Syn-Si
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB76927 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13319379_1.fastq.gz | Fastqsanger.gz | |||
| ERR13319379_2.fastq.gz | Fastqsanger.gz | |||
| ERR13319380_1.fastq.gz | Fastqsanger.gz | |||
| ERR13319380_2.fastq.gz | Fastqsanger.gz | |||
| ERR13319381_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Picocyanobacteria from the genus Synechococcus are ubiquitous in ocean waters. Their phylogenetic and genomic diversity suggests ecological niche differentiation, but the selective forces influencing this are not well defined. Marine picocyanobacteria are sensitive to Cu toxicity, so adaptations to this stress could represent a selective force within, and between, “species” also known as clades. We compared Cu stress responses in cultures and natural populations of marine Synechococcus from two co-occurring major mesotrophic clades (I and IV). Using custom microarrays and proteomics to characterize expression responses to Cu in the lab and field, we found evidence for a general stress regulon in marine Synechococcus. However, the two clades also exhibited distinct responses to copper. The Clade I representative induced expression of genomic island genes in cultures and Southern California Bight populations, while the Clade IV representative downregulated Fe-limitation proteins. Copper incubation experiments suggest that Clade IV populations may harbor stress-tolerant subgroups, and thus fitness tradeoffs may govern Cu-tolerant strain distributions. This work demonstrates that Synechococcus has distinct adaptive strategies to deal with Cu toxicity at both the clade and subclade level, implying that metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations.
2016-10-28 | GSE89262 | GEO
Project description:Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrients availability or temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to ammonium or nitrogen starvation. We found that Synechococcus has a specific response to nanomolar nitrate concentration that differs to the response showed under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentration of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural field.
2022-07-11 | PXD031142 | Pride
Project description:Microbial photoautotroph-heterotroph interactions underlie marine food webs and shape ecosystem diversity and structure in upper ocean environments. However, the high complexity of in situ ecosystems renders it difficult to study these interactions. Two-member co-culture systems of picocyanobacteria and single heterotrophic bacterial strains have been thoroughly investigated. However, in situ interactions comprise far more diverse heterotrophic bacterial associations with single photoautotrophic organisms. Here, bacterial community composition, lifestyle preference, and genomic- and proteomic-level metabolic characteristics were investigated for an open ocean Synechococcus ecotype and its associated heterotrophs over 91 days of co-cultivation. The associated heterotrophic bacterial assembly mostly constituted five classes including Flavobacteria, Bacteroidetes, Phycisphaerae, Gammaproteobacteria, and Alphaproteobacteria. The seven most abundant taxa/genera comprised >90% of the total heterotrophic bacterial community, and five of these displayed distinct lifestyle preferences (free-living or attached) and responses to Synechococcus growth phases. Six high-quality genomes from the co-culture system were reconstructed inclusive of Synechococcus and the five dominant heterotrophic bacterial populations. The only primary producer of the co-culture system, Synechococcus, displayed metabolic processes primarily involved in inorganic nutrient uptake, photosynthesis, and organic matter biosynthesis and release. Two of the flavobacterial populations, Muricauda and Winogradskyella, and an SM1A02 population, displayed preferences for initial degradation of complex compounds and biopolymers, as evinced by high abundances of TBDT, glycoside hydrolase, and peptidases proteins. In contrast, the alphaproteobacterium Oricola sp. population mainly utilized low molecular weight DOM, including Flavobacteria metabolism byproducts, through ABC, TRAP, and TTT transport systems. Polysaccharide-utilization loci present in the flavobacterial genomes encoded similar trans-membrane protein complexes as Sus/cellulosome and may influence their lifestyle preferences and close associations with phytoplankton. The heterotrophic bacterial populations exhibited complementary mechanisms for degrading Synechococcus-derived organic matter and driving nutrient cycling. In addition to nutrient exchange, removal of reactive oxygen species and vitamin trafficking also contributed to the maintenance of the Synechococcus / heterotroph co-culture system and the interactions shaping the system.
