Bioterrorism is the intentional release of of biological agents. It can be used in warfare. According to the U.S. Centers for Disease Control and Prevention bioterrorism is the deliberate release of viruses, bacteria, toxins or other harmful agents to cause illness or death in people, animals, or plants. Biological agents spread through the air, water, or in food. Some can also spread from person to person. They can be very hard to detect. They don’t cause illness for several hours or days. Biodefense uses medical measures to protect people against bioterrorism. This includes medicines and vaccinations. It also includes medical research and preparations to defend against bioterrorist attacks.

The FDA is in charge of food safety. Food safety is the process of preparing and handling food. It is done to prevent illnesses. There are certain certifications that must be passed. The 5 rules according to WHO are:

1. Prevent contaminating food with pathogens spreading from people, pets, and pests.
2. Separate raw and cooked foods to prevent contaminating the cooked foods.
3. Cook foods for the appropriate length of time and at the appropriate temperature to kill pathogens.
4. Store food at the proper temperature.
5. Do use safe water and safe raw materials.

1. Tell of all accidents immediately.
2. Keep pathways clear. Extra items should be put out of the way so no one trips or so they do not get contaminated.
3. Long hair and loose clothing should be tied up.
4. Do not taste or smell anything.
5. Safety googles should be worn.
6. Do not point test tubes at yourself.
7. Make sure your work station is clean.
8. Do not lean, hang over or sit on the laboratory tables.
9. Know where all the safety equipment in the lab is.
10. Do not eat or drink in the lab.

Water cannot be discarding untreated into lakes or streams due to environmental, and public health consideration. Primary Wastewater treatment uses physical separation methods to separate solids, particulate organic and inorganic material from water. Secondary anaerobic wastewater treatment involves a series of degradative and fermentative reactions carried out by prokaryotes in anoxic conditions. Secondary aerobic wastewater treatment uses oxidative degradation reactions carried off by microorganisms. There are advanced wastewater treatments as well. These treatments include tertiary treatment, physical-chemical treatment, or combined biological, physical treatment. Goals of advanced wastewater treatment typically include additional removal of organic matter and suspended solids. Due to new product bioremediation is needed for more than just priority pollutants. Things like fragrances, household products, and sunscreen, are continuously discharged into the environment through the release of untreated sewage.

1.Autoclaving

Pressurized steam is used to heat the material to be sterilized. It kills all microbes, spores and viruses. Autoclaving kills microbes by hydrolysis.  The intense heat comes from the steam.

2. Flaming and baking

Microbes are killed by  by oxidation of cellular components. It needs higher temperatures than autoclaving.

3. Filtration

Filters work by passing the solution through a filter with a pore diameter that is too small for microbes to pass through. Viruses and phage can pass through filters.

4. Solvents

Ethanol or isopropanol denature proteins through a process that requires water. They are good at killing microbial cells but they have no effect on spores.

5. Radiation

UV, x-rays and gamma rays are all types of electromagnetic radiation. They can penetrate DNA.

Bioremediation is the clean up of oil, toxic chemicals, or other environmental pollutants. Often it impossible to remove all contaminated material, so it is then contained. An example of a need for containment would include uranium, an inorganic pollutant. An organic pollutant, hydrocarbon, can be completely degraded by microorganisms, eventually becoming CO2. Petroleum in an oil spill is degraded by microorganisms. Because oil and water do not mix an oil spill will cause a slick layer of the water. Microorganisms will stick to this layer and degrade the oil eventually dispersing the slick. Some chemicals have never been seen by the environment, called xenobiotics. Xenobiotics include pesticides and dyes amongst other chemicals. Some xenobiotics are so chemically different that they take years to degrade, if at all. Another example of a xenobiotic is plastics.

Eukaryotic Diversity

Diplomonads

• Unicellular, flagellated protists
• Lack mitochondria and chloroplasts
• Live in anoxic habitats
  • Animal intestines
• Conserve energy from fermentation
• Can cause diseases in:
  • Fish
  • Domestic animals
  • Humans
• Contain two nuclei of equal size
• Contain mitosomes
• Reduced mitochondria lacking electron transport proteins
• Genome quite compact
  • Contains few introns in genome
• Lacks genes for metabolic pathways such as the citric acid cycle

Euglenozoans

• Unicellular
• Can be free-living or parasitic flagellated
  • Kinetoplastids and euglenids
• Kinetoplastids
  • Kinteoplast
    • Mass of DNA present in single, large mitochondrion
  • Primarily live in aquatic habitats
  • Some are parasites of animals and humans
  • Responsible for Trypanosoma cells
    • Trypanosoma brucei causes African sleeping sickness, which is a chronic and fatal disease
    • Trypanosoma cruzi causes Chagas disease
      • Spreads by a “kissing bug”
      • Can be fatal
    • Leishmania causes cutaneous and systemic leishmaniasis
  • Euglenids
    • Motile and nonpatbhogenic
    • Chemotrophic and phototrophic
    • Contain two flagella
      • Dorsal and Ventral
    • Live in aquatic habitats
      • Freshwater and Marine
    • Contain chloroplasts
    • In darkness they can lose chloroplasts and live as cheoorganotrophs
    • Many feed on cells by phagocytosis

