Biology subjects

Huber, P.

Publications and source records attributed to Huber, P..

6 recordsLinked to original sources

bioRxiv2025

Ecological processes shaping marine microbial assemblages diverge between equatorial and temperate time-series

Marine microbial communities are structured by a complex interplay of deterministic and stochastic processes, yet how these vary across latitudes remains poorly understood. Most long-term microbial observatories are restricted to temperate regions, limiting our ability to assess latitudinal contrasts in microbial dynamics. Here, we compare coastal microbial communities from two contrasting marine time-series stations using standardized molecular protocols: a new tropical site in the Equatorial Atlantic (EAMO, 6{degrees}S) and a well-studied temperate site in the Mediterranean Sea (BBMO, 41{degrees}N). Monthly 16S and 18S rRNA gene sequencing of two size-fractions (0.22-3 {micro}m and >3 {micro}m) over 41 months (from April 2013 to August 2016) revealed marked differences in taxonomic composition, temporal variability, and ecological assembly processes. Temperate communities exhibited strong seasonal turnover, higher beta-diversity, and tighter coupling with environmental variables such as temperature and daylength. In contrast, tropical communities were compositionally more stable and more governed by biotic factors and stochastic processes such as historical contingency and ecological drift. These patterns were consistent across taxonomic domains and size-fractions, though selection was generally stronger in prokaryotes and the smallest size-fraction. Co-occurrence networks at the temperate site were more densely connected and environmentally responsive compared to tropical networks, where stochastic processes and putative biological interactions gain prominence. This study highlights the importance of integrating observatories from underrepresented latitudes into global microbial monitoring efforts, particularly as climate change alters the amplitude and frequency of environmental drivers across the ocean.

ecology↗

bioRxiv2021

An objective-based prioritization approach to improve trophic complexity through ecological restoration

O_LIReassembling ecological communities and rebuilding habitats through active restoration treatments requires curating the selection of plant species to use in seeding and planting mixes. Ideally, these mixes should be assembled based on attributes that support ecosystem function and services, promote plant and animal species interactions and ecological networks in restoration while balancing project constraints. Despite these critical considerations, it is common for species mixes to be selected opportunistically. Reframing the selection of seed mixes for restoration around ecological objectives is essential for success but accessible methods and tools are needed to support this effort. C_LIO_LIWe developed a framework to optimize species seed mixes based on prioritizing plant species attributes to best support different objectives for ecosystem functions, services, and trophic relationships such as pollination, seed dispersal, and herbivory. We compared results to approaches where plant species are selected to represent plant taxonomic richness, dominant species, and at random. We tested our framework for 176 plant species found in European alpine grasslands and identified 163 associated attributes affiliated to trophic relationships, ecosystem functions, and services. C_LIO_LIIn all cases, trophic relationships, ecosystem functions, and services can be captured more efficiently through objective-based prioritization using the functional identity of plant species. Solutions (plant species lists) can be compared quantitatively, in terms of costs, species, or objectives. We confirm that a random draw of plant species from the regional plant species pool cannot be assumed to support other trophic groups and ecosystem functions and services. C_LIO_LISynthesis and Applications. Our framework is presented as a proof of concept to help restoration practitioners better apply quantitative decision-support to plant species selection in order to meet ecological restoration outcomes. Our approach may be tailored to any restoration initiative and habitat where seeding or planting mixes will be applied in active treatments. As global priority and resources are increasingly placed into restoration, this approach could be advanced to help make efficient decisions for many stages of the restoration process. C_LI

ecology↗

bioRxiv2020

The bacterial toxin ExoU requires a host trafficking chaperone for transportation and to induce necrosis

Pseudomonas aeruginosa is a causative agent in nosocomial infections, notably in ventilated or cystic fibrosis patients. P. aeruginosa isolates expressing the phospholipase ExoU, an effector of the type III secretion system, are the most pathogenic in clinics. Here, using a genome-wide screen, we discovered that ExoU toxicity requires DNAJC5, a host chaperone, to exert its necrotic activity. DNAJC5 is involved in an unconventional secretory pathway for misfolded proteins involving anterograde vesicular trafficking. DNAJC5-deficient human cells or Drosophila flies knocked-down for the DNAJC5 orthologue were largely resistant to ExoU virulence. ExoU colocalized with DNAJC5-positive vesicles in the host cytoplasm. DNAJC5 mutations preventing vesicle trafficking - identified in adult neuronal ceroid lipofuscinosis, a human congenital disease - inhibited ExoU-dependent cell lysis. These results suggest that, once injected into the host cytoplasm, ExoU docks to DNAJC5-positive secretory vesicles to reach the plasma membrane, where its phospholipase activity is triggered by binding to PI(4,5)P2.

