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Systematic Biology > Domain Archaea and Eubacteria Lab > Flashcards

Domain Archaea and Eubacteria Lab Flashcards

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1
Q

broadest of all levels of classification

A

domain

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2
Q

example of domain

A

Archaea
Eubacteria
Eukarya

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3
Q

introduced the three domain system of biological classification in 1977

A

Carl Woese et. al

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4
Q

oldest living organisms on Earth

A

Archaea

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5
Q

Resemble bacteria in morphology but have unique cell membrane and cell wall structure

A

Archaea

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6
Q

domain that are obligate anaerobes

A

archaea

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7
Q

cannot survive exposure to oxygen

A

anaerobes

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8
Q

archaea release ___ as a metabolic byproduct

A

methane

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9
Q

➢ No more closely related to bacteria than they are to eukaryotes

A

archaea

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10
Q

Represent a widely diverse group with one thing in common: they all live in extreme environments

A

archaea

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11
Q

example of extreme environments archaea lives in

A

cattle rumens and termite guts
hotsprings
geyers
submarine volcanoes

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12
Q

more complex, more common than archaea

A

eubacteria

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13
Q

Live in neutral conditions and found in human bodies, food, etc.

A

eubacteria

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14
Q

three kingdoms in domain archaea

A

crenarchaeota
euryarchaeota
korarchaeota

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15
Q

has the distinction of including microbial species with highest known growth temperatures of any organisms

A

Kingdom Crenarchaeota

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16
Q

Flourish under conditions which would kill higher organisms (kingdom)

A

Kingdom Crenarchaeota

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17
Q

grow best between 80oC to 100oC and several species will not grow below 80oC

A

Crenarchaeota

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18
Q

several species of the kingdom crenarchaeota also prefer to live under acidic conditions in dilute solutions of

A

hot sulfuric acid

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19
Q

total genera number known in crenarchaeota

A

15 genera

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20
Q

most of this type of archaea have been isolated from marine or terrestrial volcanic environments

A

hyperthermophilic

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21
Q

environment where hyperthermophilic archaea can live

A

hot springs
shallow/deep sea vents

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22
Q

recent analyses of genetic sequences obtained from environmental samples indicate the existence of these but have not yet been cultivated (kingdom)

A

low temp crenarchaeota

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23
Q

More similar to humans than to bacteria

A

crenarchaeota

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24
Q

strict anaerobe, the most extreme example of an archaean isolated from geothermally heated sea floors

A

Pyrodictium

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25
Q

Pyrodictium has a temperature minimum of

A

82 degrees

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26
Q

growth optimum temp of pyrodictium

A

105-110

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27
Q

Pyrodictium is both ____

A

organotrophic and lithotropic

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28
Q

obtains energy by oxidation of organic compounds

A

organotrophic

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29
Q

microorganism that uses inorganic substrates as a source of electron donors to drive energy acquisition

A

lithotropic

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30
Q

most common electron sources for lithotrophs

A

sulfur and H2

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31
Q

three orders in crenarchaeota

A

igneococcales
thermoproteales
sulfolobales

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32
Q

two better studied genera in crenarchaeota

A

➢ Thermoproteus
➢ Sulfolobus

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33
Q

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.

A

sulfolobolus

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34
Q

genus of crenarchaeota that are Classified as thermoacidophiles

A

Sulfolobulus

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35
Q

grow best at acidic pH values and at high temperatures

A

thermoacidophiles

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36
Q

Grow lithotrophically on surface granules in hot acid springs and soils while oxidizing the sulfur to sulfuric acid

A

sulfolobolus

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37
Q

long thin rod that can be bent or branched

A

thermoproteus

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38
Q

Strict anaerobe and grows from temperature 70-90oC and pH values between 2.5 to 6.5

A

thermoproteus

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39
Q

Found in hot springs and other hot aquatic habitats rich in sulfur

A

thermoproteus

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40
Q

very diverse kingdom which is divided into four major groups:

A

kingdom euryarchaeota

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41
Q

four major groups in kingdom euryarchaeota

A

methanogens
halobacteria
thermoplasms
thermococci

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42
Q

cells in this kingdom assume almost any shape and therefore can be:

A

euryarchaeota

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43
Q

shapes in euryarchaeota

A

rods
cocci
irregular cocci
lancet-shaped
spirilloid
discoid
triangular
square

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44
Q

generally characterized as strict anaerobes and methane is the major metabolic product

A

methanogens

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45
Q

largest group of archaeobacteria

A

methanogens

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46
Q

may be reduced to H2S without yielding energy production

A

S^O

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47
Q

At least 3 orders and 25 genera of metanogens which differ greatly (4)

