Project description:Strain SM1988T is a Gram-negative, aerobic, oxidase- and catalase-positive, unipolar flagellated, and rod-shaped bacterium capable of hydrolyzing casein, gelatin and collagens. Phylogenetic analysis revealed that strain SM1988T formed a distinct phylogenetic lineage along with known genera within the family Pseudoalteromonadaceae, with 16S rRNA gene sequence similarity being less than 93.3% to all known species in the family. Based on the phylogenetic, genomic, chemotaxonomic and phenotypic data, strain SM1988T was considered to represent a novel species in a novel genus in the family Pseudoalteromonadaceae, for which the name Flocculibacter collagenilyticus gen. nov., sp. nov. is proposed, with the type strain being SM1988T (= MCCC 1K04279T = KCTC 72761T). Strain SM1988T showed a high production (236 U/mL) of extracellular collagenases, which had high activity against both bovine collagen and codfish collagen. Biochemical tests combined with genomic and secretomic analyses indicated that the collagenases secreted by strain SM1988T are serine proteases from the S8 family. These data suggest that strain SM1988T acts as an important player in marine collagen degradation and recycling and may have a promising potential in collagen resource utilization.
Project description:The Breviatea form a lineage of free-living protists that emerged over 800 million years ago as a sister clade to opistokonta, comprising animals and fungi. Breviates conserved the ability to thrive in absence of oxygen which was an important adaptation to the low oceanic oxygen-levels that prevailed by that time. We previously found that the novel breviate, Lenisia limosa, gen. et sp. nov., was opportunistically colonized by relatives of animal-associated Arcobacter. Here we used differential proteomics to investigate how the presence/absence of symbiotic Arcobacter is manifested in Lenisia limosa's proteome. Vice versa, we also measured how symbiosis is reflected in Arcobacter's proteome. The results provide a resource to characterize the molecular underpinnings of a novel protist-prokaryote symbiosis.
2016-05-25 | PXD003275 | Pride
Project description:Ezomonas gen. nov. genome taxonomy
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..