Exam 3 Terms Flashcards
biological species concept
organisms that create fertile offspring are the same species
phylogical species concept
based on shared evolutionary history (DNA)
16S rRNA
is a chronometer to measure relatedness, ribosomal genes must be ancient, compared via PCR and alignment (reveals 3 branches of life)
informational genes
transcription and translation, generally passed on vertically
operational genes
metabolism, pathogenicity, can be traded horizontally
gene sharing
more commons between organisms in different environments
pan genome
all genes found in any strain
core genome
all genes found in all strains
pathogenicity island
region of the genome that contains virulence factors (the genetic information transferred into it to make it infect others), may contain skewed GC ratio or codon bias
shigella
genus with 4 species, all are pathogenic (S. dysenteriae, S. flexneri, S. sonnel, S. boydii, can cause body flux and kidney failure
how shingella differs from E. coli?
non-motile, does not ferment lactose, indole, lysine-decarboxylase negative, more insertion sequences, virulence plasmin, causes similar but more severe disease
how is shigella similar to E. coli
the sequencing shows they are very closely related:
- 94% same open reading frames
- causes similar diseases
- PINV plasmid, can invade other species
form species
observable characteristics
morphology
size and shape
biochemistry
composition and metabolism
ecology
habitat and tolerances
pathogenicity
ability to cause disease
paralog
same gene in same species duplicated (happens by HGT or errors in DNA repair)
reduction
organism lives in a stable, predictable environment and loses genes to reduce energy (common in nutrient poor environments and symbiosis)
evolution determinants
growth rate and strength of selection
MRSA
- treated with two rounds of antibiotic due to weakened immune system, developed small colony variant/multiple drug resistant
- mutation to S. aureus made ppGpp, normally triggered by stress
- ppGpp binded to polymerase, creating slow growth of bacteria and recycle instead of growth (shows regulatory mechanisms have large impact)
takeaway: benefit of being antibiotic resistant was greater than the cost of slow growth
E. coli long term growth experiment
takeaways: cultures evolved, every point mutation occurred
-molecular clock: mutations happen at a steady rate
-all populations evolved faster growth rates and larger cells size (rate dramatically increased more early on)
-after 33,000 generations, one culture was notably denser (cit+ mutation)
Cit+ mutation
-can use citrate as a C source, Cit- phenotype had gone extinct
-duplication copied citrate anti-porter, making citrate come in and succinate go out (behind a different promoter, CitT is usually not produced in aerobic conditions
why is CitT mutation bad?
loss of succinate, only good with gltA mutation
GltA mutation
offsets loss of succinate through the Krebs cycle
how was citT further improved?
- multiple copies of mutated citT
- increase in DctA (brings in succinate, making reversions of GltA beneficial)
- succinate using cells arose
eukaryotic tree
animals and plants are no longer together, although they are both amitochondriate groups (once had mitochondria, then lost it), reordered due to sequencng advancements
asexual reproduction
spores, germination (exit from dormancy), mycellium (mitosis), spore-producing structures (mitospores)
sexual reproduction
spores, mycellium (mitosis), plasmogamy (fusion of cytoplasm) leads to heterokaryotic stage, karyogamy (fusion of nuclei) leads to zygote (diploid), meiosis, spore producing structures
ascomycetes
many live in association with algae, lichens, yeast and hyphal morphology
glomeromycota
obligate plant mutualists, form arbuscular mycorrhizae (fungus penetrates cortical root cells and plant hormones regulated formation and they exchange sugar for fungal materials like ammonium and phosphate)
protist
not fungi but eukaryotes
protazoa
type of protists, heterotrophic single celled
primary algae
photosynthetic eukaryotes, not land plants, no roots or vascular tissues; derived from eukaryote that engulfed a cyanobacteria
secondary algae
photosynthetic eukaryotes, not land plants, no roots or vascular tissues; derived from a protozoan that engulfed a primary alga
slime molds
heterotrophic spore formers
plankton
any aquatic organism unable to swim against a current
photoplankton
phototrophic aquatic organisms unable to swim against a current
zooplankton
aquatic organisms unable to swim against a current that feed on other plankton
