Cacao, one of the world's most important perennial crops, is almost exclusively explored for chocolate manufacturing. Most cacao varieties belong to three groups: Criollo, Forastero and Trinitario that vary according to morphology, genetic and geographical origins. It is cropped under the shade of forest trees or as a monocrop without shade. Seedlings initially show an orthotropic growth with leaf emission relatively independent of climate. The maturity phase begins with the emission of plagiotropic branches that form the tree crown. At this stage environmental factors exert a large influence on plant development. Growth and development of cacao are highly dependent on temperature, which mainly affects vegetative growth, flowering and fruit development. Soil flooding decreases leaf area, stomatal conductance and photosynthetic rates in addition to inducing formation of lenticels and adventitious roots. For most genotypes drought resistance is associated with osmotic adjustment. Cacao produces caulescent flowers, which begin dehiscing in late afternoon and are completely open at the beginning of the following morning releasing pollen to a receptive stigma. Non pollinated flowers abscise 24-36 h after anthesis. The percentage of flowers setting pods is in the range 0.5 - 5%. The most important parameters determinants of yield are related to: (i) light interception, photosynthesis and capacity of photoassimilate distribution, (ii) maintenance respiration and (iii) pod morphology and seed fermentation, events that can be modified by abiotic factors. Cacao is a shade tolerant species, in which appropriate shading leads to relatively high photosynthetic rates, growth and seed yield. However, heavy shade reduces seed yield and increases incidence of diseases; in fact, cacao yields and light interception are tightly related when nutrient availability is not limiting. High production of non-shaded cacao requires high inputs in protection and nutrition of the crop. Annual radiation and rainfall during the dry season explains 70% of the variations in annual seed yields.

Six months-old seminal plants of 36 cacao genotypes grown under greenhouse conditions were subjected to two soil water regimes (control and drought) to assess, the effects of water deficit on growth, chemical composition and oxidative stress. In the control, soil moisture was maintained near field capacity with leaf water potentials (ΨWL) ranging from −0.1 to −0.5 MPa. In the drought treatment, the soil moisture was reduced gradually by withholding additional water until ΨWL reached values of between −2.0 to −2.5 MPa. The tolerant genotypes PS-1319, MO-20 and MA-15 recorded significant increases in guaiacol peroxidase activity reflecting a more efficient antioxidant metabolism. In relation to drought tolerance, the most important variables in the distinguishing contrasting groups were: total leaf area per plant; leaf, stem and total dry biomass; relative growth rate; plant shoot biomass and leaf content of N, Ca, and Mg. From the results of these analyses, six genotypes were selected with contrasting characteristics for tolerance to soil water deficit [CC-40, C. SUL-4 and SIC-2 (non-tolerant) and MA-15, MO-20, and PA-13 (tolerant)] for further assessment of the expression of genes NCED5, PP2C, psbA and psbO to water deficit. Increased expression of NCED5, PP2C, psbA and psbO genes were found for non-tolerant genotypes, while in the majority of tolerant genotypes there was repression of these genes, with the exception of PA-13 that showed an increased expression of psbA. Mutivariate analysis showed that growth variables, leaf and total dry biomass, relative growth rate as well as Mg content of the leaves were the most important factor in the classification of the genotypes as tolerant, moderately tolerant and sensitive to water deficit. Therefore these variables are reliable plant traits in the selection of plants tolerant to drought.

Flooding is common in lowlands and areas with high rainfall or excessive irrigation. A major effect of flooding is the deprivation of O₂ in the root zone, which affects several biochemical and morphophysiological plant processes. The objective of this study was to elucidate biochemical and physiological characteristics associated with tolerance to O₂ deficiency in two clonal cacao genotypes. The experiment was conducted in a greenhouse with two contrasting clones differing in flood tolerance: TSA-792 (tolerant) and TSH-774 (susceptible). Leaf gas exchange, chlorophyll (Chl) fluorescence, chemical composition and oxidative stress were assessed during 40 d for control and flooded plants. Flooding induced a decrease in net photosynthesis, stomatal conductance and transpiration of both genotypes. In flood conditions, the flood-susceptible clone showed changes in chlorophyll fluorescence, reductions in chlorophyll content and increased activity of peroxidase and polyphenol oxidase. Flooding also caused changes in macro- and micronutrients, total soluble sugars and starch concentrations in different plant organs of both genotypes. Response curves for the relationship between photosynthetically active radiation (PAR) and net photosynthetic rate (P _N) for flooded plants were similar for both genotypes. In flood conditions, the flood-susceptible clone exhibited (1) nonstomatal limitations to photosynthesis since decreased in maximum potential quantum yield of PSII (F_v/F_m) values indicated possible damage to the PSII light-harvesting complex; (2) oxidative stress; (3) increased leaf chlorosis; and (4) a reduction in root carbohydrate levels. These stresses resulted in death of several plants after 30 d of flooding.

High concentrations of Cd, Pb, Cu and Cr can cause harmful effects to the environment. These highly toxic pollutants constitute a risk for aquatic and terrestrial life. They are associated with diverse bioavailable geochemical fractions, like the water-soluble fraction and the exchangeable fraction, and non-available fractions like those associated with the crystalline net of clays and silica minerals. Depending upon their chemical and physical properties we can distinguish different mechanisms of metal toxicity in plants, such as production of reactive oxygen species from auto-oxidation, blocking and/or displacement of essential functional groups or metallic ions of biomolecules, changes in the permeability of cellular membranes, reactions of sulphydryl groups with cations, affinity for reactions with phosphate groups and active groups of ADP or ATP, substitution of essential ions, induction of chromosomal anomalies and decrease of the cellular division rate. However, some plant species have developed tolerance or resistance to these metals naturally. Such evolution of ecotypes is a classic example of local adaptation and microevolution, restricted to species with appropriate genetic variability. Phytoremediator woody species, with (i) high biomass production, (ii) a deep root system, (iii) high growth rate, (iv) high capacity to grow in impoverished soils, and (v) high capacity to allocate metals in the trunk, can be an alternative for the recovery of degraded soils due to excess of metallic elements. Phytoremediation using woody species presents advantageous characteristics as an economic and ecologically viable system, making it an appropriate, practical and successful technology.