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1.
Maé Guinet Bernard Nicolardot Cécile Revellin Vincent Durey Georg Carlsson Anne-Sophie Voisin 《Plant and Soil》2018,432(1-2):207-227
Aims
A better understanding of how plant growth, N nutrition and symbiotic nitrogen fixation (SNF) are influenced by soil inorganic N availability, for a wide range of legume species, is crucial to optimise legume productivity, N2 fixation, while limiting environmental risks such as N leaching.Methods
A comparative analysis was performed for ten legume crops, grown in a field experiment and supplied with four N fertiliser rates. Dry matter, N concentration and SNF were measured. In parallel, root elongation rates were studied in a greenhouse experiment.Results
For most species, N fertilisation had little effect on plant growth and N accumulation. SNF was reduced by soil inorganic N available at sowing but with large differences in the magnitude of the response among species. The response varied according to plant N requirements for growth and plant ability to retrieve inorganic N. Accordingly, root lateral expansion rate measured in RhizoTubes was highly correlated with plant ability to retrieve inorganic N measured in the field experiment.Conclusion
Combining SNF response to soil inorganic N, shoot N and plant ability to retrieve inorganic N, allowed a robust evaluation of differential response to soil inorganic N among a wide range of legume species.2.
Saskia Floerl Christine Druebert Andrzej Majcherczyk Petr Karlovsky Ursula Kües Andrea Polle 《BMC plant biology》2008,8(1):129
Background
Verticillium longisporum is one of the most important pathogens of Brassicaceae that remains strictly in the xylem during most stages of its development. It has been suggested that disease symptoms are associated with clogging of xylem vessels. The aim of our study was to investigate extracellular defence reactions induced by V. longisporum in the xylem sap and leaf apoplast of Brassica napus var. napus in relation to the development of disease symptoms, photosynthesis and nutrient status.Results
V. longisporum (strain VL43) did not overcome the hypocotyl barrier until 3 weeks after infection although the plants showed massive stunting of the stem and mild leaf chlorosis. During this initial infection phase photosynthetic carbon assimilation, transpiration rate and nutrient elements in leaves were not affected in VL43-infected compared to non-infected plants. Proteome analysis of the leaf apoplast revealed 170 spots after 2-D-protein separation, of which 12 were significantly enhanced in response to VL43-infection. LS-MS/MS analysis and data base searches revealed matches of VL43-responsive proteins to an endochitinase, a peroxidase, a PR-4 protein and a β-1,3-glucanase. In xylem sap three up-regulated proteins were found of which two were identified as PR-4 and β-1,3-glucanase. Xylem sap of infected plants inhibited the growth of V. longisporum.Conclusion
V. longisporum infection did not result in drought stress or nutrient limitations. Stunting and mild chlorosis were, therefore, not consequences of insufficient water and nutrient supply due to VL43-caused xylem obstruction. A distinct array of extracellular PR-proteins was activated that might have limited Verticillium spreading above the hypocotyl. In silico analysis suggested that ethylene was involved in up-regulating VL43-responsive proteins.3.
Yunbo Wang Bo Meng Shangzhi Zhong Deli Wang Jianying Ma Wei Sun 《Plant and Soil》2018,432(1-2):259-272
Background and aims
Nitrogen deposition and altered precipitation regime are likely to change plant growth, biomass allocation and community structure, which may influence susceptibility of ecosystem functions (i.e. ecosystem carbon exchange) to extreme climatic events, such as drought.Methods
In a meadow steppe, we deployed a drought treatment on a long-term water and nitrogen addition experiment to investigate resource abundance changes induced variation in the sensitivity of ecosystem carbon exchange to extreme drought.Results
Compared to the control plots, long-term water and nitrogen addition caused a strong increase in biomass, and a reduction in diversity and root/shoot ratio. Net ecosystem CO2 exchange (NEE) in water and nitrogen addition plots were more sensitive to drought stress than the control plots. The enhanced NEE drought sensitivity (SNEE) in nitrogen fertilization habitat is associated with changes in aboveground biomass and root/shoot ratio, rather than variation in species diversity, while SNEE in the unfertilized plots was controlled by root/shoot ratio. Compared to the water and nitrogen addition plots, the control plots had the highest percentage recovery of ecosystem carbon exchange (RNEE) during the rehydration period. RNEE is likely determined by aboveground biomass and level of damage in the photosynthetic organ.Conclusion
These findings suggest that long-term changes in precipitation regimes and nitrogen deposition may significant alter the susceptibility of key ecosystem processes to drought stress.4.
