Development Of Microbial Communities Flashcards
(108 cards)
1
Q
How does establishment of a community occur
A
By competition
2
Q
Different types of competition
A
Direct- interference by physical fighting over resources and physically pushing others away
Indirect- by consuming scarce resources before other organisms to outcompete them
3
Q
Cooperation in a community
A
Symbiotic relationships- depending on others for survival and both benefiting from it
4
Q
Two categories of ecological processes
A
Stochastic and deterministic
5
Q
Stochastic processes
A
Occur at random. No set rules so cant predict outcomes
6
Q
Deterministic processes
A
Follow a consistent set of rules and implies that given certain parameters, the output will always be the same
Can predict the outcome once the rules and conditions of the ecosystem are known
7
Q
Stochastic vs deterministic in a newly opened environment
A
First cells to colonise will be closest= deterministic
Specific organisms to colonise is random= stochastic
The one who takes over is determined by competition and cooperation outcomes
Both have the same opportunity to colonise
8
Q
What is microbial community succession
A
As time passes and conditions change, new niches are opened which allow for the replacement of species
Creation of new opportunity for colonisation by more species
9
Q
Two types of succession
A
Primary- environments colonised for the first time eg after volcanic eruption
Secondary- in established systems when a disturbance reduces diversity leading to renewed succession due to newly available resources or removal of competition
10
Q
What happens during succession
A
Species replacement is driven by adaptation to a narrow set of environmental conditions so when conditions change an exisiting species is outcompeted by another which are better adapted
11
Q
Driving force of microbial community succession
A
Gradients- can be metabolic side effects (eg less substrate or pH change) or purposely generated metabolites (eg bacteriocins or antibiotics)
Allow them to compete with one another
12
Q
What is a disturbance
A
Trigger of a secondary succession
Processes and events which affect species composition, structure and function in an ecosystem
Can have positive and negative effects
13
Q
What happens when a distrubance isnt too big and doesnt happen too often
A
Can be drivers of change and increase diversity
14
Q
What happens when a disturbance is too big and occurs to often
A
Can collapse a community as they cant cope with the high amount of change
15
Q
How do communities respond to a disturbance
A
Depends on how strong and how fast or long a disturbance is
Its ability to go back to how it was before is based on resistance and resilience
16
Q
Resistance to a disturbance
A
Staying essentially unchanged despite the presence of disturbances
17
Q
Resilience to a disturbance
A
Returning to the reference state (or dynamic) after a temporary disturbance
18
Q
What determines at what point in a succession a microbe grows? Because organisms in the same ecosystem must have shared traits so how is it that some grow at different times to others
A
There are early and late growers which are different to one another eg the r-K gradient
19
Q
R strategists
A
Fast growers Consume and reproduce (highly) Dont compete well Need lots of respurces Dont depend on others Extreme population fluctuations
20
Q
Example of r strategist
A
Pseudomonas
21
Q
K strategists
A
Slow growers Optimal utilization- designed to extract as much as they can from a resource Conserve energy Excel in competition with low resources Efficient but slow growing Stable population numbers
22
Q
Example of a k strategist
A
Streptomyces- can make antibiotics when in competition
23
Q
Other controls of microbial community succession
A
Parasitism- one member is harmed, other benefits
Mutualism- both species benefit
Commensalism- one benefits, other is neither harmed nor helped
Social cheaters- individuals which benefit from the cooperative behaviour of other individuals without contributing to cooperation themselves
24
Q
Factors that affect the controls of community succession
A
Competition
Cooperation
Disturbances
25
Example of competition and cheaters
One species makes siderophores which take up iron and bring it back
Same species but has undergone a mutation where it cant make the siderophores but cant still take them up and take up the iron without doing the work to make siderophores- outcompete other species but dont kill it as they require it
Species 2 makes its own siderophore and the best one (out of 1 and 2) outcompetes the other
Species 3 takes up siderophore but doesnt make them so doesnt need it but will outcompete species 1
26
Two examples of insect farmers and how it works
Leaf cutter ants and termites
They collect biomass for the feeding of microorganisms they harvest
Insects prune and select for specific phenotypes from the microorganisms
Observed across many organisms
