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Data for: Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks

The persistence of mutualisms is paradoxical, as there are fitness incentives for exploitation. This is particularly true for plant-microbe mutualisms like arbuscular mycorrhizae (AM), which are promiscuously horizontally-transmitted. Preferential allocation by hosts to the best mutualist can stabilize horizontal mutualisms, however, preferential allocation is imperfect, with its fidelity likely depending upon the spatial structure of symbionts in plant roots. In this study, we tested AM mutualisms' dependence on two dimensions of spatial structure: the initial spatial association of fungi and the ease of fungal dispersal, through three complementary experiments. We found that fitness of the beneficial AM fungus increased when fungi were initially separate, while initial spatial mixing benefited the fitness of the non-beneficial fungus. These effects were strongest when dispersal was limited, and hosts could discriminate. Additionally, we found that changes in AM fungal proportional abundance induced by spatial structure in roots of a preferentially allocating host produced positive feedbacks on plant growth, showing that interactions between spatial structure and host choice can determine the direction of plant-soil feedbacks. Our results suggest that symbiont spatial structure within plant roots may act as an important modifier of plant preferential allocation and the dynamics of mycorrhizal mutualisms, with potentially cascading effects on plant-plant interactions.

Is negative density-dependent reproduction regulated by density-induced stress in root voles? Two field experiments

Density dependence in reproduction plays an important role in stabilising population dynamics via immediate negative feedback from population density to reproductive output. Although previous studies have shown that negative density-dependent reproduction is associated with strong spacing behaviour and social interaction between individuals, the proximal mechanism for generating negative density-dependent reproduction remains unclear. In this study, we investigated the effects of density-induced stress on reproduction in root voles. Enclosed Founder populations were established by introducing six (low density) and 30 (high density) adults per sex into per enclosure (four enclosures per density in total) during the breeding season from April to July 2012 and from May to August 2015. Faecal corticosterone metabolite (FCM) levels, reproductive traits (recruitment rate and the proportion of reproductively active indivuduals), and founder population numbers were measured following repeated live-trapping in both years. The number of founders was negatively associated with recruitment rates and the proportion of reproductively active indivuduals, displaying a negative density-dependent reproduction. FCM level was positively associated with the number of founders. The number of founder females directly affected the proportion of reproductive females , and directly and indirectly through their FCM levels affected the recruitment rate; the effect of the number of male founders on the proportion of reproductive males was mediated by their FCM level. Our results showed that density-induced stress negatively affected reproductive traits and that density-induced stress is one ecological factor generating negative density-dependent reproduction.

opencc-by-4.0Apr 2022View details →

Data from: Unbiased analysis of cellular plasticity in the dorsal root ganglion after peripheral nerve injury

Sectional images of rat dorsal root ganglia (DRG) 7 or 14 days after SNI or sham injury. Sections were immunostained for neurofilament (NF), glial fibrillary acidic protein (GFAP), and glutamine synthetase (GS) and imaged using large-field (tile) microscopy. Images were segmented with a deep learning method (deepflash2). Provided are:  - 2-13 images per DRG from L4 or L5, ipsilateral (IL) or contralateral (CL)  - corresponding segmentation masks for NF, GS, and GFAP  - deep learning models for oval-shaped NF-positive structures and ring-like GS/GFAP-positive structures  - annotated data that the deep learning models were trained on

Overyielding is accounted for partly by plasticity and dissimilarity of crop root traits in maize/legume intercropping systems

