Leaf relative water content at 50% stomatal conductance measured by noninvasive NMR is linked to climate of origin in nine species of eucalypt

Stomata are the gatekeepers of plant water use and must quickly respond to changes in plant water status to ensure plant survival under fluctuating environmental conditions. The mechanism for their closure is highly sensitive to disturbances in leaf water status, which makes isolating their response to declining water content difficult to characterise and to compare responses among species. Using a small-scale non-destructive nuclear magnetic resonance spectrometer as a leaf water content sensor, we measure the stomatal response to rapid induction of water deficit in the leaves of nine species of eucalypt from contrasting climates. We found a strong linear correlation between relative water content at 50% stomatal conductance (RWCgs50 ) and mean annual temperature at the climate of origin of each species. We also show evidence for stomata to maintain control over water loss well below turgor loss point in species adapted to warmer climates and secondary increases in stomatal conductance despite declining water content. We propose that RWCgs50 is a promising trait to guide future investigations comparing stomatal responses to water deficit. It may provide a useful phenotyping trait to delineate tolerance and adaption to hot temperatures and high leaf-to-air vapour pressure deficits.

Utilising random forests in the modelling of Eragrostis curvula presence and absence in an Australian grassland system

Eragrostis curvula is an agronomically and ecologically undesirable perennial tussock grass dispersed across Australia. The objective of this study is to investigate relationships of ecologically relevant abiotic variables with the presence of E. curvula at a landscape scale in the Snowy Monaro region, Australia. Through vegetation surveys across 21 privately owned properties and freely available ancillary data on E. curvula presence, we used seven predictor variables, including Sentinel 2 NDVI reflectance, topography, distance from roads and watercourses and climate, to predict the presence or absence of E. curvula across its invaded range using a random forest (RF) algorithm. Assessment of performance metrics resulted in a pseudo-R squared of 0.96, a kappa of 0.97 and an R squared for out-of-bag samples of 0.67. Temperature had the largest influence on the model's performance, followed by linear features such as highways and rivers. Highways' high importance in the model may indicate that the presence or absence of E. curvula is related to the density of human transit, thus as a vector of E. curvula propagule dispersal. Further, humans' tendency to reside adjacent to rivers may indicate that E. curvula's presence or absence is related to human density and E. curvula's potential to spread via water courses.

The Metabolic Profile of Young, Watered Chickpea Plants Can Be Used as a Biomarker to Predict Seed Number under Terminal Drought

Chickpea is the second-most-cultivated legume globally, with India and Australia being the two largest producers. In both of these locations, the crop is sown on residual summer soil moisture and left to grow on progressively depleting water content, finally maturing under terminal drought conditions. The metabolic profile of plants is commonly, correlatively associated with performance or stress responses, e.g., the accumulation of osmoprotective metabolites during cold stress. In animals and humans, metabolites are also prognostically used to predict the likelihood of an event (usually a disease) before it occurs, e.g., blood cholesterol and heart disease. We sought to discover metabolic biomarkers in chickpea that could be used to predict grain yield traits under terminal drought, from the leaf tissue of young, watered, healthy plants. The metabolic profile (GC-MS and enzyme assays) of field-grown chickpea leaves was analysed over two growing seasons, and then predictive modelling was applied to associate the most strongly correlated metabolites with the final seed number plant^-1. Pinitol (negatively), sucrose (negatively) and GABA (positively) were significantly correlated with seed number in both years of study. The feature selection algorithm of the model selected a larger range of metabolites including carbohydrates, sugar alcohols and GABA. The correlation between the predicted seed number and actual seed number was R² adj = 0.62, demonstrating that the metabolic profile could be used to predict a complex trait with a high degree of accuracy. A previously unknown association between D-pinitol and hundred-kernel weight was also discovered and may provide a single metabolic marker with which to predict large seeded chickpea varieties from new crosses. The use of metabolic biomarkers could be used by breeders to identify superior-performing genotypes before maturity is reached.

Key issues for implementation of Genomics in Healthcare: a Policy Brief

Issue/problem

Healthcare (HC) can significantly benefit from genomic information for earlier, accurate diagnosis, effective personalized treatment with less adverse events, and accurate profiling of individuals for disease prevention. However, European countries are currently at variable maturity stages regarding the implementation of genomic medicine (GM) in healthcare, hindering the equitable delivery of personalized medicine to citizens across borders.

Description of the problem

The European 1+Million Genomes Initiative (1+MG) aims to provide cross-border access to quality genomic information and related clinical data, to advance data-driven research and HC solutions to benefit citizens. This initiative is encouraging countries to develop national GM strategies, but guidance for successful implementation is needed. In this context, the Beyond 1 Million Genomes, a supporting action to the 1+MG initiative, organized three Country Exchange Visits (CEV) to discuss critical issues, share experiences and best practices, for the implementation of sustainable GM strategies in healthcare.

Results

The United Kingdom, Estonia and Finland, which have advanced GM programs, hosted CEV describing progress and lessons learnt. Representatives of 1+MG signatory countries participated in these events and were able to present country level progress. The resulting Policy Brief (PB) captures key issues discussed at the CEVs, with real-life examples, and proposes policy recommendations for the successful implementation of GM in European healthcare systems.

Lessons

Sustainable GM implementation in HC systems requires: 1) Patient and citizens trust and engagement; 2) Sustainable infrastructure and data regulation, with solid ethical and legal frameworks; 3) Capacity building of healthcare professionals; 4) A strong ecosystem involving all stakeholders, and encouraging synergies between healthcare, research and industry to promote continuous innovation.

Key messages

• The implementation of GM in healthcare will take countries further towards making personalized medicine a reality, with remarkable health and socioeconomic benefits for patients and healthcare systems.

