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.

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.

Variety-Selective Rhizospheric Activation, Uptake, and Subcellular Distribution of Perfluorooctanesulfonate (PFOS) in Lettuce (Lactuca sativa L.).

Perfluorooctanesulfonate (PFOS) as an accumulative emerging persistent organic pollutant in crops poses severe threats to human health. Lettuce varieties that accumulate a lower amount of PFOS (low-accumulating crop variety, LACV) have been identified, but the regarding mechanisms remain unsolved. Here, rhizospheric activation, uptake, translocation, and compartmentalization of PFOS in LACV were investigated in comparison with those of high-accumulating crop variety (HACV) in terms of rhizospheric forms, transporters, and subcellular distributions of PFOS. The enhanced PFOS desorption from the rhizosphere soils by dissolved organic matter from root exudates was observed with weaker effect in LACV than in HACV. PFOS root uptake was controlled by a transporter-mediated passive process in which low activities of aquaporins and rapid-type anion channels were corrected with low expression levels of PIPs (PIP1-1 and PIP2-2) and ALMTs (ALMT10 and ALMT13) genes in LACV roots. Higher PFOS proportions in root cell walls and trophoplasts caused lower root-to-shoot transport in LACV. The ability to cope with PFOS toxicity to shoot cells was poorer in LACV relative to HACV since PFOS proportions were higher in chloroplasts but lower in vacuoles. Our findings provide novel insights into PFOS accumulation in lettuce and further understanding of multiprocess mechanisms of LACV.

Oxalic Acid in Root Exudates Enhances Accumulation of Perfluorooctanoic Acid in Lettuce.

Perfluorooctanoic acid (PFOA) is bioaccumulative in crops. PFOA bioaccumulation potential varies largely among crop varieties. Root exudates are found to be associated with such variations. Concentrations of low-molecular-weight organic acids (LMWOAs) in root exudates from a PFOA-high-accumulation lettuce variety are observed significantly higher than those from PFOA-low-accumulation lettuce variety (p < 0.05). Root exudates and their LMWOAs components exert great influences on the linear sorption-desorption isotherms of PFOA in soils, thus activating PFOA and enhancing its bioavailability. Among root exudate components, oxalic acid is identified to play a key role in activating PFOA uptake, with >80% attribution. Oxalic acid at rhizospheric concentrations (0.02-0.5 mM) can effectively inhibit PFOA sorption to soils by decreasing hydrophobic force, electrostatic attraction, ligand exchange, and cation-bridge effect. Oxalic acid enhances dissolution of metallic ions, iron/aluminum oxides, and organic matters from soils and forms oxalate-metal complexes, based on nuclear magnetic resonance spectra, ultraviolet spectra, and analyses of metal ions, iron/aluminum organometallic complexes, and dissolved organic carbon. The findings not only reveal the activation process of PFOA in soils by root exudates, particularly oxalic acid at rhizospheric concentrations, but also give an insight into the mechanism of enhancing PFOA accumulation in lettuce varieties.

Rice root exudates enhance desorption and bioavailability of phthalic acid esters (PAEs) in soil associating with cultivar variation in PAE accumulation.

Phthalic acid esters (PAEs) is a class of prevalent pollutants in agricultural soil, threating food safety through crop uptake and accumulation of PAEs. Accumulation of PAEs varies largely among crop species and cultivars. Nevertheless, how root exudates affect PAE bioavailability, dissipation, uptake and accumulation is still not well understood. In the present study, desorption and pot experiments were designed to investigate how root exudates from high-(Peizataifeng) and low-(Fengyousimiao) PAE accumulating rice cultivars affect soil PAE bioavailability, dissipation, and accumulation variation. Rice root exudates including low molecular weight organic acids (LMWOAs) of Peizataifeng and Fengyousimiao could enhance desorption of two typical PAE compounds, di-n-butyl phthalate (DBP) and di-(2-ethylhexyl) phthalate (DEHP), from aged soil to their available fractions by increasing soil dissolved organic carbon (DOC), thus improving their bioavailability in soil. Peizataifeng produced twice higher amounts of oxalic acid, critic acid and malonic acid in root exudates, and exhibited stronger effects on enhancing desorption and bioavailability of DBP and DEHP than Fengyousimiao. Higher (by about 50%) total organic carbon contents of root exudates from Peizataifeng led to higher (by 10-30%) soil microbial biomass carbon and nitrogen than Fengyousimiao, and thus promoted more PAE dissipation from soil than Fengyousimiao. Nevertheless, higher (by 20-50%) soil DOC and significantly higher PAE bioavailability in the soils planted Peizataifeng resulted in greater (by 53-93%) PAE accumulation in roots and shoots of Peizataifeng than Fengyousimiao, confirming by higher (by 1.82-3.48 folds) shoot and root bioconcentration factors of Peizataifeng than Fengyousimiao. This study reveals that the difference in root exudate extent and LMWOAs between Peizataifeng and Fengyousimiao differentiates PAE accumulation.

