Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts

The combination of ecological diversity with genetic and experimental tractability makes Drosophila a powerful model for the study of animal-associated microbial communities. Despite the known importance of yeasts in Drosophila physiology, behavior, and fitness, most recent work has focused on Drosophila-bacterial interactions. In order to get a more complete understanding of the Drosophila microbiome, we characterized the yeast communities associated with different Drosophila species collected around the world. We focused on the phylum Ascomycota because it constitutes the vast majority of the Drosophila-associated yeasts. Our sampling strategy allowed us to compare the distribution and structure of the yeast and bacterial communities in the same host populations. We show that yeast communities are dominated by a small number of abundant taxa, that the same yeast lineages are associated with different host species and populations, and that host diet has a greater effect than host species on yeast community composition. These patterns closely parallel those observed in Drosophila bacterial communities. However, we do not detect a significant correlation between the yeast and bacterial communities of the same host populations. Comparative analysis of different symbiont groups provides a more comprehensive picture of host-microbe interactions. Future work on the role of symbiont communities in animal physiology, ecological adaptation, and evolution would benefit from a similarly holistic approach.     

Yeast communities of <Emphasis Type="Italic">Formica aquilonia</Emphasis> colonies

Yeast abundance and species diversity in the colonies of Formica aquilonia ants in birch–pine grass forest near Novosibirsk, Russia, were studied. The average yeast number in the anthill material was 10³–10⁴ CFU/g, reaching 10⁵ CFU/g in the hatching chambers. Typical litter species (Trichosporon moniliiforme and Cystofilobasidium capitatum) were predominant in soil and litter around the anthills. Apart from these species, ascomycete species of the family Debaryomycetaceae, Debaryomyces hansenii, and Schwanniomyces vanrijiae were predominant in the anthill material. Yeast population of the ant’ bodies consisted exclusively of the members of the last two species. Thus, highly specific yeast communities formed in the colonies of Formica aquilonia ants differ from the communities of surrounding soil. These differences are caused by environment-forming activity of the ants.     

Influence of <Emphasis Type="Italic">Lumbricus terrestris</Emphasis> earthworms on the structure of the yeast community of forest litter

The taxonomic structure of yeast communities was studied in forest litter and soil, as well as in substrates transformed by the activity of Lumbricus terrestris earthworms (leaves in heaps, the gut contents, and coproliths). The activity of L. terrestris has a weak effect on the total yeast abundance but results in substantial changes in the community taxonomic composition. The share of ascomycetous yeasts is significantly higher in the substrates associated with the activity of earthworms. The teleomorphic ascomycetes Williopsis saturnus were isolated from the gut contents. The effect of earthworms on the composition of the yeast community in the process of forest litter destruction is more pronounced than seasonal changes.     

Multiple increase in productivity of the yeast at reducing the fraction of D<Subscript>2</Subscript>O in water

We found a two-fold increase in the productivity of baker’s yeast grown on a nutrient mixture prepared in light water with a D₂O content (127 ppm) smaller than in the distilled water (150 ppm). The number of water monomers that provides the biosynthetic activity (water transport through membrane channels) of yeast cells with an increased CO₂ yield was determined for the first time. We established that the selectivity of cell membrane channels in water of different composition depends not only on the motion of ortho-and para-spin H₂O isomers in solution, as was shown earlier, but also on the concentration of D₂O.     

Community Perceptions of the Crop-Feeding Buton Macaque (<Emphasis Type="Italic">Macaca ochreata brunnescens</Emphasis>): an Ethnoprimatological Study on Buton Island,Sulawesi

