Impact of plastic leachates on marine Prochlorococcus strains
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA484717 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7647490.fastq.gz | Fastqsanger.gz | |||
| SRR7647481.fastq.gz | Fastqsanger.gz | |||
| SRR7647491.fastq.gz | Fastqsanger.gz | |||
| SRR7647482.fastq.gz | Fastqsanger.gz | |||
| SRR7647492.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:Examining the impact of short term exposure to HDPE and PVC plastic leachates on gene transcription in Prochlorococcus cultures in vitro
2018-12-01 | GSE118155 | GEO
Project description:Prochlorococcus contributes significantly to ocean primary productivity. The link between primary productivity and iron in specific ocean regions is well established and iron limitation of Prochlorococcus cell division rates in these regions has been shown. However, the extent of ecotypic variation in iron metabolism among Prochlorococcus and the molecular basis for differences is not understood. Here, we examine the growth and transcriptional response of Prochlorococcus strains, MED4 and MIT9313, to changing iron concentrations. During steady state, MIT9313 sustains growth at an order-of-magnitude lower iron concentration than MED4. To explore this difference, we measured the whole-genome transcriptional response of each strain to abrupt iron starvation and rescue. Only four of the 1159 orthologs of MED4 and MIT9313 were differentially expressed in response to iron in both strains. However, in each strain, the expression of over a hundred additional genes changed, many of which are in labile genomic regions, suggesting a role for lateral gene transfer in establishing diversity of iron metabolism among Prochlorococcus. Furthermore, we found that MED4 lacks three genes near the iron-deficiency-induced gene (idiA) that are present and induced by iron stress in MIT9313. These genes are interesting targets for studying the adaptation of natural Prochlorococcus assemblages to local iron conditions as they show more diversity than other genomic regions in environmental metagenomic databases.
2011-01-11 | GSE26533 | GEO
Project description:We examine how the transcriptome of Prochlorococcus strain NATL2A changes in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002. Significant changes in the Prochlorococcus transcriptome were evident within six hours of co-culture, with groups of transcripts changing in different temporal waves. Many transcriptional changes persisted throughout the 48-hour experiment, indicating that the presence of the heterotroph affected a stable shift in Prochlorococcus physiology. These initial transcriptome changes largely correspond to reduced stress conditions within Prochlorococcus, as inferred from decreases in relative abundance for transcripts encoding DNA repair enzymes and many members of the ‘high-light inducible’ family of stress response proteins. Notable changes were also seen in transcripts encoding components of the photosynthetic apparatus (particularly an increase in PSI subunits and chlorophyll synthesis enzymes), ribosomal proteins and biosynthetic enzymes. Changes in secretion-related proteins and transporters also highlight the potential for metabolic exchange between the two strains.
2016-06-10 | GSE73511 | GEO
Project description:We examine how the transcriptome of Prochlorococcus strain NATL2A changes in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002. Significant changes in the Prochlorococcus transcriptome were evident within six hours of co-culture, with groups of transcripts changing in different temporal waves. Many transcriptional changes persisted throughout the 48-hour experiment, indicating that the presence of the heterotroph affected a stable shift in Prochlorococcus physiology. These initial transcriptome changes largely correspond to reduced stress conditions within Prochlorococcus, as inferred from decreases in relative abundance for transcripts encoding DNA repair enzymes and many members of the âhigh-light inducibleâ family of stress response proteins. Notable changes were also seen in transcripts encoding components of the photosynthetic apparatus (particularly an increase in PSI subunits and chlorophyll synthesis enzymes), ribosomal proteins and biosynthetic enzymes. Changes in secretion-related proteins and transporters also highlight the potential for metabolic exchange between the two strains. At each of 7 timepoints, samples from 3 biological replicate co-cultures are compared to 3 biological replicate axenic Prochlorococcus cultures that serve as a control.
2016-06-10 | E-GEOD-73511 | biostudies-arrayexpress
Project description:Prochlorococcus is an obligate marine microorganism which are dominant autotroph in tropical and subtropical central oceans. However, what is the low salinity boundary and how Prochlorococcus would response to low salinity exposure is still unknown. In this study, we first tested the growing salinity range of two Prochlorococcus strains, NATL1A and MED4, and then compared the global transcriptome of their low salinity acclimated cells and cells growing in normal seawater salinity. We found that MED4 could be acclimated in the lowest salinity of 25% and NATL1A could be acclimated in the lowest salinity of 28%. Measurement of the effective quantum yield of PSII photochemistry (Fv/Fm) indicated that both strains were stressed when growing in salinity lower than 34%. The transcriptomic response of NATL1A and MED4 were approximately different, with much more genes having changed transcript abundance in NATL1A than in MED4. To cope with low salinity, NATL1A downregulated the transcript of most genes involved in translation, ribosomal structure and biogenesis, while MED4 upregulated those genes. Moreover, low salinity acclimated NATL1A cells suppressed ATP-producing genes and induced the expression of photosynthesis related genes, while low salinity acclimated MED4 upregulated ATP-producing genes and downregulated photosynthesis related genes. These results indicate that the response to low salinity stress of different Prochlorococcus strains could be distinct. The study provided the first glimpse into the growing salinity range of Prochlorococcus cells and their global gene expression changes due to low salinity stress.
