The more, the merrier? A multi-methodological survey at the Roman town of Carnuntum

We have newly discovered the garrison of the governor’s guard, the castra singularium, in the Roman Town of Carnuntum. For a more detailed research we decided to apply a multi-method research approach on this importent archaeological site. The analysis of the different geophysical prospection methods was carried out prior to an archaeological excavation. By excavating a small area, the interpretations of the non-destructive methods could be evaluated

Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species

International audienceBeyond being a reliable nutrient provider, some bacteria will perceive the plant as a potential host and undertake root colonization leading to mutualistic or parasitic interactions. Bacteria of the Burkholderia and Paraburkholderia genera are frequently found in the rhizosphere of rice. While the latter are often described as plant growth promoting species, Burkholderia are often studied for their human opportunistic traits. Here, we used root exudate stimulation on three Burkholderia and three Paraburkholderia strains isolated from rice roots to characterize their preliminary adaptation to the rice host at the transcriptomic level. Instead of the awaited genus-dependent adaptation, we observed a strongly species-specific response for all tested strains. While all bacteria originate from the rice environment, there are great disparities in their levels of adaptation following the sensing of root exudates. We further report the shared major functions that were differentially regulated in this early step of bacterial adaptation to plant colonization, including amino acids and putrescine metabolism, the Entner-Doudoroff (ED) pathway as well as cyclic diguanylate monophosphate (c-di-GMP) cycling

Polyhydroxyalkanoate granules quantification in mixed microbial cultures using image analysis: Sudan Black B versus Nile Blue A staining

Polyhydroxyalkanoates (PHA) can be produced and intracellularly accumulated as inclusions by mixed microbial cultures (MMC) for bioplastic production and in enhanced biological phosphorus removal (EBPR) systems. Classical methods for PHA quantification use a digestion step prior to chromatography analysis, rendering them labor intensive and time-consuming. The present work investigates the use of two quantitative image analysis (QIA) procedures specifically developed for PHA inclusions identification and quantification. MMC obtained from an EBPR system were visualized by bright-field and fluorescence microscopy for PHA inclusions detection, upon Sudan Black B (SBB) and Nile Blue A (NBA) staining, respectively. The captured color images were processed by QIA techniques and the image analysis data were further treated using multivariate statistical analysis. Partial least squares (PLS) regression coefficients of 0.90 and 0.86 were obtained between QIA parameters and PHA concentrations using SBB and NBA, respectively. It was found that both staining procedures might be seen as alternative methodologies to classical PHA determination.The authors thank the Fundacao para a Ciencia e a Tecnologia (FCT) Strategic Project PEst-OE/EQB/LA0023/2013 and the Project "BioEnv - Biotechnology and Bioengineering for a sustainable world", REF. NORTE-07-0124-FEDER-000048, co-funded by the Programa Operacional Regional do Norte (ON.2 - O Novo Norte), QREN, FEDER. The authors also acknowledge the financial support to Daniela P. Mesquita through the postdoctoral grant (SFRH/BPD/82558/2011) and the project PTDC/EBB-EBI/103147/2008 provided by FCT

The origins and spread of domestic horses from the Western Eurasian steppes

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability: All collapsed and paired-end sequence data for samples sequenced in this study are available in compressed fastq format through the European Nucleotide Archive under accession number PRJEB44430, together with rescaled and trimmed bam sequence alignments against both the nuclear and mitochondrial horse reference genomes. Previously published ancient data used in this study are available under accession numbers PRJEB7537, PRJEB10098, PRJEB10854, PRJEB22390 and PRJEB31613, and detailed in Supplementary Table 1. The genomes of ten modern horses, publicly available, were also accessed as indicated in their corresponding original publications57,61,85-87.NOTE: see the published version available via the DOI in this record for the full list of authorsDomestication of horses fundamentally transformed long-range mobility and warfare. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 BC. Other longstanding candidate regions for horse domestication, such as Iberia and Anatolia, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC driving the spread of Indo-European languages. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture

Frontières adaptatives des burkholderias en interaction avec le riz : approches génétiques et fonctionnelles