2020-05-27 | PXD015067 | Pride
Project description:<p>We compared changes induced by the addition of 100 nM and 5 mM glucose on the proteome and metabolome complements in <em>Synechococcus</em> sp. strains WH8102, WH7803, and BL107 and <em>Prochlorococcus</em> sp. strains MED4, SS120, and MIT9313, grown either under standard light conditions or in darkness. Our results suggested that glucose is metabolized by these cyanobacteria, using primarily the oxidative pentoses and Calvin pathways, while no proof was found for the involvement of the Entner-Doudoroff pathway in this process. We observed differences in the effects of glucose availability, both between genera and between <em>Prochlorococcus</em> MED4 and SS120 strains, which might be related to their specific adaptations to the environment. We found evidence for fermentation in <em>Prochlorococcus</em> sp. strain SS120 and <em>Synechococcus</em> sp. strain WH8102 after 5 mM glucose addition. Our results additionally suggested that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness. Furthermore, the KaiB and KaiC proteins were also affected in <em>Synechococcus</em> sp. WH8102, pointing to a direct link between glucose assimilation and circadian rhythms in marine cyanobacteria. In conclusion, our study provides a wide overview on the metabolic effects induced by glucose availability in representative strains of the diverse marine picocyanobacteria, providing further evidence for the importance of mixotrophy in marine picocyanobacteria. The <em>Prochlorococcus sp.</em> strain PCC 9511 is genetically identical to MED4</p><p><strong>IMPORTANCE</strong> Glucose uptake by marine picocyanobacteria has been previously described and strongly suggests they are mixotrophic organisms (capable of using energy from the sun to make organic matter, but also to directly use organic matter from the environment when available). However, a detailed analysis of the effects of glucose addition on the proteome and metabolome of these microorganisms had not been carried out. Here, we analyzed three <em>Prochlorococcus</em> sp. and three <em>Synechococcus</em> sp. strains which were representative of several marine picocyanobacterial clades. We observed differential features in the effects of glucose availability, depending on both the genus and strain; our study illuminated the strategies utilized by these organisms to metabolize glucose and showed unexpected links to other pathways, such as circadian regulation. Furthermore, we found glucose addition had profound effects in the microbiome, favoring the growth of coexisting heterotrophic bacteria.</p>
2023-02-06 | MTBLS5462 | MetaboLights
Project description:Purpose: to find the potential down-stream target gene of circFAM120A Methods: mRNA profiles of decidualized human endometrial stromal cells (hESCs) after down-regulated FAM120A and control using siRNA were generated by NGS and compared by bioinformatics analysis Results: we sequenced 26414 mRNAs in hESCs between the si-NC and si-circFAM120A groups and identified 242 differentially expressed mRNAs, between which 161 were downregulated and 81 were up-regulated in si-circFAM120A group Conclusions: Our study represents the detailed analysis of decidualized hESCs transcriptomes between si-NC and si-circFAM120A groups.
2023-06-30 | GSE174495 | GEO
Project description:Primary productivity of open ocean environments, such as those inhabited by marine picocyanobacteria Synechococcus sp.WH8102, are often limited by low inorganic phosphate (P). To observe how this organism copes with P starvation, we constructed a full genome microarray and examined differences in gene expression under P-limited and P-replete growth conditions. To determine the temporal nature of the responses, comparisons were made for cells newly entered into P-stress (at a time point corresponding to the induction of extracellular alkaline phosphatase activity) and a later time point (late log phase). In almost all instances the P starvation response was transitory, with 36 genes showing significant upregulation (>log2 fold) while 23 genes were highly downregulated at the early time point; however, these changes in expression were maintained for only five of the upregulated genes. Knockout mutants were constructed for genes SYNW0947 or SYNW0948, comprising a two component regulator hypothesized to play a key role in regulating the response to P-limitation. A high degree of overlap in the sets of genes affected by P-limited conditions and in the knockout mutants supports this hypothesis; however there is some indication that other regulators may play a role in this response in Synechococcus sp. WH8102. Consistent with what has been observed in many other cyanobacteria, the Pho regulon of this strain is comprised largely of genes for alkaline phosphatases, P transport or P metabolism. Interestingly, however, the exact composition and arrangement of the Pho regulon appears highly variable in marine cyanobacteria.
2009-06-15 | GSE13170 | GEO
Project description:Combined effects of micropollutants on prokaryotic communities at the sediment-water interface
| PRJEB64322 | ENA
Project description:Combined effects of micropollutants on prokaryotic communities at the sediment-water interface
| PRJEB76198 | ENA
Project description:Marine picocyanobacteria <i>Prochlorococcus</i> and <i>Synechococcus</i>, the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, while studying the ability of picocyanobacteria to supplement photosynthetic carbon fixation with the use of exogenous organic carbon, we found the widespread occurrence of genes for breaking down chitin, an abundant source of organic carbon that exists primarily as particles. We show that cells that encode a chitin degradation pathway display chitin degradation activity, attach to chitin particles, and show enhanced growth under low light conditions when exposed to chitosan, a partially deacetylated soluble form of chitin. Marine chitin is largely derived from arthropods, which underwent major diversifications 520 to 535 Mya, close to when marine picocyanobacteria are inferred to have appeared in the ocean. Phylogenetic analyses confirm that the chitin utilization trait was acquired at the root of marine picocyanobacteria. Together this leads us to postulate that attachment to chitin particles allowed benthic cyanobacteria to emulate their mat-based lifestyle in the water column, initiating their expansion into the open ocean, seeding the rise of modern marine ecosystems. Subsequently, transitioning to a constitutive planktonic life without chitin associations led to cellular and genomic streamlining along a major early branch within <i>Prochlorococcus</i>. Our work highlights how the emergence of associations between organisms from different trophic levels, and their coevolution, creates opportunities for colonizing new environments. In this view, the rise of ecological complexity and the expansion of the biosphere are deeply intertwined processes.
2024-02-21 | MTBLS5229 | MetaboLights