Albacom
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB33361 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3419060_1.fastq.gz | Fastqsanger.gz | |||
| ERR3419060_2.fastq.gz | Fastqsanger.gz | |||
| ERR3419070_1.fastq.gz | Fastqsanger.gz | |||
| ERR3419070_2.fastq.gz | Fastqsanger.gz | |||
| ERR3419080_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 192 |
Similar Datasets
Project description:Unicellular algae, termed phytoplankton, greatly impact the marine environment by serving as the basis of marine food webs and by playing central roles in biogeochemical cycling of elements. The interactions between phytoplankton and heterotrophic bacteria affect the fitness of both partners. It is becoming increasingly understood that metabolic exchange determines the nature of such interactions, but the underlying molecular mechanisms remain underexplored. Here, we investigated the molecular and metabolic basis for the bacterial lifestyle switch, from coexistence to pathogenicity, in Sulfitobacter D7 during interactions with Emiliania huxleyi, a cosmopolitan bloom-forming phytoplankter. The interaction displays two distinct phases: first, there is a coexisting phase in which the alga grows exponentially and the bacterium grows as well. The interaction shifts to pathogenic when the virulence of Sulfitobacter D7 towards E. huxleyi is invoked upon exposure to high concentrations of algal dimethylsulfoniopropionate (DMSP), which occurs when the algae reach stationary growth or when DMSP is applied exogenously to algae in exponential growth. We aimed to unravel the response of Sulfitobacter D7 to the pathogenicity-inducing compound, DMSP, and to different algae-derived infochemicals that affect the lifestyle of the bacterium. We grew Sulfitobacter D7 in conditioned media (CM) derived from algal cultures at the different growth phases, exponential and stationary (Exp-CM and Stat-CM, respectively), in which DMSP concentration is low and high, respectively. This enabled us to separate between different phases of the interaction with E. huxleyi, i.e., Exp-CM representing the coexisting phase, and Stat-CM representing the pathogenic phase. An additional pathogenicity-inducing treatment was Exp-CM supplemented with 100 µM DMSP (herein Exp-CM+DMSP). This condition mimicked co-cultures to which we added DMSP exogenously and thus induced Sulfitobacter D7 pathogenicity, which lead to death of exponentially growing E. huxleyi. In order to identify bacterial genes that are specifically responsive to DMSP, and are not affected by other algae-derived factors, we grew Sulfitobacter D7 in defined minimal medium (MM), lacking algal metabolites, supplemented with 100 µM DMSP (herein MM+DMSP), and examined the transcriptional response. After 24 h of Sulfitobacter D7 growth in all 5 media, triplicates were taken for transcriptomic analysis. Altogether, this experimental design allowed to expand our understanding on the bacterial response to DMSP, algal infochemicals and which of these are essential for coexistence and pathogenicity.
2023-01-17 | GSE193203 | GEO
Project description:Marine phytoplankton are a diverse group of photoautotrophic organisms and key mediators in the global carbon cycle. Phytoplankton physiology and biomass accumulation are closely tied to mixed layer depth, but the intracellular metabolic pathways activated in response to changing mixed layer depths remain unexplored. Here, metatranscriptomics was used to characterize the phytoplankton community response to a mixed layer shallowing from 233 meters to 5 meters over the course of two days during the late spring in the Northwest Atlantic. Most phytoplankton genera downregulated core photosynthesis, carbon storage, and carbon fixation genes as the system transitioned from a deep to a shallow mixed layer and shifted towards catabolism of stored carbon ic pathways supportive of rapid cell growth. In contrast, phytoplankton genera exhibited divergent transcriptional strategies for photosystem light harvesting complex genes during this transition. Active infection, taken as the ratio of virus to host transcripts, increased in the Bacillariophyta (diatom) phylum and decreased in the Chlorophyta (green algae) phylum upon mixed layer shallowing. A conceptual model is proposed to provide ecophysiological context for our findings, in which light limitation during deep mixing induces populations into a transcriptional state which maximizes interrupts the oscillating levels of transcripts related to photosynthesis, carbon storage, and carbon fixation found in shallow mixed layers with relatively higher growth rates. We propose that upon sensing high light levels during mixed layer shallowing, phytoplankton resume diel oscillation of core sets of genes enabling photoprotection, biosynthesis and cell replication. Our findings highlight the shared and unique transcriptional response strategies within phytoplankton communities acclimating to the dynamic light environment associated with transient deep mixing and shallowing events during the annual North Atlantic bloom.
