Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Net interactions in an annual plant community in the Negev Desert, Israel

In most plant communities, neighbours are likely to interact in at least two ways - negatively through competition and positively by facilitation. However, typically only the end product of these interactions is measured thereby detecting only the outcome, not the interactions themselves. This thesis focuses on understanding net interactions within an annual plant community in the Negev Desert, Israel by measuring the effects of spatial pattern, seed density, plant density, and specific species effects at different life-stages (by successive measurements) and levels of abiotic stress. I first tested the assumption that seeds in seed banks are generally clumped. Using geostatistics, a consistent clump size of 85cm² was detected across time, stress level, and seed size. There was however variation in the amount of seed present on the dune over time. Subsequently, I experimentally manipulated both the fine scale spatial pattern of patches of seed and the local density of seeds in small patches. Increasing local seed density generally had negative effects on measures of plant growth, whereas patches of seed with adjacent planted patches had increased performance. These results suggest that there is interference between seeds and plants within patches but positive interactions between the patches. The more general effects of density dependence were also tested at the seed and emergent plant levels. Emergence of seedlings was negatively affected by increases in seed density which also supports the interpretation that seed-seed interference may be occurring in this plant community. Mean plant size was negatively affected by increases in plant density, but survival was unaffected. Finally, I tested the prediction that a larger annual, Erodium laciniatum, acts as a benefactor species to nearby smaller annuals. Erodium was either added to or removed from patches of seed or vegetation. In both experiments, Erodium acted as a benefactor by increasing performance of neighbours (i.e., aboveground biomass or survival). Hence, competition and facilitation both play important roles in this plant community and their relative importance is influenced by life stage but not by level of abiotic stress. These studies are the first to demonstrate facilitation similar to shrub-understorey systems but at a much finer spatial scale.Science, Faculty ofBotany, Department ofGraduat

Tree invasions : a comparative test of the dominant hypotheses and functional traits

Trees act as ecosystem engineers and invasions by exotic tree species profoundly impact recipient communities. Recently, research on invasive trees has dramatically increased, enabling the assessment of general trends in tree invasion. Analysing 90 studies dealing with 45 invasive tree species, we conducted a quantitative review and a meta-analysis to estimate the relevance of eight leading hypotheses for explaining tree invasions. We also tested whether species functional traits (growth rate, density/cover, germination, biomass and survival) equally promote tree invasiveness. Overall, our results suggest that several hypotheses, linked to invasibility or invasiveness, are pertinent to explain tree invasions. Furthermore, more than one hypothesis has been supported for a given species, which indicates that multiple factors lead to the success of invasive tree species. In addition, growth rate appears to be the most efficient predictor of invasiveness for invasive trees and could thus be used as a means to identify potential alien tree invasions. We conclude that further investigations are needed to test the consistency of some hypotheses across a broader pool of invasive tree species, whilst experimental studies with the same tree species across a larger range of sites would help to reveal the full suite of factors that affect tree invasions

Genetic differentiation and phenotypic plasticity in life-history traits between native and introduced populations of invasive maple trees

Genetically based phenotypic differentiation between native and invasive populations of exotic plants has been increasingly documented and commonly invoked to explain the success of some invasive species. Nonetheless, this basic information is lacking for invasive trees although they currently represent a major concern worldwide. Reciprocal common gardens were therefore set up in both native and introduced ranges of two exotic maple trees to assess the contribution of genetic differentiation and phenotypic plasticity to tree invasiveness. Almost 3,000 native and invasive seedlings of Acer negundo and Acer platanoides were planted in Canada and in France and their performances were compared in various life-history traits related to growth, leaf phenology and ecophysiology over 2 and 3 year periods. Invasive populations of A. negundo exhibited strong genetic differentiation in all the traits examined. Compared to their native conspecifics, they grew significantly larger in the introduced range and showed lower survival, reduced maximum assimilation rate and increased leaf area in the two gardens. They also expressed greater plasticity for growth and greater phenological sensitivity to temperature. Native and invasive populations of A. platanoides were plastic across environments but in contrast did not exhibit any genetic differentiation. This cross-continental comparison provides evidence that both genetic differentiation and phenotypic plasticity contribute synergistically to tree invasiveness. The influence of these respective processes depends on stage of invasion and the life-history strategy of each species. Plastic effects are likely more important during colonization and establishment whilst genetic effects may contribute more significantly during the spread of established populations

Ambient changes exceed treatment effects on plant species abundance in global change experiments

The responses of species to environmental changes will determine future community composition and ecosystem function. Many syntheses of global change experiments examine the magnitude of treatment effect sizes, but we lack an understanding of how plant responses to treatments compare to ongoing changes in the unmanipulated (ambient or background) system. We used a database of long-term global change studies manipulating CO2, nutrients, water, and temperature to answer three questions: (a) How do changes in plant species abundance in ambient plots relate to those in treated plots? (b) How does the magnitude of ambient change in species-level abundance over time relate to responsiveness to global change treatments? (c) Does the direction of species-level responses to global change treatments differ from the direction of ambient change? We estimated temporal trends in plant abundance for 791 plant species in ambient and treated plots across 16 long-term global change experiments yielding 2,116 experiment-species-treatment combinations. Surprisingly, for most species (57%) the magnitude of ambient change was greater than the magnitude of treatment effects. However, the direction of ambient change, whether a species was increasing or decreasing in abundance under ambient conditions, had no bearing on the direction of treatment effects. Although ambient communities are inherently dynamic, there is now widespread evidence that anthropogenic drivers are directionally altering plant communities in many ecosystems. Thus, global change treatment effects must be interpreted in the context of plant species trajectories that are likely driven by ongoing environmental changes

RecruitNet: A global database of plant recruitment networks

Plant recruitment interactions (i.e., what recruits under what) shape the composition, diversity, and structure of plant communities. Despite the huge body of knowledge on the mechanisms underlying recruitment interactions among species, we still know little about the structure of the recruitment networks emerging in ecological communities. Modeling and analyzing the community-level structure of plant recruitment interactions as a complex network can provide relevant information on ecological and evolutionary processes acting both at the species and ecosystem levels. We report a data set containing 143 plant recruitment networks in 23 countries across five continents, including temperate and tropical ecosystems. Each network identifies the species under which another species recruits. All networks report the number of recruits (i.e., individuals) per species. The data set includes >850,000 recruiting individuals involved in 118,411 paired interactions among 3318 vascular plant species across the globe. The cover of canopy species and open ground is also provided. Three sampling protocols were used: (1) The Recruitment Network (RN) protocol (106 networks) focuses on interactions among established plants ("canopy species") and plants in their early stages of recruitment ("recruit species"). A series of plots was delimited within a locality, and all the individuals recruiting and their canopy species were identified; (2) The paired Canopy-Open (pCO) protocol (26 networks) consists in locating a potential canopy plant and identifying recruiting individuals under the canopy and in a nearby open space of the same area; (3) The Georeferenced plot (GP) protocol (11 networks) consists in using information from georeferenced individual plants in large plots to infer canopy-recruit interactions. Some networks incorporate data for both herbs and woody species, whereas others focus exclusively on woody species. The location of each study site, geographical coordinates, country, locality, responsible author, sampling dates, sampling method, and life habits of both canopy and recruit species are provided. This database will allow researchers to test ecological, biogeographical, and evolutionary hypotheses related to plant recruitment interactions. There are no copyright restrictions on the data set; please cite this data paper when using these data in publications