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1.
Simone Vassiliadis Kim M. Plummer Kevin S. Powell Simone J. Rochfort 《Metabolomics : Official journal of the Metabolomic Society》2018,14(10):133
Introduction
The aphid Rhopalosiphum padi L. is a vector of Barley yellow dwarf virus (BYDV) in wheat and other economically important cereal crops. Increased atmospheric CO2 has been shown to alter plant growth and metabolism, enhancing BYDV disease in wheat. However, the biochemical influences on aphid metabolism are not known.Objectives
This work aims to determine whether altered host-plant quality, influenced by virus infection and elevated CO2, impacts aphid weight and metabolism.Methods
Untargeted 1H NMR metabolomics coupled with multivariate statistics were employed to profile the metabolism of R. padi reared on virus-infected and non-infected (sham-inoculated) wheat grown under ambient CO2 (aCO2, 400 µmol mol?1) and future, predicted elevated CO2 (eCO2, 650 µmol mol?1) concentrations. Un-colonised wheat was also profiled to observe changes to host-plant quality (i.e., amino acids and sugars).Results
The direct impacts of virus or eCO2 were compared. Virus presence increased aphid weight under aCO2 but decreased weight under eCO2; whilst eCO2 increased non-viruliferous (sham) aphid weight but decreased viruliferous aphid weight. Discriminatory metabolites due to eCO2 were succinate and sucrose (in sham wheat), glucose, choline and betaine (in infected wheat), and threonine, lactate, alanine, GABA, glutamine, glutamate and asparagine (in aphids), irrespective of virus presence. Discriminatory metabolites due to virus presence were alanine, GABA, succinate and betaine (in wheat) and threonine and lactate (in aphids), irrespective of CO2 treatment.Conclusion
This study confirms that virus and eCO2 alter host-plant quality, and these differences are reflected by aphid weight and metabolism.2.
Andrei Prodan Sultan Imangaliyev Henk S. Brand Martijn N. A. Rosema Evgeni Levin Wim Crielaard Bart J. F. Keijser Enno C. I. Veerman 《Metabolomics : Official journal of the Metabolomic Society》2016,12(9):147
Introduction
Understanding the changes occurring in the oral ecosystem during development of gingivitis could help improve prevention and treatment strategies for oral health. Erythritol is a non-caloric polyol proposed to have beneficial effects on oral health.Objectives
To examine the effect of experimental gingivitis and the effect of erythritol on the salivary metabolome and salivary functional biochemistry.Methods
In a two-week experimental gingivitis challenge intervention study, non-targeted, mass spectrometry-based metabolomic profiling was performed on saliva samples from 61 healthy adults, collected at five time-points. The effect of erythritol was studied in a randomized, controlled trial setting. Fourteen salivary biochemistry variables were measured with antibody- or enzymatic activity-based assays.Results
Bacterial amino acid catabolites (cadaverine, N-acetylcadaverine, and α-hydroxyisovalerate) and end-products of bacterial alkali-producing pathways (N-α-acetylornithine and γ-aminobutyrate) increased significantly during the experimental gingivitis. Significant changes were found in a set of 13 salivary metabolite ratios composed of host cell membrane lipids involved in cell signaling, host responses to bacteria, and defense against free radicals. An increase in mevalonate was also observed. There were no significant effects of erythritol. No significant changes were found in functional salivary biochemistry.Conclusions
The findings underline a dynamic interaction between the host and the oral microbial biofilm during an experimental induction of gingivitis.3.
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.4.
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.5.
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.6.