• Promoting cooperation, capacity building and sharing of best practices is crucial to reduce asymmetries between countries, which constrains effective and equitable cross-border personalized medicine.

Carbon isotope and soluble metabolites reflect physiological status among contrasting faba bean genotypes in response to water deficit

Identification and validation of biomarkers and bioindicators to select genotypes with superior tolerance to water deficit (WD) under field conditions are paramount to plant breeding programs. However, the co-occurrence of different abiotic stresses such as WD, heat, and radiation makes it difficult to develop generalized protocols to monitor the physiological health of the plant system. The study assessed the most abundant carbohydrates and sugar alcohols in five faba bean (Vicia faba) genotypes under field conditions and the abundance of naturally occurring carbon isotopes in bulk leaf material to predict water use efficiency (WUE). Plant water status and biomass accumulation were also assessed. Among the accumulated sugars, inter-specific variation in glucose was most prevalent and was found at a higher concentration (8.52 mg g^-1 leaf) in rainfed trial. myo-Inositol concentrations followed that of glucose accumulation in that the rainfed trial had higher amounts compared to the irrigated trial. WUE calculated from carbon isotope abundance was consistently offset with measured WUE from measurements of leaf gas exchange. All genotypes demonstrated significant relationships between predicted and measured WUE (p < 0.05) apart from control variety PBA Warda. Thus, bulk leaf-level carbon isotope abundance can be used to calculate WUE and used as an effective selection criterion for improving WUE in faba bean breeding programs under field conditions.

In situ pod growth rate reveals contrasting diurnal sensitivity to water deficit in Phaseolus vulgaris

The development of reproductive tissues determines plant fecundity and yield. Loading of resources into the developing reproductive tissue is thought to be under the co-limiting effects of source and sink strength. The dynamics of this co-limitation are unknown, largely due to an inability to measure the flux of resources into a developing sink. Here we use nuclear magnetic resonance (NMR) sensors to measure sink strength by quantifying rates of pod dry matter accumulation (pod loading) in Phaseolus vulgaris at 13-min intervals across the diel period. Rates of pod loading showed contrasting variation across light and dark periods during the onset of water deficit. In addition, rates of pod loading appeared decoupled from net photosynthetic rates when adjusted to the plant scale. Combined, these observations illustrate that the rate of pod development varies under water limitation and that continuous, non-invasive methodologies to measure sink strength provide insight into the governing processes that determine the development of reproductive tissues.

Effect of Drought and Low P on Yield and Nutritional Content in Common Bean

Common bean (Phaseolus vulgaris L.) production in the tropics typically occurs in rainfed systems on marginal lands where yields are low, primarily as a consequence of drought and low phosphorus (P) availability in soil. This study aimed to investigate the physiological and chemical responses of 12 bush bean genotypes for adaptation to individual and combined stress factors of drought and low P availability. Water stress and P deficiency, both individually and combined, decreased seed weight and aboveground biomass by ∼80%. Water deficit and P deficiency decreased photosynthesis and stomatal conductance during plant development. Maximum rates of carboxylation, electron transport, and triose phosphate utilization were superior for two common bean genotypes (SEF60 and NCB226) that are better adapted to combined stress conditions of water deficit and low P compared to the commercial check (DOR390). In response to water deficit treatment, carbon isotope fractionation in the leaf tissue decreased at all developmental stages. Within the soluble leaf fraction, combined water deficit and low P, led to significant changes in the concentration of key nutrients and amino acids, whereas no impact was detected in the seed. Our results suggest that common bean genotypes have a degree of resilience in yield development, expressed in traits such as pod harvest index, and conservation of nutritional content in the seed. Further exploration of the chemical and physiological traits identified here will enhance the resilience of common bean production systems in the tropics.

Investigating Nutrient Supply Effects on Plant Growth and Seed Nutrient Content in Common Bean

Low soil fertility commonly limits growth and yield production of common bean (Phaseolus vulgaris L.) in tropical regions. Impacts of nutrient limitations on production volume are well studied and are a major factor in reducing crop yields. This study characterised the impact of reduced nutrient supply on carbon assimilation and nutrient content of leaf, phloem sap and reproductive tissues of common bean grown in a controlled environment in order to detect chemical markers for changes in nutritional content. Leaf gas exchange measurements were undertaken over plant development to characterise changes to carbon assimilation under reduced nutrient supply. Samples of leaf, phloem sap and pod tissue of common bean were analysed for carbon isotope discrimination, mineral nutrient content, and amino acid concentration. Despite declines in nutrient availability leading to decreased carbon assimilation and reductions in yield, amino acid concentration was maintained in the pod tissue. Common bean can maintain the nutritional content of individual pods under varying nutrient availabilities demonstrating the resilience of processes determining the viability of reproductive tissues.

Phloem sap metabolites vary according to the interactive effects of nutrient supply and seasonal conditions in Eucalyptus globulus (Labill)

Improving the efficiency of fertilizer application is paramount to both the sustainability and profitability of forest plantations. Therefore, developing reliable, cost-effective tools to assess tree nutritional status is of great interest. This investigation sought to assess the use of phloem sap-derived metabolites as an indicator of nutritional status on a background of seasonal water availability of Eucalyptus globulus (Labill) trees grown under field conditions. Phloem is a central conduit for long-distance transport and signaling in plants and offers great promise in reflecting plant-scale resource limitations. Changes in the abundance of solutes and isotopes in phloem sap are sensitive to environmental cues. With a focus on both water and nutrient availability, we characterize patterns in phloem sugars, amino acids and the abundance of carbon isotopes in phloem sap obtained from E. globulus among different seasons and fertilizer treatments. Phloem-derived total amino acid concentration was found to increase with an increasing nitrogen (N) supply; however, this response was lost with the concurrent addition of phosphorus and at the highest level of N supply. Significant seasonal variation in all measured parameters was also detected, highlighting the need for caution in making quantitative relationships with growth. Broader implications of the interactive effects of both water supply and multi-nutrient additions and relationships with growth are discussed.

