Going back to the roots: the need to link plant functional biology with vadose zone processes

Soil plant atmosphere continuum concepts used in vadose zone hydrology approach plants as physical entities. This approach has proven very valuable in the past decades. The need to upscale such concepts provokes the question if plant functional biology should be considered, as larger scales also imply variation in (micro)climate and soil composition. Habitat manifestation is an expression of its evolutionary history and although the spatial distribution of habitats is largely driven by current climates, a soil's water holding capacity and hence its formation over time may have played a role. Separate mechanisms involved in the soil plant atmosphere continuum are often understood and incorporated in numerical models for predictive purposes, yet interrelationships pose challenges, especially when such relationships cross traditional scientific disciplinary boundaries. In fact, the exact driver for root water uptake is itself subject of scientific debate, as there is no consensus on whether the driver for root water uptake is soil moisture content (e.g. [1]) or soil water potential (e.g. [2]). To evaluate soil water availability in relation to crop yield prognoses and the stability of natural vegetation, integrated concepts are sorely needed, especially in the perspective of climate change [3] and global water scarcity [4]. We present considerations and possible approaches for linking plant functional biology and vadose zone processes

Spatial distribution of solute leaching with snowmelt and irrigation: measurements and simulations

Transport of a tracer and a degradable solute in a heterogeneous soil was measured in the field, and simulated with several transient and steady state infiltration rates. Leaching surfaces were used to investigate the solute leaching in space and time simultaneously. In the simulations, a random field for the scaling factor in the retention curve was used for the heterogeneous soil, which was based on the spatial distribution of drainage in an experiment with a multi-compartment sampler. As a criterion to compare the results from simulations and observations, the sorted and cumulative total drainage in a cell was used. The effect of the ratio of the infiltration rate over the degradation rate on leaching of degradable solutes was investigated. Furthermore, the spatial distribution of the leaching of degradable and non-degradable solutes was compared. The infiltration rate determines the amount of leaching of the degradable solute. This can be partly explained by a decreasing travel time with an increasing infiltration rate. The spatial distribution of the leaching also depends on the infiltration rate. When the infiltration rate is high compared to the degradation rate, the leaching of the degradable solute is similar as for the tracer. The fraction of the pore space of the soil that contributes to solute leaching increases with an increasing infiltration rate. This fraction is similar for a tracer and a degradable solute. With increasing depth, the leaching becomes more homogeneous, as a result of dispersion. The spatial distribution of the solute leaching is different under different transient infiltration rates, therefore, also the amount of leaching is different. With independent stream tube approaches, this effect would be ignored

Quantifying heterogeneous transport of a tracer and a degradable contaminant in the field, with snowmelt and irrigation

To examine the persistence of preferential flow paths in a field soil, and to compare the leaching of a degradable contaminant with the leaching of a tracer, two field experiments were performed using a multi-compartment sampler (MCS). The first experiment was carried out during the snowmelt period in early spring, characterized by high infiltration fluxes from snowmelt. The second experiment was carried out in early summer with irrigation to mimic homogeneous rainfall. During the second experiment, the soil was warmer and degradation of the degradable contaminant was observed. For both experiments, the highest tracer concentrations were found in the same area of the sampler, but the leached tracer masses of the individual locations were not highly correlated. Thus, the preferential flow paths were stable between the two experiments. With a lower infiltration rate, in the second experiment, more isolated peaks in the drainage and the leached masses were found than in the first experiment. Therefore, it is concluded that the soil heterogeneity is mainly caused by local differences in the soil hydraulic properties, and not by macropores. With higher infiltration rates, the high and low leaching cells were more clustered. The leached masses of the degradable contaminant were lower than the leached masses of the tracer, but the masses were highly correlated. The first-order degradation rate and the dispersivity were fitted with CXTFIT; the first-order degradation rate was 0.02 d-1, and the dispersivity varied between 1.9 and 7.1 cm. The persistence of the flow paths during the experiments suggests soil heterogeneity as the driver for heterogeneous flow and solute transport in this soil. At the MCS scale, heterogeneous snowmelt did not seem to have much influence on the flow and solute path

Measuring very negative water potentials with polymer tensiometers: principles, performance and applications

In recent years, a polymer tensiometer (POT) was developed and tested to directly measure matric potentials in dry soils. By extending the measurement range to wilting point (a 20-fold increase compared to conventional, water-filled tensiometers), a myriad of previously unapproachable research questions are now open to experimental exploration. Furthermore, the instrument may well allow the development of more water-efficient irrigation strategies by recording water potential rather than soil water content. The principle of the sensor is to fill it with a polymer solution instead of water, thereby building up osmotic pressure inside the sensor. A high-quality ceramic allows the exchange of water with the soil while retaining the polymer. The ceramic has pores sufficiently small to remain saturated even under very negative matric potentials. Installing the sensor in an unsaturated soil causes the high pressure of the polymer solution to drop as the water potentials in the soil and in the POT equilibrate. As long as the pressure inside the polymer chamber remains sufficiently large to prevent cavitation, the sensor will function properly. If the osmotic potential in the polymer chamber can produce a pressure of approximately 2.0 MPa when the sensor is placed in water, proper readings down to wilting point are secured. Various tests in disturbed soil, including an experiment with root water uptake, demonstrate the operation and performance of the new polymer tensiometer and illustrate how processes such as root water uptake can be studied in more detail than before. The paper discusses the available data and explores the long term perspectives offered by the instrument

Two instead of three leaves between tomato trusses: measured and simulated effects on partitioning and yield

