Taimede maa-aluse mitmekesisuse ja kooseksisteerimise väikeseskaalalised seaduspärad niiduökosüsteemides

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Teadmised taimekoosluste liigilisest mitmekesisusest ja liikide kooseksisteerimisest põhinevad uuringutele, mis käsitlevad koosluste maapealset osa. Kuigi paljudes parasvöötme niidukooslustes võib isegi kuni 75% taimsest biomassist olla paigutunud maa alla, ei ole sealsetest protsessidest kuigi palju teada, kuna varasemad meetodid ei võimaldanud välimuselt väga sarnaseid juuri ja risoome liikideks määrata. Taimede juuresüsteemid on väga laiaulatuslikud ja on ajas tunduvalt vastupidavamad kui maapealsed võsud, mistõttu võib maa all esineda samas ruumiskaalas rohkem liike kui maa peal. Doktoritöös uurisin, milliseid erinevusi võib leida maa-alustes ja maapealsetes mitmekesisuse mustrites ning täiendasin seniseid teadmisi taimekoosluse funktsioneerimisest ja taimede suhetest juurtes elavate mükoriisa seentega. Kasutades uue põlvkonna sekveneerimist leidsin, et maa-alune taimede liigirikkus on kuni kaks korda suurem kui maa peal. Määrasin juurtest ka taimedega sümbioosis olevate seente, täpsemalt arbuskulaarmükoriisa liigid ning leidsime, et seente liigiline mitmekesisus ja fülogeneetiline mitmekesisus kasvab taimede liigilise ja fülogeneetilise mitmekesisuse kasvades. Taimede liigirikkus maa peal ja maa all erines ka piki mullaviljakuse gradienti. Leidsin sarnaselt varasemate töödega, et maapealne liigirikkus langeb mullaviljakuse kasvades, kuid uudne aspekt on, et maa-aluste liikide arv kasvas mullaviljakuse kasvades. Sarnaselt elurikkusele selgus ka, et maapealne ja maa-alune taimekooslus on kokku pandud erinevate protsesside tagajärjel: maapealsete liikide kooseksisteerimine on määratud biootiliste suhete poolt, nagu näiteks valguskonkurents, samas kui maa-aluse koosluse kokkupanekut mõjutavad suuresti abiootilised ja stohhastilised protsessid (erinevad toitainete gradiendid, mulla pH, jm). Antud tulemused viitavad sellele, et vaadeldes ainult koosluse maapealset osa, näeme kõigest "jäämäe tippu", kuna tegelik liikide kooseksisteerimine leiab aset maa all. Selle doktoritöö tulemused toovad esimest korda esile taimekoosluste maa-aluse komponendi olulisuse liikide kooseksisteerimise ja ökosüsteemi protsesside uurimisel.Our current understanding about plant species diversity and coexistence is almost entirely based on studies of aboveground vegetation. In some species-rich grassland ecosystems, nearly 75% of plant biomass occurs belowground, however, little is known about below-ground processes due to difficulties in distinguishing between morphologically similar roots of different species. Belowground root systems are more extensive in space and more persistent in time than short-lived shoots, causing belowground species richness to be higher than aboveground per volume. In this thesis I explored the differences between the patterns of below-and aboveground plant diversity with adding new insights to the knowledge of mutualistic relationships between plants and root dwelling fungi and the functioning of plant communities as a whole. Application of next-generation sequencing revealed that belowground plant species richness can be up to twice as high as aboveground. By using the same root samples I identified arbuscular mycorrhizal fungi forming tight mutualistic relationships with plants and found that fungal species diversity and phylogenetic diversity increases with increasing plant diversity and phylogenetic diversity. Above- and belowground plant diversity responded differently to soil fertility gradient as well. Similar to previous studies, aboveground richness declined with increasing soil fertility; in contrast, the number of species found only belowground increased with fertility. Investigating the plant community assembly patterns above- and belowground revealed substantial differences - there is more evidence for biotic interactions, such as light competition aboveground, whereas abiotic and stochastic processes, such as soil nutrient gradients, soil pH, etc. dominate belowground. Results of this thesis suggest that by considering only aboveground vegetation we merely see the "tip of an iceberg", whereas real species coexistence occurs belowground. This thesis for the first time highlights the importance of belowground processes in the research of plant species coexistence and ecosystem processes

Sharing resources for mutual benefit: crosstalk between disciplines deepens the understanding of mycorrhizal symbioses across scales

Mycorrhizal scientists from 53 countries gathered in the city of Prague from 30 July until 4 August 2017 for the 9th International Conference on Mycorrhiza (ICOM9). They came to discuss an ancient symbiosis based on the exchange of resources between plant and fungal partners, with many impacts on plant health (van der Heijden et al., 2015). Much like this mutualistic interaction, delegates from disparate disciplines united with a strong focus on integration and sharing of resources for mutual benefit. By exchanging knowledge among researchers from the fields of molecular biology, physiology and ecology, the participants of ICOM9 made a leap forward in our understanding of symbiotic structure and function at multiple scales

Habitat preferences and functional traits drive longevity in Himalayan high-mountain plants

Plant lifespan has important evolutionary, physiological, and ecological implications related to population persistence, community stability, and resilience to ongoing environmental change impacts. Although biologists have long been puzzled over the extraordinary variation in plant lifespan and its causes, our understanding of interspecific variability in plant lifespan and the key internal and external factors influencing longevity remains limited. Here, we demonstrate the concurrent impacts of environmental, morphological, physiological, and anatomical constraints on interspecific variation in longevity among > 300 vascular dicot plant species naturally occurring at an elevation gradient (2800–6150 m) in the western Himalayas. First, we show that plant longevity (ranging from 1 to 100 years) is largely related to species' habitat preferences. Ecologically stressful habitats such as alpine and subnival host long-lived species, while productive ruderal and wetland habitats contain a higher proportion of shorter-lived species. Second, longevity is influenced by growth form with monocarpic forbs having the shortest lifespan and woody shrubs having the highest. Small-statured cushion plants with compact canopies and deep roots, most found on cold and infertile alpine and subnival soils, had a higher chance of achieving longevity. Third, plant traits reflecting plant adaptations to stress and disturbance affect interspecific differences in plant longevity. We show that longevity and growth are negatively correlated. Slow-growing species are those that have a higher chance of reaching a high age. Finally, higher longevity was associated with high leaf carbon and phosphorus, low root phosphorus and nitrogen, and with large bark-xylem ratio. Our findings suggest that plant longevity in high elevation is intricately determined by a combination of habitat preferences and growth form, as well as the plant growth rate and physiological processes.publishedVersio

Metabarcoding of soil environmental DNA to estimate plant diversity globally

IntroductionTraditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. MethodsWe sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. ResultsLarge-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. DiscussioneDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region

Global diversity and distribution of nitrogen-fixing bacteria in the soil

Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria

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

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

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

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