Topic 2: Microbial Diversity Flashcards
1
Q
What are the survival strategies of microbes
A
- repair mechanisms
- metabolic flexibility
- heat/radioactivity resistance
- sleeping mode: reduces metabolic activity/energy use
2
Q
define microbial DIVERSITY (3 factors)
A
relies on
1. species type
2. the number of species
3. the ecological diversity of species
3
Q
what is species richness
A
number of variation among species
4
Q
what do microorganisms comprise of
A
prokaryotes, viruses, viroids, filamentous fungus, yeast, microalgae, and protozoans
5
Q
what is virus vs viroids
A
virus: has nucleic acids, RNA, and protein coat
infects all orgs.
Viroids: low molec RNA, no protein coat
infects only plants
6
Q
what do soil bacteria play a role in
A
biogeochemical cycles (pathway of chemical cycling/nutrient cycling)
7
Q
why is our diversity of soil microbes limited
A
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)
8
Q
what are thermophiles
A
thrive in extreme temp
9
Q
what are psychrophiles
A
thrive in extreme temp
10
Q
what are alkaliphiles/acidophiles
A
thrive in extreme pH ranges
11
Q
what are barophiles
A
thrive in extreme pressures
12
Q
what are halophiles, what is their gram, can they form spores, what type of photosynthesis do they use
A
thrive in high salinity
many shapes, gm-, non spore forming, obligate aerobes
13
Q
what are radiophiles
A
thrive in high radiation
14
Q
what are the survival mechanisms of thermophiles
A
- change composition of amino acids/ membranes
- add repair enzymes for heat damage
- development of cell wall coatings
15
Q
what are biochemical methods that assess microbial functional diversity
A
- plate counting
- Community Physiological profiling (CLPP)
- Fatty acid methyl ester analysis (FAME)
16
Q
what is plate counting and whatre the disadvantages
A
plate counts the number of growing colonies from a culture
disadvantages:
- unculturable microbes arent present
- biased to fats growing microbes/ fungal species
17
Q
what is CLPP and what are the disadvantages
A
tells morphology and gm+/gm- of microbe
disadvantages:
- represents only culturable fraction
- biased to fast growing organisms
- sensitive to inoculum density
18
Q
what is FAME and what are its disadvantage
A
Morphology or how many cells are inside// also protein functions
Determined based off fatty acid grouping
sensitive to external environment
19
Q
what is the extramural layer
A
slime layer (protect from loss of water/nutrients) and capsule (dense) which are external to bacterial cell wall
20
Q
what are surface appendages
A
consists of flagella and pilli (project from cell surface)
important for motility/attachment
21
Q
what is the cell envelope
A
combination of cell wall, inner cell membrane, (and outer wall only in gm-)
22
Q
what is cytoplasmic inclusion
A
includes nucleoid, ribosomes, mesosomes, granules and plasmids of bacteria
23
Q
why is glycocalyx on surface coating of bacterial cells
A
plays role in pathogenic resistance/ adhesion factor
24
Q
what is fimbriae of bacterial cells
A
hair like structures on bacteria that partake in adhesion to other cells and surfaces
25
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
26
what color do endospores stain
green
27
what does cryptobiotic mean in reference to endospores
endospores exhibit no signs of life
this makes them resistance to unfavorable changes in environment
28
do all bacteria exhibit endospore ability
no
29
what triggers spore formation
unfavorable environments that especially have a limitation in carbon supply
30
when does sporulation occur in the bacterial growth cycle
later log phages/ early stationary phase
31
what components help in sporulation
complete copy of chromosome, bare min proteins and chromosomes, high conc. of calcium bound to dipicolinic acid
32
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
33
is endospore production associated with gm+ or gm- bacteria?
gm+
34
what is glycocalyx in reference to gm+ and gm- cells
polysaccharide coating outer membrane of gm- cells
(or)
peptidoglycan layer of gm+ cells
35
what is streptococcus
gm+ bacteria that forms buildup of plaque on teeth
other bacteria adhere to slime layer--> mutants can grow
36
what is isotonicity
equal conc. of solute in and out of cell
37
what is hypertonicity
high conc. of solute causing cells to shrink
38
what is hypotonicity
low conc. of solute causing cells to swell
39
eukaryotic cell walls are made of
cellulose or chitin--> prevents bursting in hypotonic environment
40
Archaean cell walls are made of
polysaccharides and proteins (NO PEPTIDOGLYCAN)
-prevents bursting in hypotonic environment
41
bacterial cell walls are made of
peptidoglycans
prevents bursting in hypotonic environment
42
what are functions of the cell membrane
1. selectively permeable membrane
2. place where transport proteins are
3. energy generating functions
4. synthesis of phospholipids
5. synthesis of murein
6. secretion of extracytoplasmic proteins
43
what is murein, what does it do
peptidoglycan-> polymer of monomers that provide rigid support but also provides some permeability to solutes.
44
what is periplasmic space
space between plasma membrane and cell wall.
