Bacteria and Archaea : the Prokaryotes

 Bacteria and Archaea : the Prokaryotes

 

· Today’s Learning objectives

· Describe the basic differences between prokaryotes And eukaryotes

· Outline the phylogeny of the major groups of Prokaryotes

· Describe the diversity of prokaryotic metabolic Strategies in terms of obtaining carbon, energy and Oxygen requirements (biological Carbon cycle)

· Describe the Nitrogen cycle and the essential roles Played by prokaryotes in this cycle

· Describe how prokaryotes impact human health

 

Identification of Diseases:

Consumption: Tuberculosis, a bacterial disease, noticeable by a significant number of cases.

The French Pox: Syphilis, another bacterial disease, highlighted by its historical name, particularly not as widespread as tuberculosis.

Smallpox: A viral disease, recognizable in the document.

Apoplexy: Identified as a stroke, a common cause of mortality in modern times.

Infant Mortality: Not explicitly labeled, but infants and young children (teething) are discernible, indicating higher mortality in these age groups.

Diseases of Nutrition: Scurvy and rickets mentioned as vitamin deficiency diseases, reflecting changes over time.

Observations on Mortality Patterns:

 

Shifts in Disease Landscape: Mortality patterns have changed over the centuries, with a decrease in bacterial and viral diseases, partly due to advancements in healthcare and disease management.

Higher Infant Mortality: Noted in the document, emphasizing the challenges in infant and child healthcare during that period.

Nutritional Diseases: Scurvy and rickets highlight nutritional deficiencies prevalent at the time.

Prokaryotes:

Prokaryotes and Disease: The prevalence of bacterial diseases, showcasing the impact of prokaryotes on historical health.

Bacterial Dominance: Even excluding the plague, many diseases were caused by bacteria, underscoring the significance of prokaryotes in historical mortality

Learning Objectives:

Phylogeny of Major Prokaryotic Groups:

outline the phylogeny of major prokaryotic groups, focusing on significant classifications.

Diversity of Prokaryotic Metabolic Strategies:

a. Carbon Acquisition: Explore the various methods prokaryotes use to obtain carbon.

b. Energy Acquisition: Describe the diversity in strategies for obtaining energy.

c. Oxygen Requirements:  variation in oxygen preferences, ranging from obligate aerobic to anaerobic conditions.

Nitrogen and Sulfur Cycles:

a. Nitrogen Cycle: Understand and describe the nitrogen cycle, emphasizing the essential roles played by prokaryotes.

b. Sulfur Cycle: Briefly explore the sulfur cycle and the involvement of prokaryotes.

Impact of Prokaryotes on Human Health:

 

a. Negative Impacts: Discuss how some prokaryotes contribute to diseases, as seen in historical mortality patterns.

b. Positive Contributions: Explore ways in which prokaryotes positively impact human health, acknowledging their beneficial roles.

 

Defining Prokaryotes:

A prokaryote is often considered a single-celled organism, with a few exceptions being multicellular in a colonial sense.

Key Feature: Lack a membrane-bound nucleus, distinguishing them from eukaryotes where genetic material is compartmentalized in a nucleus.

Prokaryotic Characteristics Clarification:

Genetic Material: Prokaryotes, including bacteria and archaea, possess both RNA and DNA, distinguishing them from viruses.

DNA Structure: The major chromosome in prokaryotes is circular, a common feature in virtually all of them.

Linear Chromosomes in Eukaryotes: A key difference is highlighted, as eukaryotes typically have linear chromosomes, although circular DNA is present in organelles like mitochondria and chloroplasts.

Asexual Reproduction: Prokaryotes reproduce asexually, but it doesn’t preclude them from sharing DNA, a concept to be further explored in genetic variability discussions.

Nuclear Structure and Gene Expression:

Nuclear Compartment: While prokaryotes lack a membrane-bound nucleus, they do have a nuclear region where genetic material is usually localized.

Transcription and Translation: Gene expression stages, transcription and translation, occur in the same compartment in prokaryotes, unlike eukaryotes where they are separated by membrane-bound organelles.

Three Major Domains of Life:

Bacterial Domain:

Prokaryotic cell organization.

