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The effects of plants on the biosphere, atmosphere and geosphere are key determinants of terrestrial ecosystem functioning. However, despite substantial progress made regarding plant belowground components, we are still only beginning to explore the complex relationships between root traits and functions. Drawing on the literature in plant physiology, ecophysiology, ecology, agronomy and soil science, we reviewed 24 aspects of plant and ecosystem functioning and their relationships with a number of root system traits, including aspects of architecture, physiology, morphology, anatomy, chemistry, biomechanics and biotic interactions. Based on this assessment, we critically evaluated the current strengths and gaps in our knowledge, and identify future research challenges in the field of root ecology. Most importantly, we found that belowground traits with the broadest importance in plant and ecosystem functioning are not those most commonly measured. Also, the estimation of trait relative importance for functioning requires us to consider a more comprehensive range of functionally relevant traits from a diverse range of species, across environments and over time series. We also advocate that establishing causal hierarchical links among root traits will provide a hypothesis-based framework to identify the most parsimonious sets of traits with the strongest links on functions, and to link genotypes to plant and ecosystem functioning.

• Plant stoichiometric coupling among all elements is fundamental to maintaining growth-related ecosystem functions. However, our understanding of nutrient balance in response to global changes remains greatly limited to plant carbon : nitrogen : phosphorus (C : N : P) coupling. • Here we evaluated nine element stoichiometric variations with one meta-analysis of 112 global change experiments conducted across global terrestrial ecosystems and one synthesis over 1900 species observations along natural environment gradients across China. • We found that experimentally increased soil N and P respectively enhanced plant N : potassium (K), N : calcium (Ca) and N : magnesium (Mg), and P : K, P : Ca and P : Mg, and natural increases in soil N and P resulted in qualitatively similar responses. The ratios of N and P to base cations decreased both under experimental warming and with naturally increasing temperature. With decreasing precipitation, these ratios increased in experiments but decreased under natural environments. Based on these results, we propose a new stoichiometric framework in which all plant element contents and their coupling are not only affected by soil nutrient availability, but also by plant nutrient demand to maintain diverse functions under climate change. • This study offers new insights into understanding plant stoichiometric variations across a full set of mineral elements under global changes.

In recent years, belowground plant ecology has experienced a booming interest. This has resulted in major advances towards a greater understanding of belowground plant and ecosystem functioning focused on fine roots, mycorrhizal associations and nutrient acquisition. Despite this, other important functions (e.g., on‐spot persistence, space occupancy, resprouting after biomass removal) exerted by different belowground plant organs (e.g., roots, rhizomes, bulbs) remain largely unexplored. Here, we propose a framework providing a comprehensive perspective on the entire set of belowground plant organs and functions. We suggest a compartment‐based approach. We identify two major belowground compartments, that is, acquisitive and nonacquisitive, associated with biomass allocation into these functions. Also, we recommend the nonacquisitive compartment to be divided into structural (e.g., functional roles carried out by rhizomes, such as sharing of resources, space occupancy) and nonstructural (e.g., functional roles exerted by carbohydrates reserve affecting resprouting ability, protection against climate adversity) subcompartments. We discuss methodological challenges—and their possible solutions—posed by changes in biomass allocation across growth forms and ontogenetic stages, and in relation to biomass partitioning and turnover. We urge the implementation of methods and approaches considering all the belowground plant compartments. This way, we would make sure that key, yet less‐studied functions would be incorporated into the belowground plant ecology research agenda. The framework has potential to advance the understanding of belowground plant and ecosystem functioning by considering relations and trade‐offs between different plant functions and organs. At last, we identify four major areas where using the proposed compartment‐based approach would be particularly important, namely (a) biomass scaling, (b) clonality‐resource acquisition relations, (c) linkages between resprouting and changing environmental conditions and (d) carbon sequestration. A plain language summary is available for this article. Plain Language Summary Foreign Language Funkční ekologie podzemních částí rostlinSummary in Czech V posledních letech zažívá ekologie podzemních částí rostlin velký zájem výzkumníků po celém světě. Tento zájem přispěl k lepšímu porozumění funkce podzemních částí rostlin, zejména jemných kořenů a mykorhizy, které hrají významnou roli při získávání vody a živin. Jiné důležité funkce rostlin, jako je přežívání na daném místě, obsazování prostoru, nebo schopnost regenerace po poškození těla, zprostředkované například zásobními kořeny a oddenky, však zůstávají opomíjeny. S cílem napravit tuto situaci, navrhujeme integrovaný přístup, který umožní komplexnější pohled na celou řadu podzemních rostlinných orgánů a jejich funkcí. Na příkladech z literatury ukazujeme, jak zaměření pouze na jemné kořeny může omezit naši schopnost poznat ekologii rostlin. Navrhujeme přístup založený na rozlišení základních funkčních specializací podzemních orgánů. Identifikujeme dva hlavní funkční podzemní kompartmenty, za prvé akviziční, tj. podílející se na získávání vody a živin, a za druhé neakviziční, tj. podílející se na propojování různých částí rostliny, na klonálním růstu a na regeneraci po narušení. Diskutujeme metodologické problémy spojené s implementací tohoto přístupu a o jejich možných řešeních. Přestavujeme rozdíly v investicích do těchto podzemních kompartmentů u různých růstových forem a během života rostliny, stejně tak problémy související se stanovením biomasy a jejím obratem. Závěrem vyzýváme výzkumníky, aby při studium ekologie aplikovali metody a přístupy, které berou v úvahu všechny podzemní orgány rostlin. Pouze tímto způsobem zajistíme, aby méně studované, avšak zcela klíčové funkce podzemních orgánů rostlin, byly začleněny do výzkumného plánu funkčních ekologů. Příkladem může být jejich využití pro lepší odhad sekvestrace uhlíku v podzemních orgánech rostlin, což je důležité pro tvorbu celosvětových geochemických modelů.

