Find research datasets worth reusing

Figure 6. Feeding variation during ENSO phenomenon. a in Life is uncertainı eat dessert first: feeding ecology and prey-predator interactions of the coffee snake Ninia atrata

Figure 6. Feeding variation during ENSO phenomenon. a) Linear regression models that relate the number of snakes with stomach content and prey abundance at microhabitats per sampling visit (n = 32). b) t-Test comparing the abundance of snakes with stomach content (n = 314) between good and bad climate years. Box represents the interquartile range, the line across the box indicates the median, the minimal and maximal values are provided with the whiskers.

Figure 4 in Life is uncertainı eat dessert first: feeding ecology and prey-predator interactions of the coffee snake Ninia atrata

Figure 4. Patterns of food intake, fat storage, and body size between sexes. a) The density of individuals with stomach contents tends to increase constantly with the increment of the body size in males. In contrast, the number of females with stomach contents start to grow nearly when their reached size of sexual maturity (>270 mm), before it, females maintain almost the same number of individuals with stomach contents despite their increase in body size (n = 264). b) Fat body area increase with the increment of the body size, being higher in females than males (n = 170). Redline depicts sexual maturity size in females.

Figure 3 in Life is uncertainı eat dessert first: feeding ecology and prey-predator interactions of the coffee snake Ninia atrata

Figure 3. Sexual dimorphism of Ninia atrata. a) Linear regression model of weight versus snout-vent length (SVL) depicting no-significative differences between sexes (n = 425). b) ANCOVA analysis depicting that males have longer heads than females in relation to their weight (n = 170).

Figure 1 in Life is uncertainı eat dessert first: feeding ecology and prey-predator interactions of the coffee snake Ninia atrata

Figure 1. Study area. Oil palm plantation (Elaeis guineensis Jacq 1897) of PALMASOL S.A. Red polygons represent the production batches sampled. Snakes collected from batches 8, 9 and 15 were fixed to perform dissections of their digestive tracts. Snakes from the Batch 13 were employed in the mark-recapture experiments.

opencc-by-4.0May 2020View details →

Slide Cast: Coffee Lecture 2

Slide Cast: Coffee Lecture 2: Planen und Strukturieren. FDM Hildesheim.

opencc-zeroJun 2020View details →

Data from: Evaluating community effects of a keystone ant, Azteca sericeasur, on Inga micheliana leaf litter decomposition in a shaded coffee agro-ecosystem

Our research examined the effect of Azteca sericeasur, a keystone arboreal ant, on the decomposition of leaf litter of the shade tree, Inga micheliana, in coffee agro-ecosystems. This interaction is important in understanding the spatial heterogeneity in decomposition. We hypothesized that A. sericeasur could affect leaf litter decomposition by excluding other ants, which could release decomposers, like collembolans, from predation pressure. Determining the relative strengths of these interactions can illuminate the importance of A. sericeasur in decomposition and nutrient cycling processes. We assessed the ant and arthropod communities surrounding 10 pairs of trees, where each pair included one shade tree with an established A. sericeasur nest. Tuna baits were used in conjunction with pitfall traps to assess the ant and arthropod community, and litterbags with I. micheliana leaf litter were used to assess decomposition. The species richness of ants did not change in proximity to A. sericeasur nests, though the ant communities were distinct. Abundance of collembola and community composition of other invertebrates did not change with the presence of an A. sericeasur nest and there were no differences in leaf litter decomposition rates. This contradicts past studies that suggests A. sericeasur reduces species richness in its territory. We suggest that other ants may avoid A. sericeasur by moving within and beneath the leaf litter. Our results indicate there is no net effect of A. sericeasur on leaf litter decomposition.

opencc-zeroAug 2020View details →

Data from: Agroforestry coffee soils increase the insect-suppressive potential offered by entomopathogenic fungi over full-sun soils: a case proposing a "bait-survival technique"

