Distribution and identification of red yeasts in deep-sea environments around the northwest Pacific Ocean

Insight into planktonic protistan and fungal communities across the nutrient-depleted environment of the South Pacific Subtropical Gyre

Ocean microorganisms constitute ~70% of the marine biomass, contribute to ~50% of the Earth's primary production, and play a vital role in global biogeochemical cycles. The marine heterotrophic and mixotrophic protistan and fungal communities have often been overlooked mainly due to limitations in morphological species identification. Despite the accumulation of studies on biogeographic patterns observed in microbial communities, our understanding of the abundance and distribution patterns within the microbial community of the largest subtropical gyre, the South Pacific Gyre (SPG), remains incomplete. Here, we investigated the diversity and vertical composition of protistan and fungal communities in the water column of the ultra-oligotrophic SPG. Our results showed apparent differences in protistan community diversity in the photic and aphotic regions. The entire protistan community diversity was significantly affected by temperature, salinity, oxygen, and nutrient concentrations, while the parasitic community diversity was also affected by chlorophyll a concentration. The parasitic protists were assigned to the class Syndiniales accounting for over 98% of the total parasitic protists, exhibiting higher relative sequence abundance along the water depth and displaying consistent patterns among different sampling stations. In contrast to the protistan community, the fungal community along the SPG primarily clustered based on the sampling station and pelagic zones. In particular, our study reveals a significant presence of parasitic protists and functionally diverse fungi in SPG and their potential impact on carbon cycling in the gyre.IMPORTANCEOur findings carry important implications for understanding the distribution patterns of the previously unrecognized occurrence of parasitic protists and functionally diverse fungi in the nutrient-limited South Pacific Gyre. In particular, our study reveals a significant presence of parasitic Syndiniales, predominantly abundant in the upper 300 m of the aphotic zone in the gyre, and a distinct presence of fungal communities in the aphotic zone at the central part of the gyre. These findings strongly suggest that these communities play a substantial role in yet insufficiently described microbial food web. Moreover, our research enhances our understanding of their contribution to the dynamics of the food webs in oligotrophic gyres and is valuable for projecting the ecological consequences of future climate warming.

Molecular Identification and Biochemical Characterization of Novel Marine Yeast Strains with Potential Application in Industrial Biotechnology

Cell-based agriculture is an emerging and attractive alternative to produce various food ingredients. In this study, five strains of marine yeast were isolated, molecularly identified and biochemically characterized. Molecular identification was realized by sequencing the DNA ITS1 and D1/D2 region, and sequences were registered in GenBank as Yarrowia lipolytica YlTun15, Rhodotorula mucilaginosa RmTun15, Candida tenuis CtTun15, Debaryomyces hansenii DhTun2015 and Trichosporon asahii TaTun15. Yeasts showed protein content varying from 26% (YlTun15) to 40% (CtTun15 and DhTun2015), and essential amino acids ranging from 38.1 to 64.4% of the total AAs (CtTun15-YlTun15, respectively). Lipid content varied from 11.15 to 37.57% with substantial amount of PUFA (>12% in RmTun15). All species had low levels of Na (<0.15 mg/100 g) but are a good source of Ca and K. Yeast cytotoxic effect was investigated against human embryonic kidney cells (HEK 293); results showed improved cell viability with all added strains, indicating safety of the strains used. Based on thorough literature investigation and yeast composition, the five identified strains could be classified not only as oleaginous yeasts but also as single cell protein (SCP) (DhTun2015 and CtTun15) and single cell oil (SCO) (RmTun15, YlTun15 and TaTun15) producers; and therefore, they represent a source of alternative ingredients for food, feed and other sectors.

First isolation and identification of Cystobasidium calyptogenae from the oral samples of an elderly patient presenting with angular cheilitis

Background

Angular cheilitis, an infection mainly caused by Candida yeasts, is featured by the appearance of inflammatory lesions at the bilateral corners of the mouth, particularly in patients with poor oral hygiene, ill-fitting dentures and old age. The first isolation of an atypical yeast, Cystobasidium calyptogenae, from oral samples of a patient presenting with angular cheilitis is discussed in this study.

Case presentation

Angular cheilitis was diagnosed in a 60-year-old denture-wearing woman who presented with an irritation fibroma on her right lower buccal sulcus over the premolar region. Primary cultures of her oral swab and oral rinse samples grew a pure culture of an uncommon yeast strain resembling Rhodotorula sp. Sequence analysis of the yeast internal transcribed spacer (ITS) gene region and D1D2 domain showed highest similarity (99.6% and 100%, respectively) to C. calyptogenae CBS 9125 type strain. Following 2 weeks of treatment with miconazole/fusidic acid and mouthwash, the oral lesion showed improvement with less erythema. C. calyptogenae was not isolated from the patient’s oral samples upon repeat sampling.

Conclusion

This is the first report on the isolation of C. calyptogenae from human oral samples. The ability of C. calyptogenae to grow at 37 °C and the fact that it was the only yeast species isolated from the patient’s oral samples suggests its pathogenic potential and possible involvement in angular cheilitis. The ubiquitous nature of the Cystobasidium yeast is believed to increase the likelihood of opportunistic infections among immunocompromised individuals. As Cystobasidium is phenotypically indistinguishable from Rhodotorula, an emerging opportunistic pathogen, surveillance using molecular identification in clinical settings is essential in providing accurate diagnosis and treatment of uncommon yeast infections.