The burkholderia group is composed of multiple bacterial genera (including Burkholderia and Paraburkholderia). Some species indulge in diverse interactions with eukaryotic hosts that range from pathogenicity to symbiosis. Many burkholderia species dwell in association with rice, making this host and ideal model for burkholderia/plant interactions. The taxonomy of burkholderia delineates a frontier between the Burkholderia genus, grouping the majority of pathogenic species, and the Paraburkholderia genus, mainly phytobeneficial and environmental species. This thesis project strived to characterize the genetic frontiers between species of both genera that share the capacity to interact with rice. First, we explored the taxonomic diversity for 124 rice-isolates using dedicated markers (16S and recA), and went into a more detailed analysis for a subset of 12 supposedly different species suing whole genome sequencing. We developed the intraspecific diversity of B. cenocepacia strains which we had found to be rice associated This was unexpected for this human pathogen and led us to describe a new species, with improved plant interaction abilities (which we propose to name B. servocepacia). We then explored the genetic bases regulating plant-adaptation of Burkholderia and Paraburkholderia species using two complementary approaches. We first undertook a transcriptomic profiling of the reaction to root exudates for six rice-isolates belonging to either genus. We thus demonstrated a strain specific response of the early plant-sensing, independent of the strain’s taxonomic attribution. We also listed the principal functions involved in exudate sensing. Our second approach focused on the rice endophyte models B. vietnamiensis LMG10929 (Bv) and P. kururiensis M130 (Pk) for which we undertook a high-throughput genetic screening of insertion mutant libraries (Tn-seq), during the root surface colonization step of two rice cultivars belonging to Oryza sativa ssp. japonica and Oryza sativa ssp. indica. We noticed a strong disparity in the adaptation for rice colonization between Bv and Pk as the display genetic requisites that differ in nature and number. Furthermore, we demonstrated a host-dependent adaptation for root colonization from both strains. Finally, we investigated on the distribution of type III secretion systems (T3SS) within burkholderia. We describe two novel T3SS types and in one instance, demonstrate its role in plant colonization for Bv. The thesis is concluded by a general discussion, summarizing the results of this project and situating them in the context of adaptative frontiers for plant interactions between Burkholderia and Paraburkholderia.Les burkholderias appartiennent à plusieurs genres bactériens (dont Burkholderia et Paraburkholderia). Certaines espèces interagissent avec de multiple hôtes eucaryotes avec lesquels elles développent une gamme d’interaction allant de la symbiose à la pathogénie. Une grande diversité d’espèces de burkholderias interagisse avec le riz, faisant de cette plante un modèle idéal pour l’étude des interactions burkholderias/plantes. Une frontière taxonomique semble se dessiner entre le genre Burkholderia, qui regroupe la majorité des espèces pathogènes, et le genre Paraburkholderia qui concentre des espèces phytobénéfiques et environnementales. Ce travail de thèse a porté sur l’étude des frontières génétiques chez des espèces de ces deux genres interagissant avec le riz. Nous avons d’abord exploré la diversité taxonomique de 124 souches isolées du riz par l’étude de marqueurs taxonomiques (16S et recA) et, pour un sous ensemble de 12 espèces potentiellement différentes, d’analyse de leurs génomes (ANI). Nous avons progressé dans la description de la diversité intraspécifique chez l’espèce Burkholderia cenocepacia dont nous possédions des isolats de racines de riz, fait étonnant pour ce pathogène humain, et qui nous a conduit à décrire une nouvelle espèce mieux adaptée à l’environnement végétale (que nous proposons de nommer B. servocepacia). Nous avons ensuite exploré les bases génétiques de l’adaptation à l’environnement plantes chez Burkholderia et Paraburkholderia par deux approches. La première portait sur les étapes précoces d’interaction avec la plante, en étudiant la réponse transcriptomique de six espèces, tirées des deux genres, stimulées aux exsudats racinaires de riz, qui nous a permis de montrer une réponse souche-spécifique indépendante de leur appartenance taxonomique, et de lister des catalogues de fonctions impliqués dans la perception des exsudats. La seconde approche a porté sur deux souches modèles endophytes du riz, Paraburkholderia kururiensis M130 (Pk) et Burkholderia vietnamiensis LMG10929 (Bv), pour lesquelles nous avons réalisé un crible génétique haut-débit de banques de mutants par Tn-Seq, visant à trouver les déterminants génétiques leur permettant de coloniser les racines des deux sous-espèces de riz, Oryza sativa ssp. japonica et Oryza sativa ssp. indica. Nous observons une forte disparité dans l’adaptation des deux souches à la colonisation racinaire puisque Bv et Pk requiert des gènes différents par leur nombre et leur nature. Par ailleurs, l’effet génotype de l’hôte induit une adaptation de la part des deux colonisateurs. En dernière partie, nous avons étudié la distribution des systèmes de sécrétion de type 3 (T3SS) chez les burkholderias. Nous décrivons deux nouveaux types de T3SS et démontrons que l’un d’eux est impliqué chez Bv dans la colonisation racinaire. Nous discutons finalement de l’ensemble des résultats de cette thèse dans le contexte de l’étude des frontières adaptatives à l’environnement plante chez les Burkholderia et Paraburkholderia

