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opencc-zeroDec 2021View details →

Mineral nitrogen nutrition of Fagus sylvatica L roots colonized by ectomycorrhizal fungi in native forest soil

The aim of this study was to examine the transcription-level response of a symbiotic system comformed by the host tree Fagus sylvatica L (European beech) and the root-associated mycobiota to fluctuations in ammonium and nitrate availability in the soil. The experiment was conducted with young trees grown at a natural regeneration forest. We used 15N stable isotopes in combination with DNA-based and RNA-based molecular methods and Illumina sequencing. We report data on the beech root-associated fungal community structure obtained by metabarcoding of the fungal ITS2 region, transcriptome data from the fungal community associated to the tree roots, and transcriptome data from Fagus sylvatica L in response to ammonium or nitrate application to the soil. We also report data from soil ammonium-N, soil-nitrate-N, tree and soil dry mass, root 15N, root N, root C, root carbohydrates, root ammonium-N, root nitrate-N, soil pH, and climate data from the experiment.

In vitro shoot regeneration and root induction of Hylocereus polyrhizus 'Da Hong' from Murashige and Skoog (MS) medium supplemented with 0.05–0.20 mg/L α-naphthaleneacetic acid (NAA).

Figure S1. In vitro shoot regeneration and root induction of Hylocereus polyrhizus ‘Da Hong’ from Murashige and Skoog (MS) medium supplemented with 0.05–0.20 mg/L α-naphthaleneacetic acid (NAA). Treatments: CS, control; TS01, 0.05 mg/L NAA; TS02, 0.10 mg/L NAA; TS03, 0.20 mg/L NAA. Bar = 5 cm.

Root tissue segmentation dataset

The PHDFM dataset is composed of fluorescence microscopy images of root tissue samples from A. thaliana, using the ratiometric fluorescent indicator 8‐hydroxypyrene‐1,3,6‐trisulfonic acid trisodium salt (HPTS). This semantic segmentation training dataset consists of 2D microscopy images (the brightfield channel for excitation at 405 nm), each containing a segmentation mask as an additional image channel (manually annotated by plant biologists). The segmentation masks classify pixels into the following 5 labels with the corresponding IDs: background (0), root tissue (1), early elongation zone (2), late elongation zone (3), and meristematic zone (4).

opencc-by-4.0Nov 2021View details →

Datasets related to publication: Microbial Consortia for Effective Biocontrol of Root and Foliar Diseases in Tomato

Datasets underlying the results presented in the Original Research Article "Microbial Consortia for Effective Biocontrol of Root and Foliar Diseases in Tomato", Frontiers in Plant Science, Volume 12, Article 756368, https://www.frontiersin.org/articles/10.3389/fpls.2021.756368/full, <a href="https://doi.org/10.3389/fpls.2021.756368">https://doi.org/10.3389/fpls.2021.756368</a> This  research  has  received  funding  from  the European  Union’s  Horizon  2020  research  and Innovation programme under grant agreement No 765290 (Name of the action: Microbe induced resistance to agricultural pests, Acronym: MiRA).

GWAS on salt stress responses in root system architecture parameters of wild tomato (S. pimpinellifolium)

The population of +/2 200 accessions of wild tomato was screened with the protocol described <a href="https://www.protocols.io/view/studying-root-system-architecture-changes-in-tomat-2mqgc5w">here</a> with the only exception that the plants were transferred 4 days after germination (rather than 3 - described in the protocol). The images were analyzed using the <a href="https://smartroot.github.io/">SmartRoot</a> for days 0, 1, 2, 3, and 4 after transfer to treatment plates (0 or 100 mM NaCl, 1/4 MS, 0.5% sucrose, 0.1% MES, 1% Dashin agar). The data analysis was performed as described <a href="https://rpubs.com/mjulkowska/BIGpimp_RSA_salt">here</a>, while the pareto front calculations were done according to Chandrasekhar & Julkowska paper (<a href="https://www.biorxiv.org/content/10.1101/2021.08.12.456185v1">preprint here</a>). The GWAS was performed using the ASReml script similar to <a href="https://onlinelibrary.wiley.com/doi/10.1111/tpj.15310">Awlia et al. (2021)</a>.

