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MBIO 1010 > Microbial Diversity > Flashcards

Microbial Diversity Flashcards

1
Q

What are the red dots on a a microorganism phylogenetic tree?

A

Phyla only known from metagenome sequencing from diverse environmental samples as they cannot be grown in the lab.

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1
Q

What are the 2 ways to describe microbial diversity?

A

Phylogenetic diversity: groups in phyla based on evolutionary relationships based on 16S rRNA gene sequence

Functional diversity: groups microbes based on the activities they carry out (e.g. anoxygenic phototrophs dispersed through several phyla)

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2
Q

What does the Microbial diversity phylogenetic tree based on 16S rRNA as of 2016?

A
  1. 92 named bacterial phyla
  2. 26 archaeal phyla
  3. 5 of the Eukaryotic super groups
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3
Q

What is the bacterial phyla tenericutes in terms of the cell wall and morphology? What is an example?

A

Mycoplasmas; phylogenetically related to Gram positives, but they don’t have a cell wall/peptidoglycan and gram stain negative. They are often pleomorphic (shapeless) as they have no cell wall. e.g. Mycoplasma genitalium.

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4
Q

What is Mycoplasma genitalium?

A

Bacteria that is the common cause of urethritis and pelvic inflammatory disease. It is the first free-living bacterium to have its genome sequenced as it is of the smallest genomes to sequecne (500 kbp)

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5
Q

What is phyla Actinobacteria and examples?

A

Second phylum of Gram positive bacteria that have a high content of Guanine and Cytosine (high GC Gram positives). Includes coryneform (club-shape) bacteria and mycobacteria. E.g. Corynebacterium diphtheriae, Propionic Acid Bacteria, Mycobacterium tuberculosis.

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6
Q

What is Corynebacterium diptheriae?

A

Actinobacteria that produces an exotoxin that inhibits protein synthesis and causes tissue death in the respiratory tract (diphtheria) and can lead to death by suffocation.

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7
Q

What is propionic acid bacteria?

A

Swiss cheese actinobacteria consume lactic acid and ferment it, producing the CO2 that creates holes in swiss cheese.

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8
Q

What are mycobacteria and a example?

A

Actinobacteria with a modified gram positive cell wall with a layer of mycolic acids outside the peptidoglycan layer, making them acid-fast.

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9
Q

What is mycobacterium tuberculosis?

A

A species of mycobacteria that is the cause of tuberculosis (slow, fatal, respiratory disease). It has a 24 hour generation time and colonies can take weeks to form on agar medium.

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10
Q

What are filamentous Actinobacteria in terms of oxygen use, morphology, gram stain, location, reproduction, and skills?

A

Genus of (mostly) obligatory aerobic filamentous Gram positives that form branching hyphae and mycelia and live in well aerated soils. Their hyphae produce reproductive spores for dispersal called conidia. They produce substances that kill or inhibit the growth of other microbes - antibiotics.

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11
Q

What are the steps to form conidia?

A
  1. Growth of hyphae
  2. curling of hyphae
  3. hyphae partitions into segments
  4. Cell walls thicken and constrict around segments
  5. Spores mature
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12
Q

What is bacteroidetes?

A

Large heterogeneous (lots of differences) phylum of Gram negative bacteria.

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13
Q

What is Bacteroides thetaioitamicron in terms of oxygen use, location and abilities?

A

Strict anaerobe of phylum bacteroidetes that is a numerically dominant microbe in the human large intestine. It produces enzymes to degrade polysaccharides to increase the variety of plant polymers that can be digested in the human gut

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14
Q

What is Acidobacteria?

A

Phyla recognized within the last 20 years, difficult to cultivate, first sequenced genome in 2009. Makes up between 20-50% of soil in microbial community.

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15
Q

What is Chlamydiae in terms of nutrition and cell wall?

A

Phyla of obligate intracellular parasites of gram negative cell wall type but lack peptidoglycan. It has a unique life cycle with two types (elementary and reticulate body)

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16
Q

What is the difference between Chlamydiae’s elementary and reticulate body?

A

Elementary body: Small dense dormant cell located outside a host cell that resists drying, allows infection of new host cells.

Reticulate body: Larger vegetative cells that multiply inside an existing host, not infective.

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17
Q

What is Chlamydia trachomatis?

A

Bactieria of phylum Chlamydiae that causes scarring, blindness, and trachoma (infection of the eye).

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18
Q

What is Planctomycetes?

A

Phyla of budding and appendaged (protein stalk for attachment) bacteria that lack peptidoglycan in the cell wall. Some have membrane-bound compartments inside the cell.

