Applications of Yeasts in Heavy Metal Remediation

Abstract

Yeasts have been extensively recognized as a type of model microorganism due to their facile cultivation, short growth cycle, and genetic stability. Different yeast strains, such as Saccharomyces cerevisiae and Rhodotorula mucilaginosa, have exhibited notable sorption capacities for heavy metals and metalloids. Yeast employs diverse pathways for detoxifying heavy metals via its cell walls, intracellular organelles, and extracellular polymeric substances (EPSs). The cell wall has many functional groups to adsorb metals, decreasing their concentrations in the environment. In intracellular regions, some proteins are capable of transporting metals into biological metabolic processes for detoxification. In extracellular regions, electrostatic as well as complexation mechanisms between protein in EPSs and heavy metals is well accepted. Meanwhile, mannose and glucose within EPSs are target sugars for complexation with metals. Many yeasts can hence work as excellent biomaterials for the bioremediation of metal pollution. Meanwhile, they can be combined with other materials to enhance remediation efficiency. This study reviews underlying mechanisms and cases of yeast-mediated metal detoxification, alongside highlighting yeasts’ industrial applications as bioremediation materials.

1. Introduction

Heavy metals (HMs) can potentially enter the environment through various anthropogenic activities, including industrial waste discharge, mining, gas utility, and agricultural practices [1,2]. HMs and metalloids differ from organic pollutants, as they can be accumulated in living organisms via the food chain [3]. HMs like lead (Pb), cadmium (Cd), chromium (Cr), mercury (Hg), and copper (Cu) and metalloids like arsenic (As) and stibium (Sb) are toxic when their concentrations surpass certain environmental thresholds [4,5].

Bioremediation exploits the innate capabilities of microorganisms and plants to transform environmental pollutants into less toxic forms, effectively degrading or detoxifying harmful substances [6]. Thus, it is recognized as an environmentally sustainable approach for addressing HM contamination [7]. Previous studies have shown that many bacteria, fungi, and algae have strong adsorption and enrichment abilities for HMs [8]. Fungal systems have higher biomass production (along with more extracellular enzymes) over the conventional bacterial systems. Therefore, they can adapt under different growth conditions with varying pH, temperature, etc. This help them to tolerate much higher metal toxicity [9,10].

Yeasts are essentially non-pathogenic microorganisms, possessing a well-established history of application in the manufacture of consumable goods. In addition, S. cerevisiae has received the designation of a safe organism by the US Food and Drug Administration [11]. Consequently, the application of yeasts to HM remediation is further underscored as a promising, environmentally friendly strategy.

Yeasts possess several advantageous traits, including ease of cultivation in well-defined media and rapid generation times. Meanwhile, they demonstrate accessibility in both molecular and genetic techniques, facilitating a deeper understanding of the underlying mechanisms [12]. Many yeast species exhibit remarkable adaptability to various environments [13], making them particularly valuable in diverse remediation contexts. In addition, yeasts are widely used in the fermentation industry, contributing approximately 15% of the total waste generated as by-products [14]. Notably, numerous yeast strains have demonstrated a strong potential for HM fixation (

Table 1. Metal sorption by yeast strains.

Strains	Sorbed Ions	Conditions	pH	References
Saccharomyces cerevisiae	As5+, As3+, Cd2+, Cr6+, Cu2+, Hg2+, Mn2+, Ni2+, Pb2+, Zn2+	0.5 g yeast dosage and incubation time 30 min (Cu2+) 30 °C, 0.1 g/L yeast biomass concentration (Mn2+) 4.5 g dry weight/L biomass concentration (Pb2+, Cr6+) 28 °C (As5+, As3+)	pH 5–7	[17,18,19,20,21,22]
Rhodotorulamucilaginosa	Cd2+, Cr6+, Cu2+, Hg2+, Pb2+, Mn2+, U6+, Zn2+	28 °C	-	[23,24,25,26]
Pichia pastoris	Cu2+	25 °C	pH 6	[27]
Pichia hampshirensis	Zn2+, Cd2+, Pb2+, Ni2+, Cr6+, As2+, Cu2+, Hg2+	30–37 °C (Cd2+)	pH 7	[28]
Meyerozyma guilliermondii	Mn2+, Cr6+, Ag+, Cu2+	incubation time 2 h, 28 °C	-	[29]
Meyerozyma caribbica	Mn2+	incubation time 2 h, 28 °C	-	[29]
Geotrichum sp.	Zn2+, Ni2+, Cu2+	initial metal concentration 80 mg/L, 28 °C, incubation time 48 h (Cu2+) 28 °C, incubation time 60 h (Zn2+, Ni2+)	-	[30]
Candida xylopsoci	Hg2+	30 °C, incubation time 36 h	-	[31]
Candida utilis	Cr6+, Cu2+, Zn2+, Cd2+, Pb2+, Mg2+	28–30 °C, accumulation time 24 h	pH 5	[32]

). In particular, S. cerevisiae and R. mucilaginosa are frequently applied for biosorption of HMs [15,16]. Both conventional yeasts, such as Saccharomycetes spp., and unconventional yeasts of the genera Pichia, Candida, and Yarrowia exhibit a significant capacity to sequester HMs [4].

