microbio chapter 6

microbes in nature

usually exist in complex, multispecies communities

pure cultures

\
contains a single species

\-used for detailed lab studies

bacterial culture media

can be liquid or solid

liquid media

allows bacteria to move freely

solid media

useful to separate mixtures of different organisms

0\.1% of bacteria 

is culturable

colonies

bacterial cells formed on solid media with agar added to make a firm surface

isolation streaking

allows for separation of colonies into pure culture

spread plate technique

\
a small amount of a previously diluted specimen is spread over the surface of a solid medium using a spreading rod to form pure colonies

\-tenfold dilutions of the original culture are spread on agar plates

early dilutions

will show confluent growth

confluent growth

growth over the entire surface of the streaked area

viable organism

organism that successfully replicates to form a colony

synthetic medium

A bacterial growth solution that contains defined, known components.

minimal medium

synthetic medium in which the components are limited to only those nutrients the organisms need in order to grow

complex/rich medium

nutrient rich but less defined

enriched media

grow fastidious organisms that have a very specific set of nutritional requirements beyond basic media

selective media

compounds in the media prevent some types of bacteria from growing, favoring the growth of one specific type

differential media

species grow equally well but compounds in the media are metabolized differently, often distinguished by a color indicator

macconkey medium

A differential, selective medium that selects for Gram-negative bacteria and can differentiate between lactose fermenters and nonfermenters.

lactose fermenters

degrade lactose and secrete acidic products that lower the pH around the colony, the acidic pH allows the indicator neutral red to enter cells and produce a red colony

nonfermenters

do not ferment lactose and no acid is produced; natural red dose not enter the cells and colonies are white

plated methods

count only living cells

direct cell counts

total numbers (living plus dead)

indirect cell counts

\
indirectly estimate cell number by measuring total biomass

\-by FACS (fluorescence-activated cell sorter) or by measuring turbidity with a spectrophotometer

bacterial growth measurement

done at the population level

binary fission

\
how most bacteria is reproduced

\-one parent cell divides and form two offspring cells

binary fission may be

symmetrical or asymmetrical

eukaryotic microbes

divide by mitosis

exponential growth

growth in which population size doubles at a fixed rate

generation time (doubling time)

In an environment with few bacteria but plenty of resources, bacteria will divide at a constant interval

phases of growth 

1\. lag phase \n 2. log phase \n 3. stationary phase \n 4. death phase

lag phase

bacteria are preparing their cell machinery for growth

log phase

growth approximates an exponential curve (straight line, on a logarithmic scale)

\
stationary phase

cells stop growing and shut down their growth machinery while turning on stress responses to help retain viability

death phase

cells begin to die at an exponential rate

chemostats

ensures exponential growth by constantly adding and removing equal amounts of culture medium

human gastrointestinal tract

\
engineered much like a chemostat

\-new nutrients in food enter from the mouth while corresponding amounts of bacterial culture exists in fecal waste.

essential nutrients

compounds a microbe cannot make itself but must gather from its immediate environment if the cell is to grow and divide

essential nutrients (elements)

carbon, nitrogen, phosphorus, hydrogen, oxygen, sulfur, magnesium, iron, potassium, trace elements like cobalt, copper, zinc

growth factors

some microbes require this to be added to culture media before they will grow

culture media

provides essential nutrients for bacteria

chemically defined media

exact chemical composition is known

complex media

contain some ingredients of unknown composition and/or concentration

chemoheterotrophs (organtrophs)

nearly all pathogenic cellular microbes

carbon (organic) compounds

essential need for all forms of life

carbon compounds

used as food, which stores energy and is a source of cellular building material for making biomass

autotrophs

make their own carbon compounds starting with CO2

how do autotrophs obtain energy?

use light energy or energy derived from oxidation of minerals to capture CO2 and convert it to complex organic molecules

heterotrophs

obtain carbon compounds from other organisms

how do heterotrophs obtain energy?

use organotrophy to gain energy by degrading complex organic compounds (polysaccharides) to smaller compounds (pyruvate). carbon from pyruvate moves through TCA cycle or Krebs and is released as CO2

why is the TCA cycle important?

without it, the carbon can end up as fermantation products, such as ethanol or acetic acid

carbon cycle

The organic circulation of carbon from the atmosphere into organisms and back again

light or chemical compounds

may be used as a source of energy by living things

phototrophs

use light as energy source

chemotrophs

use potential energy stored in chemical compounds as an energy source

lithotrophs

use inorganic chemical compounds

\
organotroph

use organic chemical compounds

nitrogen

needed by cells to make proteins and nucleic acids

nitrogen cycle

converts nitrogen to various forms

N2 gas

makes up nearly 79% of Earth's atmosphere, but cannot be used for biosynthesis.

