Microbiology 303 Exam 2

Metagenome of the microbiota

Another them for microbiota

Purple Bacteria

Are All Proteobacteria Use PSII photosystem Non-Sulfur Bacteria Use H2S as electron donor for photosystem Photoautotrophs: Fix Carbons Sulfur Bacteria Use low levels of H2S as electron donor Can be: photoautotrophs, photoheterotrophs, and by aerobic respiration

Orchid

Arent able to feed endomycorrhizae, roots are saprophytic

Rhizosphere

Assist in growth of microbes, secretes nutrients some inhibit fungal growth = causing disease plants helps microbes that help it

Iron and Manganese Cycles

At neutral pH they precipitate Fe^2+ (electron donor) --> forms H20 --> oxidative (chemolithrophy) --> Fe^3+ oxidized as product (Fe^3+ becomes electron acceptor) --> Reductive (Dissimilarity Fe^3+ reduction) --> Fe^2+ as electron donor (Fe^2+ as reduced product of anaerobic respiration) Iron can be reduced anoxically At neutral pH iron become better electron donor

Calvin Cycle

Carbon Fixation Start with Ribulose 1-5 Bisphosphate Use Enzyme: RuBisCo which adds inorganic carbon to molecule KEY PHASE: Reduction Phase: G3P Use NADPH + H+ --> NADP+ Requires 3 ATP and 2 NADPH per CO2

Microbial communities can provide stability to their environment

Carbon and Nitrogen are linked C-N-P Organism require microbes help stabilize soil Full oxidized - Nitrate (needs to be reduce) Ammonia (NH4) needs to be oxidized

CO2

CarbonDioxide can be electron accpetor and make natural gas.

Bifidobacteria

Degrades sugars in Milk

Chrome Agar

Differentiates between pathogens because each organisms has a different color. Synthetic substrate

Measuring Cell Number

Direct: Counting cant tell if its alive or dead requires a microscope Indirect: Plating Colony Forming Units (CFU) Estimating: Most Probably Number - uses dilution to extinction Light Scattering - turbidity Drawbacks: A lot of excess requirements - dilutions - microbes difficulty growing

Differential Medium

Distinguishes groups of microbes on the sample.

Anoxgenic Phototrophy

Don't Generate Oxygen Make ATP No electron donor and terminal electron acceptor (No NADPH) ETC generates PMF and returns to photosystem PSI (P840 or P798) PSII (P870) Notice High Wavelength (infrared light)

Respiration

ETC is a chain of redox reaction organized by increase ΔE Excess H+ cannot be transferred thus they are pushed out of the cell => PMF PMF can be used to do work generate ATP by ATP-synthase

History of Earth

Early Phototrophs were anoxygenic and used H2S S^0 a good from of E storage Anoxic atmosphere occured after oxygenation

Predatory

Eats cell Ex. Vampirococcus Daptobacter Myxococcus Bdellovibrio

Limitations to culture-based studies

Most microbes cant be cultured microbes in nature do not grow in pure culture - competition - symbiosis (Syntrophy) - phage and predator Microbes in nature are not usually in exponential phase Microbes in nature do not usually have unlimited nutrient and optimal growth conditions

ETC can be used Reversed

Most will go forward --> To Make ATP Some can flow backwards <-- Make NADH for reduction Reduce NAD to get NADH

Anhydride and Thioester Bond

Much less energy in a thioester bond then in a Anhydride bond Energy Storage

Microbial Communities shaped by different types of symbiosis

Mutalism Parasitism cooperation commensalism predation amensalism competition

Types of Symbiosis

Mutualism Cooperation Commensalism Predation Parasitism Pathogenesis Competition

TCA Cycle or Krebs Cycle

NADH goes to ETC to generate more ATP by Oxidative Phosphorylation 1 ATP = created by substrate level phosphorylation per pyruvate molecule 4 NAD+ = 12 ATP 1 FAD = 2 ATP

Photoheterotrophy

NADPH will help in fixing carbon to get biosynthesis ATP is required

Dead Zones

Oxygen minimum zones where chemolithoautotrophs exclusively prevail caused by influx of limiting nutrients photosynthetic microbes die and sink and consumed by chemoheterotrophs who quickly consume all oxygen and then suffocate Sewage and Pollutants that are added to waters that cause dead zones Trigger blooms of cyanobacteria and algae