Human–wildlife overlap is increasing worldwide as a result of agricultural expansion. This can reduce human tolerance of wildlife, especially if wildlife threatens human food sources. The greatest threat to the declining populations of the endemic Buton macaque (Macaca ochreata brunnescens) is habitat destruction, but as a common crop-feeding species, there is also an additional risk of retaliation killings from farmers. Finding means of reducing this risk will thus help secure the long-term future of this range-restricted subspecies. Here, we investigate variability in farmers’ perceptions of primate crop-feeding and mitigation techniques in three farming communities on Buton Island, Indonesia, which differ in wealth and agricultural resources. We employ a mixed methodology, collecting qualitative social data from focus groups and quantitative observational data to measure macaque crop-feeding occurrences. Our findings indicate that the least wealthy community used lethal control methods more frequently than the comparatively wealthier communities, even when the crop-feeding problem was less severe. The least wealthy community also expressed high levels of fear of macaques, and had the most negative perceptions of them. This community also had no knowledge of the macaques’ conservation status or their ecological roles. We recommend that efforts to protect Buton macaques focus on education and the use of effective nonlethal mitigation techniques, such as electric fencing. We also suggest that initiatives to support such measures may be most effectively directed toward communities with relatively low economic wealth and high reliance on subsistence agriculture, especially where crop-feeding wildlife is feared, even when such communities do not experience the highest losses from crop-feeding wildlife.     

Diversity and biogeographical patterns of yeast communities in Antarctic,Patagonian and tropical lakes

We investigated the distribution patterns of yeast communities in freshwater lakes along a latitudinal gradient in order to evaluate yeast biogeography at intercontinental (501–8000 km), regional (0–500 km) and local (0–1 km) geographical scales. We identified 285 yeast isolates belonging to 64 species based on sequence analysis of the ITS-5.8S region and the D1/D2 domains of the large subunit of rRNA genes. Distance decay analysis showed a significant negative slope curve at the intercontinental scale. At the intercontinental and regional scales, the dissimilarity of the yeast communities was correlated with geographical distance, with community similarity decreasing with increasing distance. The physiological profiles of the yeast communities from tropical and Patagonian lakes were similar but were different from those of Antarctic lakes. This is the first report of latitudinal patterns of lake yeast diversity along a gradient extending from Antarctic to tropical environments.     

Massive isolation and identification of <Emphasis Type="Italic">Saccharomyces paradoxus</Emphasis> yeasts from plant phyllosphere

Year-round studies of epiphytic yeast communities revealed that the number of ascosporogenous yeasts of the genus Saccharomyces inhabiting living and decaying leaves of some plants increased considerably in certain short periods (at the beginning of summer and in winter). Massive isolation of saccharomycetes was performed from 11 plant species; earlier, these yeasts had been revealed mainly in sugar-rich substrates. The isolates were identified as Saccharomyces paradoxus based on their physiological properties and RELP analysis of 5.8S-ITS. Possible reasons for short-term increases in the number of saccharomycetes in plant phyllosphere are discussed.     

Indigenous yeast communities in the environment of “Rovello bianco” grape variety and their use in commercial white wine fermentation

The indigenous yeast communities associated with several vineyard habitats were analysed. Wild yeasts were isolated, differentiated at strain level and identified. A phylogenetic tree based on partial 26S rRNA genes was constructed. The strains were characterized and the indigenous Saccharomyces cerevisiae GR1 was then used to carry out a vinification process and compared with a commercial yeast. Wines obtained were subjected to chemical and sensory analysis. The comparison between the two products highlighted differences due to the fermenting strains employed. The vineyard environment was found to strongly influence the composition of yeast communities, thus, confirming the theory of ‘terroir’ on the expression of wines. Moreover, vineyard inhabiting birds were in part responsible for the dissemination of fermentative yeasts during their feeding activities.     

Effects of habitat conditions at hatching time on growth history of offspring European anchovy, <Emphasis Type="Italic">Engraulis encrasicolus</Emphasis>, in the Central Mediterranean Sea

Species distributions are structured by regional and local determinants, which operate at multiple spatial and temporal scales. The purpose of our work was to distinguish the relative roles of local variables, climate, geographical location and post glaciation condition (i.e., delineation between supra- and subaquatic lakes during the post-glacial Ancylus Lake) in explaining variation in macrophyte community composition of all taxa, helophytes and hydrophytes. In addition, we investigated how these four explanatory variable groups affected macrophyte strategy groups based on Grime’s classification. Using partial linear regression and variation partitioning, we found that macrophyte communities are primarily filtered by local determinants together with regional characteristics at the studied spatial scale. We further evidenced that post glaciation condition indirectly influenced on local water quality variables, which in turn directly contributed to the macrophyte communities. We thus suggest that regional determinants interact with local-scale abiotic factors in explaining macrophyte community patterns and examining only regional or local factors is not sufficient for understanding how aquatic macrophyte communities are structured locally and regionally.     