cyanobacteria
green-blue algae
- only photosynthetic prokaryotes (unicellular)
- organelles sacs contain thylakoids
- adappt to non ideal conditions
- produce external toxins
heterocysts
cyanobacteria that can fixate nitrogen
akinetes
spore formating cyanobacteria
primary algae
green and red
- origin engulfed cyanobacterium, became the chloroplast
- has double membrane (one is from the cyanobacteria, one is from the host)
secondary algae
origin by engulfing primary alga, two double membranes
nucleo morph- vestigal nucleus from first host
issues with algae: the plankton paradox
limited amount of resources can support algae that need different resources
issues with algae: algal blooms
- increase in nutrient availability cause harmful toxins
- when they die, they lead to anoxic zones because they serve as food for heterotrophs that deplete O2 from the water (they all gather to feed on it)
issues with algae: red tides
- bloom of dinoflagellates
- produce neurotoxins
- dismantle Na+ ion pump
issues with algae: biofuels
extract lipids from algae
phylum
major branch of tree, distinct group of organisms
candidate phyla
new group categorized by DNA isolates
CPR
monophyletic group close to the root of the tree (unculturable, analyzed by DNA alone, do not abide by Koch)
ribosomes
make organisms seem further apart than they are
phototrophy takeaways
- color not able to be absorbed is reflected and the color that the organism appears as
- phototrophy differs depending on organism
- absorption wavelength reduces competition over light
cyanobacteria and procholorphytes
- 80% of ocean photosynthesis
- significant N fixers
- can form spores
- related ancestor of chloroplasts
proteobacteria
- photoautotrophs without O2
- purple! slay
- chromatophores produce color, more in low light, no O2
type: pelagibacteria: rhodopsin based phototrophy, Gr-, from archaea?
green S bacteria
- consortia =mutualistic relations with heterotrophic bacteria, trades food for motility
- divide in synchrony, coculturing possible
deinococci/thermus
- stain Gr+ but do not have typical Gr+; peptidoglycan layer between inner and outer membrane
- resistant to radiation and breakdown: has multiple DNA repair enzymes, tightly coiled chromosomes hold fragments
High GC Gr+ species: streptomyces morphology
- complex lifecycle and metabolisms, largest genomes
- body = hyphae (thinner than fungal), no crossbodies
- linear chromosomes
- makes lots of antibiotics
High GC Gr+ species: mycobacteria
- high lipid content; wrinkled colonies, can’t take in stains
- causes TB
- detected by acid-fast staining
High GC Gr+ species: corynebacteria
includes diphtheria pathogen
proteobacteria: pseuodomonads
rods with flagella, organoheterotrophs, aerobes
proteobacteria: neisseria
cocci or bacilli, organoheterotrophs, nonmotile, can cause gonorrehea
proteobacteria: enteric
rods, organoheterotrophs, GI tract, motile
proteobacteria: vibrios
curved rods, aquatic, bioluminescence
proteobacteria: rhizobia
N-fixers, endosymbionts of legumes
proteobacteria: rickettsia
parasites, causes human diseases transmitted by insects
proteobacteria: spirilla
pray on other Gr- bacteria, spiral shaped
Low GC Gr+ species
thick cell walls, form biofilms and endospores
Low GC Gr+ species: bacillus thuringinese
insecticidal protein, engineered into plans
Low GC Gr+ species: clostridium
can cause illness
Low GC Gr+ species: lactobacillus and listeria
dairy, fermented foods, food poisoning, invades nerve and epithelial cells
Low GC Gr+ species: staphylcoccus
boils, impetigo, skin infections, TS
Low GC Gr+ species: streptococcus
cavities, throat, pneumonia
Low GC Gr+ species: mycoplasma
no cell wall but match sequencing, have sterols and lipoglycans
proteobacteria: sheathed proteobacteria
grow within layer of protein, polysacchrides and lipids, elongated capsule
proteobacteria: stalked proteobacteria
unequal cell division: budding or polar growth, stalk is for attachment, coordinated to cell division
proteobacteria: myxobacteria
rod shaped, vegetative, aerobes, aggregates with nutrient depletion, grow in soil
elementary chlamydia
extracellular replication, inert, no cell wall
reticulate chlamydia
intracellular replication, active
verrucomicrobia
tubulin genes received via horizontal transfer
archaea
most ecologically diverse domain:
- more extreme habitats (high temperatures, low pH)
- symbioses with bacteria and eukarya
- central dogma like eukarya
- methanogenesis + rhodopsin phototroph capabilities
how can archaea adapt to high temperature?
