Methods to mitigate Escherichia coli blooms in ex vivo colon model experiments using the micro-Matrix bioreactor fermentation system.
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PROVIDER: PRJEB64237 | ENA |
REPOSITORIES: ENA
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Project description:Mitigating E. coli blooms on the microMatrix fermentation platform
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Project description:Ex vivo colon model experiments are frequently employed as a means to assess the gut microbiome modulating potential of different foods, food ingredients and dietary supplements. A number of useful models already exist; however, they tend to be relatively low in terms of throughput (3-4 samples per experiment) with a long experiment duration of one to a number of weeks. Therefore, a need for a high-throughput system with a short duration time is required to enable screening of large numbers of samples. Therefore, we report here on the development of a system based on the Applikon micro-Matrix bioreactor which has the capacity to run 24 samples with an experiment duration of 48 h. However, Escherichia coli blooms are a common problem encountered in this model. Here, we describe the factors that contribute to such blooms and provide approaches to address them, providing:•Step by step optimisation of processes involved in conducting ex vivo distal colon experiments using the micro-Matrix bioreactor fermentation platform•Recommended steps for users on how to attenuate E. coli blooms in such ex vivo colon model experiments.
| S-EPMC10577065 | biostudies-literature
Project description:Lytic viruses have been implicated in the massive cellular lysis observed during algal blooms, through which they assume a prominent role in oceanic carbon and nutrient flows. Despite their impact on biogeochemical cycling, the transcriptional dynamics of these important oceanic events is still poorly understood. Here, we employ an oligonucleotide microarray to monitor host (Emiliania huxleyi) and virus (coccolithovirus) transcriptomic features during the course of E. huxleyi blooms induced in seawater-based mesocosm enclosures. Host bloom development and subsequent coccolithovirus infection was associated with a major shift in transcriptional profile. In addition to the expected metabolic requirements typically associated with viral infection (amino acid and nucleotide metabolism, as well as transcription- and replication-associated functions), the results strongly suggest that the manipulation of lipid metabolism plays a fundamental role during host-virus interaction. The results herein reveal the scale, so far massively underestimated, of the transcriptional domination that occurs during coccolithovirus infection in the natural environment. Six mesocosm enclosures were placed in the Raunefjorden (Western Norway coast) and filled with natural community water (in June 2008). Nutrient enrichment was applied in order to trigger the development of E. huxleyi blooms. The major transcriptomic features of those blooms and consequent viral infections were monitered through the use of an oligo microarray containing a total of 3571 gene probes; 2271 (63.6%) matching E. huxleyi ESTs, and 1300 (36.4%) matching EhV-86 and EhV-163 genomic sequences. Each microarray contains 5 technical replicates. Sampling of total RNA present in 2L of water (from each enclosure) was performed once a day from day 8 to day 16. For enclosures 2 and 3 other sampling points were taken, covering the complete dial-cycle (6h,12h,18h, and 24h).
2011-11-22 | E-GEOD-24341 | biostudies-arrayexpress
Project description:Lytic viruses have been implicated in the massive cellular lysis observed during algal blooms, through which they assume a prominent role in oceanic carbon and nutrient flows. Despite their impact on biogeochemical cycling, the transcriptional dynamics of these important oceanic events is still poorly understood. Here, we employ an oligonucleotide microarray to monitor host (Emiliania huxleyi) and virus (coccolithovirus) transcriptomic features during the course of E. huxleyi blooms induced in seawater-based mesocosm enclosures. Host bloom development and subsequent coccolithovirus infection was associated with a major shift in transcriptional profile. In addition to the expected metabolic requirements typically associated with viral infection (amino acid and nucleotide metabolism, as well as transcription- and replication-associated functions), the results strongly suggest that the manipulation of lipid metabolism plays a fundamental role during host-virus interaction. The results herein reveal the scale, so far massively underestimated, of the transcriptional domination that occurs during coccolithovirus infection in the natural environment.
2011-11-22 | GSE24341 | GEO
Project description:Harmful algal blooms present severe environmental threats, impacting water quality, aquatic ecosystems, and human health. The frequency and intensity of these blooms are rising, largely driven by global warming and changing climatic conditions. There is an urgent need for innovative methods to monitor blue-green algae, also known as cyanobacteria, to enable the implementation of preventative measures. Here, we show that native mass spectrometry is an effective tool for detecting cyanobacteria directly from lake samples, both prior and during bloom formation. Our approach allows for the rapid characterization of cyanobacterial populations within lakes, offering valuable insights into the dynamics of cyanobacterial species associated with harmful algae blooms. Overall, we highlight the exceptional capability of native mass spectrometry in directly detecting and monitoring cyanobacterial blooms, which will support the development of more effective strategies to mitigate this growing environmental challenge.
2025-07-28 | PXD065745 | Pride
Project description:Utah Lakes Harmful Algal Blooms Targeted loci environmental
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Project description:Laminarin is a major storage polysaccharide in phytoplankton and an important carbon and energy source for marine microbes. How microbes compete for this labile polysaccharide in nature remains unclear. Here we investigated metaproteomes and metagenomes of bacterioplankton during four consecutive algal blooms in the North Sea to determine key laminarin consumers. We identified two specialized laminarin degraders of the Bacteroidetes group, which reached high abundances year after year. We found that these genomically streamlined bacteria of the genus Formosa have an expanded set of laminarin hydrolases, sensors and transporters that belonged to the most abundant proteins in the blooms. The respective genes are organized in three polysaccharide utilization loci. Proteomic and biochemical analyses revealed surface tethered enzymes and a laminarinase recombined with a membrane-spanning transporter, which act as a disassembly line and efficiently integrate substrate degradation and uptake in the highly diffusive, aquatic environment. We also show that the bloom bacteria couple laminarin utilization with uptake of cellular building blocks such as amino acids. This study suggests that in addition to genome reduction, enzyme fusions, transporter and enzyme expansion also the tight coupling of the carbon and nitrogen uptake make Formosa spp. efficient laminarin utilizers.
2018-07-31 | PXD007934 | Pride
Project description:Summer storms boost algal blooms that change long-term lake ecosystem dynamics
| PRJEB39507 | ENA
Project description:Microcystis aeruginosa blooms from lakes around the globe. Raw sequence reads
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Project description:Snow algal blooms decrease snow albedo and increase local melt rates. However, the causes behind the size and frequency of these blooms are still not well understood. One factor likely contributing is nutrient availability, specifically nitrogen and phosphorus. The nutrient requirements of the taxa responsible for these blooms are not known. Here, we assessed the growth of three commercial strains of snow algae under 24 different nutrient treatments that varied in both absolute and relative concentrations of nitrogen and phosphorus. After 38 days of incubation, we measured total biomass and cell size and estimated their effective albedo reduction surface. Snow algal strains tended to respond similarly and achieved bloom-like cell densities over a wide range of nutrient conditions. However, the molar ratio of nitrogen to phosphorus at which maximum biomass was achieved was between 4 and 7. Our data indicate a high requirement for phosphorus for snow algae and highlights phosphorus availability as a critical factor influencing the frequency and extent of snow algae blooms and their potential contribution to snow melt through altered albedo. Snow algae can thrive across a range of nitrogen (N) and phosphorus (P) conditions, with a higher P requirement for optimal growth. Our study suggests that increased N deposition may have a limited impact on snow algae bloom occurrence and size, emphasising P as a key factor influencing these blooms and their potential to accelerate snow melt by lowering albedo.
| S-EPMC11604572 | biostudies-literature