Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
266 Cards in this Set
- Front
- Back
|
Two scientists who worked at UCSD and reinforced the concept of prebiotic soup |
Urey-Miller |
|
|
How old is life? |
3.8 BYA |
|
|
Most scientists think life started out (hot/cold) |
hot ("warm little pond with organics") -microbes at base of tree of life are all thermophiles |
|
|
what is the alternative proposal to the prebiotic soup scienario? |
H2-dependent chemistry oftransition-metal sulfide catalysts in a hydrothermalvent setting - chemical conversions are similar to thoseoperating in microbes that use the Wood-Ljungdahl acetyl-coenzyme A pathway - Thus early life could have been chemoautotrophic |
|
|
igneous rocks formed from _____ |
cooling of lava or magma |
|
|
ultramafic rocks |
low in silica and high in magnesium andiron |
|
|
peridotite minerals |
-rock minerals are olivine andorthopyroxene |
|
|
serpentine |
-peridotite exposed to water gives this and reaction gives off hydrogen - hydroxylatedmagnesium-iron silicate |
|
|
serpentinization |
-the chemical reaction that might have produced the conditions conducive to the development of chemoautotrophic life -requires ultramafic rocks -The important part of this reaction is that ferrousiron oxidation leads to reduction of water and hydrogen formation: 2 (Fe2O)rock + H2O ➢ (Fe32O3)rock + H2 - reaction is exothermic (releasesenergy) - leads to the formation of methane andother hydrocarbons catalyzed by nickel-iron alloys |
|
|
when did serpentinization start occuring? |
The Hadean Eon 4.5 billionyears ago |
|
|
importance of alkaline pH in Hadeon eon |
natural chemiosmoticnature of alkaline hydrothermal vents in theHadean eon (chimney interior pH 9-10),oceans fluids (pH 5-6) provided energythrough an ancient ATPase |
|
|
what are the challenges of living in a serpentinization zone |
- Reduced environment results in few electronacceptors like oxygen, nitrate or sulfate |
|
|
high ph in chimneys could help _____ (serpentinization) |
ATP synthesis |
|
|
how could the formation of membranes happened in the consideration in the origin of life (vents) |
-Russell and Hall suggest that precipitation of iron sulfide, laced withnickel or tungsten, at warm vents formed a semipermeable catalyticboundary - Carboxylic acids at warm 50-200C vents can also form long chain fattyacids - which in turn can form liposomes |
|
|
Lost City |
-located by the mid atlantic ridge -ultramafic rocks -very alkaline -serpentinization -white smokers |
|
|
Two types of hydrothermal vents |
-Black smokers - lots of sulfur minerals that make darkplume. Chimney = calcium sulfate and metalsulfides. -White smokers - barium, calcium and silicon precipatesform white plume. Chimneys = calcium carbonate. Reactions between seawater and upper mantleperidotite produce methane- and hydrogen-rich fluids thatare highly alkaline (pH 9 to 11), with temperatures rangingfrom <40° to 90°C. Creates oxygenated water on surface. -> serpentinization |
|
|
Microbes Associated With the Atlantis Massif Vents |
-Lost City Methanosarcinales Group • Eat Methane • Forms Dense biofilms • Also firmicutes such as Desulfotomaculum |
|
|
Additional Locations for Serpentinization |
-Ophiolites( ultramafic rocks brought uu to surface, remnants of ancient seafloorserpentinization) • Subduction zones and mud volcanoes(associated with hydration of ocean crustduring subduction) • Other planets (Mars has evidence of pastserpentinization) - could drive hydrothermalcirculation. |
|
|
picture of subduction zone where serpentinization occurs |
|
|
|
What is the general accepted definition of life? |
Life is a self-sustained chemical systemcapable of undergoing Darwinianevolution |
|
|
What to look for when looking for life? |
-chemical disequillibrium such as that produced by sunduction and volcanism -water -moderate temperatures |
|
|
Chinese exploration of the moon |
Chang'e 3 Lunar Rover and Satellite |
|
|
Mars in the past |
-evidence of ancient volcanoes (igneous rock from mars) -believed to be a blue planet a long time ago (think there was an ocean and lots of evidence saying that there was once water on Mars) - |
|
|
current conditions on mars |
-Cold (-60oC average) - Dry Very thin atmosphere - No detectable organics -Lethal radiation - Oxidants in the soil -similar mineral composition |
|
|
Methane on Mars |
-in summer, concentrations of methane in atmosphere picks up (geological?biological?) -Curiosity has yet to detect methane |
|
|
Mars' Dark Spots |
-in ice located around South Pole -images similar to those of microbes in Lake Bonney - Colonies of photosynthetic microbesgrowing under the ice until it melts |
|
|
Viking Search for Life Experiments (1976) |
1. Gas Chromatograph- Mass Spectrometer -heat up dirt and find what material was released ( The result wasnegative, due to perchlorate in soil maybe) 2. Gas exchange experiment - looked for gases given off by an incubated soil sample after the addition of nutrients and then water (The result was negative) 3.Labeled release experiment - Soil exposedto sunlight and obtained from under a rockwas incubated with 7 Urey Miller nutrients (The results were initially positive,but subsequent experiments were negative) 4. Pyrolytic release experiment. 14C –labeled CO2 and CO was incubated with soiland the amount of fixed organic carbon wasmeasured. (The result was negative.) |
|
|
radiation resistance types |
-Gamma rays: shortest wavelengths & most energetic - radio waves: longest wavelengths & least energetic |
|
|
what blocks UV radiation |
various gases like ozone. |
|
|
what does UV radiation induce the formation of |
deleterious DNA lesions such as pyrimidine dimers. |
|
|
what are pyrimidines |
thymine or cytosine bases |
|
|
UVB can cause: |
skin cancer, cataracts and depressed immune systems. |
|
|
UV is used extensively to ___ |
