Rice root properties for internal aeration and efficient nutrient acquisition in submerged soil

Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields

Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH4) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH4 oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and 13CH4-DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH4 oxidation in supporting denitrification. Our results reveal positive relationships between CH4 oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH4 and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, 13CH4-DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating 13C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of 13C-metagenome-assembled genomes and 13C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH4 oxidation, for the coupling of CH4 oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH4 oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.

An overview of oxygen transport in plants: diffusion and convection

The movement of gases within plants is crucial for species that live in flood-prone areas with limited soil oxygen. These plants adapt to hypoxia/anoxia not by using oxygen more efficiently, but by ensuring a steady oxygen supply to their cells. Wetland plants typically form gas-filled spaces (aerenchyma) in their tissues, providing a low-resistance pathway for gas movement between shoots and roots, especially when the shoots are above water, and the roots are submerged. Oxygen movement in plant roots is mainly through diffusion. However, in certain species, such as emergent and floating-leaved plants, pressurized flows can also facilitate the movement of gases within their stems and rhizomes. Three types of pressurized (convective) flows have been identified: humidity-induced pressurization (positive pressure), thermal osmosis (positive pressure with air flow against the heat gradient), and venturi-induced suction (negative pressure) caused by wind passing over broken culms. A clear diel variation in pressurized flows exists, with higher pressures and flows during the day and negligible pressures and flows during the night. This article discusses some key aspects of these mechanisms for oxygen movement.

Mitigation of Greenhouse Gas Emissions from Rice via Manipulation of Key Root Traits

Rice production worldwide represents a major anthropogenic source of greenhouse gas emissions. Nitrogen fertilization and irrigation practices have been fundamental to achieve optimal rice yields, but these agricultural practices together with by-products from plants and microorganisms, facilitate the production, accumulation and venting of vast amounts of CO₂, CH₄ and N₂O. We propose that the development of elite rice varieties should target root traits enabling an effective internal O₂ diffusion, via enlarged aerenchyma channels. Moreover, gas tight barriers impeding radial O₂ loss in basal parts of the roots will increase O₂ diffusion to the root apex where molecular O₂ diffuses into the rhizosphere. These developments result in plants with roots penetrating deeper into the flooded anoxic soils, producing higher volumes of oxic conditions in the interface between roots and rhizosphere. Molecular O₂ in these zones promotes CH₄ oxidation into CO₂ by methanotrophs and nitrification (conversion of NH₄⁺ into NO₃^-), reducing greenhouse gas production and at the same time improving plant nutrition. Moreover, roots with tight barriers to radial O₂ loss will have restricted diffusional entry of CH₄ produced in the anoxic parts of the rhizosphere and therefore plant-mediated diffusion will be reduced. In this review, we describe how the exploitation of these key root traits in rice can potentially reduce greenhouse gas emissions from paddy fields.

Transcriptional Expression of Nitrogen Metabolism Genes and Primary Metabolic Variations in Rice Affected by Different Water Status

The era of climate change strongly requires higher efficiency of energies, such as light, water, nutrients, etc., during crop production. Rice is the world's greatest water-consuming plant, and, thus, water-saving practices such as alternative wetting and drying (AWD) are widely recommended worldwide. However the AWD still has concerns such as lower tillering, shallow rooting, and an unexpected water deficit. The AWD is a possibility to not only save water consumption but also utilize various nitrogen forms from the soil. The current study tried to investigate the transcriptional expression of genes in relation to the acquisition-transportation-assimilation process of nitrogen using qRT-PCR at the tillering and heading stages and to profile tissue-specific primary metabolites. We employed two water supply systems, continuous flooding (CF) and alternative wetting and drying (AWD), during rice growth (seeding to heading). The AWD system is effective at acquiring soil nitrate; however, nitrogen assimilation was predominant in the root during the shift from the vegetative to the reproductive stage. In addition, as a result of the greater amino acids in the shoot, the AWD was likely to rearrange amino acid pools to produce proteins in accordance with phase transition. Accordingly, it is suggested that the AWD 1) actively acquired nitrate from soil and 2) resulted in an abundance of amino acid pools, which are considered a rearrangement under limited N availability. Based on the current study, further steps are necessary to evaluate form-dependent N metabolism and root development under the AWD condition and a possible practice in the rice production system.

In situ mapping of ion distribution profiles and gene expression reveals interactions between hypoxia and Mn2+/Fe2+ availability in barley roots

Flooding stress affects soil properties thus altering the availability, uptake, and transport of mineral nutrients in plant roots. Flooding stress also increases the amount of soluble Mn²⁺ and Fe²⁺ in the soil and their uptake by plants, causing elemental toxicity. However, as oxygen profiles in plant roots are not uniform, it is still unclear how soil flooding will affect Mn²⁺/Fe²⁺ absorption and distribution in different cell types and tissues. In this study, waterlogging sensitive barley variety NasoNijo (NN) and tolerant variety TX9425 (TX) were exposed to hypoxia, metal (Mn²⁺ and Fe²⁺), and combined hypoxia + metal treatment to map the in situ ion profiles at different regions of barley root. We found that combined hypoxia and metal stress causes significantly more reduction in plant biomass compared with the single submergence or metal stress. Despite this, more Fe and Mn were accumulated under metal stress condition than those under combined stress, regardless of variety. Cultivar NN absorbed more Fe and Mn than TX in the cortical cells of the root meristem and in the mature zone under metal stress which was also verified by histochemical detection. In the mature zone, the expressions of Fe and Mn transporter genes including HvADPRibase-Mn (Manganese-dependent ADP-ribose), HvZIP1 (zinc-regulated transporter /Fe-regulated transporter-like protein 1), HvYS1 (yellow stripe 1), HvNRAMP5 (Natural Resistance-Associated Macrophage Protein 5) were significantly downregulated under all three treatments in both barley varieties except HvADPRibase-Mn HvZIP1 cortex of TX were unchanged under metal stress. Interestingly, the transcripts of HvMTP1 (metal tolerance protein 1) were significantly downregulated by metal and combined stress in stele and upregulated by hypoxia and metal stress in cortex of TX, but not affected in NN. It is concluded that Fe and Mn absorption involving HvMTP1is associated with the extent of waterlogging tolerance in barley.

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.

Iron plaque formation, characteristics, and its role as a barrier and/or facilitator to heavy metal uptake in hydrophyte rice (Oryza sativa L.)

The persistent bioavailability of toxic metal(oids) (TM) is undeniably the leading source of serious environmental problems. Through the transfer of these contaminants into food networks, sediments and the aquatic environmental pollution by TM serve as key routes for potential risks to soil and human health. The formation of iron oxyhydroxide plaque (IP) on the root surface of hydrophytes, particularly rice, has been linked to the impact of various abiotic and biotic factors. Radial oxygen loss has been identified as a key driver for the oxidation of rhizosphere ferrous iron (Fe²⁺) and its subsequent precipitation as low-to-high crystalline and/or amorphous Fe minerals on root surfaces as IP. Considering that each plant species has its unique capability of creating an oxidised rhizosphere under anaerobic conditions, the abundance of rhizosphere Fe²⁺, functional groups from organic matter decomposition and variations in binding capacities of Fe oxides, thus, impacting the mobility and interaction of several contaminants as well as toxic/non-toxic metals on the specific surface areas of the IP. More insight from wet extraction and advanced synchrotron-based analytical techniques has provided further evidence on how IP formation could significantly affect the fate of plant physiology and biomass production, particularly in contaminated settings. Collectively, this information sets the stage for the possible implementation of IP and related analytical protocols as a strategic framework for the management of rice and other hydrophytes, particularly in contaminated sceneries. Other confounding variables involved in IP formation, as well as operational issues related to some advanced analytical processes, should be considered.

