Marine metagenome
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR027336.fastq.gz | Fastqsanger.gz |
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Project description:Plants and rhizosphere microbes rely closely on each other, with plants supplying carbon to bacteria in root exudates, and bacteria mobilizing soil-bound phosphate for plant nutrition. When the phosphate supply becomes limiting for plant growth, the composition of root exudation changes, affecting rhizosphere microbial communities and microbially-mediated nutrient fluxes. To evaluate how plant phosphate deprivation affects rhizosphere bacteria, Lolium perenne seedlings were root-inoculated with Pseudomonas aeruginosa 7NR, and grown in axenic microcosms under different phosphate regimes (330 uM vs 3-6 uM phosphate). The effect of biological nutrient limitation was examined by DNA microarray studies of rhizobacterial gene expression.
2011-07-01 | E-MEXP-2812 | biostudies-arrayexpress
Project description:Temporal dynamics of bacterioplankton community in response to excessive nitrate loading in the oligotrophic coastal water
| PRJDB5020 | ENA
Project description:Marine bacterioplankton communities respond to cadmium (Cd) stress in microcosms over time
| PRJDB2337 | ENA
Project description:<p>Marine dissolved organic matter (DOM) varies in its recalcitrance to rapid microbial degradation. DOM of varying recalcitrance can be exported from the ocean surface to depth by subduction or convective mixing and oxidized over months to decades in deeper seawater. Carboxyl-rich alicyclic molecules (CRAM) are characterized as a major component of recalcitrant DOM throughout the oceanic water column. The oxidation of CRAM-like compounds may depend on specific bacterioplankton lineages with oxidative enzymes capable of catabolizing complex molecular structures like long-chain aliphatics, cyclic alkanes, and carboxylic acids. To investigate the interaction between bacteria and CRAM-like compounds, we conducted microbial remineralization experiments using several compounds rich in carboxyl groups and/or alicyclic rings, including deoxycholate, humic acid, lignin, and benzoic acid, as proxies for CRAM. Mesopelagic seawater (200 m) from the northwest Sargasso Sea was used as media and inoculum and incubated over 28 days. All amendments demonstrated significant DOC removal (2 – 11 µmol C L-1) compared to controls. Bacterioplankton abundance increased significantly in the deoxycholate and benzoic acid treatments relative to controls, with fast-growing <em>Spongiibacteracea</em>, <em>Euryarcheaota</em>, and slow-growing SAR11 enriched in the deoxycholate treatment and fast-growing <em>Alteromonas</em>, <em>Euryarcheaota</em>, and <em>Thaumarcheaota</em> enriched in the benzoic acid treatment. In contrast, bacterioplankton grew slower in the lignin and humic acid treatments, with oligotrophic SAR202 becoming significantly enriched in the lignin treatment. Our results indicate that the character of the CRAM proxy compounds resulted in distinct bacterioplankton removal rates and affected specific lineages of bacterioplankton capable of responding.</p>
2024-02-20 | MTBLS3512 | MetaboLights
Project description:This study investigates the long-term persistence of Yersinia pestis in tap water microcosms at 25°C and examines its proteomic landscape and ability to cause lethal infection in a mouse model during persistence, assessing its potential risk for waterborne transmission. Five Y. pestis strains representing different biovars and molecular profiles were studied by seeding tap water microcosms with different bacterial concentrations. All strains remained viable for approximately 120 days in High-Concentration Microcosms (HCM) and 60 days in Low-Concentration Microcosms (LCM). Mass spectrometry analysis revealed that 1,825 proteins (~72%) remained expressed in tap water for over 100 days, with 113 and 43 proteins showing differential expression at 60 and 100 days in HCM, respectively, suggesting adaptive shifts to the aquatic environment. Stress-response proteins (CspA1, CspA2, HspQ) and regulatory proteins (LysR, GntR) appeared to support survival, while virulence-associated proteins (YopE, YopB, ail, adhesins) were also expressed. Notably, mice inoculated with water from day 90 HCM succumbed to infection, underscoring the pathogen’s ability to retain infectivity even in unfavourable conditions. These findings highlight the resilience of Y. pestis in water, its prolonged survival while maintaining virulence, and the potential risks of waterborne transmission, emphasizing the need for effective mitigation strategies against biothreat agents.
