A trait-based framework linking the soil metabolome to plant-soil feedbacks

By modifying the biotic and abiotic properties of the soil, plants create soil legacies that can affect vegetation dynamics through plant-soil feedbacks (PSF). PSF are generally attributed to reciprocal effects of plants and soil biota, but these interactions can also drive changes in the identity, diversity and abundance of soil metabolites, leading to more or less persistent soil chemical legacies whose role in mediating PSF has rarely been considered. These chemical legacies may interact with microbial or nutrient legacies to affect species coexistence. Given the ecological importance of chemical interactions between plants and other organisms, a better understanding of soil chemical legacies is needed in community ecology. In this Viewpoint, we aim to: highlight the importance of belowground chemical interactions for PSF; define and integrate soil chemical legacies into PSF research by clarifying how the soil metabolome can contribute to PSF; discuss how functional traits can help predict these plant-soil interactions; propose an experimental approach to quantify plant responses to the soil solution metabolome; and describe a testable framework relying on root economics and seed dispersal traits to predict how plant species affect the soil metabolome and how they could respond to soil chemical legacies

Soil chemical legacies trigger species‐specific and context‐dependent root responses in later arriving plants

Abstract Soil legacies play an important role for the creation of priority effects. However, we still poorly understand to what extent the metabolome found in the soil solution of a plant community is conditioned by its species composition and whether soil chemical legacies affect subsequent species during assembly. To test these hypotheses, we collected soil solutions from forb or grass communities and evaluated how the metabolome of these soil solutions affected the growth, biomass allocation and functional traits of a forb ( Dianthus deltoides ) and a grass species ( Festuca rubra ). Results showed that the metabolomes found in the soil solutions of forb and grass communities differed in composition and chemical diversity. While soil chemical legacies did not have any effect on F . rubra , root foraging by D . deltoides decreased when plants received the soil solution from a grass or a forb community. Structural equation modelling showed that reduced soil exploration by D . deltoides arose via either a root growth‐dependent pathway (forb metabolome) or a root trait‐dependent pathway (grass metabolome). Reduced root foraging was not connected to a decrease in total N uptake. Our findings reveal that soil chemical legacies can create belowground priority effects by affecting root foraging in later arriving plants

Hill-Chao numbers allow decomposing gamma multifunctionality into alpha and beta components

Biodiversity-ecosystem functioning (BEF) research has provided strong evidence and mechanistic underpinnings to support positive effects of biodiversity on ecosystem functioning, from single to multiple functions. This research has provided knowledge gained mainly at the local alpha scale (i.e. within ecosystems), but the increasing homogenization of landscapes in the Anthropocene has raised the potential that declining biodiversity at the beta (across ecosystems) and gamma scales is likely to also impact ecosystem functioning. Drawing on biodiversity theory, we propose a new statistical framework based on Hill-Chao numbers. The framework allows decomposition of multifunctionality at gamma scales into alpha and beta components, a critical but hitherto missing tool in BEF research; it also allows weighting of individual ecosystem functions. Through the proposed decomposition, new BEF results for beta and gamma scales are discovered. Our novel approach is applicable across ecosystems and connects local- and landscape-scale BEF assessments from experiments to natural settings

Toward a Comprehensive and Integrated Strategy of the European Marine Research Infrastructures for Ocean Observations

Research Infrastructures (RIs) are large-scale facilities encompassing instruments, resources, data and services used by the scientific community to conduct high-level research in their respective fields. The development and integration of marine environmental RIs as European Research Vessel Operators [ERVO] (2020) is the response of the European Commission (EC) to global marine challenges through research, technological development and innovation. These infrastructures (EMSO ERIC, Euro-Argo ERIC, ICOS-ERIC Marine, LifeWatch ERIC, and EMBRC-ERIC) include specialized vessels, fixed-point monitoring systems, Lagrangian floats, test facilities, genomics observatories, bio-sensing, and Virtual Research Environments (VREs), among others. Marine ecosystems are vital for life on Earth. Global climate change is progressing rapidly, and geo-hazards, such as earthquakes, volcanic eruptions, and tsunamis, cause large losses of human life and have massive worldwide socio-economic impacts. Enhancing our marine environmental monitoring and prediction capabilities will increase our ability to respond adequately to major challenges and efficiently. Collaboration among European marine RIs aligns with and has contributed to the OceanObs’19 Conference statement and the objectives of the UN Decade of Ocean Science for Sustainable Development (2021–2030). This collaboration actively participates and supports concrete actions to increase the quality and quantity of more integrated and sustained observations in the ocean worldwide. From an innovation perspective, the next decade will increasingly count on marine RIs to support the development of new technologies and their validation in the field, increasing market uptake and produce a shift in observing capabilities and strategies.Peer reviewe

