Mikrobiologi

Wastewater Treatment: Aims

1.To remove organic matter •decrease BOD (biological oxygen demand) •BOD is increased by organic contamination, increased competition for dissolved O2 2.To reduce bacterial load and human pathogens Our water treatment infrastructure is a resource many underdeveloped countries still lack.

Biogeochemistry & Microbial Ecology

1.~ 5.0×10^30cells on earth -> 8 x number of stars in the observable universe 2.Microbes = the single largest carbon sink 3.Via - C-fixation - N-fixation - CH4metabolism - S metabolism They control global biogeochemical cycling...even in some of the most extreme environments!

What is 16S rRNA and 18S rRNA?

16S rRNA and 18S rRNA are ribosomal RNA molecules found in prokaryotes and eukaryotes, respectively. 16S ribosomal RNA is the RNA component of the 30S subunit of a prokaryotic ribosome The 16S rRNA is specific to prokaryotes and is widely used in microbial taxonomy and phylogenetic studies to identify and classify bacteria and archaea. The 18S rRNA, on the other hand, is found in the eukaryotic domain and is commonly used as a molecular marker for studying the diversity and evolutionary relationships of eukaryotic organisms, including protists, fungi, plants, and animals.

16S rRNA conservation

16S rRNA is highly conserved among different organisms, including prokaryotes. Conservation refers to the degree of similarity or preservation of a particular sequence or structure across different species. In the case of 16S rRNA, its conservation means that the sequence and structural features of this ribosomal RNA molecule are relatively consistent among diverse organisms.

Genomic G+C contents

- Genomic G+C content refers to the proportion of guanine (G) and cytosine (C) nucleotides in the DNA of an organism. - It can be used as a characteristic feature to differentiate and classify organisms, as species within a taxonomic group often exhibit similar G+C content.

Genome sequencies uses

- Metagenomics: Assessing the entire gene content of a microbial community - Transcriptomics/proteomics/metabolomics: Interactive mapping and predictive modeling - Sequence for stain identification: monitoring disease outbreakS - Diagnostics: Detecting pathogens or identifying microbes in an enviromental sample - Proteomics: Identifying drug argest and immune response

ORF prediction

- ORF (Open Reading Frame) prediction is a computational method used to identify potential protein-coding regions within a DNA or RNA sequence. - ORF prediction algorithms analyze the sequence for specific characteristics such as start codons (typically AUG), stop codons (such as UAA, UAG, or UGA), and an appropriate reading frame. - By identifying regions that meet these criteria, ORF prediction tools can determine potential protein-coding regions within a given sequence.

What are 'pathogens'?

- Pathogens: Pathogens are microorganisms, such as bacteria, viruses, fungi, or parasites, that can cause disease in their hosts. They have specific mechanisms and virulence factors that enable them to invade, colonize, and harm the host organism. - Opportunistic pathogens: Opportunistic pathogens are microorganisms that are typically harmless or present as part of the normal microbiota but can cause disease in certain situations when the host's immune system is compromised or when they gain access to normally sterile areas of the body. They take advantage of weakened host defenses or altered conditions to cause infections, particularly in individuals with underlying health conditions or weakened immune systems.

Secondary Treatment: Lagooning

1.Lagooning Primary treatment effluent flows through a large, shallow lagoon Microbes oxidize waste as it goes through, sludge removed(settling and oxidation steps combined) Requires: 1.Large enough surface area to keep water oxygenated 2.Enough land 3.Small-medium community size Advantage:Cost-effective, can even be pretty if done correctly

Secondary Treatment: Trickling Filter

2. Trickling filter A trickling filter is a type of wastewater treatment system. It consists of a fixed bed of rocks, coke, gravel, slag, polyurethane foam, sphagnum peat moss, ceramic, or plastic media over which sewage or other wastewater flows downward and causes a layer of microbial slime (biofilm) to grow, covering the bed of media. Aerobic conditions are maintained by splashing, diffusion, and either by forced-air flowing through the bed or natural convection of air if the filter medium is porous. Advantage: needs less land

Secondary Treatment: Digestion

3. Activated sludge digester •often shift between aeration and anoxic conditions •under oxicconditions: nitrification •under anoxic conditions: denitrification Advantage: needslesslandbetterremovalof N and C

Batch Culture Population Growth

4 Growth phases: •lag •exponential/log •stationary •decline/ death

Exoenzyme

An exoenzyme, or extracellular enzyme, is an enzyme that is secreted by a cell and functions outside that cell. Exoenzymes are produced by both prokaryotic and eukaryotic cells and have been shown to be a crucial component of many biological processes. Most often these enzymes are involved in the breakdown of larger macromolecules. Often by organisms in a biofilm

Sterile filtration

Bacterialand archaealcells normally have a size of 0.5-1 μm Membrane and nucleopore filters have pore sizes of 0.2 μmand stop nearly 100% of all cells

Protection from host defenses

Bacteriause differentstrategies to protectthemselvesfrom host defenses: •Multiply inside host cells -avoid phagocytosis -transferred cell-to-cell using host cell cytoplasm •Protection by capsules -prevents recognition by immune system

Toxicity

Botox: 1 ng/kg

Carbon Dioxide Fixation Pathways (6)

Calvin cycle - Bacteria: cyanobateria, purple phototrophs and lithotrophs - Energy: light - ATP/CO2: 3 3-hydroxypropionate cycle: - Bacteria: green nonsulfur bacteria - Energy: light - ATP/CO2: 1.67 Reverse TCA cycle: - Green sulfur bacteria - Energy: Light and Sulfur - ATP/CO2: 1 Reductive acetyl CoA pathway: - Anaerobic bacteria and methanogens (archaea) - Energy: Hydrogen - ATP/CO2: 0.5 Dicarboxylate/4-hydroxybutyrate cycle: - Archaea - Engergy Hydrogen and sulfur - ATP/CO2: 1.5 3-hydroxypropionate/4-hydroxybutyrate cycle - Archaea - Engergy Hydrogen and sulfur - ATP/CO2: 2

The Carbon/Oxygen Cycle

Carbon & oxygen cycles are closely connected Oxygenic photosynthesis -> removes CO2 and produces O2 Respiratory processes -> produce CO2 and remove O2

Accessory Pigments

Carotenoids • yellow, red, brown, green • absorb mainly blue light • antenna pigments • photoprotectiveagents Phycobilins • in cyanobacteria • main antenna pigments • in phycobilisomes • are attached to thylakoidmembrane

Catabolism and anabolism

Catabolism: the breakdown of complex molecules in living organisms to form simpler ones, together with the release of energy; destructive metabolism. Anabolism: the synthesis of complex molecules in living organisms from simpler ones together with the storage of energy; constructive metabolism.

Prokaryotic Cell Cycle

Cell division consists of 3 phases: - C period (S): replication of chromosome - D period (G2): cell division - G1 period (G1): normal growth/waiting period Length of each phase varies between different species and is e.g. dependant on: •Genetic characteristics •Availability of carbon and energy •Temperature

Stationary Phase

Cell division is equal to deathrate. •no net increase in population size •growth rate and death rate are in balance •new nutrients come only from lysing cells •waste products accumulate and inhibit growth •living cells are smaller •organisms capable of producing endospores do this here

Function of the cell wall

Cell walls prevent bursting due to water uptake - Due to the high osmolarity inside the cells in comparison to the out side It provides structural support and shape to the cell, protecting it from external stresses. The cell wall also helps maintain osmotic balance by preventing the cell from bursting in a hypotonic environment. Additionally, the cell wall acts as a barrier, controlling the entry and exit of molecules into the cell. Moreover, the cell wall plays a role in cell-to-cell communication and interaction with the environment.

Lag Phase

Cells: •adjust to new conditions •increase metabolism/anabolism •grow in size but don't divide •growth unbalanced •synthesize enzymes necessary for growth •start replicating the chromosome

Wastewater Treatment Challenges

Challenges of wastewater treatment •Changes in influx water (flow rate) •Changes in incoming organic compounds •Disruption in settling of flocs-Bulking sludge •Too many filamentous bacteria, floating flocs-Rising sludge •Too much nitrate present -microbial production of N2(g) •Plant operators must constantly alter plant operations to deal with these changes

Metabolic (Energy Source)

Chemo-troph: A chemotroph is an organism that obtains energy by the oxidation of electron donors in their environments. Photo-troph: A phototroph is an organism that obtaining energy from sunlight to synthesize organic compounds for nutrition.

Degradation of Biopolymers (Starch)

Ectoenzymes in/on the outer membraner breakdown the strach into Oligosaccharides. These oligosaccharides can then be transported into the Periplasm (diffusion?). In the periplasm other enzymes breakdown the oligosaccharides to monosaccharides that can be transported over in inner membrane.

Cause of death

In places like africa 56% of deaths are coursed by infections deseases

Spontaneous generation?

Louis Joblot(1645-1723) showed that microbes can't spontaneous form from decaying material. By boiling hay in water, and placing it in to different containers one covered and uncovered. Microbes grow in the uncovered one and not in the covered one. When the Cover was removed from the flask microbes grow.

Substrate-level Phosphorylation

transfer of a phosphoryl group from an organic substrate to ADP to generate ATP

The Nitrogen Cycle

Nitrification - NH4 -> NO2(-) ->NO3(-) - Oxic envirment Comammox - NH4 -> NO3(-) - Oxic conditions Denitrification - NO3(-) -> NO2(-) -> NO -> N2O -> N2 - Anoxic N2 fixation - N2 -> NH3 - Anoxic and oxic Assimilation - NH3/NH4 or NO3(-) into organic matter Ammonification .- Amino group (NH2) into NH3/NH4 Anammox - NO3(-) + NH3 -> N2 - Anoxic DNRA: dissimilatory nitrate/nitrite reduction to ammonium

Nitrite oxidation

Nitrite into nitrate, which is a key step in nitrification Nitrite oxidizers can be either autotrophic or heterotrophic, depending on the specific organism. Some nitrite oxidizers are autotrophic, meaning they can utilize inorganic carbon sources (such as carbon dioxide) for their carbon needs. However, there are also heterotrophic nitrite oxidizers that rely on organic carbon sources for their growth and metabolism.

Nitrogen Assimilation

Nitrogenassimilation from: •(organiccompounds) •ammonium or nitrate •fixation of N2

How can E. coli have a generation time of 20 min

Normal generation time is 1 h and replication is 40 min E. coli have overlapping cell cycles enable faster generation times.

Differences and similarities between Bacteria, Archaea and Eucarya

Nuclear membrane B: No A: No E: Yes Plastids B: No A: No E: Yes Peptidoglycan cell walls B: Yes A: No E: No Membrane lipids B: Ester-linked A: Ether-liked E: Ester-linked Ribosome size B: 70S A: 70S E: 80S RNA Polymerases B: 1 (4 SU) A: several (8-12 SUs) E: 3 (12-14 SUs) Transcription factors required B: No A: Yes E: Yes Promoter structure B: Pribnow box A: TATA box E: TATA box

Prokaryotes vs. Eukaryotes: Nuclear structure and function.

Nuleus with menbrane P: No E: Yes Chromosomes P: One E: Two or more Mitosis P: No E: Yes Sexual reproduction: P: Rare; only part of genome involved E: Common; all chromosomes involved Meiosis: P: No E: Yes

Microbes in Food Webs

Often primary producer or decompuseres In the ocean microbes are grazed on by invertebrates and protists or killed by viruses On land they are decompuse organic matter (they also do this in the ocean) - Decomposers: Prokaryotic microbes play a crucial role in breaking down organic matter and recycling nutrients in food webs. - Nutrient Cycling: They participate in nutrient cycling by decomposing dead organisms and organic matter, releasing essential nutrients back into the ecosystem. - Primary Production: Some prokaryotes, such as cyanobacteria, are photosynthetic and contribute to primary production by converting sunlight into organic compounds. - Symbiotic Relationships: Prokaryotes form symbiotic associations with other organisms, such as nitrogen-fixing bacteria in plant roots or gut microbiota in animals, which aid in nutrient acquisition. - Predation: Certain prokaryotes, such as predatory bacteria, can feed on other microbes, regulating population dynamics within the food web. Overall, prokaryotic microbes occupy various ecological niches and contribute significantly to the structure and functioning of food webs through nutrient cycling, primary production, symbiotic interactions, and predation.

Lake Ecosystems

Oligotrophic lakes: large, undisturbed with dilute microbe & nutrient concentrations •Epilimnion: well-mixed layer above the thermocline •Hypolimnion: anoxic •Littoral zone: upper layer shallow enough for rooted plants Eutrophiclakes: high in nutrients (P, N, organic pollutants) -> algae grow and feed bacteria -> depletion of O2(high BOD) -> fish kills

Penicillins

Penicillins work by inhibiting the synthesis of bacterial cell walls. They specifically target an enzyme called transpeptidase, which is responsible for cross-linking the peptidoglycan chains in the cell wall. By inhibiting transpeptidase, penicillins prevent the formation of a strong and stable cell wall, leading to the weakening and eventual lysis of the bacterial cell. This action is selective to bacteria because they have cell walls, while human cells do not. Penicillins are effective against a wide range of bacterial infections and are commonly used as antibiotics. Modification of N-Acylside chain can: •broaden spectrum of penicillin•enhance resistance to β-lactamase•improve oral delivery

Periplasmand Porins

Periplasmis "protected" environment between the membranes. Here degradative enzymes break down molecules to be transported into the cell. Porinsin outer membrane enable the size-selective diffusion of hydrophilic compounds (sugars, amino acids, ions). Molecules up to 700 Daltons can pass.

