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1.
Javier F. Espeleta Zoe G. Cardon K. Ulrich Mayer Rebecca B. Neumann 《Plant and Soil》2017,414(1-2):33-51
Aims
Hydro-biogeochemical processes in the rhizosphere regulate nutrient and water availability, and thus ecosystem productivity. We hypothesized that two such processes often neglected in rhizosphere models — diel plant water use and competitive cation exchange — could interact to enhance availability of K+ and NH4 +, both high-demand nutrients.Methods
A rhizosphere model with competitive cation exchange was used to investigate how diel plant water use (i.e., daytime transpiration coupled with no nighttime water use, with nighttime root water release, and with nighttime transpiration) affects competitive ion interactions and availability of K+ and NH4 +.Results
Competitive cation exchange enabled low-demand cations that accumulate against roots (Ca2+, Mg2+, Na+) to desorb NH4 + and K+ from soil, generating non-monotonic dissolved concentration profiles (i.e. ‘hotspots’ 0.1–1 cm from the root). Cation accumulation and competitive desorption increased with net root water uptake. Daytime transpiration rate controlled diel variation in NH4 + and K+ aqueous mass, nighttime water use controlled spatial locations of ‘hotspots’, and day-to-night differences in water use controlled diel differences in ‘hotspot’ concentrations.Conclusions
Diel plant water use and competitive cation exchange enhanced NH4 + and K+ availability and influenced rhizosphere concentration dynamics. Demonstrated responses have implications for understanding rhizosphere nutrient cycling and plant nutrient uptake.2.
Anlei Chen Xiaoli Xie Tida Ge Haijun Hou Wei Wang Wenxue Wei Yakov Kuzyakov 《Plant and Soil》2017,413(1-2):203-216
Aims
This study is aimed to investigate the efficiency of plant growth-promoting (PGP) strategies of Enterobacter sp. strain EG16 under metal stress and its potential application in phytoremediation.Methods
Production of siderophores and indole-3-acetic acid (IAA) by EG16 were assessed in a hydroponic system in which Hibiscus cannabinus was grown with different concentrations of Cd and Fe. A pot experiment was also carried out to evaluate the practical effect of EG16 on H. cannabinus growth and remediation efficiency.Results
Inoculation with EG16 significantly improved plant growth, probably as a result of increased plant uptake of Fe and immobilization of Cd2+, which resulted in decreased plant accumulation of Cd. Increased production of siderophores by EG16 in response to Cd exposure appeared to be the PGP strategy functioning in the EG16–H. cannabinus association. The bacterial Cd response system promoted plant and bacterial uptake of Fe, alleviated Cd-induced inhibition of bacterial IAA production, and potentially assisted in metal immobilization in the rhizosphere.Conclusions
The EG16–H. cannabinus association may be useful for phytostabilization, as it exhibits good plant growth, low plant accumulation of metals, and reduced metal bioavailability in soil.3.
Background and aims
Earthworms effect on plant growth is mediated by their dejections or “casts”, a complex mixture of organic matter, minerals and microbes. In casts, different processes such as organic matter mineralization and signal molecule production follow a complex temporal dynamics. An adaptation of root morphology to cast dynamics could allow an efficient nitrogen capture by the plant.Methods
The plant Brachypodium distachyon was grown in a laboratory experiment with different proportions of casts of increasing ages. Casts were labelled with 15N to quantify the plant N uptake from the casts. Plant biomass and morphology, especially root system structure, were analysed.Results
The age of casts had an effect on fine root length, highlighting the importance of the dynamics of cast maturation in root adaptation. Plant biomass production was affected by the interaction between the age and proportion of casts. A positive correlation between the 15N proportion in plant tissues and plant biomasses indicated that plants were more efficient in foraging N in casts than in the bulk soil.Conclusions
Our results suggested that both a timely adaptation of the root system structure and a significant proportion of casts are necessary to observe a positive effect of casts on plant growth.4.
Nadine Strehmel David Strunk Veronika Strehmel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(11):135
Introduction
Aqueous–methanol mixtures have successfully been applied to extract a broad range of metabolites from plant tissue. However, a certain amount of material remains insoluble.Objectives
To enlarge the metabolic compendium, two ionic liquids were selected to extract the methanol insoluble part of trunk from Betula pendula.Methods
The extracted compounds were analyzed by LC/MS and GC/MS.Results
The results show that 1-butyl-3-methylimidazolium acetate (IL-Ac) predominantly resulted in fatty acids, whereas 1-ethyl-3-methylimidazolium tosylate (IL-Tos) mostly yielded phenolic structures. Interestingly, bark yielded more ionic liquid soluble metabolites compared to interior wood.Conclusion
From this one can conclude that the application of ionic liquids may expand the metabolic snapshot.5.
