Microbial Ecology (#5) Flashcards
cyanobacteria that make biofilms called “microbial mats;” found in pre-cambrian rocks (extremely old) and still form today
stromatolites
where found the first microbial fossils
in microbial mats (made by stromatolites)
the study of the relationships of organisms between each other and their environment
ecology
sum of all the organisms and abiotic (nonliving) factors in a particular environment (ex: ocean, forests, desert, lakes)
ecosystem
every ecosystem has _____
microbes
T/F: some ecosystems are EXCLUSIVELY microbes
true (ex: boiling hotspring)
portion of an ecosystem where a community could reside
habitat
habitat =
PLACE
relationships where 2 organisms live in conjunction
symbiotic relationships
type of symbiotic relationships (3):
- parasitism
- mutualism
- commensalism
type of symbiotic relationship: one organism HURTS the other
parasitism
type of symbiotic relationship: both organisms benefit from each other
mutualism
type of symbiotic relationship: one benefits while the other is not affected
comensalism
a group of organisms of the SAME species in the SAME place at the SAME time
population
metabolically related microbial populations (many populations); ex: species that all use photosynthesis
guild
a habitat shared by a guild
niche
best niche for an organism; organisms DOMINATES this niche; every organism has one
prime niche
prime niche is also called:
realized niche
two or more cell populations coexisting in a certain area (habitat) at given time
community
order of ecological concepts from largest —> smallest (5):
- ecosystem (LARGEST)
- community
- guild
- population
- individual (smallest)
diversity =
variety
types of diversity (3):
- alpha diversity
- beta diversity
- gamma diversity
type of diversity: diversity WITHIN a single community (sample); can get a good look at what’s happening within a habitat
alpha diversity
components of alpha diversity (3):
- richness
- abundance
- evenness
component of alpha diversity: the total number of different SPECIES present in a particular area
richness
component of alpha diversity: the PROPORTION of each species
abundance
component of alpha diversity: how similar the abundances are (relative abundance of different species); 4 red to 6 green
evenness
alpha diversity classification: lots of different species and evenly proportioned
rich and even
alpha diversity classification: a lot of different species, but one dominates the others
rich, not even
alpha diversity classification: only has one single species
not rich or even
type of diversity: COMPARISON of samples (between community diversity); more mathematical comparison
beta diversity
type of diversity: the total species diversity for the different ecosystems within a region
gamma diversity
gamma diversity is also called _______ diverstity
landscape diversity
if you see: A vs B has 8 species, what kind of diversity are you looking at?
beta (is comparing A vs. B)
what 2 things can alter diversity?
resources + conditions
alteration of diversity examples: macronutrient, micronutrients, oxygen and other e- acceptors, inorganic e- donors
resources
alteration of diversity examples: temperature, water potential, pH, oxygen, light, and osmolarity
conditions
as you go down into anoxic sediments, you get less and less favorable _____ _______; not able to make as much ATP
electron acceptors
Legumes don’t need nitrogen fertilizers bc rhizobia in their root nodules fix _____ into ______
nitrogen into ammonia
study of biologically mediated chemical transformations
biogeochemistry
biogeochemistry involves the many ______ of activities (of essential elements) carried out by microbes
recylcing
biogeochemical cycles (4):
- carbon
- nitrogen
- sulfur
- iron
nitrogen cycle processes (5):
1) nitrification
2) denitrification
3) nitrogen fixation
4) ammonification
5) anammox
nitrogen cycle process: the oxidation of AMMONIA to NITRATE; might take 2 steps
nitrification
nitrogen cycle process: the reduction of NITRATE to NITROGEN GAS (N2); bad for soils + plants bc N2 in the atmosphere is unavailable to plants
denitrification
nitrogen cycle process: the reduction of NITROGEN GAS (N2) to AMMONIA; putting N into a form we can use
nitrogen fixation
nitrogen cycle process: the release of ammonia during the decomposition of organic nitrogen compounds (dead plants + animals)
ammonification
nitrogen cycle process: the anaerobic oxidation of AMMONIA to NITROGEN GAS (N2); denitrification but anaerobic
anammox
major reservoir of nitrogen =
atmosphere
____% of the atmosphere is composed of nitrogen gas
78% (the rest is in rocks n stuff)
______ process is bad for us/plants while ______ process is good for us/plants
denitrification; nitrogen fixation
while denitrification is bad for us, what is it good for?
waste-water treatment (removes N from waste)
2 steps of nitrification:
1) ammonia —> nitrite (NO2-)
2) nitrite (NO2-) —-> nitrate (NO3-)
what organism completes the first step of nitrification where it transforms ammonia into nitrite?
