Selective and efficient immobilization of cadmium in soil by layered double hydroxides intercalated with the mercaptosuccinic acid.

Cadmium (Cd) contamination in cropland poses a significant threat to the quality of agricultural products, but even though in-situ remediation has been extensively applied, non-selective immobilization remains an issue. In order to develop a material that specifically immobilizes Cd in soil, a layered double hydroxide, intercalated with mercaptosuccinic acid (MSA-CFA), was synthesized through co-precipitation. In this case, the MSA-CFA's maximum adsorption capacity was increased from the 513.8 mg·g-1 for unintercalated hydrotalcite CFA to 692.6 mg·g-1. Besides, MSA-CFA efficiently removed 99.25 % of Cd from soil water-extract solution and immobilized up to 70.03 % of bio-available Cd. However, interestingly, its immobilization effects on beneficial metal elements Fe, Mn and Zn were milder, being equivalent to 2/7, 5/7 and 1/2 that of lime, respectively. Moreover, XRD and XPS techniques revealed isomorphous substitution with calcium and sulfhydryl complexation during the Cd adsorption by MSA-CFA. Compared with CFA, the increased adsorption capacity of MSA-CFA for Cd was due to intercalated MSA acting as a new adsorption site, while the enhanced selectivity was contributed by sulfhydryl's affinity for Cd. Altogether, MSA-CFA showed great promise as a competitive and highly efficient candidate amendment in Cd-contaminated soil remediation.

Impact of iron and sulfur cycling on the bioavailability of cadmium and arsenic in co-contaminated paddy soil.

The biogeochemical cycling of iron (Fe) or sulfur (S) in paddy soil influences the cadmium (Cd) and arsenic (As) migration. However, the influence of coupled reduction effects and reaction precedence of Fe and S on the bioavailability of Cd and As is still not fully understood. This study aimed to reveal the influence of Fe and S reduction on soil Cd and As mobility under various pe + pH conditions and to elucidate the related mechanism in subtropical China. According to the findings, higher adsorption from Fe reduction caused high-crystalline goethite (pe + pH > 2.80) to become amorphous ferrihydrite, which in turn caused water-soluble Cd (62.0%) to first decrease. Cd was further decreased by 72.7% as a result of the transformation of SO42- to HS-/S2- via sulfate reduction and the formation of CdS and FeS. As release (an increase of 8.1 times) was consequently caused by the initial reduction and dissolution of iron oxide (pe + pH > 2.80). FeS had a lesser impact on the immobilization of As than sulfate-mediated As (V) reduction in the latter stages of the reduction process (pe + pH < 2.80). pe + pH values between 3 and 3.5 should be maintained to minimize the bioavailability of As and Cd in moderate to mildly polluted soil without adding iron oxides and sulfate amendments. The practical remediation of severely co-contaminated paddy soil can be effectively achieved by using Fe and S additions at different pe + pH conditions. This technique shows promise in reducing the bioavailability of Cd and As.

Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease.

It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.

Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections.

Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.

Controlling Factors and Predictive Models of Total Mercury and Methylmercury Accumulation in Rice (Oryza sativa L.) from Mercury-Contaminated Paddy Soils.

It is urgent to detect the major controlling factors and establish predictive models of mercury (Hg) accumulation in rice. A pot trial was conducted, exogenous Hg was added to 19 paddy soils at 4 concentration levels in this study. The major controlling factors of total Hg (THg) in brown rice were soil THg, pH and organic matter (OM) content, while those of methylmercury (MeHg) in brown rice were soil MeHg and OM. THg and MeHg in brown rice could be well predicted by soil THg, pH and clay content. The data from previous studies were collected to validate the predictive models of Hg in brown rice. The predicted values of Hg in brown rice were within the twofold prediction intervals of the observations, which demonstrated the predictive models in this study were reliable. The results could provide theoretical foundation for the risk assessment of Hg in paddy soils.

Kinetic characteristics of and critical stages for mercury accumulation in rice (Oryza sativa L.).

