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A survey for species of the genus Trichoderma occurring as endophytes of Coffea, and as mycoparasites of coffee rusts ( Hemileia ), was undertaken in Africa; concentrating on Cameroon and Ethiopia. Ninety-four isolates of Trichoderma were obtained during this study: 76 as endophytes of healthy leaves, stems and berries and, 18 directly from colonized rust pustules. A phylogenetic analysis of all isolates used a combination of three genes: translation elongation factor-1α ( tef1 ), rpb2 and cal for selected isolates. GCPSR criteria were used for the recognition of species; supported by morphological and cultural characters. The results reveal a previously unrecorded diversity of Trichoderma species endophytic in both wild and cultivated Coffea , and mycoparasitic on Hemileia rusts. Sixteen species were delimited, including four novel taxa which are described herein: T. botryosum , T. caeruloviride , T. lentissimum and T. pseudopyramidale . Two of these new species, T . botryosum and T . pseudopyramidale , constituted over 60% of the total isolations, predominantly from wild C . arabica in Ethiopian cloud forest. In sharp contrast, not a single isolate of Trichoderma was obtained using the same isolation protocol during a survey of coffee in four Brazilian states, suggesting the existence of a ‘ Trichoderma void’ in the endophyte mycobiota of coffee outside of Africa. The potential use of these African Trichoderma isolates in classical biological control, either as endophytic bodyguards—to protect coffee plants from Hemileia vastatrix , the fungus causing coffee leaf rust (CLR)—or to reduce its impact through mycoparasitism, is discussed, with reference to the on-going CLR crisis in Central America.

Coffee (Coffea spp.), a globally traded commodity, is a slow -growing tropical tree species that displays an improved photosynthetic performance when grown under elevated atmospheric CO2 concentrations ([CO2]). To investigate the mechanisms underlying this response, two commercial coffee cultivars (Catuaí and Obatã) were grown using the first free-air CO2 enrichment (FACE) facility in Latin America. Measurements were conducted in two contrasting growth seasons, which were characterized by the high (February) and low (August) sink demand. Elevated [CO2] led to increases in net photosynthetic rates (A) in parallel with decreased photorespiration rates, with no photochemical limitations to A. The stimulation of A by elevated CO2 supply was more prominent in August (56% on average) than in February (40% on average). Overall, the stomatal and mesophyll conductances, as well as the leaf nitrogen and phosphorus concentrations, were unresponsive to the treatments. Photosynthesis was strongly limited by diffusional constraints, particularly at the stomata level, and this pattern was little, if at all, affected by elevated [CO2]. Relative to February, starch pools (but not soluble sugars) increased remarkably (>500%) in August, with no detectable alteration in the maximum carboxylation capacity estimated on a chloroplast [CO2] basis. Upregulation of A by elevated [CO2] took place with no signs of photosynthetic downregulation, even during the period of low sink demand, when acclimation would be expected to be greatest.

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides ) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736  C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma’s D , suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.

Regional studies have shown that climate change will affect climatic suitability for Arabica coffee (Coffea arabica) within current regions of production. Increases in temperature and changes in precipitation patterns will decrease yield, reduce quality and increase pest and disease pressure. This is the first global study on the impact of climate change on suitability to grow Arabica coffee. We modeled the global distribution of Arabica coffee under changes in climatic suitability by 2050s as projected by 21 global circulation models. The results suggest decreased areas suitable for Arabica coffee in Mesoamerica at lower altitudes. In South America close to the equator higher elevations could benefit, but higher latitudes lose suitability. Coffee regions in Ethiopia and Kenya are projected to become more suitable but those in India and Vietnam to become less suitable. Globally, we predict decreases in climatic suitability at lower altitudes and high latitudes, which may shift production among the major regions that produce Arabica coffee.

Plant cells have the capacity to generate a new plant without egg fertilization by a process known as somatic embryogenesis (SE), in which differentiated somatic cells can form somatic embryos able to generate a functional plant. Although there have been advances in understanding the genetic basis of SE, the epigenetic mechanism that regulates this process is still unknown. Here, we show that the embryogenic development of Coffea canephora proceeds through a crosstalk between DNA methylation and histone modifications during the earliest embryogenic stages of SE. We found that low levels of DNA methylation, histone H3 lysine 9 dimethylation (H3K9me2) and H3K27me3 change according to embryo development. Moreover, the expression of LEAFY cotyledon1 (LEC1) and BABY BOOM1 (BBM1) are only observed after SE induction, whereas WUSCHEL-related homeobox4 (WOX4) decreases its expression during embryo maturation. Using a pharmacological approach, it was found that 5-Azacytidine strongly inhibits the embryogenic response by decreasing both DNA methylation and gene expression of LEC1 and BBM1. Therefore, in order to know whether these genes were epigenetically regulated, we used Chromatin Immunoprecipitation (ChIP) assays. It was found that WOX4 is regulated by the repressive mark H3K9me2, while LEC1 and BBM1 are epigenetically regulated by H3K27me3. We conclude that epigenetic regulation plays an important role during somatic embryogenic development, and a molecular mechanism for SE is proposed.

Abstract Due to the proximity between sugarcane and coffee areas in Brazil, studies are needed to evaluate the effect of different chemical ripeners in a possible drift scenario. Two open-area experiments were carried out to evaluate the effects of sugarcane’s sector commonly used ripeners on young coffee plants. In the first experiment, four ripeners were tested: glyphosate, sulfometuron-methyl, trinexapac-ethyl and ethephon, plus a control without application. The second experiment was conducted with increasing doses of the one that caused the greatest damage to the crop (glyphosate). Coffee growth and physiological parameters were assessed. For the first experiment, glyphosate (180 g a.e. ha-1) provided the greatest negative effects on coffee growth. The application of 250 g a.i. ha-1 of trinexapac-ethyl caused a positive effect on plant growth. Complete hormesis was observed on coffee plants, in which glyphosate doses up to 60 g a.e. ha-1 stimulated growth and higher doses caused deleterious effects. Our results shade light into the effect of sugarcane chemical ripeners in coffee plants, especially for supporting the choice of safe ripeners to be used in areas close to newly established coffee orchards. Resumo Devido à proximidade entre áreas de cana-de-açúcar e café no Brasil, estudos são necessários para avaliar o efeito de diferentes maturadores químicos em um possível cenário de deriva. Dois experimentos em área aberta foram conduzidos para avaliar os efeitos de maturadores comumente usados no setor de cana-de-açúcar em plantas jovens de café. No primeiro experimento, quatro maturadores foram testados: glifosato, sulfometurom-metílico, trinexapaque-etílico e etefon, além de uma testemunha sem aplicação. O segundo experimento foi conduzido com doses crescentes daquele que causou o maior dano à cultura (glifosato). Foram avaliados o crescimento do café e os parâmetros fisiológicos. Para o primeiro experimento, o glifosato (180 g e.a. ha-1) proporcionou os maiores efeitos negativos no crescimento do café. A aplicação de 250 g i.a. ha-1 de trinexapaque-etílico causou um efeito positivo no crescimento da planta. A hormesis completa foi observada nas plantas de café, em que doses de glifosato de até 60 g e.a. ha-1 estimularam o crescimento e doses mais altas causaram efeitos deletérios. Estes resultados esclarecem os efeitos dos maturadores químicos de cana-de-açúcar em plantas de café, especialmente para dar suporte à escolha de maturadores seguros a serem utilizados em áreas próximas a pomares de café recém-implantados.

