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The efficacy of nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) varies with soil types. Understanding the microbial mechanisms for this variation may lead to better modelling of NI efficacy and therefore on-farm adoption. This study addressed the response patterns of mineral nitrogen, nitrous oxide (N2O) emission, abundances of N-cycling functional guilds and soil microbiota characteristics, in relation to urea application with or without DCD or DMPP in two arable soils (an alkaline and an acid soil). The inhibition of nitrification rate and N2O emission by NI application occurred by suppressing ammonia-oxidizing bacteria (AOB) abundances and increasing the abundances of nosZI-N2O reducers; however, abundances of ammonia-oxidizing archaea (AOA) were also stimulated with NIs-added in these two arable soils. DMPP generally had stronger inhibition efficiency than DCD, and both NIs' addition decreased Nitrobacter, while increased Nitrospira abundance only in alkaline soil. N2O emissions were positively correlated with AOB and negatively correlated with nosZI in both soils and AOA only in acid soil. Moreover, N2O emissions were also positively correlated with nirK-type denitrifiers in alkaline soil, and clade A comammox in acid soil. Amendment with DCD or DMPP altered soil microbiota community structure, but had minor effect on community composition. These results highlight a crucial role of the niche differentiation among canonical ammonia oxidizers (AOA/AOB), Nitrobacter and Nitrospira, as well as nosZI- and nosZII-N2O reducers in determining the varying efficacies of DCD and DMPP in different arable soils. [ABSTRACT FROM AUTHOR]

The Hall–Petch relationship and deformation process in Ti3Al nano-polycrystalline alloys are investigated using molecular dynamics simulations in this research. The impact of different grain sizes and temperatures on mechanical characteristics was considered. Different Hall–Petch relations were detected for samples with the grain sizes ranging from 2 to 20 nm, inverse Hall–Petch relations in big grain sizes ranges, and positive Hall–Petch relations in the medium grain size region, respectively. A transition zone formed at the interception of positive and inverse Hall–Petch relations, which will vanish as the temperature rises. The critical grain size of the positive Hall–Petch relation decreases as the temperature rises from 10 to 600 K. With the grain size increases in the smaller grain size range, the yield stress increases, which is made by the grain boundary motion and rotation. Besides, temperatures affect mechanical characteristics. The rising temperatures lead to the decreasing dislocation density and a high grain boundary fraction. [ABSTRACT FROM AUTHOR]

Phosphorus (P) accumulation in croplands resulting from ever-increasing input of P fertilizer strongly influences soil microbial growth and activities, which is expected to alter the soil priming effect (PE) induced by plant residue. However, the effect of P availability on the magnitude and direction of PE remains largely unexplored and the underlying microbial mechanisms are still unclear. Therefore, a 40-day incubation experiment was established by adding C4-maize straw to C3-soils with or without long-term P fertilizer inputs to investigate PE and accompanied dynamics of microbiota. The results revealed that in both soils, straw application caused positive real PEs via a "microbial co-metabolism" mechanism, accompanied by a microbial succession from the dominance of r- and K-strategists to K-strategists (mainly fungi). In addition, long-term amendment with P increased PE by 83.2% compared with no P fertilization control, which was mainly mediated by K-strategists, especially the fungal families Chaetomiaceae and Myrmecridiaceae. The increased PE was accompanied by enhanced microbial biomass carbon, extracellular enzyme activities, and bacterial gene abundance, confirming the "stoichiometric decomposition" theory. Meanwhile, deviating from the conventional paradigm, higher phosphatase activity and lower enzymatic stoichiometry of carbon (C)-to-P ratios in high-P soil compared with that in low-P soil suggested stronger "P mining" with high-P availability. [ABSTRACT FROM AUTHOR]

Research on the structural properties of silicon crystal nucleation during solidification has been the subject of numerous classic studies in condensed matter physics and material science. The approach to structural properties of Si crystal nucleation adopted for this paper is based on molecular dynamics simulation at the cooling rate of 1010 K/s. Using the entropy of largest standard cluster and the pair distribution function, it is able to obtain microstructural evolution characteristics. The pleomorphism properties and distribution of Si crystal nucleation was presented by the visualization method. The systematic evolution diagram illustrates the competitive growth between cubic diamond and hexagonal diamond structures which shows that the crystal nucleus easily forms and then grow during a short period of time at the initial crystallization stage. The orientation characteristics after crystal nucleation in space are systematically analyzed and it is found that the nucleation and orientation of crystals are weakly dependent, that is, the orientations of crystals are homogeneous and random. In addition, the visualization results show that various twins exist in the system, including coherent twins, rotating twins and some torsional twins, which improve the structural stability to a certain degree. This study further explores crystal nucleation on the atomic scale and it is hoped that this research will contribute to expanding the understanding of the orientation distribution and crystallization behavior of amorphous silicon during the growth process. [ABSTRACT FROM AUTHOR]

