Mapping and validating predictions of soil bacterial biodiversity using European and national scale datasets

Recent research has highlighted strong correlations between soil edaphic parameters and bacterial biodiversity. Here we seek to explore these relationships across the European Union member states with respect to mapping bacterial biodiversity at the continental scale. As part of the EU FP7 EcoFINDERs project, bacterial communities from 76 soil samples taken across Europe were assessed from eleven countries encompassing Arctic to Southern Mediterranean climes, representing a diverse range of soil types and land uses (grassland, forest and arable land). We found predictable relationships between community biodiversity (ordination site scores) and land use factors as well as soil properties such as pH. Based on the modelled relationship between soil pH and bacterial biodiversity found for the surveyed soils, we were able to predict biodiversity in ∼1000 soils for which soil pH data had been collected as part of national scale monitoring. We then performed interpolative mapping utilising existing EU wide soil pH data to present the first map of bacterial biodiversity across the EU member states. The predictive accuracy of the map was assessed again using the national scale data, but this time contrasting the EU wide spatial predictions with point data on bacterial communities. Generally the maps were useful at predicting broad extremes of biodiversity reflective of low or high pH soils, though predictive accuracy was limited for Britain particularly for organic/acidic soil communities. Spatial accuracy could however be increased by utilising published maps of soil pH calculated using geostatistical approaches at both global and national scales. These findings will contribute to wider efforts to predict and understand the spatial distribution of soil biodiversity at global scales. Further work should focus on enhancing the predictive power of such maps, by harmonising global datasets on soil conditioning parameters, soil properties and biodiversity; and the continued efforts to advance the geostatistical modelling of specific components of soil biodiversity at local to global scales

Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect

To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed

Soil networks become more connected and take up more carbon as nature restoration progresses

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered

Bulletin épigraphique

Roussel Pierre, Plassart André. Bulletin épigraphique. In: Revue des Études Grecques, tome 34, fascicule 159, Octobre-décembre 1921. pp. 423-456

Bulletin épigraphique

Roussel Pierre, Plassart André. Bulletin épigraphique. In: Revue des Études Grecques, tome 34, fascicule 159, Octobre-décembre 1921. pp. 423-456

Performance analysis and modeling of SQLite embedded databases on flash file systems

International audienceDatabases are more and more used in embedded system applications and especially in consumer electronics. This comes from the need to structure user and/or system data to be more efficiently managed and accessed. The transactional database management systems widely used in embedded systems have been designed considering hard disk drives as the storage device. In embedded systems, NAND flash memory is the main storage media and its intricacies make it fundamentally different from hard drives on many points of view, in particular in terms of performance and access mode. The performance behavior of on-flash database applications remains largely unknown, and we believe a better adequacy between those applications and flash management systems would lead to strong optimizations. A first step in that process is to assess and understand the performance behavior of database applications on flash memory. For this sake, this paper presents a micro benchmarking and modeling methodology, as well as the associated results and analysis for SQLite database queries on embedded flash specific file systems. SQLite is one of the most used database application in embedded systems and especially consumer electronics. This methodology has been applied and validated on two embedded hardware platforms. Flash file systems (FFS) behavior are very specific to flash memory intricacies and the objective of this study is to highlight the interactions between flash memory, FFSs, and SQLite based applications. The model proved to be very accurate in predicting flash I/O performance for a given workload

Embedded Databases on Flash Memories: Performance and Lifetime Issues, the case of SQLite

International audienceDatabases are more and more used in embedded system applications and especially in consumer electronics. This comes from the need to structure user and/or system data to be more efficiently managed and accessed. SQLite is one of the most used database applications. This paper presents a micro benchmarking methodology and results for SQLite database requests on embedded flash specific file systems. Indeed, flash file systems behavior are very specific to flash memory intricacies and the objective of this study is to highlight the interactions between flash memory, flash file systems, and SQLite based applications

Effects of land use intensity on European soil bacterial, fungal and archaeal communities

