Factory metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA553869 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Phytoplankton community structure and diversity in industrial aquaculture
| PRJNA510476 | ENA
Project description:A functional gene microarray was developed and used to investigate phytoplankton community composition and gene expression in the English Channel. Genes encoding the CO2 fixation enzyme RuBisCO (rbcL) and the nitrate assimilation enzyme nitrate reductase (NR) representing several major groups of phytoplankton were included as oligonucleotide probes on the 'phytoarray'. Five major groups of eukaryotic phytoplankton that possess the Type 1D rbcL gene were detected, both in terms of presence (DNA) and activity (rbcL gene expression). Changes in relative signal intensity among the Type 1D rbcL probes indicated a shift from diatom dominance in the spring bloom to dominance by haptophytes and flagellates later in the summer. Because of the limitations of a smaller database, NR probes detected fewer groups, but due to the greater diversity among known NR sequences, NR probes provided higher phylogenetic resolution than did rbcL probes, and identified two uncultivated diatom phylotypes as the most abundant (DNA) and active (NR gene expression) in field samples. Unidentified chlorophytes and the diatom Phaeodactylum tricornutum were detected at both the DNA and cDNA (gene expression) levels. The reproducibility of the array was evaluated in several ways and future directions for further improvement of probe development and sensitivity are outlined. The phytoarray provides a relatively high resolution, high throughput approach to assessing phytoplankton community composition in marine environments. Keywords: seawater natural assemblages, functional gene expression Two functional genes, nitrate reductase and RuBisCO, 4 - 8 replicate features per array
2010-06-19 | E-GEOD-12742 | biostudies-arrayexpress
Project description:The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species’ abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.
2017-05-24 | GSE99220 | GEO
Project description:A functional gene microarray was developed and used to investigate phytoplankton community composition and gene expression in the English Channel. Genes encoding the CO2 fixation enzyme RuBisCO (rbcL) and the nitrate assimilation enzyme nitrate reductase (NR) representing several major groups of phytoplankton were included as oligonucleotide probes on the 'phytoarray'. Five major groups of eukaryotic phytoplankton that possess the Type 1D rbcL gene were detected, both in terms of presence (DNA) and activity (rbcL gene expression). Changes in relative signal intensity among the Type 1D rbcL probes indicated a shift from diatom dominance in the spring bloom to dominance by haptophytes and flagellates later in the summer. Because of the limitations of a smaller database, NR probes detected fewer groups, but due to the greater diversity among known NR sequences, NR probes provided higher phylogenetic resolution than did rbcL probes, and identified two uncultivated diatom phylotypes as the most abundant (DNA) and active (NR gene expression) in field samples. Unidentified chlorophytes and the diatom Phaeodactylum tricornutum were detected at both the DNA and cDNA (gene expression) levels. The reproducibility of the array was evaluated in several ways and future directions for further improvement of probe development and sensitivity are outlined. The phytoarray provides a relatively high resolution, high throughput approach to assessing phytoplankton community composition in marine environments. Keywords: seawater natural assemblages, functional gene expression
2008-09-12 | GSE12742 | GEO
Project description:Marine phytoplankton are a diverse group of photoautotrophic organisms and key mediators in the global carbon cycle. Phytoplankton physiology and biomass accumulation are closely tied to mixed layer depth, but the intracellular metabolic pathways activated in response to changing mixed layer depths remain unexplored. Here, metatranscriptomics was used to characterize the phytoplankton community response to a mixed layer shallowing from 233 meters to 5 meters over the course of two days during the late spring in the Northwest Atlantic. Most phytoplankton genera downregulated core photosynthesis, carbon storage, and carbon fixation genes as the system transitioned from a deep to a shallow mixed layer and shifted towards catabolism of stored carbon ic pathways supportive of rapid cell growth. In contrast, phytoplankton genera exhibited divergent transcriptional strategies for photosystem light harvesting complex genes during this transition. Active infection, taken as the ratio of virus to host transcripts, increased in the Bacillariophyta (diatom) phylum and decreased in the Chlorophyta (green algae) phylum upon mixed layer shallowing. A conceptual model is proposed to provide ecophysiological context for our findings, in which light limitation during deep mixing induces populations into a transcriptional state which maximizes interrupts the oscillating levels of transcripts related to photosynthesis, carbon storage, and carbon fixation found in shallow mixed layers with relatively higher growth rates. We propose that upon sensing high light levels during mixed layer shallowing, phytoplankton resume diel oscillation of core sets of genes enabling photoprotection, biosynthesis and cell replication. Our findings highlight the shared and unique transcriptional response strategies within phytoplankton communities acclimating to the dynamic light environment associated with transient deep mixing and shallowing events during the annual North Atlantic bloom.
2023-03-22 | GSE208287 | GEO
Project description:Global warming has shifted climate zones poleward or upward. However, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate).Soils were characterized for geochemistry, Illumina sequencing was used to determine microbial taxonomic communities and GeoChips 5.0 were used to determine microbial functional genes.
2017-01-10 | GSE92233 | GEO
Project description:Pilot Drug Factory Microbiome Project: Machine inner and outer parts
| PRJNA391006 | ENA
Project description:fungal community succession during pomegranate wine fermentation
| PRJDB9138 | ENA
Project description:bacterial community succession over decomposition in China
| PRJNA295335 | ENA