A coffee agroecosystem model: I. Growth and development of the coffee plant

This paper is the first of three on the coffee production system consisting of (1) the coffee plant, (2) coffee berry borer (CBB) and (3) the role of CBB parasitoids. A previous simulation model of the coffee plant was developed using data from Brazil where coffee phenology is characterized by distinct seasonal flowering (Gutierrez et al., 1998). In contrast, flowering in Colombia is continuous with low seasonality. To capture the differences in coffee phenology and growth in the two climatic regions, the Gutierrez et al. (1998) model was modified using new data from Colombia.The modifications to the model include:

(1)

The effect of solar radiation on floral buds initiation;

(2)

An age structure population model to track the daily input and development of the floral buds;

(3)

The effect of leaf water potential on breaking dormancy in flower buds, and hence on the timing and intensity of flowering;

(4)

The incorporation of both the vegetative and the reproductive demands to predict the photosynthetic rate.

(5)

The effect of low temperature on photosynthesis and defoliation.

Other aspects of the model were re-interpreted and refinements made to generalize its structure for use across coffee varieties and geographic areas. The model, without modification, realistically simulates field data from Brazil and two Colombian locations having different varieties, patterns of rainfall and hence flowering phenology.The model will be used as the base trophic level for incorporating CBB and high tropic levels effects, and for the analysis of management options in the coffee production system.     

Modelling radiative balance in a row-crop canopy: Cross-row distribution of net radiation at the soil surface and energy available to clusters in a vineyard

Distribution of energy at the soil surface in a row-crop influences mainly soil temperature and water content, and therefore root activity, nitrogen mineralization and within canopy air temperature, which all affect plant physiology. In the case of a vineyard, it is also closely related to the energy available to the berries and therefore most influential for fruit quality. The aim of this study was to develop a simplified model of available energy distribution at the soil surface and at the bottom of the rows, where most of the clusters are located. Such a model would be helpful for optimising some aspects of row-crop management like training system choice, row geometry, leaf area density, and soil surface maintenance practices.The model simulated radiation balance at the soil surface, split up into downward and upward short- and long-wave fluxes. Row shadows were calculated at any point of the inter-row space, in interaction with actual row geometry and simplified porosity distribution within row volume. All hemispheric radiations (long-wave and diffuse solar radiation) were calculated according to view factors between the row and soil surfaces. Input variables were therefore incoming solar radiation over the canopy, air temperatures near the row walls and soil surface temperatures. Parameters were row geometry, dimensions and porosities.The model was validated in a 7 years old Merlot vineyard in the Médoc area, by comparing model predictions to measured net radiation (Rns) at five positions above the inter-row soil surface. Along the row sampling was achieved by a moving device carrying the net-radiometers. Structure of the vegetation was kept constant during the experiment and gap fraction parameters were derived from pictures of shadows at the soil surface. Since Rns measurements are impracticable directly at the soil surface and horizontal distribution of Rns is heterogeneous, comparison was performed by calculating net radiation at the actual measurement height which was close to average cluster height.Model prediction agreed with field measurement in most conditions, which suggests that all short- and long-wave radiation fluxes, as well as interactions with the canopy structure, were well described. Rns, energy available to clusters, and soil surface temperature variations were all mainly driven by shading due to the rows. Coupling the model to soil heat transfer and convective fluxes to the atmosphere models will help forecasting soil temperature distribution at the surface and in depth as well as canopy microclimate. The model will also be an essential part of a more elaborate model of cluster microclimate, a key determinant of berry quality.     

Resistance and re-organization of an ecosystem in response to biological invasion: Some hypotheses

Using a dynamic model of Lake Chozas developed by Marchi et al. (2011), we tested three hypotheses about recovery of the indigenous community and water quality after radical changes caused by introduction of an invasive allochthonous crayfish, Procambarus clarkii:

1.

Can the lake resist the pressure of an invasive species, like P. clarkii, by adaptation?

2.

Can the ecosystem recover when all the crayfish are removed and low phosphorus concentrations persist in inflow water?

3.

Does the simulated recovery of submerged vegetation occur at a total phosphorus concentration below 100 mg TP m⁻³, as estimated by Scheffer et al. (1993), Scheffer (1997), Jeppesen et al. (1998) and Zhang et al. (2003)?

We obtained the following answers:

1.

Lake Chozas can at least partly resist by adaptation. A combination of possible parameter changes could lead to a significant increase in eco-exergy.

2.