sterilize surfaces -UV and the chemical agent peroxide are used in ultraclean rooms to kill microbes on the surfaces of spacecraft -Earth microbes do not contaminate extraterrestrial bodies -the spores of some Bacillus species such as Bacillus pumilus spores survive |
|
|
UCSD Professor and Nobel Prize recipient Mario Molina contributed greatly to |
the understanding of chlorofluorocarbon impacts on zone |
|
|
UV effects on Escherichia coli |
SOS stress response |
|
|
Ionizing radiation |
-form of radiation with sufficient energy to eject one or more orbital electrons from a molecule -can be electromagnetic (photons) or subatomic particles produced by alpha/beta decay, nuclear fission/fusion, solar flares... -comes from gamma-rays produced during radioactive decay |
|
|
Compton Process |
ionizing radiations ejects electrons (fast electrons) by a mechanism known as the Compton Process. |
|
|
Naturally occurring ionizing radiation comes from |
cosmic rays and naturally occurring radionuclides |
|
|
anaerobic or aerobic cultures and spores are more resistant to ionizing radiation? |
anaerobic -Anaerobes lack oxygen and hence the production of superoxide anion is reduced (O2-). -adiation resistance of spores is most likely linked to their lack of water and lack of any metabolic activity. - |
|
|
where can you find radiation resistance microbes |
hydrothermal vents, geothermal springs, and soils (especially dry soils). |
|
|
what is the largest target of ionizing radiation in the cell |
the genome |
|
|
how does UV radiation damage DNA? |
dimerization of pyrimidine bases and oxidative damage |
|
|
how does ionizing radiation damage DNA? |
causes oxidative damage in DNA and proteins via the formation of free radicals |
|
|
how can cells cope with ionizing radiation? |
Adaptation to UV and xerophily -helps to be thermophilic and alkalitolerant |
|
|
3 adaptions to be ionizing radiation resistant |
1. very efficient DNA repair processes 2. antioxidant screening pigments such as melanin in fungi and carotenoids in bacteria, 3.via additional antioxidant systems, including those using manganese. Aerobic bacteria that are resistant to ionizing radiation have high levels of manganese (not known why). |
|
|
Common hyper ionizing radiation resistant microbes |
-Deinococcus radiodurans from soil -Rubrobacter radiotolerans from soil -Thermococcus species from hydrothermal vents -The D10 values defines the dose needed to kill 90% of the population. -Resistant groups: Actinobacteria, Deinococcus-Thermus, and Thermococci. (Deinococcus radiodurans and various Rubrobacter species are very resistant to gamma radiation). -High Mn2+/Fe ratios correlate with antioxidant activity and ionizing radiation resistance in aerobic prokaryotes. |
|
|
Reactive oxygen species (H2O2, O2-) are inactivated by certain enzymes and by ____ |
Mn2+orthophosphate/organic metabolite complexes -these inactivating enzymes are dispensable for extreme radiation resistance in D. radiodurans |
|
|
Extreme resistance to ionizing radiation example: |
mesophile Escherichia coli by directed evolution -how: growing up cultures of bacteria at increasing doses of ionizing radiation exposure and selecting for mutations which confer greater fitness under this selection regime. oMutations in recombinational DNA repair, and DNA replication initiation were identified |
|
|
2 Biotechnological applications of Deinococcus radiodurans |
-cleaning up metals in radioactive areas. -Phosphate complexes with metals like uranium and precipitates them from water system |
|
|
Ancient Microbes example |
Example: The Bristlecone Pine tree can live for 5,000 years based on tree ring counts. -Plant seeds can also survive a very long time. Sacred Lotus (1,300 years), Judean Date Palm (2,000 years), and the Narrow-leafed Campion (30,000 years in Siberian permafrost) |
|
|
state of preservation is evaluated by |
examining the ratio of D to L amino acids |
|
|
Every amino acid (except glycine) can occur in two isomeric forms: |
These result from the formation of (stereoisomers) around the central carbon atom. (L- and D- forms) |
|
|
acids in proteins are all in the ____ form (L or D form) |
L |
|
|
what is used to determine quality of DNA |
D/L enantiomers of certain amino acids |
|
|
In the absence of metabolism the amino acids in proteins undergo ____ |
racemization until the ratio of the two enantiomer forms is equal |
|
|
what is the rate at which racemization occurs dependent on |
-availability of water and the temperature. - These factors also influence the depurination of DNA |
|
|
why does DNA damage accrue over time in inactive material |
due to spontaneous hydrolysis and oxidation. |
|
|
Paleomicrobiology: |
isolation or characterization of microbes from ancient materials. |
|
|
controls: |
-Wear gloves, work in filtered air. -Irradiate external surfaces of the ancient materials with UV light to destroy the DNA of any contaminating microbes. - Perform the DNA extraction and amplification in separate rooms. -PCR analyses should target short fragments not previously assayed in lab. - Do not perform (+) controls (they may contaminate your samples) -Confirm (+) results with a second test targeting a different locus |
|
|
Coprolites: |
Fossilized feces to examine the health and diets of ancient human populations |
|
|
Halites |
mineral form of NaCl` |
|
|
One type of environment where microbes may survive for tens of thousands of years: |
halite |
|
|
Many of the microbes cultures from ancient materials form ___ |
spores |
|
|
what bacterial spores were in samples of abdomens of extinct bees preserved in amber? |
Bacterial spores belonging to a Bacillus species |
|
|
Who did the study of the bacterial spores in 25-40 million year old dominican amber and what was in the amber? |
Cano and bees |
|
|
What were Cano's Amber controls |
