MCB 4150 UF

Most prokaryotic cells reside:

in the oceanic and terrestrial subsurface

Of the following, which is the strongest oxidant (i.e. best electron acceptor)?

(Exam 1, q 2)

NO3-

-strongest oxidant= is reduced

-strongest reductant= is oxidized

-positive= is reduced

-negative= is oxidized

-electron donor= is oxidized

-electron acceptor= is reduced

In anaerobic respiration with nitrate (NO3-), the oxidation of which of the following compounds would yield the most free energy?

(Exam 1, q 3)

H2

-greatest difference in reduction potential gives the greatest yield of energy

The microorganism catalyzing the following reaction is a:

NH3 + 1.5 O2 -> NO2- + H2O

chemolithoautotroph

-oxidizing inorganic compound NH3 (litho)

*Organic compound contains a C or bonded to a hydrocarbon

-obtains energy by oxidizing electron donors in environment (chemo)

-most lithotrophs are usually autotrophs

Transcription in ___ are more similar than the model found in the ___.

Archaea and Eukarya; Bacteria

Which of the following statements about Sergei Winogradsky is false?

Pioneer of pure culturing techniques

(Koch discovered it)

TRUE about Winogradsky:

-one of the first to examine elemental cycling by microbes

-developed simple enrichment technique for aerobic/anaerobic microbes

-discovered chemolithotrophy

The Archaea were originally regarded as members of the Bacteria because

all choices are correct:

-neither has membrane-bound compartments

-both typically contain a single circular chromosome

-neither has a nucleus

A fundamental difference between respiration and fermentation is that

there is an external electron acceptor in respiration

-"external" because a compound other than the substrate accepts electrons

Martinus Beijerinck was the first to isolate

all choices are correct:

-sulfate-reducing bacteria

-green algae

-nitrogen-fixing bacteria

The "cohesive force" thought to hold bacterial and archaeal species together is

periodic selection

-where on microbe persist with its adaptation, then it further diversifies again, holding together a population within a niche

-survivor of each periodic selection brings it genome, including all genes that made it able to occupy the niche

Which is one major difference between anaerobic and aerobic respiration?

electron acceptor

-aerobic respiration usually uses O2 as the e- acceptor, because it makes the greatest yield in energy with the largest difference in reduction potential from the e- donor

-anaerobic respiration can't use O2 as the e- acceptor

Which of the following statements about phylogenetic analysis of sequences is not accurate?

character state methods are based on number of sequence differences between a population of alleles

(analysis looks at molecular sequence data that was inherited by a common ancestor, to establish positional homology, NOT sequence similarity)

TRUE phylogenetic analysis:

-branch length in a tree is a measure of evolutionary distance

-the underlying assumption is the gene varieties arose form a common ancestral form

-horizontal gene transfer can skew inferred evolutionary relationships

Regarding membrane lipids, which statement is true?

Bacteria and Eukarya have ester linkages

Archaea have ether linkages

The root of the universal tree of life can be determined by the phylogenetic analysis of

ancient duplicated genes

NOT be found by:

-16S rRNA gene sequences from primitive Archaea and Bacteria

-genes known to be transferred horizontally

In selective enrichment culturing of N2-fixing bacteria,

the media does not contain a nitrogen source

-this way, only bacteria that can fix their own nitrogen will grow on the media

-the media still REQUIRES a carbon source

Identification of life's three domains has come about primarily as a result of

nucleic acid sequencing studies

-Woese studied the sequences of 16S rRNA and found methanogens are distinct from Bacteria and Eukarya -> lead to 3 Domains

-Woese demonstrated rRNA gene sequences could be useful to reveal evolutionary relationships between ALL cells

The accumulation of oxygen in Earth's atmosphere

occurred 2.4 bya and probably hundreds of millions of years after the evolution of cyanobacteria

-YEARS after cynaobacteria evolved because iron-banded formations readily reacted with the first amounts of free oxygen being produced

Which of the following statements about the polymerase chain reaction is not accurate?

No sequence information is require to amplify a region of interest

(PCR requires DNA primers for specific genetic sequences to be amplified)

TRUE about PCR:

-Mullis received a Nobel Prize in 1993 for developing the process

-DNA amplification is exponential

-use of thermostable DNA polymerase (taq from Thermus aquaticus) allows iterative cycles of amplification

An example of an electron acceptor that can be used in anaerobic respiration is

nitrate (NO3-)

- Electron Acceptors usually O2, but if anaerobic, uses OXIDIZED FORMS of N, S, C, Fe, Mn, etc

Protein synthesis studies indicate that most antibiotics that specifically affect bacterial protein synthesis

do not affect archaeal or eukaryotic protein synthesis

-Archaea and Eukarya use methionine initiator tRNA for translation

-Bacteria use formylmethionine, so it can be directly targeted by antibiotics to stop protein synthesis

-would not affect Archaea and Eukarya protein synthesis because they do not have formylmethionine

What 3 features are common to all respiratory and photosynthetic pathways?

