Clarifying the effect of biodiversity on productivity in natural ecosystems with longitudinal data and methods for causal inference.

Causal effects of biodiversity on ecosystem functions can be estimated using experimental or observational designs - designs that pose a tradeoff between drawing credible causal inferences from correlations and drawing generalizable inferences. Here, we develop a design that reduces this tradeoff and revisits the question of how plant species diversity affects productivity. Our design leverages longitudinal data from 43 grasslands in 11 countries and approaches borrowed from fields outside of ecology to draw causal inferences from observational data. Contrary to many prior studies, we estimate that increases in plot-level species richness caused productivity to decline: a 10% increase in richness decreased productivity by 2.4%, 95% CI [-4.1, -0.74]. This contradiction stems from two sources. First, prior observational studies incompletely control for confounding factors. Second, most experiments plant fewer rare and non-native species than exist in nature. Although increases in native, dominant species increased productivity, increases in rare and non-native species decreased productivity, making the average effect negative in our study. By reducing the tradeoff between experimental and observational designs, our study demonstrates how observational studies can complement prior ecological experiments and inform future ones.

Decrease of hospital- and community-acquired bloodstream infections due to Streptococcus pneumoniae and Streptococcus pyogenes during the first year of the COVID-19 pandemic: A time-series analysis in Paris region.

The impact of the COVID-19 pandemic on bloodstream infections (BSIs) due to Streptococcus pneumoniae and Streptococcus pyogenes was assessed in 25 university hospitals of Paris. Monthly BSIs incidence rates that appeared stable in 2018 and 2019, decreased for the 2 pathogens during the 2 COVID-19 lockdown periods of 2020. Containment policies, including social distancing, masking and hand hygiene strengthening in both community and hospital settings are likely to reduce BSIs due to these pathogens.

Soil properties as key predictors of global grassland production: Have we overlooked micronutrients?

Fertilisation experiments have demonstrated that nutrient availability is a key determinant of biomass production and carbon sequestration in grasslands. However, the influence of nutrients in explaining spatial variation in grassland biomass production has rarely been assessed. Using a global dataset comprising 72 sites on six continents, we investigated which of 16 soil factors that shape nutrient availability associate most strongly with variation in grassland aboveground biomass. Climate and N deposition were also considered. Based on theory-driven structural equation modelling, we found that soil micronutrients (particularly Zn and Fe) were important predictors of biomass and, together with soil physicochemical properties and C:N, they explained more unique variation (32%) than climate and N deposition (24%). However, the association between micronutrients and biomass was absent in grasslands limited by NP. These results highlight soil properties as key predictors of global grassland biomass production and point to serial co-limitation by NP and micronutrients.

Fertilized graminoids intensify negative drought effects on grassland productivity.

Droughts can strongly affect grassland productivity and biodiversity, but responses differ widely. Nutrient availability may be a critical factor explaining this variation, but is often ignored in analyses of drought responses. Here, we used a standardized nutrient addition experiment covering 10 European grasslands to test if full-factorial nitrogen, phosphorus, and potassium addition affected plant community responses to inter-annual variation in drought stress and to the extreme summer drought of 2018 in Europe. We found that nutrient addition amplified detrimental drought effects on community aboveground biomass production. Drought effects also differed between functional groups, with a negative effect on graminoid but not forb biomass production. Our results imply that eutrophication in grasslands, which promotes dominance of drought-sensitive graminoids over forbs, amplifies detrimental drought effects. In terms of climate change adaptation, agricultural management would benefit from taking into account differential drought impacts on fertilized versus unfertilized grasslands, which differ in ecosystem services they provide to society.

Broader phenology of pollinator activity and higher plant reproductive success in an urban habitat compared to a rural one.

Urban habitat characteristics create environmental filtering of pollinator communities. They also impact pollinating insect phenology through the presence of an urban heat island and the year-round availability of floral resources provided by ornamental plants.Here, we monitored the phenology and composition of pollinating insect communities visiting replicates of an experimental plant assemblage comprising two species, with contrasting floral traits: Sinapis alba and Lotus corniculatus, whose flowering periods were artificially extended. Plant assemblage replicates were set up over two consecutive years in two different habitats: rural and densely urbanized, within the same biogeographical region (Ile-de-France region, France).The phenology of pollination activity, recorded from the beginning (early March) to the end (early November) of the season, differed between these two habitats. Several pollinator morphogroups (small wild bees, bumblebees, honeybees) were significantly more active on our plant sets in the urban habitat compared to the rural one, especially in early spring and autumn. This resulted in different overall reproductive success of the plant assemblage between the two habitats. Over the course of the season, reproductive success of S. alba was always significantly higher in the urban habitat, while reproductive success of L. corniculatus was significantly higher in the urban habitat only during early flowering.These findings suggest different phenological adaptations to the urban habitat for different groups of pollinators. Overall, results indicate that the broadened activity period of pollinating insects recorded in the urban environment could enhance the pollination function and the reproductive success of plant communities in cities.

