Biodiversity loss in Latin American coffee landscapes: review of the evidence on ants, birds, and trees

Lessons from Ethiopian coffee landscapes for global conservation in a post-wild world

The reality for conservation of biodiversity across our planet is that all ecosystems are modified by humans in some way or another. Thus, biodiversity conservation needs to be implemented in multifunctional landscapes. In this paper we use a fascinating coffee-dominated landscape in southwest Ethiopia as our lens to derive general lessons for biodiversity conservation in a post-wild world. Considering a hierarchy of scales from genes to multi-species interactions and social-ecological system contexts, we focus on (i) threats to the genetic diversity of crop wild relatives, (ii) the mechanisms behind trade-offs between biodiversity and agricultural yields, (iii) underexplored species interactions suppressing pest and disease levels, (iv) how the interactions of climate change and land-use change sometimes provide opportunities for restoration, and finally, (v) how to work closely with stakeholders to identify scenarios for sustainable development. The story on how the ecology and evolution of coffee within its indigenous distribution shape biodiversity conservation from genes to social-ecological systems can inspire us to view other landscapes with fresh eyes. The ubiquitous presence of human-nature interactions demands proactive, creative solutions to foster biodiversity conservation not only in remote protected areas but across entire landscapes inhabited by people.

Effect of shade on biodiversity within coffee farms: A meta-analysis

Aligning crop production with conservation initiatives has long been a topic of debate, with agricultural intensification threatening biodiversity across the globe. Shade-grown coffee allows farmers to preserve biodiversity by providing viable habitat, but its conservation value remains unclear. In this meta-analysis, we screened existing literature using the PRISMA protocol to compare the effect of three shade intensities on species diversity and individual abundance: sun, low shade (LS) and high shade (HS). Furthermore, we examine differences between taxa, within taxa and between regions to establish which species benefit most from shade and whether these benefits vary dependent on geographical location. Out of 1889 studies, we included 69 studies in the analysis, and performed random-effects meta-analyses and meta-regressions. Overall, we found that species diversity was significantly higher in HS when compared to sun and LS, and species diversity in LS tended to be higher than in sun. In each treatment, the species diversity of birds was higher in the higher shade treatment, i.e., HS and LS. In addition, mammal and epiphyte species diversity was higher in HS when compared to LS. Similarly, studies from Latin America showed significantly higher species diversity and abundance in shaded farms when compared to sun farms. Studies conducted in Africa detailed the opposite relationship, with abundance being significantly higher in less shaded systems, highlighting that land-use strategies must be region-specific. Moving forward, strategies to conserve biodiversity within coffee farms should: 1) account for region-specific variables; 2) end further encroachment; 3) maintain connectivity; and 4) optimise yield through prioritising faunal and floral diversity.

Ecological filtering shapes the impacts of agricultural deforestation on biodiversity

The biodiversity impacts of agricultural deforestation vary widely across regions. Previous efforts to explain this variation have focused exclusively on the landscape features and management regimes of agricultural systems, neglecting the potentially critical role of ecological filtering in shaping deforestation tolerance of extant species assemblages at large geographical scales via selection for functional traits. Here we provide a large-scale test of this role using a global database of species abundance ratios between matched agricultural and native forest sites that comprises 71 avian assemblages reported in 44 primary studies, and a companion database of 10 functional traits for all 2,647 species involved. Using meta-analytic, phylogenetic and multivariate methods, we show that beyond agricultural features, filtering by the extent of natural environmental variability and the severity of historical anthropogenic deforestation shapes the varying deforestation impacts across species assemblages. For assemblages under greater environmental variability-proxied by drier and more seasonal climates under a greater disturbance regime-and longer deforestation histories, filtering has attenuated the negative impacts of current deforestation by selecting for functional traits linked to stronger deforestation tolerance. Our study provides a previously largely missing piece of knowledge in understanding and managing the biodiversity consequences of deforestation by agricultural deforestation.

Patterns of shade plant diversity in four agroforestry systems across Central America: a meta-analysis

Agroforestry systems can potentially increase tree diversity within agricultural landscapes, but to date, there is little understanding of the patterns of shade plant diversity within different agroforestry systems (AFS) at large spatial scales. Using compiled plant inventory data (from 23 sources, 2517 plots, and 148,255 individuals) encompassing four AFS (shaded coffee; shaded cocoa; dispersed trees on pastures; and live fences) across six countries in Central America we estimated different metrics of diversity to assess the conservation value of different AFS for shade plants. 458 shade plant species were recorded across the four agroforestry systems. Primary forest species accounted for 28% of the shade species recorded, but only 6% of the recorded individuals. No single AFS was consistently the most diverse across countries when considering rarefied species richness. Trees on pastures can potentially reach a similar species richness as cocoa and coffee systems but require sampled areas 7-30 times larger. In terms of composition, 29 species were shared across the agroforestry systems in different countries, illustrating the strong selection pressure of farmers for species that provide timber, firewood, and fruit. Our study highlights the potential contribution and limitations of different AFS for tree diversity conservation within agricultural landscapes.

