Midterm 1 PDF

I. Classifying Life and the Place of Fungi Systematics plays a crucial role in understanding the diversity of life. It encompasses taxonomy (description, identification, nomenclature, and classification), helping us organize and understand relationships between organi...

I. Classifying Life and the Place of Fungi Systematics plays a crucial role in understanding the diversity of life. It encompasses taxonomy (description, identification, nomenclature, and classification), helping us organize and understand relationships between organisms. Species concepts vary depending on the biological, morphological, ecological, and evolutionary perspectives considered. The starting point for modern biological nomenclature is Linnaeus's works: Systema Naturae (1735) for Animalia and Species Plantarum (1753) for Plantae. Understanding hierarchical classification and interpreting cladograms are essential for "tree thinking," visualizing evolutionary relationships. Nomenclature in mycology follows specific conventions, including the use of standard abbreviations for authorship and italicization of genus and species names. Resources like www.mycobank.org provide valuable taxonomic information. II. Evolutionary Context of Eumycota Phylogenetic studies place Eumycota within the Eukarya domain. Fungi are more closely related to animals than to plants, as evidenced by various shared traits. Key diSerences distinguish Eumycota from other kingdoms, including their heterotrophic nature with absorptive nutrition, chitinous cell walls, typically haploid nuclei, and unique mitochondrial characteristics. III. Distinctive Traits and Cellular Processes A working definition of a fungus: "Filamentous eukaryotic heterotrophs with apical growth, distinctive cell walls (composed of chitin, glucans, mannans, and sometimes melanin), and typically have haploid nuclei, although hyphae may contain more than one nucleus (dikaryotic condition)." Hyphae are the fundamental units of fungal bodies, forming the mycelium. They exhibit apical dominance mediated by the Spitzenkörper, allowing for exploration and resource capture. "Growth (biosynthesis, biomass production) occurs throughout a hypha, whereas extension occurs only at the tip." Hyphal growth is self-avoidant and autotropic. The Spitzenkörper is a dense aggregation of macrovesicles and chitosomes, orchestrating polarized hyphal growth. Macrovesicles contain enzymes and structural proteins. Chitosomes deliver inactive chitin synthases, which become activated upon contact with the cell membrane. "Vesicles are transported from Golgi apparatus to Spitzenkorper along microtubules, and then by actin microfibrils to the plasma membrane." Fungal cell walls are complex structures composed of chitin, glucans, and mannans. "β-glucan: Crucial component of the fungal cell wall and elusive MAMP in plants." Melanin can be present, contributing to structural integrity and other functions. Mitosis in fungi is a unique process characterized by a largely intact nuclear envelope (closed or semi-open mitosis).  "One of the ways in which fungal “cells” diSer from those of animals is by having closed or semi-open mitosis – the nuclear membrane remains largely intact." This contrasts with open mitosis, where the nuclear envelope breaks down, observed in most other eukaryotes. Two hypotheses for the evolution of open mitosis are: Fixation of transposable elements that induce nuclear envelope perforations. The need to accommodate larger microtubule lengths in organisms with larger genomes. Septation, the formation of cross-walls within hyphae, compartmentalizes the mycelium. "A fungal body (mycelium) is composed of hyphae, tubes or filaments characterized by a chitinous cell wall and compartmentalized by septa. Hyphal extension is governed by the Spitzenkorper." This process involves proteins like septins and formins. IV. Overall Significance Understanding the unique biological features of fungi, from their evolutionary history to their distinctive cellular structures and processes, is crucial for appreciating their ecological roles, biotechnological applications, and potential impacts on human health. 1. Defining Fungi and Their Place in the Tree of Life Fungi belong to the kingdom Mycota (Eumycota) within the domain Eukarya. Fungi are defined as "filamentous eukaryotic heterotrophs with apical growth, distinctive cell walls (composed of chitin, glucans, mannans, and sometimes melanin), and typically have haploid nuclei, although hyphae may contain more than one nucleus (dikaryotic condition)." Unlike plants (autotrophs), fungi are heterotrophic, meaning they obtain nutrients by absorbing soluble organic compounds. They are distinguished from animals by several key features, including their chitinous cell walls, haploid nuclei, persistence of the nuclear envelope during mitosis, and storage compounds such as glycogen and trehalose. 2. Hyphal Growth: The Foundation of Fungal Structure Hyphae are the fundamental units of the fungal body, collectively forming the mycelium. They exhibit apical dominance, meaning growth is concentrated at the tip and controlled by a structure called the Spitzenkörper. "Growth (biosynthesis, biomass production) occurs throughout a hypha, whereas extension occurs only at the tip." The Spitzenkörper is a dense cluster of vesicles containing enzymes and structural proteins essential for cell wall synthesis and hyphal extension. Hyphal growth is also facilitated by the cytoskeleton, particularly actin microfilaments and microtubules. "Vesicles are transported from Golgi apparatus to Spitzenkorper along microtubules, and then by actin microfibrils to the plasma membrane." 