Positive biodiversity-productivity relationships have been found in biodiversity field experiments of grassland, forestry, and other natural terrestrial ecosystems, where diversity effects were separated by complementarity (CE) and selection effects (SE). However, we know little about how CE and SE are related to root traits and root dissimilarity. A four-year field experiment was carried out with a split-plot design, where main plot was four nitrogen (N) applications (N0, N1, N2, N3) and five cropping systems (maize (Zea mays L.)/soybean (Glycine max L. Merrill.), maize/peanut (Arachis hypogaea L.) intercropped and the corresponding monocultures) with three replicates. Roots were sampled in the N0 and N2 treatments in two years. Intercropping effects were analyzed based on grain yield for four years and roots were sampled down to 60 cm depth, and analyzed with morphological parameters at different crop growth stages in two years. Intercropping significantly increased grain yield and aboveground biomass in both intercropping systems under all N treatments. The partitioning of the net intercropping effects showed that yield advantage in intercropping was due to a positive CE under the N0 treatment, and to a positive SE with N application. Maize showed greater root morphological plasticity than the legumes did, with greater changes in root length density (RLD), root weight density (RWD) and total root surface (TS) in intercropping than in monoculture. Intercropped maize occupied a larger soil space, while lateral RLD distribution of legumes was decreased by maize. The RLD, RWD, and TS of intercropped maize were constant or increased in later growth stages. SE showed a significantly positive relationship with root dissimilarity. Principal component analysis showed mean root depth and specific root length of legumes drove the positive CE in the absence of N fertilization. Root dissimilarity determined by maize explained the selection effects in overyielding. Complementarity effects under N0 were closely associated with specific root traits such as mean root depth and specific root length. Linking changes of root traits with intercropping effects aboveground helps understand yield advantages in diverse agroecosystem. In general, a cereal species with strong phenotypic plasticity intercropped with a legume species with strong physiological plasticity can maximize the yield advantage of intercropping.

Rewetting prolongs root growing season in minerotrophic peatlands and mitigates negative drought effects

Root phenology influences the timing of plant resource acquisition and carbon fluxes into the soil. This is particularly important in fen peatlands, in which peat is primarily formed by roots and rhizomes of vascular plants. However, most fens in Central Europe are drained for agriculture, leading to large carbon losses, and further threatened by increasing frequency and intensity of droughts. Rewetting fens aims to restore the original carbon sink, but how root phenology is affected by drainage and rewetting is largely unknown. We monitored root phenology with minirhizotrons in drained and rewetted fens (alder forest, percolation fen and coastal fen) as well as its soil temperature and water table depth during the 2018 drought. For each fen type, we studied a drained site and a site that was rewetted ~25 years ago, while all the sites studied had been drained for almost a century. Overall, the growing season was longer with rewetting, allowing roots to grow over a longer period in the year and have a higher root production than under drainage. With increasing depth, the growing season shifted to later in time but remained a similar length, and the relative importance of soil temperature for root length changes increased with soil depth. Synthesis and applications. Rewetting extended the growing season of roots, highlighting the importance of phenology in explaining root productivity in peatlands. A longer growing season allows a longer period of carbon sequestration in form of root biomass and promotes the peatlands' carbon sink function, especially through longer growth in deep soil layers. Thus, management practices that focus on rewetting peatland ecosystems are necessary to maintain their function as carbon sinks, particularly under drought conditions, and are a top priority to reduce carbon emissions and address climate change.

Temporal changes in nutrients in forest soil and roots and root biomass of Fagus sylvatica after P and N fertilization

We report data for nutrients in the organic layer and in mineral soil of Fagus sylvatica forests after P and N fertilization. We separated soil and roots and also report data for root biomass and nutrient contents in these soil layers. In addition, relative soil water contents and pH were measured. The samples were collected in three forests and repeatedly in spring and fall from 2016 to 2018.

opencc-by-4.0Jun 2022View details →

Supplementary material for manuscript Building Archean cratonic roots

Scripts and raw data used to plot Figures 1 and 6 of the manuscript "Building Archean cratonic roots" submitted to the Research Topic: "Interior Dynamics and Chemistry of Earth and Other Rocky Planets: Past and Present" at the journal "Frontiers in Earth Science: Solid Earth"

opencc-by-4.0Jun 2022View details →

Review of QTLs found in studies aimed at finding QTLs for bread wheat root traits (from 2005 to mid-2020)

This list contains a number of articles that have been reviewed for QTLS for bread wheat root traits from 2005 to mid-2020 publication dates.

opencc-zeroDec 2021View details →

More soil organic carbon is sequestered through the mycelium-pathway than through the root-pathway under nitrogen enrichment in an alpine forest

