Population genetics of the wild yeast Saccharomyces paradoxus

Saccharomyces paradoxus is the closest known relative of the well-known S. cerevisiae and an attractive model organism for population genetic and genomic studies. Here we characterize a set of 28 wild isolates from a 10-km(2) sampling area in southern England. All 28 isolates are homothallic (capable of mating-type switching) and wild type with respect to nutrient requirements. Nine wild isolates and two lab strains of S. paradoxus were surveyed for sequence variation at six loci totaling 7 kb, and all 28 wild isolates were then genotyped at seven polymorphic loci. These data were used to calculate nucleotide diversity and number of segregating sites in S. paradoxus and to investigate geographic differentiation, population structure, and linkage disequilibrium. Synonymous site diversity is approximately 0.3%. Extensive incompatibilities between gene genealogies indicate frequent recombination between unlinked loci, but there is no evidence of recombination within genes. Some localized clonal growth is apparent. The frequency of outcrossing relative to inbreeding is estimated at 1.1% on the basis of heterozygosity. Thus, all three modes of reproduction known in the lab (clonal replication, inbreeding, and outcrossing) have been important in molding genetic variation in this species.     

Molecular polymorphism of viral dsRNA of yeast Saccharomyces paradoxus

An analysis of 53 strains of yeast Saccharomyces paradoxus (YSP) of different geographic origins enabled us, for the first time, to find viral double-stranded RNA (L and M fractions) in YSP and to study natural polymorphism. As in the cultured Scerevisiae, the size of L dsRNA was constant (4.5 kb). The size of minor M dsRNA varied from 1.5 to 2.4 k.b. In YSP, we determined 7 types of M dsRNA (M1-M7), which were not connected with the source of isolation or geographic origin of the host strains.     

Temperature sensitive radiosensitive mutants of the yeast Saccharomyces paradoxus

Summary The properties of four radiation sensitive ts mutants of the yeast Saccharomyces paradoxus, txs ₁, txs ₂, txs ₄and txs ₅,were studied. Genetic analysis proves the mutants to be non-allelic. The mutants are sensitive to X-rays and ultraviolet. Holding at 37°C in a complete medium but not in water sharply decreases the viability. With txs ₂this effect could also be observed in water. The mutants formed filaments and showed abnormal cytokinesis under restrictive conditions, this effect being the most pronounced with txs ₄.The frequency of mitotic recombiantion induced by X-rays and UV is much lower in the mutants (except txs ₂)as compared to the wild type. Restrictive temperature somewhat increased the mitotic recombination in the mutants (excepts txs ₁).Shift of the mutants into restrictive temperature leads to immediate, inhibition of DNA synthesis; the extent of this inhibition correlates with the levels of radiation and temperature sensitivity, both being higher in txs ₂and txs ₄.Elevated temperature also decreased RNA and protein synthesis in txs ₂.It is suggested that mutation txs ₂affects a function participating at the last stages in postirradiation repair of DNA, probably DNA ligase, txs ₄seemed to affect the process of nuclear division.     

First isolation of the yeast Saccharomyces paradoxus in Western Siberia

Two ascomycetous yeast strains have been isolated near Novosibirsk from oak exudate. The strains have been identified as Saccharomyces paradoxus Bachinskaya based on the results of biochemical tests. The conspecificity of the isolates with S. paradoxus was confirmed by electrophoretic karyotyping and restriction analysis of the ITS region of its rDNA. This first isolation of S. paradoxus in Siberia provides evidence for the continuity of its natural habitats.     

Isolation and characterization of the HO gene from the yeast Saccharomyces paradoxus

A DNA fragment homologous to the homothallism (HO) gene of Saccharomyces cerevisiae was isolated from Saccharomyces paradoxus and was found to contain an open reading frame that was 90.9% identical to the coding sequence of the S. cerevisiae HO gene. The putative HO gene was shown to induce diploidization in a heterothallic haploid strain from S. cerevisiae. Phylogenetic analysis revealed that the coding and 5'-upstream regulatory regions from five Saccharomyces sensu stricto HO genes have coevolved, and that S. paradoxus is phylogenetically closer to S. cerevisiae than to S. bayanus. Finally, heterothallic haploid strains were isolated from the original homothallic type strain of S. paradoxus by disrupting the S. paradoxus HO gene with the S. cerevisiae URA3 gene.     