-a room that had not been used for similar experiment inside a laminar flow hood which excludes room air. - The amber was decontaminated before it was cracked open (tested decontamination). experimental conditions could be considered clean - probed a plain piece of amber to look for DNA |
|
|
what happened with the isolation of a 250 Million-year-old Halotolerant Bacterium from a Salt Crystal? |
- Acid and base washing of crystals used to Isolate and grow a spore-forming Bacillus speciesunder highly stringent conditions. |
|
|
what are the concerns about the Vreeland paper |
-The 16S rRNA gene sequence is too similar to that of a known moderately halophilic species from the Dead Sea. -Differences in the rate of evolution of these too genes is too low to indicate a difference in evolutionary time of 250 Mya. - If surface UV did not damage DNA inside spores, natural radiation would have -It’s argued that radioactive potassium-40 in the surrounding rock was not great enough to rule out a quarter-billion years of bacterial survival. -The brine inclusions in the salt crystals are newer than the surrounding rock. -the crystals that formed around the pockets of fluid in the experiment (and presumably bacteria) were created on or near the surface instead of far underground |
|
|
Challenger expedition recovered ____ bacteria from depths of 5,000meters |
piezotolerant |
|
|
piezotolerant |
high pressure tolerant |
|
|
approximately ___% of the total volume of the biosphere is comprised by waters with depths greater than 1000 m. |
79% |
|
|
physical characteristics of the deep sea: |
low food abundance, high pressures, low temperatures (except around hydrothermal regions), and an absence of light (other than bioluminescence) have favored the selection for organisms with many unique adaptations |
|
|
Pressure increases by 1 atmosphere (atm) for each ____ m increase in depth |
10 |
|
|
deepest regions of the oceans have pressures near _____ atms |
1,100 |
|
|
Obligately piezophilic ("pressure loving") bacteria have been isolated at depths below ____ km. |
5 |
|
|
the high pressure of the deep sea has or has not resulted in the evolution of dramatically different microbes |
has not |
|
|
Pressures higher than 100 atm inhibit ___ |
motility |
|
|
Pressures from 200 -500 atm inhibit __ |
cell division |
|
|
Pressures higher than 500 atm inhibit __ |
DNA replication |
|
|
Pressures higher than 580 atm inhibit __ |
protein synthesis |
|
|
Pressures higher than 7700 atm inhibit __ |
RNA synthesis |
|
|
Pressure changes will affect any biological process that occurs with a change in ____ |
system volume |
|
|
increases/decreases in temperature or increases/decreases in pressure tend to make lipid-based systems like membranes more rigid or viscous (choose incr or decr for both) |
-decreases -increases |
|
|
There is a compression of the lipids, resulting in tighter packing of _____ and encouragement of membrane lipid____. |
-acyl chains - gelation |
|
|
how have many deep-sea organisms, including bacteria, been found to maintain optimal membrane fluidity and function at high pressure? |
-(homeoviscous adaptation) by changing the proportion of unsaturated fatty acids in their phospholipids |
|
|
how do Phospholipid acyl chains having one or more double bonds decrease membrane fluidity |
they are kinked in structure and this align in a less orderly fashion than saturated acyl chains |
|
|
who was Regnard and what did he do |
-disciple of the pioneering microbiologist Louis Pasteur -He discovered in 1884 that bacteria obtained from 5,000 m in the ocean were more resistant to high pressure than terrestrial bacteria. |
|
|
who proposed the term barophile (later changed to piezophile) |
ZoBell and Johnson in 1949 |
|
|
who isolated the first piezophile in pure culture and isolated the first obligate piezophile |
Yayanos -1979 and 1981 |
|
|
most of the microbes in the deep sea are: are they inactive or active? |
- cyanobacteria. -inactive |
|
|
what is a pressure - retaining water sampler? |
brings back water samples that are dark, cold and at the in situ pressure. This type of instrument makes it possible to collect deep-sea microbes without any decompression. |
|
|
where in the ocean are most of the microbes present? |
deep sea |
|
|
what is High pressure culturing |
- the incubation of samples inside flexible bulbs that can effectively transmit the pressure from outside the cell culture to inside the cell culture. -These are placed in pressure vessels and incubated at high pressure |
|
|
Colonies growing at high pressure must be extracted how? |
following decompression under conditions that do not allow the cells to warm up to room temperature or to get exposed to ultraviolet light |
|
|
piezophiles have all evolved from ____ |
piezosensitive psychrophilic relatives |
|
|
world record holder for piezophilic growth is ____ |
Colwellia maniancus. It can grow up to 140 MPa. |
|
|
where does the world record holder for high temp growth live? |
deep sea -grows best with 20MPa pressure |
|
|
mesophilic bacterium Escherichia coli pressure limits and what happens at each pressure limit: |
motility stops at 10 MPA, the transport into the cell of certain nutrients stops at 26 MPa, cell division stops art 50 MPa, DNA synthesis stops at 50 MPa, growth stops at 50 MPa, protein synthesis stops at 60 MPa, RNA synthesis stops at 77 MPa, and the cells die if treated at pressures above 100 MPa. |
|
|
what are Piezophiles very sensitive to and why |
ultraviolet light because they lack the gene for DNA photolyase, an enzyme that repairs pyrimidine dimers in DNA formed after exposure to UV |
|
|
what does high pressure do to microbe lipids? |
High pressure causes the fatty acid chains within lipids to laterally compress, restricting membrane protein mobility and conformational changes needed for their activity |
|
|
how do piezophiles adapt to high pressure effects on lipids |