Ecological and Pharmacological Activities of Polybrominated Diphenyl Ethers (PBDEs) from the Indonesian Marine Sponge Lamellodysidea herbacea

Two known Polybrominated Diphenyl Ethers (PBDEs), 3,4,5-tribromo-2-(2′,4′-dibromophenoxy)phenol (1d) and 3,4,5,6-tetrabromo-2-(2′,4′-dibromophenoxy)phenol (2b), were isolated from the Indonesian marine sponge Lamellodysidea herbacea. The structure was confirmed using ¹³C chemical shift average deviation and was compared to the predicted structures and recorded chemical shifts in previous studies. We found a wide range of bioactivities from the organic crude extract, such as (1) a strong deterrence against the generalist pufferfish Canthigaster solandri, (2) potent inhibition against environmental and human pathogenic bacterial and fungal strains, and (3) the inhibition of the Hepatitis C Virus (HCV). The addition of a bromine atom into the A-ring of compound 2b resulted in higher fish feeding deterrence compared to compound 1d. On the contrary, compound 2b showed only more potent inhibition against the Gram-negative bacteria Rhodotorula glutinis (MIC 2.1 μg/mL), while compound 1d showed more powerful inhibition against the other human pathogenic bacteria and fungi. The first report of a chemical defense by compounds 1d and 2b against fish feeding and environmental relevant bacteria, especially pathogenic bacteria, might be one reason for the widespread occurrence of the shallow water sponge Lamellodysidea herbacea in Indonesia and the Indo-Pacific.

Deep-sea hydrothermal vent sediments reveal diverse fungi with antibacterial activities

Relatively little is known about the diversity of fungi in deep-sea, hydrothermal sediments. Less thoroughly explored environments are likely untapped reservoirs of unique biodiversity with the potential to augment our current arsenal of microbial compounds with biomedical and/or industrial applications. In this study, we applied traditional culture-based methods to examine a subset of the morphological and phylogenetic diversity of filamentous fungi and yeasts present in 11 hydrothermally influenced sediment samples collected from eight sites on the seafloor of Guaymas Basin, Mexico. A total of 12 unique isolates affiliating with Ascomycota and Basidiomycota were obtained and taxonomically identified on the basis of morphological features and analyses of marker genes including actin, β-tubulin, small subunit ribosomal DNA (18S rRNA), internal transcribed spacer (ITS) and large subunit ribosomal DNA (26S rRNA) D1/D2 domain sequences (depending on taxon). A total of 11 isolates possess congeners previously detected in, or recovered from, deep-sea environments. A total of seven isolates exhibited antibacterial activity against human bacterial pathogens Staphylococcus aureus ATCC-35556 and/or Escherichia coli ATCC-25922. This first investigation suggests that hydrothermal environments may serve as promising reservoirs of much greater fungal diversity, some of which may produce biomedically useful metabolites.

Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B

Red yeasts of the genus Rhodotorula are of great interest to the biotechnological industry due to their ability to produce valuable natural products, such as lipids and carotenoids with potential applications as surfactants, food additives, and pharmaceuticals. Herein, we explored the biosynthetic potential of R. mucilaginosa 50-3-19/20B collected from the Mid-Atlantic Ridge using modern genomics and untargeted metabolomics tools. R. mucilaginosa 50-3-19/20B exhibited anticancer activity when grown on PDA medium, while antimicrobial activity was observed when cultured on WSP-30 medium. Applying the bioactive molecular networking approach, the anticancer activity was linked to glycolipids, namely polyol esters of fatty acid (PEFA) derivatives. We purified four PEFAs (1–4) and the known methyl-2-hydroxy-3-(1H-indol-2-yl)propanoate (5). Their structures were deduced from NMR and HR-MS/MS spectra, but 1–5 showed no anticancer activity in their pure form. Illumina-based genome sequencing, de novo assembly and standard biosynthetic gene cluster (BGC) analyses were used to illustrate key components of the PEFA biosynthetic pathway. The fatty acid producing BGC3 was identified to be capable of producing precursors of PEFAs. Some Rhodotorula strains are able to convert inulin into high-yielding PEFA and cell lipid using a native exo-inulinase enzyme. The genomic locus for an exo-inulinase enzyme (g1629.t1), which plays an instrumental role in the PEFA production via the mannitol biosynthesis pathway, was identified. This is the first untargeted metabolomics study on R. mucilaginosa providing new genomic insights into PEFA biosynthesis.

The Mycobiota of the Deep Sea: What Omics Can Offer

The deep sea (>1000 m below sea level) represents one of the most extreme environments of the ocean. Despite exhibiting harsh abiotic conditions such as low temperatures, high hydrostatic pressure, high salinity concentrations, a low input of organic matter, and absence of light, the deep sea encompasses a great fungal diversity. For decades, most knowledge on the fungal diversity of the deep sea was obtained through culture-dependent techniques. More recently, with the latest advances of high-throughput next generation sequencing platforms, there has been a rapid increment in the number of studies using culture-independent techniques. This review brings into the spotlight the progress of the techniques used to assess the diversity and ecological role of the deep-sea mycobiota and provides an overview on how the omics technologies have contributed to gaining knowledge about fungi and their activity in poorly explored marine environments. Finally, current challenges and suggested coordinated efforts to overcome them are discussed.

Microstructure and molecular vibration of mannosylerythritol lipids from Pseudozyma yeast strains

This work highlights microstructure and molecular vibration of mannosylerythritol lipids (MELs) from Pseudozyma aphidis B1 and Pseudozyma hubeiensis TS18 strains collected from brown algae and mangrove sediments. The scanning electron microscopy (SEM) shows the elongated structures with polar budding in the cells of B1 and TS18 yeast strains. The high-resolution transmission electron microscopy (HRTEM) identifies large lipid bodies that contain MELs confirmed by the anthrone test and thin layer chromatography. The HRTEM also reveals unknown electron dense inclusions. The surface-enhanced Raman scattering (SERS) was used to analysis molecular vibrations of cells, MEL mixtures, and purified MELs (A, B, and C) extracted from the B1 and TS18 cells. The peak analysis of Raman spectra suggests a higher level of saturation per fatty acid chain in MEL-B in both B1 and TS18 cells. This work demonstrates that the out-of-plane bending vibrations of the CH bonds in the range of 840-940 cm^-1 can serve an efficient indicator for detecting MEL-A, -B, and -C.