Removal of the phosphorus represented by crayfish (by harvesting) implies complete recovery of the lake and its eco-exergy, albeit not necessarily with the same organisms having the same properties.

3.

The expected hysteresis created by introduction and harvesting of crayfish is observed under the following conditions: phytoplankton dominance at total phosphorus ≥ about 200-250 mg TP m⁻³ and submerged vegetation returns at total phosphorus < 100 mg TP m⁻³.

     

Towards a new physical theory of biotic evolution and development

Motivated by the postulates:

(a)

Matter has complementary properties: matter waves at high mass density and information oscillations at high information density.

(b)

Biological systems are information generating systems, i.e., genome capacity to generate developmental functional complexity (phenotype).

(c)

Biological information sustains the living state.

We discuss a definite model in which the life state of an organism, for successive generations, is a generalized Schrödinger's type of system which is non-conservative, nonlinear and irreversible. Vitality, the state variable, is the genome capacity to generate developmental functional complexity (phenotype). It is a function of the phenotypic variables of biological information, i.e., matter-energy growth function, life expectancy and natality.We also discuss evolution within this model. We find that the evolution of a unicellular organism, being a process through which the life function undertakes negative damping, leads to the increase of total vitality. Total vitality is a function of the system's lifespan, bio-complexity and total matter-energy metabolized or body mass. Total vitality is quantized. The derived quantization relationship provides plausible theoretical basis for punctuated equilibrium. Total bio-information (total vitality + total natality density) is conserved. The conserved quantity describes evolution and generates ecosystem, population and organism growth dynamics. Vitality has the dimension of flow-bits. Finally, a thought experiment is proposed to falsify the hypothesis.     

Definition and calculation of uncertainty in ecological process models

We present a method of multi-criteria assessment for the analysis of process model uncertainty that combines analysis of model structure, parameters and data requirements. There are three components in calculation and definition of uncertainty.

(1)

Assessment criteria: Uncertainty in a process model is reduced as the model can simultaneously simulate an increased number of assessment criteria selected to test specific aspects of the theory being investigated, and within acceptable limits set for those criteria. This reduces incomplete specification of the model—the characteristic that a model may explain some, but not all, of the observed features of a phenomenon. The calculation required is computation of the Pareto set which provides the list of simultaneously achieved criteria within specified ranges.     

Application of a three-dimensional model for assessing effects of small clear-cuttings on radiation and soil temperature

A three-dimensional model Mixfor-3D of soil–vegetation–atmosphere transfer (SVAT) was developed and applied to estimate possible effects of tree clear-cutting on radiation and soil temperature regimes of a forest ecosystem. The Mixfor-3D model consists of several closely coupled 3D sub-models describing: forest stand structure; radiative transfer in a forest canopy; turbulent transfer of sensible heat, H₂O and CO₂ between ground surface and the atmospheric surface layer; evapotranspiration of ground surface vegetation and soil; heat and moisture transfer in soil. The model operates with the horizontal grid resolution, 2 m × 2 m; vertical resolution, 1 m and primary time step, 1 h.     

Water budget and the consequent duration of canopy carbon gain in a teak plantation in a dry tropical region: Analysis using a soil–plant–air continuum multilayer model

A soil–plant–air continuum multilayer model was used to numerically simulate canopy net assimilation (A_n), evapotranspiration (ET), and soil moisture in a deciduous teak plantation in a dry tropical climate of northern Thailand to examine the influence of soil drought on A_n. The timings of leaf flush and the end of the canopy duration period (CDP) were also investigated from the perspective of the temporal positive carbon gain. Two numerical experiments with different seasonal patterns of leaf area index (LAI) were carried out using above-canopy hydrometeorological data as input data. The first experiment involved seasonally varying LAI estimated based on time-series of radiative transmittance through the canopy, and the second experiment applied an annually constant LAI. The first simulation captured the measured seasonal changes in soil surface moisture; the simulated transpiration agreed with seasonal changes in heat pulse velocity, corresponding to the water use of individual trees, and the simulated A_n became slightly negative. However, in the second simulation, A_n became negative in the dry season because the decline in stomatal conductance due to severe soil drought limited the assimilation, and the simultaneous increase in leaf temperature increased dark respiration. Thus, these experiments revealed that the leaflessness in the dry season is reasonable for carbon gain and emphasized the unfavorable soil water status for carbon gain in the dry season. Examining the duration of positive A_n (DPA) in the second simulation showed that the start of the longest DPA (LDPA) in a year approached the timing of leaf flush in the teak plantation after the spring equinox. On the other hand, the end appeared earlier than that of all CDPs. This result is consistent with the sap flow stopping earlier than the complete leaf fall, implying that the carbon assimilation period ends before the completion of defoliation. The model sensitivity analysis in the second simulation suggests that a smaller LAI and slower maximum rate of carboxylation likely extend the LDPA because soil water from the surface to rooting depth is maintained longer at levels adequate for carbon gain by decreased canopy transpiration. The experiments also suggest that lower soil hydraulic conductivity and deeper rooting depth can postpone the end of the LDPA by increasing soil water retention and the soil water capacity, respectively.     

