Bacterial Diversity Flashcards
What are the three domains?
- Bacteria
- Archaea
- Eukarya
What revolutionised classification?
16S rRNA phylogenetic
Where is the prokaryotic taxonomy catalogues?
Bergey’s Manual of Systematic Bacteriology
How are bacteria distinguished?
By Gram stain
What are the types of Gram stain?
- Gram-positive
- Gram-negative
What is a Gram-positive?
- Very simple cell wall structure
- Does not involve outer phospholipid bilayer
- Thick outer layer of peptidoglycan
- Stain purples
What is a Gram-negative?
- Phospholipid bilayer
- Thinner layer of peptidoglycan
- Thicker phospholipid bilayer (asymmetric)
- Stains pink
Which Gram stains pink?
Gram-negative
Which Gram stains purple?
Gram-positive
How do you have a greater speciation in some genera?
Using multigene analysis
How is there better speciation in some genre by using multigene analysis?
16S rRNA is further divided by multi locus sequences typing picking genes around the genome
What type of Gram is proteobacteria?
Gram-negative
How is proteobacteria divide?
- Alpha - α
- Beta-β
- Gamma - γ
- Delta - δ
- Epsilon - ε
Describe proteobacteria:
- Metabolically diverse
- Many environmental habitats (symbiont/nitrogen-fixers/aquatic environment)
- Major human pathogens exhibit chemotrophy under aerobic conditions
What is an alpha proteobacteria?
Rhizobiales
What are the genus of Rhizobiales?
Agrobacterium
Bradyrhizobium
Nitrobacter
Rhizobium
What feature does Agrobacterium have?
Plant pathogen
What feature does Bradyrhizobium have?
Symbiotic nitrogen fixer
What feature does Nitrobacter have?
Nitrifying
What feature does Rhizobium have?
Symbiotic nitrogen fixer
What do Bradyrhizobium/Rhizobium do?
- Form symbiosis with plants
- Fix nitrogen to ammonia
What is a beta proteobacteria?
Neisseriales
What are the genus of Neisseriales?
Neisseria
What are the features of neisseria?
- Human pathogen
- Characteristic diplococci
- Medically important species (Meningitis/gonorrhoea)
What is a gamma proteobacteria?
Enterobacteriales
What are the genus of Enterobacteriales?
Shigella
Escherichia
Salmonella
What are the features of Shigella/Salmonella?
- Human pathogen
- Responsible for serious food poisoning
What are the features of Escherichia?
- Human commensal, some pathogens
- Common inhabitant of intestinal tract but uncommon pathogen
- Very important research tool (e.g E.coli)
What are Enterobacteriales?
- Largest sub-group of the proteobacteria
- Most pathogenic species in this group
What is a delta proteobacteria?
Spirilla
What are the genus of Spirilla?
Bdellovibrio
What are the features of Bdellovibrio?
- Uses other bacteria as a host
- Curved bacteria
- Potential antimicrobial (wide spread in soils and aquatic environments)
What is an epsilon proteobacteria?
Campylobacterales
What are the genus of Campylobacterales?
Campylobacter
Helicobacter
What are the features of Campylobacter?
- Human pathogen
- Highly motile bacillus, curved
- Medically important species (foodborne disease)
What are the features of Helicobacter?
- Human pathogen
- Has multiple flagella
- Causes stomach ulcers
What Gram is bacteriodetes an example of?
Gram-negative
What are the four major orders of Bacteroidetes?
- Sphingobacteriales
- Cytophagales
- Flavobacteriales
- Bacteroidales
What are the types of Gram-positive bacteria divided?
- Low G+C
- High G+C
On what bases are Gram-positives divided?
Based on the %GC content in the genome
Is this a high or low G+C?
atagagctaa ttattggaaa agataaaaag gggataagaa taaataaagt tcctttacaa
Low G+C
Is this a high or low G+C?
acaatgggcg caagcctgat gcagcaacgc cgcgtgaggg acgacggcct tcgggttgta
High G+C
What are low G+C known as?
Firmicutes
What are high G+C known as?
