Five novel Candida species in insect-associated yeast clades isolated from Neuroptera and other insects

Pathogenicity of Metarhizium rileyi (Hypocreales: Clavicipitaceae) against Tenebrio molitor (Coleoptera: Tenebrionidae)

Tenebrio molitor L., also known as the mealworm, is a polyphagous insect pest that infests various stored grains worldwide. Both the adult and larval stages can cause significant damage to stored grains. The present study focused on isolating entomopathogenic fungi from an infected larval cadaver under environmental conditions. Fungal pathogenicity was tested on T. molitor larvae and pupae for 12 days. Entomopathogenic fungi were identified using biotechnological methods based on their morphology and the sequence of their nuclear ribosomal internal transcribed spacer (ITS). The results of the insecticidal activity indicate that the virulence of fungi varies between the larval and pupal stages. In comparison to the larval stage, the pupal stage is highly susceptible to Metarhizium rileyi, exhibiting 100% mortality rates after 12 days (lethal concentration 50 [LC50] = 7.8 × 106 and lethal concentration 90 (LC90) = 2.1 × 1013 conidia/mL), whereas larvae showed 92% mortality rates at 12 days posttreatment (LC50 = 1.0 × 106 and LC90 = 3.0 × 109 conidia/mL). The enzymatic analyses revealed a significant increase in the levels of the insect enzymes superoxide dismutase (4.76-10.5 mg-1) and glutathione S-transferase (0.46-6.53 mg-1) 3 days after exposure to M. rileyi conidia (1.5 × 105 conidia/mL) compared to the control group. The findings clearly show that M. rileyi is an environmentally friendly and effective microbial agent for controlling the larvae and pupae of T. molitor.

Patterns recovered in phylogenomic analysis of Candida auris and close relatives implicate broad environmental flexibility in Candida/Clavispora clade yeasts

Fungal pathogens commonly originate from benign or non-pathogenic strains living in the natural environment. The recently emerged human pathogen, Candida auris, is one example of a fungus believed to have originated in the environment and recently transitioned into a clinical setting. To date, however, there is limited evidence about the origins of this species in the natural environment and when it began associating with humans. One approach to overcome this gap is to reconstruct phylogenetic relationships between (1) strains isolated from clinical and non-clinical environments and (2) between species known to cause disease in humans and benign environmental saprobes. C. auris belongs to the Candida/Clavispora clade, a diverse group of 45 yeast species including human pathogens and environmental saprobes. We present a phylogenomic analysis of the Candida/Clavispora clade aimed at understanding the ecological breadth and evolutionary relationships between an expanded sample of environmentally and clinically isolated yeasts. To build a robust framework for investigating these relationships, we developed a whole-genome sequence dataset of 108 isolates representing 18 species, including four newly sequenced species and 18 environmentally isolated strains. Our phylogeny, based on 619 orthologous genes, shows environmentally isolated species and strains interspersed with clinically isolated counterparts, suggesting that there have been many transitions between humans and the natural environment in this clade. Our findings highlight the breadth of environments these yeasts inhabit and imply that many clinically isolated yeasts in this clade could just as easily live outside the human body in diverse natural environments and vice versa.

Clinical, Microbiological, and Molecular Characterization of Candia (Starmera) stellimalicola, a Rare Fungal Pathogen Causing Human Infections

Candia (Starmera) stellimalicola is a yeast species spread worldwide and recovered from varieties of ecological reservoirs, but human infections are rarely reported. In this study, we reported an intra-abdominal infection case caused by C. stellimalicola and described its microbiological and molecular characteristics. C. stellimalicola strains were isolated from ascites fluid of an 82-year-old male patient having diffuse peritonitis with fever and elevated WBC counts. Routine biochemical and MALDI-TOF MS methods failed to identify the pathogenic strains. Phylogenetic analysis of 18S, 26S and internal transcribed space (ITS) rDNA regions, as well as whole-genome sequence identified the strains as C. stellimalicola. Compared with other Starmera species, C. stellimalicola had unique physiological characteristics including thermal tolerance (able to grow at 42 °C), which may prompt its environmental adaptability and potential for opportunistic human infection. Fluconazole minimum inhibitory concentration (MIC) values of the strains identified in this case was 2 mg/L, and the patient had a favorable outcome after receiving fluconazole treatment. In comparison, the majority of C. stellimalicola strains previously documented had high MIC values (≥ 16 mg/L) to fluconazole. In conclusion, with the raise in human infections caused by rare fungal pathogens, molecular diagnostic remains the most efficient way for accurate species identification; and antifungal susceptibility testing is essential to guide proper patient management.

