OXYGEN DEFICIENCY AND ROOT METABOLISM: Injury and Acclimation Under Hypoxia and Anoxia

Characterization of distinct root and shoot responses to low-oxygen stress in Arabidopsis with a focus on primary C- and N-metabolism

Oxygen deficiency, caused by flooding of all or a portion of a plant, leads to significant gene regulatory and metabolic responses associated with survival. When oxygen-deprived in light, aerial organs and root systems respond in distinct manners because of their respective autotrophy and heterotrophy, as well as intrinsic differences in cell biology and organ function. To better understand organ-specific responses to oxygen deficiency, we monitored changes in the metabolome of roots and shoots of Arabidopsis thaliana seedlings using gas chromatography-mass spectrometry and (1) H-nuclear magnetic resonance spectroscopy. Only roots accumulated high amounts of γ-aminobutyrate (GABA) and lactate, whereas both organs accumulated alanine (Ala) upon hypoxia. Meta-analysis of gene regulation data revealed higher induction of mRNAs coding for fermentative enzymes in roots as compared with shoots. However, the elevation in GABA level was not correlated with changes in transcript abundance, supporting the proposal that post-translational mechanisms are important in metabolic acclimation to hypoxia. The biosynthesis, degradation and function of GABA and Ala during oxygen deprivation and re-aeration is discussed. Finally, a systematic survey of low-oxygen mediated regulation of genes associated with primary metabolism across organs and cell types reveals exciting new avenues for future studies.

Molecular and physiological responses of trees to waterlogging stress

One major effect of global climate change will be altered precipitation patterns in many regions of the world. This will cause a higher probability of long-term waterlogging in winter/spring and flash floods in summer because of extreme rainfall events. Particularly, trees not adapted at their natural site to such waterlogging stress can be impaired. Despite the enormous economic, ecological and social importance of forest ecosystems, the effect of waterlogging on trees is far less understood than the effect on many crops or the model plant Arabidopsis. There is only a handful of studies available investigating the transcriptome and metabolome of waterlogged trees. Main physiological responses of trees to waterlogging include the stimulation of fermentative pathways and an accelerated glycolytic flux. Many energy-consuming, anabolic processes are slowed down to overcome the energy crisis mediated by waterlogging. A crucial feature of waterlogging tolerance is the steady supply of glycolysis with carbohydrates, particularly in the roots; stress-sensitive trees fail to maintain sufficient carbohydrate availability resulting in the dieback of the stressed tissues. The present review summarizes physiological and molecular features of waterlogging tolerance of trees; the focus is on carbon metabolism in both, leaves and roots of trees.

Redox regulation of plant development

SIGNIFICANCE

We provide a conceptual framework for the interactions between the cellular redox signaling hub and the phytohormone signaling network that controls plant growth and development to maximize plant productivity under stress-free situations, while limiting growth and altering development on exposure to stress.

RECENT ADVANCES

Enhanced cellular oxidation plays a key role in the regulation of plant growth and stress responses. Oxidative signals or cycles of oxidation and reduction are crucial for the alleviation of dormancy and quiescence, activating the cell cycle and triggering genetic and epigenetic control that underpin growth and differentiation responses to changing environmental conditions.

CRITICAL ISSUES

The redox signaling hub interfaces directly with the phytohormone network in the synergistic control of growth and its modulation in response to environmental stress, but a few components have been identified. Accumulating evidence points to a complex interplay of phytohormone and redox controls that operate at multiple levels. For simplicity, we focus here on redox-dependent processes that control root growth and development and bud burst.

FUTURE DIRECTIONS

The multiple roles of reactive oxygen species in the control of plant growth and development have been identified, but increasing emphasis should now be placed on the functions of redox-regulated proteins, along with the central roles of reductants such as NAD(P)H, thioredoxins, glutathione, glutaredoxins, peroxiredoxins, ascorbate, and reduced ferredoxin in the regulation of the genetic and epigenetic factors that modulate the growth and vigor of crop plants, particularly within an agricultural context.

A Shoot-Specific Hypoxic Response of Arabidopsis Sheds Light on the Role of the Phosphate-Responsive Transcription Factor PHOSPHATE STARVATION RESPONSE1

Plant responses to biotic and abiotic stresses are often very specific, but signal transduction pathways can partially or completely overlap. Here, we demonstrate that in Arabidopsis (Arabidopsis thaliana), the transcriptional responses to phosphate starvation and oxygen deficiency stress comprise a set of commonly induced genes. While the phosphate deficiency response is systemic, under oxygen deficiency, most of the commonly induced genes are found only in illuminated shoots. This jointly induced response to the two stresses is under control of the transcription factor PHOSPHATE STARVATION RESPONSE1 (PHR1), but not of the oxygen-sensing N-end rule pathway, and includes genes encoding proteins for the synthesis of galactolipids, which replace phospholipids in plant membranes under phosphate starvation. Despite the induction of galactolipid synthesis genes, total galactolipid content and plant survival are not severely affected by the up-regulation of galactolipid gene expression in illuminated leaves during hypoxia. However, changes in galactolipid molecular species composition point to an adaptation of lipid fluxes through the endoplasmic reticulum and chloroplast pathways during hypoxia. PHR1-mediated signaling of phosphate deprivation was also light dependent. Because a photoreceptor-mediated PHR1 activation was not detectable under hypoxia, our data suggest that a chloroplast-derived retrograde signal, potentially arising from metabolic changes, regulates PHR1 activity under both oxygen and phosphate deficiency.

The metabolic response of cultured tomato cells to low oxygen stress

The storage of fruits and vegetables under a controlled atmosphere can induce low oxygen stress, which can lead to post-harvest losses through the induction of disorders such as core breakdown and browning. To gain better understanding of the metabolic response of plant organs to low oxygen, cultured tomato cells (Lycopersicum esculentum) were used as a model system to study the metabolic stress response to low oxygen (0 and 1 kPa O2). By adding 13C labelled glucose, changes in the levels of polar metabolites and their 13C label accumulation were quantified. Low oxygen stress altered the metabolite profile of tomato cells, with the accumulation of the intermediates of glycolysis in addition to increases in lactate and sugar alcohols. 13C label data showed reduced label accumulation in almost all metabolites except lactate and some sugar alcohols. The results showed that low oxygen stress in tomato cell culture activated fermentative metabolism and sugar alcohol synthesis while inhibiting the activity of the TCA cycle and the biosynthesis of metabolites whose precursors are derived from central metabolism, including fluxes to most organic acids, amino acids and sugars.

