Week 1 Microbiology

Microbiology: An Introduction

• Textbook title is Microbiology: An Introduction.
• Edition is the Twelfth Edition.
• Chapter 27 is titled Environmental Microbiology.
• Today's topics include introductions to the professor, course, and expectations; dissection of a journal article, the lecture topic on environmental microbiology, and a pop quiz.
• Referencing dos and don'ts are discussed; proper referencing is crucial and avoiding plagiarism is important.
• A good scientific paper has well-organized information, clear methodologies, comprehensible methods, detailed results, insightful discussion, and conclusions that support or refine the hypothesis.
• Microbial diversity and habitats include extremophiles in extreme habitats and symbiosis.
• Extremophiles live in extreme conditions (pH, temperature, and salinity). Most are members of the Archaea and have extremozymes that make growth possible.
• Symbiosis is a close association between two unlike organisms that benefits at least one or both organisms.
• Symbiotic relationships in ruminants and digestive bacteria in the rumen are described; and the relationship between roots and fungi (mycorrhizae) that extend the root surface area are also discussed; there endomycorrhizae and ectomycorrhizae examples of each.
• Not all symbiotic relationships are equivalent. Examples of symbiotic relationships are commensalism, mutualism, and parasitism. Bacteria in our microbiota are often commensals; mutualistic microorganisms benefit both parties (like E. coli synthesizing vitamin K and some B vitamins); and parasites benefit by extracting nutrients from other organisms, sometimes to the host organism's detriment.
• Mycorrhizae have considerable commercial value including Mycorrhizal infection influences the growth of many plants and Truffles are described as an important ectomycorrhiza, often found on oak trees.
• Check your understanding quizzes ask questions about extremophiles, symbiosis, and mycorrhizae; the definition of symbiosis should be understood, as well as the difference between endomycorrhizae and ectomycorrhizae.
• Soil microbiology and biogeochemical cycles involve millions of bacteria per gram of soil, with most being unable to be cultured. The largest populations exist in the top few centimeters; metagenomics is a tool to understand detail the microbial populations.
• Biogeochemical cycles are important as elements are oxidized and reduced by microorganisms to meet their needs. This recycling of elements is discussed in terms of a leaf being consumed by microbes as they metabolize organic matter.
• The Carbon Cycle is described with the important elements of photoautotrophs fixing atmospheric CO2, into organic matter using sunlight energy; the role of chemoheterotrophs using organic matter for energy, and the repeated energy and carbon dioxide releases through respiration; and understanding that decomposers oxidize organic compounds. Excessive carbon dioxide and greenhouse gases are highlighted as contributing to global warming.
• Nitrogen cycling is required to make proteins and nucleic acids. Nitrogen is abundant in the atmosphere, but it must be fixed into organic compounds by microorganisms. Nitrogen fixation bacterial processes convert nitrogen-gas to ammonia, utilizing nitrogenase enzyme which is a valuable enzyme; free-living bacteria such as Azotobacter and Beijerinckia, as well as those in the rhizosphere are discussed. Discussion on symbiotic nitrogen-fixing bacteria such as Rhizobium and Bradyrhizobium which are important associations in adapting to leguminous plants, including soybeans, peanuts, and alfalfa etc, is noted. Lichens and their importance in nitrogen cycling are listed.
• Nitrogen Cycle Steps and Processes are listed including microbial decomposition, deamination, ammonification, ammonia becoming ammonium ions in water, and the conversion of proteins/amino acids to ammonia.
• Nitrification is the oxidation of ammonium ions to nitrate, essential for plants in protein synthesis.
• Denitrification is the use of nitrate as an electron acceptor in an anaerobic environment; this processes releases nitrogen gas.
• The sulfur cycle is similar to the nitrogen cycle, with microorganisms oxidizing sulfur to be utilized by plants and animals. The reduced form of sulfur (hydrogen sulfide) is released during protein decomposition and is used for energy by microbes in anaerobic conditions and by some photosynthetic bacteria as an electron source in place of water.
• Chemoautotrophic bacteria are noted, like Beggiatoa and Acidithiobacillus which can oxidize H2S to produce NADH and feed into the electron transport chain.
• The Phosphorous Cycle describes how phosphorus changes from soluble to insoluble forms, and from organic to inorganic forms and how it exists predominately as phosphate ions which is related to pH and how acidithiobacillus produces acid to solubilize phosphate in rocks, freeing it to move through the cycle.
• Sulfur and Phosphorous cycle diagrams are also highlighted.
• Some check your understanding questions include: the common name for the group of microbes that oxidize soil nitrogen; the process bacteria of Pseudomonas undergoes in the absence of oxygen, that uses oxidized nitrogen as an electron acceptor; why non-photosynthetic bacteria accumulate sulfur granules; what serves as an energy source for organisms in darkness; and why phosphorous tends to accumulate in seas.
• The Degradation of Synthetic Chemicals in Soil and Water: Natural organic matter is easily degraded by microbes. Xenobiotics are resistant to degradation, often made of chemicals that don't occur naturally, such as plastics and DDT and the importance of bioremediation in detoxifying or degrading pollutants.
• Bioaugmentation and composting are approaches for pollutants. Composting organizes organic waste to effectively degrade waste by using microbes.
• Aquatic microbiology in natural waters and their high nutrient levels are discussed.
• Some non-photosynthetic bacteria accumulate sulfur granules within the cell using hydrogen sulfide/sulfates as energy; and the usually chemical energy source as chemical compounds that may be in darkness are noted.
• Freshwater microbiota include various zones and the microorganisms in them, including the littoral, limnetic, and benthic zones, as well as Desulfovibrio (anaerobic respiration producing H2S) and methane-producing bacteria.
• Marine microbiota includes phytoplankton, including photosynthetic cyanobacteria, prochlorococcus, synechococcus, trichodesmium, archaea, and the importance of crenarchaeota in dominating below 100 meters and large populations of archaea in seafloor sediments.
• Bioluminescence in marine organisms involve symbiotic relationships with benthic-dwelling fish, and the use of luciferase enzyme in the electron transport chain helps in emitting photon energy as light for attracting prey.
• Various checks your understanding questions are listed about reasons for some organisms to be found deep in freshwater; the role of microorganisms in water quality and its transmission of infectious diseases (biological pollution); the presence of indicator organisms to test water, and their limitations to measuring water quality.
• Water treatment involves coagulation and filtration, flocculation, filtration, disinfection (through chlorination, ozone treatment, and UV light), and various steps of sewage treatment.
• Methods for water purity testing, such as the presence of coliforms, using membrane filtration, ONPG, and MUG are identified along-with possible limitations from microbial growth in biofilms.
• Check your understanding questions are listed to better understand the reasons for microbial resistances in bacteria to metabolism from petroleum products, define bioremediation; the common names of microbes that oxidize soil nitrogen; the processes that bacteria of Pseudomonas undergoes when oxygen is absent, and other questions covering water and sewage treatment.