Research into plant gene function is crucial for developing strategies to increase crop yields. The recent introduction of large language models (LLMs) offers a means to aggregate large amounts of data into a queryable format, but the output can contain inaccurate or false claims known as hallucinations. To minimize such hallucinations and produce high‐quality knowledge‐based outputs, the s of over 60 000 plant research articles are compiled into a Chroma database for retrieval‐augmented generation (RAG). Then linguistic data are used from 13 993 Arabidopsis (Arabidopsis thaliana) phenotypes and 23 323 gene functions to fine‐tune the LLM Llama3‐8B, producing PlantGPT, a virtual expert in Arabidopsis phenotype–gene research. By evaluating answers to test questions, it is demonstrated that PlantGPT outperforms general LLMs in answering specialized questions. The findings provide a blueprint for functional genomics research in food crops and demonstrate the potential for developing LLMs for plant research modalities. To provide broader access and facilitate adoption, the online tool http://www.plantgpt.icu is developed, which will allow researchers to use PlantGPT in their scientific investigations. PlantGPT integrates 60 000+ plant research articles with Arabidopsis phenotype‐gene data through retrieval‐augmented generation and fine‐tuning of Llama3‐8B. This open‐source, specialized AI system outperforms general large language models in plant gene‐phenotype relationships, establishing a new paradigm for functional genomics research and molecular design breeding.

Background and aimsHyperaccumulator plants exhibit extreme ecophysiological characteristics, which make them suited for phytoremediation. Understanding their ecological strategies might help identify the species and functions to be favored in phytoremediation, restoration, and conservation projects for metalliferous sites.MethodsHere, we identified the hyperaccumulator species in the worldwide plant trait database TRY and cross-referenced these trait syndromes associated with the ability of plants to concentrate metals. This allows us to link trace element hyperaccumulation with broader plant ecological strategies.ResultsHyperaccumulator plant species tend to have smaller leaves and poorer competitive ability compared to non-hyperaccumulator plant species. Contrary to expectations, we found no indication of hyperaccumulator plants being more resource-conservative on the leaf economics spectrum. However, these data remain fragmentary as only 2.7% of hyperaccumulator plant species have their traits published in the TRY database.ConclusionThe recent development of trait-based models to construct plant communities providing optimal ecosystem services (e.g., phytoremediation, restoration) requires further research to identify predictable trait-service relationships. We thus call for an international collaborative sampling effort to measure traits in more hyperaccumulator plant species.

