ABSTRACT
In recent years, ‘multi-omic’ sciences have affected all aspects of fundamental and applied biological research. Yeast taxonomists, though somewhat timidly, have begun to incorporate ...complete genomic sequences into the description of novel taxa, taking advantage of these powerful data to calculate more reliable genetic distances, construct more robust phylogenies, correlate genotype with phenotype and even reveal cryptic sexual behaviors. However, the use of genomic data in formal yeast species descriptions is far from widespread. The present review examines published examples of genome-based species descriptions of yeasts, highlights relevant bioinformatic approaches, provides recommendations for new users and discusses some of the challenges facing the genome-based systematics of yeasts.
The cases in which genome data has accompanied the description of asomycetous and basidiomycetous yeasts are revised including the different methods and approaches used.
The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than ...1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina , it contains only one class compared to the 16 classes in Pezizomycotina . The third subphylum of Ascomycota , the Taphrinomycotina , consists of six classes and has approximately 10 times fewer species than the Saccharomycotina . These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families ( Lipomycetaceae , Trigonopsidaceae , Alloascoideaceae , Pichiaceae , Phaffomycetaceae , Saccharomycodaceae , and Saccharomycetaceae ), one comprises two current families ( Dipodascaceae and Trichomonascaceae ), one represents the genus Sporopachydermia , and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina , including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named.
Background and Aims
Fungicides used against the mould Botrytis cinerea can also non‐specifically affect indigenous yeasts important for the development of complex wine aroma. Our aim was to determine ...the minimal inhibitory concentration of the fungicides iprodione, pyrimethanil and fludioxonil plus cyprodinil for 109 yeasts of the grape berry microbiota.
Methods and Results
We measured the respiration activity of yeasts, changes in growth kinetics and adenosine triphosphate production. Fungicide tolerance may be a conserved feature within the yeast's genera, however, some heterogeneity between isolates remains. The viability and growth of 15 beneficial isolates were inhibited by fungicides at a residue concentration below the maximum permitted residue limits. These isolates belonged to the yeast species: Metschnikowia pulcherrima, Pichia kluyveri, Hanseniaspora uvarum and Bulleromyces albus. Furthermore, isolates of typical spoilage yeasts, such as Dekkera bruxellensis, Meyerozyma guilliermondii and Pichia membranifaciens, were found to be tolerant of a concentration of fungicides greater than that recommended for application by the suppliers.
Conclusions
Fungicide residues hindered the viability of desirable isolates and promoted the growth of several spoilage isolates and thus may have a negative impact on wine aroma.
Significance of the Study
For spontaneous fermentations the application of fungicides in the vineyard could add to the seasonal fluctuations of aroma and to the development of off‐flavours.
Summary
Campylobacter jejuni is among the most prevalent causes of human bacterial gastroenteritis worldwide. Domesticated animals and, especially, chicken meat are considered to be the main sources ...of infections. However, the contribution of surface waters and wildlife in C. jejuni transmission to humans is not well understood. We have evaluated the source attribution potential of a six‐gene multiplex PCR (mPCR) method coupled with STRUCTURE analysis on a set of 410 C. jejuni strains isolated from environment, livestock, food and humans in central Europe. Multiplex PCR fingerprints were analysed using Subclade prediction algorithm to classify them into six distinct mPCR clades. A subset of C. jejuni isolates (70%) was characterized by multilocus sequence typing (MLST) demonstrating 74% congruence between mPCR and MLST. The correspondence analysis of mPCR clades and sources of isolation indicated three distinct groups in the studied C. jejuni population—the first one associated with isolates from poultry, the second one with isolates from cattle, and the third one with isolates from the environment. The STRUCTURE analysis attributed 7.2% and 21.7% of human isolates to environmental sources based on MLST and mPCR fingerprints, respectively.
