Microbes - Origin and Evolution

What defines species boundaries in prokaryotes?

Genetic relatedness based on mutations producing phylogenetic trees.

What generates phylogeny in microbial lineages?

Random mutations, selection, and horizontal gene transfer.

What is a phylogenetic tree?

A branching diagram showing related organisms; clades represent branches.

What makes a gene ideal for building a phylogeny?

Universally present, conserved function and sequence, similar mutation rate, vertically transmitted.

Why can single-gene phylogenies be unreliable?

Different genes evolve at different rates, leading to conflicting trees

What is phylogenomics?

Using many genes/genomes to infer evolutionary relationships.

What did Carl Woese use to discover the three domains of life?

SSU rRNA gene sequencing.

What major insight came from rRNA phylogeny?

Bacteria split into two groups and Archaea recognized as distinct from Bacteria.

What traits do Archaea share with Bacteria?

Small size, circular DNA, nucleoid, operons, varied metabolism.

What traits do Archaea share with Eukarya?

Intron splicing, eukaryote-like translation, methionine initiation, antibiotic insensitivity.

What traits are unique to Archaea?

Methanogenesis, ether-linked isoprenoid lipids, absence of pathogens.

How is species identity defined using SSU rRNA?

98% sequence identity indicates same species.

How is species identity defined using ANI?

95% ANI indicates same species.

What is an ecotype?

Organisms sharing ~95% of ecological niches or metabolic traits.

What is a pangenome?

The total gene pool of a species, including core and accessory genes.

What are core genes?

Genes shared by all strains that perform essential functions

What are accessory genes?

Strain-specific genes involved in adaptation and niche specialization.

What are arbuscular mycorrhizal fungi?

Terrestrial symbionts forming mycorrhizae with >80% of land plants.

What characterizes genomic diversity in AMF?

Chromosomes vary in gene content, size, and epigenetics between strains.

What is convergent evolution?

Independent evolution of similar traits in unrelated lineages.

What is the difference between homology and analogy?

Homology = shared ancestry; analogy = similar function without shared ancestry.

Why are emerging microbial lineages difficult to classify?

They are unculturable and lack closely related species in phylogenies.

What is the origin of mitochondria and chloroplasts?

Bacterial endosymbionts that became organelles (endosymbiosis theory).

What evidence links mitochondria to bacteria?

Similarities in rRNA and other conserved genes.

What is the function of mitochondria?

Respiration via the electron transport chain.

What is the function of chloroplasts?

Photosynthesis

What are Cyanobacteria?

Oxygenic autotrophs with thylakoids and diverse light-harvesting pigments.

What is Prochlorococcus known for?

~50% of oceanic photosynthesis; contains carboxysomes with Rubisco.

What characterizes Firmicutes?

Thick peptidoglycan, S-layers, often antibiotic-resistant.

What characterizes Mycoplasma?

Wall-less, tiny genomes, often endosymbiotic or pathogenic.

What characterizes Actinobacteria?

High GC genomes; some form hyphae and spores.

What is Clostridium botulinum known for?

Producing botulinum toxin, one of the most potent neurotoxins.

Why is Mycoplasma genitalium significant?

One of the smallest genomes and naturally antibiotic resistant (no cell wall).

Why is Streptomyces coelicolor significant?

Produces many antibiotics and models microbial development.

What defines Proteobacteria?

Gram-negative, metabolically diverse group including many pathogens.

What is Thiomargarita namibiensis?

Largest known bacterium with massive nitrate-storing vacuole.

What is Nitrospira moscoviensis known for?

Complete ammonia oxidation.

What is Aquifex pyrophilus known for?

Hyperthermophile living in vents; close to LUCA.

What is unique about Planctomycetes?

Double membrane around nucleoid resembling a primitive nucleus.

What characterizes Chlamydiae?

Intracellular parasites forming elementary bodies; includes pathogens and symbionts.

What characterizes Chloroflexi?

Filamentous photoheterotrophs with chlorosomes.

What is Chloroflexus aurantiacus known for?

Thermophilic anoxygenic phototrophy and use of 3-HP bi-cycle for CO₂ fixation.

