Archives de Catégorie: Uncategorized

Use notebooks to run and share R with students during containment

Data analysis is often at the heart of our teachings, however it generates many difficulties with the use of tools such as R or Rstudio even in face-to-face situations. With confinement these problems are exacerbated because it is difficult to interact with the students’ code or even ensure that they have downloaded the right software.

However, there are effective solutions for coding, running the code, sharing it and editing it with others online. One of them is rdrr.io, which is a site that offers both the possibility to run code online and also to create « notebooks » for code, run the code, save it and share it.

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Ecological indicators explain root traits value at global scale

Graphical abstract

Plant ecological indicator values as predictors of fine‐root trait variations

First published: 07 February 2020

1. Fine‐roots play key roles in the capacity of plants to face environmental constraints and their traits reflect adaptations to the environment, including soil structure, resource availability and climate. However, the inaccuracy of global soil and climate databases to account for the large environmental variation occurring at small spatial scale prevents accurate estimations of the linkages between environmental variables and fine‐root strategies.

2. Here, using two global databases on fine‐root traits (Rhizopolis‐db) and species phylogenetic relatedness, and a regional database of species ecological indicator values (Baseflor), we quantified the predictive value of ecological indicator values, as an alternative to classical coarse soil and climate indicators, on the variation in four major fine‐root traits.

3. A strong phylogenetic signal was found among species for fine‐root mean diameter, specific root length (SRL) and root tissue density (RTD), but less so for root nitrogen concentration (RNC). After accounting for this relatedness, ecological indicators still explained a large part of trait variation in our dataset for SRL, RTD and RNC. Multi‐indicators best model R2 reached 0.40 for SRL and RTD, and 0.44 for RNC, whereas it was only 0.10 for diameter. Ecological indicators of nutrient availability and soil texture were those that most strongly related to SRL, RTD and RNC. Specifically, plant fast resources use strategies characterized by high SRL, RNC and low RTD occurred more frequently in nutrient‐rich soils and in soils with light sandy textures. Additionally, light availability and atmospheric temperature were negatively related with SRL and continentality negatively influenced RNC.

4. With respect to both nutrient and water availability ecological indicator values, opposite adaptations were observed between growth forms, particularly between woody and herbaceous species, limiting our ability to define simple, widely applicable patterns of trait‐environment relationships.

Synthesis: Our analysis demonstrates that species ecological indicator values are valuable predictors of plant below‐ground strategies. It provides original evidence that herbaceous species with fine‐root traits representative of fast resource use strategies typically occur in more favourable soil habitats (high nutrient and water availability), meanwhile woody species may show the opposite trend. Other important environmental parameters concomitantly influence fine‐root trait variation in contrasting ways.

How to use evolution sciences to improve cropping system sustainability

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Farming plant cooperation in crops

Germain Montazeaud , François Rousset , Florian Fort , Cyrille Violle , Hélène Fréville† and Sylvain Gandon†

Published:22 January 2020

https://doi.org/10.1098/rspb.2019.1290


Selection of the fittest can promote individual competitiveness but often results in the erosion of group performance. Recently, several authors revisited this idea in crop production and proposed new practices based on selection for cooperative phenotypes, i.e. phenotypes that increase crop yield through decreased competitiveness. These recommendations, however, remain difficult to evaluate without a formal description of crop evolutionary dynamics under different selection strategies. Here, we develop a theoretical framework to investigate the evolution of cooperation-related traits in crops, using plant height as a case study. Our model is tailored to realistic agricultural practices and shows that combining high plant density, high relatedness and selection among groups favours the evolution of shorter plants that maximize grain yield. Our model allows us to revisit past and current breeding practices in light of kin selection theory, and yields practical recommendations to increase cooperation among crops and promote sustainable agriculture

Roots matter for the competition

Foxx et Fort

Root and shoot competition lead to contrasting competitive outcomes under water stress: A systematic review and meta-analysis.

Foxx, Alicia J.; Fort, Florian
PLoS ONE . 12/11/2019, Vol. 14 Issue 12, p1-17. 17p.


Abstract:
Background: Competition is a critical process that shapes plant communities and interacts with environmental constraints. There are surprising knowledge gaps related to mechanisms that belie competitive processes, though important to natural communities and agricultural systems: the contribution of different plant parts on competitive outcomes and the effect of environmental constraints on these outcomes. Objective: Studies that partition competition into root-only and shoot-only interactions assess whether plant parts impose different competitive intensities using physical partitions and serve as an important way to fill knowledge gaps. Given predicted drought escalation due to climate change, we focused a systematic review–including a meta-analysis on the effects of water supply and competitive outcomes. Methods: We searched ISI Web of Science for peer-reviewed studies and found 2042 results. From which eleven suitable studies, five of which had extractable information of 80 effect sizes on 10 species to test these effects. We used a meta-analysis to compare the log response ratios (lnRR) on biomass for responses to competition between roots, shoots, and full plants at two water levels. Results: Water availability treatment and competition treatment (root-only, shoot-only, and full plant competition) significantly interacted to affect plant growth responses (p < 0.0001). Root-only and full plant competition are more intense in low water availability (-1.2 and -0.9 mean lnRR, respectively) conditions than shoot-only competition (-0.2 mean lnRR). However, shoot-only competition in high water availability was the most intense (— 0.78 mean lnRR) compared to root-only and full competition (-0.5 and 0.61 mean lnRR, respectively) showing the opposite pattern to low water availability. These results also show that the intensity of full competition is similar to root-only competition and that low water availability intensifies root competition while weakening shoot competition. Conclusions: The outcome that competition is most intense between roots at low water availability emphasizes the importance of root competition and these patterns of competition may shift in a changing climate, creating further urgency for further studies to fil knowledge gaps addressing issues of drought on plant interactions and communities.

