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SUSTROP: SUStainable management of TROPpical resources: functional genomic innovation into the service of local communities
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Transcriptomic Analyses Reveal That Coffea arabica and Coffea canephora Have More Complex Responses under Combined Heat and Drought than under Individual Stressors
Publication . Marques, Isabel; Fernandes, Isabel; Paulo, Octávio S.; Batista, Dora; Lidon, Fernando C.; Rodrigues, Ana P.; Partelli, Fábio L.; DaMatta, Fábio M.; Ribeiro-Barros, Ana I.; Ramalho, José C.; GeoBioTec - Geobiociências, Geoengenharias e Geotecnologias; MDPI - Multidisciplinary Digital Publishing Institute
Increasing exposure to unfavorable temperatures and water deficit imposes major constraints on most crops worldwide. Despite several studies regarding coffee responses to abiotic stresses, transcriptome modulation due to simultaneous stresses remains poorly understood. This study unravels transcriptomic responses under the combined action of drought and temperature in leaves from the two most traded species: Coffea canephora cv. Conilon Clone 153 (CL153) and C. arabica cv. Icatu. Substantial transcriptomic changes were found, especially in response to the combination of stresses that cannot be explained by an additive effect. A large number of genes were involved in stress responses, with photosynthesis and other physiologically related genes usually being negatively affected. In both genotypes, genes encoding for protective proteins, such as dehydrins and heat shock proteins, were positively regulated. Transcription factors (TFs), including MADS-box genes, were down-regulated, although responses were genotype-dependent. In contrast to Icatu, only a few drought- and heat-responsive DEGs were recorded in CL153, which also reacted more significantly in terms of the number of DEGs and enriched GO terms, suggesting a high ability to cope with stresses. This research provides novel insights into the molecular mechanisms underlying leaf Coffea responses to drought and heat, revealing their influence on gene expression.
Shade and altitude implications on the physical and chemical attributes of green coffee beans from Gorongosa Mountain, Mozambique
Publication . Cassamo, Crimildo T.; Mangueze, Adilson V. J.; Leitão, António Eduardo; Pais, Isabel P.; Moreira, Rita; Campa, Claudine; Chiulele, Rogério; Reis, Fabrício O.; Marques, Isabel; Scotti-Campos, Paula; Lidon, Fernando C.; Partelli, Fábio L.; Ribeiro-Barros, Ana I.; Ramalho, José C.; NOVA School of Business and Economics (NOVA SBE); GeoBioTec - Geobiociências, Geoengenharias e Geotecnologias; MDPI - Multidisciplinary Digital Publishing Institute
Coffea arabica L. is as a tropical crop that can be grown under monocrop or agroforestry (AFS) systems, usually at altitudes greater than 600 m, with suitable environmental conditions to bean quality. This study aimed to assess the effect of altitude (650, 825, and 935 m) and light conditions (deep shade—DS, and moderate shade—MS provided by native trees, and full Sun—FS) on the physical and chemical attributes of green coffee beans produced in the Gorongosa Mountain. Regardless of altitude, light conditions (mainly MS and FS) scarcely affected most of the studied physical and chemical attributes. Among the few exceptions in physical attributes, bean mass tended to lower values under FS in all three altitudes, whereas bean density increased under FS at 650 m. As regards the chemical compound contents, sporadic changes were found. The rises in trigonelline (MS and FS at 935 m), soluble sugars (FS at 935 m), and the decline in p-coumaric acid (MS and FS at 825 m), may indicate an improved sensory profile, but the rise in FQAs (FS at 825 m) could have a negative impact. These results highlight a relevant uncertainty of the quality changes of the obtained bean. Altitude (from 650 to 935 m) extended the fruit maturation period by four weeks, and altered a larger number of bean attributes. Among physical traits, the average sieve (consistent tendency), bean commercial homogeneity, mass, and density increased at 935 m, whereas the bean became less yellowish and brighter at 825 and 935 m (b*, C* colour attributes), pointing to good bean trade quality, usually as compared with beans from 650 m. Furthermore, at 935 m trigonelline and 5-CQA (MS and FS) increased, whereas FQAs and diCQAs isomers declined (in all light conditions). Altogether, these changes likely contributed to improve the sensory cup quality. Caffeine and p-coumaric acid showed mostly inconsistent variations. Overall, light conditions (FS, MS, or DS) did not greatly and consistently altered bean physical and chemical attributes, whereas altitude (likely associated with lower temperature, greater water availability (rainfall/fog), and extended maturation period) was a major driver for bean changes and improved quality.
Irradiance level and elevation shape the soil microbiome communities of Coffea arabica L.
