Draft genome sequence of [i]Pseudomonas[/i] sp. strain ADP, a bacterial model for studying the degradation of the herbicide atrazine

EAPôle BIOME & IPMWe report here the 7,259,392-bp draft genome of [i]Pseudomonas[/i] sp. strain ADP. This is a bacterial strain that was first isolated in the 1990s from soil for its ability to mineralize the herbicide atrazine. It has extensively been studied as a model to understand the atrazine biodegradation pathway. This genome will be used as a reference and compared to evolved populations obtained by experimental evolution conducted on this strain under atrazine selection pressure. Copyright 2016 Devers-Lamrani et al

“Ant” and “Grasshopper” Life-History Strategies in Saccharomyces cerevisiae

From the evolutionary and ecological points of view, it is essential to distinguish between the genetic and environmental components of the variability of life-history traits and of their trade-offs. Among the factors affecting this variability, the resource uptake rate deserves particular attention, because it depends on both the environment and the genetic background of the individuals. In order to unravel the bases of the life-history strategies in yeast, we grew a collection of twelve strains of Saccharomyces cerevisiae from different industrial and geographical origins in three culture media differing for their glucose content. Using a population dynamics model to fit the change of population size over time, we estimated the intrinsic growth rate (r), the carrying capacity (K), the mean cell size and the glucose consumption rate per cell. The life-history traits, as well as the glucose consumption rate, displayed large genetic and plastic variability and genetic-by-environment interactions. Within each medium, growth rate and carrying capacity were not correlated, but a marked trade-off between these traits was observed over the media, with high K and low r in the glucose rich medium and low K and high r in the other media. The cell size was tightly negatively correlated to carrying capacity in all conditions. The resource consumption rate appeared to be a clear-cut determinant of both the carrying capacity and the cell size in all media, since it accounted for 37% to 84% of the variation of those traits. In a given medium, the strains that consume glucose at high rate have large cell size and low carrying capacity, while the strains that consume glucose at low rate have small cell size but high carrying capacity. These two contrasted behaviors may be metaphorically defined as “ant” and “grasshopper” strategies of resource utilization. Interestingly, a strain may be “ant” in one medium and “grasshopper” in another. These life-history strategies are discussed with regards to yeast physiology, and in an evolutionary perspective

Niche-driven evolution of metabolic and life-history strategies in natural and domesticated populations of Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>Variation of resource supply is one of the key factors that drive the evolution of life-history strategies, and hence the interactions between individuals. In the yeast <it>Saccharomyces cerevisiae</it>, two life-history strategies related to different resource utilization have been previously described in strains from different industrial origins. In this work, we analyzed metabolic traits and life-history strategies in a broader collection of yeast strains sampled in various ecological niches (forest, human body, fruits, laboratory and industrial environments).</p> <p>Results</p> <p>By analysing the genetic and plastic variation of six life-history and three metabolic traits, we showed that <it>S. cerevisiae </it>populations harbour different strategies depending on their ecological niches. On one hand, the forest and laboratory strains, referred to as extreme "ants", reproduce quickly, reach a large carrying capacity and a small cell size in fermentation, but have a low reproduction rate in respiration. On the other hand, the industrial strains, referred to as extreme "grasshoppers", reproduce slowly, reach a small carrying capacity but have a big cell size in fermentation and a high reproduction rate in respiration. "Grasshoppers" have usually higher glucose consumption rate than "ants", while they produce lower quantities of ethanol, suggesting that they store cell resources rather than secreting secondary products to cross-feed or poison competitors. The clinical and fruit strains are intermediate between these two groups.</p> <p>Conclusions</p> <p>Altogether, these results are consistent with a niche-driven evolution of <it>S. cerevisiae</it>, with phenotypic convergence of populations living in similar habitat. They also revealed that competition between strains having contrasted life-history strategies ("ants" and "grasshoppers") seems to occur at low frequency or be unstable since opposite life-history strategies appeared to be maintained in distinct ecological niches.</p

Compounded Disturbance Chronology Modulates the Resilience of Soil Microbial Communities and N-Cycle Related Functions

There is a growing interest of overcoming the uncertainty related to the cumulative impacts of multiple disturbances of different nature in all ecosystems. With global change leading to acute environmental disturbances, recent studies demonstrated a significant increase in the possible number of interactions between disturbances that can generate complex, non-additive effects on ecosystems functioning. However, how the chronology of disturbances can affect ecosystems functioning is unknown even though there is increasing evidence that community assembly history dictates ecosystems functioning. Here, we experimentally examined the importance of the disturbances chronology in modulating the resilience of soil microbial communities and N-cycle related functions. We studied the impact of 3-way combinations of global change related disturbances on total bacterial diversity and composition, on the abundance of N-cycle related guilds and on N-cycle related activities in soil microcosms. The model pulse disturbances, i.e., short-term ceasing disturbances studied were heat, freeze-thaw and anaerobic cycles. We determined that repeated disturbances of the same nature can either lead to the resilience or to shifts in N-cycle related functions concomitant with diversity loss. When considering disturbances of different nature, we demonstrated that the chronology of compounded disturbances impacting an ecosystem determines the aggregated impact on ecosystem properties and functions. Thus, after 3 weeks the impact of the ‘anoxia/heat/freeze-thaw’ sequence was almost two times stronger than that of the ‘heat/anoxia/freeze-thaw’ sequence. Finally, we showed that about 29% of the observed variance in ecosystem aggregated impact caused by series of disturbances could be attributed to changes in the microbial community composition measured by weighted UniFrac distances. This indicates that surveying changes in bacterial community composition can help predict the strength of the impact of compounded disturbances on N-related functions and properties

