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opencc-by-4.0Sep 2021View details →

Annotated datasets of Scots pine cross-sectional images for root rot detection and resin detection

These are the annotated datasets used in the publication available at <a href="https://doi.org/10.1080/14942119.2024.2327247">https://doi.org/10.1080/14942119.2024.2327247</a> The first dataset is for root rot detection, the other dataset is for resin detection. Please see the publication for details.

Root:shoot ratio GWAS Arabidopsis 4M SNP mapping

The Genome Wide Association Study output files mapped using the root:shoot ratio data collected on Arabidopsis HapMap population. The GWAS was run using the ASReml script as described in Awlia et al., 2021 (<a href="https://doi.org/10.1111/tpj.15310">https://doi.org/10.1111/tpj.15310</a>). The GWAS analysis was performed by Magdalena Julkowska at King Abdullah University during her postdoc in the group of Dr. Mark Tester.

Root:shoot ratio GWAS Arabidopsis 250k SNP mapping

Arabidopsis HapMap screen for salt-induced changes in root architecture and root:shoot ratio - images BA1 experiment

Images of scanned agar plates collected for Arabidopsis accessions exposed to salt stress / control treatment. The data was collected during PhD of Magdalena Julkowska at University of Amsterdam, under supervision of Dr. Christa Testerink.

Arabidopsis HapMap screen for salt-induced changes in root architecture and root:shoot ratio - images BA2 experiment

Images of scanned agar plates collected for Arabidopsis accessions exposed to salt stress / control treatment. The data were collected during PhD of Magdalena Julkowska at University of Amsterdam, under supervision of Dr. Christa Testerink.

Arabidopsis HapMap screen for salt-induced changes in root architecture and root:shoot ratio - images BA7 experiment

Arabidopsis HapMap screen for salt-induced changes in root architecture and root:shoot ratio - images BA3 experiment

Arabidopsis HapMap screen for salt-induced changes in root architecture and root:shoot ratio - images BA6 experiment

opencc-by-4.0Nov 2022View details →

Data from: Molecular and cellular processes of deafferentation after plexus injury in human dorsal root ganglia

Dataset of human dorsal root ganglia (DRG) images and deep learning models Sections of six control and six plexus patient DRG were immunostained and imaged using large-field (tile) microscopy. Two staining combinations were investigated:  - neurofilament (NF), fatty acid binding protein 7 (FABP7), and clusterin (APOJ) - neurofilament (NF), ionized calcium-binding adapter molecule 1 (IBA1), and microtubule-associated protein 2 (MAP2)  NF-positive neurons were segmented with a deep learning method (deepflash2). FABP7 and IBA1 were segmented with a thresholding method. Provided are: - all images and corresponding segmentation masks for NF, FABP7, and IBA1  - images and annotated segmentation masks of NF-positive neurons (3 experts annotated the same 10 images, the estimated ground truth masks were used for training of deep learning models) - the deep learning model ensemble (3) for segmentation of NF-positive neurons

opencc-zeroNov 2022View details →

Lianas have a faster resource acquisition strategy than trees: belowground evidence from root traits, phylogeny, and the root economics space

1. The competitive advantage of lianas over trees has been widely documented in studies of their leaf functional traits across diverse habitats; however, the relative contribution of root functional traits to the competitive superiority of lianas over trees has not yet been evaluated. The aim of this study was to explore the root functional traits, phylogenetic structure of these traits, and root trait dimensions of lianas to clarify why lianas can outperform trees. 2. We sampled 69 liana species from tropical and temperate forests in China and measured nine key functional traits of first-order roots of each species, including morphological, architectural, anatomical, and chemical traits, as well as the percentage of mycorrhizal colonization. Data on these traits were then compared with similar data of 127 tree species from the same biome obtained from the Global Root Traits (GRooT) database and our previous studies. 3. Liana roots had lower construction costs and could acquire resources more rapidly compared with tree roots. Significant differences were observed in most tree root traits between tropical and temperate sites. However, no significant differences were observed in any of the liana root traits between tropical and temperate sites, apart from the root branching ratio. 4. Lianas showed much weaker phylogenetic conservatism in their root traits than trees when species were pooled across sites. Phylogenetic constraint was lower for nearly all root traits of both temperate lianas and trees compared with those of tropical lianas and trees. 5. The root economics space of lianas and trees had two orthogonal dimensions with "conservation" and "collaboration" axes. However, lianas occupied the trait space with higher root nitrogen concentration and greater specific root length, showing "fast" resource acquisition strategy, while trees placed opposite space and exhibited relatively "slow" strategy. 6. Synthesis. The ability of lianas to outcompete trees in harsh environments might be explained by their faster resource acquisition strategy and the lower phylogenetic constraint in root traits. Generally, lianas might play an increasingly important role in the structure and function of forest ecosystems in the future with ongoing habitat fragmentation and climate change.

