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1.
Tomoko Nozoye Motoyasu Otani Takeshi Senoura Hiromi Nakanishi Naoko K. Nishizawa 《Plant and Soil》2017,418(1-2):75-88
Background and aims
Iron (Fe) is an essential micronutrient for all higher organisms. Fe is sparingly available in calcareous soils and Fe deficiency is a major agricultural problem worldwide. Nicotianamine (NA) is a metal chelator involved in metal translocation in plants. Sweet potato is an attractive crop that can grow in poor soil and thus is useful for planting in uncultivated soil. In addition, the sweet potato has recently been suggested as a source of bioethanol. Our aim is to increase NA concentration in sweet potato to ameliorate Fe deficiency.Method
Sweet potato plants expressing the barley NA synthase 1 (HvNAS1) gene under the control of CaMV 35S promoter were produced by Agrobacterium-mediated transformation.Results
The transgenic sweet potato exhibited tolerance to low Fe availability when grown in calcareous soil. The level of tolerance to low Fe availability was positively correlated with the HvNAS1 expression level. The NA concentration of the transgenic sweet potato leaves was up to 7.9-fold greater than that of the non-transgenic (NT) plant leaves. Furthermore, the Fe and zinc concentrations were 3- and 2.9-fold greater, respectively, in transgenic sweet potato than in NT plant leaves.Conclusions
Our results suggest that increasing the NA concentration of sweet potato by overexpression of HvNAS1 could significantly improve agricultural productivity and energy source.2.
Background and aims
Iron (Fe) toxicity is a wide-spread stress in lowland rice production. The aim of this study was to differentiate between responses to acute Fe stress during the vegetative stage and chronic Fe stress throughout the growing period.Methods
Six rice genotypes were tested in a semi-artificial greenhouse setup, in which acute (almost 1500 mg L?1 Fe in soil solution during the vegetative stage) and chronic (200 to 300 mg L?1 Fe throughout the season) Fe toxicity were simulated.Results
Acute Fe stress induced early development of heavy leaf bronzing, whereas moderate symptoms occurred in the chronic treatment throughout the season. Grain yields were only reduced in the chronic stress treatment (?23 %) due to reductions in spikelet fertility, grain number and grain weight. Symptom formation during the early growth stages did not reflect yield responses in all genotypes. Only one genotype showed increases in grain Fe concentrations (24 % in the acute stress and 44 % in the chronic stress) compared to the control.Conclusions
Contrasting genotypes responded differently to acute and chronic Fe toxicity, and one genotype showed consistent tolerance and the ability to translocate excess Fe into grains. These traits can be useful in the adaptive breeding of rice for Fe toxic environments.3.
Chih-Li Yu Dafeng Hui Qi Deng E. Kudjo Dzantor Philip A. Fay Weijun Shen Yiqi Luo 《Plant and Soil》2017,420(1-2):105-117
Aims
The objective of this study was to investigate the effects of the precipitation changes on soil, microbial and root respirations of switchgrass soils, and the relationships between soil respiration and plant growth, soil moisture and temperature.Methods
A mesocosm experiment was conducted with five precipitation treatments over two years in a greenhouse in Nashville, Tennessee. The treatments included ambient precipitation, ?50%, ?33%, +33% and +50% of ambient precipitation. Soil, microbial, and root respirations were quantified during the growing seasons.Results
Mean soil and root respirations in the +50% treatment were the highest (2.48 and 0.93 μmol CO2 m?2 s?1, respectively) among all treatments. Soil microbial respiration contributed more to soil respiration, and had higher precipitation sensitivity mostly than root respiration. Increases in precipitation mostly enhanced microbial respiration while decreases in precipitation reduced both microbial and root respirations. Across precipitation treatments, soil respiration was significantly influenced by soil moisture, soil temperature, and aboveground biomass.Conclusions
Our results showed that microbial respiration was more sensitive to precipitation changes, and precipitation regulated the response of soil respiration to soil temperature. The information generated in this study will be useful for model simulation of soil respiration in switchgrass fields under precipitation changes.4.
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.5.
Xiaofang Deng Zhuqing Zhao JiaJie Zhou JinZhao Chen Chenhao Lv Xinwei Liu 《Plant and Soil》2018,433(1-2):55-64
Aims
The objectives of this study were to determine the valence state of Se and major components in Se ore powder, examine its effect on Se enrichment in crops under different cultivation patterns, and assess the safety of edible parts of crops.Methods
Se ore powder from Enshi was subjected to compositional analysis by X-ray photoelectron spectroscopy and applied to rice (wetland) and soybean (dryland) fields before planting.Results
Se was mainly present in tetravalent and zero-valent forms at a 4:6 ratio in Se ore powder. Following soil application of Se ore powder, concentrations of As, Hg, Cr, and Pb in brown rice and soybean seed were below the limit of detection, and the Cd concentration was below the European Union food regulation limit. Organic Se accounted for more than 96% of total Se in both crops, including >91% Se-methionine. Compared with dryland, the flooded environment facilitated residual Se transformation into Fe/Mn oxide-bound Se, and thus increased the potential activity of Se in the soil.Conclusions
Se ore powder can be applied for the production of Se-rich agricultural products in the short-term, and possibilities of upgrading the Se ore product should be considered in the future.6.
