Candida kunwiensis sp. nov., a yeast associated with flowers and bumblebees

Identification of fungi isolated from commercial bumblebee colonies

Fungi can have important beneficial and detrimental effects on animals, yet our understanding of the diversity and function of most bee-associated fungi is poor. Over 2 million bumblebee colonies are traded globally every year, but the presence and transport of viable fungi within them is unknown. Here, we explored whether any culturable fungi could be isolated from commercial bumblebee nests. We collected samples of various substrates from within 14 bumblebee colonies, including the honey, honey cup wall, egg cup wall, and frass then placed them on agar and recorded any growth. Fungal morphotypes were then subcultured and their ITS region sequenced for identification. Overall, we cultured 11 fungal species from the various nest substrates. These included both pathogenic and non-pathogenic fungi, such as Aspergillus sp., Penicillium sp., and Candida sp. Our results provide the first insights into the diversity of viable fungal communities in commercial bumblebee nests. Further research is needed to determine if these fungi are unique to commercial colonies or prevalent in wild bumblebee nests, and crucially to determine the ecological and evolutionary implications of these fungi in host colonies.

Nature's Most Fruitful Threesome: The Relationship between Yeasts, Insects, and Angiosperms

The importance of insects for angiosperm pollination is widely recognized. In fact, approximately 90% of all plant species benefit from animal-mediated pollination. However, only recently, a third part player in this story has been properly acknowledged. Microorganisms inhabiting floral nectar, among which yeasts have a prominent role, can ferment glucose, fructose, sucrose, and/or other carbon sources in this habitat. As a result of their metabolism, nectar yeasts produce diverse volatile organic compounds (VOCs) and other valuable metabolites. Notably, some VOCs of yeast origin can influence insects' foraging behavior, e.g., by attracting them to flowers (although repelling effects have also been reported). Moreover, when insects feed on nectar, they also ingest yeast cells, which provide them with nutrients and protect them from pathogenic microorganisms. In return, insects serve yeasts as transportation and a safer habitat during winter when floral nectar is absent. From the plant's point of view, the result is flowers being pollinated. From humanity's perspective, this ecological relationship may also be highly profitable. Therefore, prospecting nectar-inhabiting yeasts for VOC production is of major biotechnological interest. Substances such as acetaldehyde, ethyl acetate, ethyl butyrate, and isobutanol have been reported in yeast volatomes, and they account for a global market of approximately USD 15 billion. In this scenario, the present review addresses the ecological, environmental, and biotechnological outlooks of this three-party mutualism, aiming to encourage researchers worldwide to dig into this field.

Diversity and Functions of Yeast Communities Associated with Insects

Following the concept of the holobiont, insect-microbiota interactions play an important role in insect biology. Many examples of host-associated microorganisms have been reported to drastically influence insect biological processes such as development, physiology, nutrition, survival, immunity, or even vector competence. While a huge number of studies on insect-associated microbiota have focused on bacteria, other microbial partners including fungi have been comparatively neglected. Yeasts, which establish mostly commensal or symbiotic relationships with their host, can dominate the mycobiota of certain insects. This review presents key advances and progress in the research field highlighting the diversity of yeast communities associated with insects, as well as their impact on insect life-history traits, immunity, and behavior.

Factors driving metabolic diversity in the budding yeast subphylum

Background

Associations between traits are prevalent in nature, occurring across a diverse range of taxa and traits. Individual traits may co-evolve with one other, and these correlations can be driven by factors intrinsic or extrinsic to an organism. However, few studies, especially in microbes, have simultaneously investigated both across a broad taxonomic range. Here we quantify pairwise associations among 48 traits across 784 diverse yeast species of the ancient budding yeast subphylum Saccharomycotina, assessing the effects of phylogenetic history, genetics, and ecology.

