Birds and beans: Comparing avian richness and endemism in arabica and robusta agroforests in India's Western Ghats.
ABSTRACT: Coffee is a major tropical commodity crop that can provide supplementary habitat for native wildlife. In Asia, coffee production is an increasingly important driver of landscape transformation and shifts between different coffee species is a major dimension of agroforestry trends. Yet few studies have compared the ecological impacts of conversion between different coffee species. We evaluated whether or not the two species of coffee grown globally-Coffea arabica and C. canephora (denoted "robusta")-had equivalent avian conservation value in the Western Ghats, India, where robusta production has become increasingly dominant. We found that habitat specialist and functional guild diversity was higher in arabica, and that arabica was more profitable. However, robusta farms generally supported the same or slightly higher abundances of habitat specialists and functional guilds, largely due to dense canopy and landscape-level forest cover. Farming practices, chiefly pesticide use, may affect the suitability of coffee agroforests as habitat for avian specialists, and at present, robusta farmers tended to use less pesticide. Given future projections for arabica to robusta conversion in tropical Asia, our study indicates that certification efforts should prioritize maintaining native canopy shade trees and forest cover to ensure that coffee landscapes can continue providing biodiversity benefits.
Project description:The coffee berry borer (Hypothenemus hampei) is the most damaging insect pest of global coffee production. Despite its importance, our knowledge on the insect's natural habitat, range, and wild host species remains poorly known. Using archival sources (mainly herbaria but also other museum collections), we surveyed 18,667 predominantly wild-collected herbarium specimens mostly from Africa, Madagascar, and Asia for coffee berry borer occurrence. A total of 72 incidences were confirmed for presence of the coffee berry borer, with identifications assisted by micro-CT for SEM. Of the 72 positive infestations, all were from tropical African coffee (Coffea) species, of which 32 were from wild (non-cultivated) plants. Of the 32 wild occurrences, 30 were found in C. canephora (robusta coffee), 1 in C. liberica (Liberica coffee), and 1 in C. arabica (Arabica coffee). Our herbarium survey confirms literature and anecdotal reports that the coffee berry borer is indigenous to tropical Africa, and that coffee species, and particularly robusta coffee, are important hosts. We identify the wetter type of Guineo-Congolian forest as either the preferred or exclusive native habitat of the coffee berry borer. Other than coffee, we find no evidence of other naturally occurring hosts. Characters of infestation (e.g., hole position on coffee fruits) infers a certain degree of specificity between the coffee berry borer and its host.
Project description:Green Robusta beans were subjected to pre-treatment with the aim of reducing the perceived aroma difference between Arabica and Robusta coffee. Treatment was a short soaking procedure with varying concentrations of acetic acid (up to 5%). Samples were subjected to thermal treatment (roasted) and ground to a standardised particle size distribution. Aroma compounds were evaluated by headspace analysis using solid-phase microextraction and gas chromatography-mass spectrometry. Pre-treatment significantly affected aroma formation during roasting and resulted in a modified level of pyrazines, furanic compounds and sulfur-containing compounds (p?<?0.05). Principal component analysis illustrated that the aroma profile of the pre-treated Robusta coffee was closer to the target Arabica coffee after roasting. Sensory results confirmed that the aroma of the 2% acetic acid pre-treated Robusta brew was similar to Arabica; the maximum inclusion level of Robusta coffee in a blend could be increased from 20% to 80%.
Project description:Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants. Whole chloroplast genomes can now be readily obtained for plant species using new sequencing methods, giving invaluable data for plant evolution However new annotation methods are required for the efficient analysis of this data to deliver high quality phylogenetic analyses. In this study, the two main tools for chloroplast genome annotation were compared. More consistent detection and annotation of genes were produced with GeSeq when compared to the currently used Dogma. This suggests that the annotation of most of the previously annotated chloroplast genomes should now be updated. GeSeq was applied to species related to coffee, including 16 species of the Coffea and Psilanthus genera to reconstruct the ancestral chloroplast genomes and to evaluate their phylogenetic relationships. Eight genes in the plant chloroplast pan genome (consisting of 92 genes) were always absent in the coffee species analyzed. Notably, the two main cultivated coffee species (i.e. Arabica and Robusta) did not group into the same clade and differ in their pattern of gene evolution. While Arabica coffee (Coffea arabica) belongs to the Coffea genus, Robusta coffee (Coffea canephora) is associated with the Psilanthus genus. A more extensive survey of related species is required to determine if this is a unique attribute of Robusta coffee or a more widespread feature of coffee tree species.