Conservation Biological Control as an Important Tool in the Neotropical Region

The history and recent developments of conservation biological control (CBC) in the context of industrialized and small-scale agriculture are discussed from theoretical framework available in the Neotropical region. A historical perspective is presented in terms of the transition of the way pests have been controlled since ancestral times, while some of these techniques persist in some areas cultivated on a small-scale agriculture. The context of industrialized agriculture sets the stage for the transition from chemical pesticides promoted in the green revolution to the more modern concept of IPM and finds in conservation biological an important strategy in relation to more sustainable pest management options meeting new consumer demands for cleaner products and services. However, it also noted that conservation, considered within a more integrative approach, establishes its foundations on an overall increase in floral biodiversity, that is, transversal to both small-scale and industrialized areas. In the latter case, we present examples where industrialized agriculture is implementing valuable efforts in the direction of conservation and new technologies are envisioned within more sustainable plant production systems and organizational commitment having that conservation biological control has become instrumental to environmental management plans. In addition, a metanalysis on the principal organisms associated with conservation efforts is presented. Here, we found that hymenopteran parasitoids resulted in the most studied group, followed by predators, where arachnids constitute a well-represented group, while predatory vertebrates are neglected in terms of reports on CBC. Our final remarks describe new avenues of research needed and highlight the need of cooperation networks to propose research, public outreach, and adoption as strategic to educate costumers and participants on the importance of conservation as main tool in sustainable pest management.

The effect of habitat transformation on a twig epiphytic orchid: Evidence from population dynamics

The tropical Andean landscape has been dramatically transformed over the last century with remaining native forest limited to small fragments within a heterogeneous matrix of crops, cattle pastures, and urban environments. We aimed to explore the impact of habitat transformation on the population dynamics in an endemic twig epiphytic orchid located within the undisturbed forest and within modified matrix habitat in two regions with contrasting landscape structures: with a dominant shade coffee matrix and a dominant grassland matrix. Over 2 years, we surveyed 4,650 individuals of the Colombian endemic orchid, Rodriguezia granadensis. We undertook four post-breeding censuses in three sites in each region in both native forest and pasture sub-sites (12 sub-sites; 48 censuses in total), and constructed demographic transition matrices (n = 36). The transition probabilities were calculated using a Bayesian approach and population grow rates were evaluated using asymptotic models and elasticities using transient dynamics. Between regions, higher population growth rate and inertia (defined as the largest or smallest long-term population density with the same initial density distribution) was seen in the shade coffee-dominated landscape. Additionally, population growth rate and damping ratio was higher in forest compared with pasture, with lower convergence time for the forest subsites. These demographic patterns reveal the contrasting levels of population resilience of this orchid in different landscape structures with the more connected shade-coffee dominated landscape permitting some healthier populations with greater population growth and survival in forest than pasture. This study highlights that twig epiphyte colonization of isolated phorophytes in pastures should not be interpreted as a sign of a healthy population but as a temporal transitory period.

Impact of the coronavirus pandemic on financial returns of smallholder coffee plantations in Lao PDR

Laos is among the top twenty coffee producing country in the world-producing about 39,000 tonnes per year-and most of its production is currently exported to over 26 countries, contributing about 1.1% of the total export value or US$64.3 million in 2019 to Laos' national economy. COVID-19 restrictions on trade and movement of people have largely impacted on coffee markets and production. As a strategic crop in Laos, it is supported by a range of policies and programs to generate greater benefits to both independent smallholder farmers and those involved in cooperatives, including support for agroforestry production models involving coffee and tree crops. However, studies of the profitability of different coffee agroforestry models are limited. This study compares financial returns from four most popular coffee agroforestry models in two coffee production provinces of Laos, before and during COVID-19 pandemic. The data were gathered from 20 farmers, five coffee traders and an integrated coffee processing company. These data were then triangulated with, and supplemented by, interviews with coffee exporters (n = 3) and key informants (n = 4). Financial indicators suggest that all four agroforestry models were profitable before COVID, but profits for cooperative growers were higher than for smallholders due to higher crop productivity and lower costs. Despite higher prices due to COVID restrictions, other factors reduced profitability of all four models and one smallholder model became unprofitable. The reasons for such differences and related policy implications are discussed.

Data of ant community compositions and functional traits responding to land-use change at the local scale

Aim: Off-reserve conservation is a major contributor to China biodiversity conservation efforts, biodiversity conservation being achieved within afforestation and low-intensity agriculture in fragmented landscapes. Functional trait is more strongly related to ecological processes than taxonomic diversity and reflects ecosystem functioning and species responses to environmental changes. In this study, we selected five habitats that differ in degree of disturbance to explore the effects of land use on ant community compositions, traits distributions and functional diversity change. We assessed how habitat disturbance affects the ant community compositions and traits distributions and asked if ant functional diversity respond to disturbance at the local scale? Location: Lüchun County, Yunnan Province, southwest China. Methods: Pitfall traps were used to survey ant communities. Additionally, we measured four ant morphological traits (eyes diameter, distance between eyes, femur length of the hind-leg and Weber's length) to assess the functional traits distributions and functional diversity. Shade plot of ant relative abundance was used to explore species distribution amongst different habitats. Kernel density plot was used to explore ant traits distribution patterns amongst different habitats. Non-metric multi-dimensional scaling ordination, based on ant Weber's length, was used to explore the ant traits compositions amongst different habitats. The fourth corner model was used to evaluate the association between ant traits and environmental variables. The FR_ic, RaoQ and FE_ve indices were selected as three complementary measures of the multivariate functional traits space and functional redundancy of different habitats. Results: We collected 14258 ants, representing 89 species, 40 genera and seven subfamilies. Aphaenogasterschurri and Tetramoriumciliatum were the common species of secondary forest; P.sagei, P.pieli, Cardiocondylawroughtonii, Recurvidrisnuwa, Tapinnomamelanocephalum, Monomoriumpharaonis and M.orientale were the common species in plantations; and Iridomyrmexanceps and Cardiocondylanuda were the common species in managed farms. Ants had medium eye diameters, narrow distances between eyes, medium leg lengths and smaller body sizes in greatly-disturbed habitats; and ants had an increasing eye diameter and narrowing of the space between eyes, while the leg length and Weber's length became shorter in moderately-disturbed habitats. Ant trait composition, based on Weber's length, showed significantly differences amongst five habitats. The fourth corner analysis indicated that ant species traits were significantly correlated with environmental variables. The functional diversity of secondary forest, lac plantation and lac plantation-corn agroforest were higher than those in dryland farm and rice paddy. Functional diversities were significantly negatively correlated with bare ground cover and significantly positively correlated with leaf-litter cover, leaf-litter thickness and plant cover. Main conclusion: Our results indicated that ant traits distribution patterns were affected by land-use changes, followed by anthropogenic disturbance pressures at the local scale. Ant traits compositions in greatly-disturbed habitats also differed from the habitats with less disturbance. It is unfavourable for the survival of the large body-size ants in more open habitats with more anthropogenic disturbance. Compared with secondary forest, dryland farm and rice paddies were less resistant and more vulnerable and lac plantations had approximately functional diversity of ant communities, suggesting that lac plantations might be resistant as secondary forest to species loss.

