Biology subjects

Laforest-Lapointe, I.

Publications and source records attributed to Laforest-Lapointe, I..

12 recordsLinked to original sources

bioRxiv2026

Atypical immunity induced by extracellular water in plants

Microbial pathogens require nutrients and water to support their growth and proliferation. Pathogen-mediated resource acquisition is orchestrated by the secretion of virulence factors that have evolved a diversity of forms (from effector proteins to small toxins), but which have converged in function (resource acquisition). A key observable virulence mechanism employed by a large number of microbial pathogens to cause disease is to induce a water-rich niche in the extracellular space (i.e. the apoplast) of their host, known as water-soaked lesions. Given the ubiquity of this virulence mechanism, we asked whether plants respond to pathogen-induced extracellular water to activate immune programs. We find that inducing a water-soaked apoplast induces an atypical transcriptional response, yet results in a functional immune response that restricts pathogen growth as effectively as canonical pattern-triggered immunity. Genetic and functional analyses reveal a role for the immune phytohormone salicylic acid (SA) in mediating apoplastic water-induced immunity (AWII). These results suggest that plants engage in an immune-priming program in response to apoplastic water accumulation, suggesting that the pathogenic niches induced during infection may be perceived as danger signals.

plant biology↗

bioRxiv2026

Taxonomic profilers and their influence on metagenomic diversity analyses

Estimating taxonomic profiles is a central task in microbiome research. Several bioinformatic tools have been developed for this purpose, differing in algorithmic strategy, reference database flexibility, sensitivity parameters, and the type of abundance they estimate. As a result, taxonomic profiles carry an unwanted methodological signal whose driving characteristics remains understudied. While benchmarks have evaluated the performance of some of these tools, they rely on simulated data; little work has been done to compare them using real metagenomes in the presence of noise and uncharacterised diversity. Overall, the impact of taxonomic profiler choice and parameterisation on scientific conclusions remains poorly understood. First, we provide a much-needed characterisation of four taxonomic profilers to help researchers better understand the available bioinformatic tools and inform their methodological choices. Then, we leverage 1,211 shotgun metagenomes from eight datasets to compare these taxonomic profilers across 13 methodological designs. Based on diversity indices, we found substantial variability in estimated taxonomic composition depending on methodological features such as reference database and algorithmic strategy. Alpha diversity analysis was substantially sensitive totool choice (particularly among k-mer-based tools) and reference database. Beta diversity showed sensitivity to both database and parameter choices, yet this variability barely affected statistical inference. Our findings highlight the sensitivity of taxonomic diversity analyses to taxonomic profiling methodology and the importance for researchers to consider assessing the robustness of their results to choice of tool, parameter, and reference database. Crucially, differences in sample diversity across methodologies are symptomatic of differences in estimated taxonomic composition, which can affect any analysis based on taxonomic abundances. Overall, this study underscores the importance of tool selection and parametrisation, and of conducting sensitivity analyses to support robust and reliable scientific conclusions. AUTHOR SUMMARYMicrobiome research relies on bioinformatic tools to determine which microbes are present in a sample and estimate their relative abundances, a process known as taxonomic profiling. Because this task requires comparing tens of millions of DNA sequences against thousands of microbial genomes, a wide range of computational strategies have been developed to make profiling accurate and efficient. As a result, many taxonomic profilers are now available, yet do not provide the same results. Although previous studies have evaluated their precision and sensitivity, less attention has been given to how the choice of profiler may influence the scientific conclusions drawn from microbiome data. Here, we selected four widely used taxonomic profilers to examine whether researchers would reach the same biological conclusions when comparing microbiomes across groups of samples, such as healthy and diseased individuals. We show that different profilers can lead to different biological conclusions and identify key tool characteristics that contribute to these discrepancies. Moreover, we provide a comparative overview of these four profilers, offering practical guidance for researchers seeking to choose the most appropriate tool for their study. These findings highlight the importance of software choice in microbiome research and support more transparent and reproducible data analysis practices.

bioinformatics↗

bioRxiv2026

Montreal Urban Observatory: research platform to monitor urban forest ecosystems for global change adaptation and health

