Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1206561 | ENA |
REPOSITORIES: ENA
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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:Vast and diverse microbial communities exist within the ocean, performing a variety of metabolic processes that cumulatively influence global chemical cycles. Despite being globally distributed, microbial populations and ocean biochemistry vary across multiple physical scales, beyond our current ability to fully quantify. To better understand the global influence of marine microbiology, we developed a robot capable of sampling ocean biochemistry across basin-scales while still capturing the fine-scale biogeochemical processes therein.
2025-01-07 | PXD018067 | Pride
Project description:The deep marine subsurface is one of the largest unexplored biospheres on Earth, where members of the phylum Chloroflexi are abundant and globally distributed. However, the deep-sea Chloroflexi have remained elusive to cultivation, hampering a more thorough understanding of their metabolisms. In this work, we have successfully isolated a representative of the phylum Chloroflexi, designated strain ZRK33, from deep-sea cold seep sediments. Phylogenetic analyses based on 16S rRNA genes, genomes, RpoB and EF-tu proteins indicated that strain ZRK33 represents a novel class within the phylum Chloroflexi, designated Sulfochloroflexia. We present a detailed description of the phenotypic traits, complete genome sequence and central metabolisms of the novel strain ZRK33. Notably, sulfate and thiosulfate could significantly promote the growth of the new isolate, possibly through accelerating the hydrolysis and uptake of saccharides. Thus, this result reveals that strain ZRK33 may play a crucial part in sulfur cycling in the deep-sea environments. Moreover, the putative genes associated with assimilatory and dissimilatory sulfate reduction are broadly distributed in the genomes of 27 metagenome-assembled genomes (MAGs) from deep-sea cold seep and hydrothermal vents sediments. Together, we propose that the deep marine subsurface Chloroflexi play key roles in sulfur cycling for the first time. This may concomitantly suggest an unsuspected availability of sulfur-containing compounds to allow for the high abundance of Chloroflexi in the deep sea.
2024-05-22 | PXD023380 | Pride
Project description:One of the most abundant organic carbon sources in the ocean is glycolate, a compound that is commonly secreted by marine phytoplankton resulting in an estimated annual flux of one petagram of glycolate in marine environments. While it is generally accepted that glycolate is oxidized to glyoxylate by marine bacteria, the further fate of this C2 metabolite is not well understood. Here we show that ubiquitous marine Proteobacteria are able to assimilate glyoxylate via the hydroxyaspartate cycle (BHAC) that was originally proposed 56 years ago. We unravel the biochemistry of the BHAC and describe the structure of its key enzymes, including a previously unknown primary imine reductase. Overall, the BHAC allows for the direct production of oxaloacetate from glyoxylate through only four enzymatic steps, representing the most efficient glyoxylate assimilation route described to date. Analysis of marine metagenomes shows that the BHAC is globally distributed and on average 20-fold more abundant than the glycerate pathway, the only other known pathway for net glyoxylate assimilation. In a field study on a phytoplankton bloom, we show that glycolate is present in high nanomolar concentrations and taken up by prokaryotes at rates that allow a full turnover of the glycolate pool within one week. During the bloom, the BHAC is present in up to 1.5% of the bacterial community and actively transcribed, supporting its role in glycolate assimilation and suggesting a new trophic interaction between autotrophic phytoplankton and heterotrophic bacterioplankton.
