Integrated genome-transcriptome analysis unveiled the mechanism of Debaryomyces hansenii-mediated arsenic stress amelioration in rice

Globally, rice is becoming more vulnerable to arsenic (As) pollution, posing a serious threat to public food safety. Previously Debaryomyces hansenii was found to reduce grain As content of rice. To better understand the underlying mechanism, we performed a genome analysis to identify the key genes in D. hansenii responsible for As tolerance and plant growth promotion. Notably, genes related to As resistance (ARR, Ycf1, and Yap) were observed in the genome of D. hansenii. The presence of auxin pathway and glutathione metabolism-related genes may explain the plant growth-promoting potential and As tolerance mechanism of this novel yeast strain. The genome annotation of D. hansenii indicated that it contains a repertoire of genes encoding antioxidants, well corroborated with the in vitro studies of GST, GR, and glutathione content. In addition, the effect of D. hansenii on gene expression profiling of rice plants under As stress was also examined. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed 307 genes, annotated in D. hansenii-treated rice, related to metabolic pathways (184), photosynthesis (12), glutathione (10), tryptophan (4), and biosynthesis of secondary metabolite (117). Higher expression of regulatory elements like AUX/IAA and WRKY transcription factors (TFs), and defense-responsive genes dismutases, catalases, peroxiredoxin, and glutaredoxins during D. hansenii+As exposure was also observed. Combined analysis revealed that D. hansenii genes are contributing to stress mitigation in rice by supporting plant growth and As-tolerance. The study lays the foundation to develop yeast as a beneficial biofertilizer for As-prone areas.

Efficient production of single cell protein from biogas slurry using screened alkali-salt-tolerant Debaryomyces hansenii

Production of single cell protein (SCP) by recovering ammonia nitrogen from biogas slurry shows great potential against protein scarcity and unsustainable production of plant and animal proteins. Herein, a high-alkali-salt-tolerant yeast strain, Debaryomyces hansenii JL8-0, was isolated and demonstrated for high-efficient SCP production. This strain grew optimally at pH 8.50 and 2500 mg/L NH4+-N, and it could efficiently utilize acetate as the additional carbon source. Under optimal conditions, SCP biomass of 32.21 g/L and productivity of 0.32 g/L·h-1 were obtained in fed-batch fermentation. Remarkably, nearly complete (97.40 %) ammonia nitrogen from biogas slurry was recovered, probably due to its high affinity for NH4+-N. Altogether, this strain showed advantages in terms of cell biomass titer, productivity, and yield. A cultivation strategy was proposed by co-culturing D. hansenii with other compatible yeast strains to achieve high-efficient SCP production from biogas slurry, which could be a promising alternative technology for biogas slurry treatment.

Open (non-sterile) cultivations of Debaryomyces hansenii for recombinant protein production combining industrial side-streams with high salt content

The halotolerant non-conventional yeast Debaryomyces hansenii can grow in media containing high concentrations of salt (up to 4 M), metabolize alternative carbon sources than glucose, such as lactose or glycerol, and withstand a wide range of temperatures and pH. These inherent capabilities allow this yeast to grow in harsh environments and use alternative feedstock than traditional commercial media. For example, D. hansenii could be a potential cell factory for revalorizing industrial salty by-products, using them as a substrate for producing new valuable bioproducts, boosting a circular economy. In this work, three different salty by-products derived from the dairy and biopharmaceutical industry have been tested as a possible feedstock for D. hansenii's growth. The yeast was not only able to grow efficiently in all of them but also to produce a recombinant protein (Yellow Fluorescent Protein, used as a model) without altering its performance. Moreover, open cultivations at different laboratory scales (1.5 mL and 1 L) were performed under non-sterile conditions and without adding fresh water or any nutritional supplement to the cultivation, making the process cheaper and more sustainable.

Beneficial microbes to suppress Vibrio and improve the culture performance of copepod Tigriopus japonicus Mori

The use of beneficial microbes, i.e., probiotics, to reduce pathogens and promote the performance of the target species is an important management strategy in mariculture. This study aimed to investigate the potential of four microbes, Debaryomyces hansenii, Ruegeria mobilis, Lactobacillus plantarum, and Bacillus subtilis, to suppress Vibrio and increase survival, population growth and digestive enzyme activity (protease, lipase, and amylase) in the harpacticoid copepod, Tigriopus japonicus. Copepod, T. japonicus stock culture with an initial mean density of 50 individual/mL (25 adult male and 25 adult female) was distributed into five treatments (i.e., four experimental and a control, each with four replicates; repeated twice) using 20 beakers (100 mL capacity each). The copepods were fed a mixture of the dinoflagellate Alexandrium tamarense and the diatom Phyaeodactylum tricornutum (3 × 104 cells/mL-1). Each microbe's concentration was adjusted at 108 CFU/mL-1 and applied to the culture condition. D. hansenii, L. plantarum, and B. subtilis all improved the copepods' survival and population growth, likely by including a higher lipase activity (P < 0.05). In contrast, using R. mobilis did not improve the copepod's culture performance compared to control. B. subtilis was the most effective in decreasing the copepod's external and internal Vibrio loading. The probiotic concentrations in the copepod decreased within days during starvation, suggesting that routine re-application of the probiotics would be needed to sustain the microbial populations and the benefits they provide. Our results demonstrated that D. hansenii and B. subtilis are promising probiotics for mass copepod culture as live food for mariculture purposes.

Use of yeast isolates of cheese origin as adjunct culture in Beyaz cheese: Influence on sensorial, textural and quality characteristics

The effects of various yeast species isolated from raw-milk cheese were evaluated in Beyaz cheese. Four batches of cheeses were produced, in which the control cheese involved only commercial starter culture while YL, DH and KL cheeses were produced with the incorporation of individual Yarrowia lipolytica, Debaryomyces hansenii and Kluyveromyces lactis, respectively. The chemical composition, microbial counts, sensory attributes, volatile compounds and textural properties of cheeses were determined on days 1, 30, and 60 during the ripening period. The results obtained demonstrated that chemical, microbial and sensory properties of cheese varied depending on yeast species. The cheese with Y. lipolytica was the most preferred and it contained more short chain fatty acids, particularly butyric acid. This result could be due to the higher fat content and advanced lipolytic activity. The ripening index of DH was found to be higher than the other cheeses, showing an advanced proteolytic activity in relation to lower hardness in the texture profile. K. lactis was associated with lactose metabolism and promoted the development of Lactococcus spp. The results highlighted a potential use of yeasts as adjunct cultures in Beyaz cheese to develop the sensory properties such as texture and flavor.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05791-3.

Isolation of Debaryomyces hansenii and selection of an optimal strain to improve the quality of low-grade beef rump (middle gluteal) during dry aging

OBJECTIVE

The objective of this study was to evaluate the effect of Debaryomyces hansenii isolated from dry-aged beef on the tenderness and flavor attributes of low-grade beef during dry aging.

METHODS

Five D. hansenii strains were isolated from dry-aged beef samples. The rump of low-grade beef was inoculated with individual D. hansenii isolates and subjected to dry aging for 4 weeks at 5°C and 75% relative humidity. Microbial contamination levels, meat quality attributes, and flavor attributes in the dry-aged beef were measured.

RESULTS

Of the five isolates, the shear force of dry-aged beef inoculated with SMFM201812-3 and SMFM201905-5 was lower than that of control samples. Meanwhile, all five isolates increased the total free amino acid, glutamic acid, serine, glycine, alanine, and leucine contents in dry-aged beef. In particular, the total fatty acid, palmitic acid, and oleic acid contents in samples inoculated with D. hansenii SMFM201905-5 were higher than those in control samples.

CONCLUSION

These results indicate that D. hansenii SMFM201905-5 might be used to improve the quality of beef during dry aging.

Dietary Debaryomyces hansenii promotes skin and skin mucus defensive capacities in a marine fish model

The present study explores the effects of two supplementation levels of Debaryomyces hansenii (1.1% and 2.2%) as a probiotic in a reference low fish meal-based diet on the skin mucosal tissue in Sparus aurata. This study includes the evaluation of fish performance coupled with a holistic study of the skin mucosa: i) a transcriptomic study of the skin tissue, and ii) the evaluation of its secreted mucus both in terms of skin mucosal-associated biomarkers and its defensive capacity by means of co-culture analysis with two pathogenic bacteria. Results showed that after 70 days of diet administration, fish fed the diet supplemented with D. hansenii at 1.1% presented increased somatic growth and a better feed conversion ratio, compared to fish fed the control diet. In contrast, fish fed the diet including 2.2% of the probiotic presented intermediate values. Regarding gene regulation, the probiotic administration at 1.1% resulted in 712 differentially expressed genes (DEGs), among which 53.4% and 46.6% were up- and down-regulated, respectively. In particular, D. hansenii modulated some skin biological processes related to immunity and metabolism. Specifically, D. hansenii administration induced a strong modulation of some immune biological-related processes (61 DEGs), mainly involved in B- and T-cell regulatory pathways. Furthermore, dietary D. hansenii promoted the skin barrier function by the upregulation of anchoring junction genes (23 DEGs), which reinforces the physical defense against potential skin damage. In contrast, the skin showed modulated genes related to extracellular exosome and membrane organization (50 DEGs). This modulated functioning is of great interest, particularly in relation to the increased skin mucus defensive capacity observed in the bacterial co-culture in vitro trials, which could be related to the increased modulation and exudation of the innate immune components from the skin cells into the mucus. In summary, the modulation of innate immune parameters coupled with increased skin barrier function and cell trafficking potentiates the skin's physical barrier and mucus defensive capacity, while maintaining the skin mucosa's homeostatic immune and metabolic status. These findings confirmed the advantages of D. hansenii supplementation in low fish meal-based diets, demonstrating the probiotic benefits on cultured marine species.