A central paradigm in comparative ecology is that species sort out along a slow-fast resource economy spectrum of plant strategies, but this has been rarely tested for a comprehensive set of stem traits and compartments. We tested how stem traits vary across wood and bark of temperate tree species, whether a slow-fast strategy spectrum exists, and what traits make up this plant strategy spectrum. For 14 temperate tree species, 20 anatomical, chemical, and morphological traits belonging to six key stem functions were measured for three stem compartments (inner wood, outer wood, and bark). The trait variation was explained by major taxa (38%), stem compartments (24%), and species within major taxa (19%). A continuous plant strategy gradient was found across and within taxa, running from hydraulic safe gymnosperms to conductive angiosperms. Both groups showed a second strategy gradient related to chemical defense. Gymnosperms strongly converged in their trait strategies because of their uniform tracheids. Angiosperms strongly diverged because of their different vessel arrangement and tissue types. The bark had higher concentrations of nutrients and phenolics whereas the wood had stronger physical defense. The gymnosperms have a conservative strategy associated with strong hydraulic safety and physical defense, and a narrow, specialized range of trait values, which allow them to grow well in drier and unproductive habitats. The angiosperm species show a wider trait variation in all stem compartments, which makes them successful in marginal- and in mesic, productive habitats. The associations between multiple wood and bark traits collectively define a slow-fast stem strategy spectrum as is seen also for each stem compartment.

In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I–VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers’ views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.

Background and AimsBeneficial plant–microbe interactions can improve plant performance under drought; however, we know less about how drought-induced shifts in microbial communities affect plant traits.MethodsWe cultivated Zea mays in fritted clay with soil microbiomes originating from contrasting environments (agriculture or forest) under two irrigation treatments (well-watered or water limited). Using this design, we investigated whether water conditioning was carried forward through the microbiome to affect a subsequent plant cohort that was subjected to either a well-watered or water limited treatment.ResultsRegardless of the microbiome-origin, plants inoculated with a microbiome from a water limited legacy had traits that allowed them to avoid stress but conserve water. They produced longer roots to explore soil, generated greater soil dissolved organic carbon, potentially stimulating the microbiome, and slower soil water content loss during drought. A well-watered legacy resulted in plants that delayed permanent stomatal closure and higher photosynthetic nitrogen use efficiency. In plants with a forest-originated microbiome, a well-watered legacy and water treatment also resulted in higher rates of photosynthesis and stomatal conductance.ConclusionThese results demonstrate that soil microbiomes can be developed to influence plant drought performance, impacting crop resilience, using short-term microbial conditioning.

This article is a Commentary on Ramírez‐Valiente et al. (2020), 227: 794–809.

1.Ecosystem functioning relies heavily on belowground processes, which are largely regulated by plant fine-roots and their functional traits. However, our knowledge of fine-root trait distribution relies to date on local- and regional-scale studies with limited numbers of species, growth forms and environmental variation. 2.We compiled a worldwide fine-root trait dataset, featuring 1115 species from contrasting climatic areas, phylogeny and growth forms to test a series of hypotheses pertaining to the influence of plant functional types, soil and climate variables, and the degree of manipulation of plant growing conditions on species fine-root trait variation. Most particularly, we tested the competing hypotheses that fine-root traits typical of faster return on investment would be most strongly associated with conditions of limiting versus favourable soil resource availability. We accounted for both data source and species phylogenetic relatedness. 3.We demonstrate that (1) Climate conditions promoting soil fertility relate negatively to fine-root traits favouring fast soil resource acquisition, with a particularly strong positive effect of temperature on fine-root diameter and negative effect on specific root length (SRL), and a negative effect of rainfall on root nitrogen concentration; (2) Soil bulk density strongly influences species fine-root morphology, by favouring thicker, denser fine-roots; (3) Fine-roots from herbaceous species are on average finer and have higher SRL than those of woody species, and N2-fixing capacity positively relates to root nitrogen; (4) Plants growing in pots have higher SRL than those grown in the field. 4.Synthesis. This study reveals both the large variation in fine-root traits encountered globally and the relevance of several key plant functional types and soil and climate variables for explaining a substantial part of this variation. Climate, particularly temperature, and plant functional types were the two strongest predictors of fine-root trait variation. High trait variation occurred at local scales, suggesting that wide-ranging belowground resource economics strategies are viable within most climatic areas and soil conditions.