chapter 11- diversity of bacteria and archaea
Anaerobic Chemoorganotrophs- fermentation
- obtain energy by fermentation, producing ATP only by substrate-level phosphorylation - The Genus Colostrum - The Lactic Acid Bacteria - The Genus Propionibacterium ex) glucose> pyruvate(terminal electron acceptor)> lactic acid
streptomyces
-500+ species of aerobic gram + bacteria that resemble fungi in their pattern of growth form conidia -responsible for earthy odor of soil ex) streptomyces, S somanliensis (can cause infection of subcutaneous tissue) -produce antibiotics
Other Anoxygenic Phototrophs
-although green and purple bacteria most extensively studied, other anoxygenic phototrophs exist -ex. Genus Heliobacterium -gram positive endospore forming rods -related to Clostridium
Staphylococcus
-facultative anaerobic gram + cocci -can be harmless but also can cause infections -catalase +
epulopiscium
-gram + bacteria that live in the intestinal tract of surgeon fish -very large -have thousands of copies of each gene meaning necessary proteins are synthesized even in far reaches of the cell -go through odd binary fission
agrobacterium
-gram - rod shaped bacteria -they cause plant tumors which alters plants for their own benefit -Ti plasmid plays an important role
rhizobia
-gram - rods -fix nitrogen and form intimate relationships with legumes(plants that bear seed pods) -living within the nodules on the roots. The plant synthesizes the protein leghemoglobin which binds and controls levels of O2 -within this environment, the bacteria can fix nitrogen
Chlamydia and Chlamydophila
-inside host cell they are initially non infectious reticulate bodies and reproduce by binary fission -the become infectious and host cell ruptures -chlamydia trachomatis: eye infections and sti -chlamydophila pneumoniae: pneumonia -chlamydophila psittaci: psittacosis( a form of pneumonia)
Thioploca, Thiomargarita
-live in marine environments and store both sulfur and nitrate -this allows the bacteria to compensate for the fact that their energy source and terminal electron acceptor are not usually found in the same location
Caulobacter
-model for research on cellular differentiation
nanoaerchaea
-new phylum -hydrothermal vents
aerobic chemolithtrophs
-obtain energy by oxidizing reduced inorganic chemicals using O2 as a terminal electron acceptor -sulfur oxidizing bacteria -nitrifiers
bacteroids
-small strictly anaerobic gram - rods and coccobacilli -inhabit the mouth, gi tract, and genital tract -make up 1/3 of bacteria in human feces -role in digestion -responsible for abscesses and bloodstream infections
How do anoxygenic phototrophs benefit by having light-harvesting pigments that absorb wavelengths that penetrate deeper than those absorbed by chlorophyll a?
-they can harvest light in deeper areas where oxygen isnt present -they dont have to compete with other organisms
How would Pyrodictium species be grouped with respect to their temperature preference?
80-121 C
_______ gain energy via the oxidation of reduced inorganic chemicals, using O2 as a terminal electron acceptor.
Aerobic chemolithotrophs
bacteria that associate with plants
Agrobacterium and Rhizobia
extreme halophiles
An organism that lives in a highly saline environment, such as the Great Salt Lake or the Dead Sea. -archaea -pink blooms -aerobic or facultatively anaerobic ex) halobacterium, halorubrum, natronobacterium, and natronococcus
endospore formers
Bacillus - Gram + rods. facultative anaerobes and obligate aerobes. B anthracis Clostridia- gram + rods. Obligate anaerobes
______ species are Gram-negative, strictly anaerobic, make up about a third of the bacteria in fecal matter in humans, and are associated with abscesses and bloodstream infections.
Bacteroides
______species are Gram-negative curved rods that are highly motile and prey on other Gram-negative rods by boring a hole in their cell wall.
Bdellovibrio
coxiella
C burnetti :Q fever transmitted via aerosols or milk -can be in the placenta
sheathed bacteria
Chains of cells within a tube Sheath: protection, help cells attach to a solid object Sphaerotilus and Leptothrix (gram - rods)
What is the role of the Ti plasmid in plant tumor formation?
Encodes the ability to synthesize plant growth hormones
The genomes of free-living spirochetes are larger than those of ones that live within an animal host. Why would this be so?