A

overall shape
16S rRNA sequence
Cell wall chemistry and structure
membrane lipids and other features

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48
Q

methanogen cells possess these (3)

A

coenzyme M
factors 420 and 430
methanopterin

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49
Q

methanogens can assume the following shapes (4)

A

long or filamentous
curved
irregular
spirilla

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50
Q

methanogens can be (result in gram staining)

A

positive or negative

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51
Q

methanogens can be autotrophic when they grow on

A

H2 and CO2

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52
Q

representative genera of methanogens (3)

A

Methanococcus
Methanomicrobium
Methanosarcina

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53
Q

methanogens that resembles long rod or filament with pseudomurein cell wall

A

methanobacterium

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54
Q

methanogens that form irregular cocci and its cell wall is made up of heteropolysaccharide or protein

A

methanosarcina

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55
Q

third major group of archaeobacteria currently with nine genera in one family

A

halobacteria

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56
Q

halobacteria are what shaped

A

coccoid

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57
Q

halobacteria gram staining test

A

negative

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58
Q

most halobacteria are these but few are weakly motile

A

non-motile

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59
Q

weakly motile halobacteria

A

lopotrichous flagella

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60
Q

halobacteria reproduce by what

A

binary fission

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61
Q

color of colonies of halobacteria

A

red

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62
Q

some species of halobacteria contain these

A

bacteriorhopdopsin

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63
Q

used in ATP synthesis

A

light

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64
Q

representative genera of halobacteria

A

halobacterium
halococcus
natronobacterium

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65
Q

Primarily aerobic chemoorganotrophs and require high NaCl concentration for growth (>1.5M)

A

halobacteria

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66
Q

most obvious distinguishing trait of halobacteriaceae

A

absolute dependence on NaCl

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67
Q

growth optimum of halobacteria on NaCl

A

3-4M

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68
Q

thermoacidophilic, chemoorganotrophic, and pleomorphic cells lacking a cell wall

A

thermoplasms

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69
Q

Facultatively anaerobic (kingdom euryarchaeota)

A

thermoplasms

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70
Q

an organism that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation

A

facultatively anaerobic

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71
Q

plasma membrane of thermoplasms contain the following:

A

Mannose-rich glycoproteion
Lipoglycan

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72
Q

two genera of thermoplasms

A

thermoplasma
picrophilus

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73
Q

genera of thermoplasms that grows in refuse piles of coal mines

A

thermoplasma

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74
Q

thermoplasma is a ____ at 59 degrees

A

irregular filament

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75
Q

thermoplasma is what shape in lower temperatures

A

spherical

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76
Q

three orders of thermococci (atm)

A

archeoglobales
thermococcales
methanopyrales

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77
Q

Unlike thermoplasma, these have cell walls

A

thermococci

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78
Q

Strictly anaerobic and can reduce sulfur to sulfide

A

thermococci

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79
Q

Order contains one family and two genera

A

thermococcus
pyrococcus

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80
Q

Phylogenetically closer to methanogens than to thermophiles

A

thermoplasma

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81
Q

thermophiles

A

sulfolobus
thermoproteus

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82
Q

has only one family and one genus

A

archaeoglobales

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83
Q

contains gram negative, irregular coccoid cells with walls consisting of glycoprotein subunits

A

archaeoglobales

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84
Q

archeoglobales can reduce sulfate or sulfite, thiosulfate to

A

sulfide

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85
Q

Can be isolated from marine hydrothermal vents

A

archaeoglobales

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86
Q

Possesses the methanogen coenzymes factor 420 (F420) and methanopterin
but not possess coenzyme M or factor 430 (F430)

A

archeoglobales

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87
Q

also has only one family and a single genus (Methanopyrus)

A

methanopyrales

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88
Q

Extremely thermophilic rod-shaped methanogen

A

methanopyrales

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89
Q

occupies the deepest and most ancient branch of Euryarchaeotes

A

methanopyrus

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90
Q

in this kingdom there is very little information as the cells are not cultured

A

kingdom korarchaeota

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91
Q

Fall closely to the root of the three of life

A

kingdom korarchaeota

92
Q

Taxonomy of this is not very definitively worked out yet, especially higher levels of classification

A

domain eubacteria

93
Q

book that will be used in bacterial classification

A

2nd Edition of Bergey’s Manual of Systematic Biology

94
Q

how many phyla of bacteria is there

A

16 phyla

95
Q

16 phyla of bacteria

A

aquificae
xenobacteria
chrysiogenetes
➢ thermomicrobium
➢ cyanobacteria
➢ chlorobia
➢ proteobacteria
➢ firmicutes
➢ planctomyces and allies
➢ spirochetes
➢ fibrocateres
➢ bacteroides
➢ flavobacterium
➢ sphingobacteria
➢ fusobacteria
➢ verrumicrobia