making more lipid-associated fatty acids that are unsaturated. These unsaturations (carbon-carbon double bonds) produce kinks in the membranes which prevent or lessen compression. |
|
|
what is the problem associated with studying deep ocean communities |
mixing of allochthonous communities (outside communities) |
|
|
why is decompression a problem for obligate piezophiles? |
they lyse at high pressure |
|
|
piezophiles don't just produce fatty acids with a single unsaturation (double bond), they produce ___ |
polyunsaturated fatty acids (PUFAs) of the omega-3 type. It increases its ratio of total unsaturated to saturated fatty acids as it is grown at increasing pressure |
|
|
what are PUFAS and what do they prevent? |
polyunsaturated fatty acids -prevent cancer, low birth weight, AIDs, depression, hypertension, psoriasis, diabetes |
|
|
membrane proteins are sensitive to what? |
pressure |
|
|
what is ToxR? |
transmembrane transcription factor that controls what outer membrane protein is produced (depending on pressure) in membranes |
|
|
what do the ToxS and SS9 ToxR proteins do when working togther? (pertaining to pressure changes) |
senses hydrostatic pressure changes and either turns on one outer membrane protein gene, or stops blocking the expression of the other outer membrane protein gene |
|
|
DNA replication is also sensitive to high pressure. What happens if: a) a positive regulator of DNA replication is abolished ? b) a negative regulator of the initiation of DNA replication is removed? |
a) cells become more pressure-sensitive b) cells display more enhanced growth at high pressure |
|
|
Protein synthesis is highly sensitive to high pressure in the case of _______ microbes |
mesophilic |
|
|
ribsosomes dissociate when incubated at _____ pressure. |
elevated |
|
|
Flagellar motility highly dependent on ___ |
pressure |
|
|
answers to piezophily: |
-presence of modified cell walls and transfer RNA molecules - increased heavy metal resistance (may be associated with metals adsorbed onto particulate organic matter settling down to great depths) |
|
|
what are forams |
amoeboid protists that are usually less than 1 mm in size, but can get up to 20 cm |
|
|
what is Crystal Falls |
-Home of the Humungous Fungus", perhaps the world's largest and oldest living organism. -1,500 to 10,000 years old and weigh about 100 tons - species called Armillaria Bulbosa, stretches 3.5 miles |
|
|
what are one of the largest of the known bacteria |
Epulopiscium spp. |
|
|
how do Epulopiscium spp. resproduce |
produce multiple offspring intracellularly. These “daughter cells” grow inside the mother cell until they completely fill the mother cell cytoplasm. The daughter cells are eventually released from the mother cell husk |
|
|
inside what animal are there Epulopiscium species |
Surgeon fish |
|
|
what is a firmicute? |
a gram + bacteria |
|
|
why do giant microbes have a problem with their low SA to volume ratio |
they rely on diffusino to encounter nutrients |
|
|
Thiomargarita namibiensis -what does it do -how does it reproduce |
-oxidizes sulfur and reduces nitrate (accumulates nitrate in a large central vacuole) -budding |
|
|
Thioploca araucae -what does it do -where does it live -how does it get energy |
-sulfur-oxidizing bacteria (large) -lives in bundles that are surrounded by a sheath; forms thick bacterial mats on the sea floor below the oxygen-minimum zone in upwelling regions of the ocean; Most of the filaments are present near the seawater-sediment interface. But some extend down into the sediments -sulfide provides their energy source and the nitrate provides their electron acceptor |
|
|
Sulfur-oxidizing microbial communities consist of _____bacteria and ______bacteria -what do each produce |
-mega and macro -mega: multicellular filaments -macro: oxidized sulfur |
|
|
where is the largest community of visible bacteria in the world |
Peru-Chile coastline |
|
|
how do eukaryotes make better advantage of bioenergetics than prokaryotes |
mitochondrdia |
|
|
genome size is correlated with _____ size |
cell (More genome copies may make is easier for transcription, translation and protein insertion into cytoplasmic membrane to occur) |
|
|
When is Size an Advantage for a Bacterial Cell? |
-When it does not come at the expense of a high S/A (constrain metabolism, other cell processes close to the cell surface). -When it increases mobility. -When it decreases sensitivity to grazing. -When it allows the cell to carry nutrients with it in a vacuole |
|
|
why is harder for prokaryotes than eukaryotes to get large? |
prokaryotes lack the complex internal architecture of eukaryotic cells like mitochondria or other organelles. however, both of the giant microbes keep their DNA close to the membrane |
|
|
Nanoarchaeum equitans and Ignicoccus |
smallest microbe to date -thrives at temps around 100 Celsius -doesnt encode for lipids -obligate symbiont -Nanoarchaeum equitans can only be cultivated on the surface of the Archaeum Ignicoccus ("the fire sphere") -represent a quite primitive form of life, possible even a kind of living fossil from the very beginning of live on Earth. |
|
|
what are Prokaryotes |
organisms made up of cells that lack a cell nucleus or any membrane-encased organelles |
|
|
what are eukaryotes |
organisms made up of cells that possess a membrane-bound nucleus (that holds genetic material) as well as membrane-bound organelles. |
|
|
what is an Organelle |
specialized subunit within a cell that has a specific function and is usually separately enclosed within its own lipid bilayer. |
|
|
what are Membrane invaginations |
-common in photosynthetic bacteria and used to accommodate photosynthetic systems. -provides a solution to increase the membrane space to accommodate the overproduced membrane proteins. |
|
|
Magnetotactic bacteria produce organelles called ____ |
magnetosomes |
|
|
what are magnetosomes? |