Strong co-evolutionary signals
27
The symbiotic relationship with ambrosia beetles
Have a specialised structure= mycangium to carry fungus
Plant fungus in galley by inoculating wood with the fungus
Beetle is dependent on the cultivated fungi for food
Fungus is only found in active galleys where the beetles live (beetles leave, fungus dies)
28
What is bioaccumulation
In small organisms, the nutrient amounts are trace, the more they grow the more nutrients you get
29
What is biomagnification
Small organisms with trace amount of nutrients are fed to larger organisms which then have larger amounts of these nutrients
30
Leaf cutter ants and fungal gardens (symbiotic relationship)
The fungal garden providfes a source of nitrogen for the ants and the microbes in the fungal garden fix nitrogen (only microbes can do this)
N content is higher in ants than in leaves or fungi
N content is higher in N2 enriched samples
Ants get newly fixed N from gardens
31
What bacterial isolates in leaf cutter ant fungal gardens fix N
Pantoea
Klebsiella
Azospirillum
Each type of ant is associated with its own microbe/ specific for its own N fixer
32
Ants and pesticide for their fungal farms
Ants use antibiotic producing bacteria to control fungal parasites in their fungal gardens
Leads to specialised localisation of the bacterium on the ant
Strong co-evolution link between ants, bacteria and fungi
33
How does symbiosis in termites work
Termites have the microorganisms inside them
Termites eat wood to provide more SA for reactions to occur and microbe nutrient uptake to increase (extracts easy carbohydrates)
The protozoans breakdown the wood into sugars which is used by bacteria to make aas and vitamins- fatty acid absorption by host in hindgut
The waste products of the microorganisms are used by the termites to fuel them
Other microbes inside either supply essential nutrients (N) or remove waste (CO2/H2)
34
How to find out the relationship between microbes and insect hosts
Get hold of the termite, separate digestive tract into sections to get DNA/RNA/protein
Targets systems as they are in nature
Finds what is there and who is carrying the specific functions
Can link the enzymes to the microorganisms doing it
35
What is meant by ‘not all termites are the same’
Termites which eat different things all have different microbiomes depending on their dietary requirements
Eg those that eat wood have high spirochaetes as they need them to fix N as they have no other way of getting N
36
What are wolbachia
Intracellular parasites of insects- permanently live there once inside and are passed on from a mother to all offspring once inside
Gram negative bacterial genus
20-75% of all insects have it at a time
Can infect non-insect invertebrates: nematodes, mites, spiders
37
How do wolbachia have an intrusive relationship
Almost all of their genome is transferred to a chromosome and can control some of the host transcription methods/ take over
38
Ways wolbachia hates men
Feminization
Parthenogenesis
Male killing
Cytoplasmic incompatibility
39
Wolbachia feminization
Infected female + uninfected male= all offspring infected, all males turn to females by genetically manipulating offspring into full blown or pseudo-females
40
Wolbachia parthenogenesis
Can trigger an infected female to reproduce in the absence of males= full progeny, all female
41
Wolbachia male killing
Wolbachia kills infected males to ensure only infected females live (offspring of an infected female)
42
Wolbachia and cytoplasmic incompatibility
Inability of infected males to successfully reproduce with uninfected females or females infected with another strain as it is found in mature eggs but not mature sperm so no offspring will be infected if there are offspring. Stops offspring from happening
43
Wolbachia and insect diversity
They can influence the reproduction of insects and remove it totally, therefore, removing the shuffle of diversity and evolution of insects. Stops infected and uninfected insects from mating with each other
44
Three ways wolbachia can be used to control insect vector disease spread
Cytoplasmic incompatibility- embryonic death so no transfer (using infected male)
Pathogen blocking- prevents other diseases from entering as offspring are infected (using infected female)
Life shortening- all offspring have walbachia= shortens life so cant spread disease as much (using infected female)
45
Symbiosis in the bobtail squid
The microbes in them allow them to glow
| Microbes inside get fed
46
Why do bobtail squid want to glow
For reproduction- to look good
To scare away any other organisms near
Are nocturnal- a dark figure in a starry night sky will stick out, the glowing allows them to be blended in
47
How do baby bobtail squid get V.fischeri in them (the microbe that makes them glow)
The squid have ciliated appendages which beat to dray particles towards them
Mucus is produced by epithelium and the microbes are drawn to it by chemotaxis
