Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress

To explore the transcriptomic global response to osmotic stress in roots, 18 mRNA-seq libraries were generated from three triploid banana genotypes grown under mild osmotic stress (5% PEG) and control conditions. Illumina sequencing produced 568 million high quality reads, of which 70–84% were mapped to the banana diploid reference genome. Using different uni- and multivariate statistics, 92 genes were commonly identified as differentially expressed in the three genotypes. Using our in house workflow to analyze GO enriched and underlying biochemical pathways, we present the general processes affected by mild osmotic stress in the root and focus subsequently on the most significantly overrepresented classes associated with: respiration, glycolysis and fermentation. We hypothesize that in fast growing and oxygen demanding tissues, mild osmotic stress leads to a lower energy level, which induces a metabolic shift towards (i) a higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. To confirm the mRNA-seq results, a subset of twenty up-regulated transcripts were further analysed by RT-qPCR in an independent experiment at three different time points. The identification and annotation of this set of genes provides a valuable resource to understand the importance of energy sensing during mild osmotic stress

About overyielding with mixed cultures in batch processes

International audienceThis paper investigates-via modeling-several possible explanations of overyielding observed in mixed cultures cultivated in batch reactors. It is first shown that the classical model of competition of N species for a single resource cannot explain such overyielding. Then, three hypotheses are introduced and discussed at the light of numerical simulations

Effects of shortened host life span on the evolution of parasite life history and virulence in a microbial host-parasite system

<p>Abstract</p> <p>Background</p> <p>Ecological factors play an important role in the evolution of parasite exploitation strategies. A common prediction is that, as shorter host life span reduces future opportunities of transmission, parasites compensate with an evolutionary shift towards earlier transmission. They may grow more rapidly within the host, have a shorter latency time and, consequently, be more virulent. Thus, increased extrinsic (i.e., not caused by the parasite) host mortality leads to the evolution of more virulent parasites. To test these predictions, we performed a serial transfer experiment, using the protozoan <it>Paramecium caudatum </it>and its bacterial parasite <it>Holospora undulata</it>. We simulated variation in host life span by killing hosts after 11 (<it>early </it>killing) or 14 (<it>late </it>killing) days post inoculation; after killing, parasite transmission stages were collected and used for a new infection cycle.</p> <p>Results</p> <p>After 13 cycles (≈ 300 generations), parasites from the <it>early-killing </it>treatment were less infectious, but had shorter latency time and higher virulence than those from the <it>late-killing </it>treatment. Overall, shorter latency time was associated with higher parasite loads and thus presumably with more rapid within-host replication.</p> <p>Conclusion</p> <p>The analysis of the means of the two treatments is thus consistent with theory, and suggests that evolution is constrained by trade-offs between virulence, transmission and within-host growth. In contrast, we found little evidence for such trade-offs across parasite selection lines within treatments; thus, to some extent, these traits may evolve independently. This study illustrates how environmental variation (experienced by the host) can lead to the evolution of distinct parasite strategies.</p

About biomass overyielding of mixed cultures in batch processes

We study mechanisms that can produce an increase of biomass production in batch processes when considering mixed cultures, compared to pure cultures. We show that growth thresholds or variable yields can produce 'overyielding', while this is not possible in the classical batch model with multiple species. We give sufficient conditions on the characteristics of the species to obtain overyielding, and illustrate these theoretical results with numerical simulations. This work provides new insights on species complementary in models of mixed cultures, without having to consider direct interactions terms between species as, for instance in the well known Generalized Lotka-Volterra model

About biomass overyielding of mixed cultures in batch processes

International audienceWe study mechanisms that can produce an increase of biomass production in batch processes when considering mixed cultures, compared to pure cultures. We show that growth thresholds or variable yields can produce 'overyielding', while this is not possible in the classical batch model with multiple species. We give sufficient conditions on the characteristics of the species to obtain overyielding, and illustrate these theoretical results with numerical simulations. This work provides new insights on species complementary in models of mixed cultures, without having to consider direct interactions terms between species as, for instance in the well known Generalized Lotka-Volterra model

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

How different anthropogenic environments have shaped the genome of S. cerevisiae ?