cytoplasmic membrane invaginations which harbor the cells’ magnets. |
|
|
what are Intracellular vesicles? |
membranes that are completely disconnected from the cytoplasmic membrane. -inside prokaryotes, they can reflect a diseased state brought on by the infect of phage or even other bacteria |
|
|
what are planctomycetes? |
bacteria that naturally have internal membranes |
|
|
what domain do planctomycetes come from |
bacteria - deeply rooted |
|
|
what protein do planctomycetes lack and what is the effect |
universal bacterial cell division protein FtsZ and must divide their cells using another mechanism. |
|
|
are planctomycetes prokaryotic or eukaryotic |
prokaryotic |
|
|
how do planctomycetes reproduce |
budding |
|
|
where are planctomycete ATP synthase enzymes located |
cytoplasmic membrane |
|
|
ANAMMOX |
the oxidation of ammonium using nitrite as an electron acceptor. Hydrazine is an intermediate |
|
|
Organisms with ANAMMOX grow extremely _______ |
- slowly. They may take two weeks to undergo one doubling |
|
|
anammozosome is an analogue of the eukaryotic _____ because ______ |
-mitochondrion -Both organelles generate protonmotive force and use it to generate ATP outside the organelle. |
|
|
ANAMMOX planctomycetes are ______ ( _____ ______ _____) -trophs) |
chemolithoautotrophs |
|
|
how does the anammoxosome membrane prevents the release of toxic intermediates like hyderazine |
-ladderane lipids |
|
|
ANAMMOX is an important part of the global _____ cycle |
nirogen -specifically denitrification |
|
|
what is endocytosis |
cells absorb molecules by engulfing them |
|
|
what is the form of the "new tree of life" |
-bacteria as an outgroup, followed by the euryarchaeota, and the eukarya being most closely related to a group of archaeal phyla known collectively as TACK |
|
|
what is archaea Lokiarchaeota |
-new phylum was discovered in may 2015 in norway in arctic -most closely related member of TACK to eukarya ocontain lots of genes for organelles that are directly homologous to those in eukarya |
|
|
what are Viruses |
filterable infectious agents that could cause an infection and pass through a filter small enough to exclude almost all bacteria. |
|
|
facts about viruses ~~~ |
-Most are less than 100 nm in diameter, and some are much smaller than this. -by far the most abundant 'life forms' in the oceans. -reservoir of most of the genetic diversity in the sea. -There are 1030 viruses in the ocean -Microorganisms are more than 90% of the living biomass in the sea and viruses kill approximately 20% of this biomass every day. -Most abundant, but prokaryotes make up most biomass |
|
|
Acanthamoeba |
-most commonly isolated genus of all naked amoebae from freshwater and soil habitats. Giant viruses have been isolated from these protozoa -efficient hunters and engulfers of bacteria and yeast cells |
|
|
Phagocytosis |
-organism engulfing bacterium and digesting it into phagolysosomes |
|
|
Mimivirus (giant virus) discovered following an outbreak of ________ |
pneumonia (outbreak of pneumonia was perhaps linked to a pathogenic bacterium residing within these amoeba in the cooling system) |
|
|
what is an ideal host for a variety of giant bacteria? |
Acanthamoeba |
|
|
Mimivirus and Megavirus compared to a “typical virus” |
-giant viruses have far larger genome sizes and viral particle sizes than polio virus. -unlike other viruses they even carry tRNA synthetase genes, which are needed for protein synthesis. These genes are standard housekeeping genes in bacteria, and so it is extraordinary to find them encoded within a viral genome. -The giant viruses have a similar genome size to that of other bacterium, and their particles sizes are about the same size as this bacterial cell |
|
|
Pandoravirus |
-2.5 Mbp genome -encodes more than 2,500 proteins -member of the so called nucleocytoplasmic large DNA virus group. -Most of the Pandoraviruses genes do not resemble anything that is known |
|
|
what are giant viruses considered significant |
-They blur the boundary of what is considered living and what is considered non-living. -They are as large as some bacterial species and possess genomes as big as some bacteria. -They code for products previously not thought to be encoded by viruses. -They possesses genes coding for nucleotide and amino acid synthesis, which even some small obligate intracellular bacteria lack. -They do however, lack genes for ribosomal proteins, making them dependent on a host cell for protein translation and energy metabolism. -The phylogeny of giant viruses like Mimivirus is distinct from that of other nucleocytoplasmic large DNA viruses. |
|
|
scientist postulated explanation for evolution of life with RNA: |
-an original RNA cell served as the last universal common ancestor to all of life -This RNA-based life form (using RNA for both enzyme functions and for genetic information) gave rise to an RNA virus which gave rise to a DNA virus which gave rise to a DNA-based cell, which eventually gave rise to all Archaea, Bacteria and Eukarya. |
|
|
what is Sputnick? (giant viruses) |
-Mamaviruses can be infected by a virus called Sputnik. -Sputnick is considered to be a satellite virus and needs Mamavirus to grow. -mamaviruses are needed by Sputnick -Sputnick is pathogenic to mamaviruses. -Sputnick is a virophage. - Its genome contains genes related to Mimivirus, Eukarya, Archaea and Bacteria. - Some evidence suggests that Sputnick virophages may be quite broadly distributed, at least in the ocean. |
|
|
what is a virophage |
This is a virus that infects another virus. |
|
|
pressure limit for life |
130-150 MPa |
|
|
upper temperature limit for life |
122 celsius |
|
|
upper pressure limit of deep biosphere
|
10 MPa |
|
|
how do phytoplankton have an effect on the deep sea |
