Diversity of arbuscular mycorrhizal fungi in the roots of perennial plants and their effect on plant performance
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Fungi represent one of the largest and diverse kingdoms of eukaryotes, and Basidiomycota is the second most species-rich group within Fungi. Despite the ecological importance of basidial fungi, i.e., their leading role in decomposition of wood in terrestrial ecosystems, their diversity and taxonomy are insufficiently known. Fulfilling this knowledge gap, the thesis presents taxonomic studies in a class of basidal fungi called Dacrymycetes. Dacrymycetes occur only on dead wood and produce either of the two types of fruitbodies: gelatinous voluminous yellow or dry flat bleak-coloured. The latter type, also called corticioid fruitbodies, is the primary focus of this thesis. Traditionally, such corticioid fruitbodies in dacrymycetes were strictly associated with the family Cerinomycetaceae and its only genus Cerinomyces. This emphasis on a single character led to inclusion of dissimilar species into Cerinomyces, and over the time the genus became overly broad and polyphyletic. Thus, aim of the present thesis was to revise Cerinomyces and related taxa on a basis of DNA sequence-based phylogenetic analyses and morphological studies. As a result, Cerinomyces was reshaped to a more natural scope and became monophyletic. Priority for the corticioid morphology was abandoned, and gelatinous members were introduced to the genus. Instead of fruitbody type, the genus is now united by a set of microscopic characters: simple clamps, thin-walled aseptate basidiospores, and low amount of carotenoid pigments. Moreover, investigating taxa morphologically similar to Cerinomyces, the rest of dacrymycetes was partially revised. Special attention was paid to notable morphological structures called “dendrohyphidia” that are common in Cerinomyces, but were also found in other dacrymycetes. To accommodate such taxa in the Dacrymycetaceae family, a new genus Dendrodacrys was raised. In total, the thesis proposes 42 nomenclatural novelties to science, including one new genus, 27 new species, and 14 new combinations.
Knowledge of population genetics and phylogeography of living organisms are
important for conservation and management of species, since they provide
information about species viability and integrity. There have been numerous
genetic studies of brown bears in parts of the species’ range to inform local
management and conservation approaches, and due to the status of the brown
bear as a ‘model species’ in phylogeographic studies. However, there is little
information about brown bear genetics in the largest part of the distribution
area: northern continental Eurasia. The goal of this thesis was to provide new
information about the population genetics, diet and phylogeography of brown
bears in this region, to describe population genetic structure and to assess the
importance of historical and ecological conditions in generating and main-
taining structure.
Modern day human genomes are mixtures of ancient components. Thanks to advancements in ancient DNA (aDNA) research, we can detect the origins of these components and study them. However, aDNA might either not be available or be of low quality in many situations due to DNA structure being subject to degradation related to time and different environmental factors. Thankfully, we can identify and extract these ancient layers also from contemporary human genomes with local ancestry inference methods. With this approach, we can study admixed populations, which have highly divergent ancestral components, in terms of demography and functional analyses. This thesis particularly focuses on two such groups: South Asian populations, which are composed of West Eurasian and South Asian ancestries, and Ethiopian populations, which are composed of Eurasian and African ancestries. In the first part, past demographic events, diverse genomic variation and post-admixture natural selection in South Asia are investigated by generating surrogates for the two main ancestral components of contemporary South Asian genomes. In the second part, a local ancestry inference-based method is evaluated for improving selection detection in ancestral components of admixed genomes and it is applied on South Asian genomes. In the third and the last part, a similar approach to the first part is conducted for Ethiopian genomes to pinpoint the source of Eurasian ancestry in contemporary Ethiopians.