-they have electron donors and acceptors

-have an ETC made from redox reactions which create a proton gradient

-proton gradient creates a PMF, which generates production of ATP by pumping protons through ATPase

What does the root of a phylogenetic tree represent?

-is the common ancestor of all taxa present on the tree

-not all trees have a root because finding a common ancestor with all of the paralogous genes is difficult

-can use a root to hypothesize different evolutionary histories, because root DEFINES the DIRECTION of evolution for taxa plotted

What standard is currently used to delineate species of bacteria and archaea?

-NO universally accepted definition/description for a species

-"Golden" Standards are >97% similarity in 16S/18S rRNA sequences, and >70% genome hybridization

List 3 reasons why the small subunit rRNA molecule is considered a good molecular chronometer for evolutionary analysis.

-subunit is conserved in ALL cells on Earth involved in translation

Is used to COMPARE and create evolutionary history

-subunit has molecular "hour and minute hands," where some regions mutate rapdily or slowly

Times certain events or puts organisms in order in evolutionary history

-subunit makes up >80% of the RNA in a cell

Advantageous because it is a large portion of info that can be replicated in PCR, rather than small gene difficult to obtain

Name 3 properties of archaea that are thought to enhance their tolerance to high temperature.

-S-layer on cell wall

Resistant against pH, high temperatures, and lytic enzymes

-2 different hydrocarbons that make cell membrane

One can be used to make a monolayer instead of a bilayer, which is more stable in hot temperatures

-presence of histones

Tightly compact and coil DNA so they are not denatured in hot temps

What evidence supports that eukaryotic mitochondria and chloroplast organelles were derived from ancestral lineages of bacteria?

-1st evidence to support Margullis' Endosymbiotic Theory

-evidence found from analyzing duckweed/Lenma

-16S rRNA from chloroplast analyzed, and was more similar to bacteria than to other 2 domains

-gave potential origin of mitochondria and chloroplast as ancient bacterial aerobe engulfed by anaerobe and resulted in endosymbiotic relationship

Fermentative bacteria and archaea metabolize pyruvate from glycolysis to compounds such as lactate and ethanol. What is the fundamental purpose of these fermentative reactions?

-do NOT produce ATP

-recycles NAD+, because it it is an electron carrier in the Redox reaction and keeps the metabolic cycle going

How did the "pure culture paradigm" play a role in hindering understanding of microbial diversity?

-lead to a great focus on analyzing microbes cultured in lab, RATHER than microbes out in the environment

-resulted in only understanding genetic diversity of microbial life that has been cultured

-VERY small in comparison to actual number of microbes, because only 0.1% are culturable

-paradigm allowed to analyze certain strains of bacteria, but lead to studying ONLY/MAINLY cultured bacteria

List 2 differences in the way genetic information is organized on chromosomes of eukarya compared with bacteria and archaea.

-Eukaryotic chromosome has many noncoding regions, resulting in introns that are spliced out after transcription

-Bacteria/Archaea have very little noncoding regions, resulting in polycistronic mRNA coding for many things on one strand

-Bacteria and Archaea have circular chromosomes NOT in a nucleus

-Eukaryotes have compact chromosomes IN a nucleus

What evidence and constraints are used to establish that the origin of life on Earth occurred by 3.5 bya but probably not prior to 4.0 bya?

-Apex chert fossils and some stromatolites= some proof that life could have originated 3.5 billion years ago (still debate on these fossils)

-CERTAIN life could not exist 4.0 bya, because temp was VERY hot, surface bombarded by meteors and asteroids, and water only present as vapor

Life could not have easily developed, or it could have but it was eradicated by bombardments

-only after bombardments stopped and earth cooled did life begin to develop between 3.5 and 4.0 bya

B.) Although microorganisms were first described in the mid-1600s, it took another ~200 years for the first "microbiologists" to exist. Write an essay discussing the key discoveries and technical advances that led to microbiology becoming a formally recognized discipline during the 19th century.

-1600s- Leeuwenhoek invented microscope with ability to magnify by 200x

-Led to discovery and 1st description of bacteria

-Leeuwenhoek kept microscope making technique secret, so other scientists could not confirm or add to finds

-world had to wait further for development of compound microscopes after publication of his finds

-BIGGEST PROB= Belief in spontaneous generation (SG), where living things spontaneously came from nonliving things due to a "life force"

-led to assumption microbes had no evolutionary history or relationships with life

-Spallanzani- 1st tried to disprove SG with sterilized broth in concealed containers that had no growth

-people argued the "life force" was killed in the bottle, so was not accepted

-Pasteur- used Swan-necked flasks to disprove SG

-had sterilized broth in flasks, and flasks were still open but bent neck did not allow microbes to encounter broth

