Methylomarinovum strain:IN45
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ABSTRACT:
PROVIDER: PRJDB11749 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome analysis of a novel marine methanotroph, Methylomarinum sp. JGM
| PRJDB11753 | ENA
Project description:Genome analysis of a novel marine methanotroph, Methylomarinum sp. IN20
| PRJDB11751 | ENA
Project description:Previous studies have demonstrated that the iron content in marine heterotrophic bacteria is comparatively higher than that of phytoplankton. Therefore, they have been indicated to play a major role in the biogeochemical cycling of iron. In this study, we aimed to investigate the potential of viral lysis as a source of iron for marine heterotrophic bacteria. Viral lysates were derived from the marine heterotrophic bacterium, Vibrio natriegens PWH3a (A.K.A Vibrio alginolyticus). The bioavailability of Fe in the lysates was determined using a model heterotrophic bacterium, namely, Dokdonia sp. strain Dokd-P16, isolated from Fe-limited waters along Line P transect in the Northeastern Pacific Ocean. The bacteria were grown under Fe-deplete or Fe-replete conditions before being exposed to the viral lysate. Differential gene expression following exposure to the viral lysate was analyzed via RNA sequencing to identify differentially expressed genes under iron-replete and iron-deplete conditions. This study would provide novel insights into the role of viral lysis in heterotrophic bacteria in supplying bioavailable iron to other marine microorganisms under iron-limiting and non-limiting conditions. First, the marine heterotrophic bacterium genome, Dokdonia sp. strain Dokd-P16, was sequenced to provide a genomic context for the expression studies. Subsequently, the relative gene expression in Dokdonia sp. strain Dokd-P16 grown under Fe limiting and non-limiting conditions were analyzed. This transcriptomic approach would be utilized to elucidate genes regulated by Fe availability in Dokdonia sp. strain Dokd-P16, which indicate its Fe-related response viral lysate exposure. Taken together, in this study, the transcriptomic responses of Fe-limited and non-limited marine heterotrophic bacteria were analyzed, which provided novel insights into the biological availability of Fe from the viral lysates.
2021-11-01 | GSE166618 | GEO
Project description:Genome analysis of a marine methanotroph, Methylomarinovum caldicuralii IT-9
| PRJDB11744 | ENA
Project description:Using recent developments in sample preparation strategies and improvements in mass spectrometry (MS), an optimized procedure was developed to characterize the proteome of Methylocystis sp. strain SC2, a type II methanotroph. It represents one of the ecologically important groups of methane-oxidizing bacteria. The major challenge for developing an efficient analytical proteomics workflow for methanotrophic bacteria is the high amount of membrane-associated proteins that need to be efficiently solubilized and digested for downstream analysis. Therefore, each step of the workflow, including cell lysis, protein solubilization and digestion, and MS peptide quantification, was assessed and optimized. Our novel crude-lysate-MS approach proved to increase protein quantification accuracy and the proteome coverage of strain SC2. It captured 62% of predicted SC2 proteome, with 10-fold increase in membrane-associated proteins relative to less effective conditions. Use of crude cell lysate for downstream analysis showed not only to be highly efficient for strain SC2 but also for other members of the Methylocystaceae family. To validate the efficiency of our newly developed workflow, we analyzed the SC2 proteome under two contrasting nitrogen conditions, with a focus on the differential expression of proteins involved in methane and nitrogen metabolisms.
2018-07-23 | PXD009027 | Pride
Project description:This project is a proteomic comparison of Hyphomicrobium sp. MC8b grown with dichloromethane or with methanol. The datasets were obtained using the annotated genome of Hyphomicrobium sp. MC8b.
2021-09-09 | PXD021817 | Pride
Project description:Here we present the assembled genome of the facultative methanotroph, Methylocystis strain SB2, along with assessment of its transcriptome when grown on methane vs. ethanol. As expected, transcriptomic analyses indicate methane is converted to carbon dioxide via the canonical methane oxidation pathway for energy generation, and that carbon is assimilated at the level of formaldehyde via the serine cycle. When grown on ethanol, it appears this strain converts ethanol to acetyl-CoA and then utilizes the TCA cycle for energy generation and the ethylmalonyl CoA pathway for the production of biomass. All cultures were grown in triplicates for subsequent DNA and RNA extraction as well as for subsequent sequencing using Illumina. Transcriptomic analysis results presented in this Series.
2014-03-20 | E-GEOD-51345 | biostudies-arrayexpress
Project description:Genome analysis of a marine methanotroph, Methylobacter marinus MR1
| PRJDB11745 | ENA
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.
2021-01-14 | PXD023431 | Pride
Project description:Investigation of whole genome gene expression level in motile strain of Sphingomonas. sp A1 All flagellar genes in motile strain of Sphingomonas. sp A1 are highly transcribed.
2014-11-01 | GSE62901 | GEO