Domain: highest level of classification of all life
3 domains of life: Eucarya, Bacteria, Archaea
Members of each domain share certain key features with each other that members of the
other domains do not have. Members of two domains may also share features which are
not present in the third domain. Some features of organisms are easy to determine
whereas others are much more difficult to ascertain. One way to accurately classify
organisms is based on their 16S ribosomal RNA(rRNA). 16S rRNA is part of the proteinmaking machinery of all cells. It changes very slowly over time (evolves slowly) because
a large change is likely to cause the death of the organism whereas accumulated small
changes will allow the organism to live and reproduce. We can compare the 16S rRNAs
of organisms to infer evolutionary relationships between them. The more similar two
organisms’ rRNAs are to each other, the more closely related we believe those organisms
to be. Based on 16S rRNA information, we can form an evolutionary Tree of Life in
which the distances of the lines separating organisms from one another represent their
evolutionary distance from one another.
Eucarya are single or multi-celled organisms with a nuclear membrane (membrane
around their DNA). Some examples of Eucaryotes are: Animals, plants, yeast, and
protozoans.
Archaea and Bacteria are both single-celled microorganisms with no nuclear membrane
but they are as different from each other as they are from the Eucarya. Although they
have many different morphologies (sizes, shapes, colors, etc.) and physiologies
(mechanisms for using food and getting energy), they are often difficult to distinguish
and classify into Domains let alone into individual species. Some examples of Bacteria
are:
E.coli, Aquifex, Chloroflexus, Chromatium, Thermothrix, Thermoterrabacterium
Some examples of Archaea are:
Sulfolobus, Methanococcus
Anaerobe
Microorganisms that live in the absence of oxygen, and may even be killed by oxygen
(or derivatives thereof)
Aerobe
An aerobe uses oxygen to generate energy (respire).
Can be obligate, facultative, or microaerophilic
Microaerophile= Thermocrinis ruber (at Octopus Spring)
A microaerophile must have oxygen to survive but grows best when the oxygen
concentration is lower than that of the atmosphere.
*Why is presence or absence of oxygen so important?
Chemolithotrophs
Phototroph
Anoxygenic phototroph
Oxygenic phototroph
Nutritional Types
Microbial nutrition involves a source of Carbon and a source of Energy. The carbon
source provides the building blocks and the energy source drives the reactions within the
cell. The carbon source can be an organic carbon source or carbon dioxide (CO2). The
energy source can derived from light or inorganic or organic sources. An organism using
CO2 as an energy source would also need a source of protons [H] to reduce CO2 to
cellular carbon (CH2O)n. This source of [H] is called the e- donor (or the reductant) as
the e- would carry along a proton. An organism using reduced substrates as an energy
source must have an e- acceptor (an oxidant) to oxidize the cellular carbon (CH2O)n
level.
Photoautotroph (photo [light], auto [self], troph [feeding])
Energy source: light
Carbon source: CO2
e- donor: H2O, H2, or H2S, FeS
Photoheterotroph (photo [light], hetero [different], troph [feeding])
Energy source: light
Carbon source: organic compounds
Chemoautotroph/Chemolithotroph/chemolithoautotroph (chemo [chemical], auto
[self], troph [feeding])
Energy source: inorganic substrates (H2, NH3, NO2-, H2S, Fe2+)
Carbon source: CO2
e- acceptor: O2(aerobes), or S(some anaerobes), Fe 3+, NO3, SO4
Chemoheterotroph (chemo [chemical], hetero [different], troph [feeding])
Energy source: organic compounds
Carbon source: organic compounds
(The carbon and energy sources are often a single compound but may be different)
Chemolithotrophs can be grouped according to the inorganic compounds that they
oxidize for energy:
Nitrifiers-Oxidize reduced Nitrogen compounds such as NH4+
Sulfur Oxidizers- Oxidize reduced Sulfur compounds such as H2S, S0, and S2O(Thermothrix at Mammoth),
Iron Oxidizers- Oxidize reduced Iron-Fe2+ (ferrous iron), Chocolate Pots
Hydrogen Oxidizers-Oxidize Hydrogen gas-H2 (Octopus Spring)
Anoxygenic photosynthesis
Use of light energy to synthesize ATP (energy) without oxygen production
Split H2S instead of H20
Oxygenic photosynthesis
Use of light energy to synthesize ATP (energy) with oxygen production
Splits H20
Thermophile
Hyperthermophile
Mesophile
*Why is temperature important/restricting to life?
Temperature Ranges and Environments for Microbial Life
Hyperthermophile 70-113 C
opt >80 C
hot springs, volcanic areas, deep-sea
hydrothermal vents
Thermophile 45-70 C
hot springs, volcanic areas, compost
heaps, hot water heaters, deep gold
mines, deep subsurface
Mesophile 20-44 C
soil, water, pathogens
Psychrophile 0-20 C
Permafrost
Comparison between Celsius and Farenheit
Celsius
Farenheit
Example
0
32
Freezing Point of Water
4
40
Refrigerator
10
50
Chilly Evening Outdoors
21-25
70-76
Inside Room Temperature
37
98.6
Human Body Temperature
48-71
120-160
Hot Water Heater
71-82
160-180
Hot Coffee
93
200
Boiling point of Water inYellowstone
100
212
Boiling point of Water
Random facts
Purple sulfur bacteria, use sulfide and thiosulfate and deposit sulfur which can be
oxidized to sulfate, some faculative heterotrophs
Some autotrophic in low light, some obligate phototrophs
Green sulfur bacteria
strict anaerobes, and phototrophs, like the above, but sulfur formed OUTSIDE.
