Class 11: Ecosystems:

o Governed by: Biotic components Abiotic components

o Distinguished by: Climate Vegetation Stability/dynamic of ecosystem Dominate producer Dominate consumer Richness Diversity of species

o Similar ecosystems have similar communities Stratification important and controlled by temperature Productivity affected by:

o How fast cells growo Nutrientso Turnover rateso Carbon availableo Feeding strategies

Lecture Study Guide: Know all the terms discussed in class today.

o Biosphere: total living world in all aspects of the environment.o Ecology: study of the organisms and the biotic and abiotic elements of

their environment.o Ecosystem: abiotic environment and community that inhabits it o Community: self contained group of interacting organisms that share

the same habitat o Populations: self contained interacting group of the same species o Lithosphere: rocks, sediments, soils, weatheringo Hydrosphere: everything having to do with watero Atmosphere: what we and microbes can “breathe”; not just oxygeno chemical/limiting factors: pH, nutrients (trace minerals), types of

carbon available, lighto Biomass: how much living material in an ecosystem, how much is

producingo Biogeochemical cycles:

Decomposition: complex organic into simpler organic matter. Mineralization: breakdown of organic matter into inorganic.

Assimilation: transformation or incorporation by organisms/microbes converting energy into nutrients.

Immobilization: the incorporation of a simple, soluble substance into the body of an organism, making it unavailable for use by other organisms.

What types of abiotic and biotic factors are important in controlling ecosystem processes?

o Abiotic: lithosphere, hydrosphere, atmosphere, chemical/limiting factors

o Biotic: individual requirements/feeding strategies, biomass, production/productivity, decomposition, interactions (symbioses (definition: the living together or close association of two dissimilar organisms, each of these organisms being known as a symbiont), predator/prey, competition (definition: an interaction between two organisms attempting to use the same resources [nutrients, space, etc.]), population level, community level)

What are the major differences between aquatic and terrestrial environments?

o Aquatic: ~stable C:N ratio. more constant C:N ratio because of the phytoplankton microbial loop within the aquatic systems

Winter: sunlight low, inorganic nutrients high Spring blooms→ high phytoplankton biomass Spring-Summer→ Inorganic nutrients are immobilized in

phytoplankton cells, phytoplankton biomass drops Fall→ small bloom, inorganic nutrients increase in environment

o Terrestrial: declining C:N ratio because of CO2 lost to the system and plant biomass.

What controls primary production (the incorporation of CO2 into organic matter by photosynthetic organisms and chemosynthetic organisms)?

o Temperature, light, water, and nutrients Aquatic: temperature, light, nutrients Terrestrial: temperature, water, nutrients

What is net primary productivity and how would one measure it?o Rate after respiration, light-dark

Light: gross production Dark: respiration

Describe the differences in primary productivity between terrestrial and aquatic environments?

o Aquatic: controlled by temperature, light and nutrients, can get nutrients and carbon from terrestrial run-off while terrestrial

environments lose carbon primarily because plants incorporate carbon. (allochthonous)

o Terrestrial: controlled by temperature, water and nutrients, primary production from algae and cyanobacteria, terrestrial runoff, (autochthonous)

What are the major microbes that perform primary productivity in biological soils?

o Cyanobacteria, algae, and lichens What is the difference between mineralization and immobilization?

o Mineralization: the conversion of organic nutrients into inorganic material during microbial growth and metabolism

o Immobilization: the incorporation of a simple, soluble substance into the body of an organism, making it unavailable for use by other organisms. inorganic→ organic

What is decomposition controlled by? o Net rate controlled by: C:N ratios

How much energy is typically lost between trophic levels? Why?o Approximately 90% (each trophic level only receives 10% of the

energy found below it); 2nd law of thermodynamics

Class 12 Lecture Study Guide: What intrinsic properties of individuals influence population dynamics?

o Genetic composition- each individual has changes in genes that lead to physiological properties that affect ability to react.

o Physiological properties: stress tolerance, dormancy (endospores etc), plasticity (ability to adapt)

What influences population structure? Be able to describe at least two factors in detail.

o Size: smaller cells = more surface areao Density: over population, excess byproducts become toxico Age: old cells die- where in the growth cycle are cells, regulated vs

unregulated growth. o Distribution: geographic range/barriers, local populations,

microniches (small groups, specialized in certain functions) What is microbial growth controlled by?-DIP

o Density dependence: Stress Decreased reproduction Quorum sensing

Resource availability Intraspecific competition: competition within a

population Interspecific competition: between populations, within

the same communityo Interactions with different specieso Predation, disease, death

