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Thiverval-Grignon, France

Li Y.,French National Institute for Agricultural Research | Briandet R.,French National Institute for Agricultural Research | Briandet R.,Micalis Institute | Trubuil A.,French National Institute for Agricultural Research
2014 IEEE 11th International Symposium on Biomedical Imaging, ISBI 2014 | Year: 2014

Along the food chain, most wet surfaces are covered by biological pellicles called biofilms. It has also been demonstrated that bacterial stealth swimmers create transient pores that increase macromolecular transfer within the biofilm. Therefore, it is interesting to investigate the behavior of swimmers bacteria within the biofilm. In this paper we propose a novel approach to track the swimmers as well as pores within the biofilm. A direct time-lapse confocal microscopy technique enables the visualization of swimmers as well as biofilm in two color images. In these two images swimmers and pores dynamics are correlated and we reinforce the tracking of swimmers with the tracking of pores and vice and versa. The proposed algorithm is built upon U-track algorithm we modify accordingly to this particular framework where some "tracks of the past" consisting in the pores are left after the swimming of bacteria within the biofilm. We track the trajectory of swimmers in one channel by the improved U-Track. While, in the other biofilm channel we detect pores visited by swimmers and then create the other kind of trajectory for the swimmer. Finally we combine and merge these two kinds of trajectories to get more accurate trajectories. The experiment on both simulated data and real sequence demonstrates the effectiveness of the method. © 2014 IEEE. Source


Morel G.,French National Institute for Agricultural Research | Morel G.,Micalis Institute | Sterck L.,Vlaams Institute for Biotechnology | Sterck L.,Ghent University | And 32 more authors.
Scientific Reports | Year: 2015

The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi-yeasts split concomitant with the yeasts genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts. Source


Casaregola S.,French National Institute for Agricultural Research | Casaregola S.,Micalis Institute | Jacques N.,French National Institute for Agricultural Research | Jacques N.,Micalis Institute | And 4 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2013

A yeast strain was isolated from olive brines in a fermented black olive and olive oil manufacturing plant in the town of Nyons (France). On the basis of domains 1 and 2 (D1/D2) large subunit (LSU) rRNA gene and internal transcribed spacer (ITS) region sequence analyses, the strain CLIB 1303T was found to be closely related, but clearly distinct, from the three existing species of the genus Citeromyces: Citeromyces matritensis, Citeromyces siamensis and Citeromyces haiwaiiensis. Strain CLIB 1303T exhibited 6 bp, 7 bp and 12 bp divergences in the D1/D2 LSU rRNA gene with C. siamensis, C. matritensis and C. hawaiiensis, respectively. ITS region divergence amounted to more than 8 %, 4 % and 4.5 % with C. siamensis, C. matritensis and C. hawaiiensis, respectively, in addition to several indels. Like C. matritensis and C. siamensis strains, strain CLIB 1303T was shown to be halotolerant and osmotolerant. Phenotypically, strain CLIB 1303T can be distinguished from other species of the genus Citeromyces by its inability to assimilate trehalose. The strain CLIB 1303T (= CBS 12700T) was assigned to a novel species, Citeromyces nyonsensis sp. nov. © 2013 IUMS. Source


Jacques N.,French National Institute for Agricultural Research | Jacques N.,Micalis Institute | Louis-Mondesir C.,French National Institute for Agricultural Research | Louis-Mondesir C.,Micalis Institute | And 4 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2014

Three yeast strains related to members of the genus Saccharomycopsis were isolated. One strain (CLIB 1310) was isolated from olive brines of fermented black olives in France and two strains (CLIB 1454 and CLIB 1455) were isolated from a plant in French Guiana. Sequence analyses based on the D1/D2 domains of the nuclear large subunit rRNA gene, small-subunit rRNA gene and partial EF-1α gene revealed that the strains represented two novel taxa exhibiting extensive sequence divergence from the previously described species of the genus Saccharomycopsis. Two novel species are described to accommodate these newly isolated strains: Saccharomycopsis olivae sp. nov. (type strain CLIB 1310T = CBS 12701T) and Saccharomycopsis guyanensis sp. nov. (type strain CLIB 1455T = CBS 12914T and strain CLIB 1454). Both strains CLIB 1454 and CLIB 1455T displayed identical sequences but differed in their ability to metabolize sorbitol and in their morphology on agar medium. Candida amapae, Candida lassensensis and Arthroascus babjevae belonging to the Saccharomycopsis clade, are reassigned to Saccharomycopsis as novel combinations. © 2014 IUMS. Source


Mallet S.,French National Institute for Agricultural Research | Mallet S.,Micalis Institute | Weiss S.,French National Institute for Agricultural Research | Weiss S.,Micalis Institute | And 6 more authors.
PLoS ONE | Year: 2012

Among ascomycetous yeasts, the CTG clade is so-called because its constituent species translate CTG as serine instead of leucine. Though the biology of certain pathogenic species such as Candida albicans has been much studied, little is known about the life cycles of non-pathogen species of the CTG clade. Taking advantage of the recently obtained sequence of the biotechnological Millerozyma (Pichiasorbitophila) farinosa strain CBS 7064, we used MLST to better define phylogenic relationships between most of the Millerozyma farinosa strains available in public collections. This led to the constitution of four phylogenetic clades diverging from 8% to 15% at the DNA level and possibly constituting a species complex (M. farinosa) and to the proposal of two new species:Millerozyma miso sp. nov. CBS 2004T (= CLIB 1230T) and Candida pseudofarinosa sp. nov.NCYC 386T(= CLIB 1231T).Further analysis showed that M. farinosa isolates exist as haploid and inter-clade hybrids. Despite the sequence divergence between the clades, secondary contacts after reproductive isolation were evidenced, as revealed by both introgression and mitochondria transfer between clades. We also showed that the inter-clade hybrids do sporulate to generate mainly viable vegetative diploid spores that are not the result of meiosis, and very rarely aneuploid spores possibly through the loss of heterozygosity during sporulation. Taken together, these results show that in this part of the CTG clade, non-Mendelian genetic exchanges occur at high rates through hybridization between divergent strainsfrom distinct clades and subsequent massive loss of heterozygosity. This combination of mechanisms could constitute an alternative sexuality leading to an unsuspected biodiversity. © 2012 Mallet et al. Source

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