MIBO3500 Exam 3

This Knowt is meant to be used to study for Dr. Francine Scott's MIBO3500 Exam 3.

How was traditional microbial taxonomy defined?

Traditional microbial taxonomy was not rooted in evolutionary relatedness but was rather based on the diseases a microbe caused or on a process a microbe performed.

polyphasic taxonomy

a modern form of microbial taxonomy that is based on the genotype, phenotype, and evolutionary rRNA of a microbe

group Deep-Branching Thermophiles

a group of bacteria that diverged the earliest from ancestral archaea and eukaryotes that prefer to live in warm environments

Which group of bacteria have the fastest rates of binary fission?

Deep-branching thermophiles have the fastest rates of binary fission of all bacteria. Because of this, deep-branching thermophiles also have a high mutation rate.

phylum Aquificae

a phylum of group Deep-Branching Thermophiles (“water maker”) that oxidize hydrogen gas with molecular oxygen to synthesize water; phylum Aquificae have ether-linked membrane lipids which are usually found in archaeal species

thermocrinis ruber

a species of bacteria (of phylum Aquificae, group Deep-Branching Thermophiles) that grows in two different ways depending on the media that it is grown in; in standard lab media, it grows as a bacillus rod; when exposed to water current, it grows as a long “streamer”

phylum Thermotogae

a phylum of group Deep-Branching Thermophiles that have loosely-bound sheaths with an absence of a “classical” outer membrane; phylum Thermotogae have a mosaic genome of bacterial and archaeal ancestry

mosaic genome

a genome that has two or more cell lineages with different genotypes in a single organism

thermotoga maritima

a species of bacteria (of phylum Thermotogae and group Deep-Branching Thermophiles) that has a few distinct properties:

• has one of the highest recorded growth temperatures (90°C)

• during cell growth, the “sheath” extends from the poles of the cell and grows while the cytoplasm halts growth to compensate

group/phylum Cyanobacteria

the largest, most diverse group of photosynthetic bacteria

What are some properties that all Cyanobacteria share?

• all are oxygenic

• all have thick peptidoglycan walls

• all appear green because of the predominant blue and red absorption by chlorophylls

How do Cyanobacteria interact with their environment?

Cyanobacteria share many kinds of mutualistic associations with other species of bacteria in the environment; for instance, cyanobacteria will participate in multi-layered microbial mats (in which they lay on the top to photosynthesize efficiently).

microbial mat

a distinctly multi-layered sheet of microorganisms that mainly contain bacteria and archaea

What types of growth can Cyanobacteria exhibit?

these type of bacteria can exhibit filamentous, colonial, or “multicellular” communities during cell growth

heterocyst

a specialized cell used for nitrogen fixation that is produced when an organism is nitrogen deprived

How does a heterocyst prevent the diffusion of oxygen into the cell?

The thick cell wall of a heterocyst prevents the diffusion of oxygen into the heterocyst which would inactivate nitrogenase.

thylakoid

an organelle that is found in Cyanobacteria that is used for photosynthesis

carboxysome

an organelle that is found in Cyanobacteria that is used to fix carbon dioxide

phylum Firmicutes

a phylum of group Gram-Positive Bacteria that are low-GC; many form endospores and many are pathogens

genus Clostridium

a genus (of group Gram-Positive Bacteria and phylum Firmicutes) that are obligate anaerobe bacillus that can form terminal “drumstick” spores

endospore

a dormant asexual spore that is released from within a bacterial cell

What are the steps of endospore formation?

1. A septum forms near one pole of the cell. DNA replicates and extends into an axial filament.

2. The septum separates the forespore from the mother cell. DNA is pumped through the septum until each compartment gets a chromosome.

3. The mother cell engulfs the forespore by surrounding it with a second phospholipid membrane.

4. The chromosomes of the mother cell disintegrate.

5. The spore coat of the forespore is synthesized; the forespore is then released and remains dormant until germination.

What is an endospore made out of?

An endospore is composed of proteins, modified peptidoglycan (less cross-linked), DNA, RNA, ribosomes, peptidoglycan, and lipids.

clostridium botulium

a species of bacteria (of group Gram-Positive Bacteria, phylum Firmicutes, and genus Clostridium) that is the agent of foodborne botulism; they are common in the environment/soil and their spores allow for dormant survival until anaerobic conditions are met

How is infant botulism caused and how can it be treated?

