Effect of Cd(II) adsorption onto rice roots on its uptake by different indica and japonica rice varieties and toxicity effect of Cd(II) under acidic conditions.

The rapid increase in soil acidity coupled with the deleterious effects of cadmium (Cd) toxicity had led to a decline in worldwide agricultural production. Rice absorbs and accumulates Cd(II) from polluted paddy soils, increasing human health risks throughout the food chain. A 35-day hydroponic experiment with four japonica and four indica (two each of them tolerant and sensitive cultivars) was conducted in this study to investigate the adsorption and absorption of Cd(II) by rice roots as related with surface chemical properties of the roots. The results showed that the three chemical forms of exchangeable, complexed, and precipitated Cd(II) increased with the increase in Cd(II) concentration for all rice cultivars. The roots of indica rice cultivars carried more negative charges and had greater functional groups and thus adsorbed more exchangeable and complexed Cd(II) than those of japonica rice cultivars. This led to more absorption of Cd(II) by the roots and greater toxicity of Cd(II) to the roots of indica rice cultivars and more inhibition of Cd(II) stress on the growth of the roots and whole plants of indica rice cultivars compared with japonica rice cultivars, which was one of the main reasons for more declines in the biomass and length of indica rice roots and shoots than japonica rice cultivars. Cd(II) stress showed more toxicity to the sensitive rice cultivars and thus greater inhibition on the growth of the cultivars due to more exchangeable and complexed Cd(II) adsorbed by their roots induced by more negative charges and functional groups on the roots compared with tolerant rice cultivar for both indica and japonica, which resulted in greater decreases in the biomass and length of roots and shoots as well as chlorophyll contents of the sensitive cultivars than the tolerant cultivars. The roots of sensitive rice cultivars also absorbed more Cd(II) than tolerant rice cultivars due to the same reasons as above. These findings will provide useful references for the safe utilization and health risk prevention of Cd-contaminated paddy fields.

A new insight into the role of iron plaque in arsenic and cadmium accumulation in rice (Oryza sativa L.) roots.

Iron plaque, naturally iron-manganese (hydr)oxides adhered to the surface of rice roots, controls the sequestration and accumulation of arsenic (As) and cadmium (Cd) in the paddy soil-rice system. However, the effects of the paddy rice growth on the iron plaque formation and As and Cd accumulation of rice roots are often neglected. This study explores the distribution characteristics of iron plaques on rice roots and their effects on As and Cd sequestration and uptake via cutting the rice roots into 5 cm segments. Results indicated that the percentages of rice root biomass of 0-5 cm, 5-10 cm, 10-15 cm, 15-20 cm, and 20-25 cm are 57.5 %, 25.2 %, 9.3 %, 4.9 %, and 3.1 %, respectively. Iron (Fe) and manganese (Mn) concentrations in iron plaques on rice roots of various segments are 41.19-81.11 g kg-1 and 0.94-3.20 g kg-1, respectively. Increased tendency of Fe and Mn concentrations from the proximal rice roots to the distal rice roots show that iron plaque is more likely to deposit on the distal rice roots than proximal rice roots. The DCB-extractable As and Cd concentrations of rice roots with various segments are 694.63-1517.23 mg kg-1 and 9.00-37.58 mg kg-1, displaying a similar trend to the distribution characteristics of Fe and Mn. Furthermore, the average transfer factor (TF) of As (0.68 ± 0.26) from iron plaque to rice roots was significantly lower than that of Cd (1.57 ± 0.19) (P < 0.05). There was a significant positive correlation between the Cd sequestration in iron plaque and the Cd accumulation in rice roots (R = 0.97, P < 0.01). Still, a similar correlation wasn't observed between As sequestration in iron plaque and As accumulation in rice roots (R = -0.04, and P > 0.05). These results indicated that the formed iron plaque might act as a barrier to As uptake by rice roots and a facilitator to Cd uptake. This study provides insight into the role of iron plaque in the sequestration and uptake of As and Cd in paddy soil-rice systems.

