Pollen et microbes : les défis de la vie urbaine face au changement global

"La biodiversité, du plus petit des organismes au plus grand, permet aux écosystèmes de fournir d'innombrables services essentiels pour la santé des populations humaines (ex. : productivité végétale, qualité de l’air et de l’eau). Pourtant, Ripple et al. ont montré en 2017 que l’intensification actuelle des activités anthropiques (activités dues aux humains) provoque une diminution globale de la biodiversité. Aujourd’hui, la plupart des écosystèmes subissent des perturbations constantes liées aux modifications directes de l'habitat (ex. : l'urbanisation) et aux effets indirects du changement global sur les conditions abiotiques (ex. : la température). Les pertes de biodiversité et donc des services qu’elle nous procure menacent les écosystèmes et leurs habitants, y compris les humains, selon Anderson-Teixeira et al. en 2012. D’ailleurs, aucun écosystème n'évolue et ne se développe aussi rapidement que l’écosystème urbain. On estime que les personnes vivant en ville représenteront plus de 70 % de la population mondiale dans les 30 prochaines années (World Health Statistics, 2016). La synergie entre perte de biodiversité et urbanisation pourrait altérer la santé des populations humaines, entraînant alors des coûts substantiels de santé pour la société (Sandifer, Sutton-Grier, et Ward 2015). [...]

Un rôle de taille pour les microorganismes

Il est plus que jamais essentiel d’élucider le rôle des interactions entre les microorganismes et le changement global planétaire afin de protéger la santé des populations humaines et les fonctions des écosystèmes terrestres (i.e. productivité, biodiversité, résilience). Si une grande majorité des recherches portant sur l’effet du changement global envers les écosystèmes s’intéresse aux processus visibles à l’œil nu (le macroscopique), les avancées en biologie moléculaire et en microbiologie nous permettent désormais d’apprécier le pouvoir du très petit?: les microorganismes. À la lumière d’études récentes qui démontrent le rôle des microbes dans la lutte au changement global, il est crucial de fournir un effort immédiat, soutenu et concerté pour inclure de façon directe la vie microscopique dans la recherche, le développement de biotechnologies, de même que dans les décisions de politique et de gestion. Même si nous vivons dans?«?l’Anthropocène?», une période géologique définie comme l’ère de la domination de l’être humain sur la planète, force est de constater le rôle de taille que jouent les microorganismes pour les écosystèmes terrestres. Cet article présente l’état des connaissances actuelles sur les rôles des microorganismes des écosystèmes terrestres (i.e. forêts, prairies) et souligne trois avenues de recherche prometteuses visant le développement d’outils de bio-contrôle microbien pour réduire les effets négatifs du changement global: (1) l’ingénierie des interactions plantes-microbes; (2) la séquestration du carbone par les microbes du sol; et (3) les techniques de remédiation basées sur les microbes

Intraspecific variability in functional traits matters : case study of Scots pine

Although intraspecific trait variability is an important component of species ecological plasticity and niche breadth, its implications for community and functional ecology have not been thoroughly explored. We characterized the intraspecific functional trait variability of Scots pine (Pinus sylvestris) in Catalonia (NE Spain) in order to (1) compare it to the interspecific trait variability of trees in the same region, (2) explore the relationships among functional traits and the relationships between them and stand and climatic variables, and (3) study the role of functional trait variability as a determinant of radial growth. We considered five traits: wood density (WD), maximum tree height (H max), leaf nitrogen content (Nmass), specific leaf area (SLA), and leaf biomass-to-sapwood area ratio (B L:A S). A unique dataset was obtained from the Ecological and Forest Inventory of Catalonia (IEFC), including data from 406 plots. Intraspecific trait variation was substantial for all traits, with coefficients of variation ranging between 8% for WD and 24% for B L:A S. In some cases, correlations among functional traits differed from those reported across species (e.g., H max and WD were positively related, whereas SLA and Nmass were uncorrelated). Overall, our model accounted for 47% of the spatial variability in Scots pine radial growth. Our study emphasizes the hierarchy of factors that determine intraspecific variations in functional traits in Scots pine and their strong association with spatial variability in radial growth. We claim that intraspecific trait variation is an important determinant of responses of plants to changes in climate and other environmental factors, and should be included in predictive models of vegetation dynamics

