanthates in the environment.

Root-zone regulation and longitudinal translocation cause intervarietal differences for phthalates accumulation in vegetables.

Selecting and cultivating low-accumulating crop varieties (LACVs) is the most effective strategy for the safe utilization of di-(2-ethylhexyl) phthalate (DEHP)-contaminated soils, promoting cleaner agricultural production. However, the adsorption-absorption-translocation mechanisms of DEHP along the root-shoot axis remains a formidable challenge to be solved, especially for the research and application of LACV, which are rarely reported. Here, systematic analyses of the root surface ad/desorption, root apexes longitudinal allocation, uptake and translocation pathway of DEHP in LACV were investigated compared with those in a high-accumulating crop variety (HACV) in terms of the root-shoot axis. Results indicated that DEHP adsorption was enhanced in HACV by root properties, elemental composition and functional groups, but the desorption of DEHP was greater in LACV than HACV. The migration of DEHP across the root surface was controlled by the longitudinal partitioning process mediated by root tips, where more DEHP accumulated in the root cap and meristem of LACV due to greater cell proliferation. Furthermore, the longitudinal translocation of DEHP in LACV was reduced, as evidenced by an increased proportion of DEHP in the root apoplast. The symplastic uptake and xylem translocation of DEHP were suppressed more effectively in LACV than HACV, because DEHP translocation in LACV required more energy, binding sites and transpiration. These results revealed the multifaceted regulation of DEHP accumulation in different choysum (Brassica parachinensis L.) varieties and quantified the pivotal regulatory processes integral to LACV formation.

Congener-specific fate and impact of microcystins in the soil-earthworm system.

Microcystins (MCs) have a significant influence on aquatic ecosystems, but little is known about their terrestrial fate and impact. Here, we investigated the fate of two MCs (MC-LR and MC-RR) in the soil-earthworm system, with consideration of their congener-specific impact on earthworm health, soil bacteria, and soil metabolome. Although MCs had little acute lethal effect on earthworms, they caused obvious growth inhibition and setae rupture. Relative to MC-RR, MC-LR exhibited higher bioaccumulation and the resulting dermal lesions and deformation of longitudinal muscles. While the incorporation of both MCs into soils stimulated pathogenic bacteria and depressed oxidative stress tolerant bacteria, the response among soil nitrification and glutathione metabolism differed between the two congeners. The dissipation kinetics of MCs obeyed the first-order model. Earthworms stimulated soil N-cycling enzyme activities, increased the abundance of MC-degrading bacteria, and promoted bacterial metabolic functions related to glutathione metabolism, xenobiotics biodegradation, and metabolism of amino acids that comprise MCs, which accelerated the dissipation of MC-LR and MC-RR by 227% and 82%, respectively. These results provide evidence of significant congener differences in the terrestrial fate and impact of MCs, which will enable a better understanding of their role in mediating soil functions and ecosystem services.

Iron complex regulated synergistic effect between the current and peroxymonosulfate enhanced ultrafast oxidation of perfluorooctanoic acid via free radical dominant electrochemical reaction.

Iron complex regulated electrochemical reaction was triggered for revealing the reaction mechanism, degradation pathway, and applied potential of perfluorooctanoic acid (PFOA). The increased PMS concentrations, electrode spacing, and current density significantly enhanced PFOA elimination, with current density exhibiting a relatively strong interdependency to PFOA complete mineralization. The synergy between PMS and electrochemical reactions greatly accelerated PFOA decomposition by promoting the generation of key reaction sites, such as those for PMS activation and electrochemical processes, under various conditions. Furthermore, density functional theory calculations confirmed that the reciprocal transformation of Fe2+ and Fe3+ complexes was feasible under the electrochemical effect, further promoting the generation of active sites. The developed electrochemical oxidation with PMS reaction (EO/PMS) system can rapidly decompose and mineralize PFOA while maintaining strong tolerance to changing water matrices and organic and inorganic ions. Overall, it holds promise for use in treating and purifying wastewater containing PFOA.

Molecular insights into the catabolism of dibutyl phthalate in Pseudomonas aeruginosa PS1 based on biochemical and multi-omics approaches.

