Patogeensed ja arbuskulaarmükoriissed seened Eesti kartulipõldudel

A Thesis for applying for the degree of Doctor of Philosophy in Agricultural Sciences.Soil fungi have fundamental ecological roles as decomposers, mutualists, and pathogens of plants. Roots of agricultural plants are hosts for various microorganisms. These include many harmful, often soilborne, pathogens, as well as beneficial organisms such as plant growth- and health‐promoting arbuscular mycorrhizal (AM) fungi. Potato (Solanum tuberosum L.) yield and quality is very sensitive to various pathogens. Soils contain distinct AM fungal communities and most crops (including potato) naturally become colonized by AM fungi in the absence of inoculation. In the current thesis, diversity, abundance, and community composition of putative pathogenic fungi and symbiotic AM fungi in potato fields in Estonia is studied. We found that potato roots have higher AM fungal colonization levels under organic, rather than conventional, farming. However, colonization of potato roots by AM fungi is extremely low in both of these management types. Relative abundance of AM fungi is significantly higher at the end of the growing season compared to the beginning. Seasonal and cultivar-driven changes of soilborne phytopathogenic fungal communities in conventional potato production, both within roots and in soil, were studied for the first time on a large number of potato cultivars using high-throughput sequencing. Cultivar influenced root-pathogenic fungal richness and community composition more than sampling time or sampling time x cultivar interaction. Additionally, cultivar had a significant effect on root fungal pathogen relative abundance. In soil, the community composition of putative pathogenic fungi changed significantly over time. Under increasing threat of plant disease outbreaks, the speed of detection of plant disease agents is essential for avoiding large-scale crop losses. This thesis work demonstrated that the third-generation sequencing device MinION is well suited for rapid, PCR-free diagnosis of fungal pathogens and other eukaryotic organisms. However, care should be taken due to a number of possible limitations that might lead to misdiagnosis. Our findings demonstrate that AM fungi are present in Estonian conventional potato fields, but studied potato cultivars exhibit low AM root colonization levels. In order to benefit from AM fungi in potato cultivation, a potato growing technique that involves less soil disturbance could be used. The results of this thesis work also indicate the importance of plant breeding, concerning disease resistance; and offer implications for rapid pathogen diagnostics that may help to avoid large-scale crop losses caused by new, emerging pathogens that are undetectable from symptoms.Muld on elupaigaks miljonitele mikroorganismidele, sealhulgas nii taimekasvu kahjustavatele kui ka soodustavatele seentele. Kartuli (Solanum tuberosum L.) saagikust ja kvaliteeti ohustavad mitmed seenpatogeenid. Teisalt on kartul võimeline moodustama kasulike krohmseentega arbuskulaarset mükoriisat (AM). Käesolevas doktoritöös analüüsiti Eesti traditsioonilise kasvatustehnoloogiaga kartulipõldudel kartulijuuri ja mulda asustavate patogeensete seente ja taimedega sümbioosis kasvavate arbuskulaarmükoriissete seente mitmekesisuse näitajaid ning nende seoseid kartuli kasvufaasi ja sordiga. Lisaks katsetati ülikiireid protokolle taimekoest patogeenide tuvastamiseks. Käesoleva doktoritöö tulemused näitasid, et AM-seente kolonisatsioon oli üldiselt väga väike, kuid maheviljeluses oli see siiski suurem kui tavaviljeluses. Kartuli kasvuperioodi lõpus on põllumulla AM seente suhteline ohtrus võrreldes kasvuperioodi algusega oluliselt kõrgem. Selle põhjuseks võib olla kasvuperioodi alguses läbiviidavate mitmete järjestikuste mullaharimise häiringu võimalik mõju, mis aeglustab mullas looduslikult eksisteerivate AM seente ja lühikese kasvuajaga kartulitaime vahel sümbioosi tekkimist. Sekveneerimisel tuvastatud patogeensete seente suhteline ohtrus juurtes ja mullas sõltus nii taime kasvufaasist kui ka kartulisordist. Kui juurte patogeensete seente liigirikkust ja liigilist koosseisu mõjutas kartulisort, siis mulla patogeensete seeneliikide koosseisu mõjutas taime kasvufaas. Seega lubavad antud töö tulemused järeldada, et taimesortide geneetiline mitmekesisus põllul võib aidata luua põllukultuure ohustavatele patogeenidele vähem soodsa keskkonna ja seeläbi aidata luua jätkusuutlikuma agroökosüsteemi. Antud töö tulemusena leiti teadusele uudsena, et taskusekvenaatorit MinION-i saab kasutada taimekoes domineerivate patogeenide kiireks ja täpseks PCR-vabaks diagnoosimiseks. Siiski tuleb olla ettevaatlik mitmete võimalike analüüsimisel ette tulevate kõrvalekallete suhtes. Uuringute tulemused on kartulikasvatuses suure praktilise väärtusega ning kinnitavad, et krohmseened on kartulipõldudel olemas, kuid tänapäevased sordid ja kasvatustehnoloogiad ei soodusta AM seenekolonisatsiooni moodustumist. Töö tulemustest järeldub, et säästlikus kartulikasvatuses tuleb panustada rohkem sortide resistentsusaretusele ning juba aretusprogrammides võtta arvesse taim-mikroorganism vastastikuseid toimeid ja mõjusid. Antud uurimistöö tulemusena on võimalik parandada patogeenide kiiret diagnostikat, mis omakorda aitab kaasa taimepatogeenidest tingitud ulatuslike saagikadude vähendamisele.Publication of this thesis is supported by the Estonian University of Life Sciences and the European Union’s European Regional Development Fund (Estonian University of Life Sciences ASTRA project “Value-chain based bio-economy”)