Monica Calvo-Polanco Wenqing Zhang S. Ellen Macdonald Jorge Señorans Janusz J. Zwiazek 《Plant and Soil》2017,420(1-2):195-208
Aims
Reclamation following oil sands mining in northeastern Alberta (Canada) creates adverse reforestation soil conditions, including extreme pH values. We elucidated pH tolerance limits of boreal plant species and how pH affects nutrient uptake in these plants.Methods
We measured growth, gas exchange, and foliar nutrient concentration of 15 common northern boreal forest plants after eight weeks exposure to root zone pH ranging from 5.0 to 9.0. Cluster analyses were used to group these species based on their pH responses.Results
Based on their growth and gas exchange responses to pH, the 15 plant species could be divided into five groups, each of which contained species that commonly co-occur in particular boreal forest site types. For the foliar nutrient responses to pH, the 15 species could be grouped into only two categories; both showed decreases in foliar N, P, Fe and Zn concentration with increasing pH, with a more pronounced effect on the group that included trembling aspen, paper birch and chokecherry.Conclusions
The evidence of differential adaptation to pH by habitat type suggests the importance of soil pH as a factor affecting boreal plant species distribution and could be helpful for selection of species suitable for reclamation of sites with altered soil pH.7.
Liang Guo Ji Chen Eike Luedeling Jin-Sheng He Jimin Cheng Zhongming Wen Changhui Peng 《Plant and Soil》2018,425(1-2):177-188
Aims
The response of vegetation productivity to global warming is becoming a worldwide concern. While most reports on responses to warming trends are based on measured increases in air temperature, few studies have evaluated long-term variation in soil temperature and its impacts on vegetation productivity. Such impacts are especially important for high-latitude or high-altitude regions, where low temperature is recognized as the most critical limitation for plant growth.Methods
We used Partial Least Squares regression to correlate long-term aboveground net primary productivity (ANPP) data of an alpine grassland on the Qinghai-Tibetan Plateau with daily air and soil temperatures during 1997–2011. We also analyzed temporal trends for air temperature and soil temperature at different depths.Results
Soil temperatures have steadily increased at a rate of 0.4–0.9 °C per decade, whereas air temperatures showed no significant trend between 1997 and 2011. While temperature increases during the growing season (May–August) promoted aboveground productivity, warming before the growing season (March–April) had a negative effect on productivity. The negative effect was amplified in the soil layers, especially at 15 cm depth, where variation in aboveground productivity was dominated by early-spring soil warming, rather than by increasing temperature during the growing season.Conclusions
Future warming, especially in winter and spring, may further reduce soil water availability in early spring, which may slow down or even reverse the increases in grassland aboveground productivity that have widely been reported on the Qinghai-Tibetan Plateau.8.
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.9.
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.10.
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.11.
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.12.
Jamie V. de Seymour Stephanie Tu Xiaoling He Hua Zhang Ting-Li Han Philip N. Baker Karolina Sulek 《Metabolomics : Official journal of the Metabolomic Society》2018,14(6):79
Introduction
Intrahepatic cholestasis of pregnancy (ICP) is a common maternal liver disease; development can result in devastating consequences, including sudden fetal death and stillbirth. Currently, recognition of ICP only occurs following onset of clinical symptoms.Objective
Investigate the maternal hair metabolome for predictive biomarkers of ICP.Methods
The maternal hair metabolome (gestational age of sampling between 17 and 41 weeks) of 38 Chinese women with ICP and 46 pregnant controls was analysed using gas chromatography–mass spectrometry.Results
Of 105 metabolites detected in hair, none were significantly associated with ICP.Conclusion
Hair samples represent accumulative environmental exposure over time. Samples collected at the onset of ICP did not reveal any metabolic shifts, suggesting rapid development of the disease.13.
Vincent Gauthray-Guyénet Robert Schneider David Paré Alexis Achim Cédric Loi Luc Sirois 《Plant and Soil》2018,433(1-2):111-125
Background and aims
Forest composition in North America has undergone important changes since the European settlement. The effects of such alterations on soil properties remain largely unknown. This study aims to understand the long-term effects of shifts in forest composition on soil properties.Methods
Using data from 130 plots measured over an eighty-year period, the relationships between stand composition (both current and past), parent material and current soil chemical properties were studied with redundancy analyses.Results
Results indicated that the parent material remained the dominant factor explaining soil properties, followed by current tree species composition. No legacy effect of past forest composition was found, but shifts in forest composition explained part of the current soil properties. Specifically, an increase in balsam fir was related to higher C/N ratio in the O-horizon, while an increase in maple species was related to higher net nitrification in both the O and B-horizons, and higher extractable P in the B-horizon.Conclusion
Our results suggest that increasing the maple component at the expense of conifers over several decades may enhance nutrient availability in the O-horizon.14.
