Showing papers by "Marc W. Schmid published in 2018"

Contribution of epigenetic variation to adaptation in Arabidopsis.

Abstract: In plants, transgenerational inheritance of some epialleles has been demonstrated but it remains controversial whether epigenetic variation is subject to selection and contributes to adaptation. Simulating selection in a rapidly changing environment, we compare phenotypic traits and epigenetic variation between Arabidopsis thaliana populations grown for five generations under selection and their genetically nearly identical ancestors. Selected populations of two distinct genotypes show significant differences in flowering time and plant architecture, which are maintained for at least 2–3 generations in the absence of selection. While we cannot detect consistent genetic changes, we observe a reduction of epigenetic diversity and changes in the methylation state of about 50,000 cytosines, some of which are associated with phenotypic changes. Thus, we propose that epigenetic variation is subject to selection and can contribute to rapid adaptive responses, although the extent to which epigenetics plays a role in adaptation is still unclear.

Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha

Abstract: In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur during land plant reproduction, but there is little consensus on the generality and extent of epigenetic reprogramming in plants. We studied DNA methylation dynamics during the life cycle of the liverwort Marchantia polymorpha. We isolated thalli and meristems from male and female gametophytes, archegonia, antherozoids, as well as sporophytes at early and late developmental stages, and compared their DNA methylation profiles. Of all cytosines tested for differential DNA methylation, 42% vary significantly in their methylation pattern throughout the life cycle. However, the differences are limited to few comparisons between specific stages of the life cycle and suggest four major epigenetic states specific to sporophytes, vegetative gametophytes, antherozoids, and archegonia. Further analyses indicated clear differences in the mechanisms underlying reprogramming in the gametophytic and sporophytic generations, which are paralleled by differences in the expression of genes involved in DNA methylation. Differentially methylated cytosines with a gain in methylation in antherozoids and archegonia are enriched in the CG and CHG contexts, as well as in gene bodies and gene flanking regions. In contrast, gain of DNA methylation during sporophyte development is mostly limited to the CHH context, LTR retrotransposons, DNA transposons, and repeats. We conclude that epigenetic reprogramming occurs at least twice during the life cycle of M. polymorpha and that the underlying mechanisms are likely different between the two events.

Selection in response to community diversity alters plant performance and functional traits

Abstract: In grassland biodiversity experiments the positive biodiversity–ecosystem functioning relationship generally increases over time. However, we know little about the underlying short-term evolutionary processes. Using five plant species selected for twelve years in a biodiversity experiment in mixture or monoculture and plants without such a selection history, we assessed whether differential selection altered productivity, biodiversity effects, and functional trait differences within newly assembled monocultures and 2-species mixtures. Plants without a past community selection history in the biodiversity experiment produced the lowest assemblage biomass and showed the weakest biodiversity effects. In newly assembled mixtures, plants with a selection history in mixtures produced more biomass than plants with a monoculture selection history. Biodiversity effects were generally positive and differed significantly between selection histories. However, contrary to our expectations, biodiversity effects were not stronger for mixture-type plants. Biodiversity effects were influenced by both trait differences between plants and community-weighted means, but these relationships were mostly independent of selection history. Our findings suggest that twelve years of selection history in monocultures or species mixtures differentiated plants of each species into monoculture- and mixture-types. Such rapid evolution of different community-types within grassland species and its effect on ecosystem services and functioning are likely to be important for species conservation practice.

