Chapter 4; Prokaryote Diversity
Phototrophic Bacteria
-Phototrophs that contain photosynthetic lamellae -Autotrophic
Archaea Characteristics
-The cell membrane is composed of ether linkages with branched isoprene chains (as opposed to the bacterial cell membrane, which has ester linkages with unbranched fatty acids). -Their cell walls lack peptidoglycan, but some contain a structurally similar substance called pseudopeptidoglycan or pseudomurein. -Their genomes are larger and more complex than those of bacteria.
Bacteriochlorophylls
A class of primary photosynthetic pigments that do not release oxygen; they have green, purple, or blue pigments similar to chlorophyll in plants. These bacteria are classified into sulfur and nonsulfur bacteria; they are further differentiated by color.
Proteobacteria
A diverse clade of gram-negative bacteria that includes five subgroups known as alpha, beta, gamma, delta, and epsilon. (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria)
Phototrophic bacteria are not a taxon but, rather:
A group categorized by their ability to use the energy of sunlight. They include Proteobacteria and nonproteobacteria, as well as sulfur and nonsulfur bacteria colored purple or green.
Methanogens
A group of archaebacteria that produce methane as a by product of their metabolism.
Community
A group of interdependent organisms inhabiting the same region and interacting with each other
Amensalism
A relationship between organisms of two different species in which one is unaffected and the other is negatively impacted by the association
Commensalism
A relationship between two organisms in which one organism benefits and the other is unaffected
Parasitism
A relationship between two organisms of different species where one benefits and the other is harmed
Mutualism
A relationship between two species in which both species benefit
High G+C Gram Positive Bacteria
Actinobacteria
Microbiome
All of the microorganisms that live in a particular environment, such as a human body
Why are Cytophaga, Fusobacterium, and Bacteroides classified together as the CFB group?
Although they are phylogenetically diverse, bacteria of the CFB group share some similarities in the sequence of nucleotides in their DNA.
David Hendricks Bergey (1860-1937)
American microbiologist who published A Manual in Determinative Bacteriology in 1923; Included the morphological, physiological, and biochemical properties of these organisms.
Prokaryotes live in communities that interact:
Among themselves and with large organisms that they use as hosts (including humans).
Gammaproteobacteria are the largest:
And the most diverse group of Proteobacteria. Many are human pathogens that are aerobes or facultative anaerobes. Some are enteric bacteria that may be coliform or noncoliform. Escherichia coli, a member of Gammaproteobacteria, is perhaps the most studied bacterium.
Chlamydia
Another taxon of the Alphaproteobacteria. Members of this genus are gram-negative, obligate intracellular pathogens that are extremely resistant to the cellular defenses, giving them the ability to spread from host to host rapidly via elementary bodies.
Sulfur bacteria perform:
Anoxygenic photosynthesis, using sulfur compounds as donors of electrons, whereas nonsulfur bacteria use organic compounds (succinate, malate) as donors of electrons.
Serotypes
Antigenically different strains of a bacterium or other pathogen that can be distinguished by immunological means, for example by antibody-based detection tests. Also used to describe human alloantigens such as HLA and blood group antigens.
In recent years, the traditional approaches to classification of prokaryotes have been supplemented by:
Approaches based on molecular genetics.
What types of environments do Crenarchaeota prefer?
Aquadic
Planctomycetes are:
Aquatic bacteria that reproduce by budding; they may form large colonies, and develop a holdfast.
Prokaryotes are classified into domains:
Archaea and Bacteria.
Resident Microbiota
Are a part of the normal microbiota throughout life Are mostly commensal
Proteobacteria is a phylum of gram-negative:
Bacteria discovered by Carl Woese in the 1980s based on nucleotide sequence homology.
Why do scientists typically use darkfield fluorescent microscopy to visualize spirochetes?
Because they are very thin
How do Planctomycetes reproduce?
By budding
Name two Epsilonproteobacteria that cause gastrointestinal disorders.