3. Septation: Compartmentalizing the Fungal Mycelium  Septa are cross-walls that divide hyphae into compartments, providing structural support and regulating nutrient flow. Septation is a complex process involving the coordinated action of various proteins, including septins and formins. "Septin (e.g., AspB): type of GTPase, a group of hydrolase enzymes that bind to the nucleotide guanosine triphosphate (GTP) SepA: formin-type protein" 4. Mitosis in Fungi: A Unique Process Fungi exhibit closed or semi-open mitosis, where the nuclear envelope remains mostly intact throughout the process. "One of the ways in which fungal “cells” diSer from those of animals is by having closed or semi-open mitosis – the nuclear membrane remains largely intact." This contrasts with open mitosis in animals, where the nuclear envelope breaks down completely. Two hypotheses have been proposed to explain the evolution of open vs. closed mitosis: "Transposable elements that induce nuclear envelope perforations become fixed in the genome; may or may not oSer a selective advantage to the organism as a whole, but a TE with enhanced access to the genome would have a greater chance of being replicated/fixed in the genome (“selfish jumping genes”) "Size matters? Larger genomes require larger nuclei – (nuclear radius = 3√genome size) but microtubule length scales linearly with genome size. Therefore, larger genomes have microtubules longer than their radii. Breaking down the nuclear envelope (open mitosis) accommodates these ‘extra long’ microtubules." 5. Coordination of Mitosis and Septation Mitosis and septation are not always synchronized in fungi. "Mitosis may (or may not!) occur in coordination with septation. “Daughter nuclei” may co-exist in the same compartment, and nuclei do not all undergo mitotic division at once." This allows for flexibility in hyphal growth and development. Overall, this briefing document highlights the unique features of fungal biology, emphasizing hyphal growth, septation, and the distinctive process of mitosis. Understanding these characteristics is crucial for appreciating the diverse roles fungi play in various ecosystems and their potential applications in biotechnology and medicine. Defining Fungi Historically, fungi were classified based on: Biological factors: Mate recognition, phenotypic cohesion. Morphological factors: Physical characteristics. Ecological factors: Habitat and interactions. Geographic factors: Distribution. Evolutionary factors: Ancestry and relationships. Modern classification utilizes molecular data and phylogenetic analyses. This has led to significant reclassifications, exemplified by the dissolution of "Deuteromycota" (fungi lacking known sexual stages) based on the holomorphic concept: Anamorph(s) and synanamorph(s): Asexual reproductive structures.  Teleomorph: Sexual reproductive structure. Molecular tools, such as ITS (Internal Transcribed Spacer) sequencing, provide a "barcode" for fungal identification, enabling: Species delimitation: Often based on 3% sequence divergence. Phylogeographic studies: Tracing the evolutionary history and spread of species (e.g., Amanita muscaria). Discovery of novel diversity: "Many fungi remain to be discovered and/or described". A working definition of a fungus: "Filamentous eukaryotic heterotrophs with apical growth, distinctive cell walls (composed of chitin, glucans, mannans, and sometimes melanin), and typically have haploid nuclei, although hyphae may contain more than one nucleus (dikaryotic condition)." Key Traits of Eumycota (True Fungi) Eumycota are distinguished from other organisms by several key traits: TraitFungiAnimaliaPlantaeTissueFilamentous/hyphalNot hyphal, multicellularNot hyphal, multicellularNutritionHeterotrophic, absorb soluble nutrientsHeterotrophic, ingest nutrientsPhotosynthetic (autotrophic)Cell wallChitinNo cell walls (chitin in exoskeletons)Cellulose and hemicelluloseNucleiTypically haploid (n + n dikaryon)Typically diploidTypically diploidMitosis/MeiosisNuclear envelope persistsNuclear envelope breakdownNuclear envelope breakdownMitochondriaPlate or disk-like cisternaePlate or disk-like cisternaeTubular cisternaeStorage compoundsGlycogen, lipids, trehaloseGlycogen, lipids (trehalose in insects)StarchMitochondrial codon UGACodes for tryptophanCodes for tryptophanCodes for termination (stop codon)Membrane sterolsErgosterolCholesterolSitosterol and othersLysine synthesisAAA pathwayCan't synthesize lysineDAP (diamino-pimelic acid) pathwayHyphal Biology Hyphae are the fundamental units of the fungal body (mycelium). They exhibit: Apical dominance: Growth occurs primarily at the tip, regulated by the Spitzenkörper. Linear growth rate (individual hyphae): However, the colony (mycelium) grows exponentially. Self-avoidance: Hyphae typically avoid growing over each other. Diverse functions: Exploration, resource capture, formation of complex structures (rhizomorphs, fruiting bodies). The Spitzenkörper: A dense structure at the hyphal tip, orchestrating apical growth. Contains macrovesicles (secretory, containing enzymes and structural proteins) and chitosomes (delivering inactive chitin synthases). Vesicle transport to the apex is facilitated by actin microfilaments and microtubules. Cell wall: Composed of chitin, glucans, and mannans. Melanin is sometimes present, providing structural support and protection. Cell-wall lytic enzymes facilitate hyphal branching. Mitosis and Septation Fungal mitosis is unique: Closed or semi-open: The nuclear envelope remains largely intact.  