Movement of prokaryotic cells

Peritrichous: Forward motion is imparted by all flagella forming into a bundle and rotating counterclockwise (CCW). Clockwise (CW) rotation causes the bundle to break apart and the cell to tumble. A return to counterclockwise rotation leads the cell off in a new direction. Polar: CCW rotation results in running, CW rotation of the flagella results in the cell running in reverse. If the cell wanna change direction then it stop rotating the flagella and is then reoriented in a random direction

Cytoplasmic membrane: 3 main functions

Permeability barrier - Prevents leakage and functions as a gateway for transport of nutrients into and wastes out of the cell Protein anchor - Site of proteins that participate in transport, bioenergetics and chamotxis Energy conservation - Site of generation and dissipation og the proton motive force

Pathways of infection

Person to Person - Direct contact: Sex and touch --Gonorrhea - Indirect contact: drinking glass and other fomites --influenza -Airbone droplets: Sneezing and coughing -- influenza Vehicle - Waterborne: sewage --Cholera -Foodborn: contaminated food --Staphylococcal food poisoning -Soilborn: wound and contaminated soil --Tetanus Vector: - Anthropods/insects: Tickes, mosquitos -- Lyme desease, malaria

Phagolysosome

Phagolysosome the structruer that contains the engulfed bacteria Oxidative burst results in the production of toxic oxygen compounds like: •hydrogen peroxide (H2O2) •hydroxyl radical (OH*) •hypochlorusacid (HOCl) •superoxidanion (O2-) •singlet oxygen (1O2) •nitric oxide (NO

Compounds Used in Energy Transformation

Phosphoenolpyruvate (PEP) (-51.6 kJ/mol) Adenosine triphosphate (ATP) (-31.8 kj/mol) Nicotinamide adeninedinucleotide(NAD) - used to move electrones

Heterocyst cell modifications

Photosynthesis -> produces oxygen Nitrogenase-> sensitive to oxygen Differentiation of heterocysts Trick envelope with low gas permeability - A low defussion of O2 used for resiration - Also low defussion of N2 used in fixation -- N2 -> NH3 (the fixed N is send to neboring cells) PS I used to produce ATP but no O2 Heterocytes produce PatS and sends it to sorrunding cells and PatS inhibits the formation of heterocytes so that heterocytes are not formed closed together Sorrunding cells fix CO2->CH2O and gives it to the heterocytes

Lactic Acid Bacteria

•Gram-positive •Found in milk products, intestines, silage •Use Beta-Galactosidaseto split lactose to glucose and galactose •Require complex media •Ferment sugars to lactate (at least 50%) •Homofermenative-> lactate only •Heterofermentative - lactate + ethanol from hexose(+ gas production) - lactate + acetate from pentose

Clostridia

•Gram-positive bacteria •live in e.g. soil •rod shaped •obligate anaerobic bacteria •ferment many different products •here: starch fermented to butyric acid •produce spores •certain Clostridium species produce potenttoxins (tetanus, botulinumtoxin)

Factors Shaping Microbial Communities

Some habitats have continuous nutrient availability This selects for: •high-efficiency permeases -> can take up nutrients at low conc. •the ability to sustain very low growth rates, while not in stationary phase •K-strategist Some habitats have discontinuous nutrient availability (periods of rapid growth alternating with starvation) This selects for: •rapid initiation of growth (short lag time) and rapid growth rates when nutrients are present ability to spend long time periods in stationary phase •r-strategists

Glyoxylate shunt

Some microbes don't have all of TCA The Glyoxylate shunt is a metabolic pathway found in certain microorganisms and plants that allows the net synthesis of glucose from two-carbon compounds, such as acetyl-CoA, without releasing CO2. It bypasses the decarboxylation steps of the TCA cycle and uses isocitrate lyase and malate synthase enzymes to convert isocitrate into glyoxylate and then into malate. This pathway enables organisms to utilize two-carbon compounds as a carbon source, such as in the case of fatty acid metabolism during growth on fatty acids or in the germination of seeds.

Sponge/Algae and Cyanobacteria

Sponges can have photosynthetic symbionts like algae and cyanobacteria.

What are the two ways of isolating microorganisms in/on agar

Spread-plating method: The diluted sample is pipetted onto the surface of an agar plate and spread evenly over the surface. then incubated Pour-plate methode: Sample is pipetted into a steraile petridish. Sterile medium is added and mixed, it then solidify and is incubated

Cytoplasmic membrane: functions

•Impermeable barrier between cell and environment •Transmembrane proton potential central to cell bioenergetics •Reversible proton-linked ATP(synth)ase in membrane •Site of transport systems (influx and efflux) •Site of proton-translocating electron transport system in some bacteria

Coupled C/N/P Cycles

They are very inter connected because they are some of the most important nutrients in living organismens. When there is a lot of these nutrients in a lake it can cause Eutrophication.

What size will a sterile filer let through?

Things smaller the 0.2 µm So no prokaryotic cells can get through

Pathways of methanogenesis

Three kinds of substrate can be used: 1) Hydrogen(carbonaterespiration): 4H2+ HCO3-+ H+→CH4+ 3H2O (∆G°' -135 kj/mol methane) - Methanococcus 2) Acetate(acetoclasticmethanogenesis): CH3COO-+ H2O →HCO3-+ CH4 (∆G°' -31 kj/mol methane) - Methanosarcina 3) C1-compunds(e.g. methanol, methylamine) : 4CH3OH + H2O →HCO3-+ 3CH4+ H+ (∆G°' -112 kj/mol methane) - Methanolobus

Measuring Microbial Growth

Total cell count •turbidity •microscopic counts •flow cytometry Viable cell count •dilution and plating (colony forming unit (cfu) count) •membrane filtration (cfu) •most probable number (MPN)

The history of Microbiology

iÍs also a history of technical development •Mainly microscopy and cultivation techniques •Microbiologic methods (biotechnology) were used long before microbiology became a science: bread, fermentation of milk, e.g. cheese, beer, wine, soy sauce

Examples of Chemo-litho-auto-trophs

nitrifiers(NH4++O2), sulfur-oxidizers, iron-oxidizers, Knaldgas-bacteria (H2+O2)

Examples of Chemo-litho-hetero-trophs

some species of sulfide oxidizers Thiobacilus, Beggiatoa and nitrite oxidizers Nitrobacter

Mutualism

•In mutualism, each partner species benefits from the other and may fail to grow independently. •Mutualism can involve two or more microbial partners. - It can also involve one or more microbial partners with a plant or animal host. •A highly evolved form of mutualism is the lichen. - Lichens consist of an intimate symbiosis between a fungus and an alga or cyanobacterium—sometimes both

Molecular Clock

•The molecular clock is the temporal information contained in a macromolecular sequence. •Based on the acquisition of new random mutations in each round of DNA replication

Reductive Acetyl-CoA Pathway

•Used by anaerobic soil bacteria, autotrophic sulfate reducers, and methanogens •Two CO2molecules are condensed through converging pathways to form the acetyl group of acetyl-CoA; carbon monoxide is an intermediate. •Reducing agent is H2instead of NADPH. Net reaction

3-Hydroxypropionate Pathway

•Used by thermophiles(e.g. bacterium Chloroflexusand archaeonSulfolobus) • Two CO2 are fixed into one molecule of glyoxylateand ultimately into pyruvate Net reaction

Bacteriorhodopsin

•light-induced proton translocation linked to pigment isomerisation(cis/trans) of retinal •no light-harvesting antenna •no reaction centers / electron transport •well characterized •found in halophilic Archaea

Chemical sterilization

•many chemicals can kill prokaryotic microorganisms - organic compounds: e.g. ethanol, phenol, formaldehyde - halogens: e.g. iodine solution, chlorine bleach - heavy metals: e.g. mercuric chloride, silver nitrate - others: e.g. hydrogen peroxide, ozone •often they are also toxic to Eukaryotes •special case: antibiotics The out comes: •Bacteriostatic: Stones grow until removes. No major death of microbes. •Bacteriolytic: Kills microbes and in a way where both total- and viable cell count goes down • Bactericidal: Kills bactria but the total cell counts is stable

Z-Ring Formation

•minicell-forming E. coli •minC, D and Egenes responsible •Min C prevents formation of Z-ring •MinD oscillates between the poles, polymerizes MinC •are longer in the pole regions, thus Z-ring formation is inhibited here •MinE "sweeps" MinCDtowards the poles

Classic prokaryotic taxonomy (Motility)

•motile by flagella •motile by gliding •buoyancy by gas vesicles •nonmotile

Legume/Rhizobia: Root Nodules

•nitrogen-fixing rhizobia live in root nodules of legumes •bacteroidsf ix nitrogen and in return get organic acids from host plants •leghemoglobinin root nodules captures free oxygen to shape perfect conditions for nitrogen fixation and supply oxygen to the bacteroids

Factors Controlling Microbial Growth

•nutrient availability •temperature •oxygen •salinity •pressure •pH •waste products •inhibitors and more

Death Phase

•nutrients are used up •waste products accumulate to toxic levels •net decrease in cell numbers •cells die quick but with a constant speed •often cell death has a similar kinetic as exponential growth phase •not all cells die •resistant cells and endospores survive

Central metabolism consists of:

•pentose phosphate pathway •glycolysis •partial TCA cycle

Classic prokaryotic taxonomy (Other Factors)

•pigments •spore formation •cell inclusions •surface layers •pathogenicity •antibioticsensitivity

Classic prokaryotic taxonomy (Cell morphology)

•shape •size •Gram reaction •presence of flagella and their arrangement

The Phosphorus Cycle

•slow cycling as there are no gaseous intermediates •phosphorus is a limited resource and needs to be recycled •Enhanced biological phosphorus removal (EBPR) in wastewater treatment plants by poly-phosphate accumulating organisms (e.g. Candidatus Accumulibacter) The Gobal Phosphorus Pool most in rocks dead biomass dissolved inorganic nutrient

Total vs. Viable Cell Count

•total and viable cell counts can differ depending on growth phase!

Toxic Effects of Oxygen and Protection from "Active Oxygen"

"Active oxygen" speciesreact with cell components and destroy them Types of active oxygen: Superoxide (O2(-)), Hydrogen peroxide (H2O2), Hydroxyl group(OH•) Cells adapted to oxicenvironments decrease damage to cell components by detoxifying "active oxygen" species. - Catalase: catalyses H2O2 into H2O and O2 - Peroxidase: H2O2+NADH into water and NAD+ - Superoxide dismutase: O2(-) into H2O2 and O2 - and a few others Lack of tolerance to O2is due to absence of these enzymes.

Symbiosis

"Living together" •A stable association •Two organisms dependent upon one another •Each partner is called a "symbiont" •One partner has to benefit •The other may benefit, be harmed or be unaffected •Larger often termed: host

Pathogenicity Islands

"PathogenicityIsland" introduced from another bacterium by Horizontal Gene Transfer Pathogenicity islands are discrete genetic elements or regions found in the genomes of pathogenic bacteria. They contain clusters of genes that contribute to the virulence or disease-causing ability of the bacteria. These genes often encode virulence factors such as toxins, adhesins, and secretion systems that enhance the bacteria's ability to invade and survive in the host, evade the immune system, and cause disease. Pathogenicity islands can be horizontally transferred between bacteria and play a significant role in the evolution and adaptation of pathogenic strains.

Systematics

"The systematic classification of organisms and the evolutionary relationships among them; taxonomy."

Biofilms formation

- Attachment: adhesion of a few motile cells to a suitable solid surface - Colonization: intercellular communication, growth, and polysaccharide formation - Development: more growth and polysaccharide - Active Dispersal: Triggered by environmental factors such as nutrient availability

Pressure adaptations

- Barophiles: require high pressure to grow(still die if to high) - Barotolerent: organisms grow up til a certain pressure but die is the pressure is too high - Barosensitive: dies with increasing pressure

Animal digestive system

- Food goes in - Enters the stomach that have a low pH that kills many organisms - After that fast flow and the body takes op nutrients -- Few bacteria. It is advantageous to be able to attache - in the end there is turbulent flow bacteria ferment fibers and grow - Undigested fibers and microbes exits the body

Murein

- Peptidoglycanchains form foundation of cell wall - Transpeptidation forms rigid cell wall - Murein, also known as peptidoglycan, is a key component of the cell wall in bacteria. It is a complex polymer made up of repeating units of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM), cross-linked by short peptides. Murein provides structural support and rigidity to the bacterial cell wall, protecting the cell from osmotic pressure and maintaining its shape. It also serves as a target for certain antibiotics, such as penicillin, which inhibit the synthesis of murein and weaken the cell wall, leading to bacterial cell lysis.

Cell envelope of gram negative bactaria

- Pink-red when gram stained - Gram-negative bacteria have a cell envelope consisting of an inner membrane, a thin peptidoglycan layer, and an outer membrane. - The outer membrane of Gram-negative bacteria contains lipopolysaccharides (LPS), which contribute to the structural integrity of the membrane and act as an endotoxin. - The presence of an outer membrane provides an additional barrier, making Gram-negative bacteria more resistant to certain antimicrobial agents and immune responses. - The space between the inner and outer membrane is called the periplasmic space, which contains various enzymes and transport proteins involved in cell metabolism and nutrient uptake. - Gram-negative bacteria have porins in the outer membrane, which allow the passage of certain molecules into the periplasmic space. - The thin peptidoglycan layer in Gram-negative bacteria is located in the periplasmic space and provides structural support, but it is more susceptible to enzymatic degradation compared to the thick peptidoglycan layer of Gram-positive bacteria. - The presence of an outer membrane in Gram-negative bacteria can also impact the permeability of the cell envelope, affecting the entry and efflux of molecules into and out of the cell.

Cell envelope gram positive bacteria

- Purple when gram stained - Gram-positive bacteria have a cell envelope composed of a thick peptidoglycan layer. The cell envelope also contains teichoic acids, which are polymers attached to the peptidoglycan and help regulate cell wall growth and function. - The peptidoglycan layer provides structural support and rigidity to the cell. - In addition to the peptidoglycan layer, the cell envelope of Gram-positive bacteria may include proteins, lipids, and other molecules that contribute to cell surface properties and interactions with the environment. - The cell envelope of Gram-positive bacteria is susceptible to the action of lysozyme, an enzyme that can break down the peptidoglycan layer, making them more vulnerable to certain antimicrobial agents.