By studying the dynamic characteristics of and key growth stages for mercury (Hg) enrichment in rice, the Hg migration and translocation processes in this species can be better understood. In this study, a pot experiment was conducted, wherein two rice cultivars, Tianyouhuazhan (TYHZ, indica) and Zhendao 18 (ZD18, japonica), were selected and planted for analysing the Hg accumulation kinetic characteristics in rice plants. The plants were sampled at each growth stage, and the biomass and total Hg (THg) and methylmercury (MeHg) concentrations of each tissue were measured. The relative Hg contribution rates (CRs) in whole rice plants and rice grains were calculated, and the growth stage with the highest relative contribution was identified as the key growth stage for Hg accumulation. The results indicated that in rice, the MeHg translocation capability was stronger than the THg translocation capability. Significant differences in the kinetic characteristics of Hg accumulation were found between the two rice cultivars, and the TYHZ rice grains had a stronger Hg accumulation ability than the ZD18 rice grains. The key growth stages for THg accumulation in whole rice plants of both cultivars were the tillering and booting stages, while that for MeHg accumulation was the tillering stage. The key period for Hg accumulation in rice grains was the grain filling stage for both cultivars. The insights from this study could provide scientific guidance for the safe production of rice in Hg-contaminated soil.

Transfer and distribution of antibiotic resistance genes in the soil-peanut system receiving manure for years.

Antibiotic resistance gene (ARG)-contaminated food from manure application is gaining widespread interest, but little is known about the distribution and uptake of ARGs in peanuts that are subjected to manure routinely. In this study, the ARG profile and bacterial community in soil and peanut plants from a 7-year manure-fertilized field were investigated using high-throughput qPCR and 16S rRNA gene sequencing. Manure application increased the abundance of ARGs in soil and peanuts by 59-72 and 4-10 fold, respectively. The abundance of ARGs from high to low was as follows: manure, shell-sphere soil, rhizosphere soil, bulk soil, stems, shells, needles, kernels, and roots. Source-tracker analyses were used to investigate the potential source of ARGs in peanut kernels, which revealed that the ARGs in peanut kernels may be primarily absorbed by the roots from the soil. The horizontal gene transfer (HGT) of ARGs was the primary factor in the spread of ARGs, and Proteobacteria were the primary agents of HGT between different parts of peanut plants. Additionally, norank_Chloroplast from the phylum Cyanobacteria was the most important contributor to the abundance of ARGs in peanut kernels. Overall, our findings fill a gap in our understanding of the distribution patterns of ARGs in peanut plants and the migratory pathways of ARGs from soil to peanut kernels.

Metagenomic binning analyses of pig manure composting reveal potential antibiotic-degrading bacteria and their risk of antibiotic resistance genes.

Antibiotic-degrading bacteria are commonly used to treat antibiotic contamination, but the antibiotic resistance genes (ARGs) they carry are often overlooked. This study used metagenomic assembly and binning analyses to explore potential antibiotic-degrading bacteria and their ARGs during pig manure composting. The result showed that 35 metagenome-assembled genomes (MAGs) mainly containing alkyl-aryl transferase and decarboxylase genes involved in the removal of antibiotics. Multidrug (124), ß-lactam (67), macrolide-lincosamide-streptogramin (MLS) (64), and tetracycline (43) were the central ARG types detected in the 35 MAGs. Furthermore, the risk of ARGs was evaluated using the arg_ranker framework, and 19 MAGs were found to contain intermediate-high-risk ARGs with human-associated-enrichment, gene transferability, and host pathogenicity. Bin 34 of the genus of Geofilum had the highest ARG risk. Bin 6, Bin 11 and Bin 14 of the genus of Limnochorda, Chelatococcus and Niabella, had a lower ARG risk and were considered as potential antibiotic-degrading bacteria.

Double-edged effects of elevating temperature on the aging of exogenous arsenic in flooded paddy soils.

