Roles of shoots and roots in cadmium uptake and distribution in tubers of potato (<Emphasis Type="Italic">Solanum tuberosum</Emphasis> L)

Aims

We investigated whether density fractionation can be used to determine the distribution of organic phosphorus (OP) between free and mineral-associated soil organic matter (SOM).

Methods

We performed density fractionations using sodium polytungstate solution (specific gravity 1.6 g cm^?3) on 20 soils from UK semi-natural and pasture ecosystems, to obtain a light fraction (LF) and a heavy fraction (HF) for each soil. The fractions were quantified by weight, and analysed for organic carbon (OC), total N (TN), total P (TP), inorganic P (IP), and OP (by difference).

Results

Good recoveries of soil mass (96%), OC and TN (both ~ 90%) were obtained, but recovery of OP only averaged 56%. The average P:C ratio of HF SOM exceeded that of LF SOM by a factor of six, greater than the factor of two obtained for TN:OC. For the soils studied, the elements of SOM were predominantly in the HF, with averages of 75% for C, 82% for N, and 90% for P.

Conclusions

The incomplete recovery of OP demands further work. Nonetheless, the results show that HF SOM is much richer in P than LF SOM.

     

Towards understanding the traits contributing to performance of pearl millet open-pollinated varieties in phosphorus-limited environments of West Africa

Background and aims

Arbuscular mycorrhizal (AM) hyphae represent an important route for input of plant-derived C to soil, but impacts of these inputs on microbial communities and processes are poorly understood. In this study we characterised pathways of C-flow through microbial communities associated with AM hyphae and quantified impacts on mineralisation of native SOM.

Methods

Continuous, steady-state ¹³CO₂ labelling was applied throughout the growth period (60 d) of Lolium perenne. Exclusion meshes were used to control access of roots and AM hyphae to soil, and plant-derived C was quantified within microbial PLFA and NLFA, and soil CO₂ efflux was partitioned into plant- and soil organic matter (SOM) derived components.

Results

Pathways of C-flow through hyphosphere and mycorrhizosphere communities were distinct, as was the fate of plant-derived C from AM hyphae accessing soil through 37 and 1 μm meshes. Mineralisation of native SOM was increased in all treatments, relative to unplanted controls, and this priming effect was largest for AM hyphae accessing soil through the 1 μm mesh size.

Conclusions

We demonstrated that AM hyphae can strongly increase mineralisation of native SOM and identified distinct pathways of C-flow through hyphosphere communities. Our results suggest that, in addition to affecting rates of litter decomposition, AM hyphae may have a significant influence on turnover of native SOM.

     

Eighty years of maize breeding alters plant nitrogen acquisition but not rhizosphere bacterial community composition

Background and aims

Phosphorus (P) availability is crucial for forest ecosystem productivity and soil organic matter (SOM) is an important source for P. This study was conducted to reveal carbon (C), nitrogen (N) and P distributions in functional SOM fractions. We hypothesised that (1) most of the organic P (P_org) is part of the particulate SOM, (2) particulate SOM stores increasing share of P with decreasing soil P content and (3) the C:P_org ratio of mineral-associated SOM is smaller than that of particulate SOM.

Methods

We analysed soil samples from five temperate forest sites (Fagus sylvatica) under different geological parent material with a wide range of total P concentrations. Density fractionation was used to separate free light fraction (fLF), particulate SOM occluded within soil aggregates (occluded light fraction; oLF), and mineral associated SOM (heavy fraction; HF). We determined the mass balance of P in these fractions, in addition to the C and N concentrations. Additionally, the P speciation of the topsoil was analysed by X-ray absorption near edge structure (XANES) spectroscopy at the P K-edge.

Results

The fLF contained 18–54% and the oLF 1–15% of total P (P_tot). High percentage of P in these light fractions was associated to soil minerals. Phosphorous in particulate SOM within aggregates tend to increase with decreasing soil P. The HF containing mineral-associated OM, comprised 38–71% of P_tot and their C:P_org ratios were consistently lower than those of the fLF irrespective of the P status of the soil.

Conclusions

We show that all three functional SOM fractions contain variable amount of both organic and inorganic P species. The free light fraction shows no response to changing P stocks of soils.. Despite physically protected particulate SOM, oLF, becomes increasingly relevant as P cache in soils with declining P status.

     

Chemical changes in organic matter after fungal colonization in a nitrogen fertilized and unfertilized Norway spruce forest

Background and aims

Mineralization of soil organic matter (SOM) constitutes a major carbon flux to the atmosphere. The carbon use efficiency (CUE) of the saprotrophic microorganisms mineralizing SOM is integral for soil carbon dynamics. Here we investigate how the CUE is affected by temperature, metabolic conditions, and the molecular complexity of the substrate.