The yeast Saccharomyces cerevisiae plays an important role in food and beverage fermentations. In order to known how environmental constraints imposed by anthropogenic niches have shaped S. cerevisiae genomes and phenotypes, we sequenced the genome of 82 S. cerevisiae strains from various ecological origins. Using these genomic data, we found additional genetic elements acquired by introgression or by horizontal transfer. Here, we present two remarkable examples of divergent adaptation associated to yeast domestication for wine and milk fermentation. Firstly, we demonstrated the role of oligopeptide transporters encoded by FOT genes, which are recently acquired by wine yeasts from Torulaspora microellipsoides. These transporters with a broader specificity than S. cerevisiae dipeptides transporters, confer a strong competitive advantage during grape must fermentation and thus play a key role in the adaptation of wine yeasts to the nitrogen-limited wine fermentation environment. The genome of cheese strains, secondly, present some particular features. Genes of the GAL locus were replaced by their orthologues from a species apparently basal to the Saccharomyces clade. Allelic exchange of this locus in a wine strain enables improves growth speed in a media containing the two hexoses such as when released from the hydrolysis of lactose. In addition, a highly divergent high affinity transporter GAL2 and a specific allele of the regulator GAL80 were found. This work highlights the remarkable plasticity of yeast genomes as a mechanism of their adaptation to their environment

Genome-scale modeling of yeast: chronology, applications and critical perspectives

Over the last 15 years, several genome-scale metabolic models (GSMMs) were developed for different yeast species, aiding both the elucidation of new biological processes and the shift toward a bio-based economy, through the design of in silico inspired cell factories. Here, an historical perspective of the GSMMs built over time for several yeast species is presented and the main inheritance patterns among the metabolic reconstructions are highlighted. We additionally provide a critical perspective on the overall genome-scale modeling procedure, underlining incomplete model validation and evaluation approaches and the quest for the integration of regulatory and kinetic information into yeast GSMMs. A summary of experimentally validated model-based metabolic engineering applications of yeast species is further emphasized, while the main challenges and future perspectives for the field are finally addressedThis work was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of a Ph.D. grant (PD/BD/52336/2013), of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01–0145FEDER-006684) and also in the context of the EU-funded initiative ERA-NET for Industrial Biotechnology (ERA-IB-2/0003/2013), in addition to the BioTecNorte operation (NORTE-01–0145FEDER-000004) funded by European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte.info:eu-repo/semantics/publishedVersio

Brain transcriptomes of honey bees (Apis mellifera) experimentally infected by two pathogens: Black queen cell virus and Nosema ceranae.

This is the final version of the article. Available from Elsevier via the DOI in this record.Regulation of gene expression in the brain plays an important role in behavioral plasticity and decision making in response to external stimuli. However, both can be severely affected by environmental factors, such as parasites and pathogens. In honey bees, the emergence and re-emergence of pathogens and potential for pathogen co-infection and interaction have been suggested as major components that significantly impaired social behavior and survival. To understand how the honey bee is affected and responds to interacting pathogens, we co-infected workers with two prevalent pathogens of different nature, the positive single strand RNA virus Black queen cell virus (BQCV), and the Microsporidia Nosema ceranae, and explored gene expression changes in brains upon single infections and co-infections. Our data provide an important resource for research on honey bee diseases, and more generally on insect host-pathogen and pathogen-pathogen interactions. Raw and processed data are publicly available in the NCBI/GEO database: (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE81664.Sequencing was performed thanks to the EU-funded 7th Framework project BEE DOC, Grant Agreement 244956. The authors thank Maureen Labarussias for technical support during bee experiments and preparation for sequencing