Publication . Tapaça, Inocência da Piedade E.; Obieze, Chinedu C.; Pereira, Gilberto V.de Melo; Fangueiro, David; Coutinho, João; Fraga, Irene; Partelli, Fábio L.; Ramalho, José C.; Marques, Isabel; Ribeiro-Barros, Ana I.; GeoBioTec - Geobiociências, Geoengenharias e Geotecnologias; Faculdade de Ciências e Tecnologia (FCT); BioMed Central (BMC)
Background: The nexus plant-microbe-environment is essential to understand the ecosystem processes shaping plant health and fitness. Within this triangle, soils and associated microflora are among the key ecosystem’s drivers, underpinning plant productivity and evolution. In this study, we conducted a comprehensive analysis (physicochemical properties, enzyme activities, and taxonomic diversity) of soils under the canopy projection of Coffea arabica trees along a gradient of elevation (600, 800, and 900 m) and shade (0, 50, 100%). Results: While shade had no influence on most parameters, altitude shaped the dynamics of microbial communities. Available phosphorus, soil organic carbon, and nitrate were significantly higher at 800 m, likely due to the higher activities of β-glucosidase and phosphatases at this altitude. Microbial biomass (carbon and nitrogen) and moisture were significantly higher at 600 and 900 m, which might be attributed to the abundance and richness of soil microorganisms. Indeed, metabarcoding analysis revealed a complex pattern of microbial consortia (bacteria, archaea, fungi) at the three altitudes, with the lowest index of richness recorded at 800 m. The highest number of Amplicon Sequence Variants was observed in bacteria, whose functional analysis revealed distinct metabolic adaptations across different altitudes. At 900 m, the main functional attributes favored the responses to environmental stimuli and microbial interactions; at 800 m, the predominant metabolic pathways were related to organic matter, fermentation, and bioremediation; and at the lower 600 m, the pathways shifted towards the breakdown of plant-derived compounds (e.g. geraniol, limonene, and pinene degradation). Conclusion: Overall, the results indicate a higher effectiveness of the microbial consortium at 800 m, which might result in better nutrient cycling. The study highlights the importance of canopy shade species and elevation for the composition of microbial consortia in C. arabica, unveiling ecological functions beyond plant health, with implications for bio-based solutions and biotechnology.
Overexpression of Water-Responsive Genes Promoted by Elevated CO2 Reduces ROS and Enhances Drought Tolerance in Coffea Species
Publication . Marques, Isabel; Fernandes, Isabel; Paulo, Octávio S.; Batista, Dora; Lidon, Fernando C.; Partelli, Fábio; DaMatta, Fábio M.; Ribeiro-Barros, Ana I.; Ramalho, José C.; GeoBioTec - Geobiociências, Geoengenharias e Geotecnologias; MDPI - Multidisciplinary Digital Publishing Institute
Drought is a major constraint to plant growth and productivity worldwide and will aggravate as water availability becomes scarcer. Although elevated air [CO2] might mitigate some of these effects in plants, the mechanisms underlying the involved responses are poorly understood in woody economically important crops such as Coffea. This study analyzed transcriptome changes in Coffea canephora cv. CL153 and C. arabica cv. Icatu exposed to moderate (MWD) or severe water deficits (SWD) and grown under ambient (aCO2) or elevated (eCO2) air [CO2]. We found that changes in expression levels and regulatory pathways were barely affected by MWD, while the SWD condition led to a down-regulation of most differentially expressed genes (DEGs). eCO2 attenuated the impacts of drought in the transcripts of both genotypes but mostly in Icatu, in agreement with physiological and metabolic studies. A predominance of protective and reactive oxygen species (ROS)-scavenging-related genes, directly or indirectly associated with ABA signaling pathways, was found in Coffea responses, including genes involved in water deprivation and desiccation, such as protein phosphatases in Icatu, and aspartic proteases and dehydrins in CL153, whose expression was validated by qRT-PCR. The existence of a complex post-transcriptional regulatory mechanism appears to occur in Coffea explaining some apparent discrepancies between transcriptomic, proteomic, and physiological data in these genotypes.
Nutrient dynamics in the berry, bean, and husk of six Coffea canephora genotypes throughout fruit maturation
Publication . Salvador, Henzo Pezzin; Vieira, Henrique Duarte; Gontijo, Ivoney; Marques, Isabel; Ramalho, José Cochicho; Partelli, Fábio Luiz; GeoBioTec - Geobiociências, Geoengenharias e Geotecnologias; Nature Publishing Group
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.
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Fundação para a Ciência e a Tecnologia
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CEEC IND4ed
Número da atribuição
2021.01107.CEECIND/CP1689/CT0001