A simple three-dimensional macroscopic root water uptake model based on the hydraulic architecture approach

Many hydrological models including root water uptake (RWU) do not consider the dimension of root system hydraulic architecture (HA) because explicitly solving water flow in such a complex system is too time consuming. However, they might lack process understanding when basing RWU and plant water stress predictions on functions of variables such as the root length density distribution. On the basis of analytical solutions of water flow in a simple HA, we developed an "implicit" model of the root system HA for simulation of RWU distribution (sink term of Richards' equation) and plant water stress in three-dimensional soil water flow models. The new model has three macroscopic parameters defined at the soil element scale, or at the plant scale, rather than for each segment of the root system architecture: the standard sink fraction distribution <b><i>SSF</i></b>, the root system equivalent conductance <i>K</i><sub>rs</sub> and the compensatory RWU conductance <i>K</i><sub>comp</sub>. It clearly decouples the process of water stress from compensatory RWU, and its structure is appropriate for hydraulic lift simulation. As compared to a model explicitly solving water flow in a realistic maize root system HA, the implicit model showed to be accurate for predicting RWU distribution and plant collar water potential, with one single set of parameters, in dissimilar water dynamics scenarios. For these scenarios, the computing time of the implicit model was a factor 28 to 214 shorter than that of the explicit one. We also provide a new expression for the effective soil water potential sensed by plants in soils with a heterogeneous water potential distribution, which emerged from the implicit model equations. With the proposed implicit model of the root system HA, new concepts are brought which open avenues towards simple and mechanistic RWU models and water stress functions operational for field scale water dynamics simulation

Root hairs enable high transpiration rates in drying soils

What processes facilitate the ability of roots to take up water from the soil? Are root hairs advantageous for water uptake? Despite the well documented role of root hairs in phosphate uptake, their role in water extraction is controversial and the experimental data contradictory. We proposed a novel experimental method to address this question. We grew barley (Hordeum vulgare L. cv. Pallas) and its root-hairless mutant in a pressure chamber whereby the transpiration rate could be varied while monitoring the suction in the xylem. We monitored xylem water potential as function of different transpiration rate during a drying cycle. The relationship between transpiration rate and xylem suction linearly increased in wet soils and did not differ between genotypes. The slope of this increase was equal to the plant hydraulic resistance. When the soil dried the xylem water suction rapidly increased, particularly at high transpiration rates. The root-hairless mutant showed a more marked increase in the xylem suction, indicative of a lower capacity to take up water. Interestingly, the high rise in xylem suction at high transpiration rates did not quickly decrease as the transpiration rate was reduced. To quantitatively understand the relationship between transpiration rate and xylem suction and the role of root hairs, we employed a 3D root architectural model coupled with water flow in soils. The model was parametrized based on measured root architecture and soil hydraulic properties. The role of the root hairs was simulated by extending the root radius in presence of root hairs. This implicitly simulates the ability of root hairs to take up water from their tips, potential softening the drops in water potential across the rhizosphere. The simulations predicted that that as the soil dries a bigger drop in water potential develop around the roots of the root-hairless mutant. Extension of the root radius by 0.7 mm (to simulate the uptake of root hairs) reduced the drop in water potential around the roots and softened the decrease in the xylem water potential, particularly at high transpiration rates. We conclude that the root-soil interface plays a key role in root water uptake and that root hairs reduce the gradient in water potential around the roots and enable plants to sustain high transpiration rates in drying soils

Contributions of U-Th-Pb dating on the diagenesis and sediment sources of the Lower Group (BI) of the Mbuji-Mayi Supergroup (Democratic Republic of Congo)