96
Q

small group of thermophilic to hyperthermophilic, chemolithotropic bacteria

A

aquficae

97
Q

Aerobic, gram negative bacterium but can only tolerate low quantities of oxygen

A

aquifex

98
Q

what is aquifex’s energy source

A

H2S or S203^2

99
Q

aside from aquifex, the rest of the phylum of aquificae are ___

A

anaerobic

100
Q

xenobacteria comprises a number of ___

A

aerobic chemoorganotrophic baccteria

101
Q

two best studied genera of xenobacteria

A

thermus
deinococcus

102
Q

genera of xenobacteria that is thermophilic

A

thermus

103
Q

comes from Thermus aquaticus

A

enzyme Taq DNA polymerase

104
Q

Major enzyme used in polymerase chain reaction (PCR) techniques for amplifying DNA

A

enzyme Taq DNA polymerase

105
Q

best known Deinococcus species so named because of its ability to survive high doses of radiation

A

deinococcus radiodurans

106
Q

how much Gy of ionizing radiation can deinococcus radiodurans survive

A

30,000

107
Q

how much Gy can kill a human

A

5> Gy

108
Q

gram-negative bacteria and are “either immotile or possess flagella and are motile)

A

thermus

109
Q

More active at higher temperatures and more thermostable than most other enzymes

A

thermus

110
Q

thermus grow on pH (acidic/basic)

A

basic

111
Q

thermus is/is not capable of fermentation

A

is not

112
Q

substrate thermus use for growth

A

carbodydrates
amino acids
carboxylic acids
peptides

113
Q

thermus nutritional diversity

A
  • use monosaccharides (not pentoses)
114
Q

strain of thermus that use sucrose and maltose

A

icelandic strain

115
Q

used as a terminal electrany strains, some are unable to hydrolyze each substrate

A

nitrate

115
Q

high temp thermus use the following (3)

A

elastin
fibrin
casein

115
Q

metabolic studies have shown that this have a complete tricarboxylic acid cycle, giving glyoxylate bypass as well as isocitrate lyase and malate synthase

A

thermus aquaticus

115
Q

species of bacterium given its own phylum called Chrysiogenetes

A

chrysiogenetes arsenatis

115
Q

Uses chemical means to digest rock for energy and does not require organic matter for its existence

A

chemolitoautotroph

115
Q

chrysiogenetes are chemolithoautotroph by eating what

A

arsenic

116
Q

what is the crysiogenetes electron donor

A

acetate

116
Q

usually toxic to life but they use arsenite, and oxidized form of arsenic as an electron donor to create energy

A

arsenic

117
Q

example of environments that are rich in arsenite

A

Lake Coeur D’ Alene (Idaho)
Gold mine in Australia

118
Q

small phylum of chemotrophic and autotrophic bacteria

A

thermomicrobium

119
Q

best studied genera of thermomicrobium

A

thermomicrobium containing two gram negative chemotrophic series
chloroflexus

120
Q

unique in that its lipids form neither ester linkages like other bacteria, nor either linkages like the Archaea and Eukarya

A

thermomicrobium

121
Q

the lipids in thermomicrobium is made up of this instead of glycerol

A

1,2 dialcohols

122
Q

inhabitant of neutral to alkaline hot springs where it often form thick mats

A

chloroflexus

123
Q

photosynthesis is carried out by this in chloroflexus

A

bacteriochlorophyll

124
Q

can grow in the dark by means of chemo-organotrophic by aerobic respiration

A

chloroflexus spp.

125
Q

Ancient genus with a photosynthetic metabolism that is part way between that of purple bacteria and green sulfur bacteria

A

chloroflexus spp.

126
Q

May be one of the earliest photosynthetic bateria

A

chloroflexus spp.

