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openCC (other)Mar 2020View details →

Kinetic Model Data: Effect of Calcium on the Bioavailability of Dissolved Uranium (VI) in Plant Roots under Circumneutral pH

We integrated field measurements, hydroponic experiments, microscopy, and spectroscopy to investigate the effect of Ca(II) on dissolved U(VI) uptake by plants in 1 mM HCO3 − solutions at circumneutral pH. The accumulation of U in plants (3.1−21.3 mg kg−1) from the stream bank of the Rio Paguate, Jackpile Mine, New Mexico served as a motivation for this study. Brassica juncea was the model plant used for the laboratory experiments conducted over a range of U (30−700 μg L−1) and Ca (0−240 mg L−1) concentrations. The initial U uptake followed pseudo-second-order kinetics. The initial U uptake rate (V0) ranged from 4.4 to 62 μg g−1 h−1 in experiments with no added Ca and from 0.73 to 2.07 μg g−1 h−1 in experiments with 12 mg L−1 Ca. No measurable U uptake over time was detected for experiments with 240 mg L−1 Ca. Ternary Ca−U−CO3 complexes may affect the decrease in U bioavailability observed in this study. Elemental X-ray mapping using scanning transmission electron microscopy−energy dispersive spectrometry detected U−P-bearing precipitates within root cell walls in water free of Ca. These results suggest that root interactions with Ca and carbonate in solution affect the bioavailability of U in plants. This study contributes relevant information to applications related to U transport and remediation of contaminated sites.

Schizachyrium scoparium seedling root and shoot biomass: Interactive Effects of Fertility and Distribution on Plant Community Diversity and Structure

There are four levels of nitrogen, corresponding to treatments A, C, F and G in E001, applied at the same time as in that experiment. For a description of fertilizer added to E052, see file fertilization details. There are four levels of soil disturbance designated 1, 2, 3 and 4. Level 1: undisturbed Level 2: 1 pass with a 7 HP Honda rear-tined rototiller with the elevator set to till to a depth of 9 inches Level 3: 2 passes or however many required to produce about 50% bare ground Level 4: 3 passes or however many required to produce 100% bare ground. This requires 3 passes in some plots but 5 or 6 in others. In addition, all woody vegetation not destroyed by tilling is cut at the base. Rototilling is applied in late April. Each fertilization treatment receives each disturbance treatment, for a total of sixteen treatments. There are four replicates of each of the sixteen treatments. In addition, the four extreme ends (lowest N, lowest disturbance; highest N, lowest disturbance, etc. ) are replicated an additional ten times. Treatments are applied in a completely randomized design. Each of the 104 plots is 5m x 5m. Measurements taken at E052 will include: 1) species abundances, 2) community biomass allocation to leaves/roots/stems/flowers, 3) above and below ground net primary production and 4) rates of nitrogen mineralization. For a list of treatments, see the treatment layouts in file trmte52. The plots in E052 are enclosed by a fence to exclude mammalian herbivores. Galvanized welded-wire hardware cloth with 6mm x 6mm openings was buried to a depth of 50cm. Additional hardware cloth extends 60cm above the ground and poultry netting extends to 2m above the ground. In 1990, ten plots of each of four treatments (N1D1, N1D4, N4D1, N4D4, where N is the level of nitrogen added and D is the disturbance treatment) were randomly selected for the competition experiment. The above and belowground effects of neighbors on transplanted grass seedlings were measured using three

Root biomass data: Interactive Effects of Fertility and Distribution on Plant Community Diversity and Structure

Root biomass data: Plant Competition Under Different Nitrogen Levels:A Garden Experiment

This garden plot experiment is located next to the E026 gardens in Field E (Old Field 44). This garden contained monocultures of major grass species from across the grassland biome of North America, and also 3 legume species (E070). The design and purpose were similar to E026, except the plots were larger. The basic experimental design consisted of growing plants in monoculture and in various competitive combinations on each of 14 different soil mixtures. In 1988 a bulldozer was used to remove 30 inches of top soil at the site. To each plot a certain amount of black dirt, ranging from 0.3 inches to 10 inches, was added. Total carbon ranged from 0.1928% to 5.63134% and total nitrogen ranged from 0.0158% to 0.4591%. The exact amounts of black soil added to each plot are described in the field operations. Equal amounts of MgSO4, CaCO3, P2O5 \

Root carbon/nitrogen data: Multiple Traits of Multiple Plant Species Measured in Monoculture Gardens

These gardens were started in order to establish monocultures of several species of native prairie plants common to Cedar Creek.

