Notes on Taxonomy: Bacteria

· Taxonomy ○ Science of classification ○ Provides an orderly basis for the naming of organisms and for placing organisms into a category (taxon) ○ Makes use of and makes sense of the fundamental concepts of unity and diversity among living things ○ Basic principle is that members of higher-levels groups share fewer characteristics than those in lower-level groups

* Escherichia coli - rod shape and have a Gram-negative cell wall

* Even members of the same species display variations in size, shape, and other characteristics

Binomial Nomenclature • Carolus Linnaeus - credited with founding the science of taxonomy ○ Originated binomial nomenclature § System that is still used today to name all living things ○ Binomial nomenclature § Genus - first name § Specific epithet - second name, not capitalized

Strain - a subgroup of species with one or more characteristics that distinguish it from other subgroups of the same species

Dichotomous key - paired statements describing characteristics

Problems in Taxonomy • We like to classify organisms according to their phylogenetic, or evolutionary, relationships, but this is not always easy • Evolution occurs continuously and at a relatively rapid rate in microorganisms, and our knowledge of the evolutionary history of organisms is incomplete ○ It is far more important to have a taxonomic system that reflects our knowledge than to have a system that never changes • Certain problems in creating a taxonomic system that provides an organized overview of all living things and how they are related to each other ○ Deciding what constitutes a species § Taxonomists try to decide how much diversity can be tolerated within the unity of the species ○ Deciding what constitute a kingdom or in which domain a kingdom belongs § Taxonomists try to decide how to sort the diverse characteristics of living things into categories that reflect fundamental differences of evolutionary significance

* Morphology (structural characteristics) and geographic distributions also are considered in defining species

Developments Since Linnaeus' Time • Problem of classifying microorganisms - first addressed by Ernst H. Hacckel in 1866 wherein he created a 3rd Kingdom, Protista • 1956, Lynn Margulis and H. F. Copeland proposed a scheme of classifying prokaryotes and eukaryotes by the following 4-kingdom system of classification ○ Monera - all prokaryotes, including true bacteria and blue-green algae ○ Protoctista - all eukaryotic algae, protozoa, and fungi ○ Plantae - all green plants ○ Animalia - all animals derived from a zygote, a cell formed by the union of an egg and a sperm • Whittaker - proposed a taxonomic system in 1969 ○ Protista ○ Fungi ○ Monera ○ Plantae ○ Animalia

* Separated Protoctista into 2 kingdoms, Protista and Fungi

Some Characteristics of Cells - All organisms are composed of cells, and all carry out certain functions such as obtaining nutrients and getting rid of wastes. - Cell is the basic structural and functional unit of all living things. - Virus are not cells because they are not considered to be living organisms. - All cells are bounded by a cell or plasma membrane, carry genetic information in DNA, and have ribosomes where proteins are made. - Cells also contain the same kinds of organic compounds -- proteins, lipids, nucleic acids, and carbohydrates - Cells also selectively transport material between their cytoplasm and their environment

* All living organisms, regardless of the kingdom to which they are assigned, display certain characteristics that define the unity of life

* Although organisms may be classified in very diverse taxonomic groups, their cells have many similarities in structure and function

Five-Kingdom Classification System - Most widely accepted - Major advantage is the clarity with which it deals with microorganisms - Places all prokaryotes (microorganisms that lack a cell nucleus) in Kingdom Monera (Prokaryotae) - Place most unicellular eukaryotes (organisms whose cells contain a distinct nucleus) in Kingdom Protista

