Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analysis
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PROVIDER: PRJNA136009 | ENA |
REPOSITORIES: ENA
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Project description:The syntrophic growth of strain 195 with Desulfovibrio vulgaris Hildenborough (DVH) and/or Methanobacterium congolense (MC) enhanced TCE dechlorination process by faster dechlorination rate and more robust growth. Transcriptomes of strain 195 grown in isolation, co- and tri-cultures were obtained by microarray experiments to find out the differential expressed genes corresponding to the syntrophic growth. Thus we can better understand the role of DVH and MC within this syntrophy.
2011-08-01 | GSE26815 | GEO
Project description:The syntrophic growth of strain 195 with Desulfovibrio vulgaris Hildenborough (DVH) and/or Methanobacterium congolense (MC) enhanced TCE dechlorination process by faster dechlorination rate and more robust growth. Transcriptomes of strain 195 grown in isolation, co- and tri-cultures were obtained by microarray experiments to find out the differential expressed genes corresponding to the syntrophic growth. Thus we can better understand the role of DVH and MC within this syntrophy. [Transcriptomic analysis]: Cells of pure strain 195 culture, co-culture and tri-culture were collected at the early exponential phase during TCE dechlorination process for RNA extraction, cDNA synthesis, fragmentation, labelling, and hybridization on microarray. We sought to obtain differential transcription of 195 genes in pure, co- and tri- cultures, in order to understand the role of DVH and MC in the syntrophy of strain 195.
2011-07-31 | E-GEOD-26815 | biostudies-arrayexpress
Project description:Dehalococcoides ethenogenes strain 195 (DE195) was grown in a sustainable syntrophic association with Desulfovibrio vulgaris Hildenborough (DVH) as a co-culture, as well as with DVH and the hydrogenotrophic methanogen Methanobacterium congolense (MC) as a tri-culture using lactate as the sole energy and carbon source. In the co- and tri-cultures, maximum dechlorination rates of DE195 were enhanced by approximately three times (11.0±0.01 ?mol per day for the co-culture and 10.1±0.3 ?mol per day for the tri-culture) compared with DE195 grown alone (3.8±0.1 ?mol per day). Cell yield of DE195 was enhanced in the co-culture (9.0±0.5 × 10(7) cells per ?mol Cl(-) released, compared with 6.8±0.9 × 10(7) cells per ?mol Cl(-) released for the pure culture), whereas no further enhancement was observed in the tri-culture (7.3±1.8 × 10(7) cells per ?mol Cl(-) released). The transcriptome of DE195 grown in the co-culture was analyzed using a whole-genome microarray targeting DE195, which detected 102 significantly up- or down-regulated genes compared with DE195 grown in isolation, whereas no significant transcriptomic difference was observed between co- and tri-cultures. Proteomic analysis showed that 120 proteins were differentially expressed in the co-culture compared with DE195 grown in isolation. Physiological, transcriptomic and proteomic results indicate that the robust growth of DE195 in co- and tri-cultures is because of the advantages associated with the capabilities of DVH to ferment lactate to provide H(2) and acetate for growth, along with potential benefits from proton translocation, cobalamin-salvaging and amino acid biosynthesis, whereas MC in the tri-culture provided no significant additional benefits beyond those of DVH.
| S-EPMC3260503 | biostudies-literature
Project description:Global Transcriptomic and Proteomic Responses of Dehalococcoides ethenogenes Strain 195 to Fixed Nitrogen Limitation
| PRJNA140685 | ENA
Project description:Differental gene expression of three consortia: Dhc195/DVH with exogenous cobalamin, Dhc195/DVH/PF with exogenous cobalamin, Dhc195/DVH/PF without exogenous cobalamin Acronyms: Dhc195: Dehalococcoides mccartyi strain 195; DVH: Desulfovibrio vulgaris Hildenborough; PF: Pelosinus fermentans strain R7
2014-02-05 | GSE45533 | GEO
Project description:Tetrachloroethene (PCE) and trichloroethene (TCE) are prevalent groundwater contaminants that can be completely reductively dehalogenated by Dehalococcoides organisms. A Dehalococcoides-containing microbial consortium (ANAS) with the ability to degrade TCE to ethene, an innocuous end-product, was previously enriched from contaminated soil. A whole-genome photolithographic microarray was developed based on the genome of Dehalococcoides ethenogenes 195 (strain 195). This microarray contains probes designed to hybridize to >99% of the predicted protein-coding sequences in the strain 195 genome. DNA from ANAS was hybridized to the microarray to characterize the genomic content of the ANAS enrichment. The microarray revealed that the genes associated with central metabolism including an apparently incomplete carbon fixation pathway, cobalamin salvaging system, nitrogen fixation pathway, and five hydrogenase complexes are present in both strain 195 and ANAS. Although the gene encoding the TCE reductase tceA was detected, 13 of the 19 reductive dehalogenase genes present in strain 195 were not detected in ANAS. Additionally, 88% of the genes in predicted integrated genetic elements in strain 195 were not detected in ANAS, consistent with these elements being genetically mobile. Sections of the tryptophan operon and an operon encoding an ABC transporter in strain 195 were also not detected in ANAS. These insights into the diversity of Dehalococcoides genomes will improve our understanding of the physiology and evolution of these bacteria which is essential in developing effective strategies for bioremediation of PCE and TCE in the environment. Keywords: comparative genomic hybridization Genomic DNA from each culture was divided into replicate samples which were independently fragmented, labeled, and hybridized to arrays. Two microarrays were processed for the positive control (strain 195), two for the negative control (D. restrictus), and five for the ANAS enrichment culture(two analyses from one biological sample followed one year later by three analyses of a second biological sample).