Below-ground competition alters attractiveness of an insect-pollinated plant to pollinators.

Competitive interactions between plants can affect patterns of allocation to reproductive structures through modulation of resource availability. As floral traits involved in plant attractiveness to pollinators can be sensitive to these resources, competition with any neighbouring species may influence the attractiveness of insect-pollinated plants. While pollination research has primarily focused on above-ground interactions, this study aims at investigating if the presence of a competitor plant can modulate neighbouring insect-pollinated plant attractiveness to pollinators and resulting fecundity, especially through below-ground competitive interactions for soil resources. We set up a plot experiment in which we grew an insect-pollinated plant, Sinapis alba (Brassicaceae), in a mixture dominated by a wind-pollinated plant, Holcus lanatus (Poaceae). Individuals of S. alba were either subjected to or isolated from (with buried tubes in the soil) below-ground competition. Across the flowering season, floral traits involved in attractiveness of S. alba and pollinator visitation were followed at the plot and plant level to investigate different scales of attractiveness. At the end of the experiment, seeds were harvested to assess plant fecundity. Competition had a significant negative effect on plot and plant floral display size as well as flower size while nectar traits were not affected. When plants of S. alba were in competition, the time to first visit was altered: the proportion of plots that received a visit was smaller for a given time; in other words, it took more time for a given proportion of plots to be visited and some plots were even never visited. Moreover, pollinators made fewer visits per plots. The proportion of viable seeds produced by S. alba in competition was lower and probably linked to the competition itself rather than changes in pollinator visitation. This study suggests that competitive interactions between plants can modulate pollination interactions even when competing plant species are not insect-pollinated.

Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa.

To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3-V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium.

The ecology of heterogeneity: soil bacterial communities and C dynamics.

Heterogeneity is a fundamental property of soil that is often overlooked in microbial ecology. Although it is generally accepted that the heterogeneity of soil underpins the emergence and maintenance of microbial diversity, the profound and far-reaching consequences that heterogeneity can have on many aspects of microbial ecology and activity have yet to be fully apprehended and have not been fully integrated into our understanding of microbial functioning. In this contribution we first discuss how the heterogeneity of the soil microbial environment, and the consequent uncertainty associated with acquiring resources, may have affected how microbial metabolism, motility and interactions evolved and, ultimately, the overall microbial activity that is represented in ecosystem models, such as heterotrophic decomposition or respiration. We then present an analysis of predicted metabolic pathways for soil bacteria, obtained from the MetaCyc pathway/genome database collection (https://metacyc.org/). The analysis suggests that while there is a relationship between phylogenic affiliation and the catabolic range of soil bacterial taxa, there does not appear to be a trade-off between the 16S rRNA gene copy number, taken as a proxy of potential growth rate, of bacterial strains and the range of substrates that can be used. Finally, we present a simple, spatially explicit model that can be used to understand how the interactions between decomposers and environmental heterogeneity affect the bacterial decomposition of organic matter, suggesting that environmental heterogeneity might have important consequences on the variability of this process. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Trace element concentrations along a gradient of urban pressure in forest and lawn soils of the Paris region (France).

The concentration, degree of contamination and pollution of 7 trace elements (TEs) along an urban pressure gradient were measured in 180 lawn and wood soils of the Paris region (France). Iron (Fe), a major element, was used as reference element. Copper (Cu), cadmium (Cd), lead (Pb) and zinc (Zn) were of anthropogenic origin, while arsenic (As), chromium (Cr) and nickel (Ni) were of natural origin. Road traffic was identified as the main source of anthropogenic TEs. In addition, the industrial activity of the Paris region, especially cement plants, was identified as secondary source of Cd. Soil characteristics (such as texture, organic carbon (OC) and total nitrogen (tot N) contents) tell the story of the soil origins and legacies along the urban pressure gradient and often can explain TE concentrations. The history of the land-use types was identified as a factor that allowed understanding the contamination and pollution by TEs. Urban wood soils were found to be more contaminated and polluted than urban lawns, probably because woods are much older than lawns and because of the legacy of the historical management of soils in the Paris region (Haussmann period). Lawn soils are similar to the fertile agricultural soils and relatively recently (mostly from the 1950s onwards) imported from the surrounding of Paris, so that they may be less influenced by urban conditions in terms of TE concentrations. Urban wood soils are heavily polluted by Cd, posing a high risk to the biological communities. The concentration of anthropogenic TEs increased from the rural to the urban areas, and the concentrations of most anthropogenic TEs in urban areas were equivalent to or above the regulatory reference values, raising the question of longer-term monitoring.