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19
Q

What is cyanobacteria in terms of structrue?

A

Phylum of bacteria that are unicelluar, filamentous, or branching filamentous that may form heterocysts (nitrogen-fixing cells)

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20
Q

Difference between chloroplasts and cyanobacteria?

A

Cyanobacteria: gram negative cell wall type (folded thylakoid inner membrane) with peptidoglycan.

Chloroplasts: double membraned, no peptidoglycan.

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21
Q

Where are cyanobacteria from?

A

Widely distributed in terrestrial, freshwater, and marine habitats as they are have the lowest nutritional requirements of any organisms (primary producers)

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22
Q

What types of metabolism are included in phylum proteobacteria?

A
  1. Chemolithotrophs
  2. Chemoorganotrophs
  3. Phototrophs
  4. Facultative organisms that can switch from one metabolic lifestyle to another
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23
Q

What are the 6 classes of proteobacteria? What is their cell wall type?

A

Alpha, beta, gamma, delta, epsilon, zeta. All are gram negatives.

24
Q

What is an example of a nonpathogenic alphaproteobacteria?

A

Rhizobium leguminosarum: nonpathogenic bacteria that forms root nodules on legumes in a symbiotic relationship. It fixates nitrogen into a bioavailable form while the plat provides protection and nutrients from the bacteria

25
Q

What is an example of a pathogenic alphaproteobacteria?

A

Rickettsia rickettsii: obligate intracellular pathogen carried by insects and transmitted via insect bites. It causes rocky mountain spotted fever and is the closest relative to the eukaryotic mitochondrion

26
Q

What are two examples of pathogenic and non-pathogenic betaproteobacteria?

A

nonpathogenic: neisseria mucosa lives on mucous membranes

pathogenic: neisseria gonorrhoeae, causes gonorrhea

27
Q

What is gammaproteobacteria?

A

Metabolically and ecologically diverse proteobacteria that usually grow well in lab and have become important research models

28
Q

Define escherichia coli in terms of class, gram stain, cell morphology, oxygen tolerance, motility, ability, and location?

A

Class: Gammaproteobacteria

Gram stain: negative

Cell morphology: bacillus

Oxygen tolerance: facultative aerobe

Motility: peritrichous flagella

Ability: Fermentation of lactose into mixture of acids and alcohols

location: intestine of warm-blooded animals and indicator of fecal contamination

29
Q

Define Pseudomonas Aeruginosa in terms of class, gram stain, cell morphology, motility, and qualities

A

Class: gammaproteobacteria

Gram stain: negative

Cell morphology: bacillus

Motility: polar flagella

Qualities: does not ferment sugars, naturally resistant to many antibiotics and disinfectants, opportunistic pathogen (causes infections in immunocompromised patients)

30
Q

What is deltaproteobacteria?

A

Phylum of proteobacteria that contains many species with strange behaviour.

31
Q

What is Myxococcus xanthus in terms of class, motility, nutrition?

A

Class: deltaproteobacteria

Motility: gliding

Nutrition: predatory - releases exoenzymes to lyse other bacteria for nutrients

Qualities: when starved cells migrate together to form complex multicellular fruiting bodies which differentiate into myxospores for dispersal

32
Q

What is Bdellovibrio bacteriovirus in terms of class, morphology, motility and nutritoin?

A

Class: deltaproteobacteria

Morphology: curved

Motility: Highly motile, monotrichous flagella

Nutrition: parasitic; penetrates cell wall of other proteobacteria and gram negative bacteria, multiplies in periplasm, break down cell wall

33
Q

What is Desulfovibrio?

A

Part of deltaproteobacteria. An obligately anaerobic sulfate reducers that play a role in oil well souring.

34
Q

What is Epsilonproteobacteria?

A

A small class of proteobacteria famous for a few microaerophilic spirillum shaped pathogens such as Campylobacter jejuni

35
Q

What is Campylobacter jejuni?

A

Member of epsilonproteobacteria that are frequently transmitted in under-cooked chicken. One of the most common causes of food-borne illnesses (e.g. gastroenteritis and bloody diarrhea)

36
Q

What is phyla firmicutes?

A

One of two phyla with Gram positive cell walls including lactic acid bacteria and non-lactic acid bacteria.

37
Q

What is lactic acid bacteria?

A

Aerotolerant anaerobic firmicute that produce lactic acid as an end product of fermentation

38
Q

What are two examples of a lactic acid bacteria?

A

Lactobacillus delbrueckii: yogurt production

Streptococcus pyogenes: strep throat, scarlet fever, flesh eating disease.

