Microbial diversity

early earth atmosphere

• Microbes in isolation artificial, microbes will always be found in communities

• Highly anaerobic —> highly reducing atmosphere which favoured the formation of organic molecules from inorganic compounds

• All life on earth microbial from 3.7-4.3 bn years ago to the next 3bn years on

• Single celled bacterial like organisms living of hydrogen and sulphur

• Likely withstranding high temps

• Cyanobacteria popped up around 2.7-3.5bn years ago and caused the great oxygenation event

• Cyanobacteria can photosynthesise —> producing oxygen which changes the atmosphere

LUCA

 

• Everything comes from luca

• Highly diverse bacteria that we only know from DNA, haven’t cultivated

• Leading hypotheses is the 2 domain system: bacteria and arhcera are the 2 branches and eukarya come from archea

Microbial groups

• prokaryotes 

• eukaryotes 

Prokaryotes

• Bacteria and archea

  • BACTERIA: E.g: myxobacteria which form fruiting bodies or spirochetes which form spiral shapes

  • ARCHEA: E.g: haloquadratum

• Do not have a nucleus, bound by a nuclear membrane

• Previously thought that prokaryotes were limited to bacteria, due to 16S rRNA genes we can categorise diversity of life and realise that not all prokaryotes are bacteria

• difficult to classidy due to horizontal gene transfer - how much DNA do you have to pick up before considered a new species?

Microbial groups

• prokaryotes 

• eukaryotes 

Eukaryotes

• Broad groupings:

  •  fungi (including yeast)

  • protists (megagroup of things that are lumped together)

• all have mitochondria

• Contain a nucleus or membrane bound structure which contains the cells genetic material (nuclear envelope)

bacteria 

• Greatest metabolic/taxonomic diversity so can inhabit all habitats

• Can break down any compound

• Range in size from 0.5 microns to 2 microns (avg) but some can be as small as 0.2 microns or as large as 0.75 mm

• Roughly 90 bacterial phyla,

• 99% uncultured

• Have no compartmentalisation, typically single celled

• Typically have a single circular chromosome in the cytoplasm

• Largely grouped into gram neg and gram pos

  • Gram -ve: small cells wall

  • Gram +Ve: thick peptidoglycan cell wall

• Lots are facultative so can swap between 2 different metabolisms

• Critical for all biogeochemical cycling

• Ester linked lipids and shares this with eukaryotes —> this is one of the pieces of evidence for endosymbiosis theory

bacterial groups 

Actinobacteria – filamentous bacteria

• Grow in long threads

• Streptomyces produce antibiotics naturally which they use to compete eachother

Wolbachia

• Obligate intracellular bacteria which infect insects

• 80% of insects on the planet infected and affects the sexual fitness of the host —> manipulates host fertility to survive

• If the host isn’t infected with woolbachia its infertile

Nitrogen cyclers

• Nitrogen fixers

• Ammonia oxidisers

• Nitrate oxidisers

• Denitrifiers

Spirochetes

Cyanobacteria

Bdellavibrionota

• o   Predatory – attack and infect other bacteria and eat it from inside out

Archea

• Newest discovered

• Oldest organisms on the planet

• Thrive in extreme environments but are ubiquitous

• Small number isolated and studied in the lab, don’t know much about metabolic function

• A lot of methanogens (produce methane)

  • strict anaerobes (oxygen inhibits methanogenesis) found in animal gut, lake sediment etc.

  • prefer low sulphate environments as theyre out competed by sulphate reducing bacteria

  • perform several metabolic functions which all lead to methane as the product

• asgard archea are the branch that are believed to lead to eukaryotes

• ether linked lipids which are more chemically stable too deal with extreme environments

fungi

• two morphological types

  • yeast: asexual budding

  • filamentous fungi: grow on threads and form fruiting bodies

• vital for breaking down dead organic matter, more efficient than bacteria at breaking down lignin and cellulose

• release enzymes which dissolve stuff

• have membrane bound organelles and chitin in cell walls

major groups of fungi

Ascomycota

• Sac fungi, most diverse

Basidiomycota

•  Club fungi

Glomeromycota

• Ancient fungal lineage

•  Obligate symbiote with plants – gets all its carbon from plants, in exchange plants get nutrients.