Frontiers in the adaptation of rice-interacting burkholderia species : genetic and functional approaches

Les burkholderias appartiennent à plusieurs genres bactériens (dont Burkholderia et Paraburkholderia). Certaines espèces interagissent avec de multiple hôtes eucaryotes avec lesquels elles développent une gamme d’interaction allant de la symbiose à la pathogénie. Une grande diversité d’espèces de burkholderias interagisse avec le riz, faisant de cette plante un modèle idéal pour l’étude des interactions burkholderias/plantes. Une frontière taxonomique semble se dessiner entre le genre Burkholderia, qui regroupe la majorité des espèces pathogènes, et le genre Paraburkholderia qui concentre des espèces phytobénéfiques et environnementales. Ce travail de thèse a porté sur l’étude des frontières génétiques chez des espèces de ces deux genres interagissant avec le riz. Nous avons d’abord exploré la diversité taxonomique de 124 souches isolées du riz par l’étude de marqueurs taxonomiques (16S et recA) et, pour un sous ensemble de 12 espèces potentiellement différentes, d’analyse de leurs génomes (ANI). Nous avons progressé dans la description de la diversité intraspécifique chez l’espèce Burkholderia cenocepacia dont nous possédions des isolats de racines de riz, fait étonnant pour ce pathogène humain, et qui nous a conduit à décrire une nouvelle espèce mieux adaptée à l’environnement végétale (que nous proposons de nommer B. servocepacia). Nous avons ensuite exploré les bases génétiques de l’adaptation à l’environnement plantes chez Burkholderia et Paraburkholderia par deux approches. La première portait sur les étapes précoces d’interaction avec la plante, en étudiant la réponse transcriptomique de six espèces, tirées des deux genres, stimulées aux exsudats racinaires de riz, qui nous a permis de montrer une réponse souche-spécifique indépendante de leur appartenance taxonomique, et de lister des catalogues de fonctions impliqués dans la perception des exsudats. La seconde approche a porté sur deux souches modèles endophytes du riz, Paraburkholderia kururiensis M130 (Pk) et Burkholderia vietnamiensis LMG10929 (Bv), pour lesquelles nous avons réalisé un crible génétique haut-débit de banques de mutants par Tn-Seq, visant à trouver les déterminants génétiques leur permettant de coloniser les racines des deux sous-espèces de riz, Oryza sativa ssp. japonica et Oryza sativa ssp. indica. Nous observons une forte disparité dans l’adaptation des deux souches à la colonisation racinaire puisque Bv et Pk requiert des gènes différents par leur nombre et leur nature. Par ailleurs, l’effet génotype de l’hôte induit une adaptation de la part des deux colonisateurs. En dernière partie, nous avons étudié la distribution des systèmes de sécrétion de type 3 (T3SS) chez les burkholderias. Nous décrivons deux nouveaux types de T3SS et démontrons que l’un d’eux est impliqué chez Bv dans la colonisation racinaire. Nous discutons finalement de l’ensemble des résultats de cette thèse dans le contexte de l’étude des frontières adaptatives à l’environnement plante chez les Burkholderia et Paraburkholderia.The burkholderia group is composed of multiple bacterial genera (including Burkholderia and Paraburkholderia). Some species indulge in diverse interactions with eukaryotic hosts that range from pathogenicity to symbiosis. Many burkholderia species dwell in association with rice, making this host and ideal model for burkholderia/plant interactions. The taxonomy of burkholderia delineates a frontier between the Burkholderia genus, grouping the majority of pathogenic species, and the Paraburkholderia genus, mainly phytobeneficial and environmental species. This thesis project strived to characterize the genetic frontiers between species of both genera that share the capacity to interact with rice. First, we explored the taxonomic diversity for 124 rice-isolates using dedicated markers (16S and recA), and went into a more detailed analysis for a subset of 12 supposedly different species suing whole genome sequencing. We developed the intraspecific diversity of B. cenocepacia strains which we had found to be rice associated This was unexpected for this human pathogen and led us to describe a new species, with improved plant interaction abilities (which we propose to name B. servocepacia). We then explored the genetic bases regulating plant-adaptation of Burkholderia and Paraburkholderia species using two complementary approaches. We first undertook a transcriptomic profiling of the reaction to root exudates for six rice-isolates belonging to either genus. We thus demonstrated a strain specific response of the early plant-sensing, independent of the strain’s taxonomic attribution. We also listed the principal functions involved in exudate sensing. Our second approach focused on the rice endophyte models B. vietnamiensis LMG10929 (Bv) and P. kururiensis M130 (Pk) for which we undertook a high-throughput genetic screening of insertion mutant libraries (Tn-seq), during the root surface colonization step of two rice cultivars belonging to Oryza sativa ssp. japonica and Oryza sativa ssp. indica. We noticed a strong disparity in the adaptation for rice colonization between Bv and Pk as the display genetic requisites that differ in nature and number. Furthermore, we demonstrated a host-dependent adaptation for root colonization from both strains. Finally, we investigated on the distribution of type III secretion systems (T3SS) within burkholderia. We describe two novel T3SS types and in one instance, demonstrate its role in plant colonization for Bv. The thesis is concluded by a general discussion, summarizing the results of this project and situating them in the context of adaptative frontiers for plant interactions between Burkholderia and Paraburkholderia

