Root morphology acclimation to phosphorus supply by six cultivars of <Emphasis Type="Italic">Trifolium subterraneum</Emphasis> L

Aims

Trifolium subterraneum L. is the predominant annual pasture legume in southern Australia. Cultivars with improved phosphorus (P) foraging ability would improve the P-use efficiency of agricultural systems. We therefore investigated variation in root traits related to P-uptake among six cultivars.

Methods

Micro-swards were grown at six levels of P in field soil with indigenous arbuscular mycorrhizal (AM) fungi for six weeks. Dry matter yield, tissue P concentration, rhizosphere carboxylates, AM fungal colonisation and root morphological traits were measured.

Results

The cultivars showed similar shoot and root yield responses to P supply. Average root diameter did not change, specific root length (SRL) increased and root tissue density (RTD) decreased with increased P supply. Amounts of total rhizosphere carboxylates were low (<1.2 nmol cm^?1 root). The percentage of root length colonised by AM fungi was greatest (29–43 %) at an intermediate level (8 mg kg^?1 dry soil) of P supply.

Conclusions

Most differences among cultivars were reasonably consistent across P supply levels, indicating greater numbers of lines could be screened reliably at a single P level. Low colonisation by AM fungi at low P supply deserves consideration when selecting soils for cultivar comparisons. Increased SRL and decreased RTD at high P supply likely result from self-shading within the micro-swards and warrant further investigation.

     

Cultivar differences in spatial root distribution during early growth in soil,and its relation to nutrient uptake - a study of wheat,onion and lettuce

Background and aims

A study was made to quantify early root development, soil exploitation and nutrient uptake in spring wheat, onion and lettuce, and their variation among cultivars. The goal was to study genetic variation in root traits making cultivars better adapted to organic production systems or other low-input systems.

Methods

Six cultivars of each species were grown in transparent tubes to allow direct observation of early root growth. The tubes were 0.3 m deep, and 0.24 m in diameter. By placing the plants close to the edge rather than at the centre of the tubes, we could quantify the spatial distribution of the root systems as well as the general root growth and nutrient uptake.

Results

Root growth of wheat and lettuce was faster than root growth of onion, and onion showed little capacity for horizontal root system development. Significant variation in early root growth and horizontal spread of the root system was found among cultivars of all three species. In general, cultivars with strong growth and high volume of soil exploitation showed higher average nutrient concentrations.

Conclusion

Early shoot growth, root growth and nutrient uptake are intrinsically linked, making it difficult to determine whether improved root growth was the primary cause of improved performance. However, we did find cultivars where the strong root growth and superior root distribution seemed to be the driver for improved overall growth.

     

Metabolic changes of genetically engineered grapes (<Emphasis Type="Italic">Vitis vinifera</Emphasis> L.) studied by <Superscript>1</Superscript>H-NMR,metabolite heatmaps and <Emphasis Type="Italic">i</Emphasis>PLS

Introduction

The Deficiens Homologue 9-iaaM (DefH9-iaaM) gene is an ovule-specific auxin-synthesizing gene which is expressed specifically in placenta/ovules and promotes auxin-synthesis. It was introduced into the genome of two grape cultivars Thompson Seedless and Silcora and both transgenic cultivars had an increased number of berries per bunch.

Objectives

This study investigates the down-stream metabolic changes of Silcora and Thompson seedless grape cultivars when genetically modified through the insertion of the DefH9-iaaM gene into their genome.

Methods

The effects of the genetic modification upon the grape metabolome were evaluated through ¹H-NMR and exploratory data analysis. Chemometric tools such as Interval Partial Least Squares regression and metabolite heatmaps were employed for scrutinizing the changes in the transgenic metabolome as compared to the wild type one.

Results

The results show that the pleiotropic effect on the grape metabolome as a function of the gene modifications is relatively low, although the insertion of the transgene caused a decrement in malic acid and proline and an increment in p-coumaric acid content. In addition, the concentration of malic acid was successfully correlated with the number of inserted copies of transgene in the Silcora cultivar, proving that the increased production of berries, promoted by the inserted gene, is achieved at the expense of a decrement in malic acid concentration.