Free-living spirochetes will need genes to code for additional proteins to synthesize or obtain their own food from the environment around them.
legionella
Genus of bacteria responsible for the disease legionellosis (respiratory disease) -in aquatic environments living within protozoa -gram - obligate aerobes that use amino acid as a source of carbon and energy
A group of bacteria called green bacteria are ______.
Gram-negative
Prosthecate bacteria
Gram-negative bacteria that have extensions projecting from the cells, thereby increasing their surface area
Members of the family Enterobacteriaceae are _______.
Gram-negative rods
myxobacteria
Gram-negative rods that congregate to form complex structures called fruiting bodies -degraders of complex organic substances\ex) chondromyces, myxococcus, and stigmatella
Spirochetes are bacteria that are ______ and possess a unique mechanism of _______.
Gram-negative; motility
Endospore-forming bacteria are typically ______.
Gram-positive rods
During photosynthesis, anoxygenic phototrophs use _______ as a source of electrons to make reducing power.
H2S
Aside from green and purple bacteria, Gram-positive endospore forming rods of the genus ______ are also anoxygenic phototrophs.
Heliobacterium
What characteristic of Mycoplasma species separates them from other bacteria?
Mycoplasmas are distinguished phenotypically from other bacteria by their minute size and total lack of a cell wall.
Aerobic chemolithotrophs obtain energy by oxidizing reduced inorganic chemicals, using ________as a terminal electron acceptor.
O2
A reason why environments that are routinely exposed to O2 can support anaerobic growth is that ______.
O2-consuming organisms depletes the oxygen levels
Methane-generating hyperthermophiles
Oxidize H2, using CO2 as a terminal electron acceptor to yield gas. Can grow in temperatures as high as 97°C. ex) methanopyrus kandleri can grow at 122 c
Which of the following genera of organisms forms a beneficial symbiotic relationship with plants?
Rhizobium
Organisms that form storage granules include ______.
Spirillum Thioploca Thiomargarita
ecophysiology
Study of the adaptations of physiological mechanisms that prokaryotes use to live in terrestrial and aquatic environments
Why would farmers be concerned about nitrifying bacteria?
The potency and longevity of the fertilizer are affected by nitrifying bacteria converting ammonium to nitrate.
How do cyanobacteria prevent erosion in cold desert regions?
Their sheaths persist in soil, creating a sticky, fibrous network that prevents erosion.
Describe two beneficial roles of sulfur oxidizers.
They are important to the sulfur cycle
The oxidase test detects the activity of a component used in which metabolic process?
This test is used to identify microorganisms containing the enzyme cytochrome oxidase (important in the electron transport chain). It is commonly used to distinguish between oxidase negative Enterobacteriaceae and oxidase positive Pseudomadaceae.
wolbachia
a genus of bacteria which infects arthropod species, including a high proportion of insects, as well as some nematodes. It is one of the world's most common parasitic microbes and is possibly the most common reproductive parasite in the biosphere -transmitted maternally via the eggs of infected females to their offspring -bacteria increases the overall population of infected females by killing male embryos, females reproducing asexually, and causing infected males to gain female traits -lives inside worms that cause river blindness -used to prevent mosquitoes from transmitting the virus that causes zika, dengue, chikungunya and yellow fever
Thermoplasma and Picrophilus grow best in which of the following extreme conditions?
acidic and hot environments
How do Helicobacter pylori cells withstand stomach acidity?
activating its own cytoplasmic urease, which converts urea into carbon dioxide and ammonia. The ammonia first neutralises the gastric acid that enters the outer membrane of the bacteria, preventing acidification at the inner membrane.
Chemoorganotrophs that perform ______ often use sulfur or sulfate as a terminal electron acceptor.
anaerobic respiration
Which of the following were likely the earliest photosynthesizing organisms?
anoxygenic phototrophs
Most of the anaerobic chemolithotrophs that have been discovered are members of what domain?
arcaea
Nitrifiers can be described as bacteria that ______.
are Gram-negative obtain energy by oxidizing inorganic nitrogen compounds such as ammonium or nitrite
What is the habitat of Legionella species?
bodies of water
Like the green and purple bacteria, members of the genus Heliobacterium are also examples of anoxygenic phototrophs. They are ______ bacteria related to members of the genus Clostridium.