opencc-zeroNov 2022View details →

Data for the article: Coupling of leaf elemental traits with root fungal community composition reveals a plant resource acquisition strategy in a desert ecosystem

Purpose: Plant-associated microbes enhance nutrient access and stress tolerance of the host species, and therefore, are crucial for plant traits and resource strategies. However, the links between aboveground plant traits and belowground microbes related to plant resource strategies under stressful conditions remain poorly understood. Methods: We tested the relationships between leaf traits linked to water (carbon isotopic composition, δ13C) and nutrient use (elemental concentrations and stoichiometry) with microbial compositions in roots and rhizospheres of two dominant species (Artemisia ordosica and Leymus secalinus) in the Mu Us Desert, northern China. Results: L. secalinus exhibited higher Mg and Mn concentrations, N:P ratios, stoichiometric flexibility, and root fungi:bacteria ratios, but lower foliar K and Ca concentrations and δ13C values than A. ordosica. The leaf N:P of L. secalinus increased with the root fungi:bacteria ratios, whereas the leaf N:P of A. ordosica decreased with the root fungi:bacteria ratios. The plant elemental levels (P, N, K, Ca, Mn, and δ13C) of L. secalinus but not A. ordosica were significantly related to their root fungal composition. Additionally, the random forest model identified four key fungal families in predicting leaf elemental traits for both plant species. Conclusion: The results suggested tight coupling and coordination between leaf elemental traits and root microbial compositions (especially fungal communities) related to plant resource acquisition strategies. By regulating aboveground and belowground feedback loops through trait flexibility and root microbial compositions, the studied plant species can sustain their resource strategies under stressful environmental conditions.

Coordination of economics spectra in leaf, stem and root within the genus Artemisia along a large environmental gradient in China

Aim: The plant economics spectrum provides a fundamental framework for understanding functional trait variation along environmental gradients. However, it is unclear whether there is a general whole-plant economics spectrum across organs at the finer taxonomic scale (e.g. within genera), and if there is, which factors affect the trait coordination of the different organs. Here, we examined whether resource economics spectra of different organs (i.e. leaf, stem and root) can be integrated at the whole-plant level within a single genus, and how environment, intraspecific variation and taxonomic scale shape the whole-plant spectrum. Location: China. Time period: 2018. Major taxa studied: Artemisia. Results: Pairwise trait correlations and the trade-off patterns along the resource economic axis were consistent at both organ and whole-plant levels. Environmental gradients did not strongly affect the correlations among leaf, stem and root economics spectra, i.e. the intraspecific variation weakened but did not mask this coordination. Taxonomic scale did not affect the degree of trait coordination as the genus-wide whole-plant economics spectrum also emerged within each of the three subgenera. Main conclusions: Our results support the hypothesis that the coordination of economics spectra across organs forms a whole-plant economics spectrum representing "fast-slow" resource management strategy, which is robust to recent evolution (genotypic variation, even for species within a single genus) and present-day environmental variation. Further studies should elucidate in which circumstances or phylogenetic branches the coordinated pattern found for Artemisia is representative of other widely distributed genera.

opencc-by-4.0Dec 2022View details →

Competition and co-association, but not phosphorous availability, shape the benefits of phosphate solubilising root bacteria for maize (Zea mays).

Predicting the conditions under which rhizobacteria benefit plant growth remains challenging. Here we tested the hypothesis that benefits from inoculation with phosphate-solubilising rhizobacteria will depend upon two environmental conditions: phosphate availability and competition between bacteria. Maize-associated rhizobacteria with varying phosphate solubilisation ability were used in experiments in soil, sterilised soil and gnotobiotic microcosms under conditions of varying orthophosphate availability, while  we manipulated intensity of competition by varying the number of isolates in plant inocula. Growth promotion by microbes did not depend on phosphate availability but was affected by interactions between inoculants: beneficial effects of one Serratia isolate were detectable only when plants were inoculated with a single strain and beneficial effects of a competition sensitive Rhizobium was only detectable in sterilised soil or in microcosms inoculated with single strains. Moreover, microcosm experiments suggested that facilitation of a parasitic isolate, not competitive interactions between bacteria, prevented plants from gaining benefits from a potential mutualist. Competition and facilitation affected colonization of plants in microcosms but growth promotion by Serratia was more affected by inoculation treatment than culturable densities on roots. Experimental manipulation of seed inocula can reveal whether plant growth stimulation is robust with respect to competition, as well as the ecological strategies of different rhizobacteria. From an applied perspective, phosphate solubilisation may not provide the mechanism for bacterial growth promotion but may indicate mutualistic potential due to phylogenetic associations. Importantly, benefits to plants are vulnerable to interactions between rhizobacteria and may not persist in mixed inoculations.

