Microbial Trees of Life Flashcards
What is the approximate age of the earth
4.5 billion years old
When is the term microscopic used
When something is smaller than 1mm in size
Define microbes
All microscopic cellular organisms together with viruses
How long have microbes been on earth for
3.8 billion years
Evidence for the fact that microbes have lived for 3.8 billion years
Microfossils
Stromatolites can be found in rocks 3.5 billion years old and younger
There are 5x10^30 billion what on Earth
Bacteria, archaea and Protists
How many bacteria, archaea and Protists exists on earth today
5x10^30 billion
How many viruses on earth?
1031
There are 1031 what in earth
Viruses
Outline the important components of the primordial soup theory
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
How did Charles Darwin describe the primordial soup theory
Warm little pond
In what year did Darwin describe the primordial soup theory as a warm little pond
1871
Why was the primordial soup theory dismissed
Conditions thought to be too hostile
Fluctuating temperatures
Intense UV radiation
Meteor impacts
Explain the hydrothermal vent theory
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
Why is the hydrothermal vent theory plausible
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
Where did the first organisms of life evolve from
Hydrothermal vents
What caused the first cell to be formed
Synthesis of phospholipids form the membrane
What is LUCA
A population of primitive cells, found between early bacteria and early archaea
Why did life diverge into two different directions after LUCA
Perhaps due to the physiochemical differences in their niche
What does LUCA stand for
Last universal common ancestor
Heterotrophs are
Bacteria and archaea
Chemoautotrophs are
Bacteria and archaea
Photoautotrophs are
Bacteria and archaea
Ciliates are
Protists
Diatoms are
Protists
Picophytoplankton are
Protists
Amoebas are
Protists
Dinoflagellates are
Protists
Flagellates are
Protists
Prymnesiophytes are
Protists
Domain of Protists
Eukaryotes
Domain of fungi
Eukaryotes
What is a phylogenetic tree
A branching diagram showing the inferred evolutionary relationships among various biological species or other entities
What are phylogenetic trees based on
Similarities and difference in organisms physical or genetic characteristics
How many kingdoms did Linnaeus come up with and what were they
2
Vegetabilia
Animalia
How many kingdoms did Haeckel come up with and what were they
3
Protista
Plantae
Animalia
How many domains did Chatton come up with and what were they
3
Prokaryote
Eukaryote
How many kingdoms did Copeland come up with and what were they
4
Monera
Protoctista
Plantae
Animalia
How many kingdoms did Whittaker come up with and what were they
5
Monera Protoctista Fungi Plantae Animalia
How many domains did woese et al come up with and what were they
3
Bacteria
Archaea
Eukaryotes
Who was the first to classify organisms
Linnaeus
What lead to the formation of the Protista group
Invention of the microscope in the 1800s
What did woese et al use to classify organisms
Sequencing and genetics
What did everyone before use woese et al use to classify organisms
Visual features
What did Carl woese pioneer the use of
rRNA sequencing
What rRNA do bacteria and archaea have
16S
What rRNA do eukarya have
18S
What are evolutionary clocks
The variable regions on rRNA
What is the conserved region of rRNA used for?