NIR Fluorescent Probe for In Situ Bioimaging of Endogenous H2S in Rice Roots under Al3+ and Flooding Stresses.

Hydrogen sulfide (H2S) is one of the typical reactive sulfur species, which exhibits an important role in regulating both physiological and pathological processes. Recent studies indicate that H2S also serves as a key signaling molecule in a broad range of regulatory processes in plants. However, in situ imaging and detection of the levels of H2S in plant tissues remains a challenge. In this work, a NIR fluorescent probe (HBTP-H2S) was synthesized to achieve H2S imaging in living plant tissues. HBTP-H2S exhibited high sensitivity toward H2S with a large Stokes shift (250 nm). HBTP-H2S could be applied to HeLa cells to detect the fluctuation of endogenous H2S levels in response to physiological stimulations. Importantly, HBTP-H2S was utilized for direct H2S imaging of rice roots and revealed the upregulation of H2S signaling in response to aluminum ions and flooding stresses. Our work thus provides a new tool to investigate H2S-involved signal interaction and protective resistance of crops under environmental stresses.

An integrated strategy for the construction of a species-specific glycan library for mass spectrometry-based intact glycopeptide analyses.

Mass spectrometry (MS)-based strategies and related software tools using glycan mass lists have greatly facilitated the analysis of intact glycopeptides. Most glycan mass lists are derived from normal glycans of mammals and contain limited monosaccharides, which has significantly hindered high throughput studies of unusual glycosylation events observed in other species. In this work, an integrated strategy was developed for the construction of a species-specific glycan mass list from glycan structure databases and published papers. We developed a computational tool called LibGlycan, which could process the different formats of glycans. Then, the software tool generated a glycan library that contained the monoisotope mass, average mass, isotope distribution, and glycan mass list for input into Byonic software. This strategy was applied to analyze the N-glycosylation of rice roots and O-glycosylation of Acinetobacter baumannii ATCC17978, leading to the identification of 296 and 145 intact glycopeptides respectively. Combined, these results show that this strategy is a robust computational approach for the determination of glycan diversity within different complex biological systems.

Mechanism and function of root circumnutation.

Early root growth is critical for plant establishment and survival. We have identified a molecular pathway required for helical root tip movement known as circumnutation. Here, we report a multiscale investigation of the regulation and function of this phenomenon. We identify key cell signaling events comprising interaction of the ethylene, cytokinin, and auxin hormone signaling pathways. We identify the gene Oryza sativa histidine kinase-1 (HK1) as well as the auxin influx carrier gene OsAUX1 as essential regulators of this process in rice. Robophysical modeling and growth challenge experiments indicate circumnutation is critical for seedling establishment in rocky soil, consistent with the long-standing hypothesis that root circumnutation facilitates growth past obstacles. Thus, the integration of robotics, physics, and biology has elucidated the functional importance of root circumnutation and uncovered the molecular mechanisms underlying its regulation.

Calcium/calmodulin-dependent protein kinase OsDMI3 positively regulates saline-alkaline tolerance in rice roots.

Soil saline-alkalization is a major environmental stress that impairs plant growth and crop productivity. Plant roots are the primary site for the perception of soil stresses; however, the regulation mechanism engaged in the saline-alkaline stress response in plant roots is not well understood. In this study, we identified how a rice Ca2+/calmodulin-dependent protein kinase, OsDMI3, confers saline-alkaline tolerance in rice root growth. We measured the OsDMI3 activity by an in-gel kinase assay, Na+ content by NaHCO3 treatment, and Na+ and H+ fluxes by noninvasive micro-test technology (NMT). Furthermore, a real-time reverse-transcription polymerase chain reaction (RT-PCR) analysis was performed to identify the genes upregulated in response to NaHCO3 treatment in rice roots. The results showed that NaHCO3 significantly increased OsDMI3 expression and activity in rice roots. This was consistent with the results of Na+ content and NMT that indicated OsDMI3 promoted root elongation under saline-alkaline stress by reducing root Na+ and H+ influx. Moreover, real-time RT-PCR analysis revealed that OsDMI3 up-regulated the transcript levels of OsSOS1 and PM-H+-ATPase genes OsA3 and OsA8 in saline-alkaline stressed rice plants. Collectively, our results suggest that OsDMI3 could promote saline-alkaline tolerance in rice roots by modulating the Na+ and H+ influx. These findings provide an important genetic target for protection of growth in rice exposed to saline-alkaline stress.