Temperature variation can have a significant impact on arsenic (As) bioavailability in paddy soils. However, details regarding the transformation of exogenous As during the aging process in paddy soils at various temperatures remain unclear. This work investigated the effects of temperature on the As extractability and As species transformation of three paddy soils spiked with exogenous arsenate at 60 mg kg-1 under flooded aging and explored the related chemical and microbial mechanisms. The results showed that 0.05 M NH4H2PO4-extractable As decreased over time during flooded aging for 192 days, and it decreased by approximately one-third at 35 °C compared with 15 °C and 25 °C at the same aging time, indicating that higher temperatures facilitated the decrease in As extractability. As(V) reduction mainly occurred at 35 °C because the abundance and As(V)-reducing capacity of the predominant indigenous bacteria, the Bacillus sp strains, and the abundance of the arrA gene were significantly higher than those at 15 °C and 25 °C. The reduction of As(V) to As(III) and aging occurred simultaneously. The kinetic models were established, and the rate constants of the reduction and aging processes were obtained. Soil properties significantly affected the aging and reduction processes of extractable As(V). Our study indicated that elevating temperature had dual effects on the environmental risk of As in the flooded aging process. The previous definition of "aging" based on cationic metals needs to be updated according to the transformation characteristics of As species in flooded conditions. Our results addressed the necessity of impeding the reduction of As(V) in paddy soils under global warming.

Key microbial clusters and environmental factors affecting the removal of antibiotics in an engineered anaerobic digestion system.

To identify the key microbial clusters and influencing factors involved in antibiotic removal from engineered anaerobic digestion (AD) systems, the dynamic characteristics of antibiotics, physiochemical factors, microbial communities and functional genes were investigated by 16S rRNA and metagenome sequencing. The results showed that antibiotic removal occurred mainly in the first 21 days, and sulfonamides had the highest removal rate. The key microbial clusters related to the biodegradation of antibiotics consisted mainly of Firmicutes and Bacteroidetes. The key enzymes consisted of deaminases, peptidases, C-N ligases, decarboxylases and alkyl-aryl transferases. Structural equation modelling indicated that low concentrations of propionic acid promoted the biodegradation activities of key microbial clusters in the first 21 days, but their activities were inhibited by the accumulated propionic acid after 21 days. Thus, propionic acid should be regulated in engineered AD systems to prevent the adverse effect of acid inhibition on antibiotic-degrading bacteria.

Antibiotic degradation dominates the removal of antibiotic resistance genes during composting.

To identify the key hosts involved in horizontal gene transfer (HGT) and vertical gene transfer (VGT) of antibiotic resistance genes (ARGs) and to determine the extent to and ways in which environmental properties contribute to ARG removal, the changes in ARG profile and key hosts during biogas residue and pig manure composting were investigated using metagenomic sequencing coupled with network analysis. Composting significantly reduced the abundances of ARGs other than bacA. Seventy and 41 hosts from Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes were associated with HGT and VGT, respectively. The key environmental properties were determined using structural equation modelling. Antibiotics directly affected HGT and determined ARG removal. Temperature indirectly affected HGT, mainly by influencing the degradation of antibiotics. BacA was associated only with hosts involved in VGT, which may lead to its low removal rate. These findings specify the priority and pathway of antibiotics and temperature affecting ARG profile.

Polymer-coated manganese fertilizer and its combination with lime reduces cadmium accumulation in brown rice (Oryza sativa L.).

Manganese (Mn) has the potential to reduce cadmium (Cd) uptake by rice; however, the efficiency depends on its soil availability. Therefore, this study designed a slow-release Mn fertilizer by employing a polyacrylate coating. Pot trials were conducted to study the effects of coated-Mn and uncoated-Mn alone or in combination with lime on the dynamics of soil dissolved-Mn and available Cd, and the transportation of Mn and Cd within rice. The results showed that coated-Mn declined the release of Mn until the 7th day of application; however, it consistently supplied more dissolved-Mn than uncoated-Mn. As a result, coated-Mn induced a greater Cd reduction (45.8%) in brown rice than uncoated-Mn (9.7%). The total Cd of rice and its proportion in brown rice were greatly reduced by coated-Mn, indicating the inhibition of root uptake and interior transport of Cd. Additionally, lime addition prominently increased the soil pH and decreased the CaCl2-extractable Cd (90.1-93.9%). However, since lime reduced the soil dissolved-Mn, downregulated the OsHMA3 expression and upregulated the OsNramp5 expression, brown rice Cd was reduced by only 43.0%. The combined addition of lime and coated-Mn alleviated the liming effect on soil Mn and gene expression in roots, thereby reducing brown rice Cd by 71.5%.

Aging of exogenous arsenic in flooded paddy soils: Characteristics and predictive models.

