The osmotic stress tolerance of basidiomycetous yeasts

Weather and leaf age separately contribute to temporal shifts in phyllosphere community structure and composition

Microbial communities living on plant leaves can positively or negatively influence plant health and, by extension, can impact whole ecosystems. Most research into the leaf microbiome consists of snapshots, and little is known about how microbial communities change over time. Weather and host physiological characteristics change over time and are often collinear with other time-varying factors, such as substrate availability, making it difficult to separate the factors driving microbial community change. We leveraged repeated measures over the course of an entire year to isolate the relative importance of environmental, host physiological, and substrate age-related factors on the assembly, structure, and composition of leaf-associated fungal communities. We applied both culturing and sequencing approaches to investigate these communities, focusing on a foundational, widely-distributed plant of conservation concern: basin big sagebrush ( Artemisia tridentata subsp. tridentata ). We found that changes in alpha diversity were independently affected by the age of a community and the air temperature. Surprisingly, total fungal abundance and species richness were not positively correlated and responded differently, sometimes oppositely, to weather. With regard to beta diversity, communities were more similar to each other across similar leaf ages, air temperatures, leaf types, and δ 13 C stable isotope ratios. Nine different genera were differentially abundant with air temperature, δ 13 C, leaf type, and leaf age, and a set of 20 genera were continuously present across the year. Our findings highlight the necessity for longer-term, repeated sampling to parse drivers of temporal change in leaf microbial communities.

Open Research Statement

All ITS DNA amplicon sequence raw data are deposited in the NCBI Sequence Read Archive (SRA), BioProject number PRJNA1107252, data will be released upon publication. All community data, metadata, taxonomic data, and R code necessary to reproduce these results are deposited in the GitHub repository archived on Zenodo: 10.5281/zenodo.11106439.

The Culturable Mycobiota of Sediments and Associated Microplastics: From a Harbor to a Marine Protected Area, a Comparative Study

Fungi are an essential component of marine ecosystems, although little is known about their global distribution and underwater diversity, especially in sediments. Microplastics (MPs) are widespread contaminants worldwide and threaten the organisms present in the oceans. In this study, we investigated the fungal abundance and diversity in sediments, as well as the MPs, of three sites with different anthropogenic impacts in the Mediterranean Sea: the harbor of Livorno, the marine protected area “Secche della Meloria”; and an intermediate point, respectively. A total of 1526 isolates were cultured and identified using a polyphasic approach. For many of the fungal species this is the first record in a marine environment. A comparison with the mycobiota associated with the sediments and MPs underlined a “substrate specificity”, highlighting the complexity of MP-associated fungal assemblages, potentially leading to altered microbial activities and hence changes in ecosystem functions. A further driving force that acts on the fungal communities associated with sediments and MPs is sampling sites with different anthropogenic impacts.

Biological Activity of Pulcherrimin from the Meschnikowia pulcherrima Clade

Pulcherrimin is a secondary metabolite of yeasts belonging to the Metschnikowia pulcherrima clade, and pulcherrimin formation is responsible for the antimicrobial action of its producers. Understanding the environmental function of this metabolite can provide insight into various microbial interactions and enables the efficient development of new effective bioproducts and methods. In this study, we evaluated the antimicrobial and antiadhesive action of yeast pulcherrimin, as well as its protective properties under selected stressful conditions. Classical microbiological plate methods, microscopy, and physico-chemical testing were used. The results show that pure pulcherrimin does not have antimicrobial properties, but its unique hydrophilic nature may hinder the adhesion of hydrophilic bacterial cells to abiotic surfaces. Pulcherrimin also proved to be a good cell protectant against UV–C radiation at both high and low temperatures.