What are microbial growth rates controlled by?o Resource typeo Physiologyo Temperature, pH, salt, growth strategies

What are K- and r- strategies? Copiotrophs vs. oligotrophs? Why would one strategy be favored over another?

o K-selection: Grow slow Optimized to conserve environmental resources Typically resource-limited environments Stable populations Example: Comamonas acidovorans

o r-selection: High rates of reproduction (r = rapid) Populations subject to disturbances Grow in erratic bursts, depending on input Opportunistic Do not depend on others Example: Aeromonas hydrophila

o r-selection is favored in copiotrophic environments (high concentrations of organic material) and K-selection is favored in oligotrophic environments (low concentrations of organic material)

What factors influence individuals vs. populations?o Individuals: genetic composition, physiological properties,

adaptability (dormancy/persisters) o Populations: structure, dynamics, and adaptations

What is stochastic gene expression and what might happen with individuals within a population when this occurs?

o Def. = Random gene expressiono Can produce signal that affects the rest of the population (e.g.

exoenzymes, QS molecules, dormancy) What is the difference between dormancy and persisters?

o Dormancy: can be brought about by unfavorable conditions but it can also be random, no obvious change in morphology (maybe smaller because less RNA), not limited to endospores or cysts

o Persisters: during growth cells become dormant, don’t take in antibiotics because they aren’t reproducing

How does QS influence population dynamics? o 1. Production of signal moleculeo 2. Release of it into environmento 3. Recognition of that molecule by other cellso 4. Changes in the gene regulation

What are microbial cheaters? Is cheating a good strategy (for microbes, that is)?

o Take advantage of cells that are producingo Not really the best method; good for mutated cells though

Class 13 Lecture Study Guide: What is the definition and properties of a microbial community?

o Self-contained group of interacting organismso Properties: number of species, structure (relative abundance),

turnover/turnover rate, functional redundancy, niches What defines a niche? What are the properties of a niche?

o Populations/communities within a habitat, defined based on physiochemical environmental or interactions

o Can be functional (job) or physical (location)o Properties: Patchy- clumps of bacteria interacting with each other in

patches, structured by “what they’re seeing” physical and chemical environments or their interactions.

What factors influence community structure?o Interactions between species/functional nicheso Environmental heterogeneity/physical niches

What is functional redundancy? How can you tell if there is a functional redundancy in a community?

o Functional redundancy- multiple taxa with overlapping functionso Each new taxa may have a function, but at some point this levels off.

Stability of environment depends on functional redundancy- more diversity= more stability. They are capable of being stable in terms of functions they have in an environment. Redundancy makes it more likely to retain a function after stresses.

Briefly describe some ecosystem services that communities provide.

o Conservation of matter: decomposition, organic to inorganic, inorganic to organic, nutrient cycling redox reactions

What defines a stable community? Succession? o Stable community: Flexible compositions, temporal and spatial

niches, temperature niches STABLE does not = STATIC

o Succession: colonization by primary/pioneer organisms, establishment of stable community

Know the definitions of the terms in slide 16.o Disturbance: event that causes change in a habitat

Press: long-term Pulse: short-term

o Stability: when a community returns to its stable state after a disturbance

o Resistance: ability of a community to stay the same during and after a disturbance

o Sensitivity: how much a community changes during and after a disturbance

o Resilience: how fast a community recovers after a disturbance What makes up a biofilm? Briefly outline the steps in biofilm formation.

o EPS (extracellular polymeric substance), CHO, proteins, glycoproteins, glycolipids, eDNA, e-enzymes

o 1. Substratum preconditioning by ambient moleculeso 2. Cell depositiono 3. Cell adsorptiono 4. Desorption o 5. Cell-to-cell signaling and onset of exopolymer productiono 6. Convective and diffusive transport of O2 and nutrientso 7. Replication and growtho 8. Secretion of polysaccharide matrixo 9. Detachment, erosion, and sloughing

What dictates the structure of a microbial mat? Why? How is a mat different than a biofilm? Similar?

o Light and chemicals dictates structure. o They live at the interface of habitats or at the interface of biofilms o Microbial mat is a type of biofilm that is found at interfaces of

environments. o Found in places such as surfaces of plants or floating on the ocean.