• Acts as an extended root system

Chytridomycota

• Earliest diverging fungal lineage

• Motile spores (needs moisture)

• Chytridiomycosis —> devastating amphibian populations worldwide

Zygomcyota

protists

• Artificial grouping with no evolutionary heritage

• 60,000-100,000 species

• Little phylogenetic grouping, 40-50 unrelated phyla

• Don’t have any tissue organisation

protist groupings

• Used to be based on locomotion strategies

• Lots of taxonomic issues

• Broad groupings:

  • Flagellates: have flagella, free living predators  

  • Amoebae: amorphous ( no shape), free living predators and move through false feet known as pseudopodia

  • Ciliates: cilia for locomotion

  • Stationary (sporozoa): nonmobile protozoans, some undulating ridges

protist algae

• Photosynthetic protists containing chlorophyll A

• Can be single celled or complex multicellular

• Highly diverse

• Base of aquatic food web

• Fix a lot of carbon in oceans

measuring diversity

• first observed under a microscope, then began to culture them

• Culturing came up with the great plate count anomaly – only a handful of things can be physically cultures on a plate, would be different if you cultures in a liquid broth

• Molecular techniques include 16S rRNA gene sequencing

microbial functions

• Microbiomes in gut determine how healthy you are and foods you prefer

• Particular genes to break down different foods E.g: seaweed, which are particularly well picked up in Japan

• Important for climate regulation – Methanogens produce methane, some consume methane

• Nitrogen cycling – rhizobium takes up nitrogen from atm —> ammonium, another bacterium picks up ammonium to nitrite, nitrite converted to gas

  • Some bacteria can do the entire process itself

• Some fungi can induce stress in plants

• Lots of bacteria can produce compounds which can deter insects

• Some bacteria can break down pesticides

microbial interactions

• interactions between microbes determine the type of community developing 

·       positive interaction = plus, negative = minus, neutral is a circle

• Mutualism is when both partners benefit, E.g: mycorrhizal fungi – plants feed the fungus and the fungus gives nutrients back to the plant

  •  Cross feeding (example of mutualism) is when a bacteria feeds off something, E.g: sugar and produces metabolites which are needed by another bacterium. This is one of the reasons that culturing bacteria in isolation is so difficult

• Commensalism is when one bacteria benefits and the other one is unaffected. E.g: colonised by bacteria and you are unaffected but the bacteria is safe from being killed

• Parasitism is when one bacteria benefits and the other one loses out

• Amenalsim is when one bacteria has no effect, the other bacterium has a negative effect —> E.g: natural production of antibiotics by bacteria

• Competition is when the 2 bacteria are fighting eachother, both lose out

fungal highways

• Can either be a commensalism or a mutualism, depends on whether the fungus gets something back

• Fungal hyphae provide a surface for bacteria to colonise, sometimes bacteria can provide nutrients like vitamin B1

• The way that mycorrhizal fungi give phosporous to the plant is because the bacteria colonising the fungi produce phosphorous

biocrusts

• Example of a consortia of microbes algae, fungi, cyanobacteria which associate with lichens or mosses

• Generally biocrusts are the first colonisers and they reshape the environment

• Add carbon and nitrogen to the environment

• They have roles in reducing wind and water erosions, helping water retention and reducing UV pressure (production of scytonemin) the underlying soil

biofilms

• Multiple species consortia

• Release of extracellular polymetric substances – polysaccharides, DNA etc

• Resistant to perturbation and antibiotics, provides predation protection

different environments: soil

• One of the most complex environments

• High microbial abundance

• Rich in organic matter

• Lots of carbon —> ideal for colonisers

• Microbes essential for recycling nutrients, decomposing organic matter

• Microbes found up to 3km deep, could be in a dormant state waiting for water, nitrogen etc.

• Soil is so complex due to aggregates – micro and macro aggregates

  • Macroaggregates is a binding of lots of microaggregates

  • Individual particles are held together by “microbial gums” such as the polysaccharides that make up EPS of biolfim

  • Between the aggregates are pore spaces which allow the movement of air, water, microbes

pore spaces in soil

• Micro and macro aggregates have pores have pores which bacteria can exist in

• Can be beneficial as may be protected from other organisms. E.g: protists

• Oxygen and water can limit oxygen diffusion —> more denitrification and less nitrification

  • Usually water flows around macroaggregates but sometimes water can impact pore spaces between microaggregates

