Module 4 - Microbial Ecosystems Flashcards
What is the foundation of microbiology?
The study of microbes in pure culture as a pure species
What is the problem with pure cultures?
Microbes in nature do not exist under these ideal laboratory experiments
How do microbes live in nature?
As complex communities that exchange nutrients, waste products, and genetic material
How many of the total microbes are culturable?
Very few (vast majority are not culturable)
What does CFU stand for?
Colony forming unit
What is a CFU used for?
An estimation of the number of viable bacteria in a sample
How is CFU calculated?
The number of colonies that grow from a sample on solid media
Why does CFU refer to the number of bacteria in a sample?
Each individual bacterial cell can form one colony
Which environment has the lowest number of culturable bacteria?
Seawater
What is an ecosystem?
A community of living organisms in conjunction with nonliving components of the environment interacting as one system
What is life on Earth (generally)?
A collection of ecosystems
What does an ecosystem consist of?
A community of organisms interacting with each other and the environment
What does an ecosystem include?
Both biotic and abiotic factors
What are biotic factors?
Other organisms
What are abiotic factor?
Nonliving components, such as gases, minerals, and water
What defines an ecosystem?
The network of interactions between the biotic and abiotic factors
How can organisms in an ecosystem be categorized?
Based on their roles in terms of energy flow
What are the three groups of organisms, in terms of energy flow?
Producers, consumers, and decomposers
What are producers?
Organisms that capture energy and put it in a useable form
What is one of the major processes done by producers?
Photosynthesis
What does photosynthesis do?
It drives the incorporation of inorganic carbon (CO2) into organic molecules
True or false: photosynthesis is the only way communities can obtain energy
False: while the most common, photosynthesis is not the only way to obtain energy
What is a guild?
A group of organisms that carry out similar processes (but are not necessarily genetically similar)
What is microbial ecology?
The study of interactions of microbes with their surroundings
How do microbes interact with other organisms?
They may alter their metabolic activity based on competition from other organisms
What is the result of microbes interacting within their environment?
They work to modify their environment based on their metabolism
What is a niche?
The specific functional role of an organism within an ecosystem
What does a niche include?
The physiological interactions with the habitat and other organisms
How do microorganisms like to exist?
Within microenvironments
What are the characteristics of a microenvironment?
Conditions such as oxygen, pH, light, or nutrients may exist over a small distance
What happens when a microenvironment changes?
The microbes must also change in order to survive
What does the fitness of a microbe depend on?
Adaptation to the environment, and modifying metabolism through gene expression (use different nutrients to produce energy and biomass)
Where do microbes tend to grow?
On solid surfaces (biofilms)
What is a biofilm?
A collection of one or more types of microorganisms that can grow on many different surfaces
What is the purpose of a biofilm?
To allow bacteria to interact and support each other
Which microorganisms can produce biofilms?
Bacteria, fungi, and protists
What are some examples of biofilms?
The goo in the shower drain, and the plaque on teeth
What holds a biofilm together?
Extracellular polysaccharides
When are biofilms important in terms of humans?
When a human wants to rid a surface of microbes
How fast can a biofilm start forming?
Within minutes of a surface being introduced to a microbial-filled fluid
What is the first step of biofilm formation?
Specific bacteria bind to the surface and form the primary layer
What happens in biofilm formation after the primary layer is formed?
Secondary bacteria bind and secrete EPS
What does EPS stand for?
Exopolysaccharide
What is the function of EPS?
Helps protect biofilm, and form water-filled channels for transport of nutrients and wastes
What is an example of appendaged bacteria?
Caulobacter
What is special about Caulobacter?
It is specialized to attach to the surface and form the primary layer of biofilms
What is an example of EPS?
Colanic acid and alginate
What bacteria secretes colanic acid?
E. coli K 12 strain
What strains of E. coli were used to study the role of colanic acid?
A wild type strain, and a mutant strain that could not produce colanic acid
What is the result when wild type E. coli were grown in the biofilm experiment?
They formed a biofilm
What is the result when mutant E. coli were grown in the biofilm experiment?
They were able to attach to the surface, but not form a biofilm
What was the conclusion of the experiments studying E. coli biofilm formation?