-produce oxygen and biomolecules which settle as particulate matter onto sediments. - Over time these materials are buried deep into the subsurface environment. - Temperature increases with depth in Earth, and higher temperatures facilitates the breakdown and enhanced availability of some substrates for microbial metabolism. |
|
|
in the deep sea, how do complex organics get broken down |
microbial enzymes lead to the release of sugars, amino acids, long chain fatty acids, etc |
|
|
why is it important for microbial enzymes to breakdown organics in the deep sea? |
these substrates can be used for respiration with oxygen, various nitrogen compounds, manganese, iron, sulfate and carbon dioxide being used as electron acceptors |
|
|
Deep earth radioactivity, high temperatures and perhaps mechanical processes lead to the production of ________ |
energy sources such as hydrogen and hydrocarbons. |
|
|
amount of organic mater produced in the surface ocean is directly proportional to ____________ |
that which ends up in sediments |
|
|
Sediments are the largest global reservoir of __________ |
organic carbon (1.5 x 1022 g C) |
|
|
What did Thomas Gold believe |
deep hot biosphere existed that surpassed all life on Earth, oil was not produced from the remains of organisms, but rather that life first evolved to make use of the abiotic production of hydrocarbons. |
|
|
What do integrated Ocean Drilling Program and the Integrated Continental Drilling Program do? |
These programs look for deep life |
|
|
subseafloor sedimentary cell counts all (increase/decrease) with depth with about the same slope |
decrease |
|
|
Microbes present in deep sea subsurface are only _____% of Earth’s total biomass. |
~ 1% (originally thought to be 10-30%) -There are as many spores as cells in the subsurface |
|
|
How do Scientists Measure Deep SubsurfaceMicrobial Activity? |
-long deep-sea sediment drill core - processing sediment material, perhaps for cultivation, in an anaerobic hood. -use pressure-retaining samplers and subsamplers to analyses microbial activity in the absence of decompression. |
|
|
are deep-subsurface microbes alive? |
Some deep-subsurface microbes are alive and can take up nutrients and reproduce. This has been determined by using stable isotopes and by visualizing cells stained for the presence of RNA. Only metabolically active cells possess RNA (as opposed to DNA, which all cell possess) |
|
|
why do subsurface environments have a lot of oxygen? |
- the microbial activity is so low that oxygen does not get used up. The cells are lacking sufficient energy to respire oxygen and exhibit much reduced metabolic activity. -NOT BECAUSE THEYRE ALL ANAEROBIC |
|
|
what are zombies lol |
microbes that may only reproduce about every one hundred years in low nutrient deep subsurface locations |
|
|
what is necromass |
-deep subsurface microbes that have died and provides small amounts of nutrients for other microbes |
|
|
how to determine age of necromass |
-measured by the extent of aspartic acid racemization. - After death the aspartate is no longer selected to be in the L configuration and the ratio of D/L aspartate increases with sediment depth and age. It is recycled over hundreds of thousands of years |
|
|
Shimokita Peninsula located off the coast of Japan |
-2015 researchers discovered microbial life down to 2.5 km below the surface -associated with coal. It is at a temperature of 40-60ºC -concentrations of the cells vary from <10 – 104cm-3 |
|
|
how do microbes in the deep subsurface eat/live? |
-living off the small amount of organic carbon present, but others may fix inorganic carbon and get energy from hydrogen. -May be living off the organic produced directly or indirectly from photosynthesis or energy within the earth |
|
|
what kind of " "-trophs exist in the deep subsurface? |
-Both heterotrophs and lithoautotrophs exist. |
|
|
what is an autotroph |
Autotroph: fixes its own carbon (carbon dioxide) |
|
|
what is a lithotroph |
Litho: energy from inorganic chemical source i.e. hydrogen |
|
|
what does "SLiMEs" stand for and what happens there |
-Subsurface Lithoautotrophic Microbial Ecosystems -obtain hydrogen and carbon sources from diverse processes associated with serpentinization, volcanic systems, or various biological processes |
|
|
microbes influence mineral stress and fracturing, thereby liberating ________. |
hydrogen |
|
|
Methanogens Present in Deep Subsurface SettingsMay Live off of _________ |
abiotically produced hydrogen -combine hydrogen with CO2 to make methane |
|
|
Thermoanaerobacter |
They are gram positive bacteria that grow on H2 and ferric iron at temperatures ranging from 45 -75°C |
|
|
instead of phosphorous, arsenic could be used instead because _____ |
Phosphorous is needed for DNA, RNA and lipids in microbial cells. Microbes can be great at taking up phosphate present in very small quantities in the environment and can discriminate between phosphorous and arsenic. It seems unlikely that in deep subsurface locations where phosphorous is absent or greatly limiting that life will exist. -HOWEVER Deep subsurface microbes probably do need phosphate. |
|
|
Life goes down at least _______ kilometer below the seafloor |
2.5 |
|
|
Desulforudis audaxviator |
- “Sulfur rod”, “bold traveller”. -firmicute candidate bacterial species found in deep underground locations in a south African gold mine. -present in a 3-4 km deep fracture in basalt (a common volcanic rock). - The temperature is ~60°C, -pH is 9.2 -lives completely separated from the surface world - thanks to the natural radioactive decay of uranium. -Thermodynamic analyses indicate it can get all its energy from radiolytically generated chemical species - SO42- + H2. -It fixes carbon -It either fixes nitrogen or utilizes the available -resistant to free radicals produced during radiolysis of water. -It makes spores for long-term survival. ammonia |
|
|
Halicephalobus mephisto |
