Functional Traits 2.0: The power of the metabolome for ecology

Walker, T. K.; Alexander, Jake M.; Allard, Pierre‐Marie; Baines, Oliver; Baldy, Virginie; Bardgett, Richard D.; Capdevila, Pol; Coley, Phyllis D.; David, Bruno; Defossez, Emmanuel; Endara, María‐José; Ernst, Madeleine; Fernandez, Catherine; Forrister, Dale L.; Gargallo‐Garriga, Albert; Jassey, Vincent E. J.; Marr, Sue; Neumann, Steffen; Pellissier, Loïc; Peñuelas, Josep; Peters, Kristian; Rasmann, Sergio; Roessner, Ute; Sardans, Jordi; Schrodt, Franziska; Schuman, Meredith C.; Soule, Abrianna J.; Uthe, Henriette; Weckwerth, Wolfram; Wolfender, Jean‐Luc; Dam, Nicole M. van; Salguero‐Gómez, Roberto

doi:10.1111/1365-2745.13826

Cited by 62 publications

(85 citation statements)

References 126 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A formal adaption of this concept to chemical ecology of plants is lacking. Moreover, phytochemicals and their diversity are mostly neglected in trait‐based ecology despite their pivotal functional importance (Walker et al ., 2022). Here, we aim to highlight the importance of phytochemicals in plant ecology, which should be implemented in niche theory, trait‐based ecology and community ecology.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Chemical phenotype as important and dynamic niche dimension of plants

Müller

Junker

2022

New Phytologist

View full text Add to dashboard Cite

Niche theory considering the traits of species and individuals provides a powerful tool to integrate ecology and evolution of species. In plant ecology, morphological and physiological traits are commonly considered as niche dimensions, whereas phytochemical traits are mostly neglected in this context despite their pivotal functions in plant responses to their environment and in mediating interactions. The diversity of plant phytochemicals can thus mediate three key processes: niche choice, conformance and construction. Here, we integrate frameworks from niche theory with chemical ecology and argue that plants use their individual-specific diversity in phytochemicals (chemodiversity) for different niche realization processes. Our concept has important implications for ecosystem processes and stability and increases the predictive ability of chemical ecology.

show abstract

Section: Introductionmentioning

confidence: 99%

“…A formal adaption of this concept to chemical ecology of plants is lacking. Moreover, phytochemicals and their diversity are mostly neglected in trait-based ecology despite their pivotal functional importance (Walker et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Chemical phenotype as important and dynamic niche dimension of plants

Müller

Junker

2022

New Phytologist

View full text Add to dashboard Cite

show abstract

“…It is also worth mentioning that we have focused on quantifying diversity on the level of individual samples, often likely to represent individual plants. Others have instead utilized phytochemical compounds as functional traits to measure diversity on a community level (Salazar et al ., 2016), representing a complementary approach which can answer questions related to trait-based ecology and niche processes (Müller & Junker, 2022; Walker et al ., 2022).…”

Section: Resultsmentioning

confidence: 99%

Quantifying chemodiversity considering biochemical and structural properties of compounds with the R packagechemodiv

Petrén

Köllner

Junker

2022

Preprint

View full text Add to dashboard Cite

SummaryPlants produce large numbers of phytochemical compounds affecting plant physiology and interactions with their biotic and abiotic environment. Recently, chemodiversity has attracted considerable attention as an ecologically and evolutionary meaningful way to characterize the phenotype of a mixture of phytochemical compounds.Currently used measures of phytochemical diversity, and related measures of phytochemical dissimilarity, generally do not take structural or biosynthetic properties of compounds into account. Such properties can be indicative of the compounds’ function and inform about their biosynthetic (in)dependence, and should therefore be included in calculations of these measures.We introduce the R package chemodiv, which retrieves biochemical and structural properties of compounds from databases and provides functions for calculating and visualizing chemical diversity and dissimilarity for phytochemicals and other types of compounds. Our package enables calculations of diversity that takes the richness, relative abundance and – most importantly – structural and/or biosynthetic dissimilarity of compounds into account. We illustrate the use of the package with examples on simulated and real datasets.By providing the R package chemodiv for quantifying multiple aspects of chemodiversity, we hope to facilitate investigations of how chemodiversity varies across levels of biological organization, and its importance for the ecology and evolution of plants and other organisms.

