EEMB 3 Microbe Diversity

Covalent bond

two atoms (w unpaired electrons) share a pair of electrons

What about water’s chemistry makes it unique?

atoms with different electronegativities, resulting in a polar covalent bond (and hydrogen bonding)

Importance of H bonding in water

bonds can be constantly breaking and reforming (depending on state of matter)- each water molecule can H bond to up to 4 partners

Effects of H bonding in water

high boiling point, surface tensions, dissolve substances

stabilize DNA base pairs

help proteins fold into functional shapes (influences strucutresof biological molecules)

4 emergent properties of water

1. cohesion (due to H bonding, leads to surface tension, adhesion can also occur)

2. ability to moderate temperature (high specific heat capacity- sun disrupting H bonds- bonds always breaking and reforming, moderates temp fluctuations for marine environments and high heat of vaporization helps with cooling the body)

3. ice floats on liquid water (frozen = less dense, arranged in lattice formation, good for marine organisms)

4. water as solvent (surrounds materials and keeps them separated)

Stages for production of simple cells (early life on earth)

1. abiotic synthesis of small organic molecules

2. joining small molecules into macromolecules

3. packing molecules into protocells

4. origin of self replicating molecules

Earth early atmosphere

little oxygen, lots of water vapor and compounds from volcanic eruptions (nitrogen, carbon dioxide, methane, ammonia, hydrogen)

Oparin and Haldane hypothesis

early atmosphere reducing (electron removing) environment

early formation of amino acids

occurred in reducing conditions near openings of volcanoes (supported in simulated conditons)

deep sea synthesis of organic compounds on early earth

hot water, minerals, high pH (alkaline) in white smokers

meteorites as source of compounds for early life

fragments contain amino acids, lipids, simple sugars, nitrogenous bases

abiotic synthesis of macromolecules

all 4 RNA monomers can be spontaneously created by dripping water onto hot sand/clay/rock

Proto cells

earliest entity that may have been alive

relatively spherical, self organized collection of lipids

replication and metabolism

montmorillonite (mineral clay) increases rate of vesicle formation (common across early earth)

what was first genetic material

RNA- central role in protein synthesis, RNA ribozymes can catalyze many different reactions- make complementary copies of short stretches of RNA from nucleotides (helped early chemical reactions to completion)

early natural selection acted on the first proto cells

vesicles could grow and split, passing RNA to daughters

RNA could have provided template for assembly of DNA nucleotides

Fossil record

shows changes in types of organisms over time

what does fossil record include?

1. preserved body parts (bones, shells, teeth, plant material)

2. trace fossils (footprints and burrows- behavior)

3. rock layers containing fossils (when and where they lived)

Most fossils found in sedimentary rock (doesn’t degrade)

what does known fossil record favor?

species that: existed for a long time, were abundant/widespread, had hard parts (shells/skeletons)

implications of fossil record bias

1. incomplete representation of past life

2. distorted view of evolutionary patterns

3. misleading estimates of biodiversity

4. gaps in transitional forms (speciation events)

5. overemphasis on certain environments (marine)

rocks/fossils dated

radiometric dating- based on radioactive isotopes- age estimated based on ratio of C-14 (slowly decays to N-14) to C-12 (remains stable after organisms death) For carbon- can date up to 75,000 years old

for older fossils, need to track isotopes w longer half-lives- use surrounding rock, organisms wouldn’t have used these radioisotopes for shells/skeletons

origin of mammals

diverged from reptiles as the group synapsids (later evolution in terms of hinged jaw and teeth)

first single-celled organisms

stromatolites- 3.5 bya prokaryotes

fossilized on rocks

first eukaryotes

1.8 bya, fossilized cytoskeleton

single-celled, protist like organisms, formed through endosymbiosis, lived in oxygen-increasing oceans

origination of eukaryotes

endosymbiosis- prokaryotic cell engulfed small cell-evolved into mitochondrion/chloroplast (living within host cell)

serial endosymbiosis- mitochondria evolved before plastids though sequence of endosymbiotic events

origin of multicellularity

first step endosymbiosis, origin of eukaryotic cells sparked evolution of greater morphological diversity

small red algae- 1.2 bya

more diverse multicellular organisms 600 mya

cambrian explosion

many animal phyla appear (530 mya)

fossils of sponges, cnidarians, and mollusks

begins new defensive adaptions, alluding to predation (which hadn’t occurred previously)

colonization of land

prokaryotes on land 3.2 bya

fungi, plants, animals, colonizing land 500 mya

needed pollinators and adaptations to prevent dehydration

plants and fungi colonized land together (mutualistic mycorrhizae)

arthropods (first animals) 450 mya

effects of plate tectonics

distribution of animals leads to adaptive radiation and evolution as well as habitat diversity

isolation events (island biogeography)= organisms diverge & allopatric speciation

mass extinctions

triggered by disruptive global climate change

marine organisms greatly affected (more than half extinct for every event)

generally, extinction rate increases as temperature increases

Adaptive radiations

rapid period of evolutionary change, many new species arise and adapt to ecological niches

in response to: opening of niches following mass extinctions, evolution of novel characteristics, colonization of new regions w few/weak competitors

changes competition and predator-prey relationships

EX. adaptive radiation of mammals after extinction of dinosuars (66 mya)

three phenomenon that may trigger adaptive radiations

1. mass extinction events

2. colonization events

3. evolutionary innovations

How to distinguish and categorize species on Earth?