Campylobacter and Helicobacter
Betaproteobacteria
Class of diverse Gram-negative bacteria in the phylum Proteobacteria capable of growing at very low nutrient levels. Ex: The genus Neisseria, includes the bacteria N. gonorrhoeae, the causative agent of the STI gonorrhea, and N. meningitides, the causative agent of bacterial meningitis. Ex: Pertussis (whooping cough
Prokaryotes live in a:
Community
Pleomorphic
Composed of a variety of types of cells; a feature of mycoplasmas
The Five Major Phyla of Archaea
Crenarchaeota, Euryarchaeota, Korarchaeota, Nanoarchaeota, and Thaumarchaeota.
Mycoplasmas
Do not possess a cell wall and, therefore, are not stained by Gram-stain reagents, this genus is still included with the low G+C gram-positive bacteria.
Archaea
Domain of unicellular prokaryotes that have cell walls that do not contain peptidoglycan
List two families of Gammaproteobacteria
Enterobacteriaceae and Pseudomonaceae
Coliforms
Enterobacteriaceae; Gram-negative, non-spore forming bacilli that ferment lactose with acid and gas production Ex: Escherichia coli
Prokaryotes can be found:
Everywhere on our planet, even in the most extreme environments.
Some phototrophic bacteria are able to:
Fix nitrogen, providing the usable forms of nitrogen to other organisms.
Vibrionales
Found in coastal water Vibrio cholerae causes cholera V. parahaemolyticus causes gastroenteritis
Deltaproteobacteria
Gram negative, includes sulfate-reducing bacteria (SRBs), genus Bdellovibrio which are parasites of other gram-negative bacteria, and myxobacteria which lives in the soil, scavenging inorganic compounds.
Green Nonsulfur Bacteria
Gram-Negative, nonproteobacteria. Use substrates other than sulfides for oxidation. Chloroflexus is an example, it often has an orange color when it grows in the dark, but it becomes green when it grows in sunlight. It stores bacteriochlorophyll in chlorosomes, similar to Chlorobium, and performs anoxygenic photosynthesis, using organic sulfites (low concentrations) or molecular hydrogen as electron donors, so it can survive in the dark if oxygen is available.
Nonproteobacteria
Gram-negative bacteria including the spirochetes, GFC group, and planctomyces
Low G+C Gram-positive Bacteria
Have less than 50% guanine and cytosine in their DNA, and this group of bacteria includes a number of genera of bacteria that are pathogenic. Ex: Clostridium spp., Lactobacillales, Bacillus, and Staphylococcus.
Prokaryotes are unicellular microorganisms whose cells:
Have no nucleus.
Actinobacteria
High G+C gram positive bacteria The vast majority are aerobic. One distinctive feature of this group is the presence of several different peptidoglycans in the cell wall.
Gram-positive bacteria are classified into:
High G+C gram-positive and low G+C gram-positive bacteria, based on the prevalence of guanine and cytosine nucleotides in their genome
Cooperative Interactions
Independent interactions within a community which benefit the populations
Competitive Interactions
Interactions in which one population competes with another for resources.
Gammaproteobacteria
Largest and most diverse class of Proteobacteria, including purple sulfur bacteria, methane oxidizers, pseudomonads, and others.
Spirochetes
Long, slender spiral-shaped bacteria that have flexible walls and are capable of movement A type of Nonproteobacteria ex: syphilis and B. burgdorferi causes
Alphaproteobacteria
Many of which are obligate or facultative intracellular bacteria. Some species are characterized as oligotrophs, organisms capable of living in low-nutrient environments such as deep oceanic sediments, glacial ice, or deep undersurface soil. Ex: rickettsias
Transient Microbiota
May be present for days, weeks, or months
Obligate Intracellular Pathogens
Microbes that require part of their life cycle to occur inside other cells called host cells.
The totality of forms of prokaryotes (particularly bacteria) living in a certain region of the human body is called the:
Microbiota of this region.
Spirochetes are:
Motile, spiral bacteria with a long, narrow body; they are difficult or impossible to culture. Ex: syphilis and Lyme disease.
What type of Deltaproteobacteria forms fruiting bodies?
