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Many fungi are characteristically difficult to observe and collect, making the process of documenting the world’s fungal diversity challenging. The vast majority of fungal species are undescribed. The use of DNA sequencing technologies has revolutionized the study of fungal diversity by facilitating the detection of new species, the investigation of community structure and dynamics, and the elucidation of evolutionary relationships. In this dissertation, I focus on filling in some of the many gaps in our understanding of fungal diversity and community ecology in boreal pine forests through the use of DNA sequence data. In the first half of this thesis, a metabarcoding approach is used to study the composition of fungal communities found in the soil of a Lithuanian coastal pine forest and in association with the bark beetle Tomicus piniperda in Swedish pine forests. In the second half, two different approaches are taken to describe taxa detected in environmental DNA. In paper I, I demonstrate how soil microhabitats, defined based on mineral vs organic soil type and root presence or absence, vary with respect to a suite of abiotic factors and shape fungal community composition belowground. These microhabitats support functionally and taxonomically distinct fungal communities and support the overall fungal diversity of the site through niche variation. In paper II, the relationships between a) the fungal communities found on and in bark beetles from forests that have been affected by forest fire and forests that have not, b) pine phloem that has been colonized by bark beetles and phloem that has not at two different post-colonization time points, and c) phloem chemical nutrients are described. In paper III, the diversity of species within the fungal class Archaeorhizomycetes in the soil of a Swedish pine forest was studied, and two new species are described using an integrative taxonomic approach that relies on environmental DNA sequence data as taxonomical evidence.

Many fungi are characteristically difficult to observe and collect, making the process of documenting the world’s fungal diversity challenging. The vast majority of fungal species are undescribed. The use of DNA sequencing technologies has revolutionized the study of fungal diversity by facilitating the detection of new species, the investigation of community structure and dynamics, and the elucidation of evolutionary relationships. In this dissertation, I focus on filling in some of the many gaps in our understanding of fungal diversity and community ecology in boreal pine forests through the use of DNA sequence data. In the first half of this thesis, a metabarcoding approach is used to study the composition of fungal communities found in the soil of a Lithuanian coastal pine forest and in association with the bark beetle Tomicus piniperda in Swedish pine forests. In the second half, two different approaches are taken to describe taxa detected in environmental DNA. In paper I, I demonstrate how soil microhabitats, defined based on mineral vs organic soil type and root presence or absence, vary with respect to a suite of abiotic factors and shape fungal community composition belowground. These microhabitats support functionally and taxonomically distinct fungal communities and support the overall fungal diversity of the site through niche variation. In paper II, the relationships between a) the fungal communities found on and in bark beetles from forests that have been affected by forest fire and forests that have not, b) pine phloem that has been colonized by bark beetles and phloem that has not at two different post-colonization time points, and c) phloem chemical nutrients are described. In paper III, the diversity of species within the fungal class Archaeorhizomycetes in the soil of a Swedish pine forest was studied, and two new species are described using an integrative taxonomic approach that relies on environmental DNA sequence data as taxonomical evidence.

Many fungi are characteristically difficult to observe and collect, making the process of documenting the world’s fungal diversity challenging. The vast majority of fungal species are undescribed. The use of DNA sequencing technologies has revolutionized the study of fungal diversity by facilitating the detection of new species, the investigation of community structure and dynamics, and the elucidation of evolutionary relationships. In this dissertation, I focus on filling in some of the many gaps in our understanding of fungal diversity and community ecology in boreal pine forests through the use of DNA sequence data. In the first half of this thesis, a metabarcoding approach is used to study the composition of fungal communities found in the soil of a Lithuanian coastal pine forest and in association with the bark beetle Tomicus piniperda in Swedish pine forests. In the second half, two different approaches are taken to describe taxa detected in environmental DNA. In paper I, I demonstrate how soil microhabitats, defined based on mineral vs organic soil type and root presence or absence, vary with respect to a suite of abiotic factors and shape fungal community composition belowground. These microhabitats support functionally and taxonomically distinct fungal communities and support the overall fungal diversity of the site through niche variation. In paper II, the relationships between a) the fungal communities found on and in bark beetles from forests that have been affected by forest fire and forests that have not, b) pine phloem that has been colonized by bark beetles and phloem that has not at two different post-colonization time points, and c) phloem chemical nutrients are described. In paper III, the diversity of species within the fungal class Archaeorhizomycetes in the soil of a Swedish pine forest was studied, and two new species are described using an integrative taxonomic approach that relies on environmental DNA sequence data as taxonomical evidence.