Photosynthetic characteristics of giant kelp (Macrocystis pyrifera) determined in situ

Rates of net photosynthesis and nocturnal respiration by individual blades of the giant kelp Macrocystis pyrifera (L.) C. Agardh in southern California, were determined in situ by measuring oxygen production in polyethylene bags during spring/summer of 1983. Mature blades from different depths in the water column exhibited different photosynthetic characteristics. Blades from the surface canopy (0 to 1 m depth) exhibited higher photosynthetic capacity under saturating irradiance and higher photosynthetic efficiency at low irradiances than blades from 3 to 5 or 7 to 9 m depths. Saturating irradiance was lower for canopy blades than for deeper blades. Canopy blades showed no short-term photoinhibition, but photosynthetic rates of deeper blades were significantly reduced during 1 to 2 h incubations at high irradiances. Results of 1 to 2 wk acclimation experiments indicated that differences between photosynthetic characteristics of blades from different depths were primarily attributable to acclimation light conditions. Vertical displacement of blades within the kelp canopy occurred on a time-scale of 1 min to 1 h. Blades continually moved between the unshaded surface layer and deeper, shaded layers. Vertical movement did not maximize photosynthesis by individual blades; only a small proportion of blades making up a dense surface canopy maintained light-saturated photosynthetic rates during midday incubations. The relatively high photosynthetic rates exhibited by canopy blades over the entire range of light conditions probably resulted from acclimation to intermittent high and low irradiances, a consequence of vertical displacement. Vertical displacement also reduced the afternoon depression in photosynthesis of individual canopy blades. The overall effect of vertical displacement was optimization of total net photosynthesis by the kelp canopy and, therefore, optimization of whole-plant production.     

Effect of solar ultra-violet radiation on the kelp Ecklonia radiata

During spring and summer, 1982–1986, experiments were carried out near Marmion Reef, Western Australia. In summer, nearly 30% of the surface solar ultraviolet radiation (280 to 400 nm) penetrates offshore waters to 5 m depth. Experimental removal of the mature Ecklonia radiata kelp canopy in summer results in tissue damage, photopigment destruction, reduced growth, and low survivorship of subcanopy kelp sporophytes. These effects do not occur with canopy removal in winter. Laboratory experiments revealed that the UV component of radiation, rather than intense photosynthetically active radiation, was responsible for the inhibition of growth and photodamage. UV radiation probably affects survival of the settlement stages of E. radiata sporophytes, thus excluding them from otherwise suitable substrata in shallow waters. UV radiation is implicated in the reduction of canopy productivity in summer.     

Sensitivity of modelled gross primary productivity to topographic effects on surface radiation: A case study in the Cotter River Catchment, Australia

Gross primary productivity (GPP) is a critical response variable for many environmental problems, including terrestrial carbon accounting and the calculation of catchment water balances. Various approaches for modelling GPP have been developed and applied at continental and landscapes scales, but little attention has been given to the sensitivity of GPP to the spatial scale of its driving variables. A key driving variable is surface radiation (R_s) which is influenced by both meso-scale factors (latitude, time of year, cloudiness) and the topographic variables of slope, aspect and horizon shading. We compared the sensitivity of modelled GPP to two different sources of surface radiation (R_s): (1) the ANUCLIM method which only captures the meso-scaled factors; and (2) the SRAD method which incorporates the topographic effects GPP was calculated using the radiation use efficiency (RUE) model (Roderick et al., 2001) to discern general patterns of vegetation productivity at a sub-catchment (i.e. sub-water shed) scale. The radiation use efficiency approach uses the normalized difference vegetation index (NDVI) derived from satellite data (MODIS TERRA), along with estimates of solar radiation at the top of the atmosphere (R_o) and canopy (R_s). In this approach, R_o and R_s capture the influence of diffuse irradiance in canopy photosynthesis and vegetation productivity respectively. This research showed that R_s calculated using the SRAD program provides important discrimination of GPP regimes at a sub-catchment scale, as the result of minimum and maximum daily radiation varying between shaded and exposed surfaces. However, mean daily radiation at a whole-of-catchment scale did not differ between the two sources as the differences in the minimum and maximum daily values tend to cancel each other out. Applications of GPP models therefore need to consider whether topographic factors are important and select the appropriate source of R_s values. GPP models should also reflect understanding of radiation use efficiency. However, further research is required especially with respect to the influence of water stress on plant response.     