Two primary mechanisms of metal capture by yeasts are passive capture via inactive biomass (i.e., biosorption) and active uptake through living biomass (i.e., bioaccumulation) [33]. Biosorption is a physicochemical process that predominantly involves the interaction of metals (sorbates) on the surface of microbial cells [34]. The interaction occurs through complexation, chelation, coordination, or ion exchange [35]. In contrast, bioaccumulation refers to the internal sequestration of HMs within microbial cells. Beyond intracellular bioaccumulation and metabolism, and cell wall-mediated biosorption, extracellular polymeric substances (EPSs) represent an equally important mechanism (Figure 1).

2. Mechanisms of Environmental Remediation by Yeasts

2.1. Cell Wall

Yeast belongs to the fungal kingdom. The yeast cell wall constitutes a portion (ranging from 15 to 30%) of its total dry weight [36]. Fungal cell walls are primarily composed of polysaccharides (~80 wt.%) [37]. The fungal cell wall, as the outermost layer, functions as the principal interface between the cell and its immediate environment [38]. The cell wall is anchored to the cytoplasmic membrane [39]. β-1,3-glucan is the fundamental constituent of the cell wall for almost all fungi [40]. The most characteristic polysaccharide in fungal cell walls is chitin [41]. The composition of the fungal cell wall is different from the cell walls of bacteria. For example, Gram-positive bacteria feature a thick peptidoglycan layer, which is composed of alternating β-1,4-linked N-acetylmuramic acid and N-acetylglucosamine chains [42]. This reticular formation is adorned with proteins and glycopolymers [43]. In addition, it hosts wall teichoic acids (WTAs), which are attached to the peptidoglycan layer [44]. Gram-negative bacteria possess a complex cell wall comprising an outer membrane containing phospholipids, lipopolysaccharides, and outer membrane proteins [45,46].

The cell walls of yeasts determine the cell shape and integrity of the organism during growth. Three main groups of polysaccharides forming the cell wall are polymers of mannose (mannoproteins, ~40% of the cell dry mass), polymers of glucose (β-glucan, ~60% of the cell wall dry mass), and polymers of N-acetylglucosamine (chitin, ~2% of the cell wall dry mass) [47]. The different fungi might have variation of the cell wall components. For example, the cell wall of basidiomycetous organisms is characterized by relatively enriched mannan and chitinwhereas the cell wall of ascomycetous yeasts is predominantly made up of glucan and mannan [48]. Approximately 50–60% β-glucans and 35–40% mannoproteins in the cell walls have been widely accepted [36]. The highly active β-glucans usually serve as electron-transmitting components [49]. They have various sub-components. For instance, the cell wall of S. cerevisiae is primarily composed of β-1,3-glucan (~50%), with a minority of β-1,6-glucan (10–15%) [50]. Meanwhile, the electron-dense mannoproteins have a thickness of 30–40 nm. The majority of chitin is localized in bud scars. However, a minor portion is also present in the lateral cell walls [50,51]. The S. cerevisiae cell wall proteins feature N-linked outer chain mannan, which can hold up to 200 mannose residues, accompanied by shorter O-linked mannan chains containing a maximum of five mannose units [40].

Yeast cell walls exhibit considerable diversity across strains. For instance, R. rubra possesses a unique cell wall composition and architecture [52]. Chitin, owing to its intricate and highly branched structure, is widely recognized as an effective sorbent material [53,54]. Based on previous studies on R. rubra, its unique structural features likely contribute to its enhanced sorption capacity [55]. It has been documented that the coordination of metal ions to the amine N of chitin, particularly within the cell wall of R. arrhizus, facilitates sorption of uranium [26]. In addition, the red yeast cell wall contains a fucogalactomannan-type polymer, which contains both fucose and galactose units [56].

2.2. Biosorption by Cell Wall

Biosorption can manifest rapidly (within minutes). It operates independent of metabolism [11]. Surface sorption can occur in various forms, either simultaneously or independently. It includes physical interactions (such as electrostatic or Van der Waals interaction), chemical interactions, complexation, diffusion, and precipitation [57,58]. Biosorption utilizes the interaction of various functional groups, including carboxyl, amino, amide, hydroxyl, sulfhydryl, and phosphate, present in the mannoprotein layer of yeast cell walls. Notably, this process does not require substantial energy input [20,59].

Complexation refers to the process by which two or more chemical species combine to form a stable structure. The formation of mononuclear (monodentate) complexes involves the bonding of ligands to central metal ions. In contrast, a polynuclear complex forms when multiple metal cations are involved [60].

Chelation has been defined as a chelating agent interacting with a metal cation to form a stable complex [35]. An increase in ligand binding sites enhances the stability of the resulting structure. Due to the presence of multiple binding sites, chelates are more stable than simple metal complexes. Functional groups on biosorbents, such as carboxylic acids and carbon–carbon double bonds, play a key role in adsorbing Cd²⁺ ions [61]. Moreover, genetic engineering techniques have been employed to introduce histidine oligopeptides (e.g., hexa-His) on the yeast cell surface, significantly enhancing its ability to bind and sequester divalent HMs, thus enhancing sorption efficiency [62].

