Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1111332 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:To investigate the response of a dominant freshwater diatom to changes in nutrient stoichiometry, Cyclotella meneghiniana isolated from the Chaiwen River, an important tributary of the lower Yellow River, and Dongping Lake, a shallow eutrophic freshwater lake in northern China, was used as the study species. Indoor culture experiments were conducted under four nitrogen-to-phosphorus (N:P) ratios, namely 4:1, 8:1, 16:1, and 64:1. By combining nutrient monitoring with integrated transcriptomic and proteomic analyses, we investigated the physiological and molecular responses of Cyclotella meneghiniana to different N:P conditions. The results showed that lower N:P ratios were associated with higher biomass accumulation and faster nitrogen and phosphorus consumption, whereas the 64:1 treatment showed lower final biomass and reduced nutrient utilization efficiency. Integrated transcriptomic and proteomic analyses further showed that the high-N:P treatment exhibited a more distinct transcriptional profile, whereas proteomic responses were comparatively more dispersed, suggesting partial transcript–protein decoupling. GO and KEGG enrichment analyses suggested that different N:P ratios were mainly associated with changes in broadly conserved processes related to protein synthesis, energy metabolism, and cellular homeostasis, including ribosome-related functions, protein processing, oxidative phosphorylation, and glyoxylate metabolism. This study provides new insight into the physiological and molecular adaptation of a dominant freshwater diatom to altered nitrogen and phosphorus stoichiometry, and offers a basis for understanding how nutrient imbalance may influence algal responses in eutrophic waters.
2026-03-31 | PXD076358 |
Project description:Anthropogenic activities such as urbanization and agriculture can potentially pose a threat to neighboring freshwaters through nitrate and phosphorous contamination, which over time may lead to lake eutrophication. In such nitrogen-polluted environments, oxygen is depleted, and plants die and decompose. This enhances denitrifying microbes that respire under hypoxic/anoxic conditions by reducing nitrate instead of molecular oxygen and using plant remnants (lignocellulose) as carbon source. Microbial lignocellulose degradation has been well-studied for both aerobic- and anaerobic conditions; however, its degradation during denitrification remains largely unknown. Here we have applied a combination of gas kinetics and meta-omics techniques to enrich and analyze microbial communities from 10 eutrophic lakes to identify a set of core microbial metagenome-assembled genomes (MAGs) present in all the eutrophic lakes. We have further investigated their strategies and enzyme profiles for degrading lignocellulose under denitrifying conditions. We identified Pseudomonadota, Bacteroidota, Verrucomicrobiota, and Actinomycetota as the most abundant phyla and they were present in enrichments from all eutrophic lakes having a key role in denitrification and fermentation. Lignocellulose degradation was, however, dominated by species outside the core microbiome, i.e., there were differing key degraders between lakes, suggesting some level of lake-specialization. Among these we observed potential respiratory DNRA pathways, and they expressed a broad range of CAZymes targeting the various lignocellulose subfractions. Interestingly, many of the detected MAGs contained NO dismutases, enzymes postulated to convert NO to molecular oxygen and dinitrogen gas.
2026-04-30 | PXD069160 | Pride
Project description:Crude extracts of 1L cultures of fungal and bacterial strains isolated from citrus trees under high HLB pressure, grown for 1 week. All showed in vitro inhibition of Liberibacter crescens.
2020-02-21 | MSV000085000 | GNPS
Project description:Unicellular algae, termed phytoplankton, greatly impact the marine environment by serving as the basis of marine food webs and by playing central roles in biogeochemical cycling of elements. The interactions between phytoplankton and heterotrophic bacteria affect the fitness of both partners. It is becoming increasingly understood that metabolic exchange determines the nature of such interactions, but the underlying molecular mechanisms remain underexplored. Here, we investigated the molecular and metabolic basis for the bacterial lifestyle switch, from coexistence to pathogenicity, in Sulfitobacter D7 during interactions with Emiliania huxleyi, a cosmopolitan bloom-forming phytoplankter. The interaction displays two distinct phases: first, there is a coexisting phase in which the alga grows exponentially and the bacterium grows as well. The interaction shifts to pathogenic when the virulence of Sulfitobacter D7 towards E. huxleyi is invoked upon exposure to high concentrations of algal dimethylsulfoniopropionate (DMSP), which occurs when the algae reach stationary growth or when DMSP is applied exogenously to algae in exponential growth. We aimed to unravel the response of Sulfitobacter D7 to the pathogenicity-inducing compound, DMSP, and to different algae-derived infochemicals that affect the lifestyle of the bacterium. We grew Sulfitobacter D7 in conditioned media (CM) derived from algal cultures at the different growth phases, exponential and stationary (Exp-CM and Stat-CM, respectively), in which DMSP concentration is low and high, respectively. This enabled us to separate between different phases of the interaction with E. huxleyi, i.e., Exp-CM representing the coexisting phase, and Stat-CM representing the pathogenic phase. An additional pathogenicity-inducing treatment was Exp-CM supplemented with 100 µM DMSP (herein Exp-CM+DMSP). This condition mimicked co-cultures to which we added DMSP exogenously and thus induced Sulfitobacter D7 pathogenicity, which lead to death of exponentially growing E. huxleyi. In order to identify bacterial genes that are specifically responsive to DMSP, and are not affected by other algae-derived factors, we grew Sulfitobacter D7 in defined minimal medium (MM), lacking algal metabolites, supplemented with 100 µM DMSP (herein MM+DMSP), and examined the transcriptional response. After 24 h of Sulfitobacter D7 growth in all 5 media, triplicates were taken for transcriptomic analysis. Altogether, this experimental design allowed to expand our understanding on the bacterial response to DMSP, algal infochemicals and which of these are essential for coexistence and pathogenicity.
2023-01-17 | GSE193203 | GEO
Project description:Virophages are small dsDNA viruses dependent on a nucleocytoplasmic large-DNA virus infection of a cellular host for replication. Putative virophages infecting algal hosts are classified together with Polinton-like viruses, transposable elements widely found in algal genomes, yet the lack of isolated strains raises questions about their existence as independent entities. We isolated and characterized a virophage (PgVV-14T) co-infecting Phaeocystis globosa with the Phaeocystis globosa virus-14T (PgV-14T).
2023-02-11 | PXD036892 | Pride
Project description:Engineered bacterial strains with bile salt hydrolase that changed in their expression levels with high diet and diurnal changes were synthesized. These synthetic strains were cultures in BHI media with bile acids spiked in.
2024-04-20 | MSV000094578 | MassIVE