Project description:We present the draft genome of Nitrospirae bacterium Nbg-4 as a representative of this clade and couple this to in situ protein expression under sulfate-enriched and sulfate-depleted conditions in rice paddy soil. The proteins were extracted from the soil and analysed via LC-MS/MS measurements.
Project description:Streptococcus pneumoniae of serotype 3 possess a mucoid capsule and cause disease associated with high mortality rates relative to other pneumococci. Phylogenetic analysis of a complete reference genome and 81 draft sequences from clonal complex 180, the predominant serotype 3 clone in much of the world, found most sampled isolates belonged to a clade affected by few diversifying recombinations. However, other isolates indicate significant genetic variation has accumulated over the clonal complex's entire history. Two closely related genomes, one from the blood and another from the cerebrospinal fluid, were obtained from a patient with meningitis. The pair differed in their behaviour in a mouse model of disease and in their susceptibility to antimicrobials, with at least some of these changes attributable to a mutation that up-regulated the patAB efflux pump. This indicates clinically important phenotypic variation can accumulate rapidly through small alterations to the genotype. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-144]
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:Sequencing of alphaproteobacterial endosymbionts that belong to the Rickettsiales and Holosporales orders.
| PRJNA501864 | ENA
Project description:Draft Genome Sequences of three novel bacterial isolates
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. Bacteria were grown in batch culture and sampled twice during the initial, rapid phase of exponential growth and twice during the phase of slower growth that followed.
Project description:The Candidatus phylum Omnitrophica (candidate division OP3) occurs ubiquitous in anaerobic habitats, but is currently characterized only by draft genomes from metagenomes and single cells. We had visualized cells of the phylotype OP3 LiM in methanogenic cultures on limonene as small epibiontic cells. In this study, we enriched OP3 cells by double density centrifugation and obtained the first closed genome of an apparently clonal OP3 cell population applying metagenomics and PCR for gap closure. Filaments of acetoclastic Methanosaeta, the largest morphotype in limonene enrichment cultures, contained empty cells, dead cells and cells devoid of rRNA or both rRNA and DNA according to TEM, thin-section TEM, SEM, CARD-FISH and Live/Dead images. OP3 LiM cells were ultramicrobacteria (200-300 nm in diameter) and showed two physiological stages in CARD-FISH fluorescence signals: strong signals indicated many rRNA molecules and an active metabolism of OP3 LiM cells attached to Bacteria and to Archaea, whereas free-living OP3 cells had weak signals. Metaproteomics revealed that OP3 LiM lives with highly expressed secreted proteins involved in depolymerization and uptake of macromolecules, an active glycolysis and energy conservation by the utilization of pyruvate via a pyruvate:ferredoxin oxidoreductase and an RNF complex (Ferredoxin:NAD oxidoreductase). Besides sugar fermentation, a nucleotidyl transferase may contribute to energy conservation by phosphorolysis, the phosphate-dependent depolymerization of nucleic acids. Thin section TEM showed distinctive structures of predation that had been previously observed for “Velamenicoccus”. Our study demonstrated a predatory metabolism for OP3 LiM cells and we propose as name for OP3 LiM Candidatus Velamenicoccus archaeovorus gen. nov., sp. nov..