30 research outputs found

    The bacterioplankton community composition and a host genotype dependent occurrence of taxa shape the Daphnia magna gut bacterial community

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    The assembly of host-associated bacterial communities is influenced by a multitude of biotic and abiotic factors. It is essential to gain insight in the impact and relative strength of these factors if we want to be able to predict the effects of environmental change on the assembly of host-associated bacterial communities, or deliberately modify them. The environmental pool of bacteria, from which the host is colonized, and the genetic background of the host are both considered to be important in determining the composition of host-associated bacterial communities. We experimentally assessed the relative importance of these two factors and their interaction on the composition of Daphnia magna gut bacterial communities. Bacterioplankton originating from natural ponds or a laboratory culture were used to inoculate germ-free Daphnia of different genotypes. We found that the composition of the environmental bacterial community has a major influence on the Daphnia gut bacterial community, both reflected by the presence or absence of specific taxa as well as by a correlation between abundances in the environment and on the host. Our data also indicate a consistent effect of host genotype on the occurrence of specific bacterial taxa in the gut of Daphnia over different environments

    Environmental dependency of host-microbiota interactions in Daphnia magna

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    - General introduction (pg. 1) - Chapter 1: Optimization of experimental methods for investigating host-microbiota interactions in Daphnia magna (pg. 17) - Chapter 2: Food availability affects the strength of mutualistic host-microbiota interactions in Daphnia magna (pg. 39) - Chapter 3: Genotype-dependent gut microbiota drives zooplankton resistance to toxic cyanobacteria (pg. 57) - Chapter 4: Antibiotic exposure affects subsequent microbiota assembly and host performance in Daphnia (pg. 79) - General discussion (pg. 99)nrpages: 109status: publishe

    Evolutionary responses to codon usage of horizontally transferred genes in Pseudomonas aeruginosa

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    International audienceProkaryote genome evolution is characterized by the frequent gain of genes through horizontal gene transfer (HGT). For a gene, being horizontally transferred can represent a strong change in its genomic and physiological context. If the codon usage of a transferred gene deviates from that of the receiving organism, the fitness benefits it provides can be reduced due to a mismatch with the expression machinery. Consequently, transferred genes with a deviating codon usage can be selected against or elicit evolutionary responses that enhance their integration such as gene amelioration and compensatory evolution. Within bacterial species, the extent and relative importance of these different mechanisms has never been considered altogether. In this study, a phylogeny-based method was used to investigate the occurrence of these different evolutionary responses in Pseudomonas aeruginosa. Selection on codon usage of genes acquired through HGT was observed over evolutionary time, with the overall codon usage converging towards that of the core genome. Gene amelioration, through the accumulation of synonymous mutations after HGT, did not seem to systematically affect transferred genes. This pattern therefore seemed to be mainly driven by selective retention of transferred genes with an initial codon usage similar to that of the core genes. Additionally, variation in the copy number of tRNA genes was often associated with the acquisition of genes for which the observed variation could enhance their expression. This provides evidence that compensatory evolution might be an important mechanism for the integration of horizontally transferred genes

    Evolutionary responses to codon usage of horizontally transferred genes in Pseudomonas aeruginosa: gene retention, amelioration and compensatory evolution

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    International audienceProkaryote genome evolution is characterized by the frequent gain of genes through horizontal gene transfer (HGT). For a gene, being horizontally transferred can represent a strong change in its genomic and physiological context. If the codon usage of a transferred gene deviates from that of the receiving organism, the fitness benefits it provides can be reduced due to a mismatch with the expression machinery. Consequently, transferred genes with a deviating codon usage can be selected against or elicit evolutionary responses that enhance their integration, such as gene amelioration and compensatory evolution. Within bacterial species, the extent and relative importance of these different mechanisms has never been considered altogether. In this study, a phylogeny-based method was used to investigate the occurrence of these different evolutionary responses in Pseudomonas aeruginosa . Selection on codon usage of genes acquired through HGT was observed over evolutionary time, with the overall codon usage converging towards that of the core genome. Gene amelioration, through the accumulation of synonymous mutations after HGT, did not seem to systematically affect transferred genes. This pattern therefore seemed to be mainly driven by selective retention of transferred genes with an initial codon usage similar to that of the core genes. Additionally, variation in the copy number of tRNA genes was often associated with the acquisition of genes for which the observed variation could enhance their expression. This provides evidence that compensatory evolution might be an important mechanism for the integration of horizontally transferred genes