Archaeal Domain:

Prokaryotic cell organization.

Eukaryotic Domain:

Believed to be more recent than bacteria and archaea.

Likely more closely related to archaea than bacteria.

Hypothesized origin involves a symbiotic event between an archaeal cell and a bacterium, forming mitochondria.

Origin of Eukaryotes:

The eukaryotic domain likely emerged from a symbiotic event between an archaeal cell and a bacterium, leading to the formation of mitochondria.

Monophyletic Group Question:

The  consider whether prokaryotes, specifically when discussing bacteria and archaea, form a monophyletic group.

Monophyletic vs. Paraphyletic:

Prokaryotes, when considered as a group, are not monophyletic but paraphyletic.

Monophyletic groups contain the common ancestor and all its descendants, while paraphyletic groups exclude some descendants.

Prokaryotic Cell Structure:

Size: Prokaryotic cells are small, with an average length of about two microns, significantly smaller than typical eukaryotic cells.

Simplification: Due to their small size, prokaryotic cells exhibit structural simplifications compared to eukaryotic cells.

Abundance and Habitat:

Ubiquity: Prokaryotes are abundant in all habitats, including the human body, where bacterial cells outnumber human cells.

Roles in the Body: Found in the intestine and on the skin, prokaryotes play crucial roles in these locations.

Metabolic Diversity:

Eukaryotic Energy Sources: Eukaryotes primarily capture light for energy or obtain carbon from organic sources.

Prokaryotic Metabolism: Prokaryotes have diverse metabolic processes beyond those of eukaryotes, utilizing various energy sources and demonstrating intricate biochemistry.

Essential Role in Life:

Fundamental Significance: Prokaryotes are essential to all life on Earth, a concept to be elaborated on later in the lecture.

Significance of the Nitrogen Cycle:

Critical Role: The nitrogen cycle, facilitated by bacteria and nitrogen-fixing prokaryotes, is crucial for sustaining life on Earth.

Human Impact: Bacteria also play a significant role in human health, as evident from the diseases discussed earlier.

Structural Features of Bacteria:

 

DNA Structure:

Circular Chromosome: Bacterial DNA is simple, contained in a circular chromosome, folded into loops.

Cytoplasm Continuity: The DNA is not separated by a membrane, allowing continuous cytoplasm between the DNA and the rest of the cell’s metabolic processes.

Transcription and Translation: Ribosomes, associated closely with the compartment where transcription occurs, lead to direct translation, with no spatial separation.

Plasmids:

: Many bacteria have small circles of additional DNA called plasmids.

Horizontal Gene Transfer: Plasmids serve as vectors for horizontal gene transfer, carrying antibiotic resistance genes and facilitating the spread of resistance.:

Plasma Membrane: Bacteria possess a plasma membrane.

Cell Wall: Prokaryotes have a cell wall outside the plasma membrane, providing structural support.

Distinct Components: The components of the bacterial cell wall are unique and not found in eukaryotes or archaea.

Role of Cell Wall and Plasmids:

Structural Support: The cell wall outside the plasma membrane provides structural support to the bacterial cell.

Horizontal Gene Transfer: Plasmids contribute to the spread of antibiotic resistance genes, allowing bacteria to transfer resistance to related bacteria.

 

Visual Representation:

Electron Micrograph: An electron micrograph of a bacterium is shown.

Cell Wall: The outer layer is the cell wall, providing structural support.

Plasma Membrane: The plasma membrane separates the cytoplasm from the external environment.

- Note: The image appears to show a gram-negative bacterium with lipopolysaccharide on the outside and the cell wall beneath it.

 

 

 

Flagella for Motility:

Bacteria often have flagella for movement.

Flagella rotation allows forward movement or tumbling.

- Note: Bacterial flagella differ structurally from eukaryotic flagella.

 

Binary Fission and Cell Division:

Binary Fission:

Prokaryotes divide through binary fission.

DNA is replicated, and each daughter cell receives a copy of the single circular chromosome.

Motility Mechanism:

Bacteria use flagella for movement, a structurally different mechanism than eukaryotic flagella.