Chemical composition and reproductive functionality of contrasting faba bean genotypes in response to water deficit

Water deficit (WD), a major contributor to yield reductions in faba bean (Vicia faba), is a complex phenomenon that varies across daily to seasonal cycles. Several studies have identified various morphological and physiological indicators of WD tolerance, which generally show limited water use during WD. Limited information is available on the impact of WD on nutrient content and reproductive biology of the faba bean. We studied carbohydrates, amino acids, mineral nutrients and the abundance of naturally occurring carbon isotopes (δ¹³ C) in leaf and grain tissues of faba bean genotypes grown under well-watered (WW) and WD conditions. δ¹³ C of leaf tissues were found to indicate changes in water use due to WD but this was not reflected in grain tissues. Nutrient concentrations with regard to amino acids and minerals were not influenced by WD. However, carbohydrate accumulation was found to be significant for WD, specifically through the presence of a higher concentration of myo-inositol in WD leaf tissues. Alternatively, sucrose concentration in grain tissues was reduced under WD treatment. WD hampered reproductive functionality by reducing pollen viability and germination with the severity and duration of stress and this reduction was less prominent in the drought-tolerant genotype (AC0805#4912) compared to the sensitive one (11NF010c-4). It was also demonstrated that WD caused developmental impairment in the stamen and pistil, where the pistil appeared more sensitive than stamen. These findings suggest that WD impairs pollen viability and pistil function reducing yield volume, but the nutrient content of the resulting yield is not significantly affected.

Wide variation in the suboptimal distribution of photosynthetic capacity in relation to light across genotypes of wheat

Suboptimal distribution of photosynthetic capacity in relation to light among leaves reduces potential whole-canopy photosynthesis. We quantified the degree of suboptimality in 160 genotypes of wheat by directly measuring photosynthetic capacity and daily irradiance in flag and penultimate leaves. Capacity per unit daily irradiance was systematically lower in flag than penultimate leaves in most genotypes, but the ratio (γ) of capacity per unit irradiance between flag and penultimate leaves varied widely across genotypes, from less than 0.5 to over 1.2. Variation in γ was most strongly associated with differences in photosynthetic capacity in penultimate leaves, rather than with flag leaf photosynthesis or canopy light penetration. Preliminary genome-wide association analysis identified nine strong marker-trait associations with this trait, which should be validated in future work in other environments and/or materials. Our modelling suggests canopy photosynthesis could be increased by up to 5 % under sunny conditions by harnessing this variation through selective breeding for increased γ.

Over-expression of RNA interference (RNAi) core machinery improves susceptibility to RNAi in silkworm larvae

RNA interference (RNAi), one of the strategies that organisms use to defend against invading viruses, is an important tool for functional genomic analysis. In insects, the efficacy of RNAi varies amongst taxa. Lepidopteran insects are, in large part, recalcitrant to RNAi. The overall goal of this study is to overcome such insensitivity in lepidopterans to RNAi. We hypothesize that over-expression of core RNAi machinery enzymes can improve RNAi efficacy in traditionally recalcitrant species. A transgenic Bombyx mori strain, Baculovirus Immediate-Early Gene, ie1, promoter driven expression of silkworm Dicer2 coding sequence (IE1-BmDicer2), which over-expresses BmDicer2, was generated by piggyBac transposon-mediated transgenesis. Two indexes, the ratio of animals that showed a silencing phenotype and the duration of silencing, were used to evaluate silencing efficiency. Significant knockdown of target gene expression was observed at 48 h postinjection at both the transcriptional and translational levels. Furthermore, we coexpressed B. mori Argonaute 2 BmAgo2）and BmDicer 2 and found that 22% of the animals (n = 18) showed an obvious silencing effect even at 72 h, suggesting that coexpression of these two RNAi core machinery enzymes further increased the susceptibility of B. mori to injected double-stranded RNAs. This study offers a new strategy for functional genomics research in RNAi-refractory insect taxa in general and for lepidopterans in particular.

The preceding root system drives the composition and function of the rhizosphere microbiome

BACKGROUND

The soil environment is responsible for sustaining most terrestrial plant life, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere, and how it responds to agricultural management such as crop rotations and soil tillage, is vital for improving global food production.

RESULTS

This study establishes an in-depth soil microbial gene catalogue based on the living-decaying rhizosphere niches in a cropping soil. The detritusphere microbiome regulates the composition and function of the rhizosphere microbiome to a greater extent than plant type: rhizosphere microbiomes of wheat and chickpea were homogenous (65-87% similarity) in the presence of decaying root (DR) systems but were heterogeneous (3-24% similarity) where DR was disrupted by tillage. When the microbiomes of the rhizosphere and the detritusphere interact in the presence of DR, there is significant degradation of plant root exudates by the rhizosphere microbiome, and genes associated with membrane transporters, carbohydrate and amino acid metabolism are enriched.

CONCLUSIONS

The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the detritusphere microbiome in determining the metagenome of developing root systems. Modifications in root microbial function through soil management can ultimately govern plant health, productivity and food security.