Myxobacteria
Neutralism
Neither species benefits or is harmed
Noncoliforms
Non-lactose-fermenting opportunistic enterics Ex: Salmonella spp., Shigella spp., and Yersinia pestis
Alphaproteobacteria include several:
Obligate and facultative intracellular pathogens, including the rickettsias. Some can convert atmospheric nitrogen to nitrites, making nitrogen usable for other forms of life.
What is one distinctive feature of Actinobacteria?
One distinctive feature of this group is the presence of several different peptidoglycans in the cell wall.
Oligotrophs (aquatic)
Organisms capable of living in low-nutrient environments such as deep oceanic sediments, glacial ice, or deep undersurface soil.
Cyanobacteria are:
Oxygen-producing bacteria thought to have played a critical role in the forming of the earth's atmosphere.
Photosynthesis in Cyanobacteria is
Oxygenic, using the same type of chlorophyll a found in plants and algae as the primary photosynthetic pigment.
Less than 1% of prokaryotes (all of them bacteria) are thought to be human _____.
Pathogens
Cyanobacteria
Photosynthetic, oxygen-producing bacteria (formerly known as blue-green algae). Species of this group perform oxygenic photosynthesis, producing megatons of gaseous oxygen.
Crenarchaeota
Phyla of Archaea All are aquatic organisms, and they are thought to be the most abundant microorganisms in the oceans. Most, but not all, Crenarchaeota are hyperthermophiles; some of them (notably, the genus Pyrolobus) are able to grow at temperatures up to 113 °C.
Gram-negative bacteria can be further classified into:
Proteobacteria, Cytophaga-Flavobacterium-Bacteroides (CFB), and Spirochetes.
Enterobacteriaceae
Proteobacteria; most live in the intestinal tract Two groups: Coliforms and Noncoliforms
Purple Nonsulfur Bacteria
Similar to purple sulfur bacteria, except that they use hydrogen rather than hydrogen sulfide for oxidation. These microorganisms are facultative anaerobes, which are actually pink rather than purple, and can metabolize ("fix") nitrogen. Includes the genus Rhodospirillum.
Rickettsia
Small bacteria that live in lice, fleas, ticks, and mites that transmit infection to humans. An alphaproteobacteria that cannot synthesize their own adenosine triphosphate (ATP), and, therefore, rely on cells for their energy needs.
Deltaproteobacteria make up a:
Small group able to reduce sulfate or elemental sulfur. Some are scavengers and form myxospores, with multicellular fruiting bodies.
Epsilonproteobacteria make up the:
Smallest group of Proteobacteria. The genera Campylobacter and Helicobacter are human pathogens.
Name one pathogenic low G+C gram-positive bacterium and a disease it causes.
Some antibiotic-resistant strains are designated as methicillin-resistant S. aureus (MRSA) and vancomycin-resistant S. aureus (VRSA)
How can prokaryotes aide in cleaning up the environment?
Some researchers focused on the diversity and functions of prokaryotes in manmade environments. They found that some bacteria play a unique role in degrading toxic chemicals that pollute water and soil.
The phylum Euryarchaeota includes several distinct classes.
Species in the classes Methanobacteria, Methanococci, and Methanomicrobia represent Archaea that can be generally described as methanogens. Methanogens are unique in that they can reduce carbon dioxide in the presence of hydrogen, producing methane.
Gram-negative nonproteobacteria include the taxa:
Spirochetes; the Chlamydia, Cytophaga, Fusobacterium, Bacteroides group; Planctomycetes; and many representatives of phototrophic bacteria.
Actinobacteria is the:
Taxonomic name of the class of high G+C gram-positive bacteria. This class includes the genera Actinomyces, Arthrobacter, Corynebacterium, Frankia, Gardnerella, Micrococcus, Mycobacterium, Nocardia, Propionibacterium, Rhodococcus, and Streptomyces.
Betaproteobacteria are a diverse group of bacteria:
That include human pathogens of the genus Neisseria and the species Bordetella pertussis.
Cytophaga, Fusobacterium, and Bacteroides are classified together as a phylum called:
The CFB group. They are rod-shaped anaerobic organoheterotrophs and avid fermenters. Cytophaga are aquatic bacteria with the gliding motility. Fusobacteria inhabit the human mouth and may cause severe infectious diseases. Bacteroides are present in vast numbers in the human gut, most of them being mutualistic but some are pathogenic.