Colanic acid was necessary for biofilm formation, but it was not necessary for cell attachment
How do bacteria know when to secrete EPS?
Through chemical signaling
What does the chemical signaling do during biofilm formation?
It assesses population density, and changes gene expression profiles
What is one clinical example of a biofilm?
The biofilm produced during cystic fibrosis
What bacteria is responsible for cystic fibrosis?
Pseudomonas aeruginosa
What does P. aerunginosa do in the lungs?
It attaches to epithelial cells, forms microcolonies, and secretes alginate
What is alginate?
An EPS secreted by P. aerunginosa during biofilm production
What is the advantage of a biofilm in cystic fibrosis?
Protect the bacteria from the immune system, and leads to increased antibiotic resistance
What are culturable bacteria?
Bacteria that can be grown in a lab environment
True or false: if all the bacteria could be collected, they could be cultured
False: they may not be active in the environment at the time of isolation
True or false: individual species live in isolation of their natural environment
False: they are complicated interactions between an individual and its environment
What are the two broad objectives in studying microbial ecosystems?
- How many types of microorganisms are present (biodiversity)
- What are their interactions/effects in the ecosystem
What is the estimate for the total number of bacterial and archaeal cells?
~10^30 cells
What can be said about cell number and biomass in terms of microorganisms?
There is a lot of biomass production and cellularity from non-eukaryal cells
What is one technique to grow bacteria isolated from the environment?
The enrichment method
What is an example of a type of bacteria that can be isolated through the enrichment culture method?
Nitrogen fixing bacteria (Azotobacter)
What are nitrogen fixing bacteria and what do they do?
Aerobic microbes that can bind to atmospheric nitrogen and release ammonium ions
What type of microbe is Azotobacter?
Nitrogen fixing bacteria
What is the significance of nitrogen fixing bacteria?
They can take nitrogen from an unusable source (atmospheric nitrogen) and turn it into a useable source for plants (ammonium ions)
In general, what is needed to grow bacteria in the laboratory?
A source of nitrogen
What happens if growth media without nitrogen is used?
Only bacteria that can use atmospheric nitrogen can grow in the growth media
How can nitrogen fixing bacteria be isolated?
By using nitrogen deprived media, so only the nitrogen fixing bacteria can survive on the atmospheric nitrogen
What is the purpose of the enrichment culture method?
To promote the growth of desired microbes over undesired cells
Why might microbes need to be cultured through an enrichment culture method?
They may be rare in the population, or may grow slowly
What are cultivation-independent techniques?
Techniques that can identify organisms that cannot be cultured
What are some examples of cultivation-independent techniques?
Direct sequencing, metagenomics, DGGE, TRFLP, FISH, and flow cytometry
How does direct sequencing work?
A DNA sample is extracted from the environment, and amplified through PCR. The 16S rRNA gene can then be sequenced for identification
How can unknown organisms be identified through direct sequencing?
By comparing the sequence to existing databases
What is an application of direct sequencing?
It can be used to estimate the relative number of each type of organism present in the sample
If 25/100 sequenced clones match E. coli genome sequence, approximately how many of the organisms in the sample were E. coli?
25%
What is metagenomics?
The study of genetic material recovered directly from environmental samples
What are some other names for metagenomics?
Environmental genomics, ecogenomics, or community genomics
What are the steps of metagenomics?
- DNA is extracted, isolated, and digested with restriction enzymes
- DNA fragments are ligated into plasmids
- Plasmids are transformed into bacterial cells to prepare a metagenomic library
- These sequences can be studied
How can a metagenomic library be studied?
Through sequencing and/or functional analysis
What does DGGE stand for?
Denaturing gradient gel electrophoresis
What does TRFLP stand for?
Terminal restriction fragment length polymorphism
What does FISH stand for?
Fluorescent in situ hybridization
What do DGGE, TRFLP, FISH, and flow cytometry all have in common?
They are all cultivation-independent techniques
How much of the Earth’s surface is covered with water?
2/3
Where is most of the water on Earth found?
In oceans (marine environments)
True or false: all water ecosystems are the same
False: a freshwater ecosystem is very different from a marine ecosystem
How much of the marine biomass is microbes?
