Domain Archaea and Eubacteria Lab Flashcards
broadest of all levels of classification
domain
example of domain
Archaea
Eubacteria
Eukarya
introduced the three domain system of biological classification in 1977
Carl Woese et. al
oldest living organisms on Earth
Archaea
Resemble bacteria in morphology but have unique cell membrane and cell wall structure
Archaea
domain that are obligate anaerobes
archaea
cannot survive exposure to oxygen
anaerobes
archaea release ___ as a metabolic byproduct
methane
➢ No more closely related to bacteria than they are to eukaryotes
archaea
Represent a widely diverse group with one thing in common: they all live in extreme environments
archaea
example of extreme environments archaea lives in
cattle rumens and termite guts
hotsprings
geyers
submarine volcanoes
more complex, more common than archaea
eubacteria
Live in neutral conditions and found in human bodies, food, etc.
eubacteria
three kingdoms in domain archaea
crenarchaeota
euryarchaeota
korarchaeota
has the distinction of including microbial species with highest known growth temperatures of any organisms
Kingdom Crenarchaeota
Flourish under conditions which would kill higher organisms (kingdom)
Kingdom Crenarchaeota
grow best between 80oC to 100oC and several species will not grow below 80oC
Crenarchaeota
several species of the kingdom crenarchaeota also prefer to live under acidic conditions in dilute solutions of
hot sulfuric acid
total genera number known in crenarchaeota
15 genera
most of this type of archaea have been isolated from marine or terrestrial volcanic environments
hyperthermophilic
environment where hyperthermophilic archaea can live
hot springs
shallow/deep sea vents
recent analyses of genetic sequences obtained from environmental samples indicate the existence of these but have not yet been cultivated (kingdom)
low temp crenarchaeota
More similar to humans than to bacteria
crenarchaeota
strict anaerobe, the most extreme example of an archaean isolated from geothermally heated sea floors
Pyrodictium
Pyrodictium has a temperature minimum of
82 degrees
growth optimum temp of pyrodictium
105-110
Pyrodictium is both ____
organotrophic and lithotropic
obtains energy by oxidation of organic compounds
organotrophic
microorganism that uses inorganic substrates as a source of electron donors to drive energy acquisition
lithotropic
most common electron sources for lithotrophs
sulfur and H2
three orders in crenarchaeota
igneococcales
thermoproteales
sulfolobales
two better studied genera in crenarchaeota
➢ Thermoproteus
➢ Sulfolobus
members of this genus are gram negative, aerobic, irregularly-lobed spherical bacteria with a temperature optimum around 70-80oC and a pH optimum of 2-3.
sulfolobolus
genus of crenarchaeota that are Classified as thermoacidophiles
Sulfolobulus
grow best at acidic pH values and at high temperatures
thermoacidophiles
Grow lithotrophically on surface granules in hot acid springs and soils while oxidizing the sulfur to sulfuric acid
sulfolobolus
long thin rod that can be bent or branched
thermoproteus
Strict anaerobe and grows from temperature 70-90oC and pH values between 2.5 to 6.5
thermoproteus
Found in hot springs and other hot aquatic habitats rich in sulfur
thermoproteus
very diverse kingdom which is divided into four major groups:
kingdom euryarchaeota
four major groups in kingdom euryarchaeota
methanogens
halobacteria
thermoplasms
thermococci
cells in this kingdom assume almost any shape and therefore can be:
euryarchaeota
shapes in euryarchaeota
rods
cocci
irregular cocci
lancet-shaped
spirilloid
discoid
triangular
square
generally characterized as strict anaerobes and methane is the major metabolic product
methanogens
largest group of archaeobacteria
methanogens
may be reduced to H2S without yielding energy production
S^O
At least 3 orders and 25 genera of metanogens which differ greatly (4)
overall shape
16S rRNA sequence
Cell wall chemistry and structure
membrane lipids and other features
methanogen cells possess these (3)
coenzyme M
factors 420 and 430
methanopterin