Campylobacter is the most prevalent cause of bacterial gastroenteritis worldwide and it represents a significant public health risk of increasing severity due to its escalating resistance to ...clinically important quinolone and macrolide antibiotics. As a zoonotic pathogen Campylobacter is transmitted along the food chain and naturally cycles from environmental waters, feedstuff, animals and food to humans. We determined antibiotic resistance profiles, as well as multilocus sequence types and flaA-SVR types for 52 C. jejuni isolated in Slovenia from human, animal, raw and cured chicken meat and water samples. Twenty-eight different sequence types, arranged in ten clonal complexes, three new allele types and five new sequence types were identified, indicating the relatively high diversity in a small group of strains. The assignment of strains from different sources to the same clonal complexes indicates their transmission along the food supply chain. The most prevalent clonal complex was CC21, which was also the genetic group with 95% of quinolone-resistant strains. Based on the genetic relatedness of these quinolone-resistant strains identified by polymerase chain reaction with a mismatch amplification mutation assay and sequencing of the quinolone resistance-determining region of the gyrA gene, we conclude that the high resistance prevalence observed indicates the local clonal spread of quinolone resistance with CC21.
The goal of this study was the characterisation of indigenous lactic acid bacteria (LAB) and yeasts isolated from nine white pickled (BG) and nine fresh soft (ZG) artisanal cheeses collected in ...Serbia and Croatia. While LAB were present in all of the cheeses collected, yeasts were found in all BG cheeses but only in three ZG cheese samples. High LAB and yeast species diversity was determined (average H′L=0.4 and H′Y=0.8, respectively). The predominant LAB species in white pickled (BG) cheeses were Lactococcus lactis, Lactobacillus plantarum, and Leuconostoc mesenteroides, while in fresh soft (ZG) cheeses the most dominant LAB species were L. lactis, Enterococcus faecalis, and Leuconostoc pseudomesenteroides. Among the 20 yeast species found, Debaryomyces hansenii, Candida zeylanoides, and Torulaspora delbrueckii were found to be predominant in BG cheeses, while Yarrowia lipolytica was predominant in ZG cheeses. The characterisation of metabolic and technological potentials revealed that 53.4% of LAB isolates produced antimicrobial compounds, 44.3% of LAB strains showed proteolytic activity, while most of the yeast species possessed either lipolytic or proteolytic activity. In conclusion, the results obtained in this study showed that the composition of LAB and yeast populations in white pickled and fresh soft cheeses is region specific. The knowledge gained in this study could eventually be used to select region specific LAB and yeast strains for the production of white pickled and fresh soft artisanal cheeses with geographically specific origins under controlled conditions.
•Indigenous microbiota of 18 artisanal cheeses from Serbia and Croatia was determined.•LAB and yeast species were identified by using traditional and molecular methods.•High diversity of LAB and yeast populations were found.•Impact on starter culture development for traditional cheeses with defined properties•Implementation in controlled production of artisanal cheeses with geographical origin
The dynamics of the wine yeast strains presented in five spontaneous Malvasia wine fermentations have been studied. Samples were analysed for their microbiological characteristics and chemical ...substances. All 937 isolates were characterized using electrophoretic karyotyping and tested for their killer activity. The non- Saccharomyces population was identified using a combination of PCR-RFLP analysis of the rDNA spacer region and physiological testing. The total yeast population level in the must after sedimentation was 105cfu ml−1and included the following genera:Candida, Metschnikowia, Hanseniaspora, Rhodotorula, Issatchenkia and Debaryomyces. However, Saccharomyces sp. was not detected in fresh must samples plated on YEPD medium. Based on the chromosome length polymorphism among 649 isolates from the subsequent phases of fermentation, 46 different electrophoretic patterns of Saccharomyces cerevisiae were distinguished. The most abundant karyotypes were L1, L4, L12, P6. A sequential substitution of S. cerevisiae strains occurred during the different phases of fermentation. At the slow fermentation rate, karyotype L4was most abundant in almost all fermenters. At the beginning of the tumultuous fermentation phase, the most frequent karyotype became L1followed by karyotype L4. Finally, during the fermentation process, pattern L4was clearly replaced by karyotype L1followed by pattern L12. Despite the same fermentation source (grape must), differences among five spontaneous fermentations were observed. The population dynamics of S. cerevisiae yeasts, especially the dynamics of the major S. cerevisiae strains (L1, L4, and L12) were quite similar in all five fermenters in opposite to the minor strains of S. cerevisiae.
