Microbial Trees of Life Flashcards
(238 cards)
1
Q
What is the approximate age of the earth
A
4.5 billion years old
2
Q
When is the term microscopic used
A
When something is smaller than 1mm in size
3
Q
Define microbes
A
All microscopic cellular organisms together with viruses
4
Q
How long have microbes been on earth for
A
3.8 billion years
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
6
Q
There are 5x10^30 billion what on Earth
A
Bacteria, archaea and Protists
7
Q
How many bacteria, archaea and Protists exists on earth today
A
5x10^30 billion
8
Q
How many viruses on earth?
A
1031
9
Q
There are 1031 what in earth
A
Viruses
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
11
Q
How did Charles Darwin describe the primordial soup theory
A
Warm little pond
12
Q
In what year did Darwin describe the primordial soup theory as a warm little pond
A
1871
13
Q
Why was the primordial soup theory dismissed
A
Conditions thought to be too hostile
Fluctuating temperatures
Intense UV radiation
Meteor impacts
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
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
16
Q
Where did the first organisms of life evolve from
A
Hydrothermal vents
17
Q
What caused the first cell to be formed
A
Synthesis of phospholipids form the membrane
18
Q
What is LUCA
A
A population of primitive cells, found between early bacteria and early archaea
19
Q
Why did life diverge into two different directions after LUCA
A
Perhaps due to the physiochemical differences in their niche
20
Q
What does LUCA stand for
A
Last universal common ancestor
21
Q
Heterotrophs are
A
Bacteria and archaea
22
Q
Chemoautotrophs are
A
Bacteria and archaea
23
Q
Photoautotrophs are
A
Bacteria and archaea
24
Q
Ciliates are
A
Protists
25
Diatoms are
Protists
26
Picophytoplankton are
Protists
27
Amoebas are
Protists
28
Dinoflagellates are
Protists
29
Flagellates are
Protists
30
Prymnesiophytes are
Protists
31
Domain of Protists
Eukaryotes
32
Domain of fungi
Eukaryotes
33
What is a phylogenetic tree
A branching diagram showing the inferred evolutionary relationships among various biological species or other entities
34
What are phylogenetic trees based on
Similarities and difference in organisms physical or genetic characteristics
35
How many kingdoms did Linnaeus come up with and what were they
2
Vegetabilia
Animalia
36
How many kingdoms did Haeckel come up with and what were they
3
Protista
Plantae
Animalia
37
How many domains did Chatton come up with and what were they
3
Prokaryote
Eukaryote
38
How many kingdoms did Copeland come up with and what were they
4
Monera
Protoctista
Plantae
Animalia
39
How many kingdoms did Whittaker come up with and what were they
5
```
Monera
Protoctista
Fungi
Plantae
Animalia
```
40
How many domains did woese et al come up with and what were they
3
Bacteria
Archaea
Eukaryotes
41
Who was the first to classify organisms
Linnaeus
42
What lead to the formation of the Protista group
Invention of the microscope in the 1800s
43
What did woese et al use to classify organisms
Sequencing and genetics
44
What did everyone before use woese et al use to classify organisms
Visual features
45
What did Carl woese pioneer the use of
rRNA sequencing
46
What rRNA do bacteria and archaea have
16S
47
What rRNA do eukarya have
18S
48
What are evolutionary clocks
The variable regions on rRNA
49
What is the conserved region of rRNA used for?
