Gene expression profile during coffee fruit development and identification of candidate markers for phenological stages

The objective of this work was to identify genes that could be used as suitable markers for molecular recognition of phenological stages during coffee (Coffea arabica) fruit development. Four cultivars were evaluated as to their differential expression of genes associated to fruit development and maturation processes. Gene expression was characterized by both semi-quantitative and quantitative RT-PCR, in fruit harvested at seven different developmental stages, during three different seasons. No size polymorphisms or differential expression were observed among the cultivars for the evaluated genes; however, distinct expression profiles along fruit development were determined for each gene. Four out of the 28 evaluated genes exhibited a regular expression profile in all cultivars and harvest seasons, and, therefore, they were validated as candidate phenological markers of coffee fruit. The gene a-galactosidase can be used as a marker of green stage, caffeine synthase as a marker of transition to green and yellowish-green stages, and isocitrate lyase and ethylene receptor 3 as markers of late maturation.

Coffee is highly tolerant to cadmium, nickel and zinc: Plant and soil nutritional status, metal distribution and bean yield

Sewage sludge has been used to fertilize coffee, increasing the risk of metal contamination in this crop. The aim of this work was to study the effects of Cd, Zn and Ni in adult coffee plants growing under field conditions. Seven-year-old coffee plants growing in the field received one of three;loses of Cd, Zn or Ni: 15,45 and 90 g Cd plant(-1); 35, 105 and 210 g Ni plant(-1); and 100, 300 and 600 g Zn plant(-1), with all three metals in the form of sulphate salts. After three months, we noticed good penetration of the three metals into the soil, especially in the first 50 cm, which is the region where most coffee plant roots are concentrated. Leaf concentrations of K, Ca, Mg, S, B, Cu, Fe and Mn were nor affected. N levels did not change with the application of Ni or Zn but were reduced with either 45 or 90 g Cd plant(-1). Foliar P concentrations decreased with the addition of 45 and 90 g Cd plant(-1) and 600 g Zn plant(-1). Zn levels in leaves were not affected by the application of Cd or Ni. The highest concentrations. of Zn were found in branches (30-230 mg kg(-1)), leaves (7-35 mg kg(-1)) and beam (4-6.5 mg kg(-1)); Ni was found in leaves (4-45 mg kg(-1)), branches (3-18 mg kg(-1)) and beans (1-5 mg kg(-1)); and Cd was found in branches (0-6.2 mg kg(-1)) and beans (0-1.5 mg kg(-1)) but was absent in leaves. The mean yield of two harvests was not affected by Ni, but it decreased at the highest dose of Zn (600 g plant(-1)) and the two higher doses of Cd (45 and 90 g plant(-1)). Plants died when treated with the highest dose of Cd and showed symptoms of toxicity with the highest dose of Zn. Nevertheless, based on the amounts of metal used and the results obtained, we conclude that coffee plants are highly tolerant to the three metals tested. Moreover, even at high doses, there was very little transport to the beans, which is the part consumed by humans. (C) 2011 Elsevier B.V. All rights reserved.

Epiphytic orchid diversity and community composition in managed and natural moist evergreen Afromontane forest in SW Ethiopia

In SW Ethiopia, the moist evergreen Afromontane forest has become extremely fragmented and most of the remnants are intensively managed for coffee cultivation (Coffea arabica), with considerable impacts on biodiversity and ecosystem functioning. Because epiphytic orchids are potential indicators for forest quality and a proxy for overall forest biodiversity, we assessed the effect of forest management and forest fragmentation on epiphytic orchid diversity. We selected managed forest sites from both large and small forest remnants and compared their epiphytic orchid diversity with the diversity of natural unfragmented forest. We surveyed 339 canopy trees using rope climbing techniques. Orchid richness decreased and community composition changed, from the natural unfragmented forest, over the large managed forest fragments to the small managed forest fragments. This indicates that both forest management and fragmentation contribute to the loss of epiphytic orchids. Both the removal of large canopy trees typical for coffee management, and the occurrence of edge effects accompanying forest fragmentation are likely responsible for species loss and community composition changes. Even though some endangered orchid species persist even in the smallest fragments, large managed forest fragments are better options for the conservation of epiphytic orchids than small managed forests. Our results ultimately show that even though shade coffee cultivation is considered as a close-to-nature practice and is promoted as biodiversity conservation friendly, it cannot compete with the epiphytic orchid conservation benefit generated by unmanaged moist evergreen Afromontane forests.