Cell Division:

Prokaryotes utilize binary fission, distinct from eukaryotic mitosis or meiosis.

 

Small Size Significance:

Bacteria are highlighted for their small size .

Reasons:

Significance in relation to eukaryotic cells.

Impacts on their structural and functional characteristics.

Important for understanding their unique division mechanisms.

Small Size Facilitates Rapid Diffusion:

Advantage of Small Size:

Small size allows for rapid diffusion of materials over short distances.

Bacteria and archaea can rely on diffusion for material exchange between the cell’s exterior and interior.

Structural Diversity in Bacteria:

 

Common Shapes:

Rod-Shaped (E. coli): Common rod-shaped bacteria.

 

Spherical (Streptococcus): Spherical bacteria, e.g., Streptococcus.

 

Complex Structures: Some bacteria can form complex structures, like fruiting bodies, through aggregation and differentiation.

 

Reproduction and Genetic Diversity:

Prokaryotes reproduce asexually

Asexual Reproduction:

Prokaryotes, including bacteria, generally reproduce asexually.

Single-celled structures are the norm, but exceptions exist.

Genetic Diversity Source:

Mutations:

Genetic diversity primarily arises through mutations in prokaryotes.

Mutations occur in individual cells and are inherited by their offspring, leading to variation within populations.

Limitation of Single-Cell Mutations:

While mutations provide variation, they are limited to the descendants of the mutated cell.

Plasmids and Horizontal Gene Transfer:

Plasmids for Genetic Exchange:

Plasmids, small circles of DNA, play a crucial role in increasing genetic diversity.

Plasmids facilitate horizontal gene transfer, allowing the spread of genetic material between bacteria.

Horizontal gene transfer enables different cells to acquire the same new mutation, enhancing overall genetic variation in a population.

Sexual Reproduction in Bacteria:

Complex Structures (e.g., Mixobacteria):

Some bacteria, like mixobacteria, can form complex structures.

These structures involve aggregation, differentiation, and the production of environmentally resistant spores.

Importance of Genetic Diversity:

Variation in Populations:

Genetic diversity ensures variation within bacterial populations.

Mutations and horizontal gene transfer contribute to the overall diversity.

Conjugation, Transformation, Transduction:

Bacteria employ three main mechanisms for horizontal gene transfer: conjugation, transformation, and transduction.

Conjugation:

Process: Bacteria physically tethered by pilus during conjugation.

Pilus Role: Pilus pulls donor and recipient cells together.

Transfer Medium: DNA transfer occurs through the pilus, usually involving a plasmid.

Example: Donor may carry antibiotic resistance genes on the plasmid transferred to the recipient.

- Image: Bacteria linked in the process of conjugation, demonstrating pilus-mediated connection.

Transformation:

Process: Bacteria can take up naked DNA from the environment.

Source of DNA: Dead cells release DNA into the environment.

Recipient Competence: Transformation competence varies among bacterial species and strains.

 

Importance of Transformation:

Variability Increase:

Transformation allows bacteria to pick up genes from the environment, increasing genetic diversity.

Competent bacteria can incorporate genes from different sources.

Hospital Scenario:

Spread of Antibiotic Resistance:

Conjugation is a mechanism for the spread of antibiotic resistance in bacterial populations.

Transfer of antibiotic resistance plasmids from donor to recipient cells.

 

 

DNA Uptake from Environment:

Competent bacteria can take up naked DNA from the environment.

This process was discussed in the context of DNA identification as the genetic material.

Reference to Earlier Courses:

Reference to past courses (e.g., 2070) where the ability of bacteria to take up DNA and the identification of DNA as genetic material might have been discussed.

What distinguishes the Archaea from the Bacteria?

Initially distinguished based on DNA sequence differences, particularly in ribosomal DNA.

Genetic evidence indicated separate clustering of archaeal and bacterial ribosomal DNAs.

Archaeon Environments

Extreme Environments:

Early-identified archaea often found in extreme environments.

Presence in extreme conditions suggested distinctiveness from bacteria.

 

 

 

Ribosomal DNA Sequences:

Archaeal and bacterial ribosomal DNA sequences showed significant differences.