A comprehensive understanding of the molecular mechanisms underlying microbial catabolism of dibutyl phthalate (DBP) is still lacking. Here, we newly isolated a bacterial strain identified as Pseudomonas aeruginosa PS1 with high efficiency of DBP degradation. The degradation ratios of DBP at 100-1000 mg/L by this strain reached 80-99 % within 72 h without a lag phase. A rare DBP-degradation pathway containing two monobutyl phthalate-catabolism steps was proposed based on intermediates identified by HPLC-TOF-MS/MS. In combination with genomic and transcriptomic analyses, we identified 66 key genes involved in DBP biodegradation and revealed the genetic basis for a new complete catabolic pathway from DBP to Succinyl-CoA or Acetyl-CoA in the genus Pseudomonas for the first time. Notably, we found that a series of homologous genes in Pht and Pca clusters were simultaneously activated under DBP exposure and some key intermediate degradation related gene clusters including Pht, Pca, Xyl, Ben, and Cat exhibited a favorable coexisting pattern, which contributed the high-efficient DBP degradation ability and strong adaptability to this strain. Overall, these results broaden the knowledge of the catabolic diversity of DBP in microorganisms and enhance our understanding of the molecular mechanism underlying DBP biodegradation.

Arbuscular Mycorrhizal Fungus Alleviates Charged Nanoplastic Stress in Host Plants via Enhanced Defense-Related Gene Expressions and Hyphal Capture.

Contamination of small-sized plastics is recognized as a factor of global change. Nanoplastics (NPs) can readily enter organisms and pose significant ecological risks. Arbuscular mycorrhizal (AM) fungi are the most ubiquitous and impactful plant symbiotic fungi, regulating essential ecological functions. Here, we first found that an AM fungus, Rhizophagus irregularis, increased lettuce shoot biomass by 25-100% when exposed to positively and negatively charged NPs vs control, although it did not increase that grown without NPs. The stress alleviation was attributed to the upregulation of gene expressions involving phytohormone signaling, cell wall metabolism, and oxidant scavenging. Using a root organ-fungus axenic growth system treated with fluorescence-labeled NPs, we subsequently revealed that the hyphae captured NPs and further delivered them to roots. NPs were observed at the hyphal cell walls, membranes, and spore walls. NPs mediated by the hyphae were localized at the root epidermis, cortex, and stele. Hyphal exudates aggregated positively charged NPs, thereby reducing their uptake due to NP aggregate formation (up to 5000 nm). This work demonstrates the critical roles of AM fungus in regulating NP behaviors and provides a potential strategy for NP risk mitigation in terrestrial ecosystems. Consequent NP-induced ecological impacts due to the affected AM fungi require further attention.

Biodegradation of phthalate acid esters and whole-genome analysis of a novel Streptomyces sp. FZ201 isolated from natural habitats.

Di-n-butyl phthalate (DBP) is one of the most extensively used phthalic acid esters (PAEs) and is considered to be an emerging, globally concerning pollutant. The genus Streptomyces holds promise as a degrader of various organic pollutants, but PAE biodegradation mechanisms by Streptomyces species remain unsolved. In this study, a novel PAE-degrading Streptomyces sp. FZ201 isolated from natural habitats efficiently degraded various PAEs. FZ201 had strong resilience against DBP and exhibited immediate degradation, with kinetics adhering to a first-order model. The comprehensive biodegradation of DBP involves de-esterification, ß-oxidation, trans-esterification, and aromatic ring cleavage. FZ201 contains numerous catabolic genes that potentially facilitate PAE biodegradation. The DBP metabolic pathway was reconstructed by genome annotation and intermediate identification. Streptomyces species have an open pangenome with substantial genome expansion events during the evolutionary process, enabling extensive genetic diversity and highly plastic genomes within the Streptomyces genus. FZ201 had a diverse array of highly expressed genes associated with the degradation of PAEs, potentially contributing significantly to its adaptive advantage and efficiency of PAE degradation. Thus, FZ201 is a promising candidate for remediating highly PAE-contaminated environments. These findings enhance our preliminary understanding of the molecular mechanisms employed by Streptomyces for the removal of PAEs.

