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Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium [RNA-Seq]

ABSTRACT: Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS), RNA-Seq (i.e. transcriptomics), high-CO2 physiology experiments, and spatiotemporally separated samples isolated in situ (i.e. directly from the ocean) to examine the metabolic potential of genome-wide cytosine (5mC) methylation (i.e. epigenomics), its potential impacts to transcriptional dynamics under both present-day and future ocean acidification conditions, and its biogeographic conservation in the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.

ORGANISM(S): Trichodesmium erythraeum IMS101

PROVIDER: GSE86991 | GEO | 2018/03/01

REPOSITORIES: GEO

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Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium [WGBS]

Project description:Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS), RNA-Seq (i.e. transcriptomics), high-CO2 physiology experiments, and spatiotemporally separated samples isolated in situ (i.e. directly from the ocean) to examine the metabolic potential of genome-wide cytosine (5mC) methylation (i.e. epigenomics), its potential impacts to transcriptional dynamics under both present-day and future ocean acidification conditions, and its biogeographic conservation in the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.

2018-03-01 | GSE86979 | GEO

Long-term epigenomic modifications underlying trait canalization to high CO2 in the biogeochemically-important marine cyanobacterium Trichodesmium [WGBS]

Project description:Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS) and RNA-Seq (i.e. transcriptomics) to examine the long-term epigenomic dynamics of an experimenta evolution study under high CO2 in the marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly change in response to short-term high CO2 exposure, which are then maintained for 4.5 years even after adaptation (i.e. trait canalization). After 7 years of CO2 selection, high-CO2 triggered methylation levels return to ancestral, low-CO2 levels, consistent with genetic assimilation theory and observations in eukaryotic model systems. These data suggest a potential role for m5C methylation in prokaryotic trait canalization and identify genetic assimilation as an evolutionary mechanism of potential biogeochemical importance under global change factors.

2020-08-18 | GSE138174 | GEO

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Project description:The filamentous diazotrophic cyanobacteria Trichodesmium spp. supply fixed nitrogen (N) to the N-depleted oligotrophic oceans where their growth is often limited by the low availability of phosphorus(P) and/or iron. Previous studies have mostly been focused on the effects of ocean acidification on Trichodesmium under nutrient sufficient or iron-limited conditions. Only a few studies have examined the impacts of ocean acidification on Trichodesmium grown at low P concentrations using non-steady-state batch cultures. Here we cultured Trichodesmium using P-limited continuous cultures (chemostat) to mimic steady-state oceanic low P condition, and used comparative NGS-derived Trichodesmium transcriptome profiling (RNA-seq) analysis to find differentially expressed genes and cellular pathways in response to acidification.

2022-10-13 | GSE181428 | GEO

RNA-protein dynamics of high CO2-adapted, iron-phosphorus co-limited Trichodesmium reveals nutrient-limited molecular architecture of a globally significant marine nitrogen fixer in a future ocean

Project description:Our paper presents the results of a study in which we used Illumina RNA-Seq (i.e. transcriptomics) and high-CO2 nutrient limitation experiments to examine transcriptional variation of iron-limited, phosphorus-limited, and iron-phosphorus co-limited cultures following long-term (~7 years) low- (380 µatm CO2) and high-CO2 (750 µatm CO2) selection. Hence, we describe the molecular physiology of the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.

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Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium

Project description:Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium

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Long-term m5C methylome dynamics parallel phenotypic adaptation in the cyanobacterium Trichodesmium [RNA-seq]

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Project description:We present population-level epigenetic variation in Trichodesmium erythraeum IMS101 associated with steady-state Fe-limitation at two different P concentrations on both short (i.e. 2 months) and long timescales (i.e. ~1 year).

2019-12-15 | GSE101083 | GEO

Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-03-01 | GSE86992 | GEO

Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium [WGBS]

Project description:Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium [WGBS]

| PRJNA343176 | ENA

Trichodesmium field metaproteomes

Project description:This project presents field metaproteomics data from Trichodesmium colonies collected from the surface ocean. Most were collected from the tropical and subtropical Atlantic ocean, but there is also data from the long term Bermuda Atlantic Time Series and Hawaii Ocean Time Series. Trichodesmium is a globally important marine microbe and its growth and nitrogen fixation activity is limited by nutrient availability in the surface ocean. This dataset was generated to answer questions about limitations on Trichodesmium's growth and activity in the nature.

2020-05-08 | PXD016225 | Pride

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