Assessment of Diversity of Culturable Marine Yeasts Associated with Corals and Zoanthids in the Gulf of Thailand, South China Sea

Marine yeasts can occur in a wide range of habitats, including in marine invertebrates, in which they may play important roles; however, investigation of marine yeasts in marine invertebrates is scarce. Therefore, this study aims to explore the diversity of yeasts associated with corals and zoanthids in the Gulf of Thailand. Thirty-three coral and seven zoanthid samples were collected at two sampling sites near Mu and Khram islands. Fifty yeast strains were able to be isolated from 25 of the 40 samples collected. Identification based on sequence analyses of the D1/D2 domain of the large subunit rRNA gene revealed a higher number of strains in the phylum Basidiomycota (68%) than in the phylum Ascomycota. The ascomycetous yeasts comprised nine known species from four genera (Candida, Meyerozyma, Kodamaea, and Wickerhamomyces), whereas the basidiomycetous yeasts comprised 10 known species from eight genera (Vishniacozyma, Filobasidium, Naganishia, Papiliotrema, Sterigmatomyces, Cystobasidium, Rhodotorula, and Rhodosporidiobolus) and one potentially new species. The species with the highest occurrence was Rhodotorula mucilaginosa. Using principal coordinate analysis (PCoA) ordination, no marked differences were found in the yeast communities from the two sampling sites. The estimation of the expected richness of species was higher than the actual richness of species observed.

Efficient simultaneous production of extracellular polyol esters of fatty acids and intracellular lipids from inulin by a deep-sea yeast Rhodotorula paludigena P4R5

BACKGROUND

Polyol esters of fatty acids (PEFA) are a kind of promising biosurfactants and mainly secreted by Rhodotorula strains. In addition, some strains of Rhodotorula are reliable producers of microbial lipid. Therefore, it is feasible to establish a one step fermentation process for efficient simultaneous production of PEFA and microbial lipids by a suitable Rhodotorula strain.

RESULTS

A newly isolated deep-sea yeast, Rhodotorula paludigena P4R5, was shown to simultaneously produce high level of intracellular lipid and extracellular PEFA. Under the optimized conditions, it could yield 48.5 g/L of PEFA and 16.9 g/L of intracellular lipid within 156 h from inulin during 10-L batch fermentation. The PEFA consisting of a mixture of mannitol esters of 3-hydroxy C14, C16 and C18 fatty acids with variable acetylation showed outstanding surface activity and emulsifying activity, while the fatty acids of the intracellular lipid were mainly C16 and C18 and could be high-quality feedstock for biodiesel production.

CONCLUSION

The deep-sea yeast strain R. paludigena P4R5 was an excellent candidate for efficient simultaneous of biosurfactants and biodiesel from inulin. Our results also suggested that the establishment of fermentation systems with multiple metabolites production was an effective approach to improve the profitability.

Deep-Sea-Derived Butyrolactone I Suppresses Ovalbumin-Induced Anaphylaxis by Regulating Mast Cell Function in a Murine Model

Deep-sea-derived butyrolactone I (BTL-I), which was identified as a type of butanolide, was isolated from Aspergillus sp. Ovalbumin (OVA)-induced BALB/c anaphylaxis was established to explore the antifood allergic activity of BTL-I. As a result, BTL-I was able to alleviate OVA-induced allergy symptoms, reduce the levels of histamine and mouse mast cell proteinases, inhibit OVA-specific IgE, and decrease the population of mast cells in the spleen and mesenteric lymph nodes. BTL-I also significantly suppressed mast-dependent passive cutaneous anaphylaxis. Additionally, the maturation of bone marrow-derived mast cells (BMMCs) declined as BTL-I caused down-regulation of c-KIT receptors. Furthermore, molecular docking analyses revealed that BTL-I interacted with the inhibitory receptor, FcγRIIB. In conclusion, the reduction of mast cell function by deep-sea-derived BTL-I as well as its interactions with the inhibitory receptor, FcγRIIB, may contribute to BTL-I-related protection against food anaphylaxis.

Reversible naftifine-induced carotenoid depigmentation in Rhodotorula mucilaginosa (A. Jörg.) F.C. Harrison causing onychomycosis

Rhodotorula mucilaginosa was isolated from a patient with onychomycosis, and identification was confirmed by morphological and cultural characteristics as well as by DNA molecular analysis. Antifungal agents naftifine (10 mg/mL, active substance in Exoderil) and bifonazole (10 mg/mL, active substance in Canespor) were tested in different concentrations to assess in vitro effects on fungal growth and carotenoid synthesis. The antifungal mechanisms of action of naftifine and bifonazole against R. mucilaginosa isolates were similar and affected the biosynthetic pathway of ergosterol. For the first time, this research demonstrates that naftifine affects the carotenoid biosynthetic pathway, producing depigmentation of R. mucilaginosa in solid and liquid media. Furthermore, depigmentation was a reversible process; naftifine-treated yeast cells that were depigmented resumed carotenoid production upon transfer to fresh media. Raman and UV-vis spectrophotometry in conjunction with chromatographic analysis detected changes in carotenoids in yeast cells, with torulene decreasing and B-carotene increasing after repigmentation. Transmission electron micrographs revealed critical ultrastructural modifications in the depigmented cells after naftifine treatment, i.e., a low-electron-density cell wall without visible mucilage or lamellate structure.