Multifunctionality is affected by interactions between green roof plant species, substrate depth, and substrate type.

Green roofs provide ecosystem services through evapotranspiration and nutrient cycling that depend, among others, on plant species, substrate type, and substrate depth. However, no study has assessed thoroughly how interactions between these factors alter ecosystem functions and multifunctionality of green roofs. We simulated some green roof conditions in a pot experiment. We planted 20 plant species from 10 genera and five families (Asteraceae, Caryophyllaceae, Crassulaceae, Fabaceae, and Poaceae) on two substrate types (natural vs. artificial) and two substrate depths (10 cm vs. 30 cm). As indicators of major ecosystem functions, we measured aboveground and belowground biomasses, foliar nitrogen and carbon content, foliar transpiration, substrate water retention, and dissolved organic carbon and nitrates in leachates. Interactions between substrate type and depth strongly affected ecosystem functions. Biomass production was increased in the artificial substrate and deeper substrates, as was water retention in most cases. In contrast, dissolved organic carbon leaching was higher in the artificial substrates. Except for the Fabaceae species, nitrate leaching was reduced in deep, natural soils. The highest transpiration rates were associated with natural soils. All functions were modulated by plant families or species. Plant effects differed according to the observed function and the type and depth of the substrate. Fabaceae species grown on natural soils had the most noticeable patterns, allowing high biomass production and high water retention but also high nitrate leaching from deep pots. No single combination of factors enhanced simultaneously all studied ecosystem functions, highlighting that soil-plant interactions induce trade-offs between ecosystem functions. Substrate type and depth interactions are major drivers for green roof multifunctionality.

Competition with wind-pollinated plant species alters floral traits of insect-pollinated plant species.

Plant traits related to attractiveness to pollinators (e.g. flowers and nectar) can be sensitive to abiotic or biotic conditions. Soil nutrient availability, as well as interactions among insect-pollinated plants species, can induce changes in flower and nectar production. However, further investigations are needed to determine the impact of interactions between insect-pollinated species and abiotically pollinated species on such floral traits, especially floral rewards. We carried out a pot experiment in which three insect-pollinated plant species were grown in binary mixtures with four wind-pollinated plant species, differing in their competitive ability. Along the flowering period, we measured floral traits of the insect-pollinated species involved in attractiveness to pollinators (i.e. floral display size, flower size, daily and total 1) flower production, 2) nectar volume, 3) amount of sucrose allocated to nectar). Final plant biomass was measured to quantify competitive interactions. For two out of three insect-pollinated species, we found that the presence of a wind-pollinated species can negatively impact floral traits involved in attractiveness to pollinators. This effect was stronger with wind-pollinated species that induced stronger competitive interactions. These results stress the importance of studying the whole plant community (and not just the insect-pollinated plant community) when working on plant-pollinator interactions.

Mathematical and live meningococcal models for simple sequence repeat dynamics - coherent predictions and observations.

Evolvability by means of simple sequence repeat (SSR) instability is a feature under the constant influence of opposing selective pressures to expand and compress the repeat tract and is mechanistically influenced by factors that affect genetic instability. In addition to direct selection for protein expression and structural integrity, other factors that influence tract length evolution were studied. The genetic instability of SSRs that switch the expression of antibiotic resistance ON and OFF was modelled mathematically and monitored in a panel of live meningococcal strains. The mathematical model showed that the SSR length of a theoretical locus in an evolving population may be shaped by direct selection of expression status (ON or OFF), tract length dependent (α) and tract length independent factors (ß). According to the model an increase in α drives the evolution towards shorter tracts. An increase in ß drives the evolution towards a normal distribution of tract lengths given that an upper and a lower limit are set. Insertion and deletion biases were shown to skew allelic distributions in both directions. The meningococcal SSR model was tested in vivo by monitoring the frequency of spectinomycin resistance OFF→ON switching in a designed locus. The instability of a comprehensive panel of the homopolymeric SSRs, constituted of a range of 5-13 guanine nucleotides, was monitored in wildtype and mismatch repair deficient backgrounds. Both the repeat length itself and mismatch repair deficiency were shown to influence the genetic instability of the homopolymeric tracts. A possible insertion bias was observed in tracts ≤G10. Finally, an inverse correlation between the number of tract-encoded amino acids and growth in the presence of ON-selection illustrated a limitation to SSR expansion in an essential gene associated with the designed model locus and the protein function mediating antibiotic resistance.