Examination of oxygen release from plants in constructed wetlands in different stages of wetland plant life cycle

The quantification of oxygen release by plants in different stages of wetland plant life cycle was made in this study. Results obtained from 1 year measurement in subsurface wetland microcosms demonstrated that oxygen release from Phragmites australis varied from 108.89 to 404.44 mg O₂/m(2)/d during the different periods from budding to dormancy. Plant species, substrate types, and culture solutions had a significant effect on the capacity of oxygen release of wetland plants. Oxygen supply by wetland plants was estimated to potentially support a removal of 300.37 mg COD/m(2)/d or 55.87 mg NH₄-N/m(2)/d. According to oxygen balance analysis, oxygen release by plants could provide 0.43-1.12% of biochemical oxygen demand in typical subsurface-flow constructed wetlands (CWs). This demonstrates that oxygen release of plants may be a potential source for pollutants removal especially in low-loaded CWs. The results make it possible to quantify the role of plants in wastewater purification.

Rice photosynthetic productivity and PSII photochemistry under nonflooded irrigation

Nonflooded irrigation is an important water-saving rice cultivation technology, but little is known on its photosynthetic mechanism. The aims of this work were to investigate photosynthetic characteristics of rice during grain filling stage under three nonflooded irrigation treatments: furrow irrigation with plastic mulching (FIM), furrow irrigation with nonmulching (FIN), and drip irrigation with plastic mulching (DI). Compared with the conventional flooding (CF) treatment, those grown in the nonflooded irrigation treatments showed lower net photosynthetic rate (P_N), lower maximum quantum yield (F_v/F_m), and lower effective quantum yield of PSII photochemistry (Φ_PSII). And the poor photosynthetic characteristics in the nonflooded irrigation treatments were mainly attributed to the low total nitrogen content (TNC). Under non-flooded irrigation, the P_N, F_v/F_m, and Φ_PSII significantly decreased with a reduction in the soil water potential, but these parameters were rapidly recovered in the DI and FIM treatments when supplementary irrigation was applied. Moreover, The DI treatment always had higher photosynthetic productivity than the FIM and FIN treatments. Grain yield, matter translocation, and dry matter post-anthesis (DMPA) were the highest in the CF treatment, followed by the DI, FIM, and FIN treatments in turn. In conclusion, increasing nitrogen content in leaf of rice plants could be a key factor to improve photosynthetic capacity in nonflooded irrigation.

Forests on thawing permafrost: fragmentation, edge effects, and net forest loss

Much of the world's boreal forest occurs on permafrost (perennially cryotic ground). As such, changes in permafrost conditions have implications for forest function and, within the zone of discontinuous permafrost (30-80% permafrost in areal extent), distribution. Here, forested peat plateaus underlain by permafrost are elevated above the surrounding permafrost-free wetlands; as permafrost thaws, ground surface subsidence leads to waterlogging at forest margins. Within the North American subarctic, recent warming has produced rapid, widespread permafrost thaw and corresponding forest loss. Although permafrost thaw-induced forest loss provides a natural analogue to deforestation occurring in more southerly locations, we know little about how fragmentation relates to subsequent permafrost thaw and forest loss or the role of changing conditions at the edges of forested plateaus. We address these knowledge gaps by (i) examining the relationship of forest loss to the degree of fragmentation in a boreal peatland in the Northwest Territories, Canada; and (ii) quantifying associated biotic and abiotic changes occurring across forest-wetland transitions and extending into the forested plateaus (i.e., edge effects). We demonstrate that the rate of forest loss correlates positively with the degree of fragmentation as quantified by perimeter to area ratio of peat plateaus (edge : area). Changes in depth of seasonal thaw, soil moisture, and effective leaf area index (LAIe ) penetrated the plateau forests by 3-15 m. Water uptake by trees was sevenfold greater in the plateau interior than at the edges with direct implications for tree radial growth. A negative relationship existed between LAIe and soil moisture, suggesting that changes in vegetation physiological function may contribute to changing edge conditions while simultaneously being affected by these changes. Enhancing our understanding of mechanisms contributing to differential rates of permafrost thaw and associated forest loss is critical for predicting future interactions between the land surface processes and the climate system in high-latitude regions.

Nitrogen metabolism in plants under low oxygen stress

More frequent flooding and waterlogging events due to more heavy precipitation are expected worldwide in the context of climate change. Accordingly, adaptation of plants to oxygen limitation at both cellular and whole plant levels should be investigated thoroughly, that derived knowledge could be taken into account in breeding programs and agronomical practices for saving plant fitness, growth and development even when oxygen availability is low. In the present review, we highlight current knowledge on essential aspects of low oxygen stress-induced changes in nitrogen metabolism. The involvement of two possible pathways for NO production either via the reaction catalyzed by nitrate reductase or at Complex III or IV of the mitochondrial electron transport chain, thus contributing to ATP synthesis via the so-called nitrite-NO respiration, is discussed. NO is proposed to be scavenged by non-symbiotic hemoglobin (Hb) in a Hb/NO cycle, in which NAD(P)H is oxidized for the conversion of NO into NO3(-). The investigation of an additional adaptation to the decrease in oxygen availability via transcriptional and posttranslational regulation of amino acid synthesis pathways, using publicly available transcriptome and translatome data for Arabidopsis thaliana and rice is also discussed.

