Fungal pathogens distribution and dynamics in managed conifer stands after final felling

Juuremädanikud on okaspuudele suurimat majanduslikku kahju tekitavad patogeenid. Raiete järgselt tekkinud kännud on kõige ohtlikumale juuremädaniku tekitajale, s. o juurepessule (Heterobasidion spp.) heaks levimisviisiks, ning patogeeni esinemist ning tekitatud kahju ulatust on oluline uurida. Magistritöö peamine eesmärk oli kirjeldada olulisemate juuremädanike tekitajate esinemist ning dünaamikat viljakas metsamullas vahetult peale uuendusraiet ning aasta hiljem. 25-st kuuse- ning 25-st männienamusega puistust, ning sama paljudelt kontrollaladelt koguti kahel järjestikusel aastal kokku 200 mullaproovi, millest määrati Ilumina sekveneerimise meetodil mullaelustiku koosseisud. Saadud nukleotiidide järjestused määrati automaatselt taksoniteks 97 % identsusega INSD ja UNITE andmebaaside abil. Kokku tuvastati 88 976 taksonoomilist üksust, millest 82 000 kuulusid seeneriiki. Kõige enam seeni (50%) kuulus kandseente (Basidiomycota) hõimkonda, seeneliike tuvastati 1270. Kahel järjestikusel aastal ei olnud juurepessu ega külmaseene (Armillaria spp.) osakaal raiumata ja raiutud kuusikute ega männikute võrdluses statistiliselt usaldatavalt erinevad. Kuusikutes esines külmaseent ning juurepessu enam kui männikutes, samuti mädanikuga kändusid. Saadud andmemaht võimaldab erinevate seenerühmade edasist uurimist. Edasistes juuremädanike analüüsides võetakse hinnangutesse olulisi parameetreid nagu muldade keemiline koostis ja mullatüüp, ning antagonistide osakaal mullas.Root rot is one of the most dangerous pathogen on conifers and this is caused high economical loss for forestry in northern Europe. The tree stumps that are formed after felling are a good substrate for the colonization of Heterobasidion spp. Therefore, it is important to study the occurrence and extent of the damage caused by the root rot pathogens. The aim of the master thesis was to characterize pathogenic fungal communities and dynamics of 50 conifer (Pinus sylvestris and Picea abies) clear-cut areas on fertile forest site types recently after felling and one year apart, with the emphasis on root rot pathogens. Another 50 areas were chosen for control areas, where the soil samples were collected on two consecutive years. The collected samplings were analysed with Illumina sequencing to determine the structure of the fungal biota. The sequences were automatically designated to taxon units according to similarity level of 97% by INSD and UNITE databases. 88 976 taxonomic units were detected, of which 82 000 was a part of the fungi. The majority of the analysed fungi belonged to the Basidiomycota with 1270 taxon units. On the analysed consecutive years the proportions of Heterobasidion and Armillaria spp. did not differ statistically significantly depending on the management activity (clear-cut area and control area) nor the pine and spruce dominating stands. The Armillaria spp and Heterobasidion spp occurred more frequently in spruce forests. The collected data enables to study different groups of fungi more specifically. Further studies about the root rot analyses should also regard different important characteristics, e.g. the soil chemical composition, the soil type and the proportion of antagonists in the soi

Soil mycobiomes in native European aspen forests and hybrid aspen plantations have a similar fungal richness but different compositions, mainly driven by edaphic and floristic factors

BackgroundThe cultivation of short-rotation tree species on non-forest land is increasing due to the growing demand for woody biomass for the future bioeconomy and to mitigate climate change impacts. However, forest plantations are often seen as a trade-off between climate benefits and low biodiversity. The diversity and composition of soil fungal biota in plantations of hybrid aspen, one of the most planted tree species for short-rotation forestry in Northern Europe, are poorly studied.MethodsThe goal of this study was to obtain baseline knowledge about the soil fungal biota and the edaphic, floristic and management factors that drive fungal richness and communities in 18-year-old hybrid aspen plantations on former agricultural soils and compare the fungal biota with those of European aspen stands on native forest land in a 130-year chronosequence. Sites were categorized as hybrid aspen (17–18-year-old plantations) and native aspen stands of three age classes (8–29, 30–55, and 65-131-year-old stands). High-throughput sequencing was applied to soil samples to investigate fungal diversity and assemblages.ResultsNative aspen forests showed a higher ectomycorrhizal (EcM) fungal OTU richness than plantations, regardless of forest age. Short-distance type EcM genera dominated in both plantations and forests. The richness of saprotrophic fungi was similar between native forest and plantation sites and was highest in the middle-aged class (30–55-year-old stands) in the native aspen stands. The fungal communities of native forests and plantations were significantly different. Community composition varied more, and the natural forest sites were more diverse than the relatively homogeneous plantations. Soil pH was the best explanatory variable to describe soil fungal communities in hybrid aspen stands. Soil fungal community composition did not show any clear patterns between the age classes of native aspen stands.ConclusionWe conclude that edaphic factors are more important in describing fungal communities in both native aspen forest sites and hybrid aspen plantation sites than forest thinning, age, or former land use for plantations. Although first-generation hybrid aspen plantations and native forests are similar in overall fungal diversity, their taxonomic and functional composition is strikingly different. Therefore, hybrid aspen plantations can be used to reduce felling pressure on native forests; however, our knowledge is still insufficient to conclude that plantations could replace native aspen forests from the soil biodiversity perspective