List electron donors/acceptors and their products in order of energy generation.

o E- donor: CH2O → CO2, H2 → HF, CH3 → CO2, H2S → SO22-,         H2O

→ O2

Class 14 Lecture Study Guide: What is alpha diversity?

o Number of species and relative abundance within a single community What are the components to consider when studying the alpha diversity of a

community?o Number of species and relative abundanceo Species evenness

Simpson’s index (D) Measures the probability that two microbes chosen

randomly from a community will be the same species-indicative of species evenness. When D is high (~1) the evenness is low

Simpson’s diversity index (1/D). Low ratio (closer to 1) = low diversity

You have a community with 50 individuals and 10 species.

o What type of distribution would you expect for an even community? What about an uneven community?

Even: 5 individuals from each species Uneven: every species has a different number of individuals

o What would you need to change in order for the community to become more rich?

Add more species Each species has various functions

What does a rank abundance curve show? What is plotted on each axis for these types of curves? Be able to interpret a plot.

o A species’ abundance compared to the other species in its communityo X axis: ranko Y axis: abundance (percentage)

Describe two common ways to illustrate beta diversity.o Dendrogramso Ordination plots

What is the difference between weighted and unweighted methods? Why would you use one method over the other?

o Weighted: accounts for abundance of each OTUo Unweighted: + or -o Similarity or dissimilarityo Measure between similar or diverse communities or over time/space

What is Jaccard analysis? Bray-Curtis analysis?o Jaccard: unweightedo Bray-Curtis: weighted

What are the differences between Alpha and Beta Diversity?o Alpha diversity is the measure of species richness of a communityo Beta diversity is the rate of change in species composition from one

community to another (turnover rate) Be able to interpret graphs, dendrograms, and ordination plots of diversity

measures. o Graphs: ranks the samples by their abundance in the community, a

longer tail equals a more even communityo Dendrograms: nodes are sample names, determining the distance or

similarity between the two sampleso Ordination plots: closer the points are to each other, the closer the

communities are to each other (similarities wise)

Class 15 Lecture Study Guide: Know the difference between resistance and resilience.

Describe what properties contributes to stability, resistance, and resilience at all levels (in individuals, populations, and communities). Be able to define those properties.

o Resistance is a community’s ability to stay the same during and after a disturbance, resilience is how fast a community recovers after the disturbance

o Individual- Stress tolerance, Plasticity (ability to change) and Going dormant

o Population- stochastic gene expression, Growth rate, adaptability and dispersal rate

o Community- Alpha diversity, turn-over rate, Microbial interactions, functional redundancy.

Explain the difference between press and pulse disturbances. Which is more likely to change the community permanently? Why?

o Press is long-term and pulse is short-term; a press disturbance will more likely result in a permanent change because the long-term stress may permanently affect the condition of the environment and therefore affect the community that can exist there

Class 16 Lecture Study Guide Explain what symbiosis is in terms of microbial interactions

o Association between two dissimilar organisms where both benefito Definition given by Campbell- any persistent biological interaction

that can be either obligate or facultative. What is the main difference between cooperation and mutualism?

o Mutualism is an obligatory relationship, cooperation is not What is syntrophy? Give a few microbial examples of mutualistic,

cooperative, and commensal syntrophic interactions. o Syntrophy: cross-feeding between two organismso Mutualistic syntrophy: archaea-archaea: Nanoarchaeum equitans and

Ignicoccus hospitalis (housing the larger N. equitans); Chlorochromatium aggregatum (once considered 1 organism) Inner cell is a rod shaped sulfur reducing bacterium. Comamonadacae will reduce sulfate to sulfide- will utilize acetate produced as a byproduct of photosynthetic bacteria such as Chlorobium. Chlorochromatium aggregatum will use sulfide as an electron donor.

o Cooperative syntrophy: methanogens: consumes hydrogen, making fermentation of propionic acid favorable; Desulfovibrio / Chromatium D- sulfate reducing bacteria, makes sulfide  C- sulfur oxidizing. Takes sulfide and changes into sulfate. Sulfate is taken and used to grow, will produce CO2 and H2S that can be used by chromatium.

o Commensal syntrophy: two soil bacterial types, Bacillus cereus and population of Bacteroidetes; B. cereus makes peptidoglycan which promotes growth of CF rhizosphere bacteria

