Phyllosphere bacteria of 11 tree species
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA705503 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13809700.fastq.gz | Fastqsanger.gz | |||
| SRR13809701.fastq.gz | Fastqsanger.gz | |||
| SRR13809702.fastq.gz | Fastqsanger.gz | |||
| SRR13809703.fastq.gz | Fastqsanger.gz | |||
| SRR13809704.fastq.gz | Fastqsanger.gz |
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Project description:The leaf surface, known as the phylloplane, represents the initial point of contact for plants in their interaction with the aboveground environment. Although prior research has assessed how leaves respond to external pH variations, particularly in the context of acid rain, there remains a limited understanding of the molecular mechanisms through which plants detect, respond to, and mitigate cellular damage. To look at plant responses to external pH changes, we measured the phylloplane pH for five species with variable phylloplane pH that ranged in the dry control. Moreover, we investigated the phylloplane pH in response to three pH treatments (pH 6.5, 4, and 2) and found that plants can modify their phylloplane pH, and this buffering ability is species-specific. Among the species analyzed, only Gossypium displayed a strong buffering ability. For treatments where leaves were exposed to either pH 6.5 or pH 4, Gossypium alkalinized the phylloplane pH slightly higher than the dry control pH. Remarkably, when leaves were exposed to pH 2, Gossypium was able to buffer the pH to 6 within five minutes. Furthermore, our transcriptional analysis indicated that the responses to external pH changes varied among species, highlighting differentially expressed genes associated with calcium (Ca2+) signaling pathways, as well as Ca2+ and H+-ATPases pumps. These findings also suggest that pH stress negatively impacts photosynthesis, and that both wetness and moderate pH shifts may trigger additional abiotic and biotic stress signaling pathways.
2025-11-15 | GSE281272 | GEO
Project description:<p>Plants produce thousands of compounds, collectively called the metabolome, which mediate interactions with other organisms. The metabolome of an individual plant may change according to the number and nature of these interactions. We tested the hypothesis that tree diversity level affects the metabolome of four subtropical tree species in a biodiversity ecosystem-functioning experiment, BEF-China. We postulated that the chemical diversity of leaves, roots and root exudates increases with tree diversity. We expected the strength of this diversity effect to differ among leaf, root and root exudates samples. Considering their role in plant competition, we expected to find the strongest effects in root exudates. In an ecometabolomics approach, roots, root exudates and leaves of four tree species (Cinnamomum camphora, Cyclobalanopsis glauca, Daphniphyllum oldhamii, Schima superba) were sampled from selected plots in BEF-China. Samples were extracted and analysed using Liquid Chromatography-Time of Flight-Mass Spectrometry. The exudate metabolomes were normalized over their non-purgeable organic carbon level. Multivariate analyses were applied to identify the effect of both neighbouring (local) trees and plot diversity on tree metabolomes. The species and sample specific metabolites were assigned to major compound classes using the ClassyFire tool, whereas m/z features related to diversity effects were annotated manually. Individual tree species showed distinct leaf, root and root exudate metabolomes. The main compound class in leaves were the flavonoids, whereas carboxylic acids, prenol lipids and specific alkaloids were most prominent in root exudates and roots. Overall plot diversity had a stronger effect on metabolome profiles than the diversity of local, directly neighbouring trees. Leaf metabolomes responded more often to tree diversity level than exudates, whereas root metabolomes varied the least. We found not overall correlation between metabolite richness or diversity and tree diversity. Synthesis: Classification of metabolites supported initial ecological interpretation of differences among species and organs. Particularly the metabolomes of leaves and root exudates respond to differences in tree diversity. These responses were neither linear nor uniform and individual metabolites showed different dynamics. More controlled interaction experiments are needed to dissect the causes and consequences of the observed shifts in plant metabolomes.</p>
2021-08-09 | MTBLS1968 | MetaboLights
Project description:Preparation of proteins from salt-gland-enriched tissues of mangrove plant is necessary for a systematic study of proteins involved in the plant’s unique desalination mechanism. Extraction of high-quality proteins from the leaves of mangrove tree species, however, is difficult due to the presence of high levels of endogenous phenolic compounds. In our study, preparation of proteins from only a part of the leaf tissues was required, rendering extraction even more challenging. By comparing several extraction methods, we developed a reliable procedure for obtaining sufficient proteins from salt gland-enriched tissues of the mangrove species Avicennia officinalis. Protein extraction was markedly improved using a phenol-based extraction method. Despite the lower protein yield obtained, one-dimensional protein gel profiles with greater resolution could be obtained, with more than twice the number of proteins detected when 1D-LC-MS/MS analyses were compared. Further analysis of proteins that were solely present in each extraction method favoured the phenol-based extraction. Phenol-based extracts contained nearly 10 times more solely-detected proteins than those were detectable in the extracts without using phenol. The protocol established could thus be applied for downstream high-throughput proteomic analyses involving LC-MS/MS or equivalent.
2015-07-17 | PXD001691 | Pride
Project description:BackgroundThe phyllosphere is an important microbial habitat, but our understanding of how plant hosts drive the composition of their associated leaf microbial communities and whether taxonomic associations between plants and phyllosphere microbes represent adaptive matching remains limited. In this study, we quantify bacterial functional diversity in the phyllosphere of 17 tree species in a diverse neotropical forest using metagenomic shotgun sequencing. We ask how hosts drive the functional composition of phyllosphere communities and their turnover across tree species, using host functional traits and phylogeny.ResultsNeotropical tree phyllosphere communities are dominated by functions related to the metabolism of carbohydrates, amino acids, and energy acquisition, along with environmental signalling pathways involved in membrane transport. While most functional variation was observed within communities, there is non-random assembly of microbial functions across host species possessing different leaf traits. Metabolic functions related to biosynthesis and degradation of secondary compounds, along with signal transduction and cell-cell adhesion, were particularly important in driving the match between microbial functions and host traits. These microbial functions were also evolutionarily conserved across the host phylogeny.ConclusionsFunctional profiling based on metagenomic shotgun sequencing offers evidence for the presence of a core functional microbiota across phyllosphere communities of neotropical trees. While functional turnover across phyllosphere communities is relatively small, the association between microbial functions and leaf trait gradients among host species supports a significant role for plant hosts as selective filters on phyllosphere community assembly. This interpretation is supported by the presence of phylogenetic signal for the microbial traits driving inter-community variation across the host phylogeny. Taken together, our results suggest that there is adaptive matching between phyllosphere microbes and their plant hosts. Video abstract.
| S-EPMC7243311 | biostudies-literature
Project description:Annotation of small RNAs from 11 Drosophila species for the purpose of non-coding RNA annotation and comparative genomics assessment.
2017-11-20 | GSE98013 | GEO
Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces.
2013-06-21 | GSE48198 | GEO
Project description:A spectrum dataset with 329 tree leaf samples and a blank control file from Yunnan Province, Southwest China. Collection and extraction was completed in Yang Jie Group
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Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces. We designed transcriptome arrays and investigated which genes had different transcript levels in the phyllosphere of common bean (Phaseolus vulgaris) as compared to agar surfaces. Since water availability is considered an important factor in phyllosphere survival and activity, we included both high and low relative humidity treatments for the phyllosphere-grown cells. In addition, we determined the expression profile under pollutant exposure by the inclusion of two agar surface treatments, i.e. with and without 4-chlorophenol.
2013-06-21 | E-GEOD-48198 | biostudies-arrayexpress
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