Species reassignment of Geotrichum bryndzae, Geotrichum phurueaensis, Geotrichum silvicola and Geotrichum vulgare based on phylogenetic analyses and mating compatibility

Impact of algicidal fungus Aspergillus welwitschiae GF6 on harmful bloom-forming cyanobacterium Microcystis aeruginosa: Growth and physiological responses

Harmful cyanobacterial blooms (HCBs) have become a common issue in freshwater worldwide. Biological methods for controlling HCBs are relatively cost effective and environmentally friendly. The strain of ascomycete GF6 was isolated from a water sample collected from the estuarine zone of the eastern part of the Gulf of Finland. Based on cultural and morphological features and data of phylogenetic analysis, the strain was identified as Aspergillus welwitschiae GF6. The isolated GF6 strain has algicidal activity against both cyanobacteria and green algae. The highest sensitivity to the algicidal action of strain GF6 was found in cyanobacteria (98.5-100%). The algicidal effect on green algae did not exceed 63-70%. It was shown that GF6 strain exhibited an indirect attack mode by releasing metabolites that inhibit and/or degrade algal cells. In this study, significantly increased malondialdehyde content in Microcystis aeruginosa cells indicated that GF6 strain caused oxidative damage to the algal cell membrane. Enhanced production of phytosynthetic pigments, increase in lifetime chlorophyll a fluorescence and in the levels of antioxidants were noted in Microcystis aeruginosa cells. Besides this, GF6 strain could reduce the microcystins content in the medium under inhibiting the growth of M. aeruginosa. Apart from the growth inhibition and cell degradation of M. aeruginosa, GF6 strain is able to remove microcystin-LR (MC-LR). The content of MC-LR at an initial concentration of 0.51 μg/mL decreased by 61% after 72 h of A.welwitschiae GF6 strain cultivation. In the process of MC-LR biodestruction, transformation products were identified - the conjugate of microcystin with glutathione and the linearized form of MC-LR. The isolated strain with algicidal activity and the ability to degrade microcystin is of interest for further research in order to be able to use it for convergent technology to prevent the mass development of cyanobacteria and detoxification of cyanotoxins in water bodies.

Two new arthroconidial yeast species from bark and pit mud in China

A study on yeast species from the genera Geotrichum and Magnusiomyces in southwest and central China was conducted based on morphological and molecular phylogenetic analyses using the ITS region and the D1/D2 domain of the LSU rRNA gene. The research identified two new yeast species: Geotrichumhubeiense and Magnusiomycespitmudophilus. The study contributed to understanding arthroconidial yeast diversity in fermentation and natural environments and paved the way for future taxonomic and ecological studies. Descriptions, illustrations, and phylogenetic analysis results of the two new taxa are provided.

Taxonomic revision of Geotrichum and Magnusiomyces, with the descriptions of five new Geotrichum species from China

The arthroconidial yeast-like species currently classified in the asexual genera Geotrichum and Saprochaete and the sexual genera Dipodascus, Galactomyces and Magnusiomyces are frequently associated with dairy and cosmetics production, fruit rot and human infection. However, the taxonomic system of these fungi has not been updated to accommodate the new nomenclature code adopting the "one fungus, one name" principle. Here, we performed phylogenetic analyses of these yeast-like species based on the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domain of the large subunit of the rRNA gene. Two monophyletic groups were recognised from these species. One group contained Dipodascus, Galactomyces, and Geotrichum species and the other Magnusiomyces and Saprochaete species. We thus assigned the species in each group into one genus and selected the genus name Geotrichum for the first group and Magnusiomyces for the second one based on the principle of priority of publication. Five new Geotrichum species were identified from arthroconidial yeast strains recently isolated from various sources in China. The new species are described as Ge. dehoogii sp. nov., Ge. fujianense sp. nov., Ge. maricola sp. nov., Ge. smithiae sp. nov., and Ge. sinensis sp. nov.

