What this entity is
Nickel is a chemical element and metal examined through genome-wide fitness measurements. 1
Known alias: Ni. 1
No stable external identifier is specified in the source document. 1
Fitness and stress-response evidence
Nickel had a 39.3% overlap between nickel-important genes and NaCl-important genes in the cross-organism analysis, based on 17 organism × nickel comparisons. 1
In the DvH whole-genome correlation hierarchy, nickel fitness profiles correlated with NaCl fitness profiles at Pearson r=0.446. 1
Nickel’s NaCl overlap was lower than zinc at 44.6%, cobalt at 41.3%, and copper at 41.0%, but higher than uranium at 37.2%, iron at 33.3%, chromium at 29.2%, selenium at 26.8%, mercury at 23.4%, tungsten at 10.8%, and molybdenum at 9.2%. 1
The report interprets nickel’s relatively high NaCl correlation as consistent with broad toxicity involving essential-cofactor displacement or disruption of multiple cellular systems, but this is an extrapolation from fitness-profile hierarchy rather than a direct biochemical test. 1
After removing genes shared between metal and NaCl stress responses, nickel’s core-genome enrichment delta increased from +0.088 to +0.098. 1 This increase supports the conclusion that the Metal Fitness Atlas nickel signal was not produced solely by shared NaCl-stress genes. 1
The report classifies the shared NaCl and metal signal as shared-stress biology rather than evidence that chloride delivered by nickel salts is the primary driver, although the analysis did not isolate chloride from sodium or osmotic effects. 1
The metal-specificity analysis refines this broad-stress interpretation: 993 of 2,271 nickel-important gene records, or 43.7%, were classified as metal-specific because they showed significant metal fitness defects but a sick rate below 5% across non-metal experiments. 2 Thus, nickel has a substantial condition-specific component alongside the previously observed NaCl overlap. 2
Cross-metal fitness evidence
The metal cross-resistance analysis supports the broad-stress interpretation: nickel fitness profiles were positively associated with cobalt, zinc, and copper, with mean correlations of r = 0.56 across 28 organisms, r = 0.51 across 18 organisms, and r = 0.43 across 24 organisms, respectively. 3
Nickel also showed a weaker listed association with aluminum (r = 0.34), which refines the existing interpretation by indicating a universal positive direction alongside chemistry-dependent magnitudes rather than uniformly interchangeable metal responses. 3
Across the study, 98.1% of gene-level metal-fitness correlations were positive (311/317), and no metal pair showed systematically negative cross-resistance; these results support nickel’s association with shared cellular stress, while not by themselves identifying the biochemical mechanism. 3
Pan-bacterial atlas evidence
The Pan-Bacterial Metal Fitness Atlas supports the existing core-enrichment signal: across 26 nickel-profiled organisms, it identified 1,760 nickel-important genes with a core fraction of 0.877, a core-fraction delta of +0.088, OR=1.93, and p=3.0e-22. 4 This genome-wide result complements the counter-ion analysis because removing genes shared with NaCl increased the delta to +0.098, rather than eliminating the enrichment. 1
The atlas refines the interpretation of nickel resistance by placing nickel among metals whose important genes are predominantly core-genome genes, while the report’s two-tier model reserves specialized accessory functions such as efflux, sequestration, and enzymatic detoxification for a narrower resistance layer. 4 This distinction qualifies the field-versus-lab inference that specific resistance mechanisms may be accessory rather than contradicting it. 5
Field-versus-lab fitness evidence
The field-versus-lab analysis refines the broad-stress interpretation by placing nickel in a heavy-metals category whose important genes had a 71.2% core fraction among 198 genes (OR=0.77 versus baseline, FDR q=0.14); this was lower than the 76.3% all-gene baseline but not statistically significant after correction. 5
Across fitness thresholds, the heavy-metals category was 70.6%, 71.2%, 76.7%, and 76.7% core at thresholds -3.0, -2.0, -1.5, and -1.0, respectively. 5 The report supports and qualifies the existing inference about broad metal stress: it suggests the hypothesis that specific metal-resistance mechanisms, such as efflux pumps and metal-binding proteins, may be accessory, while noting that this is not a direct measurement of genomic acquisition history. 5
Environmental metal-resistance ecology
The MicrobeAtlas analysis refines nickel-specific interpretation by showing that the broader ecological association was tested for aggregate metal type diversity, not for nickel as an isolated causal factor. In the leave-one-metal-out analysis, excluding nickel retained a positive but non-significant association between metal-type diversity and inferred niche breadth (β = +0.0095, p = 0.140); the report notes that removing any one of the 7 metals also compressed predictor variance and reduced power. 6 Thus, the result supports a distributed cross-metal pattern rather than establishing that nickel alone drives ecological generalism. 6
Soil functional-genomics evidence
A separate observational soil analysis included nickel among nine measured metals and identified 2,355 significant COG–metal associations at FDR < 0.05 across 51,748 samples; COG means Cluster of Orthologous Groups functional category and FDR means false discovery rate. 7 This supports the relevance of nickel-associated functional shifts beyond laboratory fitness assays, but does not establish nickel-specific causation or effect size. 7
The soil result refines the existing cross-metal interpretation: metal co-contamination and non-independence among tests leave it unresolved whether individual associations reflect nickel itself or a broader multi-metal response, and planned partial-correlation, effect-size, and spatial analyses remain pending. 7
Related pages
- Counter Ion Effects on Metal Fitness Measurements
- Field vs Lab Gene Importance in *Desulfovibrio vulgaris* Hildenborough
- Gene-Resolution Metal Cross-Resistance Across Diverse Bacteria
- Pan-Bacterial Metal Fitness Atlas
- Metal-Specific vs General Stress Genes
- Metal Resistance Ecology — Phylogenetic Conservation vs. Environmental Selection
- Soil Metal Concentrations Drive Functional Gene Shifts
- condition-specific-fitness
- gene-essentiality
- cofitness-network-architecture
- metal-cross-resistance
- cobalt
- copper
- zinc