Target the gene
50
What is the variable region on rRNA used for
To distinguish between groups
51
Planctomycetes are
Bacteria
52
Pirellula are
Bacteria
53
Gemmata are
Bacteria
54
What do planctomycetes have that challenge the tradition concepts of prokaryotes
Complex cellular compartmentalisation
55
How many nucleotides in 16S rRNA
1540
56
How many nucleotides in 18S rRNA
1870
57
What is Magnetoglobus multicellularis
Bacteria
58
What bacteria forms tight clusters of 40 cells
Magnetoglobus multicellularis
59
What are the ancestors of mitochondria
Alphaproteobacteria
60
What are the ancestors of chloroplasts
Cyanobacteria
61
What type of parasites are virsuses
Intracellular
62
What roles do microbes play in the environment
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
63
What caused the Black Death
Yersinia pestis
64
What can Vibrio vulnificus cause
Septicaemia
65
What does Bruxelles cause in marine mammals
Abortion and mortality
66
What causes Aspergillosis in sea fans
Fungus
67
How do you know if bacteria are the same species
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
68
Vibrio coralliilytocus infects what
Corals
69
Classification of Vibrio coralliilyticus
```
Domain - bacteria
Phylum - proteobacteria
Class - gammaproteobacteria
Order - vibrionales
Family- vibrionacae
Genus - Vibrio
```
70
Last common ancestor of mitchondria
Alphaproteobacteria
71
What are the major classes of bacterioplankton
```
Others
SAR11
Roseobacter
SAR116
SAR86
Actinobacteria
Picophytoplankton
SAR202
SAR324
SAR406
```
72
What type of bacteria are roseobacter
Alphaproteobacteria
73
Roseobacter carry out what photosynthesis
```
Anoxygenic photosynthesis
(Grow aerobicslly but do not produce oxygen)
```
74
What clade makes up 30% of 16S rRNA bacteria
Roseobacter
75
What do roseobacter have a close association with
Algae blooms
76
What does candidatus mean
Cannot be cultured in agar jelly
77
Pelagibacter ubique was cultured in what year
2002
78
What was the SAR11 bacteria species in 2002
Pelagibacter ubique
79
What alphaproteobacteria makes up 25% of pelagic microbes
SAR11
80
What is a heterotroph
Organism that ingests/absorbs organic carbon in other to produce energetic and synthesis compounds
81
What do SAR11 ingest and what does this make them
```
Dimethyl sulphide (DOMs)
Heterotrophs
```
82
What bacteria type is synechoccus
Cyanobacteria
83
Where are synechococcus found
Top 20m of nearly all surface waters
84
Prochloroccus is what type of bacterioplankton
Cyanobacteria
85
What wavelengths of light do prochloroccus absorb
Blue
86
What bacteria counts for 15-40% of global carbon fixation and oxygen production
Prochloroccus
87
Trichodesmium is a type of what bacteria
Cyanobacteria
88
What bacteria is the most prominent nitrogen fixer in tropical and subtropical oceans
Trichodesium
89
What bacteria type is crocosphaera
Cyanobacteria
90
Crocosphaera does what with nitrogen
Nitrogen fixation
91
Calothrix is what type of bacteria
Cyanobacteria
92
What do calothrix do with other organisms
Fix nitrogen in a symbiotic partnership
93
What type of bacteria is candidatus atelocyanobacterium thalasso
Cyanobacteria
94
With Cyanobacteria lives in close symbiosis with prymnesiophyte algae
Candidatus atelocyanobacteria thalassa
95
What algae does candidatus atelocyanobacteria thalassa live in close symbiosis with
Prymnesiophyte algae
96
What are sulfur oxidising bacteria
Proteobacteria that grow using reduced sulfur compounds as an energy source
97
Why are sulfur oxidising bacteria free swimming
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
What are phototrophs
Use energy from sunlight to photosynthesise organic compounds for nutrition
99
What do sulfur oxidising bacteria live in association with
Phototrophs
100
What does chemolithotrophic mean
Use inorganic reduced compounds as sources of energy
101
How do chemolitrophs use inorganic reduced compounds
Accomplished through oxidation and ATP synthesis
102
What do some anaerobic sulfur oxidising bacteria use as electron acceptors
Nitrates
103
Where do anaerobic sulfur oxidising bacteria live
Anaerobic sediments beneath anoxic zones
104
What do Rimicaris shrimp graze on
Sulfur oxidising bacteria
105
What are Thioploca
Sulfur oxidising bacteria
106
What do dense blooms of Thioploca do
From giant sheathed filaments to pick up nitrates then glide down into sediments to oxidise sulphides
107
What are thiomargarita
Sulfur oxidising bacteria
108
Where do thiomargarita store nitrates
In the large vacuole
109
Where do thiomargaritas store sulfur
In granules as nutrient reservoirs
110
What are giant riftias
Tube worms
111
What do giant riftia contain
Symbiotic bacteria
112
What are the symbiotic bacteria in giant riftia close to