Root and rhizosphere soil samples of medicinal plant Huangshan Magnolia (Magnolia cylindrica) from Chinese famous national forest park of Huangshan (Yellow Mountain) were studied to determine the root colonization and the diversity of spore populations of arbuscular mycorrhizal (AM) fungi. The results showed that AM fungal colonization structures including hyphae, hyphal coils and vesicles were present in all root samples. Paris-type AM were identified in the roots according to the morphological structure. Seventeen species of AM fungi were isolated and identified from the rhizosphere soil samples. The species were of the genera Acaulospora (6 species), Glomus (8 species), Gigaspora (1 species) and Scutellospora (2 species). Based on importance value, 3 species from Acaulospora and 3 from Glomus were dominant. The AM fungi spore density ranged from 157 to 448 (average 315) per 100 g soil and the species richness ranged from 4 to 8 (average 6.5) per soil sample. Shannon-Wiener index and Evenness were calculated to evaluate the diversity of the AM fungi community associated with M. cylindrica.
Eurasian wild boar is the most widespread species of the Suidae family and its populations increased significantly in the second half of the 20th century – a change that has been largely associated with the continuing spread of agriculture, as well as the widespread practice of supplementary feeding. However, due to its omnivorous diet, high population density of wild boar can have disastrous effects on other animals, particularly on ground-nesting birds, whose populations have suffered from loss of habitat as well as predation.Wild boar can also play an important role in disease outbreaks as a reservoir of various pathogens shared between wildlife and domestic animals. The purpose of this thesis was to examine the potential consequences of supplementary feeding of wild boar for ground-nesting birds and wild boar infection with endoparasites, because increased overall abundance of wild boar and increased contact rates at feeding sites can promote the spread of various diseases.
In this study, supplementary feeding had a key role in determining wild boar abundance and grain from feeding sites constituted a major food category even in the warm season, when food availability was not hindered by low temperatures and deep snow. However, despite having access to supplemental food, wild boar acted as a predator of nests and chicks of forest grouse and the concentration of wild boar and other predators near feeding sites resulted in locally increased predation risk for ground-nesting birds. What is more, the novel molecular method applied in this study revealed that faecal diet analysis based on morphology, which is still a popular method in diet studies, underestimates the proportion of bird in wild boar diet, indicating that previous studies might suffer from the same error. In addition to its contribution to increased predation of ground-nesting birds, supplementary feeding was shown to influence endoparasite infection in wild boar both directly and indirectly through increased abundance. Supplementary feeding sites had become hot-spots for acquiring lungworm infection and parasites with a direct life cycle benefited from the overall high host abundance. These unwanted effects should be reckoned with in wild boar management.
Forests provide habitat for a huge variety of fungi that, in turn, play key roles in several forest ecosystem processes. The fungal biota is increasingly affected by human-caused transformation of forests, i.a., significant declines in the amount of coarse dead wood and large old trees. My thesis concentrates on fungi inhabiting such structures. My main focus is on polypores that belong to the dominant dead-wood composers in the forests, but I also explore lichenised fungi. Many polypores and lichens are nowadays found mainly in the remaining old-forest patches, and the occurrence of several species is thought to indicate ecological value of a forest. My general aim was to assess the forest conservation and management practices from the perspective of the fungi inhabiting dead wood and old living trees. The main method in polypore studies was fruit-body based species-inventory. In the stand scale, I found this method efficient: while all polypore species inhabiting a tree-trunk (as revealed by their DNA in the wood samples) may not produce fruit-body on the same tree, conspecific fruit-bodies can be usually found on other trunks in close vicinity. Differently from the intensively managed Fennoscandia, the old-forest associations of polypores were relatively weak in Estonia, as revealed by a comparison of old-growth, mature managed and harvested forests. Thus, fungal habitat associations and indicator value depend on regional landscape context. For the few species that were confined to old -growths, specific substrate requirements (notably large spruce trunks) were the reason. I also show that interpreting species habitat associations may me confused by “cryptic species” that have similar morphology, but differ by genetics and ecology. Thus, conservation practices might benefit from fewer, but better supported, fungal indicators. I demonstrate that fungi inhabiting dead wood and old living trees (including putative old-forest specialists) may form species-rich assemblages also in managed forests. This is possible if these forests are diverse in terms of tree species, dead-wood structures, and successional stages, including old stands. My general conclusion is that there are many possibilities for adjusting forest management to better address the fungal diversity that depends on dead wood and old living trees.