endospore-forming rod-shaped Gram-positive
What characteristic of Caulobacter species makes them important research models?
entirely different events occur in an orderly fashion at opposite ends of the cell
Prosthecate bacteria form projections called prosthecae, which are extensions of the cytoplasm and cell wall. These prosthecae ______.
facilitate absorption of nutrients
clostridium and clostridioides- anaerobic chemoorganotrophs(fermentation)
(clostridia) gram + rods that can form endospores. -in soil, intestinal tracts ex)tetaus(C. tentani), gas gangrene(C. oerfringens), botulism(C. botulinum) -some end products of fermentation can be commercially valuable like acetone and butanol
An anaerobic chemoorganotroph that uses glucose for energy and pyruvate as its terminal electron acceptor is performing ______.
fermentation
What kind of bacteria might be responsible for plugging the pipes in a sewage treatment facility?
filamentous sulfur oxidizers
Bifidobacterium
gram + irregular rod shaped anaerobes -gi tract -common in gi tract of breast fed infants -protective
Members of the Gram-negative genera Aquifex and Hydrogenobacter are hydrogen-oxidizing bacteria. An example of their metabolism involves using ______.
hydrogen as a source of energy and oxygen as a terminal electron acceptor, forming water
where are methanogens not found
in environments containing high levels of sulfate or nitrate bc microbes that use those as electron acceptors have competitive advantages
Why would breast feeding affect the composition of a baby's intestinal microbiota?
it introduces many beneficial organisms
The normal habitat of Bacteroides species in humans includes the ______.
mouth genital tract intestines
A diverse group of Gram-negative bacteria that obtain energy by oxidizing inorganic nitrogen compounds such as ammonium or nitrate are known as
nitrifiers
Bdellovibrio species ______.
prey on Gram negative bacteria like E. coli are highly motile Gram-negative curved rods bore a hole in the cell wall of their prey
Bdellovibrio
prey on other bacteria like E coli and other gram - bacteria -highly motile gram - curved rods
As a group, anaerobic chemoorganotrophs ______.
produce ATP via substrate level phosphorylation can obtain energy via fermentation
The __________bacteria have projections called prosthecae, which are extensions of the cytoplasm and cell wall that increase the surface area to facilitate absorption of nutrients.
prosthecate
What causes the purple color of the bacterial masses?
purple sulfur bacteria
What role does quorum sensing play in the behavior of bioluminescent bacteria?
quorum sensing controls bioluminescence, the ability of the bacteria to produce light
The purple bacteria are Gram-negative organisms that can appear ______ due to their light-harvesting pigments.
red, orange, or purple
By definition, obligate intracellular parasites cannot ______.
replicate outside of a host cell
How can the metabolic activities that result in this acid drainage be used in a commercially valuable manner?
to prevent acid rain by allowing the bacteria to oxidize it to sulfate which is a form that can be extracted
anoxygenic phototrophs
use hydrogen sulfide or organic compounds as a source of electrons -do not generate O2 -bogs, lakes, muds purple bacteria green bacteria
sulfur and sulfate reducing bacteria - anaerobic chemoorganotrophs
use sulfur as a terminal electron acceptor to form hydrogen sulfide -live in mud -H2S they produce causes mud and water to turn black when it reacts with iron molecules ex)desulfovibrio (gram - rods)
oxyegnic phototrophs
use water as a source of electrons -cyanobacteria
Oxygenic phototrophs use ______ as a source of electrons for reducing power, generating O2.
water
lactic acid bacteria- anaerobic chemoorganotrophs(fermentation)
gram + bacteria that produce lactic acid and can be distinguished from other bacteria that grow in the presence of O2 bc they lack the enzyme catalase ex)streptococcus, enterococcus, lactobacillus, and leuconostoc -normal microbiota, yogurt, strep throat, vagina
What will happen to the swarmer cell?
it detaches and moves to a new location, eventually loosing its flagellum and forming a polar prostheca at the opposite end so it can repeat the cycle
Relatively little is known about many obligate anaerobes. Why would this be so?
it is harder to provide the right atmospheric conditions
bacteria that form a resting stage
endospores azotobacter myxobacteria streptomyces
Bacteria that oxidize sulfur are Gram-negative rods or spirals that ______.