Genomic Analyses of a Fungemia Outbreak Caused by Lodderomyces elongisporus in a Neonatal Intensive Care Unit in Delhi, India

Lodderomyces elongisporus is a recently emerging yeast pathogen predominantly reported in adult patients who had immunosuppression and/or intravenous access devices. Here, we report a fungemia outbreak caused by L. elongisporus in a neonatal intensive care unit (NICU) in Delhi, India, from September 2021 to February 2022. All 10 neonates had low birthweight, and nine of the patients survived after amphotericin B treatment. Whole-genome sequence analyses of the patient isolates as well as those from other sources in India grouped them into two clusters: one cluster consists of isolates exclusively from stored apples and the other cluster includes isolates from patients, clinical environments, and stored apples. All outbreak strains from patients were closely related to each other and showed highly similar heterozygosity patterns across all 11 major scaffolds. While overall very similar, strains from the inanimate environment of the same neonatal intensive care unit showed loss of heterozygosity at scaffold 2 (NW_001813676) compared to the patient strains. Interestingly, evidence for recombination was found in all samples. All clinical strains were susceptible to 10 tested antifungal drugs, and comparisons with strains with high fluconazole MICs derived from the surface of stored apples revealed significant genome divergence between the clinical and apple surface strains, including 119 nonsynonymous single nucleotide polymorphisms (SNPs) in 24 triazole resistance-related genes previously found in other Candida spp. Together, our results indicate significant diversity, recombination, and persistence in the hospital setting and a high rate of evolution in this emerging yeast pathogen. IMPORTANCE Lodderomyces elongisporus was initially considered a teleomorph of Candida parapsilosis. However, DNA sequence analyses revealed it as a distinctive species. Invasive infections due to L. elongisporus have been reported globally. We report an outbreak of fungemia due to L. elongisporus in a NICU affecting 10 preterm, low-birthweight neonates during a period of 6 months. The outbreak investigation identified two environmental sites, the railing and the temperature panel of the neonate open care warmer, harboring L. elongisporus. Whole-genome sequencing confirmed that the neonate isolates were closely related to each other whereas strains from the inanimate clinical environment were related to clinical strains but showed a marked loss of heterozygosity. Further, L. elongisporus strains recovered previously from the surface of stored apples showed high fluconazole MICs and alterations in triazole resistance-related genes. Genome-wide SNP comparisons revealed recombination as an important source for genomic diversity during adaptation of L. elongisporus to different environments.

Chromosome-Level Genome Assembly of the Yeast Candida verbasci

Candida verbasci is an anamorphic ascomycetous yeast. We report the genome sequence of its type strain, 11-1055 (CBS 12699). The nuclear genome assembly consists of seven chromosome-sized contigs with a total size of 12.1 Mbp and has a relatively low G+C content (28.1%).

Torulaspora jiuxiensis sp. nov., a novel yeast species isolated from rotting wood

Two strains of a novel ascomycetous yeast species were isolated from rotting wood samples collected in Jiuxi Mountain Forest Park in Yunnan Province, southwest China. Both strains formed one or two spherical ascospores in persistent asci. Phylogenetic analysis of the concatenated sequences of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) and the D1/D2 domain of the large subunit rRNA gene revealed that the novel strains represented a phylogenetically distinct species belonging to the genus Torulaspora. This novel species differed from the type strains of the closest known species, Torulaspora nypae and Torulaspora maleeae, by 0.9 and 1.2 % nucleotide substitutions in the D1/D2 domain and 5.3 and 6 % nucleotide substitutions in the ITS region, respectively. The novel species can also be distinguished from T. nypae and T. maleeae in terms of the ability to assimilate ribitol, succinate and citrate, and its ability to grow at 37 °C. The species name of Torulaspora jiuxiensis sp. nov. is proposed with holotype CBS 16004^T (Mycobank MB 844535).

Phylogenetic and genomic analyses of two new species of Clavispora (Metschnikowiaceae, Saccharomycetales) from Central China

Species in the genus Clavispora have previously been reported primarily in the northeast and northwest regions of China; the species diversity of Clavispora in central China is not currently clear. In this study, phylogenetic inferences of Clavispora based on sequences of a single-locus (LSU D1/D2) and a two-locus (LSU D1/D2 and ITS) were conducted. Two new species isolated from rotting wood in central China, namely Clavispora xylosa sp. nov. and Clavispora paralusitaniae sp. nov., were delimited and proposed based on morphological and molecular evidence. Cl. xylosa was closely related to C. thailandica CBS 10610^T, but with 11.5% divergence in the LSU D1/D2 domains and 11.5% divergence in the ITS regions. Cl. paralusitaniae was a sister to Cl. lusitaniae CBS 6936^T from which it differs with 4.7% divergence in the LSU D1/D2 domains and 5.4% divergence in the ITS regions. Description of Cl. xylosa sp. nov. and Cl. paralusitaniae sp. nov. was also supported by morphological comparisons and genomic analyses between the two new species and their closest relatives, C. thailandica CBS 10610^T and Cl. lusitaniae CBS 6936^T. These results indicate a potentially great diversity of Clavispora spp. inhabiting rotting wood in central China, ripe for future discovery.

