Compost as an untapped niche for thermotolerant yeasts capable of high-temperature ethanol production

Dissecting an ancient stress resistance trait syndrome in the compost yeast Kluyveromyces marxianus

In the search to understand how evolution builds new traits, ancient events are often the hardest to dissect. Species-unique traits pose a particular challenge for geneticists-cases in which a character arose long ago and, in the modern day, is conserved within a species, distinguishing it from reproductively isolated relatives. In this work, we have developed the budding yeast genus Kluyveromyces as a model for mechanistic dissection of trait variation across species boundaries. Phenotypic profiling revealed robust heat and chemical-stress tolerance phenotypes that distinguished the compost yeast K. marxianus from the rest of the clade. We used culture-based, transcriptomic, and genetic approaches to characterize the metabolic requirements of the K. marxianus trait syndrome. We then generated a population-genomic resource for K. marxianus and harnessed it in molecular-evolution analyses, which found hundreds of housekeeping genes with evidence for adaptive protein variation unique to this species. Our data support a model in which, in the distant past, K. marxianus underwent a vastly complex remodeling of its proteome to achieve stress resistance. Such a polygenic architecture, involving nucleotide-level allelic variation on a massive scale, is consistent with theoretical models of the mechanisms of long-term adaptation, and suggests principles of broad relevance for interspecies trait genetics.

Yeast community succession in cow dung composting process

Yeast complexes in the composting process of cow dung prepared to fertilize the soil for growing vegetables and fruits were studied. The average abundance of yeasts changed during the four temperature stages of the composting process. The highest abundance of yeasts, 1.38 × 10⁴ cfu/g, was observed in the second stage of heating from 20 to 40 °C; the lowest was studied in the stage with the highest temperature (65 °C), 1.68 × 10³ cfu/g. A total of 19 yeast species were observed and identified: 11 ascomycetes and 8 basidiomycetes, belonging to five subphyla of Fungi: Saccharomycotina (10), Pezizomycotina (1), Agaricomycotina (5), Pucciniomycotina (2), and Ustilaginomycotina (1). The greatest diversity of yeasts was found in the initial (20 °C) and second (heating up to 40 °C) temperature stages of composting (Aureobasidium pullulans (yeast-like fungus), Candida parapsilosis, Candida saitoana, Candida santamariae, Candida tropicalis, Curvibasidium cygneicollum, Cutaneotrichosporon moniliforme, Debaryomyces fabryi, Debaryomyces hansenii, Filobasidium magnum, Kazachstania sp., Moesziomyces bullatus, Naganishia globosa, Papiliotrema flavescens, Rhodotorula mucilaginosa, Scheffersomyces insectosa, Torulaspora delbrueckii, Vanrija musci), and the lowest in the stage of maximum heating (65 °C) (C. parapsilosis, C. tropicalis, Cyberlindnera jadinii).The opportunistic yeasts C. parapsilosis and C. tropicalis were obtained not only in the initial, second and third temperature stages of the composting process, but also in mature compost in the final stage prepared for soil application. This study shows that the cow dung, used in the farm studied did not meet the microbiological safety criteria. The reduction of opportunistic yeast species was not achieved with the composting method used. The likelihood of these species entering agricultural products via compost and soil and developing as endophytes in the internal tissues of fruits is very high. Since some strains of opportunistic Candida species from cow dung exhibited virulent characteristics (they produced hydrolytic enzymes and were resistant to antifungal compounds), additional phenotypic and genetic studies of the compost strains and their comparison with clinical isolates should be pursued.