Results

We find extensive negative (traits that tend to not occur together) and positive (traits that tend to co-occur) pairwise associations among traits, as well as between traits and environments. These associations can largely be explained by the biological properties of the traits, such as overlapping biochemical pathways. The isolation environments of the yeasts explain a minor but significant component of the variance, while phylogeny (the retention of ancestral traits in descendant species) plays an even more limited role. Positive correlations are pervasive among carbon utilization traits and track with chemical structures (e.g., glucosides and sugar alcohols) and metabolic pathways, suggesting a molecular basis for the presence of suites of traits. In several cases, characterized genes from model organisms suggest that enzyme promiscuity and overlapping biochemical pathways are likely mechanisms to explain these macroevolutionary trends. Interestingly, fermentation traits are negatively correlated with the utilization of pentose sugars, which are major components of the plant biomass degraded by fungi and present major bottlenecks to the production of cellulosic biofuels. Finally, we show that mammalian pathogenic and commensal yeasts have a suite of traits that includes growth at high temperature and, surprisingly, the utilization of a narrowed panel of carbon sources.

Conclusions

These results demonstrate how both intrinsic physiological factors and extrinsic ecological factors drive the distribution of traits present in diverse organisms across macroevolutionary timescales.

Electronic supplementary material

The online version of this article (10.1186/s12915-018-0498-3) contains supplementary material, which is available to authorized users.

An atypical, pigment-producing Metschnikowia strain from a leukaemia patient

A yeast strain was isolated from the sputum sample of a leukaemia patient in the Spirito Santo Hospital of Pescara, Italy. The fungus produced a pigment that formed a reddish halo around colonies, and was identified and deposited as a Metschnikowia spp. (accession number IHEM 25107-GenBank accession number JQ921016) in the BCCM/IHEM collection of biomedical fungi and yeasts (Bruxelles, Belgium). Although the physiology of the strain was close to that of Metschnikowia sinensis, the D1/D2 sequence did not correspond to any previously described Metschnikowia species. Phylogeny of the genus Metschnikowia is complex and requires far more analysis. We present the first non-M. pulcherrima Metschnikowia spp. isolate recovered from a human, and emphasize the role of man as a transient carrier of environmental yeasts, the pathogenicity of which still needs to be defined.

Metschnikowia proteae sp. nov., a nectarivorous insect-associated yeast species from Africa

A collection of yeasts isolated from nectar of flowers of Protea caffra (Proteaceae) and associated scarab beetles (Atrichelaphinis tigrina, Cyrtothyrea marginalis, Trichostetha fascicularis and Heterochelus sp.) and drosophilid flies in South Africa, contained 28 isolates that could not be assigned to known species. Comparisons of the D1/D2 domains of the large subunit rRNA gene demonstrated the existence of three separate phylotypes with an affinity to the genus Metschnikowia and more specifically to the beetle-associated large-spored Metschnikowia clade. Twenty-six strains that had similar D1/D2 sequences were mixed in all pairwise combinations. They were found to mate and give rise to large asci typical of those in the clade. The name Metschnikowia proteae sp. nov. (type strain EBDT1Y1(T) = CBS 12522(T) = NRRL Y-48784(T); allotype strain EBDC2Y2 = CBS 12521 = NRRL Y-48785) is proposed to accommodate this novel species. The ecology of this novel yeast species is discussed in relation to its potential plant and insect host species. The additional two single strains isolated from Heterochelus sp. represent two novel undescribed species (Candida sp. 1 EBDM2Y3 and Candida sp. 2 EBDM8Y1). As these single strains are probably haploid mating types of Metschnikowia species, their description is deferred until the species are sufficiently well sampled to permit meaningful descriptions.

Species richness of yeast communities in floral nectar of southern Spanish plants

