Fungal Biology, Nutrition, and Ecological Roles Study Guide

Principles of Organismal Biology Ecology and Evolution

A general understanding of the diversity of life and how that diversity came to be through evolution by natural selection acting on organisms embedded in complex abiotic environments and biological communities.

• biodiversity
• evolution by natural selection
• abiotic environments
• biological communities
• process of science
• Archaea
• Bacteria
• Fungi
• SARs
• Red and green Algae

Components of Evolution by Natural Selection

Evolution by natural selection involves variation in a trait within a population, heritability, selection, and differential, non-random fitness.

• Evolution by natural selection
• Differential, non-random fitness
• Heritability
• Selection
• Variation in a trait within a population
• Genetic variation
• Mutations
• Distribution of fitness effects

Genetic Variation and Natural Selection

Genetic variation arises via mutations and can appear continuous or discrete, providing the variation for evolution to work on through selection.

• genetic variation
• mutations
• distribution of fitness effects
• relative fitness
• continuous variation
• discrete variation
• selection
• heritability
• differential non-random fitness

Fungi Phylogeny and Biological Characteristics

Fungi are a monophyletic lineage of large, terrestrial Eukaryotes with diversity ranging from single cells to huge multicellular structures.

• Phylogeny
• Eukaryotes
• Taxonomy
• DNA sequence data
• Sexual reproductive structures
• Monophyletic
• Mycelial cords
• Armillaria ostoyae
• Humongous Fungus
• Ecosystem functioning
• Pathogens

• Fungi: Phylogeny, Biology, and Ecological Roles

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Defining Features and Structure of Fungi

Fungi are eukaryotes that possess cell walls made of chitin and can be single-celled or made of filaments called hyphae.

• Defining features of Fungi
• Nutritional absorption
• Sexual and asexual reproduction
• Spore dispersal
• Single-celled fungi
• Yeasts
• Eukaryote vs Prokaryote
• Mycelium
• Septa

Fungal Nutrition and Ecological Impacts

Fungi utilize thin hyphae to secrete digestive enzymes externally for absorbing nutrients, driving ecological and evolutionary impacts through decomposition and symbioses.

• Fungal nutrition
• External digestive enzymes
• Lignin and cellulose decomposition
• C, N, P cycles
• Symbioses
• Lichens
• Mycorrhizae
• Batrachochytrium dendrobatidis
• Asexual reproduction
• Conidia
• Conidiophores

• Fungal Biology, Nutrition, and Ecological Roles

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Fungal Sexual Reproduction and Spore Dispersal

Fungi undergo sexual cycles involving plasmogamy, dikaryotic mycelium, karyogamy, and meiosis to produce spores for dispersal.

• plasmogamy
• dikaryotic mycelium
• karyogamy
• meiosis
• haploid spores
• basidiomycete sexual cycle
• spores
• zoospores
• airborne dispersal
• animal dispersers

• Fungal Sexual Reproduction and Spore Dispersal

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Fungal Biology and Ecological Impacts

Fungi are organisms characterized by hyphae, mycelia, and specialized reproduction stages that impact ecosystems through fermentation, bioremediation, and symbiotic mycorrhizal relationships.

• Fungal morphology
• Saprophytic nutrition
• Fungal reproduction (plasmogamy, karyogamy, meiosis)
• Spore types and germination
• Ascomycetes and Basidiomycetes
• Endomycorrhiza and ectomycorrhiza
• Bioremediation and lignin degradation
• Mating types and compatibility
• Cordyceps and insect parasitism
• Slime molds (Myxogastria)

• Fungal Biology, Structure, and Ecological Roles

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Introduction to Science and Biology

Science is a way of knowing and a system of generating reliable knowledge about things that can be measured to enable predictions.

• science
• biology
• variation
• diversity
• falsifiable
• repeatable
• evidence based
• patterns

Mechanisms and Types of Natural Selection

Natural selection leads to evolution through changes in allele frequencies and involves directional, disruptive, and stabilizing selection acting on phenotypes and variation within a population.

• Natural selection
• Directional selection
• Disruptive selection
• Stabilizing selection
• Evolution
• Allele frequencies
• Phenotypes
• Variation within a population
• Heritability
• Population mean

• Mechanisms and Types of Natural Selection

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Evolution and Modes of Natural Selection

Evolution is a change in allele frequencies involving directional selection, disruptive selection, and stabilizing selection.