Dynamics, thermodynamics, and mechanism of perfluorooctane sulfonate (PFOS) sorption to various soil particle-size fractions of paddy soil.

Soil is an important sink for perfluorooctane sulfonate (PFOS) that is a typical persistent organic pollutant with high toxicity. Understanding of PFOS sorption to various particle-size fractions of soil provides an insight into the mobility and bioavailability of PFOS in soil. This study evaluated kinetics, isotherms, and mechanisms of PFOS sorption to six soil particle-size fractions of paddy soil at environmentally relevant concentrations (0.01-1 µg/mL). The used soil particle-size fractions included coarse sand (120.4-724.4 mm), fine sand (45.7-316.2 mm), coarse silt (17.3-79.4 mm), fine silt (1.9-39.8 mm), clay (0.5-4.4 mm), and humic acid fractions (8.2-83.7 mm) labeled as F1~F6, respectively. PFOS sorption followed pseudo-second-order kinetics related to film diffusion and intraparticle diffusion, with speed-limiting phase acted by the latter. PFOS sorption isotherm data followed Freundlich model, with generally convex isotherms in larger size fractions (F1~F3) but concave isotherms in smaller size fractions (F4 and F5) and humic acid fraction (F6). Increasing organic matter content, Brunner-Emmet-Teller surface area, and smaller size fractions were conducive to PFOS sorption. Hydrophobic force, divalent metal ion-bridging effect, ligand exchange, hydrogen bonding, and protein-like interaction played roles in PFOS sorption. But hydrophobic force controlled the PFOS sorption, because its relevant organic matter governed the contribution of the soil fractions to the overall PFOS sorption. The larger size fractions dominated the PFOS sorption to the original soil because of their high mass percentages (~80%). This likely caused greater potential risks of PFOS migration into groundwater and bioaccumulation in crops at higher temperatures and ce values, based on their convex isotherms with an exothermic physical process.

AM fungi increase uptake of Cd and BDE-209 and activities of dismutase and catalase in amaranth (Amaranthus hypochondriacus L.) in two contaminants spiked soil.

Soil co-contaminated with cadmium (Cd) and decabromodiphenyl ether (BDE-209) is a widespread environmental problem, especially in electronic waste contaminated surroundings. Accumulation of Cd and BDE-209 in crops has possibly harmful effects on local human health. In order to assess the potential of arbuscular mycorrhizal (AM) fungi and amaranth (Amaranthus hypochondriacus L.) in remediation of soil co-contaminated with Cd and BDE-209, pot trials were performed to investigate interactive effects of AM fungi, Cd and BDE-209 on growth of amaranth, uptake of Cd and BDE-209, distribution of chemical forms of Cd and activities of antioxidant enzymes in shoots and dissipation of BDE-209 in soil. The present results showed that shoot biomass of non-mycorrhizal plants was significantly inhibited by increasing of Cd addition (5-15 mg kg-1), but were only slightly declined with BDE-209 addition (5 mg kg-1). The interaction of Cd and BDE-209 reduced the proportions of ethanol- and d-H2O-extractable Cd in shoots, consequently alleviated Cd toxicity to plants and enhanced root uptake of Cd and BDE-209. Inoculation of AM fungi resulted in significantly greater shoot biomass as well as higher concentrations of Cd and BDE-209 compared with non-mycorrhizal treatment. Moreover, AM fungi played a beneficial role in relieving oxidative stress on amaranth by increasing the activities of dismutase (SOD) and catalase (CAT) in shoots and significantly improved the dissipation of BDE-209 in soil. The present study suggested that combination of AM fungi and amaranth may be a potential option for remediation of Cd and BDE-209 co-contaminated soils.

