Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1105658 | ENA |
REPOSITORIES: ENA
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Project description:Castanopsis fissa is an evergreen broad-leaved species of the cone genus Castanopsis in the family Fagaceae, which is widely distributed and is an excellent native species in Guangdong Province of China. This species has a well-developed root system, excellent soil-fixing power, and better soil and water conservation ability and has the characteristics of barren tolerance, strong sprouting power, abundant and easily decomposed dead leaves, etc. Therefore, C. fissa is not only a pioneer species for postdestruction sprouting forests but also a highly potential ecological public welfare forest tree species. Moreover, due to its beautiful shape, wide canopy and various colors, it has become an ideal tree for landscaping and ornamental purposes. However, there is a basic gap in knowledge in the reports on the drought resistance or drought tolerance genes of C. fissa. Based on the above details, in this study, 2-year-old C. fissa seedlings were used as the study material to investigate the physiological response under drought stress by a potted drought experiment, and we also compared and analyzed the differentially expressed proteins (DEPs) under different periods of drought stress by TMT quantitative labeling protein to prepare a preliminary study on the physiological response and proteomic mechanism of C. fissa adaptation to drought stress.
2023-07-24 | PXD038837 | Pride
Project description:Plants are naturally associated with diverse microbial communities, which play significant roles in plant performance, such as growth promotion or fending off pathogens. The roots of Alkanna tinctoria L. are rich in naphthoquinones, particularly the medicinally used chiral compounds alkannin, shikonin and their derivatives. Former studies already have shown that microorganisms may modulate plant metabolism. To further investigate the potential interaction between A. tinctoria and associated microorganisms we performed a greenhouse experiment, in which A. tinctoria plants were grown in the presence of three distinct soil microbiomes. At four defined plant developmental stages we made an in-depth assessment of bacterial and fungal root-associated microbiomes as well as all primary and secondary metabolites. Our results showed that the plant developmental stage was the most important driver influencing the plant metabolite content, revealing peak contents of alkannin/shikonin at the fruiting stage. In contrast, the soil microbiome had the biggest impact on the plant root microbiome. Correlation analyses performed on the measured metabolite content and the abundance of individual bacterial and fungal taxa suggested a dynamic, at times positive or negative relationship between root-associated microorganisms and root metabolism. In particular, the bacterial Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group and the fungal species Penicillium jensenii were found to be positively correlated with higher content of alkannins.
2021-11-28 | ST002021 | MetabolomicsWorkbench
Project description:Deadwood plays a crucial role in forest ecosystems, but we have limited information about the specific fungal taxa and extracellular lignocellulolytic enzymes that are actively involved in the decomposition process in situ. To investigate this, we studied the fungal metaproteome of twelve deadwood tree species in a replicated, eight-year experiment. Key fungi observed included genera of white-rot fungi (Basidiomycota, e.g. Armillaria, Hypholoma, Mycena, Ischnoderma, Resinicium), brown-rot fungi (Basidiomycota, e.g. Fomitopsis, Antrodia), diverse Ascomycota including xylariacous soft-rot fungi (e.g. Xylaria, Annulohypoxylon, Nemania) and various wood-associated endophytes and saprotrophs (Ascocoryne, Trichoderma, Talaromyces). These fungi used a whole range of extracellular lignocellulolytic enzymes, such as peroxidases, peroxide-producing enzymes, laccases, cellulases, glucosidases, hemicellulases (xylanases) and lytic polysaccharide monooxygenases (LPMOs). Both the fungi and enzymes were tree-specific, with specialists and generalists being distinguished by network analysis. The extracellular enzymatic system was highly redundant, with many enzyme classes of different origins present simultaneously in all decaying logs. Strong correlations were found between peroxide-producing enzymes (oxidases) and peroxidases as well as LPMOs, and between ligninolytic, cellulolytic and hemicellulolytic enzymes. The overall protein abundance of lignocellulolytic enzymes was reduced by up to -30% in gymnosperm logs compared to angiosperm logs, and gymnosperms lacked ascomycetous enzymes, which may have contributed to the lower decomposition of gymnosperm wood. In summary, we have obtained a comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in several temperate forest tree species, which can help to improve our understanding of the complex ecological processes in forest ecosystems.
2024-04-22 | PXD041962 | Pride
Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.
