Cadmium is one of the most troublesome heavy metal contaminants in the environment, and it threatens human health even at low concentrations because it is mobile in soil, bioavailable, and prone to accumulating in living organisms. A research team reporting in Current Genetics has now taken a genomic look at a yeast strain that shrugs off this metal. The non-conventional yeast Wickerhamomyces anomalus BT3, isolated from traditional fermented beverages, tolerated cadmium chloride concentrations exceeding 1000 micromolar in laboratory assays, and whole-genome sequencing of the strain has revealed a set of genes that plausibly underpin that resistance.
The study began with a simple screening question: which yeasts can survive cadmium exposure? The researchers evaluated eight isolates from the genera Pichia and Wickerhamomyces, organisms their group had previously collected from tropical fruits, cacao fermentation, and traditional fermented beverages and shown to tolerate osmotic stress, high temperature, ethanol, organic acids, and toxic agents such as furfural. In a spot assay, cultures adjusted to roughly 108 colony-forming units per milliliter were serially diluted and spotted onto agar plates containing cadmium chloride at concentrations from 40 to 300 micromolar. The Wickerhamomyces strains proved more tolerant than the Pichia kudriavzevii isolates, whose growth was inhibited above 40 micromolar. Among the Wickerhamomyces strains, BT3 coped best with the highest exposures of 200 to 300 micromolar.
Growth curve experiments extended the picture. When BT3 was cultured in broth containing up to 200 micromolar cadmium chloride, its growth pattern did not differ significantly from that of cultures grown without the metal, and the yeast entered its logarithmic growth phase within 24 hours. At higher concentrations, however, the story changed. Above 400 micromolar, BT3 required a prolonged lag phase of 96 to 168 hours before resuming growth, yet it remained viable through that delay and subsequently entered log phase even at 1000 micromolar cadmium. By contrast, the cadmium-sensitive comparison strain Pichia kudriavzevii 1P4 could not resume growth after 400 micromolar treatment. From these data the authors concluded that BT3 has a minimum inhibitory concentration of cadmium chloride greater than 1000 micromolar. The calculated growth rates appeared higher at moderate to high cadmium concentrations when averaged over longer time windows, which the authors attribute to delayed but consistent growth after the extended lag phase rather than to any stimulatory effect of the metal.
That prolonged lag phase is itself biologically interesting. Stress can stretch the lag period as cells pause their division cycle to adapt before resuming growth, a phenomenon documented in filamentous fungi under osmotic stress and linked in bacteria to the need to build specific mechanisms for regulating intracellular metal ion levels. BT3’s ability to pause, adapt, and then grow in cadmium concentrations tenfold higher than those that block a sensitive Pichia strain suggested to the team that a cadmium-tolerant genotype resides in its genome, prompting the sequencing effort.
The genome itself is compact. Sequencing on an MGI DNBSEQ-G400 platform produced 150-base paired-end reads that, after quality filtering, de novo assembly, and polishing, yielded a genome of roughly 14 million base pairs distributed across 44 contigs, with 85.97 percent reference genome coverage, a robust 50-fold depth of coverage, and Q20 and Q30 quality scores of 98.14 percent and 93.75 percent respectively. The nucleotide composition came out as 32.62 percent adenine, 17.54 percent cytosine, 32.35 percent thymine, and 17.66 percent guanine, giving a guanine-cytosine content of 35.03 percent, close to the 34.5 percent of the reference W. anomalus strain NRRL Y-366-8 and within the range spanned by other Wickerhamomyces species, which varies from 30.5 to 40.5 percent GC.
Functional annotation pointed first to housekeeping biology. Classification against the EggNOG and KEGG databases showed that most annotated genes fall into genetic information processing, with prominent clusters of orthologous groups for translation, carbohydrate metabolism, and amino acid metabolism. Yet categories relevant to metal survival also stood out: a substantial number of genes were assigned to inorganic ion transport and metabolism, with significant representation in defense mechanisms and secondary metabolite biosynthesis, hinting at systems for responding to toxic stimuli and producing chelating or neutralizing compounds. Of the 5754 entries, about 49.6 percent of annotated genes, mapped against KEGG, 282 genes were assigned to environmental information processing, a category the authors flag as potentially corresponding to the cadmium-tolerant phenotype.
