Microbial mechanisms responsible for the variation of soil Cd availability under different pe+pH environments

Methane emission mitigation of Paenibacillus yonginensis DCY84T incorporated with silicate on paddy rice (Oryzae sativa L.) plantation revealed in soil microbiome profiling

Anthropogenic methane emissions from paddy cultivation contribute to greenhouse gas levels owing to the anaerobic conditions in flooded rice fields, which promotes the activity of methanogenic bacteria. This study explored bioremediation strategies to mitigate methane release through the application of plant growth-promoting rhizobacteria combined with silicate in rice cultivation. Rice seeds were coated with Paenibacillus yonginensis DCY84T, with and without the addition of silicate, prior to sowing. Results revealed notable reduction in methane flux during the peak growth stage of rice in seeds treated with DCY84T (27.215 ± 1.975 mg m-2 h-1), with a further reduction observed when silicate was also applied (23.592 ± 3.112 mg m-2 h-1), compared to untreated seeds (37.305 ± 2.990 mg m-2 h-1). Additionally, treatment with DCY84T (28.24 ± 0.55 g) resulted in an increase in rice yield (p < 0.05), as evidenced by a greater 1000-grain weight compared to both the control group (26.91 ± 0.09 g) and the application of silicate (27.37 ± 0.57 g). The beta diversity of the soil microbial community highlighted distinct differences between the treated and control groups, indicating DCY84T inoculation with or without silicate altered the soil microbial structure. Particularly, the treated groups showed dominance of the phylum Proteobacteria, especially the classes Alphaproteobacteria and Deltaproteobacteria. Furthermore, the addition of silicate to DCY84T-coated rice seeds resulted in a higher abundance of bacterial families, such as Anaerolinaceae, Clostridiceae, and Nitrospirae which compete with methanogens for organic substrates, thereby reducing their methane production. Notably, the DCY84T-silicate treatment group showed higher levels of methane metabolism biomarkers such as formate dehydrogenase within the soil microbiome, which correlated with the observed reduction in methane emissions. These findings suggest that coating rice seeds with DCY84T and silicate prior to sowing effectively mediates methane production and release during rice cultivation by promoting beneficial soil bacterial communities.

New insights into the stages of cadmium remediation in ryegrass enhanced by kitchen compost-derived dissolved organic matter: Activation, absorption, and storage

Dissolved organic matter (DOM) regulates plant behavior in both agricultural and environmental fields. However, the regulatory mechanisms by which DOM influences soil-plant system interactions during the phytoremediation of Cd-contaminated soils remain unclear. Therefore, this study investigated the enhanced effect of kitchen compost-derived DOM on the Cd remediation capability of ryegrass across three phases of phytoremediation. The main pathways and mechanisms of DOM-assisted phytoremediation were identified through the analysis of changes in soil microbial communities and metabolism functions. The results revealed that DOM increased the bioavailability of soil Cd and significantly enhanced the Cd enrichment capacity of ryegrass, regardless of the application rate. The application of 20 % DOM to soil with a 20 mg/kg Cd content increased the bioconcentration factors of ryegrass roots and shoots by up to 38.19 and 11.08 times, respectively, compared with the control group. The direct or indirect optimizing effects of DOM on Cd fraction transformation, microbial communities, and their metabolism functions significantly enhanced the Cd enrichment capacity of ryegrass. Notably, DOM exhibited dual effects on ryegrass growth, mainly influenced by changes in soil physicochemical properties, optimization of microbial communities, and alterations in nitrogen metabolic functions. Additionally, the Cd reserves in ryegrass, which serve as a vital indicator of phytoremediation, exhibited a positive response to DOM. This study provides insights into the various reinforcing roles of kitchen compost-derived DOM in Cd-contaminated soil phytoremediation. These findings support the development of effective agronomic strategies for precise Cd regulation.

Rhodopseudomonas palustris shapes bacterial community, reduces Cd bioavailability in Cd contaminated flooding paddy soil, and improves rice performance