traits shared due to common ancestors are use to classify organisms into groups that reflect their evolutionary history

phylogeny

evolutionary history of organism and relationship to other species

Systematics

Classifying organisms and determining evolutionary relationships

based on: taxonomy and phylogenetics

Binomial nomenclature

system for groups species in increasingly inclusive categories (ranging from broad to narrow, domain - species)

taxon = group at any level of hierarchy

what separates branches of phylogenetic tree

derived characteristics (represents common ancestor who has that characteristic)

homology

phenotypic and genetic similarities due to shared ancestry

Analogy

similarity due to convergent evolution

convergent evolution

evolution of superficial similarities in response to natural selection to similar environmental conditions

more similarity between complex structures?

more likely to be evolved from a common ancestor

homologous genes

many shared portions of nucleotide sequences between two organisms (similar bases and similar lengths)

maximum parsimony

assumes that most likely tree is one that requires fewest evolutionary events (when based on DNA, has fewest base changes)

maximum likelihood

identifies tree most likely to have produced given set of DNA data based on probability rules about how DNA changes over time

Different genes can evolve at different rates in same lineage

DNA coding for ribosomal DNA: changes slowly, can be used to detect ancient relationship

Mitochondrial DNA: evolves rapidly, can be used to explore more recent evolutionary events

Gene duplication: two genes copied produce two versions, orginal and paralog (duplicate)

Once duplicated, two copies are free to evolve independently

duplications leave detectable signatures in genomes, can help reconstruct evolutionary events

orthologous gene

homology results from gene duplication and occurs between gene copies found in different species

used for inferring phylogeny- reflects history of speciation events

lineages that diverged long ago often share many orthologous genes

paralogous gene

homology results from gene duplication and occurs between gene copies within species

reflects divergence within the same species

molecular clocks

measure of tine by counting number of nucleotide substitutions over fixed period of time

attempt to measure absolute time of evolutionary change (average rate of change, linear)

calibrated by graphing number of genetic differences against dates of branch points (known from fossil record)

horizontal gene transfer

movement of genes from one genome to another via plasmids, viral infection, possible fusion of organisms

Changes assembly of trees (fluctuating similarities between eukaryotes, prokaryotes, archea)

Why is base of tree of life so hard to resolve?

1. extreme time depth

2. HGT

3. rapid early diversification

4. gene loss and metabolic streamlining

5. long-branch attraction

current consensus on tree of life

two domain tree, with eukaryotes branching within archea

LUCA likely thermophilic autotrophic, microbe living in hydrothermal environments

prokaryote characteristics

single celled organisms (some form colonies)- make up domains bacteria and archea

adapted to diverse and extreme environments

small size (variety of shapes), rapid reproduction, rapid evolution, diverse adaptations

prokaryote cell-surface structures

cell wall (protection, maintenance of shape, prevents bursting in hypotonic environment)

bacterial cell walls can contain peptidoglycogen (network of sugar polymers and polypeptides (gram + = lots of peptido)

archea walls: variety of polysaccharides and proteins, no peptidoglycogen

sticky layer of polysaccharide/protein surrounding cell wall- adherence to substrates, prevent dehydration, protection from hosts immune system

1) capsule: dense and well defined

2) slime layer: not well organized

endospores if lacking water or nutrients (metabolically inactive, can survive extreme conditions and time)

fimbraiae: hair-like appendages to stick to substrate/individuals in colony

pili: longer than fimbriae, pulls cells together to exchange DNA

flagella for movement (42 proteins, motor, hook, and filament)

prokaryote internal organization

lacks complex compartmentalization

inner foldings of cell membrane may be specialized to perform metabolic functions

less DNA, produces fewer proteins, one circular chromosome (stored in nucleoid), may have plasmids (small rings of independantly replicating DNA)

lack a nucleus

Reproduction of prokaryotes

binary fission (occurs very quickly, short generation times)

factors that promote genetic diversity in prokaryotes

1. mutation (accumulates quickly with short generation times and large populations)

