Temporal transcriptomic microarray analysis of "Dehalococcoides ethenogenes" strain 195 during the transition into stationary phase.
David R. Johnson,Eoin L. Brodie,Alan Hubbard,Gary L. Andersen,Stephen H. Zinder,Lisa Alvarez-Cohen,Lisa Alvarez-Cohen +6 more
TL;DR: DNA microarrays were used to monitor dynamic changes in the transcriptome as “Dehalococcoides ethenogenes” strain 195 transitioned from exponential growth into stationary phase, providing molecular evidence that strain 195 can uncouple dechlorination from net growth.
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Abstract: "Dehalococcoides" bacteria can reductively dehalogenate a wide range of halogenated organic pollutants. In this study, DNA microarrays were used to monitor dynamic changes in the transcriptome as "Dehalococcoides ethenogenes" strain 195 transitioned from exponential growth into stationary phase. In total, 415 nonredundant genes were identified as differentially expressed. As expected, genes involved with translation and energy metabolism were down-regulated while genes involved with general stress response, transcription, and signal transduction were up-regulated. Unexpected, however, was the 8- to 10-fold up-regulation of four putative reductive dehalogenases (RDases) (DET0173, DET0180, DET1535, and DET1545). Another unexpected finding was the up-regulation of a large number of genes located within integrated elements, including a putative prophage and a multicopy transposon. Finally, genes encoding the dominant hydrogenase-RDase respiratory chain of this strain (Hup and TceA) were expressed at stable levels throughout the experiment, providing molecular evidence that strain 195 can uncouple dechlorination from net growth.
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Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases
Laura A. Hug,Farai Maphosa,David Leys,Frank E. Löffler,Frank E. Löffler,Hauke Smidt,Elizabeth A. Edwards,Lorenz Adrian +7 more
TL;DR: An orthologue-based classification system for the reductive dehalogenases is proposed to aid integration of new sequencing data and to unify terminology.
307
Biochar: Carbon Sequestration, Land Remediation, and Impacts on Soil Microbiology
TL;DR: In this article, the characteristics of biochar, its availability for nutrient cycling, including the beneficial and potentially negative/inhibitory impacts, and the requisite multidisciplinary analysis (physicochemical, microbiological, and molecular) to study these in detail, are explored.
Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria
TL;DR: The potential of ecogenomics approaches in developing high-throughput methods for detecting and monitoring organohalide respirers, and for providing improvements to selection, specificity and sensitivity of target biomarkers and their application to evaluate bioremediation strategies are discussed.
175
Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense : global transcriptomic and proteomic analyses
Yujie Men,Helene Feil,Nathan C Verberkmoes,Manesh B Shah,David R. Johnson,David R. Johnson,Patrick K. H. Lee,Patrick K. H. Lee,Kimberlee A. West,Stephen H. Zinder,Gary L. Andersen,Lisa Alvarez-Cohen,Lisa Alvarez-Cohen +12 more
TL;DR: 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 H2 and acetate for growth, along with potential benefits from proton translocation, cobalamin-salvaging and amino acid biosynthesis.
Monitoring Abundance and Expression of “Dehalococcoides” Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column
Sebastian Behrens,Mohammad F. Azizian,Paul J. McMurdie,Andrew R Sabalowsky,Mark E. Dolan,Lew Semprini,Alfred M. Spormann +6 more
TL;DR: It is found that 50% of the Dehalococcoides population in the first part of the column did not contain either one of the known chloroethene RDase genes, and a microbial community dominated by members of Firmicutes and Actinobacteria was revealed.
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