Global gene expression responses to waterlogging in leaves of rape seedlings

Soil waterlogging is a serious constraint to crop production. We investigated the physiological responses of rape (Brassica napus L.) seedlings to waterlogging stress and analyzed global gene transcription responses in the aerial leaves of waterlogged rape seedlings. Seedlings of 'Tammi' and 'Youngsan' cultivars were subjected to waterlogging for 3 and 6 days and recovery for 5 days. Waterlogging stress caused a significant decrease in leaf chlorophyll content and premature senescence of the leaves. Maximal quantum efficiency of PSII (F(v)/F(m)) decreased in the waterlogged seedlings compared with the control plants. To evaluate whether the observed physiological changes in the leaves are associated with the differential regulation of gene expression in response to waterlogging stress, we analyzed the global transcriptional profile of leaves of 'Tammi' seedlings that were exposed to waterlogging for a short period (36 and 72 h). SolexaQA RNA-seq analysis revealed that a total of 4,484 contigs (8.5 %) of all contigs assayed (52,747) showed a twofold change in expression after 36 h of the start of waterlogging and 9,659 contigs (18.3 %) showed a twofold change after 72 h. Major genes involved in leaf photosynthesis, including light reactions and carbon-fixing reactions, were downregulated, while a number of genes involved in the scavenging of reactive oxygen species, degradation (proteins, starch, and lipids), premature senescence, and abiotic stress tolerance were upregulated. Transcriptome analysis data suggested that the aerial leaves of waterlogged rape seedlings respond to hypoxia by regulating the expression of diverse genes in the leaves.

Comparative quantification of oxygen release by wetland plants: electrode technique and oxygen consumption model

Understanding oxygen release by plants is important to the design of constructed wetlands for wastewater treatment. Lab-scale systems planted with Phragmites australis were studied to evaluate the amount of oxygen release by plants using electrode techniques and oxygen consumption model. Oxygen release rate (0.14 g O2/m(2)/day) measured using electrode techniques was much lower than that (3.94-25.20 gO2/m(2)/day) calculated using the oxygen consumption model. The results revealed that oxygen release by plants was significantly influenced by the oxygen demand for the degradation of pollutants, and the oxygen release rate increased with the rising of the concentration of degradable materials in the solution. The summary of the methods in qualifying oxygen release by wetland plants demonstrated that variations existed among different measuring methods and even in the same measuring approach. The results would be helpful for understanding the contribution of plants in constructed wetlands toward actual wastewater treatment.

Bark and woody tissue photosynthesis: a means to avoid hypoxia or anoxia in developing stem tissues

In woody plants, oxygen transport and delivery via the xylem sap are well described, but the contribution of bark and woody tissue photosynthesis to oxygen delivery in stems is poorly understood. Here, we combined stem chlorophyll fluorescence measurements with microsensor quantifications of bark O2 levels and oxygen gas exchange measurements of isolated current-year stem tissues of beech (Fagus sylvatica L.) and pedunculate oak (Quercus robur L.) to investigate how bark and woody tissue photosynthesis impairs the oxygen status of stems. Measurements were made before bud break, when the axial path of oxygen supply via the xylem sap is impeded. At that time, bark O2 levels showed O2 concentrations below the atmospheric concentration, indicating hypoxic conditions or O2 deficiency within the inner bark, but the values were always far away from anoxic. Under illumination bark and woody tissue photosynthesis rapidly increased internal oxygen concentrations compared with plants in the dark, and thereby counteracted against localised hypoxia. The highest photosynthetic activity and oxygen release rates were found in the outermost cortex tissues. By contrast, rates of woody tissue photosynthesis were considerably lower, due to the high light attenuation of the bark and cortex tissues, as well as resistances in radial oxygen diffusion. Therefore, our results confirm that bark and woody tissue photosynthesis not only play a role in plant carbon economy, but may also be important for preventing low oxygen-limitations of respiration in these dense and metabolically active tissues.

Ethylene and reactive oxygen species are involved in root aerenchyma formation and adaptation of wheat seedlings to oxygen-deficient conditions

Exposing plants to hypoxic conditions greatly improves their anoxic stress tolerance by enhancing the activities of glycolysis and fermentation in roots. Ethylene may also be involved in these adaptive responses because its synthesis is increased in roots under hypoxic conditions. Here it is reported that pre-treatment of wheat seedlings with an ethylene precursor, 1-aminocyclopropanecarboxylic acid (ACC), enhanced accumulation of ethylene in the roots of wheat seedlings, and enhanced their tolerance of oxygen-deficient conditions through increasing the expression of genes encoding ethanol fermentation enzymes, alcohol dehydrogenase and pyruvate decarboxylase, in the roots. Lysigenous aerenchyma formation in root was induced by ACC pre-treatment and was further induced by growth under oxygen-deficient conditions. ACC pre-treatment increased the expression of three genes encoding respiratory burst oxidase homologue (a plant homologue of gp91(phox) in NADPH oxidase), which has a role in the generation of reactive oxygen species (ROS), in roots of seedlings. Co-treatment with ACC and an NADPH oxidase inhibitor, diphenyleneiodonium, partly suppressed the ACC-induced responses. These results suggest that ethylene and ROS are involved in adaptation of wheat seedlings to oxygen-deficient conditions through controlling lysigenous aerenchyma formation and the expression of genes encoding ethanol fermentation enzymes.

Analysis of the role of the pyruvate decarboxylase gene family in Arabidopsis thaliana under low-oxygen conditions

Plants under low-oxygen conditions adapt their metabolism by inducing the fermentative pathway, with ethanol as the predominant end product. Activities of pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) are required for this pathway. While a single gene encodes ADH in Arabidopsis, a family of four genes codes PDC. The availability of microarray data sets enabled the relative importance of the four PDC genes under low oxygen to be assessed, and revealed that, contrary to previous published evidence, not only PDC1 but also PDC2 plays a role under hypoxic conditions. We observed a high level of expression, both at transcript and protein levels of PDCs, even under aerobic conditions when ADH is almost absent. This suggests that PDC has a role under aerobic conditions, which is not coupled to fermentative metabolism. The expression of both PDC1 and PDC2 is strongly up-regulated under low oxygen. PDC1 is predominantly present in roots, while PDC2 appears to be leaf-specific. We showed that mutations in both PDC1 and PDC2 result in lower tolerance to submergence.