Coffee is highly sensitive to temperature and rainfall, making its cultivation vulnerable to geographic shifts in response to a changing climate. This could lead to the establishment of coffee plantations in new areas and potential conflicts with other land covers including natural forest, with consequent implications for biodiversity and ecosystem services. We project areas suitable for future coffee cultivation based on several climate scenarios and expected responses of the coffee berry borer, a principle pest of coffee crops. We show that the global climatically-suitable area will suffer marked shifts from some current major centres of cultivation. Most areas will be suited to Robusta coffee, demand for which could be met without incurring forest encroachment. The cultivation of Arabica, which represents 70% of consumed coffee, can also be accommodated in the future, but only by incurring some natural forest loss. This has corresponding implications for carbon storage, and is likely to affect areas currently designated as priority areas for biodiversity. Where Arabica coffee does encroach on natural forests, we project average local losses of 35% of threatened vertebrate species. The interaction of climate and coffee berry borer greatly influences projected outcomes.

Wild animals substantially support crop production by providing ecosystem services, such as pollination and natural pest control. However, the strengths of synergies between ecosystem services and their dependencies on land-use management are largely unknown. Here, we took an experimental approach to test the impact of land-use intensification on both individual and combined pollination and pest control services in coffee production systems at Mount Kilimanjaro. We established a full-factorial pollinator and vertebrate exclosure experiment along a land-use gradient from traditional homegardens (agroforestry systems), shaded coffee plantations to sun coffee plantations (total sample size = 180 coffee bushes). The exclusion of vertebrates led to a reduction in fruit set of ca 9%. Pollinators did not affect fruit set, but significantly increased fruit weight of coffee by an average of 7.4%. We found no significant decline of these ecosystem services along the land-use gradient. Pest control and pollination service were thus complementary, contributing to coffee production by affecting the quantity and quality of a major tropical cash crop across different coffee production systems at Mount Kilimanjaro.

The coffee plant has high nutritional demands that are lost when the crop is harvested. Understanding the dynamics of nutrient accumulation in the entire plant and on its components during coffee maturation (beans, husk and whole berries) is essential for optimizing mineral supply at different growth stages and for better fertilizer management. To this end, this study evaluated the accumulation of dry matter, macronutrients (N, P, K, Ca, Mg, S), and micronutrients (Cu, Fe, Mn, Zn, B) in the beans, husk, and the whole berries of six Coffea canephora genotypes. Berries were sampled at the end of the grain-filling stage, i.e., 33 weeks after flowering (WAF), and then taken every 14 days over nine periods, concluding at 49 WAF. Our findings reveal that fruit maturation significantly affects nutrient concentration and accumulation in beans, husk, and the whole berries, with the highest concentration typically observed in the fully mature fruits. Nitrogen accumulation was greater in beans, while potassium accumulation was more pronounced in the husk and berries throughout the maturation process. Results allow optimizing fertilization schedules. By using targeted nutrient management practices, coffee growers can avoid over-fertilization, which often leads to environmental issues such as soil degradation and water pollution.

Cultivation of Coffea arabica is highly sensitive to and has been shown to be negatively impacted by progressive climatic changes. Previous research contributed little to support forward-looking adaptation. Agro-ecological zoning is a common tool to identify homologous environments and prioritize research. We demonstrate here a pragmatic approach to describe spatial changes in agro-climatic zones suitable for coffee under current and future climates. We defined agro-ecological zones suitable to produce arabica coffee by clustering geo-referenced coffee occurrence locations based on bio-climatic variables. We used random forest classification of climate data layers to model the spatial distribution of these agro-ecological zones. We used these zones to identify spatially explicit impact scenarios and to choose locations for the long-term evaluation of adaptation measures as climate changes. We found that in zones currently classified as hot and dry, climate change will impact arabica more than those that are better suited to it. Research in these zones should therefore focus on expanding arabica's environmental limits. Zones that currently have climates better suited for arabica will migrate upwards by about 500m in elevation. In these zones the up-slope migration will be gradual, but will likely have negative ecosystem impacts. Additionally, we identified locations that with high probability will not change their climatic characteristics and are suitable to evaluate C. arabica germplasm in the face of climate change. These locations should be used to investigate long term adaptation strategies to production systems.