Yeasts from macroalgae and lichens that inhabit the South Shetland Islands, Antarctica

Antarctic terrestrial ecosystems are largely dominated by lichens, while shallow coastal environments are mainly covered by macroalgae. The aim of this study was to isolate and to evaluate the diversity of yeasts in different species of macroalgae and lichens collected in South Shetland Islands, Antarctica. A total of 405 yeasts were recovered (205 from macroalgae and 200 from lichens). The yeast community from macroalgae was most diversity than the yeast community from lichen. The dominance index was similar for both substrates. A total of 24 taxa from macroalgae and 18 from lichens were identified, and only 5 were common to both substrates. Metschnikowia australis, Mrakia sp., Rhodotorula glacialis and Glaciozyma litorale were the most abundant yeasts in macroalgae and Cryptococcus victoriae, Rhodotorula laryngis, Rhodotorula arctica, Trichosporon sp. 1 and Mrakia sp. were the most abundant in lichens. Based on molecular and phylogenetic analyses, four yeast from macroalgae and six from lichens were considered potential new species. This is the first study to report the yeast communities from the Antarctic macroalgae Himantothallus grandifolius and lichen Ramalina terebrata. Results suggest that Antarctic phyco and lichensphere represent a huge substrate for cold-adapted yeasts and enhanced the knowledge of the microbiota from extreme environments.

Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils

The effect of altitude and season on abundance and diversity of the culturable heterotrophic bacterial and yeast community was examined at four forest sites in the Italian Alps along an altitude gradient (545–2000 m). Independently of altitude, bacteria isolated at 0 °C (psychrophiles) were less numerous than those recovered at 20 °C. In autumn, psychrophilic bacterial population increased with altitude. The 1194 bacterial strains were primarily affiliated with the classes Alpha-, Beta-, Gammaproteobacteria, Spingobacteriia and Flavobacteriia. Fifty-seven of 112 operational taxonomic units represented potential novel species. Strains isolated at 20 °C had a higher diversity and showed similarities in taxa composition and abundance, regardless of altitude or season, while strains isolated at 0 °C showed differences in community composition at lower and higher altitudes. In contrast to bacteria, yeast diversity was season-dependent: site- and altitude-specific effects on yeast diversity were only detected in spring. Isolation temperature affected the relative proportions of yeast genera. Isolations recovered 719 strains, belonging to the classes Dothideomycetes, Saccharomycetes, Tremellomycetes and Mycrobotryomycetes. The presence of few dominant bacterial OTUs and yeast species indicated a resilient microbial population that is not affected by season or altitude. Soil nutrient contents influenced significantly abundance and diversity of culturable bacteria, but not of culturable yeasts.

In situ associations between marine photosynthetic picoeukaryotes and potential parasites - a role for fungi?

Photosynthetic picoeukaryotes (PPEs) are important components of the marine picophytoplankton community playing a critical role in CO2 fixation but also as bacterivores, particularly in the oligotrophic gyres. Despite an increased interest in these organisms and an improved understanding of the genetic diversity of this group, we still know little of the environmental factors controlling the abundance of these organisms. Here, we investigated the quantitative importance of eukaryotic parasites in the free-living fraction as well as in associations with PPEs along a transect in the South Atlantic. Using tyramide signal amplification-fluorescence in situ hybridization (TSA-FISH), we provide quantitative evidence of the occurrence of free-living fungi in open ocean marine systems, while the Perkinsozoa and Syndiniales parasites were not abundant in these waters. Using flow cytometric cell sorting of different PPE populations followed by a dual-labelled TSA-FISH approach, we also demonstrate fungal associations, potentially parasitic, occurring with both pico-Prymnesiophyceae and pico-Chrysophyceae. These data highlight the necessity for further work investigating the specific role of marine fungi as parasites of phytoplankton to improve understanding of carbon flow in marine ecosystems.

Draft Genome Sequence of the Deep-Sea Basidiomycetous Yeast Cryptococcus sp. Strain Mo29 Reveals Its Biotechnological Potential

Cryptococcus sp. strain Mo29 was isolated from the Rainbow hydrothermal site on the Mid-Atlantic Ridge. Here, we present the draft genome sequence of this basidiomycetous yeast strain, which has highlighted its biotechnological potential as revealed by the presence of genes involved in the synthesis of secondary metabolites and biotechnologically important enzymes.

Revisiting the pink-red pigmented basidiomycete mirror yeast of the phyllosphere

By taking advantage of the ballistoconidium‐forming capabilities of members of the genus Sporobolomyces, we recovered ten isolates from deciduous tree leaves collected from Vermont and Washington, USA. Analysis of the small subunit ribosomal RNA gene and the D1/D2 domain of the large subunit ribosomal RNA gene indicate that all isolates are closely related. Further analysis of their physiological attributes shows that all were similarly pigmented yeasts capable of growth under aerobic and microaerophilic conditions, all were tolerant of repeated freezing and thawing, minimally tolerant to elevated temperature and desiccation, and capable of growth in liquid or on solid media containing pectin or galacturonic acid. The scientific literature on ballistoconidium‐forming yeasts indicates that they are a polyphyletic group. Isolates of Sporobolomyces from two geographically separated sites show almost identical phenotypic and physiological characteristics and a monophyly with a broad group of differently named Sporobolomyces/Sporidiobolus species based on both small subunit ribosomal RNA (SSU rRNA) and D1/D2 domains of the LSU rRNA gene sequences.

Cultured and uncultured fungal diversity in deep-sea environments

The importance of fungi found in deep-sea extreme environments is becoming increasingly recognized. In this chapter, current scientific findings on the fungal diversity in several deep-sea environments by conventional culture and culture-independent methods are reviewed and discussed, primarily focused on culture-independent approaches. Fungal species detected by conventional culture methods mostly belonged to Ascomycota and Basidiomycota phyla. Culture-independent approaches have revealed the presence of highly novel fungal phylotypes, including new taxonomic groups placed in deep branches within the phylum Chytridiomycota and unknown ancient fungal groups. Future attempts to culture these unknown fungal groups may provide key insights into the early evolution of fungi and their ecological and physiological significance in deep-sea environments.