127
Q

photosynthetic, like plants, which means they use the sun’s energy to make food for themselves

A

cyanobacteria

128
Q

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

A

cyanobacteria

129
Q

Found in the water and were once thought to be blue-green algae (lack a membrane-bound nucleus and chloroplasts)

A

cyanobacteria

130
Q

where does green and blue come from (cyanobacteria)

A

green - chlorophyll
blue - phycocyanin

131
Q

photosynthetic accessory pigment

A

phycocyanin

132
Q

some cyanobacteria have this different accessory pigment other than phycocyanin

A

phycoerythrin

133
Q

pigment in cyanobacteria that gives its red hue

A

phycoerythrin

134
Q

Cyanobacteria formed symbiosis with organisms such as:

A

liverworts
ferns and cycads
fungi

135
Q

First organisms on earth to release oxygen into the atmosphere, playing a major role in making the planet suitable for animals

A

cyanobacteria

136
Q

important genera of cyanobacteria

A

stigonema
nostoc
anabaena
hapalosiphon

137
Q

heterocyst forming photoautotrophic cyanobacteria that perform oxygenic photosynthesis

A

anabaena

138
Q

during times of this, about one cell out of every ten will differentiate into heterocysts

A

low environmental nitrogen

139
Q

a differentiated cyanobacterial cell that carries out nitrogen fixation

A

heterocysts

140
Q

Supply neighboring cells with fixe nitrogen in return for the products of photosynthesis, that they can no longer performed

A

heterocysts

141
Q

Separation of functions is essential because the nitrogen fixing enzyme in heterocysts, _______, is unstable in the presence of oxygen

A

nitrogenase,

142
Q

used to prevent the entrance of oxygen into the cell the developing heterocyst builds this giving it a characteristic enlarged and rounded appearance

A

three additional layers outside the cell wall

143
Q

the first layer in heterocysts where nitrogen is fixed in an oxygen-restricted milieu

A

envelope polysaccharide layer

144
Q

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

A

photosystem II

145
Q

small phylum of 17 species sometimes referred to as Green Sulphur Bacteria

A

chlorobia

146
Q

Most species of chlorobia contain bacteriochlorophyll

A

a
c, d, or e

147
Q

trapped by bacteriochlorophylls c, d, and e is channeled to the bacteriochlorophyll a

A

light energy

148
Q

where photosynthesis take place in chlorobia

A

bacteriochlorophyll a

149
Q

is chlorobium positive/negative in gram

A

negative

150
Q

themorphilic species which forms dense microbial mats in hot springs at a high sulphide content

A

chlorobium tepidum

151
Q

some species in chlorobium have this interesting habit with other large non-phototrophic bacteria

A

consorting

152
Q

Chrolobium spp. – will be in consort with a single non-chlorobium cell in an aggregation called

A

consortia

153
Q

Both the chlorobium and non-chlorobium cells divide at

A

the same time

154
Q

second largest group of bacteria containing 1534 species or 32.3% of all known bacteria

A

proteobacteria

155
Q

Are all gram negative but otherwise represent a diverse range of organisms such as

A

proteobacteria

156
Q

type of proteobacteria

A

purple phototropic
nitrying bacteria
enteric bacteria
bacteria responsible for bioluminescens

157
Q

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

A

enteric bacteria

158
Q

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

A

escherichia

159
Q

May play a nutritional role in the intestinal tract by synthesizing vitamins, particularly vitamin K

A

escherichia

160
Q

Also help consume oxygen thus rendering the large intestine anoxic (condition which the aquatic environment does not contain dissolved oxygen)

A

escherichia

161
Q

condition which the aquatic environment does not contain dissolved oxygen

A

anoxic

162
Q

largest grouping of bacteria though because it is dominated by a number of very successful genera it contains somewhat less diversity than the proteobacteria

A

firmicutes

163
Q

Approximately 2475 in 255 genera, 40% of the species are aggregated in just 6 genera

A

firmicutes

164
Q

6 genera of firmicutes

A

lactobacillus
mycoplasma
bacillus
clostridium
streptomyces

165
Q

All gram-positive bacteria unlike the proteobacteria which are all gram-negative

A

firmicutes

166
Q

(ratio of guanine and cytosine to guanine, cytosine, adenine, thymine times 100

A

GC ratios

167
Q

non-motile, mesophilic, chemoheterotroph producing acid from glucose only aerobically

A

micrococcus

168
Q

typically rod-shaped, varying from long and slender to short, bend rods

A

lactobacillus

169
Q

Can be selectively isolated from natural materials by use of an acidic rich carbohydrate-containing medium (tomato juice peptone agar)

A

lactobacillus

170
Q

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

A

mycoplasma

171
Q

A single culture may exhibit small coccoid elements, larger, swollen forms, and filamentous forms of variable lengths, often highly branch

A

mycoplasma

172
Q

myobacterium growth often occurs in simple mineral salts medium with what as nitrogen salts

A

ammonium

173
Q

chlamydiaceae is the smaller of two families in this phylum, containing only 3 species all in the genus Chlamydia

A

planctomyces and allies

174
Q

All 3 are obligate parasites of warm blooded animals (birds, mammals, including humans); all are pathogenic:

