Leptospirillum ferrooxidans
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PROVIDER: PRJNA326909 | ENA |
REPOSITORIES: ENA
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Project description:Full title: Environmental transcriptome analysis of LfeRT32a in its natural microbial community comparing the biofilm and planktonic modes of life. Extreme acidic environments are characterized among other features by the high metal content and the lack of nutrients (oligotrophy). Macroscopic biofilms and filaments usually grow on the water-air interface or under the stream attached to solid substrates (streamers). In the Tinto River (Spain), brown filaments develop under the water stream where the Gram-negative iron-oxidizing bacteria Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans are abundant. Both microorganisms play a critical role in bioleaching processes for industrial (biominery) and environmental applications (acid mine drainage, bioremediation). The aim of this study was to investigate the physiological differences between the free living (planktonic) and the sessile (biofilm associated) lifestyles of L. ferrooxidans as part of a natural extremely acidophilic community.
2016-06-23 | GSE20267 | GEO
Project description:Purpose: Study transcriptome differences between biofilm, planktonic and stationary cultures. Methods: Total mRNA from in vitro cultures was extracted and sequenced using Ion Torrent PGM sequencer. Results: Characteristic transcriptomic profile was observed for biofilm, planktonic and stationary cultures. Biofilm and planktonic were similar biological states. Conclusions: Results suggest that H. parasuis F9 has more active metabolism during biofilm or planktonic growth when compared to stationary culture. Some identified membrane-related genes could play an important role in biofilm life.
2014-04-02 | GSE56428 | GEO
Project description:Purpose: The goal of this study was to use RNA-seq to define the Klebsiella pneumoniae transcriptome recorded under 5 different experimental conditions, and to identify signature genes of each condition by comparing global transcriptional profiles. Methods: mRNA profiles were generated for Klebsiella pneumoniae CH1034 clinical isolate, in triplicate, by deep sequencing. Total RNAs were harvested from bacteria cultured at 37°C in M63B1 minimal media under different conditions: (i) planktonic aerobic condition at OD 620nm=0.250 (exponential growth-phase), (ii) overnight planktonic aerobic condition (stationnary growth-phase), (iii) biofilm in a flow-cell chamber after 7 hours of incubation (7-hours old biofilm), (iv) biofilm in a flow-cell chamber after 13 hours of incubation (13-hours old biofilm), (v) bacteria self-dispersed from biofilm recovered in the flow-cell effluent (biofilm-dispersed bacteria). Ribosomal RNAs were removed using the Bacteria Ribo-Zero Magnetic kit (Epicentre Biotechnologies). Libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Illumina), and 50bp single-reads were obtained by HiSeq 2000 (Illumina).The sequence reads that passed FastQC quality filters were mapped to the CH1034 genome using BurrowsâWheeler Aligner (BWA) (0.7.12-r1039 version). The transcript levels were determined using HTSeq-count (0.6.1p1 version) with union mode followed by DESeq (1.16.0 version) analysis. qRTâPCR validation was performed using SYBR Green assays. Results: We found that each condition has a specific transcriptional profile, and we identify 4 robust signature genes for each. Conclusion: Our study represents the first detailed analysis of K. pneumoniae transcriptomes under different experimental conditions generated by RNA-seq technology. The data reported here should permit the dissection of complex biologic functions involved in the transition between the sessile and planktonic modes of growth. Determination of the transcriptional profiling of Klebsiella pneumoniae under 5 different experimental conditions. mRNA profiles were generated for bacteria under exponential planktonic growth-phase, stationary planktonic growth-phase, 7 hours-old biofilm, 13 hours-old biofilm and biofilm-dispersed modes, each in three biological replicates, by deep sequencing using Illumina HiSeq
2016-03-03 | E-GEOD-71754 | biostudies-arrayexpress
Project description:Purpose: Study transcriptome differences between biofilm, planktonic and stationary cultures. Methods: Total mRNA from in vitro cultures was extracted and sequenced using Ion Torrent PGM sequencer. Results: Characteristic transcriptomic profile was observed for biofilm, planktonic and stationary cultures. Biofilm and planktonic were similar biological states. Conclusions: Results suggest that H. parasuis F9 has more active metabolism during biofilm or planktonic growth when compared to stationary culture. Some identified membrane-related genes could play an important role in biofilm life. RNA profiles of 36 hours biofilm or planktonic cultures were generated and compared with stationary culture profile.