Methods

We incubated O-horizon soil samples (with either ¹³C–glucose or ¹³C–cellulose) from a boreal coniferous forest at 4, 9, 14, and 19 °C, and calculated CUEs based on the amount of ¹³C–CO₂ and ¹³C–labelled microbial biomass produced. The effects of substrate, temperature, and metabolic conditions (representing unlimited substrate supply and substrate limitation) on CUE were evaluated.

Results

CUE from metabolizing glucose was higher as compared to cellulose. A slight decrease in CUE with increasing temperature was observed in glucose amended samples (but only in the range 9–19 °C), but not in cellulose amended samples. CUE differed significantly with metabolic conditions, i.e. CUE was higher during unlimited growth conditions as compared to conditions with substrate limitation.

Conclusions

We conclude that it is integral to account for both differences in CUE during different metabolic phases, as well as complexity of substrate, when interpreting temperature dependence on CUE in incubation studies.

     

Variation of soil respiration and its components in hemiboreal Norway spruce stands of different ages

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.

     

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

Introduction

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

Objectives

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

Methods

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

Results

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

Conclusion

Further efforts are required to improve data sharing in metabolomics.

     

Maize rhizosphere priming: field estimates using <Superscript>13</Superscript>C natural abundance

Introduction

Root-mediated changes in soil organic matter (SOM) decomposition, termed rhizosphere priming effects (RPE), play crucial roles in the global carbon (C) cycle, but their mechanisms and field relevance remain ambiguous. We hypothesize that nitrogen (N) shortages may intensify SOM decomposition in the rhizosphere because of increase of fine roots and rhizodeposition.

Methods

RPE and their dependence on N-fertilization were studied using a C₃-to-C₄ vegetation change. N-fertilized and unfertilized soil cores, with and without maize, were incubated in the field for 50 days. Soil CO₂ efflux was measured, partitioned for SOM- and root-derived CO₂, and RPE was calculated. Plant biomass, microbial biomass C (MBC) and N (MBN), and enzyme activities (β-1,4-glucosidase; N-acetylglucosaminidase; L-leucine aminopeptidase) were analyzed.

Results

Roots enhanced SOM mineralization by 35 % and 126 % with and without N, respectively. This was accompanied by higher specific root-derived CO₂ in unfertilized soils. MBC, MBN and enzyme activities increased in planted soils, indicating microbial activation, causing positive RPE. N-fertilization had minor effects on MBC and MBN, but it reduced β-1,4-glucosidase and L-leucine aminopeptidase activities under maize through lower root-exudation. In contrast, N-acetylglucosaminidase activity increased with N-fertilization in planted and unplanted soils.

Conclusions

This study showed the field relevance of RPE and confirmed that, despite higher root biomass, N availability reduces RPE by lowering root and microbial activity.

     

Influence of shifts over an 80-year period in forest composition on soil properties

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.

     

Untargeted metabolomics suffers from incomplete raw data processing

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.

     

The EcoSpold 2 format—why a new format?

Purpose

This paper introduces the new EcoSpold data format for life cycle inventory (LCI).

Methods

A short historical retrospect on data formats in the life cycle assessment (LCA) field is given. The guiding principles for the revision and implementation are explained. Some technical basics of the data format are described, and changes to the previous data format are explained.

Results

The EcoSpold 2 data format caters for new requirements that have arisen in the LCA field in recent years.

Conclusions

The new data format is the basis for the Ecoinvent v3 database, but since it is an open data format, it is expected to be adopted by other LCI databases. Several new concepts used in the new EcoSpold 2 data format open the way for new possibilities for the LCA practitioners and to expand the application of the datasets in other fields beyond LCA (e.g., Material Flow Analysis, Energy Balancing).

     

KniMet: a pipeline for the processing of chromatography–mass spectrometry metabolomics data

Introduction

Data processing is one of the biggest problems in metabolomics, given the high number of samples analyzed and the need of multiple software packages for each step of the processing workflow.

Objectives

Merge in the same platform the steps required for metabolomics data processing.

Methods

KniMet is a workflow for the processing of mass spectrometry-metabolomics data based on the KNIME Analytics platform.

Results

The approach includes key steps to follow in metabolomics data processing: feature filtering, missing value imputation, normalization, batch correction and annotation.

Conclusion

KniMet provides the user with a local, modular and customizable workflow for the processing of both GC–MS and LC–MS open profiling data.

     

Pathway-based analyses

Background

New technologies for acquisition of genomic data, while offering unprecedented opportunities for genetic discovery, also impose severe burdens of interpretation andpenalties for multiple testing.