methanogens can assume the following shapes (4)
long or filamentous
curved
irregular
spirilla
methanogens can be (result in gram staining)
positive or negative
methanogens can be autotrophic when they grow on
H2 and CO2
representative genera of methanogens (3)
Methanococcus
Methanomicrobium
Methanosarcina
methanogens that resembles long rod or filament with pseudomurein cell wall
methanobacterium
methanogens that form irregular cocci and its cell wall is made up of heteropolysaccharide or protein
methanosarcina
third major group of archaeobacteria currently with nine genera in one family
halobacteria
halobacteria are what shaped
coccoid
halobacteria gram staining test
negative
most halobacteria are these but few are weakly motile
non-motile
weakly motile halobacteria
lopotrichous flagella
halobacteria reproduce by what
binary fission
color of colonies of halobacteria
red
some species of halobacteria contain these
bacteriorhopdopsin
used in ATP synthesis
light
representative genera of halobacteria
halobacterium
halococcus
natronobacterium
Primarily aerobic chemoorganotrophs and require high NaCl concentration for growth (>1.5M)
halobacteria
most obvious distinguishing trait of halobacteriaceae
absolute dependence on NaCl
growth optimum of halobacteria on NaCl
3-4M
thermoacidophilic, chemoorganotrophic, and pleomorphic cells lacking a cell wall
thermoplasms
Facultatively anaerobic (kingdom euryarchaeota)
thermoplasms
an organism that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation
facultatively anaerobic
plasma membrane of thermoplasms contain the following:
Mannose-rich glycoproteion
Lipoglycan
two genera of thermoplasms
thermoplasma
picrophilus
genera of thermoplasms that grows in refuse piles of coal mines
thermoplasma
thermoplasma is a ____ at 59 degrees
irregular filament
thermoplasma is what shape in lower temperatures
spherical
three orders of thermococci (atm)
archeoglobales
thermococcales
methanopyrales
Unlike thermoplasma, these have cell walls
thermococci
Strictly anaerobic and can reduce sulfur to sulfide
thermococci
Order contains one family and two genera
thermococcus
pyrococcus
Phylogenetically closer to methanogens than to thermophiles
thermoplasma
thermophiles
sulfolobus
thermoproteus
has only one family and one genus
archaeoglobales
contains gram negative, irregular coccoid cells with walls consisting of glycoprotein subunits
archaeoglobales
archeoglobales can reduce sulfate or sulfite, thiosulfate to
sulfide
Can be isolated from marine hydrothermal vents
archaeoglobales
Possesses the methanogen coenzymes factor 420 (F420) and methanopterin
but not possess coenzyme M or factor 430 (F430)
archeoglobales
also has only one family and a single genus (Methanopyrus)
methanopyrales
Extremely thermophilic rod-shaped methanogen
methanopyrales
occupies the deepest and most ancient branch of Euryarchaeotes
methanopyrus
in this kingdom there is very little information as the cells are not cultured
kingdom korarchaeota
Fall closely to the root of the three of life
kingdom korarchaeota
Taxonomy of this is not very definitively worked out yet, especially higher levels of classification
domain eubacteria
book that will be used in bacterial classification
2nd Edition of Bergey’s Manual of Systematic Biology
how many phyla of bacteria is there
16 phyla
16 phyla of bacteria
aquificae
xenobacteria
chrysiogenetes
➢ thermomicrobium
➢ cyanobacteria
➢ chlorobia
➢ proteobacteria
➢ firmicutes
➢ planctomyces and allies
➢ spirochetes
➢ fibrocateres
➢ bacteroides
➢ flavobacterium
➢ sphingobacteria
➢ fusobacteria
➢ verrumicrobia
small group of thermophilic to hyperthermophilic, chemolithotropic bacteria
aquficae
Aerobic, gram negative bacterium but can only tolerate low quantities of oxygen
aquifex
what is aquifex’s energy source
H2S or S203^2
aside from aquifex, the rest of the phylum of aquificae are ___
anaerobic
xenobacteria comprises a number of ___
aerobic chemoorganotrophic baccteria
two best studied genera of xenobacteria
thermus
deinococcus
genera of xenobacteria that is thermophilic
thermus
comes from Thermus aquaticus
