Horizontal transfer in the Massane Forest
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ABSTRACT:
PROVIDER: PRJEB49182 | ENA |
REPOSITORIES: ENA
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Project description:Plasmid fitness is directed by two orthogonal processes—vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical E. coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.
2022-12-23 | GSE219270 | GEO
Project description:Climate change forecasts increase the susceptibility of forest due to longer drier seasons. The adaptive management protocols have highlighted the reduction of the forest densification to improve their vulnerability to extreme climate events (i.g. drought). One of this sensitive woody species to climate change is the Abies pinsapo, a relic conifer tree endemic from the southern Spain. Previous works have shown changes in their trends because of the climate change action, being carried out experimental thinning management in their lowest distribution limit, in Sierra de las Nieves Natural Park (Malaga). Our objective is to evaluate the water improvements of thinned trees in terms of light availability by means of a shading treatment in those thinned trees. To do that we have evaluated the synergic effect of ecophysiology, metabolomics and transcriptomics in control, thinning and thinning+shading plots in wet and dry seasons for two years. The results showed strong differences between summer and spring seasons at the three studied levels. The water deficit shows a greater influence than light exposure in the ecophysiology and metabolomics tree response. And the transcriptomics suggested an improvement of thinned trees when light exposure was reduced. Our results support the necessity of adaptive forest management in order to improve the conservation status of A. pinsapo forest. The combination of different levels of tree response is paramount to understand and predict the tree physiology under water and light stress conditions.
2022-07-17 | GSE208073 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE15686: Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation (I) GSE15691: Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation (I) GSE15692: Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation (II) GSE15693: Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation (II) Refer to individual Series
2010-07-07 | E-GEOD-15803 | biostudies-arrayexpress
Project description:We report the discovery of a beta-glucosidase gene (Pgβglu-1) whose expression underpins natural resistance to a major forest pest, the spruce budworm (SBW) in white spruce (Picea glauca (Voss.) Moench). We performed a microarray experiment to compare resistant (R) and non-resistant (N-R) trees. Pgβglu-1 transcripts levels uniquely were up to 1000 times higher in phenotypically resistant trees and correlated with accumulation of acetophenones compounds that reduce SBW development. These resistance traits were heritable, temporally correlated with the emergence of the most damaging larval stages and were highly variable in the natural population across a large geographic area. The recombinant gene product specifically catalyzed the release of biologically active acetophenones from their glucoside precursors. SBW outbreaks have become more frequent and intense; therefore, the phenotypic diversity resulting from variation in Pgβglu-1 expression may be a key for the adaptability of spruce populations.
2014-05-06 | GSE57301 | GEO
Project description:We report the discovery of a beta-glucosidase gene (PgM-NM-2glu-1) whose expression underpins natural resistance to a major forest pest, the spruce budworm (SBW) in white spruce (Picea glauca (Voss.) Moench). We performed a microarray experiment to compare resistant (R) and non-resistant (N-R) trees. PgM-NM-2glu-1 transcripts levels uniquely were up to 1000 times higher in phenotypically resistant trees and correlated with accumulation of acetophenones compounds that reduce SBW development. These resistance traits were heritable, temporally correlated with the emergence of the most damaging larval stages and were highly variable in the natural population across a large geographic area. The recombinant gene product specifically catalyzed the release of biologically active acetophenones from their glucoside precursors. SBW outbreaks have become more frequent and intense; therefore, the phenotypic diversity resulting from variation in PgM-NM-2glu-1 expression may be a key for the adaptability of spruce populations. Transcriptome profiling was carried out with needles from 7 resistant and 7 non-resistant trees (harvested on June 17th, 2010), and 3 samples per tree (n=42) with a custom microarray developed for spruce species and comprising oligonucleotide probes for 23,853 unique P. glauca gene sequences (Raherison et al., 2012).
2014-05-06 | E-GEOD-57301 | biostudies-arrayexpress
Project description:ARDS-mediated lung transcriptome alterations were identified in forest musk deer. Moreover, multiple transcripts/genes involved in lung development and lung defense responses to bacteria/viruses/fungi in ARDS were filtered out in forest musk deer.
