RT-qPCR based quantitative analysis of ARO and ADH genes in Saccharomyces cerevisiae and Metschnikowia pulcherrima strains growth white grape juice

BACKGROUND

Yeast biosynthesizes fusel alcohols in fermentation through amino acid catabolism via the Ehrlich pathway. ARO8 and ARO9 genes are involved in the first step of the Ehrlich pathway, while ADH2 and ADH5 genes are involved in the last step. In this study, we describe RT-qPCR methods to determine the gene expression level of genes (ARO8, ARO9, ADH2, ADH5) found in Saccharomyces cerevisiae (Sc) and Metschnikowia pulcherrima (Mp) strains growth pasteurized white grape juice.

METHODS AND RESULTS

We used RNA extraction and cDNA synthesis protocols. The RT-qPCR efficiency of primer pairs was evaluated by generating a standard curve through serial dilution of yeast-derived cDNA. Method performance criteria were determined for each RT-qPCR assay. Then, we evaluated the gene expression levels of the four genes in all samples. RNA extraction and cDNA synthesis from yeast samples demonstrated the method's capability to generate high-yield, high-purity nucleic acids, supporting further RT-qPCR analysis. The highest normalized gene expression levels of ARO8 and ARO9 were observed in SC1, SC4, and SC5 samples. No significant difference in ADH2 gene expression among Mp strains was observed during the examination of ADH2 and ADH5 genes (p < 0.05). We observed no expression of the ADH5 gene in Mp strains except MP6 strain. The expression of ADH2 and ADH5 genes was higher in Sc strains compared to Mp strains.

CONCLUSIONS

The results suggest that the proposed RT-qPCR methods can measure gene expression of ARO8, ARO9, ADH2, and ADH5 in Sc and Mp strains growing in pasteurized white grape juice.

Bees just wanna have fungi: a review of bee associations with nonpathogenic fungi

Bee-fungus associations are common, and while most studies focus on entomopathogens, emerging evidence suggests that bees associate with a variety of symbiotic fungi that can influence bee behavior and health. Here, we review nonpathogenic fungal taxa associated with different bee species and bee-related habitats. We synthesize results of studies examining fungal effects on bee behavior, development, survival, and fitness. We find that fungal communities differ across habitats, with some groups restricted mostly to flowers (Metschnikowia), while others are present almost exclusively in stored provisions (Zygosaccharomyces). Starmerella yeasts are found in multiple habitats in association with many bee species. Bee species differ widely in the abundance and identity of fungi hosted. Functional studies suggest that yeasts affect bee foraging, development, and pathogen interactions, though few bee and fungal taxa have been examined in this context. Rarely, fungi are obligately beneficial symbionts of bees, whereas most are facultative bee associates with unknown or ecologically contextual effects. Fungicides can reduce fungal abundance and alter fungal communities associated with bees, potentially disrupting bee-fungi associations. We recommend that future study focus on fungi associated with non-honeybee species and examine multiple bee life stages to document fungal composition, abundance, and mechanistic effects on bees.

Development of a TaqMan real-time quantitative PCR assay to detect Metschnikowia bicuspidata in Chinese mitten crab Eriocheir sinensis

Milky disease of Chinese mitten crab Eriocheir sinensis caused by Metschnikowia bicuspidata is a novel disease with high mortality. No effective treatment is currently available, but a rapid, accurate detection method is required for the prevention and control of the disease. In this study, the genome-sequencing results of M. bicuspidata and similar species were used for comparative genomic analysis for genes specific to M. bicuspidata. A quantitative PCR (qPCR) detection method for M. bicuspidata was then established using the specific primers and probes designed according to the sequence of a hypothetical protein gene specific to M. bicuspidata. The assay was found to have a high degree of repeatability and reproducibility, with a linear dynamic range (R2 = 0.998) extending over 9 log10 dilutions and a high efficiency (100.7%). Furthermore, the method showed high sensitivity, being able to detect at least 11.3 copies μl-1 of recombinant plasmid, and strong specificity, without any cross-reaction with any of the 9 species of yeast that are closely related to M. bicuspidata or any of 16 species of pathogenic bacteria commonly observed in aquatic animals. The established method was used to examine 138 apparently healthy crabs collected from 22 farms, with 21 samples (15.2%) found to be M. bicuspidata-positive. Thus, the developed qPCR assay is a specific, sensitive, stable, and rapid diagnostic method for the detection and quantification of M. bicuspidata DNA from E. sinensis tissues.

