ecology, biogeochemistry, industrial micro Flashcards
doubling time of microbes
30 min
-> fast evolution, diversification.
physical environment
influences interactions of microorganisms with each other
microenvironment
specific physical location of microorganism = can be interface btw 2 environments
- impacted by fluxes of nutrients + diffusion rates of waste products
Niche
function of organism in complex system - adaptation to particular location
ppopulations
consist of cells of same species
guilds
one or more metabolically related population
= same function
abiotic constraints
moisture temp pH redox potential salinity light pressure
tolerance limits
optimal range
zone of physiological stress (low habitation)
zone of intolerance ( species absent)
bacterial species?
hard to define because species based on interbreeding + fertile offspring. but prokaryotes reproduce clonally, not sexually.
using polyphasic taxonomy
to classify species
- use combinations of genotypic AND phenotypic markers
what is exclusionary principle?
each niche is occupied by only one species
microbial ecology
environmental samples continue to reveal novel bacteria from phylum to species levels
diversity in bacteria
less in physiology than in genomes.
metabolism restricted to periodic table
species richness
species evenness:
species composition:
species dominance:
R: total number of species
E: relative abundance of species
C: which species are present
D: the most abundant species
potential niche
the niche that the organism could theoretically occupy
realized niche:
niche that the organism actually occupies
why are potential + realized niche not the same
competitive exclusion = only one species occupies a niche, but resource partitioning = niche can be divided to form narrower niche
functional redundancy = same potential niche, diff realized niche - organisms lost when outcompeted unique
negative and positive interactions btw growth rate + popln density
growth rate increases as population density increases = tapers at a point = positive
negative: popln increases, growth rate decreases due to competition
overall population density considering both +/- interactions
low popln density, low growth rate, dont have enough individuals for +interaction.
high density = low growth rate. more interactions of negative interactions. intermediate = highest growth rate.
resistance vs resilience
resistance: disturbance has little to no effect. survival.
resilience: after disturbance, recovery is high.
what are biofilms
organized microbial systems attached to surfaces
- enclosed by adhesive extracellular matrix
- creates multiple microenvironments
benefits of biofilms
intercell communication, easy access to resources as water + nutrients float by.
how actiera attach?
1 pilliattach = body turns off most genes
2. make polysaccharides + other things to attach to other bacteria + surface.
microbial mats
thick biofilms have macroscopic dimensions
- layered, each layer is a guild
- aquatic environments: when extreme, separate into layers.
soil habitat
most microbes in microcolonies
- attach to soil particles
- most grow near plant roots due to high level of nutrients
- water limitation is greatest stress (either too much or too little)
chemical distribution and biosignatures.
- through layers of water, different amounts of elements = diff organisms at each level, once one chemical is used move to next one.
two characteristics of chemical dstn and biosignatures?
- amount of energy available from chemical reactions
2. chemical constraints
lake michigan chemical dstn/biosignature
- high O2 at top of sediment btw water/sediment interface = aerobic respiration + organic matter.
O2 depletes, No3- used. fixed so used quickly. as NO3- fixed, NO2- increases
sulfate increase once NO2- decreases.
metals: better e- acceptors. needs to dissolve to be used - tricky to do
methane + CO2 in system = aerobic, fermenters, methanogens.
ammonia in deeper waters = degrade organic matter.
black sea chemical dstn/biosignature
aerobic @O2 Nitrogen-fixers @ high NO3- Mn/Fe reducing bacteria where high MN++ and FE++ NH4+ = ammonia oxidizers sulfate = sulfate oxidizers.
biogeochemical cyclins
biological + chemical processes
-ox-redox reactions that change chemical and physical characteristic of nutrients
= all nutrient cycles are linked
carbon cycle
lin O2 and C.
- photosynthesis produces O2 and removes CO2
- respiration removes O2 (aerobic) and produces CO2 (re-mineralizes)
- anaerobic resp + fermentation = diff form of C
methanotrophy from fermentation = oxidized to CO2.
aerobic carbon use
organic C + O2 => CO2 of other forms of oxidized products ( H2O, NO3-)
organic C = reduce to oxidize C H2, NH4, H2S, CO2 = chemoheterotrophs
chemo autotrophs use reduced compounds to oxidize them
anaerobic carbon use
organic matter - use other oxidant, to oxidize organic matter to CO2.
methanogens use CO2 anaerobically to produce methane
what is syntrophy
“eating together”
- all dependent on each other. one produces food for the next.
3 strains of methanobacterium omelianskii
S = unfavourable reaction energetically
MoH - favourable + spontaneous reaction
-co-culture of the 2: net reaction is favourable. so S can grow.
S is obligate syntrobe bc interspecies H transfer.
link between N cycle + C cycle = photosynthesis
high Organic C = more N2 fixation. less OC = less N2 fixation - negative feedback from N2.
high nitrate.ammonia = drive photosynthesis for more fixed carbon
microbial N cycle
Nitrogen fixation: N2 -> NH3 -> NH2OH: nitrification-> NO2 -> NO : denitrification -> N2) -> N2
oxidation: NH2OH -> NO
Anammox NO2 -> NH3
assimilation: No2 -> N2 or NH3 -> N2
Reactive Nitrogen
NO: vasodilator, free radical + destroy ozone layer N2O: greenhouse gas NO2: potent carcinogen NO3-: major water pollutant NO2: smog
N fixation
reduce N2 -> ammonia
prokaryotes only
- mass expenditure of energy, e-, and anaerobic enviro.
- aerobes + anaerobes
nitrification process
aerobic
ammonia oxidizers (reverse electron flow)
nitrite oxidizers
=N2O
anammox process
anaerobic ammonia oxidation
- produce N2 from ammonia + nitrite
- in membrane-bound organelle, intermediate it super reactive.
denitrification
anaerobic
heterotrophic (Ocarb + N-oxide (oxidant)
- lots of bacteria do this
release N2O to atmosphere
iron and manganese processes
two oxidation states each
- reduction of them in anoxic enviro = mobilize metal into soluble, oxidized form.
- lowpH, common in coal-mining, results in acid mine drainage
meta cycle
oxidized form can percipitate out + sink to bottom.
-can utilize metal a lot before precipitates out.
not re-oxidized easily. ocean marine system uses sulfate to interact with metal + percipitatte itout
what is acid mine drainage
dig mine site, pyrite precipitates + turns to sediment. when aerosolized, converted to Fe3+ = sulfide oxidized to sulfate (Hso4- = acidic)