Evaluation of yeasts in gel larval diet for Queensland fruit fly,Bactrocera tryoni

Queensland fruit fly, Bactrocera tryoni (“Q‐fly”), is Australia’s most economically important insect pest of horticultural and commercial crops especially in the eastern regions. The sterile insect technique (SIT) has been adopted as an environmentally benign and sustainable approach for management of Q‐fly outbreaks. High‐performance larval diets are required to produce the millions of flies needed each week for SIT. Yeast products contribute amino acids (protein) to fruit fly larval diets, as well as carbohydrate, fat and micronutrients, but there can be substantial variation in the nutritional composition and suitability of yeast products for use in larval diets. Gel larval diets have recently been developed for large‐scale rearing of Q‐fly for SIT, and composition of these diets requires optimization for both performance and cost, including choice of yeast products. We assessed performance of Q‐flies reared on gel larval diets that contained debittered brewer’s yeast (Lallemand LBI2240), hydrolysed yeast (Lallemand FNILS65), inactivated brewer’s yeast (Lallemand LBI2250) and inactivated torula yeast (Lallemand 2160‐50), including blends. Q‐flies performed poorly when reared on diets containing only or mostly hydrolysed yeast in terms of pupal number, pupal weight and percentage of fliers. Performance was also poor on diets containing high proportions of torula yeast. Overall, debittered brewer’s yeast is recommended as the best option for Q‐fly gel larval diet, as it is cheap, readily available, and produces flies with good performance in quality control assays. Inactivated brewer’s yeast produced flies of comparable quality with only a modest increase in cost and would also serve as an effective alternative.     

The ecology of the yeast flora in necroticOpuntia cacti and of associatedDrosophila in Australia

A survey was made of the yeast communities isolated from necrotic tissue of 4 species of prickly-pear cacti (Opuntia stricta, O. tomentosa, O. monacantha, andO. streptacantha) which have colonized in Australia. Yeast communities were sampled from a number of localities and at different times. Cactus specific yeasts accounted for 80% of the total isolates, and the 3 most common species contributed 63% of the total. Comparisons of the species compositions of the yeast communities indicated that the differences among communities were greater betweenOpuntia species than between different localities within a single cactus species, and also that differences between years were greater than average differences between localities within years. Multivariate statistical tests of association between yeast community and physical features of rots indicated that temperature, pH, and age of rot all exerted some influence on the structure of the yeast community. Similar analyses involvingDrosophila species inhabiting these cactus rots suggested the existence of complex associations betweenDrosophila community, yeast community, and physical and chemical attributes of the cactus necroses.     

Bacterial community succession in a high‐altitude subarctic glacier foreland is a three‐stage process

Alpine glaciers are retreating rapidly, exposing foreland minerals, which develop into soils. Bacterial communities in glacier forelands exhibit high rates of turnover and undergo dramatic shifts in composition within the first 50 years after deglaciation, followed by relative stabilization and convergence. This period of microbial development occurs simultaneously with plant colonization in most systems; thus, it remains unclear whether the changes in the bacterial communities occur primarily as the result of edaphic, climatic or biotic factors. We examined bacterial community structure along two replicate chronosequences within the glacial foreland of Duke River Glacier, Yukon, Canada. This foreland is estimated to include >200 years of bare soils before an appreciable grassline, likely due to the high latitude and altitude of the glacier. This enabled us to examine bacterial community development prior to plant colonization over a longer period than previous studies. We observed three successional groups in the chronosequence: (i) an ‘early’ group in soils of less than approximately 50 years since deglaciation; (ii) an ‘intermediate’ group within bare soils, after the early period but before the grassline, containing communities with a relatively high degree of variability in composition; and (iii) a ‘grassline’ group in soils collected after plant colonization with higher diversity but lower age‐group variability in community composition. These findings suggest rapid replacement and addition of species better adapted to glacier foreland conditions followed by slower community shifts over the next 150 years and, finally, indications of a possible response to plant colonization.     