Epiphytic orchid diversity found on trees and shrubs in coffee cultivated Afromontane rainforest, SW Ethiopia

The moist evergreen Afromontane forest of SW Ethiopia has become extremely fragmented and most remnants are intensively managed for cultivation of coffee (Coffea arabica). We investigated the distributions of epiphytic orchids in shade trees and their understory in forests with contrasting management intensity to determine biodiversity losses associated with coffee cultivation and to determine the capacity of coffee shrubs to act as refugia for orchid species. We studied epiphytic orchids in managed forests and natural forests and recorded orchid diversity and abundance in different tree zones of 339 trees and in the understory. Coffee management was associated with a downward shift of orchid species as orchid species were occurring in significantly lower tree zones in managed forest. The number of shrubs in the understory of managed forest was not higher than in natural forests, yet orchid abundance was higher in the understory of managed forests. Local extinctions of epiphytic orchids and species losses in the outer tree zones (a contraction of habitat) in managed forests are most likely driven by losses of large, complex-structured climax trees, and changes in microclimate, respectively. Coffee shrubs and their shade trees in managed forests are shown here to be a suitable habitat for only a limited set of orchid species. As farmers continue to convert natural forest into managed forest for coffee cultivation, further losses of habitat quality and collateral declines in regional epiphytic orchid diversity can be expected. Therefore, the conservation of epiphytic orchid diversity, as well as other components of diversity of the coffee forests, must primarily rely on avoiding coffee management intensification in the remaining natural forest. Convincing farmers to keep forest-climax trees in their coffee forest and to tolerate orchids on their coffee shrubs may also contribute to a more favorable conservation status of orchids in Ethiopian coffee agroecosystems.

Semivolatile and Volatile Compound Evolution during Pyrolysis and Combustion of Colombian Coffee Husk

Thermal characterization of coffee husk (Coffea arabica) from Colombian coffee has been studied. Different products, mostly volatile and semivolatile compounds, were analyzed, paying special attention to 16 polycyclic aromatic hydrocarbons (PAHs) classified by the United States Environmental Protection Agency (U.S. EPA) as priority pollutants, frequently used for checking toxicity in environmental samples. A fixed amount of raw material was exposed to different excess air ratios (λ = 0–2.33) and nominal temperature of 1123 K in a horizontal quartz reactor. The results show that coffee husk is a promising biomass for energetic exploitation with reduced formation of PAHs in a low air excess ratio. This implies reduction of carcinogenic potential in the limited presence of oxygen, demonstrated by calculating the carcinogenic potential (KE) for each experimental condition. Most volatile and semivolatile compounds followed different trends, with the oxygen presence prevailing their decomposition with increasing the air excess ratio.

Avaliação da atividade antimicrobiana das defensinas recombinantes de ervilha (drr230a) e café (cd1) produzidas em Pichia pastoris

The inefficiency of chemical pesticides to control phytopathogenic fungi in agriculture and the frequent incidence of human diseases caused by bacteria which are resistant to antibiotics lead to the search for alternative antimicrobial compounds. In this context, plant defensins are a promising tool for the control of both plant and human pathogenic agents. Plant defensins are cationic peptides of about 50 amino acid residues, rich in cysteine and whose tridimensional structure is considerably conserved among different plant species. These antimicrobial molecules represent an important innate component from plant defense response against pathogens and are expressed in various plant tissues, such as leaves, tubers, flowers, pods and seeds. The present work aimed at the evaluation of the antimicrobial activity of two plant defensins against different phytopathogenic fungi and pathogenic bacteria to humans. The defensin Drr230a, whose gene was isolated from pea (Pisum sativum), and the defensin CD1,whose gene was identified within coffee (Coffea arabica) transcriptome, were subcloned in yeast expression vector and expressed in Pichia pastoris. The gene cd1 was subcloned as two different recombinant forms: CD1tC, containing a six-histidine sequence (6xHis) at the peptide C-terminal region and CD1tN, containing 6xHis coding sequence at the N-terminal region. In the case of the defensin Drr230a, the 6xHis coding sequence was inserted only at the N-terminal region. Assays of the antimicrobial activity of the purified recombinant proteins rDrr230a and rCD1 against Phakopsora pachyrhizi, causal agent of soybean Asian rust, were performed to analyze the in vitro spore germination inhibition and disease severity caused by the fungus in planta. Both recombinant defensins were able to inhibit P. pachyrhizi uredospore germination, with no difference between the antimicrobial action of either CD1tC or CD1tN. Moreover, rDrr230a and rCD1 drastically reduced severity of soybean Asian rust, as demonstrated by in planta assays. In spite of the fact that rCD1 was not able to inhibit proliferation of the human pathogenic bacteria Staplylococcus aureus and Klebsiella pneumoniae, rCD1 was able to inhibit growth of the phytopathogenic fungus Fusarium tucumaniae, that causes soybean sudden death syndrome. The obtained results show that these plant defensins are useful candidates to be used in plant genetic engineering programs to control agriculture impacting fungal diseases.