Genome Replication

- Replisome binds to origin of replication and initiates synthesis - Replication forks continue synthesis in the opposite directions. - Replication forks hit the terminus of replication and collide, releasing two chromosome copies •Bacteria have one origin of replication •Archaeaand eukaryotes have multiple •Dual replication forks in circular chromosomes

Structure of the bacterial spore

- The core: The core of the spore contains the bacterium's genetic material (DNA) and essential cellular components in a dehydrated and condensed state. - Cortex: The cortex is a thick layer surrounding the core, composed of modified peptidoglycan(known as cortex murein). It provides rigidity and protection to the spore. - Spore coat: The spore coat is an outer layer consisting of proteins that provide additional protection to the spore. - Exosporium: Some bacterial spores have an outermost layer called the exosporium, which is a loose, outermost covering that can vary in composition. - Dipicolinic acid (DPA): Bacterial spores often contain high levels of dipicolinic acid, which helps to stabilize the spore's core and protect the DNA from damage. - Germination structures: Bacterial spores may possess specialized structures called germination pores or structures that allow for germination, the process of spore returning to its vegetative state.

Genome, transcription and translation

- The genome is the complete set of genetic material (DNA or RNA) of an organism. - Transcription is the process by which genetic information in the genome is copied into a complementary RNA molecule (transcript). - Translation is the process by which the information in the RNA transcript is used to synthesize proteins, using the genetic code and ribosomes. - Transcription converts DNA into RNA, and translation converts RNA into proteins, allowing the expression of genes and the synthesis of functional proteins in the cell.

Exotoxins examples

- sp. Clostridium tetani: -- Disease: tatanus -- toxin: Tatanospasmin (AB)

Ribosome composition in prokaryotes

- two subunits: large 50S and small 30S - each subunit contains both ribosomal RNA (rRNA) and many proteins - 50S = 23S rRNA + 5S rRNA + 31 proteins - 30S = 16S rRNA +21 proteins - eukaryotic ribosomes are similar but not identical

Legume/Rhizobia: Infection

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Marine Habitats

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Soil Ecosystems

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Resistance to antimicrobials

1)Prevent entry of agent -changes cell envelope and capsule -relatively unspecific 2)Efflux mechanisms -relatively unspecific 3)Intracellular destruction of agent -usuallyspecific -requires major changes (gene transfer) 4)Modification of the target -highly specific -sometimes a minor change (single base pair mutation) -may already be present in large populations (10^9)

Secondary Treatment

1.Lagooning 2.Trickling filter 3.Activated sludge digester 4.Anammox reactor 5.Membrane aerated biofilm reactor (MABR)

Classification of disease by incidence

1. Endemic: Endemic refers to the constant presence or usual prevalence of a disease within a specific geographic area or population. In an endemic situation, the disease is consistently present, and the number of cases typically remains at a relatively steady level, without major fluctuations. 2. Epidemic: An epidemic occurs when there is a sudden and significant increase in the number of cases of a particular disease within a defined geographic area or population. It represents a higher incidence of the disease than what is normally expected. Epidemics can occur in localized regions or affect larger populations. 3. Pandemic: A pandemic refers to a global or widespread epidemic. It occurs when a new infectious disease spreads over multiple countries or continents, affecting a large number of people. Pandemics are characterized by the sustained human-to-human transmission of the disease across different regions. Pandemics often involve novel or highly contagious pathogens to which a significant portion of the population has little to no immunity.

Structure of Flagellum

1. Filament: The long, helical filament is the visible part of the flagellum and extends outward from the cell. It is composed of protein subunits, such as flagellin in bacteria. 2. Hook: The hook connects the filament to the basal body and acts as a flexible joint, allowing the filament to rotate. 3. Basal Body/rotor: The basal body is embedded in the cell envelope and serves as the motor that drives flagellar rotation. It consists of a series of rings and protein complexes that anchor and support the flagellum. 4. Motor Proteins: The motor proteins, located within the basal body, provide the energy for flagellar rotation. They utilize the flow of ions, typically protons or sodium ions, across the cell membrane to generate the rotational force. Flagella rotate either: •clockwise (CW) or counterclockwise (CCW) The flagellum motor is driven by proton motive force ("protoneturbine").

Anthrax

1. Inhaled antrax spores are phagocytosed by alveolar magrophages 2. Magrophages migrates to interstitial fluid and into the lymphatic system 3. Spore germinates in a lymph node killing macrophange and miltuply in lymph node and enters blood stream LD50: 4000 spores

Intracellular pathogens: Listeria

1. Listra cell engulfed by phagosome 2. actin polymerizes around the cell --Actin is a part of the eukaryotic cytoskeleton 3. Listra makes filopod using actin assisted movement to infect neiboring cell

New Chemotaxis in E. coli

1. Sensing: E. coli possesses chemoreceptors, known as methyl-accepting chemotaxis proteins (MCPs), located on its cell surface. These MCPs detect changes in the concentration of specific chemicals in the surrounding environment. 2. Signal transduction: When a chemical gradient is detected, the MCPs undergo conformational changes, triggering a signaling cascade within the cell. This cascade involves the transfer of phosphate groups from a histidine kinase protein, called CheA, to a response regulator protein, called CheY. 3. Flagellar rotation: Phosphorylated CheY binds to the flagellar motor protein, causing a switch in the rotational direction of the flagella. When CheY is unphosphorylated, the flagella rotate counterclockwise, resulting in smooth swimming (runs). When CheY is phosphorylated, the flagella switch to clockwise rotation, leading to tumbling or changes in direction. 4. Tumbling and running: Tumbling occurs when the flagella briefly rotate clockwise, causing the bacterium to change its direction. This allows E. coli to reorient itself and move in a new direction. After tumbling, the flagella switch back to counterclockwise rotation, leading to smooth swimming in the new direction (run). By repeatedly sampling its environment, undergoing tumbling and running, E. coli can navigate towards more favorable chemical conditions or away from harmful substances. This chemotactic behavior enables the bacterium to actively respond to its surroundings and maximize its chances of survival and successful colonization.

Reconstructing phylogenetic trees

1. The first step in making a tree is to align squences 2. A distance matrix is calculated from the number of sequence differences 3. The tree is constructed by adding nodes to join lineages that have the fewest differences This is done by analyzing and comparing specific markers or sequences, such as 16S rRNA, across different organisms. Phylogenetic trees are constructed using computational algorithms that calculate the degree of similarity or dissimilarity between sequences and group them accordingly.

Stages of sporulation

1. The vegerative cell makes an asymmetric cell division 2. Engulfment: the vegetative cell engulf the prespore 3. Cortex formation 4. Spore coat, take up of Ca2+, SASPs and dipicolinic acid 5. maturation of the spore and cell lysis 6. Free spore ready to become vegetative cell •Sporulationis triggered by near depletion of nutrients. •If the nutrients are completely depleted, spores cannot be formed. •Some, but not all cells of a population start to produce spores. •Once started, the process is irreversible.

Microscopes

>0.2 nm - 0.2 µm: eletron microscope 0.2 µm - 100 µm: light microscopes >100 visable

Dilution and Plating

A method used to obtain a culture plate with a countable number of bacterial colonies. A sample is being diluted down to 1/10^4, 1/10^5 and 1/10^6. where after they are being plated. Spread-plating method: The diluted sample is pipetted onto the surface of an agar plate and spread evenly over the surface. then incubated Pour-plate methode: Sample is pipetted into a steraile petridish. Sterile medium is added and mixed, it then solidify and is incubated

What is a Promoter structure and Transcription factors binding sites?

A promoter is a specific DNA sequence located upstream of a gene that plays a crucial role in initiating gene transcription. Transcription factor binding sites are specific DNA sequences where transcription factors bind. These transcription factors regulate gene expression by promoting or inhibiting the binding of RNA polymerase to the promoter region.

immune system

A system (including the thymus and bone marrow and lymphoid tissues) that protects the body from foreign substances and pathogenic organisms by producing the immune response Innate: - Always present - Unspecific - Vaccination has no effect Adaptive: - Incuced (weeks) - Antibodies target specific sites - Vaccination helps generate anti bodies prior to infection

AB type toxins

AB-type toxins are a class of bacterial toxins consisting of two subunits: the A subunit, which is responsible for the toxic activity, and the B subunit, which facilitates the binding and entry of the toxin into host cells. 1. Binding: The B subunit of the toxin recognizes and binds to specific receptors on the surface of host cells. 2. Internalization: The bound toxin is internalized by endocytosis, where it is enclosed in a membrane-bound vesicle called an endosome. 3. Translocation: Within the endosome, the A subunit is released from the B subunit and undergoes a conformational change, allowing it to cross the endosomal membrane. 4. Intracellular action: The A subunit enters the host cell's cytoplasm and exerts its toxic effect by interfering with essential cellular processes, such as protein synthesis or cell signaling. 5. Cellular damage: The action of the A subunit disrupts normal cellular functions, leading to cell damage or death, and contributes to the overall symptoms of the infection or disease.

Active Transport: ABC Transporter

ATP binding cassette (ABC) transportersare the most common active transporters - Uptake ABC transportersare critical for transporting nutrients. - Efflux ABC transportersare generally used as multidrug efflux pumps.

Aligning Sequences

Aligning sequences refers to the process of comparing and arranging two or more sequences of DNA, RNA, or protein to identify similarities and differences between them. The goal is to determine the optimal alignment that maximizes the matching positions and considers possible gaps or mismatches. Sequence alignment is fundamental in various biological analyses, such as identifying conserved regions, studying evolutionary relationships, predicting functional elements, and detecting sequence variations.

Coupled Biogeochemical Cycles

All nutrient cycles are interconnected The C and N cycles are extremely closely coupled-other than H2O, C and N make up the bulk of living organisms These links increase the impact of changes in any of the components: Example: Increase in CO2 Increase in nitrogen fertilizers The rate of primary productivity (CO2 fixation) is controlled by several factors, in particular by the magnitude of photosynthetic biomass and by available N, often a limiting nutrient. Thus, large-scale reductions in biomass, for instance by widespread deforestation, reduce rates of primary productivity and increase levels of CO2. High levels of organic C stimulate microbial nitrogen fixation (N2 —> NH3), and this in turn adds more fixed N to the pool for primary producers; low levels of organic C have just the opposite effect. High levels of ammonia (NH3) stimulate primary production and nitrification, but inhibit nitrogen fixation. High levels of nitrate (NO3_), an excellent N source for plants and aquatic phototrophs, stimulate primary production but also increase the rate of denitrification; the latter removes fixed forms of N from the environment and feeds back in a negative way on primary production (Figure 21.6).

Cyclic vs. Linear Electron Transport

Autoheterotrophy: light -> cyclic electron transport -> transmembrane proton potential -> ATP (+Organic matter -> biomass) Photoautotrophy: light -> linear electron transport -> transmembrane proton potential -> ATP reduction of NAD(P)H - ATP and NAD(P)H can then be used to fix CO2

Secondary Treatment: Anaerobic Treatment

Anaerobic digester: Separated sludge pumped into anaerobic digester •Inflow material: undigested fiber & bacterial cells •Over time, fiber degraded, microbia lcells die or are consumed in various stages •Result: material -> CO2, CH4, late stage microbial cells •Material can be landfilled, or used as fertilizer (N-rich) •If toxic components/heavy metal present, treated •CH4 can be used to run plant or burned 1. complex polymers like polysacchires, lipids and proteins go in 2. they are then hydrolysis by microbial enzymes and broken down to monomers. 3. the monomers undergo fermentation and are made into organic acids like acetat but also CO2 and H2 4. organic acids, CO2 and H2 are used in methanogenesis

Anaerobic Respiration

Anaerobic respiration is a metabolic process that occurs in the absence of oxygen. It allows cells to generate energy from organic molecules by using electron acceptors other than oxygen, such as nitrate, sulfate, or even certain organic compounds. Unlike aerobic respiration, which produces carbon dioxide and water as byproducts, anaerobic respiration produces various end products depending on the specific electron acceptor used, such as nitrite, sulfide, or ethanol. While less efficient than aerobic respiration in terms of ATP production, anaerobic respiration enables organisms to survive and generate energy in environments with limited or no oxygen availability.

The history of Microobes

Ancestors of bacteria were the first life on Earth The first microbes were observed in 1673

Chemical defense

Antimicrobial peptides of many kinds are found in all animals •A variety of different tissues secrete antimicrobial proteins. -antimicrobial proteins are constitutive defenses •There are two classes of antimicrobial proteins -enzymes -antimicrobial peptides (AMPs) •Antimicrobial enzymes include -lysozyme, an enzyme that hydrolyzes murein -phospholipases that hydrolyze the ester linkages in phospholipids.

Ectoenzymes

Any enzyme found on the outer surface of a cell. Can also be involved in the breakdown of larger macromolecules.

Regulating Membrane Fluidity in archaea

Archaea can adjust the length, branching, and saturation of their isoprenoid side chains to modulate membrane fluidity. For example, increasing the number of branches or incorporating cyclical structures in the lipids can enhance membrane stability in harsh conditions. Monolayer membranes contribute to increased membrane rigidity

Membrane lipids

Archaea: The hydrophobic portions of archaeal lipids are comprised of isoprenoid chains synthesized from repeated units of isoprenephospholipids. This contrasts with the lipids of Bacteria and Eukarya, which have fatty acid tails. Bonded to glycerol by an ether linkage in archaea (ester in B and E) •Glycerol diethers: - Archaea can have lipid bilayers composed of phosphoglycerol diether lipids. •Diglycerol tetraethers: - Some Archaea can also have lipid monolayers composed of diphosphoglycerol tetraether lipids •Crenarchaeol: - Isoprene lipids can often contain 5- and 6-carbon rings such as those present in crenarchaeol. Bacteria: The specific composition of the phospholipids can vary among bacterial species, with variations in the length and saturation of the fatty acid chains. Additionally, some bacteria may have unique lipids, such as hopanoids or sterols, which contribute to the stability and functionality of the cell membrane.

Spread of antibiotic resistance in populations

Chromosomally-mediated resistance mutant selection - refers to the process in which mutations occur in the chromosomal DNA of a microorganism, leading to the development of resistance to antimicrobial agents. These resistant mutants are then selected for and can survive and multiply in the presence of the antimicrobial, contributing to the overall resistance of the microbial population. Plasmid-mediated resistance - Plasmid-mediated resistance refers to the acquisition and spread of resistance genes through plasmids, which are small, self-replicating DNA molecules separate from the chromosomal DNA. These plasmids can transfer resistance genes between bacteria, allowing for the rapid dissemination of antibiotic resistance traits within a microbial population.

