Bridging the Scale Gap from Leaf to Canopy in Biosphere-Atmosphere Gas and Particle Exchanges

Terrestrial ecosystems, occupying more than 25% of the Earth's surface, can serve as

`biological valves' in regulating the anthropogenic emissions of atmospheric aerosol

particles and greenhouse gases (GHGs) as responses to their surrounding environments.

While the signicance of quantifying the exchange rates of GHGs and atmospheric

aerosol particles between the terrestrial biosphere and the atmosphere is

hardly questioned in many scientic elds, the progress in improving model predictability,

data interpretation or the combination of the two remains impeded by

the lack of precise framework elucidating their dynamic transport processes over a

wide range of spatiotemporal scales. The diculty in developing prognostic modeling

tools to quantify the source or sink strength of these atmospheric substances

can be further magnied by the fact that the climate system is also sensitive to the

feedback from terrestrial ecosystems forming the so-called `feedback cycle'. Hence,

the emergent need is to reduce uncertainties when assessing this complex and dynamic

feedback cycle that is necessary to support the decisions of mitigation and

adaptation policies associated with human activities (e.g., anthropogenic emission

controls and land use managements) under current and future climate regimes.

With the goal to improve the predictions for the biosphere-atmosphere exchange

of biologically active gases and atmospheric aerosol particles, the main focus of this

dissertation is on revising and up-scaling the biotic and abiotic transport processes

from leaf to canopy scales. The validity of previous modeling studies in determining

iv

the exchange rate of gases and particles is evaluated with detailed descriptions of their

limitations. Mechanistic-based modeling approaches along with empirical studies

across dierent scales are employed to rene the mathematical descriptions of surface

conductance responsible for gas and particle exchanges as commonly adopted by all

operational models. Specically, how variation in horizontal leaf area density within

the vegetated medium, leaf size and leaf microroughness impact the aerodynamic attributes

and thereby the ultrane particle collection eciency at the leaf/branch scale

is explored using wind tunnel experiments with interpretations by a porous media

model and a scaling analysis. A multi-layered and size-resolved second-order closure

model combined with particle

uxes and concentration measurements within and

above a forest is used to explore the particle transport processes within the canopy

sub-layer and the partitioning of particle deposition onto canopy medium and forest

oor. For gases, a modeling framework accounting for the leaf-level boundary layer

eects on the stomatal pathway for gas exchange is proposed and combined with sap

ux measurements in a wind tunnel to assess how leaf-level transpiration varies with

increasing wind speed. How exogenous environmental conditions and endogenous

soil-root-stem-leaf hydraulic and eco-physiological properties impact the above- and

below-ground water dynamics in the soil-plant system and shape plant responses

to droughts is assessed by a porous media model that accommodates the transient

water

ow within the plant vascular system and is coupled with the aforementioned

leaf-level gas exchange model and soil-root interaction model. It should be noted

that tackling all aspects of potential issues causing uncertainties in forecasting the

feedback cycle between terrestrial ecosystem and the climate is unrealistic in a single

dissertation but further research questions and opportunities based on the foundation

derived from this dissertation are also brie

y discussed.

Results of the coupled atmosphere-land surface model ECHAM5-JSBACH in NetCDF format

In this study we present first results of a new model development, ECHAM5-JSBACH-wiso, where we have incorporated the stable water isotopes H218O and HDO as tracers in the hydrological cycle of the coupled atmosphere-land surface model ECHAM5-JSBACH. The ECHAM5-JSBACH-wiso model was run under present-day climate conditions at two different resolutions (T31L19, T63L31). A comparison between ECHAM5-JSBACH-wiso and ECHAM5-wiso shows that the coupling has a strong impact on the simulated temperature and soil wetness. Caused by these changes of temperature and the hydrological cycle, the d18O in precipitation also shows variations from -4 permil up to 4 permil. One of the strongest anomalies is shown over northeast Asia where, due to an increase of temperature, the d18O in precipitation increases as well. In order to analyze the sensitivity of the fractionation processes over land, we compare a set of simulations with various implementations of these processes over the land surface. The simulations allow us to distinguish between no fractionation, fractionation included in the evaporation flux (from bare soil) and also fractionation included in both evaporation and transpiration (from water transport through plants) fluxes. While the isotopic composition of the soil water may change for d18O by up to +8 permil:, the simulated d18O in precipitation shows only slight differences on the order of ±1 permil. The simulated isotopic composition of precipitation fits well with the available observations from the GNIP (Global Network of Isotopes in Precipitation) database.