Root carbon/nitrogen data: Biodiversity II: Effects of Plant Biodiversity on Population and Ecosystem Processes

Biodiversity II (E120) is designed to determine how the number of plant species affects the dynamics of ecological processes at the population, community, and ecosystem levels. By experimentally manipulating the number of species and the kinds of species, the amount of plant growth and the change from year to year, that result can be examined. Plots are large (9m x 9m actively maintained) and well-replicated, allowing responses of plant pathogens, insect herbivores, seed predators, soil parameters, invasive plant species and other variables to also be studied. Plots were seeded in May 1994 to have 1, 2, 4, 8, or 16 species, with roughly 30 replicates of each diversity level. The species composition of each plot was chosen by random draw from a pool of 18 grassland perennials that included four warm-season (C4) grasses, four cool-season (C3) grasses, four legumes, four non-legume forbs, and two woody species. All species occur in monoculture allowing comparison of responses of each species in monoculture to combinations of these same species. The experiment was established in 1994 by the lead investigators David Tilman, Peter Reich, Johannes Knops, and David Wedin. Experiment 120 is similar to Experiment 123, but it uses larger plots to provide a large capacity for long-term subexperiments.

Invasion strip root biomass: Biodiversity II: Effects of Plant Biodiversity on Population and Ecosystem Processes

Root biomass data: Natural Enemies, Plant Diversity and Plant Community Composition

The purpose of this experiment is to determine the influences of natural enemies, including plant pathogenic fungi and insect pests, influence plant community composition, productivity, and diversity over time. The experiment is being conducted in a subset of plots within the Big Biodiversity field, including monoculture, 2-species, 4-species, 8-species, 16-species, and 32-species plots. There are 5 different treatments: foliar fungicide, soil drench fungicide, foliar insecticide, the combination of all pesticides, and nontreated control. The pesticides are applied repeatedly throughout the growing season. Within the plots, community productivity, species composition, percent cover, and pest damage are being quantified over time.

opencc-zeroJun 2020View details →

Data from: Geographic scale and disturbance influence intraspecific trait variability in leaves and roots of North American understory plants

1. Considering intraspecific trait variability (ITV) in ecological studies has improved our understanding of species persistence and coexistence. These advances are based on the growing number of leaf ITV studies over local gradients, but logistical constraints have prevented a solid examination of ITV in root traits or at scales reflecting species' geographic ranges. 2. We compared the magnitude of ITV in above- and below-ground plant organs across three spatial scales (biophysical region, locality, plot). We focused on six understory species (four herbs, two shrubs) that occur both in disturbed and undisturbed habitats across boreal and temperate Canadian forests. We aimed to document ITV structure over wide ecological and geographical scales by asking: 1) What is the breadth of ITV across species range-scale?; 2) What proportion of ITV is captured at different spatial scales, particularly when local scale disturbances are considered? and 3) Is the variance structure consistent between leaf and analogous root traits, and between morphological and chemical traits? 3. Following standardized methods, we sampled 818 populations across 79 forest plots simultaneously, including disturbed and undisturbed stands, spanning four biophysical regions (~5200 km). Traits measured included specific leaf area (SLA), specific root length (SRL), and leaf and root nutrient concentrations (N, P, K, Mg, Ca). We used variance decomposition techniques to characterize ITV structure across scales. 4. Our results show that an important proportion of ITV occurred at the local scale when sampling includes contrasting environmental conditions resulting from local disturbance. A certain proportion of the variability in both leaf and root traits remained unaccounted for by the three sampling scales included in the design (36% on average) and a largest amount for SRL (54%). Substantial differences in magnitude of ITV were found among the six species, and between analogous traits, suggesting that trait distribution was influenced by species strategy and reflects the extent of understory environment heterogeneity. 5. Even for species with broad geographical distributions, a large proportion of within-species trait variability can be captured by sampling locally across ecological gradients. This has practical implications for sampling design and trait selection for both local studies and continental scale modeling.

opencc-zeroAug 2020View details →

Data from msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multi-species plant communities