Biotechnological Importance of Torulaspora delbrueckii: From the Obscurity to the Spotlight

Torulaspora delbrueckii has attracted interest in recent years, especially due to its biotechnological potential, arising from its flavor- and aroma-enhancing properties when used in wine, beer or bread dough fermentation, as well as from its remarkable resistance to osmotic and freezing stresses. In the present review, genomic, biochemical, and phenotypic features of T. delbrueckii are described, comparing them with other species, particularly with the biotechnologically well-established yeast, Saccharomyces cerevisiae. We conclude about the aspects that make this yeast a promising biotechnological model to be exploited in a wide range of industries, particularly in wine and bakery. A phylogenetic analysis was also performed, using the core proteome of T. delbrueckii, to compare the number of homologous proteins relative to the most closely related species, understanding the phylogenetic placement of this species with robust support. Lastly, the genetic tools available for T. delbrueckii improvement are discussed, focusing on adaptive laboratorial evolution and its potential.

Development of Genetic Modification Tools for Hanseniasporauvarum

Apiculate yeasts belonging to the genus Hanseniaspora are commonly isolated from viticultural settings and often dominate the initial stages of grape must fermentations. Although considered spoilage yeasts, they are now increasingly becoming the focus of research, with several whole-genome sequencing studies published in recent years. However, tools for their molecular genetic manipulation are still lacking. Here, we report the development of a tool for the genetic modification of Hanseniaspora uvarum. This was employed for the disruption of the HuATF1 gene, which encodes a putative alcohol acetyltransferase involved in acetate ester formation. We generated a synthetic marker gene consisting of the HuTEF1 promoter controlling a hygromycin resistance open reading frame (ORF). This new marker gene was used in disruption cassettes containing long-flanking (1000 bp) homology regions to the target locus. By increasing the antibiotic concentration, transformants were obtained in which both alleles of the putative HuATF1 gene were deleted in a diploid H. uvarum strain. Phenotypic characterisation including fermentation in Müller-Thurgau must showed that the null mutant produced significantly less acetate ester, particularly ethyl acetate. This study marks the first steps in the development of gene modification tools and paves the road for functional gene analyses of this yeast.

Endomycobiome associated with females of the planthopper Delphacodes kuscheli (Hemiptera: Delphacidae): A metabarcoding approach

A metabarcoding approach was performed aimed at identifying fungi associated with Delphacodes kuscheli (Hemiptera: Delphacidae), the main vector of “Mal de Río Cuarto” disease in Argentina. A total of 91 fungal genera were found, and among them, 24 were previously identified for Delphacidae. The detection of fungi that are frequently associated with the phylloplane or are endophytes, as well as their presence in digestive tracts of other insects, suggest that feeding might be an important mechanism of their horizontal transfer in planthoppers. This study draws the baseline for future research regarding mutualistic associations present in D. kuscheli as well as their physiological role in the life cycle of this important pest that might lead to developing new management strategies to keep insects populations under control.

Saccharomyces cerevisiae - Insects Association: Impacts, Biogeography, and Extent

Over the last few years, an increasing number of studies have reported the existence of an association between the budding yeast Saccharomyces cerevisiae and insects. The discovery of this relationship has called into question the hypothesis that S. cerevisiae is unable to survive in nature and that the presence of S. cerevisiae strains in natural specimens is the result of contamination from human-related environments. S. cerevisiae cells benefit from this association as they find in the insect intestine a shelter, but also a place where they can reproduce themselves through mating, the latter being an event otherwise rarely observed in natural environments. On the other hand, insects also take advantage in hosting S. cerevisiae as they rely on yeasts as nutriment to properly develop, to localize suitable food, and to enhance their immune system. Despite the relevance of this relationship on both yeast and insect ecology, we are still far from completely appreciating its extent and effects. It has been shown that other yeasts are able to colonize only one or a few insect species. Is it the same for S. cerevisiae cells or is this yeast able to associate with any insect? Similarly, is this association geographically or topographically limited in areas characterized by specific physical features? With this review, we recapitulate the nature of the S. cerevisiae-insect association, disclose its extent in terms of geographical distribution and species involved, and present YeastFinder, a cured online database providing a collection of information on this topic.

Evolutionary Relationship Between Platycerus Stag Beetles and Their Mycangium-Associated Yeast Symbionts

