Ch. 11 The Diversity of Bacteria and Archaea

extreme thermophiles

archaea found near volcanic vents and fissures that release sulfurous gases and other hot vapors others are found in hydrothermal vents in the deep sea and hot springs include some methanogens

coliforms

enteric bacteria that characteristically ferment lactose

the genus Corynebacterium

facultative anaerobes, some strict aerobes widespread in nature Gram-pos. pleomorphic rods, often club-shaped and arranged to form V shapes or palisades many species reside harmlessly in the throat, but toxin-producing strains of C. diphtheriae can cause diphtheria

thermophilic extreme acidophiles

members of 2 genera of archaea: Thermoplasma and Picrophilus are notable for growing in extremely acidic, hot environments Thermoplasma: optimal pH 2 Picrophilus: pH below 1

the genus Epulopiscium

Gram-pos. cigar-shaped bacteria that live in the intestinal tract of surgeon fish much larger than most prokaryotes and each cell has thousands of copies of chromosomes scattered throughout the cell unusual life cycle: rather than undergoing typical binary fission, get very large and lyse, releasing up to 7 daughter cells

green bacteria

anoxygenic phototrophs Gram-neg organisms that are typically green or brownish in color

purple bacteria

anoxygenic phototrophs Gram-negative organisms that appear red, orange, or purple due to their light-harvesting pigments unlike other anoxygenic phototrophs, components of photosynthetic apparatus all contained within cytoplasmic membrane

phycobiliproteins

absorb energy from wavelengths of light not well absorbed by chlorophyll

sulfur-oxidizing bacteria

aerobic chemolithotrophs Gram-negative rods or spirals, which sometimes grow in filaments obtain energy by oxidizing elemental sulfur and reduced sulfur compounds O2 serves as terminal electron acceptor, generating sulfuric acid important in sulfur cycle

leptospira

aerobic, some are free-living in aquatic environments whereas others grow within animals

extreme halophiles

archaea that live in highly saline environments require a minimum of 9% NaCl produce pigments- growth can be seen as red patches on salted fish and pink blooms in concentrated salt water ponds aerobic or facultatively anaerobic chemoheterotrophs, but some can obtain additional energy from light --> light-sensitive pigment bacteriorhodopsin- absorbs energy from the cell to create proton gradient that can be used to drive flagella or synthesize ATP come in variety of shapes, including rods, cocci, discs, and triangles

obligate intracellular parasites

cannot reproduce outside a host cell tiny Gram-neg. rods or coccobacilli

L. interrogans

cause leptospirosis- can be transmitted in urine of infected animals

filamentous anoxygenic phototrophic bacteria

form multicellular arrangements and exhibit gliding motility many have chlorosomes as a group, diverse metabolically

Bacillus and Clostridium

most common Gram-pos rod-shaped bacteria that form endospores

Agrobacterium

plant pathogens that cause tumor-like growths ability to genetically alter plants for their own benefit attach to wounded plant tissue, then transfer a portion of a plasmid to plant cell transferred DNA encodes the ability to synthesize plant growth hormones, causing uncontrolled growth of the plant tissue and resulting in a tumor

facultative anaerobes

preferentially use aerobic respiration if O2 is available, but can also ferment

the genera Chlamydia and Chlamydophila

quite different from the other obligate intracellular parasites transmitted directly from person to person, have a unique growth cycle inside host cell, initially exist as non-infectious reticulate bodies, which reproduce by binary fission later in the infection, differentiate into small, dense-appearing infectious elementary bodies, which are released when the host cell ruptures

strep and corynebacterium

reside in the respiratory tract

filamentous cyanobacteria

responsible for maintaining structure and productivity of soils in cold desert areas provide important source of nitrogen and organic carbon in otherwise nutrient-poor soils

The genera Rickettsia, Orientia, and Ehrlichia

responsible for several serious human diseases spread by blood-sucking arthropods such as ticks and lice