Proportional Belief Merging

In this paper we introduce proportionality to belief merging. Belief merging is a framework for aggregating information presented in the form of propositional formulas, and it generalizes many aggregation models in social choice. In our analysis, two incompatible notions of proportionality emerge: one similar to standard notions of proportionality in social choice, the other more in tune with the logic-based merging setting. Since established merging operators meet neither of these proportionality requirements, we design new proportional belief merging operators. We analyze the proposed operators against established rationality postulates, finding that current approaches to proportionality from the field of social choice are, at their core, incompatible with standard rationality postulates in belief merging. We provide characterization results that explain the underlying conflict, and provide a complexity analysis of our novel operators

Genetic Diversity of Type 3 Secretion System in Burkholderia s.l. and Links With Plant Host Adaptation

International audienceBurkholderia sensu lato species are prominent for their diversity of hosts. The type 3 secretion system (T3SS) is a major mechanism impacting the interactions between bacteria and eukaryotic hosts. Besides the human pathogenic species Burkholderia pseudomallei and closely affiliated species, the T3SS has received little attention in this genus as in taxonomically and evolutionary close genera Paraburkholderia , Caballeronia , Trinickia , and Mycetohabitans . We proceeded to identify and characterize the diversity of T3SS types using the genomic data from a subset of 145 strains representative of the species diversity found in the Burkholderia s.l. group. Through an analysis of their phylogenetic distribution, we identified two new T3SS types with an atypical chromosomal organization and which we propose to name BCI ( Burkholderia cepacia complex Injectisome) and PSI ( Paraburkholderia Short Injectisome). BCI is the dominant T3SS type found in Burkholderia sensu stricto ( s.s. ) species and PSI is mostly restricted to the Paraburkholderia genus. By correlating their distribution with the ecology of their strains of origin, we propose a role in plant interaction for these T3SS types. Experimentally, we demonstrated that a BCI deficient B. vietnamiensis LMG10929 mutant was strongly affected in its rice colonization capacity