Conclusion

NMR together with chemometrics is able to identify specific metabolites that were up- or down regulated in the genetically engineered plants allowing highlighting alterations in the down-stream metabolic pathways due to the up-stream genetic modifications.

     

An efficient method for medium throughput screening of cuticular wax composition in different plant species

Introduction

Most aerial plant organs are covered by a cuticle, which largely consists of cutin and wax. Cuticular waxes are mixtures of dozens of compounds, mostly very-long-chain aliphatics that are easily extracted by solvents. Over the last four decades, diverse cuticular wax analysis protocols have been developed, most of which are complex and time-consuming, and need to be adapted for each plant species or organ. Plant genomics and breeding programs often require mid-throughput metabolic phenotyping approaches to screen large numbers of individuals and obtain relevant biological information.

Objectives

To generate a fast, simple and user-friendly methodology able to capture most wax complexity independently of the plant, cultivar and organ.

Methods

Here we present a simple GC–MS method for screening relatively small wax amounts, sampled by short extraction with a versatile, uniform solvent. The method will be tested and validated in leaves and fruits from three different crop species: tomato (Solanum lycopersicum), apple (Malus domestica) and hybrid aspen (Populus tremula × tremuloides).

Results

Consistent results were obtained in tomato cultivar M82 across three consecutive years (2010–2012), two organs (leaf and fruit), and also in two different tomato (M82 and MicroTom) and apple (Golden Delicious and Granny Smith) cultivars. Our results on tomato wax composition match those reported previously, while our apple and hybrid aspen analyses provide the first comprehensive cuticular wax profile of these species.

Conclusion

This protocol allows standardized identification and quantification of most cuticular wax components in a range of species.

     

Improved sugar yields from biomass sorghum feedstocks: comparing low-lignin mutants and pretreatment chemistries

Background

For biofuel production processes to be economically efficient, it is essential to maximize the production of monomeric carbohydrates from the structural carbohydrates of feedstocks. One strategy for maximizing carbohydrate production is to identify less recalcitrant feedstock cultivars by performing some type of experimental screening on a large and diverse set of candidate materials, or by identifying genetic modifications (random or directed mutations or transgenic plants) that provide decreased recalcitrance. Economic efficiency can also be increased using additional pretreatment processes such as deacetylation, which uses dilute NaOH to remove the acetyl groups of hemicellulose prior to dilute acid pretreatment. In this work, we used a laboratory-scale screening tool that mimics relevant thermochemical pretreatment conditions to compare the total sugar yield of three near-isogenic brown midrib (bmr) mutant lines and the wild-type (WT) sorghum cultivar. We then compared results obtained from the laboratory-scale screening pretreatment assay to a large-scale pretreatment system.

Results

After pretreatment and enzymatic hydrolysis, the bmr mutants had higher total sugar yields than the WT sorghum cultivar. Increased pretreatment temperatures increased reactivity for all sorghum samples reducing the differences observed at lower reaction temperatures. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples, and reduced the differences in total sugar yields among them, but solubilized a sizable fraction of the non-structural carbohydrates. The general trends of increased total sugar yield in the bmr mutant compared to the WT seen at the laboratory scale were observed at the large-scale system. However, in the larger reactor system, the measured total sugar yields were lower and the difference in total sugar yield between the WT and bmr sorghum was larger.

Conclusions

Sorghum bmr mutants, which have a reduced lignin content showed higher total sugar yields than the WT cultivar after dilute acid pretreatment and enzymatic hydrolysis. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples. However, since deacetylation also solubilizes a large fraction of the non-structural carbohydrates, the ability to derive value from these solubilized sugars will depend greatly on the proposed conversion process.

     

A combination of stomata deregulation and a distinctive modulation of amino acid metabolism are associated with enhanced tolerance of wheat varieties to transient drought

Introduction

Mediterranean winter crops are commonly and increasingly exposed to irregular rainfall and high temperatures, which lead to transient drought events of different degrees, adversely affecting growth and yield. Hence, exploring the diverse degrees of tolerance to drought existing in the crop and the molecular strategies behind it is pivotal for the development of ad hoc breeding programs.

Objective

We investigated the physiological and metabolic response of six commercial wheat cultivars to transient water stress at the tillering and grain-filling stages.

Methods

Drought experiments in lysimeters were set up at two developmental stages including six wheat cultivars. Newly expanded youngest leaves and flag leaves were sampled during the drought and following recovery. Metabolite profiles were generated using a GC–MS based protocol. Data on transpiration were continually acquired by measuring the weight variation of pots using electronic temperature compensated load cells.

Results

The tillering stage in wheat is more sensitive to droughts than the grain filling stage. The former stage was characterized by pronounced metabolic alterations also during recovery from the drought, and plants exhibited reduced transpiration. Notably, cultivars varied considerably in their susceptibility to drought. Exceptionally only in cv Zahir was transpiration not reduced at tillering. During recovery, the transpiration rate of Yuval and Zahir was not significantly affected, while except Ruta the other varieties maintained lower values. At grain-filling, a moderate decrease in transpiration in response to drought was evident in Bar-Nir, Yuval and Zahir varieties as compared with the stronger response of Gedera, Galil and Ruta. The transpiration trend during recovery remained lower than the control plants, particularly in Gedera and Zahir, while it reached higher values than control plants in Yuval and Ruta varieties. Metabolite profiling of leaves across cultivars showed varietal specific trends of response. Particularly during tillering, amino acid metabolism was differentially regulated across cultivars. For instance, Ruta and Zahir exhibited major changes in central carbon nitrogen metabolism during stress response, accumulating large amounts of proline and threonine during tillering, while in Bar-Nir a general decrease in relative amino acid content was noted. Changes in stress related GABA were common to Galil, Ruta, Yuval and Zahir. Desiccation related raffinose family oligosaccharides were mostly associated with a later stage of grain-filling and recovery stages of response.

Conclusion

The results indicate the occurrence of stage-dependent metabolic diversification along with a physiological response during transient droughts among wheat cultivars. It can be concluded that the most tolerant cultivar was Zahir, where a combination of stomatal closure deregulation and a significant accumulation rate of stress-related metabolites were evident.

     

Optimization of fecal sample preparation for untargeted LC-HRMS based metabolomics

Introduction

Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.

Objectives

In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.

Methods

The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.

Results

A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.

Conclusion

The workflow generated repeatable and informative fingerprints for robust metabolome characterization.

     

Untargeted metabolomics approach using UPLC-ESI-QTOF-MS to explore the metabolome of fresh-cut iceberg lettuce

Introduction

The shelf-life of fresh-cut lettuce after storage is limited by several factors that affect its quality and lead to consumer rejection. Different metabolic events occur after cutting as an abiotic stress response.

Objectives

This study aims to explore the metabolome of iceberg lettuce and to understand the changes related to storage time and genetics applying an untargeted metabolomics approach.

Methods

Two cultivars with different browning susceptibility, fast-browning (FB) and slow-browning (SB), were analyzed by UPLC-ESI-QTOF-MS just after cutting (d0) and after five days of storage (d5). Extraction, metabolic profiling, and data-pretreatment procedures were optimized to obtain a robust and reliable data set.

Results

Preliminary principal component analysis and hierarchical cluster analysis of the full dataset [around 8551 extracted, aligned and filtered molecular features (MFs)] showed a clear separation between the different samples (FB-d0, FB-d5, SB-d0, and SB-d5), highlighting a clear storage time-dependent effect. After statistical analysis applying Student’s t test, 536 MFs were detected as significantly different between d0 and d5 of storage in FB and 633 in SB. Some of them (221) were common to both cultivars. Out of these significant compounds, 22 were tentatively identified by matching their molecular formulae with those previously reported in the literature. Five families of metabolites were detected: amino acids, phenolic compounds, sesquiterpene lactones, fatty acids, and lysophospholipids. All compounds showed a clear trend to decrease at d5 except phenolic compounds that increased after storage.

Conclusion

The untargeted metabolomics analysis is a powerful tool for characterizing the changes on lettuce metabolome associated with cultivar and especially with storage time. Some families of compounds affected by storage time were reported to be closely related to quality loss.

     

Epistatic determinism of durum wheat resistance to the wheat spindle streak mosaic virus

Key message

The resistance of durum wheat to the Wheat spindle streak mosaic virus (WSSMV) is controlled by two main QTLs on chromosomes 7A and 7B, with a huge epistatic effect.

Abstract

Wheat spindle streak mosaic virus (WSSMV) is a major disease of durum wheat in Europe and North America. Breeding WSSMV-resistant cultivars is currently the only way to control the virus since no treatment is available. This paper reports studies of the inheritance of WSSMV resistance using two related durum wheat populations obtained by crossing two elite cultivars with a WSSMV-resistant emmer cultivar. In 2012 and 2015, 354 recombinant inbred lines (RIL) were phenotyped using visual notations, ELISA and qPCR and genotyped using locus targeted capture and sequencing. This allowed us to build a consensus genetic map of 8568 markers and identify three chromosomal regions involved in WSSMV resistance. Two major regions (located on chromosomes 7A and 7B) jointly explain, on the basis of epistatic interactions, up to 43% of the phenotypic variation. Flanking sequences of our genetic markers are provided to facilitate future marker-assisted selection of WSSMV-resistant cultivars.

     

Does dormancy protect seeds against attack by the pathogenic fungus <Emphasis Type="Italic">Fusarium tricinctum</Emphasis> in a semiarid grassland of Northwest China?

Aims

Soil fungal pathogens can result in the failure of seedling establishment, but the effects of fungicide applications on seed/seedling survival have differed among studies. We assumed that the variation may relate to seed dormancy/germination characteristics and hypothesized that nondormant germinating seeds are more likely to be killed by fungal pathogens than dormant seeds.

Methods

Dormant and nondormant seeds of Stipa bungeana and Lespedeza davurica were inoculated with a pathogenic fungus Fusarium tricinctum under laboratory and field conditions. The outcomes of seed/seedling fate and other parameters were evaluated.

Results

In the laboratory, nondormant seeds inoculated with F. tricinctum developed white tufts of mycelium on the radicles of germinating seeds causing them to quickly die, but dormant seeds remained intact. In contrast, in the field inoculation with F. tricinctum did not cause higher mortality of nondormant than dormant seeds but resulted in higher percentages of seedling death before they emerged from soil than the controls.

Conclusions

Our results suggest that dormancy protects seeds from being attacked by some pathogens by preventing germination, but the protection is lost once germination has commenced. Further study involving various plant species with more seeds is needed to assess the generality of this pathogen-seed interaction hypothesis.

     

Inter- and intra-species intercropping of barley cultivars and legume species,as affected by soil phosphorus availability

Aims

Intercropping can improve plant yields and soil phosphorus (P) use efficiency. This study compares inter- and intra-species intercropping, and determines whether P uptake and shoot biomass accumulation in intercrops are affected by soil P availability.

Methods

Four barley cultivars (Hordeum vulgare L.) and three legume species (Trifolium subterreneum, Ornithopus sativus and Medicago truncatula) were selected on the basis of their contrasting root exudation and morphological responses to P deficiency. Monocultures and barley-barley and barley-legume intercrops were grown for 6 weeks in a pot trial at very limiting, slightly limiting and excess available soil P. Above-ground biomass and shoot P were measured.

Results

Barley-legume intercrops had 10–70% greater P accumulation and 0–40% greater biomass than monocultures, with the greatest gains occurring at or below the sub-critical P requirement for barley. No benefit of barley-barley intercropping was observed. The plant combination had no significant effect on biomass and P uptake observed in intercropped treatments.