Population Data Centre Profile - The Western Australian Data Linkage Branch

Established in 1995, the Western Australian Data Linkage Branch (DLB) is Australia's longest running data linkage agency. The Western Australian Data Linkage System (WADLS) employs an enduring linkage model spanning over 60 data collections supported by internally developed and supported software and IT infrastructure. DLB has delivered, and continues to deliver, a range of significant data linkage innovations, many of which have been adopted elsewhere. A current restructure within the Western Australian Department of Health (which we will refer to as the Department of Health) will provide an improved funding model geared toward addressing issues with staff retention, capacity and customer service, as well as fostering improvements to data management, governance and availability. Research using linked data provided by DLB has been used in over 800 projects resulting in over 2350 publications and outcomes for policy development, service delivery and public health. Demand continues to grow for data linkage services and with the Department of Health's bolstered commitment to resourcing, DLB looks forward to a future for data linkage in Western Australia that is sustainable, high quality, efficient, and safe.

Biochemical and physiological impacts of zinc sulphate, potassium phosphite and hydrogen sulphide in mitigating stress conditions in soybean

Soybean is the most widely grown oilseed in the world. It is an important source of protein and oil which are derived from its seeds. Drought stress is a major constraint to soybean yields. Finding alternative methods to mitigate the water stress for soybean is useful to maintain adequate crop yields. The aim of this study was to evaluate the morpho-physiological, biochemical and metabolic changes in soybean plants in two ontogenetic stages, under exposure to water deficit and treatment with zinc sulphate (ZS), potassium phosphite (PP) or hydrogen sulphide (HS). We carried out two independent experiments in the V4 and R1 development stages consisting of the following treatments: well-watered control (WW, 100% maximum water holding capacity, MWHC), water deficit (WD, 50% MWHC), PP + WW, PP + WD, HS + WW, HS + WD, ZS + WW and ZS + WD. The experimental design consisted of randomized blocks with eight treatments with five replicates. Morphological, physiological and metabolic analyses were performed 8 days after the start of the treatments for both experiments. We identified two tolerance mechanisms acting in response to compound application during water stress: the first involved the upregulation of antioxidant enzyme activity and the second involved the accumulation of soluble sugars, free amino acids and proline to facilitate osmotic adjustment. Both mechanisms are related to the maintenance of the photosynthetic parameters and cell membrane integrity. This report suggests the potential agricultural use of these compounds to mitigate drought effects in soybean plants.

Chemical and isotopic markers detect water deficit and its influence on nutrient allocation in Phaseolus vulgaris

The impact of drought on plant growth and yield has been widely studied and is considered a major limitation to crops reaching yield potential. Less known is the impact of water deficit on the nutritional quality of the resulting yield. This study characterised the impact of water deficit on carbon assimilation, modelled water use efficiency from carbon isotope discrimination and analysed the concentration of mineral nutrients, amino acids and sugars in leaf, phloem and pod pools collected from Phaseolus vulgaris L. (common bean) grown in a controlled environment. Water deficit led to an isohydric response, impacting on carbon isotope abundance in all tissues though not translating to any significant treatment differences in water use efficiency or nutrient content in tissues over the course of plant development. The results obtained in this study demonstrate that nutrient content of P. vulgaris yield was not impacted by the availability of water. The absence of significant changes in the nutrient content of individual seeds highlights the plasticity of developing reproductive tissue to changes in whole plant water availability.

Immune checkpoint inhibitors in mCRPC - rationales, challenges and perspectives

The advancement of immune-therapeutics in cancer treatment has proven to be promising in various malignant diseases. However, in castration resistant prostate cancer (mCRPC) major Phase III trials have been unexpectedly disappointing. To contribute to a broader understanding of the role and use of immune-therapeutics in mCRPC, we conducted a systematic review. We searched the websites ClinicalTrials.gov, PubMed and ASCO Meeting Library for clinical trials employing immune checkpoint inhibitors in mCRPC. This article not only describes the rationale of individual trials, but it also summarizes the current status of the field and sheds light on strategies for future success.

Field drought conditions impact yield but not nutritional quality of the seed in common bean (Phaseolus vulgaris L.)

Drought substantially limits seed yield of common bean (Phaseolus vulgaris L.) in the tropics. Understanding the interaction of drought on yield and the nutrient concentration of the seed is vital in order to supply nutrition to the millions of consumers who rely on common bean as a staple crop. Nevertheless, the impact of drought on common bean for both yield and nutrient concentration has not yet been concurrently investigated in a field environment. Using 10 bred lines developed by CIAT and its partners for their improved adaptation to drought and phosphorus deficiency, this study characterised the impact of drought on yield and nutrient concentration for leaf and seed tissue of common bean grown in the field. Drought significantly reduced leaf area (by ~50%), harvest index (by ~60%), yield (by ~70%), seed weight (by ~25%) and enriched carbon isotope abundance (δ13C) in the seed. Within the soluble leaf fraction, drought significantly decreased the concentration of mineral nutrients and amino acids, whereas no negative effect on the concentration of nutrients and amino acids was detected within the seed. Genotypic variation in nutrient concentration in both the leaf and seed tissue was identified and should be explored further to identify traits that may confer tolerance to abiotic stress.

Water Deficit Elicits a Transcriptional Response of Genes Governing d-pinitol Biosynthesis in Soybean (Glycine max)

d-pinitol is the most commonly accumulated sugar alcohol in the Leguminosae family and has been observed to increase significantly in response to abiotic stress. While previous studies have identified genes involved in d-pinitol synthesis, no study has investigated transcript expression in planta. The present study quantified the expression of several genes involved in d-pinitol synthesis in different plant tissues and investigated the accumulation of d-pinitol, myo-inositol and other metabolites in response to a progressive soil drought in soybean (Glycine max). Expression of myo-inositol 1-phosphate synthase (INPS), the gene responsible for the conversion of glucose-6-phosphate to myo-inositol-1-phosphate, was significantly up regulated in response to a water deficit for the first two sampling weeks. Expression of myo-inositol O-methyl transferase (IMT1), the gene responsible for the conversion of myo-inositol into d-ononitol was only up regulated in stems at sampling week 3. Assessment of metabolites showed significant changes in their concentration in leaves and stems. d-Pinitol concentration was significantly higher in all organs sampled from water deficit plants for all three sampling weeks. In contrast, myo-inositol, had significantly lower concentrations in leaf samples despite up regulation of INPS suggesting the transcriptionally regulated flux of carbon through the myo-inositol pool is important during water deficit.

