industrial, aquatic, & terrestrial microorganisms combined

the use of microorganisms to produce commercially desired products or to perform commercially desired transformations

-this may involve natural products made by wild-type microorganisms

-this may involve new, non natural products produced by genetically modified microorganisms

major products of industrial microbiology

-industrial and agricultural products

-food additives

-products for human and animal health (antibiotics and medicines)

-biofuels

types of microbial products

primary metabolites, secondary metabolites, and other microbial products

primary metabolites

-Substances synthesized by microbial cells during exponential growth phase

-Include amino acids, nucleotides, fermentation end products, and enzymes

secondary metabolities

-Primarily made during stationary phase

-Include many antibiotics and mycotoxins

other microbial products

-Antibiotics and other medical products

-Industrial and agricultural products

-Food additives: amino acids, other

-Products for human and animal health

-Biofuels: i.e., ethanol

-Cells: i.e., yeast cells for baking

Commercial food, alcohol, and fermentation processes

-Fermentation of milk: Yogurt, cheese, buttermilk, sour cream

-Fermentation of fruits and vegetables: Pickles, cabbage

-Baking

-Brewing

-Major fermentations used are lactic, propionic, and alcoholic fermentations

Example of microbial food processes fermented milks

rely on lactic acid bacteria

Example of microbial food processes cheese production

classified based on texture, hardness

Example of microbial food processes wine

Glucose fermented to ethanol and CO₂ by S. cerevisiae or S. liposideus

Example of microbial food processes production of breads

growth of S. cerevisiae under aerobic conditions

Genetic manipulation of microorganisms

-Used to produce microorganisms with new and desirable characteristics

-Classical methods of genetic exchange coupled with recombinant DNA technology play vital role in industrial microbiology

Role of microorganisms in genetic engineering

-Nearly all techniques & materials for genetic engineering, cloning, etc. are from microorganisms

genetic engineering

modification of organism's genetic information by directly changing the sequence of nucleic acids in its genome

recombinant DNA technology

procedures used to carry out genetic engineering

recombinant DNA

DNA molecule composed of DNA from 2 different sources

restriction enzymes

-Prokaryote enzymes that recognize and bind specific sequences in DNA called recognition sites

-May produce sticky ends or blunt ends

how do restriction enzymes work?

-Cleave DNA at this site or a defined distance from it in any DNA from any source

-Can combine DNA from 2 sources cut with same enzyme into 1 molecule

first recombinant molecule

-1982

-Produced new source of human insulin

-First commercial use for recombinant molecules

growing microbes in industrial settings requires

precise control of agitation, temperature, pH changes, and oxygenation

growing microbes in industrial settings occurs

in large vessels called fermentors

fermentation

any aerobic or anaerobic metabolism occurring in a fermenter for mass culture of microorganisms

-most processes are aerobic

continuous culture

continual addition of a critical nutrient prevents accumulation of undesirable metabolic waste products

microorganisms & ecosystems

-Microorganisms account for ~50% of all biomass on Earth

-They are ubiquitous (found all over) on the surface and deep within the earth and in water

-Many microorganisms are free living; others in symbiotic associations

freshwater environments

-highly variable in the resources and conditions available for microbial growth

-Water available in excess

-Oxygen, nutrients, light, temperature more variable

-Solute concentration ~0.9%

marine (salt water) environments

-Open ocean environment is saline (salty and hypertonic - 3-4%)

-Low nutrient, especially nitrogen, phosphorus, and iron

-Cooler

-Microbial activities major factors in Earth's carbon balance

zones in lakes & ponds

photic zone, freshwater upper layer (photic zone), lower layers, and lake zones

photic zone

-The water from the surface to depth to which light penetrates

-Photosynthesis can occur

Freshwater upper layer (photic zone)

-Many phytoplankton

-Oxygenic photolithoautotrophs suspended freely in water

-Includes algae and cyanobacteria

-Also protozoa and some prokaryotes

Lower layers - Profundal and Benthic

-Benthic species: microorganisms attached to bottom or sides

-Mostly anaerobic and facultative anaerobic chemoorganoheterotrophic bacteria and chemolithoautotrophs

-The activity of chemoheterotrophic microbes dependent upon primary producers

Lake zones

Benthic - bottom and sides below profundal level

Profundal zone - anoxic in deep lakes

Littoral and limnetic zone are in photic zone

Important physical factors determining which microorganisms can live in different environments

-Dissolved oxygen content: defines where strict aerobes/anaerobes reside

-CO₂: for photolithoautotrophs

-Temperature

-pH

-Light penetration: for photolithoautotrophs and chemolithoautotrophs

dissolved oxygen

-Oxygen diffuses from atmosphere

-Produced by aquatic photoautotrophs

-Varies with depth and temperature

-Decreases with depth

-Decreases with colder temperatures

nutrients

-Microbial species richness and abundance is a function of kinds and amounts of nutrients