Profiles of visual perceptual learning in feature space.

Visual perceptual learning (VPL), experience-induced gains in discriminating visual features, has been studied extensively and intensively for many years, its profile in feature space, however, remains unclear. Here, human subjects were trained to perform either a simple low-level feature (grating orientation) or a complex high-level object (face view) discrimination task over a long-time course. During, immediately after, and one month after training, all results showed that in feature space VPL in grating orientation discrimination was a center-surround profile; VPL in face view discrimination, however, was a monotonic gradient profile. Importantly, these two profiles can be emerged by a deep convolutional neural network with a modified AlexNet consisted of 7 and 12 layers, respectively. Altogether, our study reveals for the first time a feature hierarchy-dependent profile of VPL in feature space, placing a necessary constraint on our understanding of the neural computation of VPL.

Root-associated bacteria strengthen their community stability against disturbance of antibiotics on structure and functions.

Antibiotics affect bacterial community structure and functions in soil. However, the response and adaptation of root-associated bacterial communities to antibiotic stress remains poorly understood. Here, rhizobox experiments were conducted with maize (Zea mays L.) upon exposure to antibiotics ciprofloxacin or tetracycline. High-throughput sequencing analysis of bacterial community and quantitative PCR analysis of nitrogen cycling genes show that ciprofloxacin and tetracycline significantly shift bacterial community structure in bulk soil, whereas plant host may mitigate the disturbances of antibiotics on bacterial communities in root-associated niches (i.e., rhizosphere and rhizoplane) through the community stabilization. Deterministic assembly, microbial interaction, and keystone species (e.g., Rhizobium and Massilia) of root-associated bacterial communities benefit the community stability compared with those in bulk soil. Meanwhile, the rhizosphere increases antibiotic dissipation, potentially reducing the impacts of antibiotics on root-associated bacterial communities. Furthermore, rhizospheric effects deriving from root exudates alleviate the impacts of antibiotics on the nitrogen cycle (i.e., nitrification, organic nitrogen conversion and denitrification) as confirmed by functional gene quantification, which is largely attributed to the bacterial community stability in rhizosphere. The present study enhances the understanding on the response and adaptation of root-associated bacterial community to antibiotic pollution.

Concurrent attention to hetero-depth surfaces in 3-D visual space is governed by theta rhythm.

When simultaneously confronted with multiple attentional targets, visual system employs a time-multiplexing approach in which each target alternates for prioritized access, a mechanism broadly known as rhythmic attentional sampling. For the past decade, rhythmic attentional sampling has received mounting support from converging behavioral and neural findings. However, so compelling are these findings that a critical test ground has been long overshadowed, namely the 3-D visual space where attention is complicated by extraction of the spatial layout of surfaces extending beyond 2-D planes. It remains unknown how attentional deployment to multiple targets is accomplished in the 3-D space. Here, we provided a time-resolved portrait of the behavioral and neural dynamics when participants concurrently attended to two surfaces defined by motion-depth conjunctions. To characterize the moment-to-moment attentional modulation effects, we measured perceptual sensitivity to the hetero-depth surface motions on a fine temporal scale and reconstructed their neural representations using a time-resolved multivariate inverted encoding model. We found that the perceptual sensitivity to the two surface motions rhythmically fluctuated over time at ~4 Hz, with one's enhancement closely tracked by the other's diminishment. Moreover, the behavioral pattern was coupled with an ongoing periodic alternation in strength between the two surface motion representations in the same frequency. Together, our findings provide the first converging evidence of an attentional "pendulum" that rhythmically traverses different stereoscopic depth planes and are indicative of a ubiquitous attentional time multiplexor based on theta rhythm in the 3-D visual space.

Insights into the molecular network underlying phytotoxicity and phytoaccumulation of ciprofloxacin.