Debaryomyces hansenii supplementation in low fish meal diets promotes growth, modulates microbiota and enhances intestinal condition in juvenile marine fish

BACKGROUND

The development of a sustainable business model with social acceptance, makes necessary to develop new strategies to guarantee the growth, health, and well-being of farmed animals. Debaryomyces hansenii is a yeast species that can be used as a probiotic in aquaculture due to its capacity to i) promote cell proliferation and differentiation, ii) have immunostimulatory effects, iii) modulate gut microbiota, and/or iv) enhance the digestive function. To provide inside into the effects of D. hansenii on juveniles of gilthead seabream (Sparus aurata) condition, we integrated the evaluation of the main key performance indicators coupled with the integrative analysis of the intestine condition, through histological and microbiota state, and its transcriptomic profiling.

RESULTS

After 70 days of a nutritional trial in which a diet with low levels of fishmeal (7%) was supplemented with 1.1% of D. hansenii (17.2 × 10⁵ CFU), an increase of ca. 12% in somatic growth was observed together with an improvement in feed conversion in fish fed a yeast-supplemented diet. In terms of intestinal condition, this probiotic modulated gut microbiota without affecting the intestine cell organization, whereas an increase in the staining intensity of mucins rich in carboxylated and weakly sulphated glycoconjugates coupled with changes in the affinity for certain lectins were noted in goblet cells. Changes in microbiota were characterized by the reduction in abundance of several groups of Proteobacteria, especially those characterized as opportunistic groups. The microarrays-based transcriptomic analysis found 232 differential expressed genes in the anterior-mid intestine of S. aurata, that were mostly related to metabolic, antioxidant, immune, and symbiotic processes.

CONCLUSIONS

Dietary administration of D. hansenii enhanced somatic growth and improved feed efficiency parameters, results that were coupled to an improvement of intestinal condition as histochemical and transcriptomic tools indicated. This probiotic yeast stimulated host-microbiota interactions without altering the intestinal cell organization nor generating dysbiosis, which demonstrated its safety as a feed additive. At the transcriptomic level, D. hansenii promoted metabolic pathways, mainly protein-related, sphingolipid, and thymidylate pathways, in addition to enhance antioxidant-related intestinal mechanisms, and to regulate sentinel immune processes, potentiating the defensive capacity meanwhile maintaining the homeostatic status of the intestine.

Short-Term Changes in Aroma-Related Volatiles in Meat Model: Effect of Fat and D. hansenii Inoculation

This study assessed the effect of replacing pork lard with coconut oil and Debaryomyces hansenii inoculation on the biotransformation of amino acids into volatile compounds in a meat model system. Yeast counts, solid-phase microextraction, and gas chromatography/mass spectrometry were used to assess yeast growth and volatile production, respectively. Yeast growth was confirmed until 28 d, although the volatile profile changed until 39 d. Forty-three volatiles were quantified, and their odor activity values (OAVs) were calculated. The presence of fat and yeasts contributed to differences in volatiles. In pork lard models, a delayed formation of lipid-derived aldehyde compounds was observed, whereas in coconut oil models, the generation of acid compounds and their respective esters was enhanced. Yeast activity affected amino acid degradation, which produced an increase in branched-chain aldehydes and alcohols. The aroma profile in the coconut models was influenced by hexanal, acid compounds, and their respective esters, whereas in pork lard models, aroma was affected by methional (musty, potato) and 3-methylbutanal (green, cocoa). The yeast inoculation contributed to the generation of 3-methylbutanoic acid (cheesy) and phenylethyl alcohol (floral). The type of fat and yeast inoculation produced a differential effect on the aroma.

Mitigation of arsenic toxicity in rice by the co-inoculation of arsenate reducer yeast with multifunctional arsenite oxidizing bacteria

The study aimed to explicate the role of microbial co-inoculants for the mitigation of arsenic (As) toxicity in rice. Arsenate (AsV) reducer yeast Debaryomyces hansenii NBRI-Sh2.11 (Sh2.11) with bacterial strains of different biotransformation potential was attempted to develop microbial co-inoculants. An experiment to test their efficacy (yeast and bacterial strains) on plant growth and As uptake was conducted under a stressed condition of 20 mg kg-1 of arsenite (AsIII). A combination of Sh2.11 with an As(III)-oxidizer, Citrobacter sp. NBRI-B5.12 (B5.12), resulted in ∼90% decrease in grain As content as compared to Sh2.11 alone (∼40%). Reduced As accumulation in rice roots under co-treated condition was validated with SEM-EDS analysis. Enhanced As expulsion in the selected combination under in vitro conditions was found to be correlated with higher As content in the soil during their interaction with plants. Selected co-inoculant mediated enhanced nutrient uptake in association with better production of indole acetic acid (IAA) and gibberellic acid (GA) in shoot, support microbial co-inoculant mediated better biomass under stressful condition. Boosted defense response in association with enhanced glutathione-S-transferase (GST) and glutathione reductase (GR), activities under in vitro and in vivo conditions were observed. These results indicated that the As(III) oxidizer-B5.12 accelerated the As detoxification property of the As(V) reducer-Sh2.11. Henceforth, the results confer that the coupled reduction-oxidation process of the co-inoculant reduces the accumulation of As in rice grain. These co-inoculants can be further developed for field trials to achieve higher biomass with alleviated As toxicity in rice.

Selection of Autochthonous Yeasts Isolated from the Intestinal Tracts of Cobia Fish (Rachycentron canadum) with Probiotic Potential

Some yeast strains have been proposed as probiotics to improve the health of cultured fish. Cobia is a tropical benthopelagic fish species with potential for marine aquaculture; however, one of the main limitations to its large-scale production is the high mortality of fish larvae. In this study, we evaluated the probiotic potential of autochthonous yeasts from the intestines of cobia. Thirty-nine yeast isolates were recovered from the intestinal mucosa of 37 adult healthy cobia by culture methods. Yeasts were identified by sequencing of the ITS and D1/D2 regions of the 28S rRNA gene and typed by RAPD-PCR using the M13 primer. Yeast strains with unique RAPD patterns were characterized in terms of their cell biomass production ability; anti-Vibrio, enzymatic, and hemolytic activity; biofilm production; hydrophobicity; autoaggregation; polyamine production; safety; and protection of cobia larvae against saline stress. Candida haemuloni C27 and Debaryomyces hansenii C10 and C28 were selected as potential probiotics. They did not affect the survival of larvae and showed biomass production >1 g L^-1, hydrophobicity >41.47%, hemolytic activity γ, and activity in more than 8 hydrolytic enzymes. The results suggest that the selected yeast strains could be considered as potential probiotic candidates and should be evaluated in cobia larvae.

Carbohydrate Sources Influence the Microbiota and Flavour Profile of a Lupine-Based Moromi Fermentation

Lupine-based seasoning sauce is produced similarly to soy sauces and therefore generates a comparable microbiota and aroma profile. While the koji state is dominated by Aspergillus oryzae, the microbiome of the moromi differs to soy moromi, especially in yeast composition due to the absence of Zygosaccharomyces rouxii and Debaryomyces hansenii as the dominant yeast. In this study, we monitored the addition of a carbohydrate source on the microbiome and aroma profile of the resulting sauce. Compared to previous studies, the usage of a yeast starter culture resulted in a sparsely diverse microbiota that was dominated by D. hansenii and T. halophilus. This led to a pH below 5 even after four months of incubation and most of the measured aroma compounds were pyrazines and acids. The addition of wheat and buckwheat resulted in a temporary change in the yeast consortium with the appearance of Z. rouxii and additional bacterial genera. The aroma profile differs in the presence of pyrazines and esters. Since no significant differences in the taste and odour of wheat-added and buckwheat-added sauce was sensed, both substrates influence the lupine sauce in a similar way.

Structural Characterization, Antioxidant and Antitumor Activities of the Two Novel Exopolysaccharides Produced by Debaryomyces hansenii DH-1

Exopolysaccharides produced by edible microorganisms exhibit excellent constructive physicochemical and significant biological activity, which provide advantages for the food or pharmaceutical industries. Two novel exopolysaccharides produced by Debaryomyces hansenii DH-1 were characterized, named S1 and S2, respectively. S1, with a molecular weight of 34.594 kDa, primarily consisted of mannose and glucose in a molar ratio of 12.19:1.00, which contained a backbone fragment of α-D-Manp-(1→4)-α-D-Manp-(1→2)-α-D-Glcp-(1→3)-α-D-Manp-(1→3)-β-D-Glcp-(1→4)-β-D-Manp-(1→. S2, with a molecular weight of 24.657 kDa, was mainly composed of mannose and galactose in a molar ratio of 4.00:1.00, which had a backbone fragment of α-D-Manp-(1→6)-β-D-Manp-(1→2)-α-D-Manp-(1→4)-α-D-Galp-(1→3)-β-D-Manp-(1→6)-α-D-Manp-(1→. Both S1 and S2 exhibited good thermal stability and potent hydroxyl radical scavenging activity, with ~98%. Moreover, S1 possessed an additional strong iron-reducing capacity. In vitro antitumor assays showed that S1 and S2 significantly inhibited the proliferation of Hela, HepG2, and PC-9 cancer cells. Moreover, PC-9 was more sensitive to S1 compared with S2. The above results indicate that S1 and S2 have great potential to be utilized as natural antioxidants and candidates for cancer treatment in the food and pharmaceutical industries.