Kingdom Monera - Also called kingdom Prokaryotae - Consists of all organisms, including eubacteria, cyanobacteria, and archaeobacteria - All monerans are unicellular; lack true nuclei and generally lack membrane - enclosed organelles - DNA has little or no protein associated with it - Reproduction occurs mainly by binary fission - MEMBERS ○ Eubacteria: greatest concern in the health sciences ○ Cyanobacteria: formerly known as blue-green algae § Special importance in the balance of nature § Photosynthetic § Typically unicellular, although cells may sometimes connect to form threadlike filaments § Being autotrophs, they don’t invade other organisms § No health threat to humans except for toxins some release into the water § Grow in a great variety of habitats, including anaerobic ones, where they often serve as food source for more complex heterotrophic organisms § Some "fix" atmospheric nitrogen, converting it to nitrogenous compounds that algae and other organisms can use § Certain cyanobacteria also thrive in nutrient-rich water and are responsible for algal blooms (a thick layer of algae on the surface of the water that prevents light from penetrating to the water below; release toxic substances that can give the water an objectionable odor and even harm fish and livestock that drinks from it ○ Archaea: primitive eukaryotes adapted to extreme environments § Methanogens reduce carbon-containing compounds to the gas methane § Extreme halophiles live in excessively salty environments, and thermoacidophiles live in hot acidic environments (e.g. volcanic vents in ocean floor) □ There, some species of bacteria form symbiotic relationships with organisms such as giant tube-worms (up to 2m tall) ® These worms lack mouth, gut, or anus. How do they get fed? ◊ Chemolithotrophic archaeal bacteria, living inside the tubeworms, have metabolisms that fix inorganic sources into organic carbon sources via same enzymes utilized in the Calvin Cycle of certain autotrophs. Tube worms are then able to use organic carbon sources in cellular processes ® What do tubes worms do for bacteria? ◊ Tubeworms have well-vascularized plumes that trap oxygen and H2S from the thermal vents and transport these substances to the chemolithotrophs ◊ The bacteria use oxygen and H2S in their life-sustaining energy reactions, providing nutrients to their ecosystem § Believed to be of very ancient origin, archaea have been found to differ from eubacteria in several distinctive ways □ Structure of cell wall and RNA polymerase - Protista: modern protist group is very diverse but contains fewer kinds of organisms than when first defined by Hacckel § Eukaryotic § Most are unicellular, but some are organized into colonies § Have true membrane-enclosed nucleus and organelles within their cytoplasm, as do other eukaryotes § Many live in fresh water, some live in seawater, and a few live in soil § Do not develop from an embryo § Do not develop from distinctive spores § Algae (resemble plants), protozoa (resemble animals), and euglenoid (both animal and plant characteristics) § Protozoa are the greatest interest to health scientists because they can cause disease - Fungi: includes mostly multicellular and some unicellular organisms § Obtain nutrients solely by absorption of organic matter from dead organisms § Even when they invade living tissues, fungi typically kill cells and then absorb nutrients from them § Although they have some common characteristics with plants, their structures are much simpler in organization than true leaves or stems § Form spores but do not form seeds § Many pose no threat to other living thing but some attack plants, animals, and even humans § Source of food (yeast and mushrooms) - Plantae: § Most plants live on land and contain chlorophyll in organelles called chloroplasts § Interests microbiologists because some contain medicinal substances such as quinine (for microbial infections) - Animalia: includes all animals derived from zygotes (cell formed by union of two gametes) § Nearly all members are macroscopic § Certain helminths are parasitic in humans and other animals □ Include flukes, tapeworms, roundworms, leeches § Certain arthropods live on surface of the host and some spread disease □ Ticks, lice, fleas, mosquitoes

• Urkaryotes - hypothesis that earliest or original cells gave rise to eukaryotes rather than prokaryotes, obtaining organelles through endosymbiosis

The Evolution of Prokaryotic Organisms - Stromatolites: fossilized photosynthetic prokaryotes that appear as masses of cells or microbial mats ○ Commonly found associated with lagoons or hot springs ○ Do not provide any evidence for phylogenetic, or evolutionary, relationships but can be used to determine the period during which they arose ○ Studies of them indicate that life arose nearly 4B years ago, § "Age of Microorganisms" □ No multicellular living organisms □ Lasted about 3B years

Creation of Domains - Woese suggested that a new taxonomic category, the Domain - Theories about how the 3 domains may have risen ○ Standard view was that a universal common ancestor first split into Bacteria and Archaea, and then the Eukarya branched off from Archaea ○ Second view held that all 3 domains arose simultaneously from a pool of common ancestors that were able to exchange genes with one another -- universal genetic code ○ Third view sought to explain how so many genes are present in Eukarya but lack in Archaea and Bacteria § Postulated the existence of a fourth domain and directly contributed genes to the Eukarya and then became extinct

The Tree of Life is Replaced by a Shrub - As complete sequences of genomes are becoming available in increasing numbers, the concept of a universal common ancestor giving rise to linear, branching tree of life is seen as oversimplified, or just plain wrong. - There are many roots, rather than a single ancestral line, and the branches crisscross and merge again and again

