Topic 2: Microbial Diversity Flashcards
What are the survival strategies of microbes
- repair mechanisms
- metabolic flexibility
- heat/radioactivity resistance
- sleeping mode: reduces metabolic activity/energy use
define microbial DIVERSITY (3 factors)
relies on
1. species type
2. the number of species
3. the ecological diversity of species
what is species richness
number of variation among species
what do microorganisms comprise of
prokaryotes, viruses, viroids, filamentous fungus, yeast, microalgae, and protozoans
what is virus vs viroids
virus: has nucleic acids, RNA, and protein coat
infects all orgs.
Viroids: low molec RNA, no protein coat
infects only plants
what do soil bacteria play a role in
biogeochemical cycles (pathway of chemical cycling/nutrient cycling)
why is our diversity of soil microbes limited
human inability to study soil microbes
- cannot be cultured in standard lab (only 1% can be cultured and we cant assume it represent entire soil population)
what are thermophiles
thrive in extreme temp
what are psychrophiles
thrive in extreme temp
what are alkaliphiles/acidophiles
thrive in extreme pH ranges
what are barophiles
thrive in extreme pressures
what are halophiles, what is their gram, can they form spores, what type of photosynthesis do they use
thrive in high salinity
many shapes, gm-, non spore forming, obligate aerobes
what are radiophiles
thrive in high radiation
what are the survival mechanisms of thermophiles
- change composition of amino acids/ membranes
- add repair enzymes for heat damage
- development of cell wall coatings
what are biochemical methods that assess microbial functional diversity
- plate counting
- Community Physiological profiling (CLPP)
- Fatty acid methyl ester analysis (FAME)
what is plate counting and whatre the disadvantages
plate counts the number of growing colonies from a culture
disadvantages:
- unculturable microbes arent present
- biased to fats growing microbes/ fungal species
what is CLPP and what are the disadvantages
tells morphology and gm+/gm- of microbe
disadvantages:
- represents only culturable fraction
- biased to fast growing organisms
- sensitive to inoculum density
what is FAME and what are its disadvantage
Morphology or how many cells are inside// also protein functions
Determined based off fatty acid grouping
sensitive to external environment
what is the extramural layer
slime layer (protect from loss of water/nutrients) and capsule (dense) which are external to bacterial cell wall
what are surface appendages
consists of flagella and pilli (project from cell surface)
important for motility/attachment
what is the cell envelope
combination of cell wall, inner cell membrane, (and outer wall only in gm-)
what is cytoplasmic inclusion
includes nucleoid, ribosomes, mesosomes, granules and plasmids of bacteria
why is glycocalyx on surface coating of bacterial cells
plays role in pathogenic resistance/ adhesion factor
what is fimbriae of bacterial cells
hair like structures on bacteria that partake in adhesion to other cells and surfaces
what are endospores
structure that allows bacterium to survive in unfavorable condition by reducing unessential metabolic activity but preserving just enough so the cell can grow and reproduce
what color do endospores stain
green
what does cryptobiotic mean in reference to endospores
endospores exhibit no signs of life
this makes them resistance to unfavorable changes in environment
do all bacteria exhibit endospore ability
no
what triggers spore formation
unfavorable environments that especially have a limitation in carbon supply
when does sporulation occur in the bacterial growth cycle
later log phages/ early stationary phase
what components help in sporulation
complete copy of chromosome, bare min proteins and chromosomes, high conc. of calcium bound to dipicolinic acid
what is the role of dipicolinic acid in sporulation
it binds free water molecules causing spore to be dehydrated
leads to heat resistance in core of macromolecules
is endospore production associated with gm+ or gm- bacteria?