• Evolution
• Allele frequencies
• Genotype frequencies
• Directional selection
• Disruptive selection
• Stabilizing selection
• Mendelian genetics
• Phenotypes
• Mirabilis jalapa

Biosignatures and Early Microbial Life

This content examines morphological biosignatures, chemical fossils, and isotopic signatures used to identify the emergence of microbial life and stromatolites during the Archean Eon.

• morphological biosignatures
• microfossils
• macrofossils
• molecular biomarkers
• isotopic biosignatures
• stable carbon isotopic signature
• Apex chert
• stromatolites
• microbial mats
• anoxygenic photosynthesis
• oxygenic photosynthesis
• photoautotrophic microorganisms

• Biosignatures and Early Microbial Life

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Microbial Evolution and the Great Oxidation Event

The emergence of oxygenic photosynthesis by cyanobacteria led to the Great Oxidation Event, transforming Earth from anoxic to oxic environments through nutrient recycling and ozone layer formation.

• microbial sulfate reduction
• anaerobic environments
• oxygenic photosynthesis
• cyanobacteria
• Great Oxidation Event
• nutrient recycling
• heterotrophic microbes
• ozone layer formation
• aerobic microbes
• co-evolution of life and Earth

Microbial Metabolism and Redox Chemistry

Microbes are classified by how they acquire carbon and energy through redox reactions that release free energy to generate ATP.

• Heterotroph
• Chemotroph
• Photoautotroph
• Photoheterotroph
• Oxidation-reduction reactions
• Reduction potential
• Electron donors
• Electron acceptors
• ATP synthesis
• Electron transport chain
• Proton motive force
• Oxidative phosphorylation
• Redox zonation

Theories of Early Life Evolution

Theories such as primordial soup, RNA world, and hydrothermal deep sea vent explain how life first evolved on the planet through the formation of organic compounds and complex polymers.

• Primordial soup theory
• Oparin-Haldane hypothesis
• RNA world theory
• Hydrothermal deep sea vent theory
• Prebiotic chemistry
• Reducing atmosphere
• Monomers and polymers
• Amino acids
• Ribozymes
• Nucleotides
• Protocells
• Metabolism
• DNA and protein formation

Hydrothermal Vents and Origins of Life

Deep sea hydrothermal vents may have provided electrochemical gradients and metal-containing enzymes as precursors to life.

• hydrothermal vents
• electrochemical gradients
• metal-containing enzymes
• divergent plate boundaries
• mid-ocean ridges
• seafloor spreading
• chemosynthesis
• proton gradient
• porous geological structures
• organic monomers and polymers
• thermophiles

Prebiotic Chemistry and Panspermia Theories

Redox and pH gradients drive amino acid synthesis in iron oxyhydroxide mineral systems and prebiotic organic matter evolution.

• Redox and pH gradients
• Amino acid synthesis
• Iron oxyhydroxide mineral systems
• Prebiotic organic matter
• Panspermia
• RNA world hypothesis
• Autotroph
• Heterotroph
• Phototroph
• Oxidation
• Reduction
• Respiration
• Ribozyme

Microbial Redox Chemistry and Carbon Sequestration

Exploiting microbial redox chemistry to remove atmospheric carbon dioxide by storing unused plant matter in underwater brine pools through Marine Anoxic Carbon Storage.

• microbial redox chemistry
• carbon sequestration
• Marine Anoxic Carbon Storage
• atmospheric carbon dioxide removal
• organic biomass

Microbial Cell Structure and Molecular Biology

Microbes are composed of macromolecules including carbohydrates, lipids, proteins, and nucleic acids that facilitate metabolism, genetic information transfer, and reproduction.

• plasma membrane
• macromolecules
• metabolism
• genetic information
• reproduction
• DNA
• RNA
• enzymes
• central dogma of molecular biology
• transcription
• translation
• ribosome
• genetic code
• codon

Ecology and Evolution by Natural Selection

Ecology is the study of natural communities and how organisms interact with each other and their non-living environment to shape patterns of biodiversity.

• ecology
• biogeography
• evolution by natural selection
• variation within species
• abiotic environment
• biotic environment
• natural selection
• adaptation
• population
• trait variation
• fitness
• phylogeny

Mechanisms and Misconceptions of Biological Evolution

Evolution involves changes in allele frequencies in a population through natural selection, genetic drift, and sexual selection.

• Evolution
• Natural selection
• Genetic drift
• Sexual selection
• Allele frequencies
• Fitness
• Genotype
• Phenotype
• Directional selection
• Disruptive selection
• Stabilizing selection
• Mate choice
• Assortative mating
• Heritability
• Mutation

Microbial Evolution and Metagenomic Technologies

Technological advances in microbiology and metagenomics allow for the study of unculturable microbes, endosymbiosis, and the reconstruction of microbial genomes from the environment.

