MICGEN
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR299248_1.fastq.gz | Fastqsanger.gz | |||
| ERR299248_2.fastq.gz | Fastqsanger.gz | |||
| ERR299249_1.fastq.gz | Fastqsanger.gz | |||
| ERR299249_2.fastq.gz | Fastqsanger.gz |
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Project description:Validating metagenomic growth rate indicators in a coastal marine microbial community
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Project description:Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world’s oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.
2013-03-07 | GSE44448 | GEO
Project description:In estuaries and coastal areas, salinity regimes vary with river discharge, seawater evaporation, morphology of the coastal waterways, and dynamics of marine water mixing. Therefore, microalgae have to respond to salinity variations at various time scales, from daily to annual cycling. They might also adapt to physical alteration that might induce loss of connectivity and enclosure of water bodies. Here we integrate physiological-based assays, morphological plasticity with functional genomics approach to examine the regulatory change that occur during the acclimation to salinity in an estuary diatom, Thalassiosira weissflogii. We found that this diatom respond to salinity (i.e. 21, 28 and 35 psu) with minute adjustments of its physiology (i.e., carbon and silicon metabolisms, pigments concentration and photosynthetic parameters). In contrast after short- (~ 5 generations) or long-term (~ 700 generations) culture at the different salinity we found a large transcriptome reprogramming. With most of the genes being down-regulated in long-term, and only a few genes in common between short and long term experiments.
2018-10-02 | GSE73987 | GEO
Project description:Marine cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity, yet little is known of the transcriptional response of marine Synechococcus to copper shock. Global transcriptional response to two levels of copper shock was assayed in both a coastal and an open ocean strain of marine Synechococcus using whole genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus. The two strains additionally showed a reduction in photosynthetic gene transcripts. Contrastingly, the open ocean strain showed a typical stress response whereas the coastal strain exhibited a more specific oxidative or heavy metal type response. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus may in part be a result of an increased ability to sense and respond in a more specialized manner.
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Project description:Tris(4-chlorophenyl)methane (TCPM) and tris(4-chlorophenyl)methanol (TCPMOH) are two marine pollutants of emerging concern, found in marine mammals and coastal bird populations. Here, we assess the response to these compounds due to developmental (24-100 hourrs post fertilization) exposures in zebrafish embryos
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Project description:Tris(4-chlorophenyl)methane (TCPM) and tris(4-chlorophenyl)methanol (TCPMOH) are two marine pollutants of emerging concern, found in marine mammals and coastal bird populations. Here, we assess the response to these compounds due to acute exposures in zebrafish embryos (from 96-100 hours post fertilization).
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Project description:To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. 14 in the original prototype) across much of the known diversity of cultured and uncultured marine microbes. The target abundances measured by the genome proxy array were highly correlated to pyrosequence-based abundances (linear regression R2 = 0.85-0.91, p<0.0001). Fifty-seven samples from ~4-years in Monterey Bay were examined with the array, spanning the photic zone (0m), the base of the surface mixed layer (30m), and the subphotic zone (200m). A significant portion of the expanded genome proxy array’s targets showed signal (95 out of 268 targets present in ≥ 1 sample). The multi-year community survey showed the consistent presence of a core group of common and abundant targeted taxa at each depth in Monterey Bay, higher variability among shallow than deep samples, and episodic occurrences of more transient marine genotypes. The abundance of the most dominant genotypes peaked after strong episodic upwelling events. The genome-proxy array’s ability to track populations of closely-related genotypes indicated population shifts within several abundant target taxa, with specific populations in some cases clustering by depth or oceanographic season. Although 51 cultivated organisms were targeted (representing 19% of the array) the majority of targets detected and of total target signal (85% and ~92%, respectively) were from uncultivated lineages, often those derived from Monterey Bay. The array provided cost-effective (~$15 per array, for construction and use) insights into the natural history of uncultivated lineages in the wild. To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. 14 in the original prototype) across much of the known diversity of cultured and uncultured marine microbes. The target abundances measured by the genome proxy array were highly correlated to pyrosequence-based abundances (linear regression R2 = 0.85-0.91, p<0.0001). Fifty-seven samples from ~4-years in Monterey Bay were examined with the array, spanning the photic zone (0m), the base of the surface mixed layer (30m), and the subphotic zone (200m). A significant portion of the expanded genome proxy array’s targets showed signal (95 out of 268 targets present in ≥ 1 sample). The multi-year community survey showed the consistent presence of a core group of common and abundant targeted taxa at each depth in Monterey Bay, higher variability among shallow than deep samples, and episodic occurrences of more transient marine genotypes. The abundance of the most dominant genotypes peaked after strong episodic upwelling events. The genome-proxy array’s ability to track populations of closely-related genotypes indicated population shifts within several abundant target taxa, with specific populations in some cases clustering by depth or oceanographic season. Although 51 cultivated organisms were targeted (representing 19% of the array) the majority of targets detected and of total target signal (85% and ~92%, respectively) were from uncultivated lineages, often those derived from Monterey Bay. The array provided cost-effective (~$15 per array, for construction and use) insights into the natural history of uncultivated lineages in the wild.
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