CBY
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB34870 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3589654_1.fastq.gz | Fastqsanger.gz | |||
| ERR3589654_2.fastq.gz | Fastqsanger.gz | |||
| ERR3589655_1.fastq.gz | Fastqsanger.gz | |||
| ERR3589656_1.fastq.gz | Fastqsanger.gz | |||
| ERR3589657_1.fastq.gz | Fastqsanger.gz |
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Project description:DNA oligonucleotide microarrays were designed with 307 probes for 96 internal transcribed spacer (ITS1, located between 18S and 26S rRNA genes) sequences of known species and strains from the genus Pseudo-nitzschia (Bacillariophyceae). In addition, microarrays also carried 1893 probes targeting ITS1 aequences of marine Crenarchaeota and Alphaproteobacteria of SAR11 clade. In order to assign microarray profiles to Pseudo-nitzschia ribotypes and species and to 'train' the data analysis system, we grew cultures of Pseudo-nitzschia in the laboratory with identities confirmed through rDNA sequence analysis. In total, 9 cultures and 35 environmental water samples were hybridized to microarrays, in some cases, in duplicate or triplicate. Analysis of microarray data allowed us to identify and map Pseudo-nitzschia spp. in the coastal waters along Washington and Oregon coast of the Eastern Pacific Ocean, and to observe seasonal changes in diatom community composition. Total DNA was isolated from 9 Pseudo-nitzschia laboratory cultures and 35 environmental water samples collected during 7 field campaigns in 2007-2009. The environmental samples were collected at distances of 5 to 55 km from the coast, along the following transects in the Pacific Ocean covering over 300 km of the coastline: La Push (LP), Grays Harbor (GH), Columbia River (CR), and Newport Hydroline (NH). The DNA samples were subjected to PCR amplification with the primers specific for ITS1 sequences. The resultant biotin-labeled target samples were analyzed using microarray hybridization with the CombiMatrix ElectraSense 4X2K format. Out of 44 analyzed samples, 40, 2, and 2 were used for single, duplicate and triplicate hybridizations, respectively.
2012-05-31 | E-GEOD-27141 | biostudies-arrayexpress
Project description:DNA oligonucleotide microarrays were designed with 307 probes for 96 internal transcribed spacer (ITS1, located between 18S and 26S rRNA genes) sequences of known species and strains from the genus Pseudo-nitzschia (Bacillariophyceae). In addition, microarrays also carried 1893 probes targeting ITS1 aequences of marine Crenarchaeota and Alphaproteobacteria of SAR11 clade. In order to assign microarray profiles to Pseudo-nitzschia ribotypes and species and to 'train' the data analysis system, we grew cultures of Pseudo-nitzschia in the laboratory with identities confirmed through rDNA sequence analysis. In total, 9 cultures and 35 environmental water samples were hybridized to microarrays, in some cases, in duplicate or triplicate. Analysis of microarray data allowed us to identify and map Pseudo-nitzschia spp. in the coastal waters along Washington and Oregon coast of the Eastern Pacific Ocean, and to observe seasonal changes in diatom community composition.
2012-06-01 | GSE27141 | GEO
Project description:Although N2 fixation can occur in free-living cyanobacteria, the unicellular endosymbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is considered to be a dominant N2-fixing species in marine ecosystems. Four UCYN-A sublineages are known from partial nitrogenase (nifH) gene sequences. However, few studies have investigated their habitat preferences and regulation by their respective hosts in open-ocean versus coastal environments. Here, we compared UCYN-A transcriptomes from oligotrophic open-ocean versus nutrient-rich coastal waters. UCYN-A1 metabolism was more impacted by habitat changes than UCYN-A2. However, across habitats and sublineages genes for nitrogen fixation and energy production were highly transcribed. Curiously these genes, critical to the symbiosis for the exchange of fixed nitrogen for fixed carbon, maintained the same schedule of diel expression across habitats and UCYN-A sublineages, including UCYN-A3 in the open-ocean transcriptomes. Our results undersore the importance of nitrogen fixation in UCYN-A symbioses across habitats, with consequences for community interaction and global biogeochemical cycles.
