Taphrina as model phytopathogenic yeasts infecting the model plant Arabidopsis and woody plant Betula pendula

Plants constantly interact with microorganisms, including bacteria, and fungi, including yeasts. Plant-associated yeasts have not been studied as much as plant-associated fungi and bacteria. Yeast-like fungi that interact with plants can be pathogenic, neutral residents, or plant growth promoting. Yeast-like fungi can be found in or on all parts of the plant, and their role in the phyllosphere is currently receiving more attention. The plant-associated yeast species studied in this thesis are Taphrina, a genus of dimorphic yeast-like fungi, which are able to switch lifestyle from yeast to filamentous fungi when their environment is favourable. In this thesis Taphrina species were investigated as model phytopathogenic yeast-like fungi by observing the interaction of T. betulina with Betula pendula (European silver birch) and developing a Taphrina infection system with the genetic model plant, Arabidopsis thaliana (hereafter referred to as Arabidopsis). This thesis shows that T. betulina, which causes witches’ broom disease in birch, was the predominant yeast in the phylloplane of both symptomatic and asymptomatic B. pendula. Fifty-seven strains of T. betulina with seven different genotypes were found. One of the seven genotypes was found to be dominant and was common in infected trees, but was also found at lower levels in samples from healthier trees. Moreover, since T. betulina causes witches' broom disease in B. pendula, the tumour morphology in birch infected by T. betulina was characterized in this thesis. Further, the distribution of susceptible and resistant birch trees provided evidence that suggests there may be genetic resistance against T. betulina in the birch population. To develop the infection system of Taphrina in the model plant Arabidopsis, Taphrina strain M11, previously isolated from wild Arabidopsis, was used. The M11 strain caused symptoms of disease in Arabidopsis, including leaf deformations in the form of leaf bending and leaf curling. In addition, this result was supported by several tests that showed activation of auxin- and cytokinin-signalling during infection, which may be part of the pathogenic yeast invasion strategy against its host. A high-quality draft genome assembly for Taphrina strain M11 was obtained. In addition, as candidate effector proteins, 767 short secreted proteins (SSPs) were found in the M11 genome. No LysM domain containing SSPs were found, suggesting that chitin has a minor role in Taphrina-host interactions. Furthermore, infections with plant hormone signalling mutants showed that jasmonic acid and ethylene are major hormones in plant defence against Taphrina M11. In growth tests, M11 became more abundant on Arabidopsis leaves compared to related Taphrina strains and was able to form biofilms. Furthermore, M11 has been identified as a strain of T. tormentillae. Thus, this thesis shows that Taphrina has potential as a model of phytopathogenic yeasts infecting the model plant Arabidopsis and the woody plant B. pendula.Muihin kasvien kanssa tavattaviin mikrobeihin verrattuna hiivat ovat hyvin vähän tutkittuja. Hiivan tapaiset sienet vuorovaikuttavat kasvien kanssa joko patogeeneinä, pöytävierassuhteessa tai hyödyllisinä symbiontteina. Väitöskirjani kasvien kanssa vuorovaikuttavat hiivalajit kuuluvat sukuun Taphrina, jonka sienet kykenevät muuttamaan elintapansa hiivamaisesta rihmamaiseksi. Taphrina betulina aiheuttaa koivulla tuulenpesiä. Tähän tautiin keskittynyttä tutkimusta on rajallisesti, mutta saatavilla olevat harvat tutkimukset esittävät, että taudin aiheuttamaa negatiivista vaikutusta on mahdollisesti aliarvioitu. Väitöskirjallani oli kolme tavoitetta: 1) Saavuttaa käsitys tuulenpesä-sienitaudista Betula pendula -koivuissa löytämällä kasvaimen kasvun lähtöpisteenä toimiva puukudos. 2) Ymmärtää paikallista T. betulina infektioekologiaa tarkkailemalla terveessä koivussa olevia Taphrina-sieniä ja muita hiivasieniä ja vertailemalla niitä T. betulina-infektion oireita ilmentävään koivuun. 3) Määritellä molekulaariset puolustusmekanismit hiivapatogeeniä vastaan käyttämällä Arabidopsis-mallijärjestelmää, jolla selvitettiin T. betulina-patogeenin vastaisen puolustusreaktion signalointireittejä. Tässä väitöskirjassa tutkittiin T. betulina-kasvaimia ja määritettiin oireiden kehittymisen kudosspesifisyys infektioiden aikana. T. betulina-kannat on eristetty yksinomaan sairaista koivuista ja väitöskirjassa näytetään, että T. betulina-sientä löytyy myös terveistä koivuista. T. betulina oli hallitseva hiiva kasvin lehdistön pinnalla sekä sairaissa että silmämääräisesti terveissä B. pendula-koivuissa. Taphrina-infektiojärjestelmän kehittämiseksi Arabidopsis-mallikasvilla käytettiin aiemmin villiltä Arabidopsis-kasvilta eristettyä M11 Taphrina-kantaa. M11 aiheutti Arabidopsis-kasvissa taudinoireita, kuten lehtien epämuodostumia, osoittaen jossain määrin samankaltaisuutta muiden Taphrina-lajien lehtioireisiin niiden isäntäkasveissa. Väitöskirja sisältää myös M11-infektoituneen Arabidopsis-kasvin infektiofenotyyppien ja hormonivasteiden karakterisoinnin. Näin ollen tämä väitöskirjatyö osoittaa, että Taphrina-suvun lajeilla on potentiaalia malliksi fytopatogeenisista hiivoista, jotka voivat infektoida Arabidopsis-mallikasvin ja puuvartisen kasvin B. pendula