Understanding the arsenic (As) aging process is important for predicting the environmental behavior of exogenous As in paddy soils. In this work, samples of sixteen paddy soils with various soil properties were spiked with two concentrations (30 and 100 mg kg-1) of arsenate and subjected to a 360 day-long incubation under continuous flooding condition. Soil available As extracted by 0.05 M NH4H2PO4 was monitored through the aging process. Results showed that the available As%, the percentage of remaining available As in aged soils to added total As, fell from 44.2% to 41.9% on the 1st day to 22.0% and 23.0% on the 115th day for the low and high As spiked soils, respectively, then it remained basically unchanged after the 115th day. The pseudo-second order equation could adequately describe the aging kinetics of exogenous As in paddy soils. There was no significant difference in As aging parameters between the two spiked concentrations. Contents of soil free Al and Mn oxides, clay and cation exchange capacity strongly affected the aging rate of exogenous As. An empirical model, incorporating soil pH, cation exchange capacity, Olsen-P and flooding time, was developed to predict well the change of soil available As% during aging process (R2 = 0.711). The model could be potentially utilized to manage As-contaminated paddy fields and normalize ecotoxicity and bioaccumulation datasets in attempt to derive more widely applicable soil environmental quality criteria for As.

A new perspective on the toxicity of arsenic-contaminated soil: Tandem mass tag proteomics and metabolomics in earthworms.

The toxicity of low-level arsenic (As)-contaminated soil is not well understood. An integrated proteomic and metabolomic approach combined with morphological examination was used to investigate the potential biological toxicity of As-contaminated soil based on an exposure experiment with the earthworm Eisenia fetida. The results showed that the earthworm hindgut accumulated high As concentrations resulting in injury to the intestinal epithelia, chloragogenous tissues and coelom tissues. Furthermore, As-contaminated soil induced a significant increase in betaine levels and a decrease in dimethylglycine and myo-inositol levels in the earthworms, suggesting that the osmoregulatory metabolism of the earthworms may have been disturbed. The significantly altered levels of asparagine and dimethylglycine were proposed as potential biomarkers of As-contaminated soil. The upregulation of soluble calcium-binding proteins and profilin, the downregulation of sodium/potassium-transporting ATPase, and the proteins changes identified by gene ontology enrichment analysis confirmed that the earthworms suffered from osmotic stress. In addition, the significant changes in glycine-tRNA ligase activity and coelomic tissue injury revealed that As accumulation may disturb the earthworm immune system. This work provided new insight into the proteomic and metabolic toxicity of low-level As-contaminated soil ecosystems in earthworms, extended our knowledge of dual omics and highlighted the mechanisms underlying toxicity.

Selenium enhances iron plaque formation by elevating the radial oxygen loss of roots to reduce cadmium accumulation in rice (Oryza sativa L.).

The inhibition of cadmium (Cd) absorption by selenium (Se) in rice may be associated with iron plaque (IP) formation, but the driving mechanisms are still unclear. This study investigated the effects of Se on the growth, oxidative toxicity, radial oxygen loss (ROL), IP formation, and Cd absorption of rice exposed to Cd. The results of this study showed that Cd stress elevated the levels of O2- and H2O2 and depressed superoxide dismutase (SOD) and catalase (CAT) activities. The maximum ROL and IP were reduced by 43.3 % and 74.5 %, respectively. However, Se alleviated Cd toxicity by stimulating SOD and CAT activities by scavenging O2- and H2O2 and enhancing the ROL profiles. Under culture conditions without Fe2+, Se had no impact on the total Cd levels in rice (TCd). However, with the addition of Fe2+, TCd was significantly reduced by 23.3 % due to the enhancement of IP formation by Se. These results indicated that Se can reduce Cd accumulation in rice in the presence of Fe2+ treatments. However, Se just alleviated Cd toxicity in the absence of Fe2+ treatments. The enhancement of ROL was a potential reason for the elevated IP formation induced by Se.

Kinetic characteristics and predictive models of methylmercury production in paddy soils.