Alveolates

• Contain aveoli
  • Cytoplasmic sacs located under the cytoplasmic membrane
  • Helps cell maintain osmotic balance by controlling water influx and efflux
  • Some function as armor plates
• Ciliates
  • Contain cilia
    • Function in motility and some cover the cell
    • Paramecium are widely distributed species
  • Have macronuclei and micronuclei
  • Maconucleus
    • Growth and feeding
  • Micronucleus
    • Sexual reproduction
  • Parramecium
    • Hosts for endosybiotic prokaryotes and eukaryotes
  • Obligate anaerobe ciliates
    • Present in rumen of animals
    • Some can be parasites to animals
      • Balatidium coli is an intestinal parasite in animals
    • Dinoflagellates
      • Marine and freshwater phototrophic alveolates
      • Have two flagella of differents lengths and with different points of insertion
        • Transverse and longitudinal insertion points
      • Some are free-living and some share symbiotic relationships with coral reefs
      • Some are toxic
        • Gonyaulax cells or red tides
          • Kills fish and poisons humans
        • Pfiesteria
          • Infect and kill fish due to neurotoxins that affect movement and destroy skin
        • Apicomplexans
          • Nonphototrophic obligate parasites
          • Can cuase malaria, toxoplasmosis, and coccidiosis
          • Nonmotile adult stages
          • Produce sporozoites
            • Function in transmission of the parasite to a new host
          • Apicoplasts
            • Dengenerate chloroplasts that lack pigments and phototophic capacity
            • Catalyze fatty acid, isoprenoidm and heme biosynthesis and export products to cytoplasm

Stramenophiles

• Contain chemoorganotrophic and phototrophic microorganisms and macroorganisms
• Possess flagella
  • Diatoms
    • Unicellular
    • Phototrophic
    • Major component of plankton
    • Produce cell wall made of silica
      • Protects cell against predation
    • Diatom Frustule
      • Resistant to decay
    • Oomycetes
      • Water molds
        • Contain flagellated cells
      • Coenocytic hyphae
      • Cell walls are made of cellulose
      • Phytophthora infestans
        • Causes blight disease of potatoes
      • Pythium
        • Causes white rust of agricultural crops
      • Golden algae
        • Chrysophytes
        • Primarily unicellular marine and freshwater phototrophs
        • Two flagella
        • Chlorophyll c major pigment
      • Brown algae
        • Marine and multicellular
        • Typically macroscopic
        • No unicellular brown algae
        • Seaweeds are considered brown algae

Cercozoans

• Chlorarachniophytes
  • Freshwater and marine amoeba-like phototrophs
  • Develop a flagellum for dispersal
  • Acquisition of green algal chloroplasts is a prime example of secondary endosymbiosis
• Foraminifera
  • Exclusively marine and form shell-like structures called tests
    • Tests are organic materials reinforced with calcium carbonate
  • Hosts a variety of algae that form endosymbiotic relationships with the protists
  • Tests are resistant to decay and readily fossilized

Radiolarians

• Mostly planktonic marine eukaryotes
• Form threadlike pseudopodia
• Strictly heterotrophic
• Reside in the upper 100m or so of ocean waters
• Consume bacteria and particulate organic matter
• Some associate with algae that take on a symbiotic role and supply nutrients to the radiolarian
• Tests have radial symmetry

Amoebozoa

• Terrestrial and aquatic protists
• Lobe-shaped pseudopodia for movement and feeding
• Gymnamoebas
  • Free-living protists
  • Live in aquatic and soil environments
  • Amoeboid movement
    • Facilitates pseudopodia movement
  • Amoeba
    • Common organism in pond waters
  • Entamoebas
    • Parasites of vertebrates and invertebrates
    • Live in oral or intestinal tract of humans
    • Entamoeba histolytica
      • Pathogenic to humans and cause amebic dysentery
      • Forms cyst
    • Slime molds
      • Motile
      • Plasmodial slime molds
        • Vegetative form are masses of protoplasm
      • Cellular slime molds
        • Vegetative form are single amoebae
      • Live primarily on decaying plant matter
      • Form differentiated spore-like structures that can remain dormant and then germinate

Chytridiomycetes

• Earliest diverging lineage of fungi
• Fruiting body contains sexual spores
  • Flagellated and motile
• Some exists as single cells whereas others form colonies with hyphae
• Batrachochytrium dendrobatidis
  • Causes chytridiomycosis of frogs
• Some are obligate anaerobes
• Inhabit rumen of ruminant animals
• Neocallimasitx
  • Inhabits the rumen and conserves energy from the fermentation of sugars to acids