Antiparasitic potential of agrochemical fungicides on a non-target aquatic model (Daphnia × Metschnikowia host-parasite system)

Pesticides are a major anthropogenic threat to the biodiversity of freshwater ecosystems, having the potential to affect non-target aquatic organisms and disrupt the processes in which they intervene. Important knowledge gaps have been recognised concerning the ecological effects of synthetic fungicides on non-target symbiotic aquatic fungi and the ecological processes where they intervene. The goal of this work was to assess the influence of three commonly used fungicides (myclobutanil, metalaxyl and cymoxanil), which differ in their mode of action, on a host (the crustacean Daphnia magna) × parasite (the yeast Metschnikowia bicuspidata) experimental model. Using a set of life history experiments, we evaluated the effect of each fungicide on the outcome of this relationship (disease) and on the fitness of both host and parasite. Contrasting results were observed: (i) cymoxanil and metalaxyl were overall innocuous to host and parasite at the tested concentrations, although host reproduction was occasionally reduced in the simultaneous presence of parasite and fungicide; (ii) on the contrary, myclobutanil displayed a clear antifungal effect, decreasing parasite prevalence and alleviating infection signs in the hosts. This antiparasitic effect of myclobutanil was further investigated with a follow-up experiment that manipulated the timing of application of the fungicide, to understand which stage of parasite development was most susceptible: while myclobutanil did not interfere in the early stages of infection, its antifungal activity was clearly observable at a later stage of the disease (by impairing the production of transmission stages of the parasite). More research is needed to understand the broader consequences of this parasite-clearance effect, especially in face of increasing evidence that parasites are ecologically more important than their cryptic nature might suggest.

Metschnikowia bicuspidata isolated from milky diseased Eriocheir sinensis: Phenotypic and genetic characterization, antifungal susceptibility and challenge models

A severe disease occurred in farmed Eriocheir sinensis characterized by milky liquid accumulation in the pectoral cavity, in the province of Liaoning, China, during October 2018-April 2019. Diseased crabs moved sluggishly, exhibited appetite loss and readily lost legs. Under the microscopic analysis, it was observed that the milky liquid contained a large number of yeastlike microorganisms (0.8-1.2 μm × 1.5-1.9 μm), which were also present in the muscle, hepatopancreas and gills. A dominant strain was isolated from the milky liquid and other tissues of diseased crabs. It grew on nutrient agar and formed 1- to 3-mm white opaque colonies, each with a protuberance in the centre. Besides, the results of TEM and SEM also demonstrate a typical multilateral budding model of the yeast clearly. We identified the strain, which we named 2EJM001, as Metschnikowia bicuspidata based on 18S rDNA, ITS and 26S rDNA sequence analyses and on its morphological, physiological and biochemical characteristics. Phylogenetic analysis revealed that 26S rDNA of 2EJM001 was clustered with M. bicuspidata (LNES0119) as reported by Bao et al. In addition, unlike Bao et al., two challenge experiments (injection and immersion) were used in this study. The results of challenge experiments show that 2EJM001 was pathogenic to E. sinensis and caused signs similar to those found in the naturally infected crabs. At the same time, the minimum inhibitory concentrations (MIC₈₀ and MIC₉₀ ) were determined. This study further confirms that M. bicuspidata 2EJM001 was the pathogen responsible for 'milky disease' in E. sinensis from Liaoning Province.