RANS simulation of neutral atmospheric boundary layer flows over complex terrain by proper imposition of boundary conditions and modification on the k-ε model

In this study, a modelling methodology is proposed for RANS simulations of neutral Atmospheric Boundary Layer (ABL) flows on the basis of the standard k-ε model, which allows the adoption of an arbitrary shear stress model. This modelling methodology is first examined in the context of an open flat terrain in an empty domain to ascertain there are no substantial changes in the prescribed profiles. The results show that relatively good homogeneity can be achieved with this modelling methodology for various sets of inflow boundary profiles. In addition, to extend the solutions derived from the standard k-ε model to RNG k-ε model, the RNG k-ε model is in detail assembly and tuned. Finally, the topographic effects on surface wind speeds over a complex terrain are assessed with the combined use of the proposed methodology and the modified RNG model. The numerical results are in good agreement with wind tunnel testing results and long-term field observations. A discussion of the effects of horizontal homogeneity and turbulence models on the simulated wind flows over a complex terrain is also given.     

Ground water pollution by pesticides at the watershed‐soil catena scale: Lindane at the lower Colorado river basin (Argentina)

The movement of Lindane from application points at the surface soil towards the underground water and further transport within this compartment at the watershed‐soil catena scale, was inspected by measurements of the pesticide concentration in soil water at a controlled experiment where it was applied at a usual label dose. The concentrations of Lindane in soil water and the upper phreatic level were also measured at successive dates in samples obtained from a net of phreatimeter probes distributed over the area (1,500 km²) of the lower Colorado River basin (Bs. Aires, Argentina). The location of cultivated‐irrigated areas within the watershed was inferred from NDVI (Normalized Difference Vegetation Index)‐1 km‐10 day AVHRR images obtained at successive dates during the irrigation season. Feasible paths of underground gravitational water flows were computed by means of a GIS‐simulation model on the basis of local terrain slopes and aspects. The pattern of Lindane distribution over the basin was explained on the basis of the distribution of diffuse sources, the patterns of percolation and groundwater flows and the thermodynamic characteristics of the pesticide.     

Canopy structure versus physiology effects on net photosynthesis of mountain grasslands differing in land use

The present paper aims at investigating how changes in canopy structure and species physiology associated with the abandonment of mountain meadows and pastures affect their net photosynthesis. For this purpose, a multi-layer vegetation–atmosphere transfer (VAT) model is employed, which explicitly takes into account the structural and functional properties of the various canopy components and species. Three sites differing in land use are investigated, a meadow, a pasture and an abandoned area. Model simulations agree reasonably with measured canopy net photosynthetic rates, the meadow featuring the highest daily net photosynthesis, followed by the pasture and, finally, the abandoned area. A detailed process analysis suggests this ranking to be mainly due to bulk canopy physiology, which decreases from the meadow to the pasture and the abandoned area, reflecting species composition and species-specific photosynthetic capacities. Differences between the canopies with regard to canopy structure are found to be of minor importance. The amounts of green, photosynthetically active plant matter are too similar at the three sites to be a major source of variation in net photosynthesis. Large differences exist between the canopies with regard to the amount of photosynthetically inactive phytoelements. Even though a model analysis showed them to be potentially important, most of them are accumulated close to the ground surface, where they exert little influence on canopy net photosynthesis.     

Influence of cow-dung amendment on glyphosate mobility in soil

Abstract

Sorption and desorption characteristics of glyphosate on native soil and soil amended with cow dung were investigated. Sorption was pH dependent and decreased with increasing pH. Glyphosate partition coefficient ranged from 275 to 16,200?L kg^?1 in native soil, but for soil amended with cow dung it was significantly lower, viz 180–1530?L kg^?1. Glyphosate partition coefficient showed strong negative correlation with cation exchange capacity and positive correlation with surface area. Phosphate in cow dung suppressed glyphosate sorption and enhanced desorption. This study revealed that cow-dung addition to soil could raise the mobility of glyphosate towards groundwater contamination due to the presence of phosphate.     

