Biology subjects

Spaepen, S.

Publications and source records attributed to Spaepen, S..

4 recordsLinked to original sources

bioRxiv2021

Reference-based error correction of amplicon sequencing data from synthetic communities

SummarySynthetic microbial communities (SynComs) constitute an emerging and powerful tool in biological, biomedical, and biotechnological research. Despite recent advances in algorithms for the analysis of culture-independent amplicon sequencing data from microbial communities, there is a lack of tools specifically designed for analysing SynCom data, where reference sequences for each strain are available. Here we present Rbec, a tool designed for the analysis of SynCom data that accurately corrects PCR and sequencing errors in amplicon sequences and identifies intra-strain polymorphic variation. Extensive evaluation using mock bacterial and fungal communities show that our tool outperforms current methods for samples of varying complexity, diversity, and sequencing depth. Furthermore, Rbec also allows accurate detection of contaminants in SynCom experiments. Availability and implementationRbec is freely available as an open-source multi-platform R package. Release versions can be obtained via Bioconductor. The developer version is maintained and can be downloaded at: https://github.com/PengfanZhang/Rbec. Contactgarridoo@mpipz.mpg.de

bioinformatics↗

bioRxiv2019

Developmental plasticity of Brachypodium distachyon in response to P deficiency: modulation by inoculation with phosphate-solubilizing bacteria

BackgroundMineral P fertilisers must be used wisely in order to preserve rock phosphate, a limited and non-renewable resource. The use of bio-inoculants to improve soil nutrient availability and trigger an efficient plant response to nutrient deficiency is one potential strategy in the attempt to decrease P inputs in agriculture. MethodA gnotobiotic co-cultivation system was used to study the response of Brachypodium distachyon to contrasted P supplies (soluble and poorly soluble forms of P) and inoculation with P solubilizing bacteria. Brachypodiums responses to P conditions and inoculation with bacteria were studied in terms of developmental plasticity and P use efficiency. ResultsBrachypodium showed plasticity in its biomass allocation pattern in response to variable P conditions, specifically by prioritizing root development over shoot productivity under poorly soluble P conditions. Despite the ability of the bacteria to solubilize P, shoot productivity was depressed in plants inoculated with bacteria, although the root system development was maintained. The negative impact of bacteria on biomass production in Brachypodium might be attributed to inadequate C supply to bacteria, an increased competition for P between both organisms under P-limiting conditions, or an accumulation of toxic bacterial metabolites in our cultivation system. Both P and inoculation treatments impacted root system morphology. The modulation of Brachypodiums developmental response to P supplies by P solubilizing bacteria did not lead to improved P use efficiency. ConclusionOur results support the hypothesis that plastic responses of Brachypodium cultivated under P-limited conditions are modulated by P solubilizing bacteria. The considered experimental context impacts plant-bacteria interactions. Choosing experimental conditions as close as possible to real ones is important in the selection of P solubilizing bacteria. Both persistent homology and allometric analyses proved to be useful tools that should be considered when studying the impact of bio-inoculants on plant development in response to varying nutritional context.

plant biology↗

bioRxiv2019

Two Receptor-Like Kinases Required For Arabidopsis Endodermal Root Organisation Shape The Rhizosphere Microbiome

The Casparian Strip (CS) constitutes a physical diffusion barrier to water and nutrients in plant roots, and is formed by the polar deposition of lignin polymer in the endodermis. This precise pattern of lignin deposition is thought to be mediated by the scaffolding activity of membrane-bound Casparian Strip domain proteins (CASPs). However, we show that endodermis-specific receptor-like kinase 1 (ERK1) and ROP Binding Kinase1 (RBK1) are also involved in this intricate process, with the former playing an essential role both in the localization of CASP1 and in lignin deposition. We further characterised ERK1 and determined its subcellular localisation in the cytoplasm and nucleus of the endodermis, as well as provide evidence for its involvement in a signalling pathway together with the circadian clock regulator, Time for Coffee (TIC). We also show that disruption to CS organisation and increased suberisation in the endodermis due to loss of function of either ERK1 or TIC collectively leads to an altered root microbiome composition. Thus, our work reveals additional players in the complex cascade of signalling events operating in the root endodermis to establish both the CS diffusion barrier and the microbial composition of the rhizosphere.

plant biology↗

bioRxiv2019

The effects of soil phosphorous content on microbiota are driven by the plant phosphate starvation response

Phosphate starvation response (PSR) in non-mycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms - the plant microbiota - are exposed to direct influence by the soils phosphorous (P) content itself, as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient, and compared the composition of their shoot and root microbiota to wild type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota composition than P concentrations in both roots and shoots. The fungal microbiota was more sensitive to P concentrations per se than bacteria, and less depended on the soil community composition.\n\nUsing a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift is accompanied by changes in microbiota composition: the genus Burkholderia is specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrate that in the absence of Burkholderia from the SynCom, plant shoots accumulate higher phosphate levels than shoots colonized with the full SynCom, only under P starvation, but not under P-replete conditions. Therefore, P-stressed plants allow colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plants P starvation.

microbiology↗