2026-01-14 | PXD064839 | Pride
Project description:Large surface-to-volume ratios provide optimal nutrient uptake conditions for small microorganisms in oligotrophic habitats. The surface area can be increased with appendages. Here we describe chains of interconnecting vesicles protruding from cells of the flavobacterial strain Hel3_A1_48 originating from coastal free-living bacterioplankton. The chains were up to 10 µm long, had vesicles with a single membrane and a size of 80-100 nm by 50-80 nm, and emanated from the outer membrane. Cells extruded membrane tubes in the exponential phase, whereas vesicle chains dominated on cells in the stationary growth phase. This indicated a formation by pearling, which describes a physical morphogenic process: membrane tubes are protruding from liposomes and transform into chains of interconnected vesicles. Proteomes of whole cell membranes and of detached vesicles were dominated by outer membrane proteins including the type IX secretion system and surface-attached peptidases, glycoside hydrolases and endonucleases. Imported fluorescein-labeled laminarin was present in the periplasm of the cells and in the lumen of protruding vesicle chains. The appendages thus provide degradative enzymes on their surfaces and storage volume in the periplasmic extension, which seems to contribute to the high abundance of the Formosa-affiliated bacteria during laminarin utilization shortly after algal blooms.
2019-07-25 | PXD012522 | Pride
Project description:Activating the cryptic secondary metabolic gene clusters is a vital research field in Streptomyces. The marine Streptomyces sp. FJNU027 strain which could produce tirandamycins was cultured in the oligotrophic medium. Compared with normal medium, a differential product in oligotrophic culture was found by HPLC assay. After mass fermentation, 2 mg of the differential product was obtained from 30 L fermentation broth by solvent extraction, column chromatography over sephadex LH-20 and reverse phase C18, and other methods. It was identified as 4,4',5,5'-tetramethyl-[1,1'- diphenyl]-2,2'-diol by NMR and MS data. The production of this compound was enhanced with the increment of cultural time. Transcriptome sequencing analysis showed that the highest upregulated genes under oligotrophic condition were glycosidase, TraR/DksA C4-type zinc finger protein and ribonuclease encoding genes, while the expression of a MarR family transcriptional regulator was most significantly decreased under oligotrophic condition. The results indicate that oligotrophic culture is an effective method for altering the secondary metabolism of Streptomyces.
2025-12-10 | GSE278152 | GEO
Project description:Eutrophication can lead to an uncontrollable increase in algal biomass, which has repercussions for the entire microbial and pelagic community. Studies have shown how nutrient enrichment affects microbial species succession, however details regarding the impact on community functionality are rare. Here, we applied a metaproteomic approach to investigate the functional changes to algal and bacterial communities, over time, in oligotrophic and eutrophic conditions, in freshwater microcosms. Samples were taken early during algal and cyanobacterial dominance and later under bacterial dominance. 1048 proteins, from the two treatments and two timepoints, were identified and quantified by their exponentially modified protein abundance index. In oligotrophic conditions, Bacteroidetes express extracellular hydrolases and Ton-B dependent receptors to degrade and transport high molecular weight compounds captured while attached to the phycosphere. Alpha- and Beta-proteobacteria were found to capture different substrates from algal exudate (carbohydrates and amino acids, respectively) suggesting resource partitioning to avoid direct competition. In eutrophic conditions, environmental adaptation proteins from cyanobacteria suggested better resilience compared to algae in a low carbon nutrient enriched environment. This study provides insight into differences in functional microbial processes between oligo- and eutrophic conditions at different timepoints and highlights how primary producers control bacterial resources in freshwater environments.
2016-08-01 | PXD004592 | Pride
Project description:We used the previously designed oligonucleotide microarrays (BM-CM-<rgmann et al., 2007, Environmental Microbiology, 9: 2742-2755) to detect the mRNA transcripts of R. pomeroyi DSS-3 when the cells were cultured under steady-state conditions limited with ammonium (NH4Cl, 0.26 mM) but with an excess of D-ribose-5-phosphate (C5H9Na2O8P*2H2O, 0.5 mM), methylphosphonic acid (CH5PO3, 0.5 mM), or potassium phosphate (KH2PO4, 0.5 mM), or during ammonium excess (NH4Cl, 2.8 mM) but were limited with potassium phosphate (KH2PO4, 9.2 M-NM-<M). A total of 13 microarray hybridizations were performed: three biological replicates each from ribose phosphate, methylphosphonate, or potassium phosphate excess growth regimes, three biological replicates from potassium phosphate limited growth regime, and one technical replicate for the potassium phosphate excess growth regime. Data for the technical replicates were averaged and combined, resulted in a total of 12 samples.
2014-06-02 | E-GEOD-38740 | biostudies-arrayexpress