Microbiome composition and geochemical characteristics of deep subsurface high-pressure environment, Pyhäsalmi mine Finland

Pyhäsalmi mine in central Finland provides an excellent opportunity to study microbial and geochemical processes in a deep subsurface crystalline rock environment through near-vertical drill holes that reach to a depth of more than two kilometers below the surface. However, microbial sampling was challenging in this high-pressure environment. Nucleic acid yields obtained were extremely low when compared to the cell counts detected (1.4 × 10(4) cells mL(-1)) in water. The water for nucleic acid analysis went through high decompression (60-130 bar) during sampling, whereas water samples for detection of cell counts by microscopy could be collected with slow decompression. No clear cells could be identified in water that went through high decompression. The high-pressure decompression may have damaged part of the cells and the nucleic acids escaped through the filter. The microbial diversity was analyzed from two drill holes by pyrosequencing amplicons of the bacterial and archaeal 16S rRNA genes and from the fungal ITS regions from both DNA and RNA fractions. The identified prokaryotic diversity was low, dominated by Firmicute, Beta- and Gammaproteobacteria species that are common in deep subsurface environments. The archaeal diversity consisted mainly of Methanobacteriales. Ascomycota dominated the fungal diversity and fungi were discovered to be active and to produce ribosomes in the deep oligotrophic biosphere. The deep fluids from the Pyhäsalmi mine shared several features with other deep Precambrian continental subsurface environments including saline, Ca-dominated water and stable isotope compositions positioning left from the meteoric water line. The dissolved gas phase was dominated by nitrogen but the gas composition clearly differed from that of atmospheric air. Despite carbon-poor conditions indicated by the lack of carbon-rich fracture fillings and only minor amounts of dissolved carbon detected in formation waters, some methane was found in the drill holes. No dramatic differences in gas compositions were observed between different gas sampling methods tested. For simple characterization of gas composition the most convenient way to collect samples is from free flowing fluid. However, compared to a pressurized method a relative decrease in the least soluble gases may appear.

Species richness and adaptation of marine fungi from deep-subseafloor sediments

The fungal kingdom is replete with unique adaptive capacities that allow fungi to colonize a wide variety of habitats, ranging from marine habitats to freshwater and terrestrial habitats. The diversity, importance, and ecological roles of marine fungi have recently been highlighted in deep-subsurface sediments using molecular methods. Fungi in the deep-marine subsurface may be specifically adapted to life in the deep biosphere, but this can be demonstrated only using culture-based analyses. In this study, we investigated culturable fungal communities from a record-depth sediment core sampled from the Canterbury Basin (New Zealand) with the aim to reveal endemic or ubiquist adapted isolates playing a significant ecological role(s). About 200 filamentous fungi (68%) and yeasts (32%) were isolated. Fungal isolates were affiliated with the phyla Ascomycota and Basidiomycota, including 21 genera. Screening for genes involved in secondary metabolite synthesis also revealed their bioactive compound synthesis potential. Our results provide evidence that deep-subsurface fungal communities are able to survive, adapt, grow, and interact with other microbial communities and highlight that the deep-sediment habitat is another ecological niche for fungi.

Insights into deep-sea sediment fungal communities from the East Indian Ocean using targeted environmental sequencing combined with traditional cultivation

The fungal diversity in deep-sea environments has recently gained an increasing amount attention. Our knowledge and understanding of the true fungal diversity and the role it plays in deep-sea environments, however, is still limited. We investigated the fungal community structure in five sediments from a depth of ∼4000 m in the East India Ocean using a combination of targeted environmental sequencing and traditional cultivation. This approach resulted in the recovery of a total of 45 fungal operational taxonomic units (OTUs) and 20 culturable fungal phylotypes. This finding indicates that there is a great amount of fungal diversity in the deep-sea sediments collected in the East Indian Ocean. Three fungal OTUs and one culturable phylotype demonstrated high divergence (89%–97%) from the existing sequences in the GenBank. Moreover, 44.4% fungal OTUs and 30% culturable fungal phylotypes are new reports for deep-sea sediments. These results suggest that the deep-sea sediments from the East India Ocean can serve as habitats for new fungal communities compared with other deep-sea environments. In addition, different fungal community could be detected when using targeted environmental sequencing compared with traditional cultivation in this study, which suggests that a combination of targeted environmental sequencing and traditional cultivation will generate a more diverse fungal community in deep-sea environments than using either targeted environmental sequencing or traditional cultivation alone. This study is the first to report new insights into the fungal communities in deep-sea sediments from the East Indian Ocean, which increases our knowledge and understanding of the fungal diversity in deep-sea environments.

Rhodotorula portillonensis sp. nov., a basidiomycetous yeast isolated from Antarctic shallow-water marine sediment

During the characterization of the mycobiota associated with shallow-water marine environments from Antarctic sea, a novel pink yeast species was isolated. Sequence analysis of the D1/D2 domain of the LSU rDNA gene and 5.8S-ITS regions revealed that the isolated yeast was closely related to Rhodotorula pallida CBS 320(T) and Rhodotorula benthica CBS 9124(T). On the basis of morphological, biochemical and physiological characterization and phylogenetic analyses, a novel basidiomycetous yeast species, Rhodotorula portillonensis sp. nov., is proposed. The type strain is Pi2(T) ( = CBS 12733(T)  = CECT 13081(T)) which was isolated from shallow-water marine sediment in Fildes Bay, King George Island, Antarctica.