As urban populations grow, cities are increasingly seen not only as drivers of climate change but also as critical arenas for implementing mitigation and adaptation strategies. Urban forests and green infrastructure play a vital role in shaping environmental quality and human health, yet access to these benefits remains inequitable. The Montreal Urban Observatory was designed to investigate the complex relationships among biodiversity, ecosystem functioning, and human health. Twenty-five permanent plots were established across the Island of Montreal, strategically located along gradients in vegetation cover, population density, and mean household income. Interdisciplinary research within the Observatory focuses on themes including urban forest structure and function, abiotic conditions, biodiversity, ecological interactions, natures contributions to people, related human health outcomes, and developing novel methodological approaches. The Observatory supports long-term, cross-scale monitoring and fosters collaborative research on urban social-ecological systems, thus contributing to global initiatives to enhance urban sustainability and equity through nature-based solutions. Early results confirm the relevance of the main gradients for several organisms and response variables, from microbes to trees and abiotic factors. For example, sampling all trees, public and private, within a radius of 200m centered on each plot revealed significant differences in the diversity and structure of private and public trees, including an overwhelming dominance of Thuya occidentalis not captured in commonly used public tree inventories.

ecology↗

bioRxiv2025

Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients

Urban vegetation varies with socio-economic gradients, as lower-income neighborhoods often host sparser and less diverse green spaces. This disparity may affect respiratory health by influencing exposure to bioaerosols. Understanding the characteristics of this aerobiome could help anticipate risks related to allergies and other respiratory conditions. Here, we hypothesized that urban vegetation cover and socio-economic status shape urban bioaerosols. We sampled bioaerosols at 65 sites across three Canadian cities of varying population size and density using an active air sampler over four months, and characterized their bacterial, fungal, and pollen composition using amplicon sequencing. Seasonal alpha diversity varied significantly for fungi and pollen. Based on beta diversity, sampling period alone explained up to 40% of pollen, 29% of fungal, and 11% of bacterial community composition variation. In contrast, vegetation cover explained only a minor portion of the variance in bioaerosol composition, and median household income, almost none. These findings provide a critical baseline for understanding the urban aerobiome and highlight the need to study how vegetation identity and diversity, rather than cover alone, may shape bioaerosol dynamics in cities. As cities grow and urban greening initiatives expand, demystifying the aerobiome dynamics becomes an urgent public health priority.

microbiology↗

bioRxiv2025

Responses to Agricultural Practices in Apple Orchards: A Field-Based Mycobiome Study of the Phyllosphere

Microbial communities in the phyllosphere are key players in plant health and disease resistance, yet their response to agricultural management strategies remains poorly understood under field conditions. Here, we compare fungal community composition and diversity across conventional and organic apple orchards using ITS amplicon sequencing. Leaf samples were collected from six sites at three distinct time points during the 2023 growing season (in May, July, and August) corresponding approximately to monthly intervals throughout the summer. Flower samples were collected from the same trees in May. Our analyses reveal that agricultural management strategies are significantly associated with fungal community structure, with effects intensifying from May to July. Both types of management strategies showed enrichment for different genera known to include common apple tree pathogens: Alternaria and Podosphaera were associated with conventional sites, while Didymella and Ramularia were associated with organic sites. Although fungal alpha diversity was higher in May at conventional orchards compared to organic orchards, it declined over time at conventional sites while it remained stable at organic sites. Together, these patterns indicate that distinct management interventions impose contrasting selective pressures on the apple tree phyllosphere mycobiome, thus shaping both broad fungal community composition and the dominance dynamics of key fungal taxa. Our findings underscore the ecological relevance and inherent challenges of field-based microbiome research, and provide insights to inform the development of sustainable orchard management strategies grounded in fungal community dynamics.

microbiology↗

bioRxiv2024

Chloroplastic ROS bursts initiate salicylic acid biosynthesis in plant immunity

Chloroplasts are essential centers of signal integration and transduction in plants. They are involved in the biosynthesis of primary and specialized metabolites, including salicylic acid (SA), a key defense phytohormone synthesized via the conserved chorismate biosynthetic pathway. However, the identity of the signal(s) that ultimately triggers SA induction in chloroplasts upon perception of a biotic threat has remained elusive. Here, we provide evidence of a functional link between chloroplast-derived reactive oxygen species (cROS) and SA production. We observe that inhibiting ROS bursts generated from photosystem II during plant immune activation completely abrogates the induction of SA synthesis in response to immunity-inducing signals, without affecting SA-independent immune responses. Indeed, time course analyses show that the induction of SA marker genes parallels that of cROS production during an immune response. Consistent with this, preventing cROS induction is sufficient to nullify the immune protection normally conferred by activating immunity prior to an infection. Analyses of transcriptomes and photosynthetic efficiency show that two conserved effectors from the phytopathogen Pseudomonas syringae, HopM1 and AvrE1, redundantly disrupt photosynthesis and cROS bursts. These effects reduce SA accumulation and are mediated via the impact of HopM1 and AvrE1 in inducting host abscisic acid signaling. Our results suggest that a change in chloroplastic redox homeostasis induced by biotic stressors acts as an initiator of plant immunity through the production of SA, and that this response is targeted by conserved pathogen effector proteins.

