Gene Array Analysis of Sulfate-Reducing Bacteria Grown on an Iron Electrode under Conditions of Cathodic Protection
Bibliographic record
Abstract
Abstract Sulfate-reducing bacteria (SRB) can contribute to microbially-influenced corrosion (MIC) of iron. Removal of hydrogen formed at the metal surface is often regarded as a critical step in the progression of MIC. Hence SRB-mediated iron corrosion and hydrogen oxidation may be comparable processes. Because the genome sequence of the model SRB Desulfovibrio vulgaris Hildenborough (DvH) is now known, this theory can be tested by genomics technologies. D. vulgaris has four periplasmic hydrogenases to oxidize molecular hydrogen, one iron-only (Hyd), two nickel-iron (Hyn1 and Hyn2) and one nickel-iron-selenium (Hys) hydrogenase. Total RNA was extracted from lactate-grown cells, from 5%- or 50%-hydrogen-grown cells and from cells grown under conditions of cathodic protection. The lactate-and hydrogen-grown cells were planktonic, whereas the cathodic-protection-grown cells were attached to the iron electrode. Genome-wide gene expression profiles were obtained by hybridizing labelled cDNA made from the extracted RNA preparations with microarrays containing a 70-mer oligonucleotide probe for each of the approximately 3000 genes from DvH. Hyd appeared most important for planktonic growth on lactate and 50% hydrogen, whereas Hys was most important for planktonic growth at 5% hydrogen. In contrast, Hyn1 was strongly upregulated in cells grown under cathodic protection conditions. The Hmc complex, which allows transmembrane electron transfer, was similarly upregulated under these conditions. Overall the gene expression profile of cathodic-protection-grown cells most closely resembled that of 5% hydrogen-grown cells and indicated an important role for Hyn1 hydrogenase in MIC by the SRB DvH. This was confirmed by determining MIC rates, which were lower for mutants lacking Hyn1, the Hmc complex, or Hyd, as compared to the wild type.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".