Microbial Taxonomy and Classification

Microbial Diversity: Taxonomy and Classification of Microbes

• Categorizes bacteria, archaea, and eukarya as the three domains of life
• Origin of Earth was approximately 4.6 billion years ago (bya)
• Bacteria and archaea emerged around 3.8 bya
• Phototrophic bacteria appeared about 4 bya
• Cyanobacteria arose around 3 bya
• Eukarya evolved roughly 2 bya
• Both animals and vascular plants exist today
• Mammals and humans exist today

Characteristics of Domains

• Bacteria and archaea are prokaryotic, while eukarya are eukaryotic at the cellular level
• Bacteria and archaea possess a single, circular chromosome
• Eukarya have several, linear chromosomes
• Ribosomes in bacteria are 70S
• Archaeal ribosomes are similar to 70S, but the structure resembles 80S ribosomes found in eukaryotes
• Bacteria and archaea contain a unique ribosomal RNA signature sequence
• Eukaryotic cells possess a unique ribosomal RNA signature sequence
• The number of sequences shared with eukarya: bacteria (1), archaea (3), eukarya (all)
• Protein synthesis in bacteria is similar to eukarya
• Peptidoglycan is present in bacterial cell walls and absent in archaea and eukarya
• Bacterial cell membrane lipids consist of fatty acids with ester linkages
• Archaeal cell membrane lipids contain long-chain, branched hydrocarbons with ether linkages
• Eukaryotic cell membrane lipids contain fatty acids with ester linkages
• Sterols are typically absent in bacterial membranes, has some exceptions
• Sterols are sometimes present in archaeal membranes
• Sterols are present in eukaryotic membranes

Domain Archaea

• Composed of five described phyla: Nanoarcheaota, Euryarchaeota, Thaumarchaeota, Crenarchaeota, and Korarchaeota
• Have historical roots in extreme environments, with early isolates from hot, salty, or acidic sites
• Not all archaea are extremophiles

Extremophiles

• Hyperthermophiles grow best at temperatures above 80°C
• Extreme halophiles need at least 1.5 M (about 9%) NaCl for growth
• Haloferax and Natronobacterium exemplify extreme halophiles
• Acidophiles thrive below pH 5.5
• Alkaliphiles require a pH of 8 or higher for optimal growth

Bacteria

• Have a prokaryotic cell structure
• Undifferentiated single cells with lengths ranging from 0.5 to 10 um
• Typically unicellular, some can be multicellular, like Magnetoglobus
• Candidatus Magnetoglobus, a multicellular magnetotactic prokaryote, inhabits hypersaline environments
• Has 30 major phyla, with at least one species grown in culture
• Cultivated bacteria primarily belong to four phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes.
• Actinobacteria are Gram-positive with high G+C DNA
• Common in water and soil
• Firmicutes are Gram-positive, have low G+C DNA, and possess rigid cell walls containing muramic acid
• Proteobacteria are a large, diverse group of Gram-negative bacteria with rod and round shapes
• Proteobacteria's outer membrane contains LPS/LOS, triggering immune reactions, divided into five groups: alpha, beta, gamma, delta, epsilon
• Bacteroidetes are the second most common bacteria in the human gut and include Bacteroides and Prevotella.

Large Bacteria

• Epulopiscium fishelsoni
• Thiomargarita namibiensis

Endosymbiosis

• One organism lives inside another, benefitting both
• Mitochondria and chloroplasts originated as free-living bacteria absorbed by larger cells, aiding energy production

Eukarya

• Plants, animals, and fungi represent well-known eukarya groups
• The first eukaryotes were unicellular microbes
• Microbial eukaryotes come in different sizes, shape, and functions
• Nanoflagellates, tiny microbial predators, are about 2 um
• Ostreococcus, a green algae, is even smaller at 0.8 um
• Major groups are called kingdoms, not phyla
• Microbial eukaryotes are classified as protists, algae, and fungi
• Protists are eukaryotic microbes that aren't plants, animals, or fungi
• Algae are photosynthetic but are not plants
• Fungi are non-photosynthetic and have chitin cell walls (like yeasts, molds, and mushrooms)

