The Lipomycetaceae, a model family for phylogenetic studies

Walt, J. P. van der

doi:10.1007/bf00572591

Cited by 15 publications

(5 citation statements)

References 16 publications

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“…By using two more oligotrophic and nitrogen-depleted media (TMV and Brown's agar), only up to six species were be isolated. Nitrogen deficient media were previously used for the isolation of the members of the genus Lipomyces because these soil yeasts have the rare ability among yeasts to utilize nitrogen from heterocyclic compounds, such as imidazole, pyrimidine, and pyrazine [33] , [57] . These compounds were consequently included as a nitrogen source in selective media to isolate Lipomyces yeasts from soils [31] , [58] .…”

Section: Discussionmentioning

confidence: 99%

Species Accumulation Curves and Incidence-Based Species Richness Estimators to Appraise the Diversity of Cultivable Yeasts from Beech Forest Soils

2011

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BackgroundYeast-like fungi inhabit soils throughout all climatic zones in a great abundance. While recent estimations predicted a plethora of prokaryotic taxa in one gram of soil, similar data are lacking for fungi, especially yeasts.Methodology/Principal FindingsWe assessed the diversity of soil yeasts in different forests of central Germany using cultivation-based techniques with subsequent identification based on rDNA sequence data. Based on experiments using various pre-cultivation sample treatment and different cultivation media we obtained the highest number of yeasts by analysing mixed soil samples with a single nutrient-rich medium. Additionally, several species richness estimators were applied to incidence-based data of 165 samples. All of them predicted a similar range of yeast diversity, namely 14 to 16 species. Randomized species richness curves reached saturation in all applied estimators, thus indicating that the majority of species is detected after approximately 30 to 50 samples analysed.Conclusions/SignificanceIn this study we demonstrate that robust species identification as well as mathematical approaches are essential to reliably estimate the sampling effort needed to describe soil yeast communities. This approach has great potential for optimisation of cultivation techniques and allows high throughput analysis in the future.

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Section: Discussionmentioning

confidence: 99%

Species Accumulation Curves and Incidence-Based Species Richness Estimators to Appraise the Diversity of Cultivable Yeasts from Beech Forest Soils

2011

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“…Species frequently found in soil are able to grow in media with low concentrations of nutrients (Babjeva & Gorin, 1987;Kimura et al, 1998;Vishniac, 1983). In particular, nitrogen oligotrophy is a widespread adaptation of yeasts, which enables them to colonize diverse substrates such as plant surfaces (reviewed by Fonseca & Inácio, 2006), tree fluxes (Golubev, Babjeva, & Novik, 1977) and soils (Botha, 2011 and pyrazine (LaRue & Spencer, 1968;van der Walt, 1992;Cornelissen, Botha, Conradie, & Wolfaardt, 2003). Recent studies showed that the diversity of yeasts growing on imidazole is larger and includes both asco-and basidiomycetes (Cornelissen et al, 2003;Yurkov et al, 2011;Yurkov, Wehde, et al, 2016).…”

Section: Yeast Phenotypesmentioning

confidence: 99%

Yeasts of the soil – obscure but precious

Yurkov

2018

Yeast

129

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Pioneering studies performed in the nineteenth century demonstrated that yeasts are present in below‐ground sources. Soils were regarded more as a reservoir for yeasts that reside in habitats above it. Later studies showed that yeast communities in soils are taxonomically diverse and different from those above‐ground. Soil yeasts possess extraordinary adaptations that allow them to survive in a wide range of environmental conditions. A few species are promising sources of yeast oils and have been used in agriculture as potential antagonists of soil‐borne plant pathogens or as plant growth promoters. Yeasts have been studied mainly in managed soils such as vineyards, orchards and agricultural fields, and to a lesser extent under forests and grasslands. Our knowledge of soil yeasts is further biased towards temperate and boreal forests, whereas data from Africa, the Americas and Asia are scarce. Although soil yeast communities are often species‐poor in a single sample, they are more diverse on the biotope level. Soil yeasts display pronounced endemism along with a surprisingly high proportion of currently unidentified species. However, like other soil inhabitants, yeasts are threatened by habitat alterations owing to anthropogenic activities such as agriculture, deforestation and urbanization. In view of the rapid decline of many natural habitats, the study of soil yeasts in undisturbed or low‐managed biotopes is extremely valuable. The purpose of this review is to encourage researchers, both biologists and soil scientists, to include soil yeasts in future studies.

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“…In contrast to yeast species from the other major clades, it appears that there is no direct positive correlation between model similarity and trait similarity for yeast species from Lipomycetaceae , while the related model similarity is in the range of 0.87–0.96 and trait similarity is in the range of 0.40–0.89. When examining the environmental origins of the yeast species from Lipomycetaceae , it has been reported that species from this major clade had a widespread distribution [ 31 ] and could grow in the soil or in association with insects. Therefore, despite maintaining similar metabolic network structure, due to the close evolutionary distance, we speculated that the distinct growth environments may contribute to the trait variation found in some yeast species.…”

Section: Resultsmentioning

confidence: 99%

A Pan-Draft Metabolic Model Reflects Evolutionary Diversity across 332 Yeast Species

Kerkhoven

Nielsen

2022

Biomolecules

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Yeasts are increasingly employed in synthetic biology as chassis strains, including conventional and non-conventional species. It is still unclear how genomic evolution determines metabolic diversity among various yeast species and strains. In this study, we constructed draft GEMs for 332 yeast species using two alternative procedures from the toolbox RAVEN v 2.0. We found that draft GEMs could reflect the difference in yeast metabolic potentials, and therefore, could be utilized to probe the evolutionary trend of metabolism among 332 yeast species. We created a pan-draft metabolic model to account for the metabolic capacity of every sequenced yeast species by merging all draft GEMs. Further analysis showed that the pan-reactome of yeast has a ”closed” property, which confirmed the great conservatism that exists in yeast metabolic evolution. Lastly, the quantitative correlations among trait similarity, evolutionary distances, genotype, and model similarity were thoroughly investigated. The results suggest that the evolutionary distance and genotype, to some extent, determine model similarity, but not trait similarity, indicating that multiple mechanisms shape yeast trait evolution. A large-scale reconstruction and integrative analysis of yeast draft GEMs would be a valuable resource to probe the evolutionary mechanism behind yeast trait variety and to further refine the existing yeast species-specific GEMs for the community.

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The Lipomycetaceae, a model family for phylogenetic studies

Cited by 15 publications

References 16 publications

Species Accumulation Curves and Incidence-Based Species Richness Estimators to Appraise the Diversity of Cultivable Yeasts from Beech Forest Soils

Species Accumulation Curves and Incidence-Based Species Richness Estimators to Appraise the Diversity of Cultivable Yeasts from Beech Forest Soils

Yeasts of the soil – obscure but precious

A Pan-Draft Metabolic Model Reflects Evolutionary Diversity across 332 Yeast Species

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