Adult females of stag beetles (Coleoptera: Lucanidae) possess an ovipositor-associated mycangium for conveying symbiotic microorganisms. In most lucanid species, their mycangium contains yeast symbionts of the genus Scheffersomyces Kurtzman and Suzuki that are known for their xylose-fermenting capability. The lucanid genus Platycerus Geoffroy, 1762 is a group of small blue stag beetles, in which ten Japanese species constitute a monophyletic clade. Here we examined the evolutionary relationships of these Japanese Platycerus species and their yeast symbionts, together with a Korean Platycerus species and other lucanid species as outgroup taxa. Based on the internal transcribed spacer (ITS) and the intergenic spacer (IGS) sequences, the yeast symbionts of all Platycerus species were closely related to each other and formed a monophyletic clade. There is no variation in ITS sequences of the yeast symbionts of the Japanese Platycerus species. Based on IGS sequences, the yeast symbionts formed clusters that largely reflected the geographic distribution of the host insects, being shared by sympatric Platycerus species except for P. delicatulus Lewis, 1883 and P. viridicuprus Kubota & Otobe, The symbiont phylogeny was globally not congruent with the host COI-based phylogeny, although some local congruences were observed. Statistically significant correlations were detected between the genetic distances of COI sequences of the host insects and those of IGS sequences of the yeast symbionts in Japan. These results suggest that, at least to some extent, the host insects and the yeast symbionts may have experienced co-evolutionary associations. While the Japanese Platycerus species formed a monophyletic clade in the COI phylogeny, the yeast symbionts of Japanese P. viridicuprus were very closely related to those of Korean P. hongwonpyoi Imura & Choe, 1989, suggesting the possibility that a recent secondary contact of the two beetle species during a marine withdrawal, e.g., in the last glacial period, might have resulted in an inter-specific horizontal transmission of the yeast symbiont.

Microbiome of the Queensland Fruit Fly through Metamorphosis

Bactrocera tryoni (Froggatt) (Queensland fruit fly, or “Qfly”) is a highly polyphagous tephritid fruit fly and a serious economic pest in Australia. Qfly biology is intimately linked to the bacteria and fungi of its microbiome. While there are numerous studies of the microbiome in larvae and adults, the transition of the microbiome through the pupal stage remains unknown. To address this knowledge gap, we used high-throughput Next-Generation Sequencing (NGS) to examine microbial communities at each developmental stage in the Qfly life cycle, targeting the bacterial 16S rRNA and fungal ITS regions. We found that microbial communities were similar at the larval and pupal stage and were also similar between adult males and females, yet there were marked differences between the larval and adult stages. Specific bacterial and fungal taxa are present in the larvae and adults (fed hydrolyzed yeast with sugar) which is likely related to differences in nutritional biology of these life stages. We observed a significant abundance of the Acetobacteraceae at the family level, both in the larval and pupal stages. Conversely, Enterobacteriaceae was highly abundant (>80%) only in the adults. The majority of fungal taxa present in Qfly were yeasts or yeast-like fungi. In addition to elucidating changes in the microbiome through developmental stages, this study characterizes the Qfly microbiome present at the establishment of laboratory colonies as they enter the domestication process.

Occurrence and Molecular Identification of Wild Yeasts from Jimma Zone, South West Ethiopia

Yeasts are common inhabitants of most fruit trees' rhizospheres and phyllospheres. Wild yeasts are the major driving force behind several modern industrial biotechnologies. This study focused on determining the occurrence and frequency of wild yeasts associated with domestic and wild edible tree barks, fruits, and rhizosphere soil samples collected over two seasons (i.e., spring and summer) in South West Ethiopia. A total of 182 yeast strains were isolated from 120 samples. These strains belonged to 16 genera and 27 species as identified based on the sequence analysis of the D1/D2 domain of the large subunit (26S) ribosomal RNA gene. Candida blattae, Pichia kudriavzevii, Candida glabrata, Saccharomyces cerevisiae, and Candida humilis were the most dominant yeast species isolated from the bark samples. Only Pichia kudriavzevii was regularly detected from the bark, rhizosphere, fruit, and sugarcane samples. The retrieval of yeasts from bark samples was more frequent and diverse than that of soil, fruits, and sugarcane. The frequency of detection of yeasts during the spring was significantly higher than in the summer season. However, there was no significant seasonal variation in the frequency of detection of yeast species between the rhizosphere and phyllosphere samples.

The ecology of insect-yeast relationships and its relevance to human industry

Many species of yeast are integral to human society. They produce many of our foods, beverages and industrial chemicals, challenge us as pathogens, and provide models for the study of our own biology. However, few species are regularly studied and much of their ecology remains unclear, hindering the development of knowledge that is needed to improve the relationships between humans and yeasts. There is increasing evidence that insects are an essential component of ascomycetous yeast ecology. We propose a 'dispersal-encounter hypothesis' whereby yeasts are dispersed by insects between ephemeral, spatially disparate sugar resources, and insects, in turn, obtain the benefits of an honest signal from yeasts for the sugar resources. We review the relationship between yeasts and insects through three main examples: social wasps, social bees and beetles, with some additional examples from fruit flies. Ultimately, we suggest that over the next decades, consideration of these ecological and evolutionary relationships between insects and yeasts will allow prediction of where new yeast diversity is most likely to be discovered, particularly yeasts with traits of interest to human industry.

Yeast-insect associations: It takes guts

Insects interact with microorganisms in several situations, ranging from the accidental interaction to locate attractive food or the acquisition of essential nutrients missing in the main food source. Despite a wealth of studies recently focused on bacteria, the interactions between insects and yeasts have relevant implications for both of the parties involved. The insect intestine shows several structural and physiological differences among species, but it is generally a hostile environment for many microorganisms, selecting against the most sensitive and at the same time guaranteeing a less competitive environment to resistant ones. An intensive characterization of the interactions between yeasts and insects has highlighted their relevance not only for attraction to food but also for the insect's development and behaviour. Conversely, some yeasts have been shown to benefit from interactions with insects, in some cases by being carried among different environments. In addition, the insect intestine may provide a place to reside for prolonged periods and possibly mate or generate sexual forms able to mate once back in the external environments. YEA-May-17-0084.R3.