Distribution, diastereomer-specific accumulation and associated health risks of hexabromocyclododecanes (HBCDs) in soil-vegetable system of the Pearl River Delta region, South China.

The distribution and diastereomeric profiles of hexabromocyclododecanes (HBCDs, identified as persistent organic pollutants) in soil-vegetable system of open fields remain unknown. In this study, three main HBCD diastereoisomers (α-, ß-, and γ-HBCDs) were analyzed in paired soil and vegetable samples from vegetable farms in four cities (Guangzhou, Jiangmen, Huizhou, Foshan) of the Pearl River Delta region, Southern China. The sum concentrations of the three diastereoisomers (∑HBCDs) in soils varied from 0.99 to 18.4 ng/g (dry weight) with a mean of 5.77 ng/g, decreasing in the order of Jiangmen > Guangzhou > Huizhou > Foshan. The distributions of HBCDs in both soil and vegetable were diastereomer-specific, with γ-HBCD being predominant. The ∑HBCDs in vegetables ranged from 0.87 to 32.7 ng/g (dry weight) with a mean of 16.6 ng/g, generally higher than those of the corresponding soils. Thus bioconcentration factors (BCFs, the ratio of contaminant concentration in vegetable to that in soil) of HBCDs were generally greater than 1.0, implying higher accumulation in vegetable. The estimated daily intake (EDI) of ΣHBCDs via consumption of vegetables varied from 0.26 to 9.35 ng/kg bw/day with a mean of 3.60 ng/kg bw/day for adults and from 0.32 to 11.5 ng/kg bw/day with a mean of 4.41 ng/kg bw/day for Children, far lower than the oral reference dose (RfD, 2 × 105 ng/kg bw/day) proposed by US National Research Council. These results suggest that HBCD in the vegetables posed low health risk for the local population. These data are the first report on HBCD occurrence and health risk in soil-vegetable system of open fields.

Soil contamination and sources of phthalates and its health risk in China: A review.

Phthalates (PAEs) are extensively used as plasticizers and constitute one of the most frequently detected organic contaminants in the environment. With the deterioration of eco-environment in China during the past three decades, many studies on PAE occurrence in soils and their risk assessments have been conducted which allow us to carry out a fairly comprehensive assessment of soil PAE contamination on a nation-wide scale. This review combines the updated information available associated with PAE current levels, distribution patterns (including urban soil, rural or agricultural soil, seasonal and vertical variations), potential sources, and human health exposure. The levels of PAEs in soils of China are generally at the high end of the global range, and higher than the grade II limits of the Environmental Quality Standard for soil in China. The most abundant compounds, di-n-butyl phthalate (DBP) and di-(2-ethylhexyl) phthalate (DEHP), display obvious spatial distribution in different provinces. It is noted that urbanization and industrialization, application of plastic film (especially plastic film mulching in agricultural soil) and fertilizer are the major sources of PAEs in soil. Uptake of PAEs by crops, and human exposure to PAEs via ingestion of soil and vegetables are reviewed, with scientific gaps highlighted.

Variations in microbial community and di-(2-ethylhexyl) phthalate (DEHP) dissipation in different rhizospheric compartments between low- and high-DEHP accumulating cultivars of rice (Oryza sativa L.).

Di-(2-ethylhexyl) phthalate (DEHP) is a typical endocrine disrupting chemical with relatively high concentrations in agricultural soils of China. Here, a rhizobox experiment was conducted to investigate the variations in microbial community and DEHP dissipation among different soil rhizospheric compartments between low (Fengyousimiao) and high (Peizataifeng) DEHP-accumulating cultivars of rice (Oryza sativa L.) grown in DEHP spiked soil (0, 20, 100 mg/kg). The dissipation rates of DEHP in rhizospheric soils of Peizataifeng were generally significantly higher than those of Fengyousimiao, with the highest removal rate in 0-2 mm rhizosphere. The results of Illumina-HiSeq high-throughput sequencing revealed that both bacterial and fungal diversity and community structure were significantly different in rhizospheric soils of the two cultivars. DEHP dissipation rates in 0-2 mm rhizosphere of Peizataifeng were positively correlated with bacterial and fungal diversity. The relative abundance of DEHP-degrading bacterial genera Acinetobacter, Pseudomonas and Bacillus of Peizataifeng was generally higher than those in the same rhizospheric compartment of Fengyousimiao in DEHP treatments, resulting in different rhizospheric DEHP dissipation. Cultivation of Peizataifeng in agricultural soil is promising to facilitate DEHP dissipation and ensure safety of agricultural products.