98%
How much of ocean water is composed of salts?
3.5%
What are the common salt ions found in the oceans?
K, Ca, Mg, and Na
What is the highest salt found in the ocean?
NaCl (75%)
True or false: aerobic respiration can occur in oceans
True: the oceans are an oxic environment
What nutrients are low in the oceans?
Nitrogen, phosphorus, and iron
What is an example of an environment with oligotrophy?
The ocean
What is oligotrophy?
Living in an environment with very low levels of nutrients
What characteristics define an oligotroph?
Slow growth and low rates of metabolism
How can marine growth be increased?
By increasing the amount of nutrients
What happens if marine microbes are overfed?
This can lead to anoxic water conditions (dead zones)
What are dead zones?
Areas without enough oxygen to support much eukaryal life
How many identified dead zones are on the planet?
400
What is the largest dead zone on the planet?
The Baltic Sea
What has a direct connection with dead zone formation?
Agricultural activities
What are phytoplankton?
Microscopic marine plants
What is the functional role of phytoplankton?
They provide food for a wide range of sea creatures
What process do phytoplankton undergo?
They undergo photosynthesis based on the chlorophyll they have
How much of all photosynthetic activity do phytoplankton make up?
1/2
What limits the photosynthesis by phytoplankton?
Limited concentrations of nitrogen and phosphorus
What are synthetic fertilizers rich in?
Nitrogen and phosphorus
How does the Mississippi River lead to dead zones?
Fertilizers from farmland drain into the river, which drains into the Gulf of Mexico
What is the result of increased nitrogen and phosphorus in the water?
Phytoplankton bloom, increasing the amount of energy and organic carbon available
What happens when phytoplankton blooms?
There is a growth in heterotrophic microbes
What happens when there is a growth in heterotrophic microbes in the water?
They use up oxygen through cellular respiration, and create hypoxic conditions
True or false: dead zones have no life
False: they still have an active community of microbes, but not much eukaryal life
How do microbes survive in dead zones?
Not sure, but they may adapt to the low oxygen environment
What is the concentration of microbes in the ocean water?
100 million cells per mL
Compared to the microbes, how many viruses live in the oceans?
10x more viruses than microbes
How are the zones of the ocean divided?
Based on depth
What are the three zones of the ocean?
Surface zone, mid-water zone, and deep sea zone
What characterizes these three zones?
Amount of light, temperature, and pressure
True or false: light can penetrate the surface zone
True: it is the topmost layer
How deep is the surface zone?
0-200m
What are the primary producers in the surface zone?
Phytoplankton
What is an example of phytoplankton?
Cyanobacteria
What is a heterotroph?
An organism that cannot create its own food, and must take in organic substances
How is carbon and energy distributed to the other ocean layers?
Through zooplankton (consumers) feeding on phytoplankton, and virus mediated lysis
What organisms are heterotrophs?
Most bacteria, and all protists, fungi, and animals
How deep is the dark mid-water zone?
200-4000m
What is the temperature of the dark mid-water zone?
2-3 C
True or false: photosynthesis can occur in the mid-water zone
False: sunlight does not reach this zone, so photosynthesis is not possible
What materials do microorganisms feed on in the mid-water zone?
Organic matter produced by primary producers in the surface zone
What is the major characteristic of the deep sea zone?
High pressure (1000x higher than sea level)
What is the depth of the deep sea zone?
Average depth is 3500m, with the deepest being 11000m
What types of organisms can live in the deep sea zone?
Piezophiles
What are piezophiles?
Organisms that can live in high pressure environments (also called barophiles)
What helps maintain the fluidity of the plasma membrane in piezophiles?
High levels of polyunsaturated fatty acids
What is the importance of polyunsaturated fatty acids?
They help keep the plasma membrane of piezophiles fluid
How much of the primary production reaches the sea floor?
1%
True or false: primary production that reaches the sea floor is likely to biodegrade
False: biodegradation is unlikely
How come biodegradation is unlikely for primary production that reaches the sea floor?
Due to the cold conditions and lack of oxygen
What is the result of primary production not biodegrading on the sea floor?
A rich sediment is formed on the sea floor
What is the significance of the rich sediment on the sea floor?
