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Life on Earth > Microbial Trees of Life > Flashcards

Microbial Trees of Life Flashcards

1
Q

What is the approximate age of the earth

A

4.5 billion years old

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2
Q

When is the term microscopic used

A

When something is smaller than 1mm in size

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3
Q

Define microbes

A

All microscopic cellular organisms together with viruses

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4
Q

How long have microbes been on earth for

A

3.8 billion years

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5
Q

Evidence for the fact that microbes have lived for 3.8 billion years

A

Microfossils

Stromatolites can be found in rocks 3.5 billion years old and younger

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6
Q

There are 5x10^30 billion what on Earth

A

Bacteria, archaea and Protists

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7
Q

How many bacteria, archaea and Protists exists on earth today

A

5x10^30 billion

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8
Q

How many viruses on earth?

A

1031

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9
Q

There are 1031 what in earth

A

Viruses

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10
Q

Outline the important components of the primordial soup theory

A

Simple organic compounds were formed from non living inorganic molecules
They accumulated to form a rich organic ocean
They reacted with each other to form complex molecules like nucleic acids and proteins

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11
Q

How did Charles Darwin describe the primordial soup theory

A

Warm little pond

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12
Q

In what year did Darwin describe the primordial soup theory as a warm little pond

A

1871

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13
Q

Why was the primordial soup theory dismissed

A

Conditions thought to be too hostile

Fluctuating temperatures
Intense UV radiation
Meteor impacts

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14
Q

Explain the hydrothermal vent theory

A

Life arose from hydrogen, carbon dioxide, nitrogen and hydrogen sulphide with energy from geochemical gradients created at a special kind of deep sea hydrothermal gent containing tiny interconnected compartments or pores

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15
Q

Why is the hydrothermal vent theory plausible

A

Vents provided a steady and as infant supply of energy in the form of reduced compounds

Compartments or inorganic vesicles creates in alkaline deep sea vents could have produced chemical gradients very similar to the proton gradients seen in membranes of organisms today. Could have been use as a driving force of ATP synthesis or simpler equivalents

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16
Q

Where did the first organisms of life evolve from

A

Hydrothermal vents

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17
Q

What caused the first cell to be formed

A

Synthesis of phospholipids form the membrane

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18
Q

What is LUCA

A

A population of primitive cells, found between early bacteria and early archaea

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19
Q

Why did life diverge into two different directions after LUCA

A

Perhaps due to the physiochemical differences in their niche

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20
Q

What does LUCA stand for

A

Last universal common ancestor

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21
Q

Heterotrophs are

A

Bacteria and archaea

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22
Q

Chemoautotrophs are

A

Bacteria and archaea

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23
Q

Photoautotrophs are

A

Bacteria and archaea

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24
Q

Ciliates are

A

Protists

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25
Q

Diatoms are

A

Protists

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26
Q

Picophytoplankton are

A

Protists

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27
Q

Amoebas are

A

Protists

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28
Q

Dinoflagellates are

A

Protists

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29
Q

Flagellates are

A

Protists

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30
Q

Prymnesiophytes are

A

Protists

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31
Q

Domain of Protists

A

Eukaryotes

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32
Q

Domain of fungi

A

Eukaryotes

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33
Q

What is a phylogenetic tree

A

A branching diagram showing the inferred evolutionary relationships among various biological species or other entities

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34
Q

What are phylogenetic trees based on

A

Similarities and difference in organisms physical or genetic characteristics

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35
Q

How many kingdoms did Linnaeus come up with and what were they

A

2

Vegetabilia
Animalia

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36
Q

How many kingdoms did Haeckel come up with and what were they

A

3

Protista
Plantae
Animalia

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37
Q

How many domains did Chatton come up with and what were they

A

3

Prokaryote
Eukaryote

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38
Q

How many kingdoms did Copeland come up with and what were they

A

4

Monera
Protoctista
Plantae
Animalia

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39
Q

How many kingdoms did Whittaker come up with and what were they

A

5

Monera
Protoctista
Fungi
Plantae
Animalia
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40
Q

How many domains did woese et al come up with and what were they

A

3

Bacteria
Archaea
Eukaryotes

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41
Q

Who was the first to classify organisms

A

Linnaeus

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42
Q

What lead to the formation of the Protista group

A

Invention of the microscope in the 1800s

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43
Q

What did woese et al use to classify organisms

A

Sequencing and genetics

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44
Q

What did everyone before use woese et al use to classify organisms

A

Visual features

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45
Q

What did Carl woese pioneer the use of

A

rRNA sequencing

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46
Q

What rRNA do bacteria and archaea have

A

16S

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47
Q

What rRNA do eukarya have

A

18S

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48
Q

What are evolutionary clocks

A

The variable regions on rRNA

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49
Q

What is the conserved region of rRNA used for?