Spirillum volutans

forms volutin granules, which are storage form of phosphate

Clostridium species and members of Enterobacteriaceae

thrive in the intestinal tract

the genus Haemophilus

Gram-neg. coccobacilli that are "blood loving" require hematin and/or NAD many species are common microbiota of respiratory tract H. influenzae- ear infx, resp. infx, and meningitis, primarily in children

luciferase

Enzyme used in bioluminescence

spirochetes

Gram-neg. bacteria with a spiral shape and a unique motility mechanism that allows them to move through thick, viscous environments such as mud distinguishing characteristics include their spiral shape, flexible cell wall, and motility by means of endoflagella rotation of the endoflagella within the limited area between the cytoplasmic and outer membranes causes cell to move like a corkscrew, sometimes bending and twisting include free-living species that inhabit aquatic environments as well as ones that reside on or in animals

the family Enterobacteriaceae (AKA enterics)

Gram-neg rods most reside in intestinal tract of humans and other animals, although some thrive in rich soil facultative anaerobes that ferment glucose and, if motile, generally have peritrichous flagella family includes over 40 recognizable genera that can be distinguished using biochemical tests

the Genus Azobacter

Gram-neg. pleomorphic, rod-shaped bacteria that live in soil can form type of resistant cell called a cyst- have negligible metabolic activity and can withstand drying and UV radiation but not high heat also notable for ability to fix nitrogen in aerobic conditions --> nitrogenase inactivated by O2, but extremely high respiration rate consumes O2 so rapidly, creates a low O2 environment in cell, protein in cell binds nitrogenase, thereby protecting it from O2 damage

Rhizobium

Gram-neg. rod-shaped bacteria that often fix N and form intimate relationships with legumes form a mutually beneficial relationship with certain types of plants live within cells in nodules formed on the roots of plants plants synthesize protein leghemoglobin- binds and controls levels of O2 --> within resulting microaerobic environment bacteria able to fix N

the genus Spirillum

Gram-neg. spiral-shaped, microaerophilic bacteria wet mounts may be seen moving to narrow zone near edge of coverslip, where O2 availability is in optimal amount

bioluminescent bacteria

Gram-neg. straight or curved rods facultative anaerobes typically inhabit marine environment

the genus Pseudomonas

Gram-negative rods that have polar flagella and often produce pigments although most are strict aerobes, some can grow anaerobically if nitrate is available as a terminal electron acceptor do not ferment and are oxidase positive as a group, have extremely diverse biochemical capabilities --> some can metabolize more than 80 different substrates widespread, typically inhabit soil or water most harmless, some cause disease in plants and animals

the genus Staphylococcus

Gram-pos. cocci that are facultative anaerobes most reside harmlessly as part of normal microbiota of skin catalase-pos.

the genus Bifidobacterium

Gram-pos., irregular, rod-shaped anaerobes that reside primarily in intestinal tract of humans and other animals most common members of the intestinal microbiota of breast-fed infants and are thought to provide a protective function by excluding disease-causing bacteria

helicobacterium

Gram-positive endospore-forming rods related to members of genus Clostridium

the genus Propionibacterium

Gram-positive pleomorphic rods that produce propionic acid as primary fermentation end products can also ferment lactic acid --> can extract energy from waste products of other bacteria swiss cheese production --> propionic acid gives typical flavor CO2 creates characteristic holes also found in intestinal tract and in anaerobic microenvironment on skin

ecophysiology

study of physiological mechanisms bacteria and archaea have adapted to live in terrestrial and aquatic environments

the genus Clostridium

anaerobic chemoorganotrophs- fermentation gram positive rods that can form endospores common soil inhabitants, vegetative cells live in anaerobic microenvironment created when aerobic organisms consume available O2 vegetative cells that develop from endospores are responsible for a variety of diseases, including tetanus, gas gangrene, botulism, C. diff some species are normal inhabitants of intestinal tract of humans and other animals as a group, ferment wide variety of compounds including sugars and cellulose some species can ferment amino acids by an unusual process that oxidizes one amino acid, using another as a terminal electron acceptor