2022-10-19 | GSE191259 | GEO
Project description:Evidence shows that bacteria contribute actively to the decomposition of cellulose and hemicellulose in forest soil; however, their role in this process is still unclear. Here we performed the screening and identification of bacteria showing potential cellulolytic activity from litter and organic soil of a temperate oak forest. The genomes of three cellulolytic isolates previously described as abundant in this ecosystem were sequenced and their proteomes were characterized during the growth on plant biomass and on microcrystalline cellulose. Pedobacter and Mucilaginibacter showed complex enzymatic systems containing highly diverse carbohydrate-active enzymes for the degradation of cellulose and hemicellulose, which were functionally redundant for endoglucanases, -glucosidases, endoxylanases, -xylosidases, mannosidases and carbohydrate-binding modules. Luteibacter did not express any glycosyl hydrolases traditionally recognized as cellulases. Instead, cellulose decomposition was likely performed by an expressed GH23 family protein containing a cellulose-binding domain. Interestingly, the presence of plant lignocellulose as well as crystalline cellulose both trigger the production of a wide set of hydrolytic proteins including cellulases, hemicellulases and other glycosyl hydrolases. Our findings highlight the extensive and unexplored structural diversity of enzymatic systems in cellulolytic soil bacteria and indicate the roles of multiple abundant bacterial taxa in the decomposition of cellulose and other plant polysaccharides.
2016-05-02 | PXD003844 | Pride
Project description:System-level response to long-term irrigation in a drought-stressed pine forest
| PRJEB14824 | ENA
Project description:The Chinese forest musk deer (FMD; Moschus berezovskii) is an endangered artiodactyl mammal. Musk secreted by the musk gland of male FMD has extremely high economic and medicinal value. At present, little is known about the development of musk glands and the molecular mechanism of musk secretion. In the present research, using snRNA-seq and snATAC-seq association analysis performed on musk glands of forest musk deer, coupled with several bioinformatics analyses, the dynamic transcriptional cell atlas of musk gland development was revealed and the genes and transcription factors affecting musk secretion were determined. Based on uniform manifold approximation and projection (UMAP) analysis, we identified 12 cell types from musk glands, including two different acinar cells (clusters 0 and 10). In addition, the expression of core target genes and core transcription factors was verified by fluorescence in situ hybridization and immunohistochemistry. Combined with weighted gene co-expression network analysis (WGCNA), we obtained a deeper biological understanding of the relationship between core transcription factors, differentially expressed genes and musk secretion related pathways. This study lays a foundation for improving musk yield and meeting market demand. In the meantime, it also contributes to reducing the hunting and poaching of wild forest musk deer, protecting forest musk deer resources and maintaining ecological balance.
2023-08-31 | GSE182087 | GEO
Project description:Members of the fungal genus Armillaria are necrotrophic pathogens with efficient plant biomass-degrading strategies. Armillaria species are some of the largest terrestrial organisms on Earth that cause tremendous losses in diverse ecosystems. Despite their global importance, how Armillaria evolved pathogenicity in a clade of dominantly non-pathogenic wood-degraders (Agaricales) remains elusive. Here, using new genomic data, we show that Armillaria species, in addition to widespread gene duplications and de novo gene origins, appear to have acquired at least 1025 genes via 124 horizontal gene transfer (HGT) events, primarily from Ascomycota donors. Functional and expression data suggest that HGT might have affected plant biomass-degrading and virulence abilities of Armillaria, two pivotal traits in their lifestyle. HGT provides an explanation for their soft-rot like biomass degrading strategy too, which is markedly different from the primarily white rot decay mechanism of related species. Combined multi-species expression data revealed putative virulence factors, extensive regulation of horizontally acquired and wood-decay related genes as well as novel noserved pathogenicity-induced small secreted proteins (PiSSPs). Two PiSSPs induced necrosis in live plants, suggesting they are potential virulence effectors conserved across Armillaria. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits, such as plant biomass degradation and pathogenicityin one of the most influential fungal pathogens of temperate forest ecosystems.
2023-06-23 | GSE235456 | GEO