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Microbiology > Phylogeny and Diversity > Flashcards

Phylogeny and Diversity Flashcards

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Biology 101 flashcards
1
Q

Anaerobes and chemolithotrophs obtain E/Carbon from

A

CO2/H2

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2
Q

How did earth become Oxic over time?

A

cyanobacteria is the earliest oxygen-producing bactera.

o2 is the waste product (product of photosynthesis) , thus there was a gradual change from anoxic to oxic

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3
Q

Ozone

A

conversion of o2 to o3, absorbs UV radiation from the sun. UV is damaging to DNA.

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4
Q

What did ozone allow?

A

allowed organisms to inhabit earths terestiral habits and not be confined toocean and subsurface terrain.

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5
Q

So far oxygen has created ozone, which benefited life, what did it also bring?

A

Evolution of organelle-containing eukaryotic microorganisms.

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6
Q

Explain endosymbiosis

A

well-supported hypothesis for origin of eurkarotic cells,

mitochondria and chloroplasts aros from symbiotic assocation of prokaryotes w/ in another type of cell.

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7
Q

overall, development of oxic atmosphere led to evolution of?

A

new metabolic pathways that yielded more E than anaerobic metabolisms.

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8
Q

Explain mutations and why they can occur

A

-changes in nucleotide sequence of an organisms genome, and occur due to errors in the fidelity of replication, UV radiation, etc.
Adaptive mutations improve fitness of an organism, increasing its survival.
-gene duplication, horizontal gene transfer, gene loss.

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9
Q

Evolution is

A

a change in allele frequencies in a pop of organims ovetime.

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10
Q

Evolution result, allele and mutation

A
  • descent with modification, alternative versions of a given gene, and mutation is random changes in DNA sequence: neutral, deleterious, beneficial.
  • subsitutions, deletions, insertions, duplications.
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11
Q

Recombination

A

segments of DNA are broken adn rejoined to creat new combo of material.

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12
Q

selection

A

defined by fitness (ability to produce off spring.

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13
Q

genetic drift

A

random process that causes gene frequencies to change overtime, resulting in ecolution in abscence of natural selction.

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14
Q

phylogeny

A

evolutionary history of a group of organisms, inferred indirectly from nucleotide sequence data.

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15
Q

Certain genes and proteins act as ? because they can measure evolutions change (rate at which a locus accumulates mutations)

A

molecular clocks (chronometers)

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16
Q

what are the major assumptions of the molecular clock?

A

nucleotide changes occur at a constant rate and are generally neutral adn random (not all valid)

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17
Q

the most widely used molecular clocks

A

small subunit ribosomal RNA (SSU RNA)
16s/18s
functionally onstant, sufficiently conservedd (change slowly, sufficient length
nit good distincition for closely related species.

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18
Q

SSU RNA

A

found in all domains of life

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19
Q

16s rRNA

A

prokaryotes, mitochondria and chloroplasts.

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20
Q

18s

A

rRNA in eurkaryotes

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21
Q

intragenic

A

does not change repidly enough

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22
Q

comparative rRna is a routine procedure that involved

A

amplification of the gene endocing SSU rRNA. Sequencing of the amplified geen and analysis of the sequence in reference to other sequences.

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23
Q

Explain the first step in sequence analysis

A

aligning the sequence of interest with the sequence from homologous genes from other strains or species.

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24
Q

branch length on the phylogenetic tree represents

A

the number of changes that occured on the branch

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25
Q

what can be used to amplify SSU rRNA genes

A

PCR- genes are sorted out, sequenced, analyzed.

reveals key features.

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26
Q

Explain why 16s rRNA is so important

A

useful in taxonomy and is considered the gold-standarf for identiying and describing new speciies.
-proposed that a bacterium should be considered a new species iif its 16s RNA gene sequence differs by more than 3% from any name srain ad new genus if it differs by more than 5%.

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27
Q

Explain the limitations of the 16s rRNA and what is used instead.

A

the lack of divergence limits its effectiveness in discriminating btwn bacteria at species.
A multi-gene approach is used instead.

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28
Q

what type of sequence is becming more common, explain it.

A

whole-genome sequence analysis. you can see genome structure, size and numbers of chromosomes. Gene content and gene order.

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29
Q

Phylogenetic diversity is

A

the evolutionary relationships between organisms. phyla, genera, species. defined by rRNA phylogeny.

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30
Q

functional diversity

A

form and function as related to microbial physiology and ecology. organism with commmon traits/ genes.

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31
Q

gene loss, convergent evolution and horizontal gene transfer

A

reasons functional traits are seen in different species.