Limitations to using phloem sap to assess tree water and nutrient status

Rapid, reliable tools are needed to infer physiological and nutritional health for managing forest systems. Understanding the processes governing tree health is central to the development of these tools. Non-foliar approaches such as the collection of phloem sap reflect processes governing both the use and acquisition of plant water and nutrients at a wide range of temporal (diurnal to seasonal) and spatial (canopy) scales. Despite this, phloem sap is not commonly employed due to an incomplete understanding of transport and post-photosynthetic processes and their effects on chemical concentrations and carbon isotope discrimination. We highlight the need to characterize the influences of storage, remobilization and transport on the concentrations of metabolites to address the time and spatial decoupling of phloem contents to that of environmental stimuli. A conceptual framework is suggested to focus research on key phenomena regarding metabolite transport and highlight significant advantages, misconceptions and limitations to its application.

Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli

Root exudation is an important process determining plant interactions with the soil environment. Many studies have linked this process to soil nutrient mobilization. Yet, it remains unresolved how exudation is controlled and how exactly and under what circumstances plants benefit from exudation. The majority of root exudates including primary metabolites (sugars, amino acids, and organic acids) are believed to be passively lost from the root and used by rhizosphere-dwelling microbes. In this review, we synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role their exudation plays in plant nutrient acquisition strategies. Specifically, we propose a novel conceptual framework for root exudates. This framework is built upon two main concepts: (1) root exudation of primary metabolites is driven by diffusion, with plants and microbes both modulating concentration gradients and therefore diffusion rates to soil depending on their nutritional status; (2) exuded metabolite concentrations can be sensed at the root tip and signals are translated to modify root architecture. The flux of primary metabolites through root exudation is mostly located at the root tip, where the lack of cell differentiation favors diffusion of metabolites to the soil. We show examples of how the root tip senses concentration changes of exuded metabolites and translates that into signals to modify root growth. Plants can modify the concentration of metabolites either by controlling source/sink processes or by expressing and regulating efflux carriers, therefore challenging the idea of root exudation as a purely unregulated passive process. Through root exudate flux, plants can locally enhance concentrations of many common metabolites, which can serve as sensors and integrators of the plant nutritional status and of the nutrient availability in the surrounding environment. Plant-associated micro-organisms also constitute a strong sink for plant carbon, thereby increasing concentration gradients of metabolites and affecting root exudation. Understanding the mechanisms of and the effects that environmental stimuli have on the magnitude and type of root exudation will ultimately improve our knowledge of processes determining soil CO₂ emissions, ecosystem functioning, and how to improve the sustainability of agricultural production.

Corrigendum: Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli

[This corrects the article DOI: 10.3389/fpls.2019.00157.].

Source-Sink Relationships in Crop Plants and Their Influence on Yield Development and Nutritional Quality

For seed crops, yield is the cumulative result of both source and sink strength for photoassimilates and nutrients over the course of seed development. Source strength for photoassimilates is dictated by both net photosynthetic rate and the rate of photoassimilate remobilisation from source tissues. This review focuses on the current understanding of how the source-sink relationship in crop plants influences rates of yield development and the resilience of yield and nutritional quality. We present the limitations of current approaches to accurately measure sink strength and emphasize differences in coordination between photosynthesis and yield under varying environmental conditions. We highlight the potential to exploit source-sink dynamics, in order to improve yields and emphasize the importance of resilience in yield and nutritional quality with implications for plant breeding strategies.

Nitric oxide mitigates the effect of water deficit in Crambe abyssinica

Crambe abyssinica is widely cultivated in the off-season in the Midwest region of Brazil with great potential for biodeisel production. Low precipitation is characteristic of this region, which can drastically affect the productivity of C. abyssinica. Signaling molecules, such as nitric oxide (NO), can potentially alleviate the effects of water stress on plants. Here we test whether nitric oxide, applied by donor sodium nitroprusside (SNP), can alleviate the occurrence of water deficit damages in Crambe plants and maintain physiological and biochemical processes. Crambe plants were sprayed with three doses of SNP (0, 75, and 150 μM) and were submitted to two water levels (100% and 50% of the maximum water holding capacity). After 32 and 136 h, leaves were analyzed to evaluate the concentration of NO, water relations, gas exchange, chlorophyll a fluorescence, chloroplastidic pigments, proline, malondialdehyde, hydrogen peroxide, superoxide anions, and the antioxidant enzymes activity. Application of SNP allowed the maintenance of gas exchange, chlorophyll fluorescence parameters, and activities of antioxidant enzymes in plants exposed to water deficit, as well as increased the concentration of NO, proline, chloroplastidic pigments and osmotic potential. The application of SNP also decreased the concentration of malondialdehyde and reactive oxygen species in plants submitted to water deficit. Thus, the application of SNP prevented the occurrence of symptoms of water deficit in Crambe plants, maintaining the physiological and biochemical responses at reference levels, even under stress conditions.