Floral nectar of insect-pollinated plants often contains dense yeast populations, yet little quantitative information exists on patterns and magnitude of species richness of nectar-dwelling yeasts in natural plant communities. This study evaluates yeast species richness at both the plant community and plant species levels in a montane forest area in southern Spain, and also explores possible correlations between the incidence of different yeast species in nectar and their reported tolerance to high sugar concentrations, and between yeast diversity and pollinator composition. Yeast species occurring in a total of 128 field-collected nectar samples from 24 plant species were identified by sequencing the D1/D2 domain of the large subunit rDNA, and rarefaction-based analyses were used to estimate yeast species richness at the plant community and plant species levels, using nectar drops as elemental sampling units. Individual nectar samples were generally characterized by very low species richness (1.2 yeast species/sample, on average), with the ascomycetous Metschnikowia reukaufii and Metschnikowia gruessii accounting altogether for 84.7% of the 216 isolates identified. Other yeasts recorded included species in the genera Aureobasidium, Rhodotorula, Cryptococcus, Sporobolomyces, and Lecythophora. The shapes and slopes of observed richness accumulation curves were quite similar for the nectar drop and plant species approaches, but the two approaches yielded different expected richness estimates. Expected richness was higher for plant species-based than for nectar drop-based analyses, showing that the coverage of nectar yeast species occurring in the region would be improved by sampling additional host plant species. A significant correlation was found between incidence of yeast species in nectar and their reported ability to grow in a medium containing 50% glucose. Neither diversity nor incidence of yeasts was correlated with pollinator composition across plant species.

Inhospitable sweetness: nectar filtering of pollinator-borne inocula leads to impoverished, phylogenetically clustered yeast communities

Identifying the rules and mechanisms that determine the composition and diversity of naturally co-occurring species assemblages is a central topic in community ecology. Although micro-organisms represent the 'unseen majority' of species, individuals and biomass in many ecosystems and play pivotal roles in community development and function, the study of the factors influencing the assembly of microbial communities has lagged behind that of plant and animal communities. In this paper, we investigate experimentally the mechanisms accounting for the low species richness of yeast communities inhabiting the nectar of the bumble-bee-pollinated Helleborus foetidus (Ranunculaceae), and explore the relationships between community assembly rules and phylogenetic relatedness. By comparing yeast communities on the glossae of foraging bumble-bees (the potential species pool) with those eventually establishing in virgin nectar probed with bee glossae (the realized community), we address the questions: (i) does nectar filter yeast inocula, so that the communities eventually established there are not random subsamples of species on bumble-bee glossae? and (ii) do yeast communities establishing in H. foetidus nectar exhibit some phylogenetic bias relative to the species pool on bumble-bee glossae? Results show that nectar filtering leads to species-poor, phylogenetically clustered yeast communities that are a predictable subset of pollinator-borne inocula. Such strong habitat filtering is probably due to H. foetidus nectar representing a harsh environment for most yeasts, where only a few phylogenetically related nectar specialists physiologically endowed to tolerate a combination of high osmotic pressure and fungicidal compounds are able to develop.

Pollinator foraging modifies nectar sugar composition in Helleborus foetidus (Ranunculaceae):An experimental test

We experimentally tested the hypothesis that the extensive within-plant variation of nectar sugar composition in Helleborus foetidus (Ranunculaceae) and other species results from differences between flowers and nectaries in pollinator visitation history. Experiments were conducted to mimic single-nectary visits by wild-caught individuals of the main bee pollinators of H. foetidus, which were assayed for their capacity to modify the sugar composition of natural and artificial nectar. Experimental nectar probing with bee mouthparts induced extensive changes in proportional sugar composition 48 h after treatment, and bee taxa differed widely in their effects. Nectar probing by Andrena, medium-sized Anthophoridae, Apis mellifera, and Lasioglossum had no subsequent effects on nectar sugar composition, while probing by Bombus terrestris and B. pratorum induced an extensive reduction in percentage sucrose, a marked increase in percentage fructose, and a slight increase in percentage glucose. Results support the hypothesis that stochastic variations among flowers or nectaries in the taxonomic identity of recent visitors and their relative visitation frequencies may eventually generate very small-scale mosaics in nectar sugar composition. Changes in nectar sugar composition following bumblebee probing may be the consequence of nectar contamination with pollinator-borne nectarivorous yeasts.