Zygomycetes

• Known for food spoilage
• Found in soil and on decaying plant material
• Rhizopus
  • Black bread mold
  • Undergoes asexual and sexual reproduction

Glomeromycetes

• Important in mycorrhizal associations
• Form symbiotic relationship with plant roots
• Relatively small
• Obligately symbiotic and all species form relations with endomycorrhizae
• Played pivotal role in early vascular plants ability to colonize on land
• Reproduce asexually and are coencytic

Ascomycetes

• Single-celled species
  • Saccharomyces (Baker’s yeast)
• Common mold
  • Aspergillus
• Found in aquatic and terrestrial environments
• Reproduce asexually by production of conidia that form at tips of specialized hyphae
• Saccharomyces
  • Reproduce sexually in which two cells fuse, zygote

Basidiomycetes

• Basidium
  • Structure in which haploid basidiospores are formed by meiosis
  • Basidiocarp
    • Mushroom fruiting body
    • Starts out as mycelium that differentiates into a small button-shaped structure underground that then expands into the full-grown basidiocarp
  • Diakaryotic basdia
    • Borne on the underside of the basdiocarp on flat plates called gills, which are attached to the cap of the mushroom

Algae

• Red Algae
  • Rhodophytes
  • Inhabit marine environment
  • Few species found in freshwater and terrestrial habitat
  • Phototrophic and contain chlorophyll a
  • Chloroplasts contain phycobiliproteins
    • Major light harvesting pigments of cyanobacteria
  • Red color results from phycoerythrin
  • Most species are multicellular
  • Lack flagella
  • Some are filamentous, leafy, or coralline in structure
  • Unicellular
    • Cyaniadiales
      • Live in acidic hot springs at temperatures and at pH values 0.5 to 4.0
    • Green Algae
      • Chlorophytes
      • Conatain chlorophylls a and b
      • Lack phycobiliproteins
      • Chlorophytes and charophyceans
      • Chlorophytes
        • Unicellular and multicellular species
        • Volvox(colonial level)
          • Forms colonies composed of several hundred flagellated cells
            • Some are motile and carry out photosynthesis
            • Some specialize in reproduction
          • Cells are interconnected by thin strands of cytoplasm that allow the entire colony to swim in a coordinated fashion
        • Some green algae have potential for biofuels
        • Endolithic
          • Some grow inside of rocks
            • Cold and dry environments

Minerals are recovered through the leaching process. The minerals that are readily oxidized are iron and copper, but leaching also is used for gold and uranium. In the microbial leaching, the ore is dumped into a large pile and dilute sulfuric acid at pH 2 is percolated into the stack. The liquid that emerges is rich in minerals and is transported to a precipitation plant where it is purified. The liquid is then returned to the top of the pile, and the cycle is repeated.

The precipitation plant is where the Cu2+ from leaching is recovered. Cu2+ is improved by adding scrap metal iron to the precipitation pond. Temperatures in a leaching dump rise and this lead to shifts in an iron-oxidizing microbial community.

In microbial nitrogen fixation, atmospheric nitrogen is converted to ammonia by nitrogenases. Microorganisms that use nitrogen fixation include cyanobacteria, green sulfur bacteria, rhizobia, and diazotrophs. Nitrogen fixation is coupled with hydrolysis and results in the formation of H2 along with ammonia. Nitrogen fixation in incredibly diverse in the microbial world. Diazotrophs use nitrogenase generated ammonium and assimilate it into glutamate by the glutamate synthase pathway. Of note, nitrogen fixation is susceptible to oxygen and often occurs in oxygen free environments.

Rhizobia can also be found in plant nodules and facilitates nitrogen fixation to produce nitrogen compounds that help in plant growth. This relationship is also important beyond just the plant and bacterial organism in that fixed nitrogen released from dead plants help fertilize the soil. Artificial fertilization by nitrogen fixation has also been industrialized in processes such as the Haber process.

Methanogenesis is the process where methane is formed by microbial methanogens. Methanogenesis is a form of anaerobic respiration when oxygen is not used. Many methanogens are known to be obligatory anaerobes and are inhibited in growth in the presence of oxygen. In this process, the terminal electron acceptor is carbon such as acetic acid and carbon dioxide. Other carbon electron acceptors include formic acid, methanol, methylamine, dimethyl sulfide, and methanethiol. The methyl compounds are catabolized by methyl transferases.

Methanogenesis is important in that it is the final step in the degradation of biomass and organic matter. When the biomass decays, inorganic electron acceptors including sulfur, oxygen, iron, and nitrate are depleted and H2 and CO2 accumulates. Fermentation and methanogenesis takes over as the prominent catabolic processes at this stage. Methanogens are able to remove hydrogen, and carbon dioxide to flush out excess carbon accumulation in anaerobic environments.