Phylogenetic Tree of Eukarya

• Archaeplastida includes plants, green algae, and red algae, all of which are photosynthetic
• SAR Clade is diverse, has three subgroups: Stramenopiles, Alveolata, and Rhizaria.
• Stramenopiles include algae like diatoms and brown algae, which have flagella with hairs
• Alveolata includes microbes with sacs under their membranes like ciliates, dinoflagellates
• Rhizaria consists of amoeba-like organisms that use thin extensions for movement
• Excavates: unicellular organisms that lack mitochondria, ex. Euglena, Giardia
• Amoebozoa: includes amoebas and slime molds; move using pseudopodia
• Opisthokonta contains animals, fungi, and related single-celled organisms

Properties of Some Cells

• Differentiation allows cells to form new structures, like spores
• Communication allows cells to interact via chemical messengers
• Growth converts DNA into proteins, used to changes nutrients into new cells
• Evolution: chance mutations in DNA lead to new properties; phylogenetic trees depict species relationships
• Motility: some cells can self-propel with flagella
• Horizontal gene transfer: cells exchange genes

Microbial Nomenclature

• Taxonomy classifies living organisms
• Taxa are the categories used in classification
• Carl Linnaeus (1701-1778) created the basic classification rules
• Nomenclature names organisms scientifically
• Classification organizes organisms into a hierarchy
• Identification involves findings, recordings, and recognizing organisms.
• Names derive from Latin or Greek, inspired by shape, color, location, disease, or discoverer

Binomial System

• Two-name system, consisting of a capitalized genus name and a lowercase species name
• Both names are italicized or underlined if handwritten
• Staphylococcus aureus can be shortened to S. aureus after first mention
• 'sp.' indicates an unknown species
• 'spp.' is for a group of unknown species

Major Morphologies of Prokaryotic Cells

• Coccus (plural: cocci) have a round shape
• Streptococcus, Staphylococcus exemplified coccus
• Bacillus (plural: bacilli) are rod-shaped
• Escherichia coli, Bacillus subtilis exemplify bacillus
• Spirillum (plural: spirilla) are spiral-shaped
• Spirillum volutans exemplifies spirillum
• Vibrio are comma-shaped (curved rods)
• Vibrio cholerae exemplifies vibrio
• Spirochetes are flexible, long, and tightly coiled
• Treponema pallidum is an example of a spirochete
• Filamentous bacteria are thread-like chains
• Streptomyces exemplifies filamentous bacteria

Cell Arrangements

• Diplo pairs (Diplococcus)
• Streptochains (Steptococcus)
• Staphylococcus clusters (Staphylococcus)

The Eukaryotes (Fungi)

• Mycology: the study of fungi

Characteristics of fungi

• All are chemoheterotrophs
• Most are saprophytes
• Most are aerobic or facultatively anaerobic
• Few are human pathogens
• Cell walls are composed of chitin
• 50% of the global population is infected with eukaryotic pathogens
• Two microbial kingdoms: Fungi and Protista
• Subkingdoms: Protozoa (animal-like) and Algae (plant-like)

Molds & Fleshy Fungi

• Organized into three general groups based on shape: molds, yeasts, and dimorphic fungi

Molds and Fleshy Fungi

• Consist of long filaments of cells joined end to end, hyphae
• Hyphae can be 1 or 2 structural types: (genetically determined)
• Septate hyphae: joined cells have distinct separations called septa, grows by extension at the tip
• A mass of hyphae is called mycelium
• Coenocytic hyphae: consists of fused cells
• A mold mycelium produces two different versions of its hyphae
• Vegetative hyphae grow flat along surfaces & collect nutrients
• Aerial hyphae stick up off the mycelium & produce spores for reproduction

Yeasts

• Nonfilamentous, unicellular, ovaloid
• All are facultative anaerobes
• Ferment carbohydrates into alcohol and carbon dioxide in oxygen's absence
• Two types of yeasts: budding and fission
• Budding yeasts: divide by producing an outgrowth referred to as a bud
• Fission yeasts: divide by mother cell elongating and undergoing mitosis
• Daughter cells separated by forming a septa in the center (fission)
• If bud fails to separate = psuedohyphae which are not true hyphae like molds
• Hyphae = cells tightly attached by shared walls and cytoplasm
• Psuedohyphae = daughters remain stuck but separated by individual cell walls

Dimorphic Fungi

• Can grow as multicellular mold-like hyphal form or unicellular yeast-like ovaloid form depending on conditions
• Candida albicans exemplifies this trait
• 25oC, acid pH = yeast
• 37oC, neutral pH = hyphae