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.6.
Miaomiao Cheng Peter M. Kopittke Anan Wang Peter W. G. Sale Caixian Tang 《Plant and Soil》2018,430(1-2):219-231
Background and aims
Interactions between Cd and Zn occur in soils and plants but are inconsistent. This study examined how Cd/Zn interactions influence the growth of Carpobrotus rossii (Haw.) and the accumulation of Cd and Zn in plants.Methods
Plants were grown in nutrient solutions containing 5–100 μM Zn and 0, 5 or 15 μM Cd. Plant growth and tissue concentrations were measured, and the speciation of Zn within the plant tissues determined using synchrotron-based X-ray absorption spectroscopy.Results
There was an additive negative interaction between Cd and Zn on root growth. Only the highest level of Zn (100 μM) decreased Cd concentrations in root and shoot tissues (by 40–64%), whilst 100 μM Zn enhanced Cd translocation at 5 μM Cd but decreased it at 15 μM Cd. In contrast, both 5 and 15 μM Cd decreased Zn concentrations in root and shoot tissues but increased Zn translocation by 30–90%. This interaction was not associated with changes in Zn speciation within the plants, with most Zn associated with oxalate (48–87%).Conclusions
The presence of Zn and Cd resulted in an additive negative effect on root growth, but an antagonistic pattern in their accumulation in shoots of C. rossii.7.
pH as a proxy for estimating plant-available Si? A case study in rice fields in Karnataka (South India) 总被引:1,自引:0,他引:1
Jean-Dominique Meunier Kollalu Sandhya Nagabovanalli B. Prakash Daniel Borschneck Philippe Dussouillez 《Plant and Soil》2018,431(1-2):143-157
Background and aims
Soil nutrient dynamics are affected by root-microbe interactions and plant development. We investigated the influence of plant growth stage and arbuscular mycorrhiza fungi (AMF) on carbon (C) and nitrogen (N) rhizodeposition and the transfer into the microbial biomass (MB).Methods
Pea varieties (Pisum sativum L.) with (Frisson) and without mycorrhiza (P2) were 13C-15N-labelled and harvested at 45, 63, 71, and 95 days after sowing. Mycorrhization, MB, total C, N, 13C, 15N were determined in plant and soil compartments to calculate C and N derived from rhizodeposition (CdfR, NdfR).Results
Total CdfR increased until pea maturity, NdfR until end of flowering. Their relative contribution steadily decreased over time, accounting for 4–10% of total plant C and N at harvest. Rhizodeposition contributed between 1 and 6% to MB C and N, although 20% of the rhizodeposits were discovered in the MB. Frisson released more NdfR than P2 but it was not possible to accurately estimate AMF effects on C and N due to differences in biomass partitioning.Conclusions
CdfR followed an even flow from early growth until senescence. NdfR flow ceased after flowering possibly due to N relocation within the plant. Rhizodeposits contribute very little to MB in our study.8.
Daniel Cañueto Josep Gómez Reza M. Salek Xavier Correig Nicolau Cañellas 《Metabolomics : Official journal of the Metabolomic Society》2018,14(3):24
Introduction
Adoption of automatic profiling tools for 1H-NMR-based metabolomic studies still lags behind other approaches in the absence of the flexibility and interactivity necessary to adapt to the properties of study data sets of complex matrices.Objectives
To provide an open source tool that fully integrates these needs and enables the reproducibility of the profiling process.Methods
rDolphin incorporates novel techniques to optimize exploratory analysis, metabolite identification, and validation of profiling output quality.Results
The information and quality achieved in two public datasets of complex matrices are maximized.Conclusion
rDolphin is an open-source R package (http://github.com/danielcanueto/rDolphin) able to provide the best balance between accuracy, reproducibility and ease of use.9.
Arianna Filntisi Charalambos Fotakis Pantelis Asvestas George K. Matsopoulos Panagiotis Zoumpoulakis Dionisis Cavouras 《Metabolomics : Official journal of the Metabolomic Society》2017,13(12):146
Introduction
Metabolite identification in biological samples using Nuclear Magnetic Resonance (NMR) spectra is a challenging task due to the complexity of the biological matrices.Objectives
This paper introduces a new, automated computational scheme for the identification of metabolites in 1D 1H NMR spectra based on the Human Metabolome Database.Methods
The methodological scheme comprises of the sequential application of preprocessing, data reduction, metabolite screening and combination selection.Results
The proposed scheme has been tested on the 1D 1H NMR spectra of: (a) an amino acid mixture, (b) a serum sample spiked with the amino acid mixture, (c) 20 blood serum, (d) 20 human amniotic fluid samples, (e) 160 serum samples from publicly available database. The methodological scheme was compared against widely used software tools, exhibiting good performance in terms of correct assignment of the metabolites.Conclusions
This new robust scheme accomplishes to automatically identify peak resonances in 1H-NMR spectra with high accuracy and less human intervention with a wide range of applications in metabolic profiling.10.
