Unit 3 Micro

What change in state of a molecule is usually involved in cycling?

Oxidation State

Organisms contribute by redox reactions

What are the four reservoirs elements are contained in?

Terrestrial

Aquatic

Atmospheric

Living

What is the movement of elements between reservoirs called?

Flux, it will reach equilibrium over the long term

Human activities work to disrupt this equilibrium

Mescosms

Artificially enclosed ecosystems

Measure changes over time

How are radioisotopic tracers used to monitor chemical cycling?

Molécules are labeled prior to being released in a mesocosm

How the molecule moves through the mesocosm is informative on cycling methods

How do microbes influence cycling of carbon?

Metabolic activities of photosynthesis, respiration, and decomposition are all driven by microbes and maintain the balance of C distribution

Human activities disrupts these cycles, increasing atmospheric levels of greenhouse gases

What happens if CO2 fixation exceeds respiration?

Organic matter accumulates

Positive net community productivity

Why is fermentation important?

Produces partially oxidized organic end products, serves as nutrients for other organisms

Methanogensis

Production of methane (CH4) as a byproduct of biodegradation of organic carbon in anoxic environment

Consortia

Communities of interdependent organisms

Give and take pairings is called "syntrophic partnership"

hydrogenotrophic methanogens

Produce CH4 from CO2 and H2

Aerotrophic methanogens

Produce CH4 from acetate

Methanotrophy

Metabolism of CH4 into other forms

Allows greater Carbon cycling

Can occur aerobically or anaerobic ally

Méthane monoxygenase (MMO)

What aerobic methods of methanotrophy are dependent on

Where does anaerobic oxidation of methane typically occur?

In marine environments by archea

These archea have yet to be cultured

Nitrogen fixation

Conversion of N2 into NH4+ by nitrogen are complex

Carried out by aerobic/anaerobic bacteria and archea

Nitrification

Conversion of ammonia into nitrite or nitrate

*Know formulas

Denitrification

Use of nitrate/nitrite as terminal e- acceptor, producing N2

Completes N cycle

Haber-Bosch process

Produces synthetic N fertilizer

Overuse of these contributes to dead zones

What does the Oxygen cycle look like?

Reservoirs of O2, CO2, H2O

Heavily cycled back and forth btwn photosynthesis and respiration reactions

Cycling of sulfur and phosphorus

Most of either is found in rocks and dissolved water

Incorporation occurs through terrestrial and aquatic microorganisms into higher-order organisms

Decomp reactions release the elements back into the terrestrial and aquatic systems, completing the cycle

Ecosystems

interactions and exchanges of materials between organisms and their surrounding environment

Primary producers

An autotroph, usually a photosynthetic organism. Collectively, autotrophs make up the trophic level of an ecosystem that ultimately supports all other levels.

Consumer

Ingest/utilize stored photosynthetic energy

Decomposers

Recycle components back into environments

Niche

Specific functional role of an organisms within an ecosystem

What does the success of microbes in occupying particular niches depend on?

Their ability to obtain different nutrients there to produce energy and biomass

How do biofilms form?

Formation begins with appendages bacteria forming the primary layer on a surface

Secondary colonies then join

Microbes secrete exopolysacchride(EPS) which helps protect the biofilm but also helps form water-filled channels for transport of nutrients and waste

What are the two main objectives of studying microbial communities?

To understand biodiversity or the variety microbial life in nature

Understand the effects of organisms on ecosystems

Enrichment Cultures

Promote growth of desired microbes over undesired cells

Winogradsky Column

Different microbes flourish in different areas of the column that correspond to different nutritional microenvironments

Direct Sequencing

Extraction of DNA from environmental sample

Followed by PCR (often for SSU rRNA genes) and sequencing

These sequences are compared to databases of known sequences for identification

Metagenomics

DNA from an environmental sample is used to construct a genomic library

They can then be ID'd, screened, and compared

What are important details of marine ecosystems?

98+% of ocean's biomass is microbial

Most of these microbes exist in oligotrophy (using nutrients at very low conc)

Overfeeding can lead to anoxic water states (dead zones)

Dead Zones

areas without enough oxygen to support much eukaryal life

How is energy moved through a marine ecosystem?

Phytoplankton are primary producers in top levels

Carbon and energy are distributed through other levels by zooplankton (consumers) feeding on phytoplankton and through viral-mediated lysis

Describe the surface, dark mid-water zone, and the deep sea zone

Surface zone populated by phytoplankton

Dark mid-water zone: phytoplankton production drifts downward to feed zooplankton, viral lysis of phytoplankton helps release nutrients for heterotrophic microbes

Deep sea zone: 1,000x pressure than at sea level, piezophiles are microbes that can withstand these intense pressures

What are conditions like on the sea floor?