Plant response to resource stress

Freschet et al 2Allocation, morphology, physiology, architecture: the multiple facets of plant above and belowground responses to resource stress.

Grégoire T. Freschet, Cyrille Violle, Malo Y. Bourget, Michael Scherer-Lorenzen, Florian Fort

New Phytologist
First published: 01 Juin 2018

https://doi.org/10.1111/nph.15225


Plants respond to resource stress by changing multiple aspects of their biomass allocation, morphology, physiology and architecture. To date, we lack an integrated view of the relative importance of these plastic responses in alleviating resource stress and of the consistency/variability of these responses among species.

We subjected nine species (legumes, forbs and graminoids) to nitrogen and/or light shortages and measured 11 above-ground and below-ground trait adjustments critical in the alleviation of these stresses (plus several underlying traits).

Nine traits out of 11 showed adjustments that improved plants’ potential capacity to acquire the limiting resource at a given time. Above ground, aspects of plasticity in allocation, morphology, physiology and architecture all appeared important in improving light capture, whereas below ground, plasticity in allocation and physiology were most critical to improving nitrogen acquisition. Six traits out of 11 showed substantial heterogeneity in species plasticity, with little structuration of these differences within trait covariation syndromes.

Such comprehensive assessment of the complex nature of phenotypic responses of plants to multiple stress factors, and the comparison of plant responses across multiple species, makes a clear case for the high (but largely overlooked) diversity of potential plastic responses of plants, and for the need to explore the potential rules structuring them.

First paper with my student!!!

P1100244

Crop mixtures: does niche complementarity hold for belowground resources? An experimental test using rice genotypic pairs

Montazeaud G., Violle C., Fréville H., Luquet D., Ahmadi N., Courtois B., Bouhaba I., Fort F.

Plant and Soil
First published: 27 November  2017

  1. Genotypic mixtures have been receiving a growing interest as genetic diversity could increase crop productivity. Resource-use complementarity is an expected key underlying mechanism, provided that varieties in the mixture differ in resource-related traits, notably root traits. We aimed at examining how trait differences and resource-use complementarity drive biomass production of genotypic mixtures.
  2. Four rice (Oryza sativa) genotypes including two Near-Isogenic Lines only differing in root depth were grown in monoculture and in two-way mixtures in pots under two levels of phosphorus supply. We analyzed the relative difference between mixture biomass and the best monoculture biomass in relation to between-genotype phenotypic distance on ten resource-related traits.
  3. Mixtures never outperformed the best monoculture. However, relative mixture productivity increased with increasing between-genotype distance in biovolume, specific leaf area and top soil root biomass. This was mainly driven by a “selection effect”: trait differences led to competitive ability differences and the dominant genotypes tended to gain more in mixture than the subdominant genotypes lost compared to monoculture.
  4. Rather than trying to minimize competition through resource-use complementarity, we argue that promoting interactions between genotypes that have different competitive abilities may be a more promising approach to design productive crop mixtures.

Wheat roots and domestication

Roucou et al.

Agathe Roucou, Cyrille Violle, Florian Fort, Pierre Roumet, Martin Ecarnot, Denis Vile

Journal of Applied Ecology
First published: 2 December 2017

  1. Human selection, changes in environmental conditions and management practices drove the phenotypic trajectory of crops during domestication. The characterization of the crop domestication syndrome lies mostly on reproductive characters. However, biophysical and ecophysiological constraints during vegetative growth are also at play and can strongly impact crop phenotypes. It has been argued that a broadened examination of crop phenotypes through a functional trait‐based lens should improve our understanding of the domestication syndrome.
  2. We used a collection of 39 genotypes representative of key steps during tetraploid wheat domestication and grew them in a common garden experiment. We quantified the vegetative phenotype of each genotype through the measurements of 13 functional traits related to root, leaf and whole‐plant dimensions.
  3. In modern cultivars, compared to ancestral forms, leaf longevity was shorter, while net photosynthetic rate, leaf production rate and nitrogen content were higher. Modern cultivars had a shallower root system and exhibited a larger proportion of fine roots, preferring to invest biomass above‐rather than below‐ground. We found ancestral forms to be integrated phenotypes characterized by coordination between above‐ and below‐ground functioning. Conversely, in modern forms, human selection appeared to have broken this coordination and to have generated a new type of network of trait covariations.
  4. Synthesis and applications. The examination of leaf, root and whole‐plant traits of wheat accessions indicated a strong shift in plant functional strategies over the course of domestication. Elite genotypes tended to better optimize resource‐use acquisition strategies than ancestral ones. The characterization of the crop phenotype based on vegetative traits thus suggests a much more complete domestication syndrome. Our findings highlight the benefits of using a functional trait‐based characterization of crop phenotypes to document the extent of domestication syndrome and to further advance the agroecological management of cereals.