Phylogeny and Diversity Flashcards
Anaerobes and chemolithotrophs obtain E/Carbon from
CO2/H2
How did earth become Oxic over time?
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
Ozone
conversion of o2 to o3, absorbs UV radiation from the sun. UV is damaging to DNA.
What did ozone allow?
allowed organisms to inhabit earths terestiral habits and not be confined toocean and subsurface terrain.
So far oxygen has created ozone, which benefited life, what did it also bring?
Evolution of organelle-containing eukaryotic microorganisms.
Explain endosymbiosis
well-supported hypothesis for origin of eurkarotic cells,
mitochondria and chloroplasts aros from symbiotic assocation of prokaryotes w/ in another type of cell.
overall, development of oxic atmosphere led to evolution of?
new metabolic pathways that yielded more E than anaerobic metabolisms.
Explain mutations and why they can occur
-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.
Evolution is
a change in allele frequencies in a pop of organims ovetime.
Evolution result, allele and mutation
- descent with modification, alternative versions of a given gene, and mutation is random changes in DNA sequence: neutral, deleterious, beneficial.
- subsitutions, deletions, insertions, duplications.
Recombination
segments of DNA are broken adn rejoined to creat new combo of material.
selection
defined by fitness (ability to produce off spring.
genetic drift
random process that causes gene frequencies to change overtime, resulting in ecolution in abscence of natural selction.
phylogeny
evolutionary history of a group of organisms, inferred indirectly from nucleotide sequence data.
Certain genes and proteins act as ? because they can measure evolutions change (rate at which a locus accumulates mutations)
molecular clocks (chronometers)
what are the major assumptions of the molecular clock?
nucleotide changes occur at a constant rate and are generally neutral adn random (not all valid)
the most widely used molecular clocks
small subunit ribosomal RNA (SSU RNA)
16s/18s
functionally onstant, sufficiently conservedd (change slowly, sufficient length
nit good distincition for closely related species.
SSU RNA
found in all domains of life
16s rRNA
prokaryotes, mitochondria and chloroplasts.
18s
rRNA in eurkaryotes
intragenic
does not change repidly enough
comparative rRna is a routine procedure that involved
amplification of the gene endocing SSU rRNA. Sequencing of the amplified geen and analysis of the sequence in reference to other sequences.
Explain the first step in sequence analysis
aligning the sequence of interest with the sequence from homologous genes from other strains or species.
branch length on the phylogenetic tree represents
the number of changes that occured on the branch
what can be used to amplify SSU rRNA genes
PCR- genes are sorted out, sequenced, analyzed.
reveals key features.
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%.
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.
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.
Phylogenetic diversity is
the evolutionary relationships between organisms. phyla, genera, species. defined by rRNA phylogeny.
functional diversity
form and function as related to microbial physiology and ecology. organism with commmon traits/ genes.
gene loss, convergent evolution and horizontal gene transfer
reasons functional traits are seen in different species.
physiological,ecological, morphological diversity
metabolism and biochemsitry
organisms and their environment
outward appearence, shape, structure.
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.
most phototrophs are also
autotrophs
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
cyanobacteria
key genera: procholorcoccous, crocosphaera, synechococcus, trichodemiums, oscillatoria, anabaena,
-first-oxygen-evolving phototrophs
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.
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
Explain the motility of cyanobacteria
gliding motilty
-many cyanobacteria show photo/chemotaxis
? important in positioning cells in water colum where light intensity is optimal.
gas vesicles
what mucilaginous envelopes bind groups of cells/filaments together?
sheaths
hormogonia
short, motile filaments that break off to facilitate dispersal under stress.
akinetes
resting structure w/thickened outer walls that protect the organism from darkness, cold, desciccation.
cyanophycin
nitrogen storage product
Nitrogenase is sensitive to ? therefore
oxygen, so fixation cannot occurs with oxygenic photosynthesis
many cyanobacteria fix nitrogen only at
night and some transiently suppress photosynthetic activity within filaments.
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.
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.
Most abundant ocean phototrophs containing 80 percent of marine photosynthesis and 35 percent of all earths photosynthesis.
synechococcus and prochlorococcus
This is the largest phylum of bacteria and most metaboliccaly diverse and morpholically diverse
preoteobacteria
All proteobacteria is gram?
negative and include the most commonly encountered bacteria.