Entomopathogenic fungi are important natural enemies of insects. However, there is little information on the insect-suppressive potential of these fungi and possible effects of farming management on this. Meanwhile, changes in natural landscapes due to agricultural intensification have caused considerable biodiversity loss and consequent decay of ecosystem services. However, the adoption of practices such as agroforestry in agroecosystems can foster abiotic and biotic conditions that conserve biodiversity, consequently restoring the provision of ecosystems services. Here, we assessed the effect of management systems (agroforestry or full-sun) on the pest-suppressive potential of entomopathogenic fungi in Brazilian coffee plantations. We used the insect-bait method coupled with survival analyses to assess the speed of kill by entomopathogenic fungi and their presence in soil samples from both farming systems. We found that insects exposed to agroforestry soils died more quickly than insects exposed to full-sun soils. Of the fungi isolated from the insect-baits, Metarhizium was found most frequently, followed by Beauveria. Meanwhile, Fusarium was frequently isolated as primary or secondary infections. We propose that the differential survival of insects is indicative of a greater suppressive potential by entomopathogenic fungi in agroforestry, and that this could be promoted by the diversified landscape, microclimatic stability and reduced soil disturbance in agroforestry systems. Furthermore, our results provide a useful demonstration of the potential use of the insect bait method to investigate pest suppressive potential through insect-bait mortality, and we term this the "bait survival technique".

opencc-by-4.0Oct 2020View details →

1D and 2D NMR spectra of coffee from 27 countries

715 green coffee samples were gathered by Almacafé S.A. (Bogotá, Colombia) between 2012 and 2014 from 27 different countries and analyzed at the Nuclear Magnetic Resonance (NMR) laboratory at Universidad del Valle (Cali, Colombia). Over 1000 methanolic coffee extracts were prepared and a total of 4563 spectra were acquired in fully automatic mode using a 400MHz NMR spectrometer (Bruker Biospin, Germany). The dataset spans the variance that could be expected for an industrial application of origin monitoring, including samples from different harvest time, collected over several years and processed by at least two distinct operators. The resulting 1D and 2D spectra can be used to develop and evaluate feature extraction methods, multivariate algorithms and automation monitoring techniques, as a dataset for teaching, or as a reference for new studies on similar samples and approach.

opencc-zeroJan 2021View details →

Temporal dynamics and biocontrol potential of a hyperparasite on coffee leaf rust across a landscape in Arabica coffee's native range

Agroforestry systems can provide habitats for rich biodiversity including multitrophic interactions, which presents opportunities to develop natural pest control. Shade coffee systems in several coffee-growing areas of the world host such unique habitats where pests and their natural enemies interact. One of the major global challenges for coffee production, coffee leaf rust caused by the fungal pathogen Hemileia vastatrix is attacked by the fungal hyperparasite, Lecanicillium lecanii. However, we lack insights in the dynamics and biocontrol potential of the hyperparasite on coffee leaf rust from landscapes in Arabica coffee's native range. To understand the temporal dynamics across landscapes and environmental drivers of the rust and hyperparasite, and the potential for biocontrol of the rust by the hyperparasite, we studied the rust and hyperparasite during the dry and wet seasons for three consecutive years at 60 sites across a gradient of coffee management in southwestern Ethiopia. We found that coffee leaf rust was more severe during the dry season, whereas the hyperparasite was more severe during the wet season in two out of three years. The rust growth rate from the wet to the dry season transition was negatively related to the hyperparasite index during the wet season, implying a potential top-down control. Coffee leaf rust was generally more severe at lower altitudes in the dry season, whereas the hyperparasite was more severe at high altitude. The rust incidence increased with management intensity, while the hyperparasite was more common under less intensive management. This study could be interesting in that it represents a landscape where Arabica coffee originated and the rust and hyperparasite might have a long co-evolutionary history. Our findings highlight the potential of the hyperparasite to suppress the rust's growth rate from the wet to dry season transition when the rust severity could otherwise be at its peak. We show that less intensively managed landscapes with dense shade levels are likely to increase hyperparasite abundance and result in an improved top-down control of the rust. However, more detailed knowledge is needed on the interaction of these species to assess its importance for reducing rust induced yield losses or the risk of rust outbreaks.