use sulfur compounds as an energy source and oxygen as a terminal electron acceptor
How do rhizobia benefit plants?
fix nitrogen for the plant to use.
propionibacterium- anaerobic chemoorganotrophs(fermentation)
gram + pleomorphic rods that produce propionic acid as their main -swiss cheese production (propionic acid=flavor, CO2= holes)
cyanobacteria
photosynthetic gram - bacteria -inhabit freshwater, marine habitats, soils, and surfaces of rocks -can convert nitrogen gas to ammonia (nitrogen fixation) -morphologically diverse -often have gas vesicles -chlorophyll pigments and phycobiliproteins -heterocysts -Anabaena forms a relationship with the water fern Azolla -filamentous cyanobacteria are responsible for maintaining structure and productivity in cold deserts
Why would it be an advantage for a Pseudomonas species to encode enzymes for degrading certain compounds on a plasmid rather than on the chromosome?
plamids allow easy transfer to other bacterial cells so the degradation genes are more diverse
What is a trichome?
filamentous multicellular associations
lactobacillus are found
microbiota in the mouth and vagina -in the vagina they break down glycogen which results in lower ph that helps to prevent vaginal infections
Why is it important for heterocysts to minimize O2 production?
nitrogenase the enzyme that catalyzes nitrogen fixation is irreversibly inactivated by O2
Describe two beneficial contributions of the lactic acid bacteria.
-cheese -normal microbiota of the vagina which lowers the ph
treponema and borrelia
are spirochaetes. -inhabit body fluids and mucus membranes -gram - cell wall -treponema: obligate anaerobes/microaerophiles that inhabit the mouth and genital tract - T pallidum causes syphilis -B recurrentis and b hermsii causes relapsing fever -B burgdorferi causes lyme disease
mycoplasma
bacteria that lack cell wall -most have sterol to provide strength -among the smallest forms of life -they can pass through filters and easily contaminate media -M pneumoniae resistant to penicillin -M genitalium is an emerging sti
Magnetotactic bacteria
bacteria that orient along the Earth's magnetic field -allows them to move up or down in the water or sediments -gram - spiral shaped
Cyanobacteria as a group are capable of ______.
both photosynthesis and nitrogen fixation
What is the function of gas vesicles?
buoyancy control
Sulfur-oxidizing bacteria ______.
can sometimes grow in filaments can use hydrogen sulfide or thiosulfate as an energy source
obligate intracellular parasites
cannot multiply unless they invade a specific host cell and instruct its genetic and metabolic machinery to make and release new viruses -rickettsia, orientia, and ehrlichia -coxiella -chlamydia and chlamydophila -wolbachia -
How does conidia production benefit Streptomyces species?
conidia are resistant to drying and are easily spread in air currents
The earliest oxygenic phototrophs probably belonged to a group of bacteria called the
cyanobacteria
What kind of bacteria might compose the subsurface scum of polluted ponds?
cyanobacteria
Campylobacter jejuni infections are commonly associated with ______.
diarrhea
How does a Bdellovibrio cell penetrate the prey?
digestive enzymes
Hyphomicrobium
divides by budding
hydrogen- oxidizing bacteria- aerobic chemolithotrophs
gram - obligate chemolithotrophs. They use Hydrogen as an energy source and O2 as a terminal electron acceptor ex)aquifex - maximum growth temp of 95C
spirillum
gram - spiral shaped microaerophilic bacteria -forms volutin granules which are storage forms of phosphate
neisseria
gram negative cocci -common microbiota in mucus membranes -aerobes but can grow aerobically if nitrite is present -N gonorrhoeae -N meningitidis -fastidious
haemophilus
gram negative coccobacilli -"blood loving" -require hematin or NAD which is found in blood -H influenza: ear infections, respiratory infections, meningitis -haemophilus ducreyi: STD chancroid
obligate aerobes- aerobic chemoorganotrophs
none can ferment 1. micrococcus: -gram + cocci -found in soil, dust particles, and on inanimate objects and skin -airborne -form pigmented colonies -can tolerate dry conditions and salty environments ex) M luteus 2. mycobacterium: -widespread -can be harmless or harmful -they use nutrients from dead or decaying organic matter -acid-fast -pleomorphic rods can be in chains or groups Ex) M tuberculosis, M leprae 3. Pseudomonas: -gram - rods that have polar flagella and sometimes produce pigments -can grow anaerobically if needed if nitrite is available as a terminal electron acceptor -can be distinguished from the family Enterobacteriaceae because they don't ferment and are oxidase + -biochemical diverse -break down many synthetic and natural components that resist breakdown by other microorganisms -inhabit soil and water Ex) P aeruginosa: opportunistic pathogen. Can grow in nutrient-poor environments 4. Thermus and Deinococcus: thermus- thermophilic, gram - Deinococcus- gram +, resistance to gamma radiation
Sulfur-reducing hyperthermophiles
obligate anaerobes, reduces sulfur to yield H2S, eg. Pyrolobus & Pyrodictium species
Hydrogen-oxidizing bacteria such as Aquifex and Hydrogenobacter are ______.