How many classes of proteobacteria? name them?
6
alpha, beta, delta, gamma, epsilon, and zeta.
What bacteria carries out anyoxgenic photosynthesis (where no o2 is produced)
purple phototrophic bacteria
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
Nitrifying Bacteria
Grow chemolithotrophically at the expense of reduced. inorganic nitrogen compounds,most are obligate aerobes
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.)
Where is nitrifying grow? and where does it play a role.
Widespread in soil and water
Play vital role in wastewater treatment
Sulfur-Oxidizing Bacteria
Grow chemolithotrophicallyon reduced sulfur compoundsNeutrophilesand acidophiles
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
Hydrogen-Oxidizing Bacteria are ? (two)/ best studied?
Ralstonia, Paracoccus
Ralstonia, Pseudomonasand Paracoccusbest studied genera (β-, γ-, α- Prot. respectively)
How do H-oxidizing grow? Electron donor/acceptor?
Most can grow autotrophically: H2 as sole electron donor and O2as electron acceptor (so, aerobic)
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
most complex behavior among known bacteria are?
Myxobacteria–key genus Myxococcus
Microbial predators.
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
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-sensingdifferentiate into fruiting bodies (Figure 15.46) containing myxospores(specialized resistant cells)
Vegetative cells are
simple nonflagellated gram-negative rods that glide and obtain nutrients by lysing other bacteria.
Microbial Bioluminescence key genera is
Vibrio, Aliivibrio, and Photobacterium
Bioluminescence
Mostly marine; some colonize light organs of some fish and squid, producing light for signaling, avoiding predators, attracting prey.
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)
All genera within Pseudomonad group:
straight or curved rods with polar flagella, chemoorganotrophs, but cannot ferment
Pseudomonas class?
Multiple but γ-prot.
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
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 agentResistant to many common antibiotics
Aerobic and Facultative Chemoorganotrophs
Pseudomonasand the Pseudomonads Acetic Acid Bacteria Neisseria Enteric Bacteria Vibrio
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
Neisseria, Chromobacterium
Neisseria are cocci
N. gonorrhoeae(ß- prot.) causes gonorrhoeae
others are coccobacilli: rod during growth, cocci when stationary phase
Acinetobacter (γ-prot.)
common soil and water org.May cause nosocomial infections
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
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
Enterobacteriaceae
Salmonella and Shigella
Closely related to Escherichia
Usually pathogenic to humans
Salmonellacharacterized immunologically by surface antigens
Enterobacteriaceae
Proteus
rapidly motile cells; capable of swarmingFrequent cause of urinary tract infections in humans, produce urease
??? are a closely related group of organisms: Key genera –Enterobacter, Klebsiella, Serratia
Butanediol fermentators
Butanediol fermentators
More distantly related to mixed acid fermentatorsSome capable of pigment production – Ex: Serratiamarcescens
Many can be found in soil and water along with intestinal tract
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
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
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
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
Nonsporulating Gram-Positive Bacteria (Firmicutes)
Staphylococcus, Streptococcus, Lactobacillus, Listeria
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
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
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
Streptococcus pneumoniae
α- hemolytic diplococci, can cause upper respiratory infections and pneumonia
Enterococcus
genera of fecal origin (water quality indicator in marine waters esp.)
Lactobacillus
(also a lactic acid bacteria)Rod-shaped, resistant to acidic conditionsCommon in dairy products (pH 4)L. acidophilus good bacteria in yogurt
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
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
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
Nonsporulating Gram-Positive Bacteria
Lactobacillus and Listeria
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
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
form their own phylum
(Actinobacteria)
Over 30 taxonomic familiesVariety of morphology, including filamentous (Actinomycetes), usually aerobicMostly harmless commensals (Mycobacteriumare notable exceptions)Some species valuable for antibiotics and certain fermented dairy products
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
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)
Mycobacterium leprae
causes Hansen’s disease (leprosy)
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
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?
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
C. trachomatis
causes trachoma – eye disease and leading cause of blindness in humans
and the STD
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
Leptospira and Leptonema
Strictly anaerobic spirochetes
Rodents are the natural host of Leptospira,freq. transmitted via urine
cause of leptospirosis in humans