Coordination in the complex occurs when the metal atom forms coordinate covalent bonds with neighboring non-metal atoms, accepting a lone pair of electrons from them. This interaction contributes to the structural integrity and functionality of the complex. Coordinate compounds involve bonds formed by non-metal atoms donating lone electron pairs to metal ions. This provides a lone pair of electrons to an atom, which functions as the acceptor. These specific bonds define the structure of these compounds. Common coordinating groups that participate in such interactions include amino, hydroxyl, or other groups [35].

Ion exchange involves the replacement of metal ions by counter-ions on the biosorbent surface [35]. The ion-exchange process between metal ions and the cell walls of non-living yeast cells has been documented [63], further highlighting the versatility of yeasts sorption of heavy metals.

2.3. Intracellular Bioaccumulation

Bioaccumulation is an active, metabolism-driven process in which metal ions accumulate within the intracellular space of living cells [35]. This process is driven by metabolism-dependent mechanisms, such as passive diffusion, ion pumps, and carrier-mediated transport, to actively uptake HMs, thereby influencing their removal efficiency [64]. For detoxification, fungi usually tolerate elevated intracellular metal concentrations via two primary mechanisms, i.e., chelation and compartmentalization. Chelation involves the synthesis of metal-binding ligands. The three major classes of peptides are involved, metallothioneins (MTs), phytochelatins (PCs), and glutathione, which sequester heavy metals within the cytosol [65]. Their chelating abilities are due to the thiol groups of the molecule [66]. In parallel, excess metal ions are often compartmentalized into intracellular organelles such as vacuoles through polyphosphate-mediated transportation, thereby mitigating their cytotoxicity [67].

The bioaccumulation process broadly consists of five steps (see Figure 2) [68]. Certain studies suggest the formation of metal high-molecular-weight complexes (Me-HMWCs) within cellular compartments like the cytosol and organelles, though some studies consider the vacuole as the definitive destination for metals. For example, the bioaccumulation of Pb was observed within the vacuole, as confirmed by energy-dispersive X-ray spectroscopy [69]. Physiologically, transporter Cd factor 1 facilitates the sequestration of glutathione-conjugated Cd into vacuoles [70].

The translocation of HMs across the phospholipid layers of living cells involves two distinct stages. Initially, HMs adhere to the cell surface in a process that is independent of cellular metabolism. Subsequently, in the second stage, these metal ions are internalized through the cell membrane [57]. Metal species are transported inside the cells via active transport, which is a slower process [71]. Distinct from biosorption, this process is irreversible, highly depending on the metabolic activity of microbial cells [72]. The mechanism involves the conveyance of complexes into the cell interior and ionic channels and endocytosis [73].

A variety of transport proteins facilitate the translocation of metal ions within the yeast cells. The potential for Cd and Pb to be transported by the divalent metal transporter 1 (DMT1) has been proposed [74]. DMT1 is able to actively transport a diverse array of divalent cations, encompassing both essential (such as Fe and Mn) and non-essential (like Cd and Pb) metals [75]. In response to combined stress from heavy metals, yeast cells also mobilize additional intracellular ATP reserves to sustain homeostasis [76].

S. cerevisiae possesses antioxidant systems that are pivotal in mitigating HM toxicity [77]. Under heavy metal stress, yeast cells activate a response to oxidative stress. Heavy metals induce oxidative damage to fungal cell membranes primarily via the overproduction of reactive oxygen species (ROS) [65]. To mitigate ROS accumulation, fungi employ a range of antioxidant defense systems. These include enzymatic components such as NADPH-dependent thioredoxin reductases, superoxide dismutase (SOD), catalase, and various peroxidases, which collectively convert ROS into less toxic molecules, like oxygen and water. In addition to enzyme-mediated pathways, non-enzymatic antioxidants such as reduced and oxidized glutathione play a critical role in counteracting ROS-induced cellular damage. Meanwhile, GSH contributes to metal detoxification by chelating cadmium ions, thereby reducing their toxicity within the cell through vacuolar compartmentalization [76]. Then, the storage form of Cd²⁺ mainly consists of a less toxic combination of Cd [78]. In addition, GSH acts as a precursor for the formation of PCs, heavy metal-binding peptides [79]. As the genes encoding the enzyme PC synthase have been identified in yeasts [80], the GSH-dependent PC synthesis pathway is proposed [81]. Further, fermentation of specific polysaccharides by yeast may yield oligosaccharides with the potential to alleviate heavy metal-induced oxidative stress and apoptosis [82].