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32
Q

physiological,ecological, morphological diversity

A

metabolism and biochemsitry
organisms and their environment
outward appearence, shape, structure.

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33
Q

Explain phototrophic bacteria

A

originated from bacteria, first phototrophs were anoxy genic, produced water instead of 02 and used h2 iron and hydrogen sulfide instead of carbon as electron donor.

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34
Q

most phototrophs are also

A

autotrophs

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35
Q

What are the common features of phototrophic bacteria.

A

Use-chlorophyll-like and accesory pigments to harvest energy from ligh and transfer to membrane-bund rxn center to drive e transfer.

  • two types of rxn centers type 1- feS and type 2- quinone/Q-type) both are found in cyanobacteria but one or other is found in anoxygenic phototrophs.
  • pigments often found in intracellular membrane systems that allow phototrophic bacteria to better use light of low intensities.
  • many but not all fix carbon
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36
Q

cyanobacteria

A

key genera: procholorcoccous, crocosphaera, synechococcus, trichodemiums, oscillatoria, anabaena,
-first-oxygen-evolving phototrophs

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37
Q

Cyanobacteriao

A

oxygenic phototrophs with both feS and Q-type photosystems.
all fix co2 by the calvin cycle
many fix N2
most synthesis their own vitamins
-harvest enegery from light and fix co2 during day
-generate energy by fermentation or aerobix respiration of carbon storage products
-some can assimilate simple organic compounds in light (photoheterotropjhy)
-some can switch to anoxygenic photosynthesis using h2S as an electron donor.

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38
Q

Explain the physiology and phtosynthetic membranes of cyanobacteria

A

specialized membrane systems called thylakoids that increase ability to harvest light energy

  • Cell walls contrain peptidoglycan
  • photosynthesis occurs in thylakoid membrane
  • produce pigments (chlorophyll a and phycobillins) accesory pigments
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39
Q

Explain the motility of cyanobacteria

A

gliding motilty

-many cyanobacteria show photo/chemotaxis

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40
Q

? important in positioning cells in water colum where light intensity is optimal.

A

gas vesicles

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41
Q

what mucilaginous envelopes bind groups of cells/filaments together?

A

sheaths

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42
Q

hormogonia

A

short, motile filaments that break off to facilitate dispersal under stress.

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43
Q

akinetes

A

resting structure w/thickened outer walls that protect the organism from darkness, cold, desciccation.

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44
Q

cyanophycin

A

nitrogen storage product

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45
Q

Nitrogenase is sensitive to ? therefore

A

oxygen, so fixation cannot occurs with oxygenic photosynthesis

46
Q

many cyanobacteria fix nitrogen only at

A

night and some transiently suppress photosynthetic activity within filaments.

47
Q

heterocysts are formed where? what are they

A

formed on the ends of filaments or along the filament
-surrounded by thick cell wall that allows 02 diffusion and provides anoxic environment
lack photosystem 2 and cannot fix co2
exchanges material with adjacent cells
fixed carbon is important and oxidized to yeidl electrons for n2 fixation.

48
Q

Explain the importance of cyanobacteria from an ecological stand point

A

important for productivity of oceans
cyanobacterial nitrogen fixation is dominant input of new nitrogen in oceans.
widely disturbed in terrestrial and freshwater environments.

49
Q

Most abundant ocean phototrophs containing 80 percent of marine photosynthesis and 35 percent of all earths photosynthesis.

A

synechococcus and prochlorococcus

50
Q

This is the largest phylum of bacteria and most metaboliccaly diverse and morpholically diverse

A

preoteobacteria

51
Q

All proteobacteria is gram?

A

negative and include the most commonly encountered bacteria.

52
Q

How many classes of proteobacteria? name them?

A

6

alpha, beta, delta, gamma, epsilon, and zeta.

53
Q

What bacteria carries out anyoxgenic photosynthesis (where no o2 is produced)

A

purple phototrophic bacteria

54
Q

Purple phototrophic bacteria contains what pigments and is found where?

A
  • bacteriochlorphyls and cartenoid pigments

- found in illuminated anoxic zones where h2S is present and in microbial mats and salt marsh sediments

55
Q

Nitrifying Bacteria

A

Grow chemolithotrophically at the expense of reduced. inorganic nitrogen compounds,most are obligate aerobes

56
Q

Nitrification

A

(oxidation of ammonia to nitrate) occurs as two separate reactions by different groups of bacteria
Ammonia oxidizers(e.g., Nitrosococcus, gamma γ-prot.)Nitrite oxidizer(e.g., Nitrobacter, alpha α-prot.)