Commercial tomato cultivars initiate three leaves between trusses. It is expected that in a cultivar with only two leaves between trusses assimilate partitioning towards the fruits and therefore yield would be favored. However, a lower number of leaves on the plant reduces leaf area index (LAI) and may therefore reduce light interception and total biomass production, affecting yield negatively. The effect of the number of leaves between trusses was investigated in a simulation study and a greenhouse experiment. In the photosynthesis-driven model TOMSIM, two leaves per truss were simulated by reducing the sink strength of each vegetative unit by 1/3. Seven fruits per truss were assumed. Reduced vegetative sink strength increased partitioning to the fruits over a whole season from 66% to 74%. However, yield increased only marginally (1.5%), as average LAI decreased from 2.4 to 1.7 m2 m2 and hence total biomass production was reduced by 9.5%. To avoid this reduction in total biomass production, the removal of old leaves was delayed by 2 weeks. This resulted in an average LAI of 2.3 m2 m2, identical total biomass production, and yield improved compared to the control with 12.8%. In the greenhouse experiment, control plants (no leaf pruning) and plants where the second leaf of each vegetative unit was weekly removed when it was only 1-3 cm long, were grown. To compensate for a decrease in LAI, pruned plants were also grown at 3.8 plants m2. All plants were pruned to 6 fruits per truss. Leaf pruning increased partitioning to the fruits, averaged over the period from 18 February to 20 May, from 57% to 61%. Average LAI was 2.9, 2.4 and 3.6 m2 m2 for control, leaf pruning and leaf pruning & increased density, respectively. Leaf pruning significantly reduced total biomass by 11% whereas fruit yield was hardly affected. Leaf pruning & increased density unexpectedly resulted in only 58% of dry matter allocated to the fruits. Increasing density increased biomass and fruit yield per m2 by 29% and 17%, respectively. It is concluded, based on simulation results and experimental data, that a tomato cultivar with 2 instead of 3 leaves between trusses would improve yield, when combined with measures to keep LAI sufficiently high

Residual N-acetyl-α-glucosaminidase activity in fibroblasts correlates with disease severity in patients with mucopolysaccharidosis type IIIB

Background: Mucopolysaccharidosis type IIIB (MPS IIIB) is a rare genetic disorder in which the deficiency of the lysosomal enzyme N-acetyl-α-glucosaminidase (NAGLU) results in the accumulation of heparan sulfate (HS), leading to progressive neurocognitive deterioration. In MPS IIIB a wide spectrum of disease severity is seen. Due to a large allelic heterogeneity, establishing genotype-phenotype correlations is difficult. However, reliable prediction of the natural course of the disease is needed, in particular for the assessment of the efficacy of potential therapies. Methods: To identify markers that correlate with disease severity, all Dutch patients diagnosed with MPS IIIB were characterised as either rapid (RP; classical, severe phenotype) or slow progressors (SP; non-classical, less severe phenotype), based on clinical data. NAGLU activity and HS levels were measured in patients’ fibroblasts after culturing at different temperatures. Results: A small, though significant difference in NAGLU activity was measured between RP and SP patients after culturing at 37 °C (p < 0.01). Culturing at 30 °C resulted in more pronounced and significantly higher NAGLU activity levels in SP patients (p < 0.001) with a NAGLU activity of 0.58 nmol.mg-1.hr-1 calculated to be the optimal cut-off value to distinguish between the groups (sensitivity and specificity 100 %). A lower capacity of patients’ fibroblasts to increase NAGLU activity at 30 °C could significantly predict for the loss of several disease specific functions. Conclusion: NAGLU activity in fibroblasts cultured at 30 °C can be used to discriminate between RP and SP MPS IIIB patients and the capacity of cells to increase NAGLU activity at lower temperatures correlates with disease symptoms

Extension of the Pompe mutation database by linking disease-associated variants to clinical severity

Pompe disease is an autosomal recessive lysosomal storage disorder caused by disease‐associated variants in the acid alpha‐glucosidase (GAA) gene. The current Pompe mutation database provides a severity rating of GAA variants based on in silico predictions and expression studies. Here, we extended the database with clinical information of reported phenotypes. We added additional in silico predictions for effects on splicing and protein function and for cross reactive immunologic material (CRIM) status, minor allele frequencies, and molecular analyses. We analyzed 867 patients and 562 GAA variants. Based on their combination with a GAA null allele (i.e., complete deficiency of GAA enzyme activity), 49% of the 422 disease‐associated variants could be linked to classic infantile, childhood, or adult phenotypes. Predictions and immunoblot analyses identified 131 CRIM negative and 216 CRIM positive variants. While disease‐associated missense variants were found throughout the GAA protein, they were enriched up to seven‐fold in the catalytic site. Fifteen percent of disease‐associated missense variants were predicted to affect splicing. This should be confirmed using splicing assays. Inclusion of clinical severity rating in the Pompe mutation database provides an invaluable tool for diagnosis, prognosis of disease progression, treatment regimens, and the future development of personalized medicine for Pompe disease

Agricultura familiar, multifuncionalidade da agricultura e ruralidade: interfaces de uma realidade complexa.

Nas últimas décadas, assistimos à revitalização do debate em torno da agricultura familiar pela incorporação das discussões sobre as múltiplas funções da agricultura num rural que não pode mais ser visto como domínio exclusivo da atividade agrícola e dos agricultores. No contexto brasileiro, acreditamos que essa discussão deva ser permeada pela análise de como processos diferenciados de distribuição fundiária e desenvolvimento econômico e o tipo de agricultura resultante geram ruralidades específicas com características como, no caso da agricultura familiar, a manutenção de práticas sociais e de trabalho marcadas pelas relações de parentesco e vizinhança presentes numa sociedade de interconhecimento. Partindo desse princípio, este trabalho analisa a agricultura familiar de um bairro rural do município de Ouro Fino - MG, sua herança histórica e sua participação na criação de uma paisagem natural e humana que muito contribui para a atratividade da região