Effect of gut microbiota on host whole metabolome 总被引:1,自引:0,他引:1
Takeo Moriya Yoshinori Satomi Shumpei Murata Hiroshi Sawada Hiroyuki Kobayashi 《Metabolomics : Official journal of the Metabolomic Society》2017,13(9):101
Introduction
Recent advances in microbiome research have revealed the diverse participation of gut microbiota in a number of diseases. Bacteria-specific endogenous small molecules are produced in the gut, are transported throughout the whole body by circulation, and play key roles in disease establishment. However, the factors and mechanisms underlying these microbial influences largely remain unknown.Objectives
The purpose of this study was to use metabolomics to better understand the influence of microbiota on host physiology.Methods
Germ-free mice (GF) were orally administered with the feces of specific pathogen-free (SPF) mice and were maintained in a vinyl isolator for 4 weeks for establishing the so-called ExGF mice. Comparative metabolomics was performed on luminal contents, feces, urine, plasma, and tissues of GF and ExGF mice.Results
The metabolomics profile of 1716 compounds showed marked difference between GF and ExGF for each matrix. Intestinal differences clearly showed the contribution of microbiota to host digestive activities. In addition, colonic metabolomics revealed the efficient conversion of primary to secondary metabolites by microbiota. Furthermore, metabolomics of tissues and excrements demonstrated the effect of microbiota on the accumulation of metabolites in tissues and during excretion. These effects included known bacterial effects (such as bile acids and amino acids) as well as novel ones, including a drastic decrease of sphingolipids in the host.Conclusion
The diverse effects of microbiota on different sites of the host metabolome were revealed and novel influences on host physiology were demonstrated. These findings should contribute to a deeper understanding of the influence of gut microbiota on disease states and aid in the development of effective intervention strategies.7.
J. U. Regus C. E. Wendlandt R. M. Bantay K. A. Gano-Cohen N. J. Gleason A. C. Hollowell M. R. O’Neill K. K. Shahin J. L. Sachs 《Plant and Soil》2017,414(1-2):159-170
Aims
Anthropogenic nitrogen deposition can provide legumes with a cheap source of nitrogen relative to symbiotic nitrogen fixation, leading to the potential breakdown of this critical symbiosis. Here, the effects of nitrogen deposition were tested on a native symbiosis between legumes and rhizobia.Methods
Deposition rates, soil nitrogen concentration, and plant nitrogen isotopic composition were quantified along a predicted deposition gradient in California. Acmispon strigosus seedlings were exposed to fertilization spanning nitrogen concentrations observed in the plant’s California range. Both wild and experimental plants from pristine and nitrogen polluted sites were tested using rhizobial strains that varied in nitrogen fixation.Results
Deposition intensity was tightly correlated with nitrogen concentration in soils. The growth benefits of rhizobial nodulation were dramatically reduced by even modest levels of mineral nitrogen, and all Acmispon lines failed to form root nodules at high nitrogen concentrations.Conclusions
Our dataset suggests that anthropogenic deposition has greatly increased soil nitrogen concentrations in Southern California leading to significantly reduced benefits of rhizobial symbiosis. If nitrogen deposition increases continue, plant host mortality and a total collapse of the symbiosis could result.8.
Lucas Barbosa de Freitas Dirceu Maximino Fernandes Suelen Cristina Mendonça Maia Adalton Mazetti Fernandes 《Plant and Soil》2017,420(1-2):263-275
Aims
This study aimed to determine the capacity of Si to mitigate Al toxicity in upland rice plants (Oryza sativa L.) by evaluating plant growth and the Si and Al uptake kinetics.Methods
Plants were grown for 40 days, after which the Si and Al uptake kinetics (Cmin, Km and Imax) were analyzed. Then, the shoots and roots were separated, and the dry matter, root morphology and Si and Al concentration and accumulation in the plant were evaluated.Results
Aluminum decreased plant growth and the Si uptake capacity by decreasing the root growth and Si transport system efficiency in the upland rice roots (> Km and > Cmin). Silicon mitigated Al toxicity in the upland rice plants by decreasing Al transport to the plant shoots, although it did not reduce the Al uptake rate (Imax). Si treatment increased the growth of upland rice plant shoots grown in the presence of Al without influencing the root growth. The alleviation of Al toxicity by Si is more evident in the susceptible upland rice cultivar Maravilha.Conclusions
Silicon mitigated Al toxicity in the upland rice plants by decreasing Al transport to the plant shoots but did not reduce the Al uptake rate by roots.9.
Saleh Alseekh Luisa Bermudez Luis Alejandro de Haro Alisdair R. Fernie Fernando Carrari 《Metabolomics : Official journal of the Metabolomic Society》2018,14(11):148
Background
Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding.Aim of Review
We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality.Key Scientific Concepts of Review
Translational metabolomics applied to crop breeding programs.10.
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.11.
