Ontology highlight
ABSTRACT:
PROVIDER: PRJNA917192 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23006800_1.fastq.gz | Fastqsanger.gz | |||
| SRR23006800_2.fastq.gz | Fastqsanger.gz | |||
| SRR23006801_1.fastq.gz | Fastqsanger.gz | |||
| SRR23006801_2.fastq.gz | Fastqsanger.gz | |||
| SRR23006802_1.fastq.gz | Fastqsanger.gz |
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Project description:The spring bloom in the North Atlantic develops over a few weeks in response to the physical stabilization of the nutrient replete water column and is one of the biggest biological signals on earth. The composition of the phytoplankton assemblage during the spring bloom of 2008 was evaluated, using a microarray, on the basis of functional genes that encode key enzymes in nitrogen and carbon assimilation in eukaryotic and prokaryotic phytoplankton. Oligonucleotide archetype probes representing RuBisCO, nitrate reductase and nitrate transporter genes from major phytoplankton classes detected a diverse assemblage. For RuBisCO, the archetypes with strongest signals represented known phytoplankton groups, but for the nitrate related genes, the major signals were not closely related to any known phytoplankton sequences. Most of the assemblage's components exhibited consistent temporal/spatial patterns. Yet, the strongest archetype signals often showed quite different patterns, indicating different ecological responses by the main players. The most abundant phytoplankton genera identified previously by microscopy, however, were not well represented on the microarray. The lack of sequence data for well-studied species, and the inability to identify organisms associated with functional gene sequences in the environment, still limits our understanding of phytoplankton ecology even in this relatively well-studied system.
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Project description:Seasonal changes in nitrogen assimilation have been studied in the western English Channel by sampling at approximately weekly intervals for 12 months. Nitrate concentrations showed strong seasonal variations. Available nitrogen in the winter was dominated by nitrate but this was close to limit of detection from May to September, after the spring phytoplankton bloom. 15N uptake experiments showed that nitrate was the nitrogen source for the spring phytoplankton bloom but regenerated nitrogen supported phytoplankton productivity throughout the summer. The average annual f ratio was 0.35, which demonstrated the importance of ammonia regeneration in this dynamic temperate region. Nitrogen uptake rate measurements were related to the phytoplankton responsible by assessing the relative abundance of nitrate reductase (NR) genes and the expression of NR among eukaryotic phytoplankton. Strong signals were detected from NR sequences that are not associated with known phylotypes or cultures. NR sequences from the diatom Phaeodactylum tricornutum were highly represented in gene abundance and expression, and were significantly correlated with f ratio. The results demonstrate that analysis of functional genes provides additional information, and may be able to give better indications of which phytoplankton species are responsible for the observed seasonal changes in f ratio than microscopic phytoplankton identification.
2011-03-17 | GSE27998 | GEO
Project description:Seasonal changes in nitrogen assimilation have been studied in the western English Channel by sampling at approximately weekly intervals for 12 months. Nitrate concentrations showed strong seasonal variations. Available nitrogen in the winter was dominated by nitrate but this was close to limit of detection from May to September, after the spring phytoplankton bloom. 15N uptake experiments showed that nitrate was the nitrogen source for the spring phytoplankton bloom but regenerated nitrogen supported phytoplankton productivity throughout the summer. The average annual f ratio was 0.35, which demonstrated the importance of ammonia regeneration in this dynamic temperate region. Nitrogen uptake rate measurements were related to the phytoplankton responsible by assessing the relative abundance of nitrate reductase (NR) genes and the expression of NR among eukaryotic phytoplankton. Strong signals were detected from NR sequences that are not associated with known phylotypes or cultures. NR sequences from the diatom Phaeodactylum tricornutum were highly represented in gene abundance and expression, and were significantly correlated with f ratio. The results demonstrate that analysis of functional genes provides additional information, and may be able to give better indications of which phytoplankton species are responsible for the observed seasonal changes in f ratio than microscopic phytoplankton identification. NR gene diversity from seawater (two replicates of 16 blocks per array, 8 replicate features per probe, duplicate arrays for some samples) The arrays contain three sets of probes for different applications (rbcL and nitrate reductase (NR) from phytoplankton, and amoA from ammonia oxidizing bacteria). The paper to which this submission relates, and the experiments reported in it, used only the NR probe set.
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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.
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