2.4. Biosorption by EPSs

Microorganisms secrete EPSs as metabolites [83]. EPSs have three-dimensional and gel-like structures, usually serving as biofilm matrixes [84]. They are high-molecular-weight microbial polymers composed of various components, including proteins, polysaccharides, nucleic acids, lipids, etc. [85]. Proteins and polysaccharides constitute the major components of EPSs [86]. The functional groups embedded in these components serve as active sorption sites, facilitating the attraction and retention of a wide range of chemical substances, including toxic inorganic pollutants [87,88]. Some microorganisms like S. cerevisiae and Bacillus thuringiensis have evolved EPS production mechanisms that facilitate the binding of HMs, thereby preventing their internalization [89,90].

The EPSs produced by yeasts include mannans, pullulan, glucooligosaccharides, galactooligosaccharides, and a variety of heteropolysaccharides. These exopolysaccharides may share similarities with, or differ from, those on the microbial cell wall [91]. In yeasts, mannose and glucose, the predominant carbohydrates in EPSs, have a major impact on the overall structure and functionality of these extracellular secretions [92]. EPSs extracted from highly Hg-resistant Yarrowia spp. strains (Idd1 and Idd2) were isolated and evaluated for their exceptional Hg²⁺-binding capabilities. Detailed sorption models validated the intricate interaction between Hg and EPSs, involving heterogeneous multilayer sorption mechanisms [93]. Based on metal-binding assays, the crude EPS exhibits promise and potential as an active biosorbent for the remediation of HMs [94,95]. Furthermore, the red yeast R. mucilaginosa has been particularly addressed due to its abundant EPSs. Enhanced extraction methods have been shown to yield higher amounts of proteins (up to approximately 650 mg/L) and polysaccharides (up to around 2010 mg/L) [96]. This indicates that R. mucilaginosa can work as an excellent material to sorb HMs [97].

3. Remediation of Heavy Metals by Yeasts

3.1. Heavy Metals

The specific sorption of HMs depends on the type of metals. Yeasts have been successfully applied as biosorbents for Pb²⁺ cations [98,99]. For instance, Candida guilliermondii and Candida famata, isolated from wastewater, have a strong ability to sorb Pb [29,100]. At 293 K, the maximum biosorption capacity of Pb cations onto beer yeast was recorded as ~0.03 mmol g⁻¹ [19]. When employing S. cerevisiae, the removal of Cr and Pb increases with a medium pH, exhibiting a higher efficiency at a pH of 5.0 [101]. Pretreatment of yeast cells with corrosion, ethanol, and heat significantly enhances their biosorption, with a peak Pb²⁺ sorption value of 17.49 mg g⁻¹ [102]. Moreover, the biosorption capacity was enhanced at higher initial Pb²⁺ concentrations due to the stimulation by Pb stress [103,104]. Furthermore, the combined of R. mucilaginosa and phosphate minerals offers a synergistic approach to enhance Pb remediation [105]. Moreover, Pb remediation was significantly promoted by phosphate-solubilizing fungi (P. oxalicum and A. niger) combined with fluorapatite [106]. It has been demonstrated that the oxidation of yeast β-glucan with 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) yields oxidized yeast β-glucan. This further enhances the microbial ability to remediate Pb [107].

In terms of Cd sorption, yeasts exhibit the ability to remediate Cd²⁺ through both passive sorption and active intracellular accumulation. Notably, the larger specific surface area of S. cerevisiae, partially due to the thicker mannan layer, has been addressed [18]. The cell surface divalent metal transporter, Fet4p, possesses the ability to transport Cd²⁺. Yet, the aerobic repression of FET4 by the Rox1p repressor serves as a protective mechanism to shield cells from Cd toxicity [108]. In addition, the addition of Cd to yeast triggers the synthesis of glutathione (GSH) [109]. It is a soluble tripeptide, which naturally forms complexes with various metals [110]. Cd is sequestered into vacuoles through the Ycf1 protein in the form of a bis-glutathionato-Cd complex [111]. Pichia hampshirensis is also employed for Cd bioremediation. It demonstrates a remarkable capacity to remove over 20 mM/g of Cd²⁺ from aqueous systems. Moreover, chitin on the surface of Pichia hampshirensis serves as the primary binding site for Cd²⁺ [28]. Dehydrated Candida utilis cells have been utilized effectively for the removal of Cd from dilute solutions [32]. Moreover, Cd²⁺ tolerance of the mixed-species biofilms (R. mucilaginosa and Escherichia coli) was higher than for the single-species biofilms [25]. Dead cells have also emerged as highly effective biosorbents, capable of removing substantial amounts of Cd²⁺ from aqueous environments. They typically expel accumulated metal ions in living cells once a threshold intracellular concentration is reached. Consequently, the absence of efflux in dead cells leads to enhanced intracellular accumulation of Cd²⁺ [28].