Uncoordinated with septation: Daughter nuclei may co-exist in the same compartment. Asynchronous: Not all nuclei undergo mitotic division simultaneously. Septation: Compartmentalizes the hyphae, forming individual cells. Involves the formation of a septum, a cross-wall structure. Regulated by proteins like septins (GTPases) and formins. Early-Diverging Fungal Lineages Phylogeny of fungi is constantly being refined. Several early-diverging lineages include: Rozellomycota (“Cryptomycota” incertae sedis):"Cryptomycota" were initially identified from environmental DNA. Rozella, the only genus, was later linked to the eDNA sequences. They are phagotrophic (engulf food particles), unlike most fungi which are osmotrophic (absorb dissolved nutrients). Primarily endoparasites of other fungi. Microsporidia [incertae sedis]:Obligate intracellular parasites, mainly of arthropods. Possess a unique polar tube for injecting infective sporoplasm into host cells. Reduced organelles and chitinous cell walls. Aphelida [incertae sedis]:Parasites of algae and other organisms. Possess an infective stage called the amoeboid zoospore. Conclusion The study of fungal biology is continually evolving, driven by molecular data and new discoveries. Understanding the unique features of fungal cells, growth, and evolution is crucial for appreciating their ecological roles and potential applications in biotechnology and medicine. I. Defining Fungi and Their Characteristics Fungi are a kingdom of eukaryotic organisms, distinct from plants and animals. They play crucial roles in ecosystems as decomposers, symbionts, and pathogens. Key defining features of true fungi (Eumycota) include: Filamentous/Hyphal Growth: Fungi grow as hyphae, tubular structures that form a network called mycelium. Heterotrophic Nutrition: Fungi obtain nutrients by absorbing soluble organic matter from their environment. Chitinous Cell Walls: Their cell walls are composed primarily of chitin, a tough, nitrogen-containing polysaccharide. Haploid Nuclei: Fungal cells typically have haploid nuclei, but a dikaryotic stage (n+n) is common in some groups. Closed or Semi-Open Mitosis: The nuclear envelope remains largely intact during cell division. Unique Biochemical Features: Fungi use glycogen as their primary storage carbohydrate, have ergosterol as a membrane sterol, and utilize a diSerent pathway for lysine biosynthesis compared to plants and animals. II. Fungal Diversity and Classification Fungi are a highly diverse kingdom, with estimates suggesting millions of species. Molecular techniques, particularly DNA sequencing, have revolutionized our understanding of fungal phylogeny and taxonomy. The major fungal lineages include: Early-Diverging Lineages:Rozellomycota (“Cryptomycota”): Endoparasites of other fungi, primarily chytrids. Notably phagotrophic. Microsporidia: Obligate intracellular parasites, mainly of animals. Characterized by a unique polar tube used for host infection. Aphelida: Parasites of algae and other organisms, with a motile zoospore stage. Flagellated Fungi:Blastocladiomycota: Characterized by having alternating haploid and diploid generations and some exhibiting oögamous reproduction. Include parasites of plants and insects (e.g., Coelomomyces). Chytridiomycota: Aquatic fungi known for their motile zoospores with a single posterior flagellum. Some are important pathogens, such as Batrachochytrium dendrobatidis, which causes chytridiomycosis in amphibians. Monoblepharidomycota: Unique for their oogamous reproduction where a motile sperm fertilizes a non-motile egg. Non-Motile Fungi:Zoopagomycota: Include parasites of other fungi and small animals. Characterized by the production of merosporangia containing asexual spores. Mucoromycota:Mucoromycotina: Commonly known as zygomycetes. Characterized by their formation of zygospores during sexual reproduction. Include saprotrophs, parasites, and the arbuscular mycorrhizal fungi (Glomeromycotina). Glomeromycotina: Form obligate symbiotic relationships with plants, forming arbuscular mycorrhizae. Crucial for plant nutrient uptake and ecosystem functioning. III. Mycorrhizae and the Greening of Planet Earth Arbuscular mycorrhizal fungi (AMF), belonging to Glomeromycotina, played a crucial role in the colonization of land by plants. They form intimate associations with plant roots, providing them with essential nutrients, particularly phosphorus, in exchange for carbohydrates. Key points: Ancient Symbiosis: The AMF symbiosis dates back to the early Devonian, evidenced by fossilized associations in the Rhynie Chert. Widespread Occurrence: AMF associations are found in most terrestrial ecosystems and are essential for the growth and survival of many plant species. Ecosystem Function: AMF contribute significantly to nutrient cycling, soil aggregation, and plant diversity in terrestrial ecosystems. IV. Hyphal Biology and Growth Hyphae are the fundamental units of fungal growth, collectively forming the mycelium. They exhibit apical growth, driven by the Spitzenkörper, a complex structure at the hyphal tip. Key aspects of hyphal biology: Polarized Growth: The Spitzenkörper directs the delivery of enzymes and cell wall components to the hyphal tip, ensuring unidirectional growth.  