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Coffea arabica is a highly traded commodity worldwide, and its plantations are habitat to a wide range of organisms. Coffee farmers are shifting away from traditional shade coffee farms in favor of sun-intensive, higher yield farms, which can impact local biodiversity. Using plant-associated microorganisms in biofertilizers, particularly fungi collected from local forests, to increase crop yields has gained traction among coffee producers. However, the taxonomic and spatial distribution of many fungi in coffee soil, nearby forests and biofertilizers is unknown. We collected soil samples from a sun coffee system, shade coffee system, and nearby forest from Izalco, Sonsonate, El Salvador. At each coffee system, we collected soil from the surface (upper) and 10 cm below the surface (lower), and from the coffee plant drip line (drip line) and the walkway between two plants (walkway). Forest soils were collected from the surface only. We used ITS metabarcoding to characterize fungal communities in soil and in the biofertilizer (applied in both coffee systems), and assigned fungal taxa to functional guilds using FUNGuild. In the sun and shade coffee systems, we found that drip line soil had higher richness in pathotrophs, symbiotrophs, and saprotrophs than walkway soil, suggesting that fungi select for microhabitats closer to coffee plants. Upper and lower soil depths did not differ in fungal richness or composition, which may reflect the shallow root system of Coffea arabica. Soil from shade, sun, and forest had similar numbers of fungal taxa, but differed dramatically in community composition, indicating that local habitat differences drive fungal species sorting among systems. Yet, some fungal taxa were shared among systems, including seven fungal taxa present in the biofertilizer. Understanding the distribution of coffee soil mycobiomes can be used to inform sustainable, ecologically friendly farming practices and identify candidate plant-growth promoting fungi for future studies., Competing Interests: The authors have declared that no competing interests exist.

Toxicity by aluminum is a growth-limiting factor in plants cultivated in acidic soils. This metal also promotes signal transduction pathways leading to the biosynthesis of defense compounds, including secondary metabolites. In this study, we observed that Coffea arabica L. cells that were kept in the dark did not produce detectable levels of caffeine. However, irradiation with light and supplementation of the culture medium with theobromine were the best conditions for cell maintenance to investigate the role of aluminum in caffeine biosynthesis. The addition of theobromine to the cells did not cause any changes to cell growth and was useful for the bioconversion of theobromine to caffeine. During a short-term AlCl 3 -treatment (500μM) of C. arabica cells kept under light irradiation, increases in the caffeine levels in samples that were recovered from both the cells and culture media were evident. This augmentation coincided with increases in the enzyme activity of caffeine synthase (CS) and the transcript level of the gene encoding this enzyme (CS). Together, these results suggest that actions by Al and theobromine on the same pathway lead to the induction of caffeine biosynthesis., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Stomatal regulation is a key process in the physiology of Coffea arabica (C. arabica). Intrinsically linked to photosynthesis and water relations, it provides insights into the plant's adaptive capacity, survival and growth. The ability to rapidly quantify this parameter for C. arabica under different agroecological systems would be an indispensable tool. Using a Flir E6 MIR Camera, an index that is equivalent to stomatal conductance (I g ) was compared with stomatal conductance measurements (g s ) in a mature coffee plantation. In order to account for varying meteorological conditions between days, the methods were also compared under stable meteorological conditions in a laboratory and I g was also converted to absolute stomatal conductance values (g 1 ). In contrast to typical plant-thermography methods which measure indices once per day over an extended time period, we used high resolution hourly measurements over daily time series with 9 sun and 9 shade replicates. Eight daily time series showed a strong correlation between methods, while the remaining 10 were not significant. Including several other meteorological parameters in the calculation of g 1 did not contribute to any stronger correlation between methods. Total pooled data (combined daily series) resulted in a correlation of ρ=0.66 (P≤2.2e-16), indicating that our approach is particularly useful for situations where absolute values of stomatal conductance are not required, such as for comparative purposes, screening or trend analysis. We use the findings to advance the protocol for a more accurate methodology which may assist in quantifying advantageous microenvironment designs for coffee, considering the current and future climates of coffee growing regions., (Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.)

In agroforestry systems, shade trees strongly affect the physiology of the undergrown crop. However, a major paradigm is that the reduction in absorbed photosynthetically active radiation is, to a certain extent, compensated by an increase in light-use efficiency, thereby reducing the difference in net primary productivity between shaded and non-shaded plants. Due to the large spatial heterogeneity in agroforestry systems and the lack of appropriate tools, the combined effects of such variables have seldom been analysed, even though they may help understand physiological processes underlying yield dynamics. In this study, we monitored net primary productivity, during two years, on scales ranging from individual coffee plants to the entire plot. Absorbed radiation was mapped with a 3D model (MAESPA). Light-use efficiency and net assimilation rate were derived for each coffee plant individually. We found that although irradiance was reduced by 60% below crowns of shade trees, coffee light-use efficiency increased by 50%, leaving net primary productivity fairly stable across all shade levels. Variability of aboveground net primary productivity of coffee plants was caused primarily by the age of the plants and by intraspecific competition among them (drivers usually overlooked in the agroforestry literature) rather than by the presence of shade trees., (© 2017 John Wiley & Sons Ltd.)