Phototrophy can be Oxygenic and Anoxygenic

Oxygenic - generates oxygen Z path Anoxygenic - DOES NOT generate oxygen O path

Pollutants (PCDD & PDCF)

Some microbes use microbes use pollutants as electron acceptor Can reduce and make soluble against toxins

No Dormant Cells

Viable but non-culturable organisms that cant grow on a rich medium Most Organism in nature are Dormant Culture less than 1% of all microbes

Happen when there is an influx of the limiting element

a lot of growth due to influx of limiting reagents Ex. Dead Zones

ΔE Reduction Potential

can be measured and expressed for each half reaction Aox + e- --> Ared

Phosphorous and Calcium Cycles

cycles are mostly to maintain balance between organic and mineral forms of these elements Phosphorous is usually limiting for photosynthesis

Methylotrophs

oxidizes methane gas most carbons are stored in rocks and sediments 99.5% and oceans .5%

Reaction Center

site of electron excitation reaction center can be Photosystem I or II use quiniones to transfer electrons to ETC

ΔG = -nFΔE Gibbs Free Energy Change

ΔE = E(acceptor) - E(donor)

Prochloroccus

Smallest and most abundant photosynthetic organism on earth

Endergonic

+ΔG Negative ΔE not a viable lifestyle

Pristine Soil vs. Diverse Soil

Alaskan Soil (Pristine) more diverse than Wisconsin Farm Soil (Diverse)

Exergonic

-ΔG Positive ΔE Favorable reaction viable lifestyle

Step 2 of Glycolysis

1,3 Bisphosphoglycerate used to generate ATP reduces NAD+ Makes NADH and ATP 2 net ATP are made by substrate-level phosphorylation

Methylotrophs has 3 mechanism

1. Aerobic Oxidation 2. Anaerobic Oxidation 3. Coupled methane oxidation with denitrification

Aerobic Nitrification

1. Ammonia --> Nitrite 2. Nitrite --> Nitrate Nitrifying Bacteria

How is Energy Stored in Cells?

1. Membrane (PMF) 2. High Energy Bonds - Anhydrides (ATP) - Thioesters (Acetyl-CoA) - Aldehydes 3. High Energy Organic Substrates - Glycogen - PHB - Inorganic Sulfur - Starch and Fats (Eukaryotes)

Summary of Respiration

1. Protons and electons converted into NADH 2. NADH starts chain of redox reaction in the ETC 3. Electons and Protons from high-energy are passed through a chain to generate PMF 4. PMF powers ATP-synthase to generate ATP by oxidative phosphorylation used to power cellular reactions

Glycolsis

1. Start with Glucose and produce (2) Glyceraldehyde 3-P Aldehyde Group - very reactive (Preparatory Steps) 2. Energy in aldehyde bond of glyceraldehyde 3-P used to produce NADH and ATP 3. PEP, high energy phosphoanhydride. Phosphoenolpyruvate (PEP) is used to generate ATP and pyruvate (2)

Syntrophy Oxidation and Methanogen

1. Syntrophy first oxidizes reduce proton to produce H2 2. Methanogen uses H2 to reduce CO2 and produce methane Not favorable, but together it becomes favorable

Microbial diversity corresponds with redox niche

1.Notice O2 get consumed (oxic - aerobic respiration) 2. Nitrate (denitrification) 3. Iron (Fe) (Fe(III) reduction) 4. Sulfate (sulfate reduction) 5. Methane (Methanogenesis) Relative to electron acceptor

How Humans get Nitrogen

Ammonium (NH4+) or amino acids we eat Nitrate is toxic to humans

Sulfur Cycle

A lot of redox states, (can only be oxidized) SO4^2- (sulfate) most oxidized form burning fossil fuel provides sulfur to air (leads to acid rain) Sulfur/Sulfide Oxidation -(H2S --> S^0 --> Sulfate) - Anaerobic - Sulfur Chemolithotrophs -Aerobic - Purple and green bacteria Sulfate Reduction (Anaerobic) - (sulfate --> H2S) Sulfur Reduction (Anaerobic) - (S^0 --> H2S) Sulfur Disproportionation - (S2O2^2- --> H2S and sulfate) Organic Sulfur Compound oxidation and reduction CH3SH --> CO2 and H2S DMSO --> DMS Desulfurylation (organic S --> H2S) Assimilation - PAPS --> products of organic matter Dissimilation - APS --> excretion of waste product ATP consumed - Needs to be activated to get specific form (in order to become a great sink)

