An Overview of Microbial Life

Chapter 2

Elements of Cell and Viral Structures:



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.

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 QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.

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

 N

ucleus:

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

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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 QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.

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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 QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.

In actuality….

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The Tree of Life



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 three domains of life

 Comparative ribosomal RNA sequencing has defined the three

domains

Archaea

, and

Eukarya

.

of life:

Bacteria

,

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 QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.

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 that of chemoorganotrophs for themselves and • 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 QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.

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

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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?

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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 QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.

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

Eukaryotic microbial diversity

 Diplomonads: flagellates, many are parasitic –

Ex: Giardia lamblia intestinalis

and (synonymous with

Giardia duodenalis Lamblia

) 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.

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