Cell Wall Composition: The fungal cell wall provides structural integrity and protection. It is a dynamic structure composed of chitin, glucans, and other components. Septation: In many fungi, hyphae are divided into compartments by septa, perforated structures that allow for cytoplasmic flow. V. Mitosis and Septation Fungal mitosis is unique in that the nuclear envelope remains largely intact (closed or semi-open mitosis). This distinguishes it from the open mitosis seen in animals and plants. Spindle Pole Bodies (SPBs): Fungi utilize SPBs, similar to centrosomes, to organize microtubules during mitosis. Coordination with Septation: Mitosis and septation may be coordinated but not always. Daughter nuclei can coexist in the same hyphal compartment, and not all nuclei divide simultaneously. VI. Notable Quotes "Fungal morphogenesis, from the polarized growth of hyphae to complex reproduction and infection structures." - Riquelme et al. 2018. This quote highlights the diverse developmental processes governed by hyphal growth. "β-glucan: Crucial component of the fungal cell wall and elusive MAMP in plants." - Fesel and Zuccaro 2016. This quote emphasizes the importance of β- glucans in fungal cell wall structure and their role in plant-fungal interactions. "Deciphering the evolutionary history of open and closed mitosis." - Sazer et al. 2014. This paper explores the evolution of diSerent modes of mitosis, including the closed mitosis characteristic of fungi. "Early fungi from the Proterozoic era in Arctic Canada." - Loron et al. 2019. This study pushes back the fossil record of fungi, suggesting their presence in the Proterozoic. VII. Key Takeaways Fungi are a diverse and essential kingdom of eukaryotic organisms with unique biological and ecological characteristics. Understanding hyphal biology, mitosis, and septation is crucial for comprehending fungal growth and development. Mycorrhizal symbioses, particularly those involving arbuscular mycorrhizal fungi, have played a profound role in shaping terrestrial ecosystems. This briefing document provides a foundational overview of key concepts in fungal biology. Further exploration of specific topics is encouraged for a more in-depth understanding of this fascinating and important kingdom of life. I. What are Fungi? Definition: Fungi are filamentous eukaryotic heterotrophs characterized by apical growth, distinctive cell walls composed of chitin, glucans, mannans, and sometimes melanin, and typically haploid nuclei (dikaryotic condition is also common). Traits:Heterotrophic: Absorb soluble nutrients, unlike animals (ingestion) and plants (photosynthesis). Chitinous cell walls: DiSerentiate them from plants (cellulose and hemicellulose cell walls) and animals (no cell walls, chitin only in exoskeletons).  Haploid nuclei: Often exist in a dikaryotic (n+n) state, contrasting with the diploid nuclei typical of animals and plants. Unique cellular structures: Possess mitochondria with plate- or disk-like cisternae, diSering from the tubular cisternae in plants. Storage compounds: Primarily glycogen, lipids, and trehalose. Unique genetic code: Mitochondrial codon UGA codes for tryptophan, unlike in animals and plants where it's a stop codon. Ergosterol: Primary membrane sterol, unlike cholesterol in animals and sitosterol in plants. Lysine biosynthesis: Synthesized by AAA pathway, diSerent from DAP pathway in plants. II. Classification and Evolution of Fungi Molecular phylogenetics revolutionized fungal classification: DNA barcoding (e.g., using the ITS region) allows for species identification and phylogenetic analysis even in environmental samples. Hierarchical Classification: Kingdom (Mycota), Phylum (-mycota), Class (- mycetes), Order (-ales), Family (-aceae), Genus, Species. Example: Leccinum versipelle (Fr. & Hök) Snell (Agaricomycotina: Agaricomycetes: Agaricomycetidae: Boletales: Boletaceae) Early-Diverging Fungal Lineages:Rozellomycota (“Cryptomycota” incertae sedis):Endoparasites of other fungi. Phagotrophic, unlike most fungi that are osmotrophic. Microsporidia (incertae sedis):Obligate endoparasites, mainly of arthropods. Injected sporoplasm undergoes merogony (binary fission) within the host. Aphelida (incertae sedis):Parasites of algae and other fungi. Produce zoospores with a characteristic pseudopodia. Blastocladiomycota:Exhibit diverse life histories, including both saprophytic and parasitic forms. Possess flagellated zoospores. Allomyces is a well-studied model organism for its unique life cycle with alternating haploid and diploid stages. Monblepharidomycota:Characterized by oogamous reproduction, where a large non-motile egg is fertilized by a smaller motile sperm. Monoblepharis is a representative genus with a distinctive life cycle. Chytridiomycota:Often referred to as "chytrids." Known for their flagellated zoospores. Some species, like Batrachochytrium dendrobatidis, are responsible for amphibian decline. Zoopagomycota:Often parasites of other fungi or small invertebrates. Produce characteristic merosporangia and zygosporangia. Mucoromycota:Include the arbuscular mycorrhizal fungi (Glomeromycotina), which form symbiotic relationships with plants. Also encompass saprophytic and parasitic forms like Mucor and Rhizopus. Pilobulus species are known for their unique mechanism of forcibly launching sporangia. III. Hyphal Biology and Growth Hyphae: The fundamental units of the fungal body (mycelium).  