Root-emitted volatile organic compounds: can they mediate belowground plant-plant interactions?

peer reviewedBackground Aboveground, plants release volatile organic compounds (VOCs) that act as chemical signals between neighbouring plants. It is now well documented that VOCs emitted by the roots in the plant rhizosphere also play important ecological roles in the soil ecosystem, notably in plant defence because they are involved in interactions between plants, phytophagous pests and organisms of the third trophic level. The roles played by root-emitted VOCs in between- and within-plant signalling, however, are still poorly documented in the scientific literature. Scope Given that (1) plants release volatile cues mediating plant-plant interactions aboveground, (2) roots can detect the chemical signals originating from their neighbours, and (3) roots release VOCs involved in biotic interactions belowground, the aim of this paper is to discuss the roles of VOCs in between- and within-plant signalling belowground. We also highlight the technical challenges associated with the analysis of root-emitted VOCs and the design of experiments targeting volatile-mediated root-root interactions. Conclusions We conclude that root-root interactions mediated by volatile cues deserve more research attention and that both the analytical tools and methods developed to study the ecological roles played by VOCs in interplant signalling aboveground can be adapted to focus on the roles played by root-emitted VOCs in between- and within-plant signalling

Barley (Hordeum distichon L.) roots synthesise volatile aldehydes with a strong age-dependent pattern and release (E)- non-2-enal and (E,Z)-nona-2,6-dienal after mechanical injury

In the context of chemical ecology, the analysis of the temporal production pattern of volatile organic compounds (VOCs) in root tissues and the emission rate measurement of root-emitted VOCs are of major importance for setting up experiments to study the implication of these compounds in biotic interactions. Such analyses, however, remain challenging because of the belowground location of plant root systems. In this context, this study describes the evolution of the root VOC production pattern of barley (Hordeum distichon L.) at five developmental stages from germination to the end of tillering and evaluates the emission of the identified VOCs in an artificial soil. VOCs produced by crushed root tissues and released by unexcavated root systems were analysed using dynamic sampling devices coupled to a gas chromatography-mass spectrometry methodology (synchronous SCAN/SIM). The results showed that, at each analysed developmental stage, crushed barley roots produced mainly four volatile aldehydes: hexanal; (E)-hex-2-enal; (E)-non-2-enal; and (E,Z)-nona-2,6-dienal. Higher total and individual VOC concentrations were measured in 3-day-old seminal roots compared with older phenological stages. For each developmental stage, the lipoxygenase (LOX) activity was greater for linoleic acid than α-linolenic acid and the greatest LOX activities using linoleic and α- linolenic acids as substrates were measured in 7- and 3-day-old roots, respectively. The analysis of VOCs released by barley roots into the soil showed that (E)-non-2- enal and (E,Z)-nona-2,6-dienal were the only VOCs emitted in quantifiable amounts by mechanically injured roots

archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems

Quantifying plant morphology is a very challenging task that requires methods able to capture the geometry and topology of plant organs at various spatial scales. Recently, the use of persistent homology as a mathematical framework to quantify plant morphology has been successfully demonstrated for leaves, shoots, and root systems. In this paper, we present a new data analysis pipeline implemented in the R package archiDART to analyse root system architectures using persistent homology. In addition, we also show that both geometric and topological descriptors are necessary to accurately compare root systems and assess their natural complexity

archiDART 3.0

This repository contains the source codes of the R package archiDART v3.0. This version of the package was used in Delory et al archiDART v3.0: a new data analysis pipeline allowing the topological analysis of plant root systems. The manuscript was submitted to F1000Research in December 2017

archiShiny: a web app to demonstrate the capabilities of archiDART 3.0

This repository contains the source codes of the web application (archiShiny) created to illustrate the capabilities of archiDART 3.0. This version was used in Delory et al archiDART v3.0: a new data analysis pipeline allowing the topological analysis of plant root systems. The manuscript was submitted to F1000Research in December 2017