MICR 2211: Dr.Amarakoon

Prokaryotic Diversity: Bacteria

• Lecture 1 focuses on prokaryotic diversity, specifically within bacteria.
• The lecture also covers the phylogenies of bacteria, what they are, classifications, relationships, and ecological significances.

Learning Outcomes

• Describe the biochemical and metabolic diversity present in the microbial world
• Understand the major lineages of bacteria
• Describe the facultative nature of microorganisms with multiple forms of energy metabolism
• Understand human pathogens found in the environment
• Describe the significance of selected specific bacteria in agriculture, food/medicine production, and industry

Bacteria Phylogeny

• Among Bacteria, at least 80 lineages are discovered called phyla or divisions.
• Many bacterial phyla are known only from environmental sequences and are called phylotypes.
• The Proteobacteria is the largest group of bacteria.

Phylum Cyanobacteria

• Key genera include: Proclorococcus, Crocosphaera, Synechococcus, Trichodesmium, Oscillatoria, Anabaena.
• They are a large morphologically heterogeneous group of phototrophic Bacteria.
• They are distinct from purple and green bacteria
• They are obligate oxygenic phototrophs
• The name comes from the blue-green color of the pigments phycocyanin and chlorophyll
• Formerly called blue-green algae

Cyanobacteria Evolution

• Cyanobacteria have a long evolutionary history and date back 3.5 billion years.
• They are found in the earliest fossils, stromatholiths.
• Oxygen in Earth's atmosphere is thought to have originated from cyanobacterial photosynthesis.
• Cyanobacteria were the first oxygen-evolving phototrophic organisms on Earth.
• They are gram-negative and show a distant relationship to gram-positive Bacteria.

Cyanobacteria Morphology

• The three main cyanobacteria forms are unicellular, colonial, and filamentous.
• They are classified into five groups based on morphology and type of cell division.
• Cell size varies widely, ranging from 0.5-220 μm in diameter.
• Their color also varies widely.

Genera and Morphological Groupings of Cyanobacteria

• Group I (Chroococcales) is unicellular existing as single cells or aggregates dividing by binary fission; genera include Gloeothece, Gloeobacter, and Synechococcus.
• Group II (Pleurocapsales) are pleurocapsalean, reproducing by forming small spherical cells called baeocytes, produced through multiple fission (colonial); examples include Dermocarpa and Xenococcus.
• Group III (Oscillatoriales) are oscillatorian, with filamentous cells dividing by binary fission in a single plane and are non-heterocystous; this group includes Oscillatoria and Spirulina.
• Group IV (Nostocales) are nostocalean, filamentous cells that produce heterocysts, and examples are Anabaena and Nostoc.
• Group V (Stigonematales) exhibit branching, where cells divide to form branches; genera include Fischerella and Stigonema.

More Morphological Diversity

• Cyanobacteria have impressive morphological diversity.
• They can be unicellular (divide by binary fission).
• They can be unicellular (divide by multiple fission).
• They can be filamentous (with heterocysts).
• They can be filamentous (non-heterocystous).
• They can be branching filamentous.

Group I: Cyanobacteria

• Group I: Cyanobacteria - Gloeothece, unicellular, dividing by binary fission.
• Group I: unicellular cyanobacteria - Synechocystis.

Group II: Pleurocapsales

• Group II: Pleurocapsalean - Dermocarpa: dividing by multiple fission in a colonial structure.

Group III: Oscillatoriales

• Group III: Oscillatoriales - Oscillatoria: filamentous cells that divide by binary fission in a single plane; non-heterocystous.

Group IV: Cyanobacteria

• Group IV: Cyanobacteria - filamentous heterocystous, Anabaena
• Gloeotrichia are radiating colonies of heteropolar tapering filaments with a heterocyst and akinetes at the base and hair-like terminal cells at the opposite end. Each filament has a sheath, and the whole colony is enveloped in mucilage.

Group V: Stigonematales

• Group V: Stigonematales - Fischerella: filamentous branching, bright field.