lactic acid bacteria

anaerobic chemoorganotrophs- fermentation gram-positive bacteria that produce lactic acid as a major end product of their fermentative metabolism streptococcus, enterococcus, lactococcus, lactobacillus, leuconostoc most can grow in aerobic environment, but they typically only carry out fermentation can easily be distinguished from other bacteria that grow in presence of O2 because they lack catalase

sulfur oxidizers

archaea Sulfolobus species found at the surface of acidic sulfur-containing got springs such as those found in Yellowstone National Park obligate aerobes that oxidize sulfur compounds, using O2 as a terminal electron acceptor to generate sulfuric acid thermoacidiophilic, only growing above 50C at pH between 1 and 6

the genus Campylobacter

curved Gram-neg. rod microaerophile C. jejuni- diarrheal disease in humans, typically lives in intestinal tract of animals

the genus Helicobacter

curved Gram-neg. rod microaerophile H. pylori inhabits the stomach, where it can cause stomach and duodenal ulcers, also has been liked to stomach cancer, produces enzyme urease- breaks down urea to produce ammonia, which neutralizes acid in cell's immediate surroundings

oxygenic phototrophs

cyanobacteria thought to be earliest use water as source of electrons for reducing power, generates O2

prosthecate bacteria

diverse group of Gram-neg. bacteria that have projections called prosthecae- extensions of the cytoplasm and cell wall, provide increased SA to facilitate absorption of nutrients, some allow organisms to attach to solid surfaces

myxobacteria

group of aerobic Gram-neg. rods that have a unique developmental cycle as well as a resting stage when conditions favorable, cells secrete a slime layer that other cells then follow, creating a swarm of cells when nutrient levels are low, form a multicellular structure- fruiting body- cells within differentiate to become spherical, dormant forms called microcysts- much more resistant to heat, drying, and radiation than vegetative cells, but are much less resistant than endospores important in nature as degraders of complex organic substances, can digest bacteria and certain algae and fungi include genera Chondromyces, Myxococcus, and Stigmatella

primary producers

harvest energy of sunlight, using it to convert CO2 into organic compounds

Bacillus species

include both obligate aerobes and facultative anaerobes B. anthracis- anthrax

anoxygenic phototrophs

likely earliest photosynthetic organisms use H2S or organic compounds instead of H2O for electrons live in environments that have adequate light but little or no O2 typical habitats= bogs, lakes, upper lyaer of muds have unique type of chlorophyll- bacteriochlorophyll often store sulfur granules, which can later be used as as source of electrons for reducing power

the genus Legionella

most common in aquatic environments, where they often live within protozoa Gram-neg. obligate aerobes that use amino acids, but not carbohydrates, as a source of carbon and energy

anaerobic habitats

mud and tightly packed soils limit diffusion of gases, and any O2 that penetrates is quickly converted to water by aerobically respiring organisms aquatic environments if they contain nutrients that promote rapid growth of O2 consuming microbes human body: intestinal tract, skin, and oral cavity have microenvironments created by localized depletion of O2 by aerobes

The genus Thermus

obligate aerobe thermophilic valuable because of heat-stable enzymes

The genus Micrococcus

obligate aerobes Gram-positive cocci found in soil and dust particles, inanimate objects, and skin because they are often airborne, can easily contaminate bacteriological media

lactobacillus

rod-shaped bacteria common members of microbiota in mouth and healthy vagina during childbirth years also present in decomposing plant material, milk, and other dairy products

the genus Bordetella

small, Gram-neg. coccobacilli that only grow aerobically special media must be used for their cultivation because they are nutritionally fastidious B. pertussis- whooping cough B. bronchiseptica- respiratory infection in dogs