Effect of fungus Taphrina infection on birch (Betula pendula) xylem morphology and hydraulic conduction

Magistritöö Vee ja maismaa ökosüsteemide rakendusbioloogia õppekavalKäesoleva magistritöö eesmärgiks on uurida Taphrina seene avaldatavat mõju kase ksüleemi morfoloogiale ja hüdraulilisele juhtivusele. Taphrina seen on kottseente hõimkonda kuuluv parasiitseen, hõimkonna tuntuim seen on Taphrina deformans – virsikupuu lehti deformeeriv parasiitseen, mida on kõige rohkem uuritud, kuna see tekitab majanduslikku kahju. Antud töös keskendutakse kaske kahjustavale parasiitseene liigile Taphrina betula (kaseluudik), mis tekitab puuokstele visuaalselt nähtavaid kahjustusi – tuulepesi. Eesmärgi saavutamiseks koguti proove kahest kohast: Tähtvere pargist Tartu linnas ja linna külje all Ihastes asuvalt Anne looduskaitsealalt. Töö käigus uuriti ksüleemitorude suurust ja tihedust, erinevusi mõõdeti fotodelt mikroskoobi all. Selgus, et kontrollproovidel oli ksüleemitorude diameeter suurem kui nakatunud proovidel, seda 9/13, ka oli nakatunud proovidel ksüleemitorude tihedus suurem kui nakatumata proovidel. Töö tulemustes jõuame järeldusele, et Taphrina seenparasiit avaldab mõju kase puidule, mõjutades selle ksüleemitorude suurust ja tihedust. Sellest tulenevalt võib järeldada, et taime hüdrauliline juhtivus on samuti mõjutatud, kuna see sõltub ksüleemitorudest ning nende morfoloogiast, siiski hüdraulilise juhtivuse aspekt vajab tulevikus täiendavat uurimist.The aim of this Master’s thesis was to research the influance of the Taphrina fungi on the morphology and hydraulic conductivity of European white birch (Betula pendula). The Taphrina is a fungal genus within the Ascomycota phylum, the most famous species of the division is Taphrina deformans which is infamous of infecting peach trees and is most studied because of economic damage it causes. This thesis focuses on the species Taphrina betulina, which causes visible deformity in a woody plant known as Witch’s brooms. To achieve the goal, samples were collected from two places: Tähtvere Park in Tartu and the Anne Nature Reserv located in Ihaste near the City Tartu. During the study, the size and density of xylem were examined. Differences were measured from photos made by microscope. It turned out that the control samples had a larger xylem diameeter, 9 of 13 samples had larger diameeter, also infected samples had higher xylem density than noninfected samples. In the result of this thesis, we concluded that Taphrina betulina fungus affects the birch wood, affecting the size and density of its xylem. Consequently, it can be concluded that the hydraulic conductivity of the plant is also affected, since it depends on the xylem morphology, however, the aspect of hydraulic conductivity needs further investigation

Genomics and evolution of Pneumocystis species.

The genus Pneumocystis comprises highly diversified fungal species that cause severe pneumonia in individuals with a deficient immune system. These fungi infect exclusively mammals and present a strict host species specificity. These species have co-diverged with their hosts for long periods of time (> 100 MYA). Details of their biology and evolution are fragmentary mainly because of a lack of an established long-term culture system. Recent genomic advances have unlocked new areas of research and allow new hypotheses to be tested. We review here new findings of the genomic studies in relation with the evolutionary trajectory of these fungi and discuss the impact of genomic data analysis in the context of the population genetics. The combination of slow genome decay and limited expansion of specific gene families and introns reflect intimate interactions of these species with their hosts. The evolutionary adaptation of these organisms is profoundly influenced by their population structure, which in turn is determined by intrinsic features such as their self-fertilizing mating system, high host specificity, long generation times, and transmission mode. Essential key questions concerning their adaptation and speciation remain to be answered. The next cornerstone will consist in the establishment of a long-term culture system and genetic manipulation that should allow unravelling the driving forces of Pneumocystis species evolution