Candidatus Nitrosopumilus salaria BD31
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA50075 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR058923.fastq.gz | Fastqsanger.gz |
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Project description:marine archaeal group 1 strain BD31 overview
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Project description:Ammonia-oxidizing archaea (AOA) play important roles in nitrogen and carbon cycling in marine and terrestrial ecosystems. Here, we present the draft genome sequence for the ammonia-oxidizing archaeon "Candidatus Nitrosopumilus salaria" BD31, which was enriched in culture from sediments of the San Francisco Bay estuary. The genome sequences revealed many similarities to the genome of Nitrosopumilus maritimus.
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Project description:Candidatus Nitrosopumilus sediminis strain:AR2 Genome sequencing
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Project description:<p>Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mass or even their fragmentation spectra. Here we developed a novel analytical protocol based on liquid chromatography ion mobility mass spectrometry to enhance the coverage of the lipidome and characterize the conformations of archaeal lipids by their collision cross-sections (CCSs). The measurements of ion mobility revealed the gas-phase ion chemistry of representative archaeal lipids and provided further insights into their attributions to the adaptability of archaea to environmental stresses. A comprehensive characterization of the lipidome of mesophilic marine thaumarchaeon, <em>Nitrosopumilus maritimus</em> (strain SCM1) revealed potentially an unreported phosphate- and sulfate-containing lipid candidate by negative ionization analysis. It was the first time that experimentally derived CCS values of archaeal lipids were reported. Discrimination of crenarchaeol and its proposed stereoisomer was, however, not achieved with the resolving power of the SYNAPT G2 ion mobility system, and a high-resolution ion mobility system may be required for future work. Structural and spectral libraries of archaeal lipids were constructed in non-vendor-specific formats and are being made available to the community to promote research of Archaea by lipidomics. </p>
2021-12-16 | MTBLS3714 | MetaboLights
Project description:The global significance of marine non-cyanobacterial diazotrophs, notably heterotrophic bacterial diazotrophs (HBDs), has become increasingly clear. Understanding N2 fixation rates for these largely uncultured organisms poses a challenge due to uncertain growth requirements and complex nitrogenase regulation. We identified Candidatus Thalassolituus haligoni as an Oceanospirillales member, closely related to other significant γ-proteobacterial HBDs. Pangenome analysis reinforces this classification, indicating the isolate belongs to the same species as the uncultured metagenome-assembled genome Arc-Gamma-03. Analysis of the nifH gene in amplicon sequencing libraries reveals the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic and Arctic Oceans. Through combined proteomic analysis and N2 fixation rate measurements, we confirmed the isolate’s capacity for nitrate independent N2 fixation, although a clear understanding of nitrogenase regulation remains unclear. Overall, our study highlights the significance of Cand. T. haligoni as the first globally distributed, cultured model species within the understudied group of Oceanospirillales, and γ-HBDs in general.
2024-08-10 | PXD045743 | Pride
Project description:Casposase, a homolog of Cas1 integrase, is encoded by a superfamily of mobile genetic elements known as casposons. While family 2 casposase has been well documented in both function and structure, little is known about the other three casposase families. Here, we studied the family 1 casposase lacking the helix-turn-helix (HTH) domain from Candidatus Nitrosopumilus koreensis AR1 (Ca. N. koreensis). The determinants for integration by Ca. N. koreensis casposase were extensively investigated, and it was found that a 13-bp target site duplication (TSD) sequence, a minimal 3-bp leader and three different nucleotides of the TSD sequences are indispensable for target specific integration. Significantly, the casposase can site-specifically integrate a broad range of terminal inverted repeat (TIR)-derived oligonucleotides ranging from 7-nt to ∼4000-bp, and various oligonucleotides lacking the 5'-TTCTA-3' motif at the 3' end of TIR sequence can be integrated efficiently. Furthermore, similar to some Cas1 homologs, the casposase utilizes a 5'-ATAA-3' motif in the TSD as a molecular ruler to dictate nucleophilic attack at 9-bp downstream of the end of the ruler during the spacer-side integration. By characterizing the family 1 Ca. N. koreensis casposase, we have extended our understanding on mechanistic similarities and evolutionary connections between casposons and the adaptation elements of CRISPR-Cas immunity.
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Project description:Bacteria respond to stimuli in the environment using transcriptional control, but this may not be the case for most marine bacteria having small, streamlined genomes. Candidatus Pelagibacter ubique, a cultivated representative of the SAR11 clade, which is the most abundant clade in the oceans 4, has a small, streamlined genome and possesses an unusually small number of transcriptional regulators. This observation leads to the hypothesis that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. However, the extent of transcriptional control in Pelagibacter is unknown. Here we show that transcriptional control is extremely low in Pelagibacter and another oligotroph (SAR92) compared to two marine copiotrophic bacterial taxa, Polaribacter MED152 and Ruegeria pomeroyi. We found that ~0.1% of protein-encoding genes in Pelagibacter are under transcriptional control compared to >10% of genes in other marine bacteria. Regardless of the growth condition, the same genes were highly expressed while most genes were always expressed at very low levels. Quantitative RNA sequencing revealed that abundances of most Pelagibacter transcripts were <0.01 copies per cell whereas transcript abundances were 1 to 10 copies per cell in some other bacteria. Our results demonstrate that Pelagibacter can change growth without shifts in transcript levels, suggesting that transcriptional control plays a minimal role in the adaptive strategy for one of the most successful organisms in the biosphere.
2015-03-03 | GSE66443 | GEO
Project description:Candidatus Nitrosopumilus sp. DDS1 genome sequencing and assembly
| PRJNA289040 | ENA