Olivier Honnay

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Verified

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• PhD
• Professor (Full) at KU Leuven

In tropical regions, the extent of agricultural land is rapidly increasing at the expense of natural forest with associated losses of biodiversity and ecosystem services. Agroforestry has long been proposed as a more sustainable agricultural system, conserving biodiversity and ecosystem services, while providing significant local livelihood. In thi...

Species diversity is commonly hypothesized to result from trade-offs for different limiting resources, providing separate niches for coexisting species. As soil nutrients occur in multiple chemical forms, plant differences in acquisition of the same element derived from different compounds may represent unique niche dimensions. Because plant produc...

Despite the ecological significance of ericoid mycorrhizal fungi, little is known about the abiotic and biotic factors driving their diversity and community composition. To determine the relative importance of abiotic and biotic filtering in structuring ericoid mycorrhizal fungal communities, we established 156 sampling plots in two highly contrast...

Understanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GD P ) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populat...

Proximity to natural habitat is known to enhance pollination services in agricultural landscapes, particularly in large-scale industrialised farms. However, it remains unclear whether these patterns hold in tropical smallholder farms-ecologically complex landscapes that sustain millions of the world's most food-insecure communities and depend heavi...

Understanding genetic responses to forest dynamics is essential for predicting the long-term viability of understory plant populations and for developing effective conservation strategies. This study investigates genetic extinction debt and colonization credit in Circaea lutetiana, a clonal forest understory species, across its European range. Usin...

Robusta coffee, grown by 25 million farmers across more than 50 countries, plays an important role in smallholder farmers’ livelihoods and the economies of many low-income countries. Coffee establishes a mutualistic symbiosis with arbuscular mycorrhizal fungi (AMF); however, the impact of agricultural practices and soil characteristics on AMF diver...

Genetic diversity is vital for population survival, yet there is a paucity of studies focusing on the effectiveness of establishing protected areas for maintaining the population genetic diversity of threatened plant species. To evaluate the effectiveness of in situ conservation measures, we used simple sequence repeats (SSR) and single nucleotide...

In recent years, drug control institutions and national governments have emphasized the impact of coca (Erythroxylum sp.) cultivation on soil degradation. However, empirical evidence on its effects on soil quality remains limited. Here, we present a first analysis comparing the physicochemical properties of soils that have been under coca cultivati...

Coffee processing involves various steps, from harvest to the storage of dried green coffee beans, each of which can significantly affect the beans’ chemical composition and sensory qualities. Yet, a comprehensive evaluation that includes the coffee’s genetic background and chemical, sensory, and biological aspects is still uncommon for Robusta cof...

Cultivation of crops close to their wild relatives may jeopardise the integrity of wild genetic resources. Detecting cultivars among wild plants is necessary to characterise crop-wild gene flow, but can be challenging if cultivars and wild plants are phenotypically highly similar. Genomics tools can be used instead, but the selection of diagnostic...

The rapid decline of tropical rainforests, particularly in the Congo Basin, is predominantly driven by small-scale subsistence agricultural expansion. Tropical agroforestry, particularly coffee agroforestry, is seen as a potential way to balance agricultural productivity with biodiversity conservation and carbon sequestration, despite some possible...

Widespread agricultural intensification has strongly affected the biodiversity of European farmlands. Organic farming is commonly proposed as a more biodiversity-friendly alternative to mitigate this impact. However, its effectiveness for the on-field conservation of various taxa simultaneously remains unclear, especially relative to the conservati...

Robusta coffee, grown by 25 million farmers across more than 50 countries, plays an important role in smallholder farmers' livelihoods and the economies of many low-income countries. Despite robusta coffee’s growing economic importance, currently accounting for 43% of global coffee production, its association with arbuscular mycorrhizal fungus (AMF...

Biodiversity loss is a pressing global issue, necessitating effective conservation laws and compelling enforcement mechanisms. Yet, implementation issues persist. This study contributes to the development of an individual-based decision tool designed to help judicial authorities accurately assess the gravity of biodiversity offences and the harm in...

De soortenrijkdom van onze landbouwlandschappen is de afgelopen decennia dramatisch afgenomen. De oorzaak is de verregaande intensivering van de landbouw, een combinatie van diverse factoren die het landschap in grote mate ongeschikt hebben gemaakt voor het overleven van de meeste soorten. Maar hoe realistisch is het om dit intensiveringsproces ter...

Background and aims Tropical rainforests constitute a globally important biome severely threatened by anthropogenic activities. Accounting for the phylogenetic and functional dimensions can provide insights into how anthropogenic activities affect tree species community assembly. Here, we aimed to assess the effects of selective logging and forest...

Colonization by Ectomycorrhizal (EcM) fungi is key for the health and performance of plants under different stress scenarios, such as those faced by trees in urban environments. Because urban environments can be lacking EcM fungi, we here assessed the benefits of inoculating Tilia tomentosa seedlings in a pre-transplantation nursery context with th...

Meeting rising quality standards while at the same time addressing climate challenges will make the commercial cultivation of Robusta coffee increasingly difficult. Whereas breeding new varieties may be an important part of the solution, such efforts for Robusta lag behind, with much of its genetic diversity still unexplored. By screening existing...

Research on the chemical composition of coffee beans and its correlation with sensory quality is advancing, but the metabolites in coffee leaves have often been overlooked. This study investigated the metabolite profiles of roasted coffee, green beans, and coffee leaves from 39 C. canephora genotypes through LC–HRMS with an untargeted metabolomics...

Mowing is a crucial management strategy for conservation and restoration of semi-natural grasslands. In the past decades, dominant mowing methods have changed from manual to mechanical, using heavy machines causing soil compaction. Whereas the negative effects of compaction are well understood in agriculture and forestry, they have received little...

The rapid decline of tropical rainforests, particularly in the Congo Basin, is predominantly driven by small-scale subsistence agricultural expansion. Tropical agroforestry, particularly coffee agroforestry, is seen as a potential way to balance agricultural productivity with biodiversity conservation and carbon sequestration, despite some possible...

Intensivering van de landbouw is in Europa een belangrijke oorzaak van verlies aan biodiversiteit en de eraan gerelateerde ecosysteemdiensten. Biolandbouw wordt vaak naar voor geschoven als een manier om dit probleem te verminderen. In dit artikel vergelijken we de biodiversiteit en de gewas-bestuiving tussen bioappelteelt en conventionele appeltee...

Coffee processing involves various steps, from harvest to the storage of dried green coffee beans, each of which can significantly affect the beans' chemical composition and sensory qualities. Yet, a comprehensive evaluation that includes the coffee's genetic background and chemical, sensory, and biological aspects is still uncommon for Robusta cof...

Background and Aims Leaf traits are known to be strong predictors of plant performance and can be expected to (co)vary along environmental gradients. We investigated the variation, integration, environmental relationships, and evolutionary history of leaf functional traits in the genus Coffea L., typically a rainforest understory shrub, across Afri...

Introduction The genetic diversity of Robusta coffee (Coffea canephora), a cornerstone in the global coffee industry, remains not fully explored, leading to a significant gap in our understanding of its sensory intricacies. Our study evaluated the sensory quality potential of the Robusta cultivars from the INERA Coffee Collection in Yangambi (the D...

Background and aims Plant breeders are increasingly turning to crop wild relatives (CWRs) to ensure food security in a rapidly changing environment. However, CWR populations are confronted with various human-induced threats, including hybridisation with their nearby cultivated crops. This might be especially a problem for wild coffee species, which...

Agricultural intensification, afforestation and land abandonment are major drivers of biodiversity loss in semi‐natural grasslands across Europe. Reversing these losses requires the reinstatement of plant–animal interactions such as pollination. Here we assessed the differences in species composition and patterns of plant‐pollinator interactions in...

Animal-pollination is crucial in the reproduction of many crops grown in the tropics, including the self-incompatible Robusta coffee. Coffea canephora Pierre ex A. Froehner. is indigenous to the Congo basin where it is growing in the rainforest understorey yet providing very low yields. Cultivation therefore mainly occurs in either unshaded monocul...

Background and Aims Leaf traits are known to be strong predictors of plant performance and can be expected to (co)vary along environmental gradients. We investigated the variation, integration, environmental relationships, and evolutionary history of leaf functional traits in the genus Coffea L., typically a rainforest understory shrub, across Afri...

Background: The European yew Taxus baccata L. is a conifer tree species for which the autochthonous populations have become rare and endangered in many European countries after a long history of human overexploitation. The general objective of this study was to perform a population genetic analysis of rediscovered and putative autochthonous relict...

Increasing water use efficiency (WUE) in crops is critical to maintaining agricultural production under climate change-exacerbated drought. One of these approaches may consist of leveraging on the beneficial interactions between crops and arbuscular mycorrhizal fungi (AMF). In this study, we investigated how inoculation with AMF from three differen...

Climate change and the resulting increased drought frequencies pose considerable threats to forest herb populations, particularly where additional environmental challenges jeopardize responses to selection. Specifically, habitat fragmentation may hamper climate adaptation by altering the distribution of adaptive genetic variation and may also induc...

Background and aims Plant breeders are increasingly turning to crop wild relatives (CWRs) to ensure global food security amidst a rapidly changing environment. However, CWR populations are confronted with various human-induced threats, including hybridisation with their nearby cultivated crops, posing a significant threat to the wild gene pool. Her...