Metschnikowia citriensis FL01 antagonize Geotrichum citri-aurantii in citrus fruit through key action of iron depletion

Metschnikowia citriensis FL01 has great potential for biocontrol applications for its excellent biocontrol efficacy on postharvest diseases of citrus fruit, and the iron depletion by pulcherriminic acid (PA) and then formation of insoluble pigment pulcherrimin had been speculated as an important action mechanism. To identify the genes involved in pulcherrimin synthesis and reutilization in M. citriensis FL01, we de novo assembled the genome of M. citriensis FL01 based on long-read PacBio sequencing. The final assembled genome consisted of 12 contigs with a genome size of 25.74 Mb, G + C content of 49.16% and 9310 protein-coding genes. The genome-wide BLAST of the PUL genes of M. pulcherrima APC 1.2 showed that the four PUL genes were clustered and located on Contig 4 of M. citriensis FL01. In order to further clarify the role of pulcherrimin pigment on biocontrol of M. citriensis FL01, CRISPR/cas9 technology was used to knock out PUL2 gene that was responsible for PA synthesis and the pigmentless mutants with stable phenotype were obtained. The mutant strains of M. citriensis FL01 lost the ability to produce pulcherrimin pigment, and simultaneously lost the ability to inhibit the growth of Geotrichum citri-aurantii in vitro. Moreover, the biocontrol efficacy of pigmentless mutant strains against sour rot was about 80% lower than that of wild-type M. citriensis FL01. These results directly proved that the iron depletion was an important mechanism of M. citriensis FL01.

The whole-genome sequence of the novel yeast species Metschnikowia persimmonesis isolated from medicinal plant Diospyros kaki Thunb

The new yeast Metschnikowia persimmonesis KCTC 12991BP (KIOM G15050 strain) exhibits strong antimicrobial activity against some pathogens. This activity may be related to the medicinal profile of secondary metabolites that could be found in the genome of this species. Therefore, to explore its future possibility of producing some beneficial activities, including medicinal ability, we report high-quality whole-genome assembly of M. persimmonesis produced by PacBio RS II sequencer. The final draft assembly consisted of 16 scaffolds with GC content of 45.90% and comprised a fairly complete set (82.8%) of BUSCO result using Saccharomycetales lineage data set. The total length of the genome was 16.473 Mb, with a scaffold N50 of 1.982 Mb. Annotation of the M. persimmonesis genome revealed presence of 7029 genes and 6939 functionally annotated proteins. Based on the analysis of phylogenetic relationship and the average nucleotide identities, M. persimmonesis was proved to a novel species within the Metschnikowia genus. This finding is expected to significantly contribute to the discovery of high-value natural products from M. persimmonesis as well as for genome biology and evolution comparative analysis within Metschnikowia species.

Host Controls of Within-Host Disease Dynamics: Insight from an Invertebrate System

AbstractWithin-host processes (representing the entry, establishment, growth, and development of a parasite inside its host) may play a key role in parasite transmission but remain challenging to observe and quantify. We develop a general model for measuring host defenses and within-host disease dynamics. Our stochastic model breaks the infection process down into the stages of parasite exposure, entry, and establishment and provides associated probabilities for a host's ability to resist infections with barriers and clear internal infections. We tested our model on Daphnia dentifera and the parasitic fungus Metschnikowia bicuspidata and found that when faced with identical levels of parasite exposure, Daphnia patent (transmitting) infections depended on the strength of internal clearance. Applying a Gillespie algorithm to the model-estimated probabilities allowed us to visualize within-host dynamics, within which signatures of host defense could be clearly observed. We also found that early within-host stages were the most vulnerable to internal clearance, suggesting that hosts have a limited window during which recovery can occur. Our study demonstrates how pairing longitudinal infection data with a simple model can reveal new insight into within-host dynamics and mechanisms of host defense. Our model and methodological approach may be a powerful tool for exploring these properties in understudied host-parasite interactions.