2023-03-22 | GSE208287 | GEO
Project description:To investigate responses to light quality in this eukaryotic phytoplankton species, replicates were incubated for 72 hours in monochromatic light at 4umol photons m-2 s-1. We then performed gene expression profiling analysis using data obtained from RNA-seq of biological replicates in three light quality conditions.
2023-11-29 | GSE221420 | GEO
Project description:Strain N16961 was incubated with crab shell in artificial seawater media for 24 hours. cDNA from 1 ug RNA was labeled with Cy3 (planktonic bacteria) and Cy5 (crab attached bacteria). A growth condition experiment design type is where some part of the growth condition is changed for the purposes of the experiment, examples of growth conditions changed are media, temperature, humidity, light, nutrients. Keywords: growth_condition_design
2005-08-11 | GSE3102 | GEO
Project description:During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. The maternal environment during maturation can influence seed quality. RNA-seq analyses of the embryo and the endosperm of seed matured ex planta under standard or stressful condition (high temperature and/or dim light) will underly how light and temperature and a combination of both have an impact on the molecular mechanisms governing seed quality at harvest.
2020-09-29 | GSE158641 | GEO
Project description:A continuous culture of Bifidobacterium longum NCC2705 was carried out in a 2.5-l reactor (Bioengineering AG, Wald, Switzerland), equipped with a Biospectra control system (Biospectra AG, Schlieren, Switzerland) and containing 2 l of MRS, added of 0.05% cysteine, inoculated with 2 % (v/v) preculture. The temperature was maintained at 37°C and the pH at 6.0 by addition of 5 M NaOH. The culture was stirred constantly at 250 rpm using two rushton type propellers. Anaerobic conditions were maintained by flushing the headspace of the reactor with CO2. After 8 h in batch mode the culture was run in continuous mode at a dilution rate of 0.1 h-1. Fresh medium was added using a peristaltic pump (Alitea, Bioengineering AG, Wald, Switzerland), and fermented broth harvested with a second peristaltic pump (Alitea, Bioengineering AG, Wald, Switzerland) set at a slightly higher flow rate. A stabilization period of 90 h (corresponding to nine reactor volume changes) was operated prior culture monitoring (t=0). Aliquots of 2 ml taken at t=31, 134 and 211 h were centrifuged (4,000 g, 1 min, room temperature) for transcriptomic analysis. Supernatants were discarded and cell pellets snap frozen in liquid nitrogen and stored at -80ºC until RNA-extraction. Keywords: Time course of Bifidobacterium longum in continuous culture
2009-04-30 | GSE14896 | GEO
Project description:The ecological significance of light perception in non-phototrophic bacteria remains largely elusive. In terrestrial environments, diurnal oscillations in light are often temporally coupled to other environmental changes, including increased temperature and evaporation. Here we report that light functions as an anticipatory cue that triggers protective adaptations to tolerate a future rapid loss of environmental water in leaf-associated Pseudomonas syringae pv. syringae (Pss) and other terrestrial pseudomonads. Global transcriptome analyses in Pss showed that light control occurs almost entirely through a bacteriophytochrome photoreceptor that senses red, far-red and blue wavelengths and influences 30% of the Pss genome. Bacteriophytochrome-mediated light control disproportionally upregulates water-stress adaptation functions and confers enhanced fitness when cells encounter light prior to water limitation. These data demonstrate that non-phototrophic bacteria can use light as a cue to mount an adaptive anticipatory response against a physiologically unrelated but ecologically coupled stress.
2023-09-27 | GSE232095 | GEO