The most striking findings came from a targeted search for genes orthologous to known Saccharomyces cerevisiae cadmium-tolerance genes. BT3 carries YCF1, which encodes an ATP-binding cassette transporter responsible for pumping cadmium bound to glutathione into the vacuole, the yeast equivalent of a cellular waste compartment, using ATP hydrolysis to drive the process. This vacuolar sequestration of bis(glutathionato)cadmium is a classic detoxification route in baker’s yeast, where YCF1 was first shown to confer cadmium resistance. BT3 also carries GSH2, which encodes glutathione synthetase, supplying the glutathione that chelates cadmium into the transportable complex. Because cadmium exposure induces oxidative stress, causing lipid peroxidation and membrane damage in sensitive cells, the team also catalogued oxidative stress response genes: SOD1 and SOD2, encoding superoxide dismutases with copper-zinc and iron-manganese cofactors; PRX1, encoding peroxiredoxin; TRX1, encoding thioredoxin; and GLRX, encoding glutaredoxin, all of which help maintain redox balance and scavenge reactive oxygen species. Two transcription factors, CAD1 and CUP2, round out the set. CAD1 is an AP-1-like factor that binds the promoter of glutathione synthesis genes, while CUP2 activates the metallothionein genes CUP1-1 and CUP1-2, which participate in cadmium chelation. In prior studies, mutation of SOD genes or deletion of GSH2 in S. cerevisiae produced cadmium-sensitive phenotypes, underscoring why their presence in BT3 matters.
Comparative genomics placed BT3 in context. Its 6103 functional gene clusters are comparable in number to those of W. anomalus NRRL Y-366-8, with 5848 clusters, and W. ciferrii NRRL Y-1031 F-60-10, with 5462, while other tested yeasts, including Pichia kudriavzevii, Komagataella pastoris, Pichia membranifaciens, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Candida albicans, each had fewer than 5000 clusters. A total of 2212 gene clusters, representing 36 percent of BT3’s clusters and 21,914 proteins, were shared across all the compared yeast species, and 713 clusters encoding 2437 proteins were shared only within Wickerhamomyces. Most intriguingly, 121 gene clusters representing 258 proteins were unique to BT3. Gene ontology enrichment showed these unique clusters are dominated by transmembrane transport activity, with 65 genes, integral membrane components, and dimethyl sulfide monooxygenase activity, with 33 genes, and some encode proteins involved in zinc ion and metal ion binding. The authors suggest the abundance of transporter genes could equip BT3 to sense signals and import nutrients or export waste under variable conditions, while the dimethyl sulfide monooxygenase genes connect to sulfur metabolism, a pathway that in fermentative yeasts shapes the aroma profiles of fermentation products, fitting for a strain originally isolated from traditional fermented beverages.
Phylogenetic analysis based on annotated genes placed the Wickerhamomyces strains on a branch separate from the other yeast genera, and BT3 clustered closest to W. anomalus NRRL Y-366-8, indicating a recent common ancestor. Expansion and contraction analysis of gene families revealed that BT3 has one of the highest gene expansions among the compared species, with 103 expanded clusters against only 12 contracted clusters, a pattern that inflates its genome size and, the authors propose, could have generated novel functions contributing to its cadmium tolerance. The authors also speculate that BT3 may show cross-resistance to other stressors such as copper, given the presence of CUP2 and the metallothionein genes, though this remains a prediction rather than a measured phenotype.
The authors are careful about what their data do and do not show. Every cadmium-tolerance gene in BT3 was identified by orthology to characterized S. cerevisiae genes, and the physiological assays demonstrate survival and growth under cadmium exposure, not the molecular mechanism in action. They state explicitly that further studies are required to clarify the potential involvement of BT3’s unique genetic properties in coping with cadmium exposure and to explore the molecular mode of action of the identified genes. Even so, the combination of a high minimum inhibitory concentration, a food-associated origin for the strain, and a genome stocked with plausible detoxification machinery makes BT3 a candidate for bioremediation or biosensor development, applications the authors argue would be supported by comprehensive physiological and genetic analysis of these non-conventional yeasts. With very limited data currently available on cadmium bioremediation by yeast, a hardy Wickerhamomyces strain with a mapped genome offers a starting point for engineering or selecting microbes that can pull cadmium out of contaminated environments.
Subject of Research: Genomic characterization of cadmium tolerance in the non-conventional yeast Wickerhamomyces anomalus BT3
Article Title: Tolerance of the non-conventional yeast Wickerhamomyces anomalus BT3 to cadmium exposure: a genomic characterization
Article References: Afsari, N. M., Listiyowati, S., Maulana, I., & Astuti, R. I. (2025). Tolerance of the non-conventional yeast Wickerhamomyces anomalus BT3 to cadmium exposure: a genomic characterization. Current Genetics, 71(1), Article 16. https://doi.org/10.1007/s00294-025-01322-z
Image Credits: AI Generated
DOI: 10.1007/s00294-025-01322-z
Keywords: Wickerhamomyces anomalus, cadmium tolerance, whole genome sequencing, bioremediation, YCF1, glutathione, oxidative stress, gene clusters, non-conventional yeast, heavy metal contamination, comparative genomics, yeast genomics
News Source: Juliet Wilcox. (November 5, 2026). Genome of cadmium-tolerant yeast Wickerhamomyces anomalus BT3 reveals detoxification genes. Scienmag.
