Chapter 11: Characterizing and Classifying Prokaryotes

Most purple nonsulfur phototrophs are

Alphaproteobacteria

The _______ include a variety of aerobes, many of which have unusual cellular extensions called prosthecae. _______ and _______ are nitrogen fixers that are important in agriculture

Alphaproteobacteria Azospirillum Rhizobium

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.

The _______ include the nitrifying Nitrosomonas and pathogenic species such as Neisseria (gonorrhea), and Burkholderia (which colonizes the lungs of cystic fibrosis patients)

betaproteobacteria

Prokaryotes reproduce asexually by

binary fission, snapping division (a type of binary fission), spore formation, and budding.

The 3 basic shapes of bacterial cells

coccus (spherical) bacillus (rod-shaped) spiral (twisted) The spirals may be stiff (spirilla) or flexible (spirochetes)

sarcina

cuboidal arrangement

The _______ include some important human pathogens, including campylobacter and helicobacter

epsilonproteobacteria

The _______ constitute the largest class of proteobacteria; they include _______ _______ _______, intracellular pathogens, methane oxidizer, facultative anaerobes that utilizes glycolysis and the pentose phosphate pathway, and pseudomonads

gammaproteobacteria purple sulfur bacteria

Numerous human pathogens are facultatively anaerobic gammaproteobacteria that catabolize carbohydrates by

glycolysis

binary fission

A form of asexual reproduction in single-celled organisms by which one cell divides into two cells of the same size

11.7 Discuss the veracity and limitations of any taxonomic scheme

A given taxonomic scheme classifies organisms according to a set of criteria based on what is considered standard for the field at a given time. As new information becomes available, these criteria may change and require some organisms to be reclassified. Also, there is no single authoritative text for prokaryotic taxonomy, so the same organisms may be classified differently depending on the taxonomic rules used.

Environmentally resistant _______ are produced within vegetative cells of the Gram-positive genera ______ and _______. Depending on species which they formed they may be terminal, sub terminal, or terminally located

Endospores Clostridium Bacillus

Cocci may typically be found in groups including

Long chains: Streptococci Pairs: diplococci Foursomes: tetrads Cuboidal packets: sarcinae Clusters: Staphlococci

______ _____ are anaerobic bacteria that use methane for carbon and energy

Methane Oxidizers

________ are obligate anaerobes that produce methane gas and are useful in sewage treatment

Methanogens (phylum Euryarcheaota)

extremophiles

Microbes that require what humans consider to be extreme conditions of temperature, pH, pressure, and/or salinity to survive.

Are gram-positive, pleomorphic, facultative anaerobes and obligate anaerobes that lack cell walls and therefore stain pink with Gram stain. They are frequently associated with pneumonia and urinary tract infections

Mycoplasmas

The presence of mycolic acid in the cell wall characterizes

Myobacterium

Clostridia include the genus

-Clostridium (pathogenic bacteria that cause gangrene, tetanus, botulism, and diarrhea) -epulopiscium (large enough to be seen w/out microscope) -Veillonella (dental plaque)

Aquifex

-Considered to represent earliest branch of bacteria -chemoautotrophic, hyperthermophilic, and microaerophillic -derives energy and carbon from inorganic sources in very hot habitats containing little oxygen

The deltaproteobacteria include

-Desulfovibrio (important in the sulfur cycle and in corrosion of pipes) -Bdellovibrio (pathogenic to bacteria) -myxobacteria The latter form stalked fruiting bodies containing resistant, dormant myxospores

Deinococcus

-Has outer membrane similar to Gram-negatives, but stains Gram-positive -deeply branching bacteria -is extremely resistant to radiation because of the way it packages its DNA, the presence of radiation-absorbing pigments, unique lipids within its membranes, and high cytoplasmic levels of managanese that protects its DNA repair proteins from radiation damage

Halobacterium

-lacks photosynthetic pigments -rotates its flagella with energy from the proton gradient

11.8 Identify the common features of microbes in the domain Archaea.

1). They lack true peptidoglycan in their cell walls. 2). Their cytoplasmic membrane lipids have branched or ring-form hydrocarbon chains, whereas bacterial membrane lipids have straight chains. 3). The initial amino acid in their polypeptide chains, coded by the AUG start codon, is methionine (as in eukaryotes and in contrast to the N-formylmethionine used by bacteria).

binary fission steps

1. DNA Replication 2. Chromosome Segregation (when the replicated chromosomes move to different ends of cell) 3. Separation (new plasma membrane growth, cytoplasm divide, and new cell walls form around the new cells)

11.6 Explain the general purpose of Bergey's Manual of Systematic Bacteriology.

An authoritative reference in modern prokaryotic systematics; Classifies prokaryotes into 29 phyla -- 5 in Archaea, and 24 in Bacteria. The five volumes of the second edition of Bergey's Manual discuss the great diversity of prokaryotes based in large part (but not exclusively) on their possible evolutionary relationships, as reflected in their rRNA sequences.