Photosynthetic bacteria (PSB) are suitable to live and remediate cadmium (Cd) in the slightly oxygenated or anaerobic flooding paddy field. However, there is currently limited study on the inhibition of Cd accumulation in rice by PSB, and the relevant mechanisms has yet to be elucidated. In the current study, we firstly used Rhodopseudomonas palustris SC06 (a typical PSB) as research target and combined physiology, biochemistry, microbiome and metabolome to evaluate the mechanisms of remeding Cd pollution in paddy field and inhibiting Cd accumulation in rice. Microbiome analysis results revealed that intensive inoculation with R. palustris SC06 successfully survived and multiplied in flooding paddy soil, and significantly increased the relatively abundance of anaerobic bacteria including Desulfobacterota, Anaerolineaceae, Geobacteraceae, and Gemmatimonadaceae by 46.40 %, 45.00 %, 50.12 %, and 21.30 %, respectively. Simultaneously, the structure of microbial community was regulated to maintain relative stability in the rhizosphere soil of rice under Cd stress. In turn, these bacteria communities reduced bioavailable Cd and enhanced residual Cd in soil, and induced the upregulation of sugar and organic acids in the rice roots, which further inhibited Cd uptake in rice seedlings, and dramatically improved the photosynthetic efficiency in the leaves and the activities of antioxidative enzymes in the roots. Finally, Cd content of the roots, stems, leaves, and grains significantly decreased by 38.14 %, 69.10 %, 83.40 %, and 37.24 % comparing with the control, respectively. This study provides a new strategy for the remediation of Cd-contaminated flooding paddy fields and the safe production of rice.

Adsorption mechanism of Cd2+ on microbial inoculant and its potential for remediation Cd-polluted farmland soils

The adsorption characteristics and mechanism of Cd2+ on microbial inoculant (MI) mainly composed of Bacillus subtilis, Bacillus thuringiensis and Bacillus amyloliquefaciens, and its potential for remediation Cd polluted soils through batch adsorption and soil incubation experiments. It was found that the Freundlich isotherm model and the pseudo-second-order kinetics were more in line with the adsorption processes of Cd2+. The maximum adsorption capacity predicted by Langmuir isotherm model suggested that of MI was 57.38 mg g-1. Scanning electron microscopy and energy dispersive spectroscopy (SEM-EDS) images exhibited the surface structure of MI was damaged to varying degrees after adsorption, and Cd element was distributed on the surface of MI through ion exchange. X-ray diffraction (XRD) results showed that CdCO3 was formed on the surface of MI. Moreover, the functional groups (-OH, C-H, and -NH) involved in the adsorption of Cd2+ through fourier transform infrared spectroscopy (FTIR). After applying MI to Cd-contaminated soil, it was found that soil pH, conductivity (EC) and soil organic matter (SOM) increased by 0.84 %-2.43 %, 31.6 %-241.48 %, and 8.11 %-24.1 %, respectively, when compared with the control treatments. The content of DTPA-Cd in the soils was significantly (P < 0.05) reduced by 15.48 %-29.68 % in contrast with CK, and the Cd speciation was transformed into a more stable residual fraction. The activities of urease, phosphatase and sucrose were increased by 3.5 %-45.18 %, 57.00 %-134.18 % and 52.51 %-70.52 %, respectively, compared with CK. Therefore, MI could be used as an ecofriendly and sustainable material for bioremediation of Cd-contaminated soils.

Experimental and numerical study on Zn and Pb migration in the farmland soil under wastewater irrigation conditions

Long-term wastewater irrigation may lead to the accumulation, transformation, and migration of heavy metals in the farmland soil, increasing the risk of groundwater pollution. However, it is currently uncertain whether using wastewater for irrigation would lead to the migration of heavy metals zinc (Zn) and lead (Pb) into deeper layers of soil, in the local undeveloped wastewater irrigation farmland. In this study, the migration characteristics of Zn and Pb from irrigation wastewater in local farmland soil were investigated through a series of experiments including adsorption experiments, tracer, and heavy metals breakthrough experiments, as well as numerical simulations using HYDRUS-2D software. The results revealed that the Langmuir adsorption model, CDE model, and TSM model were effective in fitting the required adsorption and solute transport parameters for the simulations. Furthermore, both the soil experiments and simulation results showed that in the test soil, Pb had a stronger affinity for adsorption sites than Zn, while Zn exhibited greater mobility than Pb. After 10 years of wastewater irrigation, it was found that Zn had migrated to a maximum depth of 32.69 cm underground and Pb had only migrated to 19.59 cm. Despite their migration, the two heavy metals have not yet reached the groundwater zone. Instead, they had accumulated to higher concentrations in the local farmland soil. Moreover, the proportion of active forms of Zn and Pb decreased after flooded incubation. The present results can improve understanding of the environmental behavior of Zn and Pb in the farmland soil and can be used as a basis for risk assessment of Zn and Pb polluting groundwater.