Stay-green Drought Adaptation Trait Enhances Sorghum Production in Sub-tropical Australia, Central-Western India and Sub-Saharan Africa

Drought during grain filling is a common challenge for sorghum production in north-eastern Australia, central-western India, and sub-Saharan Africa. We show that the stay-green drought adaptation trait enhances sorghum grain yield under post-anthesis drought in these three regions. A positive relationship between stay-green and yield was generally found in breeding trials in north-eastern Australia that sampled 1668 unique hybrid combinations and 23 environments. Physiological studies in Australia also found that introgressing four individual stay-green (Stg1–4) quantitative trait loci (QTLs) into a senescent background reduced water demand before flowering and hence increased water supply during grain filling, resulting in higher grain yield relative to the senescent control. Studies in India found that various Stg QTLs affected both transpiration and transpiration efficiency, although these effects depended on the interaction between genetic background (S35 and R16) and individual QTLs. The yield variation unexplained by harvest index was related to transpiration efficiency in S35 (R2 = 0.29) and R16 (R2 = 0.72), and was related to total water extracted in S35 (R2 = 0.41) but not in R16. Finally, sixty-eight stay-green enriched lines were evaluated in six countries in sub-Saharan Africa during the 2013/14 season. Analysis of the data from Kenya indicates that stay-green and grain size were positively correlated at two sites: Kiboko (high yielding, r2=0.25) and Masongaleni (low yielding, r2=0.37). Together, these studies suggest that stay-green is a beneficial trait for sorghum production in the semi-arid tropics and is a consequence of traits altering the plant water budget.

More from less? – Efficient water use for macadamias

Macadamias, adapted to the fringes of subtropical rainforests of coastal, eastern Australia, are resilient to mild water stress. Even after prolonged drought, it is difficult to detect stress in commercial trees. Despite this, macadamia orchards in newer irrigated regions produce more consistent crops than those from traditional, rain-fed regions. Crop fluctuations in the latter tend to follow rainfall patterns. The benefit of irrigation in lower rainfall areas is undisputed, but there are many unanswered questions about the most efficient use of irrigation water. Water is used more efficiently when it is less readily available, causing partial stomatal closure that restricts transpiration more than it restricts photosynthesis. Limited research suggests that macadamias can withstand mild stress. In fact, water use efficiency can be increased by strategic deficit irrigation. However, macadamias are susceptible to stress during oil accumulation. There may be benefits of applying more water at critical times, less at others, and this may vary with cultivar. Currently, it is common for macadamia growers to apply about 20-40 L tree-1 day-1 of water to their orchards in winter and 70-90 L tree-1 day-1 in summer. Research reported water use at 20-30 L tree-1 day-1 during winter and 40-50 L tree-1 day-1 in summer using the Granier sap flow technique. The discrepancy between actual water use and farmer practice may be due to water loss via evaporation from the ground, deep drainage and/or greater transpiration due to luxury water consumption. More irrigation research is needed to develop efficient water use and to set practical limits for deficit irrigation management.

A Modeling Approach to Quantify the Effects of Stomatal Behavior and Mesophyll Conductance on Leaf Water Use Efficiency

Water use efficiency (WUE) is considered as a determinant of yield under stress and a component of crop drought resistance. Stomatal behavior regulates both transpiration rate and net assimilation and has been suggested to be crucial for improving crop WUE. In this work, a dynamic model was used to examine the impact of dynamic properties of stomata on WUE. The model includes sub-models of stomatal conductance dynamics, solute accumulation in the mesophyll, mesophyll water content, and water flow to the mesophyll. Using the instantaneous value of stomatal conductance, photosynthesis, and transpiration rate were simulated using a biochemical model and Penman-Monteith equation, respectively. The model was parameterized for a cucumber leaf and model outputs were evaluated using climatic data. Our simulations revealed that WUE was higher on a cloudy than a sunny day. Fast stomatal reaction to light decreased WUE during the period of increasing light (e.g., in the morning) by up to 10.2% and increased WUE during the period of decreasing light (afternoon) by up to 6.25%. Sensitivity of daily WUE to stomatal parameters and mesophyll conductance to CO2 was tested for sunny and cloudy days. Increasing mesophyll conductance to CO2 was more likely to increase WUE for all climatic conditions (up to 5.5% on the sunny day) than modifications of stomatal reaction speed to light and maximum stomatal conductance.

Pesticide bioconcentration factor estimate in apples.