39
Q

What are two examples of non-latic acid bacteria?

A

Staphylococcus aureus: facultative aerobe that form grape-like clusters and produces acid on mannitol salt agar; frequent cause of nosocomial infections

Staphylococcus epidermis: normal commensal on skin that can do not produce acid on mannitol salt agar

40
Q

What is Bacillus subtilis?

A

nonpathogenic, endospore-forming lab bacterium of phylum Firmicutes used as a model for gram positive cell structure, cell division, and differentiation into endospores

41
Q

What is Clostridium botulinum in terms of phylum, dormancy, oxygen tolerance, metabolism, and qualities?

A

Phylum: Firmicutes

Dormancy: endospore forming

Oxygen tolerance: Strict anaerobe

Metabolism: fermentative metabolism

Qualities: secretes variety of exoenzymes to degrade plant material and deadly neurotoxin that causes botulism.

42
Q

What are two examples of hyperthermophilic bacteria?

A

Thermus aquaticus and Deinococcus radiodurans

43
Q

What is Thermus aquaticus?

A

A hyperthermophilic chemoorganoheterotroph that has heat resistant enzymes that is an essential tool for PCR as it allows DNA synthesis reactions to be carried out quickly in high temperatures.

44
Q

What is deinococcus radiodurans in terms of abilities and cell wall?

A

A hyperthermophilic bacteria extremely resistant to radiation and have highly effective DNA repair mechanisms. In response to massive DNA damage, nucleoids from the two cells (tetrad/tetrads) fuse to facilitate repair. Has a gram negative cell wall type but stains gram positive because of thick peptidoglycan.

45
Q

What are the five archaea phyla?

A
  1. Euryarchaeota: extreme halophiles
  2. Nanoarchaeota
  3. Korarchaeota
  4. Crenarchaeota
  5. Thaumarchaeota: accomplished nitrification
46
Q

What is an example of a member of euryarchaeota?

A

Haloarchaea and Methanogenic Archaea

47
Q

What is Haloarchaea? Where is it found?

A

Member of phylum Euryarchaeota with an absolute requirement for high salt concentrations (minimum 1.5M NaCl). They are found in salt evaporation ponds and salt lakes where concentration approaches saturation (e.g. great salt lake, dead sea, soda lakes)

48
Q

How do halophiles maintain osmotic balance?

A

Accumulation or synthesis of compatible solutes for diffusion of H2O across membrane (e.g. Halobacterium salinarium pumps K into cell from environment so water flows into the cell)

49
Q

How do haloarchaea generate energy?

A

Integral membrane protein bacteriorhodopsin absorbs light energy to pump protons across the membrane to make a proton motive force which generates ATP without fixing CO2

50
Q

What is methanogenic archaea?

A

Member of phylum euryarchaeota that produce the bulk of CH4 in the atmosphere. Strict anaerobe found in many diverse anaerobic environments such as cow’s gut and sewage sludge.

51
Q

What is special about the cell wall of Methanogenic archaea?

A

Only Methanobacteriales have a pseudomurein cell wall, but other types of methanogens have an S-layer made of proteins/glycoproteins

52
Q

What is Nitrosopumilus maritimus?

A

Member of Thaumarchaeota that is abundant in open ocean water as a major player in nitrogen cycling. They are an aerobic, ammonia oxidizing chemolithoautotroph.

53
Q

What is nanoarchaeum equitans?

A

Member of Nanoarchaeota that is the obligate parasite of the crenarchaeote Ignicoccus. It is one of the smallest cellular organisms and contains one of the smallest genomes known, depending on host for most of its cellular needs.

54
Q

What is korarchaeum cryptofilum?

A

Member of korarchaeota that is a filamentous, hyperthermophilic, obligately anaerobic chemoorganotroph that lacks many core genes that depend on other members of hot springs community.

55
Q

What is crenarchaeota?

A

Phylum of archaea that are found in extremely hot environments, but some are found in extremely cold environments. They are chemoorganotrophs or chemolithotrophs that use sulfur in their metabolism.

56
Q

What is sulfolobus acidocaldarius?

A

Member of chrenarchaeota that is a hyperthermophile (90ºC) and acidophile (pH 2) that grows in sulfur rich acidic hot springs. It is an aerobic chemolithotroph that oxisizes reduced sulfur or iron.

57
Q

What is the asgard superphylum of archaea?

A

Superphylum found from sequence analyses from metagenomes with ecological functions unknown, but contain versions of genes previously thought to have been eukaryote-specific

MBIO 1010 (10 decks)

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