A

Target the gene

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50
Q

What is the variable region on rRNA used for

A

To distinguish between groups

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51
Q

Planctomycetes are

A

Bacteria

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52
Q

Pirellula are

A

Bacteria

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53
Q

Gemmata are

A

Bacteria

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54
Q

What do planctomycetes have that challenge the tradition concepts of prokaryotes

A

Complex cellular compartmentalisation

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55
Q

How many nucleotides in 16S rRNA

A

1540

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56
Q

How many nucleotides in 18S rRNA

A

1870

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57
Q

What is Magnetoglobus multicellularis

A

Bacteria

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58
Q

What bacteria forms tight clusters of 40 cells

A

Magnetoglobus multicellularis

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59
Q

What are the ancestors of mitochondria

A

Alphaproteobacteria

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60
Q

What are the ancestors of chloroplasts

A

Cyanobacteria

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61
Q

What type of parasites are virsuses

A

Intracellular

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62
Q

What roles do microbes play in the environment

A

Primary production - photosynthetic and chemosynthetic carbon dioxide fixation
Food source for other predatory microbes (esp protists)
Decomposition and transformation of materials
Changing the redox and physical state of materials
Competition and cooperation between other organisms
Microbial processes change the oxidation state of elements and move them in and out of solution - changes their immediate environment

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63
Q

What caused the Black Death

A

Yersinia pestis

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64
Q

What can Vibrio vulnificus cause

A

Septicaemia

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65
Q

What does Bruxelles cause in marine mammals

A

Abortion and mortality

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66
Q

What causes Aspergillosis in sea fans

A

Fungus

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67
Q

How do you know if bacteria are the same species

A

They have more than 70% DNA-DNA hybridisation
Their 16S rRNA gene sequences are more than 97% similar
Share a high degree of similarity with characteristics that distinguish them from other species

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68
Q

Vibrio coralliilytocus infects what

A

Corals

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69
Q

Classification of Vibrio coralliilyticus

A 
Domain - bacteria
Phylum - proteobacteria
Class - gammaproteobacteria
Order - vibrionales
Family- vibrionacae
Genus - Vibrio
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70
Q

Last common ancestor of mitchondria

A

Alphaproteobacteria

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71
Q

What are the major classes of bacterioplankton

A 
Others
SAR11
Roseobacter
SAR116
SAR86
Actinobacteria
Picophytoplankton
SAR202
SAR324
SAR406
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72
Q

What type of bacteria are roseobacter

A

Alphaproteobacteria

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73
Q

Roseobacter carry out what photosynthesis

A 
Anoxygenic photosynthesis
(Grow aerobicslly but do not produce oxygen)
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74
Q

What clade makes up 30% of 16S rRNA bacteria

A

Roseobacter

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75
Q

What do roseobacter have a close association with

A

Algae blooms

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76
Q

What does candidatus mean

A

Cannot be cultured in agar jelly

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77
Q

Pelagibacter ubique was cultured in what year

A

2002

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78
Q

What was the SAR11 bacteria species in 2002

A

Pelagibacter ubique

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79
Q

What alphaproteobacteria makes up 25% of pelagic microbes

A

SAR11

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80
Q

What is a heterotroph

A

Organism that ingests/absorbs organic carbon in other to produce energetic and synthesis compounds

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81
Q

What do SAR11 ingest and what does this make them

A 
Dimethyl sulphide (DOMs)
Heterotrophs
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82
Q

What bacteria type is synechoccus

A

Cyanobacteria

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83
Q

Where are synechococcus found

A

Top 20m of nearly all surface waters

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84
Q

Prochloroccus is what type of bacterioplankton

A

Cyanobacteria

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85
Q

What wavelengths of light do prochloroccus absorb

A

Blue

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86
Q

What bacteria counts for 15-40% of global carbon fixation and oxygen production

A

Prochloroccus

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87
Q

Trichodesmium is a type of what bacteria

A

Cyanobacteria

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88
Q

What bacteria is the most prominent nitrogen fixer in tropical and subtropical oceans