Initial genetic evidence pointed to distinct prokaryotic groups

Similar Morphology:

Archaea and bacteria may appear similar in morphology.

Lack of visible distinctions on the surface.

Expansion on Genetic Differences:

Distinct genetic clusters suggested significant evolutionary differences.

Genetic divergence supported the idea of separate evolutionary paths for archaea and bacteria.

Archaeal Diversity:

While initially identified in extreme environments, archaea are diverse and found in various habitats.

Not limited to extreme conditions, showcasing broader ecological adaptation.

Complex Phylogenetic Relationships:

The archaea has evolved to recognize the complexity of phylogenetic relationships.

Genetic, morphological, and ecological diversity challenges initial simplistic classifications.

Morphological Similarities:

Visual similarities between archaea and bacteria make morphological identification challenging.

Distinctions often require genetic or biochemical analysis.

 

 

 

Separate Evolutionary Paths:

Genetic evidence supporting separate clustering implies distinct evolutionary histories for archaea and bacteria.

Evolutionary implications of genetic divergence.

Archaea: Beyond Extreme Environments::

Archaea were initially associated with extreme environments (heat, salt, acidity).

Extremophiles were considered to thrive in areas where other organisms couldn’t.

Genetic Differences:

Genetic evidence initially distinguished archaea from bacteria.

Archaea exhibited unique genetic clusters, challenging simplistic classifications.

 

Nucleus and Membrane-Bound Organelles:

Only eukaryotes possess a nucleus and other membrane-bound organelles.

DNA Structure: :

Similarity between archaea and bacteria: DNA in a circular form.

Membrane Lipids:

Ester vs. Ether Linkages:

Archaea membranes differ in lipid structure.

Eukaryotes and bacteria use ester linkages, while archaea use ether linkages.

Photosynthesis in Archaea:

Chlorophyll Absence:

Photosynthesis occurs in archaea, but chlorophyll is not utilized.

 

High-Temperature Adaptation:

Both archaea and bacteria can grow at temperatures >80°C.

Archaea exhibit higher temperature tolerance, up to 120°C under pressure.

Histones: DNA Organization:

Histones help organize DNA into chromosomes.

Presence in eukaryotes contributes to DNA packing and regulation.

Archaea vs. Bacteria:

Shared characteristics with both bacteria and eukaryotes.

Distinctions in DNA organization, histone presence, and ribosome sensitivity.

 

 

 

 

 

Prokaryotic metabolism:

Autotrophs: Generate own carbon, often through processes like photosynthesis.

Heterotrophs: Rely on external organic sources for carbon.

Autotrophs (CO2):

· Examples: Photosynthetic organisms.

· Carbon source: Carbon dioxide (CO2) from the air.

· Heterotrophs (Organic Sources):

· Examples: Organisms consuming organic compounds.

· Carbon source: Organic materials from external sources.

Prokaryotic Metabolic Diversity

Prokaryotes encompass both autotrophic and heterotrophic organisms.

Diversity in how prokaryotes obtain and utilize carbon for metabolism.

Additional Metabolic Characteristics:

· Methane Production Capability:

· Archaea specific trait: Ability to produce methane.

Antibiotic Sensitivity:

Distinction in ribosome structure: Archaeal ribosomes differ, making them insensitive to certain antibiotics like chloramphenicol and streptomycin.

Nitrogen Fixation and Chemoautotrophy:

Shared traits between archaea and bacteria.

Nitrogen fixation and chemoautotrophy abilities not present in eukaryotes.

 

 

 

 

 

 

· Heterotrophs: Rely on organic sources for carbon.

· Autotrophs: Utilize carbon dioxide (CO2) from the air.

Metabolic Processes in Eukaryotes:

Examples:

· Heterotrophs: Animals (rely on external organic sources).

· Autotrophs: Plants (use oxygenic photosynthesis, requiring oxygen).

Prokaryotic Metabolic Flexibility:

 

Eukaryotes have limitations in metabolic pathways (e.g., oxygenic photosynthesis, aerobic respiration, and limited anaerobic respiration).

