Host specificity of plant-associated bacteria is negatively associated with genome size and host abundance along a latitudinal gradient.

Host specialization plays a critical role in the ecology and evolution of plant-microbe symbiosis. Theory predicts that host specialization is associated with microbial genome streamlining and is influenced by the abundance of host species, both of which can vary across latitudes, leading to a latitudinal gradient in host specificity. Here, we quantified the host specificity and composition of plant-bacteria symbioses on leaves across 329 tree species spanning a latitudinal gradient.

Winter Rye Cover Crops Shelter Competent Squash Phyllosphere Bacteria to Reduce pv. Growth and Angular Leaf Spot Symptoms.

Cover crops, a soil conservation practice, can contribute to reducing disease pressure caused by , considered one of the most important bacterial plant pathogens. We recently demonstrated that the phyllosphere (leaf surface) bacterial community structure changed when squash () was grown with a rye () cover crop treatment, followed by a decrease of angular leaf spot disease symptoms on squash caused by pv. .

Diversity and biogeography of plant phyllosphere bacteria are governed by latitude-dependent mechanisms.

Predicting and managing the structure and function of plant microbiomes requires quantitative understanding of community assembly and predictive models of spatial distributions at broad geographic scales. Here, we quantified the relative contribution of abiotic and biotic factors to the assembly of phyllosphere bacterial communities, and developed spatial distribution models for keystone bacterial taxa along a latitudinal gradient, by analyzing 16S rRNA gene sequences from 1453 leaf samples taken from 329 plant species in China. We demonstrated a latitudinal gradient in phyllosphere bacterial diversity and community composition, which was mostly explained by climate and host plant factors.

Data-driven identification of major axes of functional variation in bacteria.

The discovery of major axes of correlated functional variation among species and habitats has revealed the fundamental trade-offs structuring both functional and taxonomic diversity in eukaryotes such as plants. Whether such functional axes exist in the bacterial realm and whether they could explain bacterial taxonomic turnover among ecosystems remains unknown. Here, we use a data-driven approach to leverage global genomic and metagenomic datasets to reveal the existence of major axes of functional variation explaining both evolutionary differentiation within Bacteria and their ecological sorting across diverse habitats.

Soil microbial gene expression in an agricultural ecosystem varies with time and neonicotinoid seed treatments.

Neonicotinoids, a class of systemic insecticides, have been widely used for decades against various insect pests. Previous studies have reported non-target effects of neonicotinoids on some beneficial macro- and micro-organisms. Considering the crucial role the soil microbiota plays in sustaining soil fertility, it is critical to understand how neonicotinoid exposure affects the microbial taxonomic composition and gene expression.

Interplay between the Lung Microbiome, Pulmonary Immunity and Viral Reservoirs in People Living with HIV under Antiretroviral Therapy.

Pulmonary dysbiosis may predispose people living with HIV (PLWH) to chronic lung disease. Herein, we assessed whether intrapulmonary HIV reservoir size and immune disruption are associated with reduced bacterial lung diversity in PLWH. Bacterial DNA was extracted and PCR-amplified from cell-free bronchoalveolar lavage (BAL) fluid from 28 PLWH and 9 HIV-negative controls.

Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity.

Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny.

Dominance of coniferous and broadleaved trees drives bacterial associations with boreal feather mosses.

The composition of ecologically important moss-associated bacterial communities seems to be mainly driven by host species but may also be shaped by environmental conditions related with tree dominance. The moss phyllosphere has been studied in coniferous forests while broadleaf forests remain understudied. To determine if host species or environmental conditions defined by tree dominance drives the bacterial diversity in the moss phyllosphere, we used 16S rRNA gene amplicon sequencing to quantify changes in bacterial communities as a function of host species (Pleurozium schreberi and Ptilium crista-castrensis) and forest type (coniferous black spruce versus deciduous broadleaf trembling aspen) in eastern Canada.

Regional variation drives differences in microbial communities associated with sugar maple across a latitudinal range.

Climate change is prompting plants to migrate and establish novel interactions in new habitats. Because of the pivotal roles that microbes have on plant health and function, it is important to understand the ecological consequences of these shifts in host-microbe interactions with range expansion. Here we examine how the diversity of plant-associated microbes varies along the host's current range and extended range according with climate change predictions, and assess the relative influence of host genotype (seed provenance) and environment in structuring the host microbiome.

Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Diversity.

is a prevalent bacterial genus of the phyllosphere. Despite its ubiquity, little is known about the extent to which its diversity reflects neutral processes like migration and drift, versus environmental filtering of life history strategies and adaptations. In two temperate forests, we investigated how phylogenetic diversity within is structured by biogeography, seasonality, and growth strategies.

Plant-bacteria associations are phylogenetically structured in the phyllosphere.

Determining whether and how global change will lead to novel interactions between hosts and microbes is an important issue in ecology and evolution. Understanding the contribution of host and microbial ecologies and evolutionary histories in driving their contemporary associations is an important step towards addressing this challenge and predicting the fitness consequences of novel associations. Using shotgun metagenomic and amplicon sequencing of bacterial communities from the leaf surfaces (phyllosphere) of trees, we investigated how phylogenetic relatedness among hosts and among their associated bacteria influences the distribution of bacteria among hosts.

Neonicotinoid Seed Treatments Have Significant Non-target Effects on Phyllosphere and Soil Bacterial Communities.

The phyllosphere and soil are dynamic habitats for microbial communities. Non-pathogenic microbiota, including leaf and soil beneficial bacteria, plays a crucial role in plant growth and health, as well as in soil fertility and organic matter production. In sustainable agriculture, it is important to understand the composition of these bacterial communities, their changes in response to disturbances, and their resilience to agricultural practices.