Shell-isolated nanoparticle-enhanced Raman spectroscopy for characterization of living yeast cells

Studying the biochemistry of yeast cells has enabled scientists to understand many essential cellular processes in human cells. Further development of biotechnological and medical progress requires revealing surface chemistry in living cells by using a non-destructive and molecular structure sensitive technique. In this study shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) was applied for probing the molecular structure of Metschnikowia pulcherrima yeast cells. Important function of studied cells is the ability to eliminate iron from growth media by precipitating the insoluble pigment pulcherrimin. Comparative SERS and SHINERS analysis of the yeast cells in combination with bare Au and shell-isolated Au@SiO₂ nanoparticles were performed. It was observed that additional bands, such as adenine ring-related vibrational modes appear due to interaction with bare Au nanoparticles; the registered spectra do not coincide with the spectra where Au@SiO₂ nanoparticles were used. SHINERS spectra of M. pulcherrima were significantly enhanced comparing to the Raman spectra. Based on first-principles calculations and 830-nm excited Raman analysis of pulcherrimin, the SHINERS signatures of iron pigment in yeast cells were revealed. Being protected from direct interaction of metal with adsorbate, Au@SiO₂ nanoparticles yield reproducible and reliable vibrational signatures of yeast cell wall constituents.

Proteomic characterization of extracellular vesicles produced by several wine yeast species

In winemaking, the use of alternative yeast starters is becoming increasingly popular. They contribute to the diversity and complexity of wine sensory features and are typically used in combination with Saccharomyces cerevisiae, to ensure complete fermentation. This practice has drawn the interest on interactions between different oenological yeasts, which are also relevant in spontaneous and conventional fermentations, or in the vineyard. Although several interactions have been described and some mechanisms have been suggested, the possible involvement of extracellular vesicles (EVs) has not yet been considered. This work describes the production of EVs by six wine yeast species (S. cerevisiae, Torulaspora delbrueckii, Lachancea thermotolerans, Hanseniaspora uvarum, Candida sake and Metschnikowia pulcherrima) in synthetic grape must. Proteomic analysis of EV-enriched fractions from S. cerevisiae and T. delbrueckii showed enrichment in glycolytic enzymes and cell-wall-related proteins. The most abundant protein found in S. cerevisiae, T. delbrueckii and L. thermotolerans EV-enriched fractions was the enzyme exo-1,3-β-glucanase. However, this protein was not involved in the here-observed negative impact of T. delbrueckii extracellular fractions on the growth of other yeast species. These findings suggest that EVs may play a role in fungal interactions during wine fermentation and other aspects of wine yeast biology.

Comparison of Volatile Composition between Alcoholic Bilberry Beverages Fermented with Non-Saccharomyces Yeasts and Dynamic Changes in Volatile Compounds during Fermentation

The profile of volatile compounds was investigated using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) during bilberry juice fermentation with nine non-Saccharomyces yeasts, including Pachysolen tannophilus, Metschnikowia pulcherrima, Hanseniaspora uvarum, Torulaspora delbrueckii, Zygosaccharomyces bailii, Schizosaccharomyces pombe, Lachancea thermotolerans, Issatchenkia orientalis, and Saccharomycodes ludwigii. Dynamic changes in volatile compounds were determined simultaneously with the development of ethanol concentration during fermentation. H. uvarum or I. orientalis produced more ethyl acetate than other yeast strains throughout fermentation, while fermentation with M. pulcherrima resulted in high accumulation of higher alcohols. S. pombe was associated with high productions of pentane-2,3-dione, 3-hydroxybutan-2-one, 2-methylbutanal, and 3-methylbutanal. Among the 59 volatile compounds detected, generally, higher alcohols and monoterpenes accumulated constantly and reached the maximum concentration at the middle or later fermentation stage, whereas aldehydes, ketones, and acetals accumulated first followed by a significant drop. The production and accumulation dynamics of metabolites were highly dependent on the yeast species and the developing ethanol content.

Contrasting effects of yeasts and bacteria on floral nectar traits

BACKGROUND AND AIMS

Flowers can be highly variable in nectar volume and chemical composition, even within the same plant, but the causes of this variation are not fully understood. One potential cause is nectar-colonizing bacteria and yeasts, but experimental tests isolating their effects on wildflowers are largely lacking. This study examines the effects of dominant species of yeasts and bacteria on the hummingbird-pollinated shrub, Mimulus aurantiacus, in California.