Cellulosome

A multi-protein complex attached to surface of bacterial cell that binds and facilitates cellulose deconstruction

Acidophiles

ATP is free because atmosphere has protons that want to be used/donated Acidophiles have neutral insides thus H+ wouldn't all enter and kill the cell

Microbiome Resiliency

Ability to re-establish, difficulty in change of microbiota

Sinks

Adds to Atmosphere Photosynthesis, plants

Banded Iron Formations

After cyanobacteria created oxygenic photosynthesis, Fe^3+ formed and precipitated leading towards Banded Iron Formations

Iron (Energy Source)

BAD Electron Donor @ neutral pH --> spontaneous reduction (RUST) Use Oxygen as Acceptor

Great Donor and Acceptors

Best Donor - Edibles (Eat) Glucose Best Acceptor - Breathable Oxygen

Strength of Respiration

Best: Aerobic (Oxygen) 2. Nitrate 3. Manganese Reduction 4. Iron 5. Sulfate 6. Methanogens (CO2) 7. Anaerobic Reactions

Cellulose

Bioenergy Source Bound tightly, thus tough to separate Next Generation of Feedstock for biofuel Consolidating Bioprocessing (CBP) Native Plant Breaks down fibers (of solid, liquids) to form cellulose which is broken down by sugar bonds Modified Plants Consolidate bioprocessing - some organisms can use cellulose Both Pathways form Ethanol Tough to Degrade

Microbial Diversity in relations with humans

Birth --> 3 develop immune system As you age --> Microbiome less diverse --> thus microbiome disease microbinomes - fully developed unless complications

Dissimilation

Breathing A lot more Oxygen Use compounds for breathing

Chlorosomes

Bundles of chlorophyll to trap light to form ATP Light harvesting pigments

Carbon Cycle

CO2 is fixed by autotrophs or reacts with sea(WATER) to form Carbonic Acid Bicarbonate and Carbonate are formed from Carbonic Acid

Global Temperature

CO2 level have increase since industrial revolution 1. burning fossil fuel 2. deforestation Methane - is a 25x more potent gas N2O production of ammonia, excess nitrate growth isn't good

Sulfur (Energy Source)

Can be Both electron donor and acceptor Oxidation of H2S --> Inorganic Sulfur (Sulfate) Organisms can store metal in bodies for energy reserve Remember Sulfur can be acceptor need ATP to activate Sulfur as a donor - need sulfur compounds to activate (establish PMF)

Bio-synthetic Capacity

Capacity to synthesize whats necessary for itself to grow Ex. E. Coli is better than L. Mesenteriodes b/c E. Coli doesn't require amino acids, vitamins etc. It can create those things by itself

Potential Energy

Changes during redox reaction releases energy cell may capture

Hydrothermal Vents

Chemolithotroph paradise full of dynamic micro-environments (Potential Redox Tower) Can be Electron donor and acceptor Theory of Life early electron transport originally started, supported because it developed/supply H2 and S^0 Use Hydrogen as electron donor

Electron Excitation and Charge Separation

Chloro (blue) Bacterio (red) Different energy wavelengths

Measuring Turbidity

Cloudy Light Source and filter to sample the source Used with Spectrometer Optical Density (OD)

Prosthetic Group

Co-Factor is permanently attached to an enzyme Cytochromes = heme groups proteins in the ETC Donate/Accept single electron (NOT PROTONS) Flavoproteins: FAD+ and FMN+

Coenzymes

Cofactor is loosely attached to enzyme Can carry electrons and protons

How do you grow microbes?