DhDIT2 Encodes a Debaryomyces hansenii Cytochrome P450 Involved in Benzo(a)pyrene Degradation-A Proposal for Mycoremediation

Pollutants, such as polycyclic aromatic hydrocarbons (PAHs), e.g., benzo(a)pyrene (BaP), are common components of contaminating mixtures. Such compounds are ubiquitous, extremely toxic, and they pollute soils and aquatic niches. The need for new microorganism-based remediation strategies prompted researchers to identify the most suitable organisms to eliminate pollutants without interfering with the ecosystem. We analyzed the effect caused by BaP on the growth properties of Candida albicans, Debaryomyces hansenii, Rhodotorula mucilaginosa, and Saccharomyces cerevisiae. Their ability to metabolize BaP was also evaluated. The aim was to identify an optimal candidate to be used as the central component of a mycoremediation strategy. The results show that all four yeast species metabolized BaP by more than 70%, whereas their viability was not affected. The best results were observed for D. hansenii. When an incubation was performed in the presence of a cytochrome P450 (CYP) inhibitor, no BaP degradation was observed. Thus, the initial oxidation step is mediated by a CYP enzyme. Additionally, this study identified the D. hansenii DhDIT2 gene as essential to perform the initial degradation of BaP. Hence, we propose that D. hansenii and a S. cerevisiae expressing the DhDIT2 gene are suitable candidates to degrade BaP in contaminated environments.

An Integrated Process for the Xylitol and Ethanol Production from Oil Palm Empty Fruit Bunch (OPEFB) Using Debaryomyces hansenii and Saccharomyces cerevisiae

Oil palm empty fruit bunch (OPEFB) is the largest biomass waste from the palm oil industry. The OPEFB has a lignocellulose content of 34.77% cellulose, 22.55% hemicellulose, and 10.58% lignin. Therefore, this material’s hemicellulose and cellulose content have a high potential for xylitol and ethanol production, respectively. This study investigated the integrated microaerobic xylitol production by Debaryomyces hansenii and anaerobic ethanol semi simultaneous saccharification and fermentation (semi-SSF) by Saccharomyces cerevisiae using the same OPEFB material. A maximum xylitol concentration of 2.86 g/L was obtained with a yield of 0.297 g/g_xylose. After 96 h of anaerobic fermentation, the maximum ethanol concentration was 6.48 g/L, corresponding to 71.38% of the theoretical ethanol yield. Significant morphological changes occurred in the OPEFB after hydrolysis and xylitol and ethanol fermentation were shown from SEM analysis.

Exploring Biocontrol of Unwanted Fungi by Autochthonous Debaryomyces hansenii Strains Isolated from Dry Meat Products

The exploration of alternatives to the use of chemical preservatives in food is a topic that has attracted great attention. The implementation of regulations associated with the reduction of these elements directly affects the production of cured meat products, with the premise of looking for more “natural” alternatives. From a previously identified collection of 24 strains of Debaryomyces hansenii, isolated from dry meat products of the “Valle de los Pedroches” (Córdoba), a screening was carried out to determine which strains had inhibitory potential against a battery of fungi belonging to the genera Aspergillus, Penicillium, and Candida. After a series of general trials, four strains showing the greatest potential were selected by a streak inhibition assay performed at several concentrations of NaCl. The inhibitory activity of the selected D. hansenii strains was later evaluated by measuring their fungal antagonistic diffusible and volatile compound production following radial inhibition and mouth-to-mouth approaches, respectively. Growth aspects, sporulation, and morphology changes were also considered during these assays. The results support ideas already raised in previous studies, such as the presence of D. hanseniii could imply a reduction of pathogenic fungi in food. Autochthonous yeast strains inhibited not only the mycelial growth, but also sporulation, which strengthens the biocontrol activity of this yeast. Our results show that, under certain conditions, all tested D. hansenii strains were able to alter the growth/development of fungi, being especially evident in the cases of Penicillium expansum and Aspergillus niger. Finally, our research can facilitate the future comparison of results in this area, since we contributed to standardize the methodology described to date, we quantified the number of yeast cells and spores used during the experiments, we homogenized growth conditions for both, yeasts, and molds, and applied an image analyzer software to quantify the growth of the studied microorganisms in solid media.

Several Yeast Species Induce Iron Deficiency Responses in Cucumber Plants (Cucumis sativus L.)

Iron (Fe) deficiency is a first-order agronomic problem that causes a significant decrease in crop yield and quality. Paradoxically, Fe is very abundant in most soils, mainly in its oxidized form, but is poorly soluble and with low availability for plants. In order to alleviate this situation, plants develop different morphological and physiological Fe-deficiency responses, mainly in their roots, to facilitate Fe mobilization and acquisition. Even so, Fe fertilizers, mainly Fe chelates, are widely used in modern agriculture, causing environmental problems and increasing the costs of production, due to the high prices of these products. One of the most sustainable and promising alternatives to the use of agrochemicals is the better management of the rhizosphere and the beneficial microbial communities presented there. The main objective of this research has been to evaluate the ability of several yeast species, such as Debaryomyces hansenii, Saccharomyces cerevisiae and Hansenula polymorpha, to induce Fe-deficiency responses in cucumber plants. To date, there are no studies on the roles played by yeasts on the Fe nutrition of plants. Experiments were carried out with cucumber plants grown in a hydroponic growth system. The effects of the three yeast species on some of the most important Fe-deficiency responses developed by dicot (Strategy I) plants, such as enhanced ferric reductase activity and Fe²⁺ transport, acidification of the rhizosphere, and proliferation of subapical root hairs, were evaluated. The results obtained show the inductive character of the three yeast species, mainly of Debaryomyces hansenii and Hansenula polymorpha, on the Fe-deficiency responses evaluated in this study. This opens a promising line of study on the use of these microorganisms as Fe biofertilizers in a more sustainable and environmentally friendly agriculture.

Bioprocesses with Reduced Ecological Footprint by Marine Debaryomyces hansenii Strain for Potential Applications in Circular Economy

The possibility to perform bioprocesses with reduced ecological footprint to produce natural compounds and catalyzers of industrial interest is pushing the research for salt tolerant microorganisms able to grow on seawater-based media and able to use a wide range of nutrients coming from waste. In this study we focused our attention on a Debaryomyces hansenii marine strain (Mo40). We optimized cultivation in a bioreactor at low pH on seawater-based media containing a mixture of sugars (glucose and xylose) and urea. Under these conditions the strain exhibited high growth rate and biomass yield. In addition, we characterized potential applications of this yeast biomass in food/feed industry. We show that Mo40 can produce a biomass containing 45% proteins and 20% lipids. This strain is also able to degrade phytic acid by a cell-bound phytase activity. These features represent an appealing starting point for obtaining D. hansenii biomass in a cheap and environmentally friendly way, and for potential use as an additive or to replace unsustainable ingredients in the feed or food industries, as this species is included in the QPS EFSA list (Quality Presumption as Safe-European Food Safety Authority).

Bioconversion study for xylitol and ethanol production by Debaryomyces hansenii: aeration, medium and substrate composition influence

Debaryomyces hansenii has been employed to study, initially, the influence of the oxygen availability on D-xylose to xylitol fermentation, as this parameter is considered as one of the most critical variables for this bio alcohol accumulation. Apart from the air supplied in the fermentation process through the stirring vortex (0.0 v/v/min), additional aeration rates (0.1-2.0 v/v/min) effects were discussed. Furthermore, a change in the fermentative medium composition as well as a comparative analysis of D. hansenii behavior with respect to fermentation of D-glucose and D-xylose mixtures solutions, with the aim of producing both xylitol and ethanol bioproducts, were performed. For these purposes, specific growth rates, biomass productivities, specific substrate-uptake rates, overall biomass yields, specific xylitol formation rates and overall xylitol yields values have been calculated, applying a differential method to the kinetic data. Aeration influence was clearly evinced since a faster D-xylose metabolism, for aeration values close to 1.0 v/v/min, was noted. This yeast exhibited a sequential substrate consumption, firstly D-glucose and then D-xylose. The maximum xylitol yield (0.32 kg kg^{- 1}) was obtained for 0.5 v/v/min airflow, remarking a significant reduction of this parameter for both above and below the quoted air supply value.

New Cytoplasmic Virus-Like Elements (VLEs) in the Yeast Debaryomyces hansenii

Yeasts can have additional genetic information in the form of cytoplasmic linear dsDNA molecules called virus-like elements (VLEs). Some of them encode killer toxins. The aim of this work was to investigate the prevalence of such elements in D. hansenii killer yeast deposited in culture collections as well as in strains freshly isolated from blue cheeses. Possible benefits to the host from harboring such VLEs were analyzed. VLEs occurred frequently among fresh D. hansenii isolates (15/60 strains), as opposed to strains obtained from culture collections (0/75 strains). Eight new different systems were identified: four composed of two elements and four of three elements. Full sequences of three new VLE systems obtained by NGS revealed extremely high conservation among the largest molecules in these systems except for one ORF, probably encoding a protein resembling immunity determinant to killer toxins of VLE origin in other yeast species. ORFs that could be potentially involved in killer activity due to similarity to genes encoding proteins with domains of chitin-binding/digesting and deoxyribonuclease NucA/NucB activity, could be distinguished in smaller molecules. However, the discovered VLEs were not involved in the biocontrol of Yarrowia lipolytica and Penicillium roqueforti present in blue cheeses.

