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Bacteria - General
Bacteria (Procaryotes)
tremendous physiological diversity
can do photosynthesis and respiration in 100’s of ways
versus animals and plants which have
only one type of photosynthesis and two types of respiration.
can metabolize virtually any natural or manmade product
of major importance in biogeochemical cycles
dominate the biosphere in terms of numbers
(outnumber all eucaryotes combined)
more in handful of dirt than all people who have every lived
more in mouth than all people in NYC
widest tolerances for temperature, pH, salt, etc than any other kingdom of
organisms
only about 15,000 species known; estimates up to 4 million species possible
all are procaryotes
very small 1-5µm (vs eucaryotes 10-100µ long)
but Epulopiscium fishelsoni from the gut of a surgeon fish is larger than most
eucaryotic cells (500µ)
rarely occur in isolation, but form part of heterogenous microbial community
individually are invisible
but can form large multicellular aggregations when nutrients are plentiful –
then are easily visible
soil crumbs
microbial mats
sewage flocks
biofilms
bacterial blooms
tend to be embedded in matrix of water and organic molecules (glycoproteins
and polysaccharides)
in some ways these microbial communities take on characteristics of
multicellular organisms
lots of interactions and symbioses
advantages of aggregations:
provide more stable environment
protect cells from UV and heat
minimize effects of rapid changes in
environment
may offer protection from predators
highly effective in trapping nutrients
however, most environments are nutrient scarce
Bacterial Structure
no organelles – much less efficient design
but they make up for this with rapid reproductive rate and wide tolerance for
environmental conditions
Cell Wall
almost all have cell wall surrounding the cell membrane
cell wall varies from species to species also varies for each kingdom
in most Eubacteria the cell wall contains the carbohydrate = peptidoglycan,
not cellulose as in plants and some algae.
the actual composition of the cell wall varies among the different bacterial
groups:
eg Gram + and Gram – bacteria
G+ => lots of peptidoglycan
simpler structure
G- =>
less peptidoglycan
lots more lipids
often more pathogenic
lipids are often toxic
protect them from body defenses
more resistant to some antibiotics
(antibiotics inhibit synthesis of
peptidoglycan layers)
the cell wall produces the three basic shapes of bacterial cells:
cocci
bacilli (rods)
spirals
Capsule
some produce a capsule – a gelatinous, sticky layer that allows bacteria to:
attach to substrates and glues “colonies” together; also increases
pathogenic bacteria’s resistence to host’s defenses
Pili
some bacteria have pili used for attachment
and for bacterial conjugation in which genes are exchanged between two
different bacterial cells
(a type of primitive sexual reproduction)
Motility
– about half of all bacterial species are motile
can move up to 50µm/sec [~100x’s body length/sec]
ability to move and orient produces simple behavors = “taxes” or movements
toward or away from stimuli
such as light, food, oxygen, gravity, etc.
eg. + & - chemotaxes
have specific receptor molecules on cell surface to detect chemicals
movement by:
flagella
slime trail
helical filaments
Flagella
flagellum is whiplike rod that rotates like propeller to move bacteria along
Magnetic particles
– some bacteria contain rows of magnetic particles that allow them to orient
toward the earth’s magnetic field
Endospores
some bacteria can form endospores to withstand desiccation and harsh
conditions
very resistant to destruction
not for reproduction
Chromosome
not enclosed in membrane of nucleus or associated with proteins
DNA is in form of one large circular chromosome
and one or few small circular plasmids
Physiology:
Growth
growth in bacteria is measured as ability to reproduce
to reproduce all bacteria must be able to synthesize the proteins, carbos anf
fats and nucleic acids they need
also must have energy source
the kinds of raw materials bacteria use to accomplish this depend on the
species
All life has nutrient “limiting factors” => those nutrients in shortest supply that
prevent or limit growth and reproduction
eg. plants => usually N and P
eg. humans => sometimes Fe, Ca, Vitamins, etc
Most bacteria are heterotrophs => need organic food for both nutrients and
energy
nutrition at most basic level requires simple elements and an energy source
of these nutrients often the most critical is Carbon
In some aquatic environments, P or N often become a problem
other specific nutrients needed varies greatly:
eg. E. coli – glucose is ONLY organic nutrient
needed
Lactobacillus – needs all 20 amino acids,
several vitamins
other organic compounds
even when nutrients are in short supply most bacteria do not die
=> they can enter a dormant state (=anabiotic)
bacterial rates of growth and reproduction are also greatly affected by various
environmental factors:
temperature
pH
water availability
light (for photosynthetic bacteria)
every type of nutrition found in eucaryotes is found in bacteria and them some
more metabolic diversity than all other kingdoms combined
can be autotrophs
- derive all nutrients from inorganic sources;
eg CO2, NH3, etc
- any carbon source for nutrient
- must build and store organic molecules for later
breakdown and energy production
– does not require organic carbon source for
energy,
can be photoautotrophs - use sunlight as energy source