Background
In this study, we optimized the process for enhancing amylase production from Pseudomonas balearica VITPS19 isolated from agricultural lands in Kolathur, India.Methods
Process optimization for enhancing amylase production from the isolate was carried out by Response Surface Methodology (RSM) with optimized chemical and physical sources using Design expert v.7.0. A central composite design was used to evaluate the interaction between parameters. Interaction between four factors–maltose (C-source), malt extract (Nsource), pH, and CaCl2 was studied.Results
The factors pH and CaCl2 concentration were found to affect amylase production. Validation of the experiment showed a nearly twofold increase in alpha amylase production.Conclusion
Amylase production was thus optimized and increased yield was achieved.5.
Gregory D. Tredwell Jacob G. Bundy Maria De Iorio Timothy M. D. Ebbels 《Metabolomics : Official journal of the Metabolomic Society》2016,12(10):152
Introduction
Despite the use of buffering agents the 1H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples.Objectives
To investigate the acid, base and metal ion dependent 1H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture.Methods
Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl2, MgCl2, NaCl or KCl, and their 1H NMR spectra were acquired.Results
Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na+, K+, Ca2+ and Mg2+, were also measured.Conclusion
These data will be a valuable resource for 1H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for 1H NMR spectra.6.
Aim
Our objectives were to compare effects of root charge properties on Al adsorption by the roots of rice that differed in Al-tolerance, and to examine effects of different nitrogen forms on charge properties of rice roots and Al adsorption.Methods
Streaming potential and chemical methods were used to measure root zeta potential and investigate Al chemical forms adsorbed on the roots of rice obtained from solution culture experiments.Results
Rice roots of the Al-sensitive variety Yangdao-6 carried greater negative charge than the Al-tolerant variety Wuyunjing-7, which meant the roots of Yangdao-6 adsorbed more exchangeable and complexed Al. When both rice varieties were grown in NH4 +-containing nutrient solutions, there were less functional groups and lower negative surface charge on their roots, which reduced Al adsorption compared to the rice grown in NO3 ? containing nutrient solutions. The decline in nutrient solution pH due to NH4 + uptake by rice roots was responsible for the reduced numbers of functional groups and the lower negative surface charge on the roots compared to the rice grown in NO3 ? containing solutions.Conclusions
Integrated root surface charge, as expressed by zeta potential, played an important role in Al adsorption by the roots of rice with different Al-tolerance.7.
D. Jacob C. Deborde M. Lefebvre M. Maucourt A. Moing 《Metabolomics : Official journal of the Metabolomic Society》2017,13(4):36
Introduction
Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks.Objectives
The objective of NMRProcFlow is to assist the expert in this task in the best way without requirement of programming skills.Methods
NMRProcFlow was developed to be a graphical and interactive 1D NMR (1H & 13C) spectra processing tool.Results
NMRProcFlow (http://nmrprocflow.org), dedicated to metabolic fingerprinting and targeted metabolomics, covers all spectra processing steps including baseline correction, chemical shift calibration and alignment.Conclusion
Biologists and NMR spectroscopists can easily interact and develop synergies by visualizing the NMR spectra along with their corresponding experimental-factor levels, thus setting a bridge between experimental design and subsequent statistical analyses.8.
Shengnan Ouyang Yuqiang Tian Qianyuan Liu Li Zhang Ruixue Wang Xingliang Xu 《Plant and Soil》2016,398(1-2):121-137
Background and aims
To test the hypothesis that dominant plant species could acquire different nitrogen (N) forms over a spatial scale and they also have the ability to compete for available N with microbes.Methods
A short-term 15N labeling experiment was conducted in the temperate grassland ecosystem of North China in July of 2013. Three N forms (NO3 ? , NH4 + and glycine) labeled with 15N were injected into the two soil depths (0–5 and 5–15 cm) surrounding each plant to explore N acquisition by plants and microbes. Three dominant plant species (Artemisia frigida, Cleistogenes squarrosa and Artemisia capillaris) were investigated.Results
Two hours after 15N labeling, all three dominant plant species absorbed both organic and inorganic N, but different patterns were observed at two soil depths. Uptake of NO3 ? was significantly higher at 0–5 cm than at 5–15 cm soil depth among all the dominant plant species. 15N recovery by microbes was significantly higher than plants. However, 15N recovery by plants showed different patterns over soil depths.Conclusions
Dominant plant species in the temperate grassland have different patterns in acquisition of N added to soil in organic form and absorption of inorganic N, and microbes were more effectively than plants at competing for N in a short-term period.9.