Mucus production is stimulated by bacterial peptidoglycan
Symbionts enter through pores and travel down ducts to crypts- are exposed to nitric oxide and hypohalous acid
48
Once baby bobtail squid have the microbes in them, how do they stop more from coming and stop the ones there from leaving
Appendages are removed from exposure to peptidoglycan and lipopolysaccharide
Cilia disappear and so does mucus shedding
Epithelial cell lining ducts swell= ducts are narrowed and shut off
~4 days these changes are irreversible and the microbes are stuck
49
What selects for different microbial communities in the ocean
Food and resources
| Physical and chemical conditions
50
How do food and resources select for different microbial communities in the ocean
Nutrients in saltwater are limited (N, P and Fe only available in trace amounts)
Causes high amount of competition to drive evolution and speciation
51
How do physical and chemical conditions select for different microbial communities in the ocean (temperature)
Surface temp is about 35 deg
Seasonal fluctuations no more than 20 deg
Below 100m temp is 0-5 deg
Drives to microbes to evolve into these different conditions
52
How do physical and chemical conditions select for different microbial communities in the ocean (pH)
pH fluctuates between 8.3-8.5
Microbes need to go into these different niches allowing for different communities
With rising CO2, pH is decreasing and microbiomes will likely change
53
How do physical and chemical conditions select for different microbial communities in the ocean (oxygen)
Tropics and around coasts are near 0 oxygen
Due to high temps= more vibrations= less able to dissolve O2 in H2O
Coastal regions have strong freshwater regions with more nutrients= more microbes around there= more competition between the microbes
Different microbes adapted to different oxygen levels
54
What does increasing depth influence
Temperature
Pressure
Light
55
What do microbes in the ocean survive on
Availability of energy
56
Sunlight and depth of the ocean
More light penetration in open oceans than coastal waters
Closer to shore= more chance sediments are mixed= scattering light
Lots of organisms in shallower water= less ability for light to penetrate
57
Different light absorbances by microbes in the ocean
Impacts the organisms present as organisms target specific wavelengths of light
58
Photosynthesis in the ocean (not done by plants)
Photoautotrophs in sunlit waters capture energy and light
Transferred to all other organisms up the food chain
Much of marine primary production is from phytoplankton (>90%), rest from marine plants and other sources
59
Plankton distribution in the ocean and why
Productivity is heterogenous over space
| As light diminishes with increasing depth so does productivity
60
How do areas of low plankton productivity get carbon and energy
Microbial and biological carbon pumps
61
How does the microbial carbon pump work
Microbial transformation of organic carbon from liable/ easily degradable to refractory states
Long lived dissolved organic carbon from the pump is an additional reservoir of sequestered carbon in the ocean
Phytoplankton= direct release, viral lysis indirect release of this carbon, is then transferred to heterotrophic bacterial communities and passed on
62
How does the biological carbon pump work
Can transfer energy and carbon from surface to deeper waters
Export of phytoplankton-derived particular organic matter from the surface oceans to deeper depths via sinking of dead bodies, large fragments of life and their waste products
Heterotrophic bacteria then constantly convert this organic matter (as they do in the microbial carbon pump
63
What do viral shunts do in the ocean with matter
Can cause recycling of nutrients
64
What is marine snow
Waste products of organisms that have been killed and are sinking
65
What are coccolithophores
Marine phytoplankton which photosynthesis and leave fossils behind by making structures out of silica
66
How can energy be harvested from light without photosynthesis
Proteorhodopsins
67
How do Proteorhodopsins work
Rhodopsins= membrane embedded proteins that absorb photon causing a physical change
Each type links the change to a specific outcome
Conformational change can cause proton or halide to be translocated from one side of cell to the other
Can initiate a signal cascade or can be used directly to power several energy requiring cell functions
Different rhodopsins tuned to different light wavelengths to optimise sensitivity or energy yield
68
Proteorhodopsins from deep in photic zone and from shallower depths
Deep= blue absorbing
Shallower= green and blue absorbing variants
Individual photosynthetic pigments only absorb a small portion of light spectrum
69
Different uses of light in the ocean
Three photosynthesis modes: classic oxygenic photosynthesis, anaerobic anoxygenic photosynthesis, aerobic anoxygenic photosynthesis