Flooding-induced rhizosphere Clostridium assemblage prevents root-to-shoot cadmium translocation in rice by promoting the formation of root apoplastic barriers

Water managements are the most effective agricultural practices for restraining cadmium (Cd) uptake and translocation in rice, which closely correlated with rhizosphere assembly of beneficial microbiome. However, the role of the assemblage of specific microbiota in controlling root-to-shoot Cd translocation in rice remains scarcely clear. The aim of this study was to ascertain how water managements shaped rhizosphere microbiome and mediated root-to-shoot Cd translocation. To disentangle the acting mechanisms of water managements, we performed an experiment monitoring Cd uptake and transport in rice and changes in soil microbial communities in response to continuously flooding and moistening irrigation. Continuously flooding changed rhizosphere microbial communities, leading to the increased abundance of anaerobic bacteria such as Clostridium populations. Weighted gene co-expression network analysis (WGCNA) showed that a dominant OTU163, corresponding to Clostridium sp. CSP1, exhibited a strong negative correlation with root-to-shoot Cd translocation. An integrated analysis of transcriptome and metabolome further indicated that the Clostridium-secreted butyric acid was involved in the regulation of phenylpropanoid pathway in rice roots. The formation of endodermal suberized barriers and lignified xylems was remarkably enhanced in the Clostridium-treated roots, which led to more Cd retained in root cell wall and less Cd in the xylem sap. Collectively, our results indicate that the development of root apoplastic barriers can be orchestrated by beneficial Clostridium strains that are assembled by host plants grown under flooding regime, thereby inhibiting root-to-shoot Cd translocation.

Rape straw application facilitates Se and Cd mobilization in Cd-contaminated seleniferous soils by enhancing microbial iron reduction

Many naturally seleniferous soils are faced with Cd contamination problem, which severely limits crop cultivation in these areas. Straw returning has been widely applied in agricultural production due to its various benefits to soil physicochemical properties, soil fertility, and crops yield. However, effects of straw application on the fates of Se and Cd in Cd-contaminated seleniferous soils remain largely unclear. Therefore, the effects of straw application on the fates of Se and Cd in Cd-contaminated seleniferous soils were investigated in this study. The results showed that iron reduction driven by Clostridium and Anaeromyxbacter was responsible for the variations in Se and Cd fates in soil. Straw application respectively increased the gene copy numbers of Clostridium and Anaeromyxbacter by 19.5-56.3% and 33.6-39.8%, thus promoting iron reductive dissolution, eventually resulting in a high release amount of Se and Cd from Fe(III) (oxyhydr) oxides. Under reducing conditions, the released Cd was adsorbed by the newly formed metal sulfides or reacted with sulfides to generate CdS precipitates. Straw application decreased the soil exchangeable Se and soil exchangeable Cd concentration during flooding phase. However, straw application significantly increased Se/Cd in soil solution which had the highest bioavailability during flooding. In addition, straw application increased soil exchangeable Se concentration, but it had no significant effects on soil exchangeable Cd concentration after soil drainage. Taken together, straw application increased Se bioavailability and Cd mobility. Therefore, straw application is an effective method for improving Se bioavailability, but it is not suitable for the application to Cd-contaminated paddy soils. In the actual agricultural production, straw could be applied in seleniferous soils to improve Se bioavailability. At the same time, straw application should be cautious to avoid the release of Cd from Cd-contaminated soil.

Clay-hydrochar composites return to cadmium contaminated paddy soil: Reduced Cd accumulation in rice seed and affected soil microbiome

Excess cadmium (Cd) in rice precipitated by Cd contamination in paddy soils is a global human health threat and rational response is urgently needed. In this study, attapulgite-modified hydrochar (CA) and the montmorillonite-modified hydrochar (CM) were utilized in Cd-contaminated paddy soils at 0.5% (w/w) and 1% (w/w) application rates to investigate the effects of these clay-hydrochar composites on rice growth and soil Cd availability. The results show that the utility of CA and CM resulted in a significant increase in rice yield, especially at 1% application rate, which extended rice yield by 46.7-50.0% compared to 0.5% application rate. This is related to the Cd fixation and nutrient sequestration of the acidic functional groups on the surface of CA and CM. Additionally, CA-1% and CM-1% reduced the Cd concentration in rice seeds by 26.9-28.1% relative to the control. Notably, CA-1% showed the capacity to passivate Cd at the early stage of rice transplanting, lowering the proportion of Cd in the ion exchange state by 41.6% compared to the control, and this passivation effect persisted until the late stage of transplanted rice. The soil microbial community consequences showed that CA and CM did not significantly change the horizontal composition of the soil bacterial phylum and species diversity, indicating that CA and CM had excessive soil microbial adaptability. Moreover, results of correlation and Canonical Correspondence Analysis confirm that microbial genera responded significantly to the soil Cd morphologies, revealing the importance of CA and CM in the remediation of Cd-contaminated soils by influencing microorganisms. Our findings provide clay-hydrochar composites as a low-cost approach to effectively mitigate soil Cd contamination and improve the security and quality of rice.