obligate chemolithotrophs Gram-negative thermophilic
Aerobic chemoorganotrophs gain energy via the _______, using O2 as a terminal electron acceptor.
oxidation of organic compounds
Aerobic Chemoorganotrophs
oxidize organic compounds to obtain energy, using O2 as a terminal electron acceptor 1. obligate aerobes 2.facultative anaerobes
As a group, chemolithotrophs ______ to obtain energy.
oxidize reduced inorganic chemicals such as hydrogen gas
what allows cyanobacteria to absorb energy from wavelengths of light not well absorbed by chlorophyll
phycobiliproteins
How could heavily fertilized lawns foster the development of cyanobacterial blooms?
run off from lawns can get into the water ways leading to excess nitrogen that can be used by cyanobacteria
Rickettsia, Orientia, Ehrlichia
several arthropod-transmitted human pathogens -rickettsia tickettsii: rocky mountain spotted fever -R prowazekii: typhus -O tsutsugamushi: scrub typhus -E chaffeensis: human ehrlichiosis
bordetella
small gram - coccobacilli that grow aerobically -fastidious ex) bordetella fastidious (whooping cough)
spirochetes
spiral-shaped bacteria that have flexible walls and are capable of movement -gram - -can move through thick and viscous substances such as mud -mud/ anaerobic waters -endoflagella ex)L interrogans
The motile cells found in sheathed bacteria are called ______ cells, and these exit through the end of the sheath.
swarmer
Why are many spirochetes difficult to see with bright-field microscopy?
theyre too thin
extreme thermophiles
thrive in very hot environments
Nitrifiers- aerobic chemolithotrophs
gram - bacteria that obtain energy by oxidizing inorganic nitrogen compounds such as ammonium or nitrite. Use O2 as terminal electron acceptor -concern to farmers who fertilize with ammonium. The fertilizers effectiveness are effected by nitrifying bacteria -important consideration when disposing of wastes that have a high ammonium concertation bc the waters can become hypotoxic ex) Nitrosomonas and nitrosococcus: convert ammonium to nitrite Ex) Nitrobacter and nitrococcus: covert nitrite to nitrate -important in the nitrogen cycle
azotobacter
gram - pleomorphic rod shaped bacteria -live in the soil -can form a cyst that withstands drying and uv light -fix nitrogen -consumes O2 rapidly that a low O2 environment is maintained inside the cell
Describe a structural characteristic that distinguishes the purple sulfur bacteria from the green sulfur bacteria.