Bacterial microbiota similarity between predators and prey in a blue tit trophic network.

Trophic networks are composed of many organisms hosting microbiota that interact with their hosts and with each other. Yet, our knowledge of the factors driving variation in microbiota and their interactions in wild communities is limited. To investigate the relation among host microbiota across a trophic network, we studied the bacterial microbiota of two species of primary producers (downy and holm oaks), a primary consumer (caterpillars), and a secondary consumer (blue tits) at nine sites in Corsica.

Glial Cell-Derived Neurotrophic Factor Induces Enteric Neurogenesis and Improves Colon Structure and Function in Mouse Models of Hirschsprung Disease.

Background & Aims: Hirschsprung disease (HSCR) is a life-threatening birth defect in which the distal colon is devoid of enteric neural ganglia. HSCR is treated by surgical removal of aganglionic bowel, but many children continue to have severe problems after surgery. We studied whether administration of glial cell derived neurotrophic factor (GDNF) induces enteric nervous system regeneration in mouse models of HSCR.

Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest.

Background: The phyllosphere is an important microbial habitat, but our understanding of how plant hosts drive the composition of their associated leaf microbial communities and whether taxonomic associations between plants and phyllosphere microbes represent adaptive matching remains limited. In this study, we quantify bacterial functional diversity in the phyllosphere of 17 tree species in a diverse neotropical forest using metagenomic shotgun sequencing. We ask how hosts drive the functional composition of phyllosphere communities and their turnover across tree species, using host functional traits and phylogeny.

Efficacy of orally administered gabapentin in horses with chronic thoracic limb lameness.

Objective: To evaluate the analgesic effects of orally administered gabapentin on horses with chronic thoracic limb lameness.

Study Design: Randomized, crossover design.

Animals: A total of 14 adult horses with chronic thoracic limb lameness.

Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks.

Motivation: Phylogenetic trees and the methods for their analysis have played a key role in many evolutionary, ecological and bioinformatics studies. Alternatively, phylogenetic networks have been widely used to analyze and represent complex reticulate evolutionary processes which cannot be adequately studied using traditional phylogenetic methods. These processes include, among others, hybridization, horizontal gene transfer, and genetic recombination.

Limited initial impacts of biomass harvesting on composition of wood-inhabiting fungi within residual stumps.

Growing pressures linked to global warming are prompting governments to put policies in place to find alternatives to fossil fuels. In this study, we compared the impact of tree-length harvesting to more intensive full-tree harvesting on the composition of fungi residing in residual stumps 5 years after harvest. In the tree-length treatment, a larger amount of residual material was left around the residual stumps in contrast to the full-tree treatment where a large amount of woody debris was removed.

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples.

Background: Biological invasions are major drivers of environmental change that can significantly alter ecosystem function and diversity. In plants, soil microbes play an important role in plant establishment and growth; however, relatively little is known about the role they might play in biological invasions. A first step to assess whether root microbes may be playing a role in the invasion process is to find out if invasive plants host different microbes than neighbouring native plant species.

Making the Most of Trait-Based Approaches for Microbial Ecology.

There is an increasing interest in applying trait-based approaches to microbial ecology, but the question of how and why to do it is still lagging behind. By anchoring our discussion of these questions in a framework derived from epistemology, we broaden the scope of trait-based approaches to microbial ecology from one oriented mostly around explanation towards one inclusive of the predictive and integrative potential of these approaches. We use case studies from macro-organismal ecology to concretely show how these goals for knowledge development can be fulfilled and propose clear directions, adapted to the biological reality of microbes, to make the most of recent advancements in the measurement of microbial phenotypes and traits.

The prevalence of nonlinearity and detection of ecological breakpoints across a land use gradient in streams.

Human activities can alter aquatic ecosystems through the input of nutrients and carbon, but there is increasing evidence that these pressures induce nonlinear ecological responses. Nonlinear relationships can contain breakpoints where there is an unexpected change in an ecological response to an environmental driver, which may result in ecological regime shifts. We investigated the occurrence of nonlinearity and breakpoints in relationships between total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), and total dissolved carbon (DOC) concentrations and ecological responses in streams with varying land uses.

Gut microbiota-mediated Gene-Environment interaction in the TashT mouse model of Hirschsprung disease.

Based on the bilateral relationship between the gut microbiota and formation/function of the enteric nervous system (ENS), we sought to determine whether antibiotics-induced dysbiosis might impact the expressivity of genetically-induced ENS abnormalities. To address this, we took advantage of the TashT mouse model of Hirschsprung disease, in which colonic aganglionosis and hypoganglionosis are both much more severe in males. These defects result into two male-biased colon motility phenotypes: either megacolon that is lethal around weaning age or chronic constipation in adults, the latter being also associated with an increased proportion of nitrergic neurons in the distal ENS.

Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly.

The factors that govern assembly of the gut microbiota are insufficiently understood. Here, we test the hypothesis that inter-individual microbiota variation can arise solely from differences in the order and timing by which the gut is colonized early in life. Experiments in which mice were inoculated in sequence either with two complex seed communities or a cocktail of four bacterial strains and a seed community revealed that colonization order influenced both the outcome of community assembly and the ecological success of individual colonizers.

Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota.

Our knowledge of how the gut microbiome relates to mammalian evolution benefits from the identification of gut microbial taxa that are unexpectedly prevalent or unexpectedly conserved across mammals. Such taxa enable experimental determination of the traits needed for such microbes to succeed as gut generalists, as well as those traits that impact mammalian fitness. However, the punctuated resolution of microbial taxonomy may limit our ability to detect conserved gut microbes, especially in cases in which broadly related microbial lineages possess shared traits that drive their apparent ubiquity across mammals.

Variation in the leaf and root microbiome of sugar maple () 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.