Many fungi are characteristically difficult to observe and collect, making the process of documenting the world’s fungal diversity challenging. The vast majority of fungal species are undescribed. The use of DNA sequencing technologies has revolutionized the study of fungal diversity by facilitating the detection of new species, the investigation of community structure and dynamics, and the elucidation of evolutionary relationships. In this dissertation, I focus on filling in some of the many gaps in our understanding of fungal diversity and community ecology in boreal pine forests through the use of DNA sequence data. In the first half of this thesis, a metabarcoding approach is used to study the composition of fungal communities found in the soil of a Lithuanian coastal pine forest and in association with the bark beetle Tomicus piniperda in Swedish pine forests. In the second half, two different approaches are taken to describe taxa detected in environmental DNA. In paper I, I demonstrate how soil microhabitats, defined based on mineral vs organic soil type and root presence or absence, vary with respect to a suite of abiotic factors and shape fungal community composition belowground. These microhabitats support functionally and taxonomically distinct fungal communities and support the overall fungal diversity of the site through niche variation. In paper II, the relationships between a) the fungal communities found on and in bark beetles from forests that have been affected by forest fire and forests that have not, b) pine phloem that has been colonized by bark beetles and phloem that has not at two different post-colonization time points, and c) phloem chemical nutrients are described. In paper III, the diversity of species within the fungal class Archaeorhizomycetes in the soil of a Swedish pine forest was studied, and two new species are described using an integrative taxonomic approach that relies on environmental DNA sequence data as taxonomical evidence.

Many fungi are characteristically difficult to observe and collect, making the process of documenting the world’s fungal diversity challenging. The vast majority of fungal species are undescribed. The use of DNA sequencing technologies has revolutionized the study of fungal diversity by facilitating the detection of new species, the investigation of community structure and dynamics, and the elucidation of evolutionary relationships. In this dissertation, I focus on filling in some of the many gaps in our understanding of fungal diversity and community ecology in boreal pine forests through the use of DNA sequence data. In the first half of this thesis, a metabarcoding approach is used to study the composition of fungal communities found in the soil of a Lithuanian coastal pine forest and in association with the bark beetle Tomicus piniperda in Swedish pine forests. In the second half, two different approaches are taken to describe taxa detected in environmental DNA. In paper I, I demonstrate how soil microhabitats, defined based on mineral vs organic soil type and root presence or absence, vary with respect to a suite of abiotic factors and shape fungal community composition belowground. These microhabitats support functionally and taxonomically distinct fungal communities and support the overall fungal diversity of the site through niche variation. In paper II, the relationships between a) the fungal communities found on and in bark beetles from forests that have been affected by forest fire and forests that have not, b) pine phloem that has been colonized by bark beetles and phloem that has not at two different post-colonization time points, and c) phloem chemical nutrients are described. In paper III, the diversity of species within the fungal class Archaeorhizomycetes in the soil of a Swedish pine forest was studied, and two new species are described using an integrative taxonomic approach that relies on environmental DNA sequence data as taxonomical evidence.

Austropuccinia psidii, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. Austropuccinia psidii has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1 Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in TEs and a very low overall GC content of 33.8%. Compared to other Pucciniales, the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how TEs shaped the genome evolution of A. psidii and provide a greatly needed resource for strategic approaches to combat disease spread.

Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the “One Fungus = One Name” nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study.

Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the “One Fungus = One Name” nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study.