Taxonomy and physiological characterisation of Scheffersomyces titanus sp. nov., a new D-xylose-fermenting yeast species from China

Three strains of a d-xylose-fermenting yeast species were isolated from the host beetle Dorcus titanus collected from two different localities in Henan Province, Central China. These strains formed two hat-shaped ascospores in conjugated and deliquescent asci. Multilocus phylogenetic analysis that included the nearly complete small subunit (SSU), the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit (LSU) rDNAs, as well as RNA polymerase II largest subunit (RPB1) gene demonstrated that these strains represent a novel yeast species belonging to the genus Scheffersomyces. The phylogenetic analysis based on the nucleotide sequences of the xylose reductase (XYL1) gene supported the view that the new strains could be grouped as a unique species. Although this new species is highly similar to Scheffersomyces stipitis-like yeasts in terms of nrDNA sequences and morphological and physiological characteristics, the species can be clearly differentiated from its close relatives on the basis of the sequences of XYL1 and RPB1. Therefore, a novel yeast species, Scheffersomyces titanus sp. nov., is proposed to accommodate these strains. The type strain is NYNU 14712(T) (CICC 33061(T) = CBS 13926(T)).

The Gut Microbiomes of Two Pachysoma MacLeay Desert Dung Beetle Species (Coleoptera: Scarabaeidae: Scarabaeinae) Feeding on Different Diets

Micro-organisms inhabiting animal guts benefit from a protected and nutrient-rich environment while assisting the host with digestion and nutrition. In this study we compare, for the first time, the bacterial and fungal gut communities of two species of the small desert dung beetle genus Pachysoma feeding on different diets: the detritivorous P. endroedyi and the dry-dung-feeding P. striatum. Whole-gut microbial communities from 5 individuals of each species were assessed using 454 pyrosequencing of the bacterial 16S rRNA gene and fungal ITS gene regions. The two bacterial communities were significantly different, with only 3.7% of operational taxonomic units shared, and displayed intra-specific variation. The number of bacterial phyla present within the guts of P. endroedyi and P. striatum individuals ranged from 6-11 and 4-7, respectively. Fungal phylotypes could only be detected within the gut of P. striatum. Although the role of host phylogeny in Pachysoma microbiome assembly remains unknown, evidence presented in this study suggests that host diet may be a deterministic factor.

Candida vulturna pro tempore sp. nov., a dimorphic yeast species related to the Candida haemulonis species complex isolated from flowers and clinical sample

In a taxonomic study of yeasts isolated from flowers in Cagayan de Oro, Mindenao Island, The Philippines, strains were identified as representing Kabatiella microsticta, Metschnikowia koreensis and a hitherto undescribed dimorphic species. Sequences of the D1/D2 domains of the LSU 26S rRNA genes, the internal transcribed spacer (ITS) regions and the SSU 18S rRNA genes were identical in the strains of the last-named group and differed from the corresponding sequences of the type strain of the closest related species, Candida duobushaemulonii, by 4 % (D1/D2), 7 % (ITS) and 1 % (SSU). In an independent study, a strain with D1/D2 and ITS sequences very similar to those of the Philippine strains was isolated in Malaysia from the blood of a patient dying of aspiration pneumonia. Both groups of isolates were moderately sensitive to anidulafungin, caspofungin, fluconazole, itraconazole and voriconazole but resistant to amphotericin B. Molecular phylogenetic analysis of the sequences placed the Philippine and Malaysian isolates close to the Candida haemulonis complex of Candida species. To reflect the geographical location of the sites of sample collection, the novel species name Candida vulturna pro tempore sp. nov. is proposed to accommodate these strains. The type strain is 11-1170T (=CBS 14366T=CCY 094-001-001T=NCAIM-Y02177T) isolated in Cagayan de Oro, The Philippines. Mycobank: MB 817222.

Hanseniaspora uvarum from Winemaking Environments Show Spatial and Temporal Genetic Clustering

Hanseniaspora uvarum is one of the most abundant yeast species found on grapes and in grape must, at least before the onset of alcoholic fermentation (AF) which is usually performed by Saccharomyces species. The aim of this study was to characterize the genetic and phenotypic variability within the H. uvarum species. One hundred and fifteen strains isolated from winemaking environments in different geographical origins were analyzed using 11 microsatellite markers and a subset of 47 strains were analyzed by AFLP. H. uvarum isolates clustered mainly on the basis of their geographical localization as revealed by microsatellites. In addition, a strong clustering based on year of isolation was evidenced, indicating that the genetic diversity of H. uvarum isolates was related to both spatial and temporal variations. Conversely, clustering analysis based on AFLP data provided a different picture with groups showing no particular characteristics, but provided higher strain discrimination. This result indicated that AFLP approaches are inadequate to establish the genetic relationship between individuals, but allowed good strain discrimination. At the phenotypic level, several extracellular enzymatic activities of enological relevance (pectinase, chitinase, protease, β-glucosidase) were measured but showed low diversity. The impact of environmental factors of enological interest (temperature, anaerobia, and copper addition) on growth was also assessed and showed poor variation. Altogether, this work provided both new analytical tool (microsatellites) and new insights into the genetic and phenotypic diversity of H. uvarum, a yeast species that has previously been identified as a potential candidate for co-inoculation in grape must, but whose intraspecific variability had never been fully assessed.

