'rtry': An R package to support plant trait data preprocessing

Plant trait data are used to quantify how plants respond to environmental factors and can act as indicators of ecosystem function. Measured trait values are influenced by genetics, trade-offs, competition, environmental conditions, and phenology. These interacting effects on traits are poorly characterized across taxa, and for many traits, measurement protocols are not standardized. As a result, ancillary information about growth and measurement conditions can be highly variable, requiring a flexible data structure. In 2007, the TRY initiative was founded as an integrated database of plant trait data, including ancillary attributes relevant to understanding and interpreting the trait values. The TRY database now integrates around 700 original and collective datasets and has become a central resource of plant trait data. These data are provided in a generic long-table format, where a unique identifier links different trait records and ancillary data measured on the same entity. Due to the high number of trait records, plant taxa, and types of traits and ancillary data released from the TRY database, data preprocessing is necessary but not straightforward. Here, we present the 'rtry' R package, specifically designed to support plant trait data exploration and filtering. By integrating a subset of existing R functions essential for preprocessing, 'rtry' avoids the need for users to navigate the extensive R ecosystem and provides the functions under a consistent syntax. 'rtry' is therefore easy to use even for beginners in R. Notably, 'rtry' does not support data retrieval or analysis; rather, it focuses on the preprocessing tasks to optimize data quality. While 'rtry' primarily targets TRY data, its utility extends to data from other sources, such as the National Ecological Observatory Network (NEON). The 'rtry' package is available on the Comprehensive R Archive Network (CRAN; https://cran.r-project.org/package=rtry) and the GitHub Wiki (https://github.com/MPI-BGC-Functional-Biogeography/rtry/wiki) along with comprehensive documentation and vignettes describing detailed data preprocessing workflows.

Host plant height explains the effect of nitrogen enrichment on arbuscular mycorrhizal fungal communities

Nitrogen (N) enrichment is widely known to affect the root-associated arbuscular mycorrhizal fungal (AMF) community in different ways, for example, via altering soil properties and/or shifting host plant functional structure. However, empirical knowledge of their relative importance is still lacking. Using a long-term N addition experiment, we measured the AMF community taxonomic and phylogenetic diversity at the single plant species (roots of 15 plant species) and plant community (mixed roots) levels. We also measured four functional traits of 35 common plant species along the N addition gradient. We found divergent responses of AMF diversity to N addition for host plants with different innate heights (i.e. plant natural height under unfertilized treatment). Furthermore, our data showed that species-specific responses of AMF diversity to N addition were negatively related to the change in maximum plant height. When scaling up to the community level, N addition affected AMF diversity mainly through increasing the maximum plant height, rather than altering soil properties. Our results highlight the importance of plant height in driving AMF community dynamics under N enrichment at both species and community levels, thus providing important implications for understanding the response of AMF diversity to anthropogenic N deposition.

Digitized collections elucidate invasion history and patterns of awn polymorphism in Microstegium vimineum

PREMISE

Digitized collections can help illuminate the mechanisms behind the establishment and spread of invasive plants. These databases provide a record of traits in space and time that allows for investigation of abiotic and biotic factors that influence invasive species.

METHODS

Over 1100 digitized herbarium records were examined to investigate the invasion history and trait variation of Microstegium vimineum. Presence-absence of awns was investigated to quantify geographic patterns of this polymorphic trait, which serves several functions in grasses, including diaspore burial and dispersal to germination sites. Floret traits were further quantified, and genomic analyses of contemporary samples were conducted to investigate the history of M. vimineum's introduction and spread into North America.

RESULTS

Herbarium records revealed similar patterns of awn polymorphism in native and invaded ranges of M. vimineum, with awned forms predominating at higher latitudes and awnless forms at lower latitudes. Herbarium records and genomic data suggested initial introduction and spread of the awnless form in the southeastern United States, followed by a putative secondary invasion and spread of the awned form from eastern Pennsylvania. Awned forms have longer florets, and floret size varies significantly with latitude. There is evidence of a transition zone with short-awned specimens at mid-latitudes. Genomic analyses revealed two distinct clusters corresponding to awnless and awned forms, with evidence of admixture.

CONCLUSIONS

Our results demonstrate the power of herbarium data to elucidate the invasion history of a problematic weed in North America and, together with genomic data, reveal a possible key trait in introduction success: presence or absence of an awn.