Method for initially selecting Al-tolerant rice varieties based on the charge characteristics of their roots.

To explore the relationship between charge characteristics of rice roots and aluminum (Al) tolerance of rice, roots of 47 different rice genotypes were obtained by hydroponic experiment. The zeta potentials of roots were determined by streaming potential method, and the Al tolerance and the functional groups of rice were measured by relative root elongation and infrared spectroscopy (ATR-FTIR), respectively. The exchangeable, complexed and precipitated Al(III) sorbed on the root surface of rice was extracted with 1 mol L-1 KNO3, 0.05 mol L-1 EDTA-2Na and 0.01 mol L-1 HCl, respectively. There was a significant correlation between the zeta potentials and the relative elongation of rice roots, indicating that the zeta potentials of rice roots could be used to characterize rice tolerance to Al toxicity. Twelve Al-tolerant rice varieties, 25 medium Al-tolerant rice varieties, and 10 Al-sensitive rice varieties were obtained. The Al-tolerant rice varieties sorbed less complexed Al(III) and total Al(III) because there was lower negative charge on their roots compared to less tolerant genotypes. A correlation analysis showed that there were significant negative correlations between the zeta potential, relative root elongation, and the total Al(III) sorption capacity of the roots, which further confirmed the reliability of using the root zeta potential to characterize rice tolerance to Al toxicity. The results of this paper provide a new method for screening Al-tolerant rice varieties.

Microbiomes inhabiting rice roots and rhizosphere.

Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple food that feeds over 50% of the global population. Its root is a unique niche, which is often characterized by an oxic region (e.g. the rhizosphere) surrounded by anoxic bulk soil. This oxic-anoxic interface has been recognized as a pronounced hotspot that supports dynamic biogeochemical cycles mediated by various functional microbial groups. Considering the significance of rice production upon global food security and the methane budget, novel insights into how the overall microbial community (i.e. the microbiome) of the rice root system influences ecosystem functioning is the key to improving crop health and sustainable productivity of paddy ecosystems, and alleviating methane emissions. This mini-review summarizes the current understanding of microbial diversity of rice root-associated compartments to some extent, especially the rhizosphere, and makes a comparison of rhizosphere microbial community structures between rice and other crops/plants. Moreover, this paper describes the interactions between root-related microbiomes and rice plants, and further discusses the key factors shaping the rice root-related microbiomes.

Progressive drought alters architectural and anatomical traits of rice roots.

BACKGROUND: Root architectural and anatomical phenotypes are important for adaptation to drought. Many rice-growing regions face increasing water scarcity. This study describes drought responses of 11 Egyptian rice cultivars with emphasis on plastic root responses that may enhance drought adaptation. RESULTS: Eleven Egyptian rice cultivars were phenotyped for root architectural and anatomical traits after 6 weeks growth in soil mesocosms under well-watered conditions. Four of these cultivars were more intensively phenotyped under progressive drought stress in mesocosms, using a system where more moisture was available at depth than near the surface. In response to drought stress, all cultivars significantly reduced nodal root number while increasing large lateral root branching density and total lateral root length in the deepest portions of the mesocosm, where moisture was available. Nodal root cross-sectional area, but not stele area, was reduced by drought stress, especially in the basal segments of the root, and the number of late metaxylem vessels was reduced in only one cultivar. Alterations in deposition of lignin were detected by UV illumination from laser ablation tomography, enhanced by digital staining, and confirmed with standard histochemical methods. In well-watered plants, the sclerenchyma and endodermis were heavily lignified, and lignin was also visible throughout the epidermis and cortex. Under drought stress, very little lignin was detected in the outer cell layers and none in the cortex of nodal roots, but lignin deposition was enhanced in the stele. Root anatomical phenes, including cross-section area and metaxylem vessel number and lignin deposition varied dramatically along large lateral root axes under drought stress, with increasing diameter and less lignification of the stele in successive samples taken from the base to the root apex. CONCLUSIONS: Root architectural and anatomical traits varied significantly among a set of Egyptian cultivars. Most traits were plastic, i.e. changed significantly with drought treatment, and, in many cases, plasticity was cultivar-dependent. These phenotypic alterations may function to enhance water uptake efficiency. Increased large lateral root branching in the deep soil should maintain water acquisition, while water transport during drought should be secured with a more extensively lignified stele.