microbiology↗

bioRxiv2020

Environmental heterogeneity ruling the action of ecological processes over the bacterial metacommunity assembly

Determining which processes take place in the spatial distribution of bacterioplankton metacommunities has been a central goal of microbial ecology. In freshwater ecosystems, selection has been spotted as the main driver shaping bacterial community. However, its relative importance compared with others processes (dispersal, drift, diversification) may depend on spatial heterogeneity and dispersal rates within a metacommunity. Still, a decrease in the role of selection is expected with increasing dispersal homogenization. Here, we investigate the main ecological processes modulating the bacterial assembly in contrasting scenarios of environmental heterogeneity. We carried out a spatiotemporal survey in the floodplain system of Parana River. The bacterioplankton metacommunity was studied by a step-forward analysis combining different statistical inferences based on the phylogenetic and taxa turnover as well as co-occurrence networks. We found that selection was the main process even at both extremes of environmental heterogeneity and homogeneity, challenging the general view that the strength of selection is weakened due to dispersal homogenization. The ecological processes acting on the community also determined the complexity and randomness of bacterial networks. The heterogeneous selection promoted greater network complexity increasing the {beta}-diversity, and bacterial associations were more random with the increasing influence of stochasticity. Finally, the spatiotemporal heterogeneity was an important factor determining the number and identity of keystone taxa in the system. Integrating all these empirical evidences we propose a new conceptual model that elucidates how the environmental heterogeneity guides the action of ecological processes shaping the bacterial metacommunity.

ecology↗

bioRxiv2017

CLIQ-BID: A method to quantify bacteria-induced damage to eukaryotic cells by automated live-imaging of bright nuclei

Pathogenic bacteria induce eukaryotic cell damage which range from discrete modifications of signalling pathways, to morphological alterations and even to cell death. Accurate quantitative detection of these events is necessary for studying host-pathogen interactions and for developing strategies to protect host organisms from bacterial infections. Investigation of morphological changes is cumbersome and not adapted to high-throughput and kinetics measurements. Here, we describe a simple and cost-effective method based on automated analysis of live cells with stained nuclei, which allows real-time quantification of bacteria-induced eukaryotic cell damage at single-cell resolution. We demonstrate that this automated high-throughput microscopy approach permits screening of libraries composed of interference-RNA, bacterial strains, antibodies and chemical compounds in ex vivo infection settings. The use of fluorescently-labelled bacteria enables the concomitant detection of changes in bacterial growth. Using this method named CLIQ-BID (Cell Live Imaging Quantification of Bacteria Induced Damage), we were able to distinguish the virulence profiles of different pathogenic bacterial species and clinical strains.

microbiology↗

bioRxiv2017

microCT-Based Skeletal Phenomics in Zebrafish Reveals Virtues of Deep Phenotyping at the Whole-Organism Scale

Phenomics, which ideally involves in-depth phenotyping at the whole-organism scale, may enhance our functional understanding of genetic variation. Here, we demonstrate methods to profile hundreds of measures comprised of morphological and densitometric traits from a large number sites in the axial skeleton of adult zebrafish. We show the potential for vertebral patterns to confer heightened sensitivity, with similar specificity, in discriminating mutant populations compared to analyzing individual vertebrae in isolation. We identify phenotypes associated with human brittle bone disease and thyroid stimulating hormone receptor hyperactivity. Finally, we develop allometric models and show their potential to aid in the discrimination of mutant phenotypes masked by alterations in growth. Our studies demonstrate virtues of deep phenotyping in a spatially distributed organ. Analyzing phenotypic patterns may increase productivity in genetic screens, and could facilitate the study of genetic variants associated with smaller effect sizes, such as those that underlie complex diseases.

genetics↗