Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments

Fossil records indicate that life appeared in marine environments ∼3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that “hydrobacteria” and “terrabacteria” might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene origins. While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives, this lineage has obtained nearly half of its genome from terrestrial organisms. The majority of genes encoding functions critical for association with plants are among horizontally transferred genes. Our results show that transition of some aquatic bacteria to terrestrial habitats occurred much later than the suggested initial divergence of hydro- and terrabacterial clades. The birth of the genus Azospirillum approximately coincided with the emergence of vascular plants on land

Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis

Self-incompatibility has been considered by geneticists a model system for reproductive biology and balancing selection, but our understanding of the genetic basis and evolution of this molecular lock-and-key system has remained limited by the extreme level of sequence divergence among haplotypes, resulting in a lack of appropriate genomic sequences. In this study, we report and analyze the full sequence of eleven distinct haplotypes of the self-incompatibility locus (S-locus) in two closely related Arabidopsis species, obtained from individual BAC libraries. We use this extensive dataset to highlight sharply contrasted patterns of molecular evolution of each of the two genes controlling self-incompatibility themselves, as well as of the genomic region surrounding them. We find strong collinearity of the flanking regions among haplotypes on each side of the S-locus together with high levels of sequence similarity. In contrast, the S-locus region itself shows spectacularly deep gene genealogies, high variability in size and gene organization, as well as complete absence of sequence similarity in intergenic sequences and striking accumulation of transposable elements. Of particular interest, we demonstrate that dominant and recessive S-haplotypes experience sharply contrasted patterns of molecular evolution. Indeed, dominant haplotypes exhibit larger size and a much higher density of transposable elements, being matched only by that in the centromere. Overall, these properties highlight that the S-locus presents many striking similarities with other regions involved in the determination of mating-types, such as sex chromosomes in animals or in plants, or the mating-type locus in fungi and green algae

Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil

«La relation de limitation et d’exception dans le français d’aujourd’hui : excepté, sauf et hormis comme pivots d’une relation algébrique »

L’analyse des emplois prépositionnels et des emplois conjonctifs d’ “excepté”, de “sauf” et d’ “hormis” permet d’envisager les trois prépositions/conjonctions comme le pivot d’un binôme, comme la plaque tournante d’une structure bipolaire. Placées au milieu du binôme, ces prépositions sont forcées par leur sémantisme originaire dûment métaphorisé de jouer le rôle de marqueurs d’inconséquence systématique entre l’élément se trouvant à leur gauche et celui qui se trouve à leur droite. L’opposition qui surgit entre les deux éléments n’est donc pas une incompatibilité naturelle, intrinsèque, mais extrinsèque, induite. Dans la plupart des cas (emplois limitatifs), cette opposition prend la forme d’un rapport entre une « classe » et le « membre (soustrait) de la classe », ou bien entre un « tout » et une « partie » ; dans d’autres (emplois exceptifs), cette opposition se manifeste au contraire comme une attaque de front portée par un « tout » à un autre « tout ». De plus, l’inconséquence induite mise en place par la préposition/conjonction paraît, en principe, tout à fait insurmontable. Dans l’assertion « les écureuils vivent partout, sauf en Australie » (que l’on peut expliciter par « Les écureuils vivent partout, sauf [qu’ils ne vivent pas] en Australie »), la préposition semble en effet capable d’impliquer le prédicat principal avec signe inverti, et de bâtir sur une telle implication une sorte de sous énoncé qui, à la rigueur, est totalement inconséquent avec celui qui le précède (si « les écureuils ne vivent pas en Australie », le fait qu’ils « vivent partout » est faux). Néanmoins, l’analyse montre qu’alors que certaines de ces oppositions peuvent enfin être dépassées, d’autres ne le peuvent pas. C’est, respectivement, le cas des relations limitatives et des relations exceptives. La relation limitative, impliquant le rapport « tout » - « partie », permet de résoudre le conflit dans les termes d’une somme algébrique entre deux sous énoncés pourvus de différent poids informatif et de signe contraire. Les valeurs numériques des termes de la somme étant déséquilibrées, le résultat est toujours autre que zéro. La relation exceptive, au contraire, qui n’implique pas le rapport « tout » - « partie », n’est pas capable de résoudre le conflit entre deux sous énoncés pourvus du même poids informatif et en même temps de signe contraire : les valeurs numériques des termes de la somme étant symétriques et égales, le résultat sera toujours équivalent à zéro

Viral capsids: Mechanical characteristics, genome packaging and delivery mechanisms

The main functions of viral capsids are to protect, transport and deliver their genome. The mechanical properties of capsids are supposed to be adapted to these tasks. Bacteriophage capsids also need to withstand the high pressures the DNA is exerting onto it as a result of the DNA packaging and its consequent confinement within the capsid. It is proposed that this pressure helps driving the genome into the host, but other mechanisms also seem to play an important role in ejection. DNA packaging and ejection strategies are obviously dependent on the mechanical properties of the capsid. This review focuses on the mechanical properties of viral capsids in general and the elucidation of the biophysical aspects of genome packaging mechanisms and genome delivery processes of double-stranded DNA bacteriophages in particular