Galactomyces candidus diversity in the complex mycobiota of cow-milk bryndza cheese comprising antagonistic and sensitive strains

Galactomyces candidus (orthographic variant: Galactomyces candidum) is a heterogeneous species of Saccharomycetales that comprises dimorphic yeasts described previously under various names (e.g. Geotrichum, Dipodascus). Its strains are common components of the cheese surface mycobiota. This study identified genetically and physiologically heterogeneous G. candidus strains in the complex mycobiota of artisanal cow-milk bryndza samples. The traditional Slovak bryndza is a cheese produced from ewe's milk in cooler mountainous regions and from cow's milk in warmer low-land regions. The taxonomic analysis of the culturable yeasts of the latter version carried out in this study revealed considerable differences from the yeast biota previously described for ovine bryndza. However, the conventional D1/D2- and ITS-based barcode analyses could not assign unanimously all isolates to species because of the intragenomic barcode diversity in certain groups and the discordance between the D1/D2 and ITS results in other groups. The identified species and groups of isolates had different abilities to utilise the carbon and energy sources (lactose, lactate, lipids and proteins) available in milk and ripening cheese. The G. candidus strains did not metabolise lactose and lactate, hydrolysed milk proteins with diverse, usually moderate efficiency and only could grow on certain amino acids as only energy sources. Their preferred substrate was lipid. Under aerobic conditions, its hyphae penetrated the lipid droplets and degraded their content from inside by developing a dense internal mycelium. Sporulation and different MLST (multilocus sequence typing) patterns indicated that the Galactomyces strains could sexually interact and their genomes could recombine. The Galactomyces and Kluyveromyces isolates had antagonistic effects against other members of the mycobiota.

Microbial Dynamics of a Specialty Italian Raw Ewe's Milk Cheese Curdled with Extracts from Spontaneous and Cultivated Onopordum tauricum Willd

Milk coagulants prepared by maceration of flowers harvested from both spontaneous and cultivated Onopordum tauricum Willd. and a commercially available coagulant obtained from Cynara cardunculus L. (control) were assayed for small-scale manufacturing of Caciofiore, an Italian specialty raw ewe's milk cheese produced in a family run dairy farm located in the Marche region (Central Italy). The microbiota of the three thistle-based milk coagulants and their effect on the microbial dynamics of raw milk cheeses during fermentation and maturation (from day 0 up until day 60) were investigated through a combined approach based on viable counting and Illumina DNA sequencing. In both the control and experimental cheeses, despite the slight differences emerged depending on the coagulant used, Lactococcus lactis and Debaryomyces hansenii were the prevalent species among bacteria and fungi, respectively. Moreover, raw ewe's milk was the main factor affecting the evolution of both the bacterial and fungal microbiota in all cheeses. The overall similarities between control and experimental cheeses herein analyzed supports the exploitation of Onopordum tauricum Willd. as an alternative milk coagulating agent for production of Caciofiore and, more in general, raw ewe's milk cheeses.

Comparative analysis of aroma components and quality of Geotrichum candidum after space mutation breeding

Aim

The aroma-producing strain of Geotrichum candidum GDMCC60675 was taken as the research object, the composition of aroma-producing substances of G. candidum was studied, and the target strains of G. candidum suitable for food additives were screened out by mutagenesis.

Methods

Mutants were obtained by space breeding. The colony morphology and cell morphology of the mutant strain were identified, the phylogenetic tree of the two strains was constructed, and the whole-genome sequences of the wild strain and the mutant strain were compared. The aroma components and key odor compounds of the two strains were analyzed and compared by HS-SPME-GC-MS and E-nose detection, and the data were processed by using the relative odor activity value (ROAV) analysis method.

Results

A mutant strain of G. candidum was found with different characteristics of aroma production compared with wild-type G. candidum. It was found that its colony morphology and cell morphology were similar. However, it was found that the aroma-producing substances produced by the two strains were different, and the key difference compound was phenyl ethyl alcohol, which also proved that the two strains were different, and the main aroma note was different.