- proteins have hydrophobic cores, ionic residues on surface, active chaperonins
- DNA is positively supercoiled
- tetraether lipid monolayers
- hot spring/vent habitat
euryarchaeotes
major group within archaea, have methanogens, extremophiles
methanogens
aerobes, can oxidize hydrogen, most are mesophiles
halophiles
- high salt tolerance: slight, moderate, extreme
- mesophiles (normal temp),
- photoheterotrophs
- usually obligate aerobe
- some produce bacteriorhodopsin at low O2, creating H+ gradient for ATP synthesis
- have Na+ powered flagella, gas vesicles
adaptations to high salt
high GC content, more acidic, K+ in cytoplasm offsets external Na+, S-layer has acidic AA glycoproteins, stable in high Na+
ecology
interaction of organisms with each other and their environments
example of communities interacting with each other
phototrophs make O2, aerobes need O2, they take it from the anerobes in anoxxic sediments
community
organisms in given time and place
ecosystems
interconnected group of organisms and habitat
richness
number of different species
abundance
proportion of species
balance depends on nutrients, physical conditions, ability to use nutrients
guild
group of species that carry out related metabolic activities
pure cultures
remove competition, making it hard to understand the organisms
ex: plants for light, heterotrophs for carbon (enzymes tapping into new source eliminates competition)
metagenome
sum of DNA found in environmental sample (differences show DNA evolved through adaptations)
how do we sample microbial communities?
fluorescent staining highlighting living cells, 16S rRNA sequencing
how do conditions cary in small distances?
nutrients fluctuate, feast or famine (bursts of growth), natural growth rate is less than lab, habitat can change, micro colonies and films form in favorable areas, heterogeneous habitat = more niches = greater richness (more nutrients)
FISH
16S rRNA identities bacteria through fluorescent staining
microbial symbioses
binary interactions in which both organism are present (not in the real world), intensity increase with population size, third species may strengthen or counteract interaction
mutualism
obligate, needed to survive
synergism
can live without the interaction but is beneficial for growth of both organisms
syntrophism
eat each other
lichens
fungus and algae (organism is formed by mutualistic relationship)
corals
coral and algae
amensalism
one species benefits by harming the other
colonization resistance
one species dies
climate change
one consequence of CO2 increase
- positive feedback loop for methane release
- warming accelerates due to water vapor, clouds, ice albedo, soil respiration
layers of soil
Ogres (organic declines) Munch (mineral content) And (aeration decrease) Hydrate (hydration increases)
rhizoplane
plant root surface
rhizosphere
region around plant root that can receive substances from plant (fungi help plants take up minerals)
legumes
have advantange in unfertilized soil, they can get N from the fungi (needs no O2, leghemoglobin makes red)
biofilms attach by…
polysacchrides
planktonic habitat
more volume
- as depth increases, light, oxygen, and temperature decrease
- organic molecules are at the surface, minerals at the floor
- aquatic systems are generally considered oligotrophic (low N, P, Fe)
- pressure may be an issue in oceans
eutriphication
excessive nutrients leading to too many microbes, depleting water of O2, animals die
ruminents
cattle, sheep, goats, deer, elk, giraffes, buffalo etc.