Understanding the combined effects of climate change and habitat fragmentation on the adaptive potential of plant populations is essential for devising effective conservation strategies. This is particularly important where mating system variation impacts the evolutionary consequences of habitat fragmentation. Here we aimed to reveal how habitat fr...

Cultivation of Robusta coffee is likely to gain importance because of its high disease resistance and climate envelope. Robusta coffee genetic resources conserved in field genebanks can play an important role to further improve its cupping quality and other agronomic traits, but such Coffea canephora collections are limited and still poorly charact...

Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H....

Cultivation of Robusta coffee is likely to gain importance because of its high disease resistance and climate envelope, but substantial effort must be made to improve its cupping quality and other agronomic traits. Robusta coffee genetic resources conserved in field genebanks can play an important role in this context, but many of them are limited...

The current rise in the prevalence of allergies to aeroallergens is incompletely understood and attributed to interactions with environmental changes and lifestyle changes. Environmental nitrogen pollution might be a potential driver of this increasing prevalence. While the ecological impact of excessive nitrogen pollution has been widely studied a...

Recent insect pollinator declines, mainly due to the expansion and intensification of agricultural land use, are jeopardizing ecosystem service provisioning in agroecosystems. Organic farming has been suggested as a biodiversity-friendly alternative to conventional farming, but additional insights evaluating its effectiveness in perennial cropping...

Climate change and the resulting increased drought frequencies pose considerable threats to forest herb populations, particularly where additional environmental challenges jeopardize responses to selection. Specifically, habitat fragmentation may impede climate adaptation through its impact on the distribution of adaptive genetic variation, and cau...

Questions: Woody plant encroachment is known to adversely affect the biodiversity and functioning of savannah ecosystems, yet removal strategies have been shown to have variable success. Here we evaluated the effectiveness of three woody removal methods or treatments for controlling the leguminous thorny shrub Dichrostachys cinerea, and assessed pl...

Ancient semi-natural grasslands in Europe are important for ecosystem service (ES) provision. Often, the surrounding matrix contains 'Grassland Green Infrastructure' (GGI) that contain grassland species which have the potential to supplement grassland ES provision across the landscape. Here we investigate the potential for GGI to deliver a set of c...

Degradation and regeneration of tropical forests can strongly affect gene flow in understorey species, resulting in genetic erosion and changes in genetic structure. Yet, these processes remain poorly studied in tropical Africa. Coffea canephora is an economically important species, found in the understorey of tropical rainforests of Central and We...

Food security and nutrition security raise multiple questions at both the local and global levels. Experts have formulated three major challenges for the 21st century in this regard: the depletion of natural materials, the loss of environmental quality, and the assurance or guarantee of food supplies. Will we be able to produce enough food for an e...

Habitat loss is threatening natural communities worldwide. Small and isolated populations suffer from inbreeding and genetic drift, which jeopardize their long-term survival and adaptive capacities. However, the consequences of habitat loss for reciprocal coevolutionary interactions remain poorly studied. In this study, we investigated the effects...

Elevated levels of inbreeding increase the risk of inbreeding depression and extinction, yet many inbred species are widespread, suggesting that inbreeding has little impact on evolutionary potential. Here, we explore the potential for transposable elements (TEs) to maintain genetic variation in functional genomic regions under extreme inbreeding....

Biological pest control, relying on naturally occurring predator–prey dynamics, is considered a key element to achieve more sustainable farming systems. However, the combined effects of local management and landscape factors on communities of natural enemies as well as the cascading effects on pest infestations are rarely addressed, especially in p...

Ethiopian Arabica coffee is produced in different agroforestry systems which differ in forest management intensity. In forest coffee systems (FC), coffee shrubs grow naturally in the understory of Afromontane forests with little human intervention, whereas in semi-forest coffee systems (SFC) thinning of the canopy and removal of the understory is a...

Degradation and regeneration of tropical forests can strongly affect gene flow in understorey species, resulting in genetic erosion and changes in genetic structure. Yet, these processes remain poorly studied in tropical Africa. Coffea canephora is an economically important species, found in the understorey of tropical rainforests of Central and We...

Climate change is increasingly impacting temperate forest ecosystems and many forest herbs might be unable to track the changing climate due to dispersal limitation. Forest herbs with a low adaptive capacity may therefore benefit from conservation strategies that mitigate dispersal limitation and evolutionary constraints, such as assisted migration...

Species may benefit from green infrastructure, i.e. the network of natural and anthropogenic habitat remnants in human‐dominated landscapes, if it helps isolated populations in remaining habitat patches to be functionally connected. The importance of green infrastructure is therefore increasingly emphasized in conservation policy to counter biodive...