Cr is utilized in various industrial activities, e.g., electroplating and steel production, leather tanning, and manufacturing of pigments [112]. Cr⁶⁺ cations pose an evident threat to living organisms due to their extreme toxicity [113]. Yeast Candida etschellsii could remove 80% of Cr⁶⁺ after 72 h incubation [114]. When exposed to Cr⁶⁺ concentrations ranging from 10 to 30 mg L⁻¹, S. cerevisiae demonstrates an average sorption capacity of 92.6% [115]. The bioaccumulation of Cr⁶⁺ by R. mucilaginosa has also been confirmed [24]. Employing a cationic surfactant as a conditioning approach for yeast cell walls significantly bolstered their biosorption capabilities [5]. Microwave irradiation also enhances yeast mobility in a biodegradable cellulose support, offering a sustainable bioremediation option for Cr [115]. Microbial communities display a superior Cr remediation efficiency compared with pure yeast cultures, owing to the synergistic effects among different microorganisms, including yeast and bacterial strains [116]. Furthermore, the yeast extract stands out as the only amendment capable of enhancing abiotic Cr⁶⁺ removal, achieving a maximum efficiency of ~70% due to chemical oxidation [117]. In addition, a precursor derived from yeast biomass serves as a vital source of essential elements, which facilitate the formation of Ni₂P/N-BC catalyst. This enables the heterogeneous catalytic reduction of Cr⁶⁺ to Cr³⁺ [118].

A bio-sequestration experiment showed that yeast strains effectively removed >97% Hg from the medium via bioaccumulation, volatilization, and precipitation [119]. An evaluation of Hg²⁺ removal using both preexisting R. mucilaginosa biofilm and planktonic cells revealed a metal removal efficiency exceeding 90% [25]. Therefore, the biosorption for HMs by R. mucilaginosa is primarily attributed to ion exchange and surface complexation [16]. Yarrowia spp. yeast strains exhibit high self-aggregation and separability, making them suitable for biological purification of Hg-contaminated water [119]. Moreover, Candida xylopsoci, with the highest ability to remediate Hg, was isolated for Hg remediation [31]. The surface of the metalloregulatory protein MerR on S. cerevisiae enhances its ability to immobilize Hg²⁺. The surface-engineered yeast strain can effectively sorb Hg²⁺ in intricate environments, supporting biosorption and bioremediation of Hg pollution [22]. The impregnation of baker’s yeast onto activated carbon with nano-Fe₃O₄ enhances the Hg²⁺ extraction efficiency in alkaline solutions (pH > 4.0) [120].

Cu²⁺ cations can react with oxygen radicals, creating reactive oxygen species (ROS) like O²⁻, H₂O₂, and OH⁻ that are toxic to microorganisms [97]. The high capacity of Cu accumulation by yeasts is observed in many yeast strains, including R. mucilaginosa [121]. It was proposed that the cell wall removed more Cu²⁺ (21.2%) than the membrane (20.7%) and cytoplasm (18.5%) [27]. Both external and internal mechanisms within R. mucilaginosa collaborate to effectively detoxify Cu²⁺ cations [97]. While S. cerevisiae is capable of non-biological sorption of Cu, its efficiency in this regard is significantly lower when using dead yeast compared with biologically active yeasts [122]. As the temperature increases within the pH range of 3 to 4, the sorption of Cu²⁺ onto dried S. cerevisiae cells is favorable [123]. Under 9.6–19.2 mg/L Cu stress, S. cerevisiae exhibited a Cu sorption rate of 60–80%. In addition, at a pH of 7, S. cerevisiae displays a remarkable preference for removing Cu over Al and Ni [17]. During the biosorption experiment with 100 mg/L Cu²⁺, P. pastoris biomass swiftly reached equilibrium in just 15 min. Meanwhile, it achieved a remarkable maximum removal efficiency of 41.1% and a sorption capacity of 6.2 mg/g [27]. The novel yeast strain Geotrichum sp. possesses a notable capability for accumulating HMs, with Zn²⁺ being sequestered most efficiently, followed by Ni²⁺ and Cu²⁺.

Some S. cerevisiae strains have been screened for biosorption and bioaccumulation of Mn²⁺ [18]. The bioremediation of Mn²⁺ has also been investigated via the application of R. mucilaginosa [23]. In addition, Meyerozyma guilliermondii and Meyerozyma caribbica are also used as biosorbents [29]. S. cerevisiae canexhibit high Mn²⁺ biosorption, achieving a maximum at 4.8 mg Mn²⁺/L [18]. The expression of PbMTP8.1, a Mn-specific transporter localized in the pre-vacuolar compartment (PVC), enhances Mn accumulation in S. cerevisiae. Furthermore, the sequestration of Mn into the vacuole by the PbMTP8.1 transporter also imparts Mn tolerance for S. cerevisiae [124]. In addition, the yeast ion pump PMR1 in the medial Golgi is involved in directing Mn²⁺ towards the secretory pathway. Additionally, cytosolic Mn²⁺ accumulates in PMR1 mutants [125]. Moreover, mutations of PMR1 promote microbial sensitivity to the toxicity caused by extracellular Mn²⁺ [126].

3.2. Metalloid

Arsenic, a highly toxic metalloid, is widely recognized as one of the most pervasive environmental carcinogens [127]. Microbial bioremediation of arsenic pollution is feasible. During the fermentation process, yeasts exhibit a remarkable detoxification ability, effectively reducing the initial As concentration by approximately 75% [128]. The toxicity and detoxification mechanism of As in yeasts have been explained using mathematical models [129]. Significant variations were discernible among yeast strains in their resistance to As toxicity. For example, a suitable yeast strain can removed As in wine by up to 40% after fermentation [128].

