Phylogeny and Diversity 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
what can be used to amplify SSU rRNA genes
PCR- genes are sorted out, sequenced, analyzed. | reveals key features.
26
Explain why 16s rRNA is so important
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%.
27
Explain the limitations of the 16s rRNA and what is used instead.
the lack of divergence limits its effectiveness in discriminating btwn bacteria at species. A multi-gene approach is used instead.
28
what type of sequence is becming more common, explain it.
whole-genome sequence analysis. you can see genome structure, size and numbers of chromosomes. Gene content and gene order.
29
Phylogenetic diversity is
the evolutionary relationships between organisms. phyla, genera, species. defined by rRNA phylogeny.
30
functional diversity
form and function as related to microbial physiology and ecology. organism with commmon traits/ genes.
31
gene loss, convergent evolution and horizontal gene transfer
reasons functional traits are seen in different species.
32
physiological,ecological, morphological diversity
metabolism and biochemsitry organisms and their environment outward appearence, shape, structure.
33
Explain phototrophic bacteria
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.
34
most phototrophs are also
autotrophs
35
What are the common features of phototrophic bacteria.
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
36
cyanobacteria
key genera: procholorcoccous, crocosphaera, synechococcus, trichodemiums, oscillatoria, anabaena, -first-oxygen-evolving phototrophs
37
Cyanobacteriao
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.
38
Explain the physiology and phtosynthetic membranes of cyanobacteria
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
39
Explain the motility of cyanobacteria
gliding motilty | -many cyanobacteria show photo/chemotaxis
40
? important in positioning cells in water colum where light intensity is optimal.
gas vesicles
41
what mucilaginous envelopes bind groups of cells/filaments together?
sheaths
42
hormogonia
short, motile filaments that break off to facilitate dispersal under stress.
43
akinetes
resting structure w/thickened outer walls that protect the organism from darkness, cold, desciccation.
44
cyanophycin
nitrogen storage product
45
Nitrogenase is sensitive to ? therefore
oxygen, so fixation cannot occurs with oxygenic photosynthesis
46
many cyanobacteria fix nitrogen only at
night and some transiently suppress photosynthetic activity within filaments.
47
heterocysts are formed where? what are they
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
Explain the importance of cyanobacteria from an ecological stand point
important for productivity of oceans cyanobacterial nitrogen fixation is dominant input of new nitrogen in oceans. widely disturbed in terrestrial and freshwater environments.
49
Most abundant ocean phototrophs containing 80 percent of marine photosynthesis and 35 percent of all earths photosynthesis.
synechococcus and prochlorococcus
50
This is the largest phylum of bacteria and most metaboliccaly diverse and morpholically diverse
preoteobacteria
51
All proteobacteria is gram?
negative and include the most commonly encountered bacteria.
52
How many classes of proteobacteria? name them?
6 | alpha, beta, delta, gamma, epsilon, and zeta.
53
What bacteria carries out anyoxgenic photosynthesis (where no o2 is produced)
purple phototrophic bacteria
54
Purple phototrophic bacteria contains what pigments and is found where?
- bacteriochlorphyls and cartenoid pigments | - found in illuminated anoxic zones where h2S is present and in microbial mats and salt marsh sediments
55
Nitrifying Bacteria
Grow chemolithotrophically at the expense of reduced. inorganic nitrogen compounds,most are obligate aerobes
56
Nitrification
(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
Where is nitrifying grow? and where does it play a role.
Widespread in soil and water | Play vital role in wastewater treatment
58
Sulfur-Oxidizing Bacteria
Grow chemolithotrophicallyon reduced sulfur compoundsNeutrophilesand acidophiles
59
Sulfur-oxidizing Bacteria -name examples of the two bacteria. which one is best studied what is the shape?
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
Hydrogen-Oxidizing Bacteria are ? (two)/ best studied?
Ralstonia, Paracoccus | Ralstonia, Pseudomonasand Paracoccusbest studied genera (β-, γ-, α- Prot. respectively)
61
How do H-oxidizing grow? Electron donor/acceptor?
Most can grow autotrophically: H2 as sole electron donor and O2as electron acceptor (so, aerobic)
62
What binds to H2? Some are ? and grow ?