Huan Fang Hu Zhou Gareth J. Norton Adam H. Price Annette C. Raffan Sacha J. Mooney Xinhua Peng Paul D. Hallett 《Plant and Soil》2018,424(1-2):233-254
Background and aims
Drought events, agricultural practices and plant communities influence microbial and soil abiotic parameters which can feedback to fodder production. This study aimed to determine which soil legacies influence plant biomass production and nutritional quality, and its resistance and recovery to extreme weather events.Methods
In a greenhouse experiment, soil legacy effects on Lolium perenne were examined, first under optimal conditions, and subsequently during and after drought. We used subalpine grassland soils previously cultivated for two years with grass communities of distinct functional composition, and subjected to combinations of climatic stress and simulated management.Results
The soil legacy of climatic stress increased biomass production of Lolium perenne and its resistance and recovery to a new drought. This beneficial effect resulted from higher nutrient availability in soils previously exposed to climatic stresses due to lower competitive abilities and resistance of microbial communities to a new drought. This negative effect on microbial communities was strongest in soils from previously cut and fertilized grasslands or dominated by conservative grasses.Conclusion
In subalpine grasslands more frequent climatic stresses could benefit fodder production in the short term, but threaten ecosystem functioning and the maintenance of traditional agricultural practices in the long term.10.
Aims
Fungi play a central role in litter decomposition, a key process controlling the terrestrial carbon cycle and nutrient availability for plants and microorganisms. Climate change and elevated CO2 affect soil fungi, but the relative importance of the global change variables for litter decomposition is still uncertain. The main objective was therefore to assess the short-term litter decomposition and associated fungal community in a global change manipulated temperate heath ecosystem.Methods
The heath had been exposed to 6 years of warming, elevated atmospheric CO2 and an extended pre-summer drought. Litterbags with litter from heather (Calluna vulgaris) and wavy-hair grass (Deschampsia flexuosa) were incubated in the litter layer for 6 months, where after we analyzed the litter-associated fungal community, litter loss, CO2 respiration, and total content of carbon, nitrogen and phosphorus.Results
Elevated temperature tended to increase litter decomposition rates, whereas elevated CO2 had no effect on the process. The pre-summer drought treatment had a positive impact on litter decomposition, CO2 respiration and fungal abundance in the litterbags, although we observed no major changes in fungal community composition.Conclusions
The drought treatment during pre-summer had a legacy effect on litter decomposition as decomposition rates were positively affected later in the year. The community structure of litter-decomposing fungi was not affected by the drought treatment. Hence, the legacy effect was not mediated by a change in the fungal community structure.11.
Tie-juan Shao Zhi-xing He Zhi-jun Xie Hai-chang Li Mei-jiao Wang Cheng-ping Wen 《Metabolomics : Official journal of the Metabolomic Society》2016,12(4):70
Introduction
The differences in fecal metabolome between ankylosing spondylitis (AS)/rheumatoid arthritis (RA) patients and healthy individuals could be the reason for an autoimmune disorder.Objectives
The study explored the fecal metabolome difference between AS/RA patients and healthy controls to clarify human immune disturbance.Methods
Fecal samples from 109 individuals (healthy controls 34, AS 40, and RA 35) were analyzed by 1H NMR spectroscopy. Data were analyzed with principal component analysis (PCA) and orthogonal projection to latent structure discriminant (OPLS-DA) analysis.Results
Significant differences in the fecal metabolic profiles could distinguish AS/RA patients from healthy controls but could not distinguish between AS and RA patients. The significantly decreased metabolites in AS/RA patients were butyrate, propionate, methionine, and hypoxanthine. Significantly increased metabolites in AS/RA patients were taurine, methanol, fumarate, and tryptophan.Conclusion
The metabolome variations in feces indicated AS and RA were two homologous diseases that could not be distinguished by 1H NMR metabolomics.12.
