Culturable yeast community associated with grape must and honey bees sampled from apiaries located in the vineyards

AIM

In this study, we investigated culturable yeast community, present in grape must sampled from vineyards with apiaries on the borders, and in honey bees collected in these apiaries.

METHODS AND RESULTS

To this aim, yeasts isolated from spontaneously fermented grapes randomly collected in two vineyards (P1 and P2) with apiaries on the borders (A1 and A2) were compared to those isolated from spontaneously fermented grapes collected from a vineyard without apiary (P4). At the same time, yeast community was analyzed on bees collected in each apiary placed in the vineyards, in comparison to yeasts isolated from an apiary (A3) located far from the vineyards. The analysis was performed for two consecutive years (2021 and 2022). The isolated yeasts were identified by restriction analysis of amplified ITS region, followed by sequencing of ITS fragment.Our research showed that the presence of apiaries seems to increase yeast counts of grape must, in particular of Saccharomyces cerevisiae; furthermore, the permanence of apiaries in the vineyards allowed the recovering of these yeasts also from bees.

CONCLUSIONS

Our findings seem to corroborate the role of bees as vectors and reservoirs of oenologically relevant yeasts, such as a source of non-conventional yeasts with potential biotechnological applications.

Wickerhamiella lachancei f.a. sp. nov., a novel ascomycetous yeast species isolated from flowers of Lantana camara in India

Two isolates representing a novel species of the genus Wickerhamiella were obtained in India from nectar of flowers of Lantana camara, an ornamental exotic species native to Central and South America. Phylogenetic analyses of the D1/D2 domain of the 26S large subunit (LSU) rRNA gene, internal transcribed spacer (ITS) region, and physiological characteristics, supported the recognition of the novel species, that we designate Wickerhamiella lachancei sp. nov (MycoBank no. MB851709), with MCC 9929T as the holotype and PYCC 10003T as the isotype. Considering pairwise sequence similarity, the type strain of the novel species differs from the type strain of the most closely related species, Wickerhamiella drosophilae CBS 8459T, by 16 nucleotide substitutions and two gaps (3.9 % sequence variation) in the D1/D2 region (560 bp compared) and 28 nucleotide substitutions and five gaps (7.22 % sequence variation) in the ITS region (444 bp compared).

Description of lipase producing novel yeast species Debaryomyces apis f.a., sp. nov. and a modified pH indicator dye-based method for the screening of lipase producing microorganisms

Four yeast strains were isolated from the gut of stingless bee, collected in Churdhar, Himachal Pradesh, India. Physiological characterization, morphological examination, and sequence analysis of small subunit ribosomal RNA (18S rRNA) genes, internal transcribed spacer (ITS) region, and D1/D2 domain of the large subunit rRNA gene revealed that the four strains isolated from the gut of stingless bee belonged to the Debaryomyces clade. Strain CIG-23HT showed sequence divergence of 7.5% from Debaryomyces nepalensis JCM 2095T, 7.8% from Debaryomyces udenii JCM 7855T, and Debaryomyces coudertii JCM 2387T in the D1/D2 domain. In the ITS region sequences, strain CIG-23HT showed a 15% sequence divergence from Debaryomyces nepalensis JCM 2095T and Debaryomyces coudertii JCM 2387T. In 18S rRNA gene sequence, the strain CIG-23HT showed 1.14% sequence divergence from Debaryomyces nepalensis JCM 2095 and and Debaryomyces coudertii JCM 2387, and 0.83% sequence divergence from Debaryomyces hansenii NRRL Y-7426. Strain CIG-23HT can utilize more carbon sources than closely related species. The findings suggest that strain CIG-23HT is a novel species of the genus Debaryomyces, and we propose to name it as Debaryomyces apis f.a., sp. nov. The holotype is CBS 16297T, and the isotypes are MTCC 12914T and KCTC 37024T. The MycoBank number of Debaryomyces apis f.a., sp. nov. is MB836065. Additionally, a method using cresol red and Bromothymol blue pH indicator dyes was developed to screen for lipase producers, which is more sensitive and efficient than the currently used phenol red and rhodamine B dye-based screening methods, and avoids the problem of less differentiable zone of hydrolysis.

Diversity of dung beetle-associated yeasts from pristine environments of Botswana

Yeast-insect interactions are increasingly becoming an attractive source of discovery for previously unknown, unique, diverse, and industrially relevant yeast species. Despite a wealth of studies that have recently focused on yeasts in symbiotic association with Hymenopteran insects, yeasts associated with Coleopteran insects, such as lignocellulosic-rich dung-dependent beetles, remain poorly studied. Trends in yeast discovery suggest that species richness and diversity can be attributed to the ecological niche of the insect. Here, we considered the potential of dung beetles inhabiting the extreme environments of Botswana, characterized by desert-like conditions (semi-arid to arid and hot) as well as protected pristine environments, as possible attribute niches that can shape the extremophilic and diverse life history strategies of yeasts. We obtained a total of 97 phylogenetically diverse yeast isolates from six species of dung beetles from Botswana's unexplored environments, representing 19 species belonging to 11 genera. The findings suggest that the guts of dung beetles are a rich niche for non-Saccharomyces yeast species. Meyerozyma and Pichia were the most dominant genera associated with dung beetles, representing 55% (53 out of 97) of the yeast isolates in our study. Trichosporon and Cutaneotrichosporon genera represented 32% (31 out of 97) of the isolates. The remaining isolates belonged to Apiotrichum, Candida, Diutina, Naganishia, Rhodotorula, and Wickerhamiella genera (12 out of 97). We found out that about 62% (60 out of 97) of the isolates were potentially new species because of their low internal transcribed spacer (ITS) sequence similarity when compared to the most recent optimal species delineation threshold. A single isolate was unidentifiable using the ITS sequences. Using an in silico polymerase chain reaction-restriction fragment length polymorphism approach, we revealed that there was genetic diversity within isolates of the same species. Our results contribute to the knowledge and understanding of the diversity of dung beetle-associated yeasts.