Growth: Apical dominance mediated by the Spitzenkörper, a dense aggregation of macrovesicles and chitosomes. Spitzenkörper: Orchestrates polarized growth by delivering enzymes and structural components for cell wall expansion at the hyphal tip. Septation: Compartmentalizes the hyphae but allows for cytoplasmic continuity through pores. Septation process: Involves complex interplay of septins, formins, and other proteins to form a contractile ring that constricts the cell membrane and deposits new cell wall material. Variations:Rhizomorphs and Mycelial Cords: Specialized hyphal structures for resource transport and exploration. Sexual structures: Ascocarps (Ascomycota) and Basidiocarps (Basidiomycota) are complex hyphal aggregates for sexual reproduction. Mitosis: Occurs within the intact nuclear envelope (closed or semi-open mitosis). Coordination with septation: Can be synchronous or asynchronous, resulting in compartments with varying numbers of nuclei. Evolutionary significance: The prevalence of closed mitosis in fungi is debated, with hypotheses relating to transposable elements or genome size. IV. Ecological Roles of Fungi Saprotrophs: Decomposers of organic matter, playing a crucial role in nutrient cycling. Parasites: Infect plants, animals, and other fungi, sometimes causing diseases. Mutualists:Mycorrhizae: Form symbiotic relationships with plant roots, enhancing nutrient uptake. Arbuscular mycorrhizal fungi (AMF): Ancient association found in most land plants, crucial for plant colonization of land. Ectomycorrhizal fungi (EMF): Occur mainly in trees, forming a sheath around root tips. Lichens: Symbiotic partnerships between fungi (mycobiont) and algae or cyanobacteria (photobiont). Other roles:Endophytes: Live within plant tissues without causing apparent harm, potentially oSering benefits to their hosts. Pathogen vectors: Some fungi, like Olpidium, can vector plant viruses. V. Key Quotes: "A working definition for 'fungus': Filamentous eukaryotic heterotrophs with apical growth, distinctive cell walls (composed of chitin, glucans, mannans, and sometimes melanin), and typically have haploid nuclei, although hyphae may contain more than one nucleus (dikaryotic condition)." "Fungi exhibit apical dominance (polarized growth), mediated by the Spitzenkorper body. Growth (biosynthesis, biomass production) occurs throughout a hypha, whereas extension occurs only at the tip." "One of the ways in which fungal 'cells' diSer from those of animals is by having closed or semi-open mitosis - the nuclear membrane remains largely intact." VI. Notable Species and Groups: Wallemiomycetes: Some species are associated with "sick building syndrome."  Agaricomycetes: Contains many familiar mushrooms, including Agaricus, Amanita, and Boletus. Russulales: Characterized by gloeopleurous hyphae and include both saprophytic and ectomycorrhizal species. Synchytrium endobioticum: A chytrid that causes potato wart disease. Entomophthoromycotina: Includes fungi that parasitize insects. Mucoromycotina: Includes a diversity of saprobes, parasites, and the AMF. VII. Comparison of Basidia: Russula emetica: Produces homobasidia, characterized by a single, undivided cell bearing sterigmata. Ustilago maydis: Produces heterobasidia, often with septations (transverse or longitudinal), which can be further classified into phragmobasidia or teliobasidia. This briefing doc oSers a comprehensive overview of key aspects of fungal biology, highlighting the diverse nature and ecological significance of this fascinating kingdom. I. Defining Fungi & Their Evolutionary Context: Fungi are filamentous eukaryotic heterotrophs characterized by apical growth, distinctive chitinous cell walls, and predominantly haploid nuclei (with the dikaryotic condition prevalent in certain life stages). Fungi diverged from other eukaryotes early in evolutionary history. Recent molecular phylogenetics places them closer to animals than plants, challenging traditional classifications. Early-diverging fungal lineages (e.g., Rozellomycota, Microsporidia) exhibit unique characteristics like phagotrophy and obligate endoparasitism, highlighting the diversity of lifestyles within the kingdom. The evolution of non-motile fungi (e.g., Zoopagomycota, Mucoromycota) marked a shift towards saprotrophic and symbiotic lifestyles, with significant ecological and economic impacts. II. Hyphal Biology & Fungal Growth: Hyphae are the fundamental units of the fungal body (mycelium), responsible for nutrient absorption, exploration, and colonization. Apical dominance mediated by the Spitzenkörper governs hyphal extension, ensuring polarized growth and eSicient resource capture. Mitosis in fungi is a distinct process where the nuclear envelope remains largely intact (closed or semi-open mitosis), unlike in animals. Septation (cross-wall formation) compartmentalizes hyphae, allowing for diSerentiation and resource allocation. Septin proteins play a crucial role in septum formation. Vegetative growth extends beyond individual hyphae, with structures like rhizomorphs and mycelial cords facilitating resource transport and colonization. III. Key Innovations: Mycorrhizae & the Greening of Earth: Arbuscular mycorrhizal fungi (AMF) from the Mucoromycota are ancient symbionts, forming mutualistic relationships with the majority of land plants. Fossil evidence from the Rhynie Chert (~407 Ma) reveals AMF associations with early land plants, suggesting their crucial role in the colonization of terrestrial environments.  