In situ expression of nifD in Geobacteraceae in subsurface sediments.

Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
Applied and Environmental Microbiology (Impact Factor: 3.95). 01/2005; 70(12):7251-9. DOI: 10.1128/AEM.70.12.7251-7259.2004
Source: PubMed

ABSTRACT In order to determine whether the metabolic state of Geobacteraceae involved in bioremediation of subsurface sediments might be inferred from levels of mRNA for key genes, in situ expression of nifD, a highly conserved gene involved in nitrogen fixation, was investigated. When Geobacter sulfurreducens was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and Fe(III) as the electron acceptor, levels of nifD transcripts were 4 to 5 orders of magnitude higher than in chemostat cultures provided with ammonium. In contrast, the number of transcripts of recA and the 16S rRNA gene were slightly lower in the absence of ammonium. The addition of acetate to organic- and nitrogen-poor subsurface sediments stimulated the growth of Geobacteraceae and Fe(III) reduction, as well as the expression of nifD in Geobacteraceae. Levels of nifD transcripts in Geobacteraceae decreased more than 100-fold within 2 days after the addition of 100 microM ammonium, while levels of recA and total bacterial 16S rRNA in Geobacteraceae remained relatively constant. Ammonium amendments had no effect on rates of Fe(III) reduction in acetate-amended sediments or toluene degradation in petroleum-contaminated sediments, suggesting that other factors, such as the rate that Geobacteraceae could access Fe(III) oxides, limited Fe(III) reduction. These results demonstrate that it is possible to monitor one aspect of the in situ metabolic state of Geobacteraceae species in subsurface sediments via analysis of mRNA levels, which is the first step toward a more global analysis of in situ gene expression related to nutrient status and stress response during bioremediation by Geobacteraceae.

  • [Show abstract] [Hide abstract]
    ABSTRACT: Innovative methods for biogas upgrading based on biological/in-situ concepts have started to arouse considerable interest. Bioelectrochemical removal of CO2 for biogas upgrading was proposed here and demonstrated in both batch and continuous experiments. The in-situ biogas upgrading system seemed to perform better than the ex-situ one, but CO2 content was kept below 10% in both systems. The in-situ system’s performance was further enhanced under continuous operation. Hydrogenotrophic methanogenesis and alkali production with CO2 absorption could be major contributors to biogas upgrading. Molecular studies showed that all the biocathodes associated with biogas upgrading were dominated by sequences most similar to the same hydrogenotrophic methanogen species, Methanobacterium petrolearium (97–99% sequence identity). Conclusively, bioelectrochemical removal of CO2 showed great potential for biogas upgrading.
    Bioresource Technology 12/2014; 173:392–398. DOI:10.1016/j.biortech.2014.09.127 · 5.04 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Quantitative PCR (qPCR) enables rapid and sensitive gene quantification and is widely used in genomics, such as biological, medical, environmental, and food sciences. However, sample pretreatment requires the use of conventional DNA extraction kits which are time-consuming and labor intensive. In this study, we investigated four physical lysis only (PLO) methods which are rapid and could serve as alternatives to conventional DNA extraction kits. These PLO methods are bead mill, heating, sonication, and freeze-thaw. Using ethidium bromide-based assay, their performance was evaluated and compared. The effects of cell debris and its removal were also investigated. Bead mill method without cell debris removal appeared to yield the best qPCR results among the four PLO methods. In addition, bead mill method also performed better than conventional DNA extraction kits. It is probably due to the substantial loss of DNA material during the extensive purification of the conventional DNA extraction kits. The bead mill method has been demonstrated to successfully quantify 10(2) to 10(7) copies of the PAH-RHDα gene of Pseudomonas putida.
    Applied Microbiology and Biotechnology 09/2014; 98(20). DOI:10.1007/s00253-014-6064-1 · 3.81 Impact Factor
  • Source


Available from