Actinobacteria
What are the different orders of low G+C?
- Lactobacillales
- Bacillales
- Clostridiales
What are the genus of Lactobacillales?
Lactobacillus
Streptococcus
What are the genus of Bacillales?
Straphylococcus
Bacillus
What are the genus of Clostridium?
Clostridium
What are Lactoballius and Streptococcus members of?
Lactic acid bacteria
What are lactic acid bacteria?
- Produce lactic acid during metabolism
- Tolerant to low pH
What acidic by-products are produce from Straphylococcus, Bacillus and Clostridium?
- Butyric acid
- Propionic acid
- Acetic acid
What are the features of Lactobacillus?
- Lactic acid produces
- Human commensal (fermented products - yogurts)
- Variable size
What does lacto mean?
Milk
What does bacillus mean?
Rod shaped
What are the features of Streptococcus?
- Many human pathogens
- Human commensals
- Medically relevant (subdivide by haemolytic)
What does strepto mean?
Twisted chain
What does coccus mean?
Spherical/round
What are the features of Staphylococcus?
- Some human pathogens
- Medically important pathogens (boils, produces toxin/MRSA)
What does Staphyl mean?
Grape
What are the features of Bacillus?
- Rod shape
- Endospores (enables survival during extremes of environments)
- Human pathogens
- Medically important
What are the features of Clostridium?
- Anaerobes
- Endospores
- Human pathogen
- Location of spores help to identify the species
- Medically important
What an order of high G+C?
Actinomycetales
What are the genus of Actinomycetales?
Actinmyces
Frankia
Streptomyces
What are the features of Actinmyces?
- Filamentous
- Branching
- Human pathogen
- Facultative anaerobe
- Look like fungal hyphae under microscope
- Important fro soil ecology
What are the features of Frankia?
- Symbiotic nitrogen fixers
- Filamentous
- Carry out nitrogen fixation in soil
- Atmospheric N to ammonia
What are the features of Streptomyces?
- Filamentous
- Produce antibiotics
- Form mucelium
- Produce sports called conidia
- Occurs during nutrient depletion
Are conidia the same as endospores?
NO
What is must commons sub-division containing many human pathogens?
γ- proteobacteria
Why do we know so much about the Gram negative Proteobacteria, Bacteroidetes and Gram positive Firmicutes?
They are easily cultural and grown in the lab
How can we study non-culturable bacteria?
- Culture independent analyses
- Assess phylogeny into species group
- FISH (Fluorescent in situ hybridisation)
What is culture independent analysis to identifying non-culturable bacteria?
fluorescent oligonucleotides bind specific DNA
What are examples of fluorescent oligonucleotides?
- DAPI
- Acridine orange
- SYBR Green 1
What is assess phylogeny/classify bacteria into species group to identifying non-culturable bacteria?
Phylogenetically classify non-culturable bacteria you need to study the 16S rRNA gene of the bacteria
What is FISH in relation to identifying non-culturable bacteria?
Different coloured oligonucleotides match different 16S rRNA sequences
What is an ecosystem?
Sum of all organisms and abiotic factors in a particular environment
What is symbiosis?
Mutualism and commensalism
How is mutualism symbiosis?
Both species benefit
How is commensalism symbiosis?
One species benefits, the other neither harmed nor benefited
What is syntrophy?
Two or more organisms catabolising a nutrient that can not be catabolised by one on its own
What is an example of commensalism to mutualism?
Bacteria living in our large intestine supply us with vitamin K
What is species richness?
The total number of species present in an ecosystem
What is species abundance?
The proportion of each species in an ecosystem
What are Archaea more suited to?
Extreme conditions below the photic zone
What is microbial ecology interaction with plants?
- Legume-root nodule symbiosis
- Essential in fixing nitrogen and suppling to plants
What is microbial ecology interaction with mammals?
- Human microbiome project
- Gut microbiome
What is facultative anaerobe?
Makes ATP via aerobic respirations if oxygen is present BUT can also do anaerobic respiration
What is obligate aerobe?
Cannot make ATP in absence of oxygen