The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxus

Little information is presently available on the factors promoting genetic divergence in eukaryotic microbes. We studied the spatial distribution of genetic variation in Saccharomyces paradoxus, the wild relative of Saccharomyces cerevisiae, from the scale of a few centimetres on individual oak trees to thousands of kilometers across different continents. Genealogical analysis of six loci shows that isolates from Europe form a single recombining population, and within this population genetic differentiation increases with physical distance. Between different continents, strains are more divergent and genealogically independent, indicating well-differentiated lineages that may be in the process of speciation. Such replicated populations will be useful for studies in population genomics.     

Autecological investigations on marine diatoms. I. Experimental results in biogeographical studies

Summary The upper and/or lower temperature limits for growth of 43 marine diatoms have been determined. According to the extent of the temperature tolerance range for growth and its position within the ecological relevant temperature range, the diatoms were divided in oligo-eurytherm (cold-, temperate-, warm-), meso-eurytherm (cold-, warm-) and eu-eurytherm species.The definition of the terms cosmopolites and circum-tropical could be enlarged, when the experimentai results and the distribution data from literature (19 distribution maps were combined.The results showed a significant relation between lower temperature limit for growth and both volume and cell size. In this way the lower temperature limit influences the size distribution of the phytoplankton in the oceans. Large diatoms are absent in cold water because of their high lower temperature limit for growth.The use of experimental results to reduce the number of sampling stations for determination of geographical distribution of diatoms, is discussed.     

A new set of DNA macrochips for the yeast Saccharomyces cerevisiae: features and uses.

The yeast Saccharomyces cerevisiae has been widely used for the implementation of DNA chip technologies. For this reason and due to the extensive use of this organism for basic and applied studies, yeast DNA chips are being used by many laboratories for expression or genomic analyses. While membrane arrays (macroarrays) offer several advantages, for many laboratories they are not affordable. Here we report that a cluster of four Spanish molecular-biology yeast laboratories, with relatively small budgets, have developed a complete set of probes for the genome of S. cerevisiae. These have been used to produce a new type of macroarray on a nylon surface. The macroarrays have been evaluated and protocols for their use have been optimized.     

Ecological studies of Legionella species. I. Viable counts of Legionella pneumophila in cooling tower water

The occurrence and viable counts of Legionella pneumophila in acid-treated water samples of 62 cooling towers on the main island of Japan were determined by inoculating them onto plates of Wadowsky-Yee-Okuda (WYO) agar medium. WYO plate cultures of 39 (63%) of the samples yielded L. pneumophila with viable counts ranging from 10 to 10(4) colony-forming units per 100 ml. Of the L. pneumophila isolates, 157 were serologically identified as serogroup 1, and the remaining 21 were agglutinated by serogroup 3 (2 strains) and serogroup 6 (19 strains) antisera. In each culture-positive water sample, the pH and the number of other bacteria were found not be statistically significantly correlated with the viable counts of L. pneumophila. However, a higher rate of recovery of L. pneumophila was obtained with the water samples with a smaller number of other bacteria. Practical use of commercially available antialgal or antimicrobial agents was found not to be significantly effective for controlling the occurrence and growth of L. pneumophila in cooling tower water.     

Saccharomyces paradoxus and Saccharomyces cerevisiae are associated with exudates of North American oaks

Genetic hybridization and karyotypic analyses revealed the biological species Saccharomyces paradoxus and Saccharomyces cerevisiae in exudates from North American oaks for the first time. In addition, two strains collected from elm flux and from Drosophila by Phaff in 1961 and 1952 were reidentified as S. paradoxus. Each strain studied showed a unique profile of chromosomal hybridization with a probe for the retrotransposable element Ty1. The wild distribution of natural Saccharomyces sensu stricto yeasts is discussed.     