enzyme Taq DNA polymerase
Major enzyme used in polymerase chain reaction (PCR) techniques for amplifying DNA
enzyme Taq DNA polymerase
best known Deinococcus species so named because of its ability to survive high doses of radiation
deinococcus radiodurans
how much Gy of ionizing radiation can deinococcus radiodurans survive
30,000
how much Gy can kill a human
5> Gy
gram-negative bacteria and are “either immotile or possess flagella and are motile)
thermus
More active at higher temperatures and more thermostable than most other enzymes
thermus
thermus grow on pH (acidic/basic)
basic
thermus is/is not capable of fermentation
is not
substrate thermus use for growth
carbodydrates
amino acids
carboxylic acids
peptides
thermus nutritional diversity
- use monosaccharides (not pentoses)
strain of thermus that use sucrose and maltose
icelandic strain
used as a terminal electrany strains, some are unable to hydrolyze each substrate
nitrate
high temp thermus use the following (3)
elastin
fibrin
casein
metabolic studies have shown that this have a complete tricarboxylic acid cycle, giving glyoxylate bypass as well as isocitrate lyase and malate synthase
thermus aquaticus
species of bacterium given its own phylum called Chrysiogenetes
chrysiogenetes arsenatis
Uses chemical means to digest rock for energy and does not require organic matter for its existence
chemolitoautotroph
chrysiogenetes are chemolithoautotroph by eating what
arsenic
what is the crysiogenetes electron donor
acetate
usually toxic to life but they use arsenite, and oxidized form of arsenic as an electron donor to create energy
arsenic
example of environments that are rich in arsenite
Lake Coeur D’ Alene (Idaho)
Gold mine in Australia
small phylum of chemotrophic and autotrophic bacteria
thermomicrobium
best studied genera of thermomicrobium
thermomicrobium containing two gram negative chemotrophic series
chloroflexus
unique in that its lipids form neither ester linkages like other bacteria, nor either linkages like the Archaea and Eukarya
thermomicrobium
the lipids in thermomicrobium is made up of this instead of glycerol
1,2 dialcohols
inhabitant of neutral to alkaline hot springs where it often form thick mats
chloroflexus
photosynthesis is carried out by this in chloroflexus
bacteriochlorophyll
can grow in the dark by means of chemo-organotrophic by aerobic respiration
chloroflexus spp.
Ancient genus with a photosynthetic metabolism that is part way between that of purple bacteria and green sulfur bacteria
chloroflexus spp.
May be one of the earliest photosynthetic bateria
chloroflexus spp.
photosynthetic, like plants, which means they use the sun’s energy to make food for themselves
cyanobacteria
Thought of as second organisms in existence, because they give off oxygen as a byproduct, allowing aerobic organisms (ones that need to survive) to develop
cyanobacteria
Found in the water and were once thought to be blue-green algae (lack a membrane-bound nucleus and chloroplasts)
cyanobacteria
where does green and blue come from (cyanobacteria)
green - chlorophyll
blue - phycocyanin
photosynthetic accessory pigment
phycocyanin
some cyanobacteria have this different accessory pigment other than phycocyanin
phycoerythrin
pigment in cyanobacteria that gives its red hue
phycoerythrin
Cyanobacteria formed symbiosis with organisms such as:
liverworts
ferns and cycads
fungi
First organisms on earth to release oxygen into the atmosphere, playing a major role in making the planet suitable for animals
cyanobacteria
important genera of cyanobacteria
stigonema
nostoc
anabaena
hapalosiphon
heterocyst forming photoautotrophic cyanobacteria that perform oxygenic photosynthesis
anabaena
during times of this, about one cell out of every ten will differentiate into heterocysts
low environmental nitrogen
a differentiated cyanobacterial cell that carries out nitrogen fixation
heterocysts
Supply neighboring cells with fixe nitrogen in return for the products of photosynthesis, that they can no longer performed
heterocysts
Separation of functions is essential because the nitrogen fixing enzyme in heterocysts, _______, is unstable in the presence of oxygen