A 28-day microcosm experiment was conducted using three paddy soils (an alluvial paddy soil, a loess-formed paddy soil, and a yellow clayey paddy soil) to investigate the impact of procyanidin on N2O emissions and associated microbial mechanisms. The efficacy of procyanidin on N2O emissions varied among the paddy soils tested, with an average inhibition rate ranging from 2.7% in the alluvial paddy soil to 57.1% in the loess-formed paddy soil. Furthermore, suppression of N2O emissions by procyanidin occurred alongside fluctuations in nitrate reductase activity and nirS- and nirK-type denitrifiers abundance. The correlation analysis indicates that nitrate reductase, clade I nirS-denitrifiers, clade I or II, and clade III nirK-denitrifiers were closely linked to N2O emissions. These findings provide evidence that procyanidin is capable of limiting N2O emissions in paddy soils by inhibiting nitrate reductase and different clades of nirS-/nirK-denitrifiers. [ABSTRACT FROM AUTHOR]

A microcosm study was established using three arable soils differing in both physicochemical properties and AOB or AOA dominance of ammonia oxidization. Nitrification and N2O emissions were quantified under 10 Pa C2H2, 1-octyne, or 3,4-dimethylpyrazole phosphate (DMPP), and the community composition and abundance of AOA and AOB were assessed. Amendment of soil with DMPP had a comparable effect to 1-octyne on AOB activities, composition, and N2O emissions across soils. By blocking AOB activity, both DMPP and 1-octyne supported higher rates of AOA growth in both the acid and alkaline soils. Approximately, 50% of ammonia-oxidizing activity in the acid soil was attributed to AOB activity by phylotypes affiliated with Nitrosomonas communis. When AOB were blocked by DMPP or 1-octyne across all soils, recovery of AOA communities was associated with the increased abundance of Nitrososphaera viennesis. [ABSTRACT FROM AUTHOR]

Background and aims: Silicon (Si) is known to alleviate aluminum (Al) toxicity in a number of plant species; however, the mechanisms of Si-triggered Al detoxification have not been elucidated, especially in rice (Oryza sativa). We investigated the interactions between Si and Al in root and the role of cell wall polysaccharides in rice resistance to Al. Methods: Rice seedlings were grown in 0.5 mM CaCl2 solution with or without 50 µM Al and 1.0 mM H4SiO4 for 24 h. The cell expansion and oxidative injury of root were measured by histochemical analyses; Al accumulation and distribution in root apices were determined by inductively coupled plasma mass spectrometry (ICP-MS); the degree of pectin methylesterification was analyzed by immunofluorescence, and the expression of genes (e.g. OsPME) related to Al resistance was measured by quantitative real-time PCR. Results: Si relieved the inhibition of cell elongation and oxidative injury caused by Al and significantly reduced Al content (by about 41 %) in cell wall (CW). Meanwhile, Si inhibited pectin methylesterase (PME) activity and its gene expression, thereby increasing the degree of pectin methylesterification, and reduced the content of hemicellulose, which was the main binding site for Al in CW, under Al stress. Furthermore, Si decreased the non-exchangeable Al fraction of CW in root, but did not change the cation exchange capacity of CW. Conclusions: Si reduces the deposition of Al in the cell wall of rice root apex by decreasing both the degree of pectin demethylesterification and the content of hemicellulose, thereby alleviating Al stress. [ABSTRACT FROM AUTHOR]

Aims: As a vital polysaccharide related to mechanisms of plant resistance to trace metal in the root cell wall, the role of hemicellulose in cadmium (Cd) accumulation in hyperaccumulators is still unknown. We investigated hemicellulose modification in response to Cd in two populations of Sedum alfredii. Methods: Nonhyperaccumulating population (NHP) and hyperaccumulating population (HP) of S. alfredii were grown in nutrient solutions with or without 25 μM Cd for 15 d. Monosaccharide composition of root cell wall hemicellulose and its remolding mechanisms (e.g. enzyme activity and gene expression) were analyzed by using gas chromatography-mass spectrometer (GC-MS), fourier transform infrared spectrometer (FTIR), nuclear magnetic resonance (NMR) and quantitative real-time PCR techniques. Results: In 25 μM Cd treatment, root cell wall hemicellulose in the NHP significantly (P < 0.05) increased and its hemicellulose-bound Cd was nearly 2.5-fold higher than that of HP. In the presence of Cd, xylose and glucose, proved to be the main component of hemicellulose, were higher in the NHP than in the HP owing to the up-regulation of XET/XEH and encoding gene (XTH 31). 113Cd-NMR and FTIR results indicated that hemicellulose with hydroxyl and carboxyl groups of HP retained less Cd than that of NHP. Conclusion: Hemicellulose modification decreased the Cd-binding capacity of the root cell wall and increased the entry of Cd in the shoot of HP S. alfredii. [ABSTRACT FROM AUTHOR]