Prokaryotes exhibit diverse metabolic capabilities beyond eukaryotic constraints.

Prokaryotic Metabolic Pathways:

Photosynthesis in Absence of Oxygen: Anoxygenic photosynthesis.

Chemical Energy for Carbon Fixation: Chemoautotrophs.

Anaerobic Respiration without Oxygen: Exploiting different chemical compounds.

Chemo Heterotrophs and Photo Heterotrophs: Utilizing sunlight as an energy source, but relying on organic carbon.

Four Main Prokaryotic Metabolic Groups:

· Photoautotrophs: Light as an energy source, CO2 as a carbon source (e.g., some bacteria).

· Chemoheterotrophs: Chemicals as an energy source, organic carbon as a carbon source (e.g., many bacteria, animals).

· Photoheterotrophs: Light as an energy source, organic carbon as a carbon source (e.g., some bacteria).

· Chemoautotrophs: Chemicals as an energy source, CO2 as a carbon source (e.g., certain bacteria).

 

Metabolic Diversity in Prokaryotes:

 

Prokaryotes display versatile metabolic strategies.

Flexibility in utilizing different energy and carbon sources.

Contrasts with eukaryotic metabolic limitations.

        Focus on Carbon Source:

Definition: Organism’s source of carbon for biosynthesis.

Example Question: If an organism uses CO2 as a carbon source, what is the best description?

Autotrophic Organism:

        Correct Answer: Autotrophic.

Autotrophs utilize CO2 as a source of carbon for biosynthesis.

Distinct from the discussion on chemoautotrophs, which involves the energy source (chemo) for biosynthesis.

 

 

Diversity of Prokaryotic Metabolism:

· Introduction:

 the diversity in bacterial and prokaryotic metabolism.

 the fascinating diversity of biochemical pathways.

· Anoxygenic Photosynthesis:

Definition:

Photosynthesis that does not produce oxygen.

Utilizes various electron donors, distinct from the oxygenic photosynthesis seen in plants and cyanobacteria.

Example of Anoxygenic Photosynthesis:

Hydrogen Sulfide Utilization:

Organisms can use hydrogen sulfide as an electron donor instead of oxygen.

Formula is similar to oxygenic photosynthesis, with hydrogen sulfide replacing oxygen.

Results in the production of elemental sulfur as a byproduct.

Further oxidation can lead to sulfate ion formation.

 

Metabolic Diversity:

Prokaryotes exhibit diverse metabolic pathways.

Anoxygenic photosynthesis is an example of the varied strategies employed by prokaryotic organisms.

Anoxygenic Photosynthesis Features:

Distinct Characteristics:

Different electron donor (e.g., hydrogen sulfide) in place of oxygen.

Products include organic carbon sources with a unique waste product.

Oxygen is not produced during anoxygenic photosynthesis.

Organisms Performing Anoxygenic Photosynthesis:

 

· Examples:

Bacteria: Green sulfur bacteria, purple sulfur bacteria.

Archaea: Some archaea can also carry out anoxygenic photosynthesis.

 

Microbial Mats :

Microbial mats are communities found in oxygen-poor estuaries.

Stratification of metabolic activities in different layers of the mat.

 

Layers of a Microbial Mat:

 

· Top Layers:

Autotrophic metabolism dominated by oxygenic photosynthesis.

Aerobic respiration.

· Middle Layers:

Anoxygenic photosynthesis with alternative electron donors as oxygen depletes.

Anaerobic respiration.

Fermentation processes.

· Bottom Layers:

Chemoautotrophic metabolism due to the absence of light.

Utilization of chemical sources of energy to drive CO2 incorporation.

Graphical Representation of Microbial Mat Layers:

· Light Penetration:

Light penetrates a certain distance.

Oxygen levels maximize where oxygenic photosynthesis occurs.

Oxygen declines as you move down, replaced by increasing hydrogen sulfide.

· Adaptation to Oxygen-Poor Environments:

Microbial mats demonstrate metabolic versatility in oxygen-poor conditions.

Layers correspond to changing metabolic activities based on available oxygen and light.

Anoxygenic photosynthesis is a crucial component of these microbial communities.