The Archaea - Exhibit many differences from the Bacteria ○ Cell wall structure - Not all are the same - 3 major groups (based on physiological characteristics of organisms and therefore cannot be considered phylogenetic, or evolutionary, classifications ○ Methanogens § Strictly anaerobic § Isolated from such divergent anaerobic environments as waterlogged soils, lake sediments, marshes, marine sediments, and gastrointestinal tracts of animals (including humans) § As members of anaerobic food chain, they degrade organic molecules to methane ○ Extreme halophiles § Grow in highly saline environments such as the Great Salt Lake, the Dead Sea, salt evaporating ponds, and the surfaces of salt-preserved food § Generally obligate aerobes ○ Extreme thermoacidophiles § Occupy unique niches where bacteria are very rarely found, such as hot springs, geothermally heated marine sediments, and submarine hydrothermal vents § Optimum temperatures usually in excess of 80oC, that may be either obligate aerobes, facultative aerobes, or obligate anaerobes § The heat-stable enzymes known as extremozymes that are found in these organisms have become of special interest to scientists

Classification of Viruses - Viruses are acellular infectious that are smaller than cells - Contain nucleic acid (DNA or RNA) and are coated with protein - Have not been assigned to a kingdom - Display only a few characteristics associated with living organisms - Initially, were classified according to hosts they invaded and by the diseases they caused - Classified by chemical and physical characteristics such as the types and arrangement of their nucleic acids, their shape (cubical or tubular), the symmetry of the protein coat that surrounds the nucleic acid, and the presence or absence of such things as a membrane covering (called an envelope), enzymes, tail structures, or lipids - These groupings reflect only common characteristics and are not intended to represent evolutionary relationships

• Viroids and Prions

Importance of study of Viruses (Virology) - Virology is a recognized branch of microbiology, and techniques to study viruses are derived from microbiological techniques - Viruses are of concern to health scientists because many cause diseases in humans, other animals, plants, and even microorganisms

• First, let us remember the definition of chromosome. Plasmids contain genes that are needed only occasionally and are not essential for continuous use. If a large plasmid (megaplasmid) acquires a collection of “housekeeping” genes that are needed for daily life, it is then elevated to the status of chromosome. Confusingly enough, genes and plasmids can be acquired either vertically or by horizontal transfer. And, transposons can relocate genes from chromosomes into plasmids. Or, a chromosome could break, releasing a self-replicating portion of its genome into the cytoplasm. These are all ways that an ancestor with a single chromosome can develop a second chromosome.

Search for Evolutionary Relationships - Knowledge of such evolution is useful in order to understand the circumstances under which one organism becomes capable of infecting another, sometimes resulting in a symbiotic relationship and other times in the disease process - KULANG PA

Special Methods Needed for Prokaryotes - Taxonomy of most eukaryotes is based on morphology (structural characteristics) of living organisms, genetic features, and on knowledge of their evolutionary relationships from fossil records - However, morphology and fossil records provide little information about prokaryotes - Prokaryotes have left few fossil records - Stromatolites (fossilized mats of prokaryotes) have been found mainly at sites where the environment millions of years ago allowed the deposition of dense layers of bacteria ○ Also provided much of our knowledge of the origins of the Archaea ○ Most bacteria don't form mats = most ancestral prokaryotes have disappeared without a trace - Prokaryotes have few structural characteristics (subject to rapid change when the environment changes) - Large organisms tend to require a fairly long period of time to reproduce (prokaryotes reproduce rapidly) - Because of rapid mutational change rate, it is difficult to show the relationship between fossilized forms of prokaryotes and current organisms - Evolution and morphology are of little use - Metabolic reactions, genetic relatedness, and other specialized properties have been used instead to classify prokaryotes

Numerical Taxonomy - Based on the idea that increasing number of characteristics of organisms that we observe increases the accuracy with which we can detect similarities among them - If the characteristics are genetically determined, the more characteristics two organisms share, the closer their evolutionary relationship - With the use of numerical taxonomy, no single characteristic is used to arbitrarily divide all organisms into groups - If two organisms match on 90% or more of the characteristics studied, they are presumed to belong to the same species

Genetic Homology - Discovery of the structure of DNA by James Watson and Francis Crick provided new knowledge that was quickly applied by taxonomists, especially those studying taxonomic relationships and the evolution of the eukaryotes - Similarity of DNA among organisms ○ Can be studied directly by determining the base composition of the DNA, by sequencing the bases in portions of DNA or RNA, and by using DNA hybridization ○ Because an organism's proteins are determined by its DNA, similarities in DNA can be studied indirectly by preparing protein files and by analyzing amino acid sequences in proteins

Base Composition - Organisms can be grouped by comparing the relative percentages of bases present in the DNA of their cells - DNA contains four bases (A,C,T,G) - The base composition of an organism is generally stated in terms of the percentage of guanine plus cytosine and is referred to as the G–C content. Base composition only determines the total amount of each nucleotide base present; it does not give any indication of the sequence of these bases. Studies of base composition have shown that the G–C content varies from 23 to 75% in bacteria.