A

Trichodesium

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89
Q

What bacteria type is crocosphaera

A

Cyanobacteria

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90
Q

Crocosphaera does what with nitrogen

A

Nitrogen fixation

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91
Q

Calothrix is what type of bacteria

A

Cyanobacteria

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92
Q

What do calothrix do with other organisms

A

Fix nitrogen in a symbiotic partnership

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93
Q

What type of bacteria is candidatus atelocyanobacterium thalasso

A

Cyanobacteria

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94
Q

With Cyanobacteria lives in close symbiosis with prymnesiophyte algae

A

Candidatus atelocyanobacteria thalassa

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95
Q

What algae does candidatus atelocyanobacteria thalassa live in close symbiosis with

A

Prymnesiophyte algae

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96
Q

What are sulfur oxidising bacteria

A

Proteobacteria that grow using reduced sulfur compounds as an energy source

97
Q

Why are sulfur oxidising bacteria free swimming

A

They need to find the right balance between oxygen and sulfur so they’re free swimming so they can move to the area with optimal conditions

98
Q

What are phototrophs

A

Use energy from sunlight to photosynthesise organic compounds for nutrition

99
Q

What do sulfur oxidising bacteria live in association with

A

Phototrophs

100
Q

What does chemolithotrophic mean

A

Use inorganic reduced compounds as sources of energy

101
Q

How do chemolitrophs use inorganic reduced compounds

A

Accomplished through oxidation and ATP synthesis

102
Q

What do some anaerobic sulfur oxidising bacteria use as electron acceptors

A

Nitrates

103
Q

Where do anaerobic sulfur oxidising bacteria live

A

Anaerobic sediments beneath anoxic zones

104
Q

What do Rimicaris shrimp graze on

A

Sulfur oxidising bacteria

105
Q

What are Thioploca

A

Sulfur oxidising bacteria

106
Q

What do dense blooms of Thioploca do

A

From giant sheathed filaments to pick up nitrates then glide down into sediments to oxidise sulphides

107
Q

What are thiomargarita

A

Sulfur oxidising bacteria

108
Q

Where do thiomargarita store nitrates

A

In the large vacuole

109
Q

Where do thiomargaritas store sulfur

A

In granules as nutrient reservoirs

110
Q

What are giant riftias

A

Tube worms

111
Q

What do giant riftia contain

A

Symbiotic bacteria

112
Q

What are the symbiotic bacteria in giant riftia close to

A

Show characteristics of Thiobacillus

113
Q

What are yeti crabs covered in

A

Episymbiotic sulfur oxidising bacteria

114
Q

How do sulfur reducing bacteria gain energy

A

Oxidise organic compounds or hydrogen while reducing sulfate to hydrogen sulfide

115
Q

What are the electron donors in the process that sulfide reducing bacteria use to obtain energy

A

Organic compounds or hydrogen

116
Q

What bacteria are sulfide reducing bacteria

A

Deltaproteobacteria

117
Q

What is desulfovibrio

A

Deltaproteobacteria

Sulfide reducing bacteria

118
Q

What are desulfobacter

A

Deltaproteobacteria

Sulfide reducing bacteria

119
Q

Why does the break down of organic compounds into sediments by sulfur reducing bacteria form blackening

A

Due to the formation of iron sulphide

120
Q

What do sulfur reducing bacteria corrode

A

Tanks and pipes

121
Q

What type of bacteria are vibrionaceae

A

Gammaproteobacteria

122
Q

What shape are vibrios

A

Curved rods with flagella

123
Q

Major genres of the vibrionacaea are

A

Vibrio
Photobacteroium
Aliivibrio

124
Q

Where are vibrios found

A

On the surfaces of marine animals, algae and suspended organic matter

125
Q

What bacteria are important in the colonisation of surfaces and biofilms

A

The vibrios

126
Q

What two pathogen vibrio bacteria infect fish

A

Vibrio anguillarum

Vibrio salmonicida

127
Q

What do Vibrio anguillarum infect

A

Fish

128
Q

What do Vibrio salmonicida infect

A

Fish

129
Q

What Vibrio pathogens infect crustaceans

A

Vibrio harveyi

Vibrio penaeicida

130
Q

what do Vibrio harveyi infect

A

Crustaceans

131
Q

What do Vibrio penaeicida infect

A

Crustaceans

132
Q

Two bacteria that infect molluscs

A

Vibrio tubiashii

Vibrio spendidus

133
Q

3 Vibrio bacteria that infect humans

A

Vibrio cholerae
Vibrio parahaemolyticus
Vibrio vulnificus

134
Q

How many cases of cholera were reported in 2014

A

190549

135
Q

Why are cholera cases not reported

A

Countries fear trade and tourism sanctions

136
Q

What does cholera cause

A

Loss of fluids and salts due to colonisation of small intestine and production of toxins