Effects of changing climate on water and nitrogen availability with implications on the productivity of Norway spruce stands in Southern Finland

An integrated process-based model was used to study how the changing climate affects the availability of water and nitrogen, and consequently the dynamics of productivity of Norway spruce (Picea abies) on sites with different initial soil water conditions in southern Finland over a 100-year period. The sensitivity of the total stem volume growth in relation to short-term availability of water and nitrogen was also analyzed. We found that a high proportion (about 88–92%) of the total precipitation was lost in total evapotranspiration (incl. canopy evaporation (E_c), transpiration (E_t) and ground surface evaporation (E_g)), under both current and changing climate. Furthermore, under the changing climate the cumulative amount of E_c and E_g were significantly higher, while E_t was largely lower than under the current climate. Additionally, the elevated temperature and increased expansion of needle area index (L) enhanced E_c. Under the changing climate, the increasing soil water deficit (W_d) reduced the canopy stomatal conductance (g_cs), the E_t, humus yield (H, available nitrogen source) and nitrogen uptake (N_up) of the trees. During the latter phases of the simulation period, the canopy net photosynthesis (P_nc) was lower due to the reduced N_up and soil water availability. This also reduced the total stem volume production (V_s) on the site with the lower initial soil moisture content. The growth was slightly more sensitive to the change in precipitation than to the change in nitrogen content of the needles, when the elevated temperature was assumed. According to our findings, drought stress episodes may become more frequent under the changing climate. Thus, adaptive management strategies should be developed to sustain the productivity of Norway spruce in these conditions, and thus, to mitigate the adverse impacts of climate change.     

Influence of physico-chemical properties of soil clay fractions on the retention of dissolved organic carbon

This study investigated the effects of surface functional groups, cation exchange capacity (CEC), surface charge, sesquioxides and specific surface area (SSA) of three soil clay fractions (SCFs) (kaolinite–illite, smectite and allophane) on the retention of dissolved organic carbon (DOC) in soils. Physico-chemical properties of the SCFs before and after removing native carbon and/or sesquioxides were characterised, and the DOC adsorption–desorption tests were conducted by a batch method. Native organic carbon (OC)/sesquioxide removal treatments led to a small change in the CEC values of kaolinite–illite, but significant changes in those of smectite and allophane. The net negative surface charge increased in all samples with an increase in pH indicating their variable charge characteristics. The removal of native OC resulted in a slight increase in the net positive charge on soil clay surfaces, while sesquioxide removal increased the negative charge. Changes in the functional groups on the SCF surfaces contributed to the changes in CEC and zeta potential values. There was a strong relationship (R ² = 0.93, p < 0.05) between the Langmuir maximum DOC adsorption capacity (Q _max) and SSA. The Q _max value also showed a moderately strong relationship (R ² = 0.55, p < 0.05) with zeta potential (at pH 7). Q _max was only poorly correlated with CEC and native OC content. Therefore, along with SSA, the surface charge and functional groups of SCFs played the key role in determining the adsorption affinity and hence retention of DOC in soils.     

The use of35S to study sulphur cycling in forests

Estimates of the atmospheric deposition of sulphur compounds to forests can be made from measurements of throughfall and stemflow below the forest canopy if internal cycling of sulphur can be neglected. The use of³⁵SO4 as a tracer isotope to study movement of sulphate from the soil to the tree and subsequent leaching by rain is described, and illustrated by reference to a field experiment in a Scots pine forest. Application of 1.85 GBq of³⁵SO4 to an area of 35 m² of the forest floor resulted in measurable activity in both foliage and throughfall. Activity in foliage continued to increase through the winter after application in June. Activity in throughfall was initially high (20 Bq S mg⁻¹), then fell to a steady value (<2 Bq S mg⁻¹) from August onwards. There was good spatial correlation between activity in the canopy and in throughfall below canopy. The temporal changes showed that complete and rapid equilibration of the isotope with the pool of sulphur in the canopy could not be safely assumed. Laboratory experiments with excised shoots demonstrated a much smaller specific activity (Bq mg⁻1 S) in leached sulphate than in the whole needles. Nevertheless, leaching contributed only a small proportion (<15%) of the sulphate in net throughfall (throughfall + stemflow − rain), except during the period of needle expansion, which coincided with application of the isotope. The results suggest that the errors involved in neglecting internal cycling are of the same order as the uncertainties with which sulphur deposition in throughfall and stemflow can be measured. Such measurements may therefore be used to estimate sulphur deposition to forests with uncertainties comparable to those of current methods based on micrometeorological methods.