-broth remained sterile, only grew microbial life when inverted

-Pasteur showed microbial life only grew when in contact with microbes, broth remained sterile without contact, and because flask was open it still had contact with air and "life force", so his reasoning stuck

-SG disproved, but microbiology had no impact UNTIL Pasteur PROVED bacteria and pathogens are cause of many diseases

-led to boom in medical research

-Koch- developed culture media and "pure culture paradigm" for intensive study of single strains of bacteria

-Postulates used to delineate one bacteria as true causative factor, resulting in "Germ Theory"

-Beijerinck- developed enrichment selective culture

-allowed scientists to manipulate nutrients in culture to be favorable towards one bacterium and unfavorable toward another

-Beijerinck isolated N2-fixing and sulfate-reducing bacteria, and green algae

Flagellar rotation is driven by

the proton motive force

Which group of microorganisms would the Calvin Cycle least likely be found in?

anoxygenic Chloroflexus

-Chloroflexus fixes CO2 via the Hydroxypropionate Pathway (unique to phylogenetically ancient organisms)

-Calvin Cycle- takes place in chloroplasts and is important in fixing CO2, so it is present in Cyanobacteria

-Purple nonsulfur bacteria uses Calvin Cycle to fix CO2

-Majority of lithotrophs fix CO2 with Calvin Cycle

Which of the following regarding endospores and their formation is correct?

only certain species of Firmicutes form endospores

-Endopores form ONLY when central nutrient has become limited

-SASPs- "small acidic soluble proteins"

unique to endospores, binding to DNA to change b form to compact A form to be resistant to radiation and heat

-Dipicolonic Acid- complexes with Ca to bind free water and dehydrate forming spore

Inserts itself between DNA bases to further stabilize DNA from heat denaturation

Which of the following does not apply to Bdellovibrio?

attacks gram-positive Bacteria

(gram-positive NOT targets)

TRUE about Bdellovibrio:

-NOT intracellular because it pierces membrane and exists in periplasmic are of gram-NEGATIVE bacteria

-obligate aerobe

-replicates in periplasmic space

-widespread in soil and water

Methylotrophs

(study this more, question was stated to be ambiguous)

-there are facultative methylotrophs that couple the oxidation of C1 compounds with denitrification

-grow on compounds with no C-C bonds as a sole source of carbon and energy

Which of the following reactions is classified as a heterofermentation?

glucose -> lactate + ethanol + CO2

-Heterofermentative LAB oxidizes glucose into pentose sugar which splits to Gylceraldehyde 3-phosphate and Acetyl Phosphate

Glyceraldehyde 3-phosphate then forms Lactic Acid and ATP with substrate-level phosphorylation

Acetyl phosphate reduced to acetaldehyde then ethanol to regenerate NADH

Prochlorophytes were not discovered until the 1980s because

of their small size and unusual pigmentation

-found with Flow Cytometer- microfluidic device that measures size, shape, and fluorescent properties of a cell population passed through detector

During fermentation by propionic acid bacteria,

ATP is formed via substrate-level AND oxidative phosphorylation

To describe a type of photosynthesis as "oxygenic" implies that

oxygen is produced

-H2O is electron donor, and is oxidized to O2

Which of the following statements about chlorophyll or bacteriochlorophyll is correct?

None of the choices are correct

TRUE:

-Bacteriochlorophyll and chlorophyll absorb and transmit in different regions of the electromagnetic spectrum

-bacteriochlorophyll absorbs 805 nm and 870 nm, which is infrared light

-chlorophyll absorbs 680 nm red light and 480 nm blue light, which transmits/reflects green light

The most important bacteria associated with human infections are species of the genus

Bacteroides

-obligately anaerobic and found in intestinal tract of many animals

-Bacteroides species are numerically DOMINANT microbes in human intestines

In most cases, the final product in the lithotrophic oxidation of reduced sulfur compound is

sulfate/ SO4 2-

-Chemolithotrophy 1st conceived by Winogradsky while studying Beggiota

-Beggiota starved for H2S lost sulfur granules, and hypothesized H2S was being oxidized to the elemental sulfur source that was reserved in the cell

-H2S usually oxidized to SO4 2- first to be used for energy, and to elemental sulfur as a energy reserve

-but OVERALL, sulfate is final product

Which bacterial genus is though to be related to the earliest known phototroph?

Chloroflexus

-Chloroflexus uses Hydroxypropionate Pathway to fix CO2 ->

Which of the following uses gliding motility?

All choices are correct:

-Myxobacteria

-Filamentous cyanobacteria

-Cytophaga

-Gliding Motility- slower and smoother movements of the cell along long axis

-Motion linked to propulsion of cell by proteins on outside of the cell

How is ATP made by an acetogen during CO2 reduction?