Fungal diversity in shade-coffee plantations in Soconusco, Mexico

Background

As forested natural habitats disappear in the world, traditional, shade-coffee plantations offer an opportunity to conserve biodiversity and ecosystem services. Traditional coffee plantations maintain a diversity of tree species that provide shade for coffee bushes and, at the same time, are important repositories for plants and animals that inhabited the original cloud forest. However, there is still little information about shade-coffee plantation's fungal diversity despite their relevance for ecosystem functioning as decomposers, symbionts and pathogens. Specifically, it is unknown if and what mycorrhizae-forming fungi can be found on the branches and trunks of coffee bushes and trees, which hold a diversity of epiphytes. Here, we evaluate fungal communities on specific plant microsites on both coffee bushes and shade trees. We investigate the ecological roles played by this diversity, with a special focus on mycorrhizae-forming fungi that may enable the establishment and development of epiphytic plants.

Methods

We collected 48 bark samples from coffee bushes and shade trees (coffee; tree), from four plant microsites (upper and lower trunks, branches and twigs), in two shade-coffee plantations in the Soconusco region in southern Mexico, at different altitudes. We obtained ITS amplicon sequences that served to estimate alpha and beta diversity, to assign taxonomy and to infer the potential ecological role played by the detected taxa.

Results

The bark of shade trees and coffee bushes supported high fungal diversity (3,783 amplicon sequence variants). There were no strong associations between community species richness and collection site, plant type or microsite. However, we detected differences in beta diversity between collection sites. All trophic modes defined by FUNGuild database were represented in both plant types. However, when looking into guilds that involve mycorrhizae formation, the CLAM test suggests that coffee bushes are more likely to host taxa that may function as mycorrhizae.

Discussion

We detected high fungal diversity in shade-coffee plantations in Soconusco, Chiapas, possibly remnants of the original cloud forest ecosystem. Several mycorrhiza forming fungi guilds occur on the bark of coffee bushes and shade trees in this agroecosystem, with the potential of supporting epiphyte establishment and development. Thus, traditional coffee cultivation could be part of an integrated strategy for restoration and conservation of epiphytic populations. This is particularly relevant for conservation of threatened species of Orchidaceae that are highly dependent on mycorrhizae formation.

Bird Assemblages in Coffee Agroforestry Systems and Other Human Modified Habitats in Indonesia

Simple Summary

Given the high degree of deforestation in the tropics due to shifting agriculture, it is a priority for conservation to find sustainable agriculture systems. We assessed bird communities over 1228 plots from 21 sites in the highly populated island of Java, Indonesia. We found that commercial coffee polycultures (i.e., fields comprised of coffee plants, other crops and/or fruit trees, and diverse shade trees) could sustain similar levels of bird abundance, diversity, and richness than coffee systems under natural forests and community managed forests. Commercial coffee polyculture fields host higher bird abundance, diversity, and richness than sun-exposed coffee fields, fields with other crops or fruit trees, and tree farms. We provide evidence that complex commercial agroforestry systems can host similar levels of biodiversity to agroforestry systems under natural forest.

Abstract

Deforestation in the tropics is mainly driven by the need to expand agriculture and forestry land. Tropical cropland has also undergone a process of intensification, particularly evident in regions that are the main exporters of deforestation-driven commodities. Around 25 million people in the world depend on coffee production, which has a profound contribution to global biodiversity loss through agricultural extensification and intensification. Nevertheless, coffee agroforestry systems have been postulated to serve as an alternative refuge for biodiversity across different regions. We aim to compare bird abundance, diversity, and richness in commercial polyculture coffee systems (i.e., the highest degree of habitat complexity that can be achieved in coffee fields after deforestation) with other coffee agroforestry systems and human modified habitats in Java, Indonesia. We collected data in 21 sites (1228 points) on Java from February to August 2021 using the point sampling method. Via generalised additive models, we tested whether the abundance, diversity, and richness of birds were different between different human modified habitats including other potential predictors such as elevation, distance to protected areas, shade tree richness, and plant diversity. Using the non-metric multidimensional scaling, we tested whether there was a difference in terms of the composition of foraging guilds between habitats. Commercial polyculture coffee fields can sustain levels of bird abundance, diversity, and richness comparable to agroforestry systems under natural forest, and higher than sun coffee and shaded monoculture coffee, and of other human modified habitats such as crop/fruit fields and tree farms. Coffee agroforestry systems have a higher proportion of nectarivores, insectivores, and frugivores than other systems that can sustain high diversity and richness of birds such as paddy fields that mainly have granivores and carnivores. Complex polycultures can represent an avenue for the future of sustainable agriculture in conditions where deforestation rates are high and in crops such as coffee, which maintain high yield in the presence of diverse shade.