Interaction between contrasting rice genotypes and soil physical conditions induced by hydraulic stresses typical of alternate wetting and drying irrigation of soil.

BACKGROUND AND AIMS: Alternate wetting and drying (AWD) saves water in paddy rice production but could influence soil physical conditions and root growth. This study investigated the interaction between contrasting rice genotypes, soil structure and mechanical impedance influenced by hydraulic stresses typical of AWD. METHODS: Contrasting rice genotypes, IR64 and deeper-rooting Black Gora were grown in various soil conditions for 2 weeks. For the AWD treatments the soil was either maintained in a puddled state, equilibrated to -5 kPa (WET), or dried to -50 kPa and then rewetted at the water potential of -5 kPa (DRY-WET). There was an additional manipulated macropore structure treatment, i.e. the soil was broken into aggregates, packed into cores and equilibrated to -5 kPa (REPACKED). A flooded treatment (puddled soil remained flooded until harvest) was set as a control (FLOODED). Soil bulk density, penetration resistance and X-ray Computed Tomography (CT) derived macropore structure were measured. Total root length, root surface area, root volume, average diameter, and tip number were determined by WinRhizo. RESULTS: AWD induced formation of macropores and slightly increased soil mechanical impedance. The total root length of the AWD and REPACKED treatments were 1.7-2.2 and 3.5-4.2 times greater than that of the FLOODED treatment. There was no significant difference between WET and DRY-WET treatments. The differences between genotypes were minimal. CONCLUSIONS: AWD influenced soil physical properties and some root characteristics of rice seedlings, but drying soil initially to -50 kPa versus -5 kPa had no impact. Macropores formed intentionally from repacking caused a large change in root characteristics.

Effect of exogenous abscisic acid on morphology, growth and nutrient uptake of rice (Oryza sativa) roots under simulated acid rain stress.

MAIN CONCLUSION: Application of proper ABA can improve acid tolerance of rice roots by balancing endogenous hormones and promoting nutrient uptake. Abscisic acid (ABA) has an important signaling role in enhancing plant tolerance to environmental stress. To alleviate the inhibition on plant growth and productivity caused by acid rain, it is crucial to clarify the regulating mechanism of ABA on adaptation of plants to acid rain. Here, we studied the effects of exogenously applied ABA on nutrients uptake of rice roots under simulated acid rain (SAR) stress from physiological, biochemical and molecular aspects. Compared to the single SAR treatment (pH 4.5 or 3.5), exogenous 10 µM ABA alleviated the SAR-induced inhibition of root growth by balancing endogenous hormones (abscisic acid, indole-3-acetic acid, gibberellic acid and zeatin), promoting nutrient uptake (nitrate, P, K and Mg) in rice roots, and increasing the activity of the plasma membrane H+-ATPase by up-regulating expression levels of genes (OSA2, OSA4, OSA9 and OSA10). However, exogenous 100 µM ABA exacerbated the SAR-caused inhibition of root growth by disrupting the balance of endogenous hormones, and inhibiting nutrient uptake (nitrate, P, K, Ca and Mg) through decreasing the activity of the plasma membrane H+-ATPase. These results indicate that proper concentration of exogenous ABA could enhance tolerance of rice roots to SAR stress by promoting nutrients uptake and balancing endogenous hormones.

Rapid evaluation of arsenic contamination in paddy soils using field portable X-ray fluorescence spectrometry.

