Summer storms boost algal blooms
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PROVIDER: PRJEB39507 | ENA |
REPOSITORIES: ENA
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Project description:Lytic viruses have been implicated in the massive cellular lysis observed during algal blooms, through which they assume a prominent role in oceanic carbon and nutrient flows. Despite their impact on biogeochemical cycling, the transcriptional dynamics of these important oceanic events is still poorly understood. Here, we employ an oligonucleotide microarray to monitor host (Emiliania huxleyi) and virus (coccolithovirus) transcriptomic features during the course of E. huxleyi blooms induced in seawater-based mesocosm enclosures. Host bloom development and subsequent coccolithovirus infection was associated with a major shift in transcriptional profile. In addition to the expected metabolic requirements typically associated with viral infection (amino acid and nucleotide metabolism, as well as transcription- and replication-associated functions), the results strongly suggest that the manipulation of lipid metabolism plays a fundamental role during host-virus interaction. The results herein reveal the scale, so far massively underestimated, of the transcriptional domination that occurs during coccolithovirus infection in the natural environment.
2011-11-22 | GSE24341 | GEO
Project description:Lytic viruses have been implicated in the massive cellular lysis observed during algal blooms, through which they assume a prominent role in oceanic carbon and nutrient flows. Despite their impact on biogeochemical cycling, the transcriptional dynamics of these important oceanic events is still poorly understood. Here, we employ an oligonucleotide microarray to monitor host (Emiliania huxleyi) and virus (coccolithovirus) transcriptomic features during the course of E. huxleyi blooms induced in seawater-based mesocosm enclosures. Host bloom development and subsequent coccolithovirus infection was associated with a major shift in transcriptional profile. In addition to the expected metabolic requirements typically associated with viral infection (amino acid and nucleotide metabolism, as well as transcription- and replication-associated functions), the results strongly suggest that the manipulation of lipid metabolism plays a fundamental role during host-virus interaction. The results herein reveal the scale, so far massively underestimated, of the transcriptional domination that occurs during coccolithovirus infection in the natural environment. Six mesocosm enclosures were placed in the Raunefjorden (Western Norway coast) and filled with natural community water (in June 2008). Nutrient enrichment was applied in order to trigger the development of E. huxleyi blooms. The major transcriptomic features of those blooms and consequent viral infections were monitered through the use of an oligo microarray containing a total of 3571 gene probes; 2271 (63.6%) matching E. huxleyi ESTs, and 1300 (36.4%) matching EhV-86 and EhV-163 genomic sequences. Each microarray contains 5 technical replicates. Sampling of total RNA present in 2L of water (from each enclosure) was performed once a day from day 8 to day 16. For enclosures 2 and 3 other sampling points were taken, covering the complete dial-cycle (6h,12h,18h, and 24h).
2011-11-22 | E-GEOD-24341 | biostudies-arrayexpress
Project description:<p>Algal blooms are hotspots of primary production in the ocean, forming the basis of the marine food web and fueling the dissolved organic matter (DOM) pool. Marine viruses are key players in controlling algal bloom demise, thereby diverting algal biomass from higher trophic levels to the DOM pool, a process termed the ‘viral shunt’. To decode the metabolic footprint of the ‘viral shunt’ in the marine environment, we induced a bloom of <em>Emiliania huxleyi</em> and followed its succession using an untargeted exometabolomics approach. Here, we show that algal bloom succession induces dynamic changes in the exometabolic landscape. We discovered a set of novel chlorine-iodine-containing metabolites that were induced by viral infection and released during bloom demise. These metabolites were further detected in virus-infected oceanic <em>E. huxleyi</em> blooms. Therefore, we propose that halogenation with both chlorine and iodine is a distinct hallmark of the virus-induced DOM of <em>E. huxleyi</em>, providing insights into the metabolic consequences of the ‘viral shunt’ for marine DOM.</p>
2021-05-05 | MTBLS1720 | MetaboLights
Project description:Laminarin is a major storage polysaccharide in phytoplankton and an important carbon and energy source for marine microbes. How microbes compete for this labile polysaccharide in nature remains unclear. Here we investigated metaproteomes and metagenomes of bacterioplankton during four consecutive algal blooms in the North Sea to determine key laminarin consumers. We identified two specialized laminarin degraders of the Bacteroidetes group, which reached high abundances year after year. We found that these genomically streamlined bacteria of the genus Formosa have an expanded set of laminarin hydrolases, sensors and transporters that belonged to the most abundant proteins in the blooms. The respective genes are organized in three polysaccharide utilization loci. Proteomic and biochemical analyses revealed surface tethered enzymes and a laminarinase recombined with a membrane-spanning transporter, which act as a disassembly line and efficiently integrate substrate degradation and uptake in the highly diffusive, aquatic environment. We also show that the bloom bacteria couple laminarin utilization with uptake of cellular building blocks such as amino acids. This study suggests that in addition to genome reduction, enzyme fusions, transporter and enzyme expansion also the tight coupling of the carbon and nitrogen uptake make Formosa spp. efficient laminarin utilizers.