Mineral-Associated Soil Carbon is Resistant to Drought but Sensitive to Legumes and Microbial Biomass in an Australian Grassland

Drought is predicted to increase in many areas of the world with consequences for soil carbon (C) dynamics. Plant litter, root exudates and microbial biomass can be used as C substrates to form organo-mineral complexes. Drought effects on plants and microbes could potentially compromise these relative stable soil C pools, by reducing plant C inputs and/or microbial activity. We conducted a 2-year drought experiment using rainout shelters in a semi-natural grassland. We measured aboveground biomass and C and nitrogen (N) in particulate organic matter (Pom), the organo-mineral fraction (Omin), and microbial biomass within the first 15 cm of soil. Aboveground plant biomass was reduced by 50% under drought in both years, but only the dominant C4 grasses were significantly affected. Soil C pools were not affected by drought, but were significantly higher in the relatively wet second year compared to the first year. Omin-C was positively related to microbial C during the first year, and positively related to clay and silt content in the second year. Increases in Omin-C in the second year were explained by increases in legume biomass and its effect on Pom-N and microbial biomass N (MBN) through structural equation modeling. In conclusion, soil C pools were unaffected by the drought treatment. Drought resistant legumes enhanced formation of organo-mineral complexes through increasing Pom-N and MBN. Our findings also indicate the importance of microbes for the formation of Omin-C as long as soil minerals have not reached their maximum capacity to bind with C (that is, saturation).

Ecophysiological responses to excess iron in lowland and upland rice cultivars

Iron (Fe) is an essential nutrient for plants but under high concentrations, such as that found naturally in clay and waterlogged soils, its toxic effect can limit production. This study aimed to investigate the stress tolerance responses exhibited by different rice cultivars. Both lowland and upland cultivars were grown under excess Fe and hypoxic conditions. Lowland cultivars showed higher Fe accumulation in roots compared with upland cultivars suggesting the use of different strategies to tolerate excess Fe. The upland Canastra cultivar displayed a mechanism to limit iron translocation from roots to the shoots, minimizing leaf oxidative stress induced by excess Fe. Conversely, the cultivar Curinga invested in the increase of R1/A, as an alternative drain of electrons. However, the higher iron accumulation in the leaves, was not necessarily related to high toxicity. Nutrient uptake and/or utilization mechanisms in rice plants are in accordance with their needs, which may be defined in relation to crop environments. Alterations in the biochemical parameters of photosynthesis suggest that photosynthesis in rice under excess Fe is primarily limited by biochemical processes rather than by diffusional limitations, particularly in the upland cultivars. The electron transport rate, carboxylation efficiency and electron excess dissipation by photorespiration demonstrate to be good indicators of iron tolerance. Altogether, these chemical and molecular patterns suggests that rice plants grown under excess Fe exhibit gene expression reprogramming in response to the Fe excess per se and in response to changes in photosynthesis and nutrient levels to maintain growth under stress.

Post photosynthetic carbon partitioning to sugar alcohols and consequences for plant growth

The occurrence of sugar alcohols is ubiquitous among plants. Physiochemical properties of sugar alcohols suggest numerous primary and secondary functions in plant tissues and are often well documented. In addition to functions arising from physiochemical properties, the synthesis of sugar alcohols may have significant influence over photosynthetic, respiratory, and developmental processes owing to their function as a large sink for photosynthates. Sink strength is demonstrated by the high concentrations of sugar alcohols found in plant tissues and their ability to be readily transported. The plant scale distribution and physiochemical function of these compounds renders them strong candidates for functioning as stress metabolites. Despite this, several aspects of sugar alcohol biosynthesis and function are poorly characterised namely: 1) the quantitative characterisation of carbon flux into the sugar alcohol pool; 2) the molecular control governing sugar alcohol biosynthesis on a quantitative basis; 3) the role of sugar alcohols in plant growth and ecology; and 4) consequences of sugar alcohol synthesis for yield production and yield quality. We highlight the need to adopt new approaches to investigating sugar alcohol biosynthesis using modern technologies in gene expression, metabolic flux analysis and agronomy. Combined, these approaches will elucidate the impact of sugar alcohol biosynthesis on growth, stress tolerance, yield and yield quality.

Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin

Background

Climatic and edaphic conditions over geological timescales have generated enormous diversity of adaptive traits and high speciation within the genus Eucalyptus (L. Hér.). Eucalypt species occur from high rainfall to semi-arid zones and from the tropics to latitudes as high as 43°S. Despite several morphological and metabolomic characterizations, little is known regarding gene expression differences that underpin differences in tolerance to environmental change. Using species of contrasting taxonomy, morphology and physiology (E. globulus and E. cladocalyx), this study combines physiological characterizations with ‘second-generation’ sequencing to identify key genes involved in eucalypt responses to medium-term water limitation.

Results

One hundred twenty Million high-quality HiSeq reads were created from 14 tissue samples in plants that had been successfully subjected to a water deficit treatment or a well-watered control. Alignment to the E. grandis genome saw 23,623 genes of which 468 exhibited differential expression (FDR < 0.01) in one or both ecotypes in response to the treatment. Further analysis identified 80 genes that demonstrated a significant species-specific response of which 74 were linked to the ‘dry’ species E. cladocalyx where 23 of these genes were uncharacterised. The majority (approximately 80%) of these differentially expressed genes, were expressed in stem tissue. Key genes that differentiated species responses were linked to photoprotection/redox balance, phytohormone/signalling, primary photosynthesis/cellular metabolism and secondary metabolism based on plant metabolic pathway network analysis.

Conclusion

These results highlight a more definitive response to water deficit by a ‘dry’ climate eucalypt, particularly in stem tissue, identifying key pathways and associated genes that are responsible for the differences between ‘wet’ and ‘dry’ climate eucalypts. This knowledge provides the opportunity to further investigate and understand the mechanisms and genetic variation linked to this important environmental response that will assist with genomic efforts in managing native populations as well as in tree improvement programs under future climate scenarios.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3664-z) contains supplementary material, which is available to authorized users.

