Environmental Microbiology and Immunology: Cycles, Biofilms, Water Treatment, and Disease

Microbiology

Carbon Cycle

A series of processes by which carbon compounds are interconverted in the environment.

Nitrogen Cycle

The series of processes by which nitrogen and its compounds are interconverted in the environment.

Redox Reactions

Chemical reactions that involve the transfer of electrons between two species.

Respiration

The process of breaking down glucose to produce energy, typically involving oxygen.

Carbon Fixation

The process of converting inorganic carbon (CO2) into organic compounds by living organisms.

Methane Oxidation

The process by which methane is converted into carbon dioxide and water.

Methanogenesis

The biological production of methane from organic matter under anaerobic conditions.

Nitrification

The biological oxidation of ammonia to nitrate.

Denitrification

The process by which nitrates are reduced to nitrogen gas, completing the nitrogen cycle.

Nitrogen Fixation

The conversion of atmospheric nitrogen into a form usable by living organisms.

Anaerobic Respiration

Using an oxidant other than oxygen for respiration.

Symbiosis

Living together; a close interaction between two different species.

Mutualism

A type of symbiotic relationship where both species benefit and it is obligatory.

Commensalism

A type of symbiotic relationship where one species benefits and the other is unchanged.

Amensalism

A type of symbiotic relationship where one species is harmed and the other is unchanged.

Parasitism

A type of symbiotic relationship where one species benefits and the other is harmed.

Neutralism

A type of symbiotic relationship where both species are unchanged.

Oligotrophic

Describes a water body that is low in nutrients.

Eutrophic

Describes a water body that is high in nutrients.

Eutrophication

The process by which a body of water becomes overly enriched with nutrients, leading to excessive growth of algae.

Biofilms

Communities of organisms in a layer stuck to a surface.

Activated Sludge Process

A wastewater treatment process that uses microbial biomass to oxidize organic compounds.

Primary Treatment

A settling process in large basins to remove large items and settle organic matter.

Secondary Treatment

A biological process where microbes convert organics into carbon dioxide and microbial biomass through aerobic respiration.

Activated sludge

The microbial flocs used in secondary wastewater treatment.

Floc

A clump of microbes floating in the water.

Tertiary treatment

Includes several finishing processes where excess N and P can be removed, and the water is chlorinated to oxidize remaining organics and kill remaining bacteria.

Anaerobic digestor

A tank where activated sludge biomass is delivered, typically leading to the death of microbes and their consumption by anaerobic bacteria.

Stabilized sludge

The active microbial community in an anaerobic digestor.

Products of secondary treatment

Cleaner water, activated sludge biomass, carbon dioxide.

Products of the digestor

Methane, carbon dioxide, stabilized sludge biomass.

Flocculation

Causing particles to clump together, often enhanced by a flocculating agent such as a polymeric carbohydrate.

Chlorination

The process of adding chlorine to kill pathogens and oxidize organics.

Sand filters

Used for aerobic and anaerobic degradation of organic compounds by microbes.

Compost process

Involves mixing organic materials with soil in large piles called windrows, where aerobes break down materials, creating heat and eventually leading to thermophiles dominating.

In situ remediation

Leaves the waste in place, is less disruptive and costly, but may not be effective.

Ex situ remediation

Involves digging up the wastes and moving them to another location, typically an incinerator, and is more disruptive and costly but typically effective.

Nonspecific defenses

General defenses that are innate to the organism; includes physical and chemical barriers and humoral immunity.

Chemical and physical barriers

Includes tight linings with cells riveted together, blood-brain barrier, stomach acid, intestinal base, oleic acids and salts on skin surface, hypertonicity in urinary tract, and vaginal microflora.

Interferon

Interferons are a group of signaling molecules that alert neighboring cells of a viral infection.

Complement system

These are blood plasma proteins that can be activated by an immune response.

Antibody

Antibodies are protein complexes that can specifically bind to the surface proteins of bacteria, viruses and other invaders.

Basic structure of an antibody

Antibodies are composed of four proteins: two larger heavy chains for a stalk or molecular handle called the constant region, and two smaller light chains toward the specific binding end called the variable region.

Antigen

Antigens are molecules complex enough to elicit an immune response.

Antigen-antibody relationship

Antigen-antibody pairs are very specific; often an antibody only binds to one spot (epitope) on an antigen.

B-cell lymphocytes

B-cell lymphocytes differentiate into plasma cells which produce antibodies.

Activation of B-cells

B-cells are activated by an antigen-presenting cell like a macrophage or helper T-cell.