Co-incorporation of Chinese milk vetch (Astragalus sinicus L.), rice straw, and biochar strengthens the mitigation of Cd uptake by rice (Oryza sativa L.)

Soil cadmium (Cd) contamination is becoming a widespread concern because of its threat to global ecosystem health and food security. Co-incorporation of Chinese milk vetch (MV) and rice straw (RS) is a common agricultural practice in Southern China; however, the effects of combining these two materials with biochar on Cd bioavailability remain unclear. This study investigated the effects of MV, RS, rape straw biochar (RB), iron-modified biochar (FB), and their combinations on Cd uptake by rice through incubation and field experiments. The results showed that compared with the control without material input (CK), MV + RS (MR), MV + RS + RB (MRRB), and MV + RS + FB (MRFB) considerably reduced the Cd concentration in brown rice by 61.20 %, 65.38 %, and 62.65 %, respectively. Furthermore, the treatments increased the formation of iron‑manganese plaque (IMP) at different growth stages; MRRB and MRFB exhibited the highest increase rates among the treatments. Quantitatively, the Fe plaque and Mn plaque were increased by 20.61 %-47.23 % and 80.18 %-172.74 %, respectively. Compared with CK, the MRRB and MRFB treatments reduced the soil available Cd by 35.09 %-54.45 % and 38.20 %-50.20 %, respectively, at all stages. This decrease was substantially lower than that observed in the MV, RS, and MR treatments. Similar trends were observed in the incubation experiment. Additionally, the Community Bureau of Reference Sequential Extraction Analysis indicated that the MRRB and MRFB treatments converted the bioavailable Cd fractions into a stable form. Partial least squares path model and redundancy analysis revealed that pH was the major factor influencing Cd bioavailability. This study emphasized that the dual impact factors from the enhancement of Cd passivation capability and IMP formation jointly result in the reduction of Cd uptake by rice. Consequently, the co-incorporation of MV, RS, and biochar is promising for remediating Cd-contaminated paddy soils in Southern China.

Leading trait dimensions in flood-tolerant plants

BACKGROUND AND AIMS

While trait-based approaches have provided critical insights into general plant functioning, we lack a comprehensive quantitative view on plant strategies in flooded conditions. Plants adapted to flooded conditions have specific traits (e.g. root porosity, low root/shoot ratio and shoot elongation) to cope with the environmental stressors including anoxic sediments, and the subsequent presence of phytotoxic compounds. In flooded habitats, plants also respond to potential nutrient and light limitations, e.g. through the expression of leaf economics traits and size-related traits, respectively. However, we do not know whether and how these trait dimensions are connected.

METHODS

Based on a trait dataset compiled on 131 plant species from 141 studies in flooded habitats, we quantitatively analysed how flooding-induced traits are positioned in relation to the other two dominant trait dimensions: leaf economics traits and size-related traits. We evaluated how these key trait components are expressed along wetness gradients, across habitat types and among plant life forms.

KEY RESULTS

We found that flooding-induced traits constitute a trait dimension independent from leaf economics traits and size-related traits, indicating that there is no generic trade-off associated with flooding adaptations. Moreover, individual flooding-induced traits themselves are to a large extent decoupled from each other. These results suggest that adaptation to stressful environments, such as flooding, can be stressor specific without generic adverse effects on plant functioning (e.g. causing trade-offs on leaf economics traits).

CONCLUSIONS

The trait expression across multiple dimensions promotes plant adaptations and coexistence across multifaceted flooded environments. The decoupled trait dimensions, as related to different environmental drivers, also explain why ecosystem functioning (including, for example, methane emissions) are species and habitat specific. Thus, our results provide a backbone for applying trait-based approaches in wetland ecology by considering flooding-induced traits as an independent trait dimension.

Below-ground plant-soil interactions affecting adaptations of rice to iron toxicity

Iron toxicity is a major constraint to rice production, particularly in highly weathered soils of inland valleys in sub-Saharan Africa where the rice growing area is rapidly expanding. There is a wide variation in tolerance of iron toxicity in the rice germplasm. However, the introgression of tolerance traits into high-yielding germplasm has been slow owing to the complexity of the tolerance mechanisms and large genotype-by-environment effects. We review current understanding of tolerance mechanisms, particularly those involving below-ground plant-soil interactions. Until now these have been less studied than above-ground mechanisms. We cover processes in the rhizosphere linked to exclusion of toxic ferrous iron by oxidation, and resulting effects on the mobility of nutrient ions. We also cover the molecular physiology of below-ground processes controlling iron retention in roots and root-shoot transport, and also plant iron sensing. We conclude that future breeding programmes should be based on well-characterized molecular markers for iron toxicity tolerance traits. To successfully identify such markers, the complex tolerance response should be broken down into its components based on understanding of tolerance mechanisms, and tailored screening methods should be developed for individual mechanisms.

A novel mechanism study of microplastic and As co-contamination on indica rice (Oryza sativa L.)

Although the compound pollution of microplastics and arsenic (As) in paddy soil can affect the growth and quality of rice, relevant research on this phenomenon was limited. Therefore, we combined a pot experiment with computational chemistry to explore the effects and mechanism of polystyrene (PSMP) and polytetrafluoroethylene (PTFE) microplastics on As bioavailability. PSMP and PTFE interacted with rice root exudates through van der Waals forces, approached the rice root system, inhibited root activity, reduced the relative abundance of Geobacteria and Anaeromyxobacter, and consequently reduced the iron plaques on the root surfaces. Consequently, As uptake by the rice was inhibited. PSMP and PTFE reduced the hemoglobin content by directly destroying its tertiary structure, thereby retarding rice growth. In contrast, As increased the hemoglobin content by inducing reactive oxygen species in rice. Under the influence of PSMP, PTFE, and As, the activities of soluble starch synthase and pyrophosphorylase in rice grains were inhibited, and starch accumulation decreased. Thus, PSMP, PTFE, and As reduced rice biomass and yield owing to their physiological toxicity and adverse impacts on root activity. Grain yields in soil with an As content of 86.3 mg·kg^-1, 0.5% small particle-sized PSMP, and 0.5% small particle-sized PTFE decreased by 30.7%, 20.6%, and 19.4%, respectively, compared to the control. This study determined the comprehensive mechanism through which PSMP and PTFE affect As bioavailability, which is critical for managing rice biomass and low yields in As and microplastic co-contaminated soil.

Ammonium regulates redox homeostasis and photosynthetic ability to mitigate copper toxicity in wheat seedlings

As an essential plant micronutrient, copper (Cu) is required as a component of several enzymes, but it can be highly toxic to plants when present in excess quantities. Nitrogen (N) application can help to alleviate the phytotoxic effects of heavy metals, including Cu, and different N forms significantly affect the uptake and accumulation of heavy metals in plants. The aim of this study was to determine the effects of different N forms, i.e., ammonium (NH₄⁺) and nitrate (NO₃^-), on Cu detoxification in wheat seedlings. The inhibition of seedling growth under excess Cu was more obvious in wheat plants supplied with NO₃^- than in those supplied with NH₄⁺. This growth inhibition was directly induced by excess Cu accumulation and reduced absorption of other mineral nutrients by the plants. Compared with seedlings treated with NO₃^-, those treated with NH₄⁺ showed a decrease in Cu-induced toxicity as a result of increased antioxidant capacity in the leaves and a lower redox potential in the rhizosphere. Furthermore, treatment with NH₄⁺ decreased the loss of mineral nutrients in wheat seedlings exposed to excess Cu. In conclusion, compared with supplying NO₃^-, supplying NH₄⁺ to wheat seedlings under Cu stress improved their ability to maintain their nutritional and redox balance and increased their antioxidant capacity, thereby preventing a decline in photosynthesis. According to our results, NH₄⁺ is more effective than NO₃^- in reducing Cu phytotoxicity in wheat seedlings.