Stress-induced changes in carbon allocation among metabolite pools influence isotope-based predictions of water use efficiency in Phaseolus vulgaris

Understanding how major food crops respond to environmental stress will expand our capacity to improve food production with growing populations and a changing climate. This study uses chemical and physiological adaptations to heat, water deficit and elevated light stresses in Phaseolus vulgaris L. to identify changes in carbon (C) allocation that, combined with post-photosynthetic fractionation of C isotopes, influences water use efficiency (WUE) predictions. The chemical stress response was explored through changes in C allocation to the carbohydrate and cyclitol pools using GC-triple quadrupole MS. Carbon allocation to the sucrose pool fluctuated significantly among treatments, and the putative osmolytes and osmoprotectants (myo-inositol and d-ononitol) accumulated under stress. Significant osmotic adjustment (P<0.05), quantified via pressure-volume curve analysis, was detected between control and stress treatments, although this was not attributable to active accumulation of the metabolites. Compound-specific 13C isotope abundance was measured using liquid chromatography isotope ratio MS to predict intrinsic WUE. In contrast to other metabolites measured, the δ13C of the sucrose pool fluctuated according to treatment and was proportional to predicted values based upon modelled Δ13C from gas exchange data. The results suggest that the accuracy and precision of predicting WUE may be enhanced by compound-specific analysis of Δ13C and that changes in the allocation of C among metabolite pools may influence WUE predictions based upon analysis of total soluble C. Overall, the plants appeared to use a range of mechanisms to cope with adverse conditions that could be utilised to improve plant breeding and management strategies.

Carbon Isotope Composition of Carbohydrates and Polyols in Leaf and Phloem Sap of Phaseolus vulgaris L. Influences Predictions of Plant Water Use Efficiency

The use of carbon isotope abundance (δ(13)C) to assess plant carbon acquisition and water use has significant potential for use in crop management and plant improvement programs. Utilizing Phaseolus vulgaris L. as a model system, this study demonstrates the occurrence and sensitivity of carbon isotope fractionation during the onset of abiotic stresses between leaf and phloem carbon pools. In addition to gas exchange data, compound-specific measures of carbon isotope abundance and concentrations of soluble components of phloem sap were compared with major carbohydrate and sugar alcohol pools in leaf tissue. Differences in both δ(13)C and concentration of metabolites were found in leaf and phloem tissues, the magnitude of which responded to changing environmental conditions. These changes have inplications for the modeling of leaf-level gas exchange based upon δ(13)C natural abundance. Estimates of δ(13)C of low molecular weight carbohydrates and polyols increased the precision of predictions of water use efficiency compared with those based on bulk soluble carbon. The use of this technique requires consideration of the dynamics of the δ(13)C pool under investigation. Understanding the dynamics of changes in δ(13)C during movement and incorporation into heterotrophic tissues is vital for the continued development of tools that provide information on plant physiological performance relating to water use.

Site-specific responses to short-term environmental variation are reflected in leaf and phloem-sap carbon isotopic abundance of field grown Eucalyptus globulus

The carbon isotopic composition (δ(13) C) of plant material has been used extensively as an indirect measure of carbon fixation per volume of water used. More recently, the δ(13) C of phloem sap (δ(13) C(phl) ) has been used as a surrogate measure of short-term, canopy scale δ(13) C. Using a combination of δ(13) C physiological, structural and chemical indices from leaves and phloem sap of Eucalyptus globulus at sites of contrasting water availability, we sought to identify short-term, canopy scale resource limitations. Results illustrate that δ(13) C(phl) offers valid reflections of short-term, canopy scale values of leaf δ(13) C and tree water status. Under conditions limited by water, leaf and phloem sap photoassimilates differ in (13) C abundance of a magnitude large enough to significantly influence predictions of water use efficiency. This pattern was not detected among trees with adequate water supply indicating fractionation into heterotrophic tissues that may be sensitive to plant water status. Trees employed a range of physiological, biochemical and structural adaptations to acclimate to resource limitation that differed among sites providing a useful context upon which to interpret patterns in δ(13) C. Our results highlight that such easily characterized properties are ideal for use as minimally invasive tools to monitor growth and resilience of plants to variations in resource availability.

Differences in ascorbate and glutathione levels as indicators of resistance and susceptibility in Eucalyptus trees infected with Phytophthora cinnamomi

In this study we investigated the role that ascorbate (AA) and glutathione (GSH) play in the plant pathogen interaction of susceptible Eucalyptus sieberi L. A. Johnson and resistant Eucalyptus sideroxylon Woolls with Phytophthora cinnamomi Rands root infection. In a glasshouse study, seedlings were grown in soil-free plant boxes to facilitate the inoculation of the root systems by a P. cinnamomi zoospore solution. Ascorbate and GSH concentrations were measured in infected roots and leaves, along with leaf gas exchange, chlorophyll fluorescence and carbohydrate concentrations over a time course up to 312 h (13 days) post-inoculation (pi). At the early stages of infection (from 24 h pi), significant decreases in AA and GSH concentrations were observed in the infected roots and leaves of the susceptible E. sieberi seedlings. At the later stage of infection (312 h pi), the earlier AA decreases in the leaves of infected plants had become significant increases. In contrast, late, significant AA increases in the absence of any GSH changes were observed in the infected roots of the resistant E. sideroxylon seedlings. In E. sideroxylon leaves, a significant GSH increase occurred at 24 h pi; however, by 312 h pi the earlier increase had become a significant decrease, while no changes occurred in AA. In E. sieberi, photosynthesis (A), stomatal conductance (g(s)) and PSII quantum efficiency (Φ(PSII)) were reduced by ~60, 80 and 30%, respectively, in infected plants and remained significantly lower than uninfected controls for the duration of the experiment. Significant reductions in these parameters did not occur until later (120 h pi for g(s) and 312 h pi for A and Φ(PSII)), and to a lesser extent in the resistant species. Non-structural carbohydrate analysis of roots and leaves indicate that carbohydrate metabolism and resource flow between shoots and roots may have been altered at later infection stages. This study suggests that reduced antioxidant capacity, leaf physiological function and carbohydrate metabolism are associated with susceptibility in E. sieberi to P. cinnamomi infection, while AA increases and new root formation were associated with resistance in E. sideroxylon.