The use of high-energy ions or clusters to bombard graphene is emerging as a new method for the theoretical study of graphene properties. In this study, using molecular dynamics simulations and empirical potentials, the behaviors of graphene after bombardment by C60 under different initial velocities from 13.7 to 15.7 km/s were investigated. The simulations showed four types of defects: Stone–Wales defects, single vacancy defects, multiple vacancy defects, and out-of-plane carbon adatoms. The self-healing phenomenon of defective graphene was observed. In the low-speed region (< 14.5 km/s), the self-healing ability of graphene is enhanced at higher temperature. However, the effect of temperature is not obvious in the high-speed region, where velocity dominates. To repair vacancy defects in graphene, a physical method was proposed. The initial positions of lost atoms were traced, and then, the atoms were slowly dropped into the vacancy defects to effect repair. The simulations provide a fundamental understanding of bombardment between graphene and C60 and propose a new method for repairing vacancy defects in graphene. [ABSTRACT FROM AUTHOR]

In this study, soil samples from the typical rice-wheat cropping system in Jiangsu Province, China, subjected to different fertilizer application treatments-no carbon (CK), urea (UR), straw (SR), pig manure (PM), starch (ST), and glucose (GL)-were used to determine potential anaerobic ammonium oxidation (anammox) rate and its association with bacterial abundance, diversity, and activity by using DNA stable isotope probing combined with N isotope tracing and molecular techniques. The effects of different organic carbon sources on anammox were significant, in the following order: GL > ST, SR > UR > PM; anammox activity differed significantly across treatments; however, the C active anammox bacteria were only closely related to Ca. Brocadia. The anammox hydrazine synthase β subunit functional gene sequences were highly associated with the Candidatus genus Brocadia in PM and CK treatments. The different organic carbon sources had different inhibitory effects with anammox rate, which dropped from 3.19 to 1.04 nmol dinitrogen gas g dry soil h among treatments. About 4.2-22.3% of dinitrogen gas emissions were attributed to anammox and indicated that a specific population of anammox bacteria was present and varied with the addition of exogenous organic compounds in paddy soils, although a small part of dinitrogen gas was emitted from the soil via anammox. [ABSTRACT FROM AUTHOR]

Interactions between roots and microbes affect plant's resistance to abiotic stress. However, the structural and functional variation of root-associated microbiomes and their effects on metal accumulation in hyperaccumulators remain poorly understood. Here, we characterize the root-associated microbiota of a hyperaccumulating (HP) and a non-hyperaccumulating (NHP) genotype of Sedum alfredii by 16S ribosomal RNA gene profiling. We show that distinct microbiomes are observed in four spatially separable compartments: the bulk soil, rhizosphere, rhizoplane, and endosphere. Both the rhizosphere and rhizoplane were preferentially colonized by Proteobacteria, and the endosphere by Actinobacteria. The rhizosphere and endophytic microbiomes were dominated by the family of Sphingomonadaceae and Streptomycetaceae, respectively, which benefited for their survival and adaptation. The bacterial α-diversity decreases along the spatial gradient from the rhizosphere to the endosphere. Soil type and compartment were strongest determinants of root-associated community variation, and host genotype explained a small, but significant amount of variation. The enrichment of Bacteroidetes and depletion of Firmicutes and Planctomycetes in the HP endosphere compared with that of the NHP genotype may affect metal hyperaccumulation. Program PICRUSt predicted moderate functional differences in bacterial consortia across rhizocompartments and soil types. The functional categories involved in membrane transporters (specifically ATP-binding cassette transporters) and energy metabolism were overrepresented in endosphere of HP in comparison with NHP genotypes. Taken together, our study reveals substantial variation in structure and function of microbiomes colonizing different compartments, with the endophytic microbiota potentially playing an important role in heavy metal hyperaccumulation. [ABSTRACT FROM AUTHOR]