Introduction
Untargeted metabolomics is a powerful tool for biological discoveries. To analyze the complex raw data, significant advances in computational approaches have been made, yet it is not clear how exhaustive and reliable the data analysis results are.Objectives
Assessment of the quality of raw data processing in untargeted metabolomics.Methods
Five published untargeted metabolomics studies, were reanalyzed.Results
Omissions of at least 50 relevant compounds from the original results as well as examples of representative mistakes were reported for each study.Conclusion
Incomplete raw data processing shows unexplored potential of current and legacy data.15.
Wentao Luo Jordi Sardans Feike A. Dijkstra Josep Peñuelas Xiao-Tao Lü Honghui Wu Mai-He Li Edith Bai Zhengwen Wang Xingguo Han Yong Jiang 《Plant and Soil》2016,399(1-2):159-178
Background and aims
Aridity has increased in the past decades and will probably continue to increase in arid and semiarid regions. Here we decipher the plant and soil capacity to retain metal cations when climate evolves to more arid conditions.Methods
We analyzed K, Na, Ca, Mg, Fe, Mn, Zn and Cu concentrations in 580 soil samples and 666 plant (shoot and root) samples along a 3600 km aridity gradient in northern China.Results
The concentrations of soil exchangeable K, Mg, Mn, Fe and Cu clearly decreased with increasing aridity due to the relationships of aridity with soil clay content and soil pH. Increases in exchangeable Na and Ca concentrations at mid- and high-aridity levels are probably due to the soil salinization, whereas increased exchangeable Fe concentrations at extreme levels of aridity may be more related to a reduced pH. Element concentrations in both plant shoots and roots were unrelated to soil exchangeable element concentrations; instead they increased monotonously with increasing aridity, corresponding with decreases in plant size and shoot/root ratios. The shoot/root mineralomass ratios in general increased with increasing aridity. The proportional higher element contents in shoots than in roots with increasing aridity are related to increased water uptake and/or use efficiency.Conclusions
The extractability of soil elements in response to changing climate varied with the nature of specific elements that are controlled by biological and geochemical processes, i.e., some decreased linearly with increasing aridity, whereas others first decreased and then increased with different thresholds. These contrasting effects of aridity on nutrient availability could further constrain plant growth and should be incorporated into biogeochemical models. The prevailing paradigm of a positive relationship between concentrations of plant and soil elements needs to be reconsidered under changing climatic conditions.16.
Effectively processing medical term queries on the UMLS Metathesaurus by layered dynamic programming
Kaiyu Ren Albert M Lai Aveek Mukhopadhyay Raghu Machiraju Kun Huang Yang Xiang 《BMC medical genomics》2014,7(Z1):S11
Background
Mapping medical terms to standardized UMLS concepts is a basic step for leveraging biomedical texts in data management and analysis. However, available methods and tools have major limitations in handling queries over the UMLS Metathesaurus that contain inaccurate query terms, which frequently appear in real world applications.Methods
To provide a practical solution for this task, we propose a layered dynamic programming mapping (LDPMap) approach, which can efficiently handle these queries. LDPMap uses indexing and two layers of dynamic programming techniques to efficiently map a biomedical term to a UMLS concept.Results
Our empirical study shows that LDPMap achieves much faster query speeds than LCS. In comparison to the UMLS Metathesaurus Browser and MetaMap, LDPMap is much more effective in querying the UMLS Metathesaurus for inaccurately spelled medical terms, long medical terms, and medical terms with special characters.Conclusions
These results demonstrate that LDPMap is an efficient and effective method for mapping medical terms to the UMLS Metathesaurus.17.
Mai Kukumägi Ivika Ostonen Veiko Uri Heljä-Sisko Helmisaari Arno Kanal Olevi Kull Krista Lõhmus 《Plant and Soil》2017,414(1-2):265-280
Aims
Understanding the linkage of soil respiration (Rs) with forest development is essential for long-term C cycle models. We estimated the variation and temperature sensitivity (Q10 value) of Rs and its hetero-, (Rh) and autotrophic (Ra) components in relation to abiotic and biotic factors in Norway spruce stands of different ages, and the effect of trenching on microbial and soil characteristics.Methods
Trenching method was used to partition Rs into Rh and Ra. Ingrowth core method was used to estimate fine root production. Soil microbial biomass was measured using manometric respirometers.Results
Rs varied in differently aged stands demonstrating non-linear response to development stage. The variation of Rs was explained by changes in biotic factors rather than by changes in soil microclimate. Rh was more sensitive to Ts than Rs or Ra. After 4 years of trenching soil pH, N, SOM and dehydrogenase activity were significantly changed in trenched plots compared to control plots.Conclusions
Different Q10 values of Rh and Ra in stands of different ages indicate the importance of Rs partitioning. Trenching should be used during a limited number of years because of the possible changes in chemical characteristics of soil and in the activity of soil microbial community.18.
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.19.
20.
Matthew A. Hayes Amber Jesse Basam Tabet Ruth Reef Joost A. Keuskamp Catherine E. Lovelock 《Plant and Soil》2017,413(1-2):193-202