137
Q

How did cholera spread from India

A

Intercontinental transport
War
Natural disasters

138
Q

Who proved cholera is passed on via contaminated drinking water

A

John snow

139
Q

What is a causative agent

A

Biological pathogen that causes disease

140
Q

Who identified Vibrio cholera as the cause of cholera

A

Pacini

141
Q

Who showed that Vibrio cholera has a natural reservoir in coastal waters

A

Rita Colwell

142
Q

Where are Vibrio vulnificus found

A

Marine water and shellfish (especially oysters)

143
Q

How many deaths per year are caused by Vibrio vulnificus

A

50-100

144
Q

What do oceanospirillales do

A

Degrade complex organic compounds

145
Q

What do intercellular symbiotic oceanoaspirillales degrade

A

Collagen
Cholesterol
Lipids

146
Q

What do osedax worms on whale skeletons contain

A

Intercellular symbiotic oceanoaspirillales

147
Q

What degrades the oil that was released into the Gulf of Mexico

A

Bacteria related to the oceanoaspirillales

148
Q

What phyla do epulopiscium belong to

A

Firmicutes

149
Q

What gram structure is the cell wall of epulopiscium

A

Gram positive

150
Q

Where are epulopiscium found

A

Intestinal trace of herbivorous surgeon fish

In GBR and the Red Sea

151
Q

How do surgeon fish acquire epulopiscium symbionts

A

Spore formation

152
Q

What is viviparity

A

Development of an embryo inside of the parent

153
Q

what type of bacteria is Bdellovibrio bacterivorans

A

deltaproteobacteria

154
Q

what do VAMPIROCOCCUS attach to

A

Chromatium - prey bacteria

155
Q

what do methanogens do

A

produce methane

156
Q

whats the name of methane production

A

methanogenesis

157
Q

mesophillic definition

A

likes warm conditions

158
Q

thermophillic definition

A

likes hot conditions

159
Q

give three genera of methanogens

A

methanococcus
methanothermococcus
methanopyrus

160
Q

equation for the production of methane in methanogenesis

A

CO2 + 4H2 → CH4 + 2H2O

161
Q

what do VAMPIROCOCCUS do to prey

A

inject enzymes and suck out cellular contents

162
Q

why can the sea temperature increase to 110 degrees celcius at hydrothermal vents

A

due to the pressure at the bottom of the sea

163
Q

what do Bathymodiolus mussels at

hydrothermal vents harbour

A

methane-oxidizing bacteria

and sulfide-oxidizing bacteria

164
Q

what is the optimum growth temperature of Pyrococcus furiosus

A

100 degrees celcius

165
Q

what is the maximum growth temperature of Pyrococcus furiosus

A

106 degrees celcius

166
Q

how are extreme thermophiles adapted to live at high temperatures

A

adaptations of cell membranes and Tetraether lipids in membrane – limited permeability to protons so proton gradient can be maintained at high temperatures

167
Q

halophillic definitions

A

likes salt

168
Q

where do halophiles grow

A

9-35% NaCl

169
Q

why are salt pans pink

A

due to rhodopsin pigment in halophilic archaeons

170
Q

why are halophiles square

A

to stop crystals forming and piercing the membrane

171
Q

name the square halophile

A

Haloquadratum walsbyi

172
Q

what is a Haloquadratum walsbyi

A

halophile

173
Q

what is a Candidatus “Nanoarchaeum equitans”

A

hyperthermophile

174
Q

what year was Candidatus “Nanoarchaeum equitans” discovered

A

2002

175
Q

what are Candidatus “Nanoarchaeum equitans” attached to

A

the sulfur archaeon Igniococcus (Crenarchaeota)

176
Q

How did waters et al describe Candidatus “Nanoarchaeum equitans”

A

“a derived but genomically stable parasite that diverged anciently from the archaeal lineage”

177
Q

what are Chytridiomycota

A

fungi

178
Q

describe chytridiomycota

A

unicellular body with a cell wall that matures into a sporangium. Within the sporangium, develop uniflagellate zoospores