Two other light driven processes: rhosopsin based and phytochrome based
70
How to differentiate between the different light uses in the ocean
Response of different organisms to light can give clues
Improved growth in presence of light indicates and advantage
Organism doesnt die in the absence of light- benefits from it but not truly 100% dependent on it
71
How do millions of organisms survive in the ocean if they are competing for limiting resources like light
Few types of abundant microbes
Expression of genes tightly coordinated between different organisms
Transcription of proteorhodopsin and photosynthetic genes tightly synchronised to day/night cycle
Synchrony is further established by pulses of organic carbon from prochlorococcus
72
Chlorophyll changes throughout the year
Chl levels change in surface but not in deep
Linked to changes in productivity even in the deep
Phytoplankton blooms in the surface waters drive seasonality
Seasonality occurs in surface and deep water communities (bray distance)
73
What is a rumen
4 chambered stomach
Houses microorganisms
Designed for fermentation
Animal feeds microbes in the rumen, the byproducts of these microbes feed the animal
74
The 4 chambers of the ruminant stomach
```
Rumen= food churned in a rotary motion and fermentation takes place, NO SECRETIONS (9-12hr)
Reticulum= uses for regurgitation of food to increase SA for microbial attack, NO SECRETIONS
Omasum= filtering device to regulate the digesta that enters Abomasum, NO SECRETIONS
Abomasum= acidic stomach, secretes gastric juices, protein denatured, site of bacterial protein assimilation by animal
```
75
Important features of the rumen (living chemostat)
Large size= retention of food for microbial attack
High constant temperature, pH (saliva helps control pH with its carbonate)
Anaerobic environment= supports microbes in symbiotic association, ability to digest cellulose and anaerobic fermentation
76
The symbiotic relationship between ruminants and rumen microorganisms
Microbes get a home and steady food supply
Ruminant paid in energy (volatile fatty acids)
Animals dont have enzymes to breakdown cellulose so the microbes do this
77
How do we study the rumen in live animals
Fistulated animals
| Fecal samples
78
What lives in the rumen
Prokaryotes (~10^10 cells per grams of contents)
Protozoa (10^3 - 10^6 cells per gram of contents)
Fungi (difficult to quantify, ~6%)
79
Types of prokaryotes in the rumen
```
Cellulose degraders (bacteria)= fibrobacter succinogenes and ruminococcus albus
Starch degraders (bacteria)= bacteriodes ruminocola and streptococccus bovis
Lactate degraders (bacteria)= megasphaera elsdenii
Methanogens (archaea)= methanobrevibacter ruminatium
Chew through carbon= corrosion of the contents as they do this
```
80
Uniqueness of rumens
Not all the same, but provide the same/ similar functions
| Shaped by diet and species
81
Process of what the microbes in the rumen do
Hydrolyse and ferment cellulose, starch and sugars (plant feed)
Produce acetic and propanoic and butyric acids (short chain fatty acids) aswell as CO2, CH4 and H2O
Volatile fatty acids are produced, providing carbon and energy source to the animal
82
What happens to microbes that get past the rumen
Killed off so their building blocks can be harvested (provide ~90% of aa and vitamin requirements)
83
What is syntrophy
Metabolic interaction between dependent microbial partners
| Waste products handed directly from one to another= direct transfer= benefit for both
84
Example of syntrophy in the rumen
Inter species hydrogen transfer
Production of H2 by one organism and consumption of the H2 by another
Pairing of redox reactions between the two organisms
Transfers electrons and H2 to the other organism which uses CO2 as the electron acceptor
Produces methane
85
What happens in the rumen without methanogens
Partial pressure of H2 builds up and oxidation of NADH and H+ is impaired= animal malnutrition
86
What happens in the rumen with methanogens
Keeps the [H2] low by converting CO2 into CH4 and O2 through fermentation
Fermentation directed towards short chain volatile fatty acids like acetate
87
What are methanogens
Hydrogenotrophs= eat the hydrogen
Keep partial pressure of H2 low and fermentations are directed towards formation of organic acids used by the animal
Abundant in the rumen
88
Environmental outcomes of ruminant animals (especially in NZ)
Approx 500-1000L of ruminal gas is produced by fermentation are belched each day (CH4)
89
Strategies being explored to limit methane production in ruminants
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Feed additives (oils, essential oils, tannins, saponins)
Direct fed microbials (yeast)
Enzymes for fibre digestion
Farm systems
Protozoa and phage
Feeds (brassicas etc)
Animal genetics to have low/high methane
Vaccine against methanogens
Chemical inhibitors of methanogens
```
90
Getting rid of methanogens in ruminants?