This work objective was to estimate the bioconcentration factor (BCF) of thirty six pesticides used in the Brazilian integrated apple production systems (IAP), in order to select priority pesticides to be monitored in apples. A hypothetical apple orchard was assumed and the model applied was according to Paraíba (2007) [Pesticide bioconcentration modeling for fruit trees. Chemosphere (66:1468-1475)]. The model relates BCF with plant and pesticide characteristics. The octanol-water partition coefficients of pesticides and their degradation rates in the soil were used. The following plant variables were considered: growth rate, total dry biomass, daily water transpiration rate, and total volume of water necessary to produce one kg of fresh fruit per plant. The pesticide stem-water partition coefficient and the transpiration stream concentration factor were calculated using equations that relate each coefficient with the octanol-water partition coefficient. The pesticide BCF in fruits is an important indicator of the pesticide affinity to fruits, and helps to improve the integrated production systems.

Pesticide bioconcentration modelling for fruit trees.

The model presented allows simulating the pesticide concentration in fruit trees and estimating the pesticide bioconcentration factor in fruits of woody species. The model allows estimating the pesticide uptake by plants through the water transpiration stream and also the time in which maximum pesticide concentration occur in the fruits. The equation proposed presents the relationships between bioconcentration factor (BCF) and the following variables: plant water transpiration volume (Q), pesticide transpiration stream concentration factor (TSCF), pesticide stem-water partition coefficient (KWood,w), stem dry biomass (M) and pesticide dissipation rate in the soil-plant system (kEGS). The modeling started and was developed from a previous model ?Fruit Tree Model? (FTM), reported by Trapp and collaborators in 2003, to which was added the hypothesis that the pesticide degradation in the soil follows a first order kinetic equation. The model fitness was evaluated through the sensitivity analysis of the pesticide BCF values in fruits with respect to the model entry data variability.

Aspectos fisiologicos do umbuzeiro.

Realizou-se um estudo objetivando avaliar a resistencia estomatica, transpiracao e temperatura da folha do umbuzeiro (Spondias tuberosa Arr. Cam.), no seu habitat natural, no final da estacao seca e apos as primeiras chuvas. A resistencia estomatica comecou a aumentar em torno das 7 horas nos dois periodos, porem de forma mais brusca durante a seca, resultando em baixa transpiracao. Apos as primeiras chuvas, a resistencia estomatica comecou a aumentar em torno de 13 horas, quando as condicoes ambientais ainda eram favoraveis a uma grande demanda evapotranspiratoria. Estes resultados sugeram uma acentuada economia de agua pelo umbuzeiro. Nao se observaram diferencas na temperatura das folhas relativas aos dois periodos.

Estimation of water use and crop coefficients for an intensive olive orchard using sap flow measurements and modeled data

Olive tree sap flow measurements were collected in an intensive orchard near Évora, Portugal, during the irrigation seasons of 2013 and 2014, to calculate daily tree transpiration rates (T_SF). Meteorological variables were also collected to calculate reference evapotranspiration (ETo). Both data were used to assess values of basal crop coefficient (Kcb) for the period of the sap flow observations. The soil water balance model SIMDualKc was calibrated with soil, biophysical ground data and sap flow measurements collected in 2013. Validated in 2014 with collected sap flow observations, the model was used to provide estimates of dual e single crop coefficients for 2014 crop growing season. Good agreement between model simulated daily transpiration rates and those obtained with sapflow measurements was observed for 2014 (R2=0.76, RMSE=0.20 mm d-1), the year of validation, with an estimation average absolute error (AAE) of 0.20 mm d-1. Olive modeled daily actual evapotranspiration resulted in atual ETc values of 0.87, 2.05 and 0.77 mm d-1 for 2014 initial, mid- and end-season, respectively. Actual crop coefficient (Kc act) values of 0.51, 0.43 and 0.67 were also obtained for the same periods, respectively. Higher Kc values during spring (initial stage) and autumn (end-stage) were published in FAO56, varying between 0.65 for Kc ini and 0.70 for Kc end. The lower Kc mid value of 0.43 obtained for the summer (mid-season) is also inconsistent with the FAO56 expected Kc mid value of 0.70 for the period. The modeled Kc results are more consistent with the ones published by Allen & Pereira [1] for olive orchards with effective ground cover of 0.25 to 0.5, which vary between 0.40 and 0.80 for Kc ini, 0.40–0.60 for Kc mid with no active ground cover, and 0.35–0.75 for Kc end, depending on ground cover. The SIMDualKc simulation model proved to be appropriate for obtaining evapotranspiration and crop coefficient values for our intensive olive orchard in southern Portugal.