Variation in the leaf and root microbiome of sugar maple (Acer saccharum) at an elevational range limit

Background Bacteria, archaea, viruses and fungi live in various plant compartments including leaves and roots. These plant-associated microbial communities have many effects on host fitness and function. Global climate change is impacting plant species distributions, a phenomenon that will affect plant-microbe interactions both directly and indirectly. In order to predict plant responses to global climate change, it will be crucial to improve our understanding of plant-microbe interactions within and at the edge of plant species natural ranges. While microbes affect their hosts, in turn the plant’s attributes and the surrounding environment drive the structure and assembly of the microbial communities themselves. However, the patterns and dynamics of these interactions and their causes are poorly understood. Methods In this study, we quantified the microbial communities of the leaves and roots of seedlings of the deciduous tree species sugar maple (Acer saccharum Marshall) within its natural range and at the species’ elevational range limit at Mont-Mégantic, Quebec. Using high-throughput DNA sequencing, we quantified the bacterial and fungal community structure in four plant compartments: the epiphytes and endophytes of leaves and roots. We also quantified endophytic fungal communities in roots. Results The bacterial and fungal communities of A. saccharum seedlings differ across elevational range limits for all four plant compartments. Distinct microbial communities colonize each compartment, although the microbial communities inside a plant’s structure (endophytes) were found to be a subset of the communities found outside the plant’s structure (epiphytes). Plant-associated bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes while the main fungal taxa present were Ascomycota. Discussion We demonstrate that microbial communities associated with sugar maple seedlings at the edge of the species’ elevational range differ from those within the natural range. Variation in microbial communities differed among plant components, suggesting the importance of each compartment’s exposure to changes in biotic and abiotic conditions in determining variability in community structure. These findings provide a greater understanding of the ecological processes driving the structure and diversity of plant-associated microbial communities within and at the edge of a plant species range, and suggest the potential for biotic interactions between plants and their associated microbiota to influence the dynamics of plant range edge boundaries and responses to global change

Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective

Alterations in gut microbial colonization during early life have been reported in infants that later developed asthma, allergies, type 1 diabetes, as well as in inflammatory bowel disease patients, previous to disease flares. Mechanistic studies in animal models have established that microbial alterations influence disease pathogenesis via changes in immune system maturation. Strong evidence points to the presence of a window of opportunity in early life, during which changes in gut microbial colonization can result in immune dysregulation that predisposes susceptible hosts to disease. Although the ecological patterns of microbial succession in the first year of life have been partly defined in specific human cohorts, the taxonomic and functional features, and diversity thresholds that characterize these microbial alterations are, for the most part, unknown. In this review, we summarize the most important links between the temporal mosaics of gut microbial colonization and the age-dependent immune functions that rely on them. We also highlight the importance of applying ecology theory to design studies that explore the interactions between this complex ecosystem and the host immune system. Focusing research efforts on understanding the importance of temporally structured patterns of diversity, keystone groups, and inter-kingdom microbial interactions for ecosystem functions has great potential to enable the development of biologically sound interventions aimed at maintaining and/or improving immune system development and preventing disease

16S sequences for Urban Phyllosphere Paper

These are the 16S sequences associated with the manuscript entitled: "Tree Leaf Bacterial Community Structure and Diversity Differ Along a Gradient of Urban Intensity" submitted to mSystems

R Script for PeerJ paper in press entitled: "Tree Phyllosphere Bacterial Communities: exploring the magnitude of intra- and inter-individual variation among host species"

R Script for PeerJ paper in press entitled: "Tree Phyllosphere Bacterial Communities: exploring the magnitude of intra- and inter-individual variation among host species

R Code

Code for the article "Variation in the Leaf and Root Microbiome of Sugar Maple (<i>Acer saccharum</i>) at an Elevational Range Limit" submitted to Peer

All data and metadata related to the IDENT manuscript

These data files and the markdown file allow you to go through all the steps to reproduce the analyses in the manuscript entitled "Leaf bacterial diversity mediates plant diversity – ecosystem function relationships" (doi: 10.1038/nature22399)