plant biology↗

bioRxiv2023

Moss species, sections, and land use type drive moss-associated microbial taxonomy and functions in boreal forests

Moss-microbe interactions contribute to ecosystem processes in boreal forests. Yet, how host-specific characteristics and the environment drive the composition and metabolic potential of moss microbiomes is still poorly understood. In this study, we use shotgun metagenomics to identify the taxonomy and metabolic potential of the bacteria of four moss species of the boreal forests of Northern Quebec, Canada. To characterize moss bacterial community composition and diversity, we assembled the genomes of 110 potentially novel bacterial species. Our results highlight that moss genus, species, gametophyte section, and to a lesser extent soil pH and soil temperature, drive moss-associated bacterial community composition and diversity. In the brown gametophyte section, two Stigonema spp. showed partial pathway completeness for photosynthesis and nitrogen fixation, while all brown-associated Hyphomicrobiales had complete assimilatory nitrate reduction pathways and many nearly complete carbon fixation pathways. Several brown-associated species showed partial to complete pathways for coenzyme M and F420 biosynthesis, important for methane metabolism. In addition, green-associated Hyphomicrobiales (Methylobacteria spp.) displayed potential for the anoxygenic photosystem II pathway. Overall, our findings demonstrate how host-specific characteristics and environmental factors shape the composition and metabolic potential of moss bacteria, highlighting their roles in carbon fixation, nitrogen cycling, and methane metabolism in boreal forests.

microbiology↗

bioRxiv2022

Soil metatranscriptomics: An improved RNA extraction method toward functional analysis using nanopore direct RNA sequencing

Soil microbes play an undeniable role in sustainable agriculture, plant health, and soil management. A deeper understanding of soil microbial composition and function has been gained through next-generation sequencing. While soil metagenomics has provided valuable information about microbial diversity, issues stemming from RNA extraction, low RNA abundance in some microbial populations (e.g., viruses), and mRNA enrichment have slowed the progress of soil metatranscriptomics. A variety of soil RNA extraction methods have been developed so far. Yet none of the available protocols can obtain RNA with high quality, purity, and yield for third-generation sequencing. This latter requires RNA with high quality and large quantities (with no or low contamination, such as humic acids). Also, use of commercial kits for in-batch soil RNA extraction is quite expensive, and these commercial kits lack buffer composition details, which prevents the optimization of protocols for different soil types. An improved and cost-effective method for extracting RNAs from mineral and organic soils is presented in this paper. An acidic sodium acetate buffer and phosphate buffer with modifications to bead-beating and nucleic acid precipitation lead to higher RNA yields and quality. Using this method, we obtained almost DNA-free RNA. By using nanopores direct RNA sequencing, the extracted contamination-free RNAs were successfully sequenced. Lastly, taxonomic groups such as bacteria, fungi, archaea, and viruses were classified and profiled as well as functional annotation of the datasets was carried out using an in-house customized bioinformatics workflow.

microbiology↗

bioRxiv2022

Light prevents pathogen-induced aqueous microenvironments via potentiation of salicylic acid signaling

Upon establishment of an infection, many plant pathogens induce an aqueous microenvironment in the extracellular space of their host, resulting in water-soaked lesions. In the case of Pseudomonas syringae (Pst), this is accomplished through the activity of water-soaking effectors that stimulate abscisic acid (ABA) production and signaling, which results in stomatal closure. This reduces transpiration and induces a microenvironment favorable for bacterial growth. Stomata are also highly sensitive to environmental conditions, including light and circadian rhythm. Here, we show that a period of darkness is required for water-soaking, and that a constant light regime abrogates the water-soaking activity of Pst effectors. Additionally, we show that constant light induces resistance against Pst and that this effect requires salicylic acid (SA). An increase in SA production upon infection under constant light did not affect effector-induced ABA signaling, but rather abrogated ABAs ability to induce stomatal closure. Indeed, under normal diurnal light regimes, application of a SA analog is sufficient to prevent the ability of the pathogen to induce stomatal closure and a water-rich niche in the apoplast. Our results provide a novel approach to interfering with a common virulence strategy, as well as providing a physiological mechanism by which SA functions in defense against certain pathogens.

plant biology↗

bioRxiv2020

Consumption of artificially sweetened beverages during pregnancy impacts infant gut microbiota and body mass index