How are many Archaea discovered today?

Through metagenomics of environmental DNA.

Why are Archaea often difficult to study?

Many cannot be cultured and are known only from DNA sequences.

What metabolic process is unique to Archaea?

Methanogenesis.

What is unique about archaeal membranes?

Ether-linked isoprenoid lipids.

What defines Euryarchaeota?

Includes halophiles and methanogens with diverse metabolisms.

Why is Haloquadratum walsbyi unique?

Square-shaped halophile optimized for light absorption.

What defines Crenarchaeota?

Thermophiles/hyperthermophiles with sulfur-based metabolism.

What is reverse gyrase used for?

Stabilizing DNA at high temperatures via positive supercoiling.

Why is Pyrolobus fumarii notable?

Grows optimally at 113°C; among the most thermophilic organisms.

What defines Thaumarchaeota?

Ammonia-oxidizing Archaea with unique lipid (crenarchaeol).

Why is Giganthauma karukerense notable?

Giant archaeal filaments with sulfur-oxidizing ectosymbionts.

Why are Asgardarchaeota evolutionarily important?

They contain eukaryotic-like genes linked to the origin of eukaryotes.

Why is Prometheoarchaeum syntrophicum important?

Forms syntrophic relationships and models early eukaryogenesis.

What characterizes Nanoarchaeota?

Extremely small, genome-reduced, obligate symbionts.

What is Nanoarchaeum equitans known for?

Tiny ectosymbiont of Ignicoccus with extreme genome reduction.

What is the benefit of archaeal–protist endosymbiosis?

Methanogens consume H₂ from the host, aiding anaerobic survival.

What distinguishes archaeal membrane lipids across phyla?

Differences in GDGT structures, rings, side chains, and hybrid lipids.

Why is Sukunaarchaeum mirabile significant?

Nearly viral-like metabolic dependence despite being cellular.

What are Archaeasins?

Machine-learning-discovered archaeal antimicrobial peptides.

What does horizontal gene transfer do in prokaryotes?

It introduces foreign DNA that can alter evolutionary signals and complicate phylogenies.

Why is rRNA especially useful for identifying microbial lineages?

It evolves slowly and is present in all cellular organisms.

Why do some microbial classifications rely on morphology?

Because morphology can be visually observed even when genetic data is unavailable.

Why is morphology-based classification unreliable in microbes?

Convergent evolution can produce similar traits in unrelated species.

What is a clade?

A group of organisms consisting of a common ancestor and all its descendants.

What makes emerging pathogens "emerging"?

They are newly discovered or newly pathogenic due to environmental change.

Why is culturing important in microbiology?

physiological testing and direct observation of microbial traits

Why are some lineages known only from environmental DNA?

They cannot be cultured with current methods.

What causes reductive evolution in endosymbionts?

Dependency on host organisms for metabolic functions.

What is one consequence of extreme endosymbiosis?

Massive genome reduction in the symbiont.

Why are mitochondria considered descendants of bacteria?

They retain bacterial-like DNA, membranes, and ribosomes.

Why are chloroplasts considered descendants of Cyanobacteria?

They share photosynthetic machinery and genetic features with Cyanobacteria.

What major ecological role do Cyanobacteria play?

They are primary producers that oxygenate Earth’s surface environments.

What is a carboxysome?

A protein microcompartment housing Rubisco to fix CO₂.

Why are Firmicutes harder to kill with antibiotics?

Their thick peptidoglycan and protective S-layers reduce antibiotic penetration.

Why do Mycoplasma resist β-lactam antibiotics?

They lack a cell wall, the antibiotic’s target.

Why are Actinomycetes important in biotechnology?

They produce many natural antibiotics and secondary metabolites.

Why are Nitrospira important in ecosystems?

They oxidize nitrogen compounds, contributing to nitrification.

What distinguishes deep-branching Gram-negative bacteria?

They have ancient evolutionary origins and extreme environmental adaptations.

Why are archaeal lipids more stable in extreme conditions?

Their ether bonds and branched isoprenoids resist heat, acidity, and pressure.