Infant botulism is caused to due to an exposure to endospores or to toxin. A common route of exposure to endospores is the consumption of honey before the age of one; this causes infant botulism due to immature gut microflora that can’t combat clostridium botulium endospores. Infant botulism is treated with intensive care and/or an antitoxin.

How is adult botulism caused and how can it be treated?

Adult botulism is caused due to an exposure to toxins. There are many routes of exposure, but the most common route of exposure is foodborne botulism. Foodborne botulism is caused to due to the consumption of improperly canned foods. Adult botulism is treated with intensive care and/or an antitoxin.

What are some challenges related to controlling endospores?

Endospores can be resistant to heat, lytic enzymes and chemical, UV radiation, biocides, and core hydration. Endospores can maintain dormancy due to being resistant to multiple strategies of eradication.

How does UV radiation work when trying to control endospores?

UV radiation is used to surface decontamination. However, when this is used to combat endospores, the UV light can mutate endospore DNA which can make combating endospores even harder than it already is.

How does wet heat work when trying to control endospores?

Wet heat is used to clean medical/surgical supplies, growth media, and hospital waste, but not all materials can withstand wet heat. Some endospores will germinate in wet heat and some are heat resistant which renders wet heat ineffective.

autoclave

a machine used to destroy endospores in high temperature and high pressure with wet heat

What substances are not safe to use in an autoclave?

Plastics, reactive/corrosive/toxic chemicals, closed liquid containers, and radioactive material are not safe to use in an autoclave.

What is an effective multi-approach procedure to control the spread of endospores in a facility?

An effective multi-approach procedure to control the spread of endospores could look like the following:

• wash hands with soap and water frequently

• clean equipment with a sporicidal agent every time it is used

• avoid using certain antibiotics while promoting the use of probiotics

• test for endospore exposure frequently

• always wear PPE and gloves to reduce exposure to endospores

phylum Actinobacteria

a phylum of group Gram-Positive Bacteria that are high-GC; many can form multicellular filaments and are acid-fast

genus Streptomyces

a genus (of group Gram-Positive Bacteria and phylum Actinobacteria) that are:

• aerobic and non-motile

• inhabit a large amount of culturable soil microbes

• produce geosmin

• they produce secondary metabolites that are medically useful (for antibiotics and anticancer drugs)

• are nonpathogenic

• have linear chromosomes with telomeres

• they grow onto and into their substratum

geosmin

a natural bicyclic terpene with an earthly odor that is produced by genus Streptomyces

substrate mycelium

a mycelium produced by vegetative Streptomyces cells

aerial mycelium

a mycelium produced by Streptomyces cells under nutrient limitation and/or stress; this type of mycelium can “cannibalize” substrate mycelium for nutrients

arthrospore

an exospore formed from aerial mycelium that can disperse into the wind

What are some differences between an endospore and an exospore?

Some differences between endospores and exospores include:

• endospores are located within the vegetative cell while exospores are located outside of the vegetative cell

• only one endospore is produced per vegetative cell while numerous exospores can be produced per vegetative cell

broad-spectrum antibiotic

a type of antibiotic that are effective against many species of bacteria

narrow-spectrum antibiotic

a type of antibiotic that is effective against few or a single species of bacteria

bactericidal antibiotic

a type of antibiotic that kills target organisms; bacterial death occurs quickly often through the lysis of the cell

bacteriostatic antibiotic

a type of antibiotic that prevent the growth of target organisms; the immune system would eventually kill the intruding microbe or anatomical actions will “flush” out the microbe

minimum inhibitory concentration (MIC)

the lowest concentration of an antibiotic that prevents microbial growth; this varies for different bacterial species and is tested by diluting the antibiotic

What are the main targets for antibiotics?

Antibiotics target the synthesis of the cell wall, DNA/RNA, protein, and the assembly of the bacterial cell wall.

What are the four steps of peptidoglycan synthesis?