Home-field advantage meets priming effect in root decomposition: Implications for belowground carbon dynamics

1. Home-field advantage (HFA) states that litter decomposes faster in 'home' than in 'away' soil, due to the specialization of decomposer organisms in decomposing litter derived from their local plant community. Demonstration of the HFA effect has been overwhelmingly based on aboveground leaf litter despite the fact that roots play a pivotal role in carbon (C) and nutrient cycling. 2. Labile C input in root exudates and newly shed root litters can enhance the activity of soil microorganisms, which in turn can favor the breakdown of older root litter, also referred to as the priming effect. It remains, however, unclear how the addition of fresh root-derived inputs affects HFA on the decomposition of absorptive roots (ARs) and transport roots (TRs), which have a different chemical composition. 3. Here, we conducted a two-stage (endogenous C consumption versus exogenous C priming) reciprocal transplant microcosm experiment to explore the effects of HFA on the decomposition of lower-quality ARs and higher-quality TRs of two subtropical tree species (Pinus elliottii and Cunninghamia lanceolata) and their responses to either labile (glucose) or recalcitrant (fresh ARs) C additions. 4. Decomposition of lower-quality ARs exhibited neutral HFA, while decomposition of higher-quality TRs exhibited positive HFA. The absence of HFA for short-lived ARs was possibly due to the legacy effect of their chemical defenses on decomposition. The neutral HFA for ARs became negative with glucose addition, which was linked to the dissimilarity of fungal community between the home and away soils. Neither glucose nor fresh ARs additions changed the HFA pattern of TRs, implying that these long-lived roots play a reinforced role in soil C accumulation when they decompose away from their origins. 5. These results indicate that the effect of HFA on decomposition differs between ARs and TRs, and could be modified by the priming effect induced by the root-derived C input. In general, our findings highlight that complex 'HFA-priming' interactions on root decomposition should be explicitly considered in the paradigm of belowground C dynamics.

Mycorrhizal fungi alter root exudation to cultivate a beneficial microbiome for plant growth

Arbuscular mycorrhizal (AM) fungi traditionally form symbioses with most plant species. Although AM fungi have critical effects on microbial communities, the pathways showing how AM fungi shape rhizosphere bacterial communities and their functions are rarely explored. Through three systematic experiments, AM fungi-bacteria interactions were first investigated in the rhizosphere of Lotus japonicus, then the interactions were confirmed by a second experiment with wild-type and a mycorrhiza-defective mutant ljcbx of L. japonicus. The mechanisms were presented by adding core bacteria and AM fungi to the plant rhizosphere with the third experiment. We found that AM fungi-bacteria interactions enhanced host plant growth and identified a core bacterial group that uniquely enhanced host plant growth. Adding core bacteria and AM fungi promoted host growth and nutrient acquisition compared to adding AM fungi or core bacteria independently. Allelopathic substances secreted by AM fungal colonizing host roots to recruit the rhizosphere bacteria were detected by the multi-omics joint analysis, showing that arachidonic acid was the main allelopathic substance that affected AM fungi–bacteria interactions. Our findings provide direct evidence that mycorrhizal infection simulated root exudation, such as arachidonic acid, recruited a beneficial microbiome to the host rhizosphere, increasing plant growth and soil nutrient turnover.

Data for: Plant roots fuel tropical soil animal communities

Belowground life relies on plant litter, while its linkage to living roots had long been understudied, and remains unknown in the tropics. Here, we analysed the response of 30 soil animal groups to root trenching and litter removal in rainforest and plantations in Sumatra, and found that roots are similarly important to soil fauna as litter. Trenching effects were stronger in soil than in litter, with an overall decrease in animal abundance in rainforest by 42% and in plantations by 30%. Litter removal little affected animals in soil layers, but decreased the total abundance by 60% in rainforest and rubber plantations but not in oil palm plantations. Litter and root effects on animal group abundances were explained by body size or vertical distribution. Our study quantifies principle carbon pathways in soil food webs under tropical land use, providing the basis for mechanistic modelling and ecosystem-friendly management of tropical soils.