Margarita Stritzler Ana Diez Tissera Gabriela Soto Nicolás Ayub 《Biotechnology letters》2018,40(9-10):1419-1423
Objectives
Identification of novel microbial factors contributing to plant protection against abiotic stress.Results
The genome of plant growth-promoting bacterium Pseudomonas fluorescens FR1 contains a short mobile element encoding a novel type of extracellular polyhydroxybutyrate (PHB) polymerase (PhbC) associated with a type I secretion system. Genetic analysis using a phbC mutant strain and plants showed that this novel extracellular enzyme is related to the PHB production in planta and suggests that PHB could be a beneficial microbial compound synthesized during plant adaptation to cold stress.Conclusion
Extracellular PhbC can be used as a new tool for improve crop production under abiotic stress.11.
Lenin D. Sarabia Berin A. Boughton Thusitha Rupasinghe Allison M. L. van de Meene Damien L. Callahan Camilla B. Hill Ute Roessner 《Metabolomics : Official journal of the Metabolomic Society》2018,14(5):63
Introduction
Mass spectrometry imaging (MSI) is a technology that enables the visualization of the spatial distribution of hundreds to thousands of metabolites in the same tissue section simultaneously. Roots are below-ground plant organs that anchor plants to the soil, take up water and nutrients, and sense and respond to external stresses. Physiological responses to salinity are multifaceted and have predominantly been studied using whole plant tissues that cannot resolve plant salinity responses spatially.Objectives
This study aimed to use a comprehensive approach to study the spatial distribution and profiles of metabolites, and to quantify the changes in the elemental content in young developing barley seminal roots before and after salinity stress.Methods
Here, we used a combination of liquid chromatography–mass spectrometry (LC–MS), inductively coupled plasma mass spectrometry (ICP–MS), and matrix-assisted laser desorption/ionization (MALDI–MSI) platforms to profile and analyze the spatial distribution of ions, metabolites and lipids across three anatomically different barley root zones before and after a short-term salinity stress (150 mM NaCl).Results
We localized, visualized and discriminated compounds in fine detail along longitudinal root sections and compared ion, metabolite, and lipid composition before and after salt stress. Large changes in the phosphatidylcholine (PC) profiles were observed as a response to salt stress with PC 34:n showing an overall reduction in salt treated roots. ICP–MS analysis quantified changes in the elemental content of roots with increases of Na+ and decreases of K+ content.Conclusion
Our results established the suitability of combining three mass spectrometry platforms to analyze and map ionic and metabolic responses to salinity stress in plant roots and to elucidate tolerance mechanisms in response to abiotic stress, such as salinity stress.12.
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.13.
Background and aims
A study was performed to investigate the role of fungal metabolites released into the rhizosphere of replanted orchards as a potential biotic component of tree growth decline.Methods
The phytotoxicity of the gamma ray-sterilized crude culture filtrates of sixteen fungal species originating from replanted apple orchards was tested in a bioassay. Low molecular weight compounds released by Fusarium spp. were analyzed.Results
The fungal culture filtrates affected seedling growth and health with an activity that varied from growth inhibition to promotion. Three out of the six species of Fusarium tested produced species-specific mycotoxins such as equisetin and enniatin B and D (<1 μg ml?1 and <6 μg ml?1, respectively) associated with root-tip necrosis, whereas fusaric acid (80–230 μg ml?1) was associated with asymptomatic plant growth inhibition. These findings were consistent with those obtained using pure compounds. Moreover, methoxyconidiol, paecilaminol, integrastatin B and other biologically active compounds, whose fungal origin and phytotoxicity have not yet been reported, were found. in all fungal filtrates.Conclusions
Findings suggest that i) phytopathogenicity of soil borne fungi can be expressed regardless of root infection; ii) a synergistic interaction between co-occurring mycotoxins and other biologically active compounds may explain plant growth inhibition. Iii) fungal metabolites released into soil may represent an underestimated component of nonspecific replant disease.14.
