Exploring the potential of Paris polyphylla var. yunnanensis pollen manipulation in modifying seed dormancy.

Paris polyphylla var. yunnanensis, a well-known Chinese medicinal herb, shows a unique physiological trait characterized by the cyclic opening and closing of its anthers after pollen maturation. The aim of this study was to explore the implications of this phenomenon on breeding. RNA sequencing coupled with methylation sequencing was used to scrutinize and compare gene expression profiles and methylation alterations in pollen and seeds during anther opening and closing, along with cold exposure. Genes enriched within Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were examined to identify gene clusters susceptible to temperature-related methylation changes in both pollen and seeds. Four pollen treatment models, namely, normal control, "pollen protected from low temperatures," "pollen from just-opened anther," and "pollen from close-blocked anther," were used to produce corresponding seeds via artificial pollination. Subsequently, qRT-PCR was used to validate modifications in the expression patterns of marker genes in pollinated seeds under diverse treatment scenarios. Genes exhibiting significant differences in expression between anthers and normal tissues, along with gene regions linked to methylation variations attributed to low-temperature-treated pollen and seeds, were identified through transcriptomic analysis. Convergence was observed in three signaling pathways: oxidative phosphorylation (ko00190), plant hormone signal transduction (Ko04075), and zeatin biosynthesis (ko00908). Notably, gene clusters prone to temperature-induced methylation changes, such as NADH-ubiquinone oxidoreductase chain 5, plasma membrane ATPase 4, cytochrome c oxidase subunit 2, cis-zeatin O-glucosyltransferase, ABSCISIC ACID-INSENSITIVE 5-like protein 4, and indole-3-acetic acid-amido synthetase (IAAS), were identified. Evaluation using various pollen pollination models revealed altered expression patterns of five dormancy-regulating marker genes: IAAS, sucrose synthase (SUS), gibberellin 2-oxidase (GA2ox), ABA INSENSITIVE 2 (ABI2), and auxin-repressed protein (ARP), in seeds pollinated with pollen from close-blocked anthers, cold-protected pollen, and pollen from freshly opened anthers. The close-blocked anther treatment led to significantly upregulated expression of IAAS, SUS, GA2ox, and ABI2, whereas ARP expression decreased markedly, indicating a propensity toward prolonged seed dormancy. Conversely, in the low-temperature-protected anther model, SUS, ARP, GA2ox, and IAAS exhibited reduced expression levels, whereas the expression of ABI2 was upregulated, overall facilitating seed germination.

Numerical investigation of the cavitation bubble near the solid wall with a gas-entrapping hole based on a fully compressible three-phase model.

The solid surface with several cavities containing gas strongly influences the bubble's dynamical behaviors. To reveal the underlying physical mechanism of the cavitation bubble near a rigid boundary with a gas-entrapping hole, a fully compressible three-phase model, accounting for the three-phase volume transport equation, was implemented in OpenFOAM. The predicted bubble shape was validated with the corresponding experimental photos, and good agreement was achieved. The bubble's primary physical features (e.g., the expanding shock wave, upward and downward liquid jet, and high-pressure region) are well reproduced, which helps understand the underlying mechanisms. The numerical results show that the solid wall with a gas-entrapping hole could affect the morphology of both the bubble and liquid jet, as well as shortens the bubble's first oscillation period in comparison to an intact rigid wall. The relationship among the prolongation factor, the standoff distance, and the relative size ratio is analyzed. It is found the prolongation factor increases as the relative size ratio decrease. As the standoff distance decreases, the gas entrapping hole plays a significant role in the oscillation period of the bubble. The current model can be further extended to reveal the microscopic mechanism of aeration avoiding cavitation damage and investigate the interaction between air bubbles and cavitation bubbles, which is of great interest to practical applications.

Mechanistic investigation and modeling of Cd immobilization by iron (hydr)oxide-humic acid coprecipitates.

A molecular-scale understanding of aqueous metal adsorption onto humic acid-iron (hydr)oxide coprecipitates, and our ability to model these interactions, are lacking. Here, the molecular-scale mechanisms for Cd binding onto iron (hydr)oxide-humic acid (HA) composites were probed using X-ray absorption fine structure (XAFS) spectroscopy and surface complexation modeling (SCM). The immobilization of Cd in (hydr)oxide precipitation systems occurs predominantly through adsorption onto the freshly-formed (hydr)oxide nanoparticles, and SCM calculations suggest a specific surface area of 2400 m2/g available for Cd. The solution and XAFS measurements indicate that HA promotes the precipitation of both Fe clusters and Fe-Cd associations mainly through ligand exchange reactions. Site masking reactions result in a dramatic blockage of functional sites on HA and ~45% migration of the adsorbed Cd to iron (hydr)oxide binding sites at high HA:Fe mass ratios. A composite model that accounts for both site masking between Fe ions and HA and the increase of Fe hydroxyl sites simulate the distribution of Cd in the composites reasonably well. Overall, this study demonstrates that the Fe clusters play an overriding role for heavy metal stabilization in coprecipitation systems, while HA promotes the immobilization of Cd by facilitating the flocculation and dispersion of Fe clusters.

Effects of long-term fertilization on calcium-associated soil organic carbon: Implications for C sequestration in agricultural soils.