Impact of cocoa agricultural intensification on bird diversity and community composition

To meet the growing demand for chocolate, cocoa (Theobroma cacao) agriculture is expanding and intensifying. Although this threatens tropical forests, cocoa sustainability initiatives largely overlook biodiversity conservation. To inform these initiatives, we analyzed how cocoa agriculture affects bird diversity at farm and landscape scales with a meta-analysis of 23 studies. We extracted 214 Hedges' g* comparisons of bird diversity and 14 comparisons of community similarity between a forest baseline and 4 farming systems that cover an intensification gradient in landscapes with high and low forest cover, and we summarized 119 correlations between cocoa farm features and bird diversity. Bird diversity declined sharply in low shade cocoa. Cocoa with >30% canopy cover from diverse trees retained bird diversity similar to nearby primary or mature secondary forest but held a different community of birds. Diversity of endemic species, frugivores, and insectivores (agriculture avoiders) declined, whereas diversity of habitat generalists, migrants, nectarivores, and granivores (agriculture associates) increased. As forest decreased on the landscape, the difference in bird community composition between forest and cocoa also decreased, indicating agriculture associates replaced agriculture avoiders in forest patches. Our results emphasize the need to conserve forested landscapes (land sparing) and invest in mixed-shade agroforestry (land sharing) because each strategy benefits a diverse and distinct biological community.

Differences in insectivore bird diets in coffee agroecosystems driven by obligate or generalist guild, shade management, season, and year

Neotropical shade-grown coffee systems are renowned for their potential to conserve avian biodiversity. Yet, little is known about food resources consumed by insectivorous birds in these systems, the extent of resource competition between resident and migratory birds, or how management of shade trees might influence diet selection. We identified arthropods in stomach contents from obligate and generalist insectivorous birds captured in mist-nets at five coffee farms in Chiapas, Mexico between 2001-2003. Overall stomach contents from 938 individuals revealed dietary differences resulting from changes in seasons, years, and foraging guilds. Of four species sampled across all management systems, Yellow-green Vireo (Vireo flavoviridis) prey differed depending on coffee shade management, consuming more ants in shaded monoculture than polyculture systems. Diets of obligate and generalist resident insectivores were 72% dissimilar with obligate insectivores consuming more Coleoptera and Araneae, and generalist insectivores consuming more Formicidae and other Hymenoptera. This suggests that obligate insectivores target more specialized prey whereas generalist insectivores rely on less favorable, chemically-defended prey found in clumped distributions. Our dataset provides important natural history data for many Nearctic-Neotropical migrants such as Tennessee Warbler (Leiothlypis peregrina; N = 163), Nashville Warbler (Leiothlypis ruficapilla; N = 69), and Swainson's Thrush (Catharus ustulatus; N = 68) and tropical residents including Red-legged Honeycreepers (Cyanerpes cyaneus; N = 70) and Rufous-capped Warblers (Basileuterus rufifrons; N = 56). With declining arthropod populations worldwide, understanding the ecological interactions between obligate and generalist avian insectivores gives researchers the tools to evaluate community stability and inform conservation efforts.

Bird Functional Diversity in Agroecosystems and Secondary Forests of the Tropical Andes

Agricultural systems have increased in extension and intensity worldwide, altering vertebrate functional diversity, ecosystem functioning, and ecosystemic services. However, the effects of open monoculture crops on bird functional diversity remain little explored, particularly in highly biodiverse regions such as the tropical Andes. We aim to assess the functional diversity differences of bird guilds between monoculture crops (coffee, cocoa, and citrus) and secondary forests. We use four functional diversity indices (Rao Q, Functional Richness, Functional Evenness, and Functional Divergence) related to relevant morphological, life history, and behavioral traits. We find significant differences in functional diversity between agroecosystem and forest habitats. Particularly, bird functional diversity is quite homogeneous among crop types. Functional traits related to locomotion (body weight, wing-chord length, and tail length), nest type (closed), and foraging strata (canopy and understory) are dominant at the agroecosystems. The bird assemblages found at the agroecosystems are more homogeneous in terms of functional diversity than those found at the secondary forests, as a result of crop structure and management. We recommend promoting more diverse agroecosystems to enhance bird functional diversity and reduce their effects on biodiversity.

A Study of Regenerative Farming Practices and Sustainable Coffee of Ethnic Minorities Farmers in the Central Highlands of Vietnam

Coffee is highly vulnerable to climate change, thus impacting coffee-dependent livelihoods and economies. As rising temperatures continue to reduce the suitability of many historical coffee-growing regions, some farmers are practicing regenerative, organic coffee farming as a means of climate change mitigation. In the Central Highlands, the primary coffee growing region of Vietnam, conventional sun-grown, monocrop coffee requires intensive inputs, including fertilizers, pesticides and water. However, some farmers are converting their conventional sun farms to organic shade farms utilizing regenerative farming techniques for both environmental and economic reasons. This study examined regenerative farming practices and sustainable coffee in a small ethnic minority village in Lâm Ðồng province. The comparative analysis between soil samples taken from a regenerative shade-grown coffee farm and two conventional sun-grown coffee farms revealed that the soil of the regenerative farm, enriched with organic manure, is comparable to, or healthier than, the soil on the conventional farms enriched with chemical fertilizers. The results indicate that regenerative farming practices promote biodiversity; however, they also maintain microclimates that promote the growth of Roya fungus, which can decrease coffee yields. The economic analysis of farm costs and net returns found that regenerative farming practices decrease external inputs through a system of crop diversification and integrated livestock production that improves productivity and economic performance while preserving the ecological and environmental integrity of the landscape. Regenerative agriculture is an important step toward climate change adaptation and mitigation; however, in order for the farm communities in the Central Highlands to make the transition to regenerative agriculture, the success factors and benefits of this method must be demonstrated to the coffee farmers.