Complex (Rich) Medium Enrichment Medium Selective Medium Single Cell Isolation

Microbiome

Comprises all of genetic material within a microbiota (collection of microorganism in a specific niche, such as human gut)

Carotenoids and Phycobilins (Cyanobacteria)

Conjugated double bonds - which absorb stress and electron to be transferred through cell "sun block"

1% of Culturable Microorganism

Cultures that we can gain in a lab: Live in similar conditions Found in human bodies disease

Glutathione

Cytoplasm is reducing environments stores electrons on -OH group

Resources that govern microbial growth in nature

Electron Acceptors: O2, NO3-, SO4^2-, Fe3+ Macronutrients: Nitrogen and Carbon, P, S, K, Mg Energy: Light, Chemicals (H2, H2S, Fe2+...) Micronutrients: Fe, Mn, Co, Cu... (inorganic trace metals) Vitamins, Amino acids... (organic growth factors) Appropriate environmental conditions: Temp., pH, water potential, oxygen potential, light and osmotic condition

Prokaryotic Phototrophs

Electron Donor: Light - Purple/Green Bacteria Anoxygenic Use electrons to fix carbons Use H2S and Sulfur molecules to reduce carbon Generates Sulfuric Acid - Cyanobacteria Oxygenic Generate Oxygen Use H2O as reducing power

Oxygenic Phototrophy

Electron Donor: Water Uses Two photosystems Terminal Electron Acceptor: NAD(P) --> generates NAD(P)H NAD(P)H can be used for biosynthesis Flow of ETC generates PMF (normal) Water is donated to PSII, and excited by light to be a great electron donor P680 = PSII P700 = PSI 1. Non-cyclic electron generate PMF 2. Excites PSII 3. electron travel thorough Cytochrome to PSI 4. Light excites PSI 5. PSI creates Fd (Fd is used for cyclic electron generating PMF helping cytochrome get to PSI) 6. Eventually creating NAD(P)H (Reducing Power) Cycling allows to make PMF => creates ATP

Photosystems in Eukaraya vs Prokarya

Eukaryotes: Photosynthesis occur in chloroplast or chlorophyll attached to thylakoid membranes Prokaryotes: NO THYLAKOID. PMF is generated across inner membrane Water can be electron donor

Iron

Except Iron Oxidize = RUST Good Electron Acceptor Shuttles electrons from organisms to (rust) reducers Nanowires - help with breathing of metals specialized membrane to chain outside of cell to form nanowires pass electrons to allow breathing Shewanella Oneidenis (Class activity chalk board to student etc.)

Phycobilliprotiens

Extends ability of PSII to capture proteins with range of wavelength

Siderophores

Extracellular small molecules that bind Fe(III) and transport it to the cell where it is reduced

Complex (Rich) Medium

Fastest growing, best adapted to those conditions No Targeted Selection Many Microbes can grow Ex. yeast extract, beef heart etc. Best Adaptive organisms will grow first

Primitive ETC in cells

Few Protein required Iron is abundant (oxidized) Sulfur (reduced) PMF => ATP

Bacterias in Human

Firmicutes Actinobacteria Bacteriodietes Proteobacteria Cyanobacteria Fusobacteria Takes 3 years to fully develop all microbes

Flow Cytometry

Florescence-activated cell sorting Selects out single cells for analysis of growth Sorts for cell types - collection vessels etc.

Global Carbon Cycle

Fossil Fuel and CO2 --> reductive co2 fixations photo- and chemoautrophy create organic matter --> respiration and fermintation into CO2 Aerobically and Anaerobically Parts 3:1 Cyanobacteria and Diatoms --> Heterotrophs --> CO2 --> Euryachaeota --> Methylotrophs --> CO2 -> (continues cycle) CO2 --> CO2 fixation Photo and chemoautotrophy --> respiration and fermentation --> CO2 --> methanogenesis --> Methano- and methylotrophy --> CO2 (cycle continues) CO2 --> reduction --> oxidation and redox neutral --> CO2 --> reduction --> oxidation --> CO2 (cycle continues)

ETC

Found in Mitochondria 1. Chain of redox reactions organized by increasing ΔE and alternate carriers that can or cannot accept protons Small so energy can be captured by doing work. Increasing Electron Potential to smaller potential 2. Couple electron movement to generate of a protein gradient Quinones gets electrons outside the cells 3. Net = reduction of terminal electron acceptors and generations of PMF most donate to oxygen our terminal electron acceptor

