Chitin bead attached strains
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA414740 | ENA |
REPOSITORIES: ENA
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Project description:Marine picocyanobacteria <i>Prochlorococcus</i> and <i>Synechococcus</i>, the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, while studying the ability of picocyanobacteria to supplement photosynthetic carbon fixation with the use of exogenous organic carbon, we found the widespread occurrence of genes for breaking down chitin, an abundant source of organic carbon that exists primarily as particles. We show that cells that encode a chitin degradation pathway display chitin degradation activity, attach to chitin particles, and show enhanced growth under low light conditions when exposed to chitosan, a partially deacetylated soluble form of chitin. Marine chitin is largely derived from arthropods, which underwent major diversifications 520 to 535 Mya, close to when marine picocyanobacteria are inferred to have appeared in the ocean. Phylogenetic analyses confirm that the chitin utilization trait was acquired at the root of marine picocyanobacteria. Together this leads us to postulate that attachment to chitin particles allowed benthic cyanobacteria to emulate their mat-based lifestyle in the water column, initiating their expansion into the open ocean, seeding the rise of modern marine ecosystems. Subsequently, transitioning to a constitutive planktonic life without chitin associations led to cellular and genomic streamlining along a major early branch within <i>Prochlorococcus</i>. Our work highlights how the emergence of associations between organisms from different trophic levels, and their coevolution, creates opportunities for colonizing new environments. In this view, the rise of ecological complexity and the expansion of the biosphere are deeply intertwined processes.
2024-02-21 | MTBLS5229 | MetaboLights
Project description:Previous studies have demonstrated that the iron content in marine heterotrophic bacteria is comparatively higher than that of phytoplankton. Therefore, they have been indicated to play a major role in the biogeochemical cycling of iron. In this study, we aimed to investigate the potential of viral lysis as a source of iron for marine heterotrophic bacteria. Viral lysates were derived from the marine heterotrophic bacterium, Vibrio natriegens PWH3a (A.K.A Vibrio alginolyticus). The bioavailability of Fe in the lysates was determined using a model heterotrophic bacterium, namely, Dokdonia sp. strain Dokd-P16, isolated from Fe-limited waters along Line P transect in the Northeastern Pacific Ocean. The bacteria were grown under Fe-deplete or Fe-replete conditions before being exposed to the viral lysate. Differential gene expression following exposure to the viral lysate was analyzed via RNA sequencing to identify differentially expressed genes under iron-replete and iron-deplete conditions. This study would provide novel insights into the role of viral lysis in heterotrophic bacteria in supplying bioavailable iron to other marine microorganisms under iron-limiting and non-limiting conditions. First, the marine heterotrophic bacterium genome, Dokdonia sp. strain Dokd-P16, was sequenced to provide a genomic context for the expression studies. Subsequently, the relative gene expression in Dokdonia sp. strain Dokd-P16 grown under Fe limiting and non-limiting conditions were analyzed. This transcriptomic approach would be utilized to elucidate genes regulated by Fe availability in Dokdonia sp. strain Dokd-P16, which indicate its Fe-related response viral lysate exposure. Taken together, in this study, the transcriptomic responses of Fe-limited and non-limited marine heterotrophic bacteria were analyzed, which provided novel insights into the biological availability of Fe from the viral lysates.
2021-11-01 | GSE166618 | GEO
Project description:Bacteria isolated from potato scab lesions in Finland or northern Sweden were analyzed using microarrays, PCR, and sequencing. Data indicate wide genetic variability in pathogenicity islands among S.turgidiscabies and S.scabies strains.
2010-02-01 | GSE18665 | GEO
Project description:Strains VCXB21 and VCXB21 pDel were added 0.6 mM chitobiose at early log phase. Samples isolated after 30 min. cDNA from VCXB21 was prepared from 2 ug RNA and labeled with Cy3. cDNA from VCXB21pDel was prepared from 2 ug RNA and labeled with Cy5. A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out. Keywords: genetic_modification_design
2005-08-11 | GSE3103 | GEO
Project description:The DNA content of bacteriophages from Bartonella grahamii was investigated by hybridization against cellular DNA from the same organism. Phage particles were isolated from plate grown bacteria as well as from different growth phases during culture in liquid medium.
2009-07-04 | E-MEXP-2149 | biostudies-arrayexpress
Project description:Abstract: Chitin, an insoluble polymer of GlcNAc, is an abundant source of carbon, nitrogen, and energy for marine microorganisms. Microarray expression profiling and mutational studies of Vibrio cholerae growing on a natural chitin surface, or with the soluble chitin oligosaccharides (GlcNAc)(2-6), GlcNAc, or the glucosamine dimer (GlcN)2 identified three sets of differentially regulated genes. We show that (i) ChiS, a sensor histidine kinase, regulates expression of the (GlcNAc)(2-6) gene set, including a (GlcNAc)2 catabolic operon, two extracellular chitinases, a chitoporin, and a PilA-containing type IV pilus, designated ChiRP (chitin-regulated pilus) that confers a significant growth advantage to V. cholerae on a chitin surface; (ii) GlcNAc causes the coordinate expression of genes involved with chitin chemotaxis and adherence and with the transport and assimilation of GlcNAc; (iii) (GlcN)2 induces genes required for the transport and catabolism of nonacetylated chitin residues; and (iv) the constitutively expressed MSHA pilus facilitates adhesion to the chitin surface independent of surface chemistry. Collectively, these results provide a global portrait of a complex, multistage V. cholerae program for the efficient utilization of chitin. This SuperSeries is composed of the SubSeries listed below.
2006-03-08 | GSE4388 | GEO
Project description:Marine bacteria isolated from Sargassum ilicifolium macroalgae
| PRJNA1223677 | ENA
Project description:Phytoplankton-bacteria interactions are pivotal in marine ecosystems, influencing primary production and biogeochemical cycles. Diatoms engage in diverse relationships with bacteria, ranging from mutualism to pathogenicity. This study explores the interaction between a novel Alteromonas macleodii strain from the Equatorial Pacific and the model Thalassiosira pseudonana across the diatom different growth phases. We demonstrate that A. macleodii’s algicidal activity depends on the diatom’s growth phase, defensive capacity, and nutrient availability. The algicidal effect manifests during the diatom’s stationary phase or with external nutrient supplementation, implicating organic matter availability as a key driver. Transcriptomic analysis reveals that A. macleodii shifts from motility-associated to growth-associated gene expression based on the diatom’s physiology and coculture duration. Filtrate assays and fluorescence microscopy suggest a two-stage infection model: initial bacterial motility and exudate secretion induce diatom death, followed by bacterial aggregation around debris. Comparative transcriptomics with other algal hosts highlights host-specific bacterial responses, underscoring the context-dependent nature of these interactions. Our findings provide a deeper understanding of the molecular mechanisms driving diatom-bacteria interactions, shedding light on their role in marine microbial ecology and ecosystem functioning.
2026-02-10 | GSE291849 | GEO