What are some general microbial examples of commensal interactions? o All of these are considered environmental modifications (see below)o Destroying toxinso Changing pH (acidic metabolic by-products)o Removing oxygen

What are the differences in the predatory mechanisms of the following:o Myxococcus: secrete enzymes that lyses the prey, use up the organic

matter from the lysed cells and change to fruiting body stage when all the organic matter is used up. 2 growth stages- one is vegetative and one is fruiting. It is a facultative predator.

o Bdellovibrio: grows in the periplasm and eventually kills the prey and lyses the cell, and goes back into the environment. Actively searches for prey; fast enough to swim and penetrate outer cell membrane- can kill gram negative bacteria.

Why is coexistence or balance needed in parasitic interactions?o Parasite must be in host for a minimum amount of time in order to

reproduce and reach sufficient numbers to be able to colonize a new host. Ex. lysogenic virus. Ideal balance can result in long term relationship. Ex. lichens (only in book, she considers it mutualism). There must be a balance between killing the prey and surviving.   

What is amensalism? Why are bacteriocins an example? o One organism negatively affects another due to production of a

particular compound (eliminates competition)o Bacteriocins: very specific antibiotics, target strains very similar to

producer (producers have a specific protection mechanism), act by forming holes in plasma membrane

Name at least two interactions that free up resources and explain how this happens.

o Cheating- intraspecific or interspecific. Cheaters do not need to expend energy to make e-enzymes etc and can instead take in “public goods”. Can have high affinity or low affinity. Can have siderophores (iron affinity needed for microbes) or transporters. Cheaters can make a transporter and siderophores or can just have a transporter and take in iron that way.

How is cheating related to competition with the siderophore example I talked about in class?

o See above- Can be normal and produce siderophores and transporters or can have a siderophore and a transporter with low affinity, this second type is not as competitive (Unsure of this slide)

Class 17 Lecture Study Guide What types of locations can one find the microbes involved in plant-microbe

interactions?o Phyllosphere- above ground/aerial plant surface (stems and leaves)o Rhizosphere- region around a plant root- not the surfaceo Rhizoplane- plant root surface.

What is the phyllosphere? What type of microbial diversity would one expect to find there?-

o You would expect to find aerobic microbes. Exposed to rapid changes, UV light, humid environments, varied temperature. Contributes to global Carbon and Nitrogen cycling, and removal of pollutants (air, surface) and leaf decomposition

o Phyllosphere: aerial portion of plants(stems and leaves) Why are the rhizoplane and rhizosphere so rich in nutrients?

o Roots receive around 50% of the carbon produced by photosynthesis. Of this, 40 to 90% is put into the soil (plant exudates) (alcohols, sugars, amino acids, vitamins, nucleotides, etc.)

What is the difference between Ectomycorrhizae and Endomycorrhizae?o Endomycorrhizae- most common, penetrate the cell wall (arbuscular

mycorrhizae is an example) Tropical plants or crops. Fungi gets carbs from plants, plants get stress protection and nutrients (drought protection, anti pest for nematodes)

o Ectomycorrhizae (more surface type) Mostly associated with trees in cooler environments. Transfer N and P to trees, Trees give carbohydrates. Mycelium grows around the root and thickens to form a sheath

When Ectomycorrhizae are involved, how do nutrients get from the soil to the plant root cells?

o Hairs stem from the root into the soil What happens between plants and Rhizobia in nitrogen-rich soils? What

about nitrogen-poor soils?o Nitrogen-rich soils: plants secrete compounds that inhibit nodulationo Nitrogen-poor soils: inhibitory compounds are not produced, rhizobia

can invade/infect the plantso Nitrogenase is the most important enzyme

Explain how root nodules for nitrogen-fixation form. What and how do Rhizobia contribute to form the nodules? How and what do the plants contribute?

o Conversion of N2 to NH3 by enzymes o Symbiotic association between bacteria and plants-legumeso 1. Rhizobia are initially seen as invaderso 2. As a defense mechanism, the plants release an oxidative burst.