AMF facilitate nutrient uptake (especially phosphorus) for plants in exchange for photosynthetically derived carbon, contributing significantly to plant growth and ecosystem productivity. This plant-fungal mutualism has been crucial for the evolution and diversification of land plants, shaping terrestrial ecosystems as we know them. IV. Diversity & Ecological Roles of Fungal Groups: Chytridiomycota:Possess flagellated zoospores, highlighting their aquatic or moist habitats. Include significant plant pathogens (e.g., Synchytrium endobioticum causing potato wart disease) and contributors to amphibian decline (e.g., Batrachochytrium dendrobatidis). Blastocladiomycota:Exhibit a range of life histories and reproductive strategies, including the unique "oogamous" reproduction in Monoblepharidomycetes. Include parasites of plants and insects, highlighting their diverse ecological roles. Zoopagomycota:Predominantly parasites of other fungi and invertebrates. Characterized by specialized structures like merosporangia for spore dispersal. Mucoromycota:Include saprotrophs (e.g., Rhizopus causing food spoilage), pathogens (e.g., agents of mucormycosis), and the ecologically vital AMF. The production of rhizoxin by endosymbiotic bacteria in Rhizopus microsporus showcases complex symbiotic interactions and potential for biopharmaceutical applications. V. Important Facts & Observations: Fungi exhibit a wide range of hymenial (spore-bearing) morphologies, including smooth, poroid, lamellate, labyrinthoid, and hydnoid types. Basidia (the spore-producing structures in Basidiomycota) can be classified as homobasidia or heterobasidia based on their structure and septation. "Sick building syndrome" is a health concern potentially linked to fungal allergens, with Wallemiomycetes implicated as possible causative agents. Molecular phylogenetics plays a critical role in revising fungal taxonomy, revealing cryptic diversity and challenging traditional classifications based on morphology alone. Environmental DNA (eDNA) analysis is a powerful tool for exploring fungal diversity, revealing a vast array of undiscovered species and expanding our understanding of fungal ecology. VI. Quotes: "A working definition for ‘fungus’: Filamentous eukaryotic heterotrophs with apical growth, distinctive cell walls (composed of chitin, glucans, mannans, and sometimes melanin), and typically have haploid nuclei, although hyphae may contain more than one nucleus (dikaryotic condition)." “Larger genomes require larger nuclei…but microtubule length scales linearly with genome size. Therefore, larger genomes have microtubules longer than their radii. Breaking down the nuclear envelope (open mitosis) accommodates these ‘extra long’ microtubules.” VII. Future Directions: Further research using molecular and genomic tools is crucial for resolving phylogenetic relationships within the fungal kingdom.  Exploring the ecological roles of understudied fungal groups, particularly in the context of global change, is essential. Investigating the potential of fungi for bioremediation, biocontrol, and biopharmaceutical applications holds immense promise. This briefing document provides a comprehensive overview of key concepts in fungal biology, highlighting the ecological significance and remarkable diversity of this fascinating kingdom. By understanding the fundamentals of fungal biology, we can better appreciate their critical roles in ecosystems and explore their potential for addressing global challenges. I. Introduction to Fungi Fungi are eukaryotic heterotrophs characterized by apical growth, chitinous cell walls, and typically haploid nuclei, though a dikaryotic condition (n+n) is common. Mycelium, the fungal "body," comprises hyphae responsible for nutrient absorption, dispersal, and forming complex structures. Key traits distinguishing fungi from plants and animals include: Cell Wall: Chitin (vs. cellulose in plants) Nuclear Division: Closed or semi-open mitosis (vs. open in animals) Ploidy: Typically haploid (vs. diploid in animals and plants) Storage Compounds: Glycogen, lipids, trehalose (vs. starch in plants) II. Fungal Systematics and Evolution Fungal systematics involves identification, taxonomy, and nomenclature, reflecting organisms' evolutionary relationships. Molecular phylogenetics, utilizing DNA barcodes like ITS, has revolutionized fungal classification and species delimitation. Hierarchical classification: Kingdom: Fungi Phylum: -mycota Subphylum: -mycotina Class: -mycetes Order: -ales Family: -aceae Genus: Genus Species: Genus species Key evolutionary milestones: Early diverging fungal lineages include Rozellomycota, Microsporidia, and Aphelida. Loss of flagellum occurred only once in fungal evolution, uniting all non- flagellated fungi. III. Early-Diverging Fungi Characterized by unique life cycles, diverse morphologies, and ecological roles. Blastocladiomycota: Exhibit diverse life histories with alternating haploid and diploid phases. Some are parasites of plants and insects. Monoblepharidomycota: Characterized by oogamous reproduction where a motile male gamete fertilizes a non-motile female gamete.  Chytridiomycota: Aquatic fungi with motile zoospores, some causing significant diseases like potato blight and amphibian decline. IV. Non-Motile Fungi Zoopagomycota: Obligate parasites of other fungi or small animals, forming merosporangia and zygosporangia. Mucoromycota: Contains diverse lineages including: Mucoromycotina: Known for rapid growth, food spoilage, and causing mucormycosis in humans. Some species, like Pilobulus, exhibit unique spore dispersal mechanisms. Glomeromycotina: Arbuscular mycorrhizal fungi (AMF) forming symbiotic relationships with plants, critical for plant nutrition and terrestrial ecosystem evolution. V. Mycorrhizae and the Greening of Planet Earth Mycorrhizae represent symbiotic associations between fungi and plant roots. Arbuscular mycorrhizal fungi (AMF) played a crucial role in the colonization of land by plants. AMF facilitate nutrient uptake, particularly