57
Q

Where is nitrifying grow? and where does it play a role.

A

Widespread in soil and water

Play vital role in wastewater treatment

58
Q

Sulfur-Oxidizing Bacteria

A

Grow chemolithotrophicallyon reduced sulfur compoundsNeutrophilesand acidophiles

59
Q

Sulfur-oxidizing Bacteria
-name examples of the two bacteria. which one is best studied
what is the shape?

A

Thiobacillusand close relatives are best studied (beta β-Prot.)
Rod-shaped
Sulfur compounds most commonly used as electron donors are H2S, So, S2O32-; can generate sulfuric acid

Beggiatoa(gamma γ-Prot.): Filamentous, gliding bacteria, found in habitats rich in H2S
Examples: sulfur springs, decaying seaweed beds, mud layers of lakes, sewage-polluted waters, and hydrothermal vents

60
Q

Hydrogen-Oxidizing Bacteria are ? (two)/ best studied?

A

Ralstonia, Paracoccus

Ralstonia, Pseudomonasand Paracoccusbest studied genera (β-, γ-, α- Prot. respectively)

61
Q

How do H-oxidizing grow? Electron donor/acceptor?

A

Most can grow autotrophically: H2 as sole electron donor and O2as electron acceptor (so, aerobic)

62
Q

What binds to H2? Some are ? and grow ?

A

Hydrogenase enzymes bind H2 (produce ATP or for reducing power{electrons} for autotrophic growth)

Some are facultative; can grow chemoorganically

63
Q

most complex behavior among known bacteria are?

A

Myxobacteria–key genus Myxococcus

Microbial predators.

64
Q

Life cycle results in (Myxobacteria)

A

formation of multicellular structures (fruiting bodies).
often strikingly colored and morphologically elaborate (Figure 15.41)can often be seen with hand lens on decaying wood or plant material

65
Q

Myxobacteria life cycle

A

life cycle (Figure 15.42)
Vegetative cells are simple nonflagellated gram-negative rods that glide and obtain nutrients by lysing other bacteria.
Vegetative cells excrete slime trails. (Figure 15.44)
form a swarm that self-organizes, allowing them to behave as a single coordinated entity in response to environment
when nutrients exhausted, vegetative cells aggregate in mounds/heaps (Figure 15.45) likely mediated by chemotaxis or quorum-sensingdifferentiate into fruiting bodies (Figure 15.46) containing myxospores(specialized resistant cells)

66
Q

Vegetative cells are

A

simple nonflagellated gram-negative rods that glide and obtain nutrients by lysing other bacteria.

67
Q

Microbial Bioluminescence key genera is

A

Vibrio, Aliivibrio, and Photobacterium

68
Q

Bioluminescence

A

Mostly marine; some colonize light organs of some fish and squid, producing light for signaling, avoiding predators, attracting prey.

69
Q

Explain the Mechanism and ecology of bioluminescence

A

only when O2present

requires luxCDABEgenes and is catalyzed by luciferase, which uses O2, a long-chain aliphatic aldehyde (RCHO; e.g., tetradecanal) and reduced flavinmononucleotide (FMNH2)

70
Q

All genera within Pseudomonad group:

A

straight or curved rods with polar flagella, chemoorganotrophs, but cannot ferment

71
Q

Pseudomonas class?

A

Multiple but γ-prot.

72
Q

Pseudomonas is utritionally versatile, explain??

A

many organic compounds as C, and energy sources have role in biodegradationof xenobiotics

Do a lot of decomposition in the environment

73
Q

Some Psuedomonas species are pathogenic

A

P. aeurginosais a human opportunistic pathogen: urinary and resp. tract. Found in skin graft pts., catheters, cystic fibrosis sufferers; common nosocomial (hospital origin) infection agentResistant to many common antibiotics

74
Q

Aerobic and Facultative Chemoorganotrophs

A 
Pseudomonasand the Pseudomonads
Acetic Acid Bacteria
Neisseria
Enteric Bacteria
Vibrio
75
Q

Acetic Acid Bacteria

A

Acetobacter, α-Prot.)
Organisms that carry out incomplete oxidation of alcohols and sugars as starting substrates

Leads to the accumulation of organic acids as end products (converts alcohol to acetic acid, why wine becomes vinegar and sour)

Aerobic, motile rods

High tolerance to acidic conditions

Commonly found in alcoholic juices

Used in production of vinegar

76
Q

Neisseria, Chromobacterium

A

Neisseria are cocci
N. gonorrhoeae(ß- prot.) causes gonorrhoeae
others are coccobacilli: rod during growth, cocci when stationary phase

77
Q

Acinetobacter (γ-prot.)

