ese3301

• Rapid detections of microorganisms in water

  1. Motivation: Traditional methods take at least 18 hrs to obtain results and require expensive equipment and highly trained personnel

  2. Objectives: To develop a rapid monitoring method of microbial water quality
• Multi-omics approach on the ecotoxicological assessment of microplastics

  Motivation: The effect of microplastics and chemical additives on zebrafish
• What is Microbiology about

  • Study of microorganisms
  • Microscopic entities
  • Prokaryotes: Bacteria and Archaea
  • Eukaryotes
  • Single cells, cell clusters, biofilms
  • Free-living
  • Distinct from plant/animal cells, which exist only as part of multicellular organisms
  • Viruses (NOT cells)
• Microfluidic chip for understanding microbial processes

  1. Motivation: Antibiotic resistance development in biofilm

  2. Objectives: To understand biofilm formation under different concentrations of antibiotics and disinfectant in microfluidic chip

  3. Tools: Microfluidic chip, Confocal laser microscopy
• Microbiology in No aeration reciprocation MBR

  1. Motivation: Understand who they are (microbial identification) and what they do (microbial function) in engineered system

  2. Objectives: To investigate microbial ecology to reduce aeration (energy) in MBR using bioinformatic tools
• Types of organisms

  • Prokaryotes
  • Eukaryotes
• Viruses are not cells
• Typical sizes and characteristics of prokaryotes and eukaryotes
• Properties of all cells: Metabolism
• Advantages of being small in cell size

  • Greater nutrient exchange, faster growth, more chance for mutation
• Microorganisms

  • Bacteria
  • Archaea
  • Protozoa
  • Fungi
  • Algae
  • Plants
  • Animals
• Prokaryotes

  • Cell wall
  • Cytoplasmic membrane
  • Nucleoid
  • Cytoplasm
  • Plasmid
  • Ribosomes
• Opportunistic pathogenic microorganisms are not pathogens but will turn to pathogens
• Free-living organism


  An organism that is not directly dependent on another organism for survival
• Eukaryotes

  • Cell wall
  • Cytoplasmic membrane
  • Mitochondrion
  • Nuclear membrane
  • Ribosomes
  • Endoplasmic reticulum
  • Golgi complex
  • Nucleus
  • Organelles
• Difference between Prokaryotes and Eukaryotes

  Degree of specialization of cells
• Microbes interact with their physical and chemical environment. Ecosystems are influenced by microbial activities
• Cells interact with each other by chemical messengers
• Physical abiotic parameters affecting microbial activities

  • Temperature, PH, light
• Properties of all cells

  • Genetic (replication, transcription, translation)
  • Catalytic (energy, biosyntheses)
• Historical perspective of Environmental Microbiology: Water quality, fate of pathogens, pathogens control in food supply, chemicals pollutants in soil and groundwater
• Places where microorganisms exist

  • Soil, Hot springs, Fresh water, salt water, Glaciers/Antarctica
• Changes between 1900 and 2000: Understanding of disease processes, Better sanitation and public health practices, Use of antimicrobials, Active vaccination
• Microorganisms exist where their requirements are met: Water, Carbon source, Nitrogen, phosphorus, trace nutrients, Energy source
• Microorganisms do not exist in Lava, Extreme pH (pH<0, pH > 12)
• Cells evolve to display new properties. Phylogenetic trees capture evolutionary relationships
• Microorganisms change the chemical and physical properties of their habitats
• Eutrophication: Water bodies receive excess nutrients (N, P), Growth of Cyanobacteria, algae, aquatic weeds
• Properties of all cells: Metabolism - Cells take up nutrients, transform them, and expel wastes
• Reasons why environmental engineers care about microbiology: Beneficial microorganisms, Biodegradation of organic/inorganic wastes, In situ bioremediation of soils/groundwater, Wastewater treatment
• Reasons why environmental engineers care about microbiology: Harmful microorganisms, Pathogens
• Properties of some cells: Some cells can form new cell structures such as a spore
• Drinking water treatment plants

  Biological treatment is becoming more popular to remove unwanted spills, oil spills, N, P, microorganisms to remove unwanted compounds
• In situ bioremediation of soils/groundwater

  1. Accelerated in situ bioremediation: Add substrate, nutrients, or bacteria

  2. Natural attenuation: Without human intervention
• Other Beneficial Microorganisms

  • Lipid-accumulating algae for diesel
• Modern Environmental Microbiology includes better access to healthcare, imbalance in terms of income, healthcare system and living conditions, sanitation and resources, technology, immune system, proper use of antibiotics, vaccination, treatment
• Microorganisms, energy, and the environment

  • The role of microbes in production of biofuels like methane, ethanol, hydrogen
  • The role of microbes in cleaning up pollutants (bioremediation), waste to energy
• Microorganisms and the human gastrointestinal (GI) tract


  • High numbers of microorganisms occur in colon and oral cavity
  • Positive impacts: Synthesize vitamins and other nutrients, Compete with pathogens for space and resources
  • Probiotics
• Wastewater treatment plants

  1. Biological treatment is the cornerstone

  2. Activated sludge

  3. Trickling filters
• Microorganisms and agriculture

  • Many aspects of agriculture depend on microbial activities
  • Positive impacts: Nitrogen-fixing bacteria, Cellulose-degrading microbes in the rumen, Regeneration of nutrients in soil and water
  • Negative impacts: Diseases in plants and animals, in cows, bananas have a diminishing species pool