Analysis of the root diameter distribution from time series images of real and simulated Cassava root systems

The data was collected, simulated and analyzed in the framework of the CassavaStore project (a collaboration between IBG-2, Forschungszentrum Jülich, Germany and different institution from Thailand; for details see <a href="https://www.international-bioeconomy.org/cassavastore_eng">https://www.international-bioeconomy.org/cassavastore_eng</a>). Aim of this project is to get a better understanding of storage root development in cassava (Manihot esculenta Crantz) in order to optimize cassava growth with respect to variety breeding and growth management. The storage root is one of the main providers of starch in Thailand and therefore of high economic importance. Monitoring the formation of storage roots over time via quantification of the root diameter distribution of excavated root systems was one of the key aspects addressed in this project. To measure the diameters a software was developed that identifies roots in RGB images and analyzes the diameters along each identified root automatically. The published data contains 1) analyzed images from cassava roots that were acquired in a video box; 2) simulated virtual root model images with known root diameter distributions that were used to validate the analysis approach; 3) a description of the data and the folder structure.

Plantlet weight, including shoots and roots, and root/shoot ratio of Hylocereus polyrhizus 'Da Hong' grown on Murashige and Skoog (MS) medium supplemented with α-naphthaleneacetic acid (NAA) alone.

Figure S2. Plantlet weight, including shoots and roots, and root/shoot ratio of Hylocereus polyrhizus ‘Da Hong’ grown on Murashige and Skoog (MS) medium supplemented with α-naphthaleneacetic acid (NAA) alone. Treatment: CS, control; TS01, 0.05 mg/L NAA; TS02, 0.10 mg/L NAA; TS03, 0.20 mg/L NAA. Mean ± SE (n = 3, 5 segments per replicate). Means followed by different letters near the column and circle are significantly different at p = 0.05 using Fisher’s protected LSD test.

In vitro shoot regeneration and root induction of Hylocereus polyrhizus 'Da Hong' from Murashige and Skoog (MS) medium supplemented with 0.05–0.20 mg/L α-naphthaleneacetic acid (NAA).

opencc-zeroJan 2022View details →

High variation in hydraulic efficiency but not xylem safety between roots and branches in four temperate broad-leaved tree species

Xylem hydraulic safety and efficiency are key traits determining tree fitness in a warmer and drier world. While numerous plant hydraulic studies have focused on branches, our understanding of root hydraulic functioning remains limited, although roots control water uptake, influence stomatal regulation and have commonly been considered as the most vulnerable organ along the hydraulic pathway. We investigated 11 traits related to xylem safety and efficiency along the hydraulic pathway in four temperate broad-leaved tree species. Continuous vessel tapering from coarse roots to stems and branches caused considerable reduction in hydraulic efficiency. Wood density was always lowest in roots, but did not decline linearly along the flow path. In contrast, xylem embolism resistance (P50) did not differ significantly between roots and branches, except for one species. The limited variation in xylem safety between organs did not adequately reflect the corresponding reductions in vessel diameter (by ~70%) and hydraulic efficiency (by ~85%). Although we did not observe any trade-off between xylem safety and specific conductivity, vessel diameter, vessel lumen fraction and wood density were related to embolism resistance, both across and partly within organs. We conclude that coarse roots are not highly vulnerable to xylem embolism as commonly believed, indicating that hydraulic failure during soil drying might be restricted to fine roots.

opencc-zeroFeb 2022View details →

Aboveground herbivory causes belowground changes in twelve oak Quercus species: a phylogenetic analysis of root biomass and non‐structural carbohydrate storage

Plant ecosystem structure is understood to be a result of complex multitrophic interactions. Most multitrophic studies focus on plant aboveground adaptations to aboveground herbivore pressures, neglecting belowground adaptations in response to aboveground damage. Differential investment in root structures may allow plants to compensate for tissue loss or damage due to herbivores. Furthermore, phylogeny may constrain a plant's ability to adapt belowground. We examined the belowground responses of 12 species of oak (Quercus) to varying locations and intensities of simulated herbivore damage. We first established that oak belowground traits responded to aboveground herbivory by measuring patterns of investment in coarse vs fine root structures and re-allocation of non-structural carbohydrates (NSC) to root storage. We then tested whether phylogeny could explain variations in investment patterns using phylogenetic independent contrasts. Plant adaptations to aboveground herbivory included allocating biomass and carbon reserves to root structures, depending on the location and intensity of herbivore damage. NSC re-allocation to root storage was observed when oak species experienced any type of damage, but damage to lateral tissues caused a greater re-allocation than apical damage or control treatments. We found that most belowground responses to aboveground herbivory are species-specific and may be adapted for environmental conditions or type of herbivory. Some responses to herbivore damage, such as changes in fine-root mass and root sugar concentrations, were phylogenetically constrained. Phylogenetic constraints generally occur when there is severe damage at the apical meristem. Plants may adapt to aboveground tissue loss due to varying herbivore pressures (i.e. varying location and intensity of damage) by differentially investing in root types and NSC re-allocation to root storage. Understanding linkages between and phylogenetic constraints of plant belowground responses to aboveground herbivory will improve our understanding of the ecological processes involved in multitrophic interactions.