What is clean streaking and why is it important?

Clean streaking: • Steril loop is use to take inoculum • Spread in one corner of the agar plate • incubation should show confluent growth at the beging of the streak and isolated colonies at the end It is importen because • Different species needs to be sperated •Repeating streak plating will result in a clonal population Working with clonal bacterial populations offers several advantages in research and applications. It ensures genetic uniformity, allowing for consistent and reproducible results. Clonality simplifies the interpretation of experimental outcomes, as any observed variations can be attributed to specific factors rather than genetic diversity. It facilitates the study of specific traits or mutations and enables the production of large quantities of homogeneous microbial products.

cell morphology

Coccus (cocci): Round Rods: straight and slightly elongated Spirillum(spirilla): elongated and spiral Spirochete: long spiral bacteria Stalk: A bacterium with a cell body on a stalk with a holdfast(foot) Hypha: is a long, branching, filamentous structure Filamentous: Long strings

Types of heatsterilization:

Cooking (100 °C for 15 min) kills living cells but not all spores 2.Moist heat and pressure(autoclave, 121 °C, 15 psi for 15 min) kills living cells and spores 3.Dry heat (160-180 °C for 2-4 hours) kills living cells and spore

Examples of Photo-litho-auto-trophs

Cyanobacteria(H2O), Chlorobiaceae, Chromatiaceae(H2S), Chloroflexus(H2)

Biogeochemistry

Definition: Biogeochemistrydescribes the cycling, transport and transformation of chemical elements and molecules that move between the biotic ("bio-") and abiotic("-geo-") part of an ecosystem. Prokaryotesare the most important driving force in biogeochemical cycling. Many are still uncharacterized. Organisms respond to & create chemical changes in the environment The chemical processes of life involve: Redoxreactions (reduction and oxidation reactions) Reorganization reactions (simple compounds to complex compounds) Every transformation process has a reciprocal process Element cycling

Counting Chambers

Different chambers exist, e.g. Petroff-Hausser, Thoma, .... They differ in volume, please note when calculating cell concentrations!

Microbial Population Growth

Different types of microbial population growth: •batch culture: - in laboratory cultures - not often found in nature - maximum growth rate •chemostat: - continuous culture - can be optimized for high or low growth rate - good yields - closer to environmental growth •environment: - sometimes batch culture-like (exception) - slow growth rate with long G1 phases (chemostat-like)

Intoxications

Due to ingestion of a microbial toxin:pathogen does not need to multiply and establish itself in the host. 1.Botulism after ingestion, the toxin (an AB exotoxin) is absorbed into the bloodstream and taken up by nerve cells. 2.Staphylococcal food poisoning

Endotoxin

Endotoxin refers to a toxic component present in the outer membrane of certain Gram-negative bacteria. It is composed of lipopolysaccharide (LPS) and can elicit a strong immune response in the host, leading to inflammation and various symptoms associated with bacterial infections. Lipid A part of LPS found in Gram-negative bacteriaActs on: •Macrophages to produce cytokines and induce fever •Neutrophilesto produce compounds that dilate blood vessels, causing edema and shock •Complement system to induce its activation, causing inflammation

TCA =Tricarboxylic Acid; also: Krebs cycle or citric acid cycle

Energy carriers per glucose molecule: →2 ATP → 6 NADP+ H+ → 2 FADH2 Is a central metabolic pathway in aerobic organisms. It serves as a hub for the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins. The cycle begins with the entry of acetyl-CoA and combines with oxaloacetate to form citrate. Through a series of enzymatic reactions, citrate is converted back to oxaloacetate, generating energy-rich molecules such as NADH and FADH2. In addition to energy production, the TCA cycle provides intermediates for various biosynthetic pathways, including amino acid synthesis. Overall, the TCA cycle is essential for cellular respiration and the generation of ATP in aerobic organisms.

Secondary active transport (Simple/coupled transport)

Energy released by moving a driving ion down its gradient is used to move a solute up its gradient. Antiport: The actively transported molecule moves in the direction opposite to the driving ion Symport: The two molecules travel in the same direction

Tertiary Treatment: Phosphorus Removal

Enhanced Biological Phosphorus Removal (EBPR) is a wastewater treatment process that utilizes certain bacteria to remove phosphorus from wastewater. EBPR involves the cultivation of specific bacteria, called polyphosphate-accumulating organisms (PAOs), that have the ability to store phosphorus in their cells as intracellular polyphosphate. These bacteria are cultivated under anaerobic and aerobic conditions in a sequencing batch reactor or an activated sludge process. During the anaerobic phase, PAOs take up volatile fatty acids as a carbon source and convert them into polyhydroxyalkanoates (PHAs). Then, during the aerobic phase, PAOs utilize the stored PHAs as a source of energy and carbon while taking up phosphorus from the wastewater. This process effectively removes phosphorus from the wastewater, reducing its concentration to environmentally safe levels. The treated wastewater can then be safely discharged into water bodies.

Enrichment cultures (media)

Enrichment cultures with selective media: •low abundant members of the community get enriched from natural samples •as their proportion increases they can be isolated by plating •many selective media exist, e.g.: blood agar, manniteagar (Azotobacter), eosin-methyleneblue (EMB) agar (Gram-) Very very few microbes are culturable: In soil, rivers, lakes, marine, sediment only between 0.01-0.1% can be cultured 10% of the organisms from active sludge can be cultivated

Types of Cell Division

Equal products of cell division •Binary Fission - Most bacteria Unequal products of cell division •Budding - Simple budding - Budding from hyphae •Asymmetric Fission - Cell division of stalked organisms - Polar growth without differentiation of cell size

Infectious dose

Escherichia coli: 10^6-10^8cells Salmonella: > 10^5cells Cholera: 10^4-10^6cells Bacillus anthracis: 10^4spores Campylobacter jejuni: 500 cells Shigella: 10 cells Escherichia coli O157:H7: < 10 cells

Most Probable Number (MPN)

Estimates cell concentration using dilution series Sets of tubes are incubated; results are recorded and compared to table to give statistical determination

Why 16S rRNA?

General considerations •universal -essential in all cells •similar function -directly comparable •1500 bp is long enough to see useful differences •interacts with other gene products in complex assembly critical for survival -decreases likelihood of horizontal gene transfer Practical advantages •conserved regions alternate with more variable regions (because all bases are functional -compare protein) •allows reliable alignment over broad taxonomic range •conserved regions allow for use of "universal primers" for PCR •many sequences available for comparisonin online databases 9,469,124 sequences >300 bpAugust 27, 2020

What are species?

Eukaryotic species definition: "Organisms that can interbreed and produce fertile offsprings." Prokaryotic species "definition": •group of similar related strains that differ more from other strains than they do from each other •96-98% identity in the 16S rRNAgene •>70% genome hybridization estimated >10 million prokaryotic species (in contrast: approx. 1.6 million eukaryotic species are known)

Taxonomichierarchy

Example: Domain: Bacteria Phylum: Firmicutes Class: Bacilli Order: Lactobacillales Family: Lactobacillaceae Genus: Lactobacillus Species: paracasei Strain/subspecies: paracasei Lactobacillus paracaseisubsp. paracasei

Host damage

Host damage is often caused by overreaction of host defenses •High concentration of inflammatory and immune modulators at the site of microbial attack provoke responses that damage healthy cells •Modulators can also diffuse from the sites of infection to produce systemic effects such as fever

The Iron Cycle

Ferrous: Fe(2+) Ferric: Fe(3+) Ferrous iron oxidation: caused by bacteria/chemicals (Fe(2+) -> Fe(3+)) Ferrous reaction with water to form Fe(OH)3 Ferric iron reduction: Caused by bateria (Fe(3+) or Fe(OH)3 -> Fe(2+)

Extracellular structures

Flagella/Archaella: Flagella and archaella are whip-like appendages found on the surface of certain cells that enable them to move. Pili: Piliare used to attach, transfer proteins and DNA, and for motility.All Gram(-) bacteria and many Gram(+) have them. Fimbriae: Fimbriaeare used to attach to surfaces and to form biofilms. Hami: SM1 group Euryarchaealiving in the deep subsurface have hami.Hamiresemble Type IV pilibut have "grappling hooks" at the end.

Organisms that can fix N2

Free-living aerobes Phototrophs: Cyanobacteria Chemo-organotrophs: Azotobacter Free-living anaerobes Phototrophs: Purple bacteria, Green sulfur bacteria Symbiotic: Rhizobium

Microbiology today and the age of -omics

Genomics: The study of the complete set of genes (genome) within an organism, including their structure, function, and organization. Transcriptomics: The analysis of all the RNA transcripts produced by the genes in a cell or organism, providing insights into gene expression patterns and regulation. Proteomics: The study of the entire set of proteins (proteome) expressed by a cell or organism, focusing on their structure, function, and interactions. Metabolomics: The comprehensive analysis of the small molecules (metabolites) present in a biological sample, providing information about the metabolic pathways and processes occurring within a cell or organism. Exometabolomics: The study of the extracellular metabolites released by cells or organisms into their environment, helping to understand their metabolic activities and interactions with their surroundings.

Glycolysis (Embden-Meyerhof-Parnaspathway)

Glycolysis is a metabolic pathway that converts glucose into pyruvate. It occurs in the cytoplasm and involves a series of enzymatic reactions, ultimately producing ATP through Substrate-level Phosphorylation and NADH. Glycolysis is an essential process for energy production in both aerobic and anaerobic conditions. Net reaction: glucose(6C)+ 2NAD + 2ADP + 2Pi -> 2pyruvate(3C) + 2NADH + 2H+ + 2ATP Net Energy carries: 2 ADP + 2 Pi -> 2 ATP + 2 H2O 2 NAD+ + 2 H+ + 2 e- -> 2 NADH + 2 H+ Glycolysis pathway yields double the energy compared to the Enter-Doudoroffor Pentose Phosphate pathways.

Mention bacteria that form endospores

Gram positive - Aerobic : Bacillus eg subtilis - Anaerobic : Clostridium eg butyricum

Cell Divison

Gram-negative bacteria •constriction of cell envelope in the middle of the cell •constriction deepens until cells are separated Gram-positive bacteria •no constriction of their girth •formation of division septum

Growth and Death Rates

Growth rates By measuring the generation time in the exponential phase, we can assess the growth rate and reproductive capacity of the microbial population, which is useful for various applications such as studying microbial physiology, evaluating antimicrobial efficacy, or optimizing industrial processes involving microbial growth. Death rates: important for sterilization •decimal reduction time = D-value •describes the time it takes to reduce the population by one order of magnitude(90%)

Elemental composition of a prokaryotic cell

H: 8% C: 50% N: 14% O: 20% P: 3% S: 1% And a lot od essential ions like Na, Mg, Cl, K, Ca

Cofactors in Respiration

Heme groups (Heme b) Iron-sulfur closter [2Fe-2S] & [4Fe-4S] Q FMN

Metabolic (Carbon Source)

Hetero-troph: is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. Auto-troph: An autotroph is an organism that produces complex organic compounds (such as carbohydrates, fats, and proteins) using carbon from simple substances such as carbon dioxide, generally using energy from light (photosynthesis) or inorganic chemical reactions (chemosynthesis). Mixo-troph: A mixotroph is an organism that can use a mix of different sources of energy and carbon, instead of having a single trophic mode on the continuum from complete autotrophy at one end to heterotrophy at the other.

Secondary structure of 16S rRNA

High conservation of secondary structure! The secondary structure of 16S rRNA refers to the specific folding pattern and interactions within the RNA molecule. It is characterized by the formation of stem-loop structures, helices, and other structural elements resulting from base pairing between complementary nucleotides. The secondary structure of 16S rRNA is highly conserved across different organisms and plays a crucial role in its function as a component of the ribosome. The structure helps in maintaining the overall stability and integrity of the ribosome and facilitates interactions with other ribosomal components and ribosomal proteins.

Homo- vs. Heterofermentative pathway

Homofermentative: Glukose is made into 2 lactate (2 ATP) Heterofermentative Glukose is made into one lactate, one CO2 and one ethanol (1 ATP)

Horizontal gene transfer

Horizontal gene transfer (HGT) refers to the transfer of genetic material from one organism to another that is not its offspring, resulting in the acquisition of new genes or traits. It involves the transfer of genetic material between different species or even different domains of life, such as bacteria to bacteria, bacteria to archaea, or even between prokaryotes and eukaryotes. Horizontal gene transfer can occur through various mechanisms, including conjugation, transformation, and transduction. HGT plays a significant role in microbial evolution and can contribute to the spread of antibiotic resistance genes, virulence factors, and other adaptive traits among different organisms.

Differentiation in Cyanobacteria

Hormogonia - Short-chain filaments for dispersal - become transient motile by differentiating gliding cells and terminal cells with poined ends Akinetes - resistant resting stanges - limitation of C or P, temperature stress triggers formation - increased cell wall and nutrient reserves Heterocysts - Induced by nitrogen limitation - Nitrogenase is getting expressed - degradation of PS II

In contrast to Eukaryotes, transcription and translation are coupled.

In prokaryotes, such as bacteria, transcription and translation are coupled processes that occur simultaneously in the cytoplasm. As soon as a segment of DNA is transcribed into mRNA, ribosomes bind to the mRNA strand and begin translating it into a protein. This coupling allows for rapid protein synthesis and efficient coordination of gene expression in prokaryotic cells. In contrast, in eukaryotic cells, transcription occurs in the nucleus, and the mRNA transcript must undergo processing and transport to the cytoplasm for translation to take place, making the processes of transcription and translation spatially and temporally separated.

Cell membrane

In prokaryotes, the cell membrane is composed of a phospholipid bilayer. The phospholipids are arranged with their hydrophilic (water-loving) phosphate heads facing outward towards the aqueous environment, while their hydrophobic (water-fearing) fatty acid tails are oriented towards the interior of the membrane. This lipid bilayer provides a barrier that separates the cell's internal contents from the external environment. Embedded within the phospholipid bilayer are various proteins and other molecules that play roles in transport, signaling, and other cellular processes. Additionally, some prokaryotes may have additional components in their cell membrane, such as hopanoids or sterols, which help stabilize the membrane structure.