2020-03-06 | GSE146427 | GEO
Project description:The decomposition of large woody material is an important process in forest carbon cycling and nutrient release. Cord-forming saprotrophic basidiomycete fungi create non-resource limited mycelial networks between decomposing branches, logs and tree stumps on the forest floor where colonisation of new resource is often associated with the replacement of incumbent decay communities. Cord-forming species often dominate competition hierarchies in controlled paired antagonism experiments and have been shown to translocate resource to support colonisation and produce inhibitory metabolites. To date, antagonism experiments have mostly placed competing fungi in direct contact, while in nature cord-forming saprobes encounter colonised wood as mycelia in a network. Here we used soil-based microcosms that allowed foraging cord-forming Hypholoma fasciculare to encounter a wood block colonised by Trametes versicolor and conducted transcriptomic and proteomic analysis of the interaction. Cellular processes and metabolic responses to the competitive interaction were identified, where protein turnover featured strongly for both species. H. fasciculare demonstrated an exploitative profile with increased transcription of enzymes that targeted carbohydrate polymers of the substrate and in RNA and ribosome processing. T. versicolor showed a shift in signalling, energy generation and amino acid metabolism. Putative genes involved in secondary metabolite production were identified in both species. This study highlights the importance of ecologically-relevant experimental design when considering complex processes such as community development during wood decomposition
2024-09-20 | GSE245088 | GEO
Project description:Trees establish a symbiotic relationship with specialized soil fungi, called ectomycorrhizae, which is essential for nutrition, growth and health of temperate forest ecosystems. Understanding the mechanisms governing the establishment and functioning of ectomycorrhiza is important because of the role of forests in sequestering CO2 and also to develop ways to optimize tree productivity and sustainability. Here, we investigated the response of an oak species to ectomycorrhiza formation using a two dimensional differential in gel electrophoresis (2D-DIGE) and MALDI-TOF/TOF mass spectrometry proteomics approach. At the root level, changes in the abundance of 34 unique oak proteins were detected and revealed proteins involved in carbon and energy metabolism, protein processing and degradation, response to oxidative stress, lipid metabolism/transport, nitrogen and phosphorous assimilation and cell wall modification. Proteins supporting the importance of the secretory pathway functioning, in particular of the endoplasmic reticulum, during ectomycorrhiza functioning were identified. These proteins were identified as components of the endoplasmic reticulum folding/chaperoning machinery and proteins involved in the ER quality control system. This study constitutes an important contribution for the understanding of the mechanisms underlying the response of plants to ectomycorrhizal symbiosis establishment.
2017-07-14 | PXD003009 | Pride
Project description:Young Fagus sylvatica trees (approximately 7 to 8 years) were collected from a natural regeneration beech forest. The trees were excavated with intact soil cores, roots and top organic layer. The trees were then kept outdoors at the Department of Forest Botany, Georg-August-Universität Göttingen. Plants were protected from rain, and light conditions were matched to those of the natural stand using a shading net; otherwise, plants were exposed to natural climatic conditions. The soil moisture was regularly measured; plants were watered with deionized water as needed to keep soil moisture close to the original conditions. Trees was randomly relocated on a weekly basis throughout the experiment to avoid biasses caused by location or light effects. After 21 weeks, a treatment was applied to understand the physiological mechanisms of inorganic nitrogen uptake and assimilation under conditions of an inorganic nitrogen saturated forest simulation: Plants were fertilized with either a 20 mM solution of KNO3, a 20 mM solution of NH4Cl, or demineralized water (control) for 2 days. On the third day, the trees were harvested. Root tips were immediately shock-frozen in liquid nitrogen and used for RNA extraction.
2020-12-14 | E-MTAB-8931 | biostudies-arrayexpress
Project description:The leaf transcriptome of the nickel hyperaccumulator species Psychotria grandis and Psychotria costivenia (Rubiaceae) from Cuba were compared to the closely related non-accumulator Psychotria revoluta, living on Gallery forest on serpentine soil, to identity differentially expressed genes potentially involved in Ni hyperaccumulation.
2019-06-05 | GSE116050 | GEO
Project description:Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen. Both species oxidized the organic matter and accessed the organic nitrogen. The expression of those events was controlled by the availability of glucose and inorganic nitrogen. Despite those similarities, the decomposition mechanisms, including the type of genes involved as well as the patterns of their expression, differed markedly between the two species. Our results suggest that in agreement with their diverse evolutionary origins, ectomycorrhizal fungi use different decomposition mechanisms to access organic nitrogen entrapped in soil organic matter. The timing and magnitude of the expression of the decomposition activity can be controlled by the below-ground nitrogen quality and the above-ground carbon supply.
2018-11-30 | GSE110485 | GEO
Project description:The leaf transcriptome of the nickel hyperaccumulator species Homalium kanaliense (Salicaceae) endemic from New caledonia were compared to the closely related non-accumulator Homalium betulifolium, living on Gallery forest or maquis on serpentine soil, to identity differentially expressed genes potentially involved in Ni hyperaccumulation.
2019-06-05 | GSE116052 | GEO