Cyanobacteria in Mat Communities

• A microbial mat is a multi-layered sheet of microorganisms.
• Cyanobacteria form large mat-like colonies that may be toxic to other organisms

Cyanobacterial Blooms

• A harmful aspect of cyanobacterial blooms is the loss of water clarity.
• This suppresses aquatic macrophytes.
• They negatively affect inhabitativertebrate and fish habitable by this.

Cyanobacteria Physiology

• Cyanobacteria are oxygenic phototrophs that have both type I and type II photosystems.
• All species can fix CO2, and some can fix N2.
• Some filamentous species can grow in the dark on glucose.
• Some can switch from oxygenic photosynthesis to anoxygenic using H2S instead of H2O as the electron donor.

More Cyanobacteria Physiology

• Cell walls contain peptidoglycan.
• Thylakoids are specialized membrane systems that increase the cells' ability to harvest light.
• They produce chlorophyll a.
• All have characteristic phycobilin pigment needed for photosynthesis.
• Phycocyanin (class of phycobilin) is blue, and together with the green chlorophyll a, gives the blue-green color.

Cyanobacteria Cellular Structures

• Form a variety of cellular structures associated with energy storage, reproduction, and survival.
• Many produce mucilaginous envelopes or sheaths that bind groups of cells or filaments. Akinetes are cells with thickened outer walls that protect the organism during periods of darkness, desiccation, or cold. During favorable conditions, akinetes germinate by breaking down the outer wall and growing out a new vegetative filament.
• Hormogonium are short, motile filaments that break away from the longer filaments to facilitate dispersal in times of stress. They are exemplified by Oscillatoria.

Cyanobacteria Cellular and Motility Structures

• They contains storage granules which are cyanophycin, polyglucan, and lipid vacuoles.
• Cyanophycin is a nitrogen storage product.
• Motility structures such as gas vesicles helps maintain buoyancy.
• They stay in the water column where there's light.
• Many cyanobacteria display gliding motility.

Heterocysts

• Nostocales and Stigonematales facilitate N2 fixation by forming specialized cells called heterocysts either at the ends of the filaments or along the filaments.
• Heterocysts are formed in response to nitrogen starvation.
• They fix N2 from the air using nitrogenase to form ammonia.
• They lack photosystem II the oxygen requiring.

More About Heterocysts

• Thick glycolipid-rich cell walls provide a barrier to the inflow of oxygen.
• Oxygen-scavenging proteins are produced.
• Heterocysts are plugged at both ends to slow down cell-cell diffusion.
• Carbohydrates and products of photosynthesis are provided by vegetative cells in exchange for fixed nitrogen (glutamine) through intercellular channels.
• One such heterocyst is shown in nitrogen-fixing cyanobacteria.

Heterocyst Reactions

• Vegetative cells supply $CO_2$ and $H_20$ to Heterocysts, heterocyst returns glutamine to vegetative cells and vegetative cells release $O_2$.

Nitrogen Fixation Strategies

• Some cyanobacteria fix nitrogen in unspecialized cells; filamentous non-heterocystous cyanobacteria separate photosynthesis and nitrogen fixation functions, fixing nitrogen only at night and photosynthesizing during the day.
• Filamentous non-heterocyst-forming cyanobacteria form bundles of filaments with the N2 fixing filaments covered and shielded from oxygen.

Symbiotic Interactions

• Some Cyanobacteria form symbiotic interactions with a number of plants, with fixed nitrogen provided in exchange for carbohydrates.
• The signals involved appear to be different from N fixation in their own cells.
• Plants may use mucilage to attract cyanobacteria.

Symbiotic Cyanobacteia Example

• A Blasia pusilla thallus was infected in the laboratory with two different cyanobacteria.
• The two darker colonies (black arrows) contain a different Nostoc strain from the paler one (red arrow).

Gunnera Seedling

• Symbiotic interactions are present in Gunnera seedlings with red stem glands.
• The cyanobacterium penetrates Gunnera cells, and after internalization, a cyanobacterial phenotype with larger cells and numerous heterocysts (up to 80%) develops.