The interaction of Saccharomyces paradoxus with its natural competitors on oak bark

The natural history of the model yeast Saccharomyces cerevisiae is poorly understood and confounded by domestication. In nature, S. cerevisiae and its undomesticated relative S. paradoxus are usually found on the bark of oak trees, a habitat very different from wine or other human fermentations. It is unclear whether the oak trees are really the primary habitat for wild yeast, or whether this apparent association is due to biased sampling. We use culturing and high‐throughput environmental sequencing to show that S. paradoxus is a very rare member of the oak bark microbial community. We find that S. paradoxus can grow well on sterile medium made from oak bark, but that its growth is strongly suppressed when the other members of the community are present. We purified a set of twelve common fungal and bacterial species from the oak bark community and tested how each affected the growth of S. paradoxus in direct competition on oak bark medium at summer and winter temperatures, identifying both positive and negative interactions. One Pseudomonas species produces a diffusible toxin that suppresses S. paradoxus as effectively as either the whole set of twelve species together or the complete community present in nonsterilized oak medium. Conversely, one of the twelve species, Mucilaginibacter sp., had the opposite effect and promoted S. paradoxus growth at low temperatures. We conclude that, in its natural oak tree habitat, S. paradoxus is a rare species whose success depends on the much more abundant microbial species surrounding it.     

The functional biogeography of species: biogeographical species roles of birds in Wallacea and the West Indies

Biogeographical systems can be analyzed as networks of species and geographical units. Within such a biogeographical network, individual species may differ fundamentally in their linkage pattern, and therefore hold different topological roles. To advance our understanding of the relationship between species traits and large‐scale species distribution patterns in archipelagos, we use a network approach to classify birds as one of four biogeographical species roles: peripherals, connectors, module hubs, and network hubs. These roles are based upon the position of species within the modular network of islands and species in Wallacea and the West Indies. We test whether species traits – including habitat requirements, altitudinal range‐span, feeding guild, trophic level, and body length – correlate with species roles. In both archipelagos, habitat requirements, altitudinal range‐span and body length show strong relations to species roles. In particular, species that occupy coastal‐ and open habitats, as well as habitat generalists, show higher proportions of connectors and network hubs and thus tend to span several biogeographical modules (i.e. subregions). Likewise, large body size and a wide altitudinal range‐span are related to a wide distribution on many islands and across several biogeographical modules. On the other hand, species restricted to interior forest are mainly characterized as peripherals and, thus, have narrow and localized distributions within biogeographical modules rather than across the archipelago‐wide network. These results suggest that the ecological amplitude of a species is highly related to its geographical distribution within and across bio geographical subregions and furthermore supports the idea that large‐scale species distributions relate to distributions at the local community level. We finally discuss how our biogeographical species roles may correspond to the stages of the taxon cycle and other prominent theories of species assembly.     

Existence of cerebroside in Saccharomyces kluyveri and its related species

Sphingolipids are ubiquitous compounds derived from ceramide that consist of a sphingoid long-chain base with a 2-amino group amide linked to fatty acid and are present in the membranes of many organisms. As a principal sphingolipid, Saccharomyces cerevisiae contains a free ceramide and its inositol-phosphorylated derivatives (acidic types) but not a neutral glycosylated ceramide, glucosylceramide (cerebroside), which usually appears in eukaryotic cells. When 31 strains accepted in the genera Saccharomyces, Torulaspora, Zygosaccharomyces, and Kluyveromyces were analyzed for sphingolipids, cerebrosides were found in S. kluyveri, Z. cidri, Z. fermentati, K. lactis, K. thermotolerans, and K. waltii. The cerebrosides of S. kluyveri and K. lactis included 9-methyl 4-trans, 8-trans-sphingadienine and its putative metabolic intermediates. A unique characteristic of S. kluyveri was the presence of a trihydroxy sphingoid base, which rarely occurs in fungal cerebrosides. A polymerase chain reaction with primers targeted to the glucosylceramide synthase gene of other microorganisms amplified the fragments of the expected size from S. kluyveri and K. lactis and further extended to the adjacent regions. The presumed protein of S. kluyveri had 54.4% similarity to that of K. lactis, higher than the glucosylceramide synthases from Candida albicans, Pichia pastoris, and other organisms. From these observations, the divergence of S. kluyveri from the lineage of K. lactis in their evolution is discussed.     

