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Gravity
Terms in this set (48)
Are All Microbes Bad??
Only a low percentage of microbes cause disease
Many are crucial for overall life on earth
Many are useful to humans!
BAD Microbes
Only a low percentage of microbes cause disease:bacterial& viral disease,food spoilage
GOOD MICROBES
Photosynthesis by cyanobacteria-
decomposers that recycle nutrients from dead organisms
sewage treatment " regeneration of clean water"
the number of microbes/human
The human microbiome:
- 10-fold more microbial cells
than human cells in/on us*
- each of us has a unique
set of communities
(different in different sites)
- these microbes do us
much more good than harm
Microbial measurements and cell size
*- Millimeters: 1-used for non-microbes
2 - used for large groups
of microbes that form
multicellular structures:micro
- visible to naked eye
*microbial cells in Micrometers
(average bacterium ~1 mm)
*Nanometers used for viruses & subcellular
structures within bacteria
who was the first
to recognize
Microbial diversity
Carl Woese
Protist:
eukaryotic microbe
Cytoplasm with organelles: DNA in nucleus
- MEMBRANE
-mitochondria/chloroplasts
-Chromosomes in nucleus
- ribosomes in cytoplasm
- intracellular membranes
Cell membrane
Cell wall? (plants/fungi)
Bacterium:
prokaryotic microbe
Bacteria and Archaea, DNA in "nucleoid"
- NO MEMBRANE
Cytoplasm without organelles
- chromosome (DNA)
No nuclear membrane
- ribosomes in cytoplasm
- little intracellular membranes
Cell membrane
Cell wall
Viruses
-microbes- BUT NOT CELLS
- parasites that attack organisms in all 3 domains
- can't live independently
-more like each other regardless of host
- steal machinery for self-replication from host
Nucleic acid genome
- DNA (ds or ss) or RNA
Protein capsid
Delivery helpers
- tail
- envelope
- spikes
NO RIBOSOMES!!!
replicate in cytoplasm for prokaryotes,
either in cytoplasm or nucleus
for eukaryotes
How do we recognize relationshipsamong microbes?
*Classical Characteristics
-morphology: what do they look like?
-physiology: what do they do?
-biochemistry: what proteins do they have?
-ecology: where do they live?
*Molecular Characteristics
-gene sequences
Pros and cons of classical testing:
Pros: - provide information on cellular physiology and metabolism
Cons: - methods are not universal; requires a wide variety of tests
- need to grow in pure culture
- similar properties do not necessarily reflect
evolutionary relationship!
Nucleic Acid Sequencing
**Most powerful and direct method for comparing genomes
**Complete genomes can now be sequenced and compared - huge improvements in technology
*Can now sequence mixed populations without
growing in the lab!
Sequences of 16S and 18S rRNA (SSU rRNAs) are used most often in phylogenetic studies
(small subunit ribosomal RNAs - rRNAs)
what is a ribosome?
Protein synthesis machinery in all cells,
composed of small and large subunits
- prokaryotic small subunit: 16S rRNA (blue) + proteins
- eukaryotic small subunit: 18S rRNA + proteins
Three Domains of Life
Carl Woese first used SSU rRNA phylogeny to reveal the existence of the Archaea, a third group of organisms, distinct from bacteria and eukaryotes
All 3 groups derived from common ancestor
= "last common ancestor"
(no longer exists)
what is the DOMINATE LIFE ON EARTH!!!
MICROBES DOMINATE LIFE ON EARTH!!!
Viruses
Viruses are microbes too - BUT NOT CELLS!
- parasites that attack organisms in all 3 domains
- can't live independently
- don't fit into tree because lack characteristics
used to make trees
- are more like each other regardless of host
- steal machinery for self-replication from host
- can generate "trees" for viruses relative
to each other, not relative to hosts
Three Domains of Life
- Basics of DNA/RNA/protein are conserved, DNA as genetic material in all three ("Central Dogma") (some viruses do NOT follow Central Dogma!)
RETROVIRUSES - HIV
similarity in Archaea
and Eukarya
Gene expression machinery; structure of ribosomes, RNA polymerase
similarity in Bacteria and
Archaea
1-Metabolic capabilities; metabolic pathways, diversity
2-Cell structure; no nucleus, no organelles
Organelles in eukaryotes are derived from bacteria
endosymbiotic hypothesis
1-mitochondria -proteobacterium
2- chloroplasts -cyanobacterium
The timeline
Prokaryotes on Earth: 3.8 billion years ago
Humans: 200,000 years ago
Halophilic
(high salt)
Alkalophilic
(high pH)
Psychrophilic
(extreme cold)
Thermophilic
(extreme heat)
Anaerobic
(no oxygen)
obligate
REQUIRES that condition (philic = loves)
facultative
TOLERATES that condition (tolerant)
Bacteria and Archaea - reproduction
binary fission
asexual reproduction
each cell divides independently
into two new cells that are genetically identical
to the parent cell
Sporulation: a dormant state
induced by starvation
spores are very resistant
to heat, acid, base,
organic chemicals,
UV light, drying
spores are VERY difficult
to kill/clean from surfaces
- autoclave (heat+pressure)
- 120oC kills
- bleach kills
- ALCOHOL DOES NOT
bacterial "social" behavior
- work together
to wipe out prey
("wolf pack")
- form fruiting bodies
when prey are
gone
- "adventitious" cells
are the "explorers"
BY secreting small molecules
Bacterial vampires
obligate" parasite
- can't grow without prey
suck out the cytoplasm,
leave an empty cell wall
Symbiosis
squid provides a home,
bacteria provide the light at high density:"quorum sensing"
- when there are enough cells,
they ALL turn on the light!
- secrete small molecules
used as signals
- high concentration
turn on bioluminescence
Many bacteria are motile
- find new food (Myxococcus wolf pack)
- move to new home (Vibrio into squid)
- move from entry site to preferred niche
(common for pathogens)
- run from predators
Chemotaxis
sense chemical signals
- move toward attractants
- move away from toxic compounds
symbiosis
living together
mutualism
both organisms benefit
Metabolism:
total of all chemical reactions in the cell,
divided into two parts:
catabolism
the breakdown of complex organic molecules to simpler ones (energy is captured)
anabolism
the synthesis of complex organic molecules from simpler ones (energy is consumed)
Microbial ecology
- study of microbes in the environment
- interactions with each other and other organisms
- impact on chemical and physical properties of their environment
- most prominent life form on the planet when measured
in cell numbers
- estimate for the biomass in the subseafloor:
~1-3 x 1030 cells!
- approximately 1% of total living biomass on the planet
How do we know who is there?
A combination of approaches:
- traditional, laboratory-based analyses
- culturing microbes (but not all can be cultured)
- metagenomics
metagenomics
collection of total DNA sequences from a sample
- includes organisms that can't be cultured!
GENE:
DNA that encodes a single protein product
GENOME:
All of the genes in a single organism/species
(gene sequences in order, along the chromosome)
METAGENOME:
All of the DNA from a sample
(sequence fragments of DNA, don't know which come from which organism, or how assemble into genomes goal is to try to figure that out)
Culturing vs. metagenomics
overall estimate: miss >99%!
Metagenomics gives crucial new information!
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