Show characteristics of Thiobacillus
113
What are yeti crabs covered in
Episymbiotic sulfur oxidising bacteria
114
How do sulfur reducing bacteria gain energy
Oxidise organic compounds or hydrogen while reducing sulfate to hydrogen sulfide
115
What are the electron donors in the process that sulfide reducing bacteria use to obtain energy
Organic compounds or hydrogen
116
What bacteria are sulfide reducing bacteria
Deltaproteobacteria
117
What is desulfovibrio
Deltaproteobacteria
| Sulfide reducing bacteria
118
What are desulfobacter
Deltaproteobacteria
| Sulfide reducing bacteria
119
Why does the break down of organic compounds into sediments by sulfur reducing bacteria form blackening
Due to the formation of iron sulphide
120
What do sulfur reducing bacteria corrode
Tanks and pipes
121
What type of bacteria are vibrionaceae
Gammaproteobacteria
122
What shape are vibrios
Curved rods with flagella
123
Major genres of the vibrionacaea are
Vibrio
Photobacteroium
Aliivibrio
124
Where are vibrios found
On the surfaces of marine animals, algae and suspended organic matter
125
What bacteria are important in the colonisation of surfaces and biofilms
The vibrios
126
What two pathogen vibrio bacteria infect fish
Vibrio anguillarum
| Vibrio salmonicida
127
What do Vibrio anguillarum infect
Fish
128
What do Vibrio salmonicida infect
Fish
129
What Vibrio pathogens infect crustaceans
Vibrio harveyi
| Vibrio penaeicida
130
what do Vibrio harveyi infect
Crustaceans
131
What do Vibrio penaeicida infect
Crustaceans
132
Two bacteria that infect molluscs
Vibrio tubiashii
| Vibrio spendidus
133
3 Vibrio bacteria that infect humans
Vibrio cholerae
Vibrio parahaemolyticus
Vibrio vulnificus
134
How many cases of cholera were reported in 2014
190549
135
Why are cholera cases not reported
Countries fear trade and tourism sanctions
136
What does cholera cause
Loss of fluids and salts due to colonisation of small intestine and production of toxins
137
How did cholera spread from India
Intercontinental transport
War
Natural disasters
138
Who proved cholera is passed on via contaminated drinking water
John snow
139
What is a causative agent
Biological pathogen that causes disease
140
Who identified Vibrio cholera as the cause of cholera
Pacini
141
Who showed that Vibrio cholera has a natural reservoir in coastal waters
Rita Colwell
142
Where are Vibrio vulnificus found
Marine water and shellfish (especially oysters)
143
How many deaths per year are caused by Vibrio vulnificus
50-100
144
What do oceanospirillales do
Degrade complex organic compounds
145
What do intercellular symbiotic oceanoaspirillales degrade
Collagen
Cholesterol
Lipids
146
What do osedax worms on whale skeletons contain
Intercellular symbiotic oceanoaspirillales
147
What degrades the oil that was released into the Gulf of Mexico
Bacteria related to the oceanoaspirillales
148
What phyla do epulopiscium belong to
Firmicutes
149
What gram structure is the cell wall of epulopiscium
Gram positive
150
Where are epulopiscium found
Intestinal trace of herbivorous surgeon fish
In GBR and the Red Sea
151
How do surgeon fish acquire epulopiscium symbionts
Spore formation
152
What is viviparity
Development of an embryo inside of the parent
153
what type of bacteria is Bdellovibrio bacterivorans
deltaproteobacteria
154
what do VAMPIROCOCCUS attach to
Chromatium - prey bacteria
155
what do methanogens do
produce methane
156
whats the name of methane production
methanogenesis
157
mesophillic definition
likes warm conditions
158
thermophillic definition
likes hot conditions
159
give three genera of methanogens
methanococcus
methanothermococcus
methanopyrus
160
equation for the production of methane in methanogenesis
CO2 + 4H2 → CH4 + 2H2O
161
what do VAMPIROCOCCUS do to prey
inject enzymes and suck out cellular contents
162
why can the sea temperature increase to 110 degrees celcius at hydrothermal vents
due to the pressure at the bottom of the sea
163
what do Bathymodiolus mussels at
| hydrothermal vents harbour
methane-oxidizing bacteria
| and sulfide-oxidizing bacteria
164
what is the optimum growth temperature of Pyrococcus furiosus
100 degrees celcius
165
what is the maximum growth temperature of Pyrococcus furiosus
106 degrees celcius
166
how are extreme thermophiles adapted to live at high temperatures
adaptations of cell membranes and Tetraether lipids in membrane – limited permeability to protons so proton gradient can be maintained at high temperatures
167
halophillic definitions
likes salt
168
where do halophiles grow
9-35% NaCl
169
why are salt pans pink
due to rhodopsin pigment in halophilic archaeons
170
why are halophiles square
to stop crystals forming and piercing the membrane
171
name the square halophile
Haloquadratum walsbyi
172