Arsenic (As) in paddy fields is deteriorating food security and human health through rice ingestion. Rice is the dominant food source of arsenic exposure to half of the world's population. Therefore, an in situ effective method for As risk evaluation in paddy soil is strongly needed to avoid As exposure through rice ingestion. Herein, we developed a rapid analytical methodology for determination of As in plant tissues using field portable X-ray fluorescence spectrometry (FP-XRF). This method was applied to rice roots in order to evaluate the As contamination in paddy soils. The results showed that rice roots with iron plaques were superior to rhizosphere soils for generating FP-XRF signals, especially for field sites with As concentrations lower than the soil detection limit of FP-XRF (30.0mg/kg). Moreover, the strong linear relationships of As concentrations between the rice roots and corresponding leaves and grains proved that the rice root, rather than the soil, is a better predictor of As concentrations in rice grains. The research provides an efficient As monitoring method for As contaminated paddy fields by using wetland plant roots with iron plaques and XRF-based analytical techniques.

Streaming potential method for characterizing interaction of electrical double layers between rice roots and Fe/Al oxide-coated quartz in situ.

The interaction between rice roots and Fe/Al oxide-coated quartz was investigated through zeta potential measurements and column leaching experiments in present study. The zeta potentials of rice roots, Fe/Al oxide-coated quartz, and the binary systems containing rice roots and Fe/Al oxide-coated quartz were measured by a specially constructed streaming potential apparatus. The interactions between rice roots and Fe/Al oxide-coated quartz particles were evaluated/deduced based on the differences of zeta potentials between the binary systems and the single system of rice roots. The zeta potentials of the binary systems moved in positive directions compared with that of rice roots, suggesting that there were overlapping of diffuse layers of electric double layers on positively charged Fe/Al oxide-coated quartz and negatively charged rice roots and neutralization of positive charge on Fe/Al oxide-coated quartz with negative charge on rice roots. The greater amount of positive charges on Al oxide led to the stronger interaction of Al oxide-coated quartz with rice roots and the more shift of zeta potential compared with Fe oxide. The overlapping of diffuse layers on Fe/Al oxide-coated quartz and rice roots was confirmed by column leaching experiments. The greater overlapping of diffuse layers on Al oxide and rice roots led to more simultaneous adsorptions of K+ and NO3- and greater reduction in leachate electric conductivity when the column containing Al oxide-coated quartz and rice roots was leached with KNO3 solution, compared with the columns containing rice roots and Fe oxide-coated quartz or quartz. When the KNO3 solution was replaced with deionized water to flush the columns, more K+ and NO3- were desorbed from the binary system containing Al oxide-coated quartz and rice roots than from other two binary systems, suggesting that the stronger electrostatic interaction between Al oxide and rice roots promoted the desorption of K+ and NO3- from the binary system and enhanced overlapping of diffuse layers on these oppositely charged surfaces compared with other two binary systems. In conclusion, the overlapping of diffuse layers occurred between positively charged Fe/Al oxides and rice roots, which led to neutralization of opposite charge and affected adsorption and desorption of ions onto and from the charged surfaces of Fe/Al oxides and rice roots.

Effects of adhesions of amorphous Fe and Al hydroxides on surface charge and adsorption of K+ and Cd2+ on rice roots.

Iron (Fe) and aluminum (Al) hydroxides in variable charge soils attached to rice roots may affect surface-charge properties and subsequently the adsorption and uptake of nutrients and toxic metals by the roots. Adhesion of amorphous Fe and Al hydroxides onto rice roots and their effects on zeta potential of roots and adsorption of potassium (K+) and cadmium (Cd2+) by roots were investigated. Rice roots adsorbed more Al hydroxide than Fe hydroxide because of the greater positive charge on Al hydroxide. Adhesion of Fe and Al hydroxides decreased the negative charge on rice roots, and a greater effect of the Al hydroxide. Consequently, adhesion of Fe and Al hydroxides reduced the K+ and Cd2+ adsorption by rice roots. The results of attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) and desorption of K+ and Cd2+ from rice roots indicated that physical masking by Fe and Al hydroxides and diffuse-layer overlapping between the positively-charged hydroxides and negatively-charged roots were responsible for the reduction of negative charge on roots induced by adhesion of the hydroxides. Therefore, the interaction between Fe and Al hydroxides and rice roots reduced negative charge on roots and thus inhibited their adsorption of nutrient and toxic cations.