It is made using substrate level phosphorylation and a sodium ion motive force

-Acetogen= microbe that generates acetate as end product of anaerobic respiration or fermentation

-Reduction of CO2 to acetate with H2 as electron donor

sodium ion motive force used to drive Na+-dependent ATP synthase

Which of the following is incorrect regarding ammonia oxidation by nitrifying bacteria?

The process only occurs under anaerobic conditions

(use of heterocysts in aerobic situations)

TRUE of nitrifying bacteria:

-the initial steps involves an ammonia monooxygenase

-the oxidation occurs in waters that receive inputs of sewage or other waste waters

-some bacterial species are able to completely oxidize ammonia to nitrate

Which of the following conditions would be suitable for enrichment culturing of purple nonsulfur bacteria?

anoxic mineral media with an organic acid and a good light source

-Purple nonsulfur bacteria grow photoheterotrophically

-conducts anoxygenic photosynthesis

-they require a good light source (photo)

-need a source of organic carbon/acid (hetero)

Proteorhodopsin is

a light-dependnet proton pump possessed by some heterotrophic bacteria

-found in heterotrophic Candidatus Pelagibacter ubique

In photosynthesis, NADH and NADPH are produced by

reduction reactions

-NAD+/NADP+ are reduced, or electron is gained, to produce NADH/NADPH

Which of the following is not a trait of the rickettsias?

They lack cell walls

(they do have cell walls)

TRUE of rickettsias:

-None of its members have been isolated in pure culture

-most species are Alphaproteobacteria

-are obligate intracellular parasites or mutualists

-transmitted from animal to animal by arthropod vectors; mouth part of arthropods or feces

-nutrients obtained in host and multiplies until hosts bursts

-metabolizes/oxidizes glutamate or glutamine, but unable to metabolize glucose or other organic acids

Compare two different ways by which obligate intracellular bacteria propagate to new hosts.

-Wolbachia- reside in over half of the known insects, but do not cause infection

Cause Parthenogenesis in insect eggs, killing off male eggs and doubling chromosome number to make more females

Wolbachia propagate to new hosts by spreading through eggs

Remain intracellular in eggs because they are unable to live as free-living cells, and ensure propagation by making more females that will lay eggs

-Rickettsia- obligate intracellular parasite or mutualist

Primarily transmitted from animal to animal by arthropod vectors, like mouth parts of the arthropod or its feces

Move through bites of mites, ticks, or lice into a new host

They grow and multiply within a cell, taking nutrients and then they burst out of the cell, going to new host cells, and keep growing like this in intracellular environment until they are moved to a new host through bites or ingestion of arthropod feces

According to the unified concept of photosynthesis, what is the fundamental difference between oxygenic and anoxygenic photosynthesis?

-Unified concept of photosynthesis= both forms use light-dependent reactions that use electron donors from an oxidizable source to fix CO2

-Oxygenic- uses H2O has an electron donor, and oxidizes it to O2

Uses chlorophyll

-Anoxygenic- uses H2S as an electron donor, oxidizing it to elemental sulfur or SO4 2- depending on the phototroph

Uses bacteriochlorophyll

Process considered cyclic, has no excess electrons, ensuring H2O does not get oxidized to O2

Why are propionic acid bacteria referred to as secondary fermenters?

-propionic acid bacteria ferment lactic acid, which is the end product of fermentation for many bacteria

-Overall, lactic acid is an end product in one cycle, then used as a substrate in a second cycle of fermentation in propionic acid bacteria

Which two bacterial phyla dominate in the human colon? List a benefit these species provide to their host.

-Bacteroidetes and Firmicutes

-they both help break down more polysaccharides ingested than the host can ingest on their own

-release enzymes not encoded in human genome, which help to breakdown more polysaccharides to increase the amount of nutrients absorbed

-if they were not present, human digestion would not be as efficient, and the human would have to eat more food to get the same nutrients as if the 2 phyla were present

Although many nitrogen-fixing bacteria are obligate aerobes, the enzymes dinitrogenase is oxygen-sensitive. Name 2 strategies used by bacteria that allow this enzyme to function under aerobic conditions.

-Slime barrier- in cells unable to make heterocysts, they secrete a slime layer that coats the cell

Ensures oxygen does not affect the enzyme

-Heterocysts- made only under conditions when the cell is deprived of fixed nitrogen, cell differentiates to make heterocysts

Are where the enzyme and nitrogen-fixing pathways are located

Ensuring they are separated from PSII and O2 it produces so enzyme is not inhibited, so all biosynthetic pathways can occur at once

How are anoxygenic phototrophic microorganisms more physiologically diverse than oxygenic phototrophic microorganisms?