the genus Bacteroides

small, strictly anaerobic, Gram-neg. rods and coccobacilli inhabit the mouth, intestinal tract, and genital tract of humans and other animals make up ~1/3 of bacteria in human feces and play important role in digestion often responsible for abscesses and bloodstream infections that follow appendicitis and abdominal surgery many are killed by brief exposure to O2

negative side of cyanobacteria

some produce geosmin- chemical that has a distinctive "earthy" odor and makes drinking water taste odd some aquatic species produce toxins that can be deadly to an animal when consumed

the genus Borrelia

spirochetes that typically inhabit body fluids and mucous membranes of humans and other animals 3 species are pathogens, transmitted by arthropods such as ticks and lice unusual feature- genome= linear chromosome and many linear circular plasmids

the genus Treponema

spirochetes that typically inhabit body fluids and mucous membranes of humans and other animals obligate anaerobes or microaerophiles that often inhabit the mouth and genital tract T. pallidum- causes syphilis

enterococcus

typically inhabit intestinal tract of humans and other animals

the genus Deinococcus

unique in extraordinary resistance to damaging effects of gamma radiation scientists anticipate that through genetic engineering, may eventually help clean up soil and water that have been contaminated by radioactive wastes

nitrogen-fixing cyanobacteria

very important ecologically --> can incorporate both N2 + CO2 into organic material --> can then be used by other organisms like all cyanobacteria, help limit atmospheric CO2 buildup by using the gas as carbon source nitrogenase- enzyme complex that catalyzes nitrogen fixation, destroyed by O2

the genus Streptomyces

include more than 500 species of aerobic Gram-pos. bacteria that resemble fungi in their pattern of growth like the fungi, form a mycelium (visible mass of branching filaments), and this gives colonies a chalky surface filaments= hyphae, tips have chains of characteristic dormant spore- conidia- resistant to drying and are easily spread in air currents produce variety of extracellular enzymes that allow them to degrade various organic compounds also responsible for the characteristic "earthy" odor of soil naturally produce a wide array of medically useful antibiotics, including streptomycin, tertracycline, and erythromycin

lactococcus

include species used to make cheeses

streptococcus

inhabit oral cavity, generally as part of normal microbiota

the genus Mycoplasma

lack a cell wall, but most have sterols in their membrane to provide strength and rigidity among smallest forms of life, and their genomes are thought to be about the minimum size for encoding the essential functions for a free-living organism particular concern in laboratories studying viruses and eukaryotic cell physiology --> small bacteria can pass through the filters used to sterilize tissue culture media, can grow to very high number in media without casting cloudiness M. pneumoniae- "walking pneumonia"- cannot be treated with penicillin or other antibiotics that interfere with peptidoglycan synthesis

anaerobic chemolithotrophs

obtain energy by oxidizing inorganic chemicals such as hydrogen gas terminal electron acceptor- CO2 or sulfur relatively few have been discovered, most are members of domain Archaea

the genus Neisseria

Gram-neg. bacteria typically kidney-bean-shaped cocci in pairs common microbiota of animals including humans, growing in mucous membrane typically aerobes, but some can grow anaerobically if a suitable terminal electron acceptor such as nitrite is present N. gonorrheae- gonorrhea N. meningitidis- meningitis

sulfur- and sulfate-reducing bacteria

anaerobic chemoorganotrophs essential components of sulfur cycle generally live in mud that has organic material and oxidized sulfur compounds most bacteria are mesophiles or thermophiles archaea are hyperthermophiles, inhabit extreme environments such as hydrothermal vents

flashlight fish

carries bioluminescent bacteria in a light organ below its eye- by opening and closing a lid that covers the light organ, the fish can control the amount of light released, believed to confuse predators and prey

aerobic chemolithotrophs

obtain energy by oxidizing reduced inorganic chemicals, using O2 as a terminal electron acceptor

sulfur-oxidizing, nitrate-reducing marine bacteria

some marine bacteria store both sulfur (energy source) and nitrate (terminal electron acceptor) --> not found in the same location ex. Thioploca cells "commute" between the sulfur-rich sediment and the nitrate-rich waters, gathering and storing their energy source and terminal electron acceptors as needed

