MIC2011 Week 1

what process has given rise to the diversity of microbes over ~4 billion years

evolution – change in living things over time

what were the conditions on early Earth when the first microbes appeared

hot and anoxic (no oxygen)

what type of organisms were the first microbes, and how did they obtain energy

anaerobes – they obtained energy from inorganic molecules because organic molecules didn’t exist yet

what were the first photosynthetic microbes, and did they produce oxygen

anoxygenic photosynthetic microbes (purple sulfur bacteria, green sulfur bacteria) – they did not produce O₂

what major microbial event transformed Earth’s atmosphere, and what was it called

the evolution of cyanobacteria and the Great Oxygenation – oxygenic photosynthesis released massive amounts of O₂

list three major consequences of the Great Oxygenation

1. enabled aerobic life to evolve (more energy-efficient metabolism)

2. O₂ reacted with methane → reduced greenhouse effect → lowered global temperatures

3. killed many early anaerobes but created conditions for new life, including all eukaryotes

what is the evolutionary significance of cyanobacteria beyond oxygen production

cyanobacteria are the ancestors of chloroplasts, which enabled plant evolution

on the compressed timeline of Earth’s history (1 day), when did each event occur

- first cellular life

– cyanobacteria evolve

– first eukaryotic cells

– humans appear

what is the key takeaway from the “Earth history in 1 day” timeline

almost all of Earth’s history is microbial history

name the three main approaches used to understand microbial diversity, and what each reveals

• visual (microscopy) → cell size, shape, structures

• functional (culture-based) → metabolic capabilities, behaviour

• genomic (single gene or whole genome) → evolutionary relationships, predicted functions

why is the Great Oxygenation considered a transformative event for life on Earth

it created a colder, oxygenated world that enabled the evolution of energy-efficient aerobic metabolism and all eukaryotes, while fundamentally changing the planet’s chemistry and climate

what is the defining difference between prokaryotic and eukaryotic cells

presence of a membrane-bound nucleus in eukaryotes; prokaryotes lack a true nucleus

do prokaryotes have membrane-bound organelles

no, they lack membrane-bound organelles. eukaryotes have them.

give the cell plan analogy for prokaryotes vs. eukaryotes

• prokaryotes → studio apartment (some spatial organisation, no membrane separation)

• eukaryotes → house with many rooms

which domains/kingdoms are prokaryotic? which are eukaryotic (in microbiology)?

• prokaryotes: Bacteria, Archaea

• eukaryotes (microbial): Fungi, Protists

what is the evolutionary origin of eukaryotic organelles like mitochondria and chloroplasts

they have prokaryotic ancestry (endosymbiotic theory)

name four acellular entities studied in microbiology that are not technically alive

viruses, viroids, satellites, prions

true or false? prokaryotes have a nucleus but no other membrane-bound organelles

false. prokaryotes have no true nucleus and no membrane-bound organelles

based on nucleus and organelles, classify:

bacteria

fungi

archaea

protists

• bacteria → prokaryotic

• fungi → eukaryotic

• archaea → prokaryotic

• protists → eukaryotic

what are the three domains of life

Bacteria, Archaea, Eukarya

what was the problem with early (pre-molecular) classification systems like the Five Kingdoms

physical similarity does not equal evolutionary relatedness. the diversity of eukaryotes was overestimated, and all prokaryotes were lumped together in Monera

what was the first major molecular evidence that led to the three-domain classification

small subunit ribosomal RNA (SSU rRNA) sequencing, developed in the 1970s–80s

why is SSU rRNA an ideal molecule for studying evolutionary relationships (3 reasons)

1. present in all cellular life

2. changes very slowly (conserved regions allow comparison across distant organisms)

3. was technically feasible to sequence early on

what did SSU rRNA sequencing reveal about the tree of life

it revolutionised the tree of life and led to the accepted three-domain classification (Bacteria, Archaea, Eukarya)

what is the second line of evidence supporting the three-domain classification

comparative genomics (“big data”) – analysing many genes across many organisms

in comparative genomics, which genes in eukaryotes are more similar to Archaea

genes for DNA replication, transcription, and translation

im comparative genomics, which eukaryotic genes are closer to Bacteria

mitochondrial genes, chloroplast genes, and most metabolic genes

what model of evolutionary relationships does comparative genomics support, instead of a simple tree

the “Ring of Life” – eukarya is a hybrid lineage with contributions from both Archaea and Bacteria, plus unique features

true or false? the three-domain classification was originally based on phenotypic criteria like cell size and organelles

false. early classification was phenotypic; the three-domain classification came from molecular evidence (SSU rRNA and comparative genomics)