Photosynthesis

• Oxygen in the earth's atmosphere has likely originated from cyanobacterial photosynthesis.
• Cyanobacteria are obligate oxygenic phototrophs, or photoautotrophs.
• They are aerobic bacteria.
• A few display photoheterotrophy and utilize simple organic compounds such as glucose or acetate in the light.
• Also, a few use sucrose and glucose in the dark.
• Marine cyanobacteria alone produce 25% of the oxygen in the atmosphere.

Photosynthesis Reactions

• Oxygenic photosynthesis uses carbon dioxide, water, and light energy to produce glucose, oxygen, and water. The equation is: $6CO_2 + 12H_2O + \text{light energy} \rightarrow C_6H_{12}O_6 + 6O_2 + 6H_2O$.
• Anoxygenic photosynthesis uses carbon dioxide, an electron donor, and light energy to produce a carbohydrate and water. The equation is: $CO_2 + 2H_2A + \text{light energy} \rightarrow [CH_2O] + 2A + H_2O$. The electron donor can be $H_2O, H_2S, H_2$, or another electron donor.

Cyanobacteria: Photosynthesis Details

• They are oxygenic phototrophic prokaryotes.
• Photosynthesis is similar to that seen in plants and algae (Eukaryotes).
• The photosynthetic pigments are chlorophyll a and accessory pigments, the carotenoids (Beta-carotene and Zeaxanthin), and the phycobilins contained in the phycobilisomes.
• They, like plants and algae, utilize water as an electron donor and fixes carbon dioxide via the Calvin Cycle.
• Photosynthetic apparatus includes photosystem I (PS1), photosystem II (PS2), and a cytochrome b6f complex connected by electron carriers.
• The phycobilisomes make up 50% of the soluble cellular protein and enhance light harvesting.
• A phycobilisome includes: phycoerythrin, phycocyanin, allophycocyanin, with the thylakoid membrane.
• Phycocyanin absorbs orange and red light.
• Allophycocyanin absorbs orange-red light.
• Phycoerythrin absorbs green light.
• Chlorophyll and carotenoids absorb blue and red light.

Photosynthetic Spectrum

• All pigments combine to give good absorption across the visible spectrum, making cyanobacteria one of the most successful photosynthetic organisms.

Ecology

• They are an ecologically important group of bacteria.
• They occupy almost every habitat and are often pioneer phototrophic organisms in many extreme environments.
• Habitats include freshwater lakes, rivers, marine environments, hot and cold deserts, hot springs, and the interior of rocks.
• They have been suggested to have lived on Mars.
• They may be involved in oil formation.
• They are important in the global cycles of carbon, nitrogen, and oxygen.
• Carotenoids are red, orange, or yellow; the yellow of Synechococcus is exactly the same.
• Cyanobacteria give thermal springs and geyser pools beautiful color patterns - from red to purple and the complete visible spectrum of colors in between.

Toxic Cyanbacteria

• Several bloom-forming cyanobacteria produce toxic compounds called cyanotoxins.
• Cyanotoxin production is not understood.
• Bloom formation is usually seen where there is an excess of nutrients in waters causing excessive growth of bloom-forming species.
• Some species have a toxic effect on marine life and pose a risk to human health.
• An example would be a red body of water called Trichodesmium.
• Cyanotoxins are toxins produced by cyanobacteria, and can be classified as hepatotoxins, neurotoxins, and dermatotoxins.
• Microcystins are the most common hepatotoxins, produced by Anabaena, Nostoc, and Oscillatoria.
• The most potent neurotoxins are produced by Anabaena and Oscillatoria.
• Lyngbia martensiana causes dermatitis.

Economic Impacts

• Many cyanobacteria genomes have been sequenced with great potential for use in biofuel production.
• Biofuel from cyanobacterial lipids is being tested.
• spirulina or Arthrospira platensis is being consumed as a wonder food and may strenthen the immune system.
• Joule has developed a modified cyanobacteria called Helioculture that takes C02, sunlight and some nutrients to secrete transportation fuels.
• The sulpolipids appear to be medically important compounds against the AIDS virus (HIV).
• Water based extracts of Spirulina have also been shown to inhibit other diseases, especially cancers.
• Epoxyketone, also known as carmaphycin, has been isolated from cyanobacteria in the carribean and offers chemotherapy attributes.
• Apratoxins from the University of Florida show tumor selectivity and are great antitumor effects.