RMK lepinguline projekt 2016 - 2019: Kuusikute raieaja ja raieviiside mõju patogeenide levikule ja arvukusele ning puistu elurikkusele viljakates kasvukohatüüpides lõpparuande pikem versioon (LISA)

Käesolev uurimustöö on Eesti Maaülikooli ja Tartu Ülikooli kolme aastane lepinguline koostööprojekt. Iga osa koostasid või selle osa sisulist analüüsi juhtisid erinevad autorid, kes on nimetatud iga vastava aruande osa ees. Töö eesmärk on selgitada hariliku kuuse puistute majandamise (hooldus-, harvendus- ja sanitaarraie) mõju juuremädanike levikule ja kahjustusele ning seente ja epifüütide elurikkusele võrrelduna majandamata (raiumata) puistutega. Lepinguline töö jagunes järgmisteks osadeks: mullaseente elustik, lamapuidu seente elustik, seente elustik eluspuude puidus ja kändudes, samblike ja sammalde elustik, juurepessu antagonistid ning metsamajanduslik osa. Viimane sisaldab mädanike kahjude hinnanguid kuusikutes ja selle majanduslikke kalkulatsioone. Lepingulise koostööprojekti eesmärgid olid järgmised: 1. Hinnata erinevate metsamajandamise võtete, hooldusraiete korduse ning teostamise aja (puistu vanus ja aastaaeg) mõju patogeenide arvukusele, mullaelustikule ja epifüütidele viljakates kuuse-enamusega metsades. 2. Analüüsida teaduslikult kuusikute raieringi pikkuse mõju kuuse tüvepuidu sortimentide väljatulekule, tüvekahjustuste ulatusele ja elurikkusele. 3. Hinnata juuremädanikest tingitud majandusliku kahju suurust ja patogeenide arvukust viljakates kuusepuistutes (sh kändudes ja mullas) ning ühtlasi tuvastada potentsiaalseid juuremädanike antagoniste Eesti mulla- ja kliimatingimustes. 4. Koostada arvutusmudelid, mis võimaldavad erinevate sisendite (mädanike osakaal ja levik tüves, hooldusraiete aeg puistu vanusest ja vegetatsiooniperioodist lähtuvalt, mulla elurikkus) abil kirjeldada kuusikute kasvukäiku ja arvutada erinevaid tegureid arvestavad küpsusvanused, nt mahu- ja hinnaküpsus