This can be oil or gas reserves, which can be used by humans
How does the proportions of archaeons and bacteria change with depth in a marine environment?
The proportion of archaeaons increase
True or false: there are more archaeons than bacteria in the oceans
True: DNA sequencing suggests that there may be more archaeons than bacteria
Approximately how many virions live in the oceans?
~10^30 (10x more than microbes)
What is the role of viruses in the ocean ecosystem?
They supply the ecosystem with nutrients
How do viruses supply the ocean ecosystem with nutrients?
By lysing cyanobacteria, nutrients are released into the environment
What nutrients are released when lysing cyanobacteria?
Fragments of the plasma membrane, DNA, and proteins
True or false: little is known about viruses in the marine ecosystem
True: little is known about their replication cycles and their ecological impacts
True or false: viruses are integral to the proper functioning of the ecosystem
True: without viruses, the ecosystem would not function
What is needed to study the physiological and metabolic needs of microbes?
They need to be grown in pure cultures
How come microbes from the sea water cannot be cultured easily?
They cannot survive the high concentration of nutrients in the lab media
What do commercial marine isolation medias contain?
Elemental profiles similar to sea water
What are commercial marine isolation medias good for?
Isolating microbes
What are commercial marine isolation medias not good for?
Replicating the growth conditions of the natural habitat
What types of microbes are hard to culture?
Those adapted to oligotrophic conditions
How can some metabolic properties of microbes that live in sea water be studied?
Through metagenomics
What is the consequence of oligotrophic microbes?
They have a low yield of biomass, and do not support visible colonies
What technique is used to grow oligotrophic microbes from sea water?
Dilution-to-extinction
What is dilution-to-extinction?
A method to grow oligotrophic microbes from sea water
What are the steps of dilution-to-extinction?
- A sea water sample is collected, and microbes are counted using a microscope
- The sample is diluted so few cells remain in aliquot
- Autoclaved sea water is inoculated with diluted aliquots
- All samples that show growth are mixed in one bottle
True or false: dilution-to-extinction involves multiple tubes
True: multiple aliquots are needed to dilute the sample
What happens once a big bottle is generated from the dilution-to-extinction method?
The cells are centrifuged and analyzed
How are terrestrial ecosystem divided?
Into various biomes
What is a biome?
Categories of ecosystems based on vegetation characteristics
What abiotic factors distinguish biomes?
Temperature and precipitation
What are the primary producers in terrestrial biomes?
Plants
How do plants provide nutrients to the soil?
Through microbial decomposition and photosynthesis derived root exudates
What is important for the functioning of terrestrial ecosystems?
The heath of the soil
What is soil?
A thin band over the surface of Earth
How is soil formed?
Through microbial decomposition of plant and animal matter
What happens to plant and animal matter that is decomposed?
It combines with abiotic material to form soil
Where does the abiotic material to make soil come from?
The weathering of rocks
How do plants contribute to soil?
Through excreting nutrients from plant roots
How are the layers of soil determined?
Through depth
How does organic matter vary in the soil?
It is highest in the uppermost layer, and decreases with depth
What are the layers of soil (in order from highest to lowest)?
O horizon, A horizon, B horizon, C horizon, bedrock
Where is the C horizon located?
Closest to the bedrock
What is the composition of the C horizon?
Primarily inorganic material
What is another name for the B horizon?
Subsoil
What is the composition of the B horizon?
It contains some organic matter
What is another name for the A horizon?
Topsoil
What is the composition of the O horizon?
The organic matter on the soil surface
How come topsoil has the most organic material?
Due to its proximity to plant roots and decomposing biomass
Where are microbial activity and numbers highest in a terrestrial ecosystem?
Near the surface (topsoil)
What is the rhizosphere?
The area of soil immediately surrounding plant roots
What is the composition of the rhizosphere?
Large amounts of organic carbon
How come the rhizosphere has large amounts of organic carbon?
Due to the excretion of plant exudates
What is the composition of plant exudates?
Sugars, sugar alcohols, and organic acids
True or false: there are more microbes in the rhizosphere compared to the bulk soil
True: a large amount of microbes are found in the rhizosphere
How come there are more microbes in the rhizosphere than the bulk soil?