Physiological disorders affect apple susceptibility to Penicillium expansum infection and increase probability for mycotoxin patulin occurrence in apple juice

ArticlePenicillium expansum infection of apples and mycotoxin patulin (PAT) production has previously been associated with many pre- and postharvest factors other than physiological disorders. In the current study, ‘Antei’ and ‘Krameri tuviõun’ apples with and without bitter pit (BP) symptoms and ‘Talvenauding’ apples with and without superficial scald (SS) symptoms were used in order to determine if the named physiological disorders may influence susceptibility to P. expansum infection and PAT production. Apples were inoculated with 10 μL P. expansum spore suspension with the concentration of 1×105 conidia mL-1 and stored at 24 °C with relative humidity (RH) 80%. After 7 and 11 days, lesion diameters were measured, and apples were pressed into juice. PAT content was determined in pasteurized juice. Two cultivars out of three showed that in fruit with physiological disorders, Penicilllium infection and PAT production proceeded significantly faster compared to apples, which did not have physiological disorders. SS increased the risk for PAT occurrence in juice more than BP: while the juice pressed from BP–affected apples with no visual signs of fungal diseases did not contain PAT, juice pressed from apples with SS contained PAT three times above legislative limits defined by the World Health Organization (50 μg L-1)

The indigenous arbuscular mycorrhizal fungal colonisation potential in potato roots is affected by agricultural treatments

ArticlesThere is an urgent need to develop novel approaches to enhance sustainable agriculture while not reducing cr op yields. Arbuscular mycorrhizal (AM) fungi establish symbiotic associations with most crop plants improving plant performance and soil health. This study investigated the extent of colonisation of potato roots by indigenous AM fungi in the arable soil under conventional and organic farming systems. Potato roots had greater AM fungal colonisation levels under organic than conventional farming, though in general, root colonisation levels were extremely low in both farming systems . Pota to root AM fungal colonisation was lower with higher soil P content and higher with higher annual C input. Trap plant root AM fungal colonisation was considerably higher than in field potato roots and showed that soil mycorrhizal inoculum potential was hig her in organic than in conventional farming. Thus, the positive impact of manure application in organic fields to the potato AM fungal colonisation can be explained by previous higher total annual C fresh organic matter input and lower soil P content under treatment. Furthermore, the natural AM fungal abundance in the soil was sufficient to colonise trap plant roots, suggesting a low mycorrhizal dependence of the studied potato cultivar

Cultivation technology influences the occurrence of potato early blight (Alternaria solani) in an organic farming system