Yeast communities in Sphagnum phyllosphere along the temperature-moisture ecocline in the boreal forest-swamp ecosystem and description of Candida sphagnicola sp. nov

The effects of the temperature-moisture factors on the phylloplane yeast communities inhabiting Sphagnum mosses were studied along the transition from a boreal forest to a swamp biotope at the Central Forest State Biosphere Reserve (Tver region, Russia). We tested the hypothesis that microclimatic parameters affect yeast community composition and structure even on a rather small spatial scale. Using a conventional plating technique we isolated and identified by molecular methods a total of 15 species of yeasts. Total yeast counts and species richness values did not depend on environmental factors, although yeast community composition and structure did. On average, Sphagnum in the swamp biotope supported a more evenly structured yeast community. Relative abundance of ascomycetous yeasts was significantly higher on swamp moss. Rhodotorula mucilaginosa dominated in the spruce forest and Cryptococcus magnus was more abundant in the swamp. Our study confirmed the low occurrence of tremellaceous yeasts in the Sphagnum phyllosphere. Of the few isolated ascomycetous yeast and yeast-like species, some were differentiated from hitherto known species in physiological tests and phylogenetic analyses. We describe one of them as Candida sphagnicola and designate KBP Y-3887(T) (=CBS 11774(T) = VKPM Y-3566(T) = MUCL 53590(T)) as the type strain. The new species was registered in MycoBank under MB 563443.

Marine fungi: their ecology and molecular diversity

Fungi appear to be rare in marine environments. There are relatively few marine isolates in culture, and fungal small subunit ribosomal DNA (SSU rDNA) sequences are rarely recovered in marine clone library experiments (i.e., culture-independent sequence surveys of eukaryotic microbial diversity from environmental DNA samples). To explore the diversity of marine fungi, we took a broad selection of SSU rDNA data sets and calculated a summary phylogeny. Bringing these data together identified a diverse collection of marine fungi, including sequences branching close to chytrids (flagellated fungi), filamentous hypha-forming fungi, and multicellular fungi. However, the majority of the sequences branched with ascomycete and basidiomycete yeasts. We discuss evidence for 36 novel marine lineages, the majority and most divergent of which branch with the chytrids. We then investigate what these data mean for the evolutionary history of the Fungi and specifically marine-terrestrial transitions. Finally, we discuss the roles of fungi in marine ecosystems.

Molecular evidence that deep-branching fungi are major fungal components in deep-sea methane cold-seep sediments

The motile cells of chytrids were once believed to be relics from the time before the colonization of land by fungi. However, the majority of chytrids had not been found in marine but freshwater environments. We investigated fungal diversity by a fungal-specific PCR-based analysis of environmental DNA in deep-sea methane cold-seep sediments, identifying a total of 35 phylotypes, 12 of which were early diverging fungi (basal fungi, ex 'lower fungi'). The basal fungi occupied a major portion of fungal clones. These were phylogenetically placed into a deep-branching clade of fungi and the LKM11 clade that was a divergent group comprised of only environmental clones from aquatic environments. As suggested by Lara and colleagues, species of the endoparasitic genus Rozella, being recently considered of the earliest branching taxa of fungi, were nested within the LKM11 clade. In the remaining 23 phylotypes identified as the Dikarya, the majority of which were similar to those which appeared in previously deep-sea studies, but also highly novel lineages associated with Soil Clone Group I (SCGI), Entorrhiza sp. and the agaricomycetous fungi were recorded. The fungi of the Dikarya may play a role in the biodegradation of lignin and lignin-derived materials in deep-sea, because the characterized fungal species related to the frequent phylotypes within the Dikarya have been reported to possess an ability to degrade lignin.

Distribution of marine red yeasts in shrimps and the environments of shrimp culture

Populations of marine red yeast from shrimps and the environments of shrimp culture were investigated from various areas at Zhanjiang in China. All strains were studied for the production of biomass and carotenoids. We isolated 88 marine red yeast strains and the average populations of marine red yeast in seawater and the water from shrimp culture ponds were 70.0 and 172.4 CFU per 100 ml water, respectively. For shrimp samples, average populations of marine red yeast from gills, intestines, and stomachs were 178.0, 15.0, and 8.0 CFU per shrimp, respectively. The isolates were grouped into nine species belonging to three genera as follows: Rhodosporidium, Rhodotorula, and Sporidiobolus. R. sphaerocarpum had the highest average biomass yield (10.3 ± 0.88 g/l), followed by S. ruineniae (10.1 g/l) and Rh. mucilaginosa (9.9 ± 1.75 g/l). R. paludigenum had the highest average carotenoid yield (2.83 ± 0.589 mg/l), followed by S. pararoseus (2.72 mg/l) and R. sphaerocarpum (2.59 ± 0.454 mg/l). The results showed that marine red yeasts were normal microbial components in the environments of shrimp culture and shrimps, and carotenoids are abundant in these marine red yeast.

Identification and phylogeny of some species of the genera Sporidiobolus and Rhodotorula using analysis of the 5.8s rDNA gene and two ribosomal internal transcribed spacers

Due to the problems encountered in routine morphological and physiological procedures that are used in yeast identification, DNA-based methods have recently been developed. In the present study, l66 yeast strains were isolated from several apple and citrus cultivars. After analysis by basic morphological methods, the ITS1 and ITS2 regions of the isolates were amplified separately, and the isolates were grouped based on fragment size polymorphism (FSP) of the amplicons. By comparing the electrophoretic patterns of the PCR products with Rhodotorula mucilaginosa, species were identified as Rhodotorula. For precise and final identification, the ITS-PCR products were subjected to sequencing followed by Blast analysis. As a result, eight isolates were identified as belonging to the Rhodotorula genus, of which five were identified as R. mucilaginosa and three as R. glutinis, and one as a Sporidiobolus. We conclude that the method PCR-FSP, in combination with other approaches, is useful for the identification of yeast species.