Flooding and drainage induced abiotic reactions control metal solubility in soil of a contaminated industrial site

Intense industrialization has led to the increasing leaching risk of metals into groundwater at heavily polluted industrial sites. However, metal dissolution in polluted industrial soils has been neither fully investigated nor quantified before. In this study, the dissolution of Zn, Ni, and Cu in soil from a heavily contaminated industrial site during a flooding-drainage period was investigated by sequential extraction, geochemical modelling, and X-ray absorption near edge structure spectroscopy. The results showed a steady decrease in metal solubility during both reduction and oxidation stages. During reduction, with limited decrease in Eh (>100 mV), formation of carbonate precipitates rather than sulfide precipitates and adsorption on soil solids was responsible for Zn and Ni dissolution, whereas bound to soil organic matter (SOM) and iron oxides dominated Cu dissolution, due to its lower concentration and higher affinity to SOM and iron oxides compared to Zn and Ni. During oxidation, the acidity caused by ferrous oxidation was buffered by calcite dissolution, while metal precipitation ceased and adsorption on soil surface controlled metal solubility. The metal solubility and speciation during the flooding-drainage process were quantitatively predicted by geochemical model. The findings demonstrate that due to high metal concentrations and weak microbial effect in the industrial soil, metal release was largely regulated by abiotic reactions rather than biotic reactions, which is somehow different from that of the wetland or rice field soils.

Quantitative analysis of soil sustainability after applying stabilizing amendments in long-term Cd-contaminated paddy soils

Considering the biomagnification in food chains, cadmium (Cd) contamination in paddy fields has become concerning. The remediation of soil cadmium by the addition of amendments is a common agricultural practice. However, it remains ambiguous whether amendment use decreases soil environmental quality (SEQ) and sustainability. In this study, five compound amendments with different pH were utilized in long-term Cd-contaminated paddy soils. The SEQ of all treatments was quantitatively assessed according to a comprehensive evaluation mathematical model (Criteria Importance Through Inter-criteria Correlation (CRITIC)-Technique for Order Preference by Similarity to Ideal Solution (TOPSIS)), and the indicators involved in microbial functional gene (MFG) abundance, soil physicochemical and microbiological properties (CMP) and soil microbial function (N-related enzyme and transformation rate, N-ET) were measured. The results show that the SQE and remediation effect (expressed by the decrease in available Cd (A_Cd), %) in our treatments were alkaline > natural > acidic except for D alkaline treatment. The significant contradiction between soil SQE and remediation effect in D treatment attribute to its dose effects, which inhibiting microbial nitrogen assimilation and dissimilation and therefore counteracts the promoting effect of the decrease in A_Cd. Based on this discussion, three alkaline amendments (A, B and D) with similar effective remediation effect were employed in four other Cd-contaminated soils. Results indicated that both negative effect (D treatment) and promoting effect (A and B treatment) existed in the next 3 years.

Aging and phytoavailability of newly introduced and legacy cadmium in paddy soil and their bioaccessibility in rice grain distinguished by enriched isotope tracing

Phytoavailability of Cadmium (Cd) plays a critical role in its accumulation in soil-rice systems. However, differential aging and phytoavailability of newly introduced Cd (Cd_N) and legacy Cd (Cd_L) in the soil-rice system remains unknown. Moreover, distinguishing their aging and phytoavailability is challenging. Enriched ¹¹²Cd isotope was introduced into a series of pot experiments, combined with sequential extraction and isotope dilution (¹¹⁰Cd isotopic spike), to investigate the aging and distribution of Cd_N and Cd_L under different treatments. The treatments included simulated acid rain, slaked lime, and biochar. Cd_N aged quickly than Cd_L in flooded soil and its availability was similar to that of Cd_L after tillering stage. The grain Cd contents were positively correlated to Cd concentrations in the overlying water. Acid rain reduced the soil pH, increasing the grain Cd, while slaked lime reduced grain Cd content. The acidic biochar used in this study increased grain Cd, possibly through soil acidification-induced Cd release. The differences in bioaccumulation and translocation factors between Cd_N and Cd_L in rice plants under slaked lime and biochar treatments suggested their different in vivo complexations and translocations. Analysis of bioaccessibility of Cd_N and Cd_L in rice grains provided valuable insights regarding human Cd exposure.