opencc-zeroJul 2019View details →

Data from: Echolocation and roosting ecology determine sensitivity of forest-dependent bats to coffee agriculture

Species differ in vulnerability to anthropogenic landuse changes. Knowledge of the mechanisms driving differential sensitivity can inform conservation strategies but is generally lacking for species-rich taxa in the tropics. The diverse bat fauna of Southeast Asia is threatened by rapid loss of forest and expanding agricultural activities, but the associations between species, traits, vulnerability to agriculture and the underlying drivers have yet to be elucidated. We studied the responses of speciose insectivorous bat assemblages to robusta coffee cultivation in Sumatra, Indonesia. We compared abundance, species richness and assemblage structures of bats between forests and coffee farms based on trapping data and evaluated the influence of vegetation complexity on assemblage composition and species-level reactions. Bat abundance and species richness were significantly lower in coffee farms than in forests. Bat assemblage structure differed between landuses, and the overall variation can be largely explained by vegetation simplification. Species sensitive to coffee agriculture were associated with more complex vegetation structure, whereas tolerant species were associated with simpler vegetation structure. Sensitive and tolerant species differed in the type, frequency, and bandwidth of echolocation calls and roost use. Species sensitive to coffee use broadband and high-pitched frequency-modulated calls, which are efficient at detecting insects in complex vegetation, and roost in plant structures that may be lost as vegetation is simplified. In contrast, tolerant species used lower-pitched constant frequency calls and roost in caves. We advocate for greater use of trait analyses in studies seeking to clarify the influence of agriculture on diverse tropical bat faunas.

opencc-zeroDec 2017View details →

Data from: Responses of aerial insectivorous bats to local and landscape-level features of coffee agroforestry systems in Western Ghats, India

Shade coffee has shown great promise in providing crucial habitats for biodiversity outside formal protected areas. Insectivorous bats have been understudied in coffee, although they may provide pest control services. We investigated the influence of local and landscape-level features of coffee farms on aerial insectivorous bats in Chikmagalur district in the Western Ghats biodiversity hotspot, India. Bats were monitored in 20 farm sites using ultrasound detectors, and the response of bat species richness and activity to changes in tree density, proportion of built-up area in the neighborhood, and distance of farm from forest areas quantified. We examined if models built to explain the species richness and activity could also predict them in nine additional sites. We detected nine phonic types/species in the study area. The quantified predictors had no effect on assemblage-level species richness and activity of bats. Responses of edge-space and cluttered-space forager guilds mirrored those of the overall assemblage, but some species vulnerable to forest conversion like *Rhinolophus beddomei* were detected rarely. Best models explained up to 20% and 15% variation in assemblage-level species richness and activity respectively, and were poor predictors of both response variables. We conclude that coffee farms in our study area offer an important commuting space for insectivorous bats across a gradient of shade management. Further research should include species-specific responses to management decisions for at-risk species and quantification of ecosystem services like natural pest control to inform biodiversity conservation initiatives in the Western Ghats coffee landscapes.

opencc-zeroDec 2017View details →

Data from: Simplification of shade tree diversity reduces nutrient cycling resilience in coffee agroforestry