Candida spencermartinsiae sp. nov., Candida taylorii sp. nov. and Pseudozyma abaconensis sp. nov., novel yeasts from mangrove and coral reef ecosystems

Three species of yeasts are taxonomically described for strains isolated from marine environments. Candida spencermartinsiae sp. nov. (type strain CBS 10894T =NRRL Y-48663T) and Candida taylorii sp. nov. (type strain CBS 8508T =NRRL Y-27213T) are anamorphic ascomycetous yeasts in a phylogenetic cluster of marine yeasts in the Debaryomyces/Lodderomyces clade of the Saccharomycetales. The two species were isolated from multiple locations among coral reefs and mangrove habitats. Pseudozyma abaconensis sp. nov. (type strain CBS 8380T =NRRL Y-17380T) is an anamorphic basidiomycete that is related to the smut fungi of the genus Ustilago in the Ustilaginales. P. abaconensis was collected from waters adjacent to a coral reef.

The dynamics of the yeast community of the Tagus river estuary: testing the hypothesis of the multiple origins of estuarine yeasts

Yeasts are common inhabitants of different types of aquatic habitats, including marine and estuarine waters and rivers. Although numerous studies have surveyed yeast occurrence in these habitats, the identification of autochthonous populations has been problematic because several yeast species seem to be very versatile and therefore mere presence is not sufficient to establish an ecological association. In the present study we investigated the dynamics of the yeast community in the Tagus river estuary (Portugal) by combining a microbiological study involving isolation, quantification, and molecular identification of dominant yeast populations with the analysis of hydrological and hydrographical data. We set out to test the hypothesis of the multiple origins of estuarine yeast populations in a transect of the Tagus estuary and we postulate four possible sources: open sea, terrestrial, gastrointestinal and the estuary itself in the case of populations that have become resident. Candida parapsilosis and Pichia guilliermondii were correlated with Escherichia coli, which indicated an intestinal origin. Other cream-colored yeasts like Debaryomyces hansenii and Candida zeylanoides had similar dynamics, but no association with E. coli and quite distinct ecological preferences. They might represent a group of resident estuarine populations whose primary origin is diverse and can include marine, terrestrial, and gastrointestinal habitats. Another major yeast population was represented by Rhodotorula mucilaginosa. The cosmopolitan nature of that species and its moderate association with E. coli point to terrestrial sources as primary habitats.

Marine culturable yeasts in deep-sea hydrothermal vents: species richness and association with fauna

Investigations of the diversity of culturable yeasts at deep-sea hydrothermal sites have suggested possible interactions with endemic fauna. Samples were collected during various oceanographic cruises at the Mid-Atlantic Ridge, South Pacific Basins and East Pacific Rise. Cultures of 32 isolates, mostly associated with animals, were collected. Phylogenetic analyses of 26S rRNA gene sequences revealed that the yeasts belonged to Ascomycota and Basidiomycota phyla, with the identification of several genera: Rhodotorula, Rhodosporidium, Candida, Debaryomyces and Cryptococcus. Those genera are usually isolated from deep-sea environments. To our knowledge, this is the first report of yeasts associated with deep-sea hydrothermal animals.

Fungal diversity in deep-sea hydrothermal ecosystems

Deep-sea hydrothermal ecosystems are considered oases of life in oceans. Since the discovery of these ecosystems in the late 1970s, many endemic species of Bacteria, Archaea, and other organisms, such as annelids and crabs, have been described. Considerable knowledge has been acquired about the diversity of (micro)organisms in these ecosystems, but the diversity of fungi has not been studied to date. These organisms are considered key organisms in terrestrial ecosystems because of their ecological functions and especially their ability to degrade organic matter. The lack of knowledge about them in the sea reflects the widely held belief that fungi are terrestrial organisms. The first inventory of such organisms in deep-sea hydrothermal environments was obtained in this study. Fungal diversity was investigated by analyzing the small-subunit rRNA gene sequences amplified by culture-independent PCR using DNA extracts from hydrothermal samples and from a culture collection that was established. Our work revealed an unsuspected diversity of species in three of the five fungal phyla. We found a new branch of Chytridiomycota forming an ancient evolutionary lineage. Many of the species identified are unknown, even at higher taxonomic levels in the Chytridiomycota, Ascomycota, and Basidiomycota. This work opens the way to new studies of the diversity, ecology, and physiology of fungi in oceans and might stimulate new prospecting for biomolecules. From an evolutionary point of view, the diversification of fungi in the oceans can no longer be ignored.

Yeasts from high-altitude lakes: influence of UV radiation

Mountain lakes located at a high elevation are typically exposed to high UV radiation (UVR). Little is known about the ecology and diversity of yeasts inhabiting these extreme environments. We studied yeast occurrence (with special emphasis on those producing carotenoid pigments) at five high-altitude (>1400 m a.s.l.) water bodies located in the Nahuel Huapi National Park (Bariloche, Argentina). Isolates were identified using a polyphasic approach. Production of photoprotective compounds (carotenoids and mycosporines) by yeast isolates, and UVB resistance of selected species were studied. All water samples contained viable yeast cells in variable numbers, generally ranging from 49 to 209 cells L(-1). A total of 24 yeast species was found; at least four represented novel species. Carotenogenic yeasts prevailed in lakes with low water conductivity and higher transparency and chlorophyll a levels. Apparently, the ability to produce photoprotective compounds in yeasts was related to the transparency of mountain lake waters, and strains from more transparent waters developed increased UVB resistance. Our results indicate that UVR is an important environmental factor affecting the yeast community structure in aquatic habitats.