Plant roots and associated mycorrhizae exert a large influence on soil carbon (C) cycling. Yet, little was known whether and how roots and ectomycorrhizal extraradical mycelia differentially contribute to soil organic C (SOC) accumulation in alpine forests under increasing nitrogen (N) deposition. Using ingrowth cores, the relative contributions of the root-pathway (RP) (i.e., roots and rhizosphere processes) and mycelium-pathway (MP) (i.e., extraradical mycelia and hyphosphere processes) to SOC accumulation were distinguished and quantified in an ectomycorrhizal-dominated forest receiving chronic N addition (25 kg N ha-1 yr-1). Under the non-N addition, the RP facilitated SOC accumulation, while the MP reduced SOC accumulation. Nitrogen addition enhanced the positive effect of RP on SOC accumulation from +18.02 mg C g-1 to +20.55 mg C g-1 but counteracted the negative effect of MP on SOC accumulation from -5.62 mg C g-1 to -0.57 mg C g-1, as compared to the non-N addition. Compared to the non-N addition, the N-induced SOC accumulation was 1.62~2.21 mg C g-1 and 3.23~4.74 mg C g-1, in the RP and the MP, respectively. The greater contribution of MP to SOC accumulation was mainly attributed to the higher microbial C pump (MCP) efficacy (the proportion of increased microbial residual C to the increased SOC under N addition) in the MP (72.5%) relative to the RP (57%). The higher MCP efficacy in the MP was mainly associated with the higher fungal metabolic activity (i.e., the greater fungal biomass and N-acetyl glucosidase activity) and greater binding efficiency of fungal residual C to mineral surfaces than those of RP. Collectively, our findings highlight the indispensable role of mycelia and hyphosphere processes in the formation and accumulation of stable SOC in the context of increasing N deposition.

Are fine roots 'leaves underground' in terms of allometry? A test in a tropical forest successional series in southwest China

Fine roots have been hypothesized to be "leaves underground" in terms of vascular network, but this hypothesis has rarely been tested within the framework of metabolic scaling theory (MST). We measured average fine-root (diameter < 1 mm) mass (M), surface area (A), volume (V), diameter (D) and length (L) for 216 soil cores from 24 plots across four successional stages in tropical forests of Xishuangbanna (southwest China), and examined eight scaling relationships between these variables at the individual root scale. We tested whether fine-root allometries conformed to MST's model for leaf (MSTl) or model (MSTw) for woody organs (e.g. trunk). We also assessed the relative effects of environmental factors, tree size, species composition and diversity, and stand structural factors on allometric relationships using structural equation models (SEMs). Our results showed that: 1) Fine-root scaling exponents rarely conformed to MSTl's predictions. 2) The scaling exponents between fine-root M, A, V and D all conformed to MSTw's predictions in later successional forests, but showed greater deviation towards early successional stage. 3) The scaling exponents associated with fine-root length differed markedly from MSTw's predictions. 4) Changes of some fine-root scaling exponents across successional stage were mainly affected by tree size or soil fertility, and species composition affected allometry only indirectly via tree size. Our results suggested that the allometries of individual fine roots largely conform to the scaling rules governing woody organs instead of leaves, probably because leaves are nearly two-dimensional objects while the other two are three-dimensional. We showed that MSTw can well predict some fine-root allometries in later successional forests, suggesting great potential of utilizing MSTw to better estimate fine-root biomass and productivity. However, the present MSTw still needs to be improved for predicting the scaling relationships concerning fine-root length, and also for better quantifying allometric exponents in earlier successional forests.

opencc-by-4.0Jan 2023View details →

Data from: "Steroidal glycoside profile differences among primary roots system and adventitious roots in Solanum dulcamara"

The zip-file contains all chromatograms reported in vendor (.D) and open-source (.mzxml) formats.