1. Agroforestry systems are refuges for biodiversity and provide multiple ecosystem functions and services. Diverse multispecies shade tree canopies are increasingly replaced by monospecific shade, often dominated by non-native tree species. The loss of tree diversity and the nature of the dominating tree can have strong implications for ecosystem functions, e.g. nutrient cycling ultimately reducing crop production. 2. To understand direct and indirect impacts of shade trees on nutrient cycling and crop production, we studied coffee agroforestry systems in India along a gradient from native multispecies canopies to Grevillea robusta (Proteaceae) -dominated canopy cover. We identified 25 agroforests, across a broad rainfall and management gradient and assessed litter quantity and quality, decomposition, nutrient release, soil fertility and coffee nutrient limitations. 3. Increasing G. robusta dominance affected nutrient cycling predominantly by; (1) changing of litter phenology, (2) reducing phosphorus (P), potassium (K), magnesium (Mg), boron (B), and zinc (Zn) inputs via litterfall, decelerated litter decomposition and immobilization of P and Zn due to low quality litter, (3) reducing soil carbon (C) and micronutrients (especially sulphur (S), Mg and B). Coffee plants were deficient in several nutrients (nitrogen (N), calcium (Ca), manganese (Mn), Mg and S in organic and B in conventional management). (4) Overall G. robusta dominated agroforests were characterized by a reduction of P cycling due to low inputs, strong immobilization while decomposition and antagonistic effects on its release in litter mixtures with coffee. 4. Synthesis and applications. The conversion of shade cover in coffee agroforestry systems from diverse tree canopies to canopies dominated by Grevillea robusta (Proteaceae) reduces the inputs and cycling of several micro- and macronutrients. Soil fertility is therefore expected to decline in G. robusta dominated systems, with likely impacts on coffee production. These negative effects might increase under the longer dry periods projected by regional climate change scenarios due to the pronounced litter phenology of G. robusta. Maintaining diverse shade canopies can more effectively sustain micro- and macronutrients in a more seasonal climate.

opencc-zeroDec 2012View details →

Data from: The impact of climate change on the potential distribution of agricultural pests: the case of the coffee white stem borer (Monochamus leuconotus P.) in Zimbabwe

The production of agricultural commodities faces increased risk of pests, diseases and other stresses due to climate change and variability. This study assesses the potential distribution of agricultural pests under projected climatic scenarios using evidence from the African coffee white stem borer (CWB), Monochamus leuconotus (Pascoe) (Coleoptera: Cerambycidae), an important pest of coffee in Zimbabwe. A species distribution modeling approach utilising Boosted Regression Trees (BRT) and Generalized Linear Models (GLM) was applied on current and projected climate data obtained from the WorldClim database and occurrence data (presence and absence) collected through on-farm biological surveys in Chipinge, Chimanimani, Mutare and Mutasa districts in Zimbabwe. Results from both the BRT and GLM indicate that precipitation-related variables are more important in determining species range for the CWB than temperature related variables. The CWB has extensive potential habitats in all coffee areas with Mutasa district having the largest model average area suitable for CWB under current and projected climatic conditions. Habitat ranges for CWB will increase under future climate scenarios for Chipinge, Chimanimani and Mutare districts while it will decrease in Mutasa district. The highest percentage change in area suitable for the CWB was for Chimanimani district with a model average of 49.1% (3 906 ha) increase in CWB range by 2080. The BRT and GLM predictions gave similar predicted ranges for Chipinge, Chimanimani and Mutasa districts compared to the high variation in current and projected habitat area for CWB in Mutare district. The study concludes that suitable area for CWB will increase significantly in Zimbabwe due to climate change and there is need to develop adaptation mechanisms.

opencc-zeroDec 2018View details →

Data from: Canopy tree preference by insectivorous birds in shade-coffee farms: implications for migratory bird conservation

Land converted to coffee agriculture occupies >5 million hectares of what was once prime overwintering natural habitat in the American Neotropics for migrating birds. When tree canopy is retained or restored (i.e. shade-grown), coffee farms can serve as habitat refuge for wildlife. Yet few studies have examined whether canopy tree identity impacts habitat quality for biodiversity. Specifically, whether or not certain tree species are disproportionately important for foraging insectivorous birds remains unclear. In this study, we quantified bird foraging activity on 22 tree species in two Latin American Bird Friendly© coffee farms. Specifically, we conducted timed observations on focal trees to determine 1) tree preferences, 2) foraging bird abundance, 3) foraging time, and 4) species richness of birds using each canopy tree species. We found that birds did not forage randomly, and instead exhibited preferences for particular native tree species. Nitrogen-fixing Fabaceae were consistently used more frequently, supported more resident and migratory birds for longer periods of time, and supported more bird species than trees in other families. We posit that the potential mechanism contributing to tree preferences is the increase in insect abundance and diversity that provide high quality food for insectivores but do not present pest problems for coffee. Thus, tree species that support insects may provide multiple benefits for farmers in the form of bottom-up soil fertilization and top-down pest control. This study provides evidence that agroforestry land can be improved for birds of conservation concern by prioritizing canopy tree species that help birds and farm productivity.