• endosymbiosis
• nitroplast
• great plate count anomaly
• viable counts
• unculturable microbes
• metagenomics
• metagenome-assembled genomes
• CRISPR-Cas
• genome editing
• tree of life
• phylogenetic tree

Viral Characteristics and Ecological Roles

Viruses are tiny protein packages containing a DNA or RNA genome that require a host cell for replication.

• virus
• phage
• bacteria
• archaea
• horizontal gene transfer
• nutrient recycling
• Taq DNA polymerase
• polymerase chain reaction
• endosymbiosis
• eukaryogenesis
• metagenomics
• vertical inheritance
• species tree
• gene tree

Introduction to Microbes and Geomicrobiology

An introduction to microbial morphology, symbiosis, cell basics, the central dogma, and the role of microbial metabolisms in driving biogeochemical cycling.

• microbial morphology
• symbiosis
• central dogma
• geomicrobiology
• carbon cycling
• microbial evolution
• phylogenetic tree
• biomass distribution
• biogeochemical cycling
• planetary habitability

Introduction to Microbes and Microbial Causation

• microbe
• microorganism
• spontaneous generation
• Pasteur's swan-neck flask experiments
• microbial growth
• pure culture
• disease causation

Symbiosis and the Human Microbiome

Symbiosis involves microbes living in and on plants and animals, such as the human gut microbiome that helps digest food, make essential vitamins, and influence metabolism and health.

• symbiosis
• microbiome
• gut microbiome
• digestion of complex carbohydrates
• short-chain fatty acids
• vitamin production
• metabolism
• immune system training
• pathogen protection
• gut barrier maintenance
• microbial communities
• methane cycle

History of Microscopy and DNA Sequencing

A historical overview of seeing the invisible world through microscopes and the evolution of DNA sequencing and metagenomics.

• microscopes
• eukaryotic cells
• bacteria
• microfungus
• DNA sequencing
• next-generation sequencing
• high-throughput sequencing
• metagenomics
• microbial ecology
• PCR

Bacterial Genetics and Microbial Evolution

The genome stores genetic information in bacterial chromosomes and plasmids, which can be transferred via vertical or horizontal gene transfer and undergo mutations that drive evolution by natural selection.

• bacterial genome
• bacterial chromosome
• plasmids
• horizontal gene transfer
• vertical gene transfer
• conjugation
• genetic mutations
• natural selection
• experimental evolution
• transcription
• translation
• gene expression
• codon
• protein

Microbial Evolution and Eukaryotic Origins

This lecture covers the concept of endosymbiosis, vertical and horizontal evolutionary events, and the divergence of life from the Last Universal Common Ancestor.

• endosymbiosis
• eukaryotic origins
• vertical evolutionary events
• horizontal evolutionary events
• virus structure and diversity
• Last Universal Common Ancestor
• phylogenetic tree
• prokaryotes
• eukaryotes

Eukaryotic Evolution and Endosymbiotic Theory

Eukaryotic cells may have evolved through endosymbiosis, a process where organisms live inside another to create the eukaryotic cell and lineage.

• Eukaryogenesis
• Endosymbiotic Theory
• Endosymbiosis
• Mitochondria
• Chloroplasts
• First eukaryotic common ancestor
• Symbiosis as evolutionary force

Evolutionary Origins of Eukaryotes and Archaea

Exploring the genomic insights into eukaryogenesis and the evolutionary relationship between Asgard archaea, alphaproteobacteria, and eukaryotes through endosymbiosis.

• eukaryogenesis
• Asgard archaea
• endosymbiosis
• phylogenetic methods
• archaeal ancestry
• microbial dark matter
• two domains of life
• alphaproteobacteria
• cross-feeding
• eukaryotic cellular complexity
• membrane lipids
• Lokiarchaeota

Horizontal Gene Transfer and Microbial Evolution

Microbial evolution looks more like a network than a tree because horizontal gene transfer disrupts vertical inheritance.

• Vertical inheritance
• Horizontal gene transfer
• Species tree
• Gene tree
• Microbial evolution
• Phylogenetic tree

Evolution of Prokaryotes and Eukaryotes

Comparison of prokaryotic and eukaryotic cells and the evolutionary history of life including the Great Oxidation Event.

• Prokaryotes
• Eukaryotes
• Grypania
• Gunflint Chert
• Stromatolites
• Microbial mats
• Biosignatures
• Molecular biomarkers
• Anoxygenic photosynthesis
• Oxygenic photosynthesis
• Cyanobacteria
• Great Oxidation Event

Marine Algae and Evolutionary Phylogeny

This material explores marine algae, photosynthesis, and the evolutionary relationships within biological taxonomy and eukaryotic phylogeny.