1. NAG & NAM precursors are synthesized in the cytoplasm.

2. The precursors are carried across the cell membrane by bactoprenol.

3. The precursors are polymerized to the existing cell wall structure by transglycosylases.

4. The peptide side chains are cross-linked by transpeptidases.

bactoprenol

a hydrophobic alcohol that carries NAG & NAM precursors across the phospholipid bilayer of the cell membrane during peptidoglycan synthesis

transglycolsylase

an enzyme that catalyzes the polymerization of peptidoglycan from an existing cell wall structure using NAG & NAM precursors

transpeptidase

an enzyme that catalyzes the cross-link of the peptidoglycan synthesis

bacitracin

an antibiotic designed to halt peptidoglycan synthesis before NAG & NAM precursors can be transported across the cell membrane (i.e. stops bactoprenol); this antibiotic may lead to kidney toxicity if ingested, so only topical ointments of this antibiotic are advised

vancomycin

an antibiotic designed to halt peptidoglycan synthesis before NAG & NAM precursors can be polymerized and cross-linked; this antibiotic cannot transmit well across phospholipid bilayers

What are some consequences of vancomycin’s inability to penetrate phospholipid bilayers?

Some consequences of this phenomenon include:

• Gram-Negative bacterium are naturally resistant

• Gram-Positive bacterium are sensitive

• Little absorption in the human gastrointestinal tract

quinolone

a type of antibiotic designed to target DNA polymerases during DNA replication

rifampin

a type of antibiotic designed to target RNA polymerases during the transcription of DNA

tetracycline

a type of antibiotic designed to target the translation of mRNA in ribosomes

daptomycin

an antibiotic designed to alter bacterial cytoplasmic membrane fluidity that causes a cell to disassociate

What are some consequences of the fact that daptomycin is only effective on cytoplasmic membranes?

Some consequences of this phenomenon include:

• gram-negative bacterium are naturally resistant

• gram-positive bacterium are sensitive

• there is limited use of this antibiotic in oral doses

What are the three main mechanisms of antibiotic resistance?

1. A bacteria can destroy/pump out an antibiotic before it enters the cell.

2. A bacteria can add modifying groups that inactivate an antibiotic which can prevent an antibiotic from binding.

3. A bacteria can dislodge an antibiotic already bound to its target.

efflux pump

a protein pump in a bacterial membrane/periplasmic space that use specific transporters and transport complexes to pump antibiotics out of the cell

multidrug resistance (MDR) efflux pump

an efflux pump that is resistant to multiple drugs simultaneously

ribosome protection/rescue

a method of antibiotic resistance in gram-positive bacterium in which they produce proteins that bind to ribosomes and dislodge antibiotics

archaea

a domain of life that is the most ecologically diverse of the three domains; these organisms are associated with extreme habitats, but may sometimes be found in the open ocean or soil

cannulae

an extracellular structure unique to archaea that connect cells after division that creates a dense network composed to numerous cells and tubes

Why is archaeal phylogeny a challenge to define?

Archaeal phylogeny is a challenge to define because archaea are difficult to culture & PCR, their genomes are “recombinogenic”, and their classifications are frequently under revision.

psuedopeptidoglycan

a component of the archaeal cell wall that is composed of N-acetylglucosamine and N-acetyltalosaminuronic acid (NAG & NATS)

N-acetyltalosaminuronic acid (NATS)

a chemical species that is found in pseudopeptidoglycan instead of N-acetylmuramic acid (NAM)

How do cell walls differ from archaeal species to archaeal species?

Some archaea have pseudopeptidoglycan in their cell wall, but some other species might not have any pseudopeptidoglycan at all. Some species of archaea might have just an S-layer or just a capsule; it depends on the species of archaea.

How do archaeal species stain with a gram stain test?

Archaeal species can stain either gram-positive or gram-negative, so it’s generally not used for archaeal species.

How do archaeal lipids differ from bacterial lipids?

Archaeal lipids are linked by ether linkages that use L-glycerol unlike in bacterial/eukaryotic lipids that are linked by ester linkages that use D-glycerol.

How do archaeal genomes compare to bacterial and eukaryotic genomes?

Archaeal genomes are circular and contain operons like bacterial genomes and have introns and histones like eukaryotic genomes.

Can an archaea be pathogenic to other types of organisms?

No, archaea cannot be pathogenic to other organisms. Archaea can only be parasitic to other archaeal species.

What is the biochemical dynamic between a archaeal “parasite” and a archaeal host?