rumen
specialized fore stomach
- contains complicated microbial community
- came from mother after birth
animal gut ecology (rumens eat grass…)
- fibers broken down by fungi
- cellulose, starch, and AA broken down by bacteria
- glucose converted and absorbed as volatile fatty acids
- hydrogen used by methanogens
eructation (burping methane and CO2, contributes to global warming) - carbon, proteins, and vitamins produced by bacteria in the gut can be used by ruminants
- if they eat too much grains and not enough grass, acidosis results (streptococcus bovis overgrowth)
- acids from starch fermentation can kill other bacteria (cost)
eructation
burping methane and CO2, contributes to global warming
vents
heated water emerges from ocean floor
cold seeps
pressure is squeezing water through ocean sediment
lithoautotrophs
basis of local food chain (animals)
- bacteria may also attach to animals present (protection, symbiosis)
tube worms + bacteria
- worm supplies H2S and O2
- bacteria oxidizes H2S and fixes O2 (get a home in the worm away from the vent)
termites
termites “eat” wood: delivers wood fiber to gut via jaw
- protists in gut breakdown lignin
- bacteria break down cellulose
- termite absorbs fermentation product, typically acetic acid
mixotricha paradoxa (protist with 4 symbiotic bacteria)
Protist in gut of termites
- spirochete - function as flagella for movement (flagella of its own help with steering)
- anchor bacteria - related to bacterioides
- internal bacteria - take place of mitochondrion which mixo has lost
- bacteria are obtained through HGT, VGT; correlates with diet
our gut
- we gain nutrition and protection from pathogens
- diet and genetics influence gut microbiome
- fecal transplant may be needed
- imbalances can lead to disease
reserviors
pools of element
flux
movement between pools
- mediated by a process
- measured by chemical and spectroscopic analysis, radioisotope incorporation, isotope ratios
ocean (food webs describe movement)
phytoplankton, bacteria, archaea, algae (producers) goes 60% to grazers (protists and invertebrates - consumers) and 40% to viruses (decomposers)
forest (food webs describe movement)
plants (producers) goes 20% to grazers (protists and invertebrates - consumers) and 80% to fire, fungi and bacteria (decomposers)
biotic fluxes
- oxygenic PS
- lithotrophic carbon-fixation
- aerobic respiration
- acteogenesis (acetate production) - auto or heterotrophic
- anoxygenic PS
- anaerobic respiration
- fermentation
- methanogenesis (syntrophy)
- methanotrophy (oxycline - the zone between oxic and anoxic)
abiotic fluxes
- CO2 in/out of oceans
- sedimentation
- vulcanism
- burning of fossil fuels
- deforestation
role of microbes
- prokaryotes perform all known types of metabolism (eukaryotes don’t play key role)
- bacteria have dominant role in demineralization process, important in oligotrophic (low nutrient) environment
- bacteria control nutrient available to primary producers
reservoirs (where carbon is found)
from biggest to smallest:
1. crust/minerals (mostly unavailable)
2. ocean water (dissolved organic C or diss. C) - CO2 dissolves in water, produces carbonates, lowers pH
3. fossil fuels (mostly unavailable)
4. soil (decaying biomass)
5. atmosphere (increasing)
6. terrestrial + freshwater biomass (standing in trees)
human sources have accelerated processes
- agriculture (pro is more PS, con is more humans exhale CO2)
- burning of fossil fuels
- deforestation
- methane release from livestock
nitrogen cycle reservoirs
present as NH2, NH3, NO2, NO3 (N is limiting)
1. atmosphere (limited bioavailability)
- energetically expensive to fix
- industrial fixation significant
2. crust/minerals (unavailable)
3. ocean water (dissolved N2 and also available N)
4. soil
5. terrestrial biomass (grass, insects, fungi)
haber-bosch
nitrogen is fixed via combination of N + H to make NH3 (industrial process); given to plants in the form of fertilizer
downsides to fertilizer
- pollutes groundwater (excessive algae + plant growth; O2 is used + depleted to break down excessive algae creating dead zone)
- oxygen depletion leads to dead zone
- formation of N2O (greenhouse gas - leads to O2 depletion)
N fixation
fixation: N2 to 2 NH3
(consumes 8 e-, 16-24 ATP)
- N2 is not useable for most organisms
- this rxn is carried out by only bacteria + archaea (may be symbiotic with plants)
- key enzymes = dinitrogenase and dinitrogenase reductase; cofactors are iron and molybdenum; only works w/o oxygen, O2 may destroy enzymes
- 20 genes are involved (similar in bacteria + archaea) - transcription is regulated by O2, NH3, fixed N
assimilation
using NH3 to make aa, n-bases
ammonification
NH3 from breakdown of aa
nitrification
NH3 to NO2 (anaerobic) and NO2 to NO3 (aerobic)
- generally aerobic (uses O2 as the e- acceptor)
- use calvin cycle in carboxysomes for CO2 fixation
lithotrophy
oxidizing NH3 for minimal energy
nitrosifyers
NH3 to No2
nitrofyers
NO2 to NO3
denitrification
N compounds to N2
- N species used as e- acceptor for anaerobic respiration
- removes N from ecosystem - good for wastewater treatment, bad for farmers
anammox
anaerobic ammonia oxidation
- ammonia is ox, nitrite is the e- acceptor
- dissimilatory, producing N2
sulfur cycle reservoirs
- crust/minerals - weathering makes inorganic forms available
- ocean water - dissolves sulfates, vents spew H2S
- soil
- biomass
- atmosphere - volcanoes and burning of fossil fuels
sulfur cycle reservoirs
- S needed for some AA + cofactors
- reduced S often contaminates oil + coal deposits (when burned, plays a role in acid rain; S ox. bac. can clean coal)
- S bac. can also destroy concrete pipes
sulfur flux
- chemolithotrophy
- anoxygenic PS
- calvin cycle
- organoheterotrophy
- assimiliatory S rxns for AA
- inorganic fermentation (for energy, anaerobic)
sulfur reduction
- mostly anaerobes
- used as e- acceptor for anaerobic resp.