-oxygenic phototrophs only use H2O as electron donor

-anoxygenic phototrophs have a WIDE range of electron donors like: H2S, elemental sulfur, S2O3 2-, Fe 2+, or H2

Allows them to live in MUCH more diverse environments than oxygenic phototrophs, making them more physiologically diverse

Also have different structured bacteriochlorophyll that absorbs different wave lengths, which also allows more diverse environments

What specific reaction do Beta lactam antibiotics inhibit and how are some strains of Staphylococcus aureus able to persist and grow in the presence of these drugs?

-Beta lactam antibiotics inhibit cells in Transpeptidation- process that crosslinks peptidoglycan binding protein (PBP) and maeks peptidoglycan to form strong barrier on cell

-Inhibiting Transpeptidation ensures strong barrier is not made around the cell, which makes bacteria easier to lyse

-Methicillin Resistant Staph. aureus (MRSA) are NOT affected by beta lactam antibiotics

-MRSA do not have PBP, but PBP2a encoded by mecA gene

Different protein has a resistance to beta lactam antibiotics, so peptidoglycan of the cell is not affected

-MRSA are able to grow even in presence of the antibiotic because their barrier is still strong

List 3 carbon fixation pathways used by prokaryotes.

-Hydroxypropionate Pathway- may have been 1st autotrophic pathway in any phototrophic organism

-Acetyl CoA Pathway/Acetogenesis- form of anoxic CO2 reduction to acetate with H2 as electron donor

Converts acetyl-CoA to Acetate with substrate-level phosphorylation but NO GAIN of ATP

Uses Sodium Ion Motive Force to generate ATP

-Calvin Cycle- VERY important for CO2 fixation

Uses RuBisCo to catalyze 1st step, and Phosphoribulokinase to catalyze last step that regenerates RuBisCo

Compare the flagella and motility of spirochetes with that of a typical motile bacterium. What is unique about the mechanism of motility in the spirochetes?

-Spirochetes- do NOT have extracellular flagella

UNIQUE because they move in a cork-screw like manner

Have an Endoflagellum anchored at each of the poles and runs length of the cell

Cork-screw like motility due to torque endoflagellum puts on outer membrane

Can easily move through viscous material, making them more invasive in hosts

-Typical Motile Bacterium:

~Unidirectional- cell moves in one direction, stops to reorient to new direction

~Peritrichuous- cell moves when bound flagella go counterclockwise, and tumbles when flagella go clockwise

~Reversible- changes direction by turning flagella clockwise or counterclockwise

~Polar- flagellum attached to one pole

List 3 molecular adaptations found in psychrophilic microorganisms.

-more unsaturated and shorter fatty acids to make the membrane

-less hydrophobic and more polar enzymes

-some cells have IBPs (ice binding proteins) to protect the cell from different ice formations

A.) Bacteria within the SAR11 cluster of the Proteobacteria are one of the most abundant microorganisms in the world's oceans. Describe the approaches that were used to initially detect this clade in the ocean and to eventually isolate the species (e.g. Pelagibacter ubique) from this group in pure culture. Discuss at least 4 unique features of P. ubique that have been revealed by genomic sequencing and analysis.

-SAR11 cluster of Proteobacteria are one of the most abundant microorganisms, accoutning for 15% of prokaryotes in seawater worldwide, growing in low-nutrient waters

-Giovannoni took a sample of surface water from Sargasso Sea and did 16S rRNA sequencing without culturing, and led to discovery and formation of SAR11 clade

-did intense studied on SAR11 because it made up quarter of prokaryotes in oceans

-tried to culture them using "Marine Broth 2216", but unsuccessful because had TOO much C, N, and P

Believe SAR11 would grow in it because that was the pattern seen in other bacteria

-did not realize SAR11 were oligotrophic, and will only grow in low-nutrient environments

-HTC (high-throughput cultivation)- use of microtiter plates and placed 1 to 3 cells in each well

Cells grew, but concentrations never went over 1 million cell per mL, which is recorded in nature

Concentrations are small, BUT HTC increased culturability 1.4 to 120 times

FIRST isolation and pure culture of Pelagibacter ubique

-Unique of P. ubique:

~has one of the smallest genomes of all of the known bacteria

~genome is streamlined with no phage genes, pseudogenes, or replicated genes, BUT genome has ALL necessary info for biosynthesis like all other alphaproteobacteria

~is an extremely small cell, which is an advantage because it increases the surface area to volume ratio, making diffusion of nutrients and other materials more efficient

~is a heterotrophic bacteria, but contains genes for Proteorhodpsin- a light-dependent proton pump

Used to supplement energy when bacteria does not have enough nutrients, but P. ubique STILL requires organic carbon as a source of carbon and energy for biosynthesis

Superphylum of: Chlamydiae, Planctomycetes, and Verrumicrobia

-inhabit soils, aquatic systems, and in association with eukaryotic hosts

-superphylum LACKS peptidoglycan

-UNIQUE because cells have internal compartmentalization

Planctomycete

-free-living aquatic oligotrophs

-divide by budding

-Components= flagellum, stalk, and pilus

Stalk: attachment

Flagellum: movement

Pilus: budding

-S-layer Cell Wall; resistant to antibiotics that disrupt peptidoglycan synthesis

