Biology subjects

van der Putten, W.

Publications and source records attributed to van der Putten, W..

4 recordsLinked to original sources

bioRxiv2025

Connectivity of restored Atlantic Forest fragments drives composition and functionality of the fungal community in the leaf litter layer

The restoration of biodiversity and functional tropical forests is critical to mitigating global biodiversity losses. Aboveground, increasing the connectivity of regenerating forests fragments facilitates the recolonization of tropical forest biodiversity. However, restoring functional ecosystems also requires the recovery of decomposition processes as these are essential in shaping aboveground biodiversity. Therefore, we investigate the role of forest connectivity on restoring the composition and functioning of fungal communities in the leaf litter layer during a chronosequence of forest restoration. In the Brazilian Atlantic Forest, we studied secondary forests regrown between 18 to 55 years after deforestation and different levels of forest connectivity and compared their litter to recently abandoned pastures and undisturbed primary forests. We quantified how forest age and connectivity between fragments influenced the litter fungi composition in relation to tree diversity, litter chemistry, and litter isotopes. We show that fungal composition was highly heterogeneous in forest litter, whereas pasture litter exhibited a more homogeneous community. Moreover, forest connectivity had stronger effects on litter fungal composition compared to forest age. Connectivity promoted wood saprotrophs and endophytes, while suppressed soil saprotrophs, with its effects being more evident during later stages of restoration. Fungal guilds such as endophytes and saprophytes, were primarily influenced by tree diversity and leaf litter chemistry. We conclude that forest connectivity promotes the re-establishment of saprophytic fungi capable of decomposing recalcitrant litter substrates, driven mainly by enhancing tree diversity and litter quality. Practical implications of increasing connectivity may relate to forest resilience on front of future climate change scenarios.

microbiology↗

bioRxiv2024

SpeSpeNet: An interactive and user-friendly tool to create and explore microbial correlation networks

Correlation networks are commonly used to explore microbiome data. In these networks, nodes are taxa and edges represent correlations between their abundance patterns across samples. As clusters of correlating taxa (co-abundance clusters) often indicate a shared response to environmental drivers, network visualization contributes to system understanding. Currently, most tools for creating and visualizing co-abundance networks from microbiome data either require the researcher to have coding skills, or they are not user-friendly, with high time expenditure and limited customizability. Furthermore, existing tools lack focus on the relationship between environmental drivers and the structure of the microbiome, even though many edges in correlation networks can be understood through a shared relationship of two taxa with the environment. For these reasons we developed SpeSpeNet (Species-Species Network, https://tbb.bio.uu.nl/SpeSpeNet), a practical and user-friendly R-shiny tool to construct and visualize correlation networks from taxonomic abundance tables. The details of data preprocessing, network construction, and visualization are automated, require no programming ability for the web version, and are highly customizable, including associations with user-provided environmental data. Here, we present the details of SpeSpeNet and demonstrate its utility using three case studies.

ecology↗

bioRxiv2023

DNA methylation responses to stress across different plant species

O_LIChanges in environments trigger plant DNA methylation responses, potentially modulating stress responses. Studies on stress-induced DNA methylation typically focus on single species, limiting our understanding of what are general and specific responses between species. C_LIO_LIUsing reduced-representation bisulfite sequencing epiGBS, we compared DNA methylation stress-responses across seven plant species. Because methylation can be targeted at transposable elements (TEs) and because environmental plasticity may be particularly relevant in asexual species, we hypothesize that genome size and reproduction mode explain differences in methylation responses between species. C_LIO_LIWe show that enrichment of environmentally-induced methylation responses in genes and TEs is a general feature across plant species. While previous studies have emphasized methylation responses in CHH-cytosines, we observed that cytosines in all sequence contexts (CG, CHG, CHH) are equally likely to respond to stress. Larger-genome species showed a higher proportion of stress-responding cytosines, and asexual species showed more cytosines with a strong methylation response to stress than sexually responding species. C_LIO_LIOur study highlights the role of TEs in methylome plasticity and identifies causes of variation in methylome plasticity. This provides guidance to extrapolating results from models to other plant species, and may contribute to better understanding of functionality of the response. C_LI

plant biology↗

bioRxiv2019

Global distribution of earthworm diversity

Soil organisms provide crucial ecosystem services that support human life. However, little is known about their diversity, distribution, and the threats affecting them. Here, we compiled a global dataset of sampled earthworm communities from over 7000 sites in 56 countries to predict patterns in earthworm diversity, abundance, and biomass. We identify the environmental drivers shaping these patterns. Local species richness and abundance typically peaked at higher latitudes, while biomass peaked in the tropics, patterns opposite to those observed in aboveground organisms. Similar to many aboveground taxa, climate variables were more important in shaping earthworm communities than soil properties or habitat cover. These findings highlight that, while the environmental drivers are similar, conservation strategies to conserve aboveground biodiversity might not be appropriate for earthworm diversity, especially in a changing climate.\n\nOne sentence summaryGlobal patterns of earthworm diversity, abundance and biomass are driven by climate but patterns differ from many aboveground taxa.

ecology↗