Due to the high nutrients from the plant exudates present here
What occurs at the rhizosphere?
A symbiotic relationship between plants and microbes
How do plants benefit microbes?
More carbon from plants means more growth of microbes
How do microbes benefit plants?
- Production of hormones that stimulate growth
- Production of antibiotics to control plant pathogens
- Fixation of atmospheric nitrogen into a form usable by plants
- Solubilization of phosphates to be taken up by plant roots
True or false: different soil conditions can have different microbial communities
True: these different conditions can alter the microbial ecosystem
How do microbes decide how to adapt the environment to keep growing there?
Based on the nutrient availability
How has human activity impacted terrestrial ecosystems?
Dangerous chemicals get mixed into the soil
What is bioremediation?
The process of using microbes to clean up contaminants
True or false: no microbes can naturally degrade human waste
False: some natural microbes can degrade waste, but many commercial chemicals do not come from natural processes
What is an example of bioremediation?
The use of hydrocarbon degrading microbes in petroleum-contaminated areas
What are xenobiotics?
Chemicals that are not normally found in nature
What is the danger of xenobiotics?
They are usually toxic, carcinogenic, or mutagenic (bad for human health)
What are PAHs and PCBs derived from?
Petroleum
What are some examples of xenobiotics?
PAHs, PCBs, TNT, and TCE
What does PAH stand for?
Polycyclic aromatic hydrocarbons
What does PCB stand for?
Polychlorinated biphenyls
What does TCE stand for?
Trichloroethylene
What does TNT stand for?
2,4,6-trinitrotoluene
In the future, what will potentially happen with contaminated areas?
Microbes may evolve to break down these chemicals
What is the problem with waiting for microbes to evolve to clean up contaminated areas?
This will take too much time
How can contaminated areas be cleaned up without microbes?
Physically removing the contaminant, or incineration
What is the problem with physically removing the contaminant from an area, or incineration?
It can be expensive and not practical
What is the problem with natural biodegradation?
It is slow and often limited by lack of oxygen
How come natural biodegradation is limited by the lack of oxygen?
The best degradation enzymes require oxygen to function
What is biostimulation?
Providing oxygen and other nutrients to enhance the activity of microbes
What can be dome to overcome the problems of natural biodegradation?
Biostimulation
What is bioaugmentation?
The addition of a microbe that is known to degrade a particular contaminant
What is cometabolism?
The addition of a nutrient that stimulates a broad substrate-range degradation pathway
How come Earth can be seen as a “microbial world”?
Microbes has a majority of the biomass, carbon, and other nutrients compared to other forms of life
What does a consumer do?
Ingests stored photosynthetic energy
What does a decomposer do?
Breaks down dead organic matter and recycles the components back into the environment
What are some examples of guilds?
Anoxygenic phototrophs, or thermophilic methanogens
What is chemosynthesis?
The use of elements such as hydrogen sulfide to create energy
How do organisms without light obtain energy?
Through chemosynthesis
What is one chemical formula for chemosynthesis?
CO2 + O2 + 4H2S –> CH2O + 4S0 + 3H2O
Where does the energy to fix carbon come from in chemosynthesis?
The oxidation of hydrogen sulfide (H2S)
What defines a niche?
The type, quality, and quantity of sustaining resources
How come two organisms cannot occupy the same niche?
One organism will outcompete the other and take over that niche
What is the focus of studying microbes in nature?
Which metabolic types of microbes are present (not necessarily taxonomy)
True or false: taxonomy implies metabolism
False: while there are some weak correlations, they do not hold generally
What is oxidation?
Removing electrons from a compound
What is reduction?
Adding electrons to a compound
How does a biofilm lead to more growth?
Nutrients stick to the biofilm, so it can support more growth than microbes in bulk fluid
What is another name for EPS?
Extracellular polymeric substances
Besides EPS, what can be found in a biofilm?
Extracellular proteins and DNA
What does quorum-sensing do?
Allows for coordinated signaling of microbes in a biofilm
What is a Winogradsky column?
A column that allows for the study of microbial diversity
How does a Winogradsky column work?