Wickerhamiella nakhonpathomensis f.a. sp. nov., a novel ascomycetous yeast species isolated from a mushroom and a flower in Thailand

Strains SU22T (TBRC 14875T) and FLA11.5, representing a novel anamorphic yeast species, were respectively isolated from a fruiting body of a Coprinus species and an inflorescence of a Coffea species collected in Thailand. Analysis of the sequences of the D1/D2 domains of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) regions showed that the two strains differed by two nucleotide substitutions in the D1/D2 domains of the LSU rRNA gene and were identical in the ITS regions. Wickerhamiella drosophilae CBS 8459T was the most closely related species, but with 24–26 nucleotide substitutions in the D1/D2 domains of the LSU rRNA gene and 24 nucleotide substitutions in the ITS regions. A phylogenetic analysis, based on the sequences of the D1/D2 domains, indicated that the two strains represented a species in the genus Wickerhamiella which was distinct from other recognized species of the genus. Therefore, the two strains were assigned as a novel species, for which we propose the name Wickerhamiella nakhonpathomensis f.a. sp. nov. The holotype is TBRC 14875T (isotype PYCC 8914T). The MycoBank number of the novel species is MB 840833.

Trends in yeast diversity discovery

Yeasts, usually defined as unicellular fungi, occur in various fungal lineages. Hence, they are not a taxonomic unit, but rather represent a fungal lifestyle shared by several unrelated lineages. Although the discovery of new yeast species occurs at an increasing speed, at the current rate it will likely take hundreds of years, if ever, before they will all be documented. Many parts of the earth, including many threatened habitats, remain unsampled for yeasts and many others are only superficially studied. Cold habitats, such as glaciers, are home to a specific community of cold-adapted yeasts, and, hence, there is some urgency to study such environments at locations where they might disappear soon due to anthropogenic climate change. The same is true for yeast communities in various natural forests that are impacted by deforestation and forest conversion. Many countries of the so-called Global South have not been sampled for yeasts, despite their economic promise. However, extensive research activity in Asia, especially China, has yielded many taxonomic novelties. Comparative genomics studies have demonstrated the presence of yeast species with a hybrid origin, many of them isolated from clinical or industrial environments. DNA-metabarcoding studies have demonstrated the prevalence, and in some cases dominance, of yeast species in soils and marine waters worldwide, including some surprising distributions, such as the unexpected and likely common presence of Malassezia yeasts in marine habitats.

Large biodiversity of yeasts in French Guiana and the description of Suhomyces coccinellae f.a. sp. nov. and Suhomyces faveliae f.a. sp. nov

The extent of the diversity of yeasts in tropical rain forest and different environments from French Guiana was investigated. A total of 365 samples were collected from various substrates, such as plants, fruits and insects, at 13 locations, yielding 276 pure yeast isolates. Sequence analysis of the D1/D2 domains of the large subunit rRNA gene indicated that 210 isolates out of 276 belonged to 82 described species (67 Saccharomycotina, 14 Basidiomycota and 1 Pezizomycotina). In addition to these, a total of 54 Saccharomycotina isolates could not be assigned to a known species. These belonged to 14 genera and should be studied further from a taxonomic point of view. In addition, among the 43 Basidiomycotina isolates found, 12 could not be assigned to a known species. This report shows an unexpected biodiversity and indicates that oversea territories, such as French Guiana, constitute a largely unexplored reservoir for yeast diversity. Two Saccharomycotina strains, CLIB 1706 and CLIB 1725, isolated from an insect and from a fern respectively, were characterized further and were shown to belong to the Suhomyces clade on the basis of the rDNA sequence comparison. CLIB 1706^TrDNA sequences showed nine substitutions and three indels out of 556 bp (D1/D2 domains) and 32 substitutions and 12 indels out of 380 bp [internal transcribed spacer (ITS)] with that of the most closely related species Suhomyces guaymorum CBS 9823^T. CLIB 1725^T rDNA sequences presented 18 substitutions and one indel out of 549 bp (D1/D2 domains) and 48 substitutions and 11 indels out of 398 bp (ITS) with that of its closest relative Suhomyces vadensis CBS 9454^T. Two novel species of the genus Suhomyces were described to accommodate these two strains: Suhomyces coccinellae f.a. sp. nov. (CLIB 1706^T=CBS 14298^T) and Suhomyces faveliae f.a. sp. nov. (CLIB 1725^T=CBS 14299^T).