- organoheterotrophs or lithoautotrophs
phosphate cycle reservoirs
- insoluble minerals/salts
- biomass
phosphate cycle flux
- P is solubilized by bacteria, fungi, photoplankton
- passed up the food chain
*needed for DNA
why are humans a favorable environment for microbes
- nutrient dense
- controlled temp.
- pH
- osmotic balance
(some tissues have more O2 than others)
normal flora
organisms present in healthy individuals
(human cells ~ microbial cells in human)
composition of normal flora depends on
age, sex, diet, etc.
diversity of normal flora is
mostly bacteria, also archaea, fungi, protists
transient flora
organisms present in passing
(assume interaction is beneficial to microbe)
composition of transient flora depends on
exposure, disease, etc.
colonization
growth of microbe in/on body
- if its disease-causing = infection
gut-brain axis
- microbiome interacts w/ endocrine, nervous + immune systems
- affects conditions like allergies, inflammation, autism, depression, metabolism
holobiont
human = microbiota
- exists on all surfaces exposed to outside world
- starts @ birth
- natural birth vs. c section, source of milk may affect
hygiene hypothesis
gut microbiome is less diverse than before
tissues
microbes here = disease
skin
protective microbes (normal flora)
- skin is tough to penetrate, has tightly packed epithelial cells, keratins are hard to break down
- epidermis, dermis, SC layer
- shedding limits accumulation of microbes
hair follicles + sweat glands
- slightly acidic
- high salt
- nutrient rich
- contain antibacterial peptides, enzymes
skin flora includes
- mostly Gr+ (Gr- in more moist regions, fungi on scalp + feet)
- staphylococcus epidermis (harmless)
- cutibacterium acnes + related cornyebacteria (harmless, can cause odor + acne, breaks down lipids)
- staphylococcus aureus (can cause impetigo and boils)
oral cavity
moisture and food make for dense + diverse biodiversity (more than skin)
- antibacterial action of lyzozyme + lactoperoxidase
- acid production, diet high in sucrose causes cavities
- gingivitis + periodontal disease can also occur
- dental procedures may allow these organisms to enter blood + form biofilms in heart
shift in species post teething
anaerobes colonize crevices between teeth + gums
teeth = surface for attachment
- glycoprotein film from saliva covers teeth (streptococcus species can attach and make dental plaque)
- filamentous bacteria occupy root of teeth
upper respiratory tract
- microbes enter inhalation
- normal microbes prevent harmful microbes, normal flora may include pathogens in carriers
- defense includes mucus and antibodies (lysozyme)
lysozyme
enzyme that helps with immune system
lower respiratory system
not sterile as previously thought - infection from URT, viral, and secondary bac.
GI tract
- generally anaerobic
- strong pH gradient
- organisms may stay in mucus lining (H. plylori to ulcers)
- higher pH = more bacteria
- diet affects composition
- disruption of community balance can lead to water uptake issues (diarrhea)
- aerobes may cause disease if introduced to other areas (UTI)
- organisms consume + make nutrients
- bottle fed infants get mixed flora sooner
- organisms are being flushed out of system + replaced by upstream microbes
dysbiosis
out of balance community
- restored by probiotics + fecal transplant
- linked to obesity
exposure/breach in containment
organisms go where they shouldn’t
microbial virulence factors
adherence/invasion, colonization, growth toxins (factors that make microbes more virulent)
host risk factors
age, stress, diet, disease