Yeasts have developed diverse protective mechanisms to counteract As toxicity. These include limiting metal uptake, sequestering within vacuoles, and utilizing proteins/polypeptides for chelation [130,131]. S. cerevisiae possesses an arsenate reductase known as Acr2p, capable of reducing As⁵⁺ to As³⁺ [21]. It has been demonstrated that As can directly interact with and stimulate the activity of the transcription factor Arr1 [132]. Yap1 and Rpn4 are other crucial transcription factors that contribute significantly to As detoxification [127]. For example, Yap1 also participates in the elimination of ROS that are produced by As compounds [133]. In addition, the As response locus in budding yeasts serves as a key mechanism for the detoxification and subsequent expulsion of As [134].

Debaryomyces hansenii, a microorganism known for its high As tolerance, has been reported to mitigate As stress in rice [135]. Yeasts, genetically engineered to express the WaarsM gene for As methyltransferase, possess the capacity to remove As from polluted soil [136]. Under As stress, genetically modified S. cerevisiae exhibited robust As methylation and volatilization capabilities. Consequently, this engineered yeast holds significant potential to regulate As levels in soil and plants [137]. The yeast strain D. hansenii with bacterial strains has been applied to test As suppression in rice [135]. The combined bioinoculant demonstrated remarkable efficacy, achieving a substantial 90% reduction of As concentration within grain [138]. Moreover, it showed that integrating the yeast ACR3 As export system into Arabidopsis enhanced its tolerance to As [139]. Furthermore, the bioremediation of other metalloids has also been investigated. Both natural and human-induced activities contribute to the dissemination of hazardous oxyanions, including selenium (Se) and tellurium (Te), into the environment. Notably, Yarrowia lipolytica and Trichosporon cutaneum have emerged as the superior strains for effectively bioremediating these metalloids [140].

3.3. Factors Influencing Heavy Metal Remediation by Yeasts

The effectiveness of HM remediation is notably influenced by numerous environmental variables, with pH playing a crucial role [141]. This is because pH affects both the accessibility of metal-binding sites on the yeast cell surface and chemical properties of HMs [17]. Since given that cationic species constitute a significant proportion of metals in aqueous solutions, a biosorbent endowed with a higher negative charge can significantly enhance sorption efficiency. HM removal efficiency increases proportionally in acidic environments, peaking at pH 7. Low pH inhibits biosorption by blocking binding sites with hydrogen ions, making the cell surface positive and repelling positively charged ions. The cell wall acquires a net negative charge if the pH is over the isoelectric point, which strengthens its capacity to interact with HMs [142]. Elevated pH values also strengthen the binding between microbial surface groups and metal ions [143]. However, for As and molybdenum (Mo), anionic forms increase biosorption at acidic pHs (2.0–4.0) since the biomass has more positive charges to attract anions [144]. The new wastewater treatment membranes, infused with pH-responsive fillers, dynamically alter the surface properties and channel dimensions [145,146,147,148]. This enhancement, coupled with convective flow mechanisms, adjusts surface properties and accelerates contaminant removal rates [149].

Numerous factors also contribute to the sorption of HMs by yeasts. The presence of an energy source may potentially enhance Cd and Pb bioaccumulation, facilitated by DMT1 [74]. Kazachstania yasuniensis had a biosorption capacity similar to S. cerevisiae. However, Saturnispora quitensis and Kodamaea transpacifica showed an almost four times higher biosorption capacity due to their large surface areas [5]. The efficiency of contaminant removal was contingent upon the yeast strain and metal type. A strong correlation existed between this performance and biomass yields. Certain yeast strains demonstrated remarkable potential in remediating Pb²⁺ and Cd²⁺, achieving reductions of up to 96% and 40%, respectively [150]. Glucose treatment of yeast cells augments their energy availability to enhance metal accumulation from the solution [151].

Biosorption of HMs was also impacted by the dosage, contact time, and initial metal concentrations. As the abundance of adsorbent increases, the number of available adsorption sites also increases [152,153]. For example, Cu²⁺ adsorption onto biobased nanofibers (i.e., cellulose and chitin) increased linearly with surface charge content (carboxylate content) [154]. Furthermore, the mechanism of biosorption is more chemisorption than physical adsorption. It was proposed that functional groups on the cell surface contributed to the binding of metal ions via equilibrium reaction [153]. The removal efficiency gradually diminished as equilibrium was reached between the metal ion concentration and available active sites on the surfaces of fungal cells [18,155]. In addition, biosorption efficiency increases with the initial metal concentration but is eventually constrained by the saturation of binding sites [156]. Moreover, the incubation time also influences biological sorption, with a general increase in metal uptake over time [154].