Target the gene
What is the variable region on rRNA used for
To distinguish between groups
Planctomycetes are
Bacteria
Pirellula are
Bacteria
Gemmata are
Bacteria
What do planctomycetes have that challenge the tradition concepts of prokaryotes
Complex cellular compartmentalisation
How many nucleotides in 16S rRNA
1540
How many nucleotides in 18S rRNA
1870
What is Magnetoglobus multicellularis
Bacteria
What bacteria forms tight clusters of 40 cells
Magnetoglobus multicellularis
What are the ancestors of mitochondria
Alphaproteobacteria
What are the ancestors of chloroplasts
Cyanobacteria
What type of parasites are virsuses
Intracellular
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
What caused the Black Death
Yersinia pestis
What can Vibrio vulnificus cause
Septicaemia
What does Bruxelles cause in marine mammals
Abortion and mortality
What causes Aspergillosis in sea fans
Fungus
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
Vibrio coralliilytocus infects what
Corals
Classification of Vibrio coralliilyticus
Domain - bacteria Phylum - proteobacteria Class - gammaproteobacteria Order - vibrionales Family- vibrionacae Genus - Vibrio
Last common ancestor of mitchondria
Alphaproteobacteria
What are the major classes of bacterioplankton
Others SAR11 Roseobacter SAR116 SAR86 Actinobacteria Picophytoplankton SAR202 SAR324 SAR406
What type of bacteria are roseobacter
Alphaproteobacteria
Roseobacter carry out what photosynthesis
Anoxygenic photosynthesis (Grow aerobicslly but do not produce oxygen)
What clade makes up 30% of 16S rRNA bacteria
Roseobacter
What do roseobacter have a close association with
Algae blooms
What does candidatus mean
Cannot be cultured in agar jelly
Pelagibacter ubique was cultured in what year
2002
What was the SAR11 bacteria species in 2002
Pelagibacter ubique
What alphaproteobacteria makes up 25% of pelagic microbes
SAR11
What is a heterotroph
Organism that ingests/absorbs organic carbon in other to produce energetic and synthesis compounds
What do SAR11 ingest and what does this make them
Dimethyl sulphide (DOMs) Heterotrophs
What bacteria type is synechoccus
Cyanobacteria
Where are synechococcus found
Top 20m of nearly all surface waters
Prochloroccus is what type of bacterioplankton
Cyanobacteria
What wavelengths of light do prochloroccus absorb
Blue
What bacteria counts for 15-40% of global carbon fixation and oxygen production
Prochloroccus
Trichodesmium is a type of what bacteria
Cyanobacteria
What bacteria is the most prominent nitrogen fixer in tropical and subtropical oceans
Trichodesium
What bacteria type is crocosphaera
Cyanobacteria
Crocosphaera does what with nitrogen
Nitrogen fixation
Calothrix is what type of bacteria
Cyanobacteria
What do calothrix do with other organisms
Fix nitrogen in a symbiotic partnership
What type of bacteria is candidatus atelocyanobacterium thalasso
Cyanobacteria
With Cyanobacteria lives in close symbiosis with prymnesiophyte algae
Candidatus atelocyanobacteria thalassa
What algae does candidatus atelocyanobacteria thalassa live in close symbiosis with
Prymnesiophyte algae
What are sulfur oxidising bacteria
Proteobacteria that grow using reduced sulfur compounds as an energy source
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
What are phototrophs
Use energy from sunlight to photosynthesise organic compounds for nutrition
What do sulfur oxidising bacteria live in association with
Phototrophs
What does chemolithotrophic mean
Use inorganic reduced compounds as sources of energy
How do chemolitrophs use inorganic reduced compounds
Accomplished through oxidation and ATP synthesis
What do some anaerobic sulfur oxidising bacteria use as electron acceptors
Nitrates
Where do anaerobic sulfur oxidising bacteria live
Anaerobic sediments beneath anoxic zones
What do Rimicaris shrimp graze on
Sulfur oxidising bacteria
What are Thioploca
Sulfur oxidising bacteria
What do dense blooms of Thioploca do
From giant sheathed filaments to pick up nitrates then glide down into sediments to oxidise sulphides
What are thiomargarita
Sulfur oxidising bacteria
Where do thiomargarita store nitrates
In the large vacuole
Where do thiomargaritas store sulfur
In granules as nutrient reservoirs
What are giant riftias
Tube worms