New insights into the fungal community from the raw genomic sequence data of fig wasp Ceratosolen solmsi

Background

To date, biologists have discovered a large amount of valuable information from assembled genomes, but the abundant microbial data that is hidden in the raw genomic sequence data of plants and animals is usually ignored. In this study, the richness and composition of fungal community were determined in the raw genomic sequence data of Ceratosolen solmsi (RGSD-CS).

Results

To avoid the interference from sequences of C. solmsi, the unmapped raw data (about 17.1%) was obtained by excluding the assembled genome of C. solmsi from RGSD-CS. Comparing two fungal reference datasets, internal transcribed spacer (ITS) and large ribosomal subunit (LSU) of rRNA, the ITS dataset discovered a more diverse fungal community and was therefore selected as the reference dataset for evaluating the fungal community based on the unmapped raw data. The threshold of 95% sequence identity revealed many more matched fungal reads and fungal richness in the unmapped raw data than those by identities above 95%. Based on the threshold of 95% sequence identity, the fungal community of RGSD-CS was primarily composed of Saccharomycetes (88.4%) and two other classes (Agaricomycetes and Sordariomycetes, 8.3% in total). Compared with the fungal community of other reported fig wasps, Agaricomycetes and Eurotiomycetes were found to be unique to C. solmsi. In addition, the ratio of total fungal reads to RGSD-CS was estimated to be at least 4.8 × 10⁻³, which indicated that a large amount of fungal data was contained in RGSD-CS. However, rarefaction measure indicated that a deeper sequencing coverage with RGSD-CS was required to discover the entire fungal community of C. solmsi.

Conclusion

This study investigated the richness and composition of fungal community in RGSD-CS and provided new insights into the efficient study of microbial diversity using raw genomic sequence data.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0370-3) contains supplementary material, which is available to authorized users.

Pectinases from Sphenophorus levis Vaurie, 1978 (Coleoptera: Curculionidae): putative accessory digestive enzymes

The cell wall in plants offers protection against invading organisms and is mainly composed of the polysaccharides pectin, cellulose, and hemicellulose, which can be degraded by plant cell wall degrading enzymes (PCWDEs). Such enzymes are often synthesized by free living microorganisms or endosymbionts that live in the gut of some animals, including certain phytophagous insects. Thus, the ability of an insect to degrade the cell wall was once thought to be related to endosymbiont enzyme activity. However, recent studies have revealed that some phytophagous insects are able to synthesize their own PCWDEs by endogenous genes, although questions regarding the origin of these genes remain unclear. This study describes two pectinases from the sugarcane weevil, Sphenophorus levis Vaurie, 1978 (Sl-pectinases), which is considered one of the most serious agricultural pests in Brazil. Two cDNA sequences identified in a cDNA library of the insect larvae coding for a pectin methylesterase (PME) and an endo-polygalacturonase (endo-PG)-denominated Sl-PME and Sl-endoPG, respectively-were isolated and characterized. The quantitative real-time reverse transcriptase polymerase chain reaction expression profile for both Sl-pectinases showed mRNA production mainly in the insect feeding stages and exclusively in midgut tissue of the larvae. This analysis, together Western blotting data, suggests that Sl-pectinases have a digestive role. Phylogenetic analyses indicate that Sl-PME and Sl-endoPG sequences are closely related to bacteria and fungi, respectively. Moreover, the partial genomic sequences of the pectinases were amplified from insect fat body DNA, which was certified to be free of endosymbiotic DNA. The analysis of genomic sequences revealed the existence of two small introns with 53 and 166 bp in Sl-endoPG, which is similar to the common pattern in fungal introns. In contrast, no intron was identified in the Sl-PME genomic sequence, as generally observed in bacteria. These data support the theory of horizontal gene transfer proposed for the origin of insect pectinases, reinforcing the acquisition of PME genes from bacteria and endo-PG genes from fungi.