Approx 1% of primary production reaches sea floor, anoxic & cold so unlikely to biodegrade

This forms rich sediment on sea floor, but few microbes can survive these conditions

Viruses of the Ocean

Approx 10x more viruses than microbes

Little is known

Only know cyanobacteria dominating surface zone areas, they most likely liberate nutrients from cyanobacteria, making them available for heterotrophic microbes in deeper waters

Describe freshwater ecosystems

Growth can fluctuate with seasons, resulting in algal/cyanobacteria blooms

These can result in anoxia and fish-kills

Biomes

categories of ecosystems based on vegetation characteristics

What's the dominant primary producers

Plants

Describe the relevance of soils in terrestrial ecosystems

Soil layers form through microbial decomposition of plant and animal matter

They combine with abiotic minerals and excreted nutrients from plant roots

How is soil structure determined

Aggregation/clumping of soil

Binding agents include microbial substances and hum i material from incomplete breakdown of plant biomass

Microbes tend to aggregate near soil pores to get better access to nutrients & moisture

Rhizosphere

The area of soil immediately surrounding plant roots, posing large amounts of organic carbon

Often has higher numbers of microbes than bulk soil

Relationship btwn plants and microbes in rhizosphere

Complex symbiosis, promotion of plant growth yields more carbons for microbes

Plant Benefits:

- Production of hormones that stimulate growth

- Production of antibiotics to control plant pathogens

- Fixation of atmospheric nitrogen

- Solubilization of phosphate to be taken up by plant roots

Bioremediation

The use of microbes to consume and remove human-made materials from soil

ex. use of hydrocarbon degrading microbes in petroleum- contaminated areas

Xenobiotics

Chemicals not normally found in nature

Can be quite difficult to degrade quickly by microbes

Biostimulation

Provides oxygen and limiting nutrients to promote microbe activity

Cometabolism

Involves addition of a nutrient that stimulates a broad substrate-range degradation pathway

Bioaugmentation

Specific addition of a known degrading microbe to a contaminate environment

Symbiont

An organisms that has developed a longstanding relationship with another organism

Paraistism

One species does obvious harm to the other

Commensalism

One species benefits, but nothing happens to the other species

Mutalism

Both species are getting benefits

Ecotosymbiont

Live on the surface of the host, do not have to be single-celled

Endosymbionts

live within tissues or cells of the host

Lichens

Microbes/microbe symbionts

Fungal species coupled with photosynthetic species

Endophytes

plant endosymbionts

Rhizobia

Endophytes that can infect plant root cells, fixing nitrogen and forming root nodules

Benefits to plant/bacteria in symbiotic relationship?

Plant provides leghemoglobin (similar to hemoglobin)

Prevents it from damage nitrogen fixing enzymes

Bacteria provide valuable nitrogen in a form the plant cells can use (often ammonium)

Root nodule formation

Bacterial nod genes are expressed in presence of plants

An infection thread is formed to invade the root

Nodule forms, providing a low-O2 environment

Form leghemoglobin to assist

The plant provides carbon compounds to the bacteria while the bacteria provide ?

Human microbiome

The total of all microbes living in and on the body

Symbionts of human skin

Oil glands and hair follicles form microbe habitat areas

Patterns of bacteria types found on skin are emerging

By crowding out harmful competitors, these microbes may help with disease prevention

Symbionts of human vagina

Microbial populations affected by:

- Proximity to the skin and anus

- pH of the baignas tract

- Moisture levels

- Age (which often affects hormone level and pH balance)

Common symbionts include:

- Staph epidermidis

- E. coli and Enterococcus faecalis

- Candidia (yeast)

Symbionts of humans: Oral cavity

Second in colonization

Provides warm, moist, nutrient-rich area for microbes

Over 700 bacterial species, detected by 16S rRNA gene analysis, most cannot be cultured

Plaque biofilm buildup is a major cause of cavities

Includes:

- G+ Streptococci

- Anaerobic Fuso... Porphy...

Symbionts of humans: Digestive tract

Could include between 800-2,500 bacteria, a variety of bacteriophages

Anatomy/diet lead to a dynamic bacterial population changes moving along the length of the tract

How do microbes interact with the digestive tract?

They form a biofilm along the mucus that lines the interior of the intestines

What are the benefits for humans?