What do giant riftia contain
Symbiotic bacteria
What are the symbiotic bacteria in giant riftia close to
Show characteristics of Thiobacillus
What are yeti crabs covered in
Episymbiotic sulfur oxidising bacteria
How do sulfur reducing bacteria gain energy
Oxidise organic compounds or hydrogen while reducing sulfate to hydrogen sulfide
What are the electron donors in the process that sulfide reducing bacteria use to obtain energy
Organic compounds or hydrogen
What bacteria are sulfide reducing bacteria
Deltaproteobacteria
What is desulfovibrio
Deltaproteobacteria
Sulfide reducing bacteria
What are desulfobacter
Deltaproteobacteria
Sulfide reducing bacteria
Why does the break down of organic compounds into sediments by sulfur reducing bacteria form blackening
Due to the formation of iron sulphide
What do sulfur reducing bacteria corrode
Tanks and pipes
What type of bacteria are vibrionaceae
Gammaproteobacteria
What shape are vibrios
Curved rods with flagella
Major genres of the vibrionacaea are
Vibrio
Photobacteroium
Aliivibrio
Where are vibrios found
On the surfaces of marine animals, algae and suspended organic matter
What bacteria are important in the colonisation of surfaces and biofilms
The vibrios
What two pathogen vibrio bacteria infect fish
Vibrio anguillarum
Vibrio salmonicida
What do Vibrio anguillarum infect
Fish
What do Vibrio salmonicida infect
Fish
What Vibrio pathogens infect crustaceans
Vibrio harveyi
Vibrio penaeicida
what do Vibrio harveyi infect
Crustaceans
What do Vibrio penaeicida infect
Crustaceans
Two bacteria that infect molluscs
Vibrio tubiashii
Vibrio spendidus
3 Vibrio bacteria that infect humans
Vibrio cholerae
Vibrio parahaemolyticus
Vibrio vulnificus
How many cases of cholera were reported in 2014
190549
Why are cholera cases not reported
Countries fear trade and tourism sanctions
What does cholera cause
Loss of fluids and salts due to colonisation of small intestine and production of toxins
How did cholera spread from India
Intercontinental transport
War
Natural disasters
Who proved cholera is passed on via contaminated drinking water
John snow
What is a causative agent
Biological pathogen that causes disease
Who identified Vibrio cholera as the cause of cholera
Pacini
Who showed that Vibrio cholera has a natural reservoir in coastal waters
Rita Colwell
Where are Vibrio vulnificus found
Marine water and shellfish (especially oysters)
How many deaths per year are caused by Vibrio vulnificus
50-100
What do oceanospirillales do
Degrade complex organic compounds
What do intercellular symbiotic oceanoaspirillales degrade
Collagen
Cholesterol
Lipids
What do osedax worms on whale skeletons contain
Intercellular symbiotic oceanoaspirillales
What degrades the oil that was released into the Gulf of Mexico
Bacteria related to the oceanoaspirillales
What phyla do epulopiscium belong to
Firmicutes
What gram structure is the cell wall of epulopiscium
Gram positive
Where are epulopiscium found
Intestinal trace of herbivorous surgeon fish
In GBR and the Red Sea
How do surgeon fish acquire epulopiscium symbionts
Spore formation
What is viviparity
Development of an embryo inside of the parent
what type of bacteria is Bdellovibrio bacterivorans
deltaproteobacteria
what do VAMPIROCOCCUS attach to
Chromatium - prey bacteria
what do methanogens do
produce methane
whats the name of methane production
methanogenesis
mesophillic definition
likes warm conditions
thermophillic definition
likes hot conditions
give three genera of methanogens
methanococcus
methanothermococcus
methanopyrus
equation for the production of methane in methanogenesis
CO2 + 4H2 → CH4 + 2H2O
what do VAMPIROCOCCUS do to prey
inject enzymes and suck out cellular contents
why can the sea temperature increase to 110 degrees celcius at hydrothermal vents
due to the pressure at the bottom of the sea
what do Bathymodiolus mussels at
hydrothermal vents harbour
methane-oxidizing bacteria
and sulfide-oxidizing bacteria
what is the optimum growth temperature of Pyrococcus furiosus
100 degrees celcius
what is the maximum growth temperature of Pyrococcus furiosus
106 degrees celcius
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
halophillic definitions
likes salt
where do halophiles grow
9-35% NaCl
why are salt pans pink
