Role of oxidative stress in the extremely salt-tolerant yeast Hortaea werneckii

Black yeasts in hypersaline conditions

Extremotolerant and extremophilic fungi are an important part of microbial communities that thrive in extreme environments. Among them, the black yeasts are particularly adaptable. They use their melanized cell walls and versatile morphology, as well as a complex set of molecular adaptations, to survive in conditions that are lethal to most other species. In contrast to extremophilic bacteria and archaea, these fungi are typically extremotolerant rather than extremophilic and exhibit an unusually wide ecological amplitude. Some extremely halotolerant black yeasts can grow in near-saturated NaCl solutions, but can also grow on normal mycological media. They adapt to the low water activity caused by high salt concentrations by sensing their environment, balancing osmotic pressure by accumulating compatible solutes, removing toxic salt ions from the cell using membrane transporters, altering membrane composition and remodelling the highly melanized cell wall. As protection against extreme conditions, halotolerant black yeasts also develop different morphologies, from yeast-like to meristematic. Genomic studies of black yeasts have revealed a variety of reproductive strategies, from clonality to intense recombination and the formation of stable hybrids. Although a comprehensive understanding of the ecological role and molecular adaptations of halotolerant black yeasts remains elusive and the application of many experimental methods is challenging due to their slow growth and recalcitrant cell walls, much progress has been made in deciphering their halotolerance. Advances in molecular tools and genomics are once again accelerating the research of black yeasts, promising further insights into their survival strategies and the molecular basis of their adaptations. KEY POINTS: • Black yeasts show remarkable adaptability to environmental stress • Black yeasts are part of microbial communities in hypersaline environments • Halotolerant black yeasts utilise various molecular and morphological adaptations.

Understanding Fungi in Glacial and Hypersaline Environments

Hypersaline waters and glacial ice are inhospitable environments that have low water activity and high concentrations of osmolytes. They are inhabited by diverse microbial communities, of which extremotolerant and extremophilic fungi are essential components. Some fungi are specialized in only one of these two environments and can thrive in conditions that are lethal to most other life-forms. Others are generalists, highly adaptable species that occur in both environments and tolerate a wide range of extremes. Both groups efficiently balance cellular osmotic pressure and ion concentration, stabilize cell membranes, remodel cell walls, and neutralize intracellular oxidative stress. Some species use unusual reproductive strategies. Further investigation of these adaptations with new methods and carefully designed experiments under ecologically relevant conditions will help predict the role of fungi in hypersaline and glacial environments affected by climate change, decipher their stress resistance mechanisms and exploit their biotechnological potential.

Perchlorate-Specific Proteomic Stress Responses of Debaryomyces hansenii Could Enable Microbial Survival in Martian Brines

If life exists on Mars, it would face several challenges including the presence of perchlorates, which destabilize biomacromolecules by inducing chaotropic stress. However, little is known about perchlorate toxicity for microorganism on the cellular level. Here we present the first proteomic investigation on the perchlorate-specific stress responses of the halotolerant yeast Debaryomyces hansenii and compare these to generally known salt stress adaptations. We found that the responses to NaCl and NaClO₄ -induced stresses share many common metabolic features, e.g., signaling pathways, elevated energy metabolism, or osmolyte biosynthesis. Nevertheless, several new perchlorate-specific stress responses could be identified, such as protein glycosylation and cell wall remodulations, presumably in order to stabilize protein structures and the cell envelope. These stress responses would also be relevant for life on Mars, which - given the environmental conditions - likely developed chaotropic defense strategies such as stabilized confirmations of biomacromolecules and the formation of cell clusters. This article is protected by copyright. All rights reserved.

Mining for Perchlorate Resistance Genes in Microorganisms From Sediments of a Hypersaline Pond in Atacama Desert, Chile