opencc-zeroMar 2022View details →

Mycorrhizal colonization and root diameter of native and invasive plants of eastern North America

Arbuscular mycorrhizal colonization (total and arbuscules) were measured in roots of 10 species of eastern North American woody plants. Five were non-native invasive and 5 were native species. Roots were collected from ingrowth cores over three harvests during a single season, from a common garden. Diameter was estimated from published root density and specific root length values for each species.

opencc-by-4.0Feb 2022View details →

Salinity of irrigation water selects distinct bacterial communities associated with Date palm (Phoenix dactylifera L.) root

Saline water irrigation has been used extensively in date palm (Phoenix dactylifera L.) agriculture as an alternative to non-saline freshwater due to water scarcity in hyper-arid environments. However, how saline water irrigation affects date palm root-associated bacterial communities is unknown. Here, we investigated the effect of irrigation sources (non-saline vs saline water) on date palm root-associated bacterial communities and their diversity using 16S rRNA gene metabarcoding. The bacterial richness, Shannon diversity and evenness didn’t differ significantly between the irrigation sources. Soil electrical conductivity (EC) and irrigation water pH were negatively related to Shannon diversity and evenness respectively, while soil organic matter displayed a positive correlation with Shannon diversity. Of total, 40.5% OTUs were unique to non-saline water irrigation and 26% to saline water irrigation. The multivariate analyses displayed strong structuring of bacterial communities according to irrigation sources, and both soil EC and irrigation water pH were the major factors affecting communities. The genera Bacillus, Micromonospora and Mycobacterium were dominated while saline water irrigation whereas contrasting pattern was observed for Rhizobium, Streptomyces and Acidibacter. This study suggests that while saline water irrigation date palm root select specific bacterial taxa, potentially playing a crucial role in alleviating salinity stress of the host.

opencc-zeroApr 2022View details →

Interspecific differences in root foraging precision cannot be directly inferred from species' mycorrhizal status or fine root economics

Nutrient acquisition in plants can be represented by a suite of intercorrelated root traits such as root diameter, nitrogen content, root tissue density, and specific root length. However, it is unclear how a plant's ability to precisely forage for nutrients in a heterogeneous soil environment (i.e., the precision of placing roots into nutrient-rich areas) relates to these traits. Mycorrhizal symbiosis also affects the relationship between the fine root traits and root foraging precision because fungal hyphae may be used for foraging instead of roots. Hypotheses matching high root foraging precision with low mycorrhizal colonization or "fast" acquisitive strategies of plants have been raised based either on data from tree species or a limited number of herbaceous species. To test these hypotheses, we compiled data quantifying the experimentally measured degree to which root biomass responded to patchy substrate nutrient concentrations (i.e., root foraging precision) for 123 herbaceous grassland species using a partial meta-analysis. We tested root foraging precision relationship with root traits involved in nutrient acquisition and mycorrhizal symbiosis (root diameter, specific root length, root tissue density, root tissue nitrogen content, and mycorrhizal colonization). The root foraging precision data came from four different pot experiments, and the trait data were extracted from publicly available trait databases. We used a phylogenetically informed approach in order to detect the degree of conservation of the relationships. We found that root foraging precision was not significantly correlated with other fine root traits and mycorrhizal colonization. Thus, it appears unrelated to the main dimensions of the nutrient acquisition space of herbaceous species, namely acquisitive-conservative strategy and outsourcing of acquisition to the fungi. Also, we found only a very weak phylogenetic signal in root foraging precision of 123 species. Our results suggest that root foraging precision constitutes another distinct, evolutionarily independent dimension in herbaceous species' trait space.