Methods

The Pathway-based Analyses Group of the Genetic Analysis Workshop 19 (GAW19) sought reduction of multiple-testing burden through various approaches to aggregation of highdimensional data in pathways informed by prior biological knowledge.

Results

Experimental methods testedincluded the use of "synthetic pathways" (random sets of genes) to estimate power and false-positive error rate of methods applied to simulated data; data reduction via independent components analysis, single-nucleotide polymorphism (SNP)-SNP interaction, and use of gene sets to estimate genetic similarity; and general assessment of the efficacy of prior biological knowledge to reduce the dimensionality of complex genomic data.

Conclusions

The work of this group explored several promising approaches to managing high-dimensional data, with the caveat that these methods are necessarily constrained by the quality of external bioinformatic annotation.

     

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

Background

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

Methods

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

Results

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

Conclusion

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

     

Life cycle assessment of non-traditional treatments for the valorisation of dry soils in earthworks

Purpose

Sustainable development principles are leading earthwork companies to use all-natural materials extracted from the construction site to build the infrastructure. Natural materials with low characteristics must be improved. For dry soils, the common solution is to increase the compaction energy or add important quantities of water to reach the target dry density and bearing capacity. To reduce the environmental impact of their activities, the use of industrial organic products has been proposed. The aim of this study was to assess the potential benefits that could be expected from the use of these non-traditional treatments in earthworks with a well-recognised environmental impact assessment methodology.

Methods

Three non-traditional products were selected as follows: an acid solution (AS), an enzymatic solution (ES) and a calcium lignosulfonate (LS). For each of these categories, geotechnical properties such as compaction, bearing capacity, unconfined compressive strength and stiffness were first determined. Based on these results, the construction strategy for which non-traditional additives lead to greater improvement of soil properties was defined. The environmental balance of each option was then determined via a comparative process life cycle assessment study that considered ten impact categories.

Results and discussion

An experimental study showed the ability of enzymatic and lignosulfonate additives to improve soil characteristics with significant savings of water at the construction stage. The purpose of the study was also to compare the global environmental impact of each treatment strategy defined from laboratory investigations. The life cycle assessment results showed that some construction strategies lead to a significant reduction in the environmental impact compared with the reference strategy. However, these environmental improvements are strongly linked to the choice of the construction strategy and site conditions as discussed in the sensitivity analysis.

Conclusions

Within the three tested non-traditional additives, enzymatic and lignosulfonate treatments showed an association of technical and environmental interest for the compaction of dry soils. As demonstrated in the sensitivity analysis, these benefits are achieved when the production and transport steps have limited environmental impact. Thus, despite an important transportation distance for enzymatic additive, the small quantities that must be used (0.002 % by dry weight) have a limited contribution on the global environmental impact. In contrast, the production step strongly impacts the treatment with lignosulfonates. Moreover, environmental interest remains strongly dependent on the site conditions and construction strategy, which is why the adopted methodology can accurately perform an initial evaluation before implementing a soil treatment with a non-traditional product.

     

A new model for root growth in soil with macropores

Background and aims

The use of standard dynamic root architecture models to simulate root growth in soil containing macropores failed to reproduce experimentally observed root growth patterns. We thus developed a new, more mechanistic model approach for the simulation of root growth in structured soil.

Methods

In our alternative modelling approach, we distinguish between, firstly, the driving force for root growth, which is determined by the orientation of the previous root segment and the influence of gravitropism and, secondly, soil mechanical resistance to root growth. The latter is expressed by its inverse, soil mechanical conductance, and treated similarly to hydraulic conductivity in Darcy’s law. At the presence of macropores, soil mechanical conductance is anisotropic, which leads to a difference between the direction of the driving force and the direction of the root tip movement.

Results

The model was tested using data from the literature, at pot scale, at macropore scale, and in a series of simulations where sensitivity to gravity and macropore orientation was evaluated.

Conclusions

Qualitative and quantitative comparisons between simulated and experimentally observed root systems showed good agreement, suggesting that the drawn analogy between soil water flow and root growth is a useful one.

     

Differential elemental uptake in three pseudo-metallophyte C<Subscript>4</Subscript> grasses in situ in the eastern USA

Background and aims

Elemental uptake in serpentine floras in eastern North America is largely unknown. The objective of this study was to determine major and trace element concentrations in soil and leaves of three native pseudo-metallophyte C₄ grasses in situ at five sites with three very different soil types, including three serpentine sites, in eastern USA.

Methods

Pseudo-total and extractible concentrations of 15 elements were measured and correlated from the soils and leaves of three species at the five sites.

Results

Element concentrations in soils of pseudo-metallophytes varied up to five orders of magnitude. Soils from metalliferous sites exhibited higher concentrations of their characteristic elements than non-metalliferous. In metallicolous populations, elemental concentrations depended on the element. Concentrations of major elements (Ca, Mg, K) in leaves were lower than typical toxicity thresholds, whereas concentrations of Zn were higher.

Conclusions

In grasses, species can maintain relatively low metal concentrations in their leaves even when soil concentrations are richer. However, in highly Zn-contaminated soil, we found evidence of a threshold concentration above which Zn uptake increases drastically. Finally, absence of main characteristics of serpentine soil at one site indicated the importance of soil survey and restoration to maintain serpentinophytes communities and avoid soil encroachment.

     

Unimodal pattern of soil hydrophobicity along an altitudinal gradient encompassing Mediterranean,temperate, and alpine ecosystems

Background and Aims

Soil water repellency (SWR, i.e. the reduced affinity for water due to the presence of hydrophobic coatings on soil particles) has relevant hydrological implications on the rate of water infiltration, surface runoff, and overland flow. Here, we test how SWR varies along a 2490 m altitudinal gradient encompassing six ecosystems including Mediterranean, Temperate, and Alpine vegetation types.

Methods

Water repellency, measured by the Molarity of an Ethanol Droplet (MED) test, was quantified in 80 soil samples collected for 16 different elevations. Soil quality was assessed by measuring soil texture, pH, organic carbon, salinity, and nutrient availability.

Results

SWR showed a unimodal pattern along the 2490 m transect, peaking at intermediate elevations. Unexpectedly, SWR was the highest under broad-leaf deciduous forests, and the lowest under evergreen, sclerophyllous Mediterranean vegetation types. The soil organic carbon content, and the pH were the main determinants of water repellency, showing respectively a positive, and a negative correlation with the SWR. In contrast, soil texture and salinity resulted unrelated to the SWR.

Conclusions

With this study we demonstrated a linkage between SWR, vegetation type and soil pH and organic carbon content along the elevation gradient. Further studies are needed to explicitly evaluate the impact SRW on erosion risk at catchment scale in the context of climatic change.

     

Genetic variation in the TAS2R38 taste receptor contributes to the oral microbiota in North and South European locations: a pilot study

Background

Microbial communities are influenced by environmental factors including host genetics. We investigated the relationship between host bitter taste receptor genotype hTAS2R38 and oral microbiota, together with the influence of geographical location.

Methods

hTAS2R38 polymorphisms and 16S bacterial gene sequencing from oral samples were analyzed from a total of 45 healthy volunteers from different geographical locations.

Results

Genetic variation in the bitter taste receptor TAS2R38 reflected in the microbial composition of oral mucosa in Finnish and Spanish subjects. Multivariate analysis showed significant differences in the microbial composition between country and also dependent on taste genotype. Oral microbiota was shown to be more stable to the geographical location impact among AVI-homozygotes than PAV-homozygotes or heterozygotes (PAV/AVI).

Conclusion

Geographical location and genetic variation in the hTAS2R38 taste receptor impact oral mucosa microbial composition. These findings provide an advance in the knowledge regarding the interactions between taste receptor genes and oral microbiota. This study suggests the role of host-microbiota interactions on the food taste perception in food choices, nutrition, and eating behavior.

     

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

Introduction

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

Objectives

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

Methods

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

Results

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

Conclusion

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

     

Embedded rock fragments affect alpine steppe plant growth,soil carbon and nitrogen in the northern Tibetan Plateau

Background and Aims

Rock fragments within topsoil have important effects on soil properties and plant growth. This study mainly aimed to investigate the relationships between rock fragments, soil carbon (C) and nitrogen (N) densities and vegetation biomass in an alpine steppe.

Methods

Rock fragments, plant and soil samples were collected from four topographic positions (top, upper, lower, and bottom) on a hillslope.

Results

Volumetric rock fragment content within the 0–30 cm soil profile varied from 17.8 to 30.5%, the upper position value was significantly greater (P < 0.05) than those at other positions. The highest aboveground biomass was observed at the lower position (921 kg ha^?1), while the highest belowground biomass within the 0–30 cm profile was found at the upper position (4460 kg ha^?1). More fine earth and plant litter input accompanied by lower C and N losses induced by rainfall erosion resulted in higher soil organic C and total N densities (28.6 Mg C ha^?1 and 2.87 Mg N ha^?1) at the lower position.

Conclusions

Rock fragments may promote root growth but limit aboveground biomass production, and can therefore change the biomass distribution pattern. Our findings provide more evidence for scientifically assessing alpine steppe productivity.