Organic Terminal Electron Accpetors

Fumarate, DMSO and TMAO to form Succinate Reductive Dechlorination of halgoenated organic compounds

Mycorrhizae

Fungal Mutualism Delivers N and P, nutrients or water to soil to plant Plant provides carbon for fungus Can be Endo or Ecto

Major Redox Event in Glycolsis (Step 1)

G3P (glyceraldehyde-3 Phosphate) used to produce 2 NADH and add an inorganic phosphate Oxidation of Aldehyde: Highly Exothermic Formation of high-energy phosphate anhydride at C1: Endothermic REduction of NAD+ to NADH: Endothermic Net Reaction: =ΔG = +6.3 kj/mol Reduction Potential: -550 mV

Electron Acceptor

Gains Electron B becomes Reduced Ared + Box --> Aox + Bred lower potential energy "Breathable"

Deep Sea use what as resources?

Inorganic Compounds - not a lot of organic carbon present Methanogens fix its own carbon

Nitrite (Energy Source)

Good Electron Donor Nitrate --> Better Electron Donor

Nitrate

Great Electron Acceptor Useable to Plants (Soluble Forms) NO will be used by most organisms

Cultured Based Methods

Grow microbes in the lab and examine their physiological traits

Energy Source: Inorganic Energy for Chemolitotrophs

H, Nitrite, Ammonium, Sulfur, Hydrogen Sulfide, Ferrous Iron

PSI Reaction Center

Have Iron-sulfur cluster proteins in reaction center

PSII Reaction Center

Have quinones in reaction center

Green and Heliobacteria

Higher energy reaction centers, thus reduce Ferridoxin (Fd) which is high energy to reduce CO2 for anabolism Autotrophy is easy

Catabolism

How you break down substrates

Anabolism

How you synthesize biomolecules you need for life

Alternate Electron Acceptors (Breathables)

Humans breath O2 O2 is our electron accpetor

Microbes dominate all biogeochemical cycles on Earth

Humans breath out CO2 microbes do that plus re-cycle CO2 Humans CANNOT live without microbes Microbes CAN live w/o humans

Chemoorganoheterotrophs

Humans!!! Energy come from chemical source from organic things Carbon source are eaten.

Diauxic Growth

Indicates that carbon source is used, cell adapts and synthesizes new enzymes Then utilizes another carbon source

Mutualism

Insect rely on symbionts for survival - rely on symbionts for protein and amino acids changes cellouse to acetate (shields from O2) Tubeworm - act like hydrothermal vent Carbon provided by autotrophic enviroment H2S as donor and O2 as acceptor Ruminant Animals Produce hydrogen and methanogen (creates CH4+) Breakdown cellulose providing shield from anoexic atmosphere cannot digest cellulose Rumen largest fermentation operation

Primitive ETC

Iron-sulfur cluster formed protein formed around cluster Iron & sulfur around transfer of electrons to generate PMF H, S, Fe are abundent possible to do redox chemistry therefore it occurred first

Many types of symbioses

Leaf Cutting Ants Use leaf to garden on use antibiotics to kill bacteria bacteria has not developed resistant against bacteria

KEY Terms Legume-nodule

Leghemolobin - binds O2 (role) --> delivers to ETC Nod Factors --> determines specificity Rhizobia --> group of organisms Myc Factors - similar to nod factors, but used by fungi

Parasitism

Lichens - controlled fungal penetrate cell wall and take nutriens from cyanobacteria fungus provides lichen acids and protects from desiccation Phototrophs provide C and sometimes N

Photosystem

Light Harvesting complexes (antenna pigments) + reaction center How an organisms collects light molecules funnels to special pair. (molecule directly able to send them to ETC)

Retinal-Based Phototrophy

Light driven proton pump Bacteriorhodospin - light sensitive pigment retinal Use lights, and protons pumped out to create ATP

Electron Donor

Loses electrons A becomes Oxidized LEO Ared + Box --> Aox + Bred Higher potential energy electrons Edibles "We Eat"

Green Bacteria

Low light specialist Green Sulfur Bacteria PSI type photosystems Anaerobes, uses H2S as electron donor for photosystems Photoautotrophs: Fix CO2 Green Non-sulfur bacteria PSII type photosystems Can grow: photoautotroph, photoheterotroph or aerobic respiration