or chemoautotrophs – oxidizes inorganic compounds for energy
eg. H2S; NH3; Fe++, etc
or heterotrophs
- derive at least some of nutrients from complex
organic molecules
- use these same organic molecules for energy
production also
– needs organic carbon for energy and nutrient
can be chemoheterotrophs – extract both Carbon and energy
from organic molecules
eg. aerobic respiration (eg animals)
eg. saprobes, parasites
eg. fermentation
or photoheterotrophs – extract carbon from organic molecules but
energy from sunlight
most bacteria are [chemo] heterotrophs – need organic foods
nitrogen is essential for proteins and nucleic acids
other kingdoms are fairly limited in the sources they can use: NH3, NO2, NO3,
Proteins, Nucleic Acids
bacteria can metabolize many forms of nitrogen both organic and inorganic
some bacteria can fix nitrogen gas – only organisms that can do this;
(N gas makes up 80% of atmosphere but unuseable by all but
bacteria)
some of these form symbiotic root nodules with plant roots and allow these
plants to grow in poorer soil
bacteria have various requirements for oxygen:
obligate aerobes (strict aerobes) – die without
oxygen gas
obligate anaerobes (strict anaerobes) – die in
the presence of oxygen gas
facultative anaerobes – can use oxygen when
available, and do anaerobicmetabolism when its not
some (but not all!) bacteria can be grown on artificial media:
selective media – prevents the growth of certain
bacteria while allowing others to grow
enrichment media – has special nutrients that
enhance the growth of the desired bacteria
differential media – contains a specific nutrient and
an indicator the show whether the species is able to use that
nutrient
variations in the rate of growth and reproduction are greatly affected by
environment
temperature
pH
light - cyanobacteria
water
lack of organelles makes procaryotes much less efficient at metabolism
but they compensate for this by rapid reproductive rate, metabolic diversity,
and ability to withstand adverse conditions
Reproduction
bacteria reproduce by asexual binary fission
most bacterial reproduction is asexual
the single chromosome duplicates
cytoplasm splits into equal halves
time between divisions = generation time
generation time varies considerably:
Staph aureus
30 min
M. tuberculosis
18 hrs
T. pallidum
33 hrs
E coli
20 min
eg. E. coli: one cell at 8:00 am, no limiting factors:
=> 36 hrs later => 1 foot over surface of
earth
Bacterial Growth curve:
lag: transferred to new environment
log: maximum rate of reproduction
stationary: nutrients and space and env variables
become limiting and slow rate of reproduction
death: population decline, nutrients gone,
build up of toxins
no true sexual reproduction
but due to rapid life cycles, natural mutations are the main source of genetic
variations
but can exchange genetic material in several ways:
transformation
conjugation
transduction
How did bacteria, which reproduce primarily asexually evolve and diversify so
quickly?
bacteria can trade genes at a rapid pace
their DNA is loose inside cells
they often have spare strands of DNA
(extra genes)
these genes can be easily
traded,
absorbed from the environment or
moved by viruses
in early earth, UV radiation may have increased the rate of this exchange
the typical distinction between species does not apply to bacteria
“create a huge planetary gene pool that gives rise to temporarily classifiable
bacterial ‘types’ or ‘strains’ which radically and quickly change, keeping up with
the environmental conditions”
-Margulis and Sagan, 1995
Classification of Bacteria:
two procaryote kingdoms:
Archaebacteria + Eubacteria
Archaebacteria:
earliest fossils of living organisms
most primitive
most are single, simple cells
highly unusual morphologies
most have rigid cell wall but no peptidoglycan in cell walls
tend to live in extreme environments
some heterotrophs some autotrophs
unique chemical composition, structure, metabolism and DNA
unique lipids in cell membranes
unique kind of ribosomes
three groups:
1. Methanogens:
thrive in swamps, sewage, stock yards, animal
guts
strict anaerobes
use H2 to reduce CO2
produce methane as end product of energy
production:
H2 + CO2 ->CH4 + energy
gut bacteria produce 2B tons of methane/yr
affect global carbon cycle
methane collected from garbage and dung used as
renewable energy source
2. Halophiles (salt lovers)
brackish ponds, salt lakes, near deep ocean
hydrothermal vents
most are aerobic
colonies often purple or red
eg. Halobacterium
3. Thermophiles (heat lovers)
highly acidic soil, hot springs, coal mine wastes,
deep ocean hydrothermal vents
autotrophs (but chemoautotrophs not photo)
use H2S as hydrogen (electron) source to make
energy (instead of H2O)
eg. Sulfolobus:
thrives in acaidic sulfur rich hot springs
pH optimum = 2
temperature optimum = >70º C
Eubacteria:
most common bacteria are in this group
all human pathogens
most bacteria that are used to make food products
very diverse array of bactera
upper levels of classification (eg. phyla, classes) are just being worked out:
typical rods cocci and spirals
cyanobacteria
other types of photosynthetic forms
disease organisms (parasites)
many symbionts (eg. Rhizobium)
Nannobacteria??
first described in 1996
much smaller than average bacteria
1/10th the size of eubacteria
found IN rocks, clay, sand
may contribute to most geologic chemistry
may make up most of the earth’s biomass
some report growing them in lab dish
can kill other cells
may be found in blood and animal tissues
may cause human diseases
may exist on mars
may not exist at all???
