Biology subjects

Bebber, D. P.

Publications and source records attributed to Bebber, D. P..

10 recordsLinked to original sources

bioRxiv2026

Global distributions and emergence of six major tropical root-knot nematodes

Root-knot nematodes (RKN; Meloidogyne spp.) are among the most damaging plant-parasitic nematodes worldwide and present a growing threat to global food production as their geographical ranges expand. Despite their importance, the geographical distributions, proliferation risks and crop-level impacts of major RKN species remain poorly understood. Here we assess global habitat suitability for six economically significant or regulated tropical RKN species: M. arenaria, M. incognita, M. javanica, M. enterolobii, M. ethiopica and M. luci. We integrated statistical species distribution models (SDMs), mechanistic thermal-time development models and experimentally derived host-suitability metrics. Ensemble SDMs, parameterised using global occurrence records and soil-derived bioclimatic variables, indicate broad climatically suitable ranges for the four well-represented species (M. arenaria, M. incognita, M. javanica and M. enterolobii) across much of the tropics, subtropics and warm temperate regions. Suitability was lower in cooler northern latitudes and, to a degree, in the humid tropics. Predictions for M. ethiopica and M. luci remain uncertain due to limited occurrence data. Thermal-time phenological models, built from published estimates of base temperatures and Growing Degree-Day (GDD) requirements, revealed a strong latitudinal gradient in potential generation number, with life-cycle completion unlikely at higher latitudes. The risk to 26 globally important crops was evaluated by combining crop-specific reproduction factor and gall index data with global crop distribution maps, indicating highest potential impacts in southern Brazil, the central United States, parts of West and East Africa, eastern India and northern China. Together, our analyses show that most global agricultural land is suitable for the focal species establishment and proliferation, with risk shaped jointly by climate, soil conditions and crop hosts. Strengthening distributional surveys and experimentally quantifying species-specific thermal and host responses will be essential to anticipate and mitigate future threats from these crop pests under climate change.

ecology↗

bioRxiv2025

Non-target effects on the soil microbiome of a plant root exudate biocontrol for Fusarium wilt

Crop rotation and intercropping with Allium spp. (e.g. garlic, onion) are recognized as biological controls of Fusarium wilt in several crops. However, the non-target effects of this strategy on the soil microbiome are largely unknown. We evaluated the effect of cultivating Musa basjoo, Allium tuberosum (Chinese leek), and their co-cultivation on the rhizosphere and bulk soil microbiome under glasshouse conditions. We do not report the impact of Chinese leek on Foc abundances, as this has been previously reported. The bacterial and fungal communities in the rhizosphere and bulk soil varied depending on the plant type. The microbiomes of allium and bananas were consistently dissimilar, and the co-cultivation treatment contained constituent taxa from both. However, the effect of allium on soil community composition was outweighed by that of bananas in the co-cultivation scenario. Discriminative taxa for allium included members of the genera Sphingomonas, Microbacterium, Flavihumibacter, Brevundimonas, Pseudolabrys, Ramlibacter, Trichoderma, Mortierella and Fusarium. In the case of bananas, predominant biomarkers encompassed members of Rhizobacter, Noviherbaspirillum, Pseudarthrobacter, Aquabacterium, Pseudomonas, Tausonia and Humicola Biomarkers and predictions of functional gene abundances suggest that shifts in the soil microbiome induced by allium are correlated with increases in microorganisms exhibiting potential disease suppression and antibiotic or antifungal traits, whereas those in bananas are associated with plant-growth-promoting microorganisms. The biocontrol efficacy of allium co-cultivation may there involve shifts in the soil microbiome as well as direct impacts of root exudate chemistry on Fusarium plant pathogens.

ecology↗

bioRxiv2022

Climate change, biotic yield gaps and disease pressure in cereal crops

Plant diseases are major causes of crop yield losses and exert a financial burden via expenditure on disease control. The magnitude of these burdens depends on biological, environmental and management factors, but this variation is poorly understood. Here we model the effects of weather on potential yield losses due to fungal plant pathogens (the biotic yield gap, Ygb) using experimental trials of fungicide-treated and untreated cereal crops in the UK, and project future Ygb under climate change. We find that Ygb varies between 10 and 20 % of fungicide-treated yields depending on crop, and increases under warmer winter and wetter spring conditions. Ygb will increase for winter wheat and winter barley under climate change, while declining for spring crops because drier summers offset the effects of warmer winters. Potential disease impacts are comparable in magnitude to the effects of suboptimal weather and crop varieties.

ecology↗

bioRxiv2022

Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America

The global banana industry is threatened by one of the most devastating diseases: Fusarium wilt (FWB). FWB is caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc), which almost annihilated the banana production in the late 1950s. A new strain of Foc, known as tropical race 4 (TR4), attacks a wide range of banana varieties including Cavendish clones which are the source of 99% of banana exports. In 2019, Foc TR4 was reported in Colombia, and more recently (2021) in Peru. In this study, we sequenced three fungal isolates identified as Foc TR4 from La Guajira (Colombia) and compared them against 19 whole-genome sequences of Foc TR4 publicly available, including four genome sequences recently released from Peru. To understand the genetic relatedness of the Colombian Foc TR4 isolates and those from Peru, we conducted a phylogenetic analysis based on a genome-wide set of single nucleotide polymorphisms (SNPs). Additionally, we compared the genomes of the 22 available Foc TR4 isolates looking for the presence-absence of gene polymorphisms and genomic regions. Our results reveal that (i) the Colombian and Peruvian isolates are genetically distant, which could be better explained by independent incursions of the pathogen to the continent, and (ii) there is a high correspondence between the genetic relatedness and geographic origin of Foc TR4. The profile of present/absent genes and the distribution of missing genomic regions showed a high correspondence to the clades recovered in the phylogenetic analysis, supporting the results obtained by SNP-based phylogeny.

genomics↗

bioRxiv2020

A meta-analysis of the effect of organic and mineral fertilizers on soil microbial diversity

Organic agriculture, employing manures or composts, has been proposed as a way of mitigating undesirable impacts of mineral fertilizer use. Of particular interest is the effect of fertilizer regime on soil microbes, which are key to nutrient cycling, plant health and soil structure. However, the effect of fertilizers on soil microbial diversity remains poorly understood. Since biological diversity is an important determinant of ecosystem function and a fundamental metric in community ecology, the effects of fertilizer regimes on soil microbial diversity are of theoretical and applied interest. Here, we conduct a meta-analysis of 37 studies reporting microbial diversity metrics in mineral fertilized (NPK), organically fertilized (ORG) and unfertilized control (CON) soils. Of these studies, 32 reported taxonomic diversity derived from sequencing, gradient gel electrophoresis, or RFLP. Functional diversity, derived from Biolog Ecoplate measures of carbon substrate metabolism, was reported in 8 studies, with 3 studies reporting both diversity metrics. Bacterial and archaeal diversity was reported in 28 taxonomic studies, and fungal diversity in 8 taxonomic studies. We found that functional diversity was 2.8 % greater in NPK compared with CON, 7.0 % greater in ORG vs CON, and 3.8 % greater in ORG vs NPK. Bacterial and archaeal taxonomic diversity was not significantly different between NPK and CON, but on average 2.9% greater in ORG vs CON, and 2.4 % greater in ORG vs. NPK. Fungal taxonomic diversity was not significantly different between any treatment pairs. There was very high residual heterogeneity in all meta-analyses of soil diversity, suggesting that a large amount of further research is required to fully understand the influence of fertilizer regimes on microbial diversity and ecosystem function.

ecology↗

bioRxiv2020

Mapping the impacts of hurricanes Maria and Irma on banana production area in the Dominican Republic

Extreme weather events can have devastating impacts on agricultural systems, and the livelihoods that depend on them. Tools for rapid, comprehensive and cost-effective assessment of impacts, especially if carried out remotely, can be of great value in planning systematic recovery of production, as well as assessing risks from future events. Here, we use openly available remote sensing data to quantify the impacts of hurricanes Irma and Maria in 2017 on banana production area in the Dominican Republic -- the worlds largest producer of organic bananas. Further, we assess the risk to current production area if a similar extreme event were to re-occur. Hurricane associated damage was mapped using a simple change detection algorithm applied to Synthetic Aperture Radar (SAR) data over the three main banana growing provinces of northern Dominican Republic, i.e. Monte Cristi, Valverde and Santiago. The map of hurricane affected area was overlaid with banana plantation distributions for 2017 and 2019 that were mapped (accuracy = 99.8%) using a random forest classifier, and a combination of SAR and multi-spectral satellite data. Our results show that 11.35% of banana plantation area was affected by hurricane damage in 2017. Between 2017 and 2019, there was a high turnover of plantation area, but with a net gain of 10.8%. However, over a quarter (26.9%) of new plantation area spatially overlapped with regions which had seen flooding or damage from hurricanes in 2017. Our results indicate that banana production systems in northern Dominican Republic saw extensive damage in the aftermath of hurricanes Irma and Maria. While production area has recovered since then, a substantial proportion of new plantations, and a greater fraction of production area in general, occur at locations at risk from future extreme events.