-Phytoplankton are major source of organic matter

freshwater organisms

-Phytoplankton: oxygenic photolithoautotrophs

-Protozoa

-Prokaryotes

-Anaerobic and facultative anaerobic -chemoorganoheterotrophic bacteria

-Chemolithoautotrophs

marine (saltwater) organisms

-Photosynthetic microbes fix ~half the world's carbon

-Virioplankton are the most numerous members

-Phage particles are the most abundant life form on Earth

-Halotolerant microbes where freshwater meets saltwater

-Microbes in nearshore waters due to higher nutrient levels

Hydrothermal Vent Microbial Ecosystems

-Deep-sea hot springs (hydrothermal vents) support thriving animal communities

-Fueled by chemolithoautotrophic prokaryotes

Benthic marine environments

-Largest microbial biomass under the sea

-Subsurface equals that of all terrestrial and marine plants

-Some microbes are barophilic and able to tolerate atmospheric pressures up to 1,100 atm

Habitats where microorganisms reside

-Marine environments

-Freshwater environments

-Soil

Soils as a Microbial Habitat

complex and contains a large variety of habitats as a result

-microbial diversity in soils is greater than any other habitat (supported by complex physical & chemical environments)

most important factor in influencing microbial activity in surface soils

the availability of water

most important factor in influencing microbial activity subsurface environments

nutrient availability

Soil particles pore space

critical for movement of water and gases optimum environment for microbial growth

soil composition

Soils are mixtures composed of:

-composed of inorganic mineral matter (~40% of soil volume)

-organic matter (~5%) from decomposition and waste production

-air and water (~50%)

-living organisms including animals, plants, fungi, prokaryotes

-few algae or protozoa

In soils, fungi and prokaryotes are the most numerous microorganisms

-many fungi

-many prokaryotes (chemoheterotrophs & chemolithotrophs)

soil profile

-Soil is the loose outer material of Earth's surface.

-Consists of four distinct layers: O horizon, A horizon, B horizon, and C horizon

O horizon

at the surface, with undecomposed plant material

A horizon

with most microbial growth, rich in organic material and nutrients

B horizon

the subsoil where organic material leached from the A horizon gathers, little microbial activity

C horizon

the base that is directly above the bedrock and forms from the bedrock

location of microbial growth

-Most microbial growth takes place on the surfaces of soil particles

-Soil aggregates can contain many different microenvironments supporting the growth of several types of microbes

categories of soil

mineral soil and organic soil

mineral soil

from weathering of rock contains less than 20% organic carbon; most of Earth's soils are in this category.

organic soil

in bogs and marshes possesses at least 20% organic carbon

Bacteria, archaea, fungi, and protozoa use

different functional strategies to take advantage of the complex physical matrix in soi

Soil archaea

are on surfaces of soil particles

soil prokaryotes of domain Bacteria

are on surfaces within smaller soil pores

Terrestrial filamentous fungi

bridge open areas between soil particles

large numbers of terrestrial mo's in soil

only a very small fraction of them can be cultured

Soil populations play roles in

biogeochemical cycling and the carbon, nitrogen, sulfur, iron, and manganese cycles.

Molecular techniques used to help understand

the complex ecosystems found in soil environment

productivity of terrestrial mo's differs from

those operating in photic zone of the open ocean.

Plants rather than microbes

account for most primary production in terrestrial environments

microorganisms play a role in

recycling the organic matter

microbes commensalistic or mutualistic relationships with plants is...

-the major source of terrestrial primary production

-in some, the microbe is a plant pathogen and harms the host

-in all, here is a molecular signaling between the plant and microorganism for two-way communication

phyllosphere

refers to the aerial (above-group) surfaces of a plant

Phyllosphere Microorganisms

-SSU rRNA analysis shows millions of new bacteria yet to be discovered.

-Now know it can support a diverse microbial community.

Rhizosphere

volume of soil around the root influenced by materials released from root

Rhizoplane

surface of root

Plant roots receive between

30% to 60% of the net photosynthesized carbon and ~40% to 90% enters the soil

mycorrhizae

-Mutualistic fungus-plant associations

-mycorrhizal fungi colonize plant roots

-Are not saprophytic; instead use photosynthetically derived carbohydrate provided by host

-Provide enhanced nutrient uptake for plant

nitrogen fixation

-Occurs in soil as a result of a symbiotic relationship between bacteria and plants

-Results in the enzymatic conversion of gaseous nitrogen to ammonium

-important part of global nitrogen cycle