Ciprofloxacin (CIP) is frequently detected in agricultural soils and can be accumulated by crops, causing phytotoxicities and food safety concerns. However, the molecular basis of its phytotoxicity and phytoaccumulation is hardly known. Here, we analyzed physiological and molecular responses of choysum (Brassica parachinensis) to CIP stress by comparing low CIP accumulation variety (LAV) and high accumulation variety (HAV). Results showed that the LAV suffered more severe inhibition of growth and photosynthesis than the HAV, exhibiting a lower tolerance to CIP toxicity. Integrated transcriptome and proteome analyses suggested that more differentially expressed genes/proteins (DEGs/DEPs) involved in basic metabolic processes were downregulated to a larger extent in the LAV, explaining its lower CIP tolerance at molecular level. By contrast, more DEGs/DEPs involved in defense responses were upregulated to a larger extent in the HAV, showing the molecular basis of its stronger CIP tolerance. Further, a CIP phytotoxicity-responsive molecular network was constructed for the two varieties to better understand the molecular mechanisms underlying the variety-specific CIP tolerance and accumulation. The results present the first comprehensive molecular profile of plant response to CIP stress for molecular-assisted breeding to improve CIP tolerance and minimize CIP accumulation in crops.

Response and adaptation of rhizosphere microbiome to organic pollutants with enriching pollutant-degraders and genes for bioremediation: A critical review.

Phytoremediation largely involves microbial degradation of organic pollutants in rhizosphere for removing organic pollutants like polycyclic aromatic hydrocarbons, phthalates and polychlorinated biphenyls. Microbial community in rhizosphere experiences complex processes of response-adaptation-feedback up on exposure to organic pollutants. This review summarizes recent research on the response and adaptation of rhizosphere microbial community to the stress of organic pollutants, and discusses the enrichment of the pollutant-degrading microbial community and genes in the rhizosphere for promoting bioremediation. Soil pollution by organic contaminants often reduces the diversity of rhizosphere microbial community, and changes its functions. Responses vary among rhizosphere microbiomes up on different classes of organic pollutants (including co-contamination with heavy metals), plant species, root-associated niches (e.g., rhizosphere, rhizoplane and endosphere), geographical location and soil properties. Soil pollution can deplete some sensitive microbial taxa and enrich some tolerant microbial taxa in rhizosphere. Furthermore, rhizosphere enriches pollutant-degrading microbial community and functional genes including different gene clusters responsible for biodegradation of organic pollutants and their intermediates, which improve the adaptation of microbiome and enhance the remediation efficiency of the polluted soil. The knowledge gaps and future research challenges are highlighted on rhizosphere microbiome in response-adaptation-feedback processes to organic pollution and rhizoremediation. This review will hopefully update understanding on response-adaptation-feedback processes of rhizosphere microbiomes and rhizoremediation for the soil with organic pollutants.

Mechanism and Association between Microbial Nitrogen Transformation in Rhizosphere and Accumulation of Ciprofloxacin in Choysum (Brassica parachinensis).

Rhizosphere microbiota are an important factor impacting plant uptake of pollutants. However, little is known about how microbial nitrogen (N) transformation in the rhizosphere affects the uptake and accumulation of antibiotics in plants. Here, we determined recruitment of N transformation functional bacteria upon ciprofloxacin (CIP) exposure, by comparing differences in assembly processes of both rhizospheric bacterial communities and N transformation between two choysum (Brassica parachinensis) varieties differing in CIP accumulation. The low accumulation variety (LAV) of CIP recruited more host bacteria (e.g., Nitrospiria and Nitrolancea) carrying nitrification genes (mainly nxrA) but fewer host bacteria carrying denitrification genes, especially narG, relative to the high accumulation variety (HAV) of CIP. The nxrA and narG abundance in the LAV rhizosphere were, respectively, 1.6-7.8 fold higher and 1.4-3.4 fold lower than those in the HAV rhizosphere. Considering that nitrate can decrease CIP uptake into choysum through competing for the proton motive force and energy, such specific bacteria recruitment in LAV favored the production and utilization of nitrate in its rhizosphere, thus limiting its CIP accumulation with 1.6-2.4 fold lower than the HAV. The findings give insight into the mechanism underlying low pollutant accumulation, filling the knowledge gap regarding the profound effects of rhizosphere microflora and N transformation processes on antibiotic accumulation in crops.