2014-04-02 | E-GEOD-56428 | biostudies-arrayexpress
Project description:Leptospirillum ferrooxidans overview
| PRJNA73289 | ENA
Project description:Transcriptional profiling of Candida albicans cells grown under planktonic and biofilm-inducing conditions, comparing SN76 and sfl1Δ/sfl1Δ strains. Goal was to study the effect of SFL1 deletion on the transcriptomic profile of C. albicans planktonic and biofilm cells under acidic conditions, in order to reveal the function of the Sfl1 transcription factor in C. albicans biofilm development.
2023-03-03 | GSE206208 | GEO
Project description:Transcriptional profiling of Candida glabrata zap1Δ and zap1Δ::ZAP1 strains, comparing cells grown under planktonic and biofilm-inducing conditions. Goal was to analyse the effect of ZAP1 deletion in the transcriptomic profile of C. glabrata biofilm cells (in comparision to planktonic cells), under acidic conditions, in order to study the function of the Zap1 transcription factor in C. glabrata biofilm matrix production.
2024-08-08 | GSE226915 | GEO
Project description:Multispecies biofilms are the predominant form of bacterial growth in natural and human-associated environments. Although the pathways involved in monospecies biofilm have been well characterized, less is known about the metabolic pathways and emergent traits of a multispecies biofilm community. Here, we performed a transcriptome survey of the developmental stages of a 3-species biofilm community and combined it with quantitative imaging and growth experiments. We report the remodelling of central metabolism of two of the three species in this community. Specifically, we observed an increase in the expression of genes associated with glycolysis and pentose phosphate pathways in K. pneumoniae. Similarly, a decrease in the expression of the same pathways in P. protegens was observed along with an increase in expression of glyoxalate cycle genes when grown as a mixed species biofilm, suggesting reorganisation of metabolic pathways and metabolite sharing for the community biofilms. To test the possibility of cross-feeding for the community, planktonic growth experiments revealed that both the Pseudomonads grew well in TCA cycle intermediates, while K. pneumoniae grew poorly when given those carbon sources. Despite this poor growth in mono-culture, K. pneumoniae was still the dominant species in mixed species biofilms cultivated in TCA intermediates as the sole source of carbon. The biofilm growth data, combined with the transcriptomics data, suggests there is reorganisation of metabolism for the community members and may allow for cross-feeding that allows K. pneumoniae to dominate the community. We also demonstrated that sdsA1 of P. aeruginosa was induced upon exposure to the surfactant SDS and that this gene was essential in protecting mono and mixed species biofilms from surfactant stress. This also suggests that the community members can share defence mechanisms. Overall, this study describes a comprehensive transcriptomics level investigation of shared resources, metabolites and stress defence that may underpin the emergent properties of mixed species biofilm communities.
2022-10-07 | GSE214543 | GEO
Project description:Transition of microbial growth from planktonic to biofilm is associated with programmed changes in the global patterns of gene expression. These changes are likely to faciliate the appropriate physiological and metabolic adjustments that bacteria need to make during the development of biofilms. Using microarrays we have examined the changes in pattern of gene expression associated with growth of Mycobacterium smegmatis in various stages of planktonic and biofilm cultures. Keywords: developmental time course
2007-10-20 | GSE6935 | GEO
Project description:Biofilms undergo a life cycle where cells attach to a surface, grow and produce a structured community before dispersing to seed biofilms in new environments. Progression through this life cycle requires controlled temporal gene expression to maximise fitness at each stage. Previous studies have focused on the essential genome for the formation of a mature biofilm, but here we present an insight into the genes involved at different stages of biofilm formation. We used TraDIS-Xpress (a massively parallel transposon mutagenesis using transposon-located promoters to assay expression of all genes in the genome) to determine how gene essentiality and expression affects the fitness of E. coli growing as a biofilm on glass beads after 12, 24 and 48 hours. An E. coli transposon mutant library of approximately 800,000 unique mutants was grown on glass beads, and a planktonic sample was taken alongside this at each time point to compare gene essentiality and expression at each time point.
2021-06-09 | E-MTAB-9873 | biostudies-arrayexpress