Debaryomyces hansenii Is a Real Tool to Improve a Diversity of Characteristics in Sausages and Dry-Meat Products

Debaryomyces hansenii yeast represents a promising target for basic and applied biotechnological research It is known that D. hansenii is abundant in sausages and dry-meat products, but information regarding its contribution to their characteristics is blurry and contradictory. The main goal in this review was to define the biological contribution of D. hansenii to the final features of these products. Depending on multiple factors, D. hansenii may affect diverse physicochemical characteristics of meat products. However, there is general agreement about the significant generation of volatile and aromatic compounds caused by the metabolic activities of this yeast, which consequently provide a tendency for improved consumer acceptance. We also summarize current evidence highlighting that it is not possible to predict what the results would be after the inoculation of a meat product with a selected D. hansenii strain without a pivotal previous study. The use of D. hansenii as a biocontrol agent and to manufacture new meat products by decreasing preservatives are examples of exploring research lines that will complement current knowledge and contribute to prepare new and more ecological products.

Probiotic Yeasts and Vibrio anguillarum Infection Modify the Microbiome of Zebrafish Larvae

The host microbiome plays an essential role in health and disease. Microbiome modification by pathogens or probiotics has been poorly explored especially in the case of probiotic yeasts. Next-generation sequencing currently provides the best tools for their characterization. Debaryomyces hansenii 97 (D. hansenii 97) and Yarrowia lipolytica 242 (Y. lipolytica 242) are yeasts that protect wildtype zebrafish (Danio rerio) larvae against a Vibrio anguillarum (V. anguillarum) infection, increasing their survival rate. We investigate the effect of these microorganisms on the microbiome and neutrophil response (inflammation) in zebrafish larvae line Tg(Bacmpx:GFP)ⁱ¹¹⁴. We postulated that preinoculation of larvae with yeasts would attenuate the intestinal neutrophil response and prevent modification of the larval microbiome induced by the pathogen. Microbiome study was performed by sequencing the V3-V4 region of the 16S rRNA gene and prediction of metabolic pathways by Piphillin in conventionally raised larvae. Survival and the neutrophil response were both evaluated in conventional and germ-free conditions. V. anguillarum infection resulted in higher neutrophil number in the intestinal area compared to non-infected larvae in both conditions. In germ-free conditions, infected larvae pre-inoculated with yeasts showed fewer neutrophil numbers than infected larvae. In both conditions, only D. hansenii 97 increased the survival of infected larvae. Beta diversity of the microbiota was modified by V. anguillarum and both yeasts, compared to non-inoculated larvae. At 3 days post-infection, V. anguillarum modified the relative abundance of 10 genera, and pre-inoculation with D. hansenii 97 and Y. lipolytica 242 prevented the modification of 5 and 6 of these genera, respectively. Both yeasts prevent the increase of Ensifer and Vogesella identified as negative predictors for larval survival (accounting for 40 and 27 of the variance, respectively). In addition, yeast pre-inoculation prevents changes in some metabolic pathways altered by V. anguillarum’s infection. These results suggest that both yeasts and V. anguillarum can shape the larval microbiota configuration in the early developmental stage of D. rerio. Moreover, modulation of key taxa or metabolic pathways of the larval microbiome by yeasts can be associated with the survival of infected larvae. This study contributes to the understanding of yeast–pathogen–microbiome interactions, although further studies are needed to elucidate the mechanisms involved.

Debaryomyces hansenii Strains Isolated From Danish Cheese Brines Act as Biocontrol Agents to Inhibit Germination and Growth of Contaminating Molds

The antagonistic activities of native Debaryomyces hansenii strains isolated from Danish cheese brines were evaluated against contaminating molds in the dairy industry. Determination of chromosome polymorphism by use of pulsed-field gel electrophoresis (PFGE) revealed a huge genetic heterogeneity among the D. hansenii strains, which was reflected in intra-species variation at the phenotypic level. 11 D. hansenii strains were tested for their ability to inhibit germination and growth of contaminating molds, frequently occurring at Danish dairies, i.e., Cladosporium inversicolor, Cladosporium sinuosum, Fusarium avenaceum, Mucor racemosus, and Penicillium roqueforti. Especially the germination of C. inversicolor and P. roqueforti was significantly inhibited by cell-free supernatants of all D. hansenii strains. The underlying factors behind the inhibitory effects of the D. hansenii cell-free supernatants were investigated. Based on dynamic headspace sampling followed by gas chromatography-mass spectrometry (DHS-GC-MS), 71 volatile compounds (VOCs) produced by the D. hansenii strains were identified, including 6 acids, 22 alcohols, 15 aldehydes, 3 benzene derivatives, 8 esters, 3 heterocyclic compounds, 12 ketones, and 2 phenols. Among the 71 identified VOCs, inhibition of germination of C. inversicolor correlated strongly with three VOCs, i.e., 3-methylbutanoic acid, 2-pentanone as well as acetic acid. For P. roqueforti, two VOCs correlated with inhibition of germination, i.e., acetone and 2-phenylethanol, of which the latter also correlated strongly with inhibition of mycelium growth. Low half-maximal inhibitory concentrations (IC50) were especially observed for 3-methylbutanoic acid, i.e., 6.32-9.53 × 10-5 and 2.00-2.67 × 10-4 mol/L for C. inversicolor and P. roqueforti, respectively. For 2-phenylethanol, a well-known quorum sensing molecule, the IC50 was 1.99-7.49 × 10-3 and 1.73-3.45 × 10-3 mol/L for C. inversicolor and P. roqueforti, respectively. For acetic acid, the IC50 was 1.35-2.47 × 10-3 and 1.19-2.80 × 10-3 mol/L for C. inversicolor and P. roqueforti, respectively. Finally, relative weak inhibition was observed for 2-pentanone and acetone. The current study shows that native strains of D. hansenii isolated from Danish brines have antagonistic effects against specific contaminating molds and points to the development of D. hansenii strains as bioprotective cultures, targeting cheese brines and cheese surfaces.

Temporal differences in microbial composition of Époisses cheese rinds during ripening and storage

Époisses is a protected designation of origin smear-ripened cheese from the Burgundy region in France. It has an orange color and a strong flavor, both of which are generated by surface microorganisms. The objective of the present study was to investigate the microbial dynamics at the surface of Époisses cheese during ripening and postmanufacturing storage at low temperatures. Rind samples were analyzed by enumeration on agar plates and by 16S rRNA gene and internal transcribed spacer amplicon sequencing. During most of the ripening process, the counts of yeasts, which corresponded to the species Debaryomyces hansenii and Geotrichum candidum, were higher than those of the aerobic acid-sensitive bacteria. Debaryomyces hansenii reached a level of about 3 × 10⁸ cfu/cm², and its viability strongly decreased in the late stage of ripening and during storage at 4°C. Two of the inoculated bacterial species, Brevibacterium aurantiacum and Staphylococcus xylosus, did not establish themselves at the cheese surface. At the end of ripening, among the 18 most abundant bacterial species detected by amplicon sequencing, 14 were gram-negative, mainly from genera Psychrobacter, Vibrio, Halomonas, and Mesonia. It was hypothesized that the high moisture level of the Époisses rinds, due the humid atmosphere of the ripening rooms and to the frequent washings of the curds, favored growth of these gram-negative species. These species may be of interest for the development of efficient ripening cultures. In addition, because the orange color of Époisses cheeses could not be attributed to the growth of Brevibacterium, it would be interesting to investigate the type and origin of the pigments that confer color to this cheese.