gm+
what is glycocalyx in reference to gm+ and gm- cells
polysaccharide coating outer membrane of gm- cells
(or)
peptidoglycan layer of gm+ cells
what is streptococcus
gm+ bacteria that forms buildup of plaque on teeth
other bacteria adhere to slime layer–> mutants can grow
what is isotonicity
equal conc. of solute in and out of cell
what is hypertonicity
high conc. of solute causing cells to shrink
what is hypotonicity
low conc. of solute causing cells to swell
eukaryotic cell walls are made of
cellulose or chitin–> prevents bursting in hypotonic environment
Archaean cell walls are made of
polysaccharides and proteins (NO PEPTIDOGLYCAN)
-prevents bursting in hypotonic environment
bacterial cell walls are made of
peptidoglycans
prevents bursting in hypotonic environment
what are functions of the cell membrane
- selectively permeable membrane
- place where transport proteins are
- energy generating functions
- synthesis of phospholipids
- synthesis of murein
- secretion of extracytoplasmic proteins
what is murein, what does it do
peptidoglycan-> polymer of monomers that provide rigid support but also provides some permeability to solutes.
what is periplasmic space
space between plasma membrane and cell wall.
whats the difference between gm+ and gm- bacteria
gm+: thick peptidoglycan layer on the outside of bacterial cell wall –> interpeptide links easily degraded by antibiotics
gm-: thin peptidoglycan layer between 2 lipid bilayers, also covered by lipopolysaccharide (with lipid A) layer which makes it impermeable to antibiotics
what are porins
pore in gm- outer membrane
hydrophilic and allow exchange of nutrients/ also involved in pathogenesis
what is the importance of interpeptide bridges
cross links make bacteria structurally strong against things like penicillin/cephalosporins (which degrade structural link)
what are mycoplasmas
they lack cell walls which does not make bacteria gm+ or gm-
what is bacilli
typical rod shaped bacteria
what is vibrio
rod shaped bacteria but curved
what is cocci
spherical shaped bacteria
what is spirilla
spiral shaped bacteria
what are proteobacteria
gm- bacteria that include
photoautotrophs, chemoautotrophs, heterotrophs
what are hydrogenogenic CO oxidizers
bacteria that converts chemicals into H(g)
utilizes energy in the formation of hydrogen
proteobacteria
what are neutrophillic
thrive in neutral pH (6.5-7.5)
proteobacteria
what are mesophiles
grow in tolerant temperatures (not too hot nor cold)
how do prokaryotes divide and why
binary fission due to lack of cytoskeleton
elongate and constrict in middle in favorable conditions
what is the generation time for cell division
20 mins to 6 hours
more or less
what is transformation (summary)
the integration of free naked DNA into prokaryotic chromosomes
process of horizontal gene transfer
what is bacterial conjugation
process by which one bacterium transfers genetic material to another through direct contact from pilus
what is donor bacterium
donates DNA sequence (fertility (f) factor) to recipient
what is transduction
by which a virus transfers genetic material from one bacterium to another
what is archaea cell wall LINKED by
ether linkage
maintains structure stability during extreme environments
makes pseudopeptidoglycan’s
what are obligate anaerobes
bacteria that is killed by environmental conditions with oxygen
what are sulfolobus
What are its properties
acidophiles, aerobic
thrive in high temps and low pH, typically live in sulfur rich environments
what are methanogens
bacteria that form CH4 as a by product and is leading source of methane.
follow anaerobic respiration
explain karyogenic evolution of the nucleus
nucleus evolved in a single lineage in which the cellular genome became enclosed within a membrane
- membrane formation mechanism is unspecified
what is endokaryotic evolution of the nucleus
involved 2+ organisms invoking endosymbiosis or fusion to form nucleus
explain the origin of mitochondria in eukaryotes
an event in which the ancestor of eukaryotes engulfed an alpha-proteobacterium.
