AAPs rule!
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB41596 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5006050_1.fastq.gz | Fastqsanger.gz | |||
| ERR5006050_2.fastq.gz | Fastqsanger.gz | |||
| ERR5006060_1.fastq.gz | Fastqsanger.gz | |||
| ERR5006060_2.fastq.gz | Fastqsanger.gz | |||
| ERR5006070_1.fastq.gz | Fastqsanger.gz |
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Project description:Large diversity changes among aerobic anoxygenic phototrophs in a freshwater lake
| PRJEB51637 | ENA
Project description:In this study, we provide a time-series analysis of the transcriptional response of Gemmatimonas phototrophica AP64T during the dark-to-light transition under aerobic and semiaerobic conditions. By analysing its transcriptome, focussing especially on PS-related genes, we tested the hypothesis that G. phototrophica might constitute an example of an anoxygenic phototroph on its evolutionary pathway from anaerobic to aerobic life-style.
2024-02-01 | GSE253351 | GEO
Project description:In this study, we provide a time-series analysis of the transcriptional response of Gemmatimonas phototrophica AP64T during the dark-to-light transition under aerobic and semiaerobic conditions. By analysing its transcriptome, focussing especially on PS-related genes, we tested the hypothesis that G. phototrophica might constitute an example of an anoxygenic phototroph on its evolutionary pathway from anaerobic to aerobic life-style.
2024-02-01 | GSE253350 | GEO
Project description:In this study, we provide a time-series analysis of the transcriptional response of Gemmatimonas phototrophica AP64T during the dark-to-light transition under aerobic and semiaerobic conditions. By analysing its transcriptome, focussing especially on PS-related genes, we tested the hypothesis that G. phototrophica might constitute an example of an anoxygenic phototroph on its evolutionary pathway from anaerobic to aerobic life-style.
2024-02-01 | GSE253349 | GEO
Project description:Several species of aerobic anoxygenic phototrophs were identified, and genomes sequenced
| PRJNA798339 | ENA
Project description:Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-C10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium.
2016-08-16 | GSE85617 | GEO
Project description:Bacteria have evolved many strategies to spare energy when nutrients become scarce. One widespread such strategy is facultative phototrophy, which helps heterotrophs supplement their energy supply using light. Our knowledge on the impact that such behaviors have on bacterial fitness and physiology is, however, still limited. Here, we study how a representative of the genus Porphyrobacter, in which aerobic anoxygenic phototrophy is ancestral, responds to different light regimes under nutrient limitation. We show that bacterial survival in stationary phase relies on functional reaction centers and varies depending on the light regime. Under dark‑light alternance, our bacterial model presents a diphasic life history dependent on phototrophy: during dark phases, the cells inhibit DNA replication and part of the population lyses and releases nutrients, while subsequent light phases allow for the recovery and renewed growth of the surviving cells. We correlate these cyclic variations with a pervasive pattern of rhythmic transcription which reflects global changes in diurnal metabolic activity. Finally, we demonstrate that, compared to either a phototrophy null mutant or a bacteriochlorophyll a overproducer, the wild type strain is better adapted to natural environments, where regular dark‑light cycles are interspersed with additional accidental dark episodes. Overall, our results highlight the importance of light‑induced biological rhythms in a new model of aerobic anoxygenic phototroph representative of an ecologically important group of environmental bacteria.
2023-10-12 | GSE245047 | GEO
Project description:Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-CÂ10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium. Samples are 2 sets of biological replicates of a Methylobacter tundripaludum strain 21/22 mutant where the acyl-homoserine lactone (AHL) synthase gene mbaI (T451DRAFT_0796) has been deleted. The mutant strain was grown to log (48 hours) or stationary (68 hours) phase in the absence or presence of the AHL 3-OH-C10-HSL.
2016-08-16 | E-GEOD-85617 | biostudies-arrayexpress
Project description:The underlying adaptations required by anoxygenic phototrophs to oxidize Fe(II), a potential stressor, are not well constrained. We used quantitative proteomics to compare cells of the photoferrotroph Rhodopseudomonas palustris TIE-1 grown photoautotrophically with Fe(II) or H2, and photoheterotrophically with acetate. We observed unique proteome profiles for each condition with differences primarily driven by carbon source. Growth on Fe(II) was characterized by a response typical of iron homeostasis which included an increased abundance of proteins required for metal efflux (particularly copper), and decreased abundance of iron import proteins, including siderophore receptors, with no evidence of further stressors such as oxidative damage. This study suggests that the main challenge facing photoferrotrophs comes from limitations imposed by autotrophic growth and, once this challenge is overcome, iron stress can be mitigated using iron management mechanisms common to diverse bacteria.
2018-06-25 | PXD009629 | Pride