Can cut methane emissions by up to 90% (can be done with inhibitors or seaweed)
Means other organisms need to step up to reduce the partial pressure of [H2]
91
Different parts of soil and the composition
Minerals (rocks= inorganic nutrients)
Air (O2 and all other gases in the atmosphere)
Water
Organic material (live and dead biomass, carbon based molecules excreted by organisms or produced from degradation)
Composition varies between different soils. All soils have their own unique systems and compositions
92
What does not all rocks are the same mean
Different rocks provide different nutrients to organisms
Contain lots of micronutrients for sustaining life
Understanding the rocks in a soil can tell what organisms are there
93
How do rocks become soil
Weathering- changed by physical, chemical and biological processes into other soil components
Five factors driving it= parent material, climate, living organisms, topography, time
Processes include freezing and thawing, erosion by elements, roots of plants, burrowing animals, insects and microbes, water relations wetting and drying, changes in chemical composition and volume
94
Rock size and pores in soil
The larger the particles from weathering, the larger the particles allowing water (carrying nutrients) and air ( with gases such as important electron acceptors and donors) to pass through
Smaller= smaller pores
95
What else does soil structure affect
Microbiome composition and activity
| Creates selective pressures for the microbes
96
Soil and successions
Making soil takes time
| Soil development coincides with aboveground successions of plant communities
97
From rocks to soils
Parent material is weathered
Further degrading allows for colonisation of simple organisms= carbon and adds photoautotrophs
Horizons form
Multiple horizons form= well developed soil
98
Importance of addition of photoautotrophs to soils
Provides carbon and increases energy and activity
Increases degradation
Allows other species to grow there
Speeds up soil production
Plants growing and dying provides more biomass
99
Gradients in soil
Organic material at top, decreasing going down
Inorganic material at bottom, decreasing going up
Organic layer is proportional to the amount of biomass in the soil
100
How are soils classified
Using texture triangle based on grain size
101
Soils in different climates
Dessert soils= little moisture, little degradation, little amount of life
Temperate= systems developed for fast growth,
Tropical= thin layer of life due to consistent high temperature and high moisture= high degradation
102
Soil taxonomy
```
Mimics species taxonomy
Order
Suborder
Great group
Subgroup
Family
Series
```
103
The soil habitat
Consists of aggregates within aggregates- studying an average= difficult to know exactly what is going on
Microbe aggregates have different niches which lead to diversity in soils
104
Soils and selecting for microbes
Select for specific organisms and the organisms in return modify their environment
Increased biodiversity results in increased habitats= many different conditions
More gradients= more life to sustain= more gradients= more diversity
105
What do soils do for us
Extraction of raw materials and water
Physically supporting buildings and other man-made structures
Production of biomass- raw materials and other materials
Filtration, buffering, storage and chemical/ biochemical transformations
Preservation of biodiversity or potentially useful genetic material
Preservation of geogenic and cultural heritage
106
Soils and ecosystem services
Ecosystem services are the direct and indirect benefits that humans freely gain from the natural environment and form properly-functioning ecosystems
Cultural, provisioning, regulating, supporting
107
Soils and agriculture
Add pressure: the more wet, the deeper the influence of weight, decrease pore space with pressure
Not all soil on the planet can be used for growing, need to maximise production on land- using nitrogen fertilization
Get nitrogen from animal piss
Most of the nitrogen is released as nitrogen oxide into atmosphere= greenhouse gas
108
Factors determining N transformation
pH
Moisture
Carbon availability
Genetic potential
Other microbiome related factors
Many organisms and many genes are involved in N transformations
Changes in conditions modify the activity and presence of microbes harboring these genes