Plant interactions are as important belowground as aboveground. Belowground plant interactions are however inherently difficult to quantify, as roots of different species are difficult to disentangle. Although for a couple of decades molecular techniques have been successfully applied to quantify root abundance, root identification and quantification in multi-species plant communities remains particularly challenging. Here we present a novel methodology, multi-species Genotyping By Sequencing (msGBS), as a next step to tackle this challenge. First, a multi-species meta-reference database containing thousands of gDNA clusters per species is created from GBS derived High Throughput Sequencing (HTS) reads. Second, GBS derived HTS reads from multi-species root samples are mapped to this meta-reference which, after a filter procedure to increase the taxonomic resolution, allows the parallel quantification of multiple species. The msGBS signal of 111 mock-mixture root samples, with up to 8 plant species per sample, was used to calculate the within-species abundance. Optional subsequent calibration yielded the across-species abundance. The within- and across-species abundances highly correlated (R2 range 0.72-0.94 and 0.85-0.98, respectively) to the biomass-based species abundance. Compared to a qPCR based method which was previously used to analyze the same set of samples, msGBS provided similar results. Additional data on 11 congener species groups within 105 natural field root samples showed high taxonomic resolution of the method. <a>msGBS is highly scalable in terms of sensitivity and species numbers within samples, which is a major advantage compared to the qPCR method and advances our tools to reveal hidden belowground interactions.</a> This dataset belongs to the article "msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multi-species plant communities". msGBS is a technique that uses Genotyping By Sequencing on mixed plant species root samples which, after a filtering step to increase the taxonomic resolution and calibration, is able to estimate plant species abundances. The article uses data of two different experiment: <ol> <li>the Jena field survay (13 plant species) and</li> <li>the Dutch field survay (120 plant species).</li> </ol>

zenodo32/100

Data and R code used in Delory et al (2020) Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants

This repository contains the data and R markdown files supporting the findings presented in Delory et al (2020) Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants.

opengpl-3.0-or-laterAug 2020View details →

opencc-zeroSep 2020View details →

Community composition of arctic root-associated fungi mirrors host plant phylogeny

The number of plant species regarded as non-mycorrhizal increases at higher latitudes, and several plant species in the High-Arctic Archipelago Svalbard have been reported as non-mycorrhizal. We used the rRNA ITS2 and 18S gene markers to survey which fungi, as well as other micro-eukaryotes, were associated with roots of 31 arctic plant species not usually regarded as mycorrhizal in Svalbard. We assessed to what degree the root-associated fungi showed any host preference and whether the phylogeny of the plant hosts may mirror the composition of root-associated fungi. Fungal communities were largely structured according to host plant identity and to a less extent by environmental factors. We observed a positive relationship between the phylogenetic distance of host plants and the distance of fungal community composition between samples, indicating that the evolutionary history of the host plants plays a major role for which fungi colonize the plant roots. In contrast to the ITS2 marker, the 18S rRNA gene marker showed that chytrid fungi were prevalently associated with plant roots, together with a wide spectrum of amoeba-like protists and nematodes. Our study confirms that arbuscular mycorrhizal (AM) fungi are present also in arctic environments in low abundance.

opencc-zeroDec 2019View details →

Fungal root-endophytes influence plants in a species-specific manner that depends on plant's growth stage

The mycobiome (fungal microbiome) influences plants— from seed germination to full maturation. While many studies on fungal-plant interaction studies have focused on known mutualistic and pathogenic fungi, the functional role of ubiquitous endophytic fungi remains little explored. We examined how root-inhabiting fungi (endophytes) influence range expanding plant species. We isolated endophytes from three European intra-continental range-expanders and three congenerics that are native both in the range-expander's original (southern Europe) and new (northern Europe) range. To standardize our collection, endophytes were obtained from all six plant species growing under controlled conditions in northern (new range of the range-expander) and southern (native range of the range-expander) soils. We cultivated, molecularly identified and tested the effects of all isolates on seed germination, and growth of seedlings and older plants. Most of the 34 isolates could not be functionally characterized based on their taxonomic identity and literature information on functions. Endophytes affected plant growth in a plant species-endophyte specific manner, but overall differed between range-expanders and natives. While endophytes reduced germination and growth of range-expanders compared to natives, they reduced seedling growth of natives more than of range-expanders. Synthesis: We conclude that endophytic fungi have a direct effect on plant growth in a plant growth stage-dependent manner. While these effects differed between range expanders and natives, the effect strength and significance varied among the plant genera included in the present study. Nevertheless, endophytes likely influence establishment of newly arriving plants and influence vegetation dynamics

opencc-zeroJan 2021View details →

Neighboring trees regulate the root-associated pathogenic fungi on the host plant in a subtropical forest