2022-02-02 | GSE195946 | GEO
Project description:Prochlorococcus is found throughout the euphotic zone in the oligotrophic open ocean. Deep mixing and sinking in aggregates or while attached to particles can, however, transport cells below this sunlit zone, depriving them of light for extended periods of time and influencing their circulation via ocean currents. Viability of these cells over extended periods of darkness could shape the ecology and evolution of the Prochlorococcus collective. We have shown that when co-cultured with a heterotrophic microbe and subjected to repeated periods of extended darkness, Prochlorococcus cells develop a heritable dark-tolerant phenotype – through an apparent epigenetic mechanism – such that they survive longer periods of darkness. Here we examine this adaptation at the level of physiology and metabolism in co-cultures of dark-tolerant and parent strains of Prochlorococcus, each grown with the heterotroph Alteromonas under diel light:dark conditions. The relative abundance of Alteromonas is higher in dark-tolerant than parental co-cultures, while dark tolerant Prochlorococcus cells are also larger, contain less chlorophyll, and are less synchronized to the light:dark cycle. Meta-transcriptome analysis of the cultures further suggests that dark-tolerant co-cultures undergo a coupled shift in which Prochlorococcus uses more organic carbon and less photosynthesis, and Alteromonas uses more organic acids and fewer sugars. Collectively, the data suggest that dark adaptation involves a loosening of the coupling between Prochlorococcus metabolism and the light:dark cycle and a strengthening of the coupling between the carbon metabolism of Prochlorococcus and Alteromonas.
2024-04-23 | GSE264347 | GEO
Project description:Plastic pollution is a global threat to marine ecosystems. Plastic litter can leach a variety of substances into marine environments; however, virtually nothing is known regarding how this affects photosynthetic bacteria at the base of the marine food web. To address this, we investigated the effect of plastic leachate exposure on marine Prochlorococcus, widely considered the most abundant photosynthetic organism on Earth and vital contributors to global primary production and carbon cycling. Two strains of Prochlorococcus representing distinct ecotypes were exposed to leachate from common plastic items: high-density polyethylene bags and polyvinyl chloride matting. We show leachate exposure strongly impairs Prochlorococcus in vitro growth and photosynthetic capacity and results in genome-wide transcriptional changes. The strains showed distinct differences in the extent and timing of their response to each leachate. Consequently, plastic leachate exposure could influence marine Prochlorococcus community composition and potentially the broader composition and productivity of ocean phytoplankton communities.
| S-EPMC6517427 | biostudies-literature
Project description:Prochlorococcus is an abundant, cosmopolitan, marine cyanobacterium with ecotypes that vary temporally and spatially across oligotrophic regions of the global ocean. This group of organisms can serve as a model system to understand the accumulation of organic compounds synthesized by primary producers in marine ecosystems. We applied targeted metabolomics to three axenic cultures of strains that span the Prochlorococcus phylogeny: a high-light adapted HLII-clade strain, a low-light adapted LLI-clade strain, and a low-light adapted LLIV-clade strain. Intracellular metabolites were extracted from cells captured in exponential growth and extracellular metabolites were adsorbed, from the same samples, to solid-phase extraction resin. Both pools were quantified using a triple quadrupole mass spectrometer. The resulting data reveal intraspecific differences in metabolites that provide clues about the selective pressures shaping the meta-metabolism of the Prochlorococcus collective, and its interactions with the surrounding microbes that depend on them.
2018-10-23 | MTBLS567 | MetaboLights
Project description:The study aimed to explore the potential of bacterial biodegradation as a solution to the global problem of plastic pollution, specifically targeting polyethylene (PE), one of the most common types of plastic. The goals of the study were to isolate a bacterial strain capable of breaking down PE, identify the key enzymes responsible for the degradation process, and understand the metabolic pathways involved. By investigating these aspects, researchers sought to gain critical insights that could be used to optimize plastic degradation conditions and inform the development of artificial microbial communities for effective bioremediation strategies. This research has significant relevance, as it addresses the pressing need for innovative and sustainable approaches to tackle the ever-growing issue of plastic waste and its impact on the environment.
2024-01-02 | PXD041981 | Pride
Project description:We report the full transcriptome of T4-like cyanophage P-HM2 infecting Prochlorococcus in light and dark
2016-03-18 | GSE79359 | GEO