Living things are now classified into 3 domains

Archaea Bacteria Eukarya Based largely on genetic similarities

Members of the genus mycobacterium, including species that cause tuberculosis and leprosy, grow slowly and have unique, resistant cell walls containing waxy

Mycolic acids

11.11 Provide a rationale for the name deeply branching bacteria

So named because their rRNA sequences and growth characteristics lead scientists to conclude that these organisms are similar to the earliest bacteria; that is, they appear to have branched off the "tree of life" at an early stage.

taxa

group or level of organization into which organisms are classified

Methanopyrus

has an optimum growth of 98 degrees celsius and grows well in 110 degrees celsius seawater around submarine hydrothermal vents

both Legionella & Coxiella are

intracellular, pathogenic gamma-proteobacteria

Agrobacterium

is used in genetic recombination of plants

How is Halobacterium salinarum distinctive?

it is absolutely dependent on high salt concentrations to maintain its cell wall

11.10 List at least four significant roles that methanogens play in the environment

methanogens: obligate anaerobes that produce methane gas and are useful in sewage treatment 1. convert organic waste in aquatic environments ( ponds, lakes, ocean sediments) into methane gas that is subsequently released into the atmosphere. 2. In ocean sediments generate methane that becomes trapped in the mud of the ocean floor. So called " swamp gas" is actually methane generated by methanogens in the water of swamps and bogs. 3. The intestinal tracts of some terrestrial animals are inhabited by methanogens that break down organic compounds into methane gas. 4. Methanogens are used in industry, including sewage treatment and in the production of methane burned for heat and electricity.

Geogemma

record holder for surviving high temperatures- it can survive two hours at 130 degrees celsius

Endospores

remain alive for decates can remain alive in boiling water exist in a state of suspended animation

Caulobacter is used in

reproductive studies

taxonomists

scientists who classify species, use an organism's physical appearance and genetic makeup to determine its species

The type of reproduction in prokaryotes that results in paliside arrangement of cells is called

snapping division

Describes stiff, spiral-shaped prokaryotic cells

spirilla

Flexible spiral-shaped prokaryotes are

spirochetes

Pyrodictium

the cells of Pyrodictium live in deep sea hydrothermal vents, are irregular disks with elongated protein tubules that attach them to grains of sulfur that they use as final electron acceptors in cellular respiration

Why are endospores important?

their durability and potential pathogenicity. Endospores constitute a defensive strategy against hostile or unfavorable conditions. They are stable resting stages that barely metabolize and germinate when conditions improve. They can become a problem for food and health care processors, they can produce deadly toxins that cause fatal diseases like anthrax, tetanus, and gangrene.

Bacillus and Clostridium

Gram positive bacteria that produce endospores

Bacteria that convert nitrogen gas into ammonia are

nitrogen fixers

Acetobacter and Gluconobacter

Synthesize acetic acid

Halobacterium salinarium

-archaea, extreme halophile -it is a photoheterotroph that uses light energy to drive the synthesis of ATP while deriving carbon from organic compounds

11.1 Identify the six basic shapes of prokaryotic cells

1) Coccus 2) Bacillus 3) Vibrios 4) Coccobacillus 5) Spirilla spiral 6) Spirochetes spiral

snapping division

A variation of binary fission; Occurs in some Gram-positive bacilli. Only the inner portion of a cell wall is deposited across the dividing cell. As the cells grow and the new cross wall thickens, they put tension on the outer layer of the old cell wall, which still holds the two cells together. Eventually, as the tension increases, the outer wall breaks at its weakest point with a snapping movement that tears it most of the way around. The daughter cells then remain hanging together almost side by side, held at an angle by a small remnant of the original outer wall that acts like a hinge.