Functional Analysis of a MATE Gene OsFRDL2 Revealed its Involvement in Al-Induced Secretion of Citrate, but a Lower Contribution to Al Tolerance in Rice.

The multidrug and toxic compound extrusion (MATE) transporters represent a large transporter family in plants, but the role of most genes in this family has not been examined. We functionally characterized a MATE family member, OsFRDL2, in rice (Oryza sativa). OsFRDL2 showed an efflux transport activity for citrate when it was expressed in both Xenopus oocytes and cultured tobacco cells. OsFRDL2 was mainly expressed in the roots and its expression was not induced by iron (Fe) deficiency, but it was rapidly up-regulated by aluminum (Al). Furthermore, the expression of OsFRDL2 was regulated by ART1, a C2H2-type zinc-finger transcription factor for Al tolerance. OsFRDL2 protein was localized at unidentified vesicles in the cytosol, but not co-localized with either mitochondria or peroxisomes when expressed in both onion epidermal cells and cultured tobacco cells. Knockout of OsFRDL2 decreased Al-induced secretion of citrate from the roots, but did not affect the internal citrate concentration. The Al-induced inhibition of root elongation was similar between the OsFRDL2 knockout line and its wild-type rice. Knockout of OsFRDL2 did not affect the translocation of Fe from the roots to the shoots. A double mutant between osfrdl2 and osfrdl4 or osfrdl1 did not further decrease the Al-induced citrate secretion and Fe translocation compared with the single mutant. Collectively, our results indicate that although OsFRDL2 is involved in the Al-induced secretion of citrate, its contribution to high Al tolerance is relatively small in rice.

Diterpenes from the roots of Oryza sativa L. and their inhibition activity on NO production in LPS-stimulated RAW264.7 macrophages.

Two new pimarane diterpenoids, momilactone D (3) and momilactone E (5), along with three known diterpenoids, momilactone A (1), sandaracopimaradien-3-one (2), and oryzalexin A (4) were isolated from Oryza sativa roots. The chemical structures of the compounds were determined by spectroscopic data analysis. The isolated diterpenoids were evaluated for their ability to inhibit NO production and iNOS mRNA and protein expression in LPS-stimulated RAW264.7 macrophages. Compound 4 showed strong inhibition activity on NO production, and compounds 1 and 4 decreased the expression of iNOS mRNA and protein levels.

Rapid quantification of rice root-associated bacteria by flow cytometry.

UNLABELLED: To understand the mechanism of plant-bacterium interaction, it is critical to enumerate epiphytic bacteria colonizing the roots of the host. We developed a new approach, based on flow cytometry, for enumerating these bacteria and used it with rice plants, 7 and 20 days after colonization with Herbaspirillum rubrisubalbicans and Azospirillum brasilense. The results were compared with those obtained with the traditional plate count method. Both methods gave similar numbers of H. rubrisubalbicans associated with rice roots (c. 10(9) CFU g(-1) ). However, flow cytometry gave a number of viable cells of rice-associated A. brasilense that was approx. 10-fold greater than that obtained with the plate count method. These results suggest that the plate count method can underestimate epiphytic populations. Flow cytometry has the additional advantage that it is more precise and much faster than the plate count method. SIGNIFICANCE AND IMPACT OF THE STUDY: Determination of precise number of root-associated bacteria is critical for plant-bacteria interaction studies. We developed a flow cytometry approach for counting bacteria and compared it with the plate count method. Our flow cytometry assay solves two major limitations of the plate count method, namely that requires long incubation times of up to 48 h and only determines culturable cells. This flow cytometry assay provides an efficient, precise and fast tool for enumerating epiphytic cells.