Korey J. Brownstein Mahmoud Gargouri William R. Folk David R. Gang 《Metabolomics : Official journal of the Metabolomic Society》2017,13(11):133
Introduction
Botanicals containing iridoid and phenylethanoid/phenylpropanoid glycosides are used worldwide for the treatment of inflammatory musculoskeletal conditions that are primary causes of human years lived with disability, such as arthritis and lower back pain.Objectives
We report the analysis of candidate anti-inflammatory metabolites of several endemic Scrophularia species and Verbascum thapsus used medicinally by peoples of North America.Methods
Leaves, stems, and roots were analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and partial least squares-discriminant analysis (PLS-DA) was performed in MetaboAnalyst 3.0 after processing the datasets in Progenesis QI.Results
Comparison of the datasets revealed significant and differential accumulation of iridoid and phenylethanoid/phenylpropanoid glycosides in the tissues of the endemic Scrophularia species and Verbascum thapsus.Conclusions
Our investigation identified several species of pharmacological interest as good sources for harpagoside and other important anti-inflammatory metabolites.15.
Renato de Souza Pinto Lemgruber Kaspar Valgepea Mark P. Hodson Ryan Tappel Sean D. Simpson Michael Köpke Lars K. Nielsen Esteban Marcellin 《Metabolomics : Official journal of the Metabolomic Society》2018,14(3):35
Introduction
Quantification of tetrahydrofolates (THFs), important metabolites in the Wood–Ljungdahl pathway (WLP) of acetogens, is challenging given their sensitivity to oxygen.Objective
To develop a simple anaerobic protocol to enable reliable THFs quantification from bioreactors.Methods
Anaerobic cultures were mixed with anaerobic acetonitrile for extraction. Targeted LC–MS/MS was used for quantification.Results
Tetrahydrofolates can only be quantified if sampled anaerobically. THF levels showed a strong correlation to acetyl-CoA, the end product of the WLP.Conclusion
Our method is useful for relative quantification of THFs across different growth conditions. Absolute quantification of THFs requires the use of labelled standards.16.
Cicheng Zhang Xiaoyan Li Huawu Wu Pei Wang Yang Wang Xiuchen Wu Wei Li Yongmei Huang 《Plant and Soil》2017,419(1-2):169-187
Background and aims
Understanding the responses of different plant species to changes in available water sources is critical for accurately modeling and predicting species dynamics. Our study aimed to explore whether there were differences in water-use strategies between the two coexisting shrubs (Reaumuria soongorica and Nitraria sphaerocarpa) in response to different amounts of summer precipitation.Methods
We conducted 3 years of field observations at three sites along an aridity gradient from the middle to lower reaches of the Heihe River basin, northwestern China. Stable oxygen composition (δ18O) in plant xylem water, soil water and groundwater were analyzed concurrently with ecophysiological measurements at monthly intervals during the growing seasons.Results
Water source for coexisting R. soongorica and N. sphaerocarpa did not differ at the sites with high precipitation, but significantly differed in more arid locations. The N. sphaerocarpa was more sensitive to summer precipitation than R. soongorica in terms of predawn water potential, stomatal conductance and foliage carbon-isotope discrimination.Conclusions
The plants relying on groundwater maintained consistent water use strategies, but not plants that took up precipitation-derived water. We also found that the difference in water source uptake between the coexisting species was more apparent in more arid locations.17.
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.18.
Xinchang Kou Tongqing Su Ningning Ma Qi Li Peng Wang Zhengfang Wu Wenju Liang Weixin Cheng 《Plant and Soil》2018,422(1-2):129-134
Background
Seeds host bacterial inhabitants but only a limited knowledge is available on which taxa inhabit seed, which niches could be colonized, and what the routes of colonization are.Scope
Within this commentary, a discussion is provided on seed bacterial inhabitants, their taxa, and from where derive the seed colonizers.Conclusions
Seeds/and grains host specific bacteria deriving from the anthosphere, carposphere, or from cones of gymnosperms and inner tissues of plants after a long colonization from the soil to reproductive organs.19.
Nicholas J. Bond Albert Koulman Julian L. Griffin Zoe Hall 《Metabolomics : Official journal of the Metabolomic Society》2017,13(11):128
Introduction
Mass spectrometry imaging (MSI) experiments result in complex multi-dimensional datasets, which require specialist data analysis tools.Objectives
We have developed massPix—an R package for analysing and interpreting data from MSI of lipids in tissue.Methods
massPix produces single ion images, performs multivariate statistics and provides putative lipid annotations based on accurate mass matching against generated lipid libraries.Results
Classification of tissue regions with high spectral similarly can be carried out by principal components analysis (PCA) or k-means clustering.Conclusion
massPix is an open-source tool for the analysis and statistical interpretation of MSI data, and is particularly useful for lipidomics applications.20.
Yanhui Ge Mengmeng Sun Luis F. Salomé-Abarca Mei Wang Young Hae Choi 《Metabolomics : Official journal of the Metabolomic Society》2018,14(10):137