ROS- general antimicrobial but rhizobia can defend itself. o 3. Plant and rhizobia begin to exchange signals

Plant produces flavonoids to stimulate the colonization of its roots

Bacteria will attach to root hair cellso 4. Flavonoids bind to NodD (bacterial transcriptional regulator) and

activate transcription of nod genes.o 5. Plant receives Nod factor signal

Gene expression is altered in outer root cells- this re-initiates cell division to accept invading rhizobia

o 6. Interaction thread forms

Nod factors and exopolysaccharides trigger changes in the plant plasma membrane

o 7. Infection thread grows Passes through more plant cells Growth due to plant hormones and Nod factors

o 8. Infection thread reaches the inner portions of the plantso 9. Bacterium is endocytosed by the plant cell into an unwalled

membrane component Component + bacterium = symbiosome

o 10. Within the symbiosome, bacteria differentiate into bacteroids- main function to fix nitrogen to ammonia- nitrogen factories

Terminally differentiated Can no longer divide Enlarge and alter morphology

o 11. Many symbiosomes = root noduleo Plants give amino acids, carbon and energy to bacteriao Bacteria give nitrogen in amino acids to the plants

Know what leghemoglobin is- nitrogenase enzymes are O2 sensitive, so leghemoglobin is produced by both plant and bacteria. It binds to O2 to sequester it. Plant makes one part and bacteria makes the other part to make a fully functional protein.***reminded me: need to know difference between doubling time and growth rate. doubling time is the time it takes for a population to double at a constant growth rate, dt= 70/growth rateDoubling time is the amount of time it takes for a given quantity to double in size or value at a constant growth rate. We can find the doubling time for a population undergoing exponential growth by using the Rule of 70. To do this, we divide 70 by the growth rate (r).

Note: growth rate (r) must be entered as a whole number and not a decimal. For example 5% must be entered as 5 instead of 0.05.

dt = 70/r

For example, a population with a 2% annual growth would have a doubling time of 35 years.

35 = 70/2

Thanks fam

Class 18 Lecture Study Guide

Why are the endosymbionts in the giant tubeworms found near deep sea hydrothermal vents chemolithoautotrophs? (What about the environment does or does not support the growth of particular types of microbes?)

o High concentrations of hydrogen sulfide, Mn2+, H2, and CO2

o Anoxic conditions, High temperatures, high pressure, no light Explain how the Riftia symbionts obtain their substrates for growth and

energy production.o Riftia Adults-no gut, juvenile- gut. Specialized hemoglobin carries

H2S (e donor) and O2 and CO2 (carbon source)to symbiont. Trophosomes- are what used to be the gut, has a high cell density (~10^11 symbionts)

What do the symbionts supply to their hosts? What do the hosts supply to the symbionts?

o Symbionts supply: O2, CO2, and reduced carbon compounds. Succinate and glutamate transferred to worm

o Hosts supply: O2, CO2, H2S, NO3-, sulfide

Do the Lucinidae (clams) symbionts supply all the carbon necessary for their host’s survival?  How does this change with environmental change?

o Seagrasses are a good place for juvenile fish, crabs etc. When the grass dies- organic matter is produced. Sulfate reducing bacteria produce sulfide (from that organic matter). However, if there are clams present these bacteria would be in the gill cells - bacteriocytes. When housed in the gill the sulfide-oxidizing bacteria in Lucinidae (clams) give sugars to the bivalves, while the clams give the bacteria sulfide/oxygen. Less clams = higher rate of grass death because the sulfides produced by bacteria are toxic to the grass

Explain the functions of the 4 major symbionts in the Olavius algarvensis symbiosis.

o 1. 2 sulfate reducers - anaerobic deltaproteobacteria o 2. 2 sulfur oxidizers - aerobic  dentrifying gammaproteobacteriao Most spirochetes are heterotrophs, they may have something to do with the

detoxification of the worm. The advantage of having many is that they can be cycled through, hence sulfide and sulfate cycles occur directly within the worm. In addition, there is theory that there is a functional redundancy by having two of each type. They may also be able to metabolise different substances.

What is common between most of these symbioses in terms of the benefit to the host?  Compare these chemolithoautotrophc symbioses to the coral-zooxanthellae symbiosis.

o Symbioses of the three microbes listed above seems to provide metabolic pathways for the host. This is similar to that of the coral-zooxanthellae, that the algae provides materials for the coral polyps to grow and mature. Moreover, all four hosts provide safety and nutrient rich environment to prosper. However, the C-Z group uses photosynthesis, while the three listed are all chemolithoautotrophs

Class 19 Lecture Study Guide

What is/are the benefits for each member of the squid-Vibrio symbiosis?o Squid benefits:

Vibrio gives light to squid- can hide its shadow from predators o Vibrio benefits:

Safe and nutrient rich habitat How are the bobtail squid colonized with Vibrio fischeri?

o Peptidoglycan triggers the squid to secrete mucus from the immature light organ

o Mucus causes gram-negative bacteria to aggregateo In aggregates, V. fischeri outcompete the other bacteria - form a

“monoculture”o V. fischeri is extremely motile and moves up ducts into the light organo Once in the light organ, V. fischeri becomes nonmotile (loses flagella)o Establish dense populations and triggers development of light organ.