Agro-Ecological Management of Coffee Pests in Brazil

Coffee plants host several herbivorous species, but only few are considered pests. Brazil is the largest coffee producer of the world, and the two key coffee pests of the crop in the country are the coffee leaf miner Leucoptera coffeella and the coffee berry borer Hypothenemus hampei. However, in some regions or on specific conditions, species of mites and scales can also cause damage to coffee plants. Conventional management of coffee pests relies on chemical pesticides, and it is the most commonly used strategy in Brazil, but environmental problems, pest resistance, and toxicity-related issues have led coffee growers to search for alternatives for pest control. Agro-ecological strategies suitable to coffee cultivation can be adopted by farmers, based on plant diversification, in order to provide resources for natural enemies, such as nectar, pollen, shelter, microclimate conditions, and oviposition sites, thereby promoting conservation biological control. Here I revise these strategies and report the results from research in Brazil. I include results on agroforestry, use of cover crops, and non-crop plant management. These are complemented by curative measures based on the use of organic farming-approved pesticides that can be employed when the agro-ecological practices are not yet consolidated. I also present the cultural control method used by several coffee producers in Brazil to decrease coffee berry borer damage.

Cooperating With “Open Cards”—The Role of Small Intermediary Businesses in Realizing Sustainable International Coffee Supply

Despite improvements, international food supply in general and coffee supply in particular continue to cause significant greenhouse gas emissions, economic inequities, and negative impacts on human well-being. There is agreement that dominant economic paradigms need to change to comply with the sustainability principles of environmental integrity, economic resilience, and social equity. However, so far, little empirical evidence has been generated to what extent and under which conditions sustainable international coffee supply could be realized through small intermediary businesses such as roasteries, breweries, and/or retailers. This case study reports on a collaborative project between a small coffee brewery and its customers in the U.S. and a small coffee roastery and its suppliers in Mexico that demonstrates how sustainable coffee supply could look like and explores under which conditions it can be realized. A research team facilitated the cooperation using a transdisciplinary research approach, including field visits and stakeholder workshops. The project (i) assessed the sustainability challenges of the current supply and value chains; (ii) developed a vision of a joint sustainable coffee supply chain; (iii) build a strategy to achieve this vision, and (iv) piloted the implementation of the strategy. We discuss the project results against the conditions for sustainable international coffee supply offered in the literature (why they were fulfilled, or not). Overall, the study suggests that small intermediary coffee businesses might have the potential to infuse sustainability across their supply chain if cooperating with “open cards.” The findings confirm some and add some conditions, including economic resilience through cooperation, problem recognition, transparency, trust, and solidarity across the supply chain. The study concludes with reflections on study limitations and future research needs.

Diaspore Removal by Ants Does Not Reflect the Same Patterns of Ant Assemblages in Mining and Rehabilitation Areas

Mining is responsible for drastic ecosystem changes and rehabilitation is used to promote the return of functions after these impacts. In this scenario, we investigated the responses of ant assemblages and diaspore removal by ants to the transformations caused by mining and rehabilitation predicting that (a) the increase in plant density (a proxy for mining intensity) led to an increase in ant richness, percentage of diaspores removed, and changes in species composition that in turn are correlated with changes in environmental variables; (b) the increase in vegetation structure (a proxy for rehabilitation ages) led to an increase in ant richness, percentage of diaspores removed, and changes in species composition that in turn are correlated with changes in environmental variables. Additionally, we also verified which functional groups were primarily responsible for diaspore removal. We sampled arboreal and epigeic ants, diaspore removal by ants, and environmental variables. We found that ant richness and diaspore removal in mining intensity gradient are positively correlated to plant density. Although vegetation structure is positively correlated with ant richness, we found no changes in diaspore removal in rehabilitation gradient. Epigeic omnivore and epigeic generalist predator ants were the most responsible for diaspore removal. Then, we observed that mining decreases ant richness, altering ant assemblages and their functions, and rehabilitation with exotic plants is ineffective to promote the colonization by the main diaspore-removing ants.

Shade and Agronomic Intensification in Coffee Agroforestry Systems: Trade-Off or Synergy?

Despite many years of research, there is still a lack of consensus as to the nature of the relationship between shade trees and agronomic intensification in coffee agroforestry systems. While some studies find unshaded intensively managed coffee is the most productive, other studies find no trade-off between shade characteristics and productivity. Our study of 179 farms from the main coffee growing regions of Costa Rica and Guatemala analyzed how shade affected the productive response of coffee to intensification of agronomic management. Four levels of coffee productivity were differentiated for each country associated with three levels of shade development in Costa Rica and two levels in Guatemala. The highest coffee productivity group was associated with medium shade development in both countries. High shade groups had low productivity, but very low productivity groups were associated with low (Costa Rica) or medium (Guatemala) shade. Medium and high productivity farms were associated with high elevation, lower rainfall and regions with higher coffee prices. Yields with a moderate level of investment (720–1,500 USD−1) and with medium shade (LAI 0.55-1.1) were not significantly different from yields with higher investment or lower shade levels. The increase in yields with increasing N fertilizer application were similar under low, medium and high LAI, but the mean productivity significantly lower with high LAI. Agronomic intensification to increase productivity is equally effective for low and medium shade systems (LAI <1.1); low productivity farms may have high shade or low shade but are mainly limited by low investment. Intensification of production is compatible with medium shade levels that should deliver broader ecosystem services but achieving this depends on coffee prices enabling this investment.