opencc-by-4.0Apr 2022View details →

Pig rooting surveys

Description: This is a dataset on pig rooting observations in the SAFE landscape in 2021. In 2021, the Bearded Pigs of Sabah were severely affected and decimated by the African Swine Fever. These rooting surveys were conducted to provide an indication whether there were recent Bearded pig activity in the SAFE landscape. Project: This dataset was collected as part of the following SAFE research project: <a href="https://safeproject.net/projects/project_view/173">Group Dynamics of Bornean Bearded Pigs: the advantages of behavioural plasticity in changeable landscapes.</a>XML metadata: GEMINI compliant metadata for this dataset is available <a href="https://safeproject.net/datasets/xml_metadata?id=6477762">here</a>Files: This consists of 1 file: SAFE_pig_rooting_surveys_2021_for_upload.xlsxSAFE_pig_rooting_surveys_2021_for_upload.xlsxThis file contains dataset metadata and 1 data tables:<ol><li>Pig rooting observations (described in worksheet Data)Description: The observations on the presence or absence of Bearded pig rooting.Number of fields: 11Number of data rows: 88Fields: <ul><li>Date: Calender date of field survey (Field type: date)</li><li>Location: Unique ID (Field type: location)</li><li>Observers: names of the observers (Field type: id)</li><li>Distance_along_line_transect: Distance along line transect (Field type: numeric)</li><li>Left_or_right: observations about 10m along the left or the right of the transect line (Field type: categorical)</li><li>Rooting_observed: soil disturbance / rooting observed (Field type: categorical)</li><li>Age_of_rooting: rooting age (fresh = within weeks, old = 1-3 months, aged >3months) (Field type: categorical)</li><li>Pig_tracks: Presence of pig tracks (Field type: categorical trait)</li><li>Photo_ID: File name (Field type: id)</li><li>Distance_from_transect: Distance left or right from the transect (Field type: numeric)</li><li>Comments: Any additional relevant information (Field type: comments)</li></ul></li></ol>Date range: 2021-01-01 to 2021-07-14Latitudinal extent: 4.6680 to 4.6920Longitudinal extent: 117.5793 to 117.5935Taxonomic coverage: All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets.<div>&ensp;-&ensp; Animalia &ensp;-&ensp;&ensp;-&ensp; Chordata &ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp; Mammalia &ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp; Artiodactyla &ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp; Suidae &ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp; Sus &ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp;&ensp;-&ensp; Sus barbatus </div>

opencc-zeroApr 2022View details →

Phylogenomic resolution of the root of Panpulmonata, a hyperdiverse radiation of gastropods: new insight into the evolution of air breathing

Transitions to terrestriality have been associated with major animal radiations including land snails and slugs in Stylommatophora (>20,000 described species), the most successful lineage of 'pulmonates' (a non-monophyletic assemblage of air-breathing gastropods). However, phylogenomic studies have failed to robustly resolve relationships among traditional pulmonates and affiliated marine lineages that comprise clade Panpulmonata (Mollusca, Gastropoda), especially two key taxa: Sacoglossa, a group including photosynthetic sea slugs; and Siphonarioidea, intertidal limpet-like snails with a non-contractile pneumostome (narrow opening to a vascularized pallial cavity). To clarify the evolutionary history of the panpulmonate radiation, we performed phylogenomic analyses on datasets of up to 1,160 nuclear protein-coding genes for 110 gastropods, including 40 new transcriptomes for Sacoglossa and Siphonarioidea. All 18 analyses recovered Sacoglossa as the sister group to a clade we named Pneumopulmonata, within which Siphonarioidea was sister to the remaining lineages in most analyses. Comparative modeling indicated shifts to marginal habitat (estuarine, mangrove and intertidal zones) preceded and accelerated the evolution of a pneumostome, present in the pneumopulmonate ancestor along with a one-sided plicate gill. These findings highlight key intermediate stages in the evolution of air-breathing snails, supporting the hypothesis that adaptation to marginal zones played an important role in major sea-to-land transitions.

opencc-zeroApr 2022View details →

Root traits along a subarctic tundra elevational gradient

While root trait research has received increasing attention over the past two decades, the relationship between root traits and environmental factors remains elusive. At the same time, knowledge about these relationships is necessary if we are to understand plant community responses to environmental change. Here, we assessed the relationships between elevation (i.e., temperature) and fine root traits of plant species and communities. We focused on the sub-arctic tundra where plant communities are expected to experience extreme environmental change by the end of the century.

Plant-root pathogenic fungal and plant-mycorrhizal fungal association networks in a subtropical forest

Although rhizosphere fungi are essential for plant survival and ecosystem functioning, little is known about the processes that structure plant–fungal association networks. In this study, we constructed association networks between 43 plant species and two groups of root-associated fungi (mycorrhizal and pathogenic fungi; MF and PF, respectively) in a diverse subtropical forest. We then evaluated the modularity of plant–MF and plant–PF networks and linked them to the functional traits and phylogenies of both plants and fungi. We observed strong modularity in both plant–MF and plant–PF networks. Phylogenetically related fungi tended to emerge in the same modules. MF from distinct modules associated with plants with different specific root length and specific root area in plant–MF networks. PF from distinct modules associated with plants with different dark respiration rate and light compensation point in plant–PF networks. Plant affiliation to modules was explained by both plant traits and phylogeny (22% for plant–MF and 37% for plant–PF networks). In contrast, fungal affiliation to modules was explained by fungal phylogeny (16% for plant–MF and 29% for plant–PF networks). Our results elucidate the link between modularity in plant–root fungal networks and the functional traits and phylogeny of the plants and fungi. Our study highlights the importance of traits and phylogeny in governing root fungal community assembly from network perspective.

