Biology subjects

Boeckx, P.

Publications and source records attributed to Boeckx, P..

3 recordsLinked to original sources

bioRxiv2025

Revised 16S rRNA V4 hypervariable region targeting primers enhance detection of Patescibacteria and other lineages across diverse environments

Primer bias in 16S rRNA gene amplicon sequencing can distort microbial diversity estimates by underrepresenting key taxa. We introduce a modified primer pair (V4-EXT) targeting the hypervariable V4 region of bacterial and archaeal 16S rRNA genes, with improved in silico taxonomic inclusivity. To benchmark performance, we analyzed 938 samples from terrestrial, aquatic, and host-associated habitats, comparing microbial community profiles derived with V4-EXT and the currently most widely used V4-targeted primers. V4-EXT substantially improved the detection of Patescibacteria and other underrepresented lineages, such as Chloroflexota and Iainarchaeota, while enhancing recovery of novel amplicon sequence variants across sample types. Overall, V4-EXT provides broader taxonomic coverage and more inclusive microbial community profiles, particularly in high-diversity ecosystems such as groundwater and soils. We propose V4-EXT as a robust successor for comprehensive microbial community analysis across diverse habitats.

microbiology↗

bioRxiv2023

Co-habiting ants and silverfish display a converging feeding ecology

O_LISpecies from a great number of animal taxa have specialized to living with social hosts. Depending on their level of specialization, these symbiotic animals are characterized by distinct behavioural, chemical, and morphological traits that enable close heterospecific interactions. Despite its functional importance, our understanding of the feeding ecology of specialized animals living with social hosts remains limited. C_LIO_LIIn this study, we examined how host specialization of silverfish co-habiting with ants affects several components of their feeding ecology. We combined stable isotope profiling, feeding assays, phylogenetic reconstruction, and microbial community characterization of the Neoasterolepisma silverfish genus and a wider nicoletiid and lepismatid silverfish panel where divergent myrmecophilous lifestyles are observed. C_LIO_LIStable isotope profiling ({delta}13C and {delta}15N) showed that the isotopic niches (proxy for trophic niches) of granivorous Messor ants and Messor-specialized Neoasterolepisma exhibit a remarkable overlap within an ant nest. Trophic experiments and gut dissections further supported that these specialized Neoasterolepisma silverfish transitioned to a diet that includes plant seeds. In contrast, the isotopic niches of generalist Neoasterolepisma silverfish and generalist nicoletiid silverfish were clearly different from their ant hosts within the shared nest environment. C_LIO_LIThe impact of the myrmecophilous lifestyle on feeding ecology was also evident in the internal silverfish microbiome. Compared to generalists, Messor-specialists exhibited a higher bacterial density and a higher proportion of heterofermentative lactic acid bacteria. Moreover, the nest environment explained the infection profile (or the 16S rRNA genotypes) of Weissella bacteria in Messor-specialized silverfish and the ant hosts. C_LIO_LITogether, we show that social hosts are important determinants for the feeding ecology of symbiotic animals, and can induce diet convergence. C_LI

ecology↗

bioRxiv2019

Diurnal variation in xylem water isotopic signature biases depth of root-water uptake estimates

O_LIStable water isotopes are a powerful and widely used tool to derive the depth of root water uptake (RWU) in lignified plants. Uniform xylem water isotopic signature (i-H2O-xyl) along the length of a lignified plant is a central assumption, which has never been properly evaluated.\nC_LIO_LIHere we studied the effects of diurnal variation in RWU, sap flow velocity and various other soil and plant parameters on i-H2O-xyl signature within a plant using a mechanistic plant hydraulic model.\nC_LIO_LIOur model predicts significant variation in i-H2O-xyl along the full length of an individual plant arising from diurnal RWU fluctuations and vertical soil water heterogeneity. Moreover, significant differences in i-H2O-xyl emerge between individuals with different sap flow velocities. We corroborated our model predictions with field observations from French Guiana and northwestern China. Modelled i-H2O-xyl varied considerably along stem length ranging up to 18.3{per thousand} in {delta}2H and 2.2{per thousand} in {delta}18O, largely exceeding the range of measurement error.\nC_LIO_LIOur results show clear violation of the fundamental assumption of uniform i-H2O-xyl and occurrence of significant biases when using stable isotopes to assess RWU. As a solution, we propose to include monitoring of sap flow and soil water potential for more robust RWU depth estimates.\nC_LI

plant biology↗