· Microbial Mats in Estuaries:

Cyanobacteria dominate upper layers with oxygenic photosynthesis.

Purple sulfur bacteria perform anoxygenic photosynthesis using hydrogen sulfide.

Anaerobic respiration and fermentation support microbial populations in lower layers.

· Aerobic Respiration:

Organic carbon + Oxygen → CO2 + Water.

Common in eukaryotes, including humans.

· Anaerobic Respiration:

Organic carbon + Sulfur Compounds → CO2 + Hydrogen Sulfide + Water.

 

 

No molecular oxygen involved.

Different waste products compared to aerobic respiration.

Hydrothermal Vents: Extreme Environments:

· Chemoautotrophic Prokaryotes:

Base of the food chain in hydrothermal vents.

Perform chemoautotrophic metabolism.

Capture CO2, convert it to organic compounds.

Primary producers in this extreme environment.

Utilize chemical energy sources for metabolism.

      Definition:

Organism capturing CO2, converting it to organic compounds.

Fundamental in ecosystems as the basis of the food chain.

In hydrothermal vents, chemoautotrophic prokaryotes serve as primary producers.

Characteristics:

Deep-sea hydrothermal vents are extreme environments.

Chemoautotrophic prokaryotes thrive in these conditions.

Gaining carbon by reducing CO2 for energy storage and biosynthesis.

Microbial Diversity and Adaptation:

Prokaryotes showcase remarkable metabolic diversity and adaptation.

From microbial mats to hydrothermal vents, different metabolic pathways are employed

Chemoautotrophic Prokaryotes:

Capture CO2, convert to organic compounds.

Use molecules/ions (e.g., hydrogen gas, hydrogen sulfide, sulfate ion) for energy.

Don’t rely on sunlight; employ inorganic compounds as energy sources.

Demonstrates versatility in energy and carbon utilization.

Swamp Mud Metabolism:

Characterizing Prokaryotic Metabolism in Swamp Mud:

Prokaryotes thriving in swamp mud utilize anaerobic respiration.

Hydrogen sulfide gas produced as a byproduct.

Disturbance of mud releases the characteristic smell associated with anaerobic respiration.

Question: Most Likely Metabolic Process in Swamp Mud:

 

Options:

Oxygenic photosynthesis

Aerobic respiration and oxygenic photosynthesis

Anaerobic respiration

Answer: Anaerobic Respiration:

 

Explanation:

Anaerobic respiration produces hydrogen sulfide gas.

Smell associated with disturbed swamp mud is indicative of anaerobic conditions.

 Prokaryotic Roles in Sulfur and Nitrogen Cycles:

Sulfur Cycle:

Prokaryotes play crucial roles in sulfur cycling.

Sulfur is essential for organisms, including humans.

Processes involve transformations of sulfur compounds.

 

Open Question: Clarification on Oxygenic vs. Aerobic Respiration:

Sulfur Cycle:

Sulfur in Organisms:

Essential for proteins (e.g., cysteine) and biochemistry.

Plants assimilate sulfur as sulfate ions.

Sulfur Release from Decomposition:

Decomposition by fungi and bacteria releases sulfur as hydrogen sulfide.

Sulfur Conversion by Photosynthetic Bacteria:

Photosynthetic bacteria, oxygenic chemoautotrophic bacteria, and chemoautotrophic archaea convert hydrogen sulfide back to sulfate.

Essential for assimilation into organic sulfur in proteins.

        Nitrogen Fixation: :

Required for proteins and nucleic acids.

Critical component of amino acids.

Prokaryotic Nitrogen Fixation:

Bacteria play a crucial role in nitrogen fixation.

Essential for converting atmospheric nitrogen (N2) into a form usable by organisms.

Nitrogen-fixing bacteria enable the assimilation of nitrogen into organic compounds.

Prokaryotic Nitrogen Fixation:

 

 

Nitrogen is essential for amino acids and other compounds.

Nitrogen gas in the atmosphere cannot be directly utilized by eukaryotes.

Role of Nitrogen-Fixing Bacteria:

Bacteria and archaea can fix nitrogen, converting nitrogen gas into ammonia.