nitrogen fixation

process to convert N2 gas to ammonium ions which can be used for biosynthesis

nitrification

ammonia is converted to nitrate

denitrification

convert nitrate to N2

nitrogen assimilation

converting inorganic to organic nitrogen

why can't N2 gas be used for biosynthesis?

has three covalent bonds between the two nitrogen atoms

nitrogen cycle steps

1\. Nitrogen is removed from air and converted to ammonia by nitrogen fixers.

2\. Ammonia is converted to Nitrate by Nitrifiers.

3\. Nitrogen is removed from nitrate and converted to nitrogen gas by Dentrifiers.

bacteria

metabolically and physiologically diverse organisms on earth

bacterial growth consideration

\-temp and pressure

\-osmotic balance

\-pH level

normal physiologic conditions

\-temp between 20C and 40C

\-near neutral pH

\-salt concentration of 0.9%

\-ample nutrients

extremophiles

bacteria, archaea, and some eukaryotic microbes that can grow in extreme environments

pathogens are typically

mesophiles

thermophiles

\
adapted to growth at high temp

\-55C and higher

hyperthermophiles

grow at temps as high as 121C

\-occur under extreme pressure (ex ocean floor)

thermophiles and hyperthermophiles

\-have heat stable enzymes

\-proteins function at high temp

\-amino acids that make protein more heat stable are more present

\-heat-shock proteins

\-membrane has higher concentration of saturated lipids, more branched and higher in molecular weight

pyschrophiles

microbes that grow at temps as low as -10C

pyschrophiles adapted by

\-enzyme, transport systems, and proteins function well at cold temps

\-membranes have high level of unsaturated lipids (allows them to be semifluid at cold temp)

\-accumulate compatible solutes and synthesize antifreeze molecules to lower the freezing point

mesophiles

grow between 20C and 40C

\-E. Coli and Bacillus subtilis

barophiles/piezophiles

organisms adapted to grow at very high pressures

\-deep within ocean

water availability

measured as water activity (aw), a quantity approximated by concentration.

osmolarity

measure of the number of solute molecules in a solution and is inversely related to (aw)

halophiles

"salt-loving" archaea that live in environments that have very high salt concentrations

neutralophiles

bacteria that generally grow between pH 5 and 8; this includes most human pathogens

acidophiles

bacteria and archaea that live in acidic environments

alkaliphiles

occupy the opposite end of the pH spectrum, growing best at values ranging from pH 9 to pH 11

changes in pH cause

denaturation of enzymes which is detrimental for the organism

near neutral environement

maintained regardless of environment due to the prescence of cytoplasmic buffers

acidophiles (acid tolerance response)

\-occurs if pH drops below 5.5

\-involves the synthesis of proteins that will pump protons (H+) out of the cells

\-pH drops below 4.5 then acid shock proteins and heat shock proteins are synthesized

\-prevent denaturation and refold denatured proteins

neutralophiles (pH change)

exchange K+ for protons using an antiport system

alkaliphiles (pH change)

maintain internal pH close to neutral by exchanging internal sodium ions for external protons

ROS

reactive oxygen species

strict aerobes

\-Require oxygen for energy metabolism

\-Successfully detoxify reactive oxygen species (ROS)

\-Survive only in environments with oxygen

strict anaerobes

\-Do not require oxygen for energy metabolism

\-Generally unable to detoxify ROS, making oxygen toxic

\-Survive only in environments without oxygen

microaerophiles

\-Aerobic, but ROS can be toxic

\-Survive in environments with lower oxygen concentration

aerotolarant anaerobes

\-anaerobic but less susceptible to ROS, and usually lack catalase

\-prefer anaerobic conditions but can survive oxygen

facultative anaerobes

\-Aerobic AND anaerobic

\-Survive with or without oxygen

oxygen related growth zones

anaerobe jar

(for plates) where O2 is removed and CO2 is generated

anaerobic chamber

with glove ports that remove the atmosphere via vacuum and replace it with a precise mixture of N2 and CO2 gases

biofilm

mass of bacteria that stick to and multiply on a solid surface

\-can include a single species or multiple collaborating species

\-can grow on organic or inorganic surfaces

dental plague

biofilm that forms on teeth