2. HGT

3. plasmids

4. rapid reproduction

allows for natural selection and rapid evolution

genetic recombination (HGT)

combining DNA from two sources, contributing to prokaryotic diversity (via transformation, transduction, or conjugation)

generates genetic diversity, maintains genome integrity (DNA repair), accelerates evolution, enables acquisition of new metabolic or virulence traits

prokaryote transformation

incorporates foreign DNA taken up from surroundings (non pathogenic cell could become pathogenic)

prokaryote transduction

pages carry prokaryotic genes from one host cell to another, generally unintended result of phage replicative cycle

prokaryote conjugation (plasmids)

DNA transferred between two prokaryotic cells, in bacteria once cell donates and another receives via conjugation pilus and transfer of plasmid

Categorization of prokaryotes (obtain energy and carbon)

energy sources

1. phototrophs (cyanobacteria)

2. chemotrophs (can be organic or inorganic)

carbon sources

1. autotrophs

2. heterotrophs

role of oxygen in metabolism

obligate aerobes: require O2 for cellular respiration

obligate anaerobes: poisoned by O2 and live by fermentation or use substances other than O2

facultative anaerobes: can use O2 if present or carry out fermentation/anaerobic respiration if not

biofilms

cells of one or more prokaryote species cooperate to form surface-coating colonies

cells near edge release signaling molecules to recruit new cells

channels in biofilm allow nutrients to reach cells in interior and wastes to be expelled

common in nature, can be harmful/corrosive

proteobacteria

gram negative, includes: photoautotrophs, chemoautotrophs, and heterotrophs

ex. sulfur bacterium, oxidizes H2S

chlamydias

gram negative, all species parasite animal cells

spirochetes

gram negative, helical, spiral through environment by rotating internal filaments

can be free living or pathogens

ex. syphilis, lyme disease

cyanobacteria

gram negative, photoautotrophs, abundant in marine and aquatic ecosystems

gram positive bacteria

diverse group: colony forming bacteria including pathogens and soil decomposers

Archea

share some traits with both bacteria and others with eukaryotes-and have their own unique characteristics

extremophiles; high heat, saline, or pH environments

methanogenic archea

obligate anaerobes that produce methane as byproduct of metabolism

diverse environments: under ice, swamps/marshes, cattle, termites, herbivores

euryarchaeota

includes many of extreme halophiles, most methanogens, and some extreme thermophiles (most extreme thermophiles belong to another clade)

Archaea supergroup (TACK)

thaumarchaeota

aigarchaeota

crenarchaeota (most extreme thermophiles)

korarchaeota

lokiarchaeotas

recently discovered group, closely related to TACK archaeota, may represent sister group of eukaryotes

Kochs Postulates

define proof of microbial causation (one specific microorganism can cause one specific disease)

methods of microorganism identification

1. phylogenetic

2. microscopy

3. biochemical

4. molecular

protist

diverse group of eukaryotic organisms

mostly single-celled

share some characteristics with plants, animals, fungi

no longer considered its own kingdom

make up much of diversity of eukaryotes

characteristics of protists

nucleus and organized, membrane-bound organelles

well developed cytoskeleton (asymmetric, can change shape over time)

Diversity of protists

1. ancient origins

2. endosymbiotic events

3. adaptations to many environments

4. multiple nutritional strategies

5. rapid evolution in single-celled organisms

6. small, can reproduce very quickly (binary fission)

7. vary widely in cell number, size/shape, movement structure, and cell coverings

mixotrophs

combine photosynthesis and heterotrophic nutrition

protistan diversity (4 super groups)

1. excavata; excavated groove for feeding, usually unicellular (includes parabasalids, diplomonads, and euglenozoans)

2. SAR; diatoms are photosynthetic stramenopiles, rhizarian amoebas with pseudpodia (stramenopila, alveolata, rhizaria)

3. archaeplastida (supergroup including red and green algae and plants)

4. unikonta (supergroup including protists closely related to fungi and animals)

stramenopiles

important photosynthetic organisms

hairy + smooth flagellum

diatoms, oomycetes (slime molds), brown algae

alveolates

membrane-enclosed sacs (alveoli) just under plasma membrane

dinoflagellates, apicomplexans, ciliates

dinoflagellates

primary producer and nutrient cycling

2 flagella in grooves (spins)

obligate symbiants with coral, but can cause algal blooms

apicomplexans

nearly all parasites of animals

spreads through host as sporozoites

apex end of cell contains complex of organelles specialized for penetrating host/tissues

complex life cycle

Ciliates

names for use of cilia to move around and feed (usually heterotrophs)

well developed organelles

two nuclei (macro with multiple copes of genome, everyday cell function and micro as genetic backup)

9 +2 filament pattern

specialized reproduction

rhizarians

mostly amoebas (false foot to feed and move)

intricate mineral skeletons can be fossilized

important predators of microbes (remove carbon from the surface of the ocean)

amoebozoans

lobe or tube shapes pseudopodia

heterotrophs, complex life cycles

tubulinids, slime molds, entamoebas