A

common soil and water org.May cause nosocomial infections

78
Q

Family Enterobacteriaceae

A

Enteric Bacteria is unofficial name
Relatively homogeneous, facultative organisms (fermentation or aerobic respiration)
AllGamma-proteobacteria, order Enterobacteriales

Motile or non-motile, nonsporulating rods

Oxidase negative

Possess relatively simple nutritional requirements

Ferment sugars to a variety of end products: Mixed-acid

79
Q

Enterobacteriaceae

-Escherichia

A

Universal inhabitants of intestinal tract of humans and warm-blooded animals

Synthesize vitamins for host

Some strains are pathogenic: E. coli O157:H7

80
Q

Enterobacteriaceae

Salmonella and Shigella

A

Closely related to Escherichia

Usually pathogenic to humans

Salmonellacharacterized immunologically by surface antigens

81
Q

Enterobacteriaceae

Proteus

A

rapidly motile cells; capable of swarmingFrequent cause of urinary tract infections in humans, produce urease

82
Q

??? are a closely related group of organisms: Key genera –Enterobacter, Klebsiella, Serratia

A

Butanediol fermentators

83
Q

Butanediol fermentators

A

More distantly related to mixed acid fermentatorsSome capable of pigment production – Ex: Serratiamarcescens

Many can be found in soil and water along with intestinal tract

84
Q

Family Vibrionaceae - Vibrio Group

A

Gamma-proteobacteria, order Vibrionales

Cells are motile, straight or curved rods; facultative –fermentative; most are oxidase positive

Most inhabit aquatic environments, incl. marine, most are halophilic

Some are pathogenic: V. cholerae– choleraV. parahaemolyticus– diarrhea, shellfish poisoningVibrio vulnificus–sepsis from ingestion, wound infection

Some are capable of light production (bioluminescence), found in marine animals

85
Q

Distinguishing among common Gram negative rod organisms

Explain between Pseudomonas, Enterobacteriaceae, and Vibrip

A

Pseudomonas
Aerobic, motile Oxidase positive (produces certain cytochrome c oxidases- e- transport chain)
Cannot ferment

Enterobacteriaceae
Facultative, fermentative
May be motile (peritrichous flagella)
Oxidase negative

Vibrio
Facultative, fermentative
Oxidase positive
Most are motile

86
Q

Epsilonproteobacteria first described? where is it abundant?

A

Campylobacter and Helicobacterfirst described (also pathogens

Other ε-proteobacteria abundant in aquatic environment: oxic–anoxic interfaces in sulfur-rich environments
e.g., hydrothermal vents
Many are autotrophs (chemolithotrophs)
Using H2, formate, sulfide, or thiosulfate as electron donor
Pathogenic and non-pathogenic representatives

87
Q

Pathogenic: Campylobacter and Helicobacter

A

Both Gram neg. motile spirilla

Microaerophilic: cultivate under low O2

Campylobacter: several species pathogenic C. jejuni common cause of gastroenteritis: foodborne illness

Produce enterotoxins, related to cholera toxin

Helicobacter: H. pylori causes stomach ulcers

88
Q

Nonsporulating Gram-Positive Bacteria (Firmicutes)

A

Staphylococcus, Streptococcus, Lactobacillus, Listeria

89
Q

Staphylococcus

A

Facultative catalase positive, cocci

Resistant to reduced water potential, high salinity

Staphylococcus aureus: pathogen, pimples, boils, pneumonia, meningitis, MRSA nosocomial infections

S. aureus is distinguished on ability to ferment mannitol to acid – mannitol salt agar

90
Q

Lactic Acid Bacteria

A

no oxidative phosphorylation/respiratory chain; substrate level phosphorylation only

  • Produce lactic acid as a fermentation product
  • Generally need sugars: also fastidious, complex nutritional requirements
  • Aerotolerantanaerobes
91
Q

Streptococci:

A

Streptococcus, Lactococcus, Enterococcus

Streptococcus: some species are pathogenic

Hemolysis: importance in subdividing group: beta-hemolysis: complete; alpha hemolysis: discoloration

Lancefield groups: carbohydrate antigens

Streptococcus, group A: common cause of strep throat

92
Q

Streptococcus pneumoniae

A

α- hemolytic diplococci, can cause upper respiratory infections and pneumonia

93
Q

Enterococcus

A

genera of fecal origin (water quality indicator in marine waters esp.)