A

planctomyces

175
Q

3 species of planctomyces

A

C. trachomatis
C. pneumonia
C. psittaci

176
Q

causes trachoma; the leading cause of blindness in humans; otitis (non-gonococcal urethritis, urethral inflammation, lymphogranuloma venereum and cervicitis)

A

C. trachomatis

177
Q

causes a variety of respiratory problems similar to pneumonia

A

C. pneumoniae

178
Q

causes epidemic Psittacosis in birds, particularly parrots, as well as pneumonia, arthritis, and conjunctivitis in young mammals (kittens, calves, foals, and piglets)

A

C. psittaci

179
Q

another small but distinct group of bacteria, unique because of the stalk they produce, unlike that in Caulobacter is made of protein

A

planctomycetaceae

180
Q

believed to be used as a means of attachment to substrates

A

planctomycetaceae stalk

181
Q

4 genera of planctomycetaceae

A

Pirellula
Planctomyces
Gemmate
Isophaera

182
Q

gram negative , facultatively anaerobic chemoorganotrophic spherical bacterium

A

planctomyces

183
Q

Phylogenically stalked or appendaged bacterium which lack peptidoglycan in its cell wall

A

planctomyces

184
Q

distinct group of bacteria, gram-negative, chemoheterotrophic, and mesophilic (tightly coiled, long and slender and in shape)

A

spirochetes

185
Q

One or more flagella (up to 100) at each end of their cells which rotated allow them to move

A

spirochetes

186
Q

spirochetes are endosymbionts of this animal

A

spirochetes

187
Q

this genus contains only one species which lives generally within the style of molluscs such as clam and oysters

A

critispira

188
Q

genus of spirochetes to be pathogenic to humans

A

treponema

189
Q

causes syphilis in humans

A

t. pallidum

190
Q

all live in the human mouth where teeth and gums meet (3)

A

t. denticola
t. macrodentium
t. oralis

191
Q

commensals in the rumen of cattle

A

T. saccharophilum

192
Q

two aerobic genera of spirochetes

A

leptospira and leptonema

193
Q

internal parasite of mammals, normally found in rodents but can infect both humans and dogs

A

leptospira interrogans

194
Q

Causes leptospirosis in humans, a disease in the kidneys which can be fatal

A

leptospira interrogans

195
Q

microaerophilic and most pathogenic of the spirochetes and most species in this genus are parasites in animals

A

borrelia

196
Q

causing relapsing fever in humans, commonly transmitted via the body louse

A

borrelia recurrentis

197
Q

causes lyme disease which is transmitted by ticks

A

Borrelia burgdorferi

198
Q

done one of the few exceptions to the rule that ‘bacteria have circular DNA’

A

B. burgforferi

199
Q

DNA is linear, a characteristic normally only seen in Eukaryotes

A

B. burgforferi

200
Q

small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose (cellulolytic) in ruminant animals

A

fibrobacteres

201
Q

fibrobacteres genus, gram negative, chemoheterotrophic, anaerobic, and mesophilic rod-shaped bacterium; non-motile

A

fibrobacter

202
Q

with 130 species in 20 genera, this is the largest phylum of bacteria

A

bacteroides

203
Q

Most common bacteria in the human large intestine where 1010 to 1011 cells can occur per gram of faeces

A

bacteroides

204
Q

contains primarily aquatic species though they are also found in food processing plants

A

flavobacterium

205
Q

believed to be a cause of infant meningitis

A

F. meningosepticum

206
Q

includes the genera cytophaga and sporocytophaga (both have long gliding rods in form)

A

sphingobacteria

207
Q

Widespread soil species with the habit of attaching themselves to cellulose strands before digesting them

A

sphingobacteria

208
Q

Both are strict/obligate aerobes and are ecologically important as cellulose degraders in aerobic environments

A

sphingobacteria

209
Q

gram negative, chemoorganotrophic, and mesophilic; can also be pathogenic in fishes (

A

cytophaga

210
Q

causes columnaris disease

A

c. columnaris

211
Q

causes cold water disease

A

c. psychrophile

212
Q

small phylum of bacteria most all of which occur in the genus fusobacterium

A

fusobacteria

213
Q

secondary colonists on the dental plaque on your teeth

A

fusobacteria

214
Q

formed by species of Streptomyces thus thickening and reinforcing the bacterial attack on your teeth

A

fusobacteria

215
Q

recently described phylum of bacteria, contains only a described species (Verrumicrobium spinosum)

A

verumicrobia

216
Q

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

A

verumicrobia

217
Q

cause of veruccae on the feet and hands

A

verrumicrobium spinosum

218
Q

two sister phyla of verumicrobia

A

chlamydiae
lentisphaerae

219
Q
A

Systematic Biology (18 decks)

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