Isolation of an alcohol dehydrogenase cDNA from and characterization of its expression in chrysanthemum under waterlogging

A PCR strategy was used to isolate a full-length CgADH (alcohol dehydrogenase) cDNA from chrysanthemum. The gene putatively encodes a 378 residue polypeptides, which shares 95% homology with tomato alcohol dehydrogenase class III. Endogenous ethylene generated in waterlogged Chrysanthemum zawadskii was enhanced by exogenous ethylene but decreased by 1-methylcyclopropene (1-MCP), an inhibitor of ethylene action. In waterlogged roots, the transcription of the gene encoding alcohol dehydrogenase (ADH, EC 1.1.1.1) increased rapidly but transiently, peaking at 7.5 fold the non-waterlogged level after 2h of stress. Waterlogging elevated ADH activity after a prolonged episode of stress. The exogenous supply of 40μLL(-1) ethylene suppressed the production of ethanol, while that of 4μLL(-1) 1-MCP enhanced it. Ethylene appeared to suppress an acceleration of both CgADH expression and fermentation, and alleviates ethanolic fermentation probably through by as a signal to acceleration of waterlogging-induced aerenchyma formation. This supports the previously observed phenomenon that the expression level of ADH gene is regulated by the local level of physiologically active ethylene. The relevance of the CgADH gene in relation to chrysanthemum waterlogging was discussed as well.

Tolerance of anaerobic conditions caused by flooding during germination and early growth in rice (Oryza sativa L.)

Rice is semi-aquatic, adapted to a wide range of hydrologies, from aerobic soils in uplands to anaerobic and flooded fields in waterlogged lowlands, to even deeply submerged soils in flood-prone areas. Considerable diversity is present in native rice landraces selected by farmers over centuries. Our understanding of the adaptive features of these landraces to native ecosystems has improved considerably over the recent past. In some cases, major genes associated with tolerance have been cloned, such as SUB1A that confers tolerance of complete submergence and SNORKEL genes that control plant elongation to escape deepwater. Modern rice varieties are sensitive to flooding during germination and early growth, a problem commonly encountered in rainfed areas, but few landraces capable of germination under these conditions have recently been identified, enabling research into tolerance mechanisms. Major QTLs were also identified, and are being targeted for molecular breeding and for cloning. Nevertheless, limited progress has been made in identifying regulatory processes for traits that are unique to tolerant genotypes, including faster germination and coleoptile elongation, formation of roots and leaves under hypoxia, ability to catabolize starch into simple sugars for subsequent use in glycolysis and fermentative pathways to generate energy. Here we discuss the state of knowledge on the role of the PDC-ALDH-ACS bypass and the ALDH enzyme as the likely candidates effective in tolerant rice genotypes. Potential involvement of factors such as cytoplasmic pH regulation, phytohormones, reactive oxygen species scavenging and other metabolites is also discussed. Further characterization of contrasting genotypes would help in elucidating the genetic and biochemical regulatory and signaling mechanisms associated with tolerance. This could facilitate breeding rice varieties suitable for direct seeding systems and guide efforts for improving waterlogging tolerance in other crops.

A microfabricated platform for establishing oxygen gradients in 3-D constructs

Oxygen gradients are increasingly implicated in a number of biological processes, including stem cell differentiation and cancer metastasis. Unfortunately, the current in vitro tools designed to mimic conditions found in vivo lack application flexibility, simplicity in operation, and precise spatial control that most researchers require for widespread dissemination. The novel microfluidic-based device presented here addresses all the above concerns, offering a simple platform for enhanced control over the oxygen microenvironment exposed to three-dimensional cell-seeded constructs. The device utilizes an oxygen diffusion membrane approach to establish a gradient across a construct sandwiched between two continually perfused microfluidic networks. The device is capable of forming steady-state gradients at both the conditions tested-0 % to 5 % O₂ and 0 % to 21 % O₂-but a wide variety of profiles within the construct are possible. Cell viability with two model cell lines was also tested, with no adverse effects relative to the control.

Characterization of the phosphofructokinase gene family in rice and its expression under oxygen deficiency stress

Plants possess two types of phosphofructokinase proteins for phosphorylation of fructose-6-phosphate, the ATP-dependent phosphofructokinase (PFK) and the pyrophosphate-(PPi) dependent pyrophosphate-fructose-6-phosphate-phosphotransferase (PFP). During oxygen deficiency ATP levels in rice seedlings are severely reduced, and it is hypothesized that PPi is used as an alternative energy source for the phosphorylation of fructose-6-phosphate during glycolysis. In this study, we analyzed the expression of 15 phosphofructokinase-encoding genes in roots and aerial tissues of anoxia-tolerant rice seedlings in response to anoxic stress and compared our data with transcript profiles obtained from microarray analyses. Furthermore, the intracellular localization of rice PFK proteins was determined, and the PFK and PFP isoforms were grouped in a phylogenetic tree. Two PFK and two PFP transcripts accumulated during anoxic stress, whereas mRNA levels of four PFK and three PFP genes were decreased. The total specific activity of both PFK and PFP changed only slightly during a 24-h anoxia treatment. It is assumed that expression of different isoforms and their catalytic properties differ during normoxic and anoxic conditions and contribute to balanced glycolytic activity during the low-oxygen stress. These characterizations of phosphofructokinase genes and the comparison to other plant species allowed us to suggest candidate rice genes for adaptation to anoxic stress.

Genetic mechanisms conferring adaptation to submergence and drought in rice: simple or complex?

Both high and low extremes in precipitation increasingly impact agricultural productivity and sustainability as a consequence of global climate change. Elucidation of the genetic basis underlying stress tolerance facilitates development of new rice varieties with enhanced tolerance. Submergence tolerance is conferred by a single master regulator that orchestrates various acclimation responses, whereas drought tolerance is regulated by a number of small-effect loci that are largely influenced by genetic background and environment. Detailed molecular studies have uncovered the functional importance of genes and signaling components which coordinate various morphological and physiological responses to submergence and drought, providing new insight into understanding the complex regulatory mechanisms of stress tolerance in rice.