hydrogen-oxidizing bacteria

thermophilic and typically live in hot springs based on 16S rDNA studies, one of the earliest bacterial forms to exist on Earth

endoflagella

aka axial filaments contained within periplasm

spirochaeta

anaerobes or facultative anaerobes that live in muds and anaerobic waters

the genus Caulobacter

because of remarkable like cycle, serve as a model for research on cellular differentiation entirely different events occur in an orderly fashion at opposite ends of the cell have a single polar prostheca, commonly called a stalk at tip- an adhesive holdfast- structure that provides a mechanisms for attachment to multiply, cell elongates and divides by binary fission, produces a motile swarmer cell at the end opposite the stalk swarmer cell has a flagellum, located at the pole opposite the site of division swarmer cell detaches and moves to a new location, where it adheres via a holdfast near the base of its flagellum, then loses its flagellum, replacing it with a stalk

purple sulfur bacteria

cells relatively large, some motile by flagella may have gas vesicles, allowing them to move up or down to preferred level in water column most store sulfur in intracellular granules preferentially use H2S to generate reducing power, although some can use other inorganic material or organic compounds many are strict anaerobes and phototrophs, but some can grow in absence of light aerobically, oxidizing inorganic or organic compounds as source of energy

Aliivibrio fischeri

colonize special organ in certain types of squid light thought to serve as type of camouflage, masking the squid's contrast against light from above and any shadow it might otherwise cast

Pseudomonas auruginosa

common opportunistic pathogen can grow in nutrient-poor environment and is resistant to many disinfectants and antimicrobial meds

H2S

compound responsible for rotten-egg smell of many anaerobic environments formed when sulfur compounds are used as terminal electron acceptors problem to industry because it reacts with metals, corroding pipes and other structures

magnetotactic bacteria

contain a string of magnetic crystals that align cells with the Earth's magnetism --> allows them to move up or down in the water or sediments thought to allow cells to locate the microaerophilic habitats they require

nitrifiers

diverse group of Gram-negative bacteria that obtain energy by oxidizing inorganic nitrogen compounds such as ammonium or nitrite include 2 metabolically distinct groups that typically grow in close association --> together they can oxidize ammonia to form nitrate

cyanobacteria

diverse group of over 60 genera of Gram-negative bacteria play essential role in biosphere primary producers inhabit wide range of environments, including freshwater and marine habitats, soils, and the surfaces of rocks many able to convert nitrogen gas to ammonia, which can be incorporated into cellular material- nitrogen fixation morphologically diverse aquatic often have gas vesicles large numbers accumulate in stagnant lakes or other freshwater habitats have phycobiliproteins

the genus Vibrio

facultative anaerobes typically found in marine environment because most species require at least low levels of Na for growth Gram-neg. straight or slightly curved rods V. cholerae- cholera V. parahaemolyticus- milder GI disease V. vulnifus- systemic illness, particularly in pts who have an underlying illness such as liver disease some species are bioluminescent

sheathed bacteria

form chains of cells encased within a tube plays protective role, helping the bacteria attach to solid objects in favorable habitats while sheltering them from attack by predators often interfere with sewage treatment and other industrial processes by clogging pipes spread by forming motile cells called swarmer cells that exit through the unattached end of the sheath, move to a new solid surface and attach, if enough nutrients present, they can multiply and form a new sheath, which gets longer as the chain of cell grows

acidithiobacillus

found in both terrestrial and aquatic habitats where their ability to oxidize metal sulfides can be used for bioleaching-used to recover metals