(Chlorobium limicola)
Green non-sulfur bacteria
Chloroflexus grows autotrophically with either H2 or H2S as electron donor.
Has a unique pathway called hydroxypropionate pathway
Cyanobacteria
Phototrophs that are like plants, evolve oxygen when photosynthesize
Names of some of Yellowstones microbes
The temperature maxima and pH maxima are approximates. Different species and strains
will have slightly different nutritional and culturing requirements
Thermus aquaticus
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PCR (polymerase chain reaction), Taq polymerase, is the thermal-stable
polymerase (enzyme that copies DNA) that was isolated from the strain of
Thermus aquaticus, orginally isolated by Thomas Brock’s lab from Mushroom
Pool in YNP.
Thermus aquaticus belongs to the domain Bacteria.
Heterotroph
pH 7
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Temp opt. 70°C, max 80/85
Found in hot water heaters, thermal springs throughout the world. Other Thermus
species have been isolated from deep-sea vents.
Cyanidium
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Eukarya (eukaryote), alga- Rhodophyta, photosynthetic
pH 1-4
Tmax 57ϒC, T opt 45
Found parkwide, in most acid streams. Found NZ, Indonesia, Italy, Iceland,
Japan, El Salvador, Dominica, Azores
Great example in Nymph Creek.
Always present with thermophilic fungus, Dactylaria
Chromatium
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Temp 50-60 ϒC
Purple sulfur bacterium, obligate anaerobe, phototroph that only uses one
photosystem (cyanobacteria use 2 photosystems, and are the ancestors of plant
chloroplasts)
Stores sulfur in cells
Phormidium
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pH around 6.5-9
Temperature range 32-59ϒC
Produces conical stromatolites = conophytons
Often with Chloroflexus
Oscillatoria
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Cyanobacterium, gliding bacterium
Found in stream above Chocolate pots
Fixes nitrogen. Does so by making anaerobic environment (a little ball), since the
enzyme responsible for fixing nitrogen (nitrogenase) is VERY sensitive to
oxygen.
Synechococcus
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Unicellular cyanobacterium, sausage-shaped
pH near neutral
T (not higher than 75ϒC) 63-67 opt
Makes mats with Chloroflexus
Brucella
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Causes brucellosis
PCR is now being used to diagnose this disease
Zygogonium
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Eukaryotic alga, chlorophyte, red purple color, long slimy stringy mats
pH 2-3
Toptimum 20-30 ϒC
Norris geyser, amphitheatre springs, Mud volcano area, Shoshone Basin
Stores carbohydrates as starch
In moist acid soils forms mats
In water lives in close association with Euglena and Chlamydomonas
Chloroflexus
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N-fixation, energy from a wide variety of organic sources, green non-sulfur
bacterium, photosynthetic. Also the deepest photosynthetic branch in the
bacterial tree.
T up to 70ϒC
pH optimum7-7.5
Gliding bacterium, filaments
Octopus Spring, Mushroom Spring, Twin Butte Vista,
Steamboat Springs, Nevada; New Zealand, Japan, Mexico
Often in association with Synechococcus
Thermothrix
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Max temp 77-80ϒC, optimum temp about 70 ϒC, pH near neutral
Sulfur/sulfide oxidizing bacterium, obligate chemolithotroph
Uses oxygen (oxic conditions) OR nitrate (anoxic conditions) as electron acceptor
First grown in the lab, and identified as a proteobacterium which was misleading.
Turns out from 16S rRNA analysis (manuscript in prep) that the dominant
organism in these sufur mats is a member of the Aquificales (see below) and a
close relative of the pink filaments from Octopus Springs. The proteobacterium
that was cultured is probably a ‘weed’.
Found at Mammoth hotsprings
Aquificales- Thermocrinis ruber
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Pink filamentous bacteria
pH 7-9
Temperature max 88ϒC, Optimum 80ϒC
Found in the outflow of Octopus Springs
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First escaped cultivation by many scientists including Thomas Brock.
Subsequently with the use of molecular techniques the organism (and its
community) were identified as close relatives of hydrogen oxidizing bacteria, the
deepest branch in the bacterial tree of life, the Aquificales. Using this information
Karl Stetters lab in Germany was able to grow the organism under hydrogen
oxidizing conditions.
Sulfolobus
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Sulfide/pyrite/sulfur oxidizer, produces sulfuric acid, chemolithotroph, some are
heterotrophs
Temp up to 87 ϒC, Optimum 75-85 ϒC
pH 1-5, optimum 2-3
The first thermophilc archaeum to be isolated. It was only recognized as being
significantly different from other bacteria once molecular figure-prints (16S
rRNA) were determined for this novel group, and the Archaea were discovered.
Found first at Moose Pool in Mud Pots area.
Ephydra flies
Sites to visit and some of the common microorganisms
Day 1. Mammoth Hot Springs
Yellowstone microbes as analogues for life on other planets
Biomineralization
Evolution of photosynthesis and oxygen
Thermothrix, Chromatium
Day 2. Lower Geyser Basin (neutral environments)
Anoxygenic and Oxygenic photosynthesis
Stromatolites
Biotechnological applications of thermophiles (PCR)
Chloroflexus, Synechococcus, Phormidium, Thermocrinis, Thermus, Oscillatoria
Day 3. Obsidian Pool, Mutpots area, and Yellowstone Lake ecosystem
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Novel biodiversity and origins of life at high temperatures
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Acidic environments, and the Yellowstone Lake Ecosystem
Sulfolobus, Cyanidium, Zygogonium, Korarchaeota