Responses of Plant Reproductive Phenology to Winter-Biased Warming in an Alpine Meadow

Climate warming is often seasonally asymmetric with a higher temperature increase toward winters than summers. However, the effect of winter-biased warming on plant reproductive phenology has been seldom investigated under natural field conditions. The goal of this study was to determine the effects of winter-biased warming on plant reproductive phenologies. In an alpine meadow of Tibetan Plateau, we deployed six large (15 m × 15 m × 2.5 m height) open top chambers (three warmed chambers and three non-warmed chambers) to achieve winter-biased warming (i.e., a small increase in annual mean temperature with a greater increase towards winter than summer). We investigated three phenophases (onset and offset times and duration) for both the flowering and fruiting phenologies of 11 common species in 2017 and 8 species in 2018. According to the vernalization theory, we hypothesized that mild winter-biased warming would delay flowering and fruiting phenologies. The data indicated that the phenological responses to warming were species-specific (including positive, neutral, and negative responses), and the number of plant species advancing flowering (by averagely 4.5 days) and fruiting onset times (by averagely 3.6 days) was higher than those delaying the times. These changes were inconsistent with the vernalization hypothesis (i.e. plants need to achieve a threshold of chilling before flowering) alone, but can be partly explained by the accumulated temperature hypothesis (i.e. plants need to achieve a threshold of accumulative temperature before flowering) and/or the overtopping hypothesis (i.e. plants need to reach community canopy layer before flowering). The interspecific difference in the response of reproductive phenology could be attributed to the variation in plant traits including plant height growth, the biomass ratio of root to shoot, and seed mass. These results indicate that a mild winter-biased warming may trigger significant change in plant reproductive phenology in an alpine meadow.

Living Litter: Dynamic Trait Spectra Predict Fauna Composition

Understanding what drives soil fauna species composition through space and time is crucial because we should preserve soil fauna biodiversity and its key role in ecosystem functioning in this era of fast environmental change. As plant leaf litter provides both food and habitat for soil fauna, a focus on litter traits that relate to these two functions will help in understanding soil invertebrate community structure and dynamics comprehensively. To advance this agenda, we propose a conceptual framework to explicitly link the invertebrate community composition to the temporal dynamics of the litter trait space defined by two axes: a food-quality axis related to plant resource economics and chemistry and a habitat-quality axis related to litter particle size and shape.

A global growth-form database for 143,616 vascular plant species

For the majority of plant species in the world, we know little about their functional ecology, and not even one of the most basic traits-the species' growth habit. To fill the gap in availability of compiled plant growth-form data, we have assembled what is, to our knowledge, the largest global database on growth-form as a plant trait. We have, with extensive error checking and data synthesis, assembled a growth-form database from 163 data sources for 143,616 vascular plant species from 445 different plant families. This is 38.6% of the currently accepted vascular plant diversity. For our database, we have chosen seven categories to cover the majority of the diversity in plant growth forms: aquatic plants, epiphytes, hemiepiphytes, climbing plants, parasitic plants, holo-mycoheterotrophs, and freestanding plants. These categories were used because we were able to reconcile the wealth of existing definitions and types of growth-form information available globally to them clearly and unequivocally, and because they are complementary with existing databases. Plants in the database were designated into a category if their adult growth form fit the criterion. We make available two databases: first, the complete data set, including species for which there is currently conflicting information, and second, a consensus data set, where all available information supports one categorization. Of the plant species for which we found information, 103,138 (72%) are freestanding, 21,110 (15%) are epiphytes, and 4,046 (3%) are parasites. Our growth-form data can be used to produce useful summary statistics by clade. For example, current data suggests that half of pteridophytes are epiphytic, that all hemiepiphytes are eudicots, and that there are no parasitic monocots, gymnosperms, or pteridophytes. Growth form is a crucial piece of fundamental plant-trait data with implications for each species' ecology, evolution, and conservation, and thus this data set will be useful for a range of basic and applied questions across these areas of research. No copyright or proprietary restrictions are associated with the use of this data set, other than citation of the present Data Paper. A static version of this dataset is provided as Supporting Information, and a living and updating version of the dataset is available in a GitHub repository.

Contrasting Effects of Extreme Drought and Snowmelt Patterns on Mountain Plants along an Elevation Gradient

Despite the evidence that increased frequency and magnitude of extreme climate events (ECE) considerably affect plant performance, there is still a lack of knowledge about how these events affect mountain plant biodiversity and mountain ecosystem functioning. Here, we assessed the short-term (one vegetation period) effects of simulated ECEs [extreme drought (DR), advanced and delayed snowmelt (AD and DE), respectively] on the performance of 42 plant species occurring in the Bavarian Alps (Germany) along an elevational gradient of 600-2000 m a.s.l. in terms of vegetative growth and reproduction performance. We demonstrate that plant vegetative and generative traits respond differently to the simulated ECEs, but the nature and magnitude treatment effects strongly depend on study site location along the elevational gradient, species' altitudinal origin and plant functional type (PFT) of the target species. For example, the negative effect of DR treatment on growth (e.g., lower growth rates and lower leaf nitrogen content) and reproduction (e.g., lower seed mass) was much stronger in upland sites, as compared to lowlands. Species' response to the treatments also differed according to their altitudinal origin. Specifically, upland species responded negatively to extreme DR (e.g., lower growth rates and lower leaf carbon concentrations, smaller seed set), whereas performance of lowland species remained unaffected (e.g., stable seed set and seed size) or even positively responded (e.g., higher growth rates) to that treatment. Furthermore, we were able to detect some consistent differences in responses to the ECEs among three PFTs (forbs, graminoids, and legumes). For instance, vegetative growth and sexual reproduction of highly adaptable opportunistic graminoids positively responded to nearly all ECEs, likely on the costs of other, more conservative, forbs and legumes. Our results suggest that ECEs can significantly modify the performance of specific plant groups and therefore lead to changes in plant community structure and composition under ongoing climate change. Our study therefore underlines the need for more experimental studies on the effects of extreme climate events to understand the potential consequences of climate change for the alpine ecosystem.