4. Industrial Applications

Recognized as versatile model organisms with broad applications across various fields [157], yeasts have demonstrated particular promise for industrial applications [158]. Notably, multiple studies have documented the exceptional HM sorption by some yeast strains [30,83,159]. Accordingly, efforts to develop innovative materials for environmental metal remediation could leverage the advantages of yeasts. The abundant biomass, diverse metabolic activities, metal-binding peptides, unique cell walls, genetic modifiability, and resilience to harsh conditions make yeasts efficient for HM bioremediation [4].

Yeast cells, after removing heavy metals from the environment, can be recovered [160]. The desorption of heavy metals from yeast can be achieved using various eluants [161]. The ideal eluant should be non-destructive to the biomass, cost-effective, environmentally sustainable, and highly efficient [162]. The efficiency of metal recovery depends on the choice of eluant and elution conditions. Different eluants have been tested, including mineral acids, organic acids, complexing agents, etc. [163]. Multi-stage processes combining electrochemical and chemical methods have also been investigated. Following the incineration of yeast biomass, metal recovery from acid solutions can achieve a high selectivity and yield [164].

Furthermore, the reusability of yeast biomass has been proposed [165]. To prevent potential secondary environmental pollution or to enable metal recovery and biomass reuse, yeast cells must be efficiently separated from the environment for easy retrieval. Techniques for immobilization have been employed. However, they are affected by pH and the supporting matrix [20]. In addition, flocculation has been investigated as a rapid, cost-effective, and simple approach for cell separation [166]. Additionally, studies have proposed that waste adsorbents can undergo final disposal through soil burial or surface dispersion, enabling natural degradation [160].

4.1. Surface and Genetic Modification

The yeast cell wall functions as a crucial protective barrier against both biotic and abiotic stressors, characterized by a diverse array of functional groups that enhance their biosorption [167]. Through the application of physicochemical, genetic, or molecular methodologies, modifications to the yeast cell wall surface have markedly elevated its biosorption capacities [168]. Display of metallothionines (MTs) on the surface of S. cerevisiae cells has been verified [169]. By genetically engineering yeast to overexpress native membrane and vacuole transporters involved in metal detoxification, their metal accumulation can be significantly augmented [170].

Yeasts exhibit significant potential for HM sorption. Yet, critical limitations include inadequate mechanical stability, a reduced surface area relative to chemical sorbents, and difficulties in metal desorption [4]. To address these challenges, advanced bioengineering strategies have emerged to augment the yeast sorption capacity. Strategies such as chitosan/EDTA modification, ethanol/alkali pretreatment, etc., introduce or expose additional functional groups [171,172,173]. Cationic surfactants like EDTA, EDTAD (ethylenediaminetetraacetic dianhydride), heat treatment, lyophilization, and solvent treatments have been investigated [4]. Specific modifiers elicit changes in the cell wall surface through processes such as fixation, methylation, esterification, carboxylation, and phosphorylation. They can modify the functional groups and boost biosorption activity [174]. Additionally, the expression of surface metal-binding peptides, including PC and glutathione, can affect metal sorption and its toxicity to yeasts [175].

Surface modification can enhance materials with the desired characteristics for practical applications [176,177]. This strategy focuses on increasing the number of functional groups, including phosphates, carboxyl, and sulfonyl, to enhance material properties [178]. Upon EDTAD modification, S. cerevisiae biomass demonstrated an over-10-fold enhancement in Pb²⁺ and Cu²⁺ removal efficiencies [179]. Furthermore, the immobilization of effective groups onto S. cerevisiae biomass substantially augmented its sorption capacity, engineering it into a high-efficiency biosorbent [179]. Similarly, the application of chemical or biological modification techniques on activated carbon surfaces has garnered recognition [180].

The biofabrication of yeast cell surfaces through genetic modification significantly enhances their functionalization [4]. Surface peptides, including PCs, MTs, α-agglutinin anchoring proteins, hexaHis, Cys, and HP3 peptides, function as metalloregulatory proteins in S. cerevisiae and R. mucilaginosa, providing crucial biosorption sites for HMs [181,182]. The incorporation of short metal-binding NP peptides within S. cerevisiae has led to a remarkable three-fold enhancement in the biosorption capacity for Pb²⁺ [183]. Consequently, the cloning and expression of four distinct metallothionein genes from Solanum nigrum within S. cerevisiae significantly enhanced its ability to sorb Cd²⁺ at low concentrations in acidic to neutral environments [184]. In addition, the T68CadR protein with high selectivity towards Cd²⁺ has been successfully expressed in S. cerevisiae [185]. It can enable the yeast to remove up to 85% of Cd²⁺ from mixtures containing Zn²⁺ and Pb²⁺ [186]. Notably, the surface display of synthetic PCs, particularly the (Glu-Cys)₂₀Gly repeat, demonstrates a remarkable enhancement of Cd²⁺ tolerance and biosorption by S. cerevisiae. This modification also facilitates increased ethanol production in the presence of Pb²⁺, Cu²⁺, and Ni²⁺, highlighting its versatility in environmental remediation and industrial applications. Remarkably, this engineering strategy also improves the yeast’s H⁺/OH⁻ buffering capacity and its ability to immobilize Cd²⁺.