Fostering a Wildlife-Friendly Program for Sustainable Coffee Farming: The Case of Small-Holder Farmers in Indonesia

There is an urgent need for a global transition to sustainable and wildlife-friendly farming systems that provide social and economic equity and protect ecosystem services on which agriculture depends. Java is home to 60% of Indonesia’s population and harbors many endemic species; thus, managing agriculture alongside human well-being and biodiversity is vital. Within a community of ~400 coffee farmers in the province of West Java, we assessed the steps to develop a wildlife-friendly program until reaching certification between February 2019 and October 2020. We adopted an adaptive management approach that included developing common objectives through a process of stakeholder consultation and co-learning. We firstly investigated via interviews the expectations and the issues encountered by 25 farmers who converted to organic production in 2016. Their main expectations were an increase in income and an increase in coffee quality, while they had issues mainly in finding high quality fertilizers, reducing pests, and increasing productivity. We used this information to establish a problem-solving plan for the transition to community-wide wildlife-friendly practices. As part of the adaptive evaluation, we assessed the quality of coffee plantations before and after the implementation of coproduced actions. The quality of coffee significantly improved after our interventions to reduce the coffee berry borer, especially in the fields that started as inorganic and converted to organic. We uncovered additional issues to meet the standards for certification, including banning hunting and trapping activities and increasing coffee quality for international export. We describe the coproduced actions (agroforestry, conservation education, local law, organic alternatives) and phases of the program and discuss the potential barriers. We provide novel evidence of adaptive management framework successfully used to implement management actions and reach shared goals.

Local Knowledge about Ecosystem Services Provided by Trees in Coffee Agroforestry Practices in Northwest Vietnam

In recent decades in northwest Vietnam, Arabica coffee has been grown on sloping land in intensive, full sun monocultures that are not sustainable in the long term and have negative environmental impacts. There is an urgent need to reverse this negative trend by promoting good agricultural practices, including agroforestry, to prevent further deforestation and soil erosion on slopes. A survey of 124 farmers from three indigenous groups was conducted in northwest Vietnam to document coffee agroforestry practices and the ecosystem services associated with different tree species used in them. Trees were ranked according to the main ecosystem services and disservices considered to be locally relevant by rural communities. Our results show that tree species richness in agroforestry plots was much higher for coffee compared to non-coffee plots, including those with annual crops and tree plantations. Most farmers were aware of the benefits of trees for soil improvement, shelter (from wind and frost), and the provision of shade and mulch. In contrast, farmers had limited knowledge of the impact of trees on coffee quality and other interactions amongst trees and coffee. Farmers ranked the leguminous tree species Leucaena leucocephala as the best for incorporating in coffee plots because of the services it provides to coffee. Nonetheless, the farmers’ selection of tree species to combine with coffee was highly influenced by economic benefits provided, especially by intercropped fruit trees, which was influenced by market access, determined by the proximity of farms to a main road. The findings from this research will help local extension institutions and farmers select appropriate tree species that suit the local context and that match household needs and constraints, thereby facilitating the transition to a more sustainable and climate-smart coffee production practice.

Shade trees preserve avian insectivore biodiversity on coffee farms in a warming climate

AIM

Coffee is an important export for many developing countries, with a global annual trade value of $100 billion, but it is threatened by a warming climate. Shade trees may mitigate the effects of climate change through temperature regulation that can aid in coffee growth, slow pest reproduction, and sustain avian insectivore diversity. The impact of shade on bird diversity and microclimate on coffee farms has been studied extensively in the Neotropics, but there is a dearth of research in the Paleotropics.

LOCATION

East Africa.

METHODS

We created current and future regional Maxent models for avian insectivores in East Africa using Worldclim temperature data and observations from the Global Biodiversity Information Database. We then adjusted current and future bioclimatic layers based on mean differences in temperature between shade and sun coffee farms and projected the models using these adjusted layers to predict the impact of shade tree removal on climatic suitability for avian insectivores.

RESULTS

Existing Worldclim temperature layers more closely matched temperatures under shade trees than temperatures in the open. Removal of shade trees, through warmer temperatures alone, would result in reduction of avian insectivore species by over 25%, a loss equivalent to 50 years of climate change under the most optimistic emissions scenario. Under the most extreme climate scenario and removal of shade trees, insectivore richness is projected to decline from a mean of 38 to fewer than 8 avian insectivore species.

MAIN CONCLUSIONS

We found that shade trees on coffee farms already provide important cooler microclimates for avian insectivores. Future temperatures will become a regionally limiting factor for bird distribution in East Africa, which could negatively impact control of coffee pests, but the effect of climate change can be potentially mediated through planting and maintaining shade trees on coffee farms.

Natural enemy-herbivore networks along local management and landscape gradients in urban agroecosystems

Ecological networks can provide insight into how biodiversity loss and changes in species interactions impact the delivery of ecosystem services. In agroecosystems that vary in management practices, quantifying changes in ecological network structure across gradients of local and landscape composition can inform both the ecology and function of productive agroecosystems. In this study, we examined natural-enemy-herbivore co-occurrence networks associated with Brassica oleracea (cole crops), a common crop in urban agricultural systems. Specifically, we investigated how local management characteristics of urban community gardens and the landscape composition around them affect (1) the abundance of B. oleracea herbivores and their natural enemies, (2) the natural-enemy : herbivore ratio, and (3) natural-enemy-herbivore co-occurrence network metrics. We sampled herbivores and natural enemies in B. oleracea plants in 24 vegetable gardens in the California, USA central coast region. We also collected information on garden characteristics and land-use cover of the surrounding landscape (2 km radius). We found that increased floral richness and B. oleracea abundance were associated with increased parasitoid abundance, non-aphid herbivore abundance, and increased network vulnerability; increased vegetation complexity suppressed parasitoid abundance, but still boosted network vulnerability. High agricultural land-use cover in the landscape surrounding urban gardens was associated with lower predator, parasitoid, and non-aphid herbivore abundance, lower natural-enemy : herbivore ratios, lower interaction richness, and higher trophic complementarity. While we did not directly measure pest control, higher interaction richness, higher vulnerability, and lower trophic complementarity are associated with higher pest control services in other agroecosystems. Thus, if gardens function similarly to other agroecosystems, our results indicate that increasing vegetation complexity, including trees, shrubs, and plant richness, especially within gardens located in intensively farmed landscapes, could potentially enhance the biodiversity and abundance of natural enemies, supporting ecological networks associated with higher pest control services.