Microbial associates of the vine mealybug Planococcus ficus (Hemiptera: Pseudococcidae) under different rearing conditions

Sap-feeding insects harbor diverse microbial endosymbionts that play important roles in host ecology and evolution, including contributing to host pest status. The vine mealybug, Planococcus ficus, is a serious pest of grapevines, vectoring a number of pathogenic grape viruses. Previous studies have shown that virus transmission is abolished when mealybugs are raised in the laboratory on potato. To examine the possible role of microbial symbionts in virus transmission, the archaeal, bacterial, and fungal microbiota of field and laboratory P. ficus were characterized using molecular and classical microbiological methods. Lab and field colonies of P. ficus harbored different microbiota. While both were dominated by the bacterial obligate nutritional symbionts Moranella and Tremblaya, field samples also harbored a third bacterium that was allied with cluster L, a lineage of bacterial symbionts previously identified in aphids. Archaea were not found in any of the samples. Fungal communities in field-collected mealybugs were dominated by Metschnikowia and Cladosporium species, while those from laboratory-reared mealybugs were dominated by Alternaria and Cladosporium species. In conclusion, this study has identified a diverse set of microbes, most of which appear to be facultatively associated with P. ficus, depending on environmental conditions. The role of various members of the mealybug microbiome, as well as how the host plant affects microbial community structure, remains to be determined.

Winemaking and bioprocesses strongly shaped the genetic diversity of the ubiquitous yeast Torulaspora delbrueckii

The yeast Torulaspora delbrueckii is associated with several human activities including oenology, bakery, distillery, dairy industry, etc. In addition to its biotechnological applications, T. delbrueckii is frequently isolated in natural environments (plant, soil, insect). T. delbrueckii is thus a remarkable ubiquitous yeast species with both wild and anthropic habitats, and appears to be a perfect yeast model to search for evidence of human domestication. For that purpose, we developed eight microsatellite markers that were used for the genotyping of 110 strains from various substrates and geographical origins. Microsatellite analysis showed four genetic clusters: two groups contained most nature strains from Old World and Americas respectively, and two clusters were associated with winemaking and other bioprocesses. Analysis of molecular variance (AMOVA) confirmed that human activities significantly shaped the genetic variability of T. delbrueckii species. Natural isolates are differentiated on the basis of geographical localisation, as expected for wild population. The domestication of T. delbrueckii probably dates back to the Roman Empire for winemaking (∼ 1900 years ago), and to the Neolithic era for bioprocesses (∼ 4000 years ago). Microsatellite analysis also provided valuable data regarding the life-cycle of the species, suggesting a mostly diploid homothallic life. In addition to population genetics and ecological studies, the microsatellite tool will be particularly useful for further biotechnological development of T. delbrueckii strains for winemaking and other bioprocesses.

Three clustered cases of candidemia caused by Candida quercitrusa and mycological characteristics of this novel species

We investigated three nosocomial Candida quercitrusa candidemia cases occurring within 2 months in a Chinese hospital. Isolates were identifiable only by DNA sequencing of the rRNA genes. Genetic (via random amplified polymorphic DNA [RAPD]) and protein mass spectral (via matrix-assisted laser desorption ionization-time of flight mass spectrometry [MALDI-TOF MS]) analyses yielded identical profiles suggesting an outbreak. The fluconazole MICs of all the strains were 16 to 32 μg/ml.

Scheffersomyces cryptocercus: a new xylose-fermenting yeast associated with the gut of wood roaches and new combinations in the Sugiyamaella yeast clade

The gut of wood-feeding insects is a microhabitat for a specialized community of microbes, including bacteria and several groups of eukaryotes such as nematodes, parabasalids and fungi. The characterization of gut yeast communities from a variety of insects has shown that certain yeasts often are associated with the insects. The gut of wood-feeding insects is rich in ascomycete yeasts and in particular xylose-fermenting (X-F) and assimilating yeasts have been consistently present in the gut of lignicolous insects. The objective of this study was the characterization of the yeast flora from the gut of the wood roach Cryptocercus sp. (Blattodea: Cryptocercidae). Five wood roaches were collected along the Appalachian Trail near the border between Tennessee and North Carolina, USA. We isolated 18 yeast strains from the wood roaches identified as Sugiyamaella paludigena and Sugiyamaella lignohabitans, xylose-assimilating yeasts, and Scheffersomyces cryptocercus (NRRL Y-48824(T) = CBS 12658) a new species of X-F yeast. The presence of X-F and certain non X-F yeasts in the gut of the subsocial wood roach Cryptocercus sp. extends the previous findings of associations between certain ascomycete yeasts and lignicolous insects. New combinations were made for 13 asexual members of the Sugiyamaella clade.

Cryptococcus nanyangensis sp. nov., a new basidiomycetous yeast isolated from the gut of wood-boring larvae

Two strains of a novel basidiomycetous yeast species were isolated from the gut of wood-boring larvae collected in the Baotianman Nature Reserve, the central China. Sequence analysis of the D1/D2 domains of the large subunit (LSU) rRNA gene and internal transcribed spacer (ITS) regions showed that these yeasts belong to the Bulleromyces clade and formed a cluster together with eleven undescribed Cryptococcus species. The novel species differed from its closest known species, Cryptococcus rajasthanensis, by 3.3 % divergence (15 substitutions and 6 gaps over 630 bases) in the D1/D2 domains, and by 13.4 % divergence (41 substitutions and 27 gaps over 508 bases) in the ITS regions. Physiologically, the fermentation of glucose, galactose, sucrose, trehalose, and raffinose in Durham tubes was observed for the strains of this new yeast. Based on the phenotypical and molecular characteristics presented, the two strains are proposed as a new species, Cryptococcus nanyangensis sp. nov., with the type strain KCY-1(T) (=CICC 1976(T) = CBS 12474(T)).

