In memoriam: Ain Raitviir

On September 17, 2006, the distinguished Estonian mycologist, Ain Raitviir, passed away at his home in Tartu County. He was a person with a deep knowledge of mycology and general biology and with wide-ranging interests and talents in humanities.

Ultrastruktuuri ja molekulaarsete andmete rakendused tiksikseente taksonoomias

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Tiksikseened (Helotiales sensu auct., Leotiomycetes, Ascomycota) kujutavad endast ˂2 mm läbimõõduga erivärviliste kausjas-peekerjate viljakehadega seeni. Nad on eluviisilt saproobid, parasiidid või sümbiondid (endofüüdid, mükoriisaseened) erinevatel taimedel, aga ka mullas ja vees. Olles küll looduses sagedased organismid, on neid keeruline määrata, sest morfoloogilised kriteeriumid on ebaselged ja molekulaarseks määramiseks napib DNA referentsjärjestusi. Doktoritöö põhieesmärk oli panustada fülogeneesipõhise klassifikatsiooni loomisse selles väheuuritud seenerühmas. Fülogeneesi rekonstrueerimiseks sekveneeriti mitmeid geenilõike. Lisaks uuriti võrdlevalt valitud taksonite morfoloogiat, kaasates transmissioon-elektronmikroskoopia meetodeid. Tulemusena selgus, et monofüleetilised rühmad eristuvad üksteisest mitmete tunnuste kombinatsiooni, mitte üksikute tunnuste poolest, nagu eoskoti tipustruktuur. Viimastele ei peaks andma võtmetähendust, kuivõrd konvergents on selles seenerühmas laialt levinud. Heaks näiteks homoplaasia kohta on jahukirmelise vintske viljakeha välisilme alusel eristatud perekond Encoelia, mis fülogeneesi põhjal osutus polüfüleetiliseks. Kaheksa Encoelia liiki lahknesid fülogeneesipuul kuude sugukonda, kusjuures perekonna tüüpliigiga ei olnud suguluses ükski teine Encoelia liik. Fülogeneesipõhise klassifikatsiooni loomisel taaselustati kaks ajaloolist sugukonda, kirjeldati uusi perekondi ja liike ning avaldati taksonoomilised rekombinatsioonid. Multigeen-fülogeneesipuu klaadid eristusid enamasti ökoloogia poolest. Paljude tiksikseente taksonite kohta saadi olulist ökoloogilist lisateavet, analüüsides koos viljakehade ja keskkonnaproovide ITS rDNA järjestusi. See võimaldas anda nimetuse paljudele avaliku geeniandmebaasi keskkonnasekventside lähteorganismidele. Siinne töö julgustab taksonoome rohkem kasutama DNA triipkoodistamist, soodustamaks koostööd ökoloogidega, kes enamasti tuvastavad seente elutsükli varjatumat poolt – seeneniidistiku etappi.The helotialean fungi (Helotiales sensu auct., Leotiomycetes Ascomycota) have fruitbodies, which are small (˂2 mm in diameter) varicolored and discoid-cupulate. Their lifestyle is either saprobic, parasitic or symbioitic (endophytic, mycorrhizal) occurring in various plants, but also in water and soil. The general aim of this doctoral thesis was to contribute to creating a phylogeny-based classification of helotialean fungi, a group undersampled with molecular methods. For that purpose, DNA was sequenced, and comparative morphological studies were conducted, including transmission electron microscopy. The ultrastructure of apothecial hairs in the family Lachnaceae varies at the genus level, but the type of ascus apical apparatus of this family was the same except for Lachnellula. Phylogenetic analyses revealed historical characters such as the mealy appearance of apothecia and xero-tolerance to be homoplasious and the genus Encoelia to be polyphyletic with eight studied species distributed among six families. Synapomorphies were distinguished in two resurrected familes: refractive vacuolar bodies in Cenangiaceae and the presence of ionomidotic reaction in Cordieritidaceae. The substratal stromata and anamorph characteristics had also taxonomic significance. Monophyletic groups, distinguished in phylogenetic analyses indicated that helotialean taxa are defined by combination of several characters rather than individual features; reliance on the latter should be avoided. The analyses of ITS rDNA extracted from fruitbodies together with public sequences from various biological samples expanded information on the ecology of studied taxa and allowed identification of many sequenced organisms in public databases at family, genus, or species level. Based on this work taxonomists are encouraged to apply DNA barcoding and to inititate more intense cooperation with ecologists

Ungari kirjanduse retseptsioon Eestis 1991-2013

http://www.ester.ee/record=b4438251~S1*es

Fungi from Soomaa National Park : rarities and species new for Estonia

Peer reviewe

A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes

Fungi in the class Leotiomycetes are ecologically diverse, including mycorrhizas, endophytes of roots and leaves, plant pathogens, aquatic and aero-aquatic hyphomycetes, mammalian pathogens, and saprobes. These fungi are commonly detected in cultures from diseased tissue and from environmental DNA extracts. The identification of specimens from such character-poor samples increasingly relies on DNA sequencing. However, the current classification of Leotiomycetes is still largely based on morphologically defined taxa, especially at higher taxonomic levels. Consequently, the formal Leotiomycetes classification is frequently poorly congruent with the relationships suggested by DNA sequencing studies. Previous class-wide phylogenies of Leotiomycetes have been based on ribosomal DNA markers, with most of the published multi-gene studies being focussed on particular genera or families. In this paper we collate data available from specimens representing both sexual and asexual morphs from across the genetic breadth of the class, with a focus on generic type species, to present a phylogeny based on up to 15 concatenated genes across 279 specimens. Included in the dataset are genes that were extracted from 72 of the genomes available for the class, including 10 new genomes released with this study. To test the statistical support for the deepest branches in the phylogeny, an additional phylogeny based on 3156 genes from 51 selected genomes is also presented. To fill some of the taxonomic gaps in the 15-gene phylogeny, we further present an ITS gene tree, particularly targeting ex-type specimens of generic type species. A small number of novel taxa are proposed: Marthamycetales ord. nov., and Drepanopezizaceae and Mniaeciaceae fams. nov. The formal taxonomic changes are limited in part because of the ad hoc nature of taxon and specimen selection, based purely on the availability of data. The phylogeny constitutes a framework for enabling future taxonomically targeted studies using deliberate specimen selection. Such studies will ideally include designation of epitypes for the type species of those genera for which DNA is not able to be extracted from the original type specimen, and consideration of morphological characters whenever genetically defined clades are recognized as formal taxa within a classification

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

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

Fungal Systematics and Evolution: FUSE 8

In this 8th contribution to the Fungal Systematics and Evolution series published by Sydowia, the authors formally describe 11 species: Cortinarius caryae, C. flavolilacinus, C. lilaceolamellatus, C. malodorus, C. olivaceolamellatus, C. quercophilus, C. violaceoflavescens, C. viridicarneus, Entoloma meridionale (Agaricales), Hortiboletus rupicapreus (Boletales), and Paraglomus peruvianum (Paraglomerales). The following new country records are reported: Bolbitius callistus (Agaricales) from Russia and Hymenoscyphus equiseti (Helotiales) from Sweden. Hymenoscyphus equiseti is proposed as a new combination for Lanzia equiseti, based on ITS and LSU sequence data in combination with morphological study