phosphorus, and enhance plant stress tolerance. Fossil evidence from the Rhynie Chert (Early Devonian) reveals the ancient origin of AMF, coinciding with early land plant diversification. VI. Agaricomycotina: The Dikaryotic Fungi This subphylum includes smuts, rusts, and agarics, characterized by a dikaryotic phase in their life cycle. Clamp connections are specialized structures that maintain the dikaryotic state in hyphae. Hyphal DiSerentiation: Generative hyphae: Thin-walled, branching, septate, and may be mono- or dikaryotic (often with clamp connections). Skeletal hyphae: Thick-walled, long, rarely branching, aseptate, and lack clamp connections. Binding hyphae: Thick-walled, tapering branches, typically aseptate, and lack clamp connections. Basidiocarp Composition: Monomitic: Composed of generative hyphae only. Dimitic: Composed of generative hyphae and either skeletal or binding hyphae. Trimitic: Composed of generative, skeletal, and binding hyphae. Hymenium and Gill Anatomy: The hymenium is the fertile layer bearing basidia. Gill types include divergent, interwoven, and parallel trama. Basidiocarp Development: Varies among groups and involves intricate hyphal organization and diSerentiation. Septation: The formation of septa involves proteins like septin and SepA, crucial for hyphal compartmentalization. Woronin bodies, dolipores, and parenthesomes: Unique structures associated with septa in diSerent fungal groups, regulating cellular transport and compartmentalization. VII. Key Orders within Agaricomycotina  Wallemiomycetes: Xerophilic, allergenic fungi known to cause “sick building syndrome.” They produce unique compounds like wallemidone. Cantharellales: Characterized by stichic basidia, diverse basidiocarps, and ecological roles as saprotrophs and ectomycorrhizal fungi. Auriculariales: Known as “wood ears,” with longitudinally septate basidia and often edible. Geastrales: Includes earthstars and cannonball fungi with unique spore dispersal mechanisms. Hysterangiales: Mostly hypogeous or epigeous forms, with a gelatinous gleba. Many are ectomycorrhizal symbionts. Gomphales: Characterized by chiastic basidia, cyanophilic spore ornamentation, and ectomycorrhizal associations. Phallales: "Stinkhorns" with a gelatinous gleba dispersed by insects, saprotrophic in nature. Trechisporales: Corticioid basidiocarps, mostly monomitic with clamp connections. Primarily white-rot or soil saprotrophs. Hymenochaetales: Dominated by polypores and bracket fungi, featuring a continuous parenthesome. Mostly white-rot saprotrophs. Thelephorales: Diverse basidiocarps, characterized by thelephoric acid which inhibits prolyl endopeptidase. Primarily ectomycorrhizal. Polyporales: Abundant bracket fungi and other forms, major contributors to wood decay communities. Gloeophyllales: Primarily wood decay fungi, lacking unifying morphological characters. Corticiales: Mostly resupinate with smooth hymenophores, diverse ecological roles including plant pathogens, parasites, and endophytes. Russulales: Diverse group with gloeopleurous hyphae and gloeocystidia, including ectomycorrhizal and saprotrophic species like Russula and Lactarius. Agaricales: Largest order with over 13,000 species, diverse forms including gilled mushrooms, puSballs, and secotioid forms. Ecologically diverse including saprotrophs, ectomycorrhizal fungi, and even lichenized forms. Atheliales: Typically corticioid with undiSerentiated margins, including saprotrophic, ectomycorrhizal, and lichenicolous species. Boletales: Featuring poroid, gilled, or smooth hymenia, often with pileate- stipitate basidiocarps. Includes choice edibles and some poisonous species. Ecologically includes brown-rot saprotrophs, ectomycorrhizal fungi, and mycoparasites. VIII. Comparison: Russula emetica vs. Ustilago maydis Basidia Russula emetica (Agaricomycotina: Agaricales): Produces homobasidia, characterized by: Structure: Club-shaped, undivided. Sterigmata: Typically four, slender projections where basidiospores develop. Spore Discharge: Forcibly discharged. Ustilago maydis (Ustilaginomycotina: Ustilaginales): Produces heterobasidia, characterized by: Structure: Septate, divided either transversely or longitudinally. Sterigmata: Variable number, often arising laterally from septate sections.  Spore Discharge: Not forcibly discharged. IX. Conclusion This briefing document provides a comprehensive overview of fungal biology, encompassing diverse aspects from cellular structure and hyphal growth to evolutionary relationships and ecological significance. The information presented highlights the critical role of fungi in various ecosystems and their impact on human activities. I. Defining Fungi and Exploring Their Evolutionary Context: Fungi are filamentous eukaryotic heterotrophs characterized by apical growth, distinctive cell walls composed of chitin, glucans, mannans, and sometimes melanin, and typically have haploid nuclei. The presence of a dikaryotic stage is common (Lecture 2). Molecular phylogenetics, utilizing tools like ITS sequencing, revolutionized our understanding of fungal diversity and relationships, revealing a vast, undiscovered world of fungi (Lecture 5). Early-diverging fungal lineages, including Rozellomycota and Microsporidia, showcase unique features and often parasitic lifestyles. Rozella, for instance, are phagotrophic parasites of other fungi, while Microsporidia are known for their obligate intracellular parasitism in animals, particularly arthropods (Lecture 5, Lecture 6). The evolution of the hyphal habit, a defining feature of most