Biology subjects

van den Hoogen, J.

Publications and source records attributed to van den Hoogen, J..

10 recordsLinked to original sources

bioRxiv2026

Niche constraints drive differences between mycorrhizal fungal guilds in future range shifts

Mycorrhizal fungi are a diverse and ubiquitous group of plant symbionts whose distribution strongly influences ecosystem function across the globe. Yet, until now, we do not have quantitative data on the range sizes of different mycorrhizal fungal taxa, limiting our capacity to forecast future shifts in community composition and function. Here, we use 115,924 DNA sequence-derived observations to map the distribution of 651 common mycorrhizal fungal taxa and forecast future changes to their range sizes. We demonstrate that climate, plant cover, and soil factors, particularly mean annual temperature, net primary productivity, and soil organic carbon, exert major control over mycorrhizal fungal distributions. Based on these drivers, the ecological niches of mycorrhizal fungi consistently differ between arbuscular and ectomycorrhizal functional guilds. Arbuscular mycorrhizal fungal taxa generally occupy a wider niche breadth than ectomycorrhizal fungi, occurring across larger ranges of climate, soil, plant cover, topography, and disturbance conditions. Our models also predict widespread decreases in the suitable range size of mycorrhizal fungal taxa under projected future global climates, with average ranges decreasing by 13.8% or ~2.2 million km2 under high emissions scenarios (ssp5-8.5). This decrease in projected range size will be most pronounced for ectomycorrhizal fungi, strongly linked to constraints from their smaller overall niches. By generating a global atlas of common mycorrhizal fungi and their associated environmental niche, we establish a critical baseline for widely suspected declines in global fungal biodiversity.

ecology↗

bioRxiv2025

Microtubules in the coenocyte Phytophthora function in nuclear positioning and sustaining tip growth

The microtubule cytoskeleton consists of dynamic intracellular filaments and is involved in numerous processes, ranging from nuclear division to intracellular transport. Some of these microtubule-mediated processes are conserved in all eukaryotic lineages while others are specific for certain groups of organisms. Here, we focus on the microtubule cytoskeleton of oomycetes in the genus Phytophthora, a group of harmful plant pathogens. For visualizing microtubule organization and dynamics, we generated transgenic Phytophthora palmivora lines expressing GFP-tagged -tubulin. Besides a conserved localization in the mitotic spindle, we observed cytoplasmic microtubules originating from microtubule-organizing centers associated with nuclei in the coenocytic hyphae. These dynamic microtubules initiated long-lasting, antiparallel connections with microtubules originating from adjacent nuclei. After mitosis, these microtubules rapidly increased in length while maintaining their antiparallel interaction. Frequent buckling events suggest that microtubule-based force generation plays a role in nuclear spacing. This idea was strengthened by erratic nuclear motility and positioning in hyphae exposed to the microtubule depolymerizing drug oryzalin. Besides aberrant nuclear positioning we also observed defects in hyphal growth; in oryzalin-treated hyphae lacking microtubules, tip growth was less sustained than in non-treated hyphae. This suggests that microtubules radiating into the hyphal tip from the apical nucleus have a function in sustaining tip growth. Altogether, this study provides novel insights in the localization, dynamics and functions of the microtubule cytoskeleton in the coenocytic Phytophthora hyphae.

