Ektomükoriissete seente liigiline koosseis ja peremehe-eelistused Austraalia ja Aafrika ökosüsteemides

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Austraalias oli ektomükoriisaseente (ehk siis seente, kes elavad vastastikku kasulikus kooselus puittaimedega) liigirikkus suurem kui Aafrika erinevates ökosüsteemides. Austraalia seenekoosluste liigirikkus oli võrreldav põhjapoolkera parasvöötmega. Nimelt on leitud, et ektomükoriisaseente puhul on suurem liigirikkus parasvöötmes kui troopikas. Kuna Aafrika kõik proovialad jäid troopikasse, siis oli seal ka madal liigirikkus. Austraalias olid kõige tavalisemad seened rühmadest vöödikud, tomentellid-lehternahkised ja pilvikud-riisikad. Aafrikas olid puravikud vöödikute asemel. Veel uuriti, kuidas peremeespuud mõjutavad seente liigirikkust. Enamus peremeespuudest ei kasvanud mingite kindlate seeneliikidega koos. Erandiks oli Pomaderris apetala Tasmaanias, mis kasvas koos temale omaste seentega. Aafrikas eukalüptiistanduses eelistasid kindlat peremeest kolm Austraaliast sissetoodud seeneliiki, mis kasvasid ainult koos eukalüptidega. Enamus looduslikult Aafrikas kasvavatest seentest olid võimelised kasvama koos kohalike ja sissetoodud puudega. Austraaliast pärit üheksast seeneliigist neli olid võimelised kasvama koos kohalike puudega.Species richness was highest in Tasmanian wet sclerophyll forests and was comparable with species richness in Holarctic region. In contrast, in Africa, species richness was lower, and fewer fungal lineages were present. Tropical ectomycorrhizal (EcM) fungal communities are phylogenetically highly similar in different continents. There was a strong host preference among EcM fungi in a Tasmanian wet sclerophyll forest. Compared to other hosts, Pomaderris apetala hosted highly different EcM fungal communities. However, host preference was not detected among the most common fungal species in Africa. Host shifts among ectomycorrhizal fungi may occur particularly commonly, when the roots of trees intermingle. These host shifts may lead to naturalization and invasion of the introduced Eucalyptus species or spread of cointroduced EcM fungal species as detected in other ecosystems

Tidying up international nucleotide sequence databases

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

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

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

Arbuskulaar-mükoriissete seente eosekoosluste mitmekesisus looduslikes ökosüsteemides

https://www.ester.ee/record=b5496865*es

Molecular inference, multivariate morphometrics and ecological assessment are applied in concert to delimit species in the Russula clavipes complex

Species of Russula subsect. Xerampelinae are notoriously difficult to identify and name and have not been subject to molecular study. A group of species, referred to here as the R. clavipes complex, growing in association with Salix, Betula and Populus as well as coniferous tree species from temperate to arctic and alpine habitats, were examined. Analyses of the nuc rDNA internal transcribed spacer (ITS) region and a numerical analysis of morphological characters were used. The R. clavipes complex is a monophyletic group within Russula subsect. Xerampelinae, according to molecular results. The complex includes three species: R nuoljae is a phylogenetically and morphologically well-supported species while the other two, R clavipes and R pascua, are similar based on ITS data and morphology but separate based on their ecology. Russula pseudoolivascens is conspecific with R clavipes. Several combinations of characters traditionally used in the taxonomy of R subsect. Xerampelinae are inappropriate for species delimitation in this group and the adequacy of the ITS for species identification in this group is discussed. Detailed microscopic observations on the type collection of R nuoljae are presented and illustrated, along with a key to the European members of R. subsect. Xerampelinae

The role of plant mycorrhizal type and status in modulating the relationship between plant and arbuscular mycorrhizal fungal communities

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Light availability and light demand of plants shape the arbuscular mycorrhizal fungal communities in their roots

Plants involved in the arbuscular mycorrhizal (AM) symbiosis trade photosynthetically derived carbon for fungal-provided soil nutrients. However, little is known about how plant light demand and ambient light conditions influence root-associating AM fungal communities. We conducted a manipulative field experiment to test whether plants’ shade-tolerance influences their root AM fungal communities in open and shaded grassland sites. We found similar light-dependent shifts in AM fungal community structure for experimental bait plant roots and the surrounding soil. Yet, deviation from the surrounding soil towards lower AM fungal beta-diversity in the roots of shade-intolerant plants in shade suggested preferential carbon allocation to specific AM fungi in conditions where plant-assimilated carbon available to fungi was limited. We conclude that favourable environmental conditions widen the plant biotic niche, as demonstrated here with optimal light availability reducing plants’ selectivity for specific AM fungi, and promote compatibility with a larger number of AM fungal taxa