2023-02-23 | GSE206403 | GEO
Project description:A high-density oligonucleotide microarray that targets functional genes in marine microbial community was designed as a result of a multi-institutional effort. The design is based on nucleotide sequence data obtained with metagenomics and metatranscriptomics. The chip targets ~20000 gene sequences represented by 145 gene categories relevant to microbial metabolism in the open ocean and coastal environments. The three domains of life and also viruses are represented on the chip. Using this microarray we were able to compare the functional responses of microbial communities to iron and phosphate enrichments in samples from the North Pacific Subtropical Gyre. The response was attributed to individual lineages of microorganisms including uncharacterized strains. Transcription of 68% of the gene probes was detected from a variety of microorganisms, and the patterns of gene transcription indicated a relief from iron limitation and transition into nitrogen limitation. When combined with physicochemical descriptions of each system, the use of microarrays can help to develop a comprehensive understanding of the changes in microbially-driven processes. We analyzed three samples amended with phosphate and two sample amended with iron (III) after 48h of incubation
2013-03-07 | E-GEOD-44448 | biostudies-arrayexpress
Project description:The diversity and environmental distribution of the nosZ gene, which encodes the enzyme responsible for the consumption of nitrous oxide, was investigated in marine and terrestrial environments using a functional gene microarray. The microbial communities represented by the nosZ gene probes showed strong biogeographical separation, with communities from surface ocean waters and agricultural soils significantly different from each other and from those in oceanic oxygen minimum zones. Atypical nosZ genes, usually associated with incomplete denitrification pathways, were detected in all the environments, including surface ocean waters. The abundance of nosZ genes, as estimated by quantitative PCR, was highest in the agricultural soils and lowest in surface ocean waters.
2018-10-19 | GSE121473 | GEO
Project description:The absorption of visible light in aquatic environments has led to the common assumption that aquatic organisms sense and adapt to penetrative blue/green light wavelengths, but show little or no response to the more attenuated red/far-red wavelengths. Here we show that two marine diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana, possess a bona fide red/far-red light sensing phytochrome (DPH) that uses biliverdin as a chromophore and displays accentuated red-shifted absorbance peaks compared to other characterized plant and algal phytochromes. Exposure to both red and far-red light causes changes in gene expression in P. tricornutum and the responses to far-red light disappear in DPH knockout cells, demonstrating that P. tricornutum DPH mediates far-red light signaling. The identification of DPH genes in diverse diatom species widely distributed along the water column further emphasizes the ecological significance of far-red light sensing, raising questions about the sources of far-red light. Our analyses indicate that, although far-red wavelengths from sunlight are only detectable at the ocean surface, chlorophyll fluorescence and Raman scattering can generate red/far-red photons in deeper layers. This study opens up novel perspectives on phytochrome-mediated far-red light signaling in the ocean and on the light sensing and adaptive capabilities of marine phototrophs.
2016-05-09 | GSE73915 | GEO
Project description:We isolate the cultivable microbiome of a diatom and show that different bacteria have commensal, antagonistic, or synergistic effects on the diatom. One synergistic bacterium enhances growth of the diatom by production of auxin, a phytohormone. The diatom and its synergistic bacterium appear to use auxin and tryptophan as signaling molecules that drive nutrient exchange. Detection of auxin molecules and biosynthesis gene transcripts in the Pacific Ocean suggests that these interactions are widespread in marine ecosystems.
2015-05-29 | GSE65189 | GEO
Project description:Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity, at the base of marine food webs, is constrained by nutrient availability in the surface ocean, and nutrient advection from deeper waters can fuel photosynthesis. In this study, we compared the transcriptional responses by surface microbial communities after experimental deep water mixing to the transcriptional patterns of in situ microbial communities collected with high-resolution automated sampling during a bloom in the North Pacific Subtropical Gyre. Transcriptional responses were assayed with the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) marine environmental microarray, which targets all three domains of life and viruses. The experiments showed that mixing of deep and surface waters substantially affects the transcription of photosystem and nutrient response genes among photosynthetic taxa within 24 hours, and that there are specific responses associated with the addition of deep water containing particles (organisms and detritus) compared to filtered deep water. In situ gene transcription was most similar to that in surface water experiments with deep water additions, showing that in situ populations were affected by mixing of nutrients at the six sampling sites. Together, these results show the value of targeted metatranscriptomes for assessing the physiological status of complex microbial communities.
2018-09-03 | GSE109218 | GEO
Project description:Marine bacterium isolated from the Pacific Ocean
| PRJNA13902 | ENA
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