green sulfur bacteria form sulfur granules outside of the cell -purple sulfur granules are intracellular
purple bacteria- anoxygenic phototrophs
gram- organisms that appear red, orange or purple. Photosynthetic apparatus is within the cytoplasmic membrane 1. purple sulfur bacteria: -5µm, some have flagella -gas vesicles -store sulfur in granules -prefer hydrogen sulfide for reducing power but can use other inorganic compounds -most are strict anaerobes and phototrophs but some can grow in the absence of light ex)chromatium, thiospirillum, thiodictyon 2. purple nonsulfur bacteria: -prefer a variety of organic molecules rather than hydrogen sulfide as a source of electrons. -lack gas vesicles, granules form outside the cell -versatile -most can grow aerobically in the absence of light using chemotrophic metabolism ex)rhodobacter, and rhodopseudomonas
methanogens -anaerobic chemolithotrophs
group of archaea that generate ATP by oxidizing hydrogen gas, using CO2 as a terminal electron acceptor -this process generates methane (CH4) ex)methanobrevibacter, and methanosarcina -methanogens are found in anaerobic environments where H2 and CO2 are available -swamps, marine sediments, rice paddies, and digestive tracts
sulfur oxidizing bacteria-Aerobic chemolithotrophs
gram - rods/spirals which can grow in filaments. They obtain energy by oxidizing elemental sulfur and reduced sulfur compounds, O2 serves as the terminal electron acceptor -generates sulfuric acid -important in the sulfur cycle 1. filamentous sulfur oxidizers: -lives in sulfur springs, polluted waters, and on the surface of freshwater sediments -store sulfur depositing it as intracellular granules but differ in nature of filamentous growth ex)beggiatoa and thiothrix -beggiatoa moves by gliding motility -thiothrix is immobile and they attach to rocks or other cells -an overgrowth of these organisms in wastewater treatment facilities causes a problem called bulking 2. unicellular sulfur oxidizers: ex) acidithiobaciullus- -terrestrial and aquatic environments -oxidizes metal sulfides such as gold sulfide, producing sulfuric acid which lowers the Ph and converts metal to a soluble form -can be used to prevent acid rain -can cause acidic run off
green bacteria-anoxygenic phototrophs
gram - organisms that are green or brownish in color 1. green sulfur bacteria: -inhabits habitats similar to purple sulfur bacteria -use hydrogen sulfide as a source of electrons and they form sulfur granules that form outside the cell -some photosynthetic pigments are located in chlorosomes -strict anaerobes -lack flagella but have gas vesicles ex) chlorobium and pelodictyon 2. filamentous anoxygenic phototrophic bacteria: -form multicellular arrangements and exhibit gliding motility -chlorosomes -diverse metabolically as some use organic compounds to generate reducing power and others can grow in the dark aerobically using chemotrophic metabolism ex)chloroflexus -hot springs
bioluminescent bacteria
beneficial relationship between the bacteria and specific types of fish and squid. ex)aliivibrio fischeri- colonizers squids specialized organ. The light acts as camouflage which can be used to confuse predators and prey -luminescence is catalyzed by the enzyme luciferase which can be regulated by quorum sensing ex) vibrio harveyi, photobacterium phosphoreum
campylobacter and helicobacter
microaerophilic Gram-negative curved rods -camylobacter jejuni: diarrheal disease -helicobacter pylori: inhabits the stomach and has been linked with stomach cancer. Produces enzyme urease which breaks down urea to ammonia and neutralizes acid in the surroundings
What unique characteristic makes members of the genus Deinococcus noteworthy?
their resistance to gamma radiation
Why are myxobacteria important in nature?
they degrade complex organic substances and they serve as an important model for studying developmental biology
What is the role of sulfur in the metabolism of sulfur-oxidizing bacteria?
they oxidize sulfur and reduced sulfur compounds for an energy source
Facultative Anaerobes- aerobic chemoorganotrophs
-prefer to use aerobic respiration but they can ferment 1. Corynebacterium: -gram + pleomorphic rods often club-shaped and arranged to for V shapes ex) corynebacterium- most facultative anaerobes but some are string aerobes. can live harmlessly in the throat or cause diphtheria 2. Enterobacyeriaceae: -gram - rods -ferment glucose, can be motile by flagella -40 recognized genres -intestinal tract and soil ex)Enterobacter, Klebsiella, proteus, and E coli (normal microbiota) ex)shigella, salmonella enterica, and some strains of E coli (cause diarrheal disease) coliforms- enteric bacteria that ferment lactose ( E coli) 3. Vibrio: -marine environments -require low levels of NA+ for growth -gram - straight/curved rods -some are bioluminescent Ex)V chloerae and V parahaemolyricus (gi disease) Ex) V vulnificus (systemic illness)
How does Agrobacterium benefit from inducing a plant tumor?
they transfer dna which causes uncontrolled growth. The dna also encodes enzymes that direct the synthesis of opine which agrobacterium can use as a nutrient source
What metabolic process creates the rotten-egg smell characteristic of many anaerobic environments?
through anaerobic respiration of glucose using sulfate/sulfide as a terminal electron acceptor