Despite their key role in biodiversity conservation, forests in the Congo Basin are increasingly threatened by human activities, but it remains challenging to assess the impact of forest deg- radation under a more or less intact canopy. Likewise, forest recovery following agricultural abandonment remains poorly understood in the Congo Basin. Here,...

Epigenetic inheritance can drive adaptive evolution independently of DNA sequence variation. However, to what extent epigenetic variation represents an autonomous evolutionary force remains largely elusive. Through gene ontology and comparative analyses of genomic and epigenomic variation of wild strawberry plants raised in distinct drought setting...

Aims In low-input agricultural systems, arbuscular mycorrhizal fungi (AMF) play a role in plant nutrition, protection and water use. Evaluating how agricultural practices affect the composition of AMF communities is therefore an important step towards sustainable intensification. We characterized the AMF communities in enset (Ensete ventricosum) ro...

Climate change is increasingly impacting temperate forest ecosystems and many forest herbs might be unable to track the changing climate due to dispersal limitations. Forest herbs with a low adaptive capacity are prone to climate change effects and may benefit from conservation strategies mitigating dispersal limitations and evolutionary constraint...

Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Ar...

Tropical moist evergreen forests provide key ecosystem services for human well‐being. However, due to human pressure, Afromontane forests have lost much of their natural species composition and structure. In this study, vegetation surveys were carried out with the aim of investigating woody species composition and structure and their drivers of deg...

Background Attempts to restore degraded highlands by tree planting are common in East Africa. However, up till now, little attention has been given to effects of tree species choice on litter decomposition and nutrient recycling. Method In this study, three indigenous and two exotic tree species were selected for a litter decomposition study. The...

Conversion of natural ecosystems into agricultural land may strongly affect the soil microbiome and the functioning of the soil ecosystem. Alternative farming systems, such as organic farming, have therefore been advocated to reduce this impact, yet the outcomes of different agricultural management regimes often remain ambiguous and their evaluatio...

Growing concerns about the negative environmental impacts of agriculture have resulted in the increasing adoption of farming systems that try to reconcile crop production with environmental sustainability, such as organic farming. As organic farming refrains from using synthetic inputs, it heavenly reli es on maintaining soil health. However, it is...

Cassava, forming starch-rich, tuberous roots, is an important staple crop in smallholder farming systems in sub-Saharan Africa. Its relatively good tolerance to drought and nutrient-poor soils may be partly attributed to the crop’s association with arbuscular mycorrhiza fungi (AMF). Yet insights into AMF-community composition and richness of cassav...

Ons voedselsysteem, en meer in het bijzonder de manier waarop we aan landbouw doen, legt momenteel een onhoudbare druk op milieukwaliteit, biodiversiteit en klimaat. In deze bijdrage formuleren de auteurs eerst een reeks bedenkingen bij een eerder in Natuurfocus verschenen artikel waarin als oplossing voor dit probleem de agro-ecologische landbouw...

Background: Attempts to restore degraded highlands by tree planting are common in East Africa. However, up till now, little attention has been given to effects of tree species choice on litter decomposition and nutrient recycling. Method: In this study, three indigenous and two exotic tree species were selected for a litter decomposition study. The...

Background: Ecosystem restoration is as a critical tool to counteract the decline of biodiversity and recover vital ecosystem services. Restoration efforts, however, often fall short of meeting their goals. Although functionally important levels of biodiversity can significantly contribute to the outcome of ecosystem restoration, they are often ov...

We tested whether roots from indigenous wild enset in Southern Ethiopia harboured a more diverse and different AMF community compared to cultivated enset. Illumina MiSeq amplicon sequencing showed that AMF communities in both cultivated and wild enset were dominated by Glomeraceae which accounted for 64% of the 145 OTUs recorded. The majority of ra...

Despite their key role in biodiversity conservation, forests of the Congo Basin are increasingly threatened by human activities. Whereas deforestation is very conspicuous, it remains challenging to monitor the impact of forest degradation under a more or less intact canopy. Likewise, the outcomes of forest regeneration following agricultural abando...

Drastic loss in the area and quality of natural and semi‐natural habitats over the last hundred years has placed biodiversity and related ecosystem functions under substantial threat. Restoration of degraded ecosystems is among the main solutions to counteract this trend. However, past restoration efforts have not always led to the anticipated halt...

Interspecific hybridization events have played a major role in plant speciation, yet, the evolutionary origin of hybrid species often remains enigmatic. Here, we inferred the evolutionary origin of the allotetraploid species Coffea arabica, which is widely cultivated for Arabica coffee production. We estimated genetic distances between C. arabica a...