Conclusions

Barley-legume intercropping shows promise for sustainable production systems, especially at low soil P. Gains in biomass and P uptake come from inter- rather than intra-species intercropping, indicating that plant diversity resulted in decreased competition between plants for P.

     

Analysis of influencing factor of coexisting prediabetes and prehypertension in adult residents of Jilin Province

Background

To explore the risk factors of coexisting prediabetes and prehypertension, to provide theoretical basis for early intervention.

Methods

A multi-stage stratified random cluster sampling method was used to randomly select adult residents from Jilin Province in 2013 for questionnaire surveys, physical examinations, and laboratory tests.

Results

The prevalence of coexisting prediabetes and prehypertension in Jilin Province was 11.3%. The binary Logistic regression results showed that age, sex, education, triglyceride (TG), BMI, waist circumference and alcohol consumption were the effects of factor coexisting prediabetes and prehypertension.

Conclusion

It is important to pay attention to the early stage of hypertension and diabetes, control the transition from prehypertension and prediabetes to hypertension and diabetes, and improve the health of residents.

     

A metabolomics approach to uncover effects of different exercise modalities in type 1 diabetes

Introduction

Exercise-associated metabolism in type 1 diabetes (T1D) remains under-studied due to the complex interplay between exogenous insulin, counter-regulatory hormones and insulin-sensitivity.

Objective

To identify the metabolic differences induced by two exercise modalities in T1D using ultra high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC–HRMS) based metabolomics.

Methods

Twelve T1D adults performed intermittent high-intensity (IHE) and continuous-moderate-intensity (CONT) exercise. Serum samples were analysed by UHPLC–HRMS.

Results

Metabolic profiling of IHE and CONT highlighted exercise-induced changes in purine and acylcarnitine metabolism.

Conclusion

IHE may increase beta-oxidation through higher ATP-turnover. UHPLC–HRMS based metabolomics as a data-driven approach without an a priori hypothesis may help uncover distinctive metabolic effects during exercise in T1D.Clinical trial registration number is www.clinicaltrials.gov: NCT02068638.

     

How the chemical features of molecules may have addressed the settlement of metabolic steps

Introduction

While the evolutionary adaptation of enzymes to their own substrates is a well assessed and rationalized field, how molecules have been originally selected in order to initiate and assemble convenient metabolic pathways is a fascinating, but still debated argument.

Objectives

Aim of the present study is to give a rationale for the preferential selection of specific molecules to generate metabolic pathways.

Methods

The comparison of structural features of molecules, through an inductive methodological approach, offer a reading key to cautiously propose a determining factor for their metabolic recruitment.

Results

Starting with some commonplaces occurring in the structural representation of relevant carbohydrates, such as glucose, fructose and ribose, arguments are presented in associating stable structural determinants of these molecules and their peculiar occurrence in metabolic pathways.

Conclusions

Among other possible factors, the reliability of the structural asset of a molecule may be relevant or its selection among structurally and, a priori, functionally similar molecules.

     

Evaluation of metabolomics profiles of grain from maize hybrids derived from near-isogenic GM positive and negative segregant inbreds demonstrates that observed differences cannot be attributed unequivocally to the GM trait

Introduction

Past studies on plant metabolomes have highlighted the influence of growing environments and varietal differences in variation of levels of metabolites yet there remains continued interest in evaluating the effect of genetic modification (GM).

Objectives

Here we test the hypothesis that metabolomics differences in grain from maize hybrids derived from a series of GM (NK603, herbicide tolerance) inbreds and corresponding negative segregants can arise from residual genetic variation associated with backcrossing and that the effect of insertion of the GM trait is negligible.

