Eukarüootse mullaelustiku seos maakasutuse muutuse ning peremeestaime identiteediga

Väitekirja elektrooniline versioon ei sisalda publikatsiooneMullaelustiku uurimine pole lihtne – lisaks sellele, et maa-alune elu jääb inimese igapäevasest tajuruumist kõrvale, on enamik mullas elutsevaid organisme kas mikroskoopilised või vähemalt piisavalt pisikesed, et nende leidmine, rääkimata liikide eristamisest, on keeruline. Õnneks tulevad siinkohal ökoloogidele appi DNA-põhised määramismeetodid. Selle tulemusena on tormiliselt arenema hakanud ökoloogiasuund, kus samaaegselt endisaegsete loodusuurijate tööga – kes kus elab? – uuritakse maapealsel elul põhinevate teooriate paikapidavust ka maa all. Doktoritöö käigus uurisin, kuidas mõjutab inimtegevus ühe olulise maa-aluse elustikurühma – peaaegu 80% maismaa taimeliikidega sümbioosis elavate arbuskulaarmükoriissete (AM) seente – elurikkust nii globaalsel skaalal ning Eestile omastes poollooduslikes kasvukohtades. Leidsin, et inimtegevusest (või selle tegevuse lõpetamisest) tingitud stress mõjutab suuresti koosluste koosseisu, kuid ei pruugi tingimata päädida vaadeldavate organismide liigirikkuse vähenemisega. Kuna liigilist koosseisu võib teatud lähenduses käsitleda koosluse funktsiooni indikaatorina, leidsin, et inimtegevuse mõju hindamiseks ei piisa pelgalt liikide loendamisest. Samuti leidsin, et looduslike ökosüsteemide AM seente liigirikkusele on inimtekkelistel häiringutel vastassuunaline mõju – vaesemates kasvukohtades elurikkust suurendav ning rikkamates vähendav. Puisniidul erinevaid organismirühmi uurides selgus, et inimtegevuse tõttu muutunud kasvukohtades muutuvad samaaegselt ja -suunaliselt mitmed päristuumsed organismirühmad, nii mükoriisaseened kui ka mullas elavad loomad. Lisaks leidsin vastupidiselt ootustele, et vaatamata enamiku taimeliikidega koos elavate AM seente väiksele globaalsele liigirikkusele (maismaa taimeliikide ning AM seeneliikide arvu suhe on umbes 300:1) ei ole taimejuurtesse „komplekteeritud“ AM seeneliikide kogum juhuslik, vaid mükoriisavõrgustikus eelistavad teatud peremeestaimed kindlaid seeneliike (või vastupidi).Doing research on belowground organisms is troublesome – in addition to being hidden from the everyday perspective on the world, most soil-dwellers are either microscopic or at least small enough to seriously hinder detection and identification. Luckily, recent decades have advanced molecular techniques enough to allow ecologists to delimit organisms based on DNA sequences, and rapid developments in quantifying and making sense of the belowground biosphere are underway. Still, due to the hasty pace in which this field of ecology is evolving – biogeographical works resembling that of early naturalists’ are being conducted in parallel with validating old and generating new ecological principles for soil – much of the results are contradictory and gaps in knowledge can span entire ecosystems. The PhD thesis in hand dealt with global and regional anthropogenic impact on one of the ubiquitous groups of soil organisms – arbuscular mycorrhizal (AM) fungi that form symbiosis with nearly 80% of land plants. We found that stress caused by human influence (or in some cases, cessation of) strongly influences the compositional structure of AM fungi, but does not always directly translate to loss of biodiversity. As the compositional structure could be viewed as a proxy of the functional characteristics we speculate that human disturbance might influence the function of the belowground biosphere. Further, we demonstrated that human disturbance could have an opposite effect at different ends of the natural biodiversity gradient – naturally species poor sites gain in biodiversity and vice versa. In order not to be confined to a single organism group, we showed co-varying changes of different groups of soil-dwelling eukaryotes, from symbiotrophic fungi to soil animals, in response to human-mediated change of habitat. To our great surprise, we also found that despite the great imbalance of the overall diversity of AM fungal species and plant species with whom they form symbiosis with (the ratio of land plant species to AM fungal species is about 300:1), the communities of AM fungi in plant roots are not assembled randomly. Instead, the plant-fungal interaction network follows certain structural principles that promote resilience and symbiotic partners seem to prefer some species to others.https://www.ester.ee/record=b538034

Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic

Knowledge about the distribution and local diversity patterns of arbuscular mycorrhizal (AM) fungi are limited for extreme environments such as the Arctic, where most studies have focused on spore morphology or root colonization. We here studied the joint effects of plant species identity and elevation on AM fungal distribution and diversity. We sampled roots of 19 plant species in 18 locations in Northeast Greenland, using next generation sequencing to identify AM fungi. We studied the joint effect of plant species, elevation and selected abiotic conditions on AM fungal presence, richness and composition. We identified 29 AM fungal virtual taxa (VT), of which six represent putatively new VT. Arbuscular mycorrhizal fungal presence increased with elevation, and as vegetation cover and the active soil layer decreased. Arbuscular mycorrhizal fungal composition was shaped jointly by elevation and plant species identity. We demonstrate that the Arctic harbours a relatively species-rich and nonrandomly distributed diversity of AM fungi. Given the high diversity and general lack of knowledge exposed herein, we encourage further research into the diversity, drivers and functional role of AM fungi in the Arctic. Such insight is urgently needed for an area with some of the globally highest rates of climate change

Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic

Knowledge about the distribution and local diversity patterns of arbuscular mycorrhizal (AM) fungi are limited for extreme environments such as the Arctic, where most studies have focused on spore morphology or root colonization. We here studied the joint effects of plant species identity and elevation on AM fungal distribution and diversity. We sampled roots of 19 plant species in 18 locations in Northeast Greenland, using next generation sequencing to identify AM fungi. We studied the joint effect of plant species, elevation and selected abiotic conditions on AM fungal presence, richness and composition. We identified 29 AM fungal virtual taxa (VT), of which six represent putatively new VT. Arbuscular mycorrhizal fungal presence increased with elevation, and as vegetation cover and the active soil layer decreased. Arbuscular mycorrhizal fungal composition was shaped jointly by elevation and plant species identity. We demonstrate that the Arctic harbours a relatively species-rich and nonrandomly distributed diversity of AM fungi. Given the high diversity and general lack of knowledge exposed herein, we encourage further research into the diversity, drivers and functional role of AM fungi in the Arctic. Such insight is urgently needed for an area with some of the globally highest rates of climate change.Peer reviewe

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

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

User-friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences

High‐throughput sequencing (HTS) of multiple organisms in parallel (metabarcoding) has become a routine and cost‐effective method for the analysis of microbial communities in environmental samples. However, careful data treatment is required to identify potential errors in HTS data, and the large volume of data generated by HTS requires in‐house experience with command line tools for downstream analysis. This paper introduces a pipeline that incorporates the most common command line tools into an easy‐to‐use graphical interface—gDAT. By using the Python scripting language, the pipeline is compatible with the latest Windows, macOS and Linux operating systems. The pipeline supports analysis of Sanger, 454, IonTorrent, Illumina and PacBio sequences, allows custom modification of quality filtering steps, and implements both open and closed‐reference operational taxonomic unit‐picking for sequence identification. Predefined parameters are optimized for analysis of small subunit (SSU) rRNA gene amplicons from arbuscular mycorrhizal fungi, but the pipeline is widely applicable to metabarcoding studies targeting a broad range of organisms. The pipeline was additionally tested with data using general eukaryotic primers from the SSU gene region and fungal primers from the internal transcribed spacer (ITS) marker region. We describe the pipeline design and evaluate its performance and speed by conducting analysis of example data sets using different marker regions sequenced on Illumina platforms. The graphical interface, with the option to use the command line if needed, provides an accessible tool for rapid data analysis with repeatability and logging capabilities. Keeping the software open‐source maximizes code accessibility, allowing scrutiny and bug fixes by the community