Olive water use and crop coefficients from energy balance and radiometric canopy temperatures

Biophysical and meteorological variables as well as radiometric canopy temperatures were collected in an intensive orchard near Évora, Portugal, with 28% ground cover by canopy and combined in a simplified two-source energy balance model (STSEB) to independently calculate the olive tree transpiration (T_STSEB) component of the total evapotranspiration (ETc). Sap flow observations were simultaneously taken in the same orchard allowing also for independent calculations of tree transpiration (T_SF). Model water use results were compared with water use estimates from the sap flow measurements. Good agreement was observed (R2=0.86, RMSE=0.20 mm d-1), with an estimation average absolute error (AAE) of 0.17 mm d-1. From June to August, on average olive water use were 1.92 and 1.89 mm d-1 for sap flow and STSEB model respectively, and 1.38 and 1.58 mm d-1 for the month of September. Results were also used to assess the olive basal crop coefficients (Kcb). Kcb estimates of 0.33 were obtained for sap flow and STSEB model, respectively, for June to August, and of 0.44 and 0.53 for the month of September. Basal crop coefficients were lower than the suggested FAO56 average Kcb values of 0.65 for June to August, the crop mid-season growth stage, and of 0.65 for the month of September, the end-season.

Evaluation of water use, yield and water productivity of a high-density orchard (cv. Cobrançosa) subjected to different irrigation regimes – An account of four years

The impact of different irrigation scheduling regimes on the water use, yield and water productivity from a high-density olive grove cv. Cobrançosa in southern Portugal was assessed during the irrigation seasons of 2011, 2012, 2013 and 2014. The experiments were conducted in a commercial olive orchard at the Herdade Álamo de Cima, near Évora (38o 29' 49.44'' N, 7o 45' 8.83'' W; alt. 75 m) in southern Alentejo, Portugal. The orchard was established with 10-year old Cobrançosa trees in grids of 8.0 x 4.2 m (300 trees ha-1) in the E-W direction, and experiments conducted on a shallow sandy loam Regosoil Haplic soil. From mid-May to the end of September the orchard was irrigated and three plots were subjected to one of two irrigation treatments: a control treatment A, irrigated to replace 100% ETc, a moderate deficit irrigation treatment B irrigated to 70% of ETc, and a more severe deficit irrigation treatment C that provided for approximately 50% of ETc. Daily tree transpiration rates were obtained by continuously monitoring of sap flow in representative trees per treatment. Among the irrigated treatments, water use efficiency (WUE, ratio of water used to irrigation- water applied) of treatment C was the highest, with a value of 0.89, being treatment B slightly lower, with a WUE of 0.76. Olive harvest for 2012 was an exceptional “on year”. Bearing yields showed contrasting differences within years where an “on year” was followed by an “off year”. In 2011 and 2012 treatment B yields were 41 and 50% higher than treatment C, respectively. In 2013 treatment B yield was 45% higher than yield of the fully irrigated treatment A, and treatment C showed practically the same yield than treatment A. In the “on year” of 2014 treatment B averaged 48% higher yield than treatment C. Treatment B farm irrigation water productivity (WPI-Farm, ratio of yield to water applied) was the highest among all treatments. Treatment A showed the lowest conversion efficiency of all treatments, indicating treatment B as the adequate deficit irrigation treatment for our Cobrançosa orchard

Leaf water potential and sap flow as indicators of water stress in Crimson ‘seedless’ grapevines under different irrigation strategies

Vitis vinifera L. cv. Crimson Seedless is a late season red table grape developed in 1989, with a high market value and increasingly cultivated under protected environments to extend the availability of seedless table grapes into the late fall. The purpose of this work was to evaluate leaf water potential and sap flow as indicators of water stress in Crimson Seedless vines under standard and reduced irrigation strategy, consisting of 70 % of the standard irrigation depth. Additionally, two sub-treatments were applied, consisting of normal irrigation throughout the growing season and a short irrigation induced stress period between veraison and harvest. Leaf water potential measurements coherently signaled crop-available water variations caused by different irrigation treatments, suggesting that this plant-based method can be reliably used to identify water-stress conditions. The use of sap flow density data to establish a ratio based on a reference ‘well irrigated vine’ and less irrigated vines can potentially be used to signal differences in the transpiration rates, which may be suitable for improving irrigation management strategies while preventing undesirable levels of water stress. Although all four irrigation strategies resulted in the production of quality table grapes, significant differences (p ≤ 0.05) were found in both berry weight and sugar content between the standard irrigation and reduced irrigation treatments. Reduced irrigation increased slightly the average berry size as well as sugar content and technical maturity index. The 2-week irrigation stress period had a negative effect on these parameters.