Long-term nitrogen fertilization alters arbuscular mycorrhizal fungi community phylogenetic structure in plant roots across fine spatial scales

Purpose: Nitrogen deposition due to human activities is known to have a substantial impact on arbuscular mycorrhizal fungi (AMF) community in plant roots. However, the influence of elevated nitrogen on the phylogenetic structure of AMF across fine spatial scales, as well as the mechanisms behind such alterations, are remained poorly understood. Results: Nitrogen addition significantly increased the phylogenetic alpha diversity (diversity within a plot) and the 'within-treatment' phylogenetic beta diversity (dissimilarity among replicate plots) of AMF communities, which resulted in an increased 'within-treatment' phylogenetic gamma diversity (overall diversity among all the replicate plots within a treatment). These changes were caused by the relative abundance decline of a dominant genus (Glomus) and an increase in non-dominant genera. Mechanically, nitrogen addition affected phylogenetic alpha diversity mainly by influencing soil properties. Likewise, the increased 'within-treatment' dissimilarity of plant community composition and changes in soil properties caused by nitrogen addition and plot distance contributed to an increase in within-treatment phylogenetic beta diversity. Conclusions: We conclude that deterministic environmental filtering (both abiotic and biotic) and dispersal limitation effect played critical roles in AMF community assembly under global change scenarios. Insightfully, this study provides a mechanistic understanding of the response of AMF to nitrogen addition across fine scales.

opencc-by-4.0Jul 2022View details →

THREE-DIMENSIONAL VOLUMETRIC EVALUATION OF ROOT RESORPTION IN MAXILLARY ANTERIORS FOLLOWING EN-MASSE RETRACTION WITH VARYING FORCE VECTORS - A RANDOMIZED CONTROL TRIAL

To assess the severity of root resorption (RR) during retraction of maxillary anteriors with and without skeletal anchorage (three different force systems); and analyze it comprehensively using cone-beam computed tomography (CBCT) superimpositions.

The coordination between leaf and fine root litter decomposition and the difference of their controlling factors

Aim: As the two largest components of plant detritus input, leaf and root litter together determines ecosystem vegetation turnover and nutrient cycling rates. However, it remains unknown the similarities and differences between the controlling factors for their decomposition. We evaluated the relationship between leaf and fine root litter decomposition across biomes, and analyzed how litter traits, climate, soil conditions and decomposers shape their relationship. Location: Global. Time Period: 1984–2020. Major Taxa Studied: Vascular plant. Methods: We collected 352 paired leaf and fine root decomposition rates (k values) and ancillary traits, climate, soil condition and decomposer abundance data from 88 sites spanning the major global biomes. Boosted regression trees (BRTs) were applied to partition the factors that control root and leaf decomposition rates. Results: Averaged across all biomes, leaf litter decomposes significantly faster (kleaf=0.72) than fine root (kroot=0.42). The BRTs indicated that plant traits best explained the variance in both leaf and root litter decomposition. The key chemical traits of leaf litter and fine root, including C:N, [P], N:P, [lignin], [cellulose], [NSCs] and [tannins], were positively correlated. Therefore, leaf and fine root k values were positively correlated within and across biomes, even after removing the influence of climate, soil conditions and decomposers. However, climate and decomposers had different impacts on leaf and fine root decomposition. Climate induced a greater impact on fine root litter decomposition, whereas decomposers had a greater influence on leaf litter decomposition. Main Conclusions: Our finding indicates that plants evolve a coordinated nutrient supply and demand strategy. The high nutrient demand plants produce labile leaf and fine root litter, which decompose fast to meet their high nutrient requirements. However, leaf and fine root decomposition are also mediated by different combinations of trait, climate, soil condition and decomposer factors, which weakens the coordination between leaf and fine root decomposition.

Plant root growth against a mechanical obstacle: The early growth response of a maize root facing an axial resistance is consistent with the Lockhart model

Plant root growth is dramatically reduced in compacted soils, affecting the growth of the whole plant. Through a model experiment coupling force and kinematics measurements, we probed the force-growth relationship of a primary root contacting a stiff resisting obstacle, that mimics the strongest soil impedance variation encountered by a growing root. The growth of maize roots just emerging from a corseting agarose gel and contacting a force sensor (acting as an obstacle) was monitored by time-lapse imaging simultaneously to the force. The evolution of the velocity field along the root was obtained from kinematics analysis of the root texture with a PIV derived-technique. A triangular fit was introduced to retrieve the elemental elongation rate or strain rate. A parameter-free model based on the Lockhart law quantitatively predicts how the force at the obstacle modifies several features of the growth distribution (length of the growth zone, maximal elemental elongation rate, velocity) during the first 10 minutes. These results suggest a strong similarity of the early growth responses elicited either by a directional stress (contact) or by an isotropic perturbation (hyperosmotic bath).

