ArticleApplied and environmental microbiology2004
In situ expression of nifD in Geobacteraceae in subsurface sediments.
Article in Applied and environmental microbiology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed, 115 citations in OpenAlex.
- Microbial diversity and metabolic potential in long-term Cr(VI) polluted soil during in situ biostimulation: a pilot effective assay.Environmental science and pollution research international · 2025Article
- Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification.The ISME journal · 2025Article
- Rhizosphere Diazotrophs and Other Bacteria Associated with Native and Encroaching Legumes in the Succulent Karoo Biome in South Africa.Microorganisms · 2022Article
- Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids.The ISME journal · 2021Article
- Article
- Biomolecular Interaction Studies Between Cytochrome PpcA FromFrontiers in microbiology · 2018Article
- Analysis of nifH-RNA reveals phylotypes related to Geobacter and Cyanobacteria as important functional components of the NMicrobiologyOpen · 2017Article
- Evidence of Geobacter-associated phage in a uranium-contaminated aquifer.The ISME journal · 2015Article
- Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea).Frontiers in microbiology · 2014Article
- Nitrogen fixation in distinct microbial niches within a chemoautotrophy-driven cave ecosystem.The ISME journal · 2013Article
- Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community.The ISME journal · 2013Article
- Molecular analysis of the in situ growth rates of subsurface Geobacter species.Applied and environmental microbiology · 2013Article
- Characterization and transcription of arsenic respiration and resistance genes during in situ uranium bioremediation.The ISME journal · 2013Article
- Evaluation of a genome-scale in silico metabolic model for Geobacter metallireducens by using proteomic data from a field biostimulation experiment.Applied and environmental microbiology · 2012Article
- Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation.Applied and environmental microbiology · 2012Article
- Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus.The ISME journal · 2012Article
- Application of meta-transcriptomics and -proteomics to analysis of in situ physiological state.Frontiers in microbiology · 2012Article
- Gene Expression Correlates with Process Rates Quantified for Sulfate- and Fe(III)-Reducing Bacteria in U(VI)-Contaminated Sediments.Frontiers in microbiology · 2012Article
- Extracellular reduction of uranium via Geobacter conductive pili as a protective cellular mechanism.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Molecular analysis of the metabolic rates of discrete subsurface populations of sulfate reducers.Applied and environmental microbiology · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.