Low G+C Gram-positive bacteria
The class Bacilli which have less than 50% of guanine and cytosine nucleotides in their DNA.
Elementary bodies (EB)
The endospore-like form of intracellular bacteria that enter an epithelial cell, where they become active.
CFB Group
The gram-negative nonproteobacteria of the genera Cytophaga, Fusobacterium, and Bacteroides are classified together as a phylum. They are rod-shaped bacteria adapted to anaerobic environments, such as the tissue of the gums, gut, and rumen of ruminating animals.
The totality of forms of prokaryotes (particularly bacteria) living on the human body is called the:
The human microbiome, which varies between regions of the body and individuals, and changes over time.
Epsilonproteobacteria
The smallest class of Proteobacteria; which are gram-negative microaerophilic bacteria (meaning they only require small amounts of oxygen in their environment). Two clinically relevant genera of Epsilonproteobacteria are Campylobacter and Helicobacter, both of which include human pathogens.
Microbial Ecology
The study of the relationship between microorganisms and their environment
Additional characteristics that can be used to classify gram-positive prokaryotes:
Their guanine to cytosine ratios (G+C) in DNA and the composition of 16S rRNA subunits.
Purple Sulfur Bacteria
These oxidize hydrogen sulfide into elemental sulfur and sulfuric acid and get their purple color from the pigments bacteriochlorophylls and carotenoids. Bacteria of the genus Chromatium are purple sulfur Gammaproteobacteria.
Green Sulfur Bacteria
These use sulfide for oxidation and produce large amounts of green bacteriochlorophyll. These bacteria use at least four types of chlorophyll for photosynthesis. The most prevalent of these, bacteriochlorophyll, is stored in special vesicle-like organelles called chlorosomes.
Prokaryotes are ubiquitous; meaning...
They can be found everywhere on our planet, even in hot springs, in the Antarctic ice shield, and under extreme pressure two miles under water.
Assigning prokaryotes to a certain species is challenging because:
They do not reproduce sexually, so it is not possible to classify them according to the presence or absence of interbreeding. Also, they do not have many morphological features.
Prokaryotes are identified as gram-positive if they:
They have a multiple layer matrix of peptidoglycan forming the cell wall.
Deeply Branching Bacteria
They have rRNA sequences thought to be similar to those of earliest bacteria. They are autotrophic and live in hot, acidic, and anaerobic environments, often with intense exposure to sun.
Name some ways in which streptococci are classified.
They look like "bunches of grapes" They are facultative anaerobic, halophilic, and nonmotile.
Why are Neisseria classified as microaerophilic?
They require low levels of oxygen. They are cocci that live on mucosal surfaces of the human body. They are fastidious, or difficult to culture, and they require high levels of moisture, nutrient supplements, and carbon dioxide.
What characteristic makes phototrophic bacteria different from other prokaryotes?
They use solar energy to synthesize ATP through photosynthesis. When they produce oxygen, they perform oxygenic photosynthesis. When they do not produce oxygen, they perform anoxygenic photosynthesis. With the exception of some cyanobacteria, the majority of phototrophic bacteria perform anoxygenic photosynthesis.
Prokaryotes are very flexible metabolically, so they are able:
To adjust their feeding to the available natural resources.
Where do Halobacteria live?
Where there is a very high concentrations of sodium chloride in their aquatic environment. The required concentration is close to saturation, at 36%; such environments include the Dead Sea as well as some salty lakes in Antarctica and south-central Asia. One remarkable feature of these organisms is that they perform photosynthesis using the protein bacteriorhodopsin, which gives them, and the bodies of water they inhabit, a beautiful purple color
Proteobacteria are further classified into the classes:
alpha-, beta-, gamma-, delta- and epsilonproteobacteria, each class having separate orders, families, genera, and species.
Planctomycetes
they reproduce by budding. These so-called swarmer cells are motile and not attached to a surface. However, they will soon differentiate into sessile (immobile) cells with an appendage called a holdfast that allows them to attach to surfaces in the water. Only the sessile cells are able to reproduce.