Edge type affects leaf-level water relations and estimated transpiration of Eucalyptus arenacea

While edge effects on tree water relations are well described for closed forests, they remain under-examined in more open forest types. Similarly, there has been minimal evaluation of the effects of contrasting land uses on the water relations of open forest types in highly fragmented landscapes. We examined edge effects on the water relations and gas exchange of a dominant tree (Eucalyptus arenacea Marginson & Ladiges) in an open forest type (temperate woodland) of south-eastern Australia. Edge effects in replicate woodlands adjoined by cleared agricultural land (pasture edges) were compared with those adjoined by 7- to 9-year-old eucalypt plantation with a 25m fire break (plantation edges). Consistent with studies in closed forest types, edge effects were pronounced at pasture edges where photosynthesis, transpiration and stomatal conductance were greater for edge trees than interior trees (75m into woodlands), and were related to greater light availability and significantly higher branch water potentials at woodland edges than interiors. Nonetheless, gas exchange values were only ∼50% greater for edge than interior trees, compared with ∼200% previously found in closed forest types. In contrast to woodlands adjoined by pasture, gas exchange in winter was significantly lower for edge than interior trees in woodlands adjoined by plantations, consistent with shading and buffering effects of plantations on edge microclimate. Plantation edge effects were less pronounced in summer, although higher water use efficiency of edge than interior woodland trees indicated possible competition for water between plantation trees and woodland edge trees in the drier months (an effect that might have been more pronounced were there no firebreak between the two land uses). Scaling up of leaf-level water relations to stand transpiration using a Jarvis-type phenomenological model indicated similar differences between edge types. That is, transpiration was greater at pasture than plantation edges in summer months (most likely due to greater water availability at pasture edges), resulting in significantly greater estimates of annual transpiration at pasture than plantation edges (430 vs. 343lm(-2)year(-1), respectively). Our study highlights the need for landscape-level water flux models to account for edge effects on stand transpiration, particularly in highly fragmented landscapes.

Why not beans?

Changes in climate and urbanisation rapidly affecting human livelihood are particularly threatening to developing nations in tropical regions. Food production crises have focused the global development agenda on agricultural research, a proven approach for increasing crop yield. A few crops benefit from private investment, but improvement of most crops will rely on limited public funding that must be deployed strategically, pushing forward both proven approaches and new ideas. Why not invest in beans? More than 300 million people rely on this crop, considered to be the most important grain legume for human consumption. Yet the yield of beans, especially in poor regions or marginal soils, is reduced by abiotic stresses such as phosphorus deficiency, aluminum toxicity and especially drought. Is it possible to assemble resources, including genetic diversity in beans, breeding expertise, genomic information and tools, and physiological insight to generate rapid progress in developing new lines of beans more tolerant to abiotic stress? A workshop to address this question was held in November 2010 at the International Center for Tropical Agriculture (CIAT) in Colombia. The resulting 'call to action' is presented in this issue which also includes research papers focused on tolerance of beans to stress.

Polyols as biomarkers and bioindicators for 21st century plant breeding

Characterising changes in the plant metabolome is central to understanding adaptive responses to environmental change. New and improved quantitative and qualitative technologies have enabled the characterisation of plant metabolism at unprecedented scales and precision. New frontiers have therefore emerged for improving our understanding of the adaptability of plant metabolic networks. However, despite these advances, outcomes for 'in field' plant management remain largely based on subsets of plant metabolism due to broader scale network complexity. The synthesis and occurrence of polyols offer considerable promise as bioindicators of plant health and biomarkers for use as selective traits for plant improvement. Polyols are polyohydroxy compounds that may be either open chain (acyclic) alditols or cyclic compounds (cyclohexan-hexols), usually termed cyclitols or inositols. Here we highlight the functions of polyols in stress acclimation or amelioration and as sinks for carbon and indicate their potential for the development of integrated measures of plant function using new technologies in 21st century plant breeding.

Non-invasive approaches for phenotyping of enhanced performance traits in bean

Plant phenotyping is an emerging discipline in plant biology. Quantitative measurements of functional and structural traits help to better understand gene-environment interactions and support breeding for improved resource use efficiency of important crops such as bean (Phaseolus vulgaris L.). Here we provide an overview of state-of-the-art phenotyping approaches addressing three aspects of resource use efficiency in plants: belowground roots, aboveground shoots and transport/allocation processes. We demonstrate the capacity of high-precision methods to measure plant function or structural traits non-invasively, stating examples wherever possible. Ideally, high-precision methods are complemented by fast and high-throughput technologies. High-throughput phenotyping can be applied in the laboratory using automated data acquisition, as well as in the field, where imaging spectroscopy opens a new path to understand plant function non-invasively. For example, we demonstrate how magnetic resonance imaging (MRI) can resolve root structure and separate root systems under resource competition, how automated fluorescence imaging (PAM fluorometry) in combination with automated shape detection allows for high-throughput screening of photosynthetic traits and how imaging spectrometers can be used to quantify pigment concentration, sun-induced fluorescence and potentially photosynthetic quantum yield. We propose that these phenotyping techniques, combined with mechanistic knowledge on plant structure-function relationships, will open new research directions in whole-plant ecophysiology and may assist breeding for varieties with enhanced resource use efficiency varieties.