ThefirstDNAsequencesobtainedfromarbuscularendomycorrhizalfungiarereported.Theywere obtained bydirectlysequencingoverlappingamplifiedfragmentsofthenucleargenes codingforthesmallsubunit rRNA.Thesesequences were usedtodevelopa polymerasechainreactionprimer(VANSI)thatenablesthe specificamplificationofa portionofthevesicular-arbuscularendomycorrhizalfungussmallsubunitrRNA directlyfroma mixtureofplantandfungaltissues.Thespecificityofthisprimerforarbuscularendomycor- rhizalfungiwas demonstratedbytestingiton a numberoforganismsandbysequencingthefragmentamplified from colonized leek (Allium porum) roots. This approach, coupled with other molecular techniques, will facilitate rapid detection, identification, and possibly quantitation of arbuscular endomycorrhizal fungi.
A new arbuscular mycorrhizal fungus, Glomus proliferum (Glomales, Zygomycetes) is described. The description, based on a monoxenic culture established in association with a Ri T-DNA transformed carrot root, combines sequencing of the small subunit (SSU) rDNA, spore sterols and fatty acid profiles with more classical taxonomic tools such as optical and electron microscopy. The fungus forms clusters containing hundreds of small, hyaline, four-layered spores. The necessity to use different tools for identification of arbuscular mycorrhizal fungi is discussed.
Two ancestral clades of arbuscular mycorrhizal fungal species were discovered from deeply divergent ribosomal DNA sequences. They are classified here as two new families Archaeosporaceae and Paraglomaceae. Each family is phylogenetically distant from each other and from other glomalean families, despite similarities in mycorrhizal morphology and fatty acid profiles. Shared mycorrhizal morphology is not surprising, since it is highly conserved and resolves other taxa in Glomales at both family and suborder levels. At the present time, each family consists of one genus. Archaeospora (Archaeosporaceae) includes three species forming atypical Acaulospora-like spores from sporiferous saccules. Two of these species are dimorphic, forming Glomus-like spores as well. Paraglomus (Paraglomaceae) consists of two species forming spores indistinguishable from those of Glomus species. Morphological characters once considered unique, such as the sporiferous saccule defining species of Acaulosporaceae, clearly are distributed in phylogenetically distant groups. The simple design of spores of some species in Glomus also masks considerable divergence at the molecular level. It is the combination of DNA sequences, fatty acid profiles, immunological reactions against specific monoclonal antibodies, and mycorrhizal morphology which provides the basis for recognizing Archaeospora and Paraglomus. These results reinforce the value of molecular data sets in providing a clearer understanding of phylogenetic relationships, which in turn can lead to a more robust taxonomy.
We report the first molecular analysis of arbuscular mycorrhizal fungi previously classified in the genus Sclerocystis. Fungi in Sclerocystis sensu lato were distinguished by formation of complex sporocarps. Most species were transferred to Glomus, but both their taxonomic and phylogenetic relations remain the subject of controversy. Phylogenetic analysis of the 18S ribosomal subunit of G. sinuosum (= S. sinuosa) and S. coremioides shows that both species are each other's closest relatives and fall within a monophyletic clade comprising the well-characterized species, G. mosseae, G. intraradices and G. vesiculiferum, to the exclusion of several other Glomus species. This placement indicates that formation of complex sporocarps is an advanced character of some Glomus species, but the sporocarpic trait is not sufficiently unique to group these species into a separate genus Sclerocystis.