DNA and RNA Sequencing - Using PCR techniques and a DNA synthesizer, one can produce a large number of probes (single-stranded DNA fragments that have sequences complementary to those being sought - Presence or absence of the unique DNA sequence helps in identification of the specimen

DNA Hybridization - The double strands of DNA of each of two organisms are split apart, and the split strands from the two organisms are allowed to combine - The strands from different organisms will anneal (bond to each other) by base pairing (A-T, G-C) - Amount of annealing is directly proportional to the quantity of identical base sequences in the two DNAs - A high degree of homology (similarity) exists when both organisms have long, identical sequences of bases - Close DNA homology indicates that the two organisms are closely related and that they probably evolved from a common ancestor - Small degree of homology indicates that the two organisms are not very closely related

Protein Profiles and Amino Acid Sequences - Every protein molecule consists of a specific sequence of amino acids and has a particular shape with an assortment of surface charges - Protein profile is a laboratory-prepared pattern of the proteins found in a cell ○ Cell's proteins are the product of its genes ○ Cells of each gene species synthesize a unique array of proteins (as distinctive as fingerprints) - Produced by the polyacrylamide gel electrophoresis (PAGE) method ○ Separates proteins on the basis of molecular size - Each band in the profile from one kind of cell represents a different protein in that cell - Bands at the same location in profiles from different kinds of cells indicate that the same protein is present in the different cells - Determination of amino acid sequences in proteins also identifies similarities and differences among organisms - Proteins an organism contains are determined directly by the information in that organism's DNA - Both protein profiles and determinations of amino acid sequences are as significant a measure of the relatedness of organisms as are DNA homologies

Other Techniques - Properties of Ribosomes ○ Ribosomes serve as site of protein synthesis in both prokaryotic and eukaryotic cells, RNA in ribosomes can be separated into several types according to the size of the RNA units ○ rRNA molecules are easily rendered non-functional by even slight alterations in their genetic structure, mutations are rarely tolerated = ribosomes have evolved very slowly - Immunological Reactions ○ Also used to identify and study surface structures and the composition of microorganisms ○ Promises to be particularly useful in identifying specific biochemical properties of microorganisms ○ Identification of such properties will be extremely useful in determining taxonomic relationships - Phage typing ○ Involve the use of bacteriophages (viruses that attack bacteria) to determine similarities among different bacteria ○ Receptor sites for bacteriophages are highly specific, certain strains of a species of bacterium are attacked only by particular types of phages

Significance of Findings - These methods can be used to group closely related organisms and to separate them from less closely related ones - Divergent evolution ○ Occurs as certain subgroups of a species with common ancestors undergo sufficient mutation to be identified as separate species ○ Gram positive and gram negative

Bacterial Taxonomy and Nomenclature - Criteria for Classifying Bacteria ○ Other criteria used to classify bacteria § Because separating them according to cell shape, size, arrangement, presence of specific structures such as flagella, endospores, capsules. § Staining is used ○ For bacteria, a species is regarded as a collection of strains that share many common features and differ significantly from other strains § A bacterial strain consists of descendants of a single isolation in pure culture ○ Type strain - one strain of a specie designated by bacteriologists - Usually the first strain described - Name-bearer of the species and is preserved in one or more type of culture collections

The History and Significance of Bergey's Manual - Accepted reference on the identification of bacteria - Determinative information: information used to identify bacteria ○ Collected into a single volume

Problems associated with bacterial taxonomy - Those looking from the top level down can propose at least plausible divisions of the prokaryotes. Those bacteriologists looking from the bottom up can establish strains, species, and genera and can sometimes assign bacteria to higher-level groups. But too little is known about evolutionary relationships to establish clearly defined taxonomic classes and orders for many bacteria. The difficulties of classifying bacteria are greatly magnified as one proceeds with total genome sequencing and discovery of more and more examples of lateral gene transfer.

Bacterial Nomenclature - Refers to the naming of species according to internationally agreed-upon rules - When considering specific orders and families, such names have consistent endings: orders - -ales, families - -aceae

Bacteria - Obligate intracellular parasites: can only grow inside living cells

Page 266