Perchlorate is an oxidative pollutant toxic to most of terrestrial life by promoting denaturation of macromolecules, oxidative stress, and DNA damage. However, several microorganisms, especially hyperhalophiles, are able to tolerate high levels of this compound. Furthermore, relatively high quantities of perchlorate salts were detected on the Martian surface, and due to its strong hygroscopicity and its ability to substantially decrease the freezing point of water, perchlorate is thought to increase the availability of liquid brine water in hyper-arid and cold environments, such as the Martian regolith. Therefore, perchlorate has been proposed as a compound worth studying to better understanding the habitability of the Martian surface. In the present work, to study the molecular mechanisms of perchlorate resistance, a functional metagenomic approach was used, and for that, a small-insert library was constructed with DNA isolated from microorganisms exposed to perchlorate in sediments of a hypersaline pond in the Atacama Desert, Chile (Salar de Maricunga), one of the regions with the highest levels of perchlorate on Earth. The metagenomic library was hosted in Escherichia coli DH10B strain and exposed to sodium perchlorate. This technique allowed the identification of nine perchlorate-resistant clones and their environmental DNA fragments were sequenced. A total of seventeen ORFs were predicted, individually cloned, and nine of them increased perchlorate resistance when expressed in E. coli DH10B cells. These genes encoded hypothetical conserved proteins of unknown functions and proteins similar to other not previously reported to be involved in perchlorate resistance that were related to different cellular processes such as RNA processing, tRNA modification, DNA protection and repair, metabolism, and protein degradation. Furthermore, these genes also conferred resistance to UV-radiation, 4-nitroquinoline-N-oxide (4-NQO) and/or hydrogen peroxide (H2O2), other stress conditions that induce oxidative stress, and damage in proteins and nucleic acids. Therefore, the novel genes identified will help us to better understand the molecular strategies of microorganisms to survive in the presence of perchlorate and may be used in Mars exploration for creating perchlorate-resistance strains interesting for developing Bioregenerative Life Support Systems (BLSS) based on in situ resource utilization (ISRU).

A high-throughput RNA-Seq approach to elucidate the transcriptional response of Piriformospora indica to high salt stress

Piriformospora indica, a root endophytic fungus, augments plant nutrition and productivity as well as protects plants against pathogens and abiotic stresses. High salinity is a major problem faced by plants as well as by microbes. Until now, the precise mechanism of salt stress tolerance in P. indica has remained elusive. In this study, the transcriptomes of control and salt-treated (0.5 M NaCl) P. indica were sequenced via the RNA-seq approach. A total of 30,567 transcripts and 15,410 unigenes for P. indica were obtained from 7.3 Gb clean reads. Overall 661 differentially expressed genes (DEGs) between control and treated samples were retrieved. Gene ontology (GO) and EuKaryotic Orthologous Groups (KOG) enrichments revealed that DEGs were specifically involved in metabolic and molecular processes, such as "response to salt stress", "oxidoreductase activity", "ADP binding", "translation, ribosomal structure and biogenesis", "cytoskeleton", and others. The unigenes involved in "cell wall integrity", "sterol biosynthesis", and "oxidative stress" such as Rho-type GTPase, hydroxymethylglutaryl-CoA synthase, and thioredoxin peroxidase were up-regulated in P. indica subjected to salt stress. The salt-responsive DEGs have shown that they might have a potential role in salt stress regulation. Our study on the salt-responsive DEGs established a foundation for the elucidation of molecular mechanisms related to P. indica stress adaptation and a future reference for comparative functional genomics studies of biotechnologically important fungal species.

Haloadaptative Responses of Aspergillus sydowii to Extreme Water Deprivation: Morphology, Compatible Solutes, and Oxidative Stress at NaCl Saturation

Water activity (a_w) is critical for microbial growth, as it is severely restricted at a_w < 0.90. Saturating NaCl concentrations (~5.0 M) induce extreme water deprivation (a_w ≅ 0.75) and cellular stress responses. Halophilic fungi have cellular adaptations that enable osmotic balance and ionic/oxidative stress prevention to grow at high salinity. Here we studied the morphology, osmolyte synthesis, and oxidative stress defenses of the halophile Aspergillus sydowii EXF-12860 at 1.0 M and 5.13 M NaCl. Colony growth, pigmentation, exudate, and spore production were inhibited at NaCl-saturated media. Additionally, hyphae showed unpolarized growth, lower diameter, and increased septation, multicellularity and branching compared to optimal NaCl concentration. Trehalose, mannitol, arabitol, erythritol, and glycerol were produced in the presence of both 1.0 M and 5.13 M NaCl. Exposing A. sydowii cells to 5.13 M NaCl resulted in oxidative stress evidenced by an increase in antioxidant enzymes and lipid peroxidation biomarkers. Also, genes involved in cellular antioxidant defense systems were upregulated. This is the most comprehensive study that investigates the micromorphology and the adaptative cellular response of different non-enzymatic and enzymatic oxidative stress biomarkers in halophilic filamentous fungi.

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.