In this paper, we present new age constraints for the lower part of the Meso-Neoproterozoic sedimentary Mbuji-Mayi Supergroup (Democratic Republic of Congo, DRC). This Supergroup preserves a large diversity of organic-walled microfossils, evidencing the diversification of early eukaryotes for the first time in Central Africa. We use different methods such as in situ U-Pb geochronology by LA-ICP-MS and U-Th-Pb chemical datings by Electron Microprobe on diagenetic and detrital minerals such as xenotimes, monazites and zircons. We attempt to better constrain the provenance of the Mbuji-Mayi sediments and the minimum age of the Mbuji-Mayi Supergroup to constrain the age of the microfossils. Results with LA-ICP-MS and EMP provide new ages between 1030 and 1065 Ma for the diagenesis of the lower part of the sedimentary sequence. These results are consistent with data on biostratigraphy supporting the occurrence of worldwide changes at the Mesoproterozoic/Neoproterozoic boundary

Coupled root water and solute uptake - a functional structural model

Understanding the distribution and fate of solutes in the soil-plant continuum is of interest for regulatory authorities, customers and producers. For example pesticide legalization requires certain modelling and experimental studies before the substance can be released on the market. The modelling approach used in these procedures, however, does not hold detailed information about the fate of the solute in the plant root system, but treats the root system only as a linear sink term. Uptake is determined as fraction of transpiration of the concentration in the dissolved phase. With an increasing availability of more detailed modelling approaches within the last years, we focus on a more comprehensive description of pesticide uptake by plant roots. R-SWMS is a three dimensional model for water movement in soil and plant roots (1). It also includes solute transport within the roots, which is realized as a particle tracking algorithm (2). We coupled this model to Partrace, another particle tracking algorithm that solves the convection-dispersion-equation in the soil. Active or passive solute transport across the root membrane is possible. While active transport, namely Michaelis-Menten kinetics, requires energy input from the plant, passive transport can be either driven by advective water uptake and/or by the local concentration gradient between root and soil. Root membrane conductance is determined by the lipophilic properties of the solute. Within the root system solutes are transported via the advective water flux. We further implemented microbial decay and sorption to both soil and roots. Benchmarking the coupled 3D model with an analytical solution for a single root at steady state flow conditions showed a good agreement. Using this new approach we could derive global uptake parameters in silico and compare the simulation results to data from hydroponic experiments. The detailed modelling approach enables tracking solutes in time, space and phase within the soil and root system. This novel simulation tool can be used to investigate the influence of soil properties, root system architectures, solute properties, meteorological conditions as well as plant management strategies on plant solute uptake to gain a deeper understanding of solute uptake and transport parameters

Alcelaphine herpesvirus 1 genes A7 and A8 regulate viral spread and are essential for malignant catarrhal fever

Alcelaphine herpesvirus 1 (AlHV-1) is a gammaherpesvirus that is carried asymptomatically by wildebeest. Upon cross-species transmission to other ruminants, including domestic cattle, AlHV-1 induces malignant catarrhal fever (MCF), which is a fatal lymphoproliferative disease resulting from proliferation and uncontrolled activation of latently infected CD8+ T cells. Two laboratory strains of AlHV-1 are used commonly in research: C500, which is pathogenic, and WC11, which has been attenuated by long-term maintenance in cell culture. The published genome sequence of a WC11 seed stock from a German laboratory revealed the deletion of two major regions. The sequence of a WC11 seed stock used in our laboratory also bears these deletions and, in addition, the duplication of an internal sequence in the terminal region. The larger of the two deletions has resulted in the absence of gene A7 and a large portion of gene A8. These genes are positional orthologs of the Epstein-Barr virus genes encoding envelope glycoproteins gp42 and gp350, respectively, which are involved in viral propagation and switching of cell tropism. To investigate the degree to which the absence of A7 and A8 participates in WC11 attenuation, recombinant viruses lacking these individual functions were generated in C500. Using bovine nasal turbinate and embryonic lung cell lines, increased cell-free viral propagation and impaired syncytia formation were observed in the absence of A7, whereas cell-free viral spread was inhibited in the absence of A8. Therefore, A7 appears to be involved in cell-to-cell viral spread, and A8 in viral cell-free propagation. Finally, infection of rabbits with either mutant did not induce the signs of MCF or the expansion of infected CD8+ T cells. These results demonstrate that A7 and A8 are both essential for regulating viral spread and suggest that AlHV-1 requires both genes to efficiently spread in vivo and reach CD8+ T lymphocytes and induce MCF