Radial Oxygen Loss from Plant Roots—Methods

In flooded soils, an efficient internal aeration system is essential for root growth and plant survival. Roots of many wetland species form barriers to restrict radial O2 loss (ROL) to the rhizosphere. The formation of such barriers greatly enhances longitudinal O2 diffusion from basal parts towards the root tip, and the barrier also impedes the entry of phytotoxic compounds produced in flooded soils into the root. Nevertheless, ROL from roots is an important source of O2 for rhizosphere oxygenation and the oxidation of toxic compounds. In this paper, we review the methodological aspects for the most widely used techniques for the qualitative visualization and quantitative determination of ROL from roots. Detailed methodological approaches, practical set-ups and examples of ROL from roots with or without barriers to ROL are included. This paper provides practical knowledge relevant to several disciplines, including plant–soil interactions, biogeochemistry and eco-physiological aspects of roots and soil biota.

Transporters and transcription factors gene families involved in improving nitrogen use efficiency (NUE) and assimilation in rice (Oryza sativa L.)

Nitrogen (N) as a macronutrient is an important determinant of plant growth. The excessive usage of chemical fertilizers is increasing environmental pollution; hence, the improvement of crop's nitrogen use efficiency (NUE) is imperative for sustainable agriculture. N uptake, transportation, assimilation, and remobilization are four important determinants of plant NUE. Oryza sativa L. (rice) is a staple food for approximately half of the human population, around the globe and improvement in rice yield is pivotal for rice breeders. The N transporters, enzymes indulged in N assimilation, and several transcription factors affect the rice NUE and subsequent yield. Although, a couple of improvements have been made regarding rice NUE, the knowledge about regulatory mechanisms operating NUE is scarce. The current review provides a precise knowledge of how rice plants detect soil N and how this detection is translated into the language of responses that regulate the growth. Additionally, the transcription factors that control N-associated genes in rice are discussed in detail. This mechanistic insight will help the researchers to improve rice yield with minimized use of chemical fertilizers.

Root length is proxy for high-throughput screening of waterlogging tolerance in Urochloa spp. grasses

C4 perennial Urochloa spp. grasses are widely planted in extensive areas in the tropics. These areas are continuously facing waterlogging events, which limits plant growth and production. However, no commercial cultivar combining excellent waterlogging tolerance with superior biomass production and nutritional quality is available. The objective of this study was to identify root traits that can be used for selecting waterlogging tolerant species of Urochloa. Root respiration, root morphological, architectural and anatomical traits were evaluated in eight contrasting Urochloa spp. genotypes grown under aerated or deoxygenated stagnant solutions. Moreover, modelling of internal aeration was used to relate differences in root traits and root growth in waterlogged soils. Increased aerenchyma formation in roots, reduced stele area and development of a fully suberised exodermis are characteristics improving internal aeration of roots and therefore determining waterlogging tolerance in these C4 forage grasses. Waterlogging-tolerant genotypes had steeper root angles and greater root lengths than the waterlogging-sensitive genotypes. In stagnant conditions, waterlogging-tolerant genotypes had a greater proportion of aerenchyma and reduced stele area in root cross-sections, had deeper roots, steeper root angle and larger root biomass, which in turn, allowed for greater shoot biomass. Total root length had the strongest positive influence on shoot dry mass and can therefore be used as proxy for selecting waterlogging tolerant Urochloa genotypes.

Soil carbon dioxide venting through rice roots

The growth of rice in submerged soils depends on its ability to form continuous gas channels-aerenchyma-through which oxygen (O2 ) diffuses from the shoots to aerate the roots. Less well understood is the extent to which aerenchyma permits venting of respiratory carbon dioxide (CO2 ) in the opposite direction. Large, potentially toxic concentrations of dissolved CO2 develop in submerged rice soils. We show using X-ray computed tomography and image-based mathematical modelling that CO2 venting through rice roots is far greater than thought hitherto. We found rates of venting equivalent to a third of the daily CO2 fixation in photosynthesis. Without this venting through the roots, the concentrations of CO2 and associated bicarbonate (HCO3- ) in root cells would have been well above levels known to be toxic to roots. Removal of CO2 and hence carbonic acid (H2 CO3 ) from the soil was sufficient to increase the pH in the rhizosphere close to the roots by 0.7 units, which is sufficient to solubilize or immobilize various nutrients and toxicants. A sensitivity analysis of the model showed that such changes are expected for a wide range of plant and soil conditions.

Ecological floating bed (EFB) for decontamination of polluted water bodies: Design, mechanism and performance

Worldwide water quality is degrading and most of the water bodies are now being contaminated by heavy load of pollutants from various industries. Aquatic ecosystems are also disrupted affecting various flora and fauna adversely. Water bodies dominated with aquatic plants have high yielding capacity. These plants are capable of high nutrient accumulation and creating favorable condition in rhizosphere for microbial organic degradation, which can be applied in the restoration process of polluted lakes, natural streams and wetlands, etc. Ecological Floating Bed (EFB) is designed by using aquatic plants, floating like mat on the surface of water. The plant roots hang beneath the floating mat and provide a large surface area for biofilm growth. This paper reviewed the EFB concept, structure, mechanisms and functions. Screening of suitable macrophyte species, involvement of biofilm in organic removal process and necessity of growth media have been discussed briefly. Apart from this, effect of depth, buoyancy, vegetation coverage ratio are also represented. Detail mechanisms of oxygen transfer from top to bottom of water biomass have been well analyzed. Various pollutants present in wastewater like organics, solids, nitrogen, phosphorous, heavy metals etc. and their removal mechanism have also mentioned. Again biomass needs to be harvested in regular interval, else the absorbed nutrients may re-enter to the water body. Overall, EFB is an efficient and effective wastewater treatment technology and further research is necessary for its better utilization. Finally, based on reviews, recommendations have been made for future research.

Pre-aeration of the rhizosphere offers potential for phytoremediation of heavy metal-contaminated wetlands

Two solution cultures with different oxygen pretreatments were used to investigate (ⅰ) the variation in the radial oxygen loss in the roots and root morphology of Triarrhena sacchariflora seedlings and (ii) their tolerance to Cu²⁺ and Cd²⁺, as well as both the metal uptake and accumulation by pretreated seedlings. Developed aerenchyma in the roots was induced by the hypoxia pretreatment (HP) and aeration pretreatment (AP), for which root porosity, respectively, increased by 45.76%-53.39% and 84.07%-88.66%. AP altered the natural radial oxygen loss coupled to an enhanced secretion of oxygen in the root tips. AP was found to effectively improve the seedlings' tolerance to Cu²⁺ and Cd²⁺, facilitating their growth, thereby increasing their root diameter, dry weight, and number of root tips, as well as promoting shoot growth. AP was capable of promoting the uptake and bioaccumulation in seedlings of Cu²⁺ and Cd²⁺; it also induced more Cu²⁺ and Cd²⁺ immobilized in roots so that less of either metal was transported from roots to shoots, which may well be a key mechanism for strengthening seedlings' tolerance to metal ions. Our experimental results suggest that AP offers great potential for the remediation of heavy metal-contaminated wetlands.