Localized spraying in oilseeds rape crop with a conventional boom sprayer

National audienceAs a part of ECOPHYTO plan established by the French government to reduce the use of chemical plant protection products (PPP), specific spraying equipment are needed, for example to spray only the row of the crop. Often these devices have small spray boom widths and they are very expensive. The objectives of the project “PLEVOP” (development of in-row sprayer in oleaginous crops and protein crops), proposed by the technical Institute Terres-Inovia, are to define the conditions for successful localized post-emergence spraying for the herbicide application on the row using large width devices. This work is carried out in connection with a manufacturer of agricultural equipment (the Marechal company), an agricultural cooperative (CAL) and a French public Institution of Higher Education (AgroSup Dijon). The first year, experiences were conducted on oilseed rape crops using GPS-RTK as guidance system embedded on the tractor; the second year, trials were realized on oilseed rape and sunflower using a camera interface placed on the boom as guidance system. Three weeding strategies practices are compared: "full herbicide treatment" vs. "herbicide treatment on the row + inter-row hoeing" and a "no treatment". After weed counting and identification, we evaluated the biological efficiency on weeds and the effectiveness of such operations. Moreover, working with a conventional sprayer for a localized spraying, we have developed an automatic calculator tool to help farmer to determine the required amount of herbicide and water depending on its use conditions (nozzle type, nozzle height, speed of passage, boom height, field size, etc...). Oilseed rape: First trial of localized herbicide treatment with a conventional boom sprayer Experiences were conducted in the Lorraine region in France in 2017-2018 on oilseed rape crop. Plants were treated post-emergence with an herbicide at the stage four leaves. The sprayer was equipped with GPS-RTK as guidance system and the boom width was 16m (Figure 1). The sprayer characteristics were: nozzle=110°, boom height=16cm, spray band=45cm for the full herbicide treatment and nozzle=40°, boom height=27,5cm and spray band=20cm for the localized treatment. The results of this first year of experimentation show that localized treatment and full treatment have much lower infestations than the untreated reference. On the crop row, the infestations of the "localized treatment" and "full treatment" modalities are similar, which shows that on the crop row the localized treatment is as effective as a full treatment. On the inter-row, the modality " herbicide treatment on the row then hoeing" is slightly more infested in weeds than the inter-row of the modality "full treatment", which shows that the hoeing is slightly less satisfying than the full treatment. Nevertheless, when we compare the inter-row of the modality " localized treatment on the crop row and then hoeing in the inter-row" with the inter-row of the untreated reference, we notice a hoeing efficiency that is not negligible. In the modality "full treatment", we observe that the crop row is slightly dirtier than the interrow one can possibly interpret that by an umbrella effect of the rapeseed crop during the 195 treatment. In the untreated reference, we observe that the crop row is less dirty than the interrow; this is probably due to a competitive effect of rapeseed on weeds on the row. Thus, the results of modality "localized treatment on the row then hoeing" on oilseed rape crop are encouraging. The localized treatment area with no hoeing also shows that the treatment on the crop row is not enough to have a good efficiency overall surface and that hoeing is important. That is the complementarity of chemical weeding and mechanical weeding which makes it possible to obtain the 80% efficiency observed. Figure 1: Specific spraying equipment and spraying formula used for the PLEVOP project A Decision Support Tool for localized spraying A single conventional sprayer with a large spray boom (16 m) was used for both "full treatment" and "spot treatment" strategies. In both cases, complex calculations were made to determine exactly the amounts of herbicide and water. So we had to create a decision support tool (DST) to help farmers depending on their own spraying parameters but also to provide information about the environmental benefits of a localized spraying (Treatment Frequency Index (TFI) reduction for example). As an example, considering the spray parameters described previously for both treatment (full and localized) and according a tractor speed of 10km/h, a nozzle output of 0.65l/min and using an herbicide product (2litre/ha) the results of calculation are deduced from the decision support tool. They indicate that: for the "full treatment", 86.7litre of water and 2litre of herbicide are required for a field of one hectare whereas as for the treatment on the row strategy, with a spray band of 20cm, only 0.89litre of herbicide and 86.7litre of water are required for a field of one hectare. Conclusions and Future Outlook We have tested in rapeseed crop, the use of a single conventional sprayer with a spray boom of 16m for a full and localized herbicide treatment thanks to a GPS-RKT type guidance system. The "full treatment" and "localized treatment" modalities were compared to the reference "no treatment". Results were encouraging, demonstrating that "localized treatment on the crop row then hoeing" is as efficient as "full treatment" modality. During experiences, the spraying settings had to be changed for the automatic calculations of herbicide and water quantities. The guidance system with a camera interface has to be evaluated as well. Overall, we developed a decision support tool (DST) in order to assist farmers in the volume calculations of whatever their spraying settings. Thus, environmental benefits have been added to sensitize the farmer to the positive effects of herbicide reduction. We would also like to finalize the decision support tool with an economic cost estimation. Finally, we would like to test our system on other crops (protein crops for example) and using other phytopharmaceutical products