Lecture 1 - Environmental Microbiology