Impact of a heterotroph, Alteromonas MIT1002, on the transcriptome of Prochlorococcus NATL2A
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ABSTRACT:
PROVIDER: PRJNA297192 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2531970_1.fastq.gz | Fastqsanger.gz | |||
| SRR2531970_2.fastq.gz | Fastqsanger.gz | |||
| SRR2531980_1.fastq.gz | Fastqsanger.gz | |||
| SRR2531980_2.fastq.gz | Fastqsanger.gz | |||
| SRR2531990_1.fastq.gz | Fastqsanger.gz |
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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 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:We examine how the transcriptome of Prochlorococcus strain NATL2A changes in response to extended light deprivation, both when grown alone and in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002.
2018-05-01 | GSE93197 | GEO
Project description:Emergence of metabolic coupling to the heterotroph Alteromonas promotes dark survival in Prochlorococcus
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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:Due to their potential impact on ecosystems and biogeochemistry, microbial interactions, such as those between phytoplankton and bacteria, have been studied intensively using specific model organisms. Yet, to what extent interactions differ between closely related organisms, or how these interactions change over time, or culture conditions, remains unclear. Here, we characterize the interactions between five strains each of two globally abundant marine microorganisms, Prochlorococcus (phototroph) and Alteromonas (heterotroph), from the first encounter between individual strains and over more than a year of repeated cycles of exponential growth and long-term nitrogen starvation. Prochlorococcus-Alteromonas interactions had little effect on traditional growth parameters such as Prochlorococcus growth rate, maximal fluorescence, or lag phase, affecting primarily the dynamics of culture decline, which we interpret as representing cell mortality and lysis. The shape of the Prochlorococcus decline curve and the carrying capacity of the co-cultures were determined by the phototroph and not the heterotroph strains involved. Comparing various mathematical models of culture mortality suggests that Prochlorococcus death rate increases over time in mono-cultures but decreases in co-cultures, with cells potentially becoming more resistant to stress. Our results demonstrate intra-species differences in ecologically relevant co-culture outcomes. These include the recycling efficiency of N and whether the interactions are mutually synergistic or competitive. They also highlight the information-rich growth and death curves as a useful readout of the interaction phenotype.
| S-EPMC9860064 | biostudies-literature
Project description:Microbial interactions, whether direct or indirect, profoundly affect the physiology of individual cells and ultimately have the potential to shape the biogeochemistry of the Earth. For example, the growth of Prochlorococcus, the numerically dominant cyanobacterium in the oceans, can be improved by the activity of co-occurring heterotrophs. This effect has been largely attributed to the role of heterotrophs in detoxifying reactive oxygen species that Prochlorococcus, which lacks catalase, cannot. Here, we explore this phenomenon further by examining how the entire transcriptome of Prochlorococcus NATL2A changes in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002, with which it was co-cultured for years, separated and then reunited. Significant changes in the Prochlorococcus transcriptome were evident within 6 h of initiating co-culture, with groups of transcripts changing in different temporal waves. Many transcriptional changes persisted throughout the 48 h experiment, suggesting that the presence of the heterotroph affected a stable shift in Prochlorococcus physiology. These initial transcriptome changes largely corresponded to reduced stress conditions for Prochlorococcus, as inferred from the depletion of transcripts encoding DNA repair enzymes and many members of the 'high light inducible' family of stress-response proteins. Later, notable changes were seen in transcripts encoding components of the photosynthetic apparatus (particularly, an increase in PSI subunits and chlorophyll synthesis enzymes), ribosomal proteins and biosynthetic enzymes, suggesting that the introduction of the heterotroph may have induced increased production of reduced carbon compounds for export. Changes in secretion-related proteins and transporters also highlight the potential for metabolic exchange between the two strains.
| S-EPMC5148202 | biostudies-literature
Project description:Microbes evolve within complex ecological communities where biotic interactions impact both individual cells and the environment as a whole. Here we examine how cellular regulation in the marine cyanobacterium Prochlorococcus is influenced by a heterotrophic bacterium, Alteromonas macleodii, under different light conditions. We monitored the transcriptome of Prochlorococcus, grown either alone or in coculture, across a diel light:dark cycle and under the stress of extended darkness-a condition that cells would experience when mixed below the ocean's euphotic zone. More Prochlorococcus transcripts exhibited 24-h periodic oscillations in coculture than in pure culture, both over the normal diel cycle and after the shift to extended darkness. This demonstrates that biotic interactions, and not just light, can affect timing mechanisms in Prochlorococcus, which lacks a self-sustaining circadian oscillator. The transcriptomes of replicate pure cultures of Prochlorococcus lost their synchrony within 5 h of extended darkness and reflected changes in stress responses and metabolic functions consistent with growth cessation. In contrast, when grown with Alteromonas, replicate Prochlorococcus transcriptomes tracked each other for at least 13 h in the dark and showed signs of continued biosynthetic and metabolic activity. The transcriptome patterns suggest that the heterotroph may be providing energy or essential biosynthetic substrates to Prochlorococcus in the form of organic compounds, sustaining this autotroph when it is deprived of solar energy. Our findings reveal conditions where mixotrophic metabolism may benefit marine cyanobacteria and highlight new impacts of community interactions on basic Prochlorococcus cellular processes. IMPORTANCEProchlorococcus is the most abundant photosynthetic organism on the planet. These cells play a central role in the physiology of surrounding heterotrophs by supplying them with fixed organic carbon. It is becoming increasingly clear, however, that interactions with heterotrophs can affect autotrophs as well. Here we show that such interactions have a marked impact on the response of Prochlorococcus to the stress of extended periods of darkness, as reflected in transcriptional dynamics. These data suggest that diel transcriptional rhythms within Prochlorococcus, which are generally considered to be strictly under the control of light quantity, quality, and timing, can also be influenced by biotic interactions. Together, these findings provide new insights into the importance of microbial interactions on Prochlorococcus physiology and reveal conditions where heterotroph-derived compounds may support autotrophs-contrary to the canonical autotroph-to-heterotroph trophic paradigm.
| S-EPMC5974335 | biostudies-literature
Project description:We report the full transcriptome of T4-like cyanophage P-HM2 infecting Prochlorococcus in light and dark
2016-03-18 | GSE79359 | GEO