Methanogens (CO2)

Made from Archaea (that produce natural gas) Obligate anaerobies cannot tolerate oxygen very abundant in nature Reduce CO2 --> CH4 (Methane) Uses different electron chains Membrane similar to quinomes but very different for carry enzymes Chain isnt made of proteins Make Sodium Motive Force rather than PMF

Fermentation Diversity

Many microbes do fermination do them differently 1. Lactate 2. Succinate 3. Ethanol 4. Acetate 5. CO2 6. H2 clostridium butyclium generates ATP and butryic acid (distinctive smell)

Growth Rate

Measures the number of generations per time in log phase

Enrichment Medium

Medium that favors the growth of a targets microbe (usually fastidious) ex. blood agar or chocolate microbes Lyses Blood Cells

Purple Nonsulfur Bacteria

Metabolically flexible can be heterotrophs or autotrophs Can grow in light and oxygen (Can do Both) 1) grow as phototroph 2) grow via aerobic respiration

Aerobic Methane Oxidation

Methane Monooxygenase uses oxygen in two places 1. ATP 2. use in methane monooxygenase to form water and other molecules

Germ-Free Mice

Mice that germ free humanize mice - similar to human microbinome diet and genetics have effect

Microbes in Nature

Microbes do not grow in isolation like in lab Microorganism mostly exists as mixed population in nature

Light Harvesting Molecules

Molecules arranged around reaction center captures light and funnels to reaction center --> Then goes to ETC Chlorophylls Bacteriochlorophylls Absorbs at different wave length, change of different functional group

How do organisms obtain energy and carbon?

Most NADH fuel ETC and ATP synthase

Two Ways to generate ATP

Oxidative Phosphorylation Used in ATP Synthase/ETC Substrate Level Phosphorylation Used in Glycolysis

Difference between Nature and Lab

Nature 1. Resources for growth are not optimal for any given microbe 2. distribution of nutrients is not uniform 3. microorganisms in nature mostly exists as mixed populations 4. extended periods of exponential growth are rare in nature Microbes in nature grow as biofilms Lab Pure Cultures - lack of competition Ex. E. Coli in lab (20 mins) in human body/nature (12 hours)

Activation Energy

Needed to start a reaction, even if the reaction is favorable Catalyst lower the activation energy, helping reaction proceed

Pathogenic

Nematods living in soil affects insects and releases molecules killing insect use insect corpse as nutrients to reproduce

Branches of the Nitrogen Cycle

Nitrification - produces nitrate from reduce compounds nitrapyrin inhibits Denitrification - consumes nitrate, produces gas that leaves terrestrial environment (respiration of nitrate) Ammonification - produces ammonium from organic nitrogen DRNA - dissimilative reduction of nitrate or nitrite to ammonium Anammox - Reduction of Nitrite to N2 in anoxic environment Nitrogen Fixation - N2 to Ammonia (NH3)

Anaerobic Annamox

Nitrite + Ammonium --> Nitrogen Gas (N2H4) N2H4 --> N2 + 2H2O (release of N2 gas) Assists in getting rid of nitrogen toxins Occurs in Anammoxosome Membrane (Organelle) in Annamox Bacteria Organelle not a membrane

Nitrogenase

Nitrogen fixation requires oxygen-labile N2 fixation occurs in both aerobes and anaerobes Aerobes protect nitrogenase by respiration of oxygen, regulation, symbiosis etc. Cyanobacteria have Heterocyst, site where Nitrogen fixation occurs, needs to be protected Nitrogenase has FeMo-Co, and iron-molybdenum co-factor

Cooperation

Nitrogen fixing and proteobacterium (rhizobium) Grow without Nitrogen soybeans, alfalfa, beans, peas etc. excess N leaks into dead zones Rhizobia in root nodules contribute 1/4 of total annaul n-fixation not all rhizobia species can infect all legumes

Terminal Electron Acceptors other than Oxygen

Nitrogen, Sulfur, Carbon Dioxide (Methanogens or Acetogens) and Iron and Organics

Fermintation

No terminal electron acceptor present (No Oxygen or Nitrogen) Substrate Level Phosphorylation used to make ATP Need to Reoxidize NADH reuses NADH to make pyruvate into lactate 1 ATP is made only by SLP