Fungi Spores

• Asexual spores form on single organism's hyphae, clone of the parent
• Sexual spores form after fusion of 2 haploid nuclei from opposite mating type cells
• Has characteristics of both parents
• Sexual reproduction is NOT common in fungi

Life Cycle of Fungi

• Can reproduce asexually by: fragmentation of hyphae (mold), budding (budding yeast), or fission (fission yeast)
• Spores are formed on the ends of aerial hyphae

Life Cycle of Fungi: Asexual Spores

• Produced through mitosis and include DNA, an exact copy of the parent
• Sporangiospore: spores form in sporangium
• Sporangium forms at aerial hyphae's end
• It holds hundreds of sporangiospores
• Conidiosphore: spores produced at the end of aerial hyphae

Life Cycle of Fungi: Sexual Spores

• Formed by the fusion of 2 haploid nuclei into a single diploid zygote
• Zygote undergoes meiosis to generate haploid spores
• Zygospores: one thick spore between two parent hyphae
• Ascospores: 4 spores in ascus at the end of 1 hypha
• Basidiospores: 4 spores on basidium

Sexual Spore: Four Phyla of Fungi

• Fungi organized into 4 phyla based on sexual spore type
• Zygomycota: conjugation of fungi containing molds
• Contains coenocytic hyphae
• Asexual spore: sporagiospores
• Sexual spore: zygospores, ex. Rhizopus
• Ascomycota: sac fungi containing yeasts and molds
• Septate hyphae
• Asexual spores: conidiospores
• Sexual spores: ascospores
• Ex. Aspergillus, Saccharomuces
• Basidiomycota: club fungi containing mushrooms
• Septate hyphae
• Asexual spores: conidiospores
• Some sexual spores are basidiospores
• Deuteromycota: Artificial grouping of fungi where sexual reproduction is not yet observed
• Once it occurs, get placed into appropriate Phyla, ex. Penicillium

Difference Between Fungi & Bacteria

• Like acidic environment, need low moisture, require less nitrogen, and can metabolize complex carbohydrates
• Resistant to osmotic pressure
• Grow in low moisture
• Require less nitrogen
• Can metabolize complex carbohydrates

Fungi Diseases

• Few are pathogens
• Pathogenic fungi tend to be opportunistic in hosts with compromised immune systems
• Mycosis fungal infection can range from superficial (skin) to systemic (blood, organs)

Fungi and Human Society

• Use: Food and beverages production, vaccine production, drug production, and biological control of pests
• Issues; Food spoilage, crop death, and human pathogens

Algae

• Belong to different kingdoms
• Divided into four kingdoms based on gene sequencing
• Kingdom Plantae: Green (chlorophytes) and Red (Rhodophytes) algae
• Kingdom Chromista: Brown algae, Dinoflagellates, and Diatoms
• Kingdom Protozoa: Includes Fuglenozoa
• Kingdom Bacteria: Blue green algae (actually cyanobacteria)

Common Features of Algae

• All cells but one have cellulose walls
• Carry out oxygenic photosynthesis using chlorophyll in chloroplasts
• Require high moisture
• Are photoautotrophs
• Unicellular or multicellular (colonial or filamentous)
• Reproduce sexually and asexually

Five Phyla/Divisions of Algae

• Euglenoids (Euglenophycophyta)
• No cell wall, have a pellicle
• Has flagella and eye spot,
• Has chlorophyll
• Intermediate between algae and protozoa
• Green algae (Chlorophycophyta)
• Cellulose walls, chlorophyll
• Flagellated or not
• Food storage as starch, e.g., pond scum
• Golden Brown Algae (Chrysophycophyta)
• Light brown pigment + chlorophyll a
• Cellulose walls
• Flagellated
• Food storage as oils
• Special group: Diatoms
• Walls of silicon oxide (glass) box+lid
• Stores oils compressed in the earth from dead diatoms - petroleum reserves
• Brown algae (Pheophycophyta)
• Dark brown pigment + chlorophyll a
• Cellulose walls
• Non-motile
• Food storage as mannitol
• E.g. seaweeds
• Fire algae (Pyrrophycophyta)
• Cellulose walls of interlocked plated
• Contain 2 flagella
• Most dinoflagellates: ex. red tide
• Red Algae (Rhodophycophyta)
• Has pigment phycobilin and phycoerythin , masks the chlorophyll a