fungi, has occurred multiple times independently, as evidenced by groups like the Monoblepharidomycetes (Lecture 6). Fossil evidence, such as those from the Rhynie Chert, reveals the long evolutionary history of fungal-plant interactions, particularly the ancient relationship between Glomeromycotina (arbuscular mycorrhizal fungi) and early land plants (Lecture 9). II. Hyphal Biology and Growth: Hyphae are the fundamental units of the fungal body, collectively forming the mycelium. They play crucial roles in nutrient absorption, dispersal, and exploration (Lecture 2, Lecture 4). Apical growth in fungi is directed by the Spitzenkörper, a complex structure at the hyphal tip responsible for orchestrating the delivery of enzymes and structural components for cell wall expansion (Lecture 2, Lecture 4). Septation divides hyphae into compartments. This process, involving proteins like septins, is crucial for maintaining hyphal structure and function. However, unlike in plants, mitosis in fungi often occurs independently of septation, leading to multinucleate compartments (Lecture 4). Melanin, a pigment found in fungal cell walls, provides protection from environmental stresses, including UV radiation and predation (Lecture 4). III. Diversity of Form and Function in Basidiomycota: Basidiomycota are characterized by the production of basidiospores on specialized structures called basidia. This diverse group includes smuts, rusts, and agarics (Lecture 10 and 11).  Clamp connections are unique features in many basidiomycetes that ensure the maintenance of the dikaryotic state during vegetative growth. This dikaryotic phase is crucial for the formation of basidiocarps (Lecture 10 and 11). Basidiocarp morphology, including features like pileus, stipe, and hymenium, varies greatly across the Basidiomycota, reflecting diverse ecological strategies and adaptations (Lecture 10 and 11). Mycelial diSerentiation leads to the formation of generative, skeletal, and binding hyphae, which contribute to the structural complexity and strength of basidiocarps. The combination of these hyphae types defines the monomitic, dimitic, or trimitic nature of the basidiocarp (Lecture 10 and 11). Hymenial structures, responsible for spore production, come in a variety of forms, including smooth, poroid, lamellate, labyrinthoid, and hydnoid. These diSerent hymenial types reflect diSerent strategies for spore dispersal and environmental adaptation (Lecture 10 and 11). Basidiocarp development follows specific patterns in some groups, often involving the formation of a hyphal knot that diSerentiates into specialized tissues (Lecture 10 and 11). Septation in Basidiomycota is complex, involving structures like Woronin bodies, dolipores, and parenthesomes, which regulate the flow of cytoplasm and organelles between compartments (Lecture 10 and 11). Agaricomycetes, the largest class within Basidiomycota, exhibits remarkable diversity, ranging from the enigmatic Sebacinales with diverse symbiotic associations to the well-known Agaricales encompassing mushrooms with various lifestyles, including saprotrophic, ectomycorrhizal, and even lichenized forms (Lecture 10 and 11). IV. Ecological Roles and Importance: Chytridiomycota, commonly known as chytrids, play important ecological roles in aquatic ecosystems. However, some species, like Batrachochytrium dendrobatidis, have gained notoriety as pathogens of amphibians, contributing to global amphibian decline (Lecture 7). Zoopagomycota, characterized by the production of merosporangia and zygosporangia, are primarily parasites or pathogens of other fungi and invertebrates, highlighting the complex web of interactions within ecosystems (Lecture 8). Mucoromycota, including Mucoromycotina (formerly Zygomycetes) and Glomeromycotina, encompass a diverse group of fungi. Some Mucoromycotina are saprotrophs, while others cause mucormycoses in humans. Glomeromycotina are essential symbionts forming arbuscular mycorrhizae with the vast majority of land plants, playing a crucial role in nutrient uptake and ecosystem functioning (Lecture 8, Lecture 9). The greening of planet Earth was facilitated by the symbiotic relationship between early land plants and arbuscular mycorrhizal fungi, highlighting the crucial role of fungi in the evolution of terrestrial ecosystems (Lecture 9). V. Key Terminology: Holocarpic vs. eucarpic: describes whether the entire fungal thallus develops into a reproductive structure or only a portion of it.  Endobiontic vs. epibiontic: describes whether the fungus lives inside or on the surface of its host. Monocentric vs. polycentric: describes whether the fungus produces a single or multiple reproductive structures. Sporophyte vs. gametophyte: describes the diploid and haploid phases in the life cycle of some fungi. Isogamous vs. anisogamous: describes the size and morphology of gametes. Heterothallic vs. homothallic: describes whether sexual reproduction requires two compatible mating types or can occur within a single individual. Ballistospores: spores actively discharged by a mechanism involving water droplets. Homobasidia vs. heterobasidia: describes the morphology and septation of basidia. Monomitic, dimitic, trimitic: describes the composition of hyphal types in a basidiocarp. Anamorph vs. teleomorph: describes the asexual and sexual stages in the life cycle of a fungus. This briefing document provides an overview of the key concepts and important facts regarding fungal biology, highlighting the incredible diversity and ecological significance of this fascinating kingdom of life.