Abstract Nowadays, organically produced products have become more popular than ever and interest in them is still growing fast. The early blight causal pathogen Alternaria solani has not been considered a great threat to potato in northern climate conditions in the past and has not been routinely sprayed against. During our study early blight was evaluated in 2010 and 2011 on the plants of a potato cultivar 'Reet' in an organic farming experiment. In our study, both growing seasons were very favourable for early blight development. Significant differences between the two cultivation technologies were found (F 1,12 = 4.84, p = 0.048). In 2010, the area under disease progress curve (AUDPC) value was 303 on cover crop (CC) plots and 990 on CC + M (manure) plots that is three times higher, whereas in 2011, the AUDPC value was 967 on CC plots and 1195 on CC + M plots. Our results confirm that potato early blight has become a serious problem in North-East European organic potato fields and thus susceptible potato cultivars cannot be recommended for growing in an organic farming system. However, it is possible to influence the development severity of early blight by selecting the proper growing technology. Since, in the changing climate conditions and in susceptible cultivars, early blight is a potato disease that can cause early defoliation of plants and crop death, there is a need for resistant potato cultivars

Regional-scale in-depth analysis of soil fungal diversity reveals strong pH and plant species effects in Northern Europe

Soil microbiome has a pivotal role in ecosystem functioning, yet little is known about its build-up from local to regional scales. In a multi-year regional-scale survey involving 1251 plots and long-read third-generation sequencing, we found that soil pH has the strongest effect on the diversity of fungi and its multiple taxonomic and functional groups. The pH effects were typically unimodal, usually both direct and indirect through tree species, soil nutrients or mold abundance. Individual tree species, particularlyPinus sylvestris,Picea abies, andPopulus x wettsteinii, and overall ectomycorrhizal plant proportion had relatively stronger effects on the diversity of biotrophic fungi than saprotrophic fungi. We found strong temporal sampling and investigator biases for the abundance of molds, but generally all spatial, temporal and microclimatic effects were weak. Richness of fungi and several functional groups was highest in woodlands and around ruins of buildings but lowest in bogs, with marked group-specific trends. In contrast to our expectations, diversity of soil fungi tended to be higher in forest island habitats potentially due to the edge effect, but fungal richness declined with island distance and in response to forest fragmentation. Virgin forests supported somewhat higher fungal diversity than old non-pristine forests, but there were no differences in richness between natural and anthropogenic habitats such as parks and coppiced gardens. Diversity of most fungal groups suffered from management of seminatural woodlands and parks and thinning of forests, but especially for forests the results depended on fungal group and time since partial harvesting. We conclude that the positive effects of tree diversity on overall fungal richness represent a combined niche effect of soil properties and intimate associations

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold

Temporal and Cultivar-Specific Effects on Potato Root and Soil Fungal Diversity

The soil fungal community plays an important role in determining plant growth and health. In this study, we investigated the fungal diversity and community composition in the roots and soil of 21 potato (Solanum tuberosum L.) cultivars using high-throughput sequencing at three different time points across the growing season. In soil and roots, the fungal richness and relative abundance of pathogens and saprotrophs were mainly affected by sampling time. While sampling time affected fungal composition in soil, root fungal communities were also significantly affected by cultivar. The cultivar had the strongest effect on diversity of pathogens and abundance of particular pathogen species. Our results demonstrate changes in soil and root fungal communities of potato over the growing season, as well as highlighting the importance of potato cultivar on root fungal communities and abundance of pathogens

Cultivation technology influences the occurrence of potato early blight (Alternaria solani) in an organic farming system

Nowadays, organically produced products have become more popular than ever and interest in them is still growing fast. The early blight causal pathogen Alternaria solani has not been considered a great threat to potato in northern climate conditions in the past and has not been routinely sprayed against. During our study early blight was evaluated in 2010 and 2011 on the plants of a potato cultivar ‘Reet’ in an organic farming experiment. In our study, both growing seasons were very favourable for early blight development. Significant differences between the two cultivation technologies were found (F1,12 = 4.84, p = 0.048). In 2010, the area under disease progress curve (AUDPC) value was 303 on cover crop (CC) plots and 990 on CC + M (manure) plots that is three times higher, whereas in 2011, the AUDPC value was 967 on CC plots and 1195 on CC + M plots. Our results confirm that potato early blight has become a serious problem in North-East European organic potato fields and thus susceptible potato cultivars cannot be recommended for growing in an organic farming system. However, it is possible to influence the development severity of early blight by selecting the proper growing technology. Since, in the changing climate conditions and in susceptible cultivars, early blight is a potato disease that can cause early defoliation of plants and crop death, there is a need for resistant potato cultivars