179
Q

what do the zoospores in chytridiomycota do

A

swim free to new attachments and develop into new sporangium

180
Q

where do chytridiomycota live

A

outside growth substrate and produce small

rhizoids that penetrate

181
Q

what are the two main trophic modes of chytridiomycota

A

parasites

saprotroph

182
Q

how do Batrachochytrium dendrobatidis live in frogs

A 
spore freely swims to frog
spore burrows into skin of frog and develops into thallus
mature fungus develops into sporangium
4-5 days later, spores are released
120 days later frog dies
183
Q

what do chytridiomycota zoospores contain and what grazes on it

A

a lipid globule

grazed on by zooplankton

184
Q

what is a Entomophthoromycota

A

fungi

185
Q

what is a Entomophthora muscae

A

fungi

186
Q

what is a Glomeromycota

A

fungi

187
Q

what is a Gigaspora margarita

A

fungi

188
Q

what is a Amanita muscaria

A

Basidiomycota

dirkarya

189
Q

what is a Aleuria aurantia

A

Ascomycota

dirkarya

190
Q

what is a Ascomycota

A

group of fungi

191
Q

what is a Basidiomycota

A

group of fungi

192
Q

what are Ascomycota and Basidiomycota

A

the Dirkarya

193
Q

what are the ecological roles of dirkarya

A

symbiosis
parasites
pathogens
saprotrophs

194
Q

what is a Lichina pygmaea

A

lichen microbiomes

195
Q

what are Rhizaria

A

protists

196
Q

what are alveolates

A

protists

197
Q

what are stramenopiles

A

protists

198
Q

what are archaeplastids

A

protists

199
Q

what are amoebozoa

A

protists

200
Q

what are opisthokonts

A

protists

201
Q

what are excavates

A

protists

202
Q

what are plankton

A

protists

203
Q

Are diatoms and dinoflagellates protists

A

yes - theyre types of plankton

204
Q

why do most protists have flagella

A

for movement and feeding

205
Q

what causes the beating of protist flagella

A

rapid and repeated bending of the 9 pairs of peripheral and 2 pairs of central tubules

206
Q

why do the flagellates have two flagella

A

short flagellum - propels things into ‘mouth’

long flagellum - for movement

207
Q

give the genus name of grazing flagellates that are very common in coastal waters.

A

Bodo

208
Q

what are Bicosecids

A

flagellates

209
Q

what do Bicosecids eat

A

bacteria

210
Q

describe the DNA of bicosecids

A

Highly compact genome with very little non-coding DNA.

211
Q

how do chanoflagellates feed

A

a single flagellum draws water current through 30-40 tentacle like filaments which trap bacteria in food vacuoles
similar feeding mechanism to sponges

212
Q

how do dinoflagellates move

A

spinning motion of tale

213
Q

what is found under the cell membrane of dinoflagellates

A

alveoli

214
Q

what is dinoflagellate armour made of

A

alveoli containing cellulose

215
Q

types of dinoflagellates

A

Photosynthetic
heterotrophic
mixotrophic

216
Q

how are unarmoured dinoflagellates eaten

A

phagocytosis or:

the prey’s cell membrane is pierced with a peduncle, and the prey cell’s contents are sucked out

217
Q

what can Erythropsidinium cameralike

eyes see

A

polarised light to detect prey

218
Q

why cant Heterotrophic thecate dinoflagellates digest large prey directly

A

they cannot increase in volume

219
Q

how do Heterotrophic thecate dinoflagellates feed on larger prey

A

extend a pallium which surrounds the large prey. enzymes are then secreted and the prey is digested extracellularly

220
Q

what is a Protoperidinium incognitum

A

Heterotrophic thecate dinoflagellate

221
Q

what is a Protoperidinium antarcticum

A

Heterotrophic thecate dinoflagellate

222
Q

what is a Gonyaulax striata

A

Heterotrophic thecate dinoflagellate

223
Q

what do ciliates eat

A

smaller flagellates and bacteria

224
Q

what eat ciliates

A

larger protists and mesozooplankton

225
Q

where are cilliates found

A

water column sediments and microbial mats

226
Q

what are Acineria incurvata

A

ciliate

227
Q

what are Gastocirrhus monilifer

A

ciliate

228
Q

what are Aspidisca leptopsis

A

ciliates

229
Q

what do tintinnids produce

A

a ‘house’ (lorica) composed of proteins, polysaccharides and particulate debris

230
Q

what are haptophytes

A

phytoplankton

231
Q

what are haptophytes covered in

A

scales or plates

232
Q

what are Stramenopiles

A

diatoms

233
Q

what are Prymnesiophytes

A

haptophytes

234
Q

how many species of diatoms are there

A

over 10000

235
Q

what is a diatom cell enclosed in

A

a silica cell wall (SiO2)

236
Q

how much of the Total Global

Primary Production is made by diatoms

A

20%

237
Q

what is the smallest known eukaryote

A

Ostreococcus tauri

238
Q

Which group of algae is the endo parasite plasmodium most closely related

A

Dinoflagellates

Life on Earth (18 decks)

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