Some microbes produce vitamins that we absorb (K)

Some assist in digestion

They also crowd out pathogenic microbes and keep the immune system in balance

Probiotics

live microbes that when ingested benefit out gut health

Cecal fermentation

How digestive enzymes used to break down food prior to absorption

Some organisms will practice coprophisa, consumption of feces to increase nutrients uptake

Rumen

Microbes in the host break down food first, then the hosts absorb fermentation products and microbes

Termites (context of symbiotic relationships)

Higher termites feed on plant materials in soil or fungus

Lower termites feed on wood

Both depend on microbes in their gut to break down cellulose material

Not much is known bc they are not culturable

Also have relationship with nitrogen fixers to get N

Biotechnology

Use of biological processes or organisms for the production of goods or services

What are the red, white, and green groups of biotech

Red: Medical applications

White: industrial applications

Green: agricultural sector

Culture collections

Preserved specimens that other scientists can obtain at minimal cost

They help promote confirmation of findings through repeatable independent research

Bioprospecting

Searching for useful new microbes to cultivate and add to collections

Fermentation

Controlled and regulated aerobic/anaerobic culture of microbes to produce desired substances

Primary metabolite

A product of metabolic processes required for growth of the microbe

Secondary metabolite

Not required for microbial growth often produced during stationary phase

Random mutagenesis

Chemical/radiation exposure is followed by screening for desired mutations.

Used to improve microbial strains

Site-directed mutagenesis

Specific mutations at specific sites

CRISPR-Cas Genome Editing

What is Crispr gene editing

Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR associated (Cas) enzyme

Does not rely on DNA-binding protein

A powerful gene editing tool

How does Crispr work

When bacteria is exposed to pathogen, it inserts segment of DNA into repeat segments. It then transcribes this into crRNA that circulate within the cell. When pathogen is encountered, crRNA binds and targets the pathogen

How do you produce recombinant proteins

Expression vectors are used to mass-produce recombinant proteins

Insert a eukaryotic DNA sequence for a product of interest into a plasmid; put the plasmid into bacterial cells, grow, harvest

What must be done to Eukaryal genes before producing recombinant proteins

They must be reformatted to remove introns

A shine-dalgarno sequence must be added to the sequence to promote eventual translation

Appropriate stop codons must be added

What are the two major uses of microbes in the pharmaceutical industry

-Producers of secondary metabolites with therapeutic properties

-Hosts for the production of recombinant human proteins

What are some examples of secondary metabolites we use?

Antibiotics (Penicillin, Streptomycin/actinomycin)

Statins (inhibitors of cholesterol synthesis)

What are some examples of human proteins we produce with microbes?

Type 1 interferons (anti tumor and antiviral capacities)

Human insulin

What role do microbes play in industrial biotechnology?

The basic principle is to use microbes and low-cost biomass to yield products with high value and industrial use

Ex. Biofuel, Bioplastics

What is the bio refinery concept

Renewable biomass feedstock in

Microbes act on feedstock

Useful materials harvested

Ethanol (context of biofuels)

Microbes ferment sugars to produce 2-C ethanol

Can be used in internal combustion engines w/ little modification

Problems:

Commercial scaling and cost of feedstock can be difficult to overcome

Lignin/cellulose feedstocks can be difficult to break down, a way to use them would be cost-effective and environmentally friendly bc they are waste products

Butanol and acetone

Butanol (4C) can also be used in internal combustion engines and is more similar to gasoline

Currently used in latex, enamels, lacquers, and plastic additives

Production via fermentation isn't as popular but can be done

Bioplastics

Microbes can produce natural polyesters:

- Polyhydrozybutyrate (PHB) from B. megaterium

- Polyhydroxyalkanoates (PHAs)

Levels of PHA are too low, researchers working on ways to increase yields

What ways does agriculture benefit from microbes

Pesticide/herbicide production

Synthetic fertilizers

GMO

Agrobacterium

Natural genetic modifier

A. tuméfactions cause crown gall tumors by carrying a tumor producing plasmid

This plasmid is transferred into plant cells, making it a good delivery system for gene insertion into plants (Transgenic plant production)

What are some applications of transgenic plants?

Herbicide resistance

- Genetically engineered Roundup-resistant plants means farmers can use it year-round

Insect resistance

- Bt toxin is produced by B. thruingiensis

- Highly specific and lethal to certain insect larvae that feed on crops, but not naturally in plants

In what ways are microbes beneficial to use through food and water

Food preservation methods

Contamination of food/water

Perishables

Easy support microbe growth

Green salad items, fresh meat

Semi-perishable

Don't spoil as quickly

Nuts, potatoes