Sorption kinetics, isotherms, and mechanism of aniline aerofloat to agricultural soils with various physicochemical properties.

Aniline aerofloat (AAF), a high-toxic organic flotation reagent, is widely used in mineral processing industry. However, little information on its environmental fate is available. AAF sorption to four types of agricultural soils at low concentrations (1-10 mg/L) was investigated using batch experiments. AAF sorption kinetics involved both boundary layer diffusion and intraparticle diffusion, following pseudo-second-order kinetics with equilibrium time within 120 min. Both Langmuir and Freundlich models fitted well the AAF sorption with the former better. Sorption of AAF to soils was a spontaneous and favorable physical sorption that was controlled by ion bridge effect and hydrophobic interaction that was related to van der Waals force and π-π coordination based on FTIR analyses. AAF sorption was remarkably affected by soil constituents, positively correlating with the contents of organic matter and clay. The relatively higher logKoc values (3.53-4.66) of AAF at environmental concentrations (1-5 mg/L) imply that soils are serving as a sink of AAF from beneficiation wastewater, posing great potential risks to environment and human health.

Biodegradation of di-butyl phthalate (DBP) by a novel endophytic bacterium Bacillus subtilis and its bioaugmentation for removing DBP from vegetation slurry.

Di-butyl phthalate (DBP) is a widely used plasticizer, recalcitrant and hazardous organic compound with high detection frequencies and concentrations in water and soil that pose a great threat to human health. A novel endphytic bacterium strain N-1 capable of efficiently degrading DBP and utilizing it as sole carbon source was isolated from Ageratum conyzoides. This bacterium was identified as Bacillus subtilis based on its morphological characteristics and 16S rDNA sequence analysis. Under the optimal culture conditions (pH 7.0, 30 °C), degradation percentage of DBP (12.5-100 mg/L) was up to 95% within five days, and its biodegradation half-life was less than 7.23 h. Degradation percentage of high DBP concentration (200 mg/L) was relatively lower (89%) with half-life of 56.8 h. DBP was degraded by Bacillus subtilis N-1 into mono-butyl phthalate and phthalic acid as evidenced by GC-MS analysis. Bioaugmentation of Youngia japonica plant slurry with strain N-1 greatly accelerated DBP dissipation with 97.5% removal percentage (higher by 47% than non-inoculation). The results highlighted that strain N-1 has great potential for bioremediation by plant-endophyte partnerships and for lowering PAE accumulation in crops.

Genotypic variation in the uptake, accumulation, and translocation of di-(2-ethylhexyl) phthalate by twenty cultivars of rice (Oryza sativa L.).

Agricultural soil in China contains high levels of di-(2-ethylhexyl) phthalate (DEHP), especially in paddy-field soil of Guangdong province of China, but the accumulation and translocation of DEHP by rice (Oryza sativa L.) remains unknown. In the present study, twenty rice cultivars were cultivated in paddy soil spiked with DEHP, and variations in DEHP accumulation and translocation among various cultivars were investigated. Our results showed that DEHP concentrations in roots and shoots of different rice cultivars at four growth stages (i.e., ripening, tillering, jointing, and flowering stages) varied greatly from 0.26 to 11.8 mg/kg (dry weight, dw) and 0.40 to 7.58 mg/kg (dw), respectively. No obvious change over time was observed. The greatest variation in DEHP concentrations among the rice cultivars occurred at ripening stage, whereas the lowest variation at flowering stage. During ripening stage, the largest variation in DEHP concentrations among cultivars were observed in stems (varying from 0.35 to 13.2 mg/kg), whereas the least one was observed in roots (ranging from 1.01 to 5.72 mg/kg). Significant differences in DEHP concentrations in the roots, stems, leaves and grains of most rice cultivars were found. The translocation factors of DEHP from roots to stems or stems to leaves were higher than those from shoots to grains. Overall, cultivars Tianfengyou 316, Wuyou 308, and Peizataifeng, which contained low levels of DEHP in grains but high levels in shoots, were ideal cultivars for simultaneous production of safe food and phytoremediation of contaminated soil.

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.

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.

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.

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.

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.

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.