Manganese facilitates cadmium stabilization through physicochemical dynamics and amino acid accumulation in rice rhizosphere under flood-associated low pe+pH

Periodic flooding in paddy soils impacts redox behavior and induces variations in pe+pH levels. Manganese (Mn) is capable of reducing cadmium (Cd) uptake by rice. However, the processes involved in how Mn alters Cd mobilization under different pe+pH environments remain poorly understood. To investigate the mechanisms of Mn-mediated soil Cd-stabilization and subsequent inhibition of Cd uptake from flooded soils, we examined Cd immobilization in soil pot incubations, transcriptional changes in Cd-transport genes, and metabolomic analyses of roots and rhizosphere soils with or without Mn application. We found a decrease in extractable Cd concentration largely depended on irrigation-associated low pe+pH, exogenous Mn enhancement of Fe-Mn (oxyhydro)oxide-mediated Cd transformation, and Cd deposition in rice Fe/Mn plaques. Mn application led to striking effects on the expression of Cd-related genes eg. IRT, HMA, and NRAMP in rice root tissue. Exposure to Mn under variable pe+pH levels resulted in metabolic reprogramming of soil and rice roots. Mn induced amino acid synthesis in rice roots, leading to rhizosphere accumulation of free L-lysine, glycine, and glutamine, which can reportedly bind metal ions, forming complexes with Cd. Thus, secreted amino acids, low pe+pH, and free Mn can together comprise a multi-faceted approach to managing Cd toxicity in rice.

Fe(III) reduction due to low pe+pH contributes to reducing Cd transfer within a soil-rice system

Effect of Fe redox state caused by low soil pe+pH levels on Cd uptake by rice is unclear. Rice grown in pots of Cd-contaminated paddy soil were subjected to different irrigation regimes: flooding, intermittent flooding (Int-FL), and sustained soil moisture at 70% water holding capacity (WHC). Results showed low pe+pH (5.52 and 7.09) in flooding treatment significantly increased relative abundances of Fe-reducing bacteria (FeRB) (6.29% and 4.51%), especially members within the Clostridium, Geobacter and Desulfuromonadia genera. Stimulation of FeRB activity induced Fe(III) reduction and increased Fe²⁺ content in flooded soils, which promoted Cd sequestration in low-crystalline fraction of IP (IP-Feh-Cd) and Cd bonded to amorphous Fe-oxides (amFeox-Cd). The 24.9-62.4% higher amFeox-Cd content was the important factor for 20.4-44.2% lower CaCl₂-extractable Cd content in flooding treatment than those in other treatments. Soil submergence reduced Cd uptake by rice at tillering and booting stages, the critical periods of Cd transport in the soil-rice system, which was attributed to the increases in dissolved Fe²⁺ and IP-Feh-Cd contents and decrease in CaCl₂-Cd content. Therefore, maintaining flooding during the tillering and booting stages may be an effective strategy to reduce Cd uptake by rice cultivated in Cd-contaminated soil.

Improved immobilization of soil cadmium by regulating soil characteristics and microbial community through reductive soil disinfestation

Cadmium (Cd) contamination arising from industrialization has attracted increasing attention in recent years. Reductive soil disinfestation (RSD) as an effective agricultural practice has been widely applied for soil sterilization. However, there is little research regarding RSD affecting Cd immobilization. Here, five treatments, namely untreated soil (CK), flooding-treated soil (FL), RSD with 2% ethyl alcohol (EA), 2% sugarcane bagasse (SB), and 2% bean dregs (BD) were designed to detect their performance for Cd immobilization in contaminated soils, and the change of soil properties and microbial communities were monitored. The results revealed that pH significantly increased in FL and RSD-treated soils, but was negatively correlated with the exchangeable fraction of Cd (EX-Cd), while Oxidation-Reduction Potential (Eh) significantly decreased in FL and RSD-treated soils, and was positively correlated with EX-Cd. BD treatment might contribute to the increase of CaCO₃ as shown by X-Ray Diffractomer analysis and strongly decreased the EX-Cd in the soil, but increased the relative abundances of Firmicutes, Planctomycetes, Acidobacteria, and Gemmatimonadetes, which may promote Fe (III) reduction or induce resistance to Cd. Bacterial communities at the phylum and genus levels were closely related to Cd fraction. The FL and RSD treatments moderately altered bacterial specific functions, including iron respiration, which may contribute to remediation of Cd-polluted soil by Fe (III) reduction. Field experiments were conducted to confirm that BD treatment resulted in a significant increase in pH whereas the content of total available Cd was reduced in soils. Compared to the control, concentration of total available Cd of red amaranth, sweet potato, towel gourd, and cowpeas were reduced by approximately 46%, 74%, 72%, and 76% in a BD-treated field, respectively. Our study highlights the potential of RSD as an effective method for Cd immobilization in contaminated soils by improving soil characteristics and altering the composition of the microbial community.