Impacts of Bacteria on the world
1. essential for cycling nutrients (biogeochemical cycles): if they weren’t here,
we wouldn’t be
either, we would run out of nutrients
2. Deep ocean hydrothermal vents
discovered in 70’s at deep ocean ridges
hot mineral rich waters flowing out of cracks in the crust,
especially rich in hydrogen sulfide
whole community of organisms,
most are unique species;
include large worms and clams, crabs, shrimp,
fish, and dense clouds of bacteria
bacteria live inside the tissues of some of these animals;
the animals absorb hydrogen sulfide from the hot waters,
and use hemoglobin to carry this H2S to the bacteria deep in their
tissues;
the bacteria use the energy in H2S to make sugars which the animals
absorb
therefore it’s an entire ecosystem that is not based on solar energy for
autrotrophic production
3. Bacteria are used to make a wide variety of foods and drinks (see lab):
bread, bakery products,
cheeses, alcoholic beverages, etc, etc, etc,
Cheeses
The first step in making most cheeses is to prepare a curd by adding lactic acid bacteria and rennin or
bacterial enzymes to milk.
The bacteria sour the milk and enzymes coagulate the milk protein, casein, to produce a soft ‘curd’ to
make cheese and a liquid ‘whey’ which is a waste product.
The amount of whey removed determines the hardness of the cheese. eg. soft cheeses the whey is simply
drained away. Harder cheeses are heated and pressurized to remove additional whey from the mixture.
After this separation, most cheeses are ripened with inoculations of various species of bacteria and/or
fungi.
Hard Ripened Cheeses
(Cheddar, Swiss, Colby, Edam, gouda, Parmesan)
The flavor, smell and taste of these cheeses are produced by fermentations from various species of
bacteria including:
Streptococcous lactis
S. cremoris
S. durans
Lactobacillus helveticus
Proprionibacterium shermanii
The longer the incubation time the higher the acidity and the sharper the taste
Swiss Cheese
The flavor and taste of Swiss cheese is produced by the fermentation by Streptococcus lactis, S.
thermophilus and S. helveticus. The addition of Proprionibacterium species to the culture produce
various amounts of lactic and proprionic acids and produces carbon dioxide which makes the characteristic
“holes” in the cheese.
Semisoft Cheeses
(eg. Limburger, Muenster, Brick, Roquefort, Blue)
The cheese curd is ripened by bacteria and other contaminating organisms growing on the surface
including: Streptococcus lactis, S. cremoris, and Brevibacterium linens.
Soft Cheeses
(eg. Brie, Camembert)
The curd is ripened by a variety of microorganisms including Streptococcus lactis, S. cremoris, P.
camemberti and P. candidum. In this case the ripening process is aerobic and the cultures are inoculated
onto the surface of the cheese and extend hyphae throughout.
Soy Sauce
Soy sauce is produced by the fermentation of roasted soy beans and wheat using a mixture of various
bacteria and fungal species including:
bacteria: Pectococcus halophilus
Lactobacillus delbrueckii
fungi: Aspergillus soyae
A. oryzae
Saccharomyces rouxii
Candida versitilis
The starch degrading enzymes produced by the molds produces a sugar that is then fermented by the
bacteria. The entire process takes about a year.
Yogurt
Yogurt is made from milk solids which are concentrated by evaporation. The lactose in the milk is
fermented by Lactobacillus bulgaricus and Streptococcus thermophilus to produce lactic acid. The flavor
is a result of the sugar and the 2-3% lacatic acid generated by this fermentation.
Sauerkraut
Sauerkraut is produced by the natural fermentation of layers of shredded cabbage alternating with layers
of salt. The salt inhibits undesirable bacteria and draws out the juices of the cabbage. Several species of
Leuconostoc including L. mesenteroides and Lactobacillus plantarum are common in the first few days.
In two to three months the acids and esters produce the desired aromas and flavor.
Memmi
Memmi is a product made with soy sauce and used for a simple soup base for noodles.
Vinegar
Vinegar is a fermented food traditionally made by the spontaneous souring of wine. Industrial Vinegar
production begins by inoculating the fruit juice with yeasts which ferment it to an alcohol content of 1020%. Then the juice in inoculated with the bacterium, Acetobacter aceti, which convert the alcohol to acetic
acid.