Positive Feedback on Methane Release

Increasing global temperatures have a positive feedback on methane release from permafrost soils and methane hydrates.

Active transport: Group translocation

Ingroup translocation, energy is used to chemically alter the substrate during transport.Brock, Fig. 2.6Example: Phosphotransferase system (PTS) •present in all bacteria. •uses energy from phosphoenolpyruvate (PEP) to attach a phosphate to specific sugars (like Glukose -> G-6-P) •can accommodate different substrates. •Phosphate from PEP is passed along common elements of the PTS to the Enzyme II and Proteins

Penicillin inhibits transpeptidation

Inhibits only growing cells! Penicillin is an antibiotic that inhibits transpeptidation, which is a crucial step in the synthesis of the bacterial cell wall. Penicillin specifically targets the enzymes called penicillin-binding proteins (PBPs) that catalyze transpeptidation. Penicillin structurally resembles the D-alanyl-D-alanine terminus of the peptidoglycan precursor, and it competitively binds to the active site of PBPs. This binding prevents the cross-linking of adjacent peptidoglycan strands during transpeptidation. As a result, the bacterial cell wall becomes weakened and more susceptible to osmotic pressure, eventually leading to cell lysis and death. By inhibiting transpeptidation, penicillin and other beta-lactam antibiotics effectively target bacterial cells while sparing human cells, which do not have peptidoglycan cell walls.

Why is membrane fluidity important?

It is important because it affects various cellular processes such as membrane protein activity, transport of molecules across the membrane, and signal transduction. Optimal membrane fluidity allows for proper membrane protein folding, enzymatic activity, and efficient diffusion of molecules.

Koch's Postulates

Koch's Postulates are a set of four criteria proposed by the German physician Robert Koch in the late 19th century to establish a causal relationship between a microorganism and a disease. The postulates are as follows: 1. The microorganism must be present in individuals with the disease and absent in healthy individuals. 2. The microorganism must be isolated and grown in pure culture. 3. Inoculating a healthy individual with the pure culture should result in the development of the same disease. 4. The same microorganism must be re-isolated from the newly infected individual.

Lipopolysaccharide (LPS)

LPS acts as endotoxin-> lipid A part is toxic LPS from different bacteria vary in their level of endotoxicity - Lipopolysaccharide (LPS) is a complex molecule found in the outer membrane of Gram-negative bacteria. - It consists of three main components: lipid A, core oligosaccharide, and O antigen. - Lipid A is the hydrophobic region that anchors LPS in the outer membrane and serves as an endotoxin. - Core oligosaccharide connects lipid A to the O antigen, providing structural stability. - O antigen is the highly variable outermost portion of LPS and acts as an antigen, contributing to bacterial virulence and immune recognition.

Ethanol acetate fermentation

Lactate is is oxidized into pyruvate, reducing NAD+ in the process. Pyruvate is made into Acetyl-CoA Acetyl-CoA have two pathways in Ethanol acetate fermentation -Reduction of Acetyl-CoA to reoxidize NADH making Ethanol in the process - Oxidation of acetyl-CoA to produce ATP making acetat in the process

Locations of Carbon Fixation

Location and Global primary production(10^15 gC/year) Open ocean: 29.3 Coastal waters: 16.6 Polar oceans: 6.4 Rain forests: 17.8 Savannas: 16.8 Other forests and grass areas: 12.5 Agriculture and forestry: 8.0 Tundra: 0.8 Deserts: 0.5

Invasiveness and Toxicogenicity

Low invasiveness and low toxic production =Not pathogenic Low invasiveness and high toxic production = Diptheria High invasiveness and low toxic production = Gangrene High invasiveness and high toxic production = Many pathogens

Adaptive Immunity

Lymphocytes are primary effector cells - Lymphocytes B and T - Focus attack on specific pathogens - Antibodies from plasma cells and cytotoxic T cells help clear specific infections - post exposure immunity by B and T memory cells is common -- Functionof antibodies: -neutralize toxins -remove infectious agents by: clump bacteria, utilizing the filtering of the body -interact with complement to lyse certain bacteria

Lysozyme

Lysozyme is an enzyme that plays a key role in the innate immune system's defense against bacterial infections. It is found in various bodily secretions, such as tears, saliva, and mucus. The primary function of lysozyme is to hydrolyze the glycosidic bonds in peptidoglycan, which is a major component of bacterial cell walls. By breaking down peptidoglycan, lysozyme weakens the structural integrity of the bacterial cell wall, leading to cell lysis and death. Lysozyme is particularly effective against Gram-positive bacteria, which have a relatively thin peptidoglycan layer. It is less effective against Gram-negative bacteria, which have an additional outer membrane that provides some protection against lysozyme. Overall, lysozyme serves as an important defense mechanism in the body's innate immune response by targeting and destroying bacterial cells.

Germ theory of disease

Many diseases are caused by microbes

Surface growth

Many pathogens infect surfaces only Surface growth reduces the pathogen's exposure to most of the host's antimicrobial defenses. A major class of surface infections is the bacterial gastrointestinal infections. They survive the trip through the gut by competing with the normal microbiomefor attachment to the epithelial cells that line the intestinal tract

Metabolic pathway prediction

Metabolic pathway prediction is a computational approach used to infer the set of biochemical reactions and pathways that are likely to occur in an organism based on its genome sequence.

Meta-omics

Metagenome:"All the genetic material present in an environmental sample, consisting of the genomes of many individual organisms." Molecular ecology approach •advancements in sequencing techno-logiesand bioinformatics enable us to study the genomes/transcriptomesof uncultivated organisms •populations can be studied in the environment •the full prokaryotic diversity becomes accessible If you take samples from a lake at different depth you can see how the collection of microbes changes. If you also do it over cerveral mouths then a change can allso be opserved there

Types of oxygen adaptations

Microbes exhibit different adaptations to survive and thrive in the presence of oxygen. Here are some types of oxygen adaptations in microbes: 1. Obligate Aerobes: These microbes require oxygen for their growth and survival. They have efficient mechanisms for utilizing oxygen in respiration to generate energy. 2. Obligate Anaerobes: Obligate anaerobes are microbes that cannot survive in the presence of oxygen. They lack the necessary enzymes to detoxify reactive oxygen species produced during aerobic respiration. They carry out anaerobic metabolism for energy production. 3. Facultative Anaerobes: Facultative anaerobes can survive and grow in the presence or absence of oxygen. They have the ability to switch between aerobic and anaerobic metabolism depending on the availability of oxygen. In the presence of oxygen, they can utilize aerobic respiration for energy production, and in the absence of oxygen, they can switch to anaerobic fermentation or other anaerobic pathways. 4. Microaerophiles: Microaerophiles require low levels of oxygen for growth. They can tolerate oxygen to some extent but are sensitive to high concentrations. They possess mechanisms to protect themselves from oxidative damage caused by oxygen. 5. Aerotolerant Anaerobes: Aerotolerant anaerobes can tolerate the presence of oxygen but do not use it for their metabolism. They can survive in the presence of oxygen by employing various mechanisms to protect themselves from oxidative stress. These oxygen adaptations involve enzymes, protective mechanisms against reactive oxygen species, and metabolic pathways that enable microbes to adapt to different oxygen conditions in their environments.

Types of temperature adaptations

Microbes have evolved various temperature adaptations to survive and thrive in different temperature ranges. Some of the common types of temperature adaptations in microbes include: 1. Psychrophiles: These are microbes that can grow and thrive in cold temperatures, typically below 20°C. They have enzymes and cellular structures that are adapted to function optimally at low temperatures. 2. Mesophiles: Mesophiles are microbes that prefer moderate temperatures, typically ranging from 20°C to 45°C. They are often associated with environments such as the human body or moderate terrestrial and aquatic habitats. 3. Thermophiles: Thermophiles are heat-loving microbes that can grow and thrive at high temperatures, typically above 45°C. They have specialized enzymes and proteins that remain stable and functional even in extreme heat. 4. Hyperthermophiles: Hyperthermophiles are extreme thermophiles that can tolerate and grow at temperatures above 80°C, and some can even survive above 100°C. They are typically found in hot environments such as hydrothermal vents or geothermal areas. These temperature adaptations involve modifications in cellular structures, membrane composition, enzyme stability, and metabolic processes to ensure optimal functioning and survival under specific temperature conditions.

Denitrification

Microbial denitrification is a metabolic process carried out by certain bacteria and archaea, where nitrate (NO3-) is converted into nitrogen gas (N2) under anaerobic conditions, contributing to the global nitrogen cycle and reducing nitrate levels in the environment. NO3- losses 2e ->NO2- losses an e -> NO½ losses an e -> N2O½ losses an e -> N2

Iron reduction

Microbial iron reduction is a metabolic process carried out by certain microorganisms that utilize iron as an electron acceptor for respiration, converting insoluble ferric iron (Fe3+) to soluble ferrous iron (Fe2+) through enzymatic reactions. This process plays a crucial role in iron cycling in various environments and has implications in biogeochemical processes and remediation of contaminated sites. Extra: Geobacter is a genus of bacteria known for its ability to produce electrically conductive pili, also called nanowires, which allow the cells to transfer electrons to external surfaces, including minerals and electrodes. This unique feature enables Geobacter to participate in various processes, such as extracellular electron transfer, biofilm formation, and potentially applications in renewable energy and environmental remediation.

Microbial pathogenesis

Microbial pathogenesis refers to the process by which microorganisms cause disease in a host organism. It involves various mechanisms and interactions between the pathogen and the host, leading to the development of infection and the manifestation of disease. Here are some key points about microbial pathogenesis: - Adhesion: Pathogens must first adhere to host tissues or cells to establish an infection. They use various adhesion molecules or structures to bind to specific receptors on host cells. - Invasion: Once attached, pathogens can invade host tissues through various mechanisms, such as secretion of enzymes that degrade host barriers or induction of host cell uptake. - Colonization: Pathogens establish themselves in host tissues and multiply, often forming biofilms or localized infections. - Immune evasion: Pathogens have mechanisms to evade or subvert the host immune response, such as modifying their surface antigens or producing molecules that inhibit immune defenses. - Toxin production: Many pathogens produce toxins that directly damage host cells or interfere with host cellular processes, contributing to tissue damage and disease symptoms. - Host damage: The host immune response and the direct effects of the pathogen lead to tissue damage, inflammation, and other disease manifestations. - Transmission: Pathogens have strategies for spreading from one host to another, such as through respiratory droplets, contaminated food or water, vectors, or direct contact. Understanding microbial pathogenesis is crucial for developing strategies to prevent and treat infectious diseases.

Sulfate reduction

Microbial sulfate reduction is a metabolic process in which certain microorganisms use sulfate as a terminal electron acceptor, converting it to hydrogen sulfide (H2S). This process plays a crucial role in the global sulfur cycle and can be carried out by various bacteria and archaea in anaerobic environments. H2S can be excreted or assimilated into organisc sulfur compunds like cysteine

Endospore vs Vagetative cell

Microscopic appearance Cell: Nonrefractile Spore: Refractile Calcium content Cell: Low Spore: High Dipicolinic acid Cell: Absent Spore: Present Enzymatic activity Cell: High Spore: Low Respiration rate Cell: High Spore: Low or absent Macromolecular synthesis Cell: Present Spore: Absent Heat resistance Cell: Low Spore: High Radiation resistance Cell: Low Spore: High Resistance to chemicals Cell: Low Spore: High Lysozyme Cell: Sensitive Spore: Absent Water content Cell: High, 80-90% Spore: Low, 10-25% in core Small acid-soluble spore proteins Cells: Absent Spore Present

Prokaryotes vs. Eukaryotes: Cytoplasmic structures

Mitochondria P: No E: Yes (few exeptions) Chloroplast P: No E: Yes (if photosynthetic) Ribosomes P: 70S E: 80S Typical cell volume: P: <5 µm^3 E: >5 µm^3

Examples of Chemo-organo-hetero-troph

Most bacteria like E. coli and Bacillus subtilis

Microbial Culture Collections

Most commonly used and most comprehensive: American Type Culture Collection (ATCC) Deutsche Sammlung von Mikrooganismen und Zellkulturen(DSMZ)

The Gobal Nitrogen Pool

Most in Rocks Sediement Atmosphere N in rock is inaccessible to microbes! N2 (g) is highly stable; energy intensive fixation by: 1. Nitrogen-fixing bacteria & archaea 2. Haber-Bosch process (industrial)

Global Carbon Pool

Most in rocks Fossils dissolved CO2 in water dead biomass

Secondary Treatment: Anammox Reactor

NO2-+ NH4+ -> N2+ 2H2O ∆G°' = -357 KJ/mol

Regulating Membrane Fluidity

One common strategy is altering the composition of membrane lipids. Bacteria can modify the length and saturation of fatty acid chains in phospholipids to modulate fluidity. - Increasing the proportion of unsaturated fatty acids enhances membrane fluidity at lower temperatures, while incorporating more saturated fatty acids improves stability at higher temperatures. Hopanoids instead of cholesterol to regulate fluidity and stiffen membrane when needed. Hopanoids tend to make the membrane more rigid and less fluid

What are microorganisms?

Organisms that are too small to be seen with the unaided eye. Mainly single celled organisms and if not then no differentiation of cells. Viruses are not microorganisms. This incomapses all Bactria and Archaea, but only some Eukaryotes like algae and unicelluar fungi like yeast.

Metabolic (Electron Source)

Organo-troph: An organotroph is an organism that obtains hydrogen or electrons from organic substrates. Litho-troph: a diverse group of organisms using an inorganic substrate (usually of mineral origin) to obtain reducing equivalents for use in biosynthesis (e.g., carbon dioxide fixation) or energy conservation (i.e., ATP production) via aerobic or anaerobic respiration.