-he who loves not the light” - new nematode species was discovered living in 1.3 km depth fracture water, -32°C, hypoxic. - It is ~500um longa nd presumably feeds on bacteria. |
|
|
Multicellular eukarya in gold mine: |
flatworms, segmented worms, roundworm (nematode) |
|
|
what is an Ice sheet |
mass of glacial land ice extending more than 50,000 square kilometers |
|
|
Borup Pass on Ellesmere Island in the Canadian Arctic |
-Springs deliver sulfur deposits into a glacier. -The sulfur is used by sulfur oxidizing microbes, which have been found within the ice. |
|
|
Imre Friedmann |
-scientist who provided extensive characterization of endolithic life in the Antarctic Dry Valley. |
|
|
what does Endolithic mean |
Endolithic refers to “inside rocks”. |
|
|
what are lichens |
-symbioses between fungi and photosynthetic organisms -can be endolithic |
|
|
no organism can live if ______ |
frozen solid; need liquid water |
|
|
psychrophiles in ice mostly remain __________, except summer |
dormant in their frozen state |
|
|
what happens to psychrophiles in the summer? |
-still at below freezing temp -dark dust grains in the ice absorbs energy to melt a tiny pocket of liquid water -temporarily leave dormancy behind |
|
|
what kind of sea ice organisms live within the ice spaces? |
-bacteria, unicellular algae and diatoms chains, worms and crustaceans. These organisms promote the development of brine channels within the ice |
|
|
Temperatures in sea ice are about? |
~ -2°C at bottom near seawater and -35°C at top |
|
|
sea ice temperature and salinity relationship |
as temperature drops pore spaces decrease and brine salinities increase |
|
|
Ice algae may contribute more than _________% of the Arctic’s primary productivity |
50 |
|
|
Greenland Ice Sheet Project |
-microbes have been obtained from 3,043 m below the surface and about 10 m above the sediment-ice interface. -The culturable microorganisms identified in this sample could have been deposited in the ice more than 120,000 years ago. |
|
|
ometimes climate gas anomalies in ice cores (e.g. methane and nitrous oxide) are due to |
ice microbes -Microbes in deep ice cores appear to use all their metabolic energy just to repair DNA/proteins and not to grow. It has been hypothesized that the annual methane loss noted on Mars could be due to subsurface microbes |
|
|
-microbial community average DNA size (increases/decreases) with age with a half-life of about 1.1 million years. -NA present in spores might survive (longer/shorter) |
-decreases -longer |
|
|
Arctic sea ice microbes live at __________°C |
-20 |
|
|
At (low/high) temp. cells prefer to be attached to a surface |
-low -The reason for this is unknown, but could include the greater need for cells at lower temperatures to localize where nutrients tend to be (adsorbed onto surfaces) |
|
|
ice-binding proteins (IBPs) |
They bind to the prism face of ice and prevent water from joining along the a-axis, causing thermal hysteresis |
|
|
Sea-ice Algae sculpt their brine channels most likely by ___________ |
IBPs |
|
|
charactersitics of extracellular fractions from Antarctic bacteria |
-alters ice structure -may also possess IBPs -the protection of cells during freeze-thaw cycles. -This material protects Escherichia coli during repeated freezing cycles. |
|
|
Psychrophilic yeasts produce_______ |
IBPs |
|
|
IBPs prevent ice _______ |
recrystallization (essentially IBPs allow microbes to maintain ice-free zones) |
|
|
example of IBPs being important in symbiotic interactions: |
An Antarctic Moss is Protected From Freezing By IBPs Produced by Bacteria on its Leaf Surfaces. |
|
|
ice microbes can exist at least ______ km down. |
3 |
|
|
IBP sequences are conserved across (1,2, all) domains of life. |
all three |
|
|
microbes in subglacial lakes are adapted to: |
cold, dark and nutrient-poor waters. |
|
|
how may glacial lakes be interconnected? |
through aquifers in the underlying permeable basalt, -some subglacial lakes are colonized from a deeper, subterranean microbiome |
|
|
Lake Joyce |
-has access to some sunlight -has stromatolites composed of cyanobacteria and calcium carbonate |
|
|
which Antarctic lakes are endorheic? |
lake bonney, lake vida |
|
|
which antarctic lakes are subglacial? |
lake whillians, lake ellsworth, lake vostok
|
|
|
ice layer depth of Lake Bonney |
2.8-4.5 m deep |
|
|
ice layer depth of lake vida |
21 m |
|
|
ice layer depth of lake ellsworth |
3km |
|
|
ice layer depth of lake vostok |
3800m |
|
|
lake bonney and lake vida have salinities that are ____ times saltier than sea water |
6-10 and 7, respectively |
|
|
species found in lake bonney |
Halomonas, halophilic Bacillus species and Marinobacter species found |
|
|
what lake is associated with blood falls |
lake bonney |
|
|
what is blood falls |
-dramatic outflow of an iron oxide-tainted plume of saltwater, flowing from the tongue of the Taylor Glacier onto the ice-covered surface of lake bonney -contains autotrophic microbes that cycle iron, sulfur and carbon |
|
|
what is the chemical composition of lake vida? |
-reduced metals, ammonia, hydrogen (H2), dissolved organic carbon -super concentrated with nitrous oxide, nitrogen, and sulfate |
|
|
what are the two size classes of microbes in lake vida brine? |
>0.2 to 1.0-μm diameter cells are 1 × 105 cells per ml < 0.2-μm diameter cells are 5 × 107 cells per mL |
|
|
what is the effect of stress on the cells in Lake Vida? |
super small cells (ultramicrocells) are derived from some of the larger cells as a result of the stress the cells experience |
|
|
how often is water replenished in Lake Whillans and how? |
water is replenished in about a decade with meltwater from overlying ice |
|
|
how do scientists avoid contamination when sampling subglacial lakes such as lake whillans? |
a custom water treatment system designed to remove micron and sub-micron sized particles (biotic and abiotic), irradiate the drilling water with germicidal ultraviolet (UV) radiation, and pasteurize the water |