the symbiont was then locked by its host and became a mitochondrion
what is fully functional eukaryote
mitochondria with a genome and is responsible for generating energy through respiration
what are mitochondrial relics in eukaryote
partial genome with an unknown function
what are hydrogenosomes in eukaryotes
they have no genomes and generate energy by oxidation of a pyruvate
what are eukaryotes with complete loss of mitochondria
have no mitochondria and arent functional
what are the purpose of plastids
responsible for photosynthesis, storage of starch and synthesis of pigment
what is the origin of plastids
event in which ancestor of Archaeplastida engulfed cyanobacterium, symbiont was trapped by its host and became a plastid
what is primary and secondary symbiosis of plastids (chloroplast)
primary:
- green algae and red algae containing chloroplast evolve from engulfed cyanobacteria
secondary:
- green algae and red algae diverge and evolve independently
what are protists
single celled colonial eukaryotes other than fungi
what are protozoa
protists that are single celled heterotrophs
what are purposes of fungi
- recycle biomass of wood/leaves that organisms cant digest
- produce antibiotics and food products
what is mycorrhizae
fungal filaments the extend to roots of most plants
can be parasitic and pathogenic
what is absorptive nutrition (traits of fungi)
secrete enzymes and absorb broken down nutrients
what is hyphae (traits of fungi)
cell filaments that extend and to form branches and generate a mycelium (helps absorb organic matter)
what are fungal walls made of
glucans, chitin, and glycoproteins
what is sacchromyces cerevisae
single celled fungi (yeast)
makes up bakers yeast
what is candida albicans
single celled fungi (yeast)
pathogenic
how to fungus reproduce
through spores
- can be sexual (meiotic) or asexual (mitotic(
- can occur directly on fruiting bodies, hyphae, or sporangia
what is Zygomycota
nonmotile spores
- grow in tropical/subtropical regions
-essential for carbon cycle as it decomposes soil, dung, and food types
- produces ethyl alcohol
- black bread mold
what are basidiomycotan
typical mushrooms
- produce amanita phalloides that’s poisonous
- piptoporus:grow on trees
- starkish stinkhorn: attract insects
what is Chlorophyta
green algae from chloroplast and grow in upper layer of water
- unicellular w/ flagella: Chlamydomonas (model for algae research)
-multicellular: volvox
what is rhodophyta
red algae
phycoerythrin obscures chlorophyll making it red
- colonizes deep waters die to blue green light absorption
what are heterokont (diatoms)
unicellular algae
found in aquatic habitats
have shell called frustule
what is a virus
infection agent made of nucleic coat wrapped in protein coat called capsid
(bacteriophage)
do viruses belong to any kingdon, why
no they do not,
they have no organelles, cytoplasm, or cell membrane (non-cellular)
what is the virus-first/early hypothesis
hypothesis that states that viruses predated cells, contributing to the rise of cellular life
what is the regressive/reduction hypothesis
states that viruses are remnants of cellular organisms
what is the escape hypothesis
states that viruses were once part of genetic material, but escaped and evolved by pickpocketing genes using horizontal gene transfer (HGT)
what is envelope in reference to viruses
flexible, membranous layer (lipids/capbs)
- used to identify viruses
- may have enzymatic activity
- may play a role in nucleic acid replication
how do viruses recognize cells
viruses have a surface marker that match receptor site of cell,
causes specific attack processes
what is helical symmetry in viruses
nucleic acid envelope by a hollow protein cylinder with helical shape
what is isohedral symmetry of viruses
sort of spherical/rigid shape that gives protection to genome
what is the virus replication cycle
- attachment to host cell
- penetration for viral entry
- synthesis (nucleic acid/protein copies) made by cells machinery
- assembly of viral components
- release through lysis of cell
what is the main difference between lysogenic and lytic infection
lysogenic-> has temperate stage/ phage dna is integrated in bacterial dna
lytic-> includes lysis of the cell/ no temperate stage
what environment do phages best live in OUTSIDE the host cell
conditions with moisture and appropriate temp,
live longer on water resistant surfaces
how long can cold virus last outside the cell
several days, but ability to infect declines with time
how long can flu virus survive out the cell
several hours at low temp, can remain infectious for 24 hours
how long can enteric viruses survive out the cell
name 2 enteric viruses we learnt
several weeks if conditions are suitable
enteric viruses include norovirus and hep A
what is tobacco mosaic virus (TMV)
virus that infects plants –> mottled browning of tobacco leaves, and tomatoes
what is avian/bird flu
influenza spread amongst birds, can infect humans (rare)
how big is a virus (range)
seen under electron microscope–> range from 20-300 nanometers
what acellular agents do viruses have
proteins and nucleic acid
what acellular agents do viroids have
only RNA–> do not have protein coat and can only infect plants
what acellular agents do satellites have
only nucleic acids, relies on helper virus for propogation
1 gram of soil contains sufficient
DNA content
what are phytoplankton
algae fused with photosynthetic bacteria–> involved as a biological pump