Responses to flooding of plant water relations and leaf gas exchange in tropical tolerant trees of a black-water wetland

This review summarizes the research on physiological responses to flooding of trees in the seasonal black-water wetland of the Mapire River in Venezuela. Inter-annual variability was found during 8 years of sampling, in spite of which a general picture emerged of increased stomatal conductance (gs) and photosynthetic rate (PN) during the flooded period to values as high as or higher than in plants in drained wet soil. Models explaining the initial inhibitory responses and the acclimation to flooding are proposed. In the inhibitory phase of flooding, hypoxia generated by flooding causes a decrease in root water absorption and stomatal closure. An increase with flooding in xylem water potential (ψ) suggests that flooding does not cause water deficit. The PN decreases due to changes in relative stomatal and non-stomatal limitations to photosynthesis; an increase in the latter is due to reduced chlorophyll and total soluble protein content. Total non-structural carbohydrates (TNC) accumulate in leaves but their content begins to decrease during the acclimatized phase at full flooding, coinciding with the resumption of high gs and PN. The reversal of the diminution in gs is associated, in some but not all species, to the growth of adventitious roots. The occurrence of morpho-anatomical and biochemical adaptations which improve oxygen supply would cause the acclimation, including increased water absorption by the roots, increased rubisco and chlorophyll contents and ultimately increased PN. Therefore, trees would perform as if flooding did not signify a stress to their physiology.

Contrasting hypoxia tolerance and adaptation in Malus species is linked to differences in stomatal behavior and photosynthesis

We examined the potential differences in tolerance to hypoxia by two species of apple rootstocks. Stomatal behavior and photosynthesis were compared between Malus sieversii and Malus hupehensis. Plants were hydroponically grown for 15 days in normoxic or hypoxic nutrient solutions. Those of M. sieversii showed much greater sensitivity, with exposure to hypoxia resulting in higher leaf concentrations of abscisic acid (ABA) that prompted stomatal closure. Compared with the control plants of that species, stomatal density was greater in both new and mature leaves under stress conditions. In contrast, stomatal density was significantly decreased in leaves from M. hupehensis, while stomatal length was unaffected. Under stress, the net photosynthetic rate, stomatal conductance and chlorophyll contents were markedly reduced in M. sieversii. The relatively hypoxia-tolerant genotype M. hupehensis, however, showed only minor changes in net photosynthesis or chlorophyll content, and only a slight decrease in stomatal conductance due to such treatment. Therefore, we conclude that the more tolerant M. hupehensis utilizes a better protective mechanism for retaining higher photosynthetic capacity than does the hypoxia-sensitive M. sieversii. Moreover, this contrast in tolerance and adaptation to stress is linked to differences in their stomatal behavior, photosynthetic capacity and possibly their patterns of native distribution.

Low oxygen response mechanisms in green organisms

Low oxygen stress often occurs during the life of green organisms, mostly due to the environmental conditions affecting oxygen availability. Both plants and algae respond to low oxygen by resetting their metabolism. The shift from mitochondrial respiration to fermentation is the hallmark of anaerobic metabolism in most organisms. This involves a modified carbohydrate metabolism coupled with glycolysis and fermentation. For a coordinated response to low oxygen, plants exploit various molecular mechanisms to sense when oxygen is either absent or in limited amounts. In Arabidopsis thaliana, a direct oxygen sensing system has recently been discovered, where a conserved N-terminal motif on some ethylene responsive factors (ERFs), targets the fate of the protein under normoxia/hypoxia. In Oryza sativa, this same group of ERFs drives physiological and anatomical modifications that vary in relation to the genotype studied. The microalga Chlamydomonas reinhardtii responses to low oxygen seem to have evolved independently of higher plants, posing questions on how the fermentative metabolism is modulated. In this review, we summarize the most recent findings related to these topics, highlighting promising developments for the future.

Recovery of nitrogen fixation after short-term flooding of the nodulated root system of soybean

Nitrogen fixation of terrestrial legumes is strongly and rapidly diminished under flooding. Although recovery is possible with the formation of aerenchyma, information is scarce regarding recovery after draining following short-term flooding, before the appearance of morphological adaptations. This study used soybean (Glycine max) plants nodulated with Bradyrhizobium elkanii to determine xylem sap glutamine as an indication of nitrogen fixation activity during recovery from different periods of flooding. Xylem glutamine levels showed rapid recovery (within 90 min) following periods of flooding up to 4 h. Recovery was progressively slower after longer periods of flooding. After 48 h flooding very little recovery could be observed within the first 120 min after draining but recovery was possible within 48 h. Consistent with the changes in xylem glutamine, direct measurements of apparent nitrogenase activity carried out immediately on draining revealed rapid recovery after flooding for 1 h and slow recovery following 48 h of flooding. In the latter case, nitrogenase activity largely recovered 24 h after draining. Experiments with (15)N(2) incorporation into amino acids exported in the xylem sap revealed that glutamine was by far the most highly labelled amino acid in sap collected over the first 30 min of exposure to the isotope. This is conclusive evidence that xylem sap glutamine is an immediate product of N(2) fixation and export. The changes in xylem sap glutamine seen on flooding (decline) and after draining (recovery) can therefore be attributed to changes in nitrogenase activity. The data show that xylem sap glutamine is a useful means for assessing changes in nitrogenase activity, especially when the root system is submersed in water and activity cannot be measured directly.

Dehydrin, alcohol dehydrogenase, and central metabolite levels are associated with cold tolerance in diploid strawberry (Fragaria spp.)