Spatial ecology of bacteria at the microscale in soil.

Despite an exceptional number of bacterial cells and species in soils, bacterial diversity seems to have little effect on soil processes, such as respiration or nitrification, that can be affected by interactions between bacterial cells. The aim of this study is to understand how bacterial cells are distributed in soil to better understand the scaling between cell-to-cell interactions and what can be measured in a few milligrams, or more, of soil. Based on the analysis of 744 images of observed bacterial distributions in soil thin sections taken at different depths, we found that the inter-cell distance was, on average 12.46 µm and that these inter-cell distances were shorter near the soil surface (10.38 µm) than at depth (>18 µm), due to changes in cell densities. These images were also used to develop a spatial statistical model, based on Log Gaussian Cox Processes, to analyse the 2D distribution of cells and construct realistic 3D bacterial distributions. Our analyses suggest that despite the very high number of cells and species in soil, bacteria only interact with a few other individuals. For example, at bacterial densities commonly found in bulk soil (10(8) cells g(-1) soil), the number of neighbours a single bacterium has within an interaction distance of ca. 20 µm is relatively limited (120 cells on average). Making conservative assumptions about the distribution of species, we show that such neighbourhoods contain less than 100 species. This value did not change appreciably as a function of the overall diversity in soil, suggesting that the diversity of soil bacterial communities may be species-saturated. All in all, this work provides precise data on bacterial distributions, a novel way to model them at the micrometer scale as well as some new insights on the degree of interactions between individual bacterial cells in soils.

Regulation of soil organic C mineralisation at the pore scale.

Little is known about the factors that regulate C mineralisation at the soil pore scale or how these factors vary throughout the pore network. This study sought to understand how the decomposition of organic carbon varies within the soil pore network and to determine the relative importance of local environmental properties relative to biological properties as controlling factors. This was achieved by sterilising samples of soil and reinoculating them with axenic bacterial suspensions using the matric potential to target different locations in the pore network. Carbon mineralisation curves were described with two-compartment first-order models to distinguish CO2 derived from the labile organic carbon released during sterilisation from CO2 derived from organic C unaffected by sterilisation. The data indicated that the size of the labile pool of organic C, possibly of microbial origin, varied as a function of location in the pore network but that the organic carbon unaffected by sterilisation did not. The mineralisation rate of the labile C varied with the bacterial type inoculated, but the mineralisation rate of the organic C unaffected by sterilisation was insensitive to bacterial type. Taken together, the results suggest that microbial metabolism is a less significant regulator of soil organic carbon decomposition than are microbial habitat properties.

Plants may alter competition by modifying nutrient bioavailability in rhizosphere: a modeling approach.

Plants modify nutrient availability by releasing chemicals in the rhizosphere. This change in availability induced by roots (bioavailability) is known to improve nutrient uptake by individual plants releasing such compounds. Can this bioavailability alter plant competition for nutrients and under what conditions? To address these questions, we have developed a model of nutrient competition between plant species based on mechanistic descriptions of nutrient diffusion, plant exudation, and plant uptake. The model was parameterized using data of the effects of root citrate exudation on phosphorus availability. We performed a sensitivity analysis for key parameters to test the generality of these effects. Our simulations suggest the following. (1) Nutrient uptake depends on the number of roots when nutrients and exudates diffuse little, because individual roots are nearly independent in terms of nutrient supply. In this case, bioavailability profits only species with exudates. (2) Competition for nutrients depends on the spatial arrangement of roots when nutrients diffuse little but exudates diffuse widely. (3) Competition for nutrients depends on the nutrient uptake capacity of roots when nutrients and exudates diffuse widely. In this case, bioavailability profits all species. Mechanisms controlling competition for bioavailable nutrients appear to be diverse and strongly depend on soil, nutrient, and plant properties.