    Host genotype-dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria

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    The gut microbiota impacts many aspects of its host’s biology, and is increasingly considered as a key factor mediating performance of host individuals in continuously changing environments. Here we use gut microbiota transplants to show that, in the freshwater crustacean Daphnia magna, in addition to host genotype, gut microbiota mediates tolerance to toxic cyanobacteria. Interclonal variation in tolerance to cyanobacteria disappears when Daphnia are made germ-free and inoculated with an identical microbial inoculum. Instead, variation in tolerance among recipient Daphnia mirrors that of their donors. Metagenetic analyses point to host genotype and external microbial source as important determinants of gut microbiota assembly, and reveal strong differences in gut microbiota composition between tolerant and susceptible genotypes. Together, these results show that host genotype- and environmentally- induced variations in gut microbiota structure mediate Daphnia tolerance to toxic cyanobacteria, pointing to the gut microbiota as a driver of adaptation and acclimatization to cyanobacterial harmful algal blooms in zooplankton.status: publishe

    Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia

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    Abstract Background Host-associated microbiota is often acquired by horizontal transmission of microbes present in the environment. It is hypothesized that differences in the environmental pool of colonizers can influence microbiota community assembly on the host and as such affect holobiont composition and host fitness. To investigate this hypothesis, the host-associated microbiota of the invertebrate eco(toxico)logical model Daphnia was experimentally disturbed using different concentrations of the antibiotic oxytetracycline. The community assembly and host-microbiota interactions when Daphnia were colonized by the disturbed microbiota were investigated by inoculating germ-free individuals with the microbiota. Results Antibiotic-induced disturbance of the microbiota had a strong effect on the subsequent colonization of Daphnia by affecting ecological interactions between members of the microbiota. This resulted in differences in community assembly which, in turn, affected Daphnia growth. Conclusions These results show that the composition of the pool of colonizing microbiota can be an important structuring factor of the microbiota assembly on Daphnia, affecting holobiont composition and host growth. These findings contribute to a better understanding of how the microbial environment can shape the holobiont composition and affect host-microbiota interactions

    Life history and eco-evolutionary dynamics in light of the gut microbiota

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    The recent emergence of powerful genomic tools, such as high-throughput genomics, transcriptomics and metabolomics, combined with the study of gnotobiotic animals, have revealed overwhelming impacts of gut microbiota on the host phenotype. In addition to provide their host with metabolic functions that are not encoded in its own genome, evidence is accumulating that gut symbionts affect host traits previously thought to be solely under host genetic control, such as development and behavior. Metagenomics and metatranscriptomics studies further revealed that gut microbial communities can rapidly respond to changes in host diet or environmental conditions through changes in their structural and functional profiles, thus representing an important source of metabolic flexibility and phenotypic plasticity for the host. Hence, gut microbes appear to be an important factor affecting host ecology and evolution which is, however, not accounted for in life-history theory, or in classic population genetics, ecological and eco-evolutionary models. In this forum, we shed new light on life history and eco-evolutionary dynamics by viewing these processes through the lens of host-microbiota interactions. We follow a three-level approach. First, current knowledge on the role of gut microbiota in host physiology and behavior points out that gut symbionts can be a crucial medium of life history strategies. Second, the particularity of the microbiota is based on its multilayered structure, composed of both a core microbiota, under host genetic and immune control, and a flexible pool of microbes modulated by the environment, which differ in constraints on their maintenance and in their contribution to host adaptation. Finally, gut symbionts can drive the ecological and evolutionary dynamics of their host through effects on individual, population, community and ecosystem levels. In conclusion, we highlight some future perspectives for integrative studies to test hypotheses on life history and eco-evolutionary dynamics in light of the gut microbiota.status: publishe
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