Understanding the mercury (Hg) methylation process is important for the management of paddy soils contaminated by Hg. In this work, samples of eighteen paddy soils with varying soil properties were spiked with inorganic Hg and subjected to a 90 d flooding period. Soil pH and redox potential (Eh) were measured in situ at intervals, and soils were sampled for the analysis of methylmercury (MeHg). The Hg methylation efficiency increased with flooding time and reached a relatively steady state at 30 d of incubation, ranging from 0.08% to 2.52%, and was significantly correlated with the in situ soil pH and Eh. The Elovich equation could adequately describe the kinetic production of MeHg. MeHg production was well predicted by the in situ soil pH and Eh of flooded soils, in addition to the organic matter content of air-dried soil samples and flooding time. The two predictive models explained 78% and 68% of the variability of the Hg methylation efficiency. The results suggested that the methylation of inorganic Hg in paddy soils after flooding can be predicted as a function of routinely measured soil properties and flooding time, a correlation that can be utilized to improve understanding of the extent of Hg methylation and the management of Hg-contaminated paddy soils.

Toxic responses of metabolites, organelles and gut microorganisms of Eisenia fetida in a soil with chromium contamination.

The toxic sensitivity in different physiological levels of chromium (Cr) contaminated soils with environmentally equivalent concentrations (EEC) was fully unknown. The earthworm Eisenia fetida was exposed to a Cr-contaminated soil at the EEC level (referred to as Cr-CS) to characterize the induced toxicity at the whole body, organ, tissue, subcellular structure and metabolic levels. The results showed that the survival rate, weight and biodiversity of the gut microorganisms (organ) had no significant difference (p > 0.05) between control and Cr-CS groups. Qualitative histopathological and subcellular evaluations from morphology showed earthworms obvious injuries. The organelle injuries combined with the metabolic changes provided additional evidence that the Cr-CS damaged the nucleus and probably disturbed the nucleic acid metabolism of earthworms. 2-hexyl-5-ethyl-3-furansulfonate, dimethylglycine, betaine and scyllo-inositol were sensitive and relatively quantitative metabolites that were recommended as potential biomarkers for Cr-CS based on their significant weights in the multivariate analysis model. In addition, the relative abundance of Burkholderiaceae, Enterobacteriaceae and Microscillaceae of the earthworm guts in the Cr-CS group significantly increased, particularly for Burkholderiaceae (increased by 13.1%), while that of Aeromonadaceae significantly decreased by 5.6% in contrast with the control group. These results provided new insights into our understanding of the toxic effects of the EEC level of Cr contaminated soil from different physiological levels of earthworms and extend our knowledge on the composition and sensitivity of the earthworm gut microbiota in Cr contaminated soil ecosystems. Furthermore, these toxic responses from gut microorganisms to metabolites of earthworms provided important data to improve the adverse outcome pathway and toxic mechanism of the Cr-CS if the earthworm genomics and proteomics would be also gained in the future.

Influence of bacterial community composition and soil factors on the fate of phenanthrene and benzo[a]pyrene in three contrasting farmland soils.

The fate of polycyclic aromatic hydrocarbons (PAHs) determines their potential risk in soil, which may be directly affected by abiotic conditions and indirectly through the changes in decomposer communities. In comparison, the indirect effects on the fate remain largely elusive. In this study, the fate of phenanthrene and benzo[a]pyrene and the corresponding bacterial changes were investigated in three contaminated farmland soils using a 14C tracer method and Miseq sequencing. The results showed that most benzo[a]pyrene was consistently extractable with dichloromethane (DCM) after the 60-day incubation (60.4%-78.2%), while phenanthrene was mainly mineralized to CO2 during the 30-day incubation (40.4%-58.7%). Soils from Guangzhou (GZ) showed a different distribution pattern of 14C-PAHs exemplified by low mineralization and disparate bound residue formation. The PAH fate in the Shenyang (SY) and Nanjing (NJ) soils were similar to each other than to that in the GZ soil. The fate in the GZ soil seemed to be linked to the distinct edaphic properties, such as organic matter content, however soil microbial community could have influenced the distribution pattern of PAHs. This potential role of microorganisms was reflected by the unique changes in the copy numbers of Gram positive RHDα gene, and by the distinct shifts in bacterial community composition during the incubation. A quite different shift in bacterial communities was found in the GZ microcosms which may influence PAH mineralization and non-extractable residue (NER) formation.