Biology subjects

Marquis, B.

Publications and source records attributed to Marquis, B..

3 recordsLinked to original sources

bioRxiv2023

Experimental exposure to winter thaws reveals tipping point in yellow birch bud mortality and phenology in the northern temperate forest of Quebec, Canada

Climate change is expected to increase the frequency and intensity of winter thaws, which could have two contrasting effects on leaf phenology. Phenology could either be advanced through the acceleration of forcing accumulation or chilling completion, or be postponed through a reduction in chilling associated with warming air temperature. We tested the influence of winter thaws on budburst phenology by exposing 300 tree cuttings of sugar maple and yellow birch trees to five different frequencies and durations of winter thaws in the lab. In spring, half of the cuttings were exposed to air temperature in two cities representing an air temperature gradient of + 2.0 {degrees}C to mimic the ongoing climate warming and bud phenology was monitored three times a week. Irrespective of thaw treatment, yellow birch phenology occurred earlier in the warmer city, showing the importance of spring temperature in triggering budburst. The treatment with the highest frequency and duration of thawing increased bud mortality and delayed the onset of spring phenology whereas low frequency treatments did not, thereby identifying a tipping point in the impact of winter thaws on bud phenology. Past this point, winter thaws could slow the acceleration of bud phenology induced by warmer spring temperature and limit carbon uptake by delaying the closure of the canopy. Climate change simulations projected by the CMIP6 Canadian downscaled climate scenario show that winter thaws will increase in frequency. Hence the expected advance in the spring phenology associated with warmer spring is not necessarily as straightforward as previously thought. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/563331v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@68374borg.highwire.dtl.DTLVardef@631a6org.highwire.dtl.DTLVardef@a5b35corg.highwire.dtl.DTLVardef@a2679b_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2023

zDB: bacterial comparative genomics made easy

The analysis and comparison of genomes relies on different tools for tasks such as annotation, orthology prediction and phylogenetic inference. Most tools are specialized for a single task and additional efforts are necessary to integrate and visualize the results. To fill this gap, we developed zDB, an application that integrates an analysis pipeline and a visualization platform. Starting from annotated Genbank files, zDB identifies orthologs and infers a phylogeny for each orthogroup. A species phylogeny is also constructed from shared single-copy orthologs. The results can be enriched with Pfam protein domain prediction, COG and KEGG annotations and Swissprot homologs. The web application allows searching for specific genes or annotations, running Blast queries and comparing genomic regions and whole genomes. The metabolic capacities of organisms can be compared at either the module or pathway levels. Finally, users can run queries to examine the conservation of specific genes or annotations across a chosen subset of genomes and display the results as a list of genes, Venn diagram or heatmaps. Those features will make zDB useful for both bioinformaticians and researchers more accustomed to laboratory research. zDB is perfectly suited to process datasets with tens to hundred of genomes on a desktop machine. IMPORTANCEGenome comparison and analysis rely on many independent tools, leaving to scientists the burden to integrate and visualize their results for interpretation. To alleviate this burden, we have built zDB, a comparative genomics tool that includes both an analysis pipeline and a visualization platform. The analysis pipeline automates gene annotation, orthology prediction and phylogenetic inference, while the visualization platform allows scientists to easily explore the results in a web browser. Among other features, the interface allows users to visually compare whole genomes and targeted regions, assess the conservation of genes or metabolic pathways, perform Blast searches or look for specific annotations. Altogether, this tool will be useful for a broad range of applications in comparative studies between two to hundred genomes. Furthermore, it is designed to allow sharing datasets easily at local or international scale, thereby supporting exploratory analyses for non-bioinformaticians on the genome of their favorite organisms.

bioinformatics↗

bioRxiv2022

Temperature affects the host range of Rhabdochlamydia porcellionis and the infectivity of Waddlia chondrophila and Chlamydia trachomatis elementary bodies

The Rhabdochlamydiaceae family is a recent addition to the Chlamydiales order. Its members were discovered in cockroaches and woodlice but recent metagenomics surveys demonstrated the widespread distribution of this family in the environment. It was moreover estimated to be the largest family of the Chlamydiales order based on 16S rRNA encoding gene diversity. Unlike most chlamydia-like organisms, no Rhabdochlamydiaceae could be co-cultivated in amoebae and its host range remains largely unknown. Here, we tested the permissivity of various mammalian and arthropod cell lines to determine the host range of Rhabdochlamydia porcellionis, the only cultured representative of this family. While a growth could initially only be obtained in the Sf9 cell line, lowering the incubation temperature of the mammalian cells from 37 {degrees}C to 28 {degrees}C allowed R. porcellionis to grow in those cells. Furthermore, a 6 h exposure to 37 {degrees}C was sufficient to irreversibly block the replication of R. porcellionis, suggesting that this bacterium either lost or never acquired the ability to grow at 37 {degrees}C. We next sought to determine if temperature would also affect the infectivity of elementary bodies. Although we could not purify enough bacteria to reach a conclusive result for R. porcellionis, our experiment showed that the elementary bodies of Chlamydia trachomatis and Waddlia chondrophila lose their infectivity faster at 37 {degrees}C than at room temperature. Our results demonstrate that members of the Chlamydiales adapt to the temperature of their host organism and that this adaptation can in turn restrict their host range. ImportanceThe Rhabdochlamydiaceae family is part of the Chlamydiales, a bacterial order that includes obligate intracellular bacteria sharing the same biphasic developmental cycle. This family have been shown to be highly prevalent in the environment, particularly in freshwater and soil and despite being estimated to be the largest family in the Chlamydiales order, is only poorly studied. Members of the Rhabdochlamydiaceae have been detected in various arthropods like ticks, spiders, cockroaches and woodlice, but the full host range of this family is currently unknown. In this study, we showed that R. porcellionis, the only cultured representative of the Rhabdochlamydiaceae family cannot grow at 37 {degrees}C and is quickly inactivated at this temperature. A similar temperature sensitivity was also observed for elementary bodies of chlamydial species adapted to mammals. Our work demonstrates that some chlamydiae adapt to the temperature of their reservoir, making a jump between species with different body temperatures unlikely.

microbiology↗