Leaf water potential and sap flow as indicators of water stress in Crimson 'seedless' grapevines under different irrigation strategies

Abstract Vitis vinifera L. cv. Crimson Seedless is a late season red table grape developed in 1989, with a high market value and increasingly cultivated under protected environments to extend the availability of seedless table grapes into the late fall. The purpose of this work was to evaluate leaf water potential and sap flow as indicators of water stress in Crimson Seedless vines under standard and reduced irrigation strategy, consisting of 70 % of the standard irrigation depth. Additionally, two sub-treatments were applied, consisting of normal irrigation throughout the growing season and a short irrigation induced stress period between veraison and harvest. Leaf water potential measurements coherently signaled crop-available water variations caused by different irrigation treatments, suggesting that this plant-based method can be reliably used to identify water-stress conditions. The use of sap flow density data to establish a ratio based on a reference ‘well irrigated vine’ and less irrigated vines can potentially be used to signal differences in the transpiration rates, which may be suitable for improving irrigation management strategies while preventing undesirable levels of water stress. Although all four irrigation strategies resulted in the production of quality table grapes, significant differences (p ≤ 0.05) were found in both berry weight and sugar content between the standard irrigation and reduced irrigation treatments. Reduced irrigation increased slightly the average berry size as well as sugar content and technical maturity index. The 2-week irrigation stress period had a negative effect on these parameters.

Linking thermal imaging to physiological indicators in Carica papaya L. under different watering regimes

Water deficit is the most limiting factor for yield and fruit-quality parameters in papaya crop (Carica papaya L.), deficit-irrigation (DI) strategies offering a feasible alternative to manage limiting water resources. When DI is applied, it is crucial to assess the physiological status of the crop in order to maintain the plant within a threshold value of water stress so as no to affect yield or fruit-quality parameters. The aim of this work was to evaluate the feasibility of thermal imaging in young papaya plants to assess the physiological status of this crop when it is subjected to different DI regimes, studying the relationships between the changes in leaf temperature (Tleaf) and in the major physiological parameters (i.e., stomatal conductance to water vapor, gs; transpiration, E; and net photosynthesis, An). The trial was conducted in a greenhouse from March to April of 2012. Plants were grown in pots and subjected to four irrigation treatments: (1) a full irrigation treatment (control), maintained at field capacity; (2) a partial root-zone drying treatment, irrigated with 50% of the total water applied to control to only one side of roots, alternating the sides every 7 days; (3) a regulated deficit irrigation (50% of the control, applied to both sides of plant); (4) and a non-irrigated treatment, in which irrigation was withheld from both sides of the split root for 14 days, followed by full irrigation until the end of the study. Significant relationships were found between Tleaf and major physiological variables such as gs, E and An. Additionally, significant relationships were found between the difference of leaf-to-air temperature (ΔTleaf–air) and gas-exchange measurements, which were used to establish the optimum range of ΔTleaf–air as a preliminary step to the crop-water monitoring and irrigation scheduling in papaya, using thermal imaging as the main source of information. According to the results, we conclude that thermal imaging is a promising technique to monitor the physiological status of papaya during drought conditions.

Cork oak transplant: A new reality? A Physiological Approach to maximize sucess rate.

Cork oak tree (Quercus suber L.), in Portugal, is considered the national tree and have special demands and legal protection when dealing with silviculture management (pruning, debarking, thinning). Being a species of slow growth, cork oak transplanting procedures can be a valuable asset either from the economic or ecological rationales to relocate trees, re-populate areas affected by high tree mortality, increase tree density to control erosion on montado ecosystems or landscape design. This study focuses the impacts and physiological responses of ten juvenile rain fed cork oak trees (with diameter at breast height between 6 and 16cm), when subjected to transplant operations. The work was conducted in a cork oak woodland experimental plot at the campus of the University of Évora (SW Portugal), during the year of 2015. Tree’s transplants were performed with a truck-mounted hydraulic spade transplanter coupled with a proposed methodology to maximize tree survival rates, addressing techniques to limit canopy transpiration and to improve root systems prior to transplant. Tree ecophysiological indicators (sap flow, leaf water potentials and stomatal conductance) were monitored comprising the periods before and after transplant operations, and water stress avoidance practices were established to promote post-transplant tree status recovery, including irrigation to match average daily accumulated sap flow. Transplant operations were considered successful when the tree's water uptake inferred from sap flow exhibited a high correlation with solar radiation and returned to its undisturbed or pre-transplant water potential gradients in the following 2 to 3 weeks. The post-transplant tree nourishment follow up included permanent sap flow measurements and identified the time elapsed after transplantation from which the tree recovers its normal transpiration thresholds and response. Our results suggest that by following the proposed methodology the sampled cork oak trees exhibited a transplant success rate of 90%.