The Carbon Cycle

Oxic: - Oxygenic Photosynthesis: CO2 -> organic matter(CH2O)n (red.) - Chemolithotrophy: CO2 -> organic matter(CH2O)n (red.) - Respiration: organic matter(CH2O)n -> CO2 (ox.) - Methanotrophy: CH4 -> CO2 (ox) Anoxic: - Anaerobic Respiration and fermentation: organic matter(CH2O)n -> CO2 (ox.) - Anoxygenic Photosynthesis: CO2 -> organic matter(CH2O)n (red.) - Acetogenesis: CO2 -> organic matter(CH2O)n (red.) - Methanogenesis: CO2 -> CH4 (red) - Methanogenesis: organic matter(CH2O)n -> CH4 (red)

Important types of respiration

Oxygen respiration (kJ mol-1) CH2O + O2→ HCO3-+ H+ (-474 kJ/mol) Denitrification CH2O + 0.8 NO3-→ 0.4 N2+ HCO3-+ 0.4 H2O + 0.2 H+ (-448 kJ/mol) Manganese reduction CH2O + 2 MnO2+ H2O → HCO3-+ 2 Mn2++ 2 H2O + H+ (-375 kJ/mol) Iron reduction CH2O + 4 Fe(OH)3→ HCO3-+ 4 Fe(OH)2+ 2 H2O + H+ (-71 kJ/mol) Sulfate reductionCH2O + 0.5 SO42-→ HCO3-+ 0.5 H2S (-76 kJ/mol) MethanogenesisCH2O + 0.5 H2O → 0.5 HCO3-+ 0.5 CH4 (-39 kJ/mol)

Different types of Phototrophs

Oxygenic H2O -> O2 Anoxygenic H2 -> H2O H2S -> S(0), S2O3(2-), S2O4(2-) H2S -> S2O4(2-) S2O3(2-) -> SOxygenic H2O -> O2 Anoxygenic H2 -> H2O H2S -> S(0), S2O3(2-), S2O4(2-) H2S -> S2O4(2-) S2O3(2-) -> S2O4(2-) Fe(2+) -> Fe(3+)2O4(2-) Fe(2+) -> Fe(3+)

Distribution of Chlorophylls

Oxygenic: • Cyanobacteria: - Electron donor: H2O - Chloropyll a and phycobilis Anoxygenic • Purple nonsulfur bacteria: - Electron donor: Many substrates, Including H2, alcohols, organic acids, and Fe(2+) - Bacteriochloropylls a and b • Purple sulfur bacteria: - Electron donor: Reduced sulfur compunds (H2 and certain acids) - Bacteriochloropylls a and b • Green sulfur bacteria: - Electron donor: Reduced sulfur compunds (H2S and S2O4(2-)) - Bacteriochloropylls c, d and e • Heliobacteria - Electro donor: Lactate, other organic acids - - Bacteriochloropylls g

PCR

PCR stands for Polymerase Chain Reaction. It is a laboratory technique used to amplify a specific DNA sequence. PCR allows for the rapid and efficient production of multiple copies of a target DNA region, making it a valuable tool in various applications, such as DNA sequencing, genetic testing, and molecular research. Multiplex PCR (Polymerase Chain Reaction) is a molecular biology technique that allows for the simultaneous amplification of multiple DNA targets in a single reaction. It involves the use of multiple sets of primers, each specific to a different target sequence, and a DNA polymerase enzyme. By designing primers with different specificities, multiple DNA fragments can be amplified simultaneously. Multiplex PCR is a powerful tool in various applications, such as genotyping, pathogen detection, and gene expression analysis, as it saves time, resources, and sample material by allowing for the amplification of multiple targets in a single reaction.

Difference in Electron Flow in PSI and PSII

PS II is found in purple bacteria and is a cyclic process PS I is found in green sulfur bacteria and is a non cyclic process Both PSII and PSI is found in cyanobacteria and the therefore both cyclic and non cyclic

Plasmid

Plasmids are small, circular DNA molecules that exist separately from the chromosomal DNA in prokaryotic and some eukaryotic cells. They can replicate independently and are often found in multiple copies within a cell. Plasmids can carry additional genes that provide advantages to the host cell, such as antibiotic resistance or the ability to produce specific enzymes, and they can be transferred between cells through horizontal gene transfer mechanisms.

Steps of Wastewater Treatment

Primary - Removal of particulate matter Secondary - Oxidation of dissolved organic compounds, most organic matter converted to CO2 or microbial biomass Tertiary - Reduces inorganic nutrients (nitraten, phosphate and so on)

How do prokaryots cope with salty enviorments

Prokaryotes have evolved several mechanisms to cope with salty environments and maintain cellular functions under high salt conditions. Accumulation of compatible solutes: Prokaryotes can synthesize or accumulate compatible solutes, also known as osmoprotectants or osmolytes, which help maintain osmotic balance and prevent water loss from the cell. These solutes can include amino acids, sugars like sucrose , polyols, and betaines.

Marcomolecular composition of a cell in procent dry weight

Protein: 55 Lipids: 9.1 Polysaccharide: 5 Lipopolysaccarides: 3.4 DNA: 3.1 RNA: 20.5

Pseudomurein in Archaea

Pseudomurein is a structural component found in the cell walls of some archaea. It is similar in function to peptidoglycan, which is found in the cell walls of bacteria.

Pasteurization

Reduces Microvial cells by 79-99% -historical method: 63-66 °C for 30 min -modern method: 72 °C for 15 sek

Purple Bacteria PS II

Reverse Electron Transport in Type II PS 1. Oxydation of a chemical eltron donor reduces periplasmic cyt c which diffuses to oxidaze PSII when hit by light. And is then reduced back to ground state 2. Oxidation of the exited PSII reduces quinone -> quinol 3. Quinol reduces NADP+ to NADPH in two step reverse electron transport driven by the entry og protons - Her protons are pumped from the Periplasm into the cytoplasm 4. NADPH is used as a reductant in the fixation og CO2 in the calvin cycle

Reverse electron flow

Reverse electron flow (or reverse electron transport) is a mechanism observed in microbial metabolism. It is used by certain chemolithotrophs that utilize electron donors with higher redox potentials than NAD(P)+/NAD(P)H, such as nitrite or sulfur compounds. These organisms consume proton motive force to drive electrons in the reverse direction through an electron transport chain, resulting in the reduction of NAD(P)+. This process can provide the necessary energy and reducing power for autotrophs to carry out inorganic carbon fixation.

Examples of Photo-organo-hetero-trophs (some mixotrophic)

Rhodobacter, Rhodopseudomonas, Rhodospirillum, Rhodomicrobium, Heliobacterium, Chloroflexus

Vertebrate Gut Fermenters

Rumen Fermentation •ruminants cannot digest cellulose •ruminants chew plant material and later regurgitate the cud to chew it more •the rumen microbiome(bacteria, fungi, protozoa) degrade and ferment sugars; the resulting volatile fatty acids (VFA) are absorbed by ruminants

Salinity adaptations

Salinity adaptations in microbes refer to their ability to survive and function in different salt concentrations. Here are the main types of salinity adaptations: 1. Nonhalophiles: Nonhalophiles are microbes that cannot tolerate high salt concentrations and thrive in environments with low salt levels. They are typically found in freshwater or non-saline environments. 2. Halotolerant: Halotolerant microbes can tolerate a wide range of salt concentrations. They are capable of surviving in both low and high salt environments, although they may not necessarily require high salt levels for optimal growth. 3. Halophiles: Halophiles are microbes that thrive in high salt concentrations, typically above the levels tolerated by nonhalophiles or halotolerant species. They have adapted to the osmotic stress caused by high salt levels and have specific mechanisms to maintain cellular functions under these conditions. 4. Extreme Halophiles: Extreme halophiles, also known as halophilic archaea, are microbes that inhabit extremely saline environments such as salt lakes, salt pans, and hypersaline soils. They require very high salt concentrations for growth and survival and have specialized adaptations to cope with the osmotic stress and high salt levels. These adaptations to salinity involve various mechanisms such as the accumulation of compatible solutes to maintain osmotic balance, specific ion transport systems, and modifications in cell structure and metabolism to function effectively in high salt environments.

Bacterial Cytoskeleton

Shape-determining proteins •FtsZ= forms a "Z-ring" in spherical cells •MreB= forms arc-shaped patches inside rod-shaped cells •CreS"crescentin" = forms a polymer along the inner side of crescent-shaped bacteria

Antimicrobials

Site of action: - Cell wall crosslinks: -- Class: β-lactam --- Examples: Penicillin, Vancomycin - DNA gyrase -- Quinolone --- Quinolone - Protein synthesis -- Aminoglycoside --- Streptomycin - Folic acid synthesis -- Sulfa --- Sulfanilidamide

Bacteriaon/"in" thehuman body

Skin: 10^7 cells cm-2 Gut: Low small and large intestine: 10^11 cells ml-1 Most cells (10^13) can be found in the gastro-intestinal tract. Urine is steril!

Diversity in metagenomics

Soil is the most diverse by far then water then air The fewer species the more accurret the meta genome is

Tree of life

The phylogenetic tree that includes all organisms and Where the phylogeny is based on 16S rRNA for prokaryotes and 18S rRNA for eukaryotes.

Homolactic fermentation (also homofermentative):

Substrate is first oxidized and then reduced. Glucose is oxidized to pyruvat and NAD+ is reduced to NADH NAD+ is needed in the cell so pyruvat is reduced to lactate so NADH can be oxidized to NAD+ Two ATP is invested and four is produced. Net 2 ATP One glucose make two two lactate

The Sulfur Cycle

Sulfide/sulfur oxidation: H2S ->S(0) ->SO4(2-) - Both Aerbic and Anaerobic Sulfate reduction(anaerobic): SO4(2-) ->H2S Sulfur reduction(anaerobic): S(0) ->H2S Sulfate assimilation - sulfate assimilated into organic matter Desulfurylation: Organic-S -> H2S

Climate effects of Sulfur cycling

Sulfur cycling can have significant climate effects due to the production and release of sulfur-containing compounds. Some of the climate effects of sulfur cycling include: 1. Aerosol Formation: Sulfur compounds can be oxidized in the atmosphere to form sulfate aerosols, which can contribute to the scattering of sunlight and the formation of clouds. 2. Climate Cooling: Sulfate aerosols have a cooling effect on the climate by reflecting incoming solar radiation back into space, thereby reducing the amount of sunlight reaching the Earth's surface.

Other Types of Interactions

Syntrophy: a metabolic association requiring both partners to complete the metabolism with a ΔG < 0 •Synergism:an optional cooperation where both species benefit, but can grow independently •Commensalism: one partner benefits, while the other is unaffected. •Amensalism:one partner is harmed, without an intimate association. •Parasitism:an intimate association where one partner benefits, while harming a specific host

"Extreme" Prokaryotes

Temperatur: - High: Hyperthermophiles -- an Archaea found in hyperthermal vents --- minium: 90C; optimal; 106C; maxium: 122C -Low: Psychrophiles -- A Bacteria found in sea ice --- minium: -12C; optimal; 5C; maxium: 10C pH -Low: Acidophiles -- An archaea found in acidic hot springs ---minium: -0.06 ; optimal; 0.7; maxium: 4 -High: Alkaliphiles -- An archaea found in soda lakes ---minium: 8.5 ; optimal: 10; maxium: 12 Presssure: - Barophiles -- Bacteria found in deap ocean sediement ---minium: 500 atm; optimal: 700 atm; maxium: >1000 atm Salt: - Halophiles --Archaea in Salterns ---minium: 15% ; optimal: 25%; maxium: 32% (saturation)

The Electron Transport Chain

The Electron Transport Chain (ETC) is a crucial component of cellular respiration that occurs in the inner mitochondrial membrane (or the plasma membrane of prokaryotes). It is responsible for the final stages of aerobic respiration, where electrons from reduced molecules, such as NADH and FADH2, are transferred through a series of protein complexes and mobile electron carriers. As the electrons move along the ETC, they undergo a series of redox reactions, leading to the generation of a proton gradient across the membrane. This proton gradient is utilized by ATP synthase to drive the synthesis of ATP, a form of chemical energy. At the end of the chain, electrons are ultimately accepted by oxygen, which serves as the final electron acceptor, forming water. The ETC plays a vital role in energy production, as it is responsible for the majority of ATP synthesis in aerobic organisms. Complex I and IV er needed to others are optional.

Cell Division: Z-Ring

The Z-ring is a key structure involved in bacterial cell division. It is a dynamic protein complex that forms at the division site and is responsible for initiating cell constriction and septum formation. The Z-ring is composed of the protein FtsZ, which assembles into a ring-like structure at the mid-cell position.

Turbidity Measurement

The absorbance and scattering of light at a certain wave length is used to determin the optical dencity (OC) •in the course we use OD of 650 nm •samples have to be diluted if >0.3

Archaeal Cell Wall Structure

The cell wall structure in archaea is diverse and varies among different groups of archaea. Unlike bacteria, archaea do not have peptidoglycan in their cell walls. Here are some key features of archaeal cell wall structure: 1. S-Layers: Many archaea have an outermost layer called an S-layer, which is composed of repeating protein or glycoprotein subunits. S-layers provide structural stability and protection to the cell. 2. Pseudomurein: Some archaea, particularly methanogens, have a cell wall composed of pseudomurein. Pseudomurein is a polymer similar to peptidoglycan but with different sugar and amino acid components. It provides structural support to the cell. 3. Proteinaceous Cell Walls: Certain groups of archaea have cell walls predominantly composed of proteins. These proteins may form a mesh-like network or fibrillar structures that contribute to cell integrity. 4. Glycoproteins and Glycolipids: Archaeal cell walls often contain glycoproteins and glycolipids, which are molecules with carbohydrate moieties attached to proteins or lipids, respectively. These components may play a role in cell adhesion and protection. It's important to note that the exact composition and structure of the cell wall can vary greatly among different archaeal species and even within the same species under different growth conditions. The diversity of archaeal cell wall structures reflects the wide range of environments in which archaea thrive.

