CAST-R: An application to visualize circadian and heat stress-responsive genes in plants.

The circadian clock helps organisms to anticipate and coordinate gene regulatory responses to changes in environmental stimuli. Under stresses, both time of day and the circadian clock closely control the magnitude of plant responses. The identification of clock-regulated genes is, therefore, important when studying the influence of environmental factors. Here, we present CAST-R (Circadian And heat STress-Responsive), a "Shiny" application that allows users to identify and visualize circadian and heat stress-responsive genes in plants. More specifically, users can generate and export profiles and heatmaps representing transcript abundance of a single or of multiple Arabidopsis (Arabidopsis thaliana) genes over a 24-h time course, in response to heat stress and during recovery following the stress. The application also takes advantage of published Arabidopsis chromatin immunoprecipitation-sequencing datasets to visualize the connections between clock proteins and their targets in an interactive network. In addition, CAST-R offers the possibility to perform phase (i.e. timing of expression) enrichment analyses for rhythmic datasets from any species, within and beyond plants. This functionality combines statistical analyses and graphical representations to identify significantly over- and underrepresented phases within a subset of genes. Lastly, profiles of transcript abundance can be visualized from multiple circadian datasets generated in Arabidopsis, Brassica rapa, barley (Hordeum vulgare), and rice (Oryza sativa). In summary, CAST-R is a user-friendly interface that allows the rapid identification of circadian and stress-responsive genes through multiple modules of visualization. We anticipate that this tool will make it easier for users to obtain temporal and dynamic information on genes of interest that links plant responses to environmental signals.

Germination niche breadth of invasive Iris pseudacorus (L.) suggests continued recruitment from seeds with global warming.

PREMISE: Understanding recruitment processes of invasive species is central to conservation and management strategies. Iris pseudacorus, an emergent macrophyte, has established invasive populations across a broad global range, and reduces biodiversity in wetland ecosystems. Climate change is altering germination cues, yet studies on the invasion of wetland macrophytes often ignore germination ecology despite its importance to their establishment and spread. METHODS: We explored germination of seeds from invasive I. pseudacorus populations in California in response to seed coat presence or absence, and several environmental factors. Using experimental results in a thermal time model, we derived germination temperature thresholds. RESULTS: Germination of I. pseudacorus seeds did not require cold or warm stratification, and was not affected by seed coat presence or absence. Germination occurred in the dark, although germinability was two- to threefold times greater under light. At constant temperature, thermal time model estimates included 18.3 ± 1.8°C base germination temperature (Tb$({T}_{b}$ ); 28.2 ± 0.5°C optimal temperature (To$({T}_{o}$ ); and 41.0 ± 1.7°C ceiling temperature (Tc$({T}_{c}$ ). Seeds exposed to 36.0°C achieved over 10% germination, and embryos of ungerminated seeds presented 76% viability. Overall, germinability remained relatively low at constant temperatures (≤25%) but was close to 90% under alternating daily temperatures. CONCLUSIONS: Exposure to diurnally fluctuating temperatures is essential for this species to achieve high germination rates. Our study reveals that I. pseudacorus has a broad germination niche supporting its establishment in a relatively wide range of environments, including at high temperatures more frequent with climate change.

Seed source regions drive fitness differences in invasive macrophytes.

PREMISE: Worldwide, ecosystems are threatened by global changes, including biological invasions. Invasive species arriving in novel environments experience new climatic conditions that can affect their successful establishment. Determining the response of functional traits and fitness components of invasive populations from contrasting environments can provide a useful framework to assess species responses to climate change and the variability of these responses among source populations. Much research on macrophytes has focused on establishment from clonal fragments; however, colonization from sexual propagules has rarely been studied. Our objective was to compare trait responses of plants generated from sexual propagules sourced from three climatic regions but grown under common environmental conditions, using L. peploides subsp. montevidensis as a model taxon. METHODS: We grew seedlings to reproductive stage in experimental mesocosms under a mediterranean California (MCA) climate from seeds collected in oceanic France (OFR), mediterranean France (MFR), and MCA. RESULTS: Seed source region was a major factor influencing differences among invasive plants recruiting from sexual propagules of L. peploides subsp. montevidensis. Trait responses of young individual recruits from MCA and OFR, sourced from geographically distant and climatically distinct source regions, were the most different. The MCA individuals accumulated more biomass, flowered earlier, and had higher leaf N concentrations than the OFR plants. Those from MFR had intermediate profiles. CONCLUSIONS: By showing that the closer a seedling is from its parental climate, the better it performs, this study provides new insights to the understanding of colonization of invasive plant species and informs its management under novel and changing environmental conditions.

Heterogenous Impact of Water Warming on Exotic and Native Submerged and Emergent Plants in Outdoor Mesocosms.

Some aquatic plants present high biomass production with serious consequences on ecosystem functioning. Such mass development can be favored by environmental factors. Temperature increases are expected to modify individual species responses that could shape future communities. We explored the impact of rising water temperature on the growth, phenology, and metabolism of six macrophytes belonging to two biogeographic origins (exotic, native) and two growth forms (submerged, emergent). From June to October, they were exposed to ambient temperatures and a 3 °C warming in outdoor mesocosms. Percent cover and canopy height were favored by warmer water for the exotic emergent Ludwigia hexapetala. Warming did not modify total final biomass for any of the species but led to a decrease in total soluble sugars for all, possibly indicating changes in carbon allocation. Three emergent species presented lower flavonol and anthocyanin contents under increased temperatures, suggesting lower investment in defense mechanisms and mitigation of the stress generated by autumn temperatures. Finally, the 3 °C warming extended and shortened flowering period for L. hexapetala and Myosotis scorpioides, respectively. The changes generated by increased temperature in outdoor conditions were heterogenous and varied depending on species but not on species biogeographic origin or growth form. Results suggest that climate warming could favor the invasiveness of L. hexapetala and impact the structure and composition of aquatic plants communities.

Seedling Emergence from Seed Banks in Ludwigia hexapetala-Invaded Wetlands: Implications for Restoration.

Soil seed banks play a critical role in the maintenance of wetland plant communities and contribute to revegetation following disturbances. Analysis of the seed bank can therefore inform restoration planning and management. Emergence from seed banks may vary in response to hydrologic conditions and sediment disturbances. To assess the community-level impact of exotic Ludwigia hexapetala on soil seed banks, we compared differences in species composition of standing vegetation among invaded and non-invaded wetlands and the degree of similarity between vegetation and soil seed banks in northern California. To determine potential seed bank recruitment of L. hexapetala and associated plant species, we conducted a seedling emergence assay in response to inundation regime (drawdown vs. flooded) and sediment depth (surface vs. buried). Plant species richness, evenness, and Shannon's H' diversity were substantially lower in standing vegetation at L. hexapetala invaded sites as compared to non-invaded sites. Over 12 months, 69 plant taxa germinated from the seed banks, including L. hexapetala and several other exotic taxa. Seedling density varied among sites, being the highest (10,500 seedlings m-2) in surface sediments from non-invaded sites subjected to drawdown treatments. These results signal the need for invasive plant management strategies to deplete undesirable seed banks for restoration success.