Salt-stress adaptation of yeast as a simple method to improve high-gravity fermentation in an industrial medium

While Saccharomyces cerevisiae is a popular organism to produce ethanol, its fermentation performance is affected at high sugar concentrations due to osmotic stress. We hypothesized that adaptation under ionic stress conditions will improve the fermentation performance at high sugar concentrations due to cross-stress adaptation. We, therefore, adapted a high-performance yeast strain, S. cerevisiae CEN.PK 122, to increasing salt concentrations in an industrial medium. Control cells were adapted in the medium without added salt. The cells adapted to 3.5% (w/v) salt concentration demonstrated a superior performance when fermenting 10-30% (w/v) glucose. When fermenting 30% (w/v) glucose, the ethanol yields of the adapted cells (0.49 ± 0.01 g g^-1) were about 30% higher than the control cells (0.37 ± 0.01 g g^-1) and are comparable with the best reported to date for any medium employed. Similar improvements were also observed when fermenting 10% (w/v) sucrose. However, little improvement in fermentation was observed at the higher temperature tested (40 °C), even though the growth of the adapted cells was greater when tested in YPD medium. The improvements in fermentation at 30 °C were primarily related to the faster growth of the adapted cells and not to an increase in specific intake rates. Additionally, a significantly reduced lag phase was also observed when fermenting 30% (w/v) glucose. Thus, our work shows the application of a simple strategy to significantly improve high-gravity fermentation (HGF) performance through adaptation. KEY POINTS: • Cell adapted on 3.5% NaCl made 28% more ethanol when fermenting 30% glucose. • The adapted cells had reduced lag phase, grew faster, and produced less glycerol. • The improvements were not related to increased specific rates of production.

Performance of a Newly Isolated Salt-Tolerant Yeast Strain Sterigmatomyces halophilus SSA-1575 for Azo Dye Decolorization and Detoxification

The effective degradation of hazardous contaminants remains an intractable challenge in wastewater processing, especially for the high concentration of salty azo dye wastewater. However, some unique yeast symbionts identified from the termite gut system present an impressive function to deconstruct some aromatic compounds, which imply that they may be valued to work on the dye degradation for various textile effluents. In this investigation, a newly isolated and unique yeast strain, Sterigmatomyces halophilus SSA-1575, was identified from the gut system of a wood-feeding termite (WFT), Reticulitermes chinensis. Under the optimized ambient conditions, the yeast strain SSA-1575 showed a complete decolorization efficiency on Reactive Black 5 (RB5) within 24 h, where this azo dye solution had a concentration of a 50 mg/L RB5. NADH-dichlorophenol indophenol (NADH-DCIP) reductase and lignin peroxidase (LiP) were determined as the key reductase and oxidase of S. halophilus SSA-1575. Enhanced decolorization was recorded when the medium was supplemented with carbon and energy sources, including glucose, ammonium sulfate, and yeast extract. To understand a possible degradation pathway well, UV-Vis spectroscopy, FTIR and Mass Spectrometry analyses were employed to analyze the possible decolorization pathway by SSA-1575. Determination of relatively high NADH-DCIP reductase suggested that the asymmetric cleavage of RB5 azo bond was mainly catalyzed by NADH-DCIP reductase, and finally resulting in the formation of colorless aromatic amines devoid of any chromophores. The ecotoxicology assessment of RB5 after a decolorization processing by SSA-1575, was finally conducted to evaluate the safety of its metabolic intermediates from RB5. The results of Microtox assay indicate a capability of S. halophilus SSA-1575, in the detoxification of the toxic RB5 pollutant. This study revealed the effectiveness of halotolerant yeasts in the eco-friendly remediation of hazardous pollutants and dye wastewater processing for the textile industry.

Culture-dependent diversity profiling of spoilage yeasts species by PCR-RFLP comparative analysis

Spoilage caused by yeasts is a constant, widespread problem in the beverage industry that can result in major economic losses. Fruit juices provide an environment that allows the proliferation of yeast. Some factories in South Africa are not equipped with laboratory facilities to identify spoilage yeasts and outsourcing becomes a prolonged process which obstructs corrective action planning. This study aimed to establish yeast diversity and apply a rapid method for preliminary identification of spoilage yeasts associated with a small-scale fruit juice bottling factory. Yeast population in the factory was determined by isolation from the production environment, process equipment and spoiled products. PCR-RFLP analysis targeting the 5.8S-ITS region and D1/D2 sequencing was used for identification. A total of 207 yeasts belonging to 10 different genera (Candida, Lodderomyces, Wickerhamomyces, Yarrowia, Zygosaccharomyces, Zygoascus, Cryptococcus, Filobasidium, Rhodotorula/Cystobasidium and Trichosporon) were isolated and identified from the production environment and processing equipment. Candida intermedia, C. parapsilosis and Lodderomyces elongisporus were widely distributed in the factory. Zygosaccharomyces bailii, Z. bisporus, Zygoascus hellenicus and Saccharomyces cerevisiae were isolated from the spoiled products. The data provided a yeast control panel that was used successfully to identify unknown yeasts in spoiled products from this factory using polymerase chain reaction-restriction length polymorphism (PCR-RFLP) comparative analysis.