Although the contribution of calcium ion (Ca2+) to stabilizing organic carbon (OC) in soils has been known for years, we still have a limited understanding of the quantity and molecular composition of Ca2+ bound SOC (Ca-OC) evolution in response to long-term fertilization. Here we report the role of Ca2+ in the accumulation of OC in the topsoil (0-20 cm) from two long-term (25-37 years) fertilization experiment sites. Approximately 4.54-19.27% and 9.00-25.15% of SOC was bound with Ca2+ in the Ferric Acrisol and Fluvic Cambisol, respectively. The application of NPK mineral fertilizers (NPK) decreased (p < 0.05) the Ca-OC stocks from 3.40 t ha-1 to 0.96 t ha-1 and from 2.03 t ha-1 to 1.17 t ha-1 in the Ferric Acrisol and Fluvic Cambisol, respectively. Swine manure (M) addition did not change (p > 0.05) the Ca-OC stock in Ferric Acrisol, but enhanced (p < 0.05) that from 2.03 t ha-1 to 9.75 t ha-1 in Fluvic Cambisol. Fourier transform infrared and carbon (1s)-near X-ray absorption spectroscopies showed that Ca2+ was mainly bound with aromatic carbon and carboxylic carbon. Long-term M fertilization facilitated the binding of Ca2+ with O-alkyl C, suggesting an increment of Ca-linked polysaccharide. Calcium ion was preferentially associated with 13C enriched organic matter (OM). Mineral fertilization promoted the 13C-enriched organic compounds in the Ca-OC, while organic fertilization facilitated the binding of 13C-depleted organic C with Ca2+. This study suggests that Ca-OC may be a potentially vital and stable OC pool in arable soils, and provides direct evidence for the preferential association of OC with Ca2+ in edaphic environments.

Modeling of Cd adsorption to goethite-bacteria composites.

The accurate modeling of heavy metal adsorption in complex systems is fundamental for risk assessments in soils and associated environments. Bacteria-iron (hydr)oxide associations in soils and sediments play a critical role in heavy metal immobilization. The reduced adsorption of heavy metals on these composites have been widely reported using the component additivity (CA) method. However, there is a lack of a mechanism model to account for these deviations. In this study, we established models for Cd adsorption on goethite-Pseudomonas putida composites at 1:1 and 5:1 mass ratios. Cadmium adsorption on the 5:1 composite was consistent with the additivity method. However, the CA method over predicted Cd adsorption by approximately 8% on the 1:1 composite at high Cd concentration. The deviation was corrected by adding the site blockage reactions between P. putida and goethite. Both CA and "CA-site masking" models for Cd adsorption onto the composites were in line with the ITC data. These results indicate that CA method in simulating Cd adsorption on bacteria-iron oxides composites is limited to low bacterial and Cd concentrations. Therefore the interfacial complexation reactions that occur between iron (hydr)oxides and bacteria should be taken into account when high concentrations of bacteria and heavy metals are present.

Pb sorption on montmorillonite-bacteria composites: A combination study by XAFS, ITC and SCM.

Though abundant studies have targeted the characterization of heavy metal adsorption by either clay minerals or bacteria, to date, minimal literature exists which specifically assesses bacteria-clay mineral interactions in the context of metal immobilization. The adsorption of Pb onto montmorillonite, Pseudomonas putida, and their 1:1, 2:1, 6:1 and 12:1 mass ratio composites were investigated by using a combination of atomic force microscope (AFM), X-ray diffraction (XRD), surface complexation modeling (SCM), Pb-LIII edge extended X-ray absorption fine structure (EXAFS) spectroscopy and isothermal titration calorimetry (ITC). The SCM and EXAFS demonstrated that Pb ions coordinate with phosphoryl and carboxyl functional groups on bacteria at low and high concentrations, respectively. The ITC analysis found adverse enthalpy values for Pb adsorption to permanent (-2.91 kJ/mol) and variable charge sites (6.93 kJ/mol) on montmorillonite. The ternary bridging model, EXAFS and ITC provide molecular and thermodynamic evidences for the formation of enthalpy driven (-4.74 kJ/mol) ternary complex (>AlO-Pb-PO4) in the composites. The proportion for the bridging structures increased at pH > 5 and high bacterial mass ratios. The formation of ternary complex did not result in the enhanced adsorption of Pb on the composites, but promoted the allocation of Pb on the mineral fraction. The results obtained from SCM, EXAFS and ITC may provide an essential assumption for predicting the speciation and fate of Pb in soils and associated environments.

Surface complexation modeling of Cu(II) sorption to montmorillonite-bacteria composites.

Surface complexation modeling, isothermal titration calorimetry, and batch adsorption were employed to characterize the adsorption of Cu onto montmorillonite, Pseudomonas putida X4, and their composites at mass ratios of 2:1, 6:1, and 12:1, respectively. Different enthalpy values were found for Cu adsorption to permanent (-6.43kJ/mol) and variable charge sites (8.51kJ/mol) on montmorillonite. The component additivity (CA) method was used to predict the adsorption of Cu on the composites by combining end member models for montmorillonite and P. putida. A reduced adsorption was observed at pH<5.5 due to physical blocking between montmorillonite and P. putida. By contrast, the enhanced binding at high pH levels was ascribed to the formation of bridging structures among the clay mineral-Cu-bacteria complexes. These deviations in the CA method were corrected by adding reactions of >RCOOH…XNa and >RCOOCuOHXNa. The increased adsorption of the composites confirmed the decrease of permanent negative charge sites and the formation of ternary complexes. The results help elucidate the effect of Cu adsorption onto clay minerals-bacteria composites. The newly developed "CA-site masking-bridging" model can be used to predict Cu speciation in systems in which the active interaction of bacteria and clay minerals occurs.