Microbial ecology

The study of microbes ́relationship to one another and with their environment. (Eukaryota, Archaea, Bacteria, (viruses))

pH adaptations

The three types of pH adaptation observed in microbes are acidophiles, alkaliphiles, and neutrophiles. Here's a brief explanation of each: 1. Acidophiles: Acidophiles are microbes that thrive in highly acidic environments with pH levels below 3. They have specific adaptations to tolerate and grow in these extreme acidic conditions. Acidophiles often possess proton pumps that actively transport protons out of the cell, preventing intracellular acidification. They may also have enzymes and proteins that are stable and functional at low pH. 2. Alkaliphiles: Alkaliphiles are microbes that thrive in highly alkaline environments with pH levels above 9. They have adaptations to maintain cellular functions and pH homeostasis under these extreme alkaline conditions. Alkaliphiles often possess mechanisms to pump protons into the cell to counteract the high external pH. They may also have alkaline-stable enzymes and proteins that can function optimally at high pH. 3. Neutrophiles: Neutrophiles are microbes that grow optimally at neutral pH, around pH 6-8. They can tolerate a range of pH conditions within this neutral range. Neutrophiles have mechanisms to maintain pH homeostasis, which may involve proton pumps, ion transporters, and pH buffering systems. They can adapt to slight variations in pH and maintain optimal cellular functions. These pH adaptations allow microbes to colonize and thrive in diverse environments with different pH levels. They have evolved specific mechanisms to maintain intracellular pH, regulate ion transport, and stabilize proteins and enzymes to ensure their survival and growth in acidic, alkaline, or neutral pH conditions.

Transpeptidation

Transpeptidation, also known as cross-linking, is a process that occurs during the synthesis of the bacterial cell wall. It involves the formation of covalent bonds between the peptide side chains of neighboring peptidoglycan strands. Transpeptidation is catalyzed by enzymes called penicillin-binding proteins (PBPs), which are targeted by beta-lactam antibiotics like penicillin. During transpeptidation, the terminal D-alanine residue of one peptide chain is cleaved, and the resulting exposed amino group forms a new covalent bond with the neighboring peptide chain. This cross-linking process strengthens the cell wall structure and provides resistance against osmotic pressure. Inhibition of transpeptidation by beta-lactam antibiotics prevents the formation of these cross-links, leading to weakened cell walls and bacterial cell lysis. This mechanism makes transpeptidation an important target for antibiotic action.

Stickland fermentation

Two substrates (amino acids), one is oxidized and one reduced an example: - Oxidation of alanine via acetyl-CoAand ATP production - Reduction of glycine and reoxidation of NADH

Two Types of Reaction Centers in PS

Type I • ferredoxinreductases • electron acceptor is ferredoxin (iron-sulfur protein) • ferredoxinis very electronegative (-400 mV) • very potent reducing agent • most of the energy from the photon is conserved Type II • quinone reductases • reduces quinonesto quinols • quinolsare weak reducing agent (0 to -100 mV) • more energy dissipated in reaction center • less efficient than type I

Assembly of Genome

Unknown DNA sequence 1. Cleave DNA into fragments and sequence 2. Computer analysis finds overlaps 3. Consensus sequence - a consensus sequence refers to a representation of the most likely or most frequently occurring nucleotide at each position in a DNA sequence

Flow Cytometry

Used to count cells Often used together with cell sorting: fluorescence-activated cell sorting (FACS) Can sort by parameters like: -size -fluorescence (chlorophyll, stains)

What is Wastewater Treatment

Wastewater treatment is a broad field which includes: 1.Municipal wastewater treatment 2.Industrial wastewater treatment

Microbial Habitats

What are the requirements of life? 1.Liquid water 2.Electron donor 3.Energy source 4.Source of elements to make up biomass (carbon, nitrogen) This is the key to understanding life on our own planetthe emergence of life on Earth and...... other planets (astrobiology)

Antibiotics

chemical compound secreted by microbe which is toxic to other microbes. Often used more generally for any chemical compound with antimicrobial properties.

ATP synthase(ATPase)

~ 1 ATP/3.3 H+ ATP synthase, also known as ATPase, is a membrane-bound enzyme complex found in mitochondria (or the plasma membrane of prokaryotes) that plays a crucial role in cellular energy production. It utilizes the proton gradient generated by the Electron Transport Chain (ETC) to convert ADP (adenosine diphosphate) and inorganic phosphate (Pi) into ATP (adenosine triphosphate). The enzyme consists of two main components: the F0 component, embedded in the membrane and responsible for proton translocation, and the F1 component, located in the mitochondrial matrix (or cytoplasm) and responsible for ATP synthesis. ATP synthase is a key player in oxidative phosphorylation, which is the process of generating ATP from the energy released during electron transfer along the ETC.

Cell numbers

• 350-550 * 10^15 g prokaryotic biomass is equal to 60-100% of the total plant biomass Envirments and cell count Soil: 10^11 - 10^12 cells/kg Rivers and lakes: 10^9 - 10^10 cells/L Marine plankton: 10^11 - 10^12 cells/L Groundwater: 10^7 - 10^8 cells/L Sediment: 10^9 - 10^12 cells/kg Activated sludge: 10^11 - 10^13 cells/L

Pigments in Phototrophs

• Chlorophylls • Phycobilins • Carotenoids

Comammox: complete ammonia oxidation

• Comammox - NH4 -> NO3(-) - Oxic conditions • recently discovered (2015!) •energetically more favorable •distinct ammonia monooxygenasegenes in comammox-> molecular marker •present in many environments, in some abundant

Bacterial Phototrophs

• Cyanobacteria: all phototrophic • Proteobacteria: some phototrophic - Purple sulfur bacteria - Purple nonsulfurbacteria • Green sulfur bacteria: all phototrophic • Green nonsulfur bacteria: all phototrophic • Heliobacteria: subgroup of Gram+

Phagocytosis

• Phagocytosisis the killing, and digestion of invading microorganisms • Two major types of cells whose function includes phagocytosisare: -macrophages -polymorphonuclear neutrophils(PMNs) •Both types move by amoeboid motion and actively seek out invading microbe •bacterial cells getphagocytosed •form phagosome, which is a vacuole containing the engulfed pathogen •phagosomefuses with lysosometo form phagolysosome

Chlorophyll

• Principal chlorophyll in oxygenic phototrophs • spectral tuning of pigments by different side chains on tetrapyrrolering • can use different wavelengths of light • opens ecologic niches

Irradiation

• high energy radiation destroys cell components, especiallyDNA -> spores are quite tolerant to radiation -UV radiation (approx.260 nm) -ionizing radiation(Gamma-and X-rays, < 10 nm)

Green Bacteria: Chlorosomes

• located on the inside of the cytoplasmicmembrane • Bchlis not attached to proteins • FMO protein transfers energy from antennas to RC

Comparing methods for classification

•16S rDNA sequencing/ribotyping - Family - Genus - Species •Ribotyping - Genus - Species •Genomic G+C content - Genus - Species - Subspecies •DNA-DNA hybridization - Genus - Species - Subspecies •Multilocus sequence typing - Species - Subspecies - Stain •Fatty acid analysis - Species - Subspecies - Stain •Genome sequencing - Family - Genus - Species - Subspecies - Stain

Methods for classification

•16S rDNA sequencing/ribotyping - analysis of 16S rRNA gene •Multilocus sequence typing - sequencing of multiple genes and combined phylogeny •Genomic G+C content - can be characteristic for species/phylogenetic groups •DNA-DNA hybridization - genomic DNA of new strain is hybridized with know strain - percentage of hybridization tells how closely related they are •Fatty acid analysis - extraction and analysis of fatty acids •Genome sequencing - modern approach to compare species

Methanogenesis

•4H2+ CO2 →CH4+ 2H2O •requires strictly anoxic conditions •unusual cofactors (C-carriers, reductants) •only found in Archaea •sink for H2 in anoxic environments •Methanogenesis provides niches for methanotrophs (oxidize methane with O2)

Nitrification

•A kind of lithotrophyof great importance in the environment is nitrification. Happens in the pressence of oxygen. Two steps: Ammonia oxidation: •Ammonium (NH4+)→ hydroxylamine(NH2OH) → nitrite(NO2-) Nitrite oxidation: • Nitrite(NO2-) → nitrate(NO3-)

Type I/II Photosynthesis

•Also called the Oxygenic Z Pathway •Found in cyanobacteria and chloroplasts •Includes homologs of PS I and PS II •Eight photons are absorbed and two electron pairs are removed from 2H2O, ultimately producing O2 •Oxygenic photosynthesis forms 3 ATP + 2 NADPH per 2 H2O photolyzed and O2produced •The ATP and NADPH are used to fix CO2into biomass

Anammox

•Ammonium oxidation can also yield energy under anoxic conditions via oxidation by nitrite. •Process is called anaerobic ammonium oxidation (anammox) NH4+ + NO2- → N2 + 2 H2O •Doubling time: ~10 days (!) •Anammox reactors are nowadays commonly used in wastewater treatment plants •May be responsible for more than 50% of nitrogen loss in the oceans

Ammonia Oxidation

•Archaeal ammonia oxidizers (Nitrososphaeria): most abundant where NH4+ is low, e.g. in the open oceans •Bacterial ammonia oxidizers: most abundant where NH4+ is high, e.g. sewage treatment Ammonia oxidizers are microorganisms that oxidize ammonia (NH3) to nitrite (NO2-) as part of the nitrification process in the nitrogen cycle. They play a crucial role in converting toxic ammonia into nitrite, which is further oxidized to nitrate (NO3-) by nitrite-oxidizing bacteria. This process is important in wastewater treatment, soil fertility, and the overall balance of nitrogen in ecosystems. Ammonia oxidizers are typically autotrophic bacteria or archaea that obtain energy from the oxidation of ammonia.

Temperature

•At high temperatures, growth rates fall because enzymes denature. •At low temperatures, growth rates fall because of decreases in membrane fluidity and enzymatic activity. •no single species can cover the full temperature range •adaptations to the specific conditions in membrane fluidity, enzymes, etc.

Bacterial infections -a growing threat?

•Bacteria will always develop resistance •$500,000,000 / 10 years to develop a new drug •Pharmaindustry is not a charity -must maintain "shareholder value" •"Big Pharma" has largely abandoned antibacterials ->Resistance develops -short product lifetime -low profit -> Antibiotics work -take for days not rest of life -low profit -> "Superdrug" would be kept in reserve -low profit

Spores (1)

•Bacterial spores, also known as endospores, are highly resistant structures formed by certain bacterial species as a survival mechanism in response to unfavorable environmental conditions •Bacterial spores have a tough outer layer that protects the genetic material and cellular components inside. •When conditions become favorable again, the spores can germinate and give rise to active, vegetative bacterial cells. •Heat-resistant resting stages of bacteria •Discovered by John Tyndall (1820-1893) •he developed a method to effectively kill heat-resistant spores -> "tyndallization"

Exponential Growth

•Balanced growth •every time the cells divide the population doubles Population growth is proportional with size of population: dN/dt=kN N: population size k: growth rate constant (time-1, usually: hours-1) t: time Change in population size Integrated: Nt=N0*e^(kt) ⇔ ln(Nt)= k*Δt + ln(N0) N0: starting population Nt: population at time t

Nucleoid

•Circular chromosome is organizedin supercoiledloops. •DNA-binding proteins and cations(positively charged). •DNA loops protrude from a denser central core. The nucleoid is a region within the cytoplasm of prokaryotic cells where the genetic material, typically a circular chromosome, is located.

Anaerobic Methane Oxidation

•Consortia of sulfate-reducing bacteria and methane-oxidizing Archaeaoxidize methane in anoxic environments, e.g. the Black Sea. • The Sulfate-reducing bacteria makes a capsule around the methanotrophic archaea •Coupling of the carbon and sulfur cycle! • CH4 + SO4(2-) -> CO2+ HS(-) +2 H2O •some consortia with anammoxbacteria and to nitrate reducing bacteria (NC10) Microbial co-cultures (consortia) are two or more interacting microbial populations that can be found in many diverse environmental niches.

Pure culture technique (history)

•Culture bacteria on surfaces •Initially potetoes were used •later he switched to gelatin for solidification -> melts at 37C; broken down by bacteria •finally: Agar - complex polysaccharide from marine algae - melts at 100 C and solidifies at 45 C - can't be hydrolyzed by most bacteria

Nitrogenase

•Dinitrogenaseand dinitrogenasereductase •Dintrogenasereductase reduces dinitrogenase •H2 released as N2 binds •Destroyed by O2, must have anoxic surroundings •Reduces other molecules resembling N2e.g. C2H2

Distance Matrix: Algorithms

•Distance Methods (e.g. Neighbor-Joining) •Maximum Parsimony •Maximum Likelihood •Bayesian Inference

Two types of Microbial toxins

•Exotoxins •Endotoxin

Griffith's experiment: Streptococcus pneumoniae

•Experiment published in 1928 by Frederick Griffith •First evidence of transformation of genetic material •S. pneumonia that can't form a capsule (R cells) can't survive in blood:not infectious •S. pneumoniaforming a capsule (S cells) cause death in mice •heat-killed S cells don't cause death •amixture of heat-killed S cells and live R cells causes death in mice -> live S cells can be isolated from blood of dead animals

Passive Transport

•Facilitated diffusion helps solutes move across a membrane from a region of high concentration to one of lower concentration. •It does not use energy and cannot move a molecule against its gradient. •Is carried out by channels (some of which makes a confermation shift like the glycerol channel)

Pentose Phosphate Pathway

•Forms key intermediate ribulose 5-phosphate •only 1 ATP •NADPH for biosynthesis instead of NADH •many precursors for biosynthesis of cell components (eg. pentose backbones of nucleic acids) •The ribose can comes from the breakdown of DNA or RNA - It can be part of pentose pathways. Otherwise, it can be used directly to make DNA and RNA The Pentose Phosphate Pathway (PPP), also known as the hexose monophosphate shunt, is a metabolic pathway that runs parallel to glycolysis. It generates ribose-5-phosphate for nucleotide synthesis and NADPH for reductive biosynthesis and antioxidant defense. The PPP has two distinct phases: oxidative and non-oxidative. In the oxidative phase, glucose-6-phosphate is converted to ribulose-5-phosphate, generating NADPH. In the non-oxidative phase, various sugar phosphates are interconverted to produce glycolytic intermediates or regenerate glucose-6-phosphate. The PPP plays a vital role in balancing cellular energy and redox metabolism.