This study evaluated the effect of silicate fertilizer on denitrification and associated gene abundance in a paddy soil. A consecutive trial from 2013 to 2015 was conducted including the following treatments: control (CK), mineral fertilizer (NPK), NPK plus sodium metasilicate (NPK + MSF), and NPK plus slag-based silicate fertilizer (NPK + SSF). Real-time quantitative PCR (qPCR) was used to analyze the abundances of nirS, nirK, and nosZ genes. Potential NO emissions and ammonium and nitrate concentrations were related to the nirS and nirK gene abundance. Compared with the NPK treatments, the addition of a Si fertilizer decreased NO emission rates and denitrification potential by 32.4-66.6 and 22.0-59.2%, respectively, which were probably related to increased rice productivity, soil Fe availability, and soil N depletion. The abundances of nirS and nirK genes were decreased by 17.7-35.8% and 21.1-43.5% with addition of silicate fertilizers, respectively. Rates of total NO and NO from denitrification (DeNO) emission were positively correlated with the nirS and nirK gene abundance. Nitrate, exchangeable NH , and Fe concentrations were the main factors regulating the nirS and nirK gene abundance. Silicate fertilization during rice growth may serve as an effective approach to decreasing NO emissions. [ABSTRACT FROM AUTHOR]

The association between microbial communities and plant growth in long-term fertilization system has not been fully studied. In the present study, impacts of long-term fertilization have been determined on the size and activity of soil microbial communities and wheat performance in a red soil (Ultisol) collected from Qiyang Experimental Station, China. For this, different microbial communities originating from long-term fertilized pig manure (M), mineral fertilizer (NPK), pig manure plus mineral fertilizer (MNPK), and no fertilizer (CK) were used as inocula for the Ultisol tested. Changes in total bacterial and fungal community composition and structures using Ion Torrent sequencing were determined. The results show that the biomass of wheat was significantly higher in both sterilized soil inoculated with NPK (SNPK) and sterilized soil inoculated with MNPK (SMNPK) treatments than in other treatments ( P < 0.05). The activities of β-1,4- N-acetylglucosaminidase (NAG) and cellobiohydrolase (CBH) were significantly correlated with wheat biomass. Among the microbial communities, the largest Ascomycota phylum in soils was negatively correlated with β-1,4-glucosidase (βG) ( P < 0.05). The phylum Basidiomycota was negatively correlated with plant biomass (PB) and tillers per plant (TI) ( P < 0.05). Nonmetric multidimensional scaling analysis shows that fungal community was strongly correlated with long-term fertilization strategy, while the bacterial community was strongly correlated with β-1,4- N-acetylglucosaminidase activity. According to the Mantel test, the growth of wheat was affected by fungal community. Taken together, microbial composition and diversity in soils could be a good player in predicting soil fertility and consequently plant growth. [ABSTRACT FROM AUTHOR]

Background and aims: We investigated the effects of silicon (Si) on chlorophyll concentration, photosynthesis, leaf chloroplast ultrastructure, and expression of genes involved in photosynthesis to elucidate the mechanisms through which Si mediated alleviation of manganese (Mn) toxicity in rice ( Oryza sativa L.). Methods: Rice seedlings were grown hydroponically with normal Mn (6.7 μM) or high Mn (2 mM) concentrations, both with (1.5 mM) and without Si supplementation. Leaf chloroplast ultrastructure was observed by scanning and transmission electron microscopy. Differentially expressed genes relating to photosynthesis were identified by high-throughput sequencing, and their relative expression levels were evaluated by real-time quantitative PCR. Results: Chlorophyll and carotenoid concentrations and net photosynthesis decreased with chloroplast degradation under high Mn stress. High Mn concentrations may have inhibited photosynthesis through several mechanisms, including suppressing chlorophyll and ATP synthesis, decreasing light-harvesting processes, impairing photosystem I (PSI) stability and structure, and slowing activity of phosphoribulokinase. Si enhanced Mn tolerance efficiently by increasing chlorophyll concentration, light-use efficiency, and ATP concentration as well as by stabilizing the structure of PSI and promoting CO assimilation. Conclusions: Our findings suggest active involvement of Si in Mn detoxification, ranging from physiological responses to gene expression. [ABSTRACT FROM AUTHOR]