Toxigenic fungi in coffee samples: a menace to public health

Introduction - Mycotoxin contamination was reported to occur in some food and commodities, such as coffee, particularly due to the presence of toxigenic fungi such as Aspergillus, Penicillium and Fusarium spp. Aspergilli are known to produce high levels of mycotoxins, such as ochratoxin and aflatoxin. Aspergillus ochraceus has been proposed as the major cause of ochratoxin A contamination in coffee beans. Aim of the study - The aim of this work was to evaluate the prevalence of Aspergillus sections Circumdati, Flavi and Fumigati in 28 green coffee samples to be used by Portuguese coffee industry, from Coffea arabica (Arabica coffee) and Coffea canephora (Robusta coffee) species from different origins.

Fungal contamination in coffee samples: a public health concern

Introduction - Fungi are natural coffee contaminants and under certain environmental conditions have the potential to produce toxins. Many studies revealed that the important toxigenic fungal genera (Aspergillus and Penicillium) are natural coffee contaminants, and are present from the field to storage. Aspergilli from the Circumdati and Nigri sections are known to produce high levels of ochratoxin A, a mycotoxin known as nephrotoxic for animals and humans. This work aimed to evaluate fungal distribution and also the prevalence of Aspergillus sections Fumigati, Flavi, Nigri and Circumdati from Coffea arabica (Arabica coffee) and Coffea canephora (Robusta coffee) green samples.

Fertilidad del suelo con prácticas agroecológicas y manejo convencional en el cultivo de café

Las prácticas agroecológicas en plantaciones de café ( Coffea arábica L.), son necesarias para el mantenimiento y aumento de la fertilidad de los suelos y el manejo sostenible de las plantaciones. Este estudio se realizó de junio de 2009 a enero de 2010 en el Jardín Botánico y en el Centro Experimental Campos Azules, en Masatepe, Nicaragua. El propósito fue evaluar dos prácticas agroecológicas y un manejo convencional en el cultivo de café y su influencia en la fertilidad física, química y biológica del suelo. Se utilizó un arreglo unifactorial en diseño bloques completo al azar (BCA) con tres repeticiones. Las variables fueron densidad aparente, porosidad, retención de agua, materia orgánica, nitrógeno total, carbono orgánico, pH, capacidad de intercambio catiónico y cuantificación de bacterias y hongos. No existen diferencias entre los componentes de la fertilidad física y química del suelo, sin embargo, los sistemas con prácticas agroecológicas registran mayor porosidad y retención de humedad, y menor densidad aparente; así como valores más altos de materia orgánica, capacidad de intercambio catiónico, carbono orgánico, nitrógeno total y pH. No se registra diferencia en las poblaciones de bacterias, pero sí de hongos en el período lluvioso. El rendimiento acumulado de café no difiere pero existe una tendencia en los sistemas agroecológicos al aumento. Los resultados sugieren que la implementación de prácticas agroecológicas contribuye de manera sustancial con la fertilidad global del suelo.

Climate Change or Urbanization? Impacts on a Traditional Coffee Production System in East Africa over the Last 80 Years

Global environmental changes (GEC) such as climate change (CC) and climate variability have serious impacts in the tropics, particularly in Africa. These are compounded by changes in land use/land cover, which in turn are driven mainly by economic and population growth, and urbanization. These factors create a feedback loop, which affects ecosystems and particularly ecosystem services, for example plant-insect interactions, and by consequence agricultural productivity. We studied effects of GEC at a local level, using a traditional coffee production area in greater Nairobi, Kenya. We chose coffee, the most valuable agricultural commodity worldwide, as it generates income for 100 million people, mainly in the developing world. Using the coffee berry borer, the most serious biotic threat to global coffee production, we show how environmental changes and different production systems (shaded and sun-grown coffee) can affect the crop. We combined detailed entomological assessments with historic climate records (from 1929-2011), and spatial and demographic data, to assess GEC's impact on coffee at a local scale. Additionally, we tested the utility of an adaptation strategy that is simple and easy to implement. Our results show that while interactions between CC and migration/urbanization, with its resultant landscape modifications, create a feedback loop whereby agroecosystems such as coffee are adversely affected, bio-diverse shaded coffee proved far more resilient and productive than coffee grown in monoculture, and was significantly less harmed by its insect pest. Thus, a relatively simple strategy such as shading coffee can tremendously improve resilience of agro-ecosystems, providing small-scale farmers in Africa with an easily implemented tool to safeguard their livelihoods in a changing climate.