Microbial Ecology on Solar Panels in Berkeley, CA, United States

Solar panels can be found practically all over the world and represent a standard surface that can be colonized by microbial communities that are resistant to harsh environmental conditions, including high irradiation, temperature fluctuations and desiccation. These properties make them not only ideal sources of stress-resistant bacteria, but also standard devices to study the microbial communities and their colonization process from different areas of Earth. We report here a comprehensive description of the microbial communities associated with solar panels in Berkeley, CA, United States. Cultivable bacteria were isolated to characterize their adhesive capabilities, and UV- and desiccation-resistance properties. Furthermore, a parallel culture-independent metagenomic and metabolomic approach has allowed us to gain insight on the taxonomic and functional nature of these communities. Metagenomic analysis was performed using the Illumina HiSeq2500 sequencing platform, revealing that the bacterial population of the Berkeley solar panels is composed mainly of Actinobacteria, Bacteroidetes and Proteobacteria, as well as lower amounts of Deinococcus-Thermus and Firmicutes. Furthermore, a clear predominance of Hymenobacter sp. was also observed. A functional analysis revealed that pathways involved in the persistence of microbes on solar panels (i.e., stress response, capsule development, and metabolite repair) and genes assigned to carotenoid biosynthesis were common to all metagenomes. On the other hand, genes involved in photosynthetic pathways and general autotrophic subsystems were rare, suggesting that these pathways are not critical for persistence on solar panels. Metabolomics was performed using a liquid chromatography tandem mass spectrometry (LC-MS/MS) approach. When comparing the metabolome of the solar panels from Berkeley and from Valencia (Spain), a very similar composition in polar metabolites could be observed, although some metabolites appeared to be differentially represented (for example, trigonelline, pantolactone and 5-valerolactone were more abundant in the samples from Valencia than in the ones from Berkeley). Furthermore, triglyceride metabolites were highly abundant in all the solar panel samples, and both locations displayed similar profiles. The comparison of the taxonomic profile of the Californian solar panels with those previously described in Spain revealed striking similarities, highlighting the central role of both selective pressures and the ubiquity of microbial populations in the colonization and establishment of microbial communities.

Sterigmatomyces halophilus β-glucan improves the immune response and bacterial resistance in Pacific red snapper (Lutjanus peru) peripheral blood leucocytes: In vitro study

β-Glucans are naturally occurring polysaccharides that are produced by bacteria, fungi and yeast. They are considered immunostimulants in fish acting on non-specific defense mechanism. Yeast-derived glucans from cell wall (Sterigmatomyces halophilus, β-Gluc/Sh) have been used for this purpose in this study. Therefore, an in vitro assay using peripheral blood leucocytes (PBLs) from Pacific red snapper was performed to evaluate the stimulant effects of β-Gluc/Sh and zymosan A (positive control) for 12 and 24 h and after bacterial challenge with Aeromonas hydrophila at 24 h. In addition, structural characterization of this marine yeast glucan was performed by proton nuclear magnetic resonance (NMR) revealing structures containing (1-6)-branched (1-3)-β-D-glucan. PBLs responded positively to β-Gluc/Sh where cell viability was higher than 80%. After challenge, β-Gluc/Sh was able to inhibit cytotoxicity caused by A. hydrophila, highlighting that the PBLs incubated with β-Gluc/Sh significantly increased the non-specific immune response, such as phagocytic activity, respiratory burst, nitric oxide and peroxidase activities followed by an increase in superoxide dismutase and catalase activities after 12 and 24 h post-stimulation and after challenge with the pathogen. Regarding induction of antioxidant gene expression, it was more pronounced in stimulated β-Gluc/Sh leucocytes compared to other groups at all experimental times of the trial and after bacterial challenge. Indeed, our results clearly showed the ability of leucocytes to strongly react to β-Gluc/Sh with an increase in cytokine gene expression, particularly the IL-1β, IL-10 and IL-17 genes. These results confirm that S. halophilus yeast-derived β-glucan, isolated from an extreme marine environment, is beneficial for increasing innate immune response and enhancing resistance against A. hydrophila in vitro.

Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum

Diatoms are prominent marine microalgae, interesting not only from an ecological point of view, but also for their possible use in biotechnology applications. They can be cultivated in phototrophic conditions, using sunlight as the sole energy source. Some diatoms, however, can also grow in a mixotrophic mode, wherein both light and external reduced carbon contribute to biomass accumulation. In this study, we investigated the consequences of mixotrophy on the growth and metabolism of the pennate diatom Phaeodactylum tricornutum, using glycerol as the source of reduced carbon. Transcriptomics, metabolomics, metabolic modelling and physiological data combine to indicate that glycerol affects the central-carbon, carbon-storage and lipid metabolism of the diatom. In particular, provision of glycerol mimics typical responses of nitrogen limitation on lipid metabolism at the level of triacylglycerol accumulation and fatty acid composition. The presence of glycerol, despite provoking features reminiscent of nutrient limitation, neither diminishes photosynthetic activity nor cell growth, revealing essential aspects of the metabolic flexibility of these microalgae and suggesting possible biotechnological applications of mixotrophy.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.

Dietary yeast Sterigmatomyces halophilus enhances mucosal immunity of gilthead seabream (Sparus aurata L.)

A yeast was isolated from hypersaline sediments, grown and phylogenetically characterized as Sterigmatomyces halophilus strainN16. The dietary administration of this yeast was studied for its effect on skin mucosal immune and antioxidant status of gilthead seabream (Sparus aurata L.). Fish were fed a commercial diet (control, non-supplemented diet), or the same commercial diet supplemented with 0.55% or 1.1% of yeast for 15 and 30 days. One month after the end of the trial, fish from all treatments were intraperitoneally injected with pathogenic Vibrio parahaemolyticus and further fed with the same diets for one week, after which fish were also sampled. Significant increases were observed in the immune activities determined in the fish fed the yeast supplemented diets compared with the values recorded in mucus of fish from the control group. The expression levels of trypsin (one of the main digestive enzymes) and several immune-related genes (IL-1β, TNF-α, IgM, C3 and lysozyme) were also evaluated by real-time PCR in intestine and skin. Interestingly, trypsin gene expression in intestine was up regulated in both experimental diets compared with the control group, particularly in fish fed with 0.55% of S. halophilus at any time of the experimental trial. Immune-related genes in intestine and skin were strongly expressed principally in fish fed with 0.55% of S. halophilus for 15 days and 1.1% for 30 days and after infection, respectively. The present results suggest that the yeast S. halophilus can be considered as a novel fish immunostimulant. The excellent potential of marine microorganisms isolated from extreme environments with beneficial properties for fish is discussed.

Osmoadaptation strategy of the most halophilic fungus, Wallemia ichthyophaga, growing optimally at salinities above 15% NaCl

Wallemia ichthyophaga is a fungus from the ancient basidiomycetous genus Wallemia (Wallemiales, Wallemiomycetes) that grows only at salinities between 10% (wt/vol) NaCl and saturated NaCl solution. This obligate halophily is unique among fungi. The main goal of this study was to determine the optimal salinity range for growth of the halophilic W. ichthyophaga and to unravel its osmoadaptation strategy. Our results showed that growth on solid growth media was extremely slow and resulted in small colonies. On the other hand, in the liquid batch cultures, the specific growth rates of W. ichthyophaga were higher, and the biomass production increased with increasing salinities. The optimum salinity range for growth of W. ichthyophaga was between 15 and 20% (wt/vol) NaCl. At 10% NaCl, the biomass production and the growth rate were by far the lowest among all tested salinities. Furthermore, the cell wall content in the dry biomass was extremely high at salinities above 10%. Our results also showed that glycerol was the major osmotically regulated solute, since its accumulation increased with salinity and was diminished by hypo-osmotic shock. Besides glycerol, smaller amounts of arabitol and trace amounts of mannitol were also detected. In addition, W. ichthyophaga maintained relatively small intracellular amounts of potassium and sodium at constant salinities, but during hyperosmotic shock, the amounts of both cations increased significantly. Given our results and the recent availability of the genome sequence, W. ichthyophaga should become well established as a novel model organism for studies of halophily in eukaryotes.