what is a Haloquadratum walsbyi
halophile
173
what is a Candidatus “Nanoarchaeum equitans”
hyperthermophile
174
what year was Candidatus “Nanoarchaeum equitans” discovered
2002
175
what are Candidatus “Nanoarchaeum equitans” attached to
the sulfur archaeon Igniococcus (Crenarchaeota)
176
How did waters et al describe Candidatus “Nanoarchaeum equitans”
“a derived but genomically stable parasite that diverged anciently from the archaeal lineage”
177
what are Chytridiomycota
fungi
178
describe chytridiomycota
unicellular body with a cell wall that matures into a sporangium. Within the sporangium, develop uniflagellate zoospores
179
what do the zoospores in chytridiomycota do
swim free to new attachments and develop into new sporangium
180
where do chytridiomycota live
outside growth substrate and produce small
| rhizoids that penetrate
181
what are the two main trophic modes of chytridiomycota
parasites
| saprotroph
182
how do Batrachochytrium dendrobatidis live in frogs
```
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
what do chytridiomycota zoospores contain and what grazes on it
a lipid globule
| grazed on by zooplankton
184
what is a Entomophthoromycota
fungi
185
what is a Entomophthora muscae
fungi
186
what is a Glomeromycota
fungi
187
what is a Gigaspora margarita
fungi
188
what is a Amanita muscaria
Basidiomycota
| dirkarya
189
what is a Aleuria aurantia
Ascomycota
| dirkarya
190
what is a Ascomycota
group of fungi
191
what is a Basidiomycota
group of fungi
192
what are Ascomycota and Basidiomycota
the Dirkarya
193
what are the ecological roles of dirkarya
symbiosis
parasites
pathogens
saprotrophs
194
what is a Lichina pygmaea
lichen microbiomes
195
what are Rhizaria
protists
196
what are alveolates
protists
197
what are stramenopiles
protists
198
what are archaeplastids
protists
199
what are amoebozoa
protists
200
what are opisthokonts
protists
201
what are excavates
protists
202
what are plankton
protists
203
Are diatoms and dinoflagellates protists
yes - theyre types of plankton
204
why do most protists have flagella
for movement and feeding
205
what causes the beating of protist flagella
rapid and repeated bending of the 9 pairs of peripheral and 2 pairs of central tubules
206
why do the flagellates have two flagella
short flagellum - propels things into 'mouth'
| long flagellum - for movement
207
give the genus name of grazing flagellates that are very common in coastal waters.
Bodo
208
what are Bicosecids
flagellates
209
what do Bicosecids eat
bacteria
210
describe the DNA of bicosecids
Highly compact genome with very little non-coding DNA.
211
how do chanoflagellates feed
a single flagellum draws water current through 30-40 tentacle like filaments which trap bacteria in food vacuoles
similar feeding mechanism to sponges
212
how do dinoflagellates move
spinning motion of tale
213
what is found under the cell membrane of dinoflagellates
alveoli
214
what is dinoflagellate armour made of
alveoli containing cellulose
215
types of dinoflagellates
Photosynthetic
heterotrophic
mixotrophic
216
how are unarmoured dinoflagellates eaten
phagocytosis or:
| the prey’s cell membrane is pierced with a peduncle, and the prey cell’s contents are sucked out
217
what can Erythropsidinium cameralike
| eyes see
polarised light to detect prey
218
why cant Heterotrophic thecate dinoflagellates digest large prey directly
they cannot increase in volume
219
how do Heterotrophic thecate dinoflagellates feed on larger prey
extend a pallium which surrounds the large prey. enzymes are then secreted and the prey is digested extracellularly
220
what is a Protoperidinium incognitum
Heterotrophic thecate dinoflagellate
221
what is a Protoperidinium antarcticum
Heterotrophic thecate dinoflagellate
222
what is a Gonyaulax striata
Heterotrophic thecate dinoflagellate
223
what do ciliates eat
smaller flagellates and bacteria
224
what eat ciliates
larger protists and mesozooplankton
225
where are cilliates found
water column sediments and microbial mats
226
what are Acineria incurvata
ciliate
227
what are Gastocirrhus monilifer
ciliate
228
what are Aspidisca leptopsis
ciliates
229
what do tintinnids produce
a ‘house’ (lorica) composed of proteins, polysaccharides and particulate debris
230
what are haptophytes
phytoplankton
231
what are haptophytes covered in
scales or plates
232
what are Stramenopiles
diatoms
233
what are Prymnesiophytes
haptophytes
234
how many species of diatoms are there
over 10000
235
what is a diatom cell enclosed in
a silica cell wall (SiO2)
236
how much of the Total Global
| Primary Production is made by diatoms
20%
237
what is the smallest known eukaryote
Ostreococcus tauri
238
Which group of algae is the endo parasite plasmodium most closely related
Dinoflagellates