Specificity of Legume-nodule symbiosis

Nod Factors - determine specificity to plant

Nitrogen Gases

Not useable by Plants NO, N2O, N2

Respiration Location

Occurs in Plasma (inner or thalakoid membrane)

Aerobic Iron Oxidizers

Often live in acidic pH Live in specific environments with oxygen and acidic Iron

Cyanobacteria

Only aerobic oxygen producing bacteria Oxygenated Earth, produces as much oxygen as all plants on earth

Energy Sources (Edibles)

Organic 1. Glucose 2. Other Sugars 3. Starch and Carbohydrates 4. Cellulose 5. Lipids 6. Proteins Inorganic 1. Chemicals H, Nitrite, Ammonium, Sulfur, Hydrogen Sulfide, Ferrous Iron Photons (Photosynthesis)

Syntrophy

Organisms cooperate to degrade substrate anoxically Most are secondary fermentation: H2 is produced End Product: CO2 and CH4 Syntrophy doesnt occur if oxygen is present. Syntrophy cannot be grown in pure culture

Redox Reactions

Oxidation-reduction reactions Harvesting energy from donors through electron transfers

Step 3 of Glycolysis

PEP used to generate ATP 2 Net ATP are created at this step

PSI and PSII

PSI - iron sulfur culture Oxygenic only PSII - uses water as electron donor Anoxygenic only

Endomycorrhizae (Arbuscular Mycorrhizae)

Penetrate into the root Formulate intra/intercelluarly require plant, cant be grown in lab

Growth limiting elements

Phosphorus and Nitrogen are limited for photosynthesis

Photoautotrophy

Photosynthesis*** H2O isnt a great electron donor alone, but with light it becomes a great donor can Also use H2S

Chemical signals mediate initiation of symbiosis

Plant will inhibit rhibozibum if nutrients are present Flavonids initiate rhibozibum Fungi invented nod factors

Photoautotrophs

Plants!!! Energy comes from the sun Fixes Carbon

Chlorophylls

Plants, Algae, and Cyanobacteria

Sulfite Oxidase

Produce Sulfate and generate ATP by Oxidative Phosporylation and SLP

Bacteriochlorophylls

Purple and Green Bacteria Don't generate O2 Mostly purple

Forms of Nitrogen

Reduced Ammonium (NH4+) and Ammonia (NH3) Organics Nitrogen Water-Soluble Nitrogen Nitrate Nitrite Gaseous Nitrogen N2O NO N2 - biggest store of nitrogen (mostly un-used needs to be in another from N2) can be fixed, to be used NH3 lives at normal pH --> nitrification (problem for farmers) Which is Assimilation? Organic Nitrogen Which is dissimulation? Nitrate --> Nitric Oxide --> etc. Nitrogen reactions in human body rely on microbes too

Biomineralization

Reduces Metals to make it less toxic Removal or heavy metals from the ground water

Denitrification

Reduction of Nitrate --> N2 Not good for farmers because farmers not good for agriculture Good for waste water management - decrease toxicity in water

Anaerobic Methane Oxidation (ANME)

Reduction of methane hydrates at bottom of sea Archaea surrounded by sulfate reducing bacteria Creates 1 ATP (not favorable but not many can do this therefore they dont have to worry)

Sources

Release Make things available recycle Nitrogen Fixation

Hydrogenase

Removal of H from H2 1 H --> used for formation of ATP 1 H --> used for NAD reduction

N2 fixation is difficult

Requires 16 ATP N2 fixation by Haber-Bosch equals that of biological N2 fixation

Fastidious

Requires extra nutrients to grow Don't synthesis things need to survive Live close to host

Stores

Reserves Nitrogen Cycle - Nitrogen Gas Carbon Cycle - Organic carbon (fossil fuel)

Microbial Diversity corresponds to many factors and microbiomes

Resilient to perturbations microbes are able to re-establish and resilient even after rotation of water

Organic Chemical for Energy Source

Respiration (uses ETC to make PMF) 1. Aerobic (electron acceptor is oxygen) 2. Anaerbobic (electron accpetor is NOT oxygen, but could be nitrate etc.) Fermination (uses SLP to make ATP) 1. Anaerobic (no external electron acceptor)

Bacteroid

Rhizobia microcolonies surrounded by plant cytoplasmic membrane and the bacterial cell differentiate into Nitrogen-fixing cells Become Symbiosomes

Ectomycorrhizae

Sheaths around the root and colonizes trees in cooler climate Blunted root hairs

Quinones

Small hydrophobic molecules found in membrane carry both electrons and protons cycle electrons in ETC

How do you study metabolism?