METHODS

Wildflowers were inoculated with field-relevant titres of either the yeast Metschnikowia reukaufii or the bacterium Neokomagataea sp. (formerly Gluconobacter sp.), both isolated from M. aurantiacus nectar. Newly opened flowers were bagged, inoculated, harvested after 3 d and analysed for microbial abundance, nectar volume, and sugar and amino acid concentration and composition.

KEY RESULTS

Yeast inoculation reduced amino acid concentration and altered amino acid composition, but had no significant effect on nectar volume or sugar composition. In contrast, bacterial inoculation increased amino acid concentration, enhanced the proportion of nectar sugars comprised by monosaccharides, and reduced nectar volume.

CONCLUSIONS

The results presented suggest that microbial inhabitants of floral nectar can make nectar characteristics variable among flowers through divergent effects of yeasts and bacteria on nectar chemistry and availability, probably modifying plant-pollinator interactions.

Non-target effects of fungicides on nectar-inhabiting fungi of almond flowers

Nectar mediates interactions between plants and pollinators in natural and agricultural systems. Specialized microorganisms are common nectar inhabitants, and potentially important mediators of plant-pollinator interactions. However, their diversity and role in mediating pollination services in agricultural systems are poorly characterized. Moreover, agrochemicals are commonly applied to minimize crop damage, but may present ecological consequences for non-target organisms. Assessment of ecological risk has tended to focus on beneficial macroorganisms such as pollinators, with less attention paid to microorganisms. Here, using culture-independent methods, we assess the impact of two widely-used fungicides on nectar microbial community structure in the mass-flowering crop almond (Prunus dulcis). We predicted that fungicide application would reduce fungal richness and diversity, whereas competing bacterial richness would increase, benefitting from negative effects on fungi. We found that fungicides reduced fungal richness and diversity in exposed flowers, but did not significantly affect bacterial richness, diversity, or community composition. The relative abundance of Metschnikowia OTUs, nectar specialists that can impact pollination, was reduced by both fungicides. Given growing recognition of the importance of nectar microorganisms as mediators of plant-pollinator mutualisms, future research should consider the impact of management practices on plant-associated microorganisms and consequences for pollination services in agricultural landscapes.

Epidemiology of a Daphnia-multiparasite system and its implications for the red queen

The Red Queen hypothesis can explain the maintenance of host and parasite diversity. However, the Red Queen requires genetic specificity for infection risk (i.e., that infection depends on the exact combination of host and parasite genotypes) and strongly virulent effects of infection on host fitness. A European crustacean (Daphnia magna)--bacterium (Pasteuria ramosa) system typifies such specificity and high virulence. We studied the North American host Daphnia dentifera and its natural parasite Pasteuria ramosa, and also found strong genetic specificity for infection success and high virulence. These results suggest that Pasteuria could promote Red Queen dynamics with D. dentifera populations as well. However, the Red Queen might be undermined in this system by selection from a more common yeast parasite (Metschnikowia bicuspidata). Resistance to the yeast did not correlate with resistance to Pasteuria among host genotypes, suggesting that selection by Metschnikowia should proceed relatively independently of selection by Pasteuria.

N., A YEAST ASSOCIATED WITH BRINE SHRIMP

Spencer , J. F. T. (University of California, Davis), H. J. Phaff, and N. R. Gardner . Metschnikowia kamienskii sp. n., a yeast associated with brine shrimp. J. Bacteriol. 88: 758–762. 1964.—A description is given of Metschnikowia kamienskii sp. n., four strains of which were isolated from brine shrimp ( Artemia salina ) collected from a saline lake near Watrous, Saskatchewan, Canada. In addition, we obtained from N. van Uden a fifth strain which was originally isolated by L. J. Wickerham from sporocysts of the trematode Diplostomum flexicaudum parasitizing the hepatopancreas of a lymnaeid snail found in Lake Douglas, Michigan, in which material the yeast was first observed by Kathleen Hussey of Columbia University. All strains were identical and formed long club-shaped asci, containing a single needle-shaped spore, pointed at both ends. M. kamienskii differs in several of its physiological properties and by the size of its asci from the two previously isolated members of the genus, M. krissii and M. zobellii . A key differentiating the three species is given.