Aeration Increases Cadmium (Cd) Retention by Enhancing Iron Plaque Formation and Regulating Pectin Synthesis in the Roots of Rice (Oryza sativa) Seedlings

BACKGROUND

Aeration and water management increasing rhizosphere oxygen amount significantly promote rice (Oryza sativa) growth and yield, but the effect of root aeration on cadmium (Cd) toxicity and accumulation in rice seedlings under hydroponic culture remains unclear.

RESULTS

Results showed that aeration promoted rice seedling growth and alleviated Cd toxicity. Transverse section discovered that Cd accelerated root mature and senescence while aeration delayed the mature and senescence of roots. Non-invasive Micro-test Technology (NMT) showed that aeration increased net O2 and Cd2+ influxes on the surface of roots while decreased net Cd2+ influx in xylem. Perls blue staining showed that aeration and Cd treatments increased iron plaque formation on the surface of roots. Results of metal concentration analysis showed that besides increasing Cd retention in iron plaque, aeration also increasing Cd retention in the cell wall of rice roots. Cell wall component analysis showed that aeration not only increased pectin content but also decreased pectin methylesterification degree (PMD) by increasing pectin methylesterase (PME) activity.

CONCLUSIONS

All of these results indicate that aeration not only delays root mature and senescence but also increases Cd retention in roots by enhancing iron plaque formation and regulating pectin synthesis in the roots of rice seedlings.

Nitrogen supply influences arsenic accumulation and stress responses of rice (Oryza sativa L.) seedlings

In the present study, the effects of nitrogen supply (low nitrogen: LN and high nitrogen: HN) on As stress (25 μM) responses of rice seedlings were monitored for 7 d. The mean length of primary, adventitious and lateral roots and number of adventitious and lateral roots were significantly improved in LN+As, while further reduced in HN+As, as compared to As alone treatment at 7 d. The LN+As treatment resulted in significant decline in As (848 μg g^-1 DW) than that in As alone treatment (1434 μg g^-1 DW) in roots but no significant effect was seen in shoot. In contrast, HN+As treatment showed significant increase in shoot As (6.86 μg g^-1 DW) as compared to As alone treatment (3.43 μg g^-1 DW). The level of nitrate was increased in roots but declined in shoots in As alone treatment. Surprisingly, no improvement in nitrate level was seen in HN+As as compared to that in As alone treatment in both root and shoot. The expression analysis of nitrate transporters (NRT2;1, NRT2;3a, NRT2;4) showed significant differences in expression patterns in As, LN+As and HN+As treatments. In conclusion, nitrogen supply had profound influences on responses of rice plants to As.

Agricultural use of Samarco's spilled mud assessed by rice cultivation: A promising residue use?

Mining activity is one of the main responsible for accumulation of potentially toxic elements in the environment. These contaminants are absorbed by plants served as food that could be a risk to human health, such rice. Rice is a staple food with known accumulation of toxic elements. The recent collapse of a mining dam operated by Samarco Mining Company spilled around 50 million m³ of Fe-mining waste in the environment, including rivers and farming areas. In the present study, concentrations of As, Cd, Hg, Pb, Co, Zn, Mn, Cu, Fe, Al, Se, and Sr were determined in soils, roots and grains of rice plants cultivated in soil containing Samarco's residual mud (0, 16, 34 and 50%). Further, rice plant agronomic parameters (chlorophyll, carotenoids, grain yield, mass, height) were assessed. Rice cultivated at Samarco's residual mud produced grains with low levels of As, Cd and Pb. However, the excess of mud (50%) during the rice cultivation reduced roots' growth and grains yield. Chlorophyll (a and b) and carotenoids contents were significantly lower in all mud cultivations, mainly mud-50%. Our findings suggest that plant alterations induced by the mud were associated to the deficiency of nutrients and the physical properties of the mud. Soil fertilization by organic matter and top soil provided conditions for plant development. Therefore, considering the experimental conditions here used, we showed that is possible the use of the affected land for agriculture and reforestation after soil amendment.

Drying-submergence alternation enhanced crystalline ratio and varied surface properties of iron plaque on rice (Oryza sativa) roots

Iron plaque (IP) is valuable in nutrient management and contaminant tolerance for rice (Oryza sativa) because it can adsorb various nutrients and toxic ions. Crystalline ratio (CR) can be defined as the proportion of crystalline iron (CI) to total IP to describe IP crystallinity. Although the knowledge on IP has abounded, the information on the relationship among its formation condition, surface properties, and CR remains insufficient. In this study, quartz sand-soil cultivation with rice was conducted to explore the effect of drying-submergence alternation (DSA) on CI, amorphous iron (AI), CR, root oxidizing capacity (ROC), and surface properties of IP with different treatment durations and at different stages. Fourteen-day DSA treatment increased CI to 2.20 times of that after continuous submergence (CS) but decreased AI to 72.3% of that after CS. Correspondingly, CR was raised to 6.89% from 4.08%. Remarkably, CR of IP after DSA ending in submergence and ending in drying was 6.89% and 4.23%, respectively. In addition, ROC after 14-day DSA was enhanced to twice of that after CS. Results from scanning electronic microscope suggested that 14-day DSA induced thinner sheets with finer particles in IP compared to that after CS. Results from X-ray diffraction revealed that IP contained higher proportions of goethite, lepidocrocite, magnetite, and hematite after DSA than those after CS. Variable charge and surface area of IP after DSA were only 26.5% and 32.0% of those after CS, respectively. Together, our results indicated that proper strength DSA promoted ROC and transformation from AI to CI, and consequently increased CR of IP, while it changed its surface properties.

Reduced arsenic accumulation in indica rice (Oryza sativa L.) cultivar with ferromanganese oxide impregnated biochar composites amendments

The effects of biochar (BC) and ferromanganese oxide biochar composites (FMBC₁ and FMBC₂) on As (Arsenic) accumulation in rice were determined using a pot experiment. Treatments with BC or FMBC improved the dry weights of rice roots, stems, leaves, and grains in soils containing different As contamination levels. Compared to BC treatment, FMBC treatments significantly reduced As accumulation in different parts of the rice plants (P < 0.05), and FMBC₂ performed better than FMBC₁ did. Furthermore, exposure to 2% FMBC₂ decreased the total As concentration in the grain by 68.9-78.3%. The addition of FMBC increased the ratio of essential amino acids in the grain, decreased As availability in the soil, and significantly increased the Fe and Mn plaque contents. The reduced As accumulation in rice can be attributed to As(III) to As(V) oxidation by ferro - manganese binary oxide, which increased the As adsorbed by FMBC. Furthermore, Fe and Mn plaques on the rice root surface decreased the transport of As in rice. Taken together, our results demonstrated the applicability of FMBC as a potential measure for reducing As accumulation in rice, improving the amino acid content of rice grains, and effectively remediating As-polluted soil.