Role of macrophage

Macrophages are antigen-presenting cells that phagocytize the invader, destroy it, and present a surface antigen protein.

Roles of B-cells

B-cells can be plasma cells that make antibodies or differentiate into memory cells.

Plasma cells

Plasma cells produce antibodies to attack the invader directly.

Memory cells

Memory cells remember the antigens of the invader and jump start the immune response during a second infection.

Types of T-cells

T-cells can differentiate into helper T-cells, killer cells, and memory cells.

Helper T-cells

Helper T-cells enhance an immune response by activating B-cells.

Killer T-cells

Killer T-cells directly kill invaders.

Phagocyte

Phagocytic cell that can present antigens on its surface.

Phagocytosis

Engulfing an invader and taking it into the cell in a phagosome.

LPS

Gram-negative bacteria have an outer membrane of lipopolysaccharide (LPS) that is released from phagocytic cells.

Hypothalamus response

LPS stimulate interleukin production which interacts with the hypothalamus to release prostaglandins.

Body's thermostat

Hypothalamus acts as the body's thermostat.

Crisis phase

When the fever breaks and sweats start.

Wound inflammation process

First the physical barriers are broken, then the area is cordoned off with a barrier, white blood cells enter the area and attack invaders, followed by healing.

First reaction of the body after a puncture wound

First blood vessels close (vasoconstrict) to prevent the invader from becoming disseminated.

Platelets

Large cell fragments that create blood clots.

Dilation of blood vessels and edema

Small blood vessels are only one cell thick. When the vessel dilates, the expansion causes more gaps between the cells, allowing fluids to leak into the tissues from the blood, resulting in edema.

Blood cells fighting invaders

Macrophages and other phagocytic cells, with eventual involvement of B-cells and T-cells.

Nature of pus

A purulent discharge that is a mixture of tissue fluids, white blood cells, and invading microbes.

How vaccines work

Vaccines expose the body to antigens from the pathogen, creating antibodies for protection and memory cells for a strong immune response upon re-exposure.

Components of vaccines

Typically made of cell surface proteins, weakened pathogens, or killed pathogens.

Role of memory cells in acquired immunity

Memory cells remember the antigen and provide a strong and fast response when the antigen is encountered a second time.

Vaccines stimulating the immune system

They elicit antibodies and memory cells.

Classes of vaccines

Live whole agents, toxoid vaccines, subunit vaccines, and conjugated vaccines.

Common vaccines and diseases

MMR for mumps, measles, rubella; DTP for diphtheria, tetanus, pertussis; vaccines for influenza, hepatitis, venereal warts, meningitis, chickenpox, smallpox, and pneumonia.

Local infections

Infections that stay in one site.

Systemic infections

Infections that are disseminated throughout the body.

Bacteremia

When bacteria are found in the blood.

Septicemia

When the bacteria in the blood are proliferating.

Viremia

Virus in the blood.

Primary infections

The first pathogenic expression.

Secondary infections

Infections caused by a second agent that leads to greater disease, typically by an opportunistic pathogen.

Subclinical infections

Infections that do not have clear signs and symptoms.

Epidemic

An outbreak of a disease that affects many people at the same time.

Pandemic

An epidemic that has spread over multiple countries or continents.

Endemic

A disease or condition regularly found among particular people or in a certain area.

Sporadic outbreaks

Occasional cases of a disease that occur irregularly.

Contamination

Contamination means that the agent is on you or in you.

Infection

Infection means that it has colonized you.

Disease

Disease is when there is pathology.

Morbidity

Morbidity is number or rate of people sick with a disease.

Mortality

Mortality is number or rate of deaths due to the disease.

Chronic infections

Chronic infections go on for a long time.

Acute infections

Acute infections are for a short time and often more powerful than the chronic infection.

Latent diseases

Latent diseases hide in some way after infection for long periods of time, like HIV or Herpes hiding until an induction event leads to a new outbreak.

Self-limiting diseases

Self-limiting diseases will resolve without treatment.

Nosocomial infections

Nosocomial infections are acquired in a health care setting.

Pathogenicity

Pathogenicity is a measure of the capacity to cause disease.

Virulence

Virulence is a measure of the seriousness of the disease.

Virulence factors

These are features of microbes that lead to pathogenicity.

Common types of virulence factors

Adherence factors, Toxins, Capsule, Invasive enzymes.

Common adherence factors

Adherence factors are typically cell surface proteins that help the agent bind to your cells.

Endotoxin

Endotoxin would be LPS, lipopolysaccharide, released from Gram-negative outer membrane when the cell dies.