Kordia algicida OT-1
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ABSTRACT:
PROVIDER: PRJNA19315 | ENA |
REPOSITORIES: ENA
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Project description:Kordia algicida OT-1 is an algicidal bacterium against the bloom-forming microalgae. The genome sequence of K. algicida revealed a number of interesting features, including the degradation of macromolecules, the biosynthesis of carotenoid pigment and secondary metabolites, and the capacity for gliding motility, which might facilitate the understanding of algicidal mechanisms.
| S-EPMC3147531 | biostudies-literature
Project description:The genus Kordia is one of many genera affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, well known for its degradation of high molecular weight organic matters. The genus Kordia currently comprises eight species, type strains of which have been isolated from a diverse range of marine environments. As of this report, four genome sequences have been submitted for cultured strains of Kordia, but none are complete nor have they been analyzed comprehensively. In this study, we report the complete genome of Kordia antarctica IMCC3317T, isolated from coastal seawater off the Antarctic Peninsula. The complete genome of IMCC3317T consists of a single circular chromosome with 5.5 Mbp and a 33.2 mol% of G+C DNA content. The IMCC3317T genome showed features typical of chemoheterotrophic marine bacteria and similar to other Kordia genomes, such as complete gene sets for the Embden-Meyerhof-Parnas glycolysis pathway, tricarboxylic acid cycle and oxidative phosphorylation. The genome also encoded many carbohydrate-active enzymes, some of which were clustered into approximately seven polysaccharide utilization loci, thereby demonstrating the potential for polysaccharide utilization. Finally, a nosZ gene encoding nitrous oxide reductase, an enzyme that catalyzes the reduction of N2O to N2 gas, was also unique to the IMCC3317T genome.
| S-EPMC7477175 | biostudies-literature
Project description:Plankton communities consist of complex microbial consortia that change over time. These fluctuations can be only partially explained by limiting resources. Biotic factors such as herbivores and pathogens also contribute to the control of algal blooms. Here we address the effects of algicidal bacteria on a natural plankton community in an indoor enclosure experiment. The algicidal bacteria, introduced into plankton taken directly from the North Sea during a diatom bloom, caused the rapid decline of the bloom-forming Chaetoceros socialis within only 1 day. The haptophyte Phaeocystis, in contrast, is resistant to the lytic bacteria and could benefit from the removal of the competitor, as indicated by an onset of a bloom in the treated enclosures. This cascading effect caused by the bacterial pathogen accelerated the succession of Phaeocystis, which bloomed with a delay of only several weeks in the in situ waters at Helgoland Roads in the North Sea. The algicidal bacteria can thus modulate the community within the limits of the abiotic and biotic conditions of the local environment. Implications of our findings for plankton ecosystem functioning are discussed.IMPORTANCE Plankton communities change on a seasonal basis in temperate systems, with distinct succession patterns; this is mainly due to algal species that have their optimal timing relative to environmental conditions. We know that bacterial populations are also instrumental in the decay and termination of phytoplankton blooms. Here, we describe algicidal bacteria as modulators of this important species succession. Upon treatment of a natural plankton consortium with an algicidal bacterium, we observed a strong shift in the phytoplankton community structure, compared to controls, resulting in formation of a succeeding Phaeocystis bloom. Blooms of this alga have a substantial impact on global biogeochemical and ecological cycles, as they are responsible for a substantial proportion of primary production during spring in the North Sea. We propose that one of the key factors influencing such community shifts may be algicidal bacteria.
| S-EPMC6585488 | biostudies-literature
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:Non-starch soluble polysaccharides (NSPs) produced by yeasts are used in animal nutrition to improve health and performance. However, the magnitude of the effect may be dependent upon the quantity and the composition of the polysaccharides. As seaweeds are attractive sources of NSPs, this study was set up to evaluate their potential to improve intestinal health. The effect of NSP extracts prepared from Saccharomyces cerevisiae containing β-glucan and mannan (PSY1, positive control) or a mixture of mannanoligosaccharides (PSY2, positive control), micro algae containing β-glucan (PSA1), brown macro algae containing fucoidan and laminarin (PSA2), and green macro algae containing ulvan (PSA3) on intestinal porcine epithelial cells J2 (IPEC-J2) was studied in the presence and absence of the enterotoxigenic bacterium Escherichia coli k99 strain (ETEC) as an in vitro challenge. The E.coli-k99 strain with adhesion factor F41 (41/32) was isolated from a mastitis-infected udder. In addition, a mixed extract prepared from vegatal orgin supplemented with phenolic compounds from vegetal origin, zinc and selenium (9631), and ZnO were tested to compare responses to NSP extracts. Gene expression was measured in IPEC-J2 cells after 2 and 6 hours of incubation using “whole genome” porcine microarrays (submission as a conference paper at the SEAGRICULTURE 2017 6th International Seaweed Conference).
2023-06-01 | GSE100838 | GEO
Project description:Spatially resolved transcriptomics (SRT) measures mRNA transcripts at thousands of locations within a tissue slice, revealing spatial variations in gene expression and distribution of cell types. In recent studies, SRT has been applied to tissue slices from multiple timepoints during the development of an organism. Alignment of this spatiotemporal transcriptomics data can provide insights into the gene expression programs governing the growth and differentiation of cells over space and time. We introduce DeST-OT (Developmental SpatioTemporal Optimal Transport), a method to align SRT slices from pairs of developmental timepoints using the framework of optimal transport (OT). DeST-OT uses semi-relaxed optimal transport to precisely model cellular growth, death, and differentiation processes that are not well-modeled by existing alignment methods. We demonstrate the advantage of DeST-OT on simulated slices. We further introduce two metrics to quantify the plausibility of a spatiotemporal alignment: a growth distortion metric which quantifies the discrepancy between the inferred and the true cell type growth rates, and a migration metric which quantifies the distance traveled between ancestor and descendant cells. DeST-OT outperforms existing methods on these metrics in the alignment of spatiotemporal transcriptomics data from the development of axolotl brain.
| S-EPMC10942402 | biostudies-literature
Project description:The formose reaction in reverse micelles of aerosol-OT (AOT), triton X-100 (TX), and hexadecyltrimethylammonium bromide (CTAB) was investigated. Time-conversion data have indicated that the interfacial water layer of AOT reverse micelles is a medium that accelerates formation of glycolaldehyde in the formose reaction. The 13C NMR spectra for the products of the formose reaction using formaldehyde-13C as starting material are indicative of the formation of ethylene glycol as a major product.
| S-EPMC5238542 | biostudies-literature