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.
What did we find in 2023-2024?
This was another big year for the undergraduate class -they discovered two new yeast species, which we hope to publish in 2025.
What did we find in 2022-2023?
The students produced the first genome sequences of Schwanniomyces capriottii . They also collaborated with Dr Richard McLaughlin from Gateway Technical College, Kenosha, to publish the genome sequences of two isolates of Candida zeylanoides.
McLaughlin RW, Hession C, Bergin S, Cosgrove A, Dowd A, Garvey N, Litovskich G, Osaigbovo E, Popa D, Thuku C, Butler G, Wolfe KH, Byrne KP.Microbiol Resour Announc. 2024 Mar 12;13(3):e0108123. doi: 10.1128/mra.01081-23. Epub 2024 Feb 9.PMID: 38334401
Heneghan PG, Ryan AP, Ó Cinnéide E, Davies J, Bracken C, Ogundipe V, Doheny M, Lenihan L, Passalaris A, Walker R, Wolfe KH, Butler G, Byrne KP.Microbiol Resour Announc. 2024 Mar 12;13(3):e0107323. doi: 10.1128/mra.01073-23. Epub 2024 Feb 5.PMID: 38315016 Free PMC article.
What did we find in 2021-2022?
2021/2022, was an important year for the undergraduate classes. 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 menglaensis
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 menglaensis 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.
What did we find in 2018-2019?
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
What did we find in 2017-2018?
The students published 3 short papers describing the genomes that they sequenced.
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
The UCD undergraduate students also discovered a new species in soil from a park in Dundrum, belonging to the Hanseniapora genus. Primary school students found more isolates in 2019, in soil samples collected by pupils from St Bernard’s NS (Abbeylara) in Co. Longford and from Kilcommon NS in Co. Tipperary. The smae species was discovered by a group in China, and named Hanseniaspora menglaensis. We published teh first genome sequence of this species in 2024.
Genome Analysis of a Newly Discovered Yeast Species, Hanseniaspora menglaensis.
Ryan AP, Groenewald M, Smith MT, Holohan C, Boekhout T, Wolfe KH, Butler G.J Fungi (Basel). 2024 Feb 28;10(3):180. doi: 10.3390/jof10030180.PMID: 38535189