~GENES for peptidoglycan synthesis still found, may be purposed in different ways from other bacteria

-some are nucleated: Nucleoid is surrounded by nuclear envelope

-> DNA covalently closed, circular, and supercoiled

-> nuclear membrane is invagination in cytoplasmic membrane

-some members are nitrifying bacteria that oxidize ammonia

Anammox

-anoxic ammonia oxidation

(classic nitrifying bacteria are aerobes, but ammonia can also be oxidized under anoxic conditions)

-oxidation of ammonia with Nitrite/NO2- as external electron acceptor to yield gaseous nitrogen

Anammox Reaction

NH4+ + NO2- -> N2 + 2H2O

Delta G= -357 kJ

-Nitrite reduced to nitric oxide by Nitrite Reductase, then Hydrazine Synthase mediates nitric oxide reacting with ammonia to produce hydrazine (very strong reductant), then Hydrazine Dehydrogenase oxidizes hydrazine to form N2 gas

-electrons generated funneled into ETC where they form a PMF, and electrons also donated to initial reductive steps

-ATPase is in the membrane of anammoxosome for ATP generation

Enzymes:

~Nitrite Reductase

~Hydrazine Synthase

~Hydrazine Dehydrogenase

REDOX Reaction:

~Ammonia= e- donor

~Nitrite= e- acceptor

~Hydrazine= strong reductant

Brocadia anammoxidans

-member of Planctomycetes

-autotroph

-catalyzes anammox

-fixes CO2 via Acetyl-CoA Pathway

Anammoxosome

-unit membrane structure where anammox reaction occurs

-protects the cell from toxic intermediates produced during anammox reaction

-made of DISTINT lipids: Ladderane Lipids, forming dense membrane structure preventing diffusion of substance from anammoxosome to cytoplasm

-> ester AND ether bonds

Chlamydiae

-obligately intracellular parasites

-simplest biochemical capabilities of ALL known bacteria

-thought to be "energy parasites", but have genes for ATP synthesis, peptidoglycan biosynthesis, and some "eukaryotic-like" genes

~"eukaryotic-like" means they were horizontally inherited from the host

-gram negative cell wall, LACK peptidoglycan

~lack sensitivity to penicillin

~still has genes for peptidoglycan synthesis -> chemically different form not yet detectable from current chemical methods

-divide by binary fission

Chlamydia Life Cycle

-Elementary Body: small, dense cell with rigid cell wall relatively resistant to drying, is nongrowing, and infectious

-> NOT capable of multiplying

-Reticulate Body: fragile cell wall, multplying by binary fission, and NONinfectious because on goal is to multiply

-> vegetative form of species

->converts from Elementary Body to Reticulate Body to multiply

-transferred primarily as AEROSOLS that enter through the respiratory system

2 Groups of Chlamydiae

-Animal Parasites

-"Environmental" Species: possess virulence factors found in modern pathogenic Chlamydiae

-Chlamydiae-like endocytobionts found in protozoan hosts, where this adaptation to intracellular environment may have been vital to generation of pathogenic species

-last common ancetsor for both arose 700 mya, and already adapted to intracellular survival in eukaryotes

-Chlamydiae are FIRST to exploit eukaryotes as hosts

-Have not been pure cultured yet, but do readily grow in lab in protozoa hosts

Genus Thermus

radiation-sensitive thermophiles or hyperthermophiles

Genus Deinococcus

radiation-resistant and desiccation-resistant thermophiles, mesophiles, and psychrophiles

Thermus aquaticus

-1st discovered by Brock in Yellowstone hot springs

-source of heat-resistant Taq DNA Pol enzyme in PCR

-described to have pink filaments, and REQUIRED higher temps to grow

Deinococcus radiodurans

-1 of the MOST radioresistant organisms known

-found when using ionizing radiation to sterilize canned meat, and saw this endured

-ionizing radiation is string enough to strip off e-, forming ions

->Radiation, heat, and dehydration damages cells by causing DOUBLE STRAND BREAKS

-D. radiodurans can endure 100x IR levels that kill otehr bacteria, and 2000X higher lethal human dose

-DNA is ordered into tetrad doughnut-like structure/ring-like toroidal structure

-> tightly packed DNA so when DS-breaks occur, they are held in close proximity

-cannot precent DNA damage from IR, but has repairing abilities to survive extensive chromosomal breakage

2 Possibilities

~D. rad uses same DNA-repair strategies (RecA or D-loop) as others, but more effective

~uses DNA repair system with novel components

-IR resistance doe NOT provide selective advantage

~ability of D. rad to repair DNA came form selective pressure to survive desiccation/dehydration

Candidate Phyla Radiation (CPR)