Nitrosomonas
what organism completes the second step of nitrification where it transforms nitrite into nitrate?
Nitrobacter
nitrification is a ______ process
oxidation
denitrification is a _____ process
reduction
plants can assimilate nitrogen from ______ or ______
ammonia or nitrate (NO3-)
plants prefer to assimilate _____ bc it is easier
nitrate (compared to ammonia)
can be easily leeched from soil and get into ground water
nitrate
nitrate in ground water can cause what disease?
blue baby syndrome
in blue baby syndrome, nitrate binds to _______ making it less able to carry oxygen
hemoglobin
the legume-root nodule is a plant-bacterial _______ type of symbiosis
mutualism
plants with seeds that grow in PODS (ex: soybeans, clover, alfalfa, beans, peas, and peanuts)
legumes
infection of legumes by nitrogen-fixing bacteria, known as _______, leads to the formation of root nodules
rhizobia
live in roots and take nitrogen gas from the atmosphere and fix it to ammonia; gives plants a source of Nitrogen; both benefit from it
rhizobia
bc of rhizobia, legumes can grow well in what type of soil?
nitrogen deficient soil
legumes play a key role in _____ _____
crop rotation (replenish soil with nitrogen)
_____ leaves = not getting enough nitrogen
yellow
T/F: plants NOT infected by rhizobia grow better
false
herbivorous mammals that posses a rumen
ruminants
examples of ruminant animals
cows, sheep, and goats (not horses)
digestive organ within which cellulose and other plant polysaccharides are digested by microbes
rumen
order of food particles through a ruminant animal (5):
1) esophagus
2) reticulum
3) omasum
4) abomasum
5) small intestine
part of ruminant digestive tract: sorting room; sorts large and small particles (small can pass)
reticulum
part of ruminant digestive tract: acidic stomach
abomasum
part of ruminant digestive tract: moving organ; mixes plant material microbes in rumen digest plant material (cellulose to sugars) and the rest ferment sugars into volatile fatty acids which are absorbed into the bloodstream by the walls of this
rumen
main source of energy for ruminant animals comes from the _____
rumen (absorption through walls)
in the rumen, microbes digest cellulose into sugars and the rest ferment sugars into _____ ______ _____ which are absorbed into the bloodstream through the walls
volatile fatty acids
the reticulum sends small particles to the ______ and large particles to the ______
omasum; rumen
what is not digested in the rumen is ________ so cows can continue to chew and break it down to smaller pieces
regurgitated
man-made hole in cow for scientific purposes
fistula (can stick your FIST in it)
microbes in the rumen are mostly _______
anaerobes
there are ____ to ______ microbes per gram of rumen contents
10^10 to 10^11 microbes
cellulolytic microbes hydrolyze ____ to free ______
cellulose to free sugars
fermentation of sugars in the rumen yields what 3 things?
- volatile fatty acids
- CO2
- CH4
pass through rumen wall into bloodstream; serve as the ruminant’s MAIN energy source
volatile fatty acids
volatile fatty acids/fermentation products (3):
- acetate
- propionate
- butyrate
volatile fatty acids are produced in an ______ environment with a constant _____
anoxic; pH
microbial environments in nature are _____ and constantly _______
complex + constantly changing
microbial environment conditions are determined in part by ______ _____ of the community
metabolic activties
resources in microbial environments are highly _____ and often _______
variable; suboptimal
there is a “_____________” existence of resources for bacteria; doubling exponentially is actually RARE bc of this
“feast-or-famine”
microbes also have to deal with _______ substances when trying to acquire resources
inhibitory substances
microbial environments in nature have a ______ or ______ relationship
competition or cooperation
in a soil particle, each layer counts as a different _________
microenvironement
assemblages of bacterial cells attached to a surface
biofilm
biofilms are a ______ community
heterogenous
what makes biofilms a heterogenous community (2)?
- metabolic differences
- location
biofilms are enclosed in an _______ _______
adhesive matrix
adhesive matrix traps _____ for microbial growth and help prevent _____ of cells
nutrients; detachment
biofilms provide _____ for cells
protection
microbial interactions within biofilms (3):
- metabolic exchange
- DNA uptake
- quorum sensing
microbial interaction within biofilm: increases diversity; helps pick up advantageous genes
DNA uptake
quorum sensing is _____ dependent
density
