Bacteria associated with acute oak decline
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ABSTRACT:
PROVIDER: PRJEB10225 | ENA |
REPOSITORIES: ENA
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Project description:Acute Oak Decline (AOD) is a decline-disease currently spreading in Britain, threatening oak trees. Here, we analyze and compare the proteomes of inner bark tissue sampled from oak stems of trees symptomatic with AOD and non-symptomatic trees.
2018-02-07 | PXD004991 | Pride
Project description:Beetle-bacteria interactions in Acute Oak Decline
| PRJEB69286 | ENA
Project description:The UK's native oak is under serious threat from Acute Oak Decline (AOD). Stem tissue necrosis is a primary symptom of AOD and several bacteria are associated with necrotic lesions. Two members of the lesion pathobiome, Brenneria goodwinii and Gibbsiella quercinecans, have been identified as causative agents of tissue necrosis. However, additional bacteria including Lonsdalea britannica and Rahnella species have been detected in the lesion microbiome, but their role in tissue degradation is unclear. Consequently, information on potential genome-encoded mechanisms for tissue necrosis is critical to understand the role and mechanisms used by bacterial members of the lesion pathobiome in the aetiology of AOD. Here, the whole genomes of bacteria isolated from AOD-affected trees were sequenced, annotated and compared against canonical bacterial phytopathogens and non-pathogenic symbionts. Using orthologous gene inference methods, shared virulence genes that retain the same function were identified. Furthermore, functional annotation of phytopathogenic virulence genes demonstrated that all studied members of the AOD lesion microbiota possessed genes associated with phytopathogens. However, the genome of B. goodwinii was the most characteristic of a necrogenic phytopathogen, corroborating previous pathological and metatranscriptomic studies that implicate it as the key causal agent of AOD lesions. Furthermore, we investigated the genome sequences of other AOD lesion microbiota to understand the potential ability of microbes to cause disease or contribute to pathogenic potential of organisms isolated from this complex pathobiome. The role of these members remains uncertain but some such as G. quercinecans may contribute to tissue necrosis through the release of necrotizing enzymes and may help more dangerous pathogens activate and realize their pathogenic potential or they may contribute as secondary/opportunistic pathogens with the potential to act as accessory species for B. goodwinii. We demonstrate that in combination with ecological data, whole genome sequencing provides key insights into the pathogenic potential of bacterial species whether they be phytopathogens, part-contributors or stimulators of the pathobiome.
| S-EPMC6412055 | biostudies-literature
Project description:Rhizosphere microbiome of cork oak under forest decline disturbance
| PRJEB33831 | ENA
Project description: Not available
| S-EPMC10673434 | biostudies-literature
Project description:The pathological interaction between oak trees and Phytophthora cinnamomi has implications in the cork oak decline observed over the last decades in the Iberian Peninsula. During host colonization, the phytopathogen secretes effector molecules like elicitins to increase disease effectiveness. The objective of this study was to unravel the proteome changes associated to with the cork oak immune response triggered by P. cinnamomi inoculation in a long-term assay, through SWATH-MS quantitative proteomics performed in the oak leaves. Using the Arabidopis thaliana proteome database as a reference, 424 proteins have been confidently quantified in cork oak leaves, of which 80 proteins showed a p-value below 0.05 or a fold-change greater than 2 or less than 0.5 in their levels between control and inoculated samples being considered as altered. The inoculation of cork oak roots with P. cinnamomi increased the levels of proteins associated with protein-DNA complex assembly, lipid oxidation, response to endoplasmic reticulum stress, and pyridine-containing compound metabolic process in the leaves. In opposition, several proteins associated with cellular metabolic compound salvage and monosaccharide catabolic process had significantly decreased abundances. The most significant abundance variations were observed for the Ribulose 1,5-Bisphosphate Carboxylase small subunit (RBCS1A), Heat Shock protein 90-1 (Hsp90-1), Lipoxygenase 2 (LOX2) and Histone superfamily protein H3.3 (A8MRLO/At4G40030) revealing a pertinent role for these proteins in the host-pathogen interaction mechanism. This work represents the first SWATH-MS analysis performed in cork oak plants inoculated with P. cinnamomi and highlights host proteins that have a relevant action in the homeostatic states that emerge from the interaction between the oomycete and the host in the long term and in a distal organ.
2021-01-04 | PXD021455 | Pride
Project description:The transcriptome of Phanerochaete chrysosporium control mycelium was compared to the transcriptome of mycelium grown on oak acetonic extractives containing medium. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Phanerochaete chrysosporium genome sequence version 1. The aim of this study was to determine gene expression changes in Phanerochaete chrysosporium grown on oak extract with a special focus on detoxification systems.
2014-08-13 | GSE54542 | GEO
Project description:The periderm is basic for land plants due to its protective role during radial growth, which is achieved by the polymers deposited in the cell walls. Despite the research on the topic has unravelled the role of several enzymes and transcription factors, many questions remain open, especially those regarding cell development. Here we use the outer bark of cork oak (cork), holm oak (rhytidome), and their natural hybrids’ to further understand the mechanisms underlying periderm development. Cork is an outstanding model as it consists of a thick and very homogeneous periderm produced by a permanent mother-cell layer (phellogen). Conversely, holm oak contains a more heterogeneous bark including several thin periderms mixed with phloem, also known as a rhytidome. The inclusion of hybrid samples showing rhytidome-type and cork-type barks is valuable to approach cork development, allowing an accurate identification of candidate genes and processes. The present study underscores that biotic stress and cell death signalling are enhanced in rhytidome-type barks while lipid metabolism and cell cycle are enriched in cork-type barks. Based on the DEGs most expressed related to development, we highlight that cell division, cell expansion, and cell differentiation could account for the differences found between cork and rhytidome-type barks.
2024-06-12 | GSE227020 | GEO