Preferable inorganic fertilization over the last decades has led to fertility degradation of black soil in Northeast China. However, how fertilization regimes impact denitrification and its related bacterial community in this soil type is still unclear. Here, taking advantage of a suit of molecular ecological tools in combination of assaying the potential denitrification (DP), we explored the variation of activity, community structure, and abundance of nirS and nirK denitrifiers under four different fertilization regimes, namely no fertilization control (N0M0), organic pig manure (N0M1), inorganic fertilization (N1M0), and combination of inorganic fertilizer and pig manure (N1M1). The results indicated that organic fertilization increased DP, but inorganic fertilization had no impacts. The increase of DP was mirrored by the shift of nirS denitrifiers' community structure but not by that of nirK denitrifiers'. Furthermore, the change of DP coincided with the variation of abundances of both denitrifiers. Shifts of community structure and abundance of nirS and nirK denitrifiers were correlated with the change of soil pH, total nitrogen (TN), organic matter (OM), C:P, total phosphorus (TP), and available phosphorus (Olsen P). Our results suggest that the change of DP under these four fertilization regimes was closely related to the shift of denitrifying bacteria communities resulting from the variation of properties in the black soil tested. [ABSTRACT FROM AUTHOR]

Background and aims: The role of polysaccharide modification in metal accumulation in hyperaccumulators is still unknown. Our aim was to compare the differences in the role of root cell-wall polysaccharides in cadmium (Cd) accumulation between hyperaccumulating (HE) and non-hyperaccumulating ecotype (NHE) of Sedm alfredii. Methods: Hydroponic experiments were performed to characterize root-to-shoot Cd translocation, cadmium species and polysaccharide modification in root cell-wall of S. alfredii using stable isotope tracing, X-ray absorption near edge structure and immunofluorescence localization techniques. Results: Cd absorbed was more readily available for transport to the shoots by the HE roots than by the NHE roots, which is confirmed by a 6-fold higher Cd concentration in xylem sap. Root Cd efflux originated mainly from the cell walls. The concentration of cell-wall polysaccharides and activity of pectin methylesterase were higher in the NHE than in the HE in the absence of Cd, and even higher in the presence of Cd. More pectins were methylated in the HE than in the NHE, indicating more free pectic acid residues in the NHE. The cell-wall-bound Cd was retained more tightly in the NHE than in the HE. Conclusions: Cadmium hyperaccumulation by HE of S. alfredii is associated with its enhanced Cd flux into the xylem, which is partly regulated by cell-wall polysaccharide modification in roots. [ABSTRACT FROM AUTHOR]

The two-layer nanotubes consisted of carbon atoms on the outside layer and silicon atoms on the inside layer (CNT@SiNT) show a series of diversity in the shape transitions, for instance transforming from a circle through an oval to a rectangle. In this paper, we investigate this geometric change from three perspectives. In the first aspect, we stationary time, followed by quantize in the three-dimensional Z-axis of nanotubes. In the second aspect, we stationary Z-axis, followed by quantize in the time. Finally, we tracked distance of nanotubes flattest section and roundest section. At the stationary time, the overall image of different Z-axis distance distributions is similar to a plan view of multiple ice creams, regardless of whether CNT or SiNT are on the same Z-axis, their slice plans are circle or rectangle of the projection of the Z-axis section on the XOY plane. In the stationary Z-axis, the nanotubes periodically change from a circle to an oval, and then from an oval to a rectangle at different times. Most remarkably, the distance value of deformation which we track the flattest and roundest is a constant value, and in the same distance period, there is only one roundest circle and one longest rectangle at different section and different time. The geometric analysis provided theoretical reference for the preparation of various devices and semiconductor nano-heterojunctions. [ABSTRACT FROM AUTHOR]

Abiotic and biotic stresses are the major factors limiting plant growth worldwide. Plants exposed to abiotic and biotic stresses often cause reduction in plant biomass as well as crop yield, resulting in plant biomass carbon loss. As a beneficial and quasi-essential element, silicon accumulation in rhizosphere and plants can alleviate the unfavorable effects of the major forms of abiotic and biotic stress through several resistance mechanisms and thus increases plant biomass accumulation and crop yield. The beneficial effects of silicon on plant growth and crop yield have been widely reviewed over the last years. However, carbon accumulation of silicon-associated plant biomass under abiotic and biotic stresses has not yet been systematically addressed. This review article focuses on both the main mechanisms of silicon-mediated alleviation of abiotic and biotic stresses and their effects on plant biomass carbon accumulation in terrestrial ecosystems. The major points are the following: (1) the recovery of plant biomass via silicon mediation usually exhibits a bell-shaped response curve to abiotic stress severity and an S-shaped response curve to biotic stress severity; (2) although carbon concentration of plant biomass decreases with silicon accumulation, more than 96% of the recovered plant biomass contributes to plant biomass carbon accumulation; (3) silicon-mediated recovery generally increases plant biomass carbon by 35% and crop yield by 24%. In conclusion, silicon can improve plant growth and enhance plant biomass carbon accumulation under abiotic and biotic stresses in terrestrial ecosystems. [ABSTRACT FROM AUTHOR]