Photosystem II

•Found in Alphaproteobacteria, "purple nonsulfur" bacteria •Separates an electron from bacteriochlorophyll itself •Electrons are then transferred to an ETS •Ultimately, an electron is returned to bacteriochlorophyll - This process, which generates ATP, is called cyclic photophosphorylation •PS II, unlike PS I, provides no directway to make NADH or NADPH for reductive biosynthesis

Photosystem I

•Found in Chlorobia, "green sulfur" bacteria and Heliobacteria •Electrons donors: H2S, organic carbon such as succinate, or reduced iron (Fe2+) •Electrons are eventually transferred to NAD+ or NADP+ via ferredoxin (Fd). - The reduced carrier (NADH or NADPH) provides reductive energy for CO2 fixation and biosynthesis. •Bacteria using PSI also generate a net proton gradient to drive ATP synthesis.

Non-protein toxins

•General indicator of presence of bacteria -not necessarily pathogen -behind mucosal barrier •Gram-negative bacteria: -Lipopolysaccharide (LPS) (= endotoxin) •Gram-positive bacteria: -Lipoteichoic acid (LTA) •Bind to opsonins and stimulate phagocytosis

Teichoic acids in Gram-positives

•Glycerol or ribitolphosphodiester chains •Change surface of cells •Promote adherence to surfaces (pathogenicity factor) - Composition: Teichoic acids are composed of repeating units of glycerol or ribitol phosphate, with additional modifications such as D-alanine or sugars. - Attachment to Peptidoglycan: Teichoic acids are covalently linked to the peptidoglycan layer of the cell wall. They can extend outward from the cell surface or be embedded within the peptidoglycan layer. - Functions: Teichoic acids play important roles in the physiology and virulence of Gram-positive bacteria. They contribute to the maintenance of cell shape and stability, regulate cell division, and help in the binding of cations like calcium and magnesium.

Staining Techniques

•Gram staining (Crystal violet, counter stain with Safranin) •Spore staining (Malachite green) •Capsule staining (Ink) •DNA staining (DAPI: 4',6-diamidino-2-phenylindole) •Fluorescence in situ hybridization (FISH) •Live-dead staining

Calvin-Benson Cycle

•In photoautotrophs and chemoautotrophs •Only pathway for aerobic autotrophic bacteria •CO2 fixation step catalyzed by ribulose 1,5 bisphosphate carboxylase/oxygenase (Rubisco) •Ribulose bisphosphate regenerated from 5/6 of triose-phosphate, 1/6 is product •12 NADPH and 18 ATP are required to synthesize Glucose from 6 CO2 • The Clavin cycle needs a lot of ATP to fix CO2. However, this energy demand is usually not a problem for photosynthetic organisms because ATP is generated through the light-dependent reactions of photosynthesis by photophosphorylation. • Phosphoribulokinase: Its main function is to phosphorylate ribulose 5-phosphate (RuBP), a five-carbon sugar, using ATP as a phosphate donor. This phosphorylation step converts RuBP into a more reactive molecule called 1,5-bisphosphoribulose, which can then undergo subsequent reactions to incorporate carbon dioxide and initiate the synthesis of organic compounds, such as glucose. In essence, phosphoribulokinase helps drive the carbon fixation process in photosynthetic organisms.

Sterilization

•Killing of all living cells and all spores •Not all methods are 100% effective -> reduction of germs •depending on material that needs to be sterilized different methods are used: - heat sterilization - Pasteurization - irradiation sterilization - sterile filtration - chemical sterilization

Types of photosynthetic machinery

•Lamellar membrane stacks: Purple bacteria •Thylakoids: Cyanobacteria •Chlorosomes: Green bacteria

Phagocytes

•Macrophages -form of lymphocyte -found virtually everywherewithin the body -long-lived -have mitochondria -have an oxidative metabolism •Polymorphonuclearneutrophils(PMNs) -a form of leukocyte (white blood cell) -found mainly in blood -they leave the blood and migrate to site of active infections (inflammation) -short-lived, continually replaced-lack mitochondria-depend on fermentation of glucose

The advantage of being small

•Microbes process their nutrients 10 to 1000 times faster per gram than mammalian cells. •High surface to volume ratio allows quick chemical exchange.

Sulfide/Sulfur oxidizers

•Obtain energy through oxidation of reduced sulfur compounds, including elemental sulfur, hydrogen sulfide, thiosulfate •Example: endosymbionts of the tube worm Riftiapachyptila •Lithotrophicmicrobes fuel life in deep ocean hydrothermal seeps •HS(-) + 2 O2→ SO4(2-) + 1H(+) Reverse electron flow??

Normal Microbiota

•Often called the Human Microbiome •10^13 to 10^14 cells per human (10^13 human cells) •Thousands of different species •Metagenomeis larger than human genome -sequenced by "Human MicrobiomeProject"

Killing pathways

•Phagosome-lysosomefusion results in: - Oxygen-independent killing pathways ->Lysozyme, lactoferrin, and defensins - Oxygen-dependent killing pathways ->Superoxide anion (•O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (•OH) - Reactive nitrogen intermediates ->Nitric oxide (NO), nitrite (NO2-), and nitrate (NO3-) •These mechanisms cause the oxidative burst. - Large increase in oxygen consumption

Host defenses

•Physical/chemical barriers -skin and mucous membranes -ciliated cells in respiratory system -stomach acids and bile salts •Protection against successful invaders -low available iron -phagocytes -protective proteins •Adaptive and inducible defenses (immune system) -specifically induced by exposure to an invader

Transpeptidation forms rigid cell wall

•Precursor is transported over membrane with the help of bactoprenol •Autolysin breaks glycosidicbonds in peptidoglycan to open gap •Transglycolase inserts precursor into gap and makes new glycosidicbonds •Transpeptidation connects the chains

Peptidoglycan synthesis

•Precursor is transported over membrane with the help of bactoprenol •Autolysin breaks glycosidicbonds in peptidoglycanto open gap •Transglycolaseinserts precursor into gap and makes new glycosidicbonds•Transpeptidationconnects the chains

Flagella/Archaella

•Prokaryotes that are motile generally swim by means of rotary flagella (called archaellain Archaea) •Peritrichous cells (a) have flagella randomly distributed around cell -The flagella rotate together in a bundle behind the swimming cell •Polar/monotrichous(b) cells have a single flagellum •Lophotrichous(c) cells have flagella at the end(s)

Rubisco

•Rubiscoconsists of 8 small (S) and 8 large (L) subunits. •Catalyzes the condensation of CO2 to ribulose 1,5-bisphosphate, and the splitting of the unstable 6C intermediate into two 3C PGA molecules •many organisms have Rubiscoin carboxysomes

Capsules

•Slime or capsule covering the cells to protect them. •Consist of high-molecular weight polysaccharides. •Often produced under specific conditions (pathogenicityfactor).

Protein toxins (Exotoxins)

•Specific proteins produced by pathogens•Cause the symptoms of disease•Types of toxins: -Enterotoxins affect intestinal water uptake - Neurotoxins affect nerve conduction - Cytotoxins destroy cells -Pyrogenic toxins cause fever and shock

Biofilm

•Switch from planktonicto sessile lifestyle •Most moist surfaces are covered in biofilms •Cells attach, produce matrix made of exopolymericsubstances (EPS) •Shaping of environment: protection, resistance, chemical gradients, etc. •Quorum sensing required for biofilmformation. Quorum sensing (QS) is a bacterial cell-cell communication process that involves the production, detection, and response to extracellular signaling molecules called autoinducers (AIs).

Reverse Citric Acid Cycle

•TCA cycle functions in "reverse" •Allows the reduction of CO2to regenerate acetyl-CoAand build sugars •Reduction (addition of 2H+ + 2e-) is performed by NADPH or NADH and by reduced ferredoxin(FDH2) • There are four enzymes that differ from the TCA cycle: 1. Fumarate reductace: reduces Fumarate to Succinate 2. α-KG synthase: Succinyl-CoA+ CO2 -> α-KetoGlutarate 3. Citrate lyase: Citrate -> Acetyl-CoA Pyruvate synthase: Acetyl-CoA + CO2 -> Pyruvate A mechanism for autotrophy in green sulfur bacteria and a few other autotrophic Bacteria, and also in some Archaea Net reaction:

Host microbiome

•The human microbiomeis usually protective to the host •The human microbiomeprevents the body from being colonized by other, more harmful, parasites •Some species from the human microbiomeoccasionally causes disease •Some species may become serious pathogens if they get to other areas of the body. •Other species can be serious pathogens in their normal niche if conditions allow them to proliferate to a greater than normal extent

Chemotaxis system in E. coli

•Uses two-component signal transduction •Sensor kinase: senses enviromental signal •Response regulator - Gets phosphorlated and activated by sensor kinase - transfers signaæ - can e.g. controle transription, regulate the flagellar motors Mechanism of chemotaxis in Escherichia coli. Methyl-accepting chemotaxis proteins (MCPs) within chemoreceptor arrays form a complex with the sensor kinase CheA and the coupling protein CheW. Binding of an attractant to MCP (or an empty MCP) inhibits CheA kinase activity. Without phosphorylation of CheY, the flagellar switch continues in a counterclockwise (CCW) rotation and cell running toward the attractant occurs, (b) Binding of a repellent to MCP stimulates CheA, which can then phosphorylate the response regulators CheB and CheY. Binding of phosphorylated CheY (CheY-P) to the flagellar motor switch results in clockwise (CW) rotation and cell tumbling. CheZ is responsible for dephosphorylating CheY-P so that the response can continue or cease depending on the activity of CheA. CheR continually adds methyl groups to the MCP, while CheB-P(but not CheB) removes them. The degree of methylation of the MCPs controls their ability to respond to attractants and repellents and leads to adaptation.

Modern cultivation

•after over 100 years all "low hanging fruits" (microorganisms) are isolated •some abundant and important cladesstill not cultivated •trying to get around cultivation bias by using: - low nutrient media - undefined media - dilution to extinction - microencapsulation - cell sorting •mainly molecular -> often new techniques are used here first •first genome of a free-living organism: Haemophilusinfluenzae(1995)

Chemostat

•always new nutrients •no accumulation of waste products •growth rate is set by dilution rate •unlimited operation time

Inflammation

•bacteriaget introduced by a cut •damaged cells release cytokines and chemokines •this attracts first resident macrophages •later, neutrophilesget recruited from the capillaries (extravasation

Cholera Toxin

•cholera toxin subunit A permanently activates adenylatecyclase •high cAMPconcentrations in cell inhibit Na+pump •Cl- is lost to the intestinal lumen and water follows it

Classic prokaryotic taxonomy (Nutrition and Physiology)

•energy conservation: phototroph, chemoorganotroph, chemolithotroph •aerob, anaerobe •temperature optimum •pH optimum •salt requirements/tolerances •ability to use carbon, nitrogen and sulfur sources •growth factor requirements

Classic prokaryotic taxonomy (Colony morphology)

•formation of colonies •shape of colonies •pigmentation of colonies •exopolymer production

Photocomplexes

•formed of reaction centers and light harvesting antenna pigments •pigments are attached to proteins •photocomplexes consist of 50-300 chlorophyll/bacteriochlorophyll molecules •found in oxygenic phototrophs and purple anoxygenic phototrophs •housed within photosynthetic membranes

Nitrogen Fixation ("Diazotrophy")

•found only in Bacteria and Archaea •essential in maintaining biogeochemical nitrogen cycle by recycling N2 lost by denitrification and anammox •symbiosis between bacteria and plants is important (for example Rhizobium and legumes) N2+ 8H++ 8e-+ 16 ATP2 → NH3+ H2+ 16 ADP + 16 P

Habitats that prokaryotes can be found in:

•from -10 °C to +120°C •in freshwater, saltwater and saltponds •from acidic (pH < 1) to alkaline (pH > 10) conditions •inoxicand anoxic environments •from the air to the subsurface •from high nutrient (eutrophic) to low nutrient (oligiotrophic) conditions

Molecular phylogeny

•genotypic characterization, not phenotypic •more potential "targets" you can use •does not need isolation of organisms •based on selected "target" gene more or less phylogeneticinformation available Main "targets": •16S rRNA(SSU rRNA) gene •proteincoding genes ("housekeeping" genes)

Human gut microbiome

•gut microbiome develops over time, protects host •differences based on region your are from, diet, stage of your life •"healthy" gut microbiome is resistant to perturbations; hard to define "healthy" •suspected link of gut microbiome to obesity, diabetes, stress, etc.

Azotobacter

•has characteristic two short rod morphology •forms cysts to survive adverse conditions •forms a capsule under oxicconditions•has alternative nitrogenase (VFe, FeFe)

Fermentation

•in anoxic environments •no terminal electron acceptors for respiration are available •electron shuttles reduced during glycolysis (NADH) need to be oxidized again •energy conservation (ATP generation) by substrate level phosphorylation only

Two Types of Growth

•individual cell grows in size (anabolism) •population grows because cells are dividing

Population Growth

•individual cells grow and eventually divide •as a result the amount of cells in the culture/environment increases →population growth

Chemolithotrophs

•inorganicelectron donors (NH4+, NO2-, H2S) - oxidized (usually by O2) -> energy - oxidized to produce NADPH for CO2fixation •low energy yields •low biomass but high activities •unique ecological niche - do not compete for organics •NADPH needed to reduce CO2 generated by "reverse electron transport" at the expense of the proton potential

Examples of Continuous Cultures

•intestines •WWTP: activated sludge •many environments

Genome Sequencing

•isolate and purify the DNA •shear DNA into smaller fragments •preparation for sequencing; dependent on sequencing method •DNA sequencing: Sanger, 454 pyrosequencing, SolexaIllumina •quality control of reads •assembly of single reads to a genome •prediction of open reading frames (ORFs) •annotation of ORFs•metabolic pathway analysis

New prokaryotic species

•isolate new organism •characterize it: physiological test, genome •deposit it as typestrain at a culture collection •publish in International Journal of Systematic and Evolutionary Microbiology (IJSEM) with a proposed name → with publication name is official •later species will be included in overview literature like Bergey'sManual of Systematic Bacteriology