Key aroma compounds and metabolic profiling of Debaryomyces hansenii L1-1-fermented Flos Sophorae

The extract from Debaryomyces hansenii L1-1-fermented Flos Sophorae has a unique aroma and could be used as a natural spice. The influence of yeast growth and culture medium pH on organoleptic properties of fermented substrates, as well as on the content of volatile aromatic compounds, total sugars, polysaccharides, reducing sugars, total proteins, and amino acids, were analyzed. Metabolic pathways were annotated to compare and contrast key aromatic compounds and metabolic profiles of water and ethanol extracts of D. hansenii L1-1-fermented Flos Sophorae. We found that cells grew most rapidly, pH values changed significantly, and the largest consumption of sugars and amino acids occurred within 48 hr, producing bouquet-like, fruity, and sweet odors, as well as the highest content of volatile aromatic compounds in the extracts. The main aroma metabolites were 2-phenylethanol, linalool, and α-terpineol. The sensory quality of the ethanol extracts was superior to that of the water extracts. Five aromatic compounds, isoamyl alcohol, 2-methylbutan-1-ol, isobutyric acid, 2,3-hexanedione, and 1-hexanol, were positively correlated with the water extract group and negatively correlated with the ethanol extract group, whereas 13 aromatic compounds, styrene, acetophenone, 2-octen-1-ol, linalool, naphthalene, α-terpineol, dihydrocarveol, (-)-myrtenol, methyl anthranilate, eugenol, γ-nonanolactone, jasmone, and β-ionone, showed the converse trend. Although 2-phenylethanol displayed the highest concentration in the extracts, it did not significantly contribute to the separation of ethanol and water extracts. In Flos Sophorae medium, D. hansenii mainly produces 2-phenylethanol from phenylalanine by the Ehrlich reaction, whereas it produces linalool and α-terpineol by the terpenoid backbone and monoterpenoid biosynthetic pathways; the variable contents of proline, arginine, and glutamate could respond to the arginine and proline metabolic pathways. PRACTICAL APPLICATIONS: Flos Sophorae, a collection of buds of Sophora japonica L., is a traditional Chinese medicinal and edible plant for its good aroma, taste, and nutritional value. Debaryomyces hansenii is a common, aroma-producing yeast. D. hansenii L1-1-fermented Flos Sophorae had a unique, bouquet-like aroma, slightly softer than the typical Flos Sophorae-like aroma. This study enriches our understanding of predominant aroma components and determines their contribution to the profiles of Flos Sophorae ferments obtained using D. hansenii L1-1. Researchers and manufacturers specializing in spices making can use these data to improve the aromatic profiles of natural spices produced by microorganisms, thereby obtaining unique aromas.

CRISPR/Cas9-Mediated Genome Engineering Reveals the Contribution of the 26S Proteasome to the Extremophilic Nature of the Yeast Debaryomyces hansenii

The marine yeast Debaryomyces hansenii is of high importance in the food, chemical, and medical industries. D. hansenii is also a popular model for studying molecular mechanisms of halo- and osmotolerance. The absence of genome editing technologies hampers D. hansenii research and limits its biotechnological application. We developed novel and efficient single- and dual-guide CRISPR systems for markerless genome editing of D. hansenii. The single-guide system allows high-efficiency (up to 95%) mutation of genes or regulatory elements. The dual-guide system is applicable for efficient deletion of genomic loci. We used these tools to study transcriptional regulation of the 26S proteasome, an ATP-dependent protease complex whose proper function is vital for all cells and organisms. We developed a genetic approach to control the activity of the 26S proteasome by deregulation of its essential subunits. The mutant strains were sensitive to geno- and proteotoxic stresses as well as high salinity and osmolarity, suggesting a contribution of the proteasome to the extremophilic properties of D. hansenii. The developed CRISPR systems allow efficient D. hansenii genome engineering, providing a genetic way to control proteasome activity, and should advance applications of this yeast.

A physiological characterization in controlled bioreactors reveals a novel survival strategy for Debaryomyces hansenii at high salinity

Debaryomyces hansenii is traditionally described as a halotolerant non-conventional yeast and has served as a model organism for the study of osmotolerance and salt tolerance mechanisms in eukaryotic systems for the past 30 years. However, unraveling of D. hansenii's biotechnological potential has always been difficult due to the persistent limitations in the availability of efficient molecular tools described for this yeast. Additionally, there is a lack of consensus and contradictory information along the recent years that limits a comprehensive understanding of its central carbon metabolism, mainly due to a lack of physiological studies in controlled and monitored environments. Moreover, there is little consistency in the culture conditions (media composition, temperature, and pH among others) used by different groups, which makes it complicated when trying to get prevalent conclusions on behavioral patterns. In this work, we present for the first time a characterization of D. hansenii in batch cultivations using highly controlled lab-scale bioreactors. Our findings contribute to a more complete picture of the central carbon metabolism and the external pH influence on the yeast's ability to tolerate high Na⁺ and K⁺ concentrations, pointing to a differential effect of both salts, as well as a positive effect in cell performance when low environmental pH values are combined with a high sodium concentration in the media. Finally, a novel survival strategy at very high salinity (2 M) is proposed for this yeast, as well as potential outcomes for its use in industrial biotechnology applications. TAKE AWAY: High salt concentrations stimulate respiration in Debaryomyces hansenii. Sodium exerts a stronger positive impact on cell performance than potassium. μ_max is higher at a combination of low pH, high salt, and high temperature. Concentrations of 2 M salt result in slower growth but increased biomass yield. The positive effect of salts is enhanced at low glucose concentration.

Tolerance to Oxidative Stress in Budding Yeast by Heterologous Expression of Catalases A and T from Debaryomyces hansenii

The function of catalases A and T from the budding yeast Saccharomyces cerevisiae (ScCta1 and ScCtt1) is to decompose hydrogen peroxide (H₂O₂) to mitigate oxidative stress. Catalase orthologs are widely found in yeast, suggesting that scavenging H₂O₂ is crucial to avoid the oxidative damage caused by reactive oxygen species (ROS). However, the function of catalase orthologs has not yet been experimentally characterized in vivo. Here, we heterologously expressed Debaryomyces hansenii DhCTA1 and DhCTT1 genes, encoding ScCta1 and ScCtt1 orthologs, respectively, in a S. cerevisiae acatalasemic strain (cta1Δ ctt1Δ). We performed a physiological analysis evaluating growth, catalase activity, and H₂O₂ tolerance of the strains grown with glucose or ethanol as carbon source, as well as under NaCl stress. We found that both genes complement the catalase function in S. cerevisiae. Particularly, the strain harboring DhCTT1 showed improved growth when ethanol was used as carbon source both in the absence or presence of salt stress. This phenotype is attributed to the high catalase activity of DhCtt1 detected at the exponential growth phase, which prevents intracellular ROS accumulation and confers oxidative stress resistance.

Intestinal mucosal bacterial diversity of antibiotic-associated diarrhea (AAD) mice treated with Debaryomyces hansenii and Qiweibaizhu powder

The aim was to investigate the combined effect of Debaryomyces hansenii and Qiweibaizhu powder (QWBZP) on the bacterial diversity of the intestinal mucosa of antibiotic-associated diarrhea (AAD) mice, for the potential treatment of diarrhea, especially which is induced by administration of antibiotics. Eighteen (18) mice were randomly assigned to three equal groups of six mice, namely Normal (mn group), Placebo control (mm group) and D. hansenii and QWBZP (DQ) treatment (mdq group). Mice were gavaged with a solution (23.33 mL·kg^-1·day^-1) consisting of gentamicin and cefradine to establish AAD. The DQ treatment group was gavaged with DQ for 4 days, and sterile water was used as a placebo control. The metagenome DNA of the intestinal mucosal microbiota was extracted, and the 16S rRNA gene was sequenced. Analysis showed that there were 288 OTUs for the normal group, 443 for the placebo control group, and 229 for the DQ treatment group. Phylogenetically, the gut microbiota of the DQ treatment group and the normal group were closer to each other than to the placebo control group. Both the DQ and placebo-treated groups included Stenotrophomonas, Robinsoniella, Bacteroidales S24-7 group norank, Citrobacter, and Glutamicibacter, but their abundances were significantly higher in the DQ treatment group than in the placebo control group. This suggested that the combined use of D. hansenii and QWBZP overcame the influence of dysbacteriosis and could lead to the recovery of intestinal mucosal microbiota homeostasis. This positive effect is likely related to short-chain fatty acid (SCFA)-producing bacteria, such as members of Micrococcaceae, Lachnospiraceae, and Bacteroidales S24-7 group, which could play beneficial roles in protecting the mucosal barrier and stimulating the immune response in mice.

Competitiveness of three biocontrol candidates against ochratoxigenic Penicillium nordicum under dry-cured meat environmental and nutritional conditions

The environmental conditions during the ripening of dry-cured meats and their nutritional composition promote the colonisation of their surface by Penicillium spp., including P. nordicum producer of ochratoxin A (OTA). The objective of this work was to study the competitiveness of three potential biocontrol candidates (Debaryomyces hansenii FHSCC 253H, Enterococcus faecium SE920 and Penicillium chrysogenum CECT, 20922) against the ochratoxigenic P. nordicum FHSCC4 under environmental and nutritional conditions simulating the ripening of dry-cured meat products. For this, the nutritional utilisation pattern, niche overlap index (NOI), interactions by dual-culture assays and OTA production were determined. The number of carbon sources (CSs) metabolised depended on the microorganism and the interacting water activity (a_w) x temperature conditions. The number of CSs utilised by both filamentous fungi was quite similar and higher than those utilised by D. hansenii and E. faecium. The yeast isolate metabolised a number of CSs much larger than the bacterium. The NOI values showed that, in general, P. nordicum nutritionally dominated E. faecium and D. hansenii regardless of the environmental conditions evaluated. The relationship between the toxigenic and non-toxigenic fungal isolates depended on the a_w x temperature combinations, although in none of the conditions a dominance of P. nordicum was observed. According to the interaction assays, both D. hansenii and P. chrysogenum decreased the growth of P. nordicum. The effect of D. hansenii could be attributed to the production of some extra-cellular compounds, while the action of P. chrysogenum is likely related to nutritional competition. In addition, both P. chrysogenum and D. hansenii reduced the OTA levels produced by P. nordicum. The effect of the yeast was more pronounced decreasing the concentration of OTA at quantities lower than the limit established by the Italian legislation. Therefore, P. chrysogenum and D. hansenii can be suggested as biocontrol candidates in the manufacture of dry-cured meat products.

Effect of Debaryomyces hansenii combined with Qiweibaizhu powder extract on the gut microbiota of antibiotic-treated mice with diarrhea

The aim of this study was to investigate the effects of an extract of Qiweibaizhu powder combined with Debaryomyces hansenii on the gut microbiota of antibiotic-treated mice with diarrhea. Mice were gavaged with a mixture of gentamycin sulfate and cefradine to induce diarrhea. After diarrhea was observed, 25% dose of ultra-micro Qiweibaizhu powder extract combined with 25% dose of Debaryomyces hansenii (QCD) was gavaged to mice with diarrhea. DNA of intestinal contents in mice was extracted for 16S rRNA gene sequence analysis by high-throughput sequencing following treatment finished. The results showed that the QCD increased the species richness and diversity, but did not recover the diversity to the original level. Antibiotics and QCD significantly altered the composition of gut microbiota at different taxonomic levels. At the genus level, the relative abundance of Bacteroidales S24-7 group_unidentified and Bacteroides returned to baseline after QCD treatment. Additionally, QCD suppressed the growth of Oscillospira and Ruminococcus, and promoted the proliferation of Erysipelotrichaceae_norank and Blautia compared with the healthy and diarrheal mice. Our results indicated that QCD modulated the diversity and composition of the gut microbiota in antibiotic-treated mice with diarrhea. The synergistic effect between Qiweibaizhu powder extract and Debaryomyces hansenii may be related to Bifidobacterium and Bacteroidales S24-7 group_unidentified.

Overlapping responses between salt and oxidative stress in Debaryomyces hansenii

Debaryomyces hansenii is a halotolerant yeast of importance in basic and applied research. Previous reports hinted about possible links between saline and oxidative stress responses in this yeast. The aim of this work was to study that hypothesis at different molecular levels, investigating after oxidative and saline stress: (i) transcription of seven genes related to oxidative and/or saline responses, (ii) activity of two main anti-oxidative enzymes, (iii) existence of common metabolic intermediates, and (iv) generation of damages to biomolecules as lipids and proteins. Our results showed how expression of genes related to oxidative stress was induced by exposure to NaCl and KCl, and, vice versa, transcription of some genes related to osmotic/salt stress responses was regulated by H₂O₂. Moreover, and contrary to S. cerevisiae, in D. hansenii HOG1 and MSN2 genes were modulated by stress at their transcriptional level. At the enzymatic level, saline stress also induced antioxidative enzymatic defenses as catalase and glutathione reductase. Furthermore, we demonstrated that both stresses are connected by the generation of intracellular ROS, and that hydrogen peroxide can affect the accumulation of in-cell sodium. On the other hand, no significant alterations in lipid oxidation or total glutathione content were observed upon exposure to both stresses tested. The results described in this work could help to understand the responses to both stressors, and to improve the biotechnological potential of D. hansenni.

Development of an Efficient Transformation System for Halotolerant Yeast Debaryomyces hansenii CBS767

Debaryomyces hansenii is one of the most osmotolerant and halotolerant yeasts. Further, its association with traditional cheese and meat products imparting special flavors to these products project this yeast with enormous biotechnological potential in the agrofood sector. However, lack of an efficient transformation system in D. hansenii still direct the complementation based assay in S. cerevisiae mutants for functional analysis of D. hansenii genes. Here, we have described the development of an efficient transformation system for D. hansenii that is based on a histidine auxotrophic recipient strain, DBH9 (generated by UV induced random mutagenesis), and the DhHIS4 gene as the selectable marker. Moreover, the same method has also been employed for gene disruption in D. hansenii by homologous recombination.

Transcription Profiling Reveals Cooperative Metabolic Interactions in a Microbial Cheese-Ripening Community Composed of Debaryomyces hansenii, Brevibacterium aurantiacum, and Hafnia alvei

Ripening cultures containing fungi and bacteria are widely used in smear-ripened cheese production processes, but little is known about the biotic interactions of typical ripening microorganisms at the surface of cheese. We developed a lab-scale mini-cheese model to investigate the biotic interactions of a synthetic community that was composed of Debaryomyces hansenii, Brevibacterium aurantiacum, and Hafnia alvei, three species that are commonly used for smear-ripened cheese production. Transcriptomic analyses of cheese samples produced with different combinations of these three species revealed potential mechanisms of biotic interactions concerning iron acquisition, proteolysis, lipolysis, sulfur metabolism, and D-galactonate catabolism. A strong mutualistic interaction was observed between H. alvei and B. aurantiacum. We propose an explanation of this positive interaction in which B. aurantiacum would benefit from siderophore production by H. alvei, and the latter would be stimulated by the energy compounds liberated from caseins and triglycerides through the action of the proteases and lipases secreted by B. aurantiacum. In the future, it would be interesting to take the iron acquisition systems of cheese-associated strains into account for the purpose of improving the selection of the ripening culture components and their association in mixed cultures.

Denitrase activity of Debaryomyces hansenii reduces the oxidized compound 3-nitrotyrosine in mice liver with colitis

The oxidation of tyrosine to 3-nitrotyrosine is irreversible, and due to this characteristic, 3-nitrotyrosine is used as a marker for oxidative stress in a range of diverse chronic and degenerative diseases. It has been established that the yeast Debaryomyces hansenii (D. hansenii) can assimilate free 3-nitrotyrosine as unique source of nitrogen, and during saline stress, has a high denitrase activity to detoxify this compound in a reaction that involves the liberation of nitrogen dioxide from 3-nitrotyrosine. However, until now it has not been determined whether D. hansenii can detoxify protein-bound 3-nitrotyrosine such as nitrated proteins present in different chronic illnesses. TThe aim of the present study was to evaluate the denitrase activity of D. hansenii to reduce 3-nitrotyrosine from liver proteins of mice with colitis. Firstly, the levels of reactive oxygen species of liver tissue of colitic and control mice were measured by the reaction with the 2'7'-dichlorofluorescein diacetate. Denitrase activity of D. hansenii was evaluated by incubating cell extracts of the yeast with protein extracts from livers of mice with colitis. Following incubation, 3-nitrotyrosine was measured, and to corroborate that denitrase reaction had occurred, the production of nitrites was measured. In samples of liver tissue from mice with colitis, the maximum levels of reactive oxygen species were up to two times higher compared with the control livers. Following the incubation of colitic liver samples with cell extracts of D. hansenii, it was observed that 3-nitrotyrosine decreased to the basal concentration of control liver samples, and that the concentration of nitrites was increased. These results indicate that denitrase of D. hansenii extracts can effectively detoxify 3-nitrotyrosine bound to proteins and that the extracts could be used to decrease protein oxidation damage in chronic degenerative diseases.

Biocontrol of aflatoxigenic Aspergillus parasiticus by native Debaryomyces hansenii in dry-cured meat products

Dry-cured meat products, such as dry-cured ham or dry-fermented sausages, are characterized by their particular ripening process, where a mould population grows on their surface. Some of these moulds are hazardous to the consumers because of their ability to produce mycotoxins including aflatoxins (AFs). The use of native yeasts could be considered a potential strategy for controlling the presence of AFs in dry-cured meat products. The aim of this work was to evaluate the antagonistic activity of two native Debaryomyces hansenii strains on the relative growth rate and the AFs production in Aspergillus parasiticus. Both D. hansenii strains significantly reduced the growth rates of A. parasiticus when grown in a meat-model system at different water activity (a_w) conditions. The presence of D. hansenii strains caused a stimulation of AFs production by A. parasiticus at 0.99 a_w. However, at 0.92 a_w the yeasts significantly reduced the AFs concentration in the meat-model system. The relative expression levels of the aflR and aflS genes involved in the AFs biosynthetic pathway were also repressed at 0.92 a_w in the presence of both D. hansenii strains. These satisfactory results were confirmed in dry-cured ham and dry-fermented sausage slices inoculated with A. parasiticus, since both D. hansenii strains significantly reduced AFs amounts in these matrices. Therefore, both tested D. hansenii strains could be proposed as biocontrol agents within a HACCP framework to minimize the hazard associated with the presence of AFs in dry-cured meat products.

Hyper-Osmotic Stress Elicits Membrane Depolarization and Decreased Permeability in Halotolerant Marine Debaryomyces hansenii Strains and in Saccharomyces cerevisiae

The use of seawater and marine microorganisms can represent a sustainable alternative to avoid large consumption of freshwater performing industrial bioprocesses. Debaryomyces hansenii, which is a known halotolerant yeast, possess metabolic traits appealing for developing such processes. For this purpose, we studied salt stress exposure of two D. hansenii strains isolated from marine fauna. We found that the presence of sea salts during the cultivation results in a slight decrease of biomass yields. Nevertheless, higher concentration of NaCl (2 M) negatively affects other growth parameters, like growth rate and glucose consumption rate. To maintain an isosmotic condition, the cells accumulate glycerol as compatible solute. Flow cytometry analysis revealed that the osmotic adaptation causes a reduced cellular permeability to cell-permeant dye SYBR Green I. We demonstrate that this fast and reversible phenomenon is correlated to the induction of membrane depolarization, and occurred even in presence of high concentration of sorbitol. The decrease of membrane permeability induced by osmotic stress confers to D. hansenii resistance to cationic drugs like Hygromycin B. In addition, we describe that also in Saccharomyces cerevisiae the exposure to hyper-osmotic conditions induced membrane depolarization and reduced the membrane permeability. These aspects are very relevant for the optimization of industrial bioprocesses, as in the case of fermentations and bioconversions carried out by using media/buffers containing high nutrients/salts concentrations. Indeed, an efficient transport of molecules (nutrients, substrates, and products) is the prerequisite for an efficient cellular performance, and ultimately for the efficiency of the industrial process.

Cheese yeasts

Numerous traditionally aged cheeses are surface ripened and develop a biofilm, known as the cheese rind, on their surfaces. The rind of such cheeses comprises a complex community of bacterial and fungal species that are jointly responsible for the typical characteristics of the various cheese varieties. Surface ripening starts directly after brining with the rapid colonization of the cheese surface by yeasts. The initially dominant yeasts are acid and salt-tolerant and are capable of metabolizing the lactate produced by the starter lactic acid bacteria and of producing NH₃ from amino acids. Both processes cause the pH of the cheese surface to rise dramatically. This so-called deacidification process enables the establishment of a salt-tolerant, Gram-positive bacterial community that is less acid-tolerant. Over the past decade, knowledge of yeast diversity in cheeses has increased considerably. The yeast species with the highest prevalence on surface-ripened cheeses are Debaryomyces hansenii and Geotrichum candidum, but up to 30 species can be found. In the cheese core, only lactose-fermenting yeasts, such as Kluyveromyces marxianus, are expected to grow. Yeasts are recognized as having an indispensable impact on the development of cheese flavour and texture because of their deacidifying, proteolytic, and/or lipolytic activity. Yeasts are used not only in the production of surface-ripened cheeses but also as adjunct cultures in the vat milk in order to modify ripening behaviour and flavour of the cheese. However, yeasts may also be responsible for spoilage of cheese, causing early blowing, off-flavour, brown discolouration, and other visible alterations of cheese.

Septic shock due to Candida famata (Debaryomyces hansenii) candidemia in an ICU immunocompetent trauma-patient

Sepsis related to Candida famata (C. famata) fungemia is extremely rare in immunocompetent patients. Moreover, septic shock has not been reported due to this yeast. A previously healthy young multi-trauma male, presented septic shock from C. famata, after he had been admitted in the Intensive Care Unit (ICU) due to haemorrhagic shock. Risk factors for candidemia in ICU patients are the presence of a central venous catheter (CVC), Total Parenteral Nutrition (TPN), use of broad-spectrum antimicrobials, immunosuppression and the length of ICU stay. The presence of CVCs, prior use of antibiotics, prolonged hospitalization, disruption of skin flora and immunocompromised states have been identified as predisposing risk factors for C. famata fungemia. It is worth noting that the present case concerns a non-immunocompromised patient, but long ICU stay and brain injury may indicate a state of immunoparalysis. Identification of the yeast was performed by partial amplification and sequencing of the 26S ribosomal DNA gene [hypervariable region D1/D2; partial sequencing of the act1 gene confirmed the identity of the strain as Debaryomyces hansenii (GenBank submission ID: 1688297)] The patient quickly recovered from sepsis after initiation of amphotericin B and was discharged on the 60th day.

Inhibitory Effect of PgAFP and Protective Cultures on Aspergillus parasiticus Growth and Aflatoxins Production on Dry-Fermented Sausage and Cheese

Aflatoxigenic molds can grow and produce aflatoxins on dry-fermented meat and cheese. The small, basic, cysteine-rich antifungal protein PgAFP displays a time-limited inhibitory ability against unwanted molds by increasing reactive oxygen species (ROS), which can lead to increased aflatoxin production. However, calcium abolishes the inhibitory effect of PgAFP on certain Aspergillus spp. To maximize the antifungal effect, this protein may be combined with protective cultures. Yeasts and lactic acid bacteria may counteract the impact of calcium on PgAFP fungal inhibition. The objective of this work was to study the effect of PgAFP and different combined treatments with Debaryomyces hansenii and/or Pediococcus acidilactici against growth of and aflatoxin production by an aflatoxigenic strain of Aspergillus parasiticus in both culture media and dry-fermented foods with low or high calcium levels. Aflatoxins production was increased by PgAFP but dramatically reduced by P. acidilactici in low calcium culture medium, whereas in the Ca-enriched culture medium, all treatments tested led to low aflatoxins levels. To study whether PgAFP and the protective microorganisms interfere with ROS and aflatoxin production, the relative expression of genes foxA, which is involved in peroxisomal β-oxidation, and aflP, which is required for aflatoxin biosynthesis, were evaluated. The aflatoxin overproduction induced by PgAFP seems not to be linked to peroxisomal β-oxidation. The combination of PgAFP and D. hansenii provided a successful inhibitory effect on A. parasiticus growth as well as on aflatoxin production on sliced dry-fermented sausage and cheese ripened up to 15 days, whereas P. acidilactici did not further enhance the protective effect of the two former agents. Therefore, the combined treatment of PgAFP and D. hansenii seems to provide a promising protective mean against aflatoxin-producing A. parasiticus on dry-fermented foods.

Non-canonical Activities of Hog1 Control Sensitivity of Candida albicans to Killer Toxins From Debaryomyces hansenii

Certain yeasts secrete peptides known as killer toxins or mycocins with a deleterious effect on sensitive yeasts or filamentous fungi, a common phenomenon in environmental species. In a recent work, different Debaryomyces hansenii (Dh) strains isolated from a wide variety of cheeses were identified as producing killer toxins active against Candida albicans and Candida tropicalis. We have analyzed the killer activity of these toxins in C. albicans mutants defective in MAPK signaling pathways and found that the lack of the MAPK Hog1 (but not Cek1 or Mkc1) renders cells hypersensitive to Dh mycocins while mutants lacking other upstream elements of the pathway behave as the wild type strain. Point mutations in the phosphorylation site (T174A-176F) or in the kinase domain (K52R) of HOG1 gene showed that both activities were relevant for the survival of C. albicans to Dh killer toxins. Moreover, Hog1 phosphorylation was also required to sense and adapt to osmotic and oxidative stress while the kinase activity was somehow dispensable. Although the addition of supernatant from the killer toxin- producing D. hansenii 242 strain (Dh-242) induced a slight intracellular increase in Reactive Oxygen Species (ROS), overexpression of cytosolic catalase did not protect C. albicans against this mycocin. This supernatant induced an increase in intracellular glycerol concentration suggesting that this toxin triggers an osmotic stress. We also provide evidence of a correlation between sensitivity to Dh-242 killer toxin and resistance to Congo red, suggesting cell wall specific alterations in sensitive strains.

Effects of Debaryomyces hansenii treatment on intestinal microorganisms in mice with antibiotics-induced diarrhea

To investigate the influence of Debaryomyces hansenii treatment on intestinal microorganisms in mice with antibiotics-induced diarrhea, mouse model of antibiotics-induced diarrhea was created by gavaging mice with mixed antibiotics (23.33 mL/kg/days) composed of gentamycin sulfate and cefradine for 5 days. Mice with the symptom of diarrhea were then treated with D. hansenii by intragastric administration. The control group mice were given with sterile water. After 4 day treatment, total DNA of intestinal microflora of treated and control mice was extracted, and their quantities were measured by sequencing the V4 region of 16S rDNA. The results showed that when compared to the control (sterile water), treatment with D. hansenii increased the operational taxonomic units (OTUs) of intestinal bacteria. The Chao index in diarrhea treated group was higher than diarrhea control group and was similar to healthy control group, while all differences had no significance (P > 0.05). D. hansenii treatment increased the Shannon index but not significantly (P > 0.05). Moreover, there was not significant impact on density and diversity of intestinal bacterial population at phylum and genus levels (P > 0.05). Interestingly, D. hansenii treatment recovered the population density of certain bacterium species, such as Bacteroidaceae (in family level) (P < 0.05). Our results indicate that D. hansenii has potency of adjusting the density and diversity of intestinal bacteria and recovering the population density of Bacteroidaceae in family level.

Debaryomyces hansenii up regulates superoxide dismutase gene expression and enhances the immune response and survival in Pacific red snapper (Lutjanus peru) leukocytes after Vibrio parahaemolyticus infection

Application of yeast is increasing to improve welfare and promotes growth in aquaculture. The halotolerant yeast Debaryomyces hansenii is normally a non-pathogenic yeast with probiotic properties and potential source of antioxidant enzymes as superoxide dismutase. Here, first, we characterized the sequence features of MnSOD and icCu/ZnSOD from Pacific red snapper, and second, we evaluated the potential antioxidant immune responses of the marine yeast Debaryomyces hansenii strain CBS004 in leukocytes which were then subjected to Vibrio parahaemolyticus infection. In silico analysis revealed that LpMnSOD consisted of 1186 bp, with an ORF of 678 bp encoding a 225 amino acid protein and LpicCu/ZnSOD consisted of 1090 bp in length with an ORF of 465 bp encoding a 154 amino acid protein. Multiple alignment analyzes revealed many conserved regions and active sites among its orthologs. In vitro assays using head-kidney and spleen leukocytes immunostimulated with D. hansenii and zymosan in response to V. parahaemolyticus infection reveled that D. hansenii strain CBS004 significantly increased transcriptions of MnSOD and icCu/ZnSOD genes. Flow cytometry assay showed that D. hansenii was able to inhibit apoptosis caused by V. parahaemolyticus in the Pacific red snapper leukocytes and enhanced the phagocytic capacity in head-kidney leukocytes. Immunological assays reveled an increased in superoxide dismutase and peroxidase activities, as well as, in nitric oxide production and reactive oxygen species production (respiratory burst) in fish stimulated with D. hansenii. Finally, our results. These results strongly support the idea that marine yeast Debaryomyces hansenii strain CBS004 can stimulate the antioxidant immune mechanism in head-kidney and spleen leukocytes.

Screening of Debaryomyces hansenii Strains for Flavor Production under a Reduced Concentration of Nitrifying Preservatives Used in Meat Products

A total of 15 Debaryomyces hansenii strains from different food origins were genetically characterized and tested on a culture medium resembling the composition of fermented sausages but different concentrations of nitrifying preservatives. Genetic typing of the D. hansenii strains revealed two levels of discrimination: isolation source or strain specific. Different abilities to proliferate on culture media containing different concentrations of nitrate and nitrite, as sole nitrogen sources and in the presence of amino acids, were observed within D. hansenii strains. Overall metabolism of amino acids and generation of aroma compounds were related to the strain origin of isolation. The best producers of branched aldehydes and ethyl ester compounds were strains isolated from pork sausages. Strains from cheese and llama sausages were good producers of ester compounds and branched alcohols, while vegetable strains produced mainly acid compounds. Nitrate and nitrite reduction affected in different ways the production of volatiles by D. hansenii.

New kids on the block: emerging oleaginous yeast of biotechnological importance

There is growing interest in using oleaginous yeast for the production of a variety of fatty acids and fatty acid-derived oleochemicals. This is motivated by natural propensity for high flux through lipid biosynthesis that has naturally evolved, making them a logical starting point for additional genetic engineering to improve titers and productivities. Much of the academic and industrial focus has centered on yeast that have significant genetic engineering tool capabilities, such as Yarrowia lipolytica, and those that have naturally high lipid accumulation, such as Rhodosporidium toruloides and Lipomyces starkeyi; however, there are oleaginous yeast with phenotypes better aligned with typically inhibitory process conditions, such as high salt concentrations and lignocellulosic derived inhibitors. This review addresses the foundational work in characterizing two emerging oleaginous yeast of interest: Debaryomyces hansenii and Trichosporon oleaginosus. We focus on the physiological and metabolic properties of these yeast that make each attractive for bioprocessing of lignocellulose to fuels and chemicals, discuss their respective genetic engineering tools and highlight the critical barriers facing the broader implementation of these oleaginous yeast.

Vacuolar control of subcellular cation distribution is a key parameter in the adaptation of Debaryomyces hansenii to high salt concentrations

Debaryomyces hansenii is a halotolerant and Na⁺-includer yeast that can be isolated from different food and low-water activity products. It has also been defined as a marine-occurring yeast but key aspects for this salt tolerant behavior are far from being understood. Here, we searched for clues helping to elucidate the basis of this ability. Our results on growth, Rb⁺ transport, total K⁺ and Na⁺ content and vacuolar fragmentation are compatible with a yeast species adapted to cope with salt stress. On the other hand, we confirmed the existence of D. hansenii strategies that are generally observed in sensitive organisms, such as the production of glycerol as a compatible solute and the efficient vacuolar sequestration of Na⁺. We propose a striking role of D. hansenii vacuoles in the maintenance of constant cytosolic K⁺ values, even in the presence of extracellular Na⁺ concentration values more than two orders of magnitude higher than extracellular K⁺. Finally, the ability to deal with cytosolic Na⁺ levels significantly higher than those found in S. cerevisiae, shows the existence of important and specific salt tolerance mechanisms and determinants in D. hansenii.

The serine/threonine phosphatase DhSIT4 modulates cell cycle, salt tolerance and cell wall integrity in halo tolerant yeast Debaryomyces hansenii

The highly conserved family of Phosphoprotein phosphatases (PPP) regulates several major physiological processes in yeast. However, very little is known about the PPP orthologs from the yeast species inhabiting extreme environmental niches. In the present study we have identified DhSIT4, a member of PPP6 class of serine threonine phosphatases from the halotolerant yeast Debaryomyces hansenii. Deletion of DhSIT4 in D. hansenii was not lethal but the mutant exhibited reduced growth due to its effect on the cell cycle. The knock out mutant Dhsit4Δ showed sensitivity towards Li⁺, Na⁺ and cell wall damaging agents. The expression of DhSit4p rescued salt, caffeine and calcofluor white sensitivity of Dhmpk1Δ strain and thereby indicating a genetic interaction of this phosphatase with the cell wall integrity pathway in this species. Our study also demonstrated the antagonistic roles of DhSit4p and DhPpz1p in maintaining the cell cycle and ion homeostasis in D. hansenii.

Postharvest biocontrol ability of killer yeasts against Monilinia fructigena and Monilinia fructicola on stone fruit

The antagonistic effects of Debaryomyces hansenii KI2a, D. hansenii MI1a and Wickerhamomyces anomalus BS91 were tested against Monilinia fructigena and Monilinia fructicola in in vitro and in vivo trials. All yeast strains demonstrated antifungal activity at different levels depending on species, strain and pathogen. D hansenii KI2a and W. anomalus BS91 showed the highest biocontrol activity in vitro; the production of hydrolytic enzymes, killer toxins and volatile organic compounds (VOCs) were hypothesized as their main mechanisms of action against pathogens. D hansenii KI2a and W. anomalus BS91 significantly reduced brown rot incidence and severity on peach and plum fruits artificially inoculated with M. fructigena and M. fructicola, especially when applied 24 h before pathogen inoculation. On the opposite, D. hansenii MI1a exhibited weak antagonistic activity towards M. fructigena on peach and plum fruits and was ineffective against M. fructicola. The noticeable ability of W. anomalus BS91 to control brown rot could be also correlated with its high capacity to colonize the wound tissue and to increase its population density. Accordingly, the antagonistic strains of D. hansenii and W. anomalus could be proposed as active ingredients for the development of biofungicides against Monilinia species that are responsible for considerable economic losses in stone fruit crops.

Investigation of the Activity of the Microorganisms in a Reblochon-Style Cheese by Metatranscriptomic Analysis

The microbial communities in cheeses are composed of varying bacteria, yeasts, and molds, which contribute to the development of their typical sensory properties. In situ studies are needed to better understand their growth and activity during cheese ripening. Our objective was to investigate the activity of the microorganisms used for manufacturing a surface-ripened cheese by means of metatranscriptomic analysis. The cheeses were produced using two lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus), one ripening bacterium (Brevibacterium aurantiacum), and two yeasts (Debaryomyces hansenii and Geotrichum candidum). RNA was extracted from the cheese rinds and, after depletion of most ribosomal RNA, sequencing was performed using a short-read sequencing technology that generated ~75 million reads per sample. Except for B. aurantiacum, which failed to grow in the cheeses, a large number of CDS reads were generated for the inoculated species, making it possible to investigate their individual transcriptome over time. From day 5 to 35, G. candidum accounted for the largest proportion of CDS reads, suggesting that this species was the most active. Only minor changes occurred in the transcriptomes of the lactic acid bacteria. For the two yeasts, we compared the expression of genes involved in the catabolism of lactose, galactose, lactate, amino acids, and free fatty acids. During ripening, genes involved in ammonia assimilation and galactose catabolism were down-regulated in the two species. Genes involved in amino acid catabolism were up-regulated in G. candidum from day 14 to day 35, whereas in D. hansenii, they were up-regulated mainly at day 35, suggesting that this species catabolized the cheese amino acids later. In addition, after 35 days of ripening, there was a down-regulation of genes involved in the electron transport chain, suggesting a lower cellular activity. The present study has exemplified how metatranscriptomic analyses provide insight into the activity of cheese microbial communities for which reference genome sequences are available. In the future, such studies will be facilitated by the progress in DNA sequencing technologies and by the greater availability of the genome sequences of cheese microorganisms.

Identification and Partial Characterization of Antilisterial Compounds Produced by Dairy Yeasts

Food-grade yeasts make significant contributions to flavor development in fermented foods. Some yeast species also inhibit undesirable bacteria, yeasts and molds, apparently by producing antimicrobial compounds called mycocins. The aim of this study was to evaluate the ability of wild yeasts, isolated from raw milk and cheese in the Quebec province area, to produce antilisterial compounds. Based on an agar-membrane screening test, 22 of 95 isolates, namely one Candida catenulata, one Candida parapsilosis, five Candida tropicalis, four Debaryomyces hansenii, one Geotrichum candidum, nine Pichia fermentans and one Pichia anomala, exhibited a significant inhibitory effect against Listeria ivanovii HPB28. Four in particular, namely C. tropicalis LMA-693, D. hansenii LMA-916, P. fermentans LMA-256 and P. anomala LMA-827, produced substances extractable from culture supernatant and capable of decreasing 18-h growth of L. ivanovii by, respectively, 97, 92, 84 and 78 %. Heating the extracted material (100 °C for 10 min) decreased these values to 72, 62, 58 and 31 %, respectively, while treatment with trypsin or pronase E decreased them to as little as 27 %. The extracts reduced the numbers of viable Listeria monocytogenes by as much as four log cycles within an hour. Transmission electron microscopy revealed a high proportion of lysis among the cells, apparently due to pore formation. This study clearly shows the potential of these four yeast isolates for use as bio-preservatives in a variety of dairy products.