The influence of extremely low frequency electromagnetic fields on net photosynthesis, transpiration, photosynthetic pigment concentration, and gene expression of ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit (RBCS1), during in vitro establishment, in vitro multiplication and acclimatization phases of coffee seedlings were investigated. Untreated coffee plants were considered as control, whereas treated plants were exposed to a 60 Hz sinusoidal magnetic field of 2 mT of magnetic induction during 3 min. This magnetic field was generated by an electromagnet, connected to a wave generator. The results revealed that magnetically treated plants showed a significant increase in net photosynthesis (85.4% and 117.9%, in multiplication and acclimatization phases, respectively), and in photosynthetic pigment concentration (66.6% for establishment phase, 79.9% for multiplication phase, and 43.8% for acclimatization phase). They also showed a differential RBCS1 gene expression (approximately twofold) and a decrease of transpiration rates in regard to their control plants. In conclusion, the findings suggest that the application of 60 Hz magnetic field to in vitro coffee plants may improve the seedlings quality by modifying some photosynthetic physiological and molecular processes, increasing their vigor, and ensuring better plant development in later stages., (© 2014 Wiley Periodicals, Inc.)

Coffee (Coffea arabica L.) has been traditionally considered as shade-demanding, although it performs well without shade and even out-yields shaded coffee. Here we investigated how coffee plants adjust their metabolic machinery to varying light supply and whether these adjustments are supported by a reprogramming of the primary and secondary metabolism. We demonstrate that coffee plants are able to adjust its metabolic machinery to high light conditions through marked increases in its antioxidant capacity associated with enhanced consumption of reducing equivalents. Photorespiration and alternative pathways are suggested to be key players in reductant-consumption under high light conditions. We also demonstrate that both primary and secondary metabolism undergo extensive reprogramming under high light supply, including depression of the levels of intermediates of the tricarboxylic acid cycle that were accompanied by an up-regulation of a range of amino acids, sugars and sugar alcohols, polyamines and flavonoids such as kaempferol and quercetin derivatives. When taken together, the entire dataset is consistent with these metabolic alterations being primarily associated with oxidative stress avoidance rather than representing adjustments in order to facilitate the plants from utilizing the additional light to improve their photosynthetic performance.

In this study, the combined effects of light and water availability on the functional relationships of the relative growth rate (RGR), leaf chemical composition, construction and maintenance costs, and benefits in terms of payback time for Coffea arabica are presented. Coffee plants were grown for 8 months in 100% or 15% full sunlight and then a four-month water shortage was implemented. Plants grown under full sunlight were also transferred to shade and vice versa. Overall, most of the traits assessed were much more responsive to the availability of light than to the water supply. Larger construction costs (12%), primarily associated with elevated phenol and alkaloid pools, were found under full sunlight. There was a positive correlation between these compounds and the RGR, the mass-based net carbon assimilation rate and the carbon isotope composition ratio, which, in turn, correlated negatively with the specific leaf area. The payback time was remarkably lower in the sun than in shade leaves and increased greatly in water-deprived plants. The differences in maintenance costs among the treatments were narrow, with no significant impact on the RGR, and there was no apparent trade-off in resource allocation between growth and defence. The current irradiance during leaf bud formation affected both the specific leaf area and leaf physiology upon transferring the plants from low to high light and vice versa. In summary, sun-grown plants fixed more carbon for growth and secondary metabolism, with the net effect of an increased RGR.

Based on indirect evidence, it was previously suggested that shading could attenuate the negative impacts of drought on coffee (Coffea arabica), a tropical crop species native to shady environments. A variety (47) of morphological and physiological traits were examined in plants grown in 30-l pots in either full sunlight or 85% shade for 8 months, after which a 4-month water shortage was implemented. Overall, the traits showed weak or negligible responses to the light × water interaction, explaining less than 10% of the total data variation. Only slight variations in biomass allocation were observed in the combined shade and drought treatment. Differences in relative growth rates were mainly associated with physiological and not with morphological adjustments. In high light, drought constrained the photosynthetic rate through stomatal limitations with no sign of apparent photoinhibition; in low light, such constraints were apparently linked to biochemical factors. Sun-grown plants displayed osmotic adjustments, decreased tissue elasticities and improved long-term water use efficiencies, especially under drought. Regardless of the water availability, higher concentrations of lipids, total phenols, total soluble sugars and lignin were found in high light compared to shade conditions, in contrast to the effects on cellulose and hemicellulose concentrations. Proline concentrations increased in water-deprived plants, particularly those grown under full sun. Phenotypic plasticity was much higher in response to the light than to the water supply. Overall, shading did not alleviate the negative impacts of drought on the coffee tree., (Copyright © Physiologia Plantarum 2011.)