-obligate anaerobic microbes that make 15% of ALL living organisms

-monophyletic group

-ultra small cells and have very small genomes

-lack genes for free-living (amino acid synthesis, incomplete TCA cycle, no ETC complexes, lack ATP synthase)

Parasites of other microbes

-obligate fermenters

-discovered in sampling of aquifer well, where groundwater was prefiltered through 1.2 microns, then subsequent 0.2 and 0.1 filters to catch the bacterium

-did NOT readily bind to SSU primers, because they had insertion sequences that made their 16S rRNA divergent from normal ones studied

Shadow Biosphere

-could consist of lineages that do not share a common ancestor with known life, OR diverged from common life of descent shortly after origin of life

-likely inherently biased against different lifeforms, because we use PCR for known 16S rRNA, but what if other lifeforms do not have it

-> PCR is BIASED

-Metagenomics is PCR-independent

-> is UNBIASED: take direct sample from environment and gets partial to complete genomes

-> largest fraction of diversity accessible ONLY via cultivation-independent approaches

-no proof of a "shadow biosphere"

Aquificales

-hyperthermophilic, chemolithotrophic, and microaerophilic bacteria

-found in hydrothermal vents

-Aquifex pyrophilus is "type strain"- MOST thermophilic in cultivation growing optimally from 85-95*C

-deepest branching lineage within bacterial domain

-most thermophiles either anaerobes or micoraeropiles, due to low solubility of O2 in water, and early life didn't have excess O2

-most are chemoautotrophs and canNOT grow heterotrophically

~fix CO2 via reverse/reductive TCA cycle

~few use acetate and formate as C source

Microaerophile

oxidizes H2, H2S, or SO3 2- with O2 or NO3 2-

Thermotoga maritimus

-hyperthermophilic bacterium capable of growth to 90*C

-sheath-like membrane/ "toga"= outer membrane

-anaerobic, fermentative chemoorganotroph

~CATABOLIZES sugars and polymers like starch, cellulose, and xylan to PRODUCE lactate, acetate, CO2, and H2

-can grow on H2 and use Fe 3+ or elemental sulfur as electron acceptor

-EVIDENCE for horizontal gene transfer between Archaea and bacteria in T. maritima genome:

~25% genes similar to archaea

~conservation of gene order shows possible transfer from thermophilic archaea to thermophilic bacteria

~majority genes for housekeeping (transcrip, transl, and replic) are BACTERIAL

Thermodesulfobacterium

-thermophilic, sulfate reducing bacterium

-separate from Thermotoga and Aquifex

-strict anaerobe, growing optimally at 70*C

-e- donors= lactate, pyruvate, or ethanol

-UNIQUE= ether-linked lipids, like in archaea

Upper temp limits for: phototrophy, chemoorganotrophy, and chemolithotrophy

-only archaea capable of growth >95*C

~habitats are devoid of phototrophs, so they are only primary producers here

-temps >110*C, ONLY H2-oxidizing archaea known

~physiological relic of ancient metabolism

~H2= e- donor

~elemental sulfur, NO3-, Fe 3+, or O2= e- acceptor

Thermococcus and Pyrococcus

-hyperthemophilic Euryarchaeota

-similar to hyperthermophilic crenarchaeotes

-Proteins, starch, or maltose oxidized as e- DONORS and elemental sulfur as e- ACCEPTOR

-Thermococcus= 70-95*C

~most frequently isolate hyperthermophile

~produce Protease and Lipase enzymes used in industry

-Pyrococcus= 70-106*C

Archaeglobus

-TRUE sulfate-reducing hyperthermophile

-grow optimally at 83*C

-ONLY archaea able to reduce SO4 2- to H2S

~couples oxidation of H2, lactate, pyruvate, glucose, or complex organic compounds to reduction of SO4 2-

-MANY coenzymes in common with methanogens, producing small amounts of methane during growth

Ferroglobus

-iron-oxidizing chemolithotrophic autotroph

-conserves energy from oxidation of Fe 2+ to Fe 3+ coupled with reduction of NO3- to NO2- and NO-

-ONLY use H2 or H2S as e- donors

-ability to oxidize Fe 2+ under anaerobic conditions is interesting

~Makes dating origin of cyanobacteria hard because Banded Iron Formations may not have occured because of O2 from cyanobacteria, but because of Ferroglobus

Sulfur Metabolism in Crenarchaeota

Sulfur Reduction:

~Chemolithotrophic-

Hs + S0 -> H2S

~Chemoorganotrophic-

organic compound + S0 -> H2S + CO2

Sulfur Oxidation:

~Chemolithotrophic-

2 S0 + 3 O2 + 2 H2O -> 2 H2SO4

-use elemental sulfur as e- donor or acceptor, depending on presence of O2

~Aerobic= oxidizes S0 to H2SO4, so S0 is e- donor

~Anaerobic= S0 is reduced, so it is an e- acceptor, forming H2S

Sulfulobus

-acidophilic hyperthermophilic member of the Crenarchaeota

-grow in sulfur rich hotsprings 90*C and pH 1-5

-grows aerobically and autotrophically, oxidizing H2S oe elemental sulfur to H2SO4 and Fe 2+ to Fe 3+

~can also grow chemoorganotrophically

-1st prokaryote shown to be able to grow over 80*C

-cells are more or less spherical, but have distinct lobes

-cells tightly adhere to sulfur crystals, where they can be seen microscopically with fluorescent dyes

Pyrodictum and Pyrolobus

-Pyrodictum occultum: 105*C

~strict anaerobe

~chemolithotroph on H2 with elemental sulfur as e- acceptor

~can also be chemoorganotroph

~hollow filaments for attachment

-Pyrolobus fumarii: 106*C

~MOST thermophilic, with growth up to 113*C

~lives in "black smoker" hydrothermal vent chimneys

~autotrophic metabolism gives organic carbon in otherwise inorganic environ

Ignicoccus islandicus

-Strictly anaerobic and H2/S0 based

~H2 as e- donor and S0 as e- acceptor

-optimal 90*C

-UNIQUE contains an outer membrane like gram-negative bacteria

-volume of periplasm is 2-3x that of cytoplasm

-membrane bound vesicles that may function in exporting substances out of the cell

-perisplasmic space host to Nanoarchaeum, where it uses Ignicoccus for carbon and energy

~N. equitans lacks biosynthesis pathways, glycolysis, and some genes for functional ATPase

~ must be directly attached to host

~N. equitans is ONLY archaeal symbiont known

Nanoarchaeum equitans

Archaeal "parasite" that needs its archaeal host (Ignicoccus hospitalis) to produce lipids, amino acids, and nucleotides; directly connected to host through a pore

lacks biosynthesis pathways, glycolysis, and some genes for functional ATPase

~ must be directly attached to host

ONLY archaeal symbiont known for Ignicoccus islandicus

Molecular Adaptations to Hyperthermophily

-proteins have highly hydrophobic cores and more ionic interactions on the surface

-Thermosomes (chaperones)- keep the cell's proteins properly folded and functional

-Reverse DNA gyrase that stabilizes DNA by inducing positive supercoils in DNA

-histones wind and compact DNA into nucleosome

-dibiphytanyl tetraether lipids to form monolayer membranes

Methanogens

-obligate anaerobes with key role in terminal step of organic C mineralization

-utilize H2 and reduce CO2 to methane/CH4

~methane also made from acetate and other substrates

-85% of energy from glucose remains in methane

-Habitats:

~anoxic sediments

~animal digestive tracts

~hydrothermal vents

~Artificial biodegradation facilities

~endosymbionts of various anaerobic protozoa

from who did the methanogens gain the ability to form CH4 from H2/CO2?

Euryarchaeota

All methanogens are within which biological Domain?

euryarchaeota

Substrates converted to methane by methanogenesis

CO2 reduction pathway:

-CO2 + 4 H2 -> CH4 + H2O

Methylotrophic Pathways:

-CH3OH + H2 -> CH4 + H2O

-4 CH3OH -> 3 CH4 + CO2 + 2 H2O

Acetoclastic pathway:

-CH3COO- + H2O -> CH4 + HCO3-

Methanogen Cell Wall Chemistries

-methanobacterium have psuedopeptidoglycan

- methanosarcina cell wall polymer similar in structure to chondroitin

- methanocaldococcus protein and glycoprotein walls

-methanospirillum has an S-layer

Methanogenesis

-CO2(e- acceptor) reduced with H2(e- doner) and attached to methanofuran in form of formyl group

-MF-bound formyl group transferred to methanopterin where it is dehydrated and reduced(using e- from CoF) to methylene and methyl

-methyl group transferred from MP to CoM (highly exergonic resulting in a Na motive force)

-Methyl-CoM reduced by methyl reductase complex using e- donated form CoB

Generates CH4 and forms heterodisulfide bond

-Free CoM and CoB regenerated in reduction of heterodisulfide by heterodisulfide reductase

->associated with generation ETC and PMF with extrusion of protons

Unique coenzymes:

~C1 Carriers- carries C units along pathways

~Methanofuran/MF

~Methanopterin/MP

~CoM

~CoB

~CoF420- absorbs light at 420 nm and fluoresces blue-green in oxidized form

->convenient way to identify methanogens under microscope

Autotrophy in Methanogens via Acetyl-CoA Pathway

-carbonyl group of acetate produced during autotrophic growth derived from enzyme CO dehydrogenase

-methyl groups abundant from e- donors or made during methanogenesis

what do methanogens lack to fix CO2

lack enzymes for tetrahydrofolate driven reactions that produce methyl groups

what is the largest sink for methane?

atmosphere