• Marine algae
• Photosynthesis
• Phylogenetic tree
• Monophyletic group
• Sister groups
• Common descent
• Biological taxonomy
• Five kingdom system
• Eukaryotic phylogeny
• Polyphyletic groups

Evolutionary Relationships of Eukaryotic Supergroups

A phylogenetic tree illustrates the evolutionary relationships between major eukaryotic supergroups including Archaeplastids, Stramenopiles, and photosynthetic organisms.

• Archaeplastids
• Eukaryotic supergroups
• Phylogenetic tree
• Stramenopiles
• Alveolates
• Rhizarians
• Discobids
• Metamonads
• Excavates
• Photosynthetic organisms

Evolution of Photosynthesis and Marine Algae

This topic explores the endosymbiotic origin of chloroplasts from cyanobacteria, the spread of photosynthesis through eukaryotic lineages, and the biological characteristics of marine phytoplankton, brown algae, and red algae.

• oxygenic photosynthesis
• Great Oxidation Event
• endosymbiotic origin of chloroplasts
• primary endosymbiosis
• secondary endosymbiosis
• cyanobacteria
• phytoplankton
• diatoms
• brown algae (Phaeophytes)
• kelp forests
• keystone species
• trophic cascades
• alternation of generations
• gametophyte
• sporophyte
• red algae
• coralline red algae
• monophyletic groups
• sister taxa

Diversification and Evolutionary Relationships

This lecture explores phylogeny as a hypothesis about evolutionary relationships and examines diversification rates and extinction rates within lineages.

• phylogeny
• evolutionary relationships
• diversification rates
• extinction rates
• common ancestor
• extant species
• lineages
• cladistics

Mechanisms of Speciation and Diversification

Speciation occurs through reduced gene flow, different evolution via selection or drift, and reproductive isolation.

• speciation
• reduced gene flow
• different evolution
• selection
• genetic variation
• drift
• reproductive isolation
• sympatric speciation
• geographic separation
• sexual selection
• diversification rates
• environmental heterogeneity
• ecological opportunity
• adaptive radiation

Human Influences on Ecology and Evolution

Human influences and industrialization impact ecology, selection, and evolution through climate change, phenotypic plasticity, and altered landscape connectivity.

• human influences
• ecology
• selection
• evolution
• biotic factors
• abiotic gradients
• convergent evolution
• niches
• industrialization
• phenotypic plasticity
• genotype
• phenotypes
• climate change
• spring migration
• loss of diversity
• landscape connectivity

Speciation, Evolution, and Environmental Change

This topic explores how species respond to environmental change through adaptation via evolution, phenotypic plasticity, and the complex role of gene flow in speciation.

• speciation
• evolutionary adaptation
• gene flow
• hybridization
• reproductive isolation
• phenotypic plasticity
• natural selection
• artificial selection
• directional selection
• phylogeny
• habitat fragmentation
• selection pressure

Mechanisms and Types of Natural Selection

Evolution by natural selection involves variation in a trait within a population, selection, and differential, non-random fitness.

• Evolution by natural selection
• Differential, non-random fitness
• Variation in a trait within a population
• Distribution of fitness effects
• Continuous variation
• Discontinuous or discrete variation
• Biological variation
• Mutation

Mechanisms and Types of Natural Selection

Natural selection causes a shift in the distribution of variation and changes in allele frequencies within a population.

• natural selection
• differential, non-random fitness
• directional selection
• disruptive selection
• stabilizing selection
• phenotypes
• allele frequencies
• variation within a population
• continuous trait distribution
• incomplete dominance

Mechanisms and Misconceptions of Evolution

Evolution is a change in allele frequencies in a population caused by natural selection, genetic drift, and sexual selection.

• Evolution
• Allele frequencies
• Genotype frequencies
• Natural selection
• Genetic drift
• Sexual selection
• Directional selection
• Disruptive selection
• Stabilizing selection
• Mutation
• Fitness
• Reproductive success
• Sampling error

Evolutionary Processes and Population Genetics

The sources explain how evolution is defined as a change in allele frequencies in a population and discuss the differences between genotype frequencies, phenotypes, and alleles.

• evolution
• allele frequencies
• genotype frequencies
• phenotype
• selection
• disruptive selection
• stabilizing selection
• assortative mating
• Mendelian genetics
• co-dominant
• species vs population
• natural selection
• population genetics