|
|
what was found to be present in Lake Whillans |
-presence of nitrogen, iron and sulfur oxidizing chemolithoautotrophic microorganisms -NO EUKARYOTES |
|
|
what is the turn over rate in Lake Ellsworth? |
700 years |
|
|
which lake could not be drilled through to reach the lake surface due to not having enough fuel? |
lake Ellsworth |
|
|
how long does it take for lake vostok to renew its waters |
10,000 years |
|
|
which lake is the largest subglacial lake in Antarctica? |
lake vostok |
|
|
what is the lowest temp in lake vostok |
-89°C |
|
|
unlike lake vida, which has liquid brine due to high salinty, how does lake vostok keep its fresh water in liquid form? |
by the pressure of the ice overburden (equivalent to <350 atm) and, perhaps, by geothermal heating |
|
|
what were the results of the Lake Vostok samples |
-Bacterial 16S ribosomal DNA genes revealed low diversity -Microbes were found in accreted ice above the lake at a depth of about 3590meters. -complex community of bacteria and eukaryotes, plus a few archaea. -Some of the microbes are psycrophilic/tolerant and some appear to be thermophilic. -Many halophiles and marine-related microbes were also found -not collected in a manner suitable for microbiology -if the data are valid they suggest Lake Vostok is not a pristine freshwater lake after all. It may have a marine-like salinity and it may also be influenced by geothermal activity. |
|
|
Many microbial symbionts reduce their ________ to eliminate unnecessary biosynthetic pathways |
genomes |
|
|
example of microbial symbiosis |
Coral animals and their zooxanthellae partners, or isopods with ecosymbiotic cyanobacteria – microbes photosynthesize and assimilate CO2 into organic carbon for animal host |
|
|
For animals and plants, symbionts can be internal or ______. |
external |
|
|
The symbionts can be a monoculture (or near-monoculture) or they can be _______ |
part of a complex community |
|
|
Symbionts can be acquired either horizontally (from the external environment) or ________ |
vertically (from a parent) |
|
|
what is host-symbiont coevolution and what does it depend on? |
-both organisms have a comparable evolutionary history. -This can depend on the method of transmission; vertical transmission is more likely to result in coevolution |
|
|
what is an adaptation animals have for hosting symbionts? |
have specialized organs that are exclusively for housing symbionts. -Examples include stink bugs, bobtail squid, and Amazonian ants |
|
|
what are some examples of the importance of microbial natural products due to symbioses |
-Many bacteria make bioactive small molecules o -The actinomycete clade is particularly enriched in this capacity -genomics revolution has greatly expanded our knowledge of microbial biosynthetic potential – we can now find gene clusters predicted to make natural products without growing the microbe. |
|
|
Hawaiian bobtail squid and Vibrio fischeri a) what is the important enzyme in this symbiosis b) how do they work together |
a) Luciferase is the enzyme that catalyzes the light producing reactions (Acquired horizontally, Encoded by lux genes, Regulated by quorum sensing) b) uses bioluminescence as counterillumination to avoid predators during nocturnal behavior; each day at dawn the hosts bury into the sand and expel 95% of their light organ symbionts (Light organ lies in the center of body cavity) |
|
|
examples of Natural products from symbionts: |
-taxol for breast cancer drug from bark of pacific yew tree, penicillum from fungi, actinomycetes for antibiotics. Many natural products have recognizable gene clusters. |
|
|
Apterostigma ants and Pseudonocardia bacteria relationship |
a) Ants cultivate fungal gardens deep underground byforag organic matter on the surface and feed their fungi with it; ants defend their food source (fungal gardens) through a symbiosis with antibiotic-producing actinobacteria; Ants produce an antifungal molecule that is specific to the parasitic fungus and not active against the fungal gardens |
|
|
Didemnid ascidians and Prochloron didemni relationship |
-Prochloron use chlorophyll a and b for photosynthesis (unlike most cyanos but like plants) -Have thylakoid like structures -Relatively large cells |
|
|
Theonella sponges and symbiotic bacteria |
-Sponge has a vast amount of symbionts (not yet cultivated) -Sponges from different locations have distinct chemotypes |
|
|
Osedax (bone eating worms) and Oceanospirallales relationship |
-Whale falls in the deep sea provide an extreme environment for several branches of life -No gut or mouth on the worms meaning they might have a nutritional partnership with symbionts -Gram negative double membrane -Fatty acid signatures of worms match those of symbionts, not free-living bacteria in water column. -Dna probes confirmed presence of the clades thought to be enriched in osedax |
|
|
Primary sources of chemical energy for microbes in serpentinite environments: |
hydrogen oxidation, methanotrophy, methanogenesis, sulfate reduction and anaerobic methane oxidation |
|
|
Serpentinization provided one of the most abundant forms of biological energy on the early earth, at least until ______ |
photosynthesis |
|
|
Analyses of microbes in ultrabasic continental serpentine spring have indicated the presence of _____ and ______ in _______ rich environemtns |
-Hydrogenophaga -Erysipelothrix -hydrogen |
|
|
When availability of water and pore space were not limiting factors and where fresh solutions had sufficient time to be reduced in open conductive ultramafic rock systems, bulk _____ generation occurred |
H2 |
|
|
at the interface between seawater and reduced alkaline solutions, ______ formed, providing favorable conditions for_________ |
- sharp thermodynamic gradients - microbial life |