Environmental constraints disturb plant metabolism and are often associated with photosynthetic impairments and yield reductions. Among them, low positive temperatures are of up most importance in tropical plant species, namely in Coffea spp. in which some acclimation ability has been reported. To further explain cold tolerance, the impacts on photosynthetic functioning and the expression of photosynthetic-related genes were analyzed. The experiments were carried out along a period of slow cold imposition (to allow acclimation), after chilling (4°C) exposure and in the following rewarming period, using 1.5-year-old coffee seedlings of 5 genotypes with different cold sensitivity: Coffea canephora cv. Apoatã, Coffea arabica cv. Catuaí, Coffea dewevrei and 2 hybrids, Icatu (C. arabica×C. canephora) and Piatã (C. dewevrei×C. arabica). All genotypes suffered a significant leaf area loss only after chilling exposure, with Icatu showing the lowest impact, a first indication of a higher cold tolerance, contrasting with Apoatã and C. dewevrei. During cold exposure, net photosynthesis and Chl a fluorescence parameters were strongly affected in all genotypes, but stomatal limitations were not detected. However, the extent of mesophyll limitation, reflecting regulatory mechanisms and/or damage, was genotype dependent. Overnight retention of zeaxanthin was common to Coffea genotypes, but the accumulation of photoprotective pigments was highest in Icatu. That down-regulated photochemical events but efficiently protected the photosynthetic structures, as shown, e.g., by the lowest impacts on A(max) and PSI activity and the strongest reinforcement of PSII activity, the latter possibly reflecting the presence of a photoprotective cycle around PSII in Icatu (and Catuaí). Concomitant to these protection mechanisms, Icatu was the sole genotype to present simultaneous upregulation of caCP22, caPI and caCytf, related to, respectively, PSII, PSI and to the complex Cytb(6)/f, which could promote better repair ability, contributing to the maintenance of efficient thylakoid functioning. We conclude that Icatu showed the best acclimation ability among the studied genotypes, mostly due to a better upregulation of photoprotection and repair mechanisms. We confirmed the presence of important variability in Coffea spp. that could be exploited in breeding programs, which should be assisted by useful markers of cold tolerance, namely the upregulation of antioxidative molecules, the expression of selected genes and PSI sensitivity., (Copyright © 2011 Elsevier GmbH. All rights reserved.)

Background and Aims: Using two parental clones of outcrossing Trifolium ambiguum as a potential model system, we examined how during seed development the maternal parent, number of seeds per pod, seed position within the pod, and pod position within the inflorescence influenced individual seed fresh weight, dry weight, water content, germinability, desiccation tolerance, hardseededness, and subsequent longevity of individual seeds., Methods: Near simultaneous, manual reciprocal crosses were carried out between clonal lines for two experiments. Infructescences were harvested at intervals during seed development. Each individual seed was weighed and then used to determine dry weight or one of the physiological behaviour traits., Key Results: Whilst population mass maturity was reached at 33-36 days after pollination (DAP), seed-to-seed variation in maximum seed dry weight, when it was achieved, and when maturation drying commenced, was considerable. Individual seeds acquired germinability between 14 and 44 DAP, desiccation tolerance between 30 and 40 DAP, and the capability to become hardseeded between 30 and 47 DAP. The time for viability to fall to 50 % (p(50)) at 60 % relative humidity and 45 degrees C increased between 36 and 56 DAP, when the seed coats of most individuals had become dark orange, but declined thereafter. Individual seed f. wt at harvest did not correlate with air-dry storage survival period. Analysing survival data for cohorts of seeds reduced the standard deviation of the normal distribution of seed deaths in time, but no sub-population showed complete uniformity of survival period., Conclusions: Variation in individual seed behaviours within a developing population is inherent and inevitable. In this outbreeder, there is significant variation in seed longevity which appears dependent on embryo genotype with little effect of maternal genotype or architectural factors.

Coffee berry disease (CBD), caused by Colletotrichum kahawae, is a major constraint for Arabica coffee cultivation in Africa. The disease is specific to green berries and can lead to 60% harvest losses. In Cameroon, mixed cropping systems of coffee with other crops, such as fruit trees, are very widespread agricultural practices. Fruit trees are commonly planted at random on coffee farms, providing a heterogeneous shading pattern for coffee trees growing underneath. Based on a recent study of CBD, it is known that those plants can reduce disease incidence. To assess the specific effect of shade, in situ and in vitro disease development was compared between coffee trees shaded artificially by a net and trees located in full sunlight. In the field, assessments confirmed a reduction in CBD on trees grown under shade compared with those grown in full sunlight. Artificial inoculations in the laboratory showed that shade did not have any effect on the intrinsic susceptibility of coffee berries to CBD. Coffee shading mainly acts on environmental parameters in limiting disease incidence. In addition to reducing yield losses, agroforestry system may also be helpful in reducing chemical control of the disease and in diversifying coffee growers' incomes.