NEEDS AUTO-INDUCER N-ACETYLHOMOSERINE LACTONE (recognize this at best)

o Once cell numbers reach a certain point, quorum sensing leads to light production

o In the morning, squid almost empties its light organ of bacteria, and bacteria regrow

What selective pressures contribute to the specificity of this interaction between the squid and bacteria?

o Gram-negative selection by mucuso NO (nitric oxide) gas- common defense by animal against pathogens,

strong oxidant, present in the mucus/ light organs. V fischeri can tolerate

What about this process is similar/different to the Legume-Rhizobia symbiosis?

o Similar: both use QS to communicate (p.153)o Both use AHL’s to communicate with each other (Quorum-sensing)o The bacteria is given a safe place to reside with a nutrient rich environmento The plant receives nutrients and the organism gets a tactical advantage

What general characteristics does the environment in the rumen have?

o pH between 5.5-6.5o Protozoa also present but in smaller numbers, Total mass ends up

being about the same for rumen and protozoa. If pH gets too acidic then protozoa die. Saliva buffers pH

Explain the basic process of degradation of plant materials into VFAs by ruminants and their microbes.

o Microbes break down cellulose into glucose o Glucose is fermented by bacteria into VFAs (acetate, propionate,

butyrate) which the cows can use for energy. What changes in the microbial community occur when cows are fed a poor

foliage diet, a grass diet, and a starch diet? Why?o Poor foliage: fungi and high in complex plant material like cellulose

and lignin (more Chytridiomycetes)o Grass: High in cellulose (more Ruminococcus albus and Fibrobacter

flavefaciens)o High Grain diet-Starch (increases acidity of stomach). This can be a

problem because the pH will be too low in the rumen. (more acid-resistant pathogens such as E. coli and Prevotella)

What ruminant diet leads to an increase in human pathogens? Which human pathogens? Why?

o Grain Diet. This diet makes the environment more acidic and, since E. coli are resistant to acidosis, they become more prevalent in the cow’s gut and muscles. So, when people eat the meat from these cows, they often get food poisoning. Farmers often switch the cow’s diet from a grain diet to a grass diet before butchering in order to reduce the amount of E. coli in the stomach.

o THANK YOU whoever put this up <3  You’re very velcome :)

https://quizlet.com/_2l3pze

Class 11 Notes:

1. Termsa. Biosphere: total living world in all aspects of the environment

i. Thin layer on earth, but microbes expand it. b. Ecology: study of the organisms and the biotic and abiotics of their

environment c. Ecosystem: abiotic environment and the community that inhabits itd. Community: self contained group of interacting organisms, share the

same habitate. Population: self contained interacting group of the same species

f. Biome: regional ecosystem (habitat)2. Ecosystems:

a. Abiotic componentsi. Lithosphere: rocks, sediments, soils, weathering

ii. Hydrosphere: everything having to do with wateriii. Atmosphere: what we and microbes can “breathe”, not just O2

iv. Chemical/limiting factors: pH, nutrients (trace minerals), types of carbon available, light

b. Biotic groups:i. Individual

ii. Populationiii. Community

3. Biotic factors:a. Individual requirements/feeding strategiesb. Biomass: how much living material in ecosystemc. Production/productivity: how much is producingd. Decompositione. Interactions

i. Symbiosesii. Predator/prey

iii. Competitioniv. Population levelv. Community level

4. Ecosystem Processesa. Biogeochemical cycles

i. C, N, P, Sii. Decomposition: organic to organic

1. Higher under anaerobic conditions iii. Mineralization: organic matter into inorganic matteriv. Assimilation: transformation or incorporate organisms/into

microbes converting into nutrientsv. Immobilization: the incorporation of a simple soluble substance