KEYLINK: Towards a more integrative soil representation for inclusion in ecosystem scale models - II: Model description, implementation and testing

New knowledge on soil structure highlights its importance for hydrology and soil organic matter (SOM) stabilization, which however remains neglected in many wide used models. We present here a new model, KEYLINK, in which soil structure is integrated with the existing concepts on SOM pools, and elements from food web models, that is, those from direct trophic interactions among soil organisms. KEYLINK is, therefore, an attempt to integrate soil functional diversity and food webs in predictions of soil carbon (C) and soil water balances. We present a selection of equations that can be used for most models as well as basic parameter intervals, for example, key pools, functional groups' biomasses and growth rates. Parameter distributions can be determined with Bayesian calibration, and here an example is presented for food web growth rate parameters for a pine forest in Belgium. We show how these added equations can improve the functioning of the model in describing known phenomena. For this, five test cases are given as simulation examples: changing the input litter quality (recalcitrance and carbon to nitrogen ratio), excluding predators, increasing pH and changing initial soil porosity. These results overall show how KEYLINK is able to simulate the known effects of these parameters and can simulate the linked effects of biopore formation, hydrology and aggregation on soil functioning. Furthermore, the results show an important trophic cascade effect of predation on the complete C cycle with repercussions on the soil structure as ecosystem engineers are predated, and on SOM turnover when predation on fungivore and bacterivore populations are reduced. In summary, KEYLINK shows how soil functional diversity and trophic organization and their role in C and water cycling in soils should be considered in order to improve our predictions on C sequestration and C emissions from soils. © 2021 PeerJ Inc.. All rights reserved.The following grant information was disclosed by the authors: COST (European Cooperation in Science and Technology): FP1305 (BioLink) and ES1406 (KEYSOM). Short Term Scientific Mission (STSM) programs. Spanish Ministry of Science, Innovation and Universities. Spanish Ministry of Economy and Competitiveness (MINECO): IBERYCA (CGL2017-84723-P). BC3 María de Maeztu Excellence Accreditation: MDM-2017-0714. Basque Government: BERC 2018-2021. This article is based upon work from COST Actions FP1305 (BioLink) and ES1406 (KEYSOM), supported by COST (European Cooperation in Science and Technology), and their Short Term Scientific Mission (STSM) programs. Omar Flores’ work was funded by FPU PhD grant program of the Spanish Ministry of Science, Innovation and Universities. Jorge Curiel Yuste received funding from the Spanish Ministry of Economy and Competitiveness (MINECO) under projects IBERYCA (CGL2017-84723-P) and the BC3 María de Maeztu excellence accreditation (MDM-2017-0714). Jorge Curiel Yuste also received funding from the Basque Government through the BERC 2018-2021 program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

A new model for root growth in soil with macropores

Abstract: Background and aimsThe 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

Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families

Our understanding of basic evolutionary processes in bacteria is still very limited. For example, multiple recent dating estimates are based on a universal inter-species molecular clock rate, but that rate was calibrated using estimates of geological dates that are no longer accepted. We therefore estimated the short-term rates of mutation and recombination in Helicobacter pylori by sequencing an average of 39,300 bp in 78 gene fragments from 97 isolates. These isolates included 34 pairs of sequential samples, which were sampled at intervals of 0.25 to 10.2 years. They also included single isolates from 29 individuals (average age: 45 years) from 10 families. The accumulation of sequence diversity increased with time of separation in a clock-like manner in the sequential isolates. We used Approximate Bayesian Computation to estimate the rates of mutation, recombination, mean length of recombination tracts, and average diversity in those tracts. The estimates indicate that the short-term mutation rate is 1.4×10−6 (serial isolates) to 4.5×10−6 (family isolates) per nucleotide per year and that three times as many substitutions are introduced by recombination as by mutation. The long-term mutation rate over millennia is 5–17-fold lower, partly due to the removal of non-synonymous mutations due to purifying selection. Comparisons with the recent literature show that short-term mutation rates vary dramatically in different bacterial species and can span a range of several orders of magnitude