Soil CO2 venting as one of the mechanisms for tolerance of Zn deficiency by rice in flooded soils

We sought to explain rice (Oryza sativa) genotype differences in tolerance of zinc (Zn) deficiency in flooded paddy soils and the counter-intuitive observation, made in earlier field experiments, that Zn uptake per plant increases with increasing planting density. We grew tolerant and intolerant genotypes in a Zn-deficient flooded soil at high and low planting densities and found (a) plant Zn concentrations and growth increased with planting density and more so in the tolerant genotype, whereas the concentrations of other nutrients decreased, indicating a specific effect on Zn uptake; (b) the effects of planting density and genotype on Zn uptake could only be explained if the plants induced changes in the soil to make Zn more soluble; and (c) the genotype and planting density effects were both associated with decreases in dissolved CO₂ in the rhizosphere soil solution and resulting increases in pH. We suggest that the increases in pH caused solubilization of soil Zn by dissolution of alkali-soluble, Zn-complexing organic ligands from soil organic matter. We conclude that differences in venting of soil CO₂ through root aerenchyma were responsible for the genotype and planting density effects.

The Key to Mn Homeostasis in Plants: Regulation of Mn Transporters

Plants only require small amounts of manganese (Mn) for healthy growth, but Mn concentrations in soil solution vary from sub-micromolar to hundreds of micromolar across the growth period. Therefore, plants must deal with large Mn concentration fluctuations, but the molecular mechanisms underlying how plants cope with low and high Mn concentrations are poorly understood. In this Opinion we discuss the role of Mn transporters in the uptake, distribution, and detoxification of Mn in response to changes in Mn concentrations through their regulation at the transcriptional and protein levels, mainly focusing on rice, an Mn-tolerant and -accumulating species. We also propose mechanisms involved in the hyperaccumulation of Mn and future prospects for studying this specific trait.

Rice Genotype Differences in Tolerance of Zinc-Deficient Soils: Evidence for the Importance of Root-Induced Changes in the Rhizosphere

Zinc (Zn) deficiency is a major constraint to rice production and Zn is also often deficient in humans with rice-based diets. Efforts to breed more Zn-efficient rice are constrained by poor understanding of the mechanisms of tolerance to deficiency. Here we assess the contributions of root growth and root Zn uptake efficiency, and we seek to explain the results in terms of specific mechanisms. We made a field experiment in a highly Zn-deficient rice soil in the Philippines with deficiency-tolerant and -sensitive genotypes, and measured growth, Zn uptake and root development. We also measured the effect of planting density. Tolerant genotypes produced more crown roots per plant and had greater uptake rates per unit root surface area; the latter was at least as important as root number to overall tolerance. Tolerant and sensitive genotypes took up more Zn per plant at greater planting densities. The greater uptake per unit root surface area, and the planting density effect can only be explained by root-induced changes in the rhizosphere, either solubilizing Zn, or neutralizing a toxin that impedes Zn uptake (possibly [Formula: see text] or Fe(2+)), or both. Traits for these and crown root number are potential breeding targets.

A natural rice rhizospheric bacterium abates arsenic accumulation in rice (Oryza sativa L.)

A natural rice rhizospheric isolate abates arsenic uptake in rice by increasing Fe plaque formation on rice roots. Rice (Oryza sativa L.) is the staple food for over half of the world's population, but its quality and yield are impacted by arsenic (As) in some regions of the world. Bacterial inoculants may be able to mitigate the negative impacts of arsenic assimilation in rice, and we identified a nonpathogenic, naturally occurring rice rhizospheric bacterium that decreases As accumulation in rice shoots in laboratory experiments. We isolated several proteobacterial strains from a rice rhizosphere that promote rice growth and enhance the oxidizing environment surrounding rice root. One Pantoea sp. strain (EA106) also demonstrated increased iron (Fe)-siderophore in culture. We evaluated EA106's ability to impact rice growth in the presence of arsenic, by inoculation of plants with EA106 (or control), subsequently grew the plants in As-supplemented medium, and quantified the resulting plant biomass, Fe and As concentrations, localization of Fe and As, and Fe plaque formation in EA106-treated and control plants. These results show that both arsenic and iron concentrations in rice can be altered by inoculation with the soil microbe EA106. The enhanced accumulation of Fe in the roots and in root plaques suggests that EA106 inoculation improves Fe uptake by the root and promotes the formation of a more oxidative environment in the rhizosphere, thereby allowing more expansive plaque formation. Therefore, this microbe may have the potential to increase food quality through a reduction in accumulation of toxic As species within the aerial portions of the plant.

Host and non-host roots in rice: cellular and molecular approaches reveal differential responses to arbuscular mycorrhizal fungi

Oryza sativa, a model plant for Arbuscular Mycorrhizal (AM) symbiosis, has both host and non-host roots. Large lateral (LLR) and fine lateral (FLR) roots display opposite responses: LLR support AM colonization, but FLR do not. Our research aimed to study the molecular, morphological and physiological aspects related to the non-host behavior of FLR. RNA-seq analysis revealed that LLR and FLR displayed divergent expression profiles, including changes in many metabolic pathways. Compared with LLR, FLR showed down-regulation of genes instrumental for AM establishment and gibberellin signaling, and a higher expression of nutrient transporters. Consistent with the transcriptomic data, FLR had higher phosphorus content. Light and electron microscopy demonstrated that, surprisingly, in the Selenio cultivar, FLR have a two-layered cortex, which is theoretically compatible with AM colonization. According to RNA-seq, a gibberellin inhibitor treatment increased anticlinal divisions leading to a higher number of cortex cells in FLR. We propose that some of the differentially regulated genes that lead to the anatomical and physiological properties of the two root types also function as genetic factors regulating fungal colonization. The rice root apparatus offers a unique tool to study AM symbiosis, allowing direct comparisons of host and non-host roots in the same individual plant.

O2 dynamics in the rhizosphere of young rice plants (Oryza sativa L.) as studied by planar optodes

BACKGROUND AND AIMS

Radial O2 loss (ROL) strongly affect the O2 availability in the rhizosphere of rice. The ROL create an oxic zone around the roots, protecting the plant from toxic reduced chemical species and regulates the redox chemistry in the soil. This study investigates the spatio-temporal variability in O2 dynamics in the rice rhizosphere.

METHOD

Applying high-resolution planar optode imaging, we investigated the O2 dynamics of plants grown in water saturated soil, as a function of ambient O2 level, irradiance and plant development, for submerged and emerged plants.

RESULTS

O2 leakage was heterogeneously distributed with zones of intense leakage around roots tips and young developing roots. While the majority of roots exhibited high ROL others remained surrounded by anoxic soil. ROL was affected by ambient O2 levels around the plant, as well as irradiance, indicating a direct influence of photosynthetic activity on ROL. At onset of darkness, oxia in the rhizosphere was drastically reduced, but subsequently oxia gradually increased, presumably as root and/or soil respiration declined.

CONCLUSION

The study demonstrates a high spatio-temporal heterogeneity in rhizosphere O2 dynamics and difference in ROL between different parts of the rhizosphere. The work documents that spatio-temporal measurements are important to fully understand and account for the highly variable O2 dynamics and associated biogeochemical processes and pathways in the rice rhizosphere.