The use of artificial freezing tests, identification of biomarkers linked to or directly involved in the low-temperature tolerance processes, could prove useful in applied strawberry breeding. This study was conducted to identify genotypes of diploid strawberry that differ in their tolerance to low-temperature stress and to investigate whether a set of candidate proteins and metabolites correlate with the level of tolerance. 17 Fragaria vesca, 2 F. nilgerrensis, 2 F. nubicola, and 1 F. pentaphylla genotypes were evaluated for low-temperature tolerance. Estimates of temperatures where 50 % of the plants survived (LT₅₀) ranged from -4.7 to -12.0 °C between the genotypes. Among the F. vesca genotypes, the LT₅₀ varied from -7.7 °C to -12.0 °C. Among the most tolerant were three F. vesca ssp. bracteata genotypes (FDP821, NCGR424, and NCGR502), while a F. vesca ssp. californica genotype (FDP817) was the least tolerant (LT₅₀) -7.7 °C). Alcohol dehydrogenase (ADH), total dehydrin expression, and content of central metabolism constituents were assayed in select plants acclimated at 2 °C. The LT₅₀ estimates and the expression of ADH and total dehydrins were highly correlated (r(adh) = -0.87, r (dehyd) = -0.82). Compounds related to the citric acid cycle were quantified in the leaves during acclimation. While several sugars and acids were significantly correlated to the LT₅₀ estimates early in the acclimation period, only galactinol proved to be a good LT₅₀ predictor after 28 days of acclimation (r(galact) = 0.79). It is concluded that ADH, dehydrins, and galactinol show great potential to serve as biomarkers for cold tolerance in diploid strawberry.

Can Stress Enhance Phytoremediation of Polychlorinated Biphenyls?

Phytoremediation-plant-facilitated remediation of polluted soil and groundwater-is a potentially effective treatment technology for the remediation of heavy metals and certain organic compounds. However, contaminant attenuation rates are often not rapid enough to make phytoremediation a viable option when compared with alternative treatment approaches. Different strategies are being employed to enhance the efficacy of phytoremediation, including modification to the plant genome, inoculation of the rhizosphere with specialized and/or engineered bacteria, and treatment of the soil with supplementary chemicals, such as surfactants, chelators, or fertilizers. Despite these efforts, greater breakthroughs are necessary to make phytoremediation a viable technology. Here, we introduce and discuss the concept of integrating controlled environmental stresses as a strategy for enhancing phytoremediation. Plants have a diverse suite of defense mechanisms that are only induced in response to stress. Here, we examine some stress-response mechanisms in plants, focusing on defenses involving physiological changes that alter the soil microenvironment (rhizosphere), and outline how these defense mechanisms can be co-opted to enhance the effectiveness of phytoremediation of polychlorinated biphenyls and other contaminants.

De-submergence responses of antioxidative defense systems in two wetland plants having escape and quiescence strategies

Fast recovery after de-submergence requires efficient protection against oxidative injuries. We investigated whether de-submergence responses of antioxidant systems differ in two wetland plants, Alternanthera philoxeroides and Hemarthria altissima, characterized by 'escape' and 'quiescence' strategies of flood tolerance, respectively. The antioxidant capacity was assessed in the two species during 10d of recovery following 20d of complete submergence (low light+low O(2)) or severe shading (low light+ambient O(2)). The activities of superoxide dismutase and catalase were measured in leaf and root tissues, along with the concentrations of reduced ascorbate, malondialdehyde, and acetaldehyde. In addition, formation of superoxide (O(2)(-)) and hydrogen peroxide (H(2)O(2)) was detected in leaves by chemical staining. Following de-submergence, plants of A. philoxeroides showed a transient burst of acetaldehyde, while the concentration of acetaldehyde increased slowly and stayed high in leaves of H. altissima. In leaves of A. philoxeroides, the variations in O(2)(-) and H(2)O(2) correlated with the levels of light and O(2), respectively, whereas neither of the two reactive oxygen species was detected in H. altissima. For A. philoxeroides, the antioxidant capacities changed mainly in leaves during the recovery. For H. altissima, changes in reduced ascorbate were found in leaves and those of antioxidant enzyme activities in roots. De-submergence caused some lipid peroxidation in leaves of both species. We conclude that de-submergence responses of the detoxification systems differ between A. philoxeroides and H. altissima, especially in leaves. Dynamic changes were found in A. philoxeroides (having the escape strategy), as opposed to little or slow changes in H. altissima (having the quiescence strategy). Whereas the antioxidant capacities are often strongly influenced by light environments, the toxic compounds and lipid peroxidation indicate harmful effects of changing O(2) concentration which accompanies submergence and de-submergence.

Proteomic study of low-temperature responses in strawberry cultivars (Fragaria x ananassa) that differ in cold tolerance

To gain insight into the molecular basis contributing to overwintering hardiness, a comprehensive proteomic analysis comparing crowns of octoploid strawberry (Fragaria × ananassa) cultivars that differ in freezing tolerance was conducted. Four cultivars were examined for freeze tolerance and the most cold-tolerant cultivar ('Jonsok') and least-tolerant cultivar ('Frida') were compared with a goal to reveal how freezing tolerance is achieved in this distinctive overwintering structure and to identify potential cold-tolerance-associated biomarkers. Supported by univariate and multivariate analysis, a total of 63 spots from two-dimensional electrophoresis analysis and 135 proteins from label-free quantitative proteomics were identified as significantly differentially expressed in crown tissue from the two strawberry cultivars exposed to 0-, 2-, and 42-d cold treatment. Proteins identified as cold-tolerance-associated included molecular chaperones, antioxidants/detoxifying enzymes, metabolic enzymes, pathogenesis-related proteins, and flavonoid pathway proteins. A number of proteins were newly identified as associated with cold tolerance. Distinctive mechanisms for cold tolerance were characterized for two cultivars. In particular, the 'Frida' cold response emphasized proteins specific to flavonoid biosynthesis, while the more freezing-tolerant 'Jonsok' had a more comprehensive suite of known stress-responsive proteins including those involved in antioxidation, detoxification, and disease resistance. The molecular basis for 'Jonsok'-enhanced cold tolerance can be explained by the constitutive level of a number of proteins that provide a physiological stress-tolerant poise.