Global patterns in endemicity and vulnerability of soil fungi

Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms

Connecting the multiple dimensions of global soil fungal diversity

15 páginas.- 5 figuras.- 99 referenciasHow the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.This work was supported by the Estonian Science Foundation: PRG632 (to L.T.), Estonian Research Council: PRG1615 (to R.D.), Estonian Research Council: PRG1170 (to U.K. and Ka.Po.), Estonian Science Foundation: MOBTP198 (to St.An.), Novo Nordisk Fonden: NNF20OC0059948 (to L.T.), Norway-Baltic financial mechanism: EMP442 (to L.T., K.-A.B., and M.T.), King Saud University: DFSP-2020-2 (to L.T.), King Saud University: Highly Cited Program (to L.T.), European Regional Development Fund: Centre of Excellence EcolChange TK131 (to M.O., M.Z., Ü.M., U.K., and M.E.), Estonian Research Council: PRG1789 (to M.O. and I.H.), British Ecological Society: LRB17\1019 (MUSGONET) (to M.D.-B.), Spanish Ministry of Science and Innovation: PID2020-115813RA-I00 (to M.D.-B.), Spanish Ministry of Science and Innovation: SOIL4GROWTH (to M.D.-B.), Marie Sklodowska-Curie: 702057 (CLIMIFUN) (to M.D.- B.), European Research Council (ERC): grant 647038 [BIODESERT] (to F.T.M.), Generalitat Valenciana: CIDEGENT/2018/041 (to F.T.M.), Spanish Ministry of Science and Innovation: EUR2022-134048 (to F.T.M.), Estonian Research Council: PRG1065 (to M.M. and M.Z.), Swedish Research Council Formas: 2020-00807 (to Mo.Ba.), Swedish Research Council: 2019-05191 (to Al. An.), Swedish Foundation for Strategic Environmental Research MISTRA: Project BioPath (to Al. An.), Kew Foundation (to Al.An.), EEA Financial Mechanism Baltic Research Programme in Estonia: EMP442 (to Ke.Ar. and Je.An.), Ghent University Special Research Fund (BOF): Metusalem (to N.S.), Estonian Research Council: PSG825 (to K.R.), European Research Council (ERC): 101096403 (MLTOM23415R) (to Ü.M.), European Regional Development Fund (ERDF): 1.1.1.2/VIAA/2/18/298 (to D.K.), Estonian Research Council: PUT1170 (to I.H.), German Federal Ministry of Education and Research (BMBF): 01DG20015FunTrAf (to K.T.I., M.P., and N.Y.), Proyecto SIA: SA77210019 (ANID—Chile) (to C.M.), Fondecyt: 1190642 (ANID—Chile) (to R.G.), European Research Council (ERC): Synergy Grant 856506—LIFEPLAN (to T.R.), Academy of Finland: grant 322266 (to T.R.), U.S. National Science Foundation: DEB-0918591 (to T.H.), U.S. National Science Foundation: DEB-1556338 (to T.H.), U.S. National Science Foundation: DEB 1737898 (to G.B.), UNAM-PAPIIT: IV200223 (to R.G.-O.), Czech Science Foundation: 21-26883S (to J.D.), Estonian Research Council: PRG352 (to M.E.), NERC core funding: the BAS Biodiversity, Evolution and Adaptation Team (to K.K.N.), NERC-CONICYT: NE/P003079/1 (to E.M.B.), Carlsberg Foundation: CF18-0267 (to E.M.B.), Qatar Petroleum: QUEX-CAS-QP-RD-18/19 (to Ju.Al.), Russian Ministry of Science and Higher Education: 075-15-2021-1396 (to V.F. and V.O.), Secretaria de Ciencia y Técnica (SECYT) of Universidad Nacional de Córdoba and CONICET (to E.N.), HighLevel Talent Recruitment Plan of Yunnan Province 2021:“High-End Foreign Experts” (to Pe.Mo.), AUA grant from research council of UAE University: G00003654 (to S.M.), Ghent University: Bijzonder Onderzoeksfonds (to A.V.), Ghent University: Bijzonder Onderzoeksfonds (BOF-PDO2017-001201) (to E.D.C.), Ghent University: The Faculty Committee Scientific Research, FCWO (to E.D.C. and A.V.), The King Leopold III Fund for Nature Exploration and Conservation (to A.V. and E.D.C.), The Research Foundation—Flanders (FWO) (to E.D.C. and A.V.), The High-Level Talent Recruitment Plan of Yunnan Provinces: “Young Talents” Program (to D.-Q.D.), The HighLevel Talent Recruitment Plan of Yunnan Provinces: “High-End Foreign Experts" Program (to N. N.W.), IRIS scholarship for progressive and ambitious women (to L.H.), Estonian University of Life Sciences: P190250PKKH (to Kr.Pa.), Hungarian Academy of Sciences: Lendület Programme (96049) (to J.G.), Eötvös Loránd Research Network (to J.G.), Botswana International University of Science and Technology (to C.N.), and Higher Education Commision (HEC, Islamabad, Pakistan): Indigenous and International research support initiative program (IRSIP) scholarship (to M.S.)Peer reviewe