show abstract

“…This involves mass feature detection, alignment among samples, MS spectral deconvolution, feature normalization, missing value imputation, and multilevel statistical analyses, as reviewed by Li and Gaquerel (2021) . Despite major advances in omic sciences, metabolomic aspects are still major bottlenecks because of the high diversity of secondary plant compounds and unresolved biosynthetic pathways ( Peters et al, 2018 ; Walker et al, 2022 ). However, the development of powerful analytical tools based on combinations of high-resolution MS and increasingly advanced bioinformatic tools is raising capacities to acquire and translate metabolomic information into usable data to merge with other forms of omic information ( Peters et al, 2018 ; Walker et al, 2022 ).…”

Section: Eco-metabolomics Of Plant-arthropod Interactionsmentioning

confidence: 99%

“…Despite major advances in omic sciences, metabolomic aspects are still major bottlenecks because of the high diversity of secondary plant compounds and unresolved biosynthetic pathways ( Peters et al, 2018 ; Walker et al, 2022 ). However, the development of powerful analytical tools based on combinations of high-resolution MS and increasingly advanced bioinformatic tools is raising capacities to acquire and translate metabolomic information into usable data to merge with other forms of omic information ( Peters et al, 2018 ; Walker et al, 2022 ). Moreover, statistical descriptors from information-theoretical frameworks have been transposed to score indices of diversity and specialization from metabolome profiles, thereby allowing quantification of the reprogramming of metabolome diversity according to ecological interactions ( Li et al, 2020 ; Li and Gaquerel, 2021 ; Walker et al, 2022 ).…”

Section: Eco-metabolomics Of Plant-arthropod Interactionsmentioning

confidence: 99%

Evolutionary Ecology of Plant-Arthropod Interactions in Light of the “Omics” Sciences: A Broad Guide

et al. 2022

View full text Add to dashboard Cite

Aboveground plant-arthropod interactions are typically complex, involving herbivores, predators, pollinators, and various other guilds that can strongly affect plant fitness, directly or indirectly, and individually, synergistically, or antagonistically. However, little is known about how ongoing natural selection by these interacting guilds shapes the evolution of plants, i.e., how they affect the differential survival and reproduction of genotypes due to differences in phenotypes in an environment. Recent technological advances, including next-generation sequencing, metabolomics, and gene-editing technologies along with traditional experimental approaches (e.g., quantitative genetics experiments), have enabled far more comprehensive exploration of the genes and traits involved in complex ecological interactions. Connecting different levels of biological organization (genes to communities) will enhance the understanding of evolutionary interactions in complex communities, but this requires a multidisciplinary approach. Here, we review traditional and modern methods and concepts, then highlight future avenues for studying the evolution of plant-arthropod interactions (e.g., plant-herbivore-pollinator interactions). Besides promoting a fundamental understanding of plant-associated arthropod communities’ genetic background and evolution, such knowledge can also help address many current global environmental challenges.

show abstract

Functional Traits 2.0: The power of the metabolome for ecology

Abstract: Nicole M. van Dam and Roberto Salguero-Gómez joint last authorship.

Cited by 62 publications

References 126 publications

Chemical phenotype as important and dynamic niche dimension of plants

Chemical phenotype as important and dynamic niche dimension of plants

Quantifying chemodiversity considering biochemical and structural properties of compounds with the R packagechemodiv

Evolutionary Ecology of Plant-Arthropod Interactions in Light of the “Omics” Sciences: A Broad Guide

Contact Info

Product

Resources

About