Methylmercury production in sediment from agricultural and non-agricultural wetlands in the Yolo Bypass, California, USA

As part of a larger study of mercury (Hg) biogeochemistry and bioaccumulation in agricultural (rice growing) and non-agricultural wetlands in California's Central Valley, USA, seasonal and spatial controls on methylmercury (MeHg) production were examined in surface sediment. Three types of shallowly-flooded agricultural wetlands (white rice, wild rice, and fallow fields) and two types of managed (non-agricultural) wetlands (permanently and seasonally flooded) were sampled monthly-to-seasonally. Dynamic seasonal changes in readily reducible 'reactive' mercury (Hg(II)R), Hg(II)-methylation rate constants (kmeth), and concentrations of electron acceptors (sulfate and ferric iron) and donors (acetate), were all observed in response to field management hydrology, whereas seasonal changes in these parameters were more muted in non-agricultural managed wetlands. Agricultural wetlands exhibited higher sediment MeHg concentrations than did non-agricultural wetlands, particularly during the fall through late-winter (post-harvest) period. Both sulfate- and iron-reducing bacteria have been implicated in MeHg production, and both were demonstrably active in all wetlands studied. Stoichiometric calculations suggest that iron-reducing bacteria dominated carbon flow in agricultural wetlands during the growing season. Sulfate-reducing bacteria were not stimulated by the addition of sulfate-based fertilizer to agricultural wetlands during the growing season, suggesting that labile organic matter, rather than sulfate, limited their activity in these wetlands. Along the continuum of sediment geochemical conditions observed, values of kmeth increased approximately 10,000-fold, whereas Hg(II)R decreased 100-fold. This suggests that, with respect to the often opposing trends of Hg(II)-methylating microbial activity and Hg(II) availability for methylation, microbial activity dominated the Hg(II)-methylation process, and that along this biogeochemical continuum, conditions that favored microbial sulfate reduction resulted in the highest calculated MeHg production potential rates. Rice straw management options aimed at limiting labile carbon supplies to surface sediment during the post-harvest fall-winter period may be effective in limiting MeHg production within agricultural wetlands.

Waterlogging-induced changes in root architecture of germplasm accessions of the tropical forage grass Brachiaria humidicola

Waterlogging is one of the major factors limiting the productivity of pastures in the humid tropics. Brachiaria humidicola is a forage grass commonly used in zones prone to temporary waterlogging. Brachiaria humidicola accessions adapt to waterlogging by increasing aerenchyma in nodal roots above constitutive levels to improve oxygenation of root tissues. In some accessions, waterlogging reduces the number of lateral roots developed from main root axes. Waterlogging-induced reduction of lateral roots could be of adaptive value as lateral roots consume oxygen supplied from above ground via their parent root. However, a reduction in lateral root development could also be detrimental by decreasing the surface area for nutrient and water absorption. To examine the impact of waterlogging on lateral root development, an outdoor study was conducted to test differences in vertical root distribution (in terms of dry mass and length) and the proportion of lateral roots to the total root system (sum of nodal and lateral roots) down the soil profile under drained or waterlogged soil conditions. Plant material consisted of 12 B. humidicola accessions from the gene bank of the International Center for Tropical Agriculture, Colombia. Rooting depth was restricted by 21 days of waterlogging and confined to the first 30 cm below the soil surface. Although waterlogging reduced the overall proportion of lateral roots, its proportion significantly increased in the top 10 cm of the soil. This suggests that soil flooding increases lateral root proliferation of B. humidicola in the upper soil layers. This may compensate for the reduction of root surface area brought about by the restriction of root growth at depths below 30 cm. Further work is needed to test the relative efficiency of nodal and lateral roots for nutrient and water uptake under waterlogged soil conditions.

Enhancing phosphorus and zinc acquisition efficiency in rice: a critical review of root traits and their potential utility in rice breeding

BACKGROUND

Rice is the world's most important cereal crop and phosphorus (P) and zinc (Zn) deficiency are major constraints to its production. Where fertilizer is applied to overcome these nutritional constraints it comes at substantial cost to farmers and the efficiency of fertilizer use is low. Breeding crops that are efficient at acquiring P and Zn from native soil reserves or fertilizer sources has been advocated as a cost-effective solution, but would benefit from knowledge of genes and mechanisms that confer enhanced uptake of these nutrients by roots.

SCOPE

This review discusses root traits that have been linked to P and Zn uptake in rice, including traits that increase mobilization of P/Zn from soils, increase the volume of soil explored by roots or root surface area to recapture solubilized nutrients, enhance the rate of P/Zn uptake across the root membrane, and whole-plant traits that affect root growth and nutrient capture. In particular, this review focuses on the potential for these traits to be exploited through breeding programmes to produce nutrient-efficient crop cultivars.

CONCLUSIONS

Few root traits have so far been used successfully in plant breeding for enhanced P and Zn uptake in rice or any other crop. Insufficient genotypic variation for traits or the failure to enhance nutrient uptake under realistic field conditions are likely reasons for the limited success. More emphasis is needed on field studies in mapping populations or association panels to identify those traits and underlying genes that are able to enhance nutrient acquisition beyond the level already present in most cultivars.

Alleviation of chromium toxicity in rice seedlings by applying exogenous glutathione

The effect of exogenous reduced glutathione (GSH) on alleviation of hexavalent chromium (Cr(6+)) toxicity to rice seedlings and its physiological mechanisms were comprehensively investigated in a series of experiments. Our results showed that growth and nutrient uptake of rice seedlings were dramatically reduced under 100 μM Cr(6+) stress, and the reduction was significantly alleviated by exogenous GSH. Cr(6+) stress also reduced cell viability in root tips and damaged ultrastructure of both chloroplasts and root cells, while the addition of GSH alleviates those negative effects. Cr-induced toxicity and GSH-caused Cr alleviation differed significantly between Cr-tolerant Line 117 (L117) and Cr-sensitive Line 41 (L41). Under Cr(6+) stress, cystine content was increased and GSH content was decreased in rice plants, exogenous GSH, however, mitigated the Cr-toxicity by reversing the Cr-induced changes of the two compounds. The types of Cr-induced secretion of organic acids varied between the genotypes, where reduction in the contents of acetic and lactic acids and tartaric and malic acids were observed in L117 and L41, respectively. The addition of GSH alleviated the reduction of secretion of these organic acids. Exogenous GSH also altered the forms of Cr ions in the rhizosphere and the fraction of distribution at subcellular level in both shoots and roots. It may be concluded that the alleviation of Cr(6+) toxicity by exogenous GSH is directly attributed to its regulation on forms of Cr ions in rhizosphere and their distribution at subcellular levels.

Knockdown of a rice stelar nitrate transporter alters long-distance translocation but not root influx

Root nitrate uptake is well known to adjust to the plant's nitrogen demand for growth. Long-distance transport and/or root storage pools are thought to provide negative feedback signals regulating root uptake. We have characterized a vascular specific nitrate transporter belonging to the high-affinity Nitrate Transporter2 (NRT2) family, OsNRT2.3a, in rice (Oryza sativa ssp. japonica 'Nipponbare'). Localization analyses using protoplast expression, in planta promoter-β-glucuronidase assay, and in situ hybridization showed that OsNRT2.3a was located in the plasma membrane and mainly expressed in xylem parenchyma cells of the stele of nitrate-supplied roots. Knockdown expression of OsNRT2.3a by RNA interference (RNAi) had impaired xylem loading of nitrate and decreased plant growth at low (0.5 mm) nitrate supply. In comparison with the wild type, the RNAi lines contained both nitrate and total nitrogen significantly higher in the roots and lower in the shoots. The short-term [(15)N]NO(3)(-) influx (5 min) in entire roots and NO(3)(-) fluxes in root surfaces showed that the knockdown of OsNRT2.3a in comparison with the wild type did not affect nitrate uptake by roots. The RNAi plants showed no significant changes in the expression of some root nitrate transporters (OsNRT2.3b, OsNRT2.4, and OsNAR2.1), but transcripts for nia1 (nitrate reductase) had increased and OsNRT2.1 and OsNRT2.2 had decreased when the plants were supplied with nitrate. Taken together, the data demonstrate that OsNRT2.3a plays a key role in long-distance nitrate transport from root to shoot at low nitrate supply level in rice.

Investigation of the mechanism of uptake and accumulation of zwitterionic tetracyclines by rice (Oryza sativa L.)

The uptake and accumulation of organic contaminants by plants can be detrimental to the plant itself as well as consumers. Tetracycline antibiotics are present at trace levels in soil and water. Under typical environmental conditions, they exist as zwitterions. Comparatively little is known of their uptake and accumulation by plants, or the mechanism by which this occurs. To examine this, rice (Oryza sativa L.) was employed, together with a static diffusion cell equipped with a cellulose membrane as a model for the uptake process. For rice, kinetic results suggested that the zwitterions were behaving similarly to neutral organic compounds, with a passive uptake process. The diffusion cell provided qualitatively similar results. When exposed to aqueous concentrations of zwitterionic tetracyclines of 50 mg L(-1) over 15 days, no translocation to shoots or detrimental effects on plants was observed. Despite relatively low root lipid contents, concentrations in root tissue of greater than 1000 mg kg(-1) (d.w.) were determined with maximum Root Concentration Factors of the order of 2000 L kg(-1) (d.w.). Overall, for the tetracyclines investigated, kinetic and accumulation behavior in plants together with permeation in the diffusion cell were all governed by compound hydrophobicity.

Spatial expression and regulation of rice high-affinity nitrate transporters by nitrogen and carbon status

The high affinity nitrate transport system (HATS) plays an important role in rice nitrogen acquisition because, even under flooded anaerobic cultivation when NH(4)(+) dominates, significant nitrification occurs on the root surface. In the rice genome, four NRT2 and two NAR2 genes encoding HATS components have been identified. One gene OsNRT2.3 was mRNA spliced into OsNRT2.3a and OsNRT2.3b and OsNAR2.1 interacts with OsNRT2.1/2.2 and OsNRT2.3a to provide nitrate uptake. Using promoter-GUS reporter plants and semi-quantitative RT-PCR analyses, it was observed that OsNAR2.1 was expressed mainly in the root epidermal cells, differently from the five OsNRT2 genes. OsNAR2.1, OsNRT2.1, OsNRT2.2, and OsNRT2.3a were up-regulated by nitrate and suppressed by NH(4)(+) and high root temperature (37 °C). Expression of all these genes was increased by light or external sugar supply. Root transcripts of OsNRT2.3b and OsNRT2.4 were much less abundant and not affected by temperature. Expression of OsNRT2.3b was insensitive to the form of N supply. Expression of OsNRT2.4 responded to changes in auxin supply unlike all the other NRT2 genes. A region from position -311 to -1, relative to the translation start site in the promoter region of OsNAR2.1, was found to contain the cis-element(s) necessary for the nitrate-, but not light- and sugar-dependent activation. However, it was difficult to define a conserved cis-element in the promoters of the nitrate-regulated OsNRT2/OsNAR2 genes. The results imply distinct physiological functions for each OsNRT2 transporter, and differential regulation pathways by N and C status.

Physiological and proteomic characterization of manganese sensitivity and tolerance in rice (Oryza sativa) in comparison with barley (Hordeum vulgare)

BACKGROUND AND AIMS

Research on manganese (Mn) toxicity and tolerance indicates that Mn toxicity develops apoplastically through increased peroxidase activities mediated by phenolics and Mn, and Mn tolerance could be conferred by sequestration of Mn in inert cell compartments. This comparative study focuses on Mn-sensitive barley (Hordeum vulgare) and Mn-tolerant rice (Oryza sativa) as model organisms to unravel the mechanisms of Mn toxicity and/or tolerance in monocots.

METHODS

Bulk leaf Mn concentrations as well as peroxidase activities and protein concentrations were analysed in apoplastic washing fluid (AWF) in both species. In rice, Mn distribution between leaf compartments and the leaf proteome using 2D isoelectric focusing IEF/SDS-PAGE and 2D Blue native BN/SDS-PAGE was studied.

KEY RESULTS

The Mn sensitivity of barley was confirmed since the formation of brown spots on older leaves was induced by low bulk leaf and AWF Mn concentrations and exhibited strongly enhanced H2O2-producing and consuming peroxidase activities. In contrast, by a factor of 50, higher Mn concentrations did not produce Mn toxicity symptoms on older leaves in rice. Peroxidase activities, lower by a factor of about 100 in the rice leaf AWF compared with barley, support the view of a central role for these peroxidases in the apoplastic expression of Mn toxicity. The high Mn tolerance of old rice leaves could be related to a high Mn binding capacity of the cell walls. Proteomic studies suggest that the lower Mn tolerance of young rice leaves could be related to Mn excess-induced displacement of Mg and Fe from essential metabolic functions.

CONCLUSIONS

The results provide evidence that Mn toxicity in barley involves apoplastic lesions mediated by peroxidases. The high Mn tolerance of old leaves of rice involves a high Mn binding capacity of the cell walls, whereas Mn toxicity in less Mn-tolerant young leaves is related to Mn-induced Mg and Fe deficiencies.

The effects of water regime on phosphorus responses of rainfed lowland rice cultivars

BACKGROUND AND AIMS

Soil phosphorus (P) solubility declines sharply when a flooded soil drains, and an important component of rice (Oryza sativa) adaptation to rainfed lowland environments is the ability to absorb and utilize P under such conditions. The aim of this study was to test the hypothesis that rice cultivars differ in their P responses between water regimes because P uptake mechanisms differ.

METHODS

Six lowland rice cultivars (three considered tolerant of low P soils, three sensitive) were grown in a factorial experiment with three water regimes (flooded, moist and flooded-then-moist) and four soil P levels, and growth and P uptake were measured. Small volumes of soil were used to maximize inter-root competition and uptake per unit root surface. The results were compared with the predictions of a model allowing for the effects of water regime on P solubility and diffusion.

KEY RESULTS

The plants were P stressed but not water stressed in all the water regimes at all P levels except the higher P additions in the flooded soil. The cultivar rankings scarcely differed between the water regimes and P additions. In all the treatments, the soil P concentrations required to explain the measured uptake were several times the concentration of freely available P in the soil.

CONCLUSIONS

The cultivar rankings were driven more by differences in growth habit than specific P uptake mechanisms, so the hypothesis cannot be corroborated with these data. Evidently all the plants could tap sparingly soluble forms of P by releasing a solubilizing agent or producing a greater root length than measured, or both. However, any cultivar differences in this were not apparent in greater net P uptake, possibly because the restricted rooting volume meant that additional P uptake could not be converted into new root growth to explore new soil volumes.