Variation in species-level plant functional traits over wetland indicator status categories

Wetland indicator status (WIS) describes the habitat affinity of plant species and is used in wetland delineations and resource inventories. Understanding how species-level functional traits vary across WIS categories may improve designations, elucidate mechanisms of adaptation, and explain habitat optima and niche. We investigated differences in species-level traits of riparian flora across WIS categories, extending their application to indicate hydrologic habitat. We measured or compiled data on specific leaf area (SLA), stem specific gravity (SSG), seed mass, and mature height of 110 plant species that occur along the Colorado River in Grand Canyon, Arizona. Additionally, we measured leaf δ13C, δ15N, % carbon, % nitrogen, and C/N ratio of 56 species with C3 photosynthesis. We asked the following: (i) How do species-level traits vary over WIS categories? (ii) Does the pattern differ between herbaceous and woody species? (iii) How well do multivariate traits define WIS categories? (iv) Which traits are correlated? The largest trait differences among WIS categories for herbaceous species occurred for SSG, seed mass, % leaf carbon and height, and for woody species occurred for height, SSG, and δ13C. SSG increased and height decreased with habitat aridity for both woody and herbaceous species. The δ13C and hence water use efficiency of woody species increased with habitat aridity. Water use efficiency of herbaceous species increased with habitat aridity via greater occurrence of C4 grasses. Multivariate trait assemblages differed among WIS categories. Over all species, SLA was correlated with height, δ13C, % leaf N, and C/N; height was correlated with SSG and % leaf C; SSG was correlated with % leaf C. Adaptations of both herbaceous and woody riparian species to wet, frequently inundated habitats include low-density stem tissue. Adaptations to drier habitats in the riparian zone include short, high-density cavitation-resistant stem tissue, and high water use efficiency. The results enhance understanding about using traits to describe plant habitat in riparian systems.

Balancing competition for resources with multiple pest regulation in diversified agroecosystems: a process-based approach to reconcile diversification and productivity

Agroecosystem plant diversification can enhance pest biological regulation and is a promising alternative to pesticide application. However, the costs of competition for resources between plants may exceed the benefits gained by pest regulation. To disentangle the interactions between pest regulation and competition, we developed a generic process‐based approach that accounts for the effects of an associated plant and leaf and root pests on biomass production. We considered three crop–plant associations that differ in competition profiles, and we simulated biomass production under wide ranges of both pest regulation rates and resources’ availability. We analyzed outputs to quantify the pest regulation service level that would be required to attain monoculture yield and other production goals. Results showed that pest regulation requirements were highly dependent on the profile of resource interception of the associated plant and on resources’ availability. Pest regulation and the magnitude of competition between plants interacted in determining the balance between nitrogen and radiation uptake by the crop. Our findings suggest that productivity of diversified agroecosystems relative to monoculture should be optimized by assembling plants whose characteristics balance crops’ resource acquisition. The theoretical insights from our study draw generic rules for vegetation assemblage to optimize trade‐offs between pest regulation and production. Our findings and approach may have implications in understanding, theorizing and implementing agroecosystem diversification. By its generic and adaptable structure, our approach should be useful for studying the effects of diversification in many agroecosystems.

Quantitative assessment of the differential impacts of arbuscular and ectomycorrhiza on soil carbon cycling

A significant fraction of carbon stored in the Earth's soil moves through arbuscular mycorrhiza (AM) and ectomycorrhiza (EM). The impacts of AM and EM on the soil carbon budget are poorly understood. We propose a method to quantify the mycorrhizal contribution to carbon cycling, explicitly accounting for the abundance of plant-associated and extraradical mycorrhizal mycelium. We discuss the need to acquire additional data to use our method, and present our new global database holding information on plant species-by-site intensity of root colonization by mycorrhizas. We demonstrate that the degree of mycorrhizal fungal colonization has globally consistent patterns across plant species. This suggests that the level of plant species-specific root colonization can be used as a plant trait. To exemplify our method, we assessed the differential impacts of AM : EM ratio and EM shrub encroachment on carbon stocks in sub-arctic tundra. AM and EM affect tundra carbon stocks at different magnitudes, and via partly distinct dominant pathways: via extraradical mycelium (both EM and AM) and via mycorrhizal impacts on above- and belowground biomass carbon (mostly AM). Our method provides a powerful tool for the quantitative assessment of mycorrhizal impact on local and global carbon cycling processes, paving the way towards an improved understanding of the role of mycorrhizas in the Earth's carbon cycle.