Coffee
After coffee beans are picked they are soaked in water containing natural cultures of Erwinia dissolvens
and Saccharomyces spp. to loosen the berry skins before roasting. Some fermentation occurs which is
believed to produce some of the unique flavors of various varieties of coffee.
Cocoa
Microbial fermentation by Candida krusei and Geotrichum spp. is used to help remove the cocoa beans
from the pulp covering them in the pod. The products of this fermentation contribute to the flavor of the
cocoa.
Cured (Fermented) Beef or Pork Sausages
eg. Pepperoni, Salami, Thuringer, Polsa
These are generally produced by adding seasoning agents to the ground meats, stuffing the meat into
casings and incubating them at warm temperatures. Mixed acids produced from the fermentation of
carbohydrates by such bacteria as Pedicoccus cerevisiae and Micrococcus spp. in the meat give the
sausage its unique flavor and aroma.
Pickles
Pickles are made by fermenting cucumbers in a mixture of bacteria normally found growing on them
including Lactobacillus plantarum and Pedicoccus cerevisiae.
Butter
Butter is produced by inoculating pasteurized cream or milk with a lactic starter culture which includes
Streptococcus cremoris, S. diacetylactis and S. lactis. and allowing the fermentation to proceed until the
required amount of acidity is obtained. The acidified cream is churned until the thick butter forms. It is
then worked to remove excess liquid, washed, salted, and packaged. The characteristic aroma and taste of
butter result from the compound diacetyl, which is formed by bacteria such as Streptococcus diacetylactis
and other microorganisms.
Buttermilk
Buttermilk is the liquid remaining after cream is churned for butter production. It can also be prepared by
inoculating skim milk with a starter culture of Streptococcus cremoris, S. diacetylactis or S. lactis which
produce lactic acid making the sour taste and curdling the milk. Leuconostoc citrovorum and L.
dextranicum help to create the desired odors.
Sour Cream
Cultured sour cream is prepared by fermenting pasteurized light cream with a lactic starter with the same
organisms as for making buttermilk; including Streptococcus cremoris, S. diacetylactis or S. lactis.
Acidophilus Milk
Lactobacillus acidophilus is added to milk to produce an acidity of 2-3% lactic acid.
Sourdough Bread
Wheat flour is fermented using S. exiguus and Lactobacillus sanfrancisco to produce the tart, acidy flavor
Spirulina
Spirulina is a cyanobacterium that is used as a protein supplement in various dishes and soups
Green Olives
Fermented by Leuconostoc mesenteroides and Lacrtobacillus plantarum
Kimchi
Made from shredded cabbage fermented with lactic acid bacteria
4. Industrial microbiology: uses large cultures of bacteria and other
microorganisms to produce
various industrial chemicals such as amino acids, citric acid, enzymes,
pharmaceuticals, etc
5. Some bacteria are used for energy (methane) production
6. Genetically engineered bacteria are increasing the variety of products we
can produce from bacteria
7. Some bacteria are pathogens:
A. Tuberculosis (Mycobacterium tuberculosis)
an ancient disease
also called consumption
has been called the worlds most neglected epidemic
kills more people worldwide than any other infectious disease
about half of the worlds population is infected, with 8-10 million
new cases each year
about 2-3 million people die each year from the disease
no longer a major disease in US,
esp in urban poor, homeless, and AIDS folks
easily combated if caught early,
difficult to get rid of in advanced cases
slow growing pathogen – respiratory disease
infection in lungs causes formation of ‘tubercles’
90% of infected people remain infected for life but never develop
symptoms of the disease = asymptomatic
two new strains have appeared: a fast growing form and a
completely antibiotic
resistant form
B. Anthrax (Bacillus anthracis)
common soil organism
produces spores that can persist for years
is a zoonosis – animal disease that people can catch
preferred biowarfare agent since it lasts long and can be relatively
easily dispersed
need pretty high exposure to spores to actually get the disease
C. Syphilis (Treponema pallidum)
STD once more abundant than it is today in US
first recognized in 1500’s.
thought it may have been a disease picked up by Native Americans
and spread to Europeans,
new evidence doubts this, it was in Europe before contact with
Americas
easily treated in early stages,
difficult to treat in advanced stages
progresses through three major stages:
1st – after sexual contact, the bacteria
produce open sores in genital area
they persist for several weeks
2nd – several months later the bacteria
have spread throughout the body,
fever, headaches, sore throat, rash, etc. symptoms
disappear in a few weeks
3rd – latent period lasts up to 20 years,
about 30% of patients untreated will
show severe pathology, rupture of blood vessels, heart
damage, blindness, derangement, convulsions, brain
damage, death.