Data and R scripts for: Ant invasions is associated with lower root density and different root distribution of a foundational savanna tree species

Some invasive ants have worldwide distributions and impose substantial impacts on human society and native biodiversity. Yet we know little about how ants impact soil ecosystems in general, much less how soil ecosystems shift when invasive ants move in. We excavated the coarse roots of a monodominant savanna tree in invaded and uninvaded areas to test the hypothesis that the presence of invasive ants would be associated with changes in root distribution and biomass across the landscape. We found that in the presence of invasive ants, trees had a shifted distribution of lateral coarse roots, with proportionally less root biomass near the surface and far from tree stems. In addition, the density of lateral coarse-root biomass was ~20% lower for trees within invaded landscapes. Our results suggest that soil-nesting invasive ants can drive important changes in rooting strategy for a tree species that serves a foundational role in the biogeochemical cycles of vertisol savannas.

Data for: Roots originating from different shoot parts are functionally different in running bamboo, Phyllostachys glauca

Running bamboos are a group of clonal plants exhibiting rapid and widespread expansion. They possess two root subsystems, arising from different shoot parts, culm roots and rhizome roots. To date, it remains unclear what the functional differences are between the two root subsystems and what their relation is to the remarkably competitive ability of running bamboos. A typical running bamboo, Phyllostachys glauca, which dominates in a highly heterogenous habitat of limestone hills, was sampled to compare the morphology, architecture, anatomy, chemical composition, mechanics, and nutrient acquisition of the two root subsystems to explore their differences in functional traits. Compared with rhizome roots, culm roots possessed greater tensile strength, modulus of elasticity, stele diameter to root diameter ratio, root tissue density, root length density, rooting depth, basal diameter of shoot-borne roots, and more lignified cells. Culm roots also had a higher phosphorus (P) concentration (>0.4 mg g-1), which was nearly twice that of rhizome roots. By contrast, rhizome roots exhibited a greater specific root area, specific root length, cortex thickness to root radius ratio, total branch order, and greater P-uptake capacity than culm roots. Our findings revealed distinct differences in functional traits between culm roots and rhizome roots in P. glauca. Culm roots are considered to primarily provide anchorage, but also function in resource acquisition and nutrient storage, while rhizome roots mainly play a role in resource acquisition. Except for the anchorage and resource acquisition of culm roots, the extra resource acquisition by rhizome roots and the high concentration of a limiting nutrient (P) in culm roots enhance the performance in a highly heterogenous habitat which offers a physiological explanation for P. glauca dominating on limestone hills. The functional differentiation between culm roots and rhizome roots provides insight into the mechanism underpinning the remarkable expansion of running bamboos and offers a new perspective to explain the strong competitive ability of clonal plants with dimorphic roots.

opencc-by-4.0Dec 2022View details →

Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root

Supplemental datasets for "Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root".

Drought effects on root and shoot traits and their decomposability

1. Drought can induce phenotypic plasticity in a range of plant root and shoot traits. These traits have been shown to explain differences in root and shoot litter decomposability between species. However, it is unknown how drought-induced plasticity of root and shoot traits alters their decomposability. 2. To investigate this issue across a range of species, we grew a grass (Lolium perenne), a forb (Plantago lanceolata) and a legume (Trifolium repens) common to European temperate grasslands and subjected them to a 5-week moderate drought treatment. We compared morphological and chemical root and shoot traits of the droughted plants to well-watered controls. We then conducted a decomposition assay of the senesced root and shoot material over 16 weeks, with mass loss measurements at five timepoints. 3. Drought had significant and sometimes strong effects on morphological and chemical root and shoot traits of all three species, sometimes similar to differences between species and generally in line with a shift to a more resource-conservative strategy. Drought also increased the labile litter fraction in roots of Lolium perenne, which was associated with a substantial increase in non-structural carbohydrates. Drought decreased the labile litter fraction in shoots of Plantago lanceolata, but this could not be explained by the traits we measured. Drought effects on litter decomposability were weaker than on plant traits. 4. Our results suggest that plant trait-mediated effects of drought on litter decomposability can either increase or decrease vegetation feedbacks to climate change. They also show that drought-induced plasticity in root and shoot traits does not automatically translate into equivalent changes in litter decomposability.