A novel yeast strain Geotrichum sp. CS-67 capable of accumulating heavy metal ions

Bioremediation, which has several advantages over traditional methods, represents an alternative means of dealing with heavy metal pollution. We screened for microorganisms showing heavy metal tolerance in polluted mangrove soils. A novel yeast, Geotrichum sp. CS-67, was discovered and tested for tolerance of Cu²⁺, Zn²⁺, and Ni²⁺. Zn²⁺ was the most efficiently sequestered by Geotrichum sp. CS-67 followed by Ni²⁺ and Cu²⁺. Zn²⁺ and Ni²⁺ were actively taken up into the cell, while Cu²⁺ was adsorbed to the cell wall. We used RNA-Seq to show that a large number of genes involved in the physiological and biochemical processing of heavy metals were differentially expressed in this yeast when it was subjected to Zn²⁺ and Ni²⁺ stress. From this panel, we selected the SED1, GDI1 and ZRT1 genes for validation by qRT-PCR and discovered that, during Zn²⁺ and Ni²⁺ stress, SED1 and GDI1 were upregulated, while ZRT1 was downregulated, which was consistent with the RNA-Seq results and the biochemical function of these genes. In conclusion, the novel yeast Geotrichum sp. CS-67 has a marked ability to accumulate heavy metal ions, making it of great interest as a possible microbial agent for heavy metal pollution remediation in the future.

Unusual Stylar-End Breakdown and Sour Rot on Key Lime (Citrus aurantiifolia) in Pre-Harvest Condition in Italy

Key lime (Citrus aurantiifolia) is an emerging crop in Italy, especially in the Southern regions, where the environmental conditions are suitable for its cultivation. A field survey in Sicily in a commercial orchard of Key lime revealed the widespread presence of water-soaked spots and sunken/dry lesions at the stylar-end, mainly in pre-harvest condition. Water-soaked spots were attributed to Geotrichum citri-aurantii, an agent of sour rot on Citrus spp., whereas the sunken/dry lesion was attributed to the physiological disorder known as stylar-end breakdown. Sour rot and stylar-end breakdown are usually considered post-harvest diseases and rarely found in the field on fruit still attached to the tree. Although Geotrichum citri-aurantii is not responsible for the stylar-end breakdown, its association with this alteration reveals the importance of the environmental conditions and the agronomic practices in diseases/disorders development. In addition, to our knowledge, this is the first report of Geotrichum citri-aurantii on Key lime in Europe.

Machinery Mold (Galactomyces geotrichum) Survival following Thermal and Hydrostatic Pressure Processing

HIGHLIGHTS

Enrichment, isolation, and biodegradation potential of long-branched chain alkylphenol degrading non-ligninolytic fungi from wastewater

4-t-Octylphenol (4-t-OP) has become a serious environmental concern due to the endocrine disruption in animals and humans. The biodegradation of 4-t-OP by pure cultures has been extensively investigated only in bacteria and wood-decaying fungi. In this study we isolated and identified 14 filamentous fungal strains from wastewater samples in Taiwan using 4-t-OP as a sole carbon and energy source. The isolates were identified based on sequences from different DNA regions. Of 14 fungal isolates, 10 strains grew effectively on solid medium with a wide variety of endocrine disrupting chemicals as the sole carbon and energy source. As revealed by high-performance liquid chromatography analysis, the most effective 4-t-OP degradation (>70%) in liquid medium was observed in Fusarium falciforme after 15days. To our knowledge, this is the first report on the degradation of 4-t-OP as a sole carbon and energy source by non-ligninolytic fungi.

Aerobic degradation of estrogenic alkylphenols by yeasts isolated from a sewage treatment plant

Long-chain alkylphenols including octylphenol (OP) are well-known toxic pollutants prevailing in the environment due to the massive demand of these chemicals in industry and have been identified as endocrine disrupting chemicals (EDCs).