Back to the Salt Mines: Genome and Transcriptome Comparisons of the Halophilic Fungus Aspergillus salisburgensis and Its Halotolerant Relative Aspergillus sclerotialis

Salt mines are among the most extreme environments as they combine darkness, low nutrient availability, and hypersaline conditions. Based on comparative genomics and transcriptomics, we describe in this work the adaptive strategies of the true halophilic fungus Aspergillus salisburgensis, found in a salt mine in Austria, and compare this strain to the ex-type halotolerant fungal strain Aspergillus sclerotialis. On a genomic level, A. salisburgensis exhibits a reduced genome size compared to A. sclerotialis, as well as a contraction of genes involved in transport processes. The proteome of A. sclerotialis exhibits an increased proportion of alanine, glycine, and proline compared to the proteome of non-halophilic species. Transcriptome analyses of both strains growing at 5% and 20% NaCl show that A. salisburgensis regulates three-times fewer genes than A. sclerotialis in order to adapt to the higher salt concentration. In A. sclerotialis, the increased osmotic stress impacted processes related to translation, transcription, transport, and energy. In contrast, membrane-related and lignolytic proteins were significantly affected in A. salisburgensis.

Overview of Oxidative Stress Response Genes in Selected Halophilic Fungi

Exposure of microorganisms to stress, including to high concentrations of salt, can lead to increased production of reactive oxygen species in the cell. To limit the resulting damage, cells have evolved a variety of antioxidant defenses. The role of these defenses in halotolerance has been proposed before. Whole genome sequencing for some of the most halotolerant and halophilic fungal species has enabled us to investigate the possible links between oxidative and salt stress tolerance on the genomic level. We identified genes involved in oxidative stress response in the halophilic basidiomycete Wallemia ichthyophaga, and halotolerant ascomycetous black yeasts Hortaea werneckii and Aureobasidium pullulans, and compared them to genes from 16 other fungi, both asco- and basidiomycetes. According to our results, W. ichthyophaga can survive salinities detrimental to most other organisms with only a moderate number of oxidative stress response genes. In other investigated species, however, the maximum tolerated salinity correlated with the number of genes encoding three major enzymes of the cellular oxidative stress response: superoxide dismutases, catalases, and peroxiredoxins. This observation supports the hypothetical link between the antioxidant capacity of cells and their halotolerance.

Recent Advances in Halophilic Protozoa Research

Most research on microorganisms adapted to hypersaline habitats has focused on Archaea and Bacteria, with microbial eukaryotes receiving much less attention. Over the past 15 yr, our knowledge of phagotrophic microbial eukaryotes, i.e. protozoa, from hypersaline habitats has greatly improved through combinations of microscopy, molecular phylogenetics, environmental sequencing, transcriptomics and growth experiments. High salinity waters from salterns, other landlocked water masses and deep hypersaline anoxic basins contain unique and diverse halophilic protozoan assemblages. These have the potential to exert substantial grazing pressure on prokaryotes and other eukaryotes. They represent many separate evolutionary lineages; species of Heterolobosea, Bicosoecida, and Ciliophora have been most intensively characterized, with several proven to be extreme (or borderline extreme) halophiles. Transcriptomic examinations of the bicosoecid Halocafeteria (and the heteroloboseid Pharyngomonas) indicate that high-salt adaptation is associated with a subtle shift in protein amino acid composition, and involves the differential expression of genes participating in ion homeostasis, signal transduction, stress management, and lipid remodeling. Instances of gene duplication and lateral transfer possibly conferring adaptation have been documented. Indirect evidence suggests that these protozoa use "salt-out" osmoadaptive strategies.

Adaptations to High Salt in a Halophilic Protist: Differential Expression and Gene Acquisitions through Duplications and Gene Transfers