The number and diversity of yeasts on grape berry surfaces are influenced by several factors, such as grape variety, degree of grape maturity at harvest, climatological conditions, geographic ...location, physical damage of grapes, the intensity of pest management etc. Cviček is a typical Slovene wine, which has obtained a special protection under the Slovene Wine Law for its geographical origin. This blended red wine is produced from different grape varieties (
Vitis vinifera L.), mostly from red grapes of Žametovka and Modra frankinja and from white grapes of Kraljevina. The aim of this study was to evaluate the impact of geographical locations in the Dolenjska vine-growing region and to obtain precise information about the influence of different grape varieties on the composition of yeast community on grape berries. The restriction fragment length polymorphism of PCR-amplified fragments from the rDNA gene cluster (PCR RFLP of rDNA) has been used for the differentiation of yeast species. The standard identification procedure has been performed on representative strains that shared identical RFLP profiles. The number of yeasts and yeast species isolated varied according to different grape varieties, Žametovka, Modra frankinja and Kraljevina (
V. vinifera L.) and according to different sampling location. On the surface of grape berries 13 different yeast species have been identified.
Saccharomyces cerevisiae has not been found.
Biocontrol activities of different yeast species and strains isolated from grape/must/ wine environments have been compared to those of commercially available antagonistic yeast species of Candida ...oleophila. A total of 591 yeast isolates were tested in a preliminary screening on agar to select isolates showing inhibitory effect against Botrytis cinerea, the plant pathogen causing grey mould disease on grape. Yeast species Aureobasidium pullulans, Metschnikowia pulcherrima and Pichia guilliermondii showed, on average, higher biocontrol activity than commercially used yeast Candida oleophila. Furthermore, these three species and Saccharomyces cerevisiae, which is potentially interesting biocontrol agent against grey mould of grapes, were selected for their inhibitory effects and assayed in vitro on different solid synthetic media for their antagonistic capacity towards B. cinerea. The results indicate that the composition of the medium had an impact on the biocontrol activity of yeast species and strains, as Saccharomyces cerevisiae showed the highest antagonistic activity against B. cinerea when tested on media with increased concentrations of glucose. The antagonistic activity of selected yeast strains was finally determined on wounded and sound grape berries of cultivars Rebula and Chardonnay for their ability to inhibit infection by B. cinerea moulds. Results suggest that antagonist yeasts with the potential to control B. cinerea on grape can be found among the microflora associated with the berries. Key words: biocontrol agents, Botrytis cinerea, grey mould, antagonism, grapes, wine yeasts
Wine yeast strains were isolated from seven fermentations of the red wines ‘Refošk’ and ‘Teran’, produced in the southwestern part of Slovenia. Among 613 isolated yeast strains, 22 expressed killer ...activity against the supersensitive strain Saccharomyces cerevisiae. Killer strains were isolated at different stages of wine fermentation but did not dominate in any of them. Species identification was based on the combination of RFLP analysis of an amplified rDNA region and biochemical–physiological tests. Killer isolates were identified as S. cerevisiae, Pichia anomala, Pichia kluyveri, Pichia pijperi, Hanseniaspora uvarum and Candida rugosa. Electrophoretic karyotyping was used to differentiate strains of the same species. Fermentation properties of four S. cerevisiae strains that possessed stable killer activity were characterized in fermentations of Malvasia must by studying their population dynamics and chemical composition and by sensory analysis of the wines produced. In order to compare the results, spontaneous fermentations and fermentations induced by commercial yeast starters were performed concomitantly. The local killer strain SS12/10 showed the best fermentation properties and produced wine with favourable characteristics.
PDF
