| 1. |
- Kõljalg, Urmas, et al.
(author)
-
Towards a unified paradigm for sequence-based identification of fungi.
- 2013
-
In: Molecular ecology. - : Wiley. - 1365-294X .- 0962-1083. ; 22:21, s. 5271-7
-
Journal article (peer-reviewed)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
|
|
| 2. |
- Oja, Jane, et al.
(author)
-
Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands
- 2017
-
In: Mycorrhiza. - : Springer Science and Business Media LLC. - 0940-6360 .- 1432-1890. ; 27:4, s. 355-367
-
Journal article (peer-reviewed)abstract
- Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in species-rich temperate semi-natural grasslands, the persistence of which depends on moderate physical disturbances, such as grazing and mowing. The aim of this study was to test whether the diversity, structure and composition of OrM fungal community are influenced by the orchid patches and management intensity in semi-natural grasslands. We detected putative OrM fungi from 0 to 32 m away from the patches of host orchid species (Orchis militaris and Platanthera chlorantha) in 21 semi-natural calcareous grasslands using pyrosequencing. In addition, we assessed different ecological conditions in semi-natural grasslands but primarily focused on the effect of grazing intensity on OrM fungal communities in soil. We found that investigated orchid species were mostly associated with Ceratobasidiaceae and Tulasnellaceae and, to a lesser extent, with Sebacinales. Of all the examined factors, the intensity of grazing explained the largest proportion of variation in OrM fungal as well as total fungal community composition in soil. Spatial analyses showed limited evidence for spatial clustering of OrM fungi and their dependence on host orchids. Our results indicate that habitat management can shape OrM fungal communities, and the spatial distribution of these fungi appears to be weakly structured outside the orchid patches.
|
|
| 3. |
- Pölme, Sergei, et al.
(author)
-
Host preference and network properties in biotrophic plant-fungal associations
- 2018
-
In: New Phytologist. - : WILEY. - 0028-646X .- 1469-8137. ; 217:3, s. 1230-1239
-
Journal article (peer-reviewed)abstract
- Analytical methods can offer insights into the structure of biological networks, but mechanisms that determine the structure of these networks remain unclear. We conducted a synthesis based on 111 previously published datasets to assess a range of ecological and evolutionary mechanisms that may influence the plant-associated fungal interaction networks. We calculated the relative host effect on fungal community composition and compared nestedness and modularity among different mycorrhizal types and endophytic fungal guilds. We also assessed how plant-fungal network structure was related to host phylogeny, environmental and sampling properties. Orchid mycorrhizal fungal communities responded most strongly to host identity, but the effect of host was similar among all other fungal guilds. Community nestedness, which did not differ among fungal guilds, declined significantly with increasing mean annual precipitation on a global scale. Orchid and ericoid mycorrhizal fungal communities were more modular than ectomycorrhizal and root endophytic communities, with arbuscular mycorrhizal fungi in an intermediate position. Network properties among a broad suite of plant-associated fungi were largely comparable and generally unrelated to phylogenetic distance among hosts. Instead, network metrics were predominantly affected by sampling and matrix properties, indicating the importance of study design in properly inferring ecological patterns.
|
|
| 4. |
- Ranheim Sveen, Tord, et al.
(author)
-
Plant-microbe interactions in response to grassland herbivory and nitrogen eutrophication
- 2021
-
In: Soil Biology & Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 156
-
Journal article (peer-reviewed)abstract
- Plant-soil feedback is increasingly recognized as a vital framework to analyze multi-trophic interactions involving herbivores, plants and microbes, but research is still lacking on understanding such feedback in the context of global change. In grasslands, patterns of herbivory are expected to be affected by global change, further modifying existing plant-soil feedbacks. We tested this by evaluating the individual and combined impacts of aboveground herbivory by a generalist leaf-chewer and nitrogen (N) eutrophication, simulating elevated N deposition, on soil microbial communities and root colonization of arbuscular mycorrhizal fungi and related these to existing data on plant functional types and community composition. We found that colonization of arbuscular mycorrhizal fungi in the plant roots responded differently to treatments depending on host plant species in patterns consistent with the changes in the plant community composition and biomass. Further, the effect of aboveground herbivory on plant-soil interactions was comparable and even exceeded that of N-eutrophication, with the additive effects of herbivory and N-eutrophication on the soil microbiome being stronger than each factor separately. Our results suggest that plant-soil feedback in response to N-eutrophication is contingent on biotic variables such as herbivory and plant species, and that biotic and abiotic disturbances may have additive effects on the soil microbiome structure.
|
|
| 5. |
- Tedersoo, Leho, et al.
(author)
-
Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of ITS sequences of mycorrhizal fungi
- 2011
-
In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:9
-
Journal article (peer-reviewed)abstract
- Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.
|
|
| 6. |
- Vahter, Tanel, et al.
(author)
-
Co-introduction of native mycorrhizal fungi and plant seeds accelerates restoration of post-mining landscapes
- 2020
-
In: Journal of Applied Ecology. - : Wiley. - 0021-8901 .- 1365-2664. ; 57:9, s. 1741-1751
-
Journal article (peer-reviewed)abstract
- Grasslands are among the most threatened terrestrial biomes, and habitat conservation alone will be insufficient to meet biodiversity goals. While restoration of indigenous grasslands is a priority, conflict with economic objectives means that incorporation of alternative habitats is necessary to offset grassland loss. With up to 800,000 km2 of land affected by mining globally, there is an opportunity to create additional grassland habitat in post-mining landscapes. We aimed to assess whether co-introduction of native arbuscular mycorrhizal (AM) fungi and plants is an efficient means of initializing species-rich vegetation recovery in barren post-mining landscapes. We established an experiment in three post-mining areas in Estonia, where we seeded plots with native plant seeds and inoculated them with trap-cultured native AM fungi from a similar habitat. We measured the abundance and composition of soil AM fungal and above-ground plant communities in two consecutive years using relevés, high-throughput sequencing and fatty acid profiling. Our results demonstrate that co-introduction of native plants and AM fungi is an effective way to establish species-rich vegetation in post-mining areas. Co-introduction of symbiotic partners resulted in higher richness, diversity and abundance of plants and AM fungi than when either partner was introduced individually. However, the plant and AM fungal communities in sown and inoculated plots were not distinct from those in uninoculated treatments; they rather formed a subset of all taxa present on the sites but exhibited higher diversity than in uninoculated plots. Synthesis and applications. This study shows that managing the below-ground microbiome is an essential part of vegetation restoration. The availability of symbiotic partners can be considered a key aspect determining the diversity of restored vegetation. Targeted inoculations with native and habitat-specific native arbuscular mycorrhizal fungi could therefore increase restoration success.
|
|