Rapid identification of 6328 isolates of pathogenic yeasts using MALDI-ToF MS and a simplified, rapid extraction procedure that is compatible with the Bruker Biotyper platform and database

Rapid and accurate identification of yeast isolates from clinical samples is essential, given their innately variable antifungal susceptibility profiles, and the proposal of species-specific antifungal susceptibility interpretive breakpoints. Here we have evaluated the utility of MALDI-ToF MS analysis for the identification of clinical isolates of pathogenic yeasts. A simplified, rapid extraction method, developed in our laboratory, was applied to 6343 isolates encompassing 71 different yeast species, which were then subjected to MALDI-ToF MS analysis using a Bruker Microflex and the resulting spectra were assessed using the supplied Bruker database. In total, 6328/6343 (99.8%) of isolates were correctly identified by MALDI-ToF MS. Our simplified extraction protocol allowed the correct identification of 93.6% of isolates, without the need for laborious full extraction, and a further 394 (6.2%) of isolates could be identified after full extraction. Clinically relevant identifications with both extraction methods were achieved using the supplied Bruker database and did not require the generation of bespoke, in-house databases created using profiles obtained with the adapted extraction method. In fact, the mean LogScores obtained using our method were as robust as those obtained using the recommended, published full extraction procedures. However, an in-house database can provide a useful additional identification tool for unusual or rarely encountered organisms. Finally, the proposed methodology allowed the correct identification of over 75% of isolates directly from the initial cultures referred to our laboratory, without the requirement for additional sub-culture on standardised mycological media.

Genome Sequence of Lactobacillus plantarum 19L3, a Strain Proposed as a Starter Culture for Slovenska Bryndza Ovine Cheese

The genome sequence of Lactobacillus plantarum isolated from ovine cheese is presented here. This bacterium is proposed as a starter strain, named 19L3, for Slovenská bryndza cheese, a traditional Slovak cheese fulfilling European Food Safety Authority (EFSA) requirements.

Identification of medically relevant species of arthroconidial yeasts by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was used for an extensive identification study of arthroconidial yeasts, using 85 reference strains from the CBS-KNAW yeast collection and 134 clinical isolates collected from medical centers in Qatar, Greece, and Romania. The test set included 72 strains of ascomycetous yeasts (Galactomyces, Geotrichum, Saprochaete, and Magnusiomyces spp.) and 147 strains of basidiomycetous yeasts (Trichosporon and Guehomyces spp.). With minimal preparation time, MALDI-TOF MS proved to be an excellent diagnostic tool that provided reliable identification of most (98%) of the tested strains to the species level, with good discriminatory power. The majority of strains were correctly identified at the species level with good scores (>2.0) and seven of the tested strains with log score values between 1.7 and 2.0. The MALDI-TOF MS results obtained were consistent with validated internal transcribed spacer (ITS) and/or large subunit (LSU) ribosomal DNA sequencing results. Expanding the mass spectrum database by increasing the number of reference strains for closely related species, including those of nonclinical origin, should enhance the usefulness of MALDI-TOF MS-based diagnostic analysis of these arthroconidial fungi in medical and other laboratories.

The treasure trove of yeast genera and species described by Johannes van der Walt (1925-2011)

Yeast taxonomy and systematics have in recent years been dealt with intensively primarily by a small group of individual researchers with particular expertise. Amongst these was Johannes P. van der Walt, who had a major role in shaping our current understanding of yeast biodiversity and taxonomy. Van der Walt based his taxonomic studies not only on available cultures, but also by going into the field to isolate yeasts from various substrates. This pioneering work led to the discovery of many new genera and species, which were deposited in the Centraalbureau voor Schimmelcultures (CBS) collections for future studies in taxonomy, genomics, and industrial uses. These treasures collected during more than 60 years provide an outstanding legacy to the yeast community and will continue to exist in his absence. This contribution provides a comprehensive overview of the current nomenclatural and taxonomic status of the yeast genera and species introduced by van der Walt during his career.