Pichia anomala, from UC Davis.

Belongs within: Saccharomycetales.

In a Pichia
Published 8 October 2015
Culture of Pichia membranifaciens, from Tomas Linder.

In my previous post, I alluded to the revolutionary effect that DNA analysis had on the classification of bacteria. A similar thing happened for the study of yeasts. Previously, the taxonomy of yeasts (i.e. unicellular fungi) had suffered for the same reasons as bacterial taxonomy: a dearth of usable morphological features combined with uncertainty about the significance or otherwise of metabolic variations. With the availability of genetic information, the relations between yeast taxa became far easier to ascertain.

Needless to say, this lead to a significant shake-up in our understanding of individual yeast taxa. One of the harder-hit taxa was the genus Pichia, previously recognised as a large genus of close to 100 species. Molecular phylogenetic analyses showed that the various species of Pichia were widely scattered within the Saccharomycotina, a fungal clade that includes a large number of yeast species (including such familiar taxa as the brewer’s or baker’s yeast Saccharomyces cerevisiae). This probably did not come as a huge shock: part of the reason for Pichia‘s size was that it had not been very stringently defined. Members of this genus were characterised by multilateral budding (that is, buds could develop anywhere along the side of the yeast cell) on a narrow base. They could produce hyphae and/or pseudohyphae (except when they didn’t), they might ferment sugars (except when they couldn’t), and nitrate might be used as their sole source of nitrogen (except when it wasn’t). Pichia spores might be hat-shaped, hemispheroidal or spherical, and they might or might not have a ledge or rim around the equator (Kurtzman 2011).

All of which adds up to a genus that probably tended to be defined as ‘the genus that includes any yeast not belonging to these other genera’. In other words, the classic concept of a wastebasket taxon. As a result, the genus has been progressively pared down to a smaller array of species concentrated around the type, Pichia membranifaciens. This is a yeast commonly found as a spoilage organism on foods such as fruit or cheese. Among its other sins, it may grow as a film in the surface of wine, giving the wine an off taste. However, it’s not all bad news: recently, P. membranifaciens has been studied as a potential biocontrol agent as it may produce a toxin that has an inhibitory effect on other contaminating fungi (Santos et al. 2009).

A growing culture of Komagataella pastoris, from here.

Somewhat unfortunately, one of the species to be expelled from Pichia is perhaps the best-studied: the yeast formerly known as Pichia pastoris (now supposed to be referred to as Komagataella pastoris though a quick Google Scholar search suggests that a great many authors are pretending that hasn’t happened). This species can be grown using methanol as a sole carbon source, and protocols were developed in the 1970s for growing it in high densities at an industrial scale. The original plan was for it to be used for high-protein stock-feed using methanol produced as a by-product of oil refining (the modern agricultural industry has been described as the process of turning oil into food; this would have been a somewhat literal example). Rising oil prices rendered this proposal economically inviable but the P. pastoris industry was to have a reprieve, as the culture method was adopted as a means of producing active proteins (Cereghino & Cregg 2000). Procedures were developed for inserting foreign genes into the yeast, with the resulting pure methanol-based culture allowing the target protein to be generated at a greater rate and higher purity than might be possibly with a culture of the original source organism. Enzymes for laboratory studies, vaccines, medical products such as insulin: whatsitsname pastoris has been used in the production of them all.

Systematics of Pichia
Pichia Hansen 1904 (see below for synonymy)KC01
|--+--‘Williopsis’ salicorniaeYK99
| `--+--‘Candida’ kruseiYK99
| `--P. membranifaciensYK99
`--+--P. anomala [=*Hansenula anomala]YK99
`--Williopsis Zender 1925YK99, KC01
|--W. mucosaYK99
`--W. saturnusSL02
|--W. s. var. saturnusSL02
`--W. s. var. mrakiiSL02

Pichia incertae sedis:
‘Hyphopichia’ burtoniiFB20
P. canadensisLO02 [incl. Hansenula wingeiBS-L99]
P. capsulataSL02
P. ciferriiSL02
P. farinosaSL02
P. haplophilaSL02
P. minutaSL02
P. ofunaensisSL02
P. pastorisSL02
P. pijperiSL02
P. piniSL02
P. quercuumSL02
P. tannicolaSL02

Pichia Hansen 1904 [incl. Azymohansenula Novák & Zsolt 1961, Byrrha Bat., Monnier & Silveira 1959, Hansenula Syd. & Syd. 1919, Hyphopichia Arx & Van der Walt 1976, Komagataella Yamada, Matsuda et al. 1995, Kuraishia Yamada, Maeda & Mikata 1994, Nakazawaea Yamada, Maeda & Mikata 1994, Ogataea Yamada, Maeda & Mikata 1994, Petasospora Boidin & Abadie 1955, Willia Hansen 1904 non Müll. Hal. 1890, Yamadazyma Billon-Grand 1989, Zygohansenula Lodder 1932, Zygopichia (Klöcker) Kudrjanzev 1960, Zygowillia (Klöcker) Kudrjanzev 1960, Zymopichia Novák & Zsolt 1961]KC01

*Type species of generic name indicated


[BS-L99] Burger, G., D. Saint-Louis, M. W. Gray & B. F. Lang. 1999. Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea: cyanobacterial introns and shared ancestry of red and green algae. Plant Cell 11: 1675–1694.

Cereghino, J. L., & J. M. Cregg. 2000. Heterologous protein expression in the methylotrophic yeast Pichia pastoris. FEMS Microbiology Reviews 24: 45–66.

[FB20] Felden, A., J. W. Baty, M. Bulgarella, R. L. Brown, J. Dobelmann, M. A. M. Gruber, O. Quinn & P. J. Lester. 2020. Viral and fungal pathogens associated with Pneumolaelaps niutirani (Acari: Laelapidae): a mite found in diseased nests of Vespula wasps. Insectes Sociaux 67: 83–93.

[KC01] Kirk, P. M., P. F. Cannon, J. C. David & J. A. Stalpers. 2001. Ainsworth & Bisby’s Dictionary of the Fungi 9th ed. CAB International: Wallingford (UK).

Kurtzman, C. P. 2011. Phylogeny of the ascomycetous yeasts and the renaming of Pichia anomala to Wickerhamomyces anomalus. Antonie van Leeuwenhoek 99: 13–23.

[LO02] Lang, B. F., C. O’Kelly, T. Nerad, M. W. Gray & G. Burger. 2002. The closest unicellular relatives of animals. Current Biology 12: 1773–1778.

Santos, A., M. San Mauro, E. Bravo & D. Marquina. 2009. PMKT2, a new killer toxin from Pichia membranifaciens, and its promising biotechnological properties for control of the spoilage yeast Brettanomyces bruxellensis. Microbiology 155: 624–634.

[SL02] Schweigkofler, W., K. Lopandic, O. Molnár & H. Prillinger. 2002. Analysis of phylogenetic relationships among Ascomycota with yeast phases using ribosomal DNA sequences and cell wall sugars. Organisms Diversity & Evolution 2: 1–17.

[YK99] Yamada, Y., H. Kawasaki, Y. Nagatsuka, K. Mikata & T. Seki. 1999. The phylogeny of the cactophilic yeasts based on the 18S ribosomal RNA gene sequences: the proposals of Phaffomyces antillensis and Starmera caribaea, new combinations. Bioscience, Biotechnology, and Biochemistry 63: 827–832.

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