list four shared features of all cellular microbes

1. too small to be seen with naked eye

2. inhabit every environment that supports life

3. found in complex communities

4. fundamental to human/animal/planetary health

what is the typical size range for cellular microbes, and why is small size advantageous

typically <100 µm. small size maximises surface area:volume ratio for efficient nutrient uptake and waste removal

what is universal about the cytoplasmic membrane in cellular microbes

all cells have a phospholipid bilayer (hydrophilic faces, hydrophobic core) separating the cell from its environment. most also have a cell wall

what is the “universal language of life” shared by all cellular microbes

DNA (information storage), RNA (information conversion), and protein (function). the machinery is highly conserved

do all cellular microbes use ATP

yes. all produce energy and use ATP as the universal energy currency, though they use a wide variety of nutrient sources

how do all cellular microbes adapt and evolve

all can evolve via mutation (vertical evolution). many also exchange DNA via horizontal gene transfer (important for traits like antimicrobial resistance). haploid genomes + short generation times = rapid adaptation

name four types of cell shapes (morphologies) found in prokaryotes, with examples

• rods (bacilli) – Shigella flexneri, E. coli

• spheres (cocci) – Staphylococcus aureus

• spiral – Borrelia burgdorferi (Lyme disease)

• square (rare) – Haloquadratum (salt lakes, WA)

does cell shape reliably indicate evolutionary relatedness

no. shape is not universal and does not reliably indicate evolutionary relatedness

list the range of habitats where microbes can live

ocean, soil, human/animal/plant hosts, extreme environments (hydrothermal vents, salt lakes, pH 0–11, temperature –15°C to 121°C)

name three types of microbial lifestyles

free-living, parasitic, symbiotic, or part of complex communities

give examples of microbial metabolic capabilities

photosynthesis, nitrogen fixation, carbon fixation, fermentation, aerobic/anaerobic respiration

what are four common (but NOT universal) microbial abilities

1. motility (flagella, pili)

2. chemical communication (quorum sensing)

3. differentiation

4. horizontal gene transfer (most, but not all, prokaryotes)

name rare or unusual microbial abilities

• multicellularity

• predation

• magnetotaxis (magnetic organelles – magnetosomes)

• extreme survival (pH 0–11, temp –15 to 121°C)

how many major phyla exist for Bacteria vs. Archaea

Bacteria: 30–80 major phyla; Archaea: 5–12 phyla

do Archaea include known pathogens

no known pathogens (reason unknown – may change with more research). bacteria include many human, plant, and animal pathogens

which domain is less studied, and what is the approximate genome count

Archaea are less studied (~30,000 genomes for all Archaea combined)

what bias exists in our knowledge of “typical” prokaryotes

our knowledge is biased toward human pathogens, “domesticated” lab strains, easily cultured organisms, and a few species

describe a “typical” microbe in the wild (6 characteristics)

• bacterial (not archaeal or eukaryotic)

• 1–2 µm in length, circular genome

• adapted to temperate conditions

• free-living (not an obligate parasite/symbiont)

• heterotrophic (uses organic carbon)

• present in low-nutrient conditions, embedded in a community, often attached to a surface

what is a biofilm

a community of surface-attached microbial cells embedded in a self-produced matrix

why do microbes attach to surfaces to form biofilms (3 reasons)

1. greater nutrient access

2. protection from predators/physical disturbance

3. stability in a hospitable environment

give three examples of surfaces where biofilms form

biological (plant roots, teeth, seashells) or abiotic (catheters, rocks). examples: dental plaque, hot spring communities, sewage sludge

why are biofilms important in microbial ecology

the biofilm matrix protects from stress and facilitates microbe-microbe interactions

define: Microbe/Microorganism

a life form too small to be seen with the human eye (exceptions exist)

define: Microbiome

a community occupying a well-defined habitat with long-term association

define: Culture (in microbiology)

a collection of microbial cells grown in nutrient medium

define: Microbial growth

increase in cell number due to replication (not increase in cell size)

define: Colony

a visible mass of cells arising from a single cell

what is the resolution range of light microscopy, and what can it visualise

500 nm – 10 mm. can visualise bacteria, archaea, and some viruses. can sometimes visualise living cells

what is the advantage of fluorescence microscopy

it visualises specific cellular components and growth information, sometimes in living cells, within the light microscopy range

why is electron microscopy not suitable for living cells

it always kills cells. resolution is 0.1 nm – 100 μm; visualises most viruses and prokaryotic cell structures

what type of microscopy is required to see most viruses

electron microscopy

approximately how large is a paramecium (eukaryote), and is it visible to the naked eye

~0.1 mm – near the visible limit of the human eye