ecology↗

bioRxiv2020

The global burden of plant disease tracks crop yields under climate change

Global food security is strongly determined by crop production. Climate change-induced losses to production can occur directly, or indirectly, including via the distributions and impacts of plant pathogens. However, the likely changes in pathogen pressure in relation to global crop production are poorly understood. Here we show that temperature-dependent infection risk, r(T), for 80 fungal and oomycete crop pathogens will track projected yield changes in 12 crops over the 21st Century. For most crops, both yields and r(T) are likely to increase at high latitudes. In contrast, while the tropics will see little or no productivity gains, r(T) is also likely to decline. In addition, the USA, Europe and China may experience major changes in pathogen assemblages. The benefits of yield gains may therefore be tempered by the increased burden of crop protection due to increased and unfamiliar pathogens.

ecology↗

bioRxiv2019

Geometry and evolution of the ecological niche in plant-associated microbes

The ecological niche of a species can be conceptualized as a volume in multidimensional space, where each dimension describes an abiotic condition or biotic resource. The shape and size of this volume strongly determines interactions among species and influences their global distribution, but the geometry of the niche is poorly understood. Here, we analyse temperature response functions and host plant ranges for hundreds of fungi and oomycetes. We demonstrate that niche specialization is independent on abiotic and biotic axes, that host interactions restrict fundamental niche breadth to form the realized niche, and that both abiotic and biotic niches show limited phylogenetic constraint. Such niche adaptability makes plant pathogens a formidable threat to agriculture and forestry.

ecology↗

bioRxiv2019

The Brazilian Amazon Protected Area Network was largely unaffected by recent fires

August 2019 saw dramatic increases in wildfires in the Brazilian Amazon, leading to arguments between Brazil and G7 leaders and widespread concern among conservationists. Popular media reports suggested that swathes of the Amazon rainforest in Brazil are on fire. Here we investigate the spatial distribution of fires through August 2019, showing that fires were largely restricted to deforested regions and areas with low canopy cover, particularly in unprotected areas that comprise half the region. In contrast, Brazils protected areas had one third as many fires, and forest in protected areas with high canopy cover was almost entirely unaffected by fire. Protected areas reduce deforestation and carbon emissions, and have proved largely untouched by recent fires. However, fires in closed-canopy forest cannot readily be detected by satellite remote-sensing and so this analysis likely underestimates the burned area in intact forest, both in protected and unprotected areas.

ecology↗

bioRxiv2019

Many unreported crop pests and pathogens are probably already present

Biotic invasions threaten global biodiversity and ecosystem function, and present challenges to agriculture where invasive pest species require major economic investment in control and can cause significant production losses. Pest Risk Analysis (PRA) is key to prioritizing agricultural biosecurity efforts, but is hampered by incomplete knowledge of current crop pest and pathogen distributions. Here we develop predictive models of current pest distributions and test these models using new observations at sub-national resolution. We apply generalized linear models (GLM) to estimate presence probabilities for 1901 crop pests in the CABI pest distribution database. We test model predictions for 100 unobserved pests in the Peoples Republic of China (PRC), against observations of these pests abstracted from the Chinese literature which has hitherto been omitted from databases on global pest distributions. Finally, we predict occurrences of all unobserved pests globally. Presence probability increases with host presence, presence in neighbouring regions, and global prevalence, and decreases with mean distance from coast, per capita GDP, and host number. The models are good predictors of pest presence in Provinces of the PRC, with AUC values of 0.76 - 0.80. Large numbers of currently unobserved, but probably present pests, are predicted in China, India, southern Brazil and some countries of the former USSR. GLMs can predict presences of pseudo-absent pests at sub-national resolution. Controlling for countries scientific capacity improves model fit. The Chinese scientific literature has been largely inaccessible to Western academia but contains important information that can support PRA. Prior studies have often assumed that unreported pests in a global distribution database is a true absence. Our analysis provides a method for quantifying pseudo-absences to enable improved PRA and species distribution modelling.

ecology↗