cell biology↗

bioRxiv2024

Large-scale recovery in Costa Rica's Payment for Ecosystem Service Program

Costa Rica implemented the worlds first national-scale Payment for Ecosystem Service (PES) program in 1996 and now protects over 200,000 hectares. By distributing wealth towards local land-stewards, Costa Ricas program has helped to limit deforestation at a national scale, but the large-scale ecological implications have yet remained unclear. Here, we use a massive ecoacoustic dataset to evaluate how this program has impacted the ecological integrity of PES forests across the entire Nicoya Peninsula. At the times and frequencies that are indicative of native biological activity, we reveal dramatic increases in the integrity of PES soundscapes, relative to those of natural protected areas. Specifically, natural regeneration sites were 97.79% more acoustically similar to reference forests (absolute mean similarity of 0.539) than they were to disturbed pastures, while acoustic recovery of plantations lags behind (79.66%; 0.489). These findings are strongly suggestive of large-scale ecological recovery, constituting some of the most robust evidence to date that restoration initiatives can benefit biodiversity on large spatial scales. Study overviewCosta Ricas PES program pays landowners to encourage forest recovery and compensate them for opportunity costs. Most payments subsidize land conservation, in which participants allow existing forests to naturally regenerate. Some payments are also offered to produce timber through plantations, which are often monocultures of exotic tree species. Despite the programs importance to Costa Ricas conservation efforts, little is known about whether these forest systems are recovering their natural characteristics. To investigate the dynamics of the PES program, we recorded continuous 6-day soundscapes in 119 sites across the Nicoya Peninsula of Costa Rica (Supplementary Figure 1). Specifically, we characterized the soundscapes across 4 land-use types: (i) 19 reference pastures, (ii) 43 PES monoculture tree plantations, (iii) 39 PES natural regeneration sites, and (iv) 18 reference forests. Sites from each land-use type are distributed across the Nicoya Peninsulas climate and edaphic gradient, allowing us to capture substantial variation in ecological outcomes. We determined the areas of acoustic space where most animals vocalize and where ecological responses to recovery were most likely to be detected (Figure 1). We then identified how and to what extent the soundscapes of natural regeneration and plantation sites had changed over the last 27 years. We find evidence that naturally regenerating forests within the PES have recovered substantially when compared to reference forests, while plantation systems lag behind (Figure 3). Our findings reaffirm the importance of ecosystem conservation, while suggesting redistributive policy mechanisms can accelerate nature protection at scale. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/610944v1_fig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1e23f8org.highwire.dtl.DTLVardef@cbac64org.highwire.dtl.DTLVardef@1a2daaborg.highwire.dtl.DTLVardef@c2157e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Tailoring the acoustic space to improve acoustic analyses. Soundscape analyses can be improved by identifying the times and frequencies associated with the dynamics of interest. Using manual annotations and modelling approaches we determined that differences in the activity of native fauna, shown here in black, were best understood within frequencies 1 - 9 kHz (on the y-axis) and the times listed along the x-axis in yellow. Outside of this region of acoustic space, differences between land-use types are better explained by climatic differences or other acoustic events (shown in grey). C_FIG O_FIG O_LINKSMALLFIG WIDTH=134 HEIGHT=200 SRC="FIGDIR/small/610944v1_fig3.gif" ALT="Figure 3"> View larger version (17K): org.highwire.dtl.DTLVardef@111505org.highwire.dtl.DTLVardef@17b36cborg.highwire.dtl.DTLVardef@4a5057org.highwire.dtl.DTLVardef@e08a29_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 3:C_FLOATNO Soundscape comparisons reveal substantial recovery in PES natural regeneration sites. (A) Scaled similarity values to reference forests are shown for the remaining three land-use types, higher values indicate more shared acoustic characteristics. Box plots show the quantile ranges and median values for each land-use type. Colored points represent mean similarities for all 10-minute time bins included in the analysis, colored by the time of period of the day, while outliers are plotted again in black. Brackets indicate the results of a Wilcoxon post-hoc statistical test. (B) 24-hour cycles of SPMN for each land-use type are shown for the frequency bands in which similarities between natural regeneration sites and reference forests were highest (3 - 4 and 6 - 7 kHz). C_FIG

ecology↗

bioRxiv2024

Macro-environment strongly interacts with warming in a global analysis of decomposition

Empirical studies worldwide show substantial variability in plant litter decomposition responses to warming, leaving the overall impact of climate change on this process uncertain. We conducted a meta-analysis of 109 experimental warming studies across seven continents, utilizing natural and standardized plant material, to assess the overarching effect of warming on decomposition and identify potential moderating factors. Warming influences decomposition differently across macro-environmental gradients of moisture and temperature. Negative warming effects on decomposition in warmer, low-moisture areas were counterbalanced by the positive, though not significant, warming effects in colder areas, resulting in an overall non-significant effect. We determine that at least 5.2 degrees of warming is required for a significant increase in decomposition. This is particularly relevant given the past decades global warmth in higher latitudes, holding a significant proportion of terrestrial carbon. Low-quality plant litter was more sensitive to warming. Therefore, future vegetation changes toward low-quality, temperature-sensitive plants could increase carbon release and reduce the net supply of stored organic matter in the soil by increasing the decomposition of low-quality litter with warming. Our findings emphasize the connection between warming responses, macro-environment, and litter characteristics, refining predictions of climate changes consequences on key ecosystem processes and its contextual dependencies.

ecology↗

bioRxiv2022

Globally invariant metabolism but density-diversity mismatch in springtails

Soil life supports the functioning and biodiversity of terrestrial ecosystems1, 2. Springtails (Collembola) are among the most abundant soil animals regulating soil fertility and flow of energy through above- and belowground food webs3-5. However, the global distribution of springtail diversity and density, and how these relate to energy fluxes remains unknown. Here, using a global dataset collected from 2,470 sites, we estimate total soil springtail biomass at 29 Mt carbon (threefold higher than wild terrestrial vertebrates6) and record peak densities up to 2 million individuals per m{superscript 2} in the Arctic. Despite a 20-fold biomass difference between tundra and the tropics, springtail energy use (community metabolism) remains similar across the latitudinal gradient, owing to the increase in temperature. Neither springtail density nor community metabolism were predicted by local species richness, which was highest in the tropics, but comparably high in some temperate forests and even tundra. Changes in springtail activity may emerge from latitudinal gradients in temperature, predation7, 8, and resource limitation7, 9, 10 in soil communities. Contrasting temperature responses of biomass, diversity and activity of springtail communities suggest that climate warming will alter fundamental soil biodiversity metrics in different directions, potentially restructuring terrestrial food webs and affecting major soil functions.