Actinomycetes resemble fungi in that they produce spores and form filaments; this group includes

Actinomyces (normally found in human mouths) Nocardia (useful in degradation of pollutants) Streptomyces (produces important antibiotics

Phylum Proteobacteria is a very large group of Gram-negative bacteria divided into 5 classes

Alpha- Beta- Gamma- Delta- Epsilonproteobacteria-

11.2 Describe the formation and function of bacterial endospores

An endospore is a dormant, tough, non-reproductive structure produced by a small number of bacteria from the Firmicute family. The primary function of most endospores is to ensure the survival of a bacterium through periods of environmental stress.3 ways it forms: Centrally, subterminally (near one end), terminally (at one end)

Spores

Asexual reproductive or resting cell capable of developing into a new organism without fusion with another cell, in contrast to a gamete Example: Actinomycetes

Low G + C Gram Positive bacilli and cocci important to human health and industry include _______ (which contains species that cause anthrax and food poisoning and includes beneficial bacteria that produces Bt toxin.), _______ (which causes bacteremia and meningitis), _______(used to produce yogurt and pickles), _______, _______, and _______ each of which causes a number of diseases

Bacillus Listeria Lactobacillus Streptococcus, Enterococcus, and Staphylococcus

Domains

Bacteria, Archaea, Eukarya the largest most inclusive taxa

Which genus is the most common anaerobic pathogen

Bacteroides

_______ include Bacteroides, an obligate anaerobic rod that inhabits the digestive tract, and Cytophaga, an aerobic rod that degrades wood and raw sewage

Bacteroids

The most authoritative reference in modern prokaryotic systematics is ______, second edition. Currently there are five known phyla of Archaea and 24 phyla of bacteria. The organization of this texts survey of prokaryotes largely follows Bergeys classification scheme

Bergey's Manual of Systemic Bacterialogy

11.4 Describe snapping division as a type of binary fission

Binary Fission: A form of asexual reproduction in single-celled organisms by which one cell divides into two cells of the same size Occurs in some Gram positive species: Snapping Division: The type of reproduction in prokaryotes that results in a palisade arrangement of cells. --Only the inner portion of the cell wall is formed. --As daughter cell grows, the tension snaps the outer portion. --original outer wall acts like a hinge hanging the daughter cell

11.3 List three common types of reproduction in prokaryotes.

Binary fission, spore formation, and budding.

_______ are Gram negative cocci typified by genus Chlamydia; they cause neonatal blindness, pneumonia, and a sexually transmitted disease

Chlamydias

The phylum Firmicutes contains bacteria with a G+C content of less than 50%. Firmicutes includes

Colostridia Mycoplasmas And other low G+C cocci and bacilli

Are high G+C Gram Positive bacteria that are classified in phylum Actinobacteria

Corynebacterium Mycobacterium Actinomycetes

Bacteria in ________ stores phosphates in _______ ______; ______ causes diphtheria

Corynebacterium C. diphtheriae

Phototrophic bacteria trap light energy with photosynthetic lamellar. The 5 groups of phototrophic bacteria are

Cyanobacteria Green Sulfur Bacteria Green Nonsulfur Bacteria Purple Sulfur Bacteria Purple Nonsulfur Bacteria

Many _______ reduce atmospheric N2 to NH3 via a process called ______ ______. Cyanobacteria must separate (in either time and space) the metabolic pathways of nitrogen fixation from those of oxygenic photosynthesis because nitrogen fixation is inhibited by the oxygen generated during photosynthesis. Many Cyanobacteria fix nitrogen in thick walled cells called _______.

Cyanobacteria Nitrogen fixation Heterocysts

_______ _______ _______ have rRNA sequences thought to be similar to those of earliest bacteria. They are autotrophic and live in acidic, and anaerobic environments, often with intense exposure to sun

Deeply branching bacteria

photosynthetic lamellae

Elaborate internal membrane systems found in cyanobacteria that are used for photosynthesis

viviparty

Epulopiscium, a giant bacterium that lives inside surgeonfish, and many of its relatives have a truly unique method of reproduction among prokaryotes: They give "birth" to as many as 12 live offspring that emerge from the body of their dead mother cell; The production of live offspring within a mother

The domain of Archaea includes ________, microbes that require extreme conditions of temperature, pH, pressure, and/or salinity to survive

Extremophiles

Greenhouse gas

Gases such as carbon dioxide, methane, nitrous oxide, water vapor, and ozone in the atmosphere which are involved in the global warming

________ depend on high concentrations of salt to keep their cells walls intact. Halophiles such as ________ ________ synthesize purple proteins called ________ that harvest light energy to synthesize ATP

Halophiles (phylum Euryarcheaota) Halobacterium Salinarum Bacteriorthodospins

Budding

In prokaryotes and yeasts, reproductive process in which an outgrowth of the parent cell receives a copy of the genetic material, enlarges, and detaches. Example: Plantomyces

Some members of the alphaproteobacteria are ______ ______, which oxidize NH3 to NO3 via a process called ________. Nitrifying alphaproteobacteria are int the genus Nitrobacter

Nitrifying bacteria Nitrification

Methanogens

Obligate anaerobes that convert CO2, H2, and organic acids into methane gas (CH4), which is the major component of natural gas.