Green sulfur bacteria

found in habitats similar to those preferred by purple sulfur bacteria use H2S as source of electrons for reducing power and form sulfur granules outside cell accessory pigments located in structures- chlorosomes lack flagella, but many have gas vesicles all are strict anaerobes and none can use chemotrophic metabolisms

purple non-sulfur bacteria

found in wide variety of aquatic habitats, including moist soils, bogs, and rice paddies important characteristic that distinguishes them from the purple sulfur= preferentially use a variety of organic molecules rather than H2S as source of electrons for reducing power lack gas vesicles and if they story sulfur, granules form outside the cell remarkably versatile metabolically most can grow aerobically in absence of light using chemotrophic metabolism

methanogens

group of archaea that generate ATP by oxidizing hydrogen gas, using CO2 as a terminal electron acceptor many can also use alternative energy sources such as formate, methanol, or acetate representative genera= Methanospirillum and Methanosarcina found in anaerobic environment where H2 and CO2 are both available generally not found in environments containing high levels of sulfate, nitrate, or other inorganic electron acceptors commonly found in: swamps, marine sediments, rice paddies, and dig tracts of humans and other animals

the genus Bdellovibrio

highly motile Gram-neg. curved rods that prey on E. coli and other Gram-neg. bacteria when attacks, it strikes its prey with such force that it propels the prey a short distance parasite then attaches to its host and rotates with a spinning motion at the same time, makes digestive enzymes that break down lipids and peptidoglycan, eventually forming a hole in the cell wall of prey over period of several hours, degrades and utilizes prey's cellular contents derives energy by aerobically oxidizing amino acids and acetate increases in length, ultimately dividing to form several motile daughter cells when host cell lyses, progeny are released to find new hosts, repeating the cycle

the genus Hyphomicrobium

in many ways similar to Caulobacter except they have a distinct method of reproduction single polar prostheca of parent cell enlarges at tip to form a bud, continues enlarging and also develops a flagellum, eventually giving rise to a motile daughter cell daughter cell (swarmer cell) then detaches and moves to a new location, eventually losing its flagellum and forming a polar prostheca at the opposite end to repeat the cycle

Sulfur-reducing hyperthermophiles

obligate anaerobic archaea that use sulfur as a terminal electron acceptor, generating H2S harvest energy by oxidizing organic compounds and/or H2 can be isolated from hot sulfur-containing environments such as sulfur hot springs and hydrothermal vents include some of the most thermophilic organisms known

the genus Coxiella

obligate intracellular parasites only characterized species= C. burnetti- obligate intracellular bacterium that survives well outside the host cell during its intracellular growth, forms spore-like structures- small-cell variants (SCVs) that later allow it to survive in the environment causes Q fever of humans- most often acquired by inhaling bacteria shed from infected animals

the genus Wolbachia

obligate intracellular parasites only know species= W. pipentis- infects arthropods and parasitic worms primarily transmitted maternally via the eggs of infected females to their offspring in arthropods, uses unique strategies to increase the overall population of infected females does not infect mammals, but its medical importance has been recognized with the discovery that it resides within filarial worms that cause the disease river blindness and elephantiasis

obligate aerobes

obtain energy using respiration exclusively

chemotrophs

organisms that harvest energy by oxidizing chemicals

filamentous sulfur oxidizers

overgrowth in wastewater at treatment facilities causes problem called bulking- because masses of filamentous organisms do not settle easily, bulking interferes with processes that separate solid and liquid portions of waste

anaerobic chemoorganotrophs

oxidize organic compounds such as glucose to obtain energy often use sulfur or sulfate as a terminal electron acceptor

aerobic chemoorganotrophs

oxidize organic compounds to obtain energy, using O2 as terminal electron acceptors include wide assortment of bacteria, ranging from some that inhabit very specific environments to others that are ubiquitous

the genus Mycobacterium

widespread in nature and include harmless saprophytes- live on dead and decaying matter- as well as pathogens waxy cell wall (mycolic acids) acid-fast: once stained, resist destaining even with acidic decolorizing solution generally pleomorphic rods: often occur in chains that sometimes branch, or bunch together to cord-like groups M. tuberculosis- tuberculosis M. leprae- leprosy more resistant to disinfectants than most other vegetative bacteria resistant to many of the most common antimicrobial medications