The yearly incidence of root colonization and extramatrical spores of vesicular-arbuscular (-VA) mycorrhizal fungi were determined for six agronomic crops grown in monoculture for 7 yr on a newly cleared woodland site in northwest Florida. Thirteen species of VA-mycorrhizal fungi were identified from the test site from 1972 to 1978. Sorghum yielded the greatest number of species (12) from a single crop during this period. The highest number of spores was associated with soybean and the lowest number of spores was found in the native woodland. Spores of Gigaspora margarita, G. gregaria, and G. gigantea were most numerous from soil around soybeans while Glomus fasciculatus and G. clarus were most numerous around roots of bahia grass. Acaulospora spp. were most abundant from soil around cotton and peanut. The yearly incidence of Gigaspora margarita spores increased while G. gregaria and G. gigantea decreased in numbers during the 7-yr study. Glomus macrocarpus var. geosporus and G. fasciculatus were observed in 1971 and/or 1972 but were not recovered again until 1978. Only two species, Gigaspora margarita and G. gregaria, were recovered each yr that samples were taken. The highest level of root colonization occurred in 1972 and was followed by a decline in 1973–1974, but mycorrhizae showed a general increase in 1975–1976. It is suggested that the observed changes in the incidence of VA-mycorrhizal fungi were primarily due to the agricultural system of monoculture.
Spores of Gigaspora and Scutellospora species predominated in the root zones of three major plant species growing in the barrier dunes extending from northern New Jersey to Virginia. Similarity in edaphic factors, vegetation, daylength during the growing season, and precipitation along a 355 km transect permitted study of the composition of the VAM fungal community in response to temperature. Twenty-three species of VAM fungi were recovered. Dominant species along the transect were G. gigantea, Acaulospora scrobiculata, and S. dipapillosa. Some species were more abundant in the northern (cooler) regions of the transect and others were more abundant in the southern regions. Average VAM fungal species richness was positively correlated with distance south along the transect and with temperature parameters. Temperature effects on the VAM fungal community may be separated into two components, a direct effect on the fungi and an indirect effect mediated through the host plant. Plots of rank/log Importance Value depicted the structure of the VAM fungal community and were of use in identifying severe habitats where heat stress appeared to be the controlling factor. Dominance by a single fungal species was inversely correlated with distance south and with temperature parameters. It was most pronounced in northern sites and in the root zones of heat-stressed Ammophila breviligulata plants growing near the species' southern limit.
The storage of inoculum (mycorrhizal spores and roots in soil) as prerequisite treatment for increasing axenic spore germination was investigated with a tropical isolate of Glomus clarum. Prolonged dry storage of the inoculum, for up to 6 months at 25–30 C, increased percentage spore germination significantly on water agar. If, following dry storage, the extracted spores were then stored at 4 C for at least 2 weeks, germination was further enhanced. Incubation temperatures of 25–35 C and medium pH of 5–8 were most favorable for germination. These requirements may be significant in understanding the ecophysiology of vesicular-arbuscular mycorrhizal fungi in their natural environment.
Describes how pattern and structure at different levels of plant organization (communities, populations and individuals) are influenced by abiotic factors such as climate and soil and by biotic interactions including competition with other plants, attack by herbivores and pathogens, and relationships with mutualistic organisms. Patterns of distribution and abundance are interpreted as the outcome of dynamic processes involving gains and losses. The species richness of communities, for instance, is seen as the resolution of immigration and extinction; population density reflects the balance of recruitment and mortality within a single species; and the size of individual plants is a consequence of the births and deaths of modular component parts. The ultimate aim is to measure the impact of processes which influence the fitness of individual phenotypes. Chapters are on: structure of plant communities; resources, competition and the dynamics of plant communities; canopy gaps and the dynamics of a neotropical forest; structure of plant populations; plant population dynamics; ecology of pollination and seed dispersal; breeding structure and genetic variation; life history and environment; dynamics of growth and form; individual plants as genetic mosaics - ecological organisms vs evolutionary individuals; photosynthesis; and the acquisition and utilization of resources.-after Editor