Methods

Four NK603-positive and negative segregant inbred males were crossed with two different females (testers). The resultant hybrids, as well as conventional comparator hybrids, were then grown at three replicated field sites in Illinois, Minnesota, and Nebraska during the 2013 season. Metabolomics data acquisition using gas chromatography–time of flight-mass spectrometry (GC–TOF-MS) allowed the measurement of 367 unique metabolite features in harvested grain, of which 153 were identified with small molecule standards. Multivariate analyses of these data included multi-block principal component analysis and ANOVA-simultaneous component analysis. Univariate analyses of all 153 identified metabolites was conducted based on significance testing (α = 0.05), effect size evaluation (assessing magnitudes of differences), and variance component analysis.

Results

Results demonstrated that the largest effects on metabolomic variation were associated with different growing locations and the female tester. They further demonstrated that differences observed between GM and non-GM comparators, even in stringent tests utilizing near-isogenic positive and negative segregants, can simply reflect minor genomic differences associated with conventional back-crossing practices.

Conclusion

The effect of GM on metabolomics variation was determined to be negligible and supports that there is no scientific rationale for prioritizing GM as a source of variation.

     

Heterogeneity in arbuscular mycorrhizal fungal communities may contribute to inconsistent plant-soil feedback in a Neotropical forest

Background and aims

Plant-soil feedback may vary across host species and environmental gradients. The relative importance of these biotic versus abiotic drivers of feedback will determine the stability of plant and microbial communities across environments. If plant hosts are the main driver of soil microbial communities, plant-soil feedback may be stable across changing environments. However, if microbial communities vary with environmental gradients, feedback may also vary, limiting its capacity to predict plant distributions.

Methods

We characterized arbuscular mycorrhizal (AM) fungi across tree plantations and a primary Neotropical rainforest. We then performed a plant-soil feedback pot experiment of AM fungi from these plantations on three plant species and related feedback and AM fungal communities in the field.

Results

In the field, temporal and spatial variation in AM fungal composition was similar in magnitude to variation across plant host species. Composition of AM fungi in the pot experiment significantly differed from the field plots. Furthermore, differential feedback was explained by shifts in AM fungal composition only for one plant host species (Hyeronima alchorneoides) in the pot experiment.

Conclusions

Natural AM fungal communities were temporally and spatially heterogeneous and AM fungal communities in the greenhouse did not reflect natural soils. These factors led to heterogeneous and unpredictable feedback responses, which suggests that applying greenhouse derived plant-soil feedback trends to predict plant coexistence in natural systems may be misleading.

     

Pseudo current density maps of electrophysiological heart,nerve or brain function and their physical basis

Background

In recent years the visualization of biomagnetic measurement data by so-called pseudo current density maps or Hosaka-Cohen (HC) transformations became popular.

Methods

The physical basis of these intuitive maps is clarified by means of analytically solvable problems.

Results

Examples in magnetocardiography, magnetoencephalography and magnetoneurography demonstrate the usefulness of this method.

Conclusion

Hardware realizations of the HC-transformation and some similar transformations are discussed which could advantageously support cross-platform comparability of biomagnetic measurements.

     

Workflow to improve patient recruitment for clinical trials within hospital information systems – a case-study

Background

The identification of suitable patients is a common problem in clinical trials that is especially evident in tertiary care hospitals.

Methods

We developed and analysed a workflow, which uses routine data captured during patient care in a hospital information system (HIS), to identify potential trial subjects. Study nurses or physicians are notified automatically by email and verify eligibility.

Results

As a case study we implemented the system for acute myeloid leukemia (AML) trials in Münster. During a test period of 50 days 41 patients were identified by the system. 13 could be included as new trial patients, 7 were already included during earlier visits. According to review of paper records no AML trial patient was missed by the system. In addition, the hospital information system further allowed to preselect patients for specific trials based on their disease status and individual characteristics.

Conclusion

Routine HIS data can be used to support patient recruitment for clinical trials by means of an automated notification workflow.

     

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it

Introduction

Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.

Objectives

(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.

Methods

A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.

Results

Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.

Conclusion

Further efforts are required to improve data sharing in metabolomics.