Domain Bacteria

• Phylum Cyanobacteria
• Order Phrochlorales

Prochlorophytes Details

• Prochlorophytes are phylogenetically related to cyanobacteria and are oxygenic phototrophic prokaryotes.
• They contain chlorophyll a or b, but lack phycobilins.
• These are similar to plant and algae possessing chlorophyll b.
• Prochloron is found in symbiotic associations with marine ascidians
• Prochlorothrix is a filamentous freshwater species
• Prochlorococcus occupies the open oceans.The first group is a spherical shaped single called prochloron, who display both chlorophyll A and B, and lacks phycobilins

Prochloron

• Photosynthetic Membranes.
• Extensive thylakoid membranes similar to that of chloroplast, found in symbiotic association with marine invertebrates. Spherical shapes can be found in several ascidians and display both chlorophyll A and B, but they lack phycobilins

Lissoclinum bistratum

• an ascidian host of prochloron.
• Prochlorothrix strains are rare with isolates to only two locations and contains a and b chlorophyll.

Prochlorococcus Details

• Prochlorococcus were discovered in 1986.
• This is the smallest photosynthetic organism known with diameter 0.5-0.8 µm diameter.
• Coccoid shape, free-living, motile.
• They are abundant in oligotrophic regions of the oceans.
• Possibly the most abundant organism on earth.
• Prochlorococcus contains divinyl chlorophyll a and b is the smallest photosynethic organisim, similar to the carotene which only has prokaryotes
• They are found in tropical and temperate oceans
• Appears to be the most abundant and productive photosynthetic bateria
• Plays a very important part in the carbon cycle
• Contribute 30 - 80% to primary production in the oceans
• There are two genetically distinct types: one that is high light adapted, and light adapted
• Divinyl chlorophylls are not true chlorophyll and allow light scavange through the depth of oceans
• They have not been found in fresh water ways or terrestrial ecosystems

Chloroplasts

• Structure of Chloroplast contains: Inner/outermembrane, intermembrane space, thylakoid, stroma, lamella and the granum stack.
• Choroplasts are known as the chlorophyll containing which conduct photosythesis. They have a permeable outer membrane and a much less premeable inner membrane
• The inside structure called the "stroma" contains both light reactions/components that are located on the flattened membrane disc "thylakoids"
• Chloroplast was proposed to be formed by the oxygenic prokaryote within the cell and by being established in early eukaryotes

Eukaryotic Chloroplast Phylogeny

• An endosymbiotic theory states that chloroplasts are thought to be ancestrally cyanobacteria, and thus, were the earliest oxygenic phototrophs.
• This process is said to have ignited an Explosion in biological diversity.
• While containing chlorophyll a, like cyano, chloroplasts do not contain phycobilins unlike the previous phylogentic group
• Chlorophyll A gives a visual look throughthe diagram

Green Sulphur Bacteria

• Table of the variety of the pigements across of cholorplasts in groups
• Key generas inclue: Chlorobium, Chlorobaculum, and Chlorochromatium Phylogenetically distinct

More About Green Sulfur Bacteria

• Non-motile
• anoxygenic phototrophic bacteria
• Utilize H2S as an electron donor
• Contain only obligate anaerobic species among cultured isolates
• The group includes bacteria that have short to long rods
• Green- and brown-colored species exist
• They are known to have sulfur granules

C. clathratiforme

• In contrast to C. clathratiforme, photosynthesis uses sunlight instead of oxygen and is known to be the only 80% abundant species of cells. They only account for 15% of ammonium usage.
• Green Sulphur are able to oxidze $H_2S$ into $SO_4$. They also display similar qualities to purple sulfur yet do not depose the sulfur outside the cell.

