Fantastic Yeasts and Where to Find Them

Staff involved in teaching: Prof Geraldine Butler, Prof Ken Wolfe, Dr Tadhg Ó’Cróinín, Assoc Prof Peadar Ó Gaora, Dr Kevin Byrne, Dr Lisa Lombardi, plus many PhD students.

Welcome to the Wild Yeast Project at University College Dublin. Did you know that there are more organisms in a teaspoon of soil than there are people on the entire planet? Since 2017, UCD undergraduate students in Genetics and Microbiology have been surveying the yeasts living in Irish soil. Yeasts are fungi – they belong to the same family as mushrooms. However, yeasts often have have only one or a few cells, so they are easier to work with, and to grow in the lab. We don’t know what kinds of yeasts live in Irish soil, but we do know that they are required to keep the soil healthy. Climate change may affect the yeasts, so we want to find out what kinds (species) are living here as soon as possible. We are also interested in finding new species, and in sequencing the genomes of species that are poorly studied.

The students take part in two undergraduate research modules. In the first module, they collect soil samples from around Ireland, and use microbiological and genetic techniques to identify yeast species living in the soil. They then choose some interesting isolates, and in the second module they work out their genetic code (sequence and assemble the genomes). The students have identified some new yeast species, and sequenced the genomes of 10 species for the first time.

In 2021/2022, the undergraduate students gathered soil from the UCD campus. We found the first European isolates of the parent of lager yeasts, Saccharomyces eubayanus which you can read about here.

The class also published two short papers, describing the genome sequences of two yeasts for the first time.

Draft Genome Sequence of the Yeast Blastobotrys aristata Strain UCD613, Isolated from Soil in Ireland. Microbiol Resour Announc. 2022 Nov 17;11(11):e0095722. doi: 10.1128/mra.00957-2

Draft Genome Sequence of the Yeast Torulaspora quercuum Strain UCD657, Isolated from Soil in Ireland. Microbiol Resour Announc. 2022 Nov 17;11(11):e0095222. doi: 10.1128/mra.00952-22.

What did we find in 2019-2021?

In 2020/21 only the bioinformatics module was offered, because of lab shutdowns associated with the Covid-19 pandemic. In 2019/2020 primary school pupils helped us to collect soil samples (see below).

You can see the location of the 15 primary schools from 13 counties in Ireland who helped us on the map below. If you click on the spots you will find more information about the schools.

We found one species that has only been described once before. This is called Ogataea degrootiae, and it was collected by pupils from Kilglass NS, Co. Sligo. This species was first discovered in 2018 by school pupils in the Netherlands (see here). However, the Netherlands study didn’t sequence the genome (work out the genetic code) of the species. UCD students were the first to do that, and they published their work here, with an acknowledgement to the children from Kilglass.

Papers from the 2019-21 classes

Draft Genome Sequence of the Yeast Ogataea degrootiae Strain UCD465, Isolated from Soil in Ireland. Microbiol Resour Announc. 2021 Sep 30;10(39):e0073621. doi: 10.1128/MRA.00736-21.

Draft Genome Sequence of a Diploid and Hybrid Candida Strain, Candida sanyaensis UCD423, Isolated from Compost in Ireland. Microbiol Resour Announc. 2021 Sep 23;10(38):e0076121. doi: 10.1128/MRA.00761-21

Species identified soil samples from primary schools (species in bold chosen for further study)

St Finians NS, Garryhill, Co. Carlow: Pichia fermentans, Schwanniomyces capriotti, Candida sake, Kazachstania servazzii

Urhan NS, Co. Cork: Barnettozyma californica, Kazachstania servazzii, Cyberlindnera suaveolens 

Leap NS, Co. Cork: Hanseniaspora uvarum

Knockaderry NS, Co. Kerry: Wickerhamomyces anomalus

Allen NS, Co. Kildare: Wickerhamomyces anomalus

Abbeyleix South NS, Co. Laois: Vanrija albida

St. Brigid’s NS, Co. Limerick: Barnettozyma californica

St. Bernard’s NS Co. Longford: Kazachstania servazzii, Hanseniaspora scholastica

Whitecross Primary School, Co. Meath: Torulaspora delbrueckii

St. Ciarán’s NS, Co. Offaly: Saccharomyces paradoxus, Kazachstania servazzii

Castleplunkett NS, Co. Roscommon: Wickerhamomyces anomalus

Kilglass NS, Co. Sligo: Naumovozyma castellii, Ogataea degrootiae, Saccharomyces paradoxus

Kilcommon NS, Co. Tipperary: Hanseniaspora uvarum, Hanseniaspora scholastica, Saccharomyces paradoxus, Barnettozyma californica

New Ross Educate Together NS, Co. Wexford: Candida tropicalis

Gorey Educate Together, Co.  Wexford: Kazachstania servazzii, Kazachstania marxianus, Hanseniaspora uvarum, Torulaspora delbrueckii.

In 2018/2019, the students published 3 short papers.

Draft Genome Sequence of the Birch Tree Fungal Pathogen Taphrina betulina UCD315. Microbiol Resour Announc. 2019 Nov 27;8(48):e01255-19. doi: 10.1128/MRA.01255-19.

Draft Genome Sequences of Two Isolates of the Yeast Kazachstania servazzii Recovered from Soil in Ireland. Microbiol Resour Announc. 2019 Oct 31;8(44):e01257-19. doi: 10.1128/MRA.01257-19

Draft Genome Sequence of a Red Basidiomycete Yeast, Symmetrospora coprosmae Strain UCD350, Isolated from Soil in Ireland. Microbiol Resour Announc. 2019 Oct 31;8(44):e01256-19. doi: 10.1128/MRA.01256-19

In 2017, UCD undergraduate students discovered a new species in soil from a park in Dundrum. They called it Hanseniaspora scholastica (named after student). Primary school students found this twice in 2019, in soil samples collected by pupils from St Bernard’s NS (Abbeylara) in Co. Longford and from Kilcommon NS in Co. Tipperary. We now know that Hanseniaspora scholastica is probably quite common in Ireland. We are still working on publishing a description (and the genome) of this species. The students published 3 other short papers.

Draft Genome Sequence of a Highly Heterozygous Yeast Strain from the Metschnikowia pulcherrima Subclade, UCD127. Genome Announc. 2018 Jun 21;6(25):e00550-18. doi: 10.1128/genomeA.00550-18

Draft Genome Sequence of the Yeast Nadsonia starkeyi-henricii UCD142, Isolated from Forest Soil in Ireland. Genome Announc. 2018 Jun 21;6(25):e00549-18. doi: 10.1128/genomeA.00549-18

Draft Genome Sequences of Two Natural Isolates of the Yeast Barnettozyma californica from Ireland, UCD09 and UCD89. Genome Announc. 2018 Jun 21;6(25):e00548-18. doi: 10.1128/genomeA.00548-18