45
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
46
what are porins
pore in gm- outer membrane
hydrophilic and allow exchange of nutrients/ also involved in pathogenesis
47
what is the importance of interpeptide bridges
cross links make bacteria structurally strong against things like penicillin/cephalosporins (which degrade structural link)
48
what are mycoplasmas
they lack cell walls which does not make bacteria gm+ or gm-
49
what is bacilli
typical rod shaped bacteria
50
what is vibrio
rod shaped bacteria but curved
51
what is cocci
spherical shaped bacteria
52
what is spirilla
spiral shaped bacteria
53
what are proteobacteria
gm- bacteria that include
photoautotrophs, chemoautotrophs, heterotrophs
54
what are hydrogenogenic CO oxidizers
bacteria that converts chemicals into H(g)
utilizes energy in the formation of hydrogen
proteobacteria
55
what are neutrophillic
thrive in neutral pH (6.5-7.5)
proteobacteria
56
what are mesophiles
grow in tolerant temperatures (not too hot nor cold)
57
how do prokaryotes divide and why
binary fission due to lack of cytoskeleton
elongate and constrict in middle in favorable conditions
58
what is the generation time for cell division
20 mins to 6 hours
more or less
59
what is transformation (summary)
the integration of free naked DNA into prokaryotic chromosomes
process of horizontal gene transfer
60
what is bacterial conjugation
process by which one bacterium transfers genetic material to another through direct contact from pilus
61
what is donor bacterium
donates DNA sequence (fertility (f) factor) to recipient
62
what is transduction
by which a virus transfers genetic material from one bacterium to another
63
what is archaea cell wall LINKED by
ether linkage
maintains structure stability during extreme environments
makes pseudopeptidoglycan's
64
what are obligate anaerobes
bacteria that is killed by environmental conditions with oxygen
65
what are sulfolobus
What are its properties
acidophiles, aerobic
thrive in high temps and low pH, typically live in sulfur rich environments
66
what are methanogens
bacteria that form CH4 as a by product and is leading source of methane.
follow anaerobic respiration
67
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
68
what is endokaryotic evolution of the nucleus
involved 2+ organisms invoking endosymbiosis or fusion to form nucleus
69
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
70
what is fully functional eukaryote
mitochondria with a genome and is responsible for generating energy through respiration
71
what are mitochondrial relics in eukaryote
partial genome with an unknown function
72
what are hydrogenosomes in eukaryotes
they have no genomes and generate energy by oxidation of a pyruvate
73
what are eukaryotes with complete loss of mitochondria
have no mitochondria and arent functional
74
what are the purpose of plastids
responsible for photosynthesis, storage of starch and synthesis of pigment
75
what is the origin of plastids
event in which ancestor of Archaeplastida engulfed cyanobacterium, symbiont was trapped by its host and became a plastid
76
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
77
what are protists
single celled colonial eukaryotes other than fungi
78
what are protozoa
protists that are single celled heterotrophs
79
what are purposes of fungi
1. recycle biomass of wood/leaves that organisms cant digest
2. produce antibiotics and food products
80
what is mycorrhizae
fungal filaments the extend to roots of most plants
can be parasitic and pathogenic
81
what is absorptive nutrition (traits of fungi)
secrete enzymes and absorb broken down nutrients
82
what is hyphae (traits of fungi)
cell filaments that extend and to form branches and generate a mycelium (helps absorb organic matter)
83
what are fungal walls made of
glucans, chitin, and glycoproteins
84
what is sacchromyces cerevisae
single celled fungi (yeast)
makes up bakers yeast
85
what is candida albicans
single celled fungi (yeast)
pathogenic
86
how to fungus reproduce
through spores
- can be sexual (meiotic) or asexual (mitotic(
- can occur directly on fruiting bodies, hyphae, or sporangia
87
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
88
what are basidiomycotan
typical mushrooms
- produce amanita phalloides that's poisonous
- piptoporus:grow on trees
- starkish stinkhorn: attract insects
89
what is Chlorophyta
green algae from chloroplast and grow in upper layer of water
- unicellular w/ flagella: Chlamydomonas (model for algae research)
-multicellular: volvox
90
what is rhodophyta
red algae
phycoerythrin obscures chlorophyll making it red
- colonizes deep waters die to blue green light absorption
91
what are heterokont (diatoms)
unicellular algae
found in aquatic habitats
have shell called frustule
92
what is a virus
infection agent made of nucleic coat wrapped in protein coat called capsid
(bacteriophage)
93
do viruses belong to any kingdon, why
no they do not,
they have no organelles, cytoplasm, or cell membrane (non-cellular)
94
what is the virus-first/early hypothesis
hypothesis that states that viruses predated cells, contributing to the rise of cellular life
95
what is the regressive/reduction hypothesis
states that viruses are remnants of cellular organisms
96
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)
97
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
98
how do viruses recognize cells
viruses have a surface marker that match receptor site of cell,
causes specific attack processes
99
what is helical symmetry in viruses
nucleic acid envelope by a hollow protein cylinder with helical shape
100
what is isohedral symmetry of viruses
sort of spherical/rigid shape that gives protection to genome
101
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
102
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
103
what environment do phages best live in OUTSIDE the host cell
conditions with moisture and appropriate temp,
live longer on water resistant surfaces
104
how long can cold virus last outside the cell
several days, but ability to infect declines with time
105
how long can flu virus survive out the cell
several hours at low temp, can remain infectious for 24 hours
106
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
107
what is tobacco mosaic virus (TMV)
virus that infects plants --> mottled browning of tobacco leaves, and tomatoes
108
what is avian/bird flu
influenza spread amongst birds, can infect humans (rare)
109
how big is a virus (range)
seen under electron microscope--> range from 20-300 nanometers
110
what acellular agents do viruses have
proteins and nucleic acid
111
what acellular agents do viroids have
only RNA--> do not have protein coat and can only infect plants
112
what acellular agents do satellites have
only nucleic acids, relies on helper virus for propogation
113
1 gram of soil contains sufficient
DNA content
114
what are phytoplankton
algae fused with photosynthetic bacteria--> involved as a biological pump