Rhizosphere bacterial community composition depends on plant diversity legacy in soil and plant species identity

Abstract: Soil microbes are known to be involved in a number of essential ecosystem processes such as nutrient cycling, plant productivity and the maintenance of plant species diversity. However, how plant species diversity and identity affect soil microbial diversity and community composition is largely unknown. We tested whether, over the course of 11 years, distinct soil bacterial communities developed under plant monocultures and mixtures, and if over this timeframe plants with a monoculture or mixture history changed in the microbial communities they associated with. For eight species, we grew offspring of plants that had been grown for 11 years in the same monocultures or mixtures (monoculture- or mixture-type plants) in pots inoculated with microbes extracted from the monoculture and mixture soils. After five months of growth in the glasshouse, we collected rhizosphere soil from each plant and used 16S-rRNA gene sequencing to determine the community composition and diversity of the bacterial communities. Microbial community structure in the plant rhizosphere was primarily determined by soil legacy (monoculture vs. mixture soil) and by plant species identity, but not by plant legacy (monoculture- vs. mixture-type plants). In seven out of the eight plant species bacterial abundance was larger when inoculated with microbes from mixture soil. We conclude that plant diversity can strongly affect belowground community composition and diversity, feeding back to the assemblage of rhizosphere microbial communities in newly establishing plants. Thereby our work demonstrates that concerns for plant biodiversity loss are also concerns for soil biodiversity loss.

Evidence for rapid evolution in a grassland biodiversity experiment

Abstract: In long-term grassland biodiversity experiments positive effects of biodiversity on plant productivity commonly increase with time. Previously it was shown that differential selection in monoculture and mixed-species grassland communities could lead to the rapid emergence of monoculture and mixture phenotypes. Underlying mechanisms for such rapid phenotypic responses are however still unclear. We hypothesized that in biodiversity experiments pre-adapted genotypes or epigenetic variants could be sorted out from the standing genetic or epigenetic variation. To test if biodiversity acted as a selective environment, we grew offspring from plants that were exposed for twelve years to a monoculture or mixture environment in a biodiversity experiment (Jena Experiment) under controlled greenhouse conditions. Using epiGBS, a genotyping-by-sequencing approach combined with bisulfite conversion to provide integrative genetic and epigenetic data, we showed that plants with a monoculture or mixture background were genetically distinct. Our data reveal strong genetic and epigenetic divergence within species according to selection history and suggest variation in epigenetic variation to be largely under genetic control. This pattern was consistently observed across six perennial grassland species. Our results suggest that selection of genetic variants caused the rapid emergence of monoculture and mixture types in the Jena Experiment.

Diversity loss selects for altered plant phenotypic responses to local arbuscular mycorrhizal communities

Abstract: 1. Biodiversity loss not only impairs ecosystem functioning but can also alter the selection for traits in plant communities. At high diversity selection favours traits that allow for greater niche partitioning, whereas at low diversity selection may favour greater defence against pathogens. However, it is unknown whether changes in plant diversity also select for altered interactions with soil organisms. 2. We assessed whether the responses in plant growth and functional traits to their local arbuscular mycorrhizal fungal (AMF) communities have been altered by the diversity of the plant communities from which both plants and AMF communities were obtained. We grew plants with AMF communities that originated from either plant monocultures or mixtures in a fully factorial design that included both negative and positive controls, by inoculating no AMF or a foreign AMF respectively. 3. We found that AMF from plant mixtures were more beneficial than monoculture AMF for two out of five plant species. Plants from mixtures generally grew better than those from monocultures, but suffered greater damage by leaf pathogens. Although plant growth and phenotypic responses were dependent on the AMF communities with which they associated, we found little evidence for plant growth responses specific to their local AMF communities and results differed between species and traits. 4. Our results show that plants from mixtures were selected for increased growth at the expense of reduced defence and vice versa for plants from monocultures, providing evidence for plant diversity-dependent selection on competitive growth vs. defence. Furthermore, our study suggests that effects of a common history between plants and AMF do not follow a general pattern leading to increased or decreased mutualism. 5. Synthesis: Here we provide evidence that biodiversity loss can alter evolutionary trajectories of plant phenotypes and responses to their local AMF communities. However, the selection for altered plant-AMF interactions differ between plant species. To understand how plant communities respond and evolve under a changing environment requires further knowledge about life strategies of plant species and their above-belowground interactions.