nitrogenase,
used to prevent the entrance of oxygen into the cell the developing heterocyst builds this giving it a characteristic enlarged and rounded appearance
three additional layers outside the cell wall
the first layer in heterocysts where nitrogen is fixed in an oxygen-restricted milieu
envelope polysaccharide layer
to lower the amount of oxygen within the cell, the presence of this is eliminated while the rate of respiration is stepped up to use excess oxygen
photosystem II
small phylum of 17 species sometimes referred to as Green Sulphur Bacteria
chlorobia
Most species of chlorobia contain bacteriochlorophyll
a
c, d, or e
trapped by bacteriochlorophylls c, d, and e is channeled to the bacteriochlorophyll a
light energy
where photosynthesis take place in chlorobia
bacteriochlorophyll a
is chlorobium positive/negative in gram
negative
themorphilic species which forms dense microbial mats in hot springs at a high sulphide content
chlorobium tepidum
some species in chlorobium have this interesting habit with other large non-phototrophic bacteria
consorting
Chrolobium spp. – will be in consort with a single non-chlorobium cell in an aggregation called
consortia
Both the chlorobium and non-chlorobium cells divide at
the same time
second largest group of bacteria containing 1534 species or 32.3% of all known bacteria
proteobacteria
Are all gram negative but otherwise represent a diverse range of organisms such as
proteobacteria
type of proteobacteria
purple phototropic
nitrying bacteria
enteric bacteria
bacteria responsible for bioluminescens
characterized phenotypically as follows:
➢ Gram negative
➢ Nonsporulating rods
➢ Non-motile or motile by peritrichous flagellea
➢ Facultative anaerobes
➢ Oxidase negative with relatively simple nutritional requirements, fermenting sugars to a variety of end sugars
enteric bacteria
almost universal inhabitants of the intestinal tract of humans and warm-blooded animals, although they are by no means the dominant organisms in these habitats
escherichia
May play a nutritional role in the intestinal tract by synthesizing vitamins, particularly vitamin K
escherichia
Also help consume oxygen thus rendering the large intestine anoxic (condition which the aquatic environment does not contain dissolved oxygen)
escherichia
condition which the aquatic environment does not contain dissolved oxygen
anoxic
largest grouping of bacteria though because it is dominated by a number of very successful genera it contains somewhat less diversity than the proteobacteria
firmicutes
Approximately 2475 in 255 genera, 40% of the species are aggregated in just 6 genera
firmicutes
6 genera of firmicutes
lactobacillus
mycoplasma
bacillus
clostridium
streptomyces
All gram-positive bacteria unlike the proteobacteria which are all gram-negative
firmicutes
(ratio of guanine and cytosine to guanine, cytosine, adenine, thymine times 100
GC ratios
non-motile, mesophilic, chemoheterotroph producing acid from glucose only aerobically
micrococcus
typically rod-shaped, varying from long and slender to short, bend rods
lactobacillus
Can be selectively isolated from natural materials by use of an acidic rich carbohydrate-containing medium (tomato juice peptone agar)
lactobacillus
organism without cell wall, although not staining gram positively since they lack cell walls, they are clearly phylogenetically related to low GC, gram positive bacteria
mycoplasma
A single culture may exhibit small coccoid elements, larger, swollen forms, and filamentous forms of variable lengths, often highly branch
mycoplasma
myobacterium growth often occurs in simple mineral salts medium with what as nitrogen salts
ammonium
chlamydiaceae is the smaller of two families in this phylum, containing only 3 species all in the genus Chlamydia
planctomyces and allies
All 3 are obligate parasites of warm blooded animals (birds, mammals, including humans); all are pathogenic:
planctomyces
3 species of planctomyces
C. trachomatis
C. pneumonia
C. psittaci