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

Background: Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks. Results: We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. Conclusions: Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification

Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community

Pesticides are intentionally applied to agricultural fields for crop protection. They can harm non-target organisms such as soil microorganisms involved in important ecosystem functions with impacts at the global scale. Within the frame of the pesticide registration process, the ecotoxicological impact of pesticides on soil microorganisms is still based on carbon and nitrogen mineralization tests, despite the availability of more extensive approaches analyzing the abundance, activity or diversity of soil microorganisms. In this study, we used a high-density DNA microarray (PhyloChip) and 16S rDNA amplicon next-generation sequencing (NGS) to analyze the impact of the organophosphate insecticide chlorpyrifos (CHL), the phenyl-urea herbicide isoproturon (IPU), or the triazole fungicide tebuconazole (TCZ) on the diversity and composition of the soil bacterial community. To our knowledge, it is the first time that the combination of these approaches are applied to assess the impact of these three pesticides in a lab-to-field experimental design. The PhyloChip analysis revealed that although no significant changes in the composition of the bacterial community were observed in soil microcosms exposed to the pesticides, significant differences in detected operational taxonomic units (OTUs) were observed in the field experiment between pesticide treatments and control for all three tested pesticides after 70 days of exposure. NGS revealed that the bacterial diversity and composition varied over time. This trend was more marked in the microcosm than in the field study. Only slight but significant transient effects of CHL or TCZ were observed in the microcosm and the field study, respectively. IPU was not found to significantly modify the soil bacterial diversity or composition. Our results are in accordance with conclusions of the Environmental Food Safety Authority (EFSA), which concluded that these three pesticides may have a low risk toward soil microorganisms

Génétique et amélioration des plantes au sein du réseau PhytoMic

National audienc

Adaptive strategies to contrasted environments in saccharomyces cerevisiae

Malgré une utilisation séculaire de Saccharomyces cerevisiae comme modèle en biologie moléculaire et génétique, l étude de son écologie et son évolution n en est qu à ses débuts. Un phénotypage fin des populations naturelles et domestiquées manque encore. L objectif de cette thèse est d explorer la variabilité phénotypique et l évolution des populations de S. cerevisiae provenant d habitats divers en se concentrant sur les traits d histoire de vie et l utilisation des ressources. Utilisant une approche de biologie des populations, nous avons montré que les souches naturelles et domestiquées présentaient de la variation phénotypique pour les traits d histoire de vie et les caractères métaboliques. Les corrélations génétiques entre traits définissent deux stratégies d histoire de vie extrêmes : En fermentation, les Cigales se reproduisent lentement, sont de grande taille cellulaire mais atteignent une faible capacité biotique ; les Fourmis démontrant les caractéristiques opposées. Les Cigales consomment les ressources à des vitesses comparables aux Fourmis mais elles produisent moins d éthanol. Elles semblent stocker les ressources plutôt que de secréter des métabolites secondaires. Développant une approche d évolution expérimentale, nous avons étudié l évolution de 6 souches présentant des caractéristiques variées dans 4 régimes de sélection différant par la quantité de ressources et la durée des saisons. Nous avons montré que la sélection tend à homogénéiser des populations initialement distinctes vers un optimum local dans chaque traitement. Les stratégies extrêmes Fourmis et Cigales semblent être des stratégies adaptatives à des environnements contrastés.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Influence of abiotic and biotic soil characteristics on Listeria monocytogenes survival in the environment

National audienceListeria monocytogenes is a food born pathogen responsible for the potentially fatal disease listeriosis. Initial contamination of plants vegetables and fruits may occur in cropping systems and originate from soil (that may act as a reservoir), water or organic amendments. The aim of this study was to identify major biotic and abiotic soils characteristics which determine L. monocytogenes survival in soil. Survival of L. monocytogenes was evaluated in a set of 100 soil microcosms representative of land use and pedology of French soils. These soils originated from the RMQS network were thoroughly characterized including chemical properties (pH, ionic content), texture (clay, sand and silt content), land use, and spatial localization. A sub-set of 9 Gamma-radiation sterilized soils was used to investigate whether soil microflora may affect L. monocytogenes survival. Microcosms were inoculated with 106 L. monocytogenes per gram of soil. L. monocytogenes populations were monitored after 7, 14 and 84 days of incubation at 20°C by plate-counts on selective PALCAM media. L. monocytogenes was able to persist in most of the tested soils but survival rates were strongly variable. A short term and a long term survival of L. monocytogenes were reported in 71% and 21% of tested soils, respectively. In 8% of soils, L. monocytogenes was either absent or below detection limits as soon as 7 days after inoculation. This suggests that L. monocytogenes survival depends on abiotic and/or biotic factors. Statistical analysis evidenced that land use and spatial localization of soils did not significantly affect L. monocytogenes survival. Variance partitioning demonstrated that 60% of the differences between survival rates at 7 and 14 days were explained by soil chemical properties. Basic cation saturation ratio was the major soil chemical characteristic explaining short-term survival. Cationic exchange capacity and exchangeable calcium further explained survival of L. monocytogenes at 7 days and 14 days respectively. Long-term survival was driven mainly by soil texture (11% of the variance), especially clay content. Survival of L. monocytogenes in sterile soils differed markedly. Indeed, 4 sterilised soils supported growth of L. monocytogenes while the rate of decrease was lower in the other sterilised soils than when microflora was active. This result points out the critical role played by both the soil microflora and the soil physico-chemical properties in determining the survival rate of L. monocytogenes