Saprophagous insect larvae,Drosophila melanogaster,profit from increased species richness in beneficial microbes

Female fruit flies, Drosophila melanogaster, lay their eggs on decaying plant material. Foraging fly larvae strongly depend on the availability of dietary microbes, such as yeasts, to reach the adult stage. In contrast, strong interference competition with filamentous fungi can cause high mortality among Drosophila larvae. Given that many insects are known for employing beneficial microbes to combat antagonistic ones, we hypothesized that fly larvae engaged in competition with the noxious mould Aspergillus nidulans benefit from the presence of dietary yeast species, especially when they are associated with increasingly species rich yeast communities (ranging from one to six yeast species per community). On a nutrient‐limited fruit substrate infested with A. nidulans, both larval survival and development time were positively affected by more diverse yeast communities. On a mould‐free fruit substrate, merely larval development but not survival was found to be affected by increasing species richness of dietary yeasts. Not only yeast diversity had an effect on D. melanogaster life‐history traits, but also the identity of the yeast combinations. These findings demonstrate the importance of the structure and diversity of microbial communities in mutualistic animal–microbe interactions.     

Characterization of yeast groupings in the phyllosphere of <Emphasis Type="Italic">Sphagnum</Emphasis> mosses

Significant differences were revealed in the taxonomic structure of the epiphytic yeast communities formed on Sphagnum mosses and on the leaves of vascular plants. On mosses, low abundance of red yeasts was found (the most typical epiphytes on vascular plant leaves), along with a relatively high content and diversity of nonpigmented dimorphic basidiomycetes related to the order Leucosporidiales. The species composition of epiphytic yeasts from mosses is different from that of both forest and meadow grasses and of the parts of vascular plants submerged in the turf. The specific composition of the Sphagnum mosses yeast community is probably determined by the biochemical characteristics of this environment, rather than by the hydrothermal regime in the turf.     

Testing a ‘genes‐to‐ecosystems’ approach to understanding aquatic–terrestrial linkages

A ‘genes‐to‐ecosystems’ approach has been proposed as a novel avenue for integrating the consequences of intraspecific genetic variation with the underlying genetic architecture of a species to shed light on the relationships among hierarchies of ecological organization (genes → individuals → communities → ecosystems). However, attempts to identify genes with major effect on the structure of communities and/or ecosystem processes have been limited and a comprehensive test of this approach has yet to emerge. Here, we present an interdisciplinary field study that integrated a common garden containing different genotypes of a dominant, riparian tree, Populus trichocarpa, and aquatic mesocosms to determine how intraspecific variation in leaf litter alters both terrestrial and aquatic communities and ecosystem functioning. Moreover, we incorporate data from extensive trait screening and genome‐wide association studies estimating the heritability and genes associated with litter characteristics. We found that tree genotypes varied considerably in the quality and production of leaf litter, which contributed to variation in phytoplankton abundances, as well as nutrient dynamics and light availability in aquatic mesocosms. These ‘after‐life’ effects of litter from different genotypes were comparable to the responses of terrestrial communities associated with the living foliage. We found that multiple litter traits corresponding with aquatic community and ecosystem responses differed in their heritability. Moreover, the underlying genetic architecture of these traits was complex, and many genes contributed only a small proportion to phenotypic variation. Our results provide further evidence that genetic variation is a key component of aquatic–terrestrial linkages, but challenge the ability to predict community or ecosystem responses based on the actions of one or a few genes.     