2010-06-20 | E-GEOD-9612 | biostudies-arrayexpress
Project description:Tetrachloroethene (PCE) and trichloroethene (TCE) are prevalent groundwater contaminants that can be completely reductively dehalogenated by Dehalococcoides organisms. A Dehalococcoides-containing microbial consortium (ANAS) with the ability to degrade TCE to ethene, an innocuous end-product, was previously enriched from contaminated soil. A whole-genome photolithographic microarray was developed based on the genome of Dehalococcoides ethenogenes 195 (strain 195). This microarray contains probes designed to hybridize to >99% of the predicted protein-coding sequences in the strain 195 genome. DNA from ANAS was hybridized to the microarray to characterize the genomic content of the ANAS enrichment. The microarray revealed that the genes associated with central metabolism including an apparently incomplete carbon fixation pathway, cobalamin salvaging system, nitrogen fixation pathway, and five hydrogenase complexes are present in both strain 195 and ANAS. Although the gene encoding the TCE reductase tceA was detected, 13 of the 19 reductive dehalogenase genes present in strain 195 were not detected in ANAS. Additionally, 88% of the genes in predicted integrated genetic elements in strain 195 were not detected in ANAS, consistent with these elements being genetically mobile. Sections of the tryptophan operon and an operon encoding an ABC transporter in strain 195 were also not detected in ANAS. These insights into the diversity of Dehalococcoides genomes will improve our understanding of the physiology and evolution of these bacteria which is essential in developing effective strategies for bioremediation of PCE and TCE in the environment. Keywords: comparative genomic hybridization
2008-09-01 | GSE9612 | GEO
Project description:Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing D. ethenogenes strain 195 to fixed nitrogen limitation (FNL). As expected, the nitrogen-fixing (nif) genes were differentially up-regulated in the transcriptome and proteome of strain 195 during FNL. Aside from the nif operon, a putative methylglyoxal synthase-encoding gene (DET1576), which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly up-regulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally down regulated in response to FNL and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition while others were associated with general stress responses. A number of genes related to the biological functions of nucleotide synthesis, replication, transcription, translation, and post-translational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate cellular nitrogen status in the environment. Dehalococcoides ethenogenes strain 195 was grown with or without ammonium in batch cultures with trichloroethene as the electron acceptor, acetate as the carbon source, and hydrogen as the electron donor. Microarrays were used to compare the transcriptome during fixed nitrogen limitation and triplicate biological samples were prepared for each condition. Differentially expressed genes between the two growth conditions were identified using a two-tailed Student's t-test, a false discovery rate of less than 1%, an absolute hybridization signal intensity of 300 or greater in one of the two conditions, and an expression ratio of two-fold or greater.
2012-04-25 | E-GEOD-28855 | biostudies-arrayexpress
Project description:Purpose: The is a major paucity of knowledge regarding the biology of Trypanosoma congolense, a protozoan parasite primarily responsible for Animal African Trypanosomiasis. In contrast, the closely related species T. brucei, is far better understood. To characterise core metabolism in T. congolense, comparative RNAseq analysis was undertaken to assess similarities and differences in transcript levels of genes associated with metabolism Methods: Samples from both in vitro culture and ex vivo (isolated from murine infections) bloodstream-form T. brucei and T. congolense were RNA-sequenced. Data was analyzed using a pipeline that allows for inter-species comparison Results: T. congolense exhibits increased transcript abundance in genes associated with the glycosomal succinate shunt, as well as mitochondrial metabolism, in particular the catabolism of pyruvate to acetate, compared to T. brucei. These differences occur both in vitro and ex vivo. Furthermore there are differences in nucleotide metabolism, and transcript levels of genes involved in fatty acid synthesis are reduced in T. congolense compared to T. brucei. Conclusions: Comparative RNAseq between two closely related species provided a detailed overview of similarities and differences in core metabolism. This carries significant implications for adaptation to in vitro culture, and drug efficacy, mode of action and mode of resistance.
2021-01-22 | GSE165290 | GEO