Ammonia can further be converted to nitrite or nitrate.

Plants can uptake ammonia, nitrite, or nitrate and incorporate organic nitrogen into their structures.

Symbiosis in Legumes:

Example of legumes (e.g., soybeans) forming associations with nitrogen-fixing bacteria.

Bacteria convert nitrogen gas into a usable form for plants.

Symbiotic relationship benefits both the plant and the bacteria.

Bacterial Diversity:

Many prokaryotes have not been cultured in laboratories.

 about them primarily comes from DNA sequences.

Example from the Sargasso Sea:

Collection of water samples from the Sargasso Sea.

Sequencing revealed 1800 distinct types of bacteria.

Indicates a vast diversity of bacterial species in oceans and likely other environments.

 

Rare Biosphere:

 the number of sequences and their proximity to known bacteria.

 the existence of a diverse and vast “rare biosphere” with many unknown species.

Implies numerous bacteria, particularly in deep-sea and other less-explored environments, are yet to be studied and cultured.

  

 

Prokaryotic Dominance:

Prokaryotes, including bacteria and archaea, exhibit a vast diversity of life.

 the tree of life highlights the dominance of prokaryotes, particularly bacteria and archaea.

The blue section represents bacteria, and the green section represents archaea.

 

Increased Archaeal Diversity:

The diversity of archaea has expanded since the drawing of the tree, indicating a much broader range than depicted.

There is a considerable amount of prokaryotic diversity compared to eukaryotes.

Phylogeny of Bacteria:

The   diversity within the bacterial realm and plans to explore specific bacterial groups separately.

 

 

 

 

 

 

 

Photosynthetic Bacteria:

Cyanobacteria carry out oxygenic photosynthesis.

Other photosynthetic bacteria, like purple sulfur and green sulfur bacteria, perform an anoxygenic form of photosynthesis.

Photosynthesis occurs in different bacterial groups throughout the bacterial tree.

Gram-Positive and Gram-Negative Bacteria:

Gram staining is one of the oldest methods of classifying bacteria based on the thickness of the peptidoglycan layer in their cell wall.

Gram-Positive Bacteria:

Thick peptidoglycan layer.

Cytoplasmic membrane below the peptidoglycan layer.

Gram-Negative Bacteria:

Peptidoglycan layer, but thinner than in gram-positive bacteria.

Outer membrane with lipopolysaccharide (LPS) wall outside the peptidoglycan layer.

 

Structural Differences:

Gram-positive bacteria appear dark in the gram stain.

Gram-negative bacteria have a more complex structure, appearing differently in the gram stain.

Gram-Negative Bacteria:

         Gram Staining:

Gram-negative bacteria have a thinner peptidoglycan layer in their cell wall.

The gram stain does not stain the peptidoglycan as strongly.

Proteobacteria:

Proteobacteria is a major group of gram-negative bacteria.

E. coli is an example of a gram-negative bacterium in the

 Proteobacteria group.

Proteobacteria are diverse and abundant, with significant importance in various environments, including the human gut.

Cholera bacterium is an example of a pathogenic gram-negative bacterium.

Gram-Positive Bacteria: Firmicutes:

 

Clostridium botulinum:

Gram-positive bacterium known for causing botulism.

Produces resistant spores.

Streptomyces:

Gram-positive bacterium forming branched structures.

Significant as a source of antibiotics, including streptomycin.

 

Found in soil and contributes to the production of antibiotics.

Cyanobacteria:

Oxygenic Photosynthetic Bacteria:

Cyanobacteria are oxygenic photosynthetic bacteria.

Diverse group, ranging from small single-celled species to larger colony-forming bacteria.

 

Ecological Impact:

Cyanobacteria contribute to the formation of pond scum.

Involved in harmful algae blooms, such as those in Lake Erie.

 

 

 

 

 

Diverse Forms:

Cyanobacteria exhibit diverse forms, including single-celled species, filamentous structures, and those with differentiated cell types.

Some species have specialized cells like heterocysts, capable of nitrogen fixation alongside photosynthesis.

 

Structures Inside Cyanobacteria:

Extracellular envelope made of polysaccharides.