Dynamic changes in microbiota and mycobiota during spontaneous ‘Vino Santo Trentino’ fermentation

Vino Santo is a sweet wine produced from late harvesting and pressing of Nosiola grapes in a small, well‐defined geographical area in the Italian Alps. We used metagenomics to characterize the dynamics of microbial communities in the products of three wineries, resulting from spontaneous fermentation with almost the same timing and procedure. Comparing fermentation dynamics and grape microbial composition, we show a rapid increase in a small number of wine yeast species, with a parallel decrease in complexity. Despite the application of similar protocols, slight changes in the procedures led to significant differences in the microbiota in the three cases of fermentation: (i) fungal content of the must varied significantly in the different wineries, (ii) Pichia membranifaciens persisted in only one of the wineries, (iii) one fermentation was characterized by the balanced presence of Saccharomyces cerevisiae and Hanseniaspora osmophila during the later phases. We suggest the existence of a highly winery‐specific ‘microbial‐terroir’ contributing significantly to the final product rather than a regional ‘terroir’. Analysis of changes in abundance during fermentation showed evident correlations between different species, suggesting that fermentation is the result of a continuum of interaction between different species and physical–chemical parameters.     

Competition dynamics in long‐term propagations of Schizosaccharomyces pombe strain communities

Experimental evolution studies with microorganisms such as bacteria and yeast have been an increasingly important and powerful tool to draw long‐term inferences of how microbes interact. However, while several strains of the same species often exist in natural environments, many ecology and evolution studies in microbes are typically performed with isogenic populations of bacteria or yeast. In the present study, we firstly perform a genotypic and phenotypic characterization of two laboratory and eight natural strains of the yeast Schizosaccharomyces pombe. We then propagated, in a rich resource environment, yeast communities of 2, 3, 4, and 5 strains for hundreds of generations and asked which fitness‐related phenotypes—maximum growth rate or relative competitive fitness—would better predict the outcome of a focal strain during the propagations. While the strain''s growth rates would wrongly predict long‐term coexistence, pairwise competitive fitness with a focal strain qualitatively predicted the success or extinction of the focal strain by a simple multigenotype population genetics model, given the initial community composition. Interestingly, we have also measured the competitive fitness of the ancestral and evolved communities by the end of the experiment (≈370 generations) and observed frequent maladaptation to the abiotic environment in communities with more than three members. Overall, our results aid establishing pairwise competitive fitness as good qualitative measurement of long‐term community composition but also reveal a complex adaptive scenario when trying to predict the evolutionary outcome of those communities.     

Community Structure of Yeast Fungi in Forest Biogeocenoses

The results of longterm studies of yeasts inhabiting soil, plant surfaces, and plant residues in typical subboreal forests of the European part of Russia are summarized. The cell number and species diversity of yeast communities in the array of substrates corresponding to succession stages in plant residue decomposition are shown to steadily decline. Each stage is characterized by its specific set of dominating species. The yeast diversity in forest biogeocenoses is shown to surpass that in other geographic zones. This manifests itself in a greater number of species occurring in similar arrays of substrates, in the absence of conspicuous dominants on the biogeocenotic level, and in a higher differentiation of the yeast population with respect to its habitat type. The forest yeast populations are also characterized by a high diversity of yeasts of ascomycetous affinity and of the anamorphic stages of Taphrinales and Tremellales and by the presence of typical pedobiont species (except Lipomyces spp.).     

Analysis of the community structure of yeasts associated with the decaying stems of cactus. II.Opuntia species

A survey was made of yeast species associated with the decaying pads of 3 prickly pear cacti (Opuntia phaeacantha, O. ficus-indica, andO. lindheimeri) in Arizona and Texas. Yeast communities from 12 localities were compared among localities, amongOpuntia species, and with previous data on yeast communities associated with columnar cacti. The results indicate thatOpuntia necroses contain relatively more yeast species with broader physiological abilities in their communities than columnar necroses. It is argued that differences in chemistry of the opuntias and columnar forms in concert with the insect vectors specific for these cacti account for the differences in yeast community structure. It is further hypothesized that the differences in yeast community structure have been important in the evolution and maintenance of species diversity forDrosophila species which live in the decaying stems or cladodes of various cacti. Most of the yeast community evolution in the cacti is postulated to have proceeded by evolution in situ and not by additions and replacements from outside of the system.