Sporobolomyces koalae sp. nov., a basidiomycetous yeast isolated from nasal smears of Queensland koalas kept in a Japanese zoological park

Three strains (JCM 15063(T), JCM 15098 and JCM 15099) of a novel basidiomycetous yeast species belonging to the genus Sporobolomyces were isolated from nasal smears of Queensland koalas kept in a Japanese zoological park. Analyses of sequences of the nuclear rDNA internal transcribed spacer region and the 26S rDNA D1/D2 domain and morphological studies indicated that these strains represent a novel species with a close phylogenetic relationship to Sporobolomyces carnicolor and Sporobolomyces japonicus in the Sporidiobolus lineage, for which the name Sporobolomyces koalae sp. nov. is proposed (type strain JCM 15063(T) =CBS 10914(T) =DSM 19992(T)).

Sympodiomycopsis lanaiensis sp. nov., a basidiomycetous yeast (Ustilaginomycotina: Microstromatales) from marine driftwood in Hawai'i

A previously unknown basidiomycetous yeast is described for which the name Sympodiomycopsis lanaiensis is proposed. The type strain, LM418(T), was isolated from driftwood collected on a beach on Lana'i (Hawai'i). On the basis of ribosomal DNA sequence analysis [large subunit (LSU), internal transcribed spacer (ITS) 1 & 2, and 18S], LM418(T) belongs to the order Microstromatales, which includes the genera Sympodiomycopsis, Rhodotorula, Microstroma, Volvocisporium and Quambalaria. The strain is described as a new species in the genus Sympodiomycopsis on the basis of morphological and physiological characteristics and the phylogenetic relationship to Sympodiomycopsis paphiopedili. Sexual reproduction was not observed in LM418(T). GenBank accession numbers for nucleotide sequences of regions of the LSU, ITS and 18S regions of the ribosomal operon in LM418(T) are DQ990016, DQ990017 and DQ990018, respectively. LM418(T) has been deposited in the DSMZ as DSM 18755, in the ATCC as MYA-4092, in the Agricultural Research Service Culture Collection as NRRL Y-48466, and the Centraalbureau voor Schimmelcultures as CBS 10858.

Diversity of soil yeasts isolated from South Victoria Land, Antarctica

Unicellular fungi, commonly referred to as yeasts, were found to be components of the culturable soil fungal population in Taylor Valley, Mt. Discovery, Wright Valley, and two mountain peaks of South Victoria Land, Antarctica. Samples were taken from sites spanning a diversity of soil habitats that were not directly associated with vertebrate activity. A large proportion of yeasts isolated in this study were basidiomycetous species (89%), of which 43% may represent undescribed species, demonstrating that culturable yeasts remain incompletely described in these polar desert soils. Cryptococcus species represented the most often isolated genus (33%) followed by Leucosporidium (22%). Principle component analysis and multiple linear regression using stepwise selection was used to model the relation between abiotic variables (principle component 1 and principle component 2 scores) and yeast biodiversity (the number of species present at a given site). These analyses identified soil pH and electrical conductivity as significant predictors of yeast biodiversity. Species-specific PCR primers were designed to rapidly discriminate among the Dioszegia and Leucosporidium species collected in this study.

Dipodascus tetrasporeus sp. nov., an ascosporogenous yeast isolated from deep-sea sediments in the Japan Trench

Dipodascus tetrasporeus sp. nov. is described as a novel yeast species in the family Dipodascaceae to accommodate an isolate recovered from sediments collected on the deep-sea floor in the north-western Pacific Ocean. In the clade comprising the genera Dipodascus, Galactomyces and Geotrichum, this is the only species that forms asci that bear four ascospores. The ascospore is surrounded by an irregular exosporium wall, similar to what is observed in the genus Galactomyces, but they are released by rupture, which is characteristic of Dipodascus and not Galactomyces. D. tetrasporeus is remarkably divergent (>10 % difference) in its D1/D2 26S rDNA sequence from any other known species. Although maximum-likelihood analysis of combined 18S rDNA and D1/D2 26S rDNA sequences cannot elucidate a reliable position for this species, it was placed among Geotrichum carabidarum, Geotrichum cucujoidarum, Geotrichum fermentans and Geotrichum histeridarum, which also have morphological and physiological affinity with the species. The species is homothallic. The type strain of Dipodascus tetrasporeus sp. nov. is strain SY-277T (=NBRC 103136T =CBS 10071T).

Chemical Investigations of a Deep Water Marine-Derived Fungus: Simple Amino Acid Derivatives from an Arthrinium sp

The saltwater culture of an Arthrinium sp. derived from a marine sediment collected at −550 meters was a source of tyrosol (1) and a new compound, tyrosol carbamate (2). This is only the third report of novel secondary metabolites discovered from the saltwater culture of a deep-water marine-derived fungus.

Yeasts in high Arctic glaciers: the discovery of a new habitat for eukaryotic microorganisms

Recently a new habitat for microbial life has been discovered at the base of polythermal glaciers. In ice from these subglacial environments so far only non-photosynthetic bacterial communities were discovered, but no eukaryotic microorganisms. We found high numbers of yeast cells, amounting to a maximum of 4,000 CFU ml(-1) of melt ice, in four different high Arctic glaciers. Twenty-two distinct species were isolated, including two new yeast species. Basidiomycetes predominated, among which Cryptococcus liquefaciens was the dominant species (ca. 90% of total). Other frequently occurring species were Cryptococcus albidus, Cryptococcus magnus, Cryptococcus saitoi and Rhodotorula mucilaginosa. The dominant yeast species were psychrotolerant, halotolerant, freeze-thaw resistant, unable to form mycelium, relatively small-sized and able to utilize a wide range of carbon and nitrogen sources. This is the first report on the presence of yeast populations in subglacial ice.