Quantitative assessment of trace and macro element compositions of Cassava (Manihot esculenta) storage roots enriched with Β-Carotene as influenced by genotypes and growing locations

Cassava's important mineral contents depends on some factors, including genetic and growing locational factors. The study aimed to evaluate the influence of genotype and growing locations on the mineral concentrations in yellow-fleshed cassava root genotypes. Twenty-five pipeline yellow-fleshed cassava genotypes and three white-fleshed varieties (check samples) were planted at five different experimental fields for two seasons, each representing the major agroecological zones in Nigeria. Standard laboratory protocols were employed in the sampling to ensure zero contamination, and the trace and macro elements were determined using the inductively coupled plasma optical emission spectroscopic method (ICPOES). The trace and macro elements identified in all the genotypes and varieties investigated were Fe, Mn, B, Cu, Mo, Co, Ni, Zn, and Al; Ca, Mg, Na, K. P, and S respectively. Genotype and growing location had a highly significant (p < 0.05) effect on all the trace elements except Ti and Cr. However, there was no interactive effect between genotype and growing location on all the trace elements except for Pb and Zn. Among the explanatory variables, the variable growing location was the most influential on macro and trace elements. Conclusively, genotypes 01/1442 and 01/1273 have outstanding trace and macro element concentrations.

Areal (+)-borneol modulates root morphology, auxin signalling and meristematic activity in Arabidopsis roots

One of the characteristic aspects of odour sensing in humans is the activation of olfactory receptors in a slightly different manner to different enantiomers. Here, we focused on whether plants showed enantiomer-specific responses similar to that in humans. We exposed Arabidopsis seedlings to methanol (control) and (+)- or (−)-borneol, and found that only (+)-borneol reduced the root length. Furthermore, the root-tip width was more increased upon (+)-borneol exposure than upon (−)-borneol exposure. In addition, root-hair formation was observed near the root tip in response to (+)-borneol. Auxin signalling was strongly reduced in the root tip following exposure to (+)-borneol, but was detected following exposure to (−)-borneol and methanol. Similarly, in the root tip, the activity of Cyclin B1:1 was detected on exposure to (−)-borneol and methanol, but not on exposure to (+)-borneol, indicating that (+)-borneol inhibits the meristematic activity in the root. These results partially explain (+)-borneol-specific reduction in the root length of Arabidopsis. Our results indicate the presence of a sensing system specific for (+)-borneol in Arabidopsis.

Root penetration index 3, a major quantitative trait locus (QTL) associated with root system penetrability in Arabidopsis.

Soil mechanical impedance precludes root penetration, confining root system development to shallow soil horizons where mobile nutrients are scarce. Using a two-phase-agar system, we characterized Arabidopsis thaliana responses to low and high mechanical impedance at three root penetration stages. We found that seedlings whose roots fail to penetrate agar barriers show a significant reduction in leaf area, root length and elongation zone and an increment in root diameter, while those capable of penetrating show only minor morphological effects. Analyses using different auxin-responsive reporter lines, exogenous auxins and inhibitor treatments suggest that auxin responsiveness and PIN-mediated auxin distribution play an important role in regulating root responses to mechanical impedance. The assessment of 21 Arabidopsis accessions revealed that primary root penetrability (PRP) varies widely among accessions. To search for quantitative trait loci (QTLs) associated to root system penetrability, we evaluated a recombinant inbred population (RIL) derived from Landsberg erecta (Ler-0, with a high PRP) and Shahdara (Sha, with a low PRP) accessions. QTL analysis revealed a major-effect QTL localized in chromosome 3 (q-RPI3), which accounted for 29.98% (LOD = 8.82) of the total phenotypic variation. Employing an introgression line (IL-321), with a homozygous q-RPI3region from Sha in the Ler-0 genetic background, we demonstrated that q-RPI3 plays a crucial role in root penetrability. This multiscale study revels new insights into root plasticity during the penetration process in hard agar layers, natural variation and genetic architecture behind primary root penetrability in Arabidopsis.