causes trachoma; the leading cause of blindness in humans; otitis (non-gonococcal urethritis, urethral inflammation, lymphogranuloma venereum and cervicitis)
C. trachomatis
causes a variety of respiratory problems similar to pneumonia
C. pneumoniae
causes epidemic Psittacosis in birds, particularly parrots, as well as pneumonia, arthritis, and conjunctivitis in young mammals (kittens, calves, foals, and piglets)
C. psittaci
another small but distinct group of bacteria, unique because of the stalk they produce, unlike that in Caulobacter is made of protein
planctomycetaceae
believed to be used as a means of attachment to substrates
planctomycetaceae stalk
4 genera of planctomycetaceae
Pirellula
Planctomyces
Gemmate
Isophaera
gram negative , facultatively anaerobic chemoorganotrophic spherical bacterium
planctomyces
Phylogenically stalked or appendaged bacterium which lack peptidoglycan in its cell wall
planctomyces
distinct group of bacteria, gram-negative, chemoheterotrophic, and mesophilic (tightly coiled, long and slender and in shape)
spirochetes
One or more flagella (up to 100) at each end of their cells which rotated allow them to move
spirochetes
spirochetes are endosymbionts of this animal
spirochetes
this genus contains only one species which lives generally within the style of molluscs such as clam and oysters
critispira
genus of spirochetes to be pathogenic to humans
treponema
causes syphilis in humans
t. pallidum
all live in the human mouth where teeth and gums meet (3)
t. denticola
t. macrodentium
t. oralis
commensals in the rumen of cattle
T. saccharophilum
two aerobic genera of spirochetes
leptospira and leptonema
internal parasite of mammals, normally found in rodents but can infect both humans and dogs
leptospira interrogans
Causes leptospirosis in humans, a disease in the kidneys which can be fatal
leptospira interrogans
microaerophilic and most pathogenic of the spirochetes and most species in this genus are parasites in animals
borrelia
causing relapsing fever in humans, commonly transmitted via the body louse
borrelia recurrentis
causes lyme disease which is transmitted by ticks
Borrelia burgdorferi
done one of the few exceptions to the rule that ‘bacteria have circular DNA’
B. burgforferi
DNA is linear, a characteristic normally only seen in Eukaryotes
B. burgforferi
small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose (cellulolytic) in ruminant animals
fibrobacteres
fibrobacteres genus, gram negative, chemoheterotrophic, anaerobic, and mesophilic rod-shaped bacterium; non-motile
fibrobacter
with 130 species in 20 genera, this is the largest phylum of bacteria
bacteroides
Most common bacteria in the human large intestine where 1010 to 1011 cells can occur per gram of faeces
bacteroides
contains primarily aquatic species though they are also found in food processing plants
flavobacterium
believed to be a cause of infant meningitis
F. meningosepticum
includes the genera cytophaga and sporocytophaga (both have long gliding rods in form)
sphingobacteria
Widespread soil species with the habit of attaching themselves to cellulose strands before digesting them
sphingobacteria
Both are strict/obligate aerobes and are ecologically important as cellulose degraders in aerobic environments
sphingobacteria
gram negative, chemoorganotrophic, and mesophilic; can also be pathogenic in fishes (
cytophaga
causes columnaris disease
c. columnaris
causes cold water disease
c. psychrophile
small phylum of bacteria most all of which occur in the genus fusobacterium
fusobacteria
secondary colonists on the dental plaque on your teeth
fusobacteria
formed by species of Streptomyces thus thickening and reinforcing the bacterial attack on your teeth
fusobacteria
recently described phylum of bacteria, contains only a described species (Verrumicrobium spinosum)
verumicrobia
number as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive ectosymbionts of protist and endosymbionts of nematodes residing in their gamets
verumicrobia
cause of veruccae on the feet and hands
verrumicrobium spinosum
two sister phyla of verumicrobia
chlamydiae
lentisphaerae