Candida sirachaensis sp. nov. and Candida sakaeoensis sp. nov. two anamorphic yeast species from phylloplane in Thailand

Three strains (LM008(T), LM068 and LM078(T)), representing two novel yeast species were isolated from the phylloplane of three plant species by an enrichment technique. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and the sequence analysis of the D1/D2 domain of the large subunit rRNA gene and the internal spacer region, the three strains were assigned as two novel Candida species. Strain LM008(T) was assigned to be Candida sirachaensis sp. nov. (type strain LM008(T) = BCC 47628(T) = NBRC 108605(T) CBS 12094(T)) in the Starmerella clade. Two strains (LM068 and LM078(T)) represent a single species in the Lodderomyces-Spathaspora clade for which the name Candida sakaeoensis sp. nov. is proposed with the type strain LM078(T) = BCC 47632(T) = NBRC 108895(T) = CBS 12318(T).

Dimorphic cycle in Candida citri sp. nov., a novel yeast species isolated from rotting fruit in Borneo

Five dimorphic yeast strains were isolated from rotting lime fruits in Borneo. The sequences of the D1/D2 domains of the 26S rRNA genes, the internal transcribed spacer (ITS) chromosomal regions and the 18S rRNA genes were identical in the isolates and differed from the corresponding sequences of all known yeast species. Based on the sequence differences (12-15% in the D1/D2 domain) from the closest relatives and the different pattern of taxonomic traits, the new isolates are assigned the status of a new species, for which the name Candida citri sp. nov. is proposed. Its type strain is 11-469(T) , which has been deposited in Centralbureau voor Schimmelcultures (Utrecht, the Netherlands) as CBS 11858(T) , Culture Collection of Yeasts (Bratislava, Slovakia) as CCY 29-181-1(T) and the National Collection of Agricultural and Industrial Microorganisms (Budapest, Hungary) as NCAIM Y.01978(T) . MycoBank number: MB 519100. The GenBank accession numbers for nucleotide sequences of its D1/D2 domain, ITS and 18S regions are HM803241, HM803242 and HM803243, respectively. Candida citri produces invasive mycelium composed of true septate hyphae that grow towards nutrient-rich parts of the medium and develop large vacuoles at the nongrowing ends of their cells. The hyphae produce blastoconidia, which can establish satellite yeast colonies in the invaded solid substrate.

The yeast Wickerhamomyces anomalus (Pichia anomala) inhabits the midgut and reproductive system of the Asian malaria vector Anopheles stephensi

While symbiosis between bacteria and insects has been thoroughly investigated in the last two decades, investments on the study of yeasts associated with insects have been limited. Insect-associated yeasts are placed on different branches of the phylogenetic tree of fungi, indicating that these associations evolved independently on several occasions. Isolation of yeasts is frequently reported from insect habitats, and in some cases yeasts have been detected in the insect gut and in other organs/tissues. Here we show that the yeast Wickerhamomyces anomalus, previously known as Pichia anomala, is stably associated with the mosquito Anopheles stephensi, a main vector of malaria in Asia. Wickerhamomyces anomalus colonized pre-adult stages (larvae L(1)-L(4) and pupae) and adults of different sex and age and could be isolated in pure culture. By a combination of transmission electron microscopy and fluorescent in situ hybridization techniques, W. anomalus was shown to localize in the midgut and in both the male and female reproductive systems, suggesting multiple transmission patterns.

Negative fitness consequences and transmission dynamics of a heritable fungal symbiont of a parasitic wasp

Heritable bacterial symbionts are widespread in insects and can have many important effects on host ecology and fitness. Fungal symbionts are also important in shaping their hosts' behavior, interactions, and evolution, but they have been largely overlooked. Experimental tests to determine the relevance of fungal symbionts to their insect hosts are currently extremely rare, and to our knowledge, there have been no such tests for strictly predacious insects. We investigated the fitness consequences for a parasitic wasp (Comperia merceti) of an inherited fungal symbiont in the Saccharomycotina (Ascomycota) that was long presumed to be a mutualist. In comparisons of wasp lines with and without this symbiont, we found no evidence of mutualism. Instead, there were significant fitness costs to the wasps in the presence of the yeast; infected wasps attacked fewer hosts and had longer development times. We also examined the relative competitive abilities of the larval progeny of infected and uninfected mothers, as well as horizontal transmission of the fungal symbiont among larval wasps that shared a single host cockroach egg case. We found no difference in larval competitive ability when larvae whose infection status differed shared a single host. We did find high rates of horizontal transmission of the fungus, and we suggest that this transmission is likely responsible for the maintenance of this infection in wasp populations.