Some Like It Hot: The Influence and Implications of Climate Change on Coffee Berry Borer (Hypothenemus hampei) and Coffee Production in East Africa

The negative effects of climate change are already evident for many of the 25 million coffee farmers across the tropics and the 90 billion dollar (US) coffee industry. The coffee berry borer (Hypothenemus hampei), the most important pest of coffee worldwide, has already benefited from the temperature rise in East Africa: increased damage to coffee crops and expansion in its distribution range have been reported. In order to anticipate threats and prioritize management actions for H. hampei we present here, maps on future distributions of H. hampei in coffee producing areas of East Africa. Using the CLIMEX model we relate present-day insect distributions to current climate and then project the fitted climatic envelopes under future scenarios A2A and B2B (for HADCM3 model). In both scenarios, the situation with H. hampei is forecasted to worsen in the current Coffea arabica producing areas of Ethiopia, the Ugandan part of the Lake Victoria and Mt. Elgon regions, Mt. Kenya and the Kenyan side of Mt. Elgon, and most of Rwanda and Burundi. The calculated hypothetical number of generations per year of H. hampei is predicted to increase in all C. arabica-producing areas from five to ten. These outcomes will have serious implications for C. arabica production and livelihoods in East Africa. We suggest that the best way to adapt to a rise of temperatures in coffee plantations could be via the introduction of shade trees in sun grown plantations. The aims of this study are to fill knowledge gaps existing in the coffee industry, and to draft an outline for the development of an adaptation strategy package for climate change on coffee production. An abstract in Spanish is provided as Abstract S1.

Sustentabilidade de uma lavoura cafeeira orgânica manejada sob sistema agroflorestal no Sul de Minas Gerais.

Diante da atual crise ecológica e econômica da cafeicultura convencional, o presente trabalho tem como objetivos analisar a produtividade, os aspectos econômicos e ambientais de um sistema agroflorestal conduzido em Machado, sul de Minas Gerais há onze anos, tendo como principais produtos o café (Coffea arabica) orgânico certificado pela BCS, que é exportado para outros países, a banana e a madeira, que também possuem certificação orgânica e são vendidos no comércio local. A metodologia da pesquisa foi baseada no DRP (Diagnóstico Rural Participativo) utilizando-se principalmente do diálogo semi-estruturado, valorizando o conhecimento empírico adquirido pelos agricultores. Ao contrário dos sistemas convencionais de produção, o sistema agroflorestal em estudo evidencia a viabilidade do modelo de produção nas dimensões produtiva, ecológica e econômica do ideal de sustentabilidade. A baixa produtividade do sistema agroflorestal cafeeiro é compensada pela venda do café no mercado internacional, pela produção e comercialização da banana, do eucalipto e obtenção de uma diversidade de alimentos saudáveis para a subsistência das famílias. A diversidade de produtos (café, banana, eucalipto) destinada à comercialização e à subsistência (frutas, milho, feijão, mandioca e arroz) possibilita um balanço econômico positivo ao agricultor, devido os baixos custos de produção do sistema agroflorestal.

Sistema agroflorestal no sul de Minas Gerais: café, frutíferas e madeireiras.

Diante da atual crise ambiental e econômica enfrentada pela agricultura moderna, o presente trabalho teve como objetivos analisar a produtividade, os aspectos econômicos e ambientais de um sistema agroflorestal conduzido em Machado, sul de Minas Gerais há onze anos, tendo como principais produtos o café (Coffea arabica) orgânico certificado pela BCS, que é exportado para outros países, a banana e o eucalipto, que também possuem certificação orgânica e são vendidos no comércio local. A metodologia da pesquisa foi baseada no DRP (Diagnóstico Rural Participativo). Ao contrário dos sistemas convencionais de produção, o sistema agroflorestal estudado evidenciou a viabilidade do modelo de produção nas dimensões produtiva, ecológica e econômica. A baixa produtividade do café no sistema agroflorestal é compensada pela venda do café no mercado internacional, pela produção e comercialização da banana, do eucalipto e obtenção de uma diversidade de alimentos saudáveis para a subsistência das famílias.

Uma ferramenta semiautomática para medição da área de lesões de Mancha Alvo em folhas de café.

Este documento apresenta uma ferramenta semiautomática que requer apenas algumas poucas interações com o usuário para medir lesões associadas com a doença mancha-alvo em folhas de café.

Alterações na flora espontânea em sistemas agroecológicos de produção de café.

2014