Filamentous structures with multiple cells.

Differentiated cell types, e.g., heterocysts for nitrogen fixation.

Thylakoid membranes are crucial for photosynthesis.

Thylakoid Membranes:

Location of Photosynthesis:

Thylakoid membranes are stacked structures within cyanobacteria where photosynthesis occurs.

These membranes contain chlorophyll, the energy center for cyanobacteria.

Analogous structures are found in chloroplasts of eukaryotic plant cells.

Significance of Thylakoid Membranes:

Thylakoid membranes in cyanobacteria are fundamental to photosynthesis.

The term “thylakoid membrane” is introduced for further relevance.

A link is established with chloroplasts in plant cells.

Cyanobacteria in Symbiotic Evolution:

Origin of Eukaryotes:

Cyanobacteria play a role in the origin of eukaryotes.

The  a symbiotic event between a eukaryotic cell and a cyanobacterium, leading to the formation of photosynthetic plants.

The connection is made with thylakoid membranes and circular DNA in chloroplasts.

 

 

 

Oxygenic Photosynthesis:

Cyanobacteria are the only prokaryotes capable of oxygenic photosynthesis.

Their significance extends beyond their structural diversity to their crucial role in producing oxygen through photosynthesis.

Cyanobacteria and Oxygen Production:

Cyanobacteria are the only prokaryotes capable of oxygenic photosynthesis.

They played a crucial role in introducing oxygen to the Earth’s atmosphere.

Oxygen Production Timeline:

In the first 2 billion years, virtually no oxygen was present in the atmosphere.

Around 2.5 billion years ago, oxygen began to rise, correlating with the evolution of cyanobacteria.

Cyanobacteria contributed to an early burst of oxygen, laying the foundation for the oxygen-rich atmosphere we depend on today.

 

 

Source of Antibiotics:

Cyanobacteria are not a source of antibiotics.

Streptomycin, an important antibiotic, is derived from Streptomyces bacteria.

Archaea and Methanogens:

Archaea are found not only in extreme environments but also in the deep ocean and other areas of the biosphere.

Methanogens:

Methanogens, a group of archaea, are the only known biological sources of methane.

Found in the rumen of cows, methanogens contribute to methane production during fermentation.

Methanogens in Cow Rumen:

Biochemistry of Methanogens:

Methanogens, a group of archaea, produce methane as part of their biochemical processes.

Found in the anaerobic environment of the cow’s rumen, contributing to methane production during food digestion.:

Discovery of Asgard Archaea:

The Asgard group of archaea, including potential ancestors of eukaryotes, was discovered more recently.

Asgard archaea are now recognized as a distinct and abundant group in the microbial world.

Phylogeny of Archaea and Eukaryotes:

The phylogeny suggests that eukaryotes branch out from within the Asgard archaea.

This challenges the idea of archaea as a monophyletic group, as eukaryotes are excluded, making archaea paraphyletic.

 

Prokaryotes and Human Health:

Prokaryotes, particularly bacteria, have had a significant impact on human health throughout history.

Examples include diseases caused by prokaryotic pathogens like the plague bacillus.

The human microbiota, comprising bacteria living on and inside humans, influences various health conditions.

 

Microbiota and Human Health:

 

Microbiota Variations and Human Conditions:

Variations in microbiota composition are associated with various human conditions, such as obesity.

The question arises whether these microbiota differences are a cause or an effect of the associated human conditions.

Associations may not always imply causation; microbiota changes could be related to rather than causing the condition.

 

 

Diversity of Human Microbiome:

 

 

Bacteria are present in various parts of the body, including the gastrointestinal (GI) tract, airways, skin, and urogenital tract.

The human microbiome is diverse, and different bacterial communities are associated with different body regions.

 

Roles of Bacteria in the Human Body:

Positive Roles of Bacteria:

Bacteria in the GI tract contribute positively to human health by producing essential compounds like vitamins B12 and K.

Bacteria protect against pathogenic invaders, both in the GI tract and on the skin.

Bacteria in the GI tract assist in the digestion process, playing a role in nutrient breakdown.