94
Q

Lactobacillus

A

(also a lactic acid bacteria)Rod-shaped, resistant to acidic conditionsCommon in dairy products (pH 4)L. acidophilus good bacteria in yogurt

95
Q

Listeria

A

related but not a lactic acid genus)

Gram-positive coccobacilli

Form chains 3–5 cells long

Require full oxicor microoxicconditions for growth

L. monocyto genes causes listeriosis– foodborne illness, in prepared food products like ham, hot dogs, cheese

96
Q

Endospore-Forming Gram-Positive Bacteria (Firmicutes) key genera

A

Bacillus, Clostridium

Distinguished on the basis of cell morphology, shape and cellular position of endospore

Generally found in soils

Endospores are advantageous for soil microorganisms

Isolate by heating sample (80 C), then streaking

97
Q

Bacillus and Paenibacillus

A

Many produce extracellular hydrolytic enzymes that break down polymers (e.g. amylase)

Many bacilli produce antibiotics

Paenibacilluspopilliaeand Bacillus thuringiensis produce insect larvicides, Bttoxin has been introduced to GM plants

Aerobe and facultative species

Some species are pathogenic

98
Q

Nonsporulating Gram-Positive Bacteria

A

Lactobacillus and Listeria

99
Q

Clostridium

A

Lack a respiratory chain – only do substrate-level phosphorylation (fermentation), obligately anaerobic

Some Clostridia perform Stickland reactions

Metabolism of pair of amino acids (1 e-donor, other e-acceptor)

Responsible for putrefaction oftentimes

Mainly found in anaerobic pockets in the soil. Also live in mammalian intestinal tract

Very important for N2fixation in soil, breakdown of soil organic matter

Some are pathogenic - diseases such as botulism (C. botulinum), tetanus (C. tetani), and gangrene (C. perfringens); all toxin-producing

100
Q

Cell-Wall-Less Gram-Positive Bacteria:

A

Mycoplasmas
Key genera: Mycoplasma, Spiroplasma

Lack cell walls

Some of the smallest organisms capable of autonomous growth – simple cells and small genomes

Parasites that inhabit animal and plant hosts

M. pneumoniae– atypical pneumonia cause

Key components of peptidoglycan are missing; important role of sterols

101
Q

form their own phylum

A

(Actinobacteria)
Over 30 taxonomic familiesVariety of morphology, including filamentous (Actinomycetes), usually aerobicMostly harmless commensals (Mycobacteriumare notable exceptions)Some species valuable for antibiotics and certain fermented dairy products

102
Q

Propionic Acid Bacteria

A

First discovered in Swiss cheese

Gram-positive anaerobes

Have metabolic strategy called secondary fermentation

Obtain energy from fermentation products produced by other bacteria

Also causative of acne

103
Q

Mycobacterium

A

Rod-shaped organisms, exhibit acid-fastness;

Not readily stained by Gram stain because of high surface lipid content but considered Gram +

M. tuberculosis exhibits cord-like growth

“cord factor”, the virulence factor leading to cord-like growth (glycolipid in cell wall)

104
Q

Mycobacterium leprae

A

causes Hansen’s disease (leprosy)

105
Q

Filamentous Actinobacteria: Streptomyces & Others

A

Filamentous, gram-positive bacteria

Produce mycelium analogous to mycelium of filamentous fungi

Streptomycesspores are called conidia

Primarily soil microorganisms, responsible for earthy odor of soil (geosmins)

Strict aerobes that produce many extracellular enzymes

106
Q

Streptomyces

A

50% of all isolated Streptomycesproduce antibiotics

Over 500 distinct antibiotics produced by Streptomyces

Some produce more than one antibiotic

Genomes are typically quite large (8 Mbpand larger)

Knowledge of the ecology of Streptomycesremains poor, i.e. why produce so many antibiotics?

107
Q

Explain The Chlamydia

A

Obligatelyparasitic with poor metabolic capacities, intracellular parasites

Gram –based on biochemical analyses

Some of the simplest biochemical capacities of all known bacteria

108
Q

C. trachomatis

A

causes trachoma – eye disease and leading cause of blindness in humans
and the STD

109
Q

Spirochetes
Treponema
Spirochaeta
Borrelia

A

Treponema
Anaerobic host-associated spirochetes that are commensal or parasites of humans –Treponemapallidum: syphilis

Spirochaeta

Free-living, anaerobic and facultatively anaerobic spirochetes

Borrelia
Majority are human or animal pathogens

Borrelia burgdorferiis the causative agent of Lyme disease

110
Q

Leptospira and Leptonema

A

Strictly anaerobic spirochetes

Rodents are the natural host of Leptospira,freq. transmitted via urine
cause of leptospirosis in humans

Microbiology (12 decks)

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