Soil oxidation-reduction in wetlands and its impact on plant functioning

Soil flooding in wetlands is accompanied by changes in soil physical and chemical characteristics. These changes include the lowering of soil redox potential (Eh) leading to increasing demand for oxygen within the soil profile as well as production of soil phytotoxins that are by-products of soil reduction and thus, imposing potentially severe stress on plant roots. Various methods are utilized for quantifying plant responses to reducing soil conditions that include measurement of radial oxygen transport, plant enzymatic responses, and assessment of anatomical/morphological changes. However, the chemical properties and reducing nature of soil environment in which plant roots are grown, including oxygen demand, and other associated processes that occur in wetland soils, pose a challenge to evaluation and comparison of plant responses that are reported in the literature. This review emphasizes soil-plant interactions in wetlands, drawing attention to the importance of quantifying the intensity and capacity of soil reduction for proper evaluation of wetland plant responses, particularly at the process and whole-plant levels. Furthermore, while root oxygen-deficiency may partially account for plant stress responses, the importance of soil phytotoxins, produced as by-products of low soil Eh conditions, is discussed and the need for development of methods to allow differentiation of plant responses to reduced or anaerobic soil conditions vs. soil phytotoxins is emphasized.

Molecular cloning and biochemical characterization of three phosphoglycerate kinase isoforms from developing sunflower (Helianthus annuus L.) seeds

Three cDNAs encoding different phosphoglycerate kinase (PGK, EC 2.7.2.3) isoforms, two cytosolic (HacPGK1 and HacPGK2) and one plastidic (HapPGK), were cloned and characterized from developing sunflower (Helianthus annuus L.) seeds. The expression profiles of these genes showed differences in heterotrophic tissues, such as developing seeds and roots, where HacPGK1 was predominant, while HapPGK was highly expressed in photosynthetic tissues. The cDNAs were expressed in Escherichia coli, and the corresponding proteins purified to electrophoretic homogeneity, using immobilized metal ion affinity chromatography, and biochemically characterized. Despite the high level of identity between sequences, the HacPGK1 isoform showed strong differences in terms of specific activity, temperature stability and pH sensitivity in comparison to HacPGK2 and HapPGK. A polyclonal immune serum was raised against the purified HacPGK1 isoform, which showed cross-immunoreactivity with the other PGK isoforms. This serum allowed the localization of high expression levels of PGK isozymes in embryo tissues.

Local root apex hypoxia induces NO-mediated hypoxic acclimation of the entire root

Roots are very sensitive to hypoxia and adapt effectively to a reduced availability of oxygen in the soil. However, the site of the root where oxygen availability is sensed and how roots acclimate to hypoxia remain unclear. In this study, we found that the root apex transition zone plays central roles in both sensing and adapting to root hypoxia. The exposure of cells of the root apex to hypoxia is sufficient to achieve hypoxic acclimation of the entire root; particularly relevant in this respect is that, of the entire root apex, the transition zone cells show the highest demand for oxygen and also emit the largest amount of nitric oxide (NO). Local root apex-specific oxygen deprivation dramatically inhibits the oxygen influx peak in the transition zone and simultaneously stimulates a local increase in NO emission. The hypoxia-induced efflux of NO is strictly associated with the transition zone and is essential for hypoxic acclimation of the entire root.

Peptidyl-prolyl cis-trans isomerase ROF2 modulates intracellular pH homeostasis in Arabidopsis

Intracellular pH must be kept close to neutrality to be compatible with cellular functions, but the mechanisms of pH homeostasis and the responses to intracellular acidification are mostly unknown. In the plant Arabidopsis thaliana, we found that intracellular acid stress generated by weak organic acids at normal external pH induces expression of several chaperone genes, including ROF2, which encodes a peptidyl-prolyl cis-trans isomerase of the FK506-binding protein class. Loss of function of ROF2, and especially double mutation of ROF2 and the closely related gene ROF1, results in acid sensitivity. Over-expression of ROF2 confers tolerance to intracellular acidification by increasing proton extrusion from cells. The activation of the plasma membrane proton pump (H(+) -ATPase) is indirect: over-expression of ROF2 activates K(+) uptake, causing depolarization of the plasma membrane, which activates the electrogenic H(+) pump. The depolarization of ROF2 over-expressing plants explains their tolerance to toxic cations such as lithium, norspermidine and hygromycin B, whose uptake is driven by the membrane potential. As ROF2 induction and intracellular acidification are common consequences of many stresses, this mechanism of pH homeostasis may be of general importance for stress tolerance.

Physiological and biochemical parameters controlling waterlogging stress tolerance in Prunus before and after drainage

Waterlogging is associated with poor soil drainage. As a consequence oxygen levels decrease in the root environment inducing root asphyxia and affecting plant growth. Some plants can survive under these conditions triggering complex anatomical and biochemical adaptations, mostly in the roots. Long- and short-term responses to waterlogging stress were compared in two trials using a set of two myrobalans (Prunus cerasifera Erhr), 'P.2175' and 'P.2980', as tolerant rootstocks and two almond × peach [Prunus amygdalus Batsch ×Prunus persica (L.) Batsch] interspecific hybrids, 'Garnem' and 'Felinem', as sensitive ones in two consecutive years. Stomatal conductance and chlorophyll content were measured in the long-term trials to assess survival performance, while the enzyme activities of superoxide dismutase (SOD, EC 1.15.1.1), guaiacol peroxidase (POD, EC 1.11.1.7), and catalase (CAT, EC 1.11.1.6) were measured in the short-term trials to study early antioxidant response. The incidence of the stress in the root environment was different as a result of the different plant development at the moment of the treatment, as a consequence of different environmental conditions both before and during the treatment between the 2 years. The activity of the different enzymes was higher in the sensitive genotype 'Felinem' than in the tolerant 'P.2175'. This result shows an activation of the antioxidant system and has been observed to depend of the different nature of the roots between the 2 years. As the antioxidant enzymes seem to work more efficiently when roots are more aerated, we cannot conclude that they are responsible for the higher tolerance observed in the myrobalan plums.