Spatial variation of active microbiota in the rice rhizosphere revealed by in situ stable isotope probing of phospholipid fatty acids

This report is part of a serial study applying stable isotope labelling to rice microcosms to track the utilization of recently photosynthesized carbon by active microbiota in the rhizosphere. The objective of the present study was to apply phospholipid fatty acid-based stable isotope probing (PLFA-SIP) to detect the spatial variation of active microorganisms associated with rhizosphere carbon flow. In total, 49 pulses of 13CO2 were applied to rice plants in a microcosm over a period of 7 days. Rhizosphere soil was separated from bulk soil by a root bag. Soil samples were taken from rhizosphere and bulk soil, and the bulk soil samples were further partitioned both vertically (up layer and down layer) and horizontally with increasing distance to the root bag. Incorporation of 13C into PLFAs sharply decreased with distance to the roots. The labelling of 16:1omega9, 18:1omega7, 18:1omega9, 18:2omega6,9 and i14:0 PLFAs was relatively stronger in the rhizosphere while that of i15:0 and i17:0 increased in the bulk soil. The microorganisms associated with 16:1omega9 were active in both up- and down-layer soils. The microorganisms represented by i14:0, 18:1omega7 and 18:2omega6,9 exhibited a relatively higher activity in up-layer soil, whereas those represented by i15:0 and i17:0 were more active in down-layer soil. These results suggest that in the rhizosphere Gram-negative and eukaryotic microorganisms were most actively assimilating root-derived C, whereas Gram-positive microorganisms became relatively more important in the bulk soil. The active populations apparently differed between up- and down-layer soil and in particular changed with distance to the roots, demonstrating systematic changes in the activity of the soil microbiota surrounding roots.

Conditions leading to high CO2 (>5 kPa) in waterlogged-flooded soils and possible effects on root growth and metabolism

AIMS

Soil waterlogging impedes gas exchange with the atmosphere, resulting in low P(O2) and often high P(CO2). Conditions conducive to development of high P(CO2) (5-70 kPa) during soil waterlogging and flooding are discussed. The scant information on responses of roots to high P(CO2) in terms of growth and metabolism is reviewed.

SCOPE

P(CO2) at 15-70 kPa has been reported for flooded paddy-field soils; however, even 15 kPa P(CO2) may not always be reached, e.g. when soil pH is above 7. Increases of P(CO2) in soils following waterlogging will develop much more slowly than decreases in P(O2); in soil from rice paddies in pots without plants, maxima in P(CO2) were reached after 2-3 weeks. There are no reliable data on P(CO2) in roots when in waterlogged or flooded soils. In rhizomes and internodes, P(CO2) sometimes reached 10 kPa, inferring even higher partial pressures in the roots, as a CO2 diffusion gradient will exist from the roots to the rhizomes and shoots. Preliminary modelling predicts that when P(CO2) is higher in a soil than in roots, P(CO2) in the roots would remain well below the P(CO2) in the soil, particularly when there is ventilation via a well-developed gas-space continuum from the roots to the atmosphere. The few available results on the effects of P(CO2) at > 5 kPa on growth have nearly all involved sudden increases to 10-100 kPa P(CO2); consequently, the results cannot be extrapolated with certainty to the much more gradual increases of P(CO2) in waterlogged soils. Nevertheless, rice in an anaerobic nutrient solution was tolerant to 50 kPa CO2 being suddenly imposed. By contrast, P(CO2) at 25 kPa retarded germination of some maize genotypes by 50%. With regard to metabolism, assuming that the usual pH of the cytoplasm of 7.5 was maintained, every increase of 10 kPa CO2 would result in an increase of 75-90 mM HCO3(-) in the cytoplasm. pH maintenance would depend on the biochemical and biophysical pH stats (i.e. regulatory systems). Furthermore, there are indications that metabolism is adversely affected when HCO3(-) in the cytoplasm rises above 50 mM, or even lower; succinic dehydrogenase and cytochrome oxidase are inhibited by HCO3(-) as low as 10 mM. Such effects could be mitigated by a decrease in the set point for the pH of the cytoplasm, thus lowering levels of HCO3(-) at the prevailing P(CO2) in the roots.

CONCLUSIONS

Measurements are needed on P(CO2) in a range of soil types and in roots of diverse species, during waterlogging and flooding. Species well adapted to high P(CO2) in the root zone, such as rice and other wetland plants, thrive even when P(CO2) is well over 10 kPa; mechanisms of adaptation, or acclimatization, by these species need exploration.

The potential for nitrification and nitrate uptake in the rhizosphere of wetland plants: a modelling study

BACKGROUND AND AIMS

It has recently found that lowland rice grown hydroponically is exceptionally efficient in absorbing NO3-, raising the possibility that rice and other wetland plants growing in flooded soil may absorb significant amounts of NO3- formed by nitrification of NH4+ in the rhizosphere. This is important because (a) this NO3- is otherwise lost through denitrification in the soil bulk; and (b) plant growth and yield are generally improved when plants absorb their nitrogen as a mixture of NO3- and NH4+ compared with growth on either N source on its own. A mathematical model is developed here with which to assess the extent of NO3- absorption from the rhizosphere by wetland plants growing in flooded soil, considering the important plant and soil processes operating.

METHODS

The model considers rates of O2 transport away from an individual root and simultaneous O2 consumption in microbial and non-microbial processes; transport of NH4+ towards the root and its consumption in nitrification and uptake at the root surface; and transport of NO3- formed from NH4+ towards the root and its consumption in denitrification and uptake by the root. The sensitivity of the model's predictions to its input parameters is tested over the range of conditions in which wetland plants grow.

KEY RESULTS

The model calculations show that substantial quantities of NO3- can be produced in the rhizosphere of wetland plants through nitrification and taken up by the roots under field conditions. The rates of NO3- uptake can be comparable with those of NH4+. The model also shows that rates of denitrification and subsequent loss of N from the soil remain small even where NO3- production and uptake are considerable.

CONCLUSIONS

Nitrate uptake by wetland plants may be far more important than thought hitherto. This has implications for managing wetland soils and water, as discussed in this paper.

Rice: sulfide-induced barriers to root radial oxygen loss, Fe2+ and water uptake, and lateral root emergence

BACKGROUND AND AIMS

Akagare and Akiochi are diseases of rice associated with sulfide toxicity. This study investigates the possibility that rice reacts to sulfide by producing impermeable barriers in roots.

METHODS

Root systems of rice, Oryza sativa cv. Norin 36, were subjected to short-term exposure to 0.174 mm sulfide (5.6 ppm) in stagnant solution. Root growth was monitored; root permeability was investigated in terms of polarographic determinations of oxygen efflux from fine laterals and the apices of adventitious roots, water uptake, anatomy and permeability to Fe2+ using potassium ferricyanide.

KEY RESULTS

Both types of root responded rapidly to the sulfide with immediate cessation of growth, decreased radial oxygen loss (ROL) to the rhizospheres and reduced water uptake. Profiles of ROL measured from apex to basal regions of adventitious roots indicated that more intense barriers to ROL than normal were formed around the apices. Absorption of Fe2+ appeared to be impeded in sulfide-treated roots. In adventitious roots, deposition of lipid material (suberisation) and thickenings of walls within the superficial cell layers were obvious within a week after lifting the treatment and could prevent the emergence of laterals and commonly result in their upward longitudinal growth within the cortex. Death of laterals sometimes occurred prior to emergence; emergent laterals eventually died. In adventitious roots, blockages formed within the vascular and aeration systems in response to the sulfide.

CONCLUSIONS

In both adventitious and lateral roots, sulfide-induced cell wall suberization and thickening of the superficial layers were correlated with reduced permeability to O2, water and Fe2+. This study sheds light on some of the symptoms of diseases such as Akiochi. The results correlate with the authors' previous findings on the effects on roots of sulfide and lower organic acids in Phragmites and of acetic acid in rice.