Artificial sweetener consumption by pregnant women has been associated with an increased risk of infant obesity, but the underlying mechanisms are unknown. We aimed to determine if maternal consumption of artificially sweetened beverages (ASB) during pregnancy is associated with modifications of infant gut bacterial community composition during the first year of life, and whether these alterations are linked with infant body mass index (BMI) at one year of age. This research included 100 infants from the prospective Canadian CHILD Cohort Study, selected based on maternal ASB consumption during pregnancy (50 non-consumers and 50 daily consumers). We identified four microbiome clusters, of which two recapitulated the maturation trajectory of the infant gut bacterial communities from immature to mature and two deviated from this trajectory. Maternal ASB consumption was associated with the depletion of several Bacteroides sp. and higher infant BMI. As we face an unprecedented rise in childhood obesity, future studies should evaluate the causal role of gut microbiota in the association between maternal ASB consumption, infant development and metabolism, and body composition.

microbiology↗

bioRxiv2019

Contribution of fungal microbiome to intestinal physiology, early-life immune development and mucosal inflammation in mice

Gut microbiomes make major contributions to the physiological and immunological development of the host, but the relative importance of their bacterial and fungal components, and how they interact, remain largely unknown. We applied carefully controlled experiments in gnotobiotic mice colonized with defined communities of bacteria, fungi, or both to differentiate the direct role of fungi on microbiome assembly, host development, and susceptibility to colitis and airway inflammation. Our results revealed that fungal colonization alone was insufficient to promote the intestinal anatomic and physiological changes seen in mice colonized by bacteria, and had limited impact on the fecal metabolome. However, fungal colonization promoted major shifts in bacterial microbiome ecology, and had an independent effect on the innate and adaptive immune development in young mice. Fungi further exacerbated some aspects of the inflammatory effects of the bacterial community during OVA-induced airway inflammation by promoting macrophage infiltration in the airway. Our results demonstrate a dominant ecological and physiological role of bacteria in gut microbiomes, but highlight fungi as an ecological factor shaping the assembly of the bacterial community and a direct capacity to impact immune system and modulate disease susceptibility. These findings demonstrate that studies focused on bacteria alone provide an incomplete portrayal on microbiome ecology and functionality, and prompt for the inclusion of fungi in human microbiome studies.

microbiology↗

bioRxiv2019

Exposure to parasitic protists and helminths changes the intestinal community structure of bacterial microbiota but not of eukaryotes in a cohort of mother-child binomial from a semi-rural setting in Mexico

Around 3.5 billion people are colonized by intestinal parasites worldwide. Intestinal parasitic eukaryotes interact not only with the host, but also with the intestinal microbiota. In this work, we studied the relationship between the presence of multiple enteric parasites and the community structure of the bacterial and eukaryote intestinal microbiota in an asymptomatic cohort of mother-child binomials from a semi-rural community in Mexico. The intestinal parasites identified were Blastocystis hominis, Entamoeba histolytica/dispar, Endolimax nana, Chilomastix mesnili, Iodamoeba butshlii, Entamoeba coli, Hymenolepis nana and Ascaris lumbricoides. We sequenced bacterial 16S rDNA and eukaryotic 18S rDNA in fecal samples of 46 mothers and their respective children, with ages ranging from two to twenty months. Although we did not find significant alpha-diversity changes, we found a significant effect of parasite exposure on bacterial beta-diversity, which explained between 5.2% and 15.0% of the variation of the bacterial community structure. Additionally, exposure to parasites was associated with significant changes in relative abundances of bacterial taxa, characterized by increases in the Clostridia and decreased Actinobacteria and Bacteroidia abundances. There were no significant changes of intestinal microeukaryote abundances associated with parasite exposure. However, we found several significant positive correlations between intestinal bacteria and eukaryotes, including co-occurrence of the fungi Candida tropicalis with Bacteroides and Actinomyces, and Saccharomycetales with Bifidobacterium and Prevotella copri. These bacterial community structure changes associated with parasite exposure imply effects on microbial metabolic routes, host nutrient uptake abilities and intestinal immunity regulation in host-parasite interactions.\n\nIMPORTANCEThe impact of intestinal eukaryotes on the prokaryotic microbiome composition of asymptomatic carriers has not been extensively explored, especially in children and in hosts with multiple parasites. In this work, we studied the relationship between protist and helminth parasite colonization and intestinal microbiota structure in an asymptomatic population of mother-child binomials from the semi-rural community of Morelos in Mexico. We found that the presence of parasitic eukaryotes correlated with changes in the bacterial community structure in the intestinal microbiota in an age-dependent way. This was characterized by an increase of the relative abundance of the class Clostridia and the decrease of Actinobacteria and Bacteroidia. While there were no significant associations between the presence of parasites and microeukaryote community structure, we observed strong positive correlations between bacterial and eukaryote taxa, identifying novel relationships between prokaryotes and fungi, and reflecting the diet of the human population studied.

microbiology↗