Novel Prunus rootstock somaclonal variants with divergent ability to tolerate waterlogging

Plants require access to free water for nutrient uptake, but excess water surrounding the roots can be injurious or even lethal because it blocks the transfer of free oxygen between the soil and the atmosphere. Genetic improvement efforts in this study were focused on the increased tolerance in roots to waterlogging. Among a pool of clones generated in vitro from leaf explants of rootstock Mr.S.2/5 of Prunus cerasifera L., the S.4 clone was flood tolerant whereas the S.1 clone was sensitive. The S.4 clone formed adventitious roots on exposure to flooding. Moreover, the chlorophyll content and mitochondrial activity in the leaf and root, soluble sugar content, alcohol dehydrogenase activity and ethylene content were different between the clones. The sorbitol transporter gene (SOT1) was up-regulated during hypoxia, the alcohol dehydrogenase genes (ADH1 and ADH3) were up-regulated in the leaves and down-regulated in the roots of the S.4 clone during hypoxia, and the 1-aminocyclopropane-1-oxidase gene (ACO1) was up-regulated in the leaves and roots of the S.4 clone during hypoxia and down-regulated in the wild-type roots. In addition, in the S.4 root, hypoxia induced significant down-regulation of a glycosyltransferase-like gene (GTL), which has a yet-undefined role. Although the relevant variation in the S.4 genome has yet to be determined, genetic alteration clearly conferred a flooding-tolerant phenotype. The isolation of novel somaclonals with the same genomic background but with divergent tolerance to flooding may offer new insights in the elucidation of the genetic machinery of resistance to flooding and aid in the selection of new Prunus rootstocks to be used in various adverse environments.

Ethylene reduces plant gas exchange and growth of lettuce grown from seed to harvest under hypobaric and ambient total pressure

Naturally occurring high levels of ethylene can be a problem in spaceflight and controlled environment agriculture (CEA) leading to sterility and irregular plant growth. There are engineering and safety advantages of growing plants under hypobaria (low pressure) for space habitation. The goals of this research were to successfully grow lettuce (Lactuca sativa cv. Buttercrunch) in a long-term study from seed to harvest under hypobaric conditions, and to investigate how endogenously produced ethylene affects gas exchange and plant growth from seed germination to harvest under hypobaric and ambient total pressure conditions. Lettuce was grown under two levels of total gas pressure [hypobaric or ambient (25 or 101 kPa)] in a long-term, 32-day study. Significant levels of endogenous ethylene occurred by day-15 causing reductions in photosynthesis, dark-period respiration, and a subsequent decrease in plant growth. Hypobaria did not mitigate the adverse ethylene effects on plant growth. Seed germination was not adversely affected by hypobaria, but was reduced by hypoxia (6 kPa pO(2)). Under hypoxia, seed germination was higher under hypobaria than ambient total pressure. This research shows that lettuce can be grown from seed to harvest under hypobaria (≅25% of normal earth ambient total pressure).

Differential responses in sympatric tree species exposed to waterlogging

Climate change is projected to have a significant ecological impact on natural ecosystems, most notably through direct and indirect modifications of local precipitation regimes. In addition, anthropic activities such as the removal of vegetation, soil proofing due to building, the absence of storm drains and crop over-irrigation will all increase the occurrence of flooding. As a result, forest species, and more specifically trees, will increasingly be exposed to soil waterlogging. It is now well established that such flooding events can lead to changes in forest distribution and composition. For such reasons, it is becoming increasingly important to study forest ecosystems and more particularly the adaptive potential of tree species to better understand the ecological plasticity of forest communities to environmental modifications.

Effect of flooding on C metabolism of flood-tolerant (Quercus robur) and non-tolerant (Fagus sylvatica) tree species

Flooding is assumed to cause an energy crisis in plants because-due to a lack of O(2)-mitochondrial respiration is replaced by alcoholic fermentation which yields considerably less energy equivalents. In the present study, the effect of flooding on the carbon metabolism of flooding-tolerant pedunculate oak (Quercus robur L.) and flooding-sensitive European beech (Fagus sylvatica L.) seedlings was characterized. Whereas soluble carbohydrate concentrations dropped in roots of F. sylvatica, they were constant in Q. robur during flooding. At the same time, root alcohol dehydrogenase activities were decreased in beech but not in oak, suggesting substrate limitation of alcoholic fermentation in beech roots. Surprisingly, leaf and phloem sap sugar concentrations increased in both species but to a much higher degree in beech. This finding suggests that the phloem unloading process in flooding-sensitive beech was strongly impaired. It is assumed that root-derived ethanol is transported to the leaves via the transpiration stream. This mechanism is considered an adaptation to flooding because it helps avoid the accumulation of toxic ethanol in the roots and supports the whole plant's carbon metabolism by channelling ethanol into the oxidative metabolism of the leaves. A labelling experiment demonstrated that in the leaves of flooded trees, ethanol metabolism does not differ between flooded beech and oak, indicating that processes in the roots are crucial for the trees' flooding tolerance.

Quinclorac resistance: a concerted hormonal and enzymatic effort in Echinochloa phyllopogon

BACKGROUND

Quinclorac (3,7-dichloro-quinoline-carboxylic acid) is a selective herbicide widely used to control annual grasses and certain broadleaf weeds. Echinochloa phyllopogon (Stapf) Koss. is the most noxious grass weed in California rice fields and has evolved resistance to multiple herbicides with different modes of action. A quinclorac-resistant (R) E. phyllopogon biotype found in a Sacramento Valley rice field where quinclorac has never been applied was investigated.

RESULTS

Resistant to susceptible (S) GR(50) (herbicide rate for 50% growth reduction) ratios ranged from 6 to 17. The cytochrome P450 inhibitor malathion (200 mg L(-1)) caused R plants to become as quinclorac susceptible as S plants. Quinclorac rapidly (6 HAT) stimulated ethylene formation in S plants, but only marginally in R plants. Malathion pretreatment did not reduce ethylene formation by quinclorac-treated S and R plants. Activity of β-cyanoalanine synthase (β-CAS) in tissue extracts was 2-3-fold greater in R than in S plants, and incubation of shoot extracts with 1 mM malathion reduced β-CAS activity by 40% in both biotypes.

CONCLUSION

Resistance to quinclorac in R E. phyllopogon involved at least two mechanisms: (a) insensitivity along the response pathway whereby quinclorac induces ethylene production; (b) enhanced β-CAS activity, which should enable greater HCN detoxification following quinclorac stimulation of ethylene biosynthesis. This unveils new resistance mechanisms for this multiple-resistant biotype widely spread throughout California rice fields.