Project description:Caffeine is a metabolite of great economic importance, especially in coffee, where it influences the sensorial and physiological impacts of the beverage. Caffeine metabolism in the Coffea species begins with the degradation of purine nucleotides through three specific N-methyltransferases: XMT, MXMT and DXMT. A comparative analysis was performed to clarify the molecular reasons behind differences in caffeine accumulation in two Coffea species, namely Coffea arabica and Coffea canephora var. robusta. Three different genes encoding N-methyltransferase were amplified in the doubled haploid Coffea canephora: CcXMT1, CcMXMT1 and CcDXMT. Six genes were amplified in the haploid Coffea arabica: CaXMT1, CaXMT2, CaMXMT1, CaMXMT2, CaDXMT1, and CaDXMT2. A complete phylogenic analysis was performed to identify specific key amino acids defining enzymatic function for each protein identified. Furthermore, a quantitative gene-expression analysis was conducted on leaves and on maturing coffee beans, simultaneously analyzing caffeine content. In the different varieties analyzed, caffeine accumulation is higher in leaves than in the coffee bean maturation period, higher in Robusta than in Arabica. In Robusta, CcXMT1 and CcDXMT gene expressions are predominant and transcriptional activity is higher in leaves than in maturing beans, and is highly correlated to caffeine accumulation. In Arabica, the CaXMT1 expression level is high in leaves and CaDXMT2 as well to a lesser extent, while global transcriptional activity is weak during bean maturation, suggesting that the transcriptional control of caffeine-related genes differs within different organs and between Arabica and Robusta. These findings indicate that caffeine accumulation in Coffea species has been modulated by a combination of differential transcriptional regulation and genome evolution.
Project description:Aroma is one of the main characteristics of coffee specimens. Different mixtures of Arabica and Robusta coffees are usually found in the market to offer specific aroma or flavor profiles to consumers. However, the mixed samples or their proportions are not always identified in the product labels. Since the price of Arabica is much higher than that of Robusta, this lack of information is not only an economical issue but a possible fraud to consumers, besides the potential allergic reaction that these mixtures may trigger in some individuals. In this paper, two sample preparation techniques were compared before the analysis of the total volatile organic compounds (VOCs) found in Robusta, Arabica, and in the mixture from both coffee types. The comparison of the signals obtained from the analyses showed that the VOCs concentration levels obtained from the headspace (HS) analyses were clearly higher than those obtained from the pre-concentration step where an adsorbent, an active charcoal strip (ACS + HS), was used. In the second part of this study, the possibility of using the headspace gas-chromatography ion mobility spectrometry (HS-GC-IMS) for the discrimination between Arabica, Robusta, and mixed coffee samples (n = 30) was evaluated. The ion mobility sum spectrum (IMSS) obtained from the analysis of the HS was used in combination with pattern recognition techniques, namely linear discrimination analysis (LDA), as an electronic nose. The identification of individual compounds was not carried out since chromatographic information was not used. This novel approach allowed the correct discrimination (100%) of all of the samples. A characteristic fingerprint for each type of coffee for a fast and easy identification was also developed. In addition, the developed method is ecofriendly, so it is a good alternative to traditional approaches.
Project description:Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single-nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high-density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora-derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high-density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.