Hydrogenase enzymes bind H2 (produce ATP or for reducing power{electrons} for autotrophic growth) Some are facultative; can grow chemoorganically
63
most complex behavior among known bacteria are?
Myxobacteria–key genus Myxococcus | Microbial predators.
64
Life cycle results in (Myxobacteria)
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
Myxobacteria life cycle
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
Vegetative cells are
simple nonflagellated gram-negative rods that glide and obtain nutrients by lysing other bacteria.
67
Microbial Bioluminescence key genera is
Vibrio, Aliivibrio, and Photobacterium
68
Bioluminescence
Mostly marine; some colonize light organs of some fish and squid, producing light for signaling, avoiding predators, attracting prey.
69
Explain the Mechanism and ecology of bioluminescence
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
All genera within Pseudomonad group:
straight or curved rods with polar flagella, chemoorganotrophs, but cannot ferment
71
Pseudomonas class?
Multiple but γ-prot.
72
Pseudomonas is utritionally versatile, explain??
many organic compounds as C, and energy sources have role in biodegradationof xenobiotics Do a lot of decomposition in the environment
73
Some Psuedomonas species are pathogenic
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
Aerobic and Facultative Chemoorganotrophs
``` Pseudomonasand the Pseudomonads Acetic Acid Bacteria Neisseria Enteric Bacteria Vibrio ```
75
Acetic Acid Bacteria
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
Neisseria, Chromobacterium
Neisseria are cocci N. gonorrhoeae(ß- prot.) causes gonorrhoeae others are coccobacilli: rod during growth, cocci when stationary phase
77
Acinetobacter (γ-prot.)
common soil and water org.May cause nosocomial infections
78
Family Enterobacteriaceae
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
Enterobacteriaceae | -Escherichia
Universal inhabitants of intestinal tract of humans and warm-blooded animals Synthesize vitamins for host Some strains are pathogenic: E. coli O157:H7
80
Enterobacteriaceae | Salmonella and Shigella
Closely related to Escherichia Usually pathogenic to humans Salmonellacharacterized immunologically by surface antigens
81
Enterobacteriaceae | Proteus
rapidly motile cells; capable of swarmingFrequent cause of urinary tract infections in humans, produce urease
82
??? are a closely related group of organisms: Key genera –Enterobacter, Klebsiella, Serratia
Butanediol fermentators
83
Butanediol fermentators
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
Family Vibrionaceae - Vibrio Group
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
Distinguishing among common Gram negative rod organisms | Explain between Pseudomonas, Enterobacteriaceae, and Vibrip
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
Epsilonproteobacteria first described? where is it abundant?
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
Pathogenic: Campylobacter and Helicobacter
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
Nonsporulating Gram-Positive Bacteria (Firmicutes)
Staphylococcus, Streptococcus, Lactobacillus, Listeria
89
Staphylococcus
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
Lactic Acid Bacteria
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
Streptococci:
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
Streptococcus pneumoniae
α- hemolytic diplococci, can cause upper respiratory infections and pneumonia
93
Enterococcus
genera of fecal origin (water quality indicator in marine waters esp.)
94
Lactobacillus
(also a lactic acid bacteria)Rod-shaped, resistant to acidic conditionsCommon in dairy products (pH 4)L. acidophilus good bacteria in yogurt
95
Listeria
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
Endospore-Forming Gram-Positive Bacteria (Firmicutes) key genera
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
Bacillus and Paenibacillus
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
Nonsporulating Gram-Positive Bacteria
Lactobacillus and Listeria
99
Clostridium
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
Cell-Wall-Less Gram-Positive Bacteria:
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
form their own phylum
(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
Propionic Acid Bacteria
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
Mycobacterium
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
Mycobacterium leprae
causes Hansen’s disease (leprosy)
105
Filamentous Actinobacteria: Streptomyces & Others
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
Streptomyces
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
Explain The Chlamydia
Obligatelyparasitic with poor metabolic capacities, intracellular parasites Gram –based on biochemical analyses Some of the simplest biochemical capacities of all known bacteria
108
C. trachomatis
causes trachoma – eye disease and leading cause of blindness in humans and the STD
109
Spirochetes Treponema Spirochaeta Borrelia
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
Leptospira and Leptonema
Strictly anaerobic spirochetes Rodents are the natural host of Leptospira,freq. transmitted via urine cause of leptospirosis in humans