Gustavo Boitt Amanda Black Steve A. Wakelin Richard W. McDowell Leo M. Condron 《Plant and Soil》2018,427(1-2):163-174
Aims
We assessed and quantified the cumulative impact of 20 years of biomass management on the nature and bioavailability of soil phosphorus (P) accumulated from antecedent fertiliser inputs.Methods
Soil (0–2.5, 2.5–5, 5–10 cm) and plant samples were taken from replicate plots in a grassland field experiment maintained for 20 years under contrasting plant biomass regimen- biomass retained or removed after mowing. Analyses included dry matter production and P uptake, root biomass, total soil carbon (C), total nitrogen (N), total P, soil P fractionation, and 31P NMR spectroscopy.Results
Contemporary plant production and P uptake were over 2-fold higher for the biomass retained compared with the biomass removed regimes. Soil C, total P, soluble and labile forms of inorganic and organic soil P were significantly higher under biomass retention than removal.Conclusions
Reserves of soluble and labile inorganic P in soil were significantly depleted in response to continued long-term removal of P in plant biomass compared to retention. However, this was only sufficient to sustain plant production at half the level observed for the biomass retention after 20 years, which was partly attributed to limited mobilisation of organic P in response to P removal.13.
Gaoxiang Qi Lian Xiong Xiaoqing Lin Chao Huang Hailong Li Xuefang Chen Xinde Chen 《Biotechnology letters》2017,39(1):97-104
Objective
To investigate the inhibiting effect of formic acid on acetone/butanol/ethanol (ABE) fermentation and explain the mechanism of the alleviation in the inhibiting effect under CaCO3 supplementation condition.Results
From the medium containing 50 g sugars l?1 and 0.5 g formic acid l?1, only 0.75 g ABE l?1 was produced when pH was adjusted by KOH and fermentation ended prematurely before the transformation from acidogenesis to solventogenesis. In contrast, 11.4 g ABE l?1 was produced when pH was adjusted by 4 g CaCO3 l?1. The beneficial effect can be ascribed to the buffering capacity of CaCO3. Comparative analysis results showed that the undissociated formic acid concentration and acid production coupled with ATP and NADH was affected by the pH buffering capacity of CaCO3. Four millimole undissociated formic acid was the threshold at which the transformation to solventogenesis occurred.Conclusion
The inhibiting effect of formic acid on ABE fermentation can be alleviated by CaCO3 supplementation due to its buffering capacity.14.
Background
There are few in-flight studies of cognition-related cerebral oxygen status in helicopter pilots.Methods
Four male helicopter pilots volunteered for nine sorties during visual flight in a BK117 and UH-60J. The pilots' pre-frontal oxy-hemoglobin (O2Hb) and deoxy-hemoglobin (HHb) concentration were continuously monitored from the right/left sections of the forehead using near-infrared spectrophotometers with a consideration of motion artifacts.Results
The concentration of O2Hb progressively increased (13.98 μmol?L-1 as a maximum increased concentration) in both the right/left sections of the forehead from the basal level during the heightened cognitive demand of helicopter flight. There was comparatively little change (4.32 μmol?L-1 as a maximum increased concentration) in HHb concentration during measurement of helicopter flight. HHb changes were apparently not affected by a heightened cognitive demand of helicopter pilots.Conclusion
These results demonstrate that near-infrared spectroscopy, especially O2Hb measurements, provides a sensitive method for the monitoring of cognitive demand (maneuvers) in helicopter pilots.15.
