An Overview of Microbial Life Chapter 2

3 Domains: Archae, Eubacteria, Eukaryota Two structural types of cells are recognized: the prokaryote and the eukaryote. Prokaryotic cells have a simpler internal structure than eukaryotic cells, lacking membrane-enclosed organelles. Viruses: –Viruses are not cells but depend on cells for their replication. Elements of Cell and Viral Structures:

Cells from each domain Bacteria Archae Eukarya

The basic components.. All microbial cells share certain basic structures in common, such as cytoplasm, a cytoplasmic membrane, ribosomes, and (usually) a cell wall. –Note: Animal cells typically do not have a cell wall The major components dissolved in the cytoplasm include –Macromolecules –Inorganic ions

Eukaryotic Cells Larger and structurally more complex Euk. microorganisms include algae, fungi and protozoa Membrane enclosed organelles –Nucleus –Mitochondria –Chloroplasts (photosynthetic cells only)

Prokaryotic Cells Lack membrane enclosed organelles Include Bacteria and Archae Smaller than eukaryotic cells (Typically ~1-5 um long and ~1um in width) However, can vary greatly in size

Viruses Not cells Static structures which rely on cells for replication and biosynthetic machinery Many cause disease and can have profound effects on the cells they infect –Cancer, HIV However, can alter genetic material and improve the cell

Arrangement of DNA in Microbial Cells Genes govern the properties of cells, and a cell's complement of genes is called its genome. DNA is arranged in cells to form chromosomes. In prokaryotes, there is usually a single circular chromosome; whereas in eukaryotes, several linear chromosomes exist.

Nucleus vs. Nucleoid Nucleus: a membrane- enclosed structure that contains the chromosomes in eukaryotic cells. Nucleoid: aggregated mass of DNA that constitutes the chromosome of cells of Bacteria and Archaea

Prokaryotic DNA Most DNA is circular Most have only a single chromosome Single copy of genes –Haploid Many also contain plasmids

Plasmids Plasmids are circular extrachromosomal genetic elements (DNA), nonessential for growth, found in prokaryotes. Typically contain genes that confer special properties (ie unique metabolic properties) Useful in biotechnology

Eukaryotic DNA Organized into linear molecules Packaged into chromosomes –Number varies Typically contain two copies of each gene –Diploid

Genes, genomes, and proteins E.coli genome= a single circular chromosome of 4.68 million base pairs # of genes: 4,300 A single cell contains: –1,900 different proteins –2.4 million protein molecules –Abundance of proteins varies

Genome size, complexity, and the C-value paradox Genome size does not necessarily correlate with organismal complexity

In actuality….

Evolution: change in allelic frequencies over generations The evolutionary relationships between life forms are the subject of the science of phylogeny. Phylogenetic relationships are deduced by comparing ribosomal sequences The Tree of Life

The three domains of life Comparative ribosomal RNA sequencing has defined the three domains of life: Bacteria, Archaea, and Eukarya.

What has this sequencing revealed?? Molecular sequencing has shown that the major organelles of Eukarya have evolutionary roots in the Bacteria Mitochondria and chloroplasts were once free-living cells that established stable residency in cells of Eukarya eons ago. –The process by which this stable arrangement developed is known as endosymbiosis.

What has this sequencing revealed?? Cont. Although species of Bacteria and Archaea share a prokaryotic cell structure, they differ dramatically in their evolutionary history. Archae are more closely related to eukaryotes than are species of bacteria

Molecular sequencing and microbiology Overall rRNA sequencing technology has helped reveal the overall evolutionary connections between all cells –In particular prokaryotes Impacted subdispiciplines –Microbial classification and ecology –Clinical diagnostics Can identify organisms without having to culture them

Microbial Diversity Cell size and morphology Metabolic strategies (physiology) Motility Mechanisms of cell division Pathogenesis Developmental biology Adaptation to environmental extremes And many more

Physiological Diversity of Microorganisms All cells need carbon and energy sources Energy can be obtained in 3 ways: –Organic chemicals –Inorganic chemicals –Light Types of physiological diversity: –Chemoorganotrophs –Chemolithotrophs –Phototrophs –Heterotrophs and Autotrophs –Habitats and Extreme environments

Chemoorganotrophs Chemoorganotrophs obtain their energy from the oxidation of organic compounds. –Energy conserved as ATP All natural and even synthetic organic compounds can be used as an energy source Aerobes Anaerobes Most microorganisms that have been cultured are chemoorganotrophs

Chemolithotrophs Chemolithotrophs obtain their energy from the oxidation of inorganic compounds. Found only in prokaryotes Can use a broad spectrum of inorganic compounds Advantageous because can utilize waste products of chemoorganotrophs