Project description:Temperate savannas and grasslands are globally threatened. In the Midwest United States of America (USA), for example, oak savannas persist today at a small percentage of recent historic coverage. Therefore, restoration of habitats of low and intermediate canopy cover is a landscape conservation priority that often emphasizes returning tree density to a savanna-like target value. Understanding how animal species react to such changes in vegetation structure is important for assessing the value of these restoration plans. We examined how butterfly community attributes in northwest Indiana USA, including community composition, richness, and abundance responded to a grassland-to-forest gradient of canopy cover. Butterfly community composition under intermediate canopy cover differed significantly from community composition in the most open or closed-canopy habitats. Composition of the plant community in flower was a significant predictor of three assessed attributes of the butterfly community-composition, richness, and abundance. Phenology, expressed as day-of-the-year, was also a strong predictor of these butterfly community attributes. Few butterfly species were habitat specialists as adults although canopy cover was a more important predictor of adult community composition than of richness or abundance of butterflies. Therefore, adult butterfly community differences along the canopy cover gradient were less about butterfly communities filled with habitat specialists for different canopy-defined habitats and more about gradual changes in community composition along this gradient. Overall, butterfly community richness was predicted to peak at about 34% canopy cover, butterfly abundance at about 53% canopy cover, community conservation value at about 59% canopy cover, and a combination of desirable conservation attributes-high diversity, high abundance, and high conservation value-was predicted to reach a peak of co-occurrence at about 67% canopy cover suggesting that habitats of intermediate canopy cover might be particularly effective for butterfly conservation in this region.
Project description:We report on the analysis of volatile compounds by SPME-GC-MS for individual roasted coffee beans. The aim was to understand the relative abundance and variability of volatile compounds between individual roasted coffee beans at constant roasting conditions. Twenty-five batches of Arabica and robusta species were sampled from 13 countries, and 10 single coffee beans randomly selected from each batch were individually roasted in a fluidised-bed roaster at 210?°C for 3?min. High variability (CV?=?14.0-53.3%) of 50 volatile compounds in roasted coffee was obtained within batches (10 beans per batch). Phenols and heterocyclic nitrogen compounds generally had higher intra-batch variation, while ketones were the most uniform compounds (CV?<?20%). The variation between batches was much higher, with the CV ranging from 15.6 to 179.3%. The highest variation was observed for 2,3-butanediol, 3-ethylpyridine and hexanal. It was also possible to build classification models based on geographical origin, obtaining 99.5% and 90.8% accuracy using LDA or MLR classifiers respectively, and classification between Arabica and robusta beans. These results give further insight into natural variation of coffee aroma and could be used to obtain higher quality and more consistent final products. Our results suggest that coffee volatile concentration is also influenced by other factors than simply the roasting degree, especially green coffee composition, which is in turn influenced by the coffee species, geographical origin, ripening stage and pre- and post-harvest processing.
Project description:High-field and low-field proton NMR spectroscopy were used to analyse lipophilic extracts from ground roast coffees. Using a sample preparation method that produced concentrated extracts, a small marker peak at 3.16?ppm was observed in 30 Arabica coffees of assured origin. This signal has previously been believed absent from Arabicas, and has been used as a marker for detecting adulteration with robusta. Via 2D 600?MHz NMR and LC-MS, 16-O-methylcafestol and 16-O-methylkahweol were detected for the first time in Arabica roast coffee and shown to be responsible for the marker peak. Using low-field NMR, robusta in Arabica could be detected at levels of the order of 1-2%?w/w. A surveillance study of retail purchased "100% Arabica" coffees found that 6 out of 60 samples displayed the 3.16?ppm marker signal to a degree commensurate with adulteration at levels of 3-30%?w/w.
Project description:Monitoring coffee quality as a means of detecting and preventing economically motivated fraud is an important aspect of international commerce today. Therefore, there is a compelling need for rapid high throughput validated analytical techniques such as quantitative proton nuclear magnetic resonance (NMR) spectroscopy for screening and authenticity testing. For this reason, we sought to validate an 1H NMR spectroscopic method for the routine screening of coffee for quality and authenticity. A factorial experimental design was used to investigate the influence of the NMR device, extraction time, and nature of coffee on the content of caffeine, 16-O-methylcafestol (OMC), kahweol, furfuryl alcohol, and 5-hydroxymethylfurfural (HMF) in coffee. The method was successfully validated for specificity, selectivity, sensitivity, and linearity of detector response. The proposed method produced satisfactory precision for all analytes in roasted coffee, except for kahweol in canephora (robusta) coffee. The proposed validated method may be used for routine screening of roasted coffee for quality and authenticity control (i.e., arabica/robusta discrimination), as its applicability was demonstrated during the recent OPSON VIII Europol-Interpol operation on coffee fraud control.