opencc-zeroDec 2015View details →

Data from: Intraspecific trait variation across multiple scales: the leaf economics spectrum in coffee

Understanding species differences in plant functional traits has been critical in developing a mechanistic understanding of terrestrial ecological processes. Greater attention is now being placed on understanding the extent, causes and consequences of intraspecific trait variation (ITV). ITV is especially important in governing ecological processes in cropping systems, where only a small number of species or genotypes exist in high abundances. However, it remains unclear if key principles of trait-based ecology – namely the leaf economics spectrum (LES) – also describe intraspecific variation in crop functional biology. There also remains a need to understand whether ITV within crops is random, or structured across environmental, management-related or biological levels of organization in agroecosystems. We employed a nested design field survey to evaluate ITV in leaf traits in coffee (Coffea arabica), one of the world's most widespread tropical crops. We evaluated ITV in eight physiological, morphological and chemical leaf traits, across five nested categorical levels (sites, management systems, spatial location, plant identity, branch identity). We compared patterns of LES trait covariation in coffee, to interspecific patterns observed across over 700 wild plant species. Patterns of bivariate and multivariate ITV in coffee were broadly consistent with, but considerably weaker than, interspecific patterns associated with the LES, indicating that crops may systematically diverge from global patterns of trait trade-offs observed in wild plants. Physiological traits varied most widely (coefficient of variation (cv) 42–107%), followed by morphological traits (cv = 15–38%) and chemical traits (cv = 3–11%). Physiological ITV was best explained by the site in which a coffee plant was growing (17–55% explained), while ITV for chemical traits was best explained by management treatments within sites (25–36%); morphological ITV was higher even at the individual tree level or branch level and remained largely unexplained. Our results support the hypothesis that artificial selection and high-resource agricultural environments lead crops to systematically deviate from patterns of leaf trait covariation observed across wild plants species. Coupled with an understanding of how different traits vary systematically across multiple levels of biological organization, these findings help integrate ITV into future analyses of agroecosystem structure and function.

opencc-zeroApr 2020View details →

Impact of smoking cessation, coffee and bread consumption on the intestinal microbial composition among Saudis: A cross-sectional study

The gut microbiota is often affected by the dietary and lifestyle habits of the host, resulting in a better efficacy that favors energy harvesting from the consumed food. Our objective was to characterize the composition of gut microbiota in adult Saudis and investigate possible association with lifestyle and dietary practices. Feces from 104 Saudi volunteers (48% males) were tested for microbiota by sequencing the V3-V4 region of bacterial 16S ribosomal RNA (rRNA). For all participants, data were collected related to their lifestyle habits and dietary practices. The relative abundance (RA) of Fusobacteria was significantly higher in normal weight Saudis ( p =0.005, FDR=0.014). Individuals who consumed more coffee presented marginally significant more RA of Fusobacteria ( p =0.02, FDR=0.20) in their gut microbiota compared to those reporting low or no coffee intake, but the RA of Fusobacteria was significantly higher in smokers compared to non-smokers p =0.009, FDR=0.027) . The RA of Fusobacteria was also significantly higher in those reporting daily consumption of bread ( p =0.005, FDR=0.015). At the species level, the gut microbiota of people who consumed coffee was dominated by Bacteroidetes thetaiotaomicron followed by Phascolarctobacterium faecium and Eubacteriumrectale . Similarly, the gut microbiota of smokers was also enriched by B. thetaiotaomicron and Lactobacillus amylovorus. Smoking cessation, bread and coffee consumption induce changes in the intestinal microbial composition of Saudis. This indicates the significance of diet and lifestyle practices in the determination of the composition of the gut microbiota, which could possibly lead later to changes in metabolic profile and weight.