L1 - Microbial Diversity Flashcards
Describe what a microbe is and th difficulty of defining it.
- Anything NOT a multicellular animal or plant
- Not a taxonomic term
- Microbes from all 3 kingdoms of life
Describe the prokaryotes
How are species within the prokaryotes defined?
- Bacterial (Eubacterial) and Archaeal Kingdoms
- Biological species concept doesn’t work (no sexual reproduction)
- Defined operationally as collection of strains with very similar traits
- E.g. >70% DNA-DNA hybridisation or >97% 16S rRNA similarity
Give a characteristic that separates the bacteria into two groups
Gram negative:
- cells w/ outer lipopolysaccharide membrane surrounds peptidoglycan cell wall
- Most bacteria
Gram positive:
- no outer membrane, thicker peptidoglycan cell wall
Describe the major two groups of gram negative bacteria
Describe the major two groups of gram positive bacteria
Gram negative:
Proteobacteria:
- Contains many species using plant-microbe interactions e.g. Rhizobium
Cyanobacteria:
- Oxygenic phototrophs
- E.g. Anabaena cylindrica, in low N certain cells differentiate to N2 fixing non-photosynthetic heterocysts
Gram positive:
Firmicutes:
- Low genomic GC content
Actinobacteria:
- High (>50%) GC content
Detail how the cell walls seen in archaea compare to those seen in bacteria?
Give 6 points
Archaea:
- more diverse cell walls
- no peptidoglycan
- generally lack outer membrane
- most commonly have S-layer, paracrytalline layer of glycoprotein, providing osmotic protection
- S-layer also seen combined w/ polysaccharide layer e.g. pseudomurein
Bacteria:
- S-layers also found, mainly in gram positive
Eukaryotic microbes: Fungi
How many fungi species are there?
- At least 1.5M, up to 5M
Describe the three major groups relevant to this course
Ascomycota (sac fungi)
- 64,000 sp. (all sp. probably underestimate)
- Septate hyphae
- Spores produced inside ascus (sac)
Basidiomycota (club fungi)
- 32,000 sp.
- Septate hyphae w/ clamp connections
- Spores produced externally from basidium
- Includes all toadstalls and mushrooms
Glomeromycotina (Arbuscular mycorrhizal fungi)
- 640 sp.
- Non-septate hyphae
- Large multinucleate spores
- Obligate biotroph, forms arbuscles in host tissue
Eukaryotic microbes: Algae
Outline the algae, no. of species, diversity, evolutionary history
- 30,000 - 1M species
- Both macroalgae (seaweeds) and microalgae (unicellular or aggregations)
- 3 basal groups evolved after primary endosymbiosis between primitive eukaryotic cell and photosynthetic cyanobacteria
Name the 3 basal algae groups and the photosynthetic pigment(s) used
Chlorophyta (Green algae)
- “Green” plastids, use Chl a + b
- Plants evolved from chlorophyta
Rhodophyta (Red algae)
- “Red” plastids, use Chl a and phycobilins
Glaucophyta
- Use Clh a and phycobilisomes
- Most basal group
Why is there so much diversity in algal forms, especially in the Red Algae and Green Algae lineages?
- Large number of secondary + tertiary endosymbioses in chlorophyta and rhodophyta
- Pigment variation allows many ecological niches, e.g. water depth gives varying light quantity + quality from Rayleigh scattering. More red light deeper = different pigment
- Plastid loss in many lineages e.g. non-photosynthetic malaria parasite (Plasmodium)
What is metagenomics and why is it beneficial?
Give an important example of a previously unknown clade that was discovered through metagenomics
- Identifies many microbial clades using only sequence information
- Reduces bias towards microbes that can be cultured
- SAR86 clade of 𝜸 - proteobacteria
- Hugely abundant in ocean
- Identified from 16S rRNA sequences, uncultured
- Inc. genes for glutathione transport + metabolism = potential sulphur source?
Describe an important paper that relied on metagenomics
- Luo et al. (2014)
- Global warming could have significant effects on microbial communities
- Significant changes in microbe populations in grassland soil samples heated by 2˚C for 10 years
Outline a big case study on fungal diversity that used metagenomics
- Global Fungal Diversity (Tendersoo et al. 2014)
- 365 sites sampled globally and metagenomics applied
- Relative proportions of main fungal groups varied significantly across biomes e.g. spike in EctoMycorrhizal fungi with northern pine forests
- Ratio between plant + fungal richness declines exponentially as you move away from the equator
Outline a second case study related to microbes in the sea
Sketch the relevant diagram
- Bermuda Atlantic Time-series Study (BATS) (Giovannoni and Vergin, 2012)
- Fixed locations sampled monthly in Sargasso Sea and microbes profiled
- Winter: turbulent oceans mixes nutrients into photic zone, reducing cell density
- Spring: eukaryotic phytoplankton use sunlight + nutrients = “Spring Bloom” population
- Summer: Prokaryotic phytoplankton dominate in three communities:
a) Upper Euphotic Zone community (UEZ) - heterotrophic bacteria
b) Deep Chlorophyll Maximum (DCM) - cyanobacterial sp. e.g. Prochlorococcus
c) Upper Mesopelagic Zone (UMP) - heterotrophic bacteria, feed on sinking nutrients
See diagram on pg. 7