Highly Efficient and Simultaneous Analysis of Three Common Fluorotelomer Alcohols in Vegetables and Soils.

Fluorotelomer alcohols (FTOHs), as precursors of perfluoroalkyl carboxylic acids, are difficult to analyze due to their high volatility and matrix interference. A method based on single-factor experiments and response surface methodology design was developed for simultaneous analysis of three common FTOHs in vegetables and soils, using single extraction, dispersive solid phase extraction cleanup, and gas chromatography-mass spectrometry in negative chemical ionization. The method improved the extraction efficiency up to ∼40 folds and showed a commendable linearity range (1-100 ng/mL, R2 > 0.991), low limit of detection (0.025-0.897 ng/g, dry weight (dw)), and high accuracy and precision (83 ± 7.2-117 ± 6.0% recoveries at 2-20 ng/g fortification levels). It was successfully applied to determine the FTOHs in real vegetables and soils, demonstrating its feasibility for routine analysis. Concentrations of the FTOHs ranged from 3.5 to 37.9 ng/g (dw) and from 6.5 to 141.0 ng/g (dw), respectively, in the vegetables and soils collected nearby fluorochemical factories, which warrants further investigations on FTOH pollution and food safety concerns for which the developed method will be useful.

Substrate-enzyme interactions and catalytic mechanism in a novel family VI esterase with dibutyl phthalate-hydrolyzing activity.

Microbial degradation has been confirmed as effective and environmentally friendly approach to remediate phthalates from the environment, and hydrolase is an effective element for contaminant degradation. In the present study, a novel dibutyl phthalate (DBP)-hydrolyzing carboxylesterase (named PS06828) from Pseudomonas sp. PS1 was heterogeneously expressed in E. coli, which was identified as a new member of the lipolytic family VI. Purified PS06828 could efficiently degrade DBP with a wide range of temperature (25-37 °C) and pH (6.5-9.0). Multi-spectroscopy methods combined with molecular docking were employed to study the interaction of PS06828 with DBP. Fluorescence and UV-visible absorption spectra revealed the simultaneous presence of static and dynamic component in the fluorescence quenching of PS06828 by DBP. Synchronous fluorescence and circular dichroism spectra showed inconspicuous alteration in micro-environmental polarity around amino acid residues but obvious increasing of α-helix and reducing of ß-sheet and random coil in protein conformation. Based on the information on exact binding sites of DBP on PS06828 provided by molecular docking, the catalytic mechanism mediated by key residues (Ser113, Asp166, and His197) was proposed and subsequently confirmed by site-directed mutagenesis. The results can strengthen our mechanistic understanding of family VI esterase involved in hydrolysis of phthalic acid esters, and provide a solid foundation for further enzymatic modification.

Development, Evaluation, and Application of Machine Learning Models for Accurate Prediction of Root Uptake of Per- and Polyfluoroalkyl Substances.

Machine learning (ML) models were developed for understanding the root uptake of per- and polyfluoroalkyl substances (PFASs) under complex PFAS-crop-soil interactions. Three hundred root concentration factor (RCF) data points and 26 features associated with PFAS structures, crop properties, soil properties, and cultivation conditions were used for the model development. The optimal ML model, obtained by stratified sampling, Bayesian optimization, and 5-fold cross-validation, was explained by permutation feature importance, individual conditional expectation plot, and 3D interaction plot. The results showed that soil organic carbon contents, pH, chemical logP, soil PFAS concentration, root protein contents, and exposure time greatly affected the root uptake of PFASs with 0.43, 0.25, 0.10, 0.05, 0.05, and 0.05 of relative importance, respectively. Furthermore, these factors presented the key threshold ranges in favor of the PFAS uptake. Carbon-chain length was identified as the critical molecular structure affecting root uptake of PFASs with 0.12 of relative importance, based on the extended connectivity fingerprints. A user-friendly model was established with symbolic regression for accurately predicting RCF values of the PFASs (including branched PFAS isomerides). The present study provides a novel approach for profound insight into the uptake of PFASs by crops under complex PFAS-crop-soil interactions, aiming to ensure food safety and human health.