Root-associated fungi and host-specific pathogens are major determinants of species coexistence in forests. Phylogenetically related neighboring trees can strongly affect the fungal community structure of the host plant, which, in turn, will affect the ecological processes. Unfortunately, our understanding of the factors influencing fungal community composition in forests is still limited. In particular, investigation of the relationship between the phytopathogenic fungal community and neighboring trees is incomplete. In the current study, we tested the host specificity of members of the root-associated fungal community collected from seven tree species and determined the influence of neighboring trees and habitat variation on the composition of the phytopathogenic fungal community of the focal plant in a subtropical evergreen forest. Using high-throughput sequencing data with respect to the internal transcribed spacer (ITS) region, we characterized the community composition of the root-associated fungi and found significant differences with respect to fungal groups among the seven tree species. The density of conspecific neighboring trees had a significantly positive influence on the relative abundance of phytopathogens, especially host-specific pathogens, while the heterospecific neighbor density had a significant negative impact on the species richness of host-specific pathogens, as well as phytopathogens. Our work provides evidence that the root-associated phytopathogenic fungi of a host plant depends greatly on the tree neighbors of the host plant.

opencc-zeroDec 2016View details →

Data from: Archaea and bacteria mediate the effects of native species root loss on fungi during plant invasion

Although invasive plants can drive ecosystem change, little is known about the directional nature of belowground interactions between invasive plants, native roots, bacteria, archaea and fungi. We used detailed bioinformatics and a recently developed root assay on soils collected in fescue grassland along a gradient of smooth brome (Bromus inermis Leyss) invasion to examine the links between smooth brome shoot litter and root, archaea, bacteria and fungal communities. We examined (1) aboveground versus belowground influences of smooth brome on soil microbial communities, (2) the importance of direct versus microbe-mediated impacts of plants on soil fungal communities, and (3) the web of roots, shoots, archaea, bacteria and fungi interactions across the A and B soil horizons in invaded and non-invaded sites. Archaea and bacteria influenced fungal composition, but not vice versa, as indicated by redundancy analyses. Co-inertia analyses suggested that bacterial–fungal variance was driven primarily by 12 bacterial operational taxonomic units (OTUs). Brome increased bacterial diversity via smooth brome litter in the A horizon and roots in the B horizon, which then reduced fungal diversity. Archaea increased abundance of several bacterial OTUs, and the key bacterial OTUs mediated changes in the fungi's response to invasion. Overall, native root diversity loss and bacterial mediation were more important drivers of fungal composition than were the direct effects of increases in smooth brome. Critically, native plant species displacement and root loss appeared to be the most important driver of fungal composition during invasion. This causal web likely gives rise to the plant–fungi feedbacks, which are an essential factor determining plant diversity in invaded grassland ecosystems.

opencc-zeroDec 2013View details →

Data from: Plant-herbivore interactions: silicon concentration in tussock sedges and population dynamics of root voles

1. It has been hypothesized that the induction of silicon (Si)-based plant defence in response to herbivore damage may engender rodent population cycles. Many studies have also considered accumulation of Si as a process controlled by geo-hydrological factors. 2. To test these ideas, we investigated the relationship between concentration of Si in fibrous tussock sedge (Carex appropinquata) and the population density of a major sedge consumer, the root vole (Microtus oeconomus), in field enclosures in natural habitat under a variety of natural water regimes and weather conditions. 3. We found that a high density of voles at the end of summer resulted in the immediate accumulation of Si by rhizomes, followed by accumulation of Si in leaves with a one-year lag time. The level of river flooding in the same year had an additional impact on Si concentration in rhizomes but did not affect silicification of leaves. 4. Overwinter changes in concentration of Si in sedges were influenced by fluctuations in ambient temperature and the depth of snow cover (multiple freeze-thaw cycles), thus affecting the quality of winter food available for voles. 5. Smaller voles had lower mortality during early winter than large voles, which seemed to be connected with changes in the quality of the autumn rather than the winter food base. Winter survival of voles was not associated with Si concentration in their faeces, however. 6. Our results suggest that changes in Si concentration in fibrous tussock sedge can be induced by changes in vole population density and are also additionally affected by the amount of flooding and weather conditions.