Whilst the importance of soils and their contribution to ecosystem services provision are well recognised, there is a paucity of knowledge on how particular land-use practices affect different types of soil organisms, and subsequently whether this affects soil functioning. The seventh framework programme EcoFINDERS project (Ecological Function and Biodiversity Indicators in European Soils) aims to “Decipher the links between soil biodiversity, activities, functioning and ecosystem services”. Through this project we have examined soil microbes at a number of European locations ranging from Iberian grassland to boreal forest. At each field site a gradient of land-use intensification has been established permitting investigation of the effects of different land management strategies on microbial communities across a range of climatic zones and soil types. This work focuses on how the diversity and community structure of the different microbial groups are affected at local and regional scales, and the environmental parameters responsible for the perceived differences. We specifically targeted bacteria, archaea and fungi as indicators, and present molecular data showing differential effects in response to anthropogenic and natural environmental gradients. Our results highlight the effect of land-use change on soil microbial communities across Europe and adds to the understanding of how belowground organisms are affected by above ground practices

Restons groupés ! La construction discursive des relations sociales

Que signifie « appartenir à un groupe » lorsque les pratiques communautaires s’estompent ou sont au contraire le prétexte d’un rejet de l’autre ? Les discours jouent à cet égard un rôle crucial : ce sont à travers eux que les individus donnent du sens à leurs relations sociales, les font naître, exister, se transformer. Les textes réunis dans ce dossier visent à rendre compte de ces constructions discursives. Elles se donnent à voir dans la mise en question, par les locuteurs eux-mêmes, des dénominations qui réfèrent aux groupes – par exemple pieds-noirs, harkis ou Algériens dans l’article de Mailys Kydjian – ou des désignations du lien censé les unir – la « nationalité » dans l’article de Suzanne Forbes et Anna Plassart ou le « patriotisme » dans celui de Marie Plassart. Elles peuvent même être saisies au croisement des deux dimensions, comme dans le cas d’Amnesty International, en quête d’un principe de regroupement – l’« expertise » ou l’« engagement » ? – à même d’atténuer les distinctions entre le groupe des « salariés » et le groupe des « bénévoles » (Amaia Errecart). Elles apparaissent enfin, de manière à la fois plus individuelle et plus indirecte, dans les dispositifs énonciatifs auxquels les individus ont recours lorsqu’ils évoquent leurs relations à des collectifs, comme le montre Thomas Liano à propos de Jean Genet et des Black Panthers. What does “belonging to a group” mean when community practices tend to fade out or when they are a pretext for rejecting others? Discourses play a crucial role at that point: individuals give life and meaning to their social relations, as well as transform them, through discourse. This collection of articles proposes an account of the discursive construction of groups. The latter is made visible in the questioning of group-naming by the speakers themselves, as with the words pieds-noirs, harkis or Algerians in Mailys Kydjian’s article, or with the naming of what is supposed to unite the group – “nationality” in the article by Suzanne Forbes and Anna Plassart or “patriotism” in Marie Plassart’s article. The discursive construction of groups can be grasped at the intersection of two dimensions, as is the case with Amnesty International, either defined by “expertise” or “engagement”, in a quest for ways to smooth out the distinctions between its “employees” and its “volunteers” (Amaia Errecart). The discursive construction of groups also appears more individually and less directly in the enunciative patterns devised by individuals when the evoke their relation to groups, as shown by Thomas Liano with his study of Jean Genet and the Black Panthers. ¿Qué significará «pertenecer a un grupo» cuándo las prácticas comunitarias se van borrando o, por el contrario, son el pretexto para rechazar el otro? Los discursos juegan en esa cuestión un papel crucial: es a través de ellos que los individuos atribuyen un sentido a sus relaciones sociales, los hacen nacer, existir, transformarse. Los textos reunidos en este dossier buscan trabajar sobre estas construcciones discursivas. Permiten rendir cuentas del cuestionamiento, por los mismos locutores, de las denominaciones que se refieren a los grupos – como por ejemplo los pieds-noirs, harkis o Algériens en el artículo de Mailys Kydjian – o de las designaciones del lazo que supuestamente los une – la «nacionalidad» en el artículo de Suzanne Forbes y de Anna Plassart o el «patriotismo» en el de Marie Plassart. También pueden ser analizadas en la encrucijada de dos dimensiones, como en el caso de Amnesty International, en busqueda de un principio de agrupamiento – la «pericia» o el «compromiso»? – capaz de mitigar las distinciones entre el grupo de los «asalariados» y el grupo de los «voluntarios» (Amaia Errecart). Finalmente aparecen, de un modo a más individual e indirecto, en los dispositivos enunciativos a los cuales los individuos apelan cuando evocan sus relaciones con colectivos, como lo muestra Thomas Liano a propósito de Jean Genet con los Black Panthers

Evaluation of the ISO Standard 11063 DNA extraction procedure for assessing soil microbial abundance and community structure

Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities