Thiorhodococcus drewsii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA63013 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme’s response (R2, 0.51–0.80, p < 0.01 in all cases). Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide (latitude 62.2°S–16°N, MAT –1.4ºC–29.5ºC) validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility, confirm the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response
2023-02-07 | PXD039714 | Pride
Project description:The aim of the current study was to characterize the differential cellular and exosomal miRNAs during inflammation or high fat diet-induced obesity in mice. Mesenteric adipose tissue (MAT) and abdominal aorta (AA) from mice fed a normal chow diet (NCD) or a high fat diet (HFD) were harvested for miRNA profiling. MAT-derived adipocytes (MAT-Ad) challenged with either lipopolysaccharide (LPS, 1 µg/ml) or PBS were harvested for miRNA profiling. Meanwhile, miRNAs encapsulated in MAT-Ad-derived exosomes (MAT-Ad-EX) were also analyzed. Hierarchical clustering analysis performed on most significantly regulated miRNAs (HFD vs NCD in tissues; LPS challenge vs PBS in the cells) showed a set of miRNAs that are differentially expressed in obese versus lean MAT or AA tissues, and in LPS-challenged versus PBS-treated MAT-Ads. The dysregulated of miRNAs in MAT-Ad-EX was also generated and hierarchically clustered, induced by prolonged exposure to microbial product.
2019-12-29 | GSE126808 | GEO
Project description:We have determined the draft genome sequences of Thiorhodococcus mannitoliphagus and Thiorhodococcus minor for comparison with those of T. drewsii and Imhoffiella purpurea According to average nucleotide identity (ANI) and whole-genome phylogenetic comparisons, these two species are clearly distinct from the Imhoffiella species and T. drewsii.
| S-EPMC7118184 | biostudies-literature
Project description:Tracing autotroph and heterotroph photosynthetic catalytic carbon cycling within a microbial mat, confirming biomass 13C incorporation into extracellular polymeric substances through proteomics.
2023-07-20 | PXD012190 | Pride
Project description:Samples collect to investigate the gene activity from microbial populations in marine steel corrosion, and to compare with gene activity in water and bed sediment samples from the surrounding area. The study was undertaken to (1) investigate mechanisms of microbially influenced corrosion (MIC) of marine steel, and (2) compare microbial population gene activity between corrosion and the surrounding environment. Purified DNA (1µg) was labelled with Cy3, purified and hybridised at 42°C for 16h with the GeoChipTM 5.0 on a MAUI hybridisation station (BioMicro, USA).
2019-11-01 | E-MTAB-8364 | biostudies-arrayexpress
Project description:Polyamines, such as putrescine and spermidine, are aliphatic organic compounds with multiple amino groups. They are found ubiquitously in marine systems. However, compared with the extensive studies on the concentration and fate of other dissolved organic nitrogen compounds in seawater, such as dissolved free amino acids (DFAA), investigations of bacterially-mediated polyamine transformations have been rare. Bioinformatic analysis identified genes encoding polyamine transporters in 74 of 109 marine bacterial genomes surveyed, a surprising frequency for a class of organic nitrogen compounds not generally recognized as an important source of carbon and nitrogen for marine bacterioplankton. The genome sequence of marine model bacterium Silicibacter pomeroyi DSS-3 contains a number of genes putatively involved in polyamine use, including six four-gene ATP-binding cassette transport systems. In the present study, polyamine uptake and metabolism by S. pomeroyi was examined to confirm the role of putative polyamine-related genes, and to investigate how well current gene annotations reflect function. A comparative whole-genome microarray approach (Bürgmann et al., 2007) allowed us to identify key genes for transport and metabolism of spermidine in this bacterium, and specify candidate genes for in situ monitoring of polyamine transformations in marine bacterioplankton communities.
2008-12-31 | GSE13781 | GEO
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:Vibrio species represent one of the most diverse genera of marine bacteria known for their ubiquitous presence in natural aquatic systems. Several members of this genus including Vibrio harveyi are receiving increasing attention lately because they are becoming a source of health problems, especially for some marine organisms widely used in sea food industry. To learn about adaptation changes triggered by V. harveyi during its long-term persistence at elevated temperatures, we studied adaptation of this marine bacterium in sea water microcosms at 30 oC that closely mimicks the upper limits of sea surface temperatures recorded around the globe.
2019-02-05 | GSE113564 | GEO
Project description:Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity, at the base of marine food webs, is constrained by nutrient availability in the surface ocean, and nutrient advection from deeper waters can fuel photosynthesis. In this study, we compared the transcriptional responses by surface microbial communities after experimental deep water mixing to the transcriptional patterns of in situ microbial communities collected with high-resolution automated sampling during a bloom in the North Pacific Subtropical Gyre. Transcriptional responses were assayed with the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) marine environmental microarray, which targets all three domains of life and viruses. The experiments showed that mixing of deep and surface waters substantially affects the transcription of photosystem and nutrient response genes among photosynthetic taxa within 24 hours, and that there are specific responses associated with the addition of deep water containing particles (organisms and detritus) compared to filtered deep water. In situ gene transcription was most similar to that in surface water experiments with deep water additions, showing that in situ populations were affected by mixing of nutrients at the six sampling sites. Together, these results show the value of targeted metatranscriptomes for assessing the physiological status of complex microbial communities.
2018-09-03 | GSE109218 | GEO
Project description:Competition for limited iron resources is a key driver of microbial community structure in many regions of the surface ocean. The bacterial siderophores ferrioxamine and amphibactin have been identified in marine surface waters, suggesting that they may represent an important bacterial strategy for obtaining iron from a scarcely populated pool. We screened several strains of marine Vibrio for the presence of putative amphibactin biosynthesis gene homologues and amphibactin production. Whole cell proteomics, siderophore isolation, and isotopically labeled iron uptake experiments were performed. Here, we show that an amphibactin-producing marine bacterium, Vibrio cyclitrophicus str. 1F-53, harbors an independently regulated uptake pathway for ferrioxamines. Proteomic analyses identified upregulation of the amphibactin NRPS system and a putative amphibactin siderophore transporter in response to low iron concentrations. In addition, multiple other transporters were upregulated, however when desferrioxamine was present, amphibactin production decreased and the ferrioxamine receptor increased in abundance. Such cheating phenotypes, which appear widespread among marine amphibactin producers, highlight the strategies that contribute to the fitness of marine bacteria in the face of iron stress. These results demonstrate siderophore producer and cheater phenotypes and highlight the cellular restructuring which is involved due to competition for iron, that shapes the community structure of marine ecosystems.
2021-04-19 | PXD011427 | Pride