More Details of the Chlorosomes

• For identification and function purposes we can look at Bacteriochlorophyll (BChl)
• The bacteriochlorohyll function in green sulfur (BChl a)

Structure

• Ligth is transfered by the Bchl which helps with photosynthetic processes/energy and to conduct and convert ATP in the cytoplasmic membrane and function.
• A "Chlorosome" can also describe the Bchl as they can hold reaction. Examples inclue:

Light from light, CsmX1, CsmD etc

More Description In Depth with Structure

• Green sulfur come in many colors to help describe each one of their characeristics
• Such as Clorobaculum is known for (brown carotenoids)
• Chlorobaculum tepidum who display the only chrolophilic
• Green sulphur bacteria are known to live aquatic enviroments which have strong sulphide qualities. Even more, green sulphur is able to tolerate sulfide in higher potentcies
• Green sulphur bacteria also display symbiotic behaviour within their self.

Green Sulphur Bacteria Consortia

• The consortium bacteria/ green sulphur forms an intimate member association with what they call the bacterium "chemoorganotrophic".
• The symbiotic benefit in ways: organism benefits and symbiotic
• Some have a phototrophic or a Chemotrophic component

A and B details

• The phototrophic is refered to the 2 members (epibiont) and both phsycially attacted, while, non-phototrophic. (An 209 diagram shows the difference)

Green Sulphate

• Using 16S rRNA
• FISH green with the central cell. There is a theory where cells postion for phsytosyntheis where it is able for cell to extract for their own benfit as organic nutrients (diagram looks like a sun dial)
• One could show by diagrams of bacteria with hair
• We have determined "colonies of colonie" that it should be (lacking - PT contact to the epibm)
• That it attaches a function (ECL chains)

Phylium Section

Phylum Chloroflexi is what contains

Green Non-Sulphur Bacterium

• It is known as phylengentic from other bacterias. Only has few genera such is the ability to use Chloroflexus. Contains themomicroium , displays little amounts of bacterial/polumers
• The unusual Lipids of Thermomicrobium diagrams. These lipids do not have an ester ether/linkages.
• Chloroselxus helps a little bit, with this being a result from being a phylum

Chloroflexus Description Continued

• Help contain neuatral to hot alkaline sprungs and is most important for the cyanobacteria formation
• Anoxygneic diagrams and is able to transfer and get pigments.
• There is a structural location for photothetic with the help of what cells you live in of course.

Phyosology Information

• Phtotoautotrophy and has what cells are. In the Chloroflexa they call it habitats...

Other Properties

• Roseiflexus will not exist as cultured when it comes to the species, instead cells that are filamentious are yellow and orrange
• Can not cultrue Heliothrix, can be flamentious and display yellow orange due to lack to carotenoid (more or less color differences)

Phylum Spirochaetes

• This includes: Key Genera: Spirochaeta, Treponema, Cristispira, Leptospira, Borrelia (with 8 type to classify)

Morphology of these key type in the Phylum Spirochaetes

• Gram negative, known for moving/ and tightly coil up for shapes, unique. They have wide aquatics areas and is in animals as.
• Causes syphillis of corse.

Motility

• They show move and can not move or get by the cell wall/the cylinder. They do not single flagel and help that emertges out from each pole. They call this diagram name for this"motility 8.8 and outer cell/ and cylinder structure"
• "The spirochetes move or fold back are they periplasm to cell?"

Treponma and the related properties

• Its not eacape or to the human side.
• We need have microaerophillic
• Have other "what about what I menton is a bad idea like bad/gums" Diagrams would also have help for "T. Saccharo"

Treponma Sacro/Another Diagram

• Has "termite"
• Can fix nitrogen, not only has are it is or any type a way, "but what in the gum"

LeptospiRa "diagram time"

• Is useing " fatty cells/ acids" to help carbon source which thins out the cell
• In humans this is well know to cause failure to organ that may death

Treatment

• Can affect the body or the membrane of the urine and is in contact. Cured and with drugs?

Borrelia Details

• Is know for or affecting the human body like fever Diagram of course and help guide as the best we can with Lyme also is something to look for as well.

Diagram and Other Affects/Reservoir Factors

• With that said, more could be result with pains that to go "limbs", "vision" and with drug to help

Phylum Details

Phylum is able include to

Thermales

• That all we need now, hope fully we are able to complete and or to add the file.