Teklab Gebregiworgis Fatema Bhinderwala Vinee Purohit Nina V. Chaika Pankaj K. Singh 《Metabolomics : Official journal of the Metabolomic Society》2018,14(12):156
Introduction
Gemcitabine is an important component of pancreatic cancer clinical management. Unfortunately, acquired gemcitabine resistance is widespread and there are limitations to predicting and monitoring therapeutic outcomes.Objective
To investigate the potential of metabolomics to differentiate pancreatic cancer cells that develops resistance or respond to gemcitabine treatment.Results
We applied 1D 1H and 2D 1H–13C HSQC NMR methods to profile the metabolic signature of pancreatic cancer cells. 13C6-glucose labeling identified 30 key metabolites uniquely altered between wild-type and gemcitabine-resistant cells upon gemcitabine treatment. Gemcitabine resistance was observed to reprogram glucose metabolism and to enhance the pyrimidine synthesis pathway. Myo-inositol, taurine, glycerophosphocholine and creatinine phosphate exhibited a “binary switch” in response to gemcitabine treatment and acquired resistance.Conclusion
Metabolic differences between naïve and resistant pancreatic cancer cells and, accordingly, their unique responses to gemcitabine treatment were revealed, which may be useful in the clinical setting for monitoring a patient’s therapeutic response.16.
Background
Maize seedlings are constantly exposed to inorganic phosphate (Pi)-limited environments. To understand how maize cope with low Pi (LP) and high Pi (HP) conditions, physiological and global proteomic analysis of QXN233 genotype were performed under the long-term Pi starvation and supplementation.Methods
We investigated the physiological response of QXN233 genotype to LP and HP conditions and detected the changes in ion fluxes by non-invasive micro-test technology and gene expression by quantitative real-time polymerase chain reaction. QXN233 was further assessed using vermiculite assay, and then proteins were isolated and identified by nano-liquid chromatography-mass spectrometry.Results
A negative relationship was observed between Na+ and Pi, and Na+ efflux was enhanced under HP condition. Furthermore, a total of 681 and 1374 were identified in the leaves and roots, respectively, which were mostly involved in metabolism, ion transport, and stress response. Importantly, several key Pi transporters were identified for breeding potential. Several ion transporters demonstrated an elaborate interplay between Pi and other ions, together contributing to the growth of QXN233 seedlings.Conclusion
The results from this study provide insights into the response of maize seedlings to long-term Pi exposure.17.
Aims
The role of different soil types for beech productivity and drought sensitivity is unknown. The aim of this experimental study was to compare mycorrhizal diversity between acid sandy and calcareous soils and to investigate how this diversity affects tree performance, nitrogen uptake and use efficiency (NUE).Methods
Beech trees were germinated and grown in five different soil types (pH 3.8 to 6.7). One-and-a-half-year-old plants were exposed for 6 weeks to sufficient or low soil humidity. Tree biomass, root tip mycorrhizal colonization and community structure, root tip mortality, leaf area, photosynthesis, nitrogen concentrations, NUE and short-term 15N uptake from glutamine were determined.Results
Soil type did not affect photosynthesis or biomass formation, with one exception in calcareous soil, where root mortality was higher than in the other soil types. Beech in acid soils showed lower mycorrhizal colonization, higher nitrogen tissue concentrations, and lower NUE than those in calcareous soils. Drought had no effect on nitrogen concentrations or NUE but caused reductions in mycorrhizal colonization. Mycorrhizal species richness correlated with nitrogen uptake and NUE. Nitrogen uptake was more sensitive to drought in calcareous soils than in acid soils.Conclusions
Beech may be more drought-susceptible on calcareous sites because of stronger decrease of organic nitrogen uptake than on acid soils.18.
N. Cesbron A.-L. Royer Y. Guitton A. Sydor B. Le Bizec G. Dervilly-Pinel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(8):99
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.19.
Lei Chen Xiaoming Yi Fajun Deng Wei Fang Xuecheng Zhang Xiaotang Wang Zemin Fang Yazhong Xiao 《Biotechnology letters》2016,38(3):471-476
Objectives
To produce and characterize novel laccases with ethanol tolerance from Trametes versicolor using agriculture by-products as energy source.Results
Trametes versicolor 1017 produces two laccase isoenzymes with a total activity of 10 U ml?1 within 8 days when using wheat bran and peanut powder as energy sources in liquid culture medium. A novel isoenzyme, named Tvlac, was identified, purified and characterized. Its optimum pH and temperature were from 4.5 to 5 and 55 to 60 °C, respectively. Its activity was stimulated by ethanol at 10 % (v/v) which increased the V 0.Conclusions
The biochemical properties of Tvlac substantiate the potential of this enzyme for applications under an aqueous ethanol mixture environment.20.