Studying nutritional requirements of a pure culture by adding specific nutrient to culture medium

Sulfur/Sulfate

Sulfate requires ATP to make it a better electron accpetor ATP to make APS Reduction of SO4^2- to H2S is done by Dissimilative Reduction Reaction Need 8 electrons to reduce Sulfate to Hyrdogen Sulfide How do they make ATP - Both because APT can use

Biogeochemical Cycling

Sum of Microbial, physical, and chemical processes that drive flow of elements between sediments, water and atmosphere elemental cycles (C, N, S, Fe, P and Mn) can be reduce/intermediate/oxidize and redox state. Ability to be electon donor

Metabolism

Sum of all biochemical reactions that occur in a cell

Assimilation

Takes something and makes it there own Biosynthesis - Not a lot of O2 present

Selective Medium

Target microbe growth, non-targeted microbes are killed or inhibited Pros: Select Desired metabolic capacity Cons: Only get certain types and you have KNOW what you are looking for

Generation Time

Time it takes to divide generations per time N = No2^n N = final cell number No = initial cell number n = # of generations during period of exponential growth

Purple Bacteria (Anoxygenic Phototrophs)

Use high energy electron donor to replenish P670 and run the ETC in reverse to reduce NAD Autotrophy is costly

Phototrophs

Use light as electron donor

Chemolithotrophs are autotrophs

Use oxygen as terminal electron acceptor Inorganic energy and electon source --> uses ETC to make PMF --> ATP (via Ox. Phosphorylation) Carbon source (CO2) --> use NADPH and ATP --> Biosynthesis Need to do carbon fixation Require more energy for reduction of NAD+ to get NADH Use ETC in reverse to reduce NAD

Hydrogen (H2) Energy Source

Used as Electron Donor, used by most chemolithotrophs Commonly produced by Fermentation

Methanogenesis

Used by early archaea 3.7 BYA (as well as acetogenesis (early bacteria))

Chlorophyll-Based Phototrophy

Used light for energy transfer to ETC ETC makes PMF PMF does Photo-Phosphorylation --> ATP Forms Carbon (like plants)

ATP ATP Synthase

Uses ATP to make PMF or PMF to make ATP Every turn = 3 ATP Reversible rotary motor

Direct Counts

Viable Counts - LiveDead Strains

Membranes (PMF)

dissipation of protons motive force coupled by ATP synthesis

Human Gut Microbiome

less diverse than other environments 85% similar in Humans Most bacteria in large intestine - found Colon bacteria found in throughout GI Esophagus, stomach, small intestine and large intestine

Rhodopsin-based Phototrophy

light gets asorbed into (rhodospin complex) generates PMF PMF does Photo-Phosphorylation to create ATP Consume Carbon --> Organically

Catalyst

lower the activation energy, helping reaction proceed Ex. Ribozymes Enzymes - some use cofactors - prosthetic group - coenzymes

Methanotrophs

methylotrophs that use methane as sole source of C and E use methane to form all products (lipids, methanol, organic acids etc.) Methane Monooxygenase - MMO substrate recognition Used in Bioremediation: chlorinated solvents, xenobiotics Used in Biosynthesis: complex materials from methane plus oxygen

Communities are physically separated

microbes are primary catalyst of all nutrients cycles in nature Type of reactions: Species Richness - # of species per sample Species Abundance - Rates of microbial activities depends on nutrients and growth conditions of the environment

Global Warming

microbes fix 1/2 carbon on earth methane hydrates source of greenhouse gas highest 800k years ocean absorbs CO2 and acidifies by .1 pH

Bacteria Phototroph are...

mostly anoxygenic anaerboic phototroph

Root nodule in a legume

secrete node factors --> Rhizobia start symbiosis plants provide leghemoglobin to bind up free oxygen