opencc-by-4.0Dec 2021View details →

Plasmid Sequences for Brophy et al., 2022: Synthetic genetic circuits as a means of reprogramming plant roots

Plasmid Sequences for Brophy et. al. 2022: Synthetic genetic circuits as a means of reprogramming plant roots

opencc-zeroAug 2022View details →

Visualization and quantification of carbon 'rusty sink' by rice root iron plaque: mechanisms, functions, and global implications

Paddies contain 78% higher organic carbon (C) stocks than adjacent upland soils, and iron (Fe) plaque formation on rice roots is one of the mechanisms that traps C. The process sequence, extent and global relevance of this C stabilization mechanism under oxic/anoxic conditions remains unclear. We quantified and localized the contribution of Fe plaque to C stabilization in a microoxic area (rice rhizosphere) and evaluated the role of this C trap toward global C sequestration in paddy soils. Visualization and localization of pH by imaging with planar optodes, enzyme activities by zymography, and root exudation by 14C imaging, as well as upscale modeling enabled linkage of three groups of rhizosphere processes that are responsible for C stabilization from the micro- (root) to the macro- (ecosystem) level. The 14C activity in soil (reflecting stabilization of rhizodeposits) with Fe2+ addition was 1.4−1.5 times higher than that in the control and phosphate addition soils. Perfect co-localization of the hotspots of β-glucosidase activity (by zymography) with exudation showed that labile C and high enzyme activities were localized within Fe plaques. Fe2+ addition to soil and its microbial oxidation to Fe3+ by radial oxygen release from rice roots increased Fe plaque (Fe3+) formation by 1.7−2.5 times. The C trapped by Fe plaque was 1.1 times higher after Fe2+ addition. Therefore, Fe plaque formed from amorphous and complex Fe on root surface act as a "rusty sink" for C. Upscaling by model revealed the global significance of C preservation within Fe3+ complexes in paddy soils. Considering the area of coverage of paddy soils globally, radial oxygen loss from roots and bacterial Fe oxidation may trap up to 130 Mg C in Fe plaques per rice season. This represents an important annual surplus of new and stable C to the existing C pool under long-term rice cropping.

opencc-by-4.0Aug 2022View details →

Archive data supporting the results in the paper: Increase in carbon input by enhanced fine root turnover in a long-term warmed forest soil

This is the archive data supporting the results in the paper: Increase in carbon input by enhanced fine root turnover in a long-term warmed forest soil; submitted to the Journal Science of the Total Environment.

opencc-zeroFeb 2021View details →

Phylogenomic analyses of 2,786 genes in 158 lineages support a root of the eukaryotic tree of life between opisthokonts and all other lineages

Advances in phylogenetic methods and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolutionary history of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most 'popular' (i.e. in textbooks and reviews) hypothesis for the root is between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single gene fusion and a limited sampling of eukaryotic lineages. Subsequent highly-cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within the Excavata. However, concatenation of genes neither considers phylogenetically-informative events (i.e. gene duplications and losses) nor provides an estimate of the root. A more recent study using gene tree-species tree reconciliation methods suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we apply a gene tree – species tree reconciliation approach to a gene-rich and taxon-rich dataset (i.e. 2,786 gene families from two sets of ~158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. Our results estimate a root between Fungi and all other eukaryotes, or between Opisthokonta and all other eukaryotes, and reject alternative popular roots from the literature. Based on further analysis of genome size, we propose Opisthokonta + others as the most likely root. Finding the root of the eukaryotic tree of life is critical for the field of comparative biology as it allows us to understand the timing and mode of evolution of characters across the evolutionary history of eukaryotes.