Connecting the multiple dimensions of global soil fungal diversity

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes

Occurrence of the root rot after thinning on spruce stands

Juuremädaniku tekitaja Heterobasidion spp. tekitab hariliku kuuse puistutes tõsist majanduslikku kahju. Harvendusraiete mõju juurepessu levikule on märkimisväärne. Bakalaureusetöö eesmärgiks on välja selgitada kui ulatuslikult ja mis liiki juuremädanike tekitajatega on hariliku kuuse puistud viljakates kasvukohatüüpides (jänesekapsa, naadi ja sinilille) harvendusraiete järgselt nakatunud; hinnata mädaniku esinemist, arvestades alade ajalugu, puistu vanust, liigilist koosseisu ning kasvukohatüüpe. Uurimuse jaoks koguti 2013. aasta sügisel andmeid kümnelt proovitükilt hariliku kuuse puistust ja 99-lt puult, Tartumaa metskonnast ning Järvselja Õppe- ja Katsemetskonnast. Harvendusraied olid läbi viidud erinevatel aegadel: talvel, varakevadel ja suvel. Kolmel katsealal oli tehtud kaks ja enam harvendusraiet. Kogutud juurdekasvuproove analüüsiti laboris mädaniku hindamiseks ning liikide määramiseks. Resistograafiga saadud andmeid kasutati samuti mädanikuga puude hindamiseks puistus ning saadud andmed võrreldi juurdekasvuproovidega. Kümnest uuritud kuuse enamusega puistust olid juuremädanike tekitajatega nakatunud kaheksa. Rohkem määrati kuuse-juurepessu (Heterobasidion parviporum) esinemist, kuid kahest kuusepuistust leiti ka männi-juurepessu (Heterobasidion annosum). Külmaseent (Armillaria spp.) uuritud puudel ei esinenud. Tüvemädanikku esines viies puistus, neist ühel alal märgiti mädaniku esinemine 10-st puust neljal, teises puistutes oli mädanikuga puude osakaal väiksem. Huvitava asjaoluna selgus, et juurepessuga nakatunud puid oli vähem suvistel ja varakevadel teostatud harvendusraiete aladel võrreldes talvel teostatud raietega. Kõige ulatuslikumalt osutus juurepessu poolt kahjustatuks puistu sinilille kasvukohatüübis, seejärel naadi kasvukohatüübi puistud ning siis jänesekapsa kasvukohatüüp. Alad jäävad püsikatsealadeks ning proove kogutakse 2-aastase intervalliga, selgitamaks juurepessu levimise kiirust harvendusraiete järgselt.Root rot Heterobasidion causes serious economical damage in Norway spruce stands. Thinning thereby affects considerably the spread of the Heterobasidion. Objectives of this bachelor’s thesis was to investigate species and spread of the root rots in fertile site types after thinnings, also to estimate spread of the decay in consideration of site history, age, composition of stand and forest site type. For research were selected ten Norway spruce stands in Tartumaa forest district and Järvselja Training and Experimental Forest Centre where data from 99 trees were collected. Thinnings were carried out in winter, early-spring and summer. On three plots, two or more thinnings were carried out. Increment borer samples were collected to estimate decay and determine species of the pathogen. Resistograph data were collected and used to estimate decayed trees and data was compared with increment samples data. Eight out of ten plots were infected with Heterobasidion root rot. Mostly, H. parviporum was determined, however two plots were infected by H. annosum. Armillaria spp. was not found in investigated areas. Butt rot appeared in five stands, one of them with extensive decay (4 out of 10 trees), percentage of the decay in other stands were lower. As interesting circumstance, there were higher percentage of infected stands in winter thinning areas compared to summer and early-spring thinnings. Hepatica site type was the most extensively infected, after that Aegopodium site type and then Oxalis site type. Experimental plots will remain as permanent plots and samples will be collected in 2- years interval to investigate the rapidity of the Heterobasidion spread after thinning

Global patterns in endemicity and vulnerability of soil fungi

Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.The full acknowledgements are provided in Table S6. The bulk of the funding is derived from the Estonian Science Foundation (grants PRG632, PRG1170, PRG1615, MOBTP198), EEA Financial Mechanism Baltic Research Programme (EMP442), and Novo Nordisk Fonden (NNF20OC0059948). All collected soil samples are preserved in collection of DNA and environmental samples of University of Tartu Natural History Museum

Global patterns in endemicity and vulnerability of soil fungi

Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms

Towards understanding diversity, endemicity and global change vulnerability of soil fungi

Fungi play pivotal roles in ecosystem functioning, but little is known about their global patterns of diversity, endemicity, vulnerability to global change drivers and conservation priority areas. We applied the high-resolution PacBio sequencing technique to identify fungi based on a long DNA marker that revealed a high proportion of hitherto unknown fungal taxa. We used a Global Soil Mycobiome consortium dataset to test relative performance of various sequencing depth standardization methods (calculation of residuals, exclusion of singletons, traditional and SRS rarefaction, use of Shannon index of diversity) to find optimal protocols for statistical analyses. Altogether, we used six global surveys to infer these patterns for soil-inhabiting fungi and their functional groups. We found that residuals of log-transformed richness (including singletons) against log-transformed sequencing depth yields significantly better model estimates compared with most other standardization methods. With respect to global patterns, fungal functional groups differed in the patterns of diversity, endemicity and vulnerability to main global change predictors. Unlike α-diversity, endemicity and global-change vulnerability of fungi and most functional groups were greatest in the tropics. Fungi are vulnerable mostly to drought, heat, and land cover change. Fungal conservation areas of highest priority include wetlands and moist tropical ecosystems