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ENVIRONMENTAL MICROBIOLOGY

ENVIRONMENTAL MICROBIOLOGY. What is Microbiology?!. Microbiology is a branch of biology dealing with microscopic forms of life. Who discovered microbiology?. Aristotle, Ancient Egyptians and Ancient Chinese Robert Hooke (1635- 1703) Anton Van Leeuwenhoek (1632-1723)

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ENVIRONMENTAL MICROBIOLOGY

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  1. ENVIRONMENTAL MICROBIOLOGY

  2. What is Microbiology?!

  3. Microbiology is a branch of biology dealing with microscopic forms of life.

  4. Who discovered microbiology? Aristotle, Ancient Egyptians and Ancient Chinese Robert Hooke (1635- 1703) Anton Van Leeuwenhoek (1632-1723) Francesco Redi (1626-1678) Louis Pasteur (1822-1895) Joseph Lister (1827-1912) Robert Koch (1843-1910)

  5. Environmental microbiologyis the study of microscopic organisms found in natural environments. Microbes may be eukaryotes or prokaryotes. Bacteria, cyanobacteria, dinoflagellates, algae, and protozoans, are examples of microbes. Associated with water, soil sediments, intestinal tracts of animals, and plants. May be heterotrophic or autotrophic.

  6. Microbes live in virtually every environmental niche Extremes - pH, salinity, pressure, temperature Aerobic, anaerobic conditions Biofilms Geothermal vents and subterranean deposits

  7. Microbes make up a majority of the biomass on Earth ≥ 99% are not culturable at present, but may hold valuable products for humans. 5-20% of biomass in seawater. Rich bacterial communities in sub-surface strata (600 m depth) - up to 2 x 104 tons-equivalent to 2 m layer over entire planet. More than all flora and fauna combined!

  8. Ways to classify bacteria

  9. Many Gram Negative bacteria species are pathogenic or disease causing such as: • Escherichia coli • Salmonella • Pseudomonas • Cyanobacteria • Many Gram Positive bacteria species are non-pathenogenic with the exception of: • Streptococcus • Staphylococcus • Bacillus

  10. Observations • 98% of all water on Earth from marine environment. • 75% of the ocean below 1000 m and averages 3° C. • Deepest part of oceans ~11,000 m and ~1000 atm. • Many marine bacteria have absolute requirements • for sodium, potassium, and magnesium ions. • Large pressure differences lead to microorganisms • being present at different depths. Microbes vary in • their ability to deal with pressure and salinity. • Microorganisms are involved in many geochemical • cycles in ocean waters and sediments including • carbon, nitrogen, sulfur, and phosphorus cycles.

  11. Marine Microbial Food Web Phage Protozoa Autotrophic Bacteria Heterotrophic Bacteria Dissolved Organic Matter - DOM Fish Corals Sponges Algae

  12. Classical Marine Food Web Fish Herbivores Zooplankton Big Algae Nutrients (P,N,Fe) Heterotrophic Bacteria Particulate Organic Matter (POM) Dissolved Organic Matter (DOM) Bacteria as Remineralizers

  13. Note: In marine environments bacteria and fungi play a major role in recycling nutrients by converting organic detritus to a more useable form. Example: breakdown of sea grasses and mangrove leaves. Plant material is mostly cellulose and not easily digested by many marine organisms. Decomposition by microbial action releases phosphorus, nitrogen, and sulfur which is in digestible form.

  14. Carbon cycle

  15. Phosphorus cycle

  16. Nitrogen cycle

  17. Sulfur cycle

  18. Abundance of organisms in 1 ml of seawater • Viruses/Phage 10,000,000 • Heterotrophic Bacteria 1,000,000 • Photosynthetic Bacteria 100,000 • Protozoa 4,000 • Algae 3,000 • Zooplankton <<1

  19. Abundance of Microbes (cells per ml) • Groundwater 1 x 104 - 4 x 105 • Central Atlantic Ocean 2 x 105 - 8 x 105 • Mediterranean Sea 2 x 105 - 7 x 105 • Antarctic coastal areas 2 x 105- 7x 105 • Coastal lagoons 7 x 105 - 2 x 106 • Continental lakes 1 x 106 - 43 x 106 • Eutrophic lakes 6 x 106 - 3 x 107 • Hyperhaline ponds up to 108

  20. Direct Counts with Epifluorescent Microscopy Use a vacuum to pull 10 ml seawater through a 0.02 mm glass filter Incubate with dsDNA stain Place filter on slide Visualize on an epifluorescent microscope Hobbie (1977) Appl Environ Microbiol Moriarty et al (1985) Mar Biol - 1st counts on coral reefs

  21. Cultured vs Uncultured Coral-Associated Microbes Airbrush or crush coral Uncultured Cultured Extract DNA Plate onto marine agar PCR with primers specific to 16S rDNA Isolate 100 colonies Extract DNA Clone and Transform Sequence 16S rDNA Pick 100 colonies Isolate plasmid DNA Compare 16S rDNA sequences against each other Sequence 16S rDNA

  22. Methods to study bacteria

  23. B a c t 3 5 8 B a c t 5 1 7 B a c t 2 7 F 5 ﾕ 3 ﾕ V 1 V 2 V 3 B a c t 1 4 9 2 R transcription translation DNA RNA Protein RIBOSOME 16S rDNA a gene that encodes small subunit ribosomal RNA rDNA is present in all known organisms

  24. mucus or tissue samples (multiple species) Identifying uncultured bacteria gradient gel electrophoresis of 16S PCR products to identify uncultured bacteria by sequencing of individual unique bands

  25. Summary Microbes are a key component of environment and may contain valuable compounds/info. They are responsible for important geochemical cycling. Bacteria occupy various ecological “niches” based on their tolerance (or lack thereof) for salinities, temperatures, and baro-tolerance. Many methods may be employed to study specific environmental microbiology/ecology questions.

  26. QUESTIONS?

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