Distinct arbuscular mycorrhizal fungal communities associate with different manioc landraces and Amazonian soils

Manioc (Manihot esculenta Crantz) is an important tropical crop that depends on arbuscular mycorrhizal (AM) association for its nutrition. However, little is known about the richness and species composition of AM fungal communities associating with manioc and possible differences across soils and manioc landraces. We studied the diversity and composition of AM fungal communities present in the roots of different manioc landraces and surrounding soils in indigenous shifting cultivation fields on different Amazonian soil types. A total of 126 AM fungal virtual taxa (VT; phylogenetically defined taxonomic units) were recovered from soil and root samples using 454 sequencing of AM fungal SSU rRNA gene amplicons. Different AM fungal communities occurred in different soil types. Minor differences occurred in the composition of AM fungal community associating with different manioc landraces, but AM fungal richness was not different among them. There was a low similarity between the AM fungal communities colonizing manioc roots and those recorded in the soil, independently of differences in soil properties or the manioc landrace evaluated. Rhizophagus manihotis and Glomus VT126 were the most abundant AM fungal species colonizing manioc roots. Contrasting with the results of earlier spore-based investigations, all the AM fungi identified as indicator species of particular manioc landraces were morphologically unknown Glomus species. In conclusion, different manioc landraces growing in common conditions associated with distinct AM fungal communities, whereby AM fungal communities in soils did not necessarily reflect the AM fungal communities colonizing manioc roots

Diversity of root-associated arbuscular mycorrhizal fungal communities in a rubber tree plantation chronosequence in Northeast Thailand

Rubber tree (Hevea brasiliensis) is of major economic importance in Southeast Asia and for small land holders in Thailand in particular. Due to the high value of latex, plantations are expanding into unsuitable areas, such as the northeast province of Thailand where soil fertility is very low and therefore appropriate management practices are of primary importance. Arbuscular mycorrhizal fungi (AMF) contribute to plant growth through a range of mechanisms and could play a key role in a more sustainable management of the rubber plantations. We described the diversity of AMF associated with rubber tree roots in Northeast Thailand in relation to tree age and soil parameters along a chronosequence of rubber tree plantations. Cassava fields were included for comparison. Rubber tree and cassava roots harbored high diversity of AMF (111 Virtual Taxa, VT), including 20 novel VT. AMF VT richness per sample was consistently high (per site mean 16 to 21 VT per sample) along the chronosequence and was not related to soil properties. The composition of AMF communities differed between cassava and rubber tree plantations and was influenced by soil texture and nutrient content (sand, K, P, Ca). AMF community composition gradually shifted with the age of the trees. Our results suggest that the high diversity of AMF in this region is potentially significant for maintaining high functionality of AMF communities. (Résumé d'auteur

Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate-dependent

International audienceArbuscular mycorrhizal (AM) fungi are known to exhibit high intra-organism genetic variation. However, information about intra- vs. interspecific variation among the genes commonly used in diversity surveys is limited. Here, the nuclear small subunit (SSU) rRNA gene, internal transcribed spacer (ITS) region and large subunit (LSU) rRNA gene portions were sequenced from 3 to 5 individual spores from each of two isolates of Rhizophagus irregularis and Gigaspora margarita. A total of 1482 Sanger sequences (0.5 Mb) from 239 clones were obtained, spanning ~4370 bp of the ribosomal operon when concatenated. Intrasporal and intra-isolate sequence variation was high for all three regions even though variant numbers were not exhausted by sequencing 12–40 clones per isolate. Intra-isolate nucleotide variation levels followed the expected order of ITS > LSU > SSU, but the values were strongly dependent on isolate identity. Single nucleotide polymorphism (SNP) densities over 4 SNP/kb in the ribosomal operon were detected in all four isolates. Automated operational taxonomic unit picking within the sequence set of known identity overestimated species richness with almost all cut-off levels, markers and isolates. Average intraspecific sequence similarity values were 99%, 96% and 94% for amplicons in SSU, LSU and ITS, respectively. The suitability of the central part of the SSU as a marker for AM fungal community surveys was further supported by its level of nucleotide variation, which is similar to that of the ITS region; its alignability across the entire phylum; its appropriate length for next-generation sequencing; and its ease of amplification in single-step PCR