ecology↗

bioRxiv2021

Global trade-offs in tree functional traits

AO_SCPLOWBSTRACTC_SCPLOWDue to massive energetic investments in woody support structures, trees are subject to unique physiological, mechanical, and ecological pressures not experienced by herbaceous plants. When considering trait relationships across the entire plant kingdom, plant trait frameworks typically must omit traits unique to large woody species, thereby limiting our understanding of how these distinct ecological pressures shape trait relationships in trees. Here, by considering 18 functional traits--reflecting leaf economics, wood structure, tree size, reproduction, and below-ground allocation--we quantify the major axes of variation governing trait expression of trees worldwide. We show that trait variation within and across angiosperms and gymnosperms is captured by two independent processes: one reflecting tree size and competition for light, the other reflecting leaf photosynthetic capacity and nutrient economies. By exploring multidimensional relationships across clusters of traits, we further identify a representative set of seven traits which captures the majority of variation in form and function in trees: maximum tree height, stem conduit diameter, specific leaf area, seed mass, bark thickness, root depth, and wood density. Collectively, this work informs future trait-based research into the functional biogeography of trees, and contributes to our fundamental understanding of the ecological and evolutionary controls on forest biodiversity and productivity worldwide.

ecology↗

bioRxiv2021

A geospatial mapping pipeline for ecologists

Geospatial modelling can give fundamental insights in the biogeography of life, providing key information about the living world in current and future climate scenarios. Emerging statistical and machine learning approaches can help us to generate new levels of predictive accuracy in exploring the spatial patterns in ecological and biophysical processes. Although these statistical models cannot necessarily represent the essential mechanistic insights that are needed to understand global biogeochemical processes under ever-changing environmental conditions, they can provide unparalleled predictive insights that can be useful for exploring the variation in biophysical processes across space. As such, these emerging tools can be a valuable approach to complement existing mechanistic approaches as we aim to understand the biogeography of Earths ecosystems. Here, we present a comprehensive methodology that efficiently handles large datasets to produce global predictions. This mapping pipeline can be used to generate quantitative, spatially explicit predictions, with a particular emphasis on spatially-explicit insights into the evaluation of model uncertainties and inaccuracies.

ecology↗

bioRxiv2021

Mapping tree species for restoration potential resilient to climate change

The restoration of forest ecosystems is associated with key benefits for biodiversity and ecosystem services. Where possible, ecosystem restoration efforts should be guided by a detailed knowledge of the native flora to regenerate ecosystems in a way that benefits natural biodiversity, ecosystem services, and natures contribution to people. Machine learning can map the ecological suitability of tree species globally, which then can guide restoration efforts, especially in regions where knowledge about the native tree flora is still insufficient. We developed an algorithm that combines ecological niche modelling and geographic distributions that allows for the high resolution (1km) global mapping of the native range and suitability of 3,987 tree species under current and future climatic conditions. We show that in most regions where forest cover could be potentially increased, heterogeneity in ecological conditions and narrow species niche width limit species occupancy, so that in several areas with reforestation potential, a large amount of potentially suitable species would be required for successful reforestation. Local tree planting efforts should consider a wide variety of species to ensure that the equally large variety of ecological conditions can be covered. Under climate change, a large fraction of the surface for restoration will suffer significant turnover in suitability, so that areas that are suitable for many species under current conditions will not be suitable in the future anymore. Such a turnover due to shifting climate is less pronounced in regions containing species with broader geographical distributions. This indicates that if restoration decisions are solely based on current climatic conditions, a large fraction of the restored area will become unsuitable in the future. Decisions on forest restoration should therefore take the niche width of a tree species into account to mitigate the risk of climate-driven ecosystem degradation.

ecology↗

bioRxiv2019

The genome of Peronospora belbahrii reveals high heterozygosity, a low number of canonical effectors and CT-rich promoters

Along with Plasmopara destructor, Peronosopora belbahrii has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was ca. 35.4 Mbp in length, with an N50 scaffold length of ca. 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of ca. 40.1 kbp. From the repeat-masked genome 9049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16 % of the genome consists of repetitive sequences, and based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of Pe. belbahrii. Peronospora belbahrii has undergone a high degree of convergent evolution, reflecting its obligate biotrophic lifestyle. Features of its secretome, signalling networks, and promoters are presented, and some patterns are hypothesised to reflect the high degree of host specificity in Peronospora species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.

genomics↗

bioRxiv2018

Attempts to implement CRISPR/Cas9 for genome editing in the oomycete Phytophthora infestans

Few techniques have revolutionized the molecular biology field as much as genome editing using CRISPR/Cas9. Recently, a CRISPR/Cas9 system has been developed for the oomycete Phytophthora sojae, and since then it has been employed in two other Phytophthora spp. Here, we report our progress on efforts to establish the system in the potato late blight pathogen Phytophthora infestans. Using the original constructs as developed for P. sojae, we did not obtain any transformants displaying a mutagenized target gene. We made several modifications to the CRISPR/Cas9 system to pinpoint the reason for failure and also explored the delivery of pre-assembled ribonucleoprotein complexes. With this report we summarize an extensive experimental effort pursuing the application of a CRISPR/Cas9 system for targeted mutagenesis in P. infestans and we conclude with suggestions for future directions.

molecular biology↗