Green and purple bacteria use bacteriochlorophylls for anoxygenic photosynthesis. Nonsulfur forms derive electrons from _____ _____; sulfur forms derive electrons from ______

Organic compounds H2S

Halophiles

Organisms that inhabit extremely saline habitats, such as the Dead Sea, the Great Salt Lake, and solar evaporation ponds used to concentrate salt for use in seasoning and for production of fertilizer. Can also colonize and spoil such foods as salted fish, sausages, and pork.

Bacilli are found singly, in pairs, in chains, or in a

Palaside arrangement

Bacteriorhodopsin

Pigmented protein found in abundance in the plasma membrane of the salt-loving archaeon. It absorbs light energy to pump protons across the cytoplasmic membrane to establish a proton gradient. Cells use the energy of protein gradients to produce ATP

Hyperthermophiles

Prokaryotes that require temperatures over 80 degrees celsius.

Thermophiles

Prokaryotes whose DNA, RNA, cytoplasmic membranes, and proteins do not function properly at temperatures lower than about 45 degrees celsius.

11.12- Explain the function of heterocyst in terms of both photosynthesis and nitrogen fixation.

Protein which is implicated in heterocyst formation. A heterocyst is a differentiated cyanobacteria cell that carries out nitrogen fixation. The heterocyst function as the sites for nitrogen fixation under aerobic conditions. They are formed in response to a lack of fixed nitrogen

________, including pathogenic Pseudomonas and nitrogen fixing Azobacter and Azomonas, utilize the Entner-Dourdoff and pentose phosphate pathways for catabolism of glucose

Pseudomonads

Pathogenic alphaproteobacteria include

Rickettsia (typhus and Rocky Mountain spotted fever) Brucella (brucellosis)

Sporulation

The process of endospore formation, requires 8-10 hours and proceeds in seven steps. Depending on the species, a vegetative cell forms an endospore either centrally, subterminally (near one end), or terminally (at one end).

What are two representative genera of thermophilic archaea?

Thermococcus and Pyrodictium.

________ and _______ live at temperatures above 45 degrees Celsius and 80 degrees Celsius respectively; because their DNA, membranes and proteins do not function properly at lower temperatures

Thermophiles Hyperthermophiles

11.9 Compare and contrast the two kinds of extremophiles discussed in this section

Thermophiles: are prokaryotes whose DNA , RNA, cytoplasmic membranes, and proteins do not function properly at temperature lower than about 45 degrees Celsius. Scientists use thermophiles and their enzymes in recombinant DNA technology applications because thermophiles cellular structure and enzymes are stable and functional at temperatures that denature most proteins and nucleic acid and kill other cells. Halophiles: depend on high concentrations of salt, above 9%.

Thermococcus and Pyrodictum

These microorganisms live in acidic hot springs such as those found in deep ocean rifts and similar terrestrial volcanic habitats

Other Betaproteobacteria include

Thiobacillus (ecologically important) Zooglea (useful in sewage treatment) Sphaerotilus (hampers sewage treatment)

Spirochetes are flexible, helical bacteria that live in diverse environments. The pathogens _______ and ______ are important spirochetes

Treponema (syphilis) Borrelia (lyme disease)

Variations In shapes of prokaryotes include

Vibrios (slightly curved rods) Coccobacilli (intermediate to cocci and bacilli) Pleomorphic (variable shape and size)

Scientists discovered __________ using metagenomic sequencing, which entails sequencing all the DNA from a site so as to ascertain all microbes present. _________ oxidize iron in marine environments

Zetaproteobacteria

vegetative cell

a cell that has not formed spores or other resting stages

Palisade

a side by side arrangement of Example: Corynebacterium diphtheriae, the causative agent of diphtheria, divide by snapping division, the daughter cells remain attached to form V-shapes and a palisade

The thick walled reproductive spores produced in the middle of cyanobacterial filaments

akinetes

Photosynthetic bacteria that also fix nitrogen are

cyanobacteria