The archaeal parasite cannot synthesize lipids, amino acids, and nucleotides on its own, so it needs a host cell to assist in the synthesis of these essential molecules. Highly colonized archaeal hosts are growth impaired due to constantly being drained by archaeal “parasites”.

How are archaeal parasites and archaeal hosts hypothesized to be connected?

Archaeal parasite and archaeal hosts are hypothesized to be connected through a pore in the cell wall.

ammonia oxidizing archaea (AOA)

a type of archaea that can be found in the open ocean and the human skin

• in the ocean, they recycle ammonia and act as a source of nitrite for marine phytoplankton

• on the human skin, they metabolize ammonia and contribute to the control of the pH of the skin

methanogens

a type of archaea that release methane from the soil and digestive habitats that contribute to human and animal digestion

eukaryote

a domain of life defined by the presence of a nucleus and other membrane-bound organelles

Why do eukaryotes pose a challenge to define?

Eukaryotes are a challenge to define for a few reasons:

• complex eukaryotic cells frequently lose structures through reductive (degenerative) evolution

• superficially similar forms of organisms have evolved independently in distantly related taxa

• the evolution of eukaryotes includes multiple events of endosymbiosis

reductive evolution

the loss of genes and their corresponding functions as a result of evolution over a large volume of generations

convergent evolution

the evolution of similar morphological traits between unrelated organisms in different taxonomical groups

endosymbiosis

a symbiosis in which one organism lives inside of another organism in which both organisms don’t hinder each other

group Opisthokonts

a group of eukaryotic organisms that include animals and fungi that have the presence of unpaired flagellum at some point in their life cycle; organisms of this group share several key gene insertions (EF1α gene) and deletions

class Choanoflagellates

a class of group Opisthokonts that diverged most recently from animals that have collared cells that closely resemble the choanocyte cells of colonial sponges

choanocyte

a flagellated cell found in colonial sponges that circulate water and digest food particles

absorptive nutrition

a form of consumption observed in fungi in which fungi secrete enzymes and then absorb the broken-down nutrients

hyphae

multinucleate cell filaments found in fungi that can extend and form branches that generate mycelium

chitin

a chemical species found in the cell wall of fungi

ergosterol

a chemical species found in the cell membranes of fungi

yeast

a unicellular fungal organism that serves as a model for many human cellular processes

candida albicans

a fungal organism that is a part of the normal flora; this organism can cause a yeast infection on the skin or in mucosal membranes in healthy individuals as a result of the disruption of flora or by sexual contact

What can be used to treat candida albicans?

candida albicans can be treated using anti-fungals such as Monistat and Thrush; these anti-fungals work by preventing the formation of the fungal cell membrane which causes cell contents to leak out

pseudopod

a lobe-shaped extension of amoebic organisms that controls the flow of liquid through the cytoplasm through its extension; these have been studied closely for their relevance to human white blood cells

naegleria fowleri

an amoebic organism that thrives in warm freshwater lakes, rivers, and streams; while transmission to humans is rare, infections are almost always fatal (i.e. the “brain-eating” amoeba)

Dimitri Ivanovsky

he studied Tabacco Mosaic Disease that causes the mottling, stunting, and wrinkling of tabacco leaves; he observed that the agent of disease was not removed by filters

Beijernick

he studied Tabacco Mosaic Disease that causes the mottling, stunting, and wrinkling of tabacco leaves; he observed that the agent of disease was not removed by filters and proposed that the agent must be so small that it passes through filters

Loeffler & Frosch

two scientists who were former students of Robert Koch who studied Foot & Mouth Disease in livestock; they observed that the agent of disease was not removed by a filter

Peyton Rous

he studied sarcomas (tumors) in chickens; he observed that cell free “filtrate” from diseased chickens could transmit tumors to healthy chickens by a “virus”

June Almeida

she was the first to use an electron microscope to observe coronaviruses

What are some general properties of viruses?

Some general properties of viruses include:

• they are composed of about one molecule of DNA/RNA enclosed in a coat of protein

• they cannot reproduce independent of living cells nor carry out cell division

• they can exist extraceullarly

nucleocapsid

a viral structure composed of the capsid and a nucleic acid

capsid

a protein coat that protects the DNA/RNA of a virus