Combining forecast probabilities with graphical visualization for improved reporting of antimicrobial susceptibility testing

Abstract: Sir, Antimicrobial susceptibility testing (AST) reports are used by clinicians to guide antibiotic treatment of patients suffering from infectious diseases. AST reports, such as those based on the Kirby– Bauer disc diffusion test, in general do not include raw data, but an interpretation of the data in clinical categories (resistant, intermediate, susceptible), which reflect the likelihood of therapeutic success. This practice is intended to provide clinicians with clear and unambiguous clinical information. However, it entails a major loss of data. In contrast to results from clinical chemistry or haematology, where methodological precision measurements and quantitative results are implemented in the reports, these are absent in AST reports, where a mere classification into clinical categories is performed on the basis of inhibition zone measurements or MIC determinations. As a consequence, AST reports do not allow estimation of the probabilities of miscategorization, especially for measurements close to the clinical breakpoints (CBPs), where the error probability is higher. Since 2014, AST categorization of most drug/species combinations has depended exclusively on MIC and/or inhibition zone measurements. However, AST methods still suffer from a notable methodological variability, which can lead to miscategorization of a clinical isolate. Different miscategorization types are defined on the basis of the therapeutic implications. Erratic classifications of true-susceptible isolates as resistant are considered major errors (MEs), misclassifications of true-resistant isolates as susceptible are referred to as very major errors (vMEs) and false assignments of bacterial isolates to adjacent interpretative categories (S!I, I!S, I!R) are considered minor errors (mEs). The rates of MEs, vMEs and mEs depend on a number of factors: (i) presence and width of an intermediate zone; (ii) position of a population relative to the CBP; and (iii) methodological variation. The latter parameter includes both the methodological imprecision (inoculum size, agar composition, incubation time, disc content, interand intra-person variability in the reading) and the biological variation. Here we report on Antibiotrust, a software that visualizes the antibiogram and the reliability of the categorization. Antibiotrust was developed with the aim of conveying a graphic report displaying AST data from Kirby–Bauer disc diffusion testing. However, this approach can also be used for data based on MIC determination. As shown in Figure 1, Antibiotrust reports display the inhibition zone diameters of antibiotic panels used for the various bacterial groups (e.g. Enterobacteriaceae). The rectangular boxes correspond to the various antibiotics and are partitioned into the interpretative categories [resistant (r) in red, intermediate (i) in yellow and susceptible (s) in green]. Inhibition zone diameter distributions within the susceptible WT population appear in green shades, which become darker with higher prevalences. The distributions are based on local data and are updated each year. This feature is particularly relevant for susceptible clinical isolates, as it visualizes the position of the tested clinical isolate relative to the distribution of the WT population as derived from local epidemiological data. Black boxes and error bars indicate the inhibition zone diameter along with the methodological variation. The latter significantly influences the classification reliability and thereby the rate of MEs and vMEs. The width of the error bars is continuously updated for each combination of antibiotic and species or bacterial group and is given by the 2-fold standard deviation of weekly repeated measurements of inhibition zones of a quality-control strain. The interpretative category is displayed on the left side of the antibiotic box and is accompanied by the reliability of the categorization, which is calculated separately for all antibiotics using a normal model. Intrinsic antibiotic resistances are displayed in blue (e.g. ampicillin for Klebsiella pneumoniae). Monochromatic boxes display interpretative categorizations that are deduced from other antibiotics (i.e. ciprofloxacin and levofloxacin from norfloxacin) in agreement with EUCAST-derived in-house expert interpretation rules. Reliabilities are not determined for intrinsic resistances, deduced interpretations and for antibiotic/species combinations classified as intermediate. Several studies have shown a good correlation between MIC values and inhibition zone diameters in several bacterial species. A prospective integration of MIC values inferred from disc diffusion assays by Antibiotrust may further advance the accuracy of the AST reports and allow a better estimate of the antimicrobial susceptibility patterns. The additional information provided by Antibiotrust will help in choosing the most appropriate antibiotic, as clinicians will be in the