The capacity of halophiles to thrive in extreme hypersaline habitats derives partly from the tight regulation of ion homeostasis, the salt-dependent adjustment of plasma membrane fluidity, and the increased capability to manage oxidative stress. Halophilic bacteria, and archaea have been intensively studied, and substantial research has been conducted on halophilic fungi, and the green alga Dunaliella. By contrast, there have been very few investigations of halophiles that are phagotrophic protists, i.e., protozoa. To gather fundamental knowledge about salt adaptation in these organisms, we studied the transcriptome-level response of Halocafeteria seosinensis (Stramenopiles) grown under contrasting salinities. We provided further evolutionary context to our analysis by identifying genes that underwent recent duplications. Genes that were highly responsive to salinity variations were involved in stress response (e.g., chaperones), ion homeostasis (e.g., Na+/H+ transporter), metabolism and transport of lipids (e.g., sterol biosynthetic genes), carbohydrate metabolism (e.g., glycosidases), and signal transduction pathways (e.g., transcription factors). A significantly high proportion (43%) of duplicated genes were also differentially expressed, accentuating the importance of gene expansion in adaptation by H. seosinensis to high salt environments. Furthermore, we found two genes that were lateral acquisitions from bacteria, and were also highly up-regulated and highly expressed at high salt, suggesting that this evolutionary mechanism could also have facilitated adaptation to high salt. We propose that a transition toward high-salt adaptation in the ancestors of H. seosinensis required the acquisition of new genes via duplication, and some lateral gene transfers (LGTs), as well as the alteration of transcriptional programs, leading to increased stress resistance, proper establishment of ion gradients, and modification of cell structure properties like membrane fluidity.

Seawater as Alternative to Freshwater in Pretreatment of Date Palm Residues for Bioethanol Production in Coastal and/or Arid Areas

The large water consumption (1.9-5.9 m(3) water per m(3) of biofuel) required by biomass processing plants has become an emerging concern, which is particularly critical in arid/semiarid regions. Seawater, as a widely available water source, could be an interesting option. This work was to study the technical feasibility of using seawater to replace freshwater in the pretreatment of date palm leaflets, a lignocellulosic biomass from arid regions, for bioethanol production. It was shown that leaflets pretreated with seawater exhibited lower cellulose crystallinity than those pretreated with freshwater. Pretreatment with seawater produced comparably digestible and fermentable solids to those obtained with freshwater. Moreover, no significant difference of inhibition to Saccharomyces cerevisiae was observed between liquids from pretreatment with seawater and freshwater. The results showed that seawater could be a promising alternative to freshwater for lignocellulose biorefineries in coastal and/or arid/semiarid areas.

Microbially-driven strategies for bioremediation of bauxite residue

Globally, 3 Gt of bauxite residue is currently in storage, with an additional 120 Mt generated every year. Bauxite residue is an alkaline, saline, sodic, massive, and fine grained material with little organic carbon or plant nutrients. To date, remediation of bauxite residue has focused on the use of chemical and physical amendments to address high pH, high salinity, and poor drainage and aeration. No studies to date have evaluated the potential for microbial communities to contribute to remediation as part of a combined approach integrating chemical, physical, and biological amendments. This review considers natural alkaline, saline environments that present similar challenges for microbial survival and evaluates candidate microorganisms that are both adapted for survival in these environments and have the capacity to carry out beneficial metabolisms in bauxite residue. Fermentation, sulfur oxidation, and extracellular polymeric substance production emerge as promising pathways for bioremediation whether employed individually or in combination. A combination of bioaugmentation (addition of inocula from other alkaline, saline environments) and biostimulation (addition of nutrients to promote microbial growth and activity) of the native community in bauxite residue is recommended as the approach most likely to be successful in promoting bioremediation of bauxite residue.

Melanin is crucial for growth of the black yeast Hortaea werneckii in its natural hypersaline environment

Melanin has an important role in the ability of fungi to survive extreme conditions, like the high NaCl concentrations that are typical of hypersaline environments. The black fungus Hortaea werneckii that has been isolated from such environments has 1,8-dihydroxynaphthalene-melanin incorporated into the cell wall, which minimises the loss of glycerol at low NaCl concentrations. To further explore the role of melanin in the extremely halotolerant character of H. werneckii, we studied the effects of several melanin biosynthesis inhibitors on its growth, pigmentation and cell morphology. The most potent inhibitors were a 2,3-dihydrobenzofuran derivative and tricyclazole, which restricted the growth of H. werneckii on high-salinity media, as shown by growth curves and plate-drop assays. These inhibitors promoted release of the pigments from the H. werneckii cell surface and changed the medium colour. Inhibitor-treated H. werneckii cells exposed to high salinity showed both decreased and increased cell lengths. We speculate that this absence of melanin perturbs the integrity of the cell wall in H. werneckii, which affects its cell division and exposes it to the harmful effects of high NaCl concentrations. Surprisingly, melanin had no effect on H. werneckii survival under H₂O₂ oxidative stress.

Tinea nigra by Hortaea werneckii, a report of 22 cases from Mexico

Tinea nigra is a superficial mycosis caused by Hortaea werneckii. It is an infrequent asymptomatic infection that affects human palms and soles, and is mostly observed in tropical countries. We evaluate retrospectively twenty-two confirmed cases of tinea nigra from a total of eleven yr (1997–2007) and discuss the epidemiology, clinical features and treatment of this disease. In twelve cases, adults were involved, in 10, children. In nineteen cases the disorder was located on palms of hands and in three on soles of feet. In all cases, the obtained isolates were morphologically identified as Hortaea werneckii and the identification of ten isolates was retrospectively confirmed with the help of sequences of the internal transcribed spacer regions of the ribosomal DNA. The patients received topical treatment with Whitfield ointment, ketoconazole, bifonazole, or terbinafine. Treatment with keratolytic agents and topical antifungals was effective.

Adaptation of extremely halotolerant black yeast Hortaea werneckii to increased osmolarity: a molecular perspective at a glance

Halophilic adaptations have been studied almost exclusively on prokaryotic microorganisms. Discovery of the black yeast Hortaea werneckii as the dominant fungal species in hypersaline waters enabled the introduction of a new model organism to study the mechanisms of salt tolerance in eukaryotes. Its strategies of cellular osmotic adaptations on the physiological and molecular level revealed novel, intricate mechanisms to combat fluctuating salinity. H. werneckii is an extremely halotolerant eukaryotic microorganism and thus a promising source of transgenes for osmotolerance improvement of industrially important yeasts, as well as in crops.

Fungal adaptation to extremely high salt concentrations

Hypersaline environments support substantial microbial communities of selected halotolerant and halophilic organisms, including fungi from various orders. In hypersaline water of solar salterns, the black yeast Hortaea werneckii is by far the most successful fungal representative. It has an outstanding ability to overcome the turgor loss and sodium toxicity that are typical for hypersaline environments, which facilitates its growth even in solutions that are almost saturated with NaCl. We propose a model of cellular responses to high salt concentrations that integrates the current knowledge of H. werneckii adaptations. The negative impact of a hyperosmolar environment is counteracted by an increase in the energy supply that is needed to drive the energy-demanding export of ions and synthesis of compatible solutes. Changes in membrane lipid composition and cell-wall structure maintain the integrity and functioning of the stressed cells. Understanding the salt responses of H. werneckii and other fungi (e.g., the halophilic Wallemia ichthyophaga) will extend our knowledge of fungal stress tolerance and promote the use of the currently unexploited biotechnological potential of fungi that live in hypersaline environments.

The MAP kinase HwHog1 from the halophilic black yeast Hortaea werneckii: coping with stresses in solar salterns

Background

Hortaea werneckii is one of the most salt-tolerant species among microorganisms. It has been isolated from hypersaline waters of salterns as one of the predominant species of a group of halophilic and halotolerant melanized yeast-like fungi, arbitrarily named as "black yeasts". It has previously been shown that H. werneckii has distinct mechanisms of adaptation to high salinity environments that are not seen in salt-sensitive and only moderately salt-tolerant fungi. In H. werneckii, the HOG pathway is important for sensing the changes in environmental osmolarity, as demonstrated by identification of three main pathway components: the mitogen-activated protein kinase (MAPK) HwHog1, the MAPK kinase HwPbs2, and the putative histidine kinase osmosensor HwHhk7.

Results

In this study, we show that the expression of HwHOG1 in salt-adapted cells depends on the environmental salinity and that HwHOG1 transcription responds rapidly but reciprocally to the acute hyper-saline or hypo-saline stress. Molecular modelling of HwHog1 reveals an overall structural homology with other MAPKs. HwHog1 complements the function of ScHog1 in the Saccharomyces cerevisiae multistress response. We also show that hyper-osmolar, oxidative and high-temperature stresses activate the HwHog1 kinase, although under high-temperature stress the signal is not transmitted via the MAPK kinase Pbs2. Identification of HOG1-like genes from other halotolerant fungi isolated from solar salterns demonstrates a high degree of similarity and excellent phylogenetic clustering with orthologues of fungal origin.

Conclusion

The HOG signalling pathway has an important role in sensing and responding to hyper-osmolar, oxidative and high-temperature stresses in the halophilic fungi H. werneckii. These findings are an important advance in our understanding of the HOG pathway response to stress in H. werneckii, a proposed model organism for studying the salt tolerance of halophilic and halotolerant eukaryotes.