Biology subjects

Motte, H.

Publications and source records attributed to Motte, H..

4 recordsLinked to original sources

bioRxiv2026

Structure-activity relationship study in soil identifies an effective broad-spectrum inhibitor of archaeal nitrification

Ammonia-oxidizing archaea (AOA) can contribute substantially to nitrification in agricultural soils, yet the portfolio of AOA-targeting nitrification inhibitors (NIs) with demonstrated efficacy under soil conditions remains limited. Moreover, the performance of candidate inhibitors in soil is often difficult to predict from pure-culture assays because their activity is strongly influenced by soil-dependent factors. In this study, we employed a recently developed high-throughput miniaturized soil incubation assay to perform a soil-based structure-activity relationship (SAR) analysis of SIAS (Specific Inhibitor of AOA in Soil), a pyrazolo-pyridine derivative previously identified as an AOA-targeting compound with strong additive nitrification inhibition effects when combined with the AOB-targeting inhibitor DMP (3,4-dimethyl-1H-pyrazole). To identify structural features associated with improved and more robust soil efficacy, a library of 27 SIAS-derived pyrazolo-pyridine analogues was evaluated directly in soil. The SAR analysis showed that inhibitory activity was governed by a specific combination of structural features and led to the discovery of Optimized SIAS (Opt. SIAS), a simplified analogue that consistently outperformed the original lead compound across diverse agricultural soils. Correlation analysis further revealed that soil pH and, particularly, silt content were major determinants of Opt. SIAS efficacy. The strong additive effects obtained through combined application of Opt. SIAS and DMP highlight the contribution of AOA to residual nitrification following AOB inhibition and demonstrate the potential of simultaneously targeting both groups. Together, these results expand the limited portfolio of effective AOA-targeting nitrification inhibitors and provide a foundation for the development of next-generation nitrification inhibition strategies aimed at improving nitrogen-use efficiency and reducing nitrogen losses from agricultural soils.

microbiology↗

bioRxiv2025

Unified nonparametric analysis of single-molecule spatial omics data using probabilistic indices

Spatial omics technologies localize individual molecules at subcellular resolution, shedding light on the spatial micro-organisation of living organisms. Yet the development of analysis methods struggles to keep pace with growing numbers of molecules, features and replicates being measured, and with new scientific questions arising on single molecules localization patterns. To meet this need, we present smoppix, a nonparametric analysis method based on the probabilistic index, which unifies tests for several univariate and bivariate localization patterns, such as aggregation of transcripts or colocalization of transcript pairs, in a single framework. These tests can be performed across tissues as well as within cells, while accounting for nested design structures. The high-dimensionality of the data is exploited for variance weighting and for providing a meaningful background null distribution, unique for every individual molecule. smoppix sidesteps segmentation, warping, edge correction and density estimation, and scales to high numbers of molecules and replicates thanks to an exact permutation null distribution. We demonstrate its power by unearthing spatial patterns in four published datasets from different kingdoms, and validate some findings experimentally on Selaginella moellendorfii roots. Our method is available from Bioconductor as the R-package smoppix.

bioinformatics↗

bioRxiv2024

New high-throughput screening assays for nitrification inhibitors identify an oxazolidine-thione as biological nitrification inhibitor

Nitrification is a microbial two-step process whereby ammonia (NH3) is first oxidized into nitrite (NO2-), by ammonia-oxidizing microorganisms, and then into nitrate (NO3-) by nitrite-oxidizing bacteria (NOB) in a mutualistic symbiosis. Due to high nitrogen (N) input in agriculture, this process needs to be slowed down as NO2- and NO3- easily leach, becoming unavailable for plants and leading to eutrophication. Moreover, they may be further processed into the very strong greenhouse gas nitrous oxide (N2O). Nitrification thus results in inefficient use of fertilizer and leads to detrimental environmental impact. Inhibitors can be used to mitigate these negative effects and are shown to positively affect plant growth and crop yield and strongly reduce nitrogen (N) pollution. However, currently, only a limited portfolio of nitrification inhibitors is commonly available. These show a variable efficiency and come with logistic complexities. As such, there is a high demand for a broader portfolio of novel molecules. To contribute to the discovery phase of new inhibitors and enable the evaluation of a large number of molecules, we developed miniaturized high-throughput screening assays on the soil-borne ammonia-oxidizing bacteria (AOB) Nitrosomonas europaea and Nitrosospira multiformis. We give a detailed overview of the procedure and illustrate its use by testing structural variants of oxazolidine-thiones that were previously discovered as nitrification inhibitors. This led to the discovery of the natural compound goitrin as a new biological nitrification inhibitor (BNI). Overall, the presented assays are promising discovery tools, as demonstrated by the newly discovered BNI, and may contribute to the advancement of a more sustainable agriculture.

microbiology↗

bioRxiv2022

Cellular and gene expression patterns associated with root bifurcation in Selaginella

The roots of lycophytes branch through dichotomy or bifurcation, which means that the root apex splits into two daughter roots. This is morphologically distinct from lateral root (LR) branching in the extant euphyllophytes, where LRs develop along the root axis at different distances from the apex. The process of root bifurcation is poorly understood, while such knowledge can be important, as it may represent an evolutionarily ancient strategy that roots recruited to form new stem cells or meristems. In this study, we examined root bifurcation in the lycophyte Selaginella moellendorffii. We characterized an in vitro developmental time-frame based on repetitive apex bifurcations, allowing us to sample different stages of dichotomous root branching and analyze the root meristem and root branching in S. moellendorffii at the microscopical and transcriptional level. Our results show that, in contrast to previous assumptions, initial cells in the root meristem are mostly not tetrahedral but rather show an irregular shape. Tracking down the early stages during root branching argues for the occurrence of a symmetric division of the single initial cell resulting in two apical stem cells allowing for root meristem bifurcation. Moreover, we generated a S. moellendorffii root branching transcriptome, which resulted in the delineation of a subset of core meristem genes. The occurrence of multiple meristem-related orthologues in this dataset, including inversely correlated expression profiles of a SCARECROW (SCR) versus a RETINOBLASTOMA-RELATED1 (RBR1) homologue suggests the presence of conserved pathways in the control of meristem and root stem cell establishment or maintenance. One-sentence summaryThe root of the spike moss Selaginella moellendorffii bifurcates following a symmetric cell division of the single stem cell and involves conserved genetic modules known from angiosperm roots.

plant biology↗