The purification and characterization of DNA topoisomerases I and II of the yeast Saccharomyces cerevisiae

The ATP-independent type I and the ATP-dependent type II DNA topoisomerase of the yeast Saccharomyces cerevisiae have been purified to near homogeneity, and the purification procedures are reported. Both purified topoisomerases are single subunit enzymes with monomer weights of Mr = 90,000 and 150,000 for the type I and type II enzyme, respectively. Sedimentation and gel filtration data suggest that the type I enzyme is monomeric and the type II enzyme is dimeric. Similar to other purified eukaryotic topoisomerases, the yeast type I enzyme does not require a divalent cation for activity, but is stimulated 10-20-fold in the presence of 7-10 mM Mg(II) or Ca(II). Mn(II) is about 25% as efficient as Mg(II) in this stimulation but Co(II) is inhibitory. The yeast type II topoisomerase has an absolute requirement for a divalent cation: Mg(II) is the most effective, whereas Mn(II), Ca(II), or Co(II) supports the reaction to a lesser extent. The type II enzyme also requires ATP or dATP; the nonhydrolyzable ATP analogues adenylyl imidodiphosphate and adenylyl (beta,gamma-methylene)diphosphonate are potent inhibitors. Both yeast topoisomerases are completely inhibited by N-ethylmaleimide at 0.5 mM. In addition, the type II enzyme, but not the type I enzyme, is inhibited to various extents by coumermycin, ethidium, and berenil. Both topoisomerases are nuclear enzymes; no topoisomerase specific to mitochondria has been detected.     

Assessing biogeographical relationships of ecologically related species using favourability functions: a case study on British deer

Aim Using six free‐living deer species in Great Britain as a case study, we studied biogeographical relationships of ecologically related species composed of both native and introduced species. Location Great Britain. Methods  We modelled the environmental favourability for the deer species using variables related with spatial location, climate, topography, human disturbances and habitat structure. Favourability values of each pair of native (naturalized)‐introduced species were used to estimate the fuzzy overlap index (FOvI) as a measure of overall similarity between the environmental requirements for the species in Great Britain. The absolute local overlap values (FOvI‐L) were also used to measure the degree to which a given location was favourable simultaneously for each pair of species. We assessed the trends of species favourability across a range defined by the absolute local overlap values and studied the shape of the obtained curves since they informs us about the favourability balance between the studied species. Results Muntjac and Chinese water deer attained higher favourability values than native species in localities with intermediate values of FOvI‐L (a reduced number in the study area), suggesting that if competitive relationships were established in these localities the introduced deer species may have some advantages over natives. Sika deer only achieved higher values than fallow deer in those localities clearly unfavourable for the naturalized species. Our analyses predicted that fallow deer will be less affected by the introduced deer species than native species. Main conclusions We developed an approach based on the favourability function to describe biogeographical relationships between species, natives and introduced and to assess from a biogeographical perspective if introduced species could pose a competitive risk to natives. Although the results of present analyses do not conclusively demonstrate competitive exclusion, they provide directional hypotheses that can be tested in experimental field and laboratory studies.     

Immunologically related proteins in cytoplasmic and mitochondrial ribosomes of yeast Saccharomyces cerevisiae

Summary Ribosomal proteins from the cytoplasm and mitochondria of the yeast Saccharomyces cerevisiae were compared by immunoblotting techniques. Antibodies raised against cytoplasmic ribosomal proteins cross-react with five mitochondrial ribosomal proteins, four of which are located in the large and one in the small mitochondrial subunits. The possible existence of common ribosomal proteins for cytoplasmic and mitochondrial ribosomes is discussed.Abbreviations cyto cytoplasmic - mito mitochondrial     

Sympatric natural Saccharomyces cerevisiae and S. paradoxus populations have different thermal growth profiles

Saccharomyces cerevisiae and its close congener S. paradoxus are typically indistinguishable by the phenotypic criteria of classical yeast taxonomy, but they are evolutionarily distinct as indicated by hybrid spore inviability and genomic sequence divergence. Previous work has shown that these two species coexist in oak-associated microhabitats at natural woodland sites in North America. Here, we show that sympatric populations of S. cerevisiae and S. paradoxus from a single natural site are phenotypically differentiated in their growth rate responses to temperature. Our main finding is that the S. cerevisiae population exhibits a markedly higher growth rate at 37 degrees C than the S. paradoxus population; we also find possible differences in growth rate between these populations at two lower temperatures. We discuss the implications of our results for the coexistence of these yeasts in natural environments, and we suggest that thermal growth response may be an evolutionarily labile feature of these organisms that could be analyzed using genomic approaches.