Vertical stratification of seed-dispersing vertebrate communities and their interactions with plants in tropical forests

Vertical stratification (VS) is a widespread phenomenon in plant and animal communities in forests and a key factor for structuring their species richness and biodiversity, particularly in tropical forests. The organisms composing forest communities adjust and shape the complex three-dimensional structure of their environment and inhabit a large variety of niches along the vertical gradient of the forest. Even though the degree of VS varies among different vertebrate groups, patterns of compositional stratification can be observed across taxa. Communities of birds, bats, primates, and non-flying small mammals are vertically stratified in terms of abundance, species richness, diversity, and community composition. Frugivorous members of these taxa play important roles as seed dispersers and forage on fruit resources that, in turn, vary in quantity and nutritional value along the vertical gradient. As a consequence, plant-seed disperser interaction networks differ among strata, which is manifested in differences in interaction frequencies and the degree of mutual specialization. In general, the canopy stratum is composed of strong links and generalized associations, while the lower strata comprise weaker links and more specialized interactions. Investigating the VS of communities can provide us with a better understanding of species habitat restrictions, resource use, spatial movement, and species interactions. Especially in the face of global change, this knowledge will be important as these characteristics can imply different responses of species and taxa at a fine spatial scale.

Soil microbial composition varies in response to coffee agroecosystem management

Soil microbes are essential to the continued productivity of sustainably managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability and coffee productivity have been demonstrated, but the effects of management on the composition of the soil microbial communities remains relatively unexplored. To further understand how management modulates the soil microbiome, the soil fungal and bacterial communities, soil chemistry, and canopy composition were surveyed in a Nicaraguan coffee cooperative, across 19 individual farms. Amplicon sequencing analyses showed that management (organic or conventional), stand age and previous land use affected the soil microbiome, albeit in different ways. Bacterial communities were most strongly associated with soil chemistry, while fungal communities were more strongly associated with the composition of the canopy and historical land use of the coffee plantation. Notably, both fungal and bacterial richness decreased with stand age. In addition to revealing the first in-depth characterization of the soil microbiome in coffee plantations in Nicaragua, these results highlight how fungal and bacterial communities are simultaneously modulated by long-term land use legacies (i.e. an agricultural plot's previous land use) and short-term press disturbance (i.e. farm age).

Review of Remote Sensing Methods to Map Coffee Production Systems

The coffee sector is working towards sector-wide commitments for sustainable production. Yet, knowledge of where coffee is cultivated and its environmental impact remains limited, in part due to the challenges of mapping coffee using satellite remote sensing. We recognize the urgency to capitalize on recent technological advances to improve remote sensing methods and generate more accurate, reliable, and scalable approaches to coffee mapping. In this study, we provide a systematic review of satellite-based approaches to mapping coffee extent, which produced 43 articles in the peer-reviewed and gray literature. We outline key considerations for employing effective approaches, focused on the need to balance data affordability and quality, classification complexity and accuracy, and generalizability and site-specificity. We discuss research opportunities for improved approaches by leveraging the recent expansion of diverse satellite sensors and constellations, optical/Synthetic Aperture Radar data fusion approaches, and advances in cloud computing and deep learning algorithms. We highlight the need for differentiating between production systems and the need for research in important coffee-growing geographies. By reviewing the range of techniques successfully used to map coffee extent, we provide technical recommendations and future directions to enable accurate and scalable coffee maps.

Bee diversity in secondary forests and coffee plantations in a transition between foothills and highlands in the Guatemalan Pacific Coast

Background

Although conservation of pristine habitats is recognized in many countries as crucial for maintaining pollinator diversity, the contribution of secondary forest conservation is poorly recognized in the Latin American context, such as in Guatemala. San Lucas Tolimán (SLT) is a high-quality coffee production region from the Atitlan Province, which has the second highest deciduous forest cover in Guatemala and pristine forest is prioritized for conservation. In contrast, secondary forest protection is undetermined, since these forests are normally removed or strongly affected by coffee farming practices. This situation may affect the diversity of native pollinators, mainly bees, which usually rely on the secondary forest for food resources.

Methods

We conducted a study to investigate the importance of secondary forests around the SLT coffee plantations (Coffea arabica L.) for pollinators. We compared bee diversity (richness, abundance and composition) in secondary forests of different age and coffee plantations with diverse farming techniques. Being the first study of pollinators in Guatemalan coffee plantations, we also recorded data for an entire year (2013–2014) in order to describe bee seasonality.

Results

We found significant differences in bee diversity between the coffee plantations and secondary forests, particularly early secondary forests showed higher bee abundances but diversity indices were similar between different vegetation type plots. In the early dry season, secondary forests showed the greatest native bee diversity. During the late dry season, when the coffee was flowering, honey bees were dominant in the same plots. This study provides important management insights to support the conservation of pollinators, since our results offer guidelines to improve coffee production by increasing native pollinator diversity.

Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador

Coffea arabica is a highly traded commodity worldwide, and its plantations are habitat to a wide range of organisms. Coffee farmers are shifting away from traditional shade coffee farms in favor of sun-intensive, higher yield farms, which can impact local biodiversity. Using plant-associated microorganisms in biofertilizers, particularly fungi collected from local forests, to increase crop yields has gained traction among coffee producers. However, the taxonomic and spatial distribution of many fungi in coffee soil, nearby forests and biofertilizers is unknown. We collected soil samples from a sun coffee system, shade coffee system, and nearby forest from Izalco, Sonsonate, El Salvador. At each coffee system, we collected soil from the surface (upper) and 10 cm below the surface (lower), and from the coffee plant drip line (drip line) and the walkway between two plants (walkway). Forest soils were collected from the surface only. We used ITS metabarcoding to characterize fungal communities in soil and in the biofertilizer (applied in both coffee systems), and assigned fungal taxa to functional guilds using FUNGuild. In the sun and shade coffee systems, we found that drip line soil had higher richness in pathotrophs, symbiotrophs, and saprotrophs than walkway soil, suggesting that fungi select for microhabitats closer to coffee plants. Upper and lower soil depths did not differ in fungal richness or composition, which may reflect the shallow root system of Coffea arabica. Soil from shade, sun, and forest had similar numbers of fungal taxa, but differed dramatically in community composition, indicating that local habitat differences drive fungal species sorting among systems. Yet, some fungal taxa were shared among systems, including seven fungal taxa present in the biofertilizer. Understanding the distribution of coffee soil mycobiomes can be used to inform sustainable, ecologically friendly farming practices and identify candidate plant-growth promoting fungi for future studies.

Patterns of biodiversity response along a gradient of forest use in Eastern Amazonia, Brazil

The preservation of tropical forests is increasingly at risk, including forests located within human-modified landscapes that retain high conservation value. People modify and interact with these landscapes through a wide range of uses. However, our knowledge of how different forest uses affect biodiversity is limited. Here, we analyse the responses of different taxa to four distinct categories of forest management, namely old-growth forest, Brazil nut extraction areas, reduced impact logging areas, and eucalyptus plantations. Within six independent replicates of each category, we sampled three taxa (fruit-feeding butterflies, dung beetles, and trees) in eastern Amazonia. Forests under moderate use (Brazil nut extraction and reduced-impact logging) had similar, albeit slightly lower, diversity levels relative to old-growth forests, while communities in plantations were significantly less diverse. Only 4%, 20%, and 17%, of the sampled butterfly, dung beetle, and tree species, respectively, were restricted to old-growth forests. This study provides further empirical evidence of the importance of old-growth forest conservation in the context of human-modified landscapes. It also suggests that landscape matrices integrating forest uses at varying intensities are well positioned to reconcile biodiversity conservation with the production of goods that support local livelihoods.

Overlooked biodiversity loss in tropical smallholder agriculture

Smallholder agriculture is the main driver of deforestation in the western Amazon, where terrestrial biodiversity reaches its global maximum. Understanding the biodiversity value of the resulting mosaics of cultivated and secondary forest is therefore crucial for conservation planning. However, Amazonian communities are organized across multiple forest types that support distinct species assemblages, and little is known about smallholder impacts across the range of forest types that are essential for sustaining biodiversity. We addressed this issue with a large-scale field inventory of birds (point counts) and trees (transects) in primary forest and smallholder agriculture in northern Peru across 3 forest types that are key for Amazonian biodiversity. For birds smallholder agriculture supported species richness comparable to primary forest within each forest type, but biotic homogenization across forest types resulted in substantial losses of biodiversity overall. These overall losses are invisible to studies that focus solely on upland (terra firma) forest. For trees biodiversity losses in upland forests dominated the signal across all habitats combined and homogenization across habitats did not exacerbate biodiversity loss. Proximity to forest strongly predicted the persistence of forest-associated bird and tree species in the smallholder mosaic, and because intact forest is ubiquitous in our study area, our results probably represent a best-case scenario for biodiversity in Amazonian agriculture. Land-use planning inside and outside protected areas should recognize that tropical smallholder agriculture has pervasive biodiversity impacts that are not apparent in typical studies that cover a single forest type. The full range of forest types must be surveyed to accurately assess biodiversity losses, and primary forests must be protected to prevent landscape-scale biodiversity loss.

Managing the farmscape for connectivity increases conservation value for tropical bird species with different forest-dependencies

Land clearing for agricultural use is a primary driver of biodiversity loss and fragmentation of natural ecosystems. Restoring natural habitat connectivity by retaining quality habitats and increasing on-farm tree cover contributes to species' mobility and persistence in agricultural landscapes. Nonetheless, remarkably few studies have quantified the impacts of on-farm practices for species' mobility measured as functional connectivity within the context of farm and broader spatial levels of landscape organization. We tested how adding and removing trees in different configurations on a farm comprised of coffee plantations and cattle pastures can help evaluate species' mobility at the farmscape level (an area comprising the farm plus a 1.5 km buffer area). We coupled bird capture data and scenario modeling to assess species mobility of five neotropical bird species with distinct life history characteristics representing a gradient of forest dependency. We used seven years of mist-netting data to estimate species habitat affinity and to predict species mobility using the Circuitscape model across a 4371 ha farmscape in Costa Rica. Circuitscape allowed us to estimate changes in movement probability and relative changes in resistance to movement that species experience during dispersal (measured as resistance distance and passage area through which species can move) under four farmscape management scenarios. The four land-use scenarios included: (a) the 2011 farmscape land-use composition and configuration, b) converting all existing live fences to post-and-wire fence lines in the farm c) converting simplified coffee agroforests to multistrata coffee agroforests in the farm, and d) placing multistrata live fences around the perimeter of every parcel and roads on the farm. Model results suggest that existing multistrata live fences maintain the sporadic movement of all five species irrespective of forest dependence. Likewise, adding multistrata live fences around individual fields presents a more efficient strategy for increasing species mobility than multistrata coffee agroforestry systems in the assessed farmscape, by doubling the passage areas available to all species, although it created labyrinths with "dead-ends" for two species. While retaining large habitat patches remains important for conservation, managing on-farm connectivity complements these efforts by increasing movement probability and reducing dispersal resistance for forest-dependent bird species.