Phototrophs Phototrophs contain pigments that allow them to use light as an energy source. –ATP generated from light energy –Cells are colored Oxygenic photosynthesis: –O 2 involved –Cyanobacteria and relatives Anoxygenic photosynthesis: –No O 2 –Purple and green bacteria

Autotrophs and Heterotrophs All cells require carbon as a major nutrient Microbial cells are either: –Autotrophs use carbon dioxide as their carbon source, whereas heterotrophs use organic carbon from one or more organic compounds. –Autotrophs considered primary producers Synthesize organic matter from CO 2 for themselves and that of chemoorganotrophs All organic matter on earth has been synthesized from primary producers

Habitats and Extreme Environments Microorganisms are everywhere on Earth that can support life Extremophiles: organisms inhabiting extreme environments –Boiling hot springs, –Within ice, extreme pH, salinity, pressure

Examples of Extremophiles:

Prokaryotic Diversity Several lineages are present in the domains Bacteria and Archaea An enormous diversity of cell morphologies and physiologies are represented rRNA analysis has shown dramatic differences in phenotypic characteristics within a given phylogenetic group

Bacteria

Proteobacteria The Proteobacteria is the largest division (called a phylum) of Bacteria A major lineage of bacteria that contains a large number of gram(-) rods and cocci Represent majority of known gram(-) medical, industrial, and agricultural bacteria of significance Extreme metabolic diversity: –Chemorganotrophs: E.coli –Photoautotrophs: Purple sulfur bacterium –Chemolithotrophs: Pseudomonas, Aztobacter –Pathogens: Salmonella, Rickettsia, Neisseria

Proteobacteria examples Chemolithotrophic sulfur-oxidizing bacteria Achromatium Neisseria gonorrhoeae

Gram-positive bacteria United by a common cell wall structure Examples: Spore forming: –Clostridium, Bacillus Antibiotic producing: –Streptomyces Lactic acid bacteria: –Streptococcus –Lactobacillus Mycoplasmas: –Lack cell wall –Small genomes –Often pathogenic

Cyanobacteria The Cyanobacteria are phylogenetic relatives of gram- positive bacteria and are oxygenic phototrophs. First oxygenic phototrophs to have evolved on Earth

Planctomyces Characterized by distinct cells with stalks that allow for attachment to solid surfaces Aquatic

Spirochetes Helical shaped Morphologically and phylogenetically distinct Widespread in nature and some cause disease –Most notable sp cause Syphilis and Lyme Disease Spirochaeta zuelzerae

Green sulfur and non-sulfur bacteria Contain similar photosynthetic pigments Can grow as autotrophs Chloroflexus –Inhabits hot springs and shallow marine bays –Dominant organism in stratified microbial mats –Important link in the evolution of photosynthesis

Chlamydia Most species are pathogens Obligate intracellular parasites How would this affect an immune response?

Deinococcus Contain sp with unusual cell walls and high level of resistance to radiation Cells usually exist in pairs or tetrads Can reassemble its chromosome after high radiation

Aquifex, Thermotoga, Env-OP2 Sp that branch early on the tree Unified in that they grow at very high temps: hyperthermophily Inhabitats of hot springs

Archaea There are two lineages of Archaea: the Euryarchaeota and the Crenarchaeota Many are extremophiles All are chemotrophic –Many using organic carbon –While others are chemolithotrophs

Euryarchaeota & Crenarchaeota Physiologically diverse groups Many inhabit extreme environments –From extreme pH, temperature, salinity

Limitations of Phylogenetic analyses Not all Archaea are extremophiles Difficult to culture Based on molecular microbial ecology, the extent of diversity is much greater than once thought

Eukaryotic Microorganisms Collectively, microbial eukaryotes are known as the Protista. Microbial eukaryotes are a diverse group that includes algae, protozoa, fungi, and slime molds Cells of algae and fungi have cell walls, whereas the protozoa do not. The “early-branching” Eukarya are structurally simple eukaryotes lacking mitochondria and other organelles –Ex Giardia

Eukaryotic microbial diversity

Diplomonads: flagellates, many are parasitic –Ex: Giardia lamblia (synonymous with Lamblia intestinalis and Giardia duodenalis) is a flagellated protozoan parasite flagellated protozoan parasite Trichomonads: anaerobic protist, many are pathogenic –Ex. Trichomonas vaginalis Flagellates: all protozoa in this group utilize flagella for motility, free-living, and pathogenic –Ex. Trypanosomes Slime molds: resemble fungi and protozoa –Ex. Dictyostelium discoideum

Algae Fungi Protozoa

Lichens Some algae and fungi have developed mutualistic associations called lichens.