Mud from a swamp or pond is added to a clear cylinder, which is then exposed to light
What is the result of the Winogradsky column?
Different microbes will proliferate at different levels of the column
What microbes are at the top of the Winogradsky column?
Aerobic cyanobacteria
What microbes are in the middle of the Winogradsky column?
Green and purple sulfur bacteria
What microbes are at the bottom of the Winogradsky column?
Anaerobic sulfur-reducing bacteria
How can the different microbes be visualized in a Winogradsky column?
Based on differences in coloration
How can traditional cultivation approaches be used to get specific microbes?
By adding specific molecules to help growth
What molecules can be added to traditional cultivation approaches to help in growth?
Quorum-sensing molecules, siderophores, and vitamins
What do siderophores do?
Helps microorganisms acquire iron
What part of the rRNA is used to determine phylogeny?
The hypervariable regions
How can primers be used with 16S rRNA?
They can be used to identify all rRNA, or only rRNA from specific taxons
What is the problem with direct sequencing of rRNA genes?
The primers may be biased, and it may be hard to extract DNA
What is SIP?
A cultivation-independent method to analyze microbes in a community
What does SIP stand for?
Stable isotope probing
What are the two types of SIP?
DNA-SIP and RNA-SIP
True or false: metagenomics lead to the sequencing of an entire organism
True: this creates a DNA library for that organism
True or false: metagenomics requires cloning
False: the genes can be sequenced directly, without a cloning step
Outside of the microbial world, what is the standard measure of diversity?
The number of species
What does OTU stand for?
Operational taxonomic unit
What is an OTU?
Any group of organisms that share at least 97% small subunit rRNA gene sequence identity
What are some problems with OTU?
Low abundance can lead to noise
What is microbial dark matter?
Genomes recovered from poorly explored microbes
Besides cyanobacteria, what are some examples of phytoplankton?
Diatoms (Thalassiosira) and dinoflagellates (Ceratium)
True or false: cyanobacteria can fix nitrogen
True: this is important for the marine ecosystem
What is commonly found in marine bacteria?
Proteorhodopsin
What is the general question with cultivation-independent methods?
Who is there
What is the general question with cultivation-dependent methods?
What do they do
How do freshwater environments differ from marine environments?
Freshwater environments contain much higher nutrients and organic matter due to runoff
Why are lakes separated into zones?
Based on the temperature dependent density of water
What are the three zones of a lake (in order of increasing depth)?
Epilimnion, thermocline, and hypolimnion
What is the epilimnion?
An oxic, warmer low-density water environment
What is the hypolimnion?
An anoxic, colder high-density water environment
What is the thermocline?
A thin region where temperature and density rapidly changes
True or false: photosynthesis can occur in the hypolimnion
True: sunlight can reach this layer, so photosynthesis can occur
Why do some lakes mix?
Based on water from the bottom of the lake freezing and rising to the top
What is the importance of mixing the layers of a lake?
It redistributes nutrients
How is soil categorized taxonomically?
Based on physical characteristics
What is the texture of a soil?
The proportion of particle sizes that make up the mineral components of the soil
What is the importance of soil texture?
It is important in water retention and the concentration and interconnectedness of soil microbial communities
What can be said about soils with larger particle sizes?
They tend to have fewer microbes per unit volume, but increased diversity
What is humic material?
The incomplete breakdown of plant biomass
What is the importance of humic material?
It aids in the aggregation of soil
How are microbes arranged in the soil?
Non-uniformly, in a biofilm near soil pores
What is a major component of humic material?
Lignin
How come lignin is a major component of humic material?
It is resistant to degradation
How does diversity correlate to soil pH?
A neutral soil has more diversity than acidic or alkaline soil
What is brown rot?
The degradation of cellulose and hemicellulose, but not lignin
What is white rot?
The degradation of cellulose and hemicellulose, and the mineralization of lignin
What is the role of fungi in the soil ecosystem?
The degradation of plant matter
What is the importance of actinomycetes?
They help break down substances in terrestrial ecosystems by releasing enzymes
What is an example of cometabolism?
The methane or toluene pathways can degrade TCE
True or false: bioremediation can only occur in terrestrial ecosystems
False: they can also occur in marine ecosystems