Andrea Pitzschke 《Plant and Soil》2018,422(1-2):135-154
Aims
The pseudo-cereal quinoa has an outstanding nutritional value. Seed germination is unusually fast, and plant tolerance to salt stress exceptionally high. Seemingly all seeds harbor bacterial endophytes. This work examines mitogen-activated protein kinase (MAPK) activities during early development. It evaluates possible contribution of endophytes to rapid germination and plant robustness.Methods
MAPK activities were monitored in water- and NaCl-imbibed seeds over a 4-h-period using an immunoblot-based approach. Cellulolytic and pectinolytic abilities of bacteria were assessed biochemically, and cellular movement, biofilm, elicitor and antimicrobial compound synthesis genes sequenced. GyrA-based, cultivation-independent studies provided first insight into endophyte diversity.Results
Quinoa seeds and seedlings exhibit remarkably complex and dynamic MAPK activity profiles. Depending on seed origin, variances exist in MAPK patterns and probably also in endophyte assemblages. Mucilage-degrading activities enable endophytes to colonize seed surfaces of a non-host species, chia, without apparent adverse effects.Conclusions
Owing to their motility, cell wall-loosening and elicitor-generating abilities, quinoa endophytes have the potential to drive cell expansion, move across cell walls, generate damage-associated molecular patterns and activate MAPKs in their host. Bacteria may thus facilitate rapid germination and confer a primed state directly upon seed rehydration. Transfer into non-native crops appears both desirable and feasible.12.
Background
Fevers of unknown origin constitute a substantial disease burden in Southeast Asia. In majority of the cases, the cause of acute febrile illness is not identified.Methods
We used MassTag PCR, a multiplex assay platform, to test for the presence of 15 viral respiratory agents from 85 patients with unexplained respiratory illness representing six disease clusters that occurred in Cambodia between 2009 and 2012.Results
We detected a virus in 37 (44%) of the cases. Human rhinovirus, the virus detected most frequently, was found in both children and adults. The viruses most frequently detected in children and adults, respectively, were respiratory syncytial virus and enterovirus 68. Sequence analysis indicated that two distinct clades of enterovirus 68 were circulating during this time period.Conclusions
This is the first report of enterovirus 68 in Cambodia and contributes to the appreciation of this virus as an important respiratory pathogen.13.
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.14.
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.15.
Rachel A. Spicer Christoph Steinbeck 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):16
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.16.
Lia Bally Cédric Bovet Christos T. Nakas Thomas Zueger Jean-Christophe Prost Jean-Marc Nuoffer Alexander B. Leichtle Georg Martin Fiedler Christoph Stettler 《Metabolomics : Official journal of the Metabolomic Society》2017,13(7):78
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: NCT02068638.17.
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.18.
Joaquín Moreno Alejandro Terrones Ana Juan María Ángeles Alonso 《Plant and Soil》2018,430(1-2):185-204
Aims
Establishing a vegetation-soil model in Mediterranean saltmarshes based on the relationships between the plant communities and the abiotic factors, considering temporary variation.Methods
Relationships between perennial plant species abundances and plant communities were analysed by DCAs. A CCA was performed to study the relationships between floristic composition and edaphic variables. Sixteen soil variables and Pearson correlations between them were considered. Marginal and conditional effects were supported by mixed ANOVA. Statistical analyses were performed to check temporary variation.Results
DCAs results showed eight vegetation types. CCA showed E.C. as the main gradient, with the succulent halophyte communities growing in high E.C. soils. SAR and percentage of sand were considered as secondary gradients. Finally, the highest values of the edaphic variables were observed, in general, during the cold period.Conclusions
The main gradient of salinity, together with sodicity and texture gradients, would markedly influence the plant distribution in Mediterranean saltmarshes. Two principal plant zones were observed: succulent zone vs. non-succulent zone, with a specific edaphic distribution for each plant community and for the proposed Limonium morphotypes treatment. A plant-soil model based on these three gradients is here proposed. Our results would complement the previous knowledge about plant-soil relationships in Mediterranean saltmarshes.19.
H. S. Arathi L. Bjostad E. Bernklau 《Metabolomics : Official journal of the Metabolomic Society》2018,14(6):86