Algae and Human Society

• Produce 80% of oxygen on earth
• Basis for several food chains, fixes carbon dioxide into glucose
• Petroleum deposit
• Sources of food as nori (red algae)
• Source of agar

Protozoa

• All unicellular and chemoheterotrophs
• Reproduce sexually and asexually
• Most are aerobic and require high moisture
• Usually covered with a pellicle (no wall)

Protozoa's Life Cycle

• Switch between two forms
• Trophozite; Vegetative phase, feeding, and growth
• Cyst; Survival, formed when conditions are bad or need to move to the next host

Three Major Phyla Based on Locomotion

• Sarcomastigophora;
• Sarcodin, Rhizopoda, move via pseudopodia (ameoboid)
• Mastigophora: move via flagella (zooflagellates)
• Ciliophora; move via cilia, ex. Paramecium

Apicomplexa

• Non-motile
• Usually intracellular parasites
• Complex lifecycle

Slime Molds

• Show fungal, amoeba-like characteristics
• Hunters of bacteria and fungi
• Produce spores in difficult conditions

Two Phyla of Slime Molds:

• Cellular slime molds
  • Exists as a "amoeba", In conditions,
  • Congregate form a "mushroom" in others Plasmodial Slime molds
  • Plasmodium is their favorable state, can move "amoeba", mold-like state, during Conditions,

Survey of the Microbial World

• Microorganisms are tiny life forms that need a magnifying glass

Cellular Microorganisms

• Cells can organize, grow, reproduce, and send genetic data
• Cytoplasmic membranes delimit the cells. Cells can be or Eukaryotic, be or EUKARYOTIC CELLS;
  • Have membrane-bound organelles that serve unique tasks
  • The nucleus contains the DNA
• PROKARYOTIC CELLS; Do not have a nucleus or cellular Microorganisms from an ancestor, Eukarya formed, and bacteria

Acellular Microorganism

• Are missing an cellular setup

Viruses

• Cannot complete life tasks
• Replicate the organism's cells
• Are not cells

Sizes and Shapes of a Virus

• Vary from around 5 to 300 nanometers
• Are smaller than bacteria: submicroscopic
• Helical Viruses, nucleic encapsulated by a cylinder, uses structure Polyhedral, has a shell , and
• Covered Viruses, which have helical

Structure of a Virus

• A virion explains a virus, has a role in infection and genome translocation C the protein shell and acids
• E, covers the nucleocapsid

Genome virus

• Baltimore, divides viruses by characteristics such as the host.
• Prions: infectious agent .
• Viroids act as plant pathogens.

Scheme of a Microorganism

• 7 Categories: kingdoms- several.
• kingdom- several sections
• Family classes
• classes several orders

The Kingdom of Organisms

. The method

• The process
• The process

Comparison of Eukaryotic Cells: Microbial Cell Structure

Concept PROKARYOTIC

• Unicellular (cell)
• Differentiated factors, like configuration
• key
• Bacterial
• Antiagents
• Plasmid data such resistance

Three Basic bacteria shapes

Coccus, and spiral The shapes come heredity.

External Cellular Structures

• G protects and creates an , it can be unorganized
• can bacterial and host bacteria Substances.

The Flagella and Biofilm

: Bacteria's

• Polar: is
• : all over the.
• Bacteria
• Acid/base that is.
• Axial's: can and can.

Structure

• axial has.
• There pili that can for. Cell bacteria

Walls

• Maintains and has cells. Cells are vulnerable.
• Composition characteristics. that provides
• Murein helps
• Wall components bacteria but not
• Amino found in and Bacteria,
• Gram +/-, each walls

Wall Primary Stain

• Gram: for in bacteria.
• The cells may have. Internal to wall,surrounds the the small surrounds both The a cell to interact with.

Cell Bacterial Membrane: Phospholipid

: Like molecules like that. Actions:

• Quarry, and can. Materials Membrane Does
• . passive is power requires and . process requires with power .
• Net water moves, requires.
• The active require energy. Bacterial's similar but different.

Archeola

. from

Components of the cell

• refers to within
• single to with. Plasmids from, in. The are from and and.

Inclusions

Accumulations:

• reserves in and with.
• in, or essential,. Usually or.

Microbial Nutrition and Growth

• supplying,.
• Nutrients with for.
• supply to that.