due to rhodopsin pigment in halophilic archaeons
why are halophiles square
to stop crystals forming and piercing the membrane
name the square halophile
Haloquadratum walsbyi
what is a Haloquadratum walsbyi
halophile
what is a Candidatus “Nanoarchaeum equitans”
hyperthermophile
what year was Candidatus “Nanoarchaeum equitans” discovered
2002
what are Candidatus “Nanoarchaeum equitans” attached to
the sulfur archaeon Igniococcus (Crenarchaeota)
How did waters et al describe Candidatus “Nanoarchaeum equitans”
“a derived but genomically stable parasite that diverged anciently from the archaeal lineage”
what are Chytridiomycota
fungi
describe chytridiomycota
unicellular body with a cell wall that matures into a sporangium. Within the sporangium, develop uniflagellate zoospores
what do the zoospores in chytridiomycota do
swim free to new attachments and develop into new sporangium
where do chytridiomycota live
outside growth substrate and produce small
rhizoids that penetrate
what are the two main trophic modes of chytridiomycota
parasites
saprotroph
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
what do chytridiomycota zoospores contain and what grazes on it
a lipid globule
grazed on by zooplankton
what is a Entomophthoromycota
fungi
what is a Entomophthora muscae
fungi
what is a Glomeromycota
fungi
what is a Gigaspora margarita
fungi
what is a Amanita muscaria
Basidiomycota
dirkarya
what is a Aleuria aurantia
Ascomycota
dirkarya
what is a Ascomycota
group of fungi
what is a Basidiomycota
group of fungi
what are Ascomycota and Basidiomycota
the Dirkarya
what are the ecological roles of dirkarya
symbiosis
parasites
pathogens
saprotrophs
what is a Lichina pygmaea
lichen microbiomes
what are Rhizaria
protists
what are alveolates
protists
what are stramenopiles
protists
what are archaeplastids
protists
what are amoebozoa
protists
what are opisthokonts
protists
what are excavates
protists
what are plankton
protists
Are diatoms and dinoflagellates protists
yes - theyre types of plankton
why do most protists have flagella
for movement and feeding
what causes the beating of protist flagella
rapid and repeated bending of the 9 pairs of peripheral and 2 pairs of central tubules
why do the flagellates have two flagella
short flagellum - propels things into ‘mouth’
long flagellum - for movement
give the genus name of grazing flagellates that are very common in coastal waters.
Bodo
what are Bicosecids
flagellates
what do Bicosecids eat
bacteria
describe the DNA of bicosecids
Highly compact genome with very little non-coding DNA.
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
how do dinoflagellates move
spinning motion of tale
what is found under the cell membrane of dinoflagellates
alveoli
what is dinoflagellate armour made of
alveoli containing cellulose
types of dinoflagellates
Photosynthetic
heterotrophic
mixotrophic
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
what can Erythropsidinium cameralike
eyes see
polarised light to detect prey
why cant Heterotrophic thecate dinoflagellates digest large prey directly
they cannot increase in volume
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
what is a Protoperidinium incognitum
Heterotrophic thecate dinoflagellate
what is a Protoperidinium antarcticum
Heterotrophic thecate dinoflagellate
what is a Gonyaulax striata
Heterotrophic thecate dinoflagellate
what do ciliates eat
smaller flagellates and bacteria
what eat ciliates
larger protists and mesozooplankton
where are cilliates found
water column sediments and microbial mats
what are Acineria incurvata
ciliate
what are Gastocirrhus monilifer
ciliate
what are Aspidisca leptopsis
ciliates
what do tintinnids produce
a ‘house’ (lorica) composed of proteins, polysaccharides and particulate debris
what are haptophytes
phytoplankton
what are haptophytes covered in
scales or plates
what are Stramenopiles
diatoms
what are Prymnesiophytes
haptophytes
how many species of diatoms are there
over 10000
what is a diatom cell enclosed in
a silica cell wall (SiO2)
how much of the Total Global
Primary Production is made by diatoms
20%
what is the smallest known eukaryote
Ostreococcus tauri
Which group of algae is the endo parasite plasmodium most closely related
Dinoflagellates