Metschnikowia noctiluminum sp. nov., Metschnikowia corniflorae sp. nov., and Candida chrysomelidarum sp. nov., isolated from green lacewings and beetles

Fourteen yeast isolates belonging to the Metschnikowia clade were isolated from the digestive tracts of lacewings (Neuroptera: Chrysopidae), soldier beetles and leaf beetles (Coleoptera: Cantharidae and Chrysomelidae), and a caddisfly (Trichoptera: Hydropsychidae). The insect hosts were associated with sugary substances of plants, a typical habitat for yeasts in this clade. Based on DNA sequence comparisons and phenetic characters, the yeasts were identified as Candida picachoensis, Candida pimensis, and four undescribed taxa. Among the undescribed taxa, three yeasts were distinguished from one another and from other described taxa by nucleotide differences in the ribosomal DNA repeat, which were sufficient to consider them as new species. Two of the novel yeast species are described as Metschnikowia noctiluminum (NRRL Y-27753(T)) and M. cornifloraespp. nov. (NRRL Y-27750(T)) based in part on production of needle-shaped ascospores, which are found in most Metschnikowia species. Sexual reproduction was not observed in the third new yeast, Candida chrysomelidarumsp. nov. (NRRL Y-27749(T)). A fourth isolate, NRRL Y-27752, was not significantly distinct from Metschnikowia viticola and Candida kofuensis to be described as a new species. Phylogenetic analysis of the D1/D2 loop sequences placed M. noctiluminum within the M. viticola clade, while C. chrysomelidarum was a sister taxon of Candida rancensis. Metschnikowia corniflorae was phylogenetically distinct from other new species and fell outside of the large-spored Metschnikowia group.

Analysis of yeast isolates related to Metschnikowia pulcherrima using the partial sequences of the large subunit rDNA and the actin gene; description of Metschnikowia andauensis sp. nov

Thirty-two yeast isolates were cultured from guts or excrements of three different pests of corn or from the stem of healthy corn. The strains were analyzed using MSP-PCR (micro/minisatellite-primed polymerase chain reaction), sequences of the D1/D2 region of the large subunit rDNA and a 979 bp long part of the actin gene (act-1). They seem to belong to three groups that are all sister groups of Metschnikowia pulcherrima, M. fructicola and M. chrysoperlae. A new species, Metschnikowia andauensis (HA 1657T) is described. In contrast to M. pulcherrima and M. fructicola, M. andauensis is well separated in the act-1 phylogenetic tree too.

Discrimination between Candida albicans and Candida dubliniensis isolated from HIV-positive patients by using commercial method in comparison with PCR assay

Nineteen clinical isolates of Candida albicans and C. dubliniensis were isolated from patients (majority of them HIV-positive) in Slovakia, Brazil, Thailand and Japan. Species discrimination was performed by using growth on CHROMagar Candida, commercial biochemical set API 20C AUX, germ-tube test in human serum, growth at 42 and 45 degrees C on Sabouraud-dextrose agar as well as on CHROMagar Candida, assimilation of D-xylose and methyl alpha-D-glucoside by glass-tube test, and production of chlamydospores. These tests were completed by PCR using Cd-oligo2/F and Cd-oligo2/R primer pair specific for C. dubliniensis. Six clinical isolates were confirmed to be C. dubliniensis, remaining 13 strains were determined as C. albicans. The use of conventional method showed that the determination is markedly influenced by personal evaluation suggesting the necessity of using the combination of many tests to obtain correct results comparing with accurate and rapid PCR assay. For discrimination between C. albicans and C. dubliniensis we recommend the combination of primo-cultivation on CHROMagar, followed by germ-tube test and PCR.

Metschnikowia kunwiensis comb. nov., the teleomorph of Candida kunwiensis

The teleomorph of Candida kunwiensis Hong, Bae, Herzberg, Titze, Lachance, Metschnikowia kunwiensis, is described. Repeated attempts to obtain ascospore formation succeeded using modified V8 sporulation media and extended incubation times. The asci are ovoid, with only a small protrusion caused by the spore(s). The species is diplontic, possibly homothallic, with one or two ascospores per ascus. Aside from having atypical ovoid asci, the acicular shape of the spores is characteristic of the genus Metschnikowia. The type strain is CBS 9676(T).