  • Water dries and created bridges which lock off the oxygen in the pore —> can form an anaerobic environment

water and oxygen relationship

• Solid aqueous phase and gas phase in soil

• Wet soils have trouble diffusing oxygen

• Dry soils have problems diffusing nutrients

• Very dry soils limit microbial activity as they need water for metabolism

biogeography

• The study of organisms in space and time

• Closer to the equator more species diversity for most organisms except bacteria —> they peak in temperate regions

• Hypothesis for this is that they avoid competition with fungi by doing this

Different environments: plants

Phyllosphere

• Above ground

• Bacteria grow on leaves

• Infection can occur through the stomata

• Also colonise trichomes

Rhizosphere

• Below the ground

• Hotspot of biogeochemical activity around the roots of the plants

• Different from the soil environment as plants change the local environment through oxygen conc, pH, sugars, amino acids, secondary metabolites.

• A particular group of bacteria which are enriched —> high turnover, high growth rate

• Certain taxa which don’t like that environment

communication with the environment

• Plants produce exodates —> carbon compounds that act as food sources for microorganisms

• Plants produce volatiles or phenolics which herbivores react to eat —> plants try to avoid releasing these

• Plants release strigolactones in phosphorous limiting conditions which triggers arbuscular mycorhhizal fungi to colonise

• BUT the germination of parasitic plants is also triggered by strigolactones

mycorrhizal fungi and plant interactions

Ectomycorrhizal and arbuscular mycorrhizal fungi

• Ectomycorrhizal – grows outside the fungi

• Arbuscular – respond to strigolactones, enter the cells and produce arbusclues which exchange nutrients

• Bacteria like rhizobium can infect a legumous plant and form nodules —> forms a mutualism

different environments: oceans

• Exist in every element of marine settings

• Biological pump – phytoplankton photosynthesise and put carbon into the system, sinks, gets sequestered into deep sediment (never sequestered for ever) at some point gets eaten,

• Microbial loop – phytoplankton produce carbon, cells explode and carbon is released, heterotrophic bacteria eat that and produce carbon dioxide which goes back into the atmosphere

Phycosphere

• Is a hotspot of microbial activity which surrounds phytoplankton when they die

• Analogous to the rhizosphere

• Bacteria use chemotaxis to swarm towards the phycosphere

Different environments: animals

• Animals associate with microbes

• Can be categorised into pathogenic or symbiotic relationship

• Can have organ specific microbiomes —> skin microbiome which acts as a physical barrier, gut microbiome

different environments: insects

• Infect up to 65% of all insect species

• Manipulate insect reproduction by

  • Cytoplasmic incompatibility

  •  feminisation

  • Male killing

• By releasing uninfected Wolbachia, they will reproduce but their offsring are infertile

termite gut mutualisms

• One of the most efficient bioreactors in the planet

• Termite gut community has a symbiotic relationship in gut essential for survival

• Lignin and cellulose are broken down to provide rich carbon source

• However, they do not contain nitrogen so nitrogen fixers required to produce bioavailable nitrogen

• Also contain protists within the gut —> protist eats the wood in the gut which causes the breakdown

fungal parasites - zombie ants

• Fungi infects insects and hijacks their behaviour – causes the insect to attach to the underside of the leaf for spore dissemination

microbial behaviour

• In consortia microbes communicate via quorum sensing mediated by autoinducers

• At a certain density of cells will switch on or off a certain behaviour

• Density-dependent communication strategy

• Cyanobacteria at a certain density produce this structure called heterocysts which is the format needed for nitrogen fixation

extremophiles

• Microbes which live in extreme environments that are detrimental for other forms of life

• Acidophiles – live between pH 3-5 but can be lower

  • Pump out protons to counter the acid

  • Have proteins which are extremely stable

• Alkaliphiles – live in alkaline environments

  • Pump in protons to counter high pH

• Halophiles – love high salinity (3-15% moderate halophiles, 15-30% extreme)

  • High salt levels cause proteins to aggregate which can cause cell dessication from osmosis

  • As a result produce osmoprotectants (amino acids, sugars, betaines) which accumulate inside cell to balance osmotic difference

• Thermophiles – exist in habitats over 100 degrees

  • Proteins denatures and so have chaperone proteins which can prevent this

• Pschrophiles – low temperatures (-20-+10 degrees)

  • Can produce antifreezes

  • Lipid membranes which are chemically resistant

  • Enzymes which retain activity at low temperatures

• Xerophiles – arid deserts

  • Scytomenin is a compound for UV absorption

  • Has a state of anhydrobiosis (state of low metabolic activity) to counter the low cell water content