2019-10-14 | PXD013274 | Pride
Project description:Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis
2016-02-12 | MSV000079512 | MassIVE
Project description:Bdellovibrio bacteriovorus HD100 is a predatory bacterium which attacks a wide range of gram negative bacterial pathogens and is proposed to be a potential living antibiotic. In the current study, we evaluated the effects of indole, a bacterial signaling molecule commonly produced within the gut, on the predatory ability of B. bacteriovorus HD100. Indole significantly delayed predation on E. coli MG1655 and S. enterica KACC 11595 at physiological concentrations (0.25 to 1 mM) and completely inhibited predation when present at 2 mM. Microscopic analysis revealed that indole blocked the predator from attacking the prey. Furthermore, indole was not toxic to the predator but slowed down its motility. Microarray and RT-qPCR analyses confirmed this as the gene group showing the greatest down-regulation in the presence of 1 and 2 mM indole was flagellar assembly and motility genes. Aside from this group, indole also caused a wide spectrum changes in gene expression including the general down-regulation of genes involved in ribosome assembly and RNA translation. Furthermore, indole addition to the predatory culture after the entrance of B. bacteriovorus into the prey periplasm slowed down bdelloplast lysis. In conclusion, indole is an important gut-related signaling molecule that can have significant impacts on the predation efficiency and predator behavior. These findings should be taken into consideration especially if B. bacteriovorus is to be applied as a probiotic or living antibiotic.
2013-11-19 | GSE52455 | GEO
Project description:In this study, we used whole genome comparative oligonucleotide microarrays to investigate the brain transcriptomic response to predator cues using the threespine stickleback, Gasteroteus aculeatus. We showed that exposure to olfactory, visual and tactile cues of a predator (rainbow trout, Oncorhynchus mykiss) for six days resulted in subtle but significant transcriptomic changes in the brain of sticklebacks. Gene functional analysis and gene ontology (GO) enrichment revealed that the majority of the transcripts differentially expressed between the fish exposed to predator cues and the control group are primarily related to antigen processing and presentation (involving primarily the major histocompatibility complex (MHC)), transmission of synaptic signals, brain metabolic processes, gene regulation, or visual perception. Pathway analysis identified synaptic long-term depression, RAN signaling, relaxin signaling and phototransduction as the top four pathways that were over-represented. Adult fish were placed in six different 26L tanks with three fish per tank in a partially recirculating flow-through system. Half of the tanks were assigned to the control group and the other half to the experimental group.10 samples were selected for microarray analysis. The ten samples comprised five biological replicates in the experimental group (fish exposed to predator cues) and five biological replicates in the control group (fish not exposed to predator cues), and were evenly distributed across tanks. The cDNA labeling (single color), hybridization, washing and scanning steps were performed in the NimbleGen microarray gene expression service department.
2011-04-24 | E-GEOD-21599 | biostudies-arrayexpress
Project description:Complete genomes of 30 globally distributed Group A Streptococcus isolates
| PRJNA454341 | ENA
Project description:Bdellovibrio bacteriovorus HD100 is a predatory bacterium which attacks a wide range of gram negative bacterial pathogens and is proposed to be a potential living antibiotic. In the current study, we evaluated the effects of indole, a bacterial signaling molecule commonly produced within the gut, on the predatory ability of B. bacteriovorus HD100. Indole significantly delayed predation on E. coli MG1655 and S. enterica KACC 11595 at physiological concentrations (0.25 to 1 mM) and completely inhibited predation when present at 2 mM. Microscopic analysis revealed that indole blocked the predator from attacking the prey. Furthermore, indole was not toxic to the predator but slowed down its motility. Microarray and RT-qPCR analyses confirmed this as the gene group showing the greatest down-regulation in the presence of 1 and 2 mM indole was flagellar assembly and motility genes. Aside from this group, indole also caused a wide spectrum changes in gene expression including the general down-regulation of genes involved in ribosome assembly and RNA translation. Furthermore, indole addition to the predatory culture after the entrance of B. bacteriovorus into the prey periplasm slowed down bdelloplast lysis. In conclusion, indole is an important gut-related signaling molecule that can have significant impacts on the predation efficiency and predator behavior. These findings should be taken into consideration especially if B. bacteriovorus is to be applied as a probiotic or living antibiotic. Bdellovibrio bacteriovorus HD100 was incubated for 30 min at 30°C in HEPES buffer supplemented with 0,1, and 2 mM indole. RNA was then extracted from each sample and purified. 100 ng of RNA from each sample were used for microarray experiment. For zero and 1 mM indole treatments, three independant samples were tested while for 2 mM indole treatment, two samples were tested. A total of 8 arrays were used.
2013-11-19 | E-GEOD-52455 | biostudies-arrayexpress