2018-07-31 | PXD007934 | Pride
Project description:Summer mortality of the Pacific oyster Crassostrea gigas is the result of a complex interaction between oysters, their environment and pathogens. Heredity appears to be a major factor determining the sensitivity of oysters to summer mortality, allowing resistant (R) and susceptible (S) lines to be produced. We conducted genome-wide expression profiling of R and S gonads during the 3-month period preceding a summer mortality event using a 9K cDNA microarray that we designed. This transcriptional analysis provides new indications to define markers for Quantitative Trait Loci searches and functional studies, and evaluates the potential role of each gene in the resistance to summer mortality
2009-08-15 | GSE16448 | GEO
Project description:A natural product algal extract and its major component, cymopol, have demonstrated anti-oxidant and anti-inflammatory activity in vitro and in vivo. RNA transcript levels of Nqo1 and Hmox1 were discovered in multiple organs following oral gavage of 2 doses of the extract and cympopol for 3 consecutive days. The highest change in gene expression was noted in the digestive tract.
2017-12-03 | GSE107623 | GEO
Project description:Protein present in phytoplankton represents a large fraction of the organic nitrogen and carbon transported from its synthesis in surface waters to marine sediments. Yet relatively little is known about the longevity of identifiable protein in situ, or the potential modifications to proteins that occur during bloom termination, protein recycling and degradation. To address this knowledge gap, diatom-dominated phytoplankton was collected during the Bering Sea spring blooms of 2009 and 2010, and incubated under darkness in separate shipboard degradation ex periments spanning 11 and 53 d, respectively. In each experiment, the protein distribution was monited over time using shotgun proteomics, along with total hydrolyzable amino acids (THAAs), total protein, particulate organic carbon (POC) and nitrogen (PN), and bacterial cell abundance. Identifiable proteins, total protein and THAAs were rapidly lost during the first 5 d of enclosure in darkness in both incubations. Thereafter the loss rate was slower, and it declined further after 22 d. The initial loss of identifiable biosynthetic, glycolysis, metabolism and translation proteins after 12 h may represent shutdown of cellular activity among algal cells. Additional peptides with glycan modifications were identified in early incubation time points, suggesting that such protein modifications could be used as a marker for internal recycling processes and possibly cell death. Protein recycling was not uniform, with a subset of algal proteins including fucoxanthin chlorophyll binding proteins and RuBisCO identified after 53 d of degradation. Non-metric multidimensional scaling was used to compare the incubations with previous environmental results. The results confirmed recent observations that some fraction of algal proteins can survive water column recycling and undergo transport to marine sediments, thus contributing organic nitrogen to the benthos.
2017-05-19 | PXD006417 | Pride
Project description:A better understanding of innate responses induced by vaccination is critical for designing optimal vaccines. Here, we studied the diversity and dynamics of the NK cell compartment after prime-boost immunization with the modified vaccinia virus Ankara using cynomolgus macaques as a model. Mass cytometry was used to deeply characterize blood NK cells. The NK cell subphenotype composition was modified by the prime. Certain phenotypic changes induced by the prime were maintained over time and, as a result, the NK cell composition prior to boost differed from that before prime. The key phenotypic signature that distinguished NK cells responding to the boost from those responding to the prime included stronger expression of several cytotoxic, homing, and adhesion molecules, suggesting that NK cells at recall were functionally distinct. Our data reveal potential priming or imprinting of NK cells after the first vaccine injection. This study provides novel insights into prime-boost vaccination protocols that could be used to optimize future vaccines.
2019-02-19 | E-MTAB-7697 | biostudies-arrayexpress
Project description:Investigation of transcriptome dynamics of Japanese cedar (Cryptomeria japonica) in winter (Dec. 22-23, 2011) and summer (July 30-31, 2012). We investigated seasonal and diurnal transcriptome dynamics of Japanese cedar (Cryptomeria japonica) by analyzing shoot samples collected at four-hour interval for two days in winter and summer, respectively. We first collected sequence data of expressed genes from shoots to designed microarray probes. Microarray analysis revealed the significant difference of transcripts between summer and winter, and the diurnal transcriptome dynamic in summer.Statistical analysis indicated that about 7.7 % of unique genes showed diurnal rhythms with more than two-fold of peak-to-trough amplitude in summer.
2014-09-29 | GSE53945 | GEO
Project description:Similar with others, our data proved that antigen-specific CD8+ T cells from mice primed with DNA and boosted by VACV were much more sensitive to antigen stimulation than those from DNA-boost. Since the mechanisms of in vivo tuning of antigen sensitivity (also termed functional avidity) is still not defined, we compared this two vaccination regimen at gene expression level. Results provide important information of which genes were selectively activated by VACV boost vaccination. For example, data shows that the expression levels of genes involved in Cancer and Wnt signaling pathways is more higher in DNA prime-VACV boost regimen that DNA prime-DNA boost vaccination. To obtain sufficient of antigen-specific cells for microarray analysis, the OVA-specific CD8+ T cells from OT-1 mice were adoptively transferred into wild type mice and then immunized by DNA and VACV vaccine encoding OVA. Four week later, mice were scarificed and antigen-specific CD8+ T cells were emriched by CD45.1-PE antibody and anti-PE MicroBeads from splenocytes.Total RNA was extracted by the RNeasy Mini Kit (QIAGEN, Germany). Followed by amplification and biotin labeling, the samples were hybridized using Illumina Total Prep RNA Amplification Kit (Ambion, USA). Mouse WG-6v2 Expression BeadChips were used for analysis of transcriptome.
2013-10-30 | E-GEOD-51849 | biostudies-arrayexpress