In another example, genetic modification of S. cerevisiae can fuse a gene encoding PC to the α-agglutinin protein, displaying PC on the cell surface. This modification not only enhanced Cd²⁺ sorption efficiency but also boosted Cd²⁺ tolerance, underscoring its potential for bioremediation [182]. In addition, genetic engineering of Ralstonia eutropha CH34 by incorporating mouse MT on its cell surface resulted in the creation of the MTB strain. This engineered strain demonstrated a significant improvement in its ability to sequester Cd²⁺ in soil [187].

4.2. Composite Materials

The development of yeast-based composite materials presents a promising strategy for enhancing the removal of HMs. For instance, a novel sorbent composed of a combination of mineral vermiculite and S. cerevisiae has been effectively utilized to remove Cd²⁺ from aqueous solutions [188]. Similarly, the successful synthesis of nano-ZnO/yeast composites via an alkaline hydrothermal process facilitates the formation of ZnO nanoparticles directly onto the yeast surface. This approach not only enhances the roughness of the composite material but also significantly augments its specific surface area. Notably, the resultant nano-ZnO/yeast composites exhibited an exceptional sorption capacity for Pb²⁺ (surpassing 30 mg g⁻¹) [99]. Furthermore, the synthesis of hydroxyapatite (HAp)/yeast biomass composites can be efficiently achieved via a straightforward alkaline ultrasound cavitation technique. This innovative nano-ZnO/yeast composite serves as an efficient sorbent for the removal of Pb²⁺. Its remarkable Pb²⁺ removal capability is attributed to the synergistic effect of apatite and the augmented accessibility of functional groups present on the yeast surface [99]. Moreover, yeast-MnO₂ composites can be synthesized by treating S. cerevisiae with KMnO₄ under acidic conditions for Cd²⁺ removal. [189]. Recent studies have also explored the potential of integrating phosphogypsum with fungal materials, further expanding the scope of bioremediation based on solid wastes [190].

An eco-friendly hybrid aerogel was crafted by immobilizing yeasts onto chitin nanofibers, resulting in a three-dimensional honeycomb-like structure utilized for the effective remediation of Cd [191]. The inclusion of yeast biomass in the hybrid aerogel design notably improved its sorption abilities and wet compression reversibility, leading to an increase in Cd²⁺ removal efficiency. Immobilized yeasts in a stable honeycomb structure support the creation of biocomponent carbon nanomaterials (CNs), enabling swift Cd sorption due to improved permeability [192]. The concept of utilizing a bio-separator and bio-synthesizer stands out as a promising candidate for bioremediation. These devices are synchronized to generate nanoparticles from the deceased R. mucilaginosa cells [193]. Moreover, a material comprising metal–organic frameworks and cellulose aerogels was developed [194]. Compared with normal yeasts, the thermal stability and sorption capacity of Pb²⁺ of the synthesized yeast were improved [195].

Activated carbon is the most conventional adsorbent for both organic and inorganic contaminants [196,197,198]. A novel activated carbon-based composite with nano-Fe₃O₄-impregnated yeast can effectively remove Hg²⁺ from water as a magnetic nano-sorbent [120].

Fungi and soil modifiers containing chicken manure can be combined to restore rare earth mine wasteland [199]. Poultry manure compost can be effectively employed for the remediation of Cu-contaminated soils due to its enhancing properties for metal sorption, which ultimately decreases the bioavailability of Cu [200]. Therefore, yeasts may be used in combination with manure to remediate soil HM pollution.

5. Future Perspectives

It is imperative to explore novel yeast strains possessing robust HM enrichment capabilities. The standardized ISO/OECD methods in the bacterial field are encouraged. For bacteria, it has been confirmed that toxicity data vary greatly depending on the performed conditions [201]. Therefore, in evaluating yeasts, it is recommended that a standardized toxicity testing protocol should be developed for sample preparation, incubation, and analytical techniques.

Surface modification and genetic recombination of yeast, along with the investigation of diverse yeast composite materials, represent viable strategies for advancing the remediation potential of yeasts. Introducing active functional groups or binding sites for target-metal biosorption by chemical reaction improves cell-surface functionalization. The introduction of many chemical agents can further increase the capacity of sorption. In addition, genetically modified yeast cells, overexpressing metalloregulatory proteins or cysteine-rich peptides, are anticipated to bolster their metal-binding selectivity and bioaccumulation potential. Additionally, integrating inorganic nanomaterials into organic biomass can amplify its effectiveness in HM remediation.

Advancements in biotechnological tools, including genetic engineering and genetically modified organisms, have significantly enhanced the performance of bioremediation. Additionally, peptide-library technology provides a robust framework for identifying peptides with high affinity for HM binding. In future, more engineering yeasts will be applied for repairing metal pollution in the environment. For instance, permeable reactive barrier (PRB) with immobilized microbial technology has been developed. However, maintaining the genetic stability of these engineered yeast strains remains a persistent challenge.