into the body of an organism, making it unavailable by use by other organisms

5. Kinds of Ecosystems:a. Governed by:

i. Biotic componentsii. Abiotic components

b. Distinguishing ecosystems:i. Climate

ii. Vegetationiii. Stabilityiv. Dominate producerv. Dominate consumer

vi. Richnessvii. Diversity of species

c. Major typesi. Aquatic

ii. Terrestrial6. Production/productivity

a. Fix energyi. Photosynthesis

ii. Chemosynthesisb. Primary productivity

i. Gross: photosynthetic production of organic compounds (rate)ii. Net: rate after respiration

iii. Measured as kcal/m2/yr or gC/m2/yriv. ½ global productivity is by microbes

7. Primary Production in aquatic environmentsa. Controlled by temperature, light and nutrientsb. Stratification important and controlled by temperature

8. Primary production in terrestrial systemsa. Controlled by temperature, water and nutrientsb. Plants, algae, and cyanobacteria

9. Decomposition/mineralization and immobilization a. Terrestrial: C:N ratio decliningb. Aquatic: C:N ratio are more constant because of the zitoplankton

10.Balance between processes?a. Energy conservationb. Differences in where carbon/nutrients come from and end up between

aquatic and terrestrial ecosystemsi. Terrestrial: autochthonous

ii. Aquatic: allochthonous, terrestrial runoff11.Energy flow in Ecosystems

a. Kinds of energy: solar, chemical, mechanicalb. Productivity

i. How fast cells growii. Nutrients

iii. Turnover ratesiv. Carbon available

v. Feeding strategies

Class 12 Notes:

1. Individualsa. Genetic compositionb. Physiological properties

i. Stress toleranceii. Dormancy

iii. Plasticity: ability to adapt2. Adaptability

a. Physiological heterogeneity: variation of individuals within a population

i. “Developmental noise”1. Stochastic (random) gene expression2. dormancy/persisters

ii. Quorum sensingiii. Mutants

1. Cheaters2. HGT of antibiotic resistance

3. Stochastic gene expressiona. Subpopulations most influential

i. Can produce signal that affects rest of populationii. Examples: exoenzymes, QS molecules, dormancy

4. Dormancy/Persistersa. Can be brought about by unfavorable conditions but it can also be

randomb. Not limited to endospores or cystsc. No obvious change in morphology, maybe smaller because less RNAd. Persisters: during growth cells become dormante. Some 80-90% of cells in environment could be dormant

5. Quorum Sensinga. Steps:

i. Production of signal moleculeii. Release into environment

iii. Recognition of that molecule by other cellsiv. Changes in the gene regulation

6. Cheater Cellsa. Don’t want to use energy, don’t have to produceb. Stealing, randomc. Antibiotic resistance

d. Exoenzymese. QS moleculesf. Ion-scavengingg. Can take advantage of the cells that are producing

7. Microbial Populationsa. Structure, dynamics and adaptationsb. Structure

i. Sizeii. Density

iii. Ageiv. Distribution

1. Geographic range2. Local populations3. Microniches

c. Dynamicsi. extinction/bottlenecks

ii. Dispersal1. Types: geographic, physical, competition, predation2. Factors involved: nutrients, perspiration, escape from

predators so they will disperse or sink  iii. Growthiv. Ratesv. Growth strategies

vi. Adaptability within a population (individual) 8. Population Growth

a. VBNC (viable but not culturable) genetic response to starvation b. Growth rate: K = n/tc. Doubling time: g = 1/kd. Carrying capacity: maximum sustainable population size, depends on

the environment but in microbes because too many byproducts inhibit reactions

9. Overall Growth Controlled by?a. Density dependence

i. Stressii. Decreased reproduction

iii. Quorum sensingiv. Resource availability

1. Intraspecific competition: competition within a population

2. Interspecific competition: between populations, in the same community

b. Predation, disease, deathc. Interactions with different species

10.Growth Ratesa. Other factors: temperature, pH, salt, growth strategiesb. How active a cell migth be

11.Growth Strategiesa. R-selection

i. High rates of reproduction (r)ii. Populations subject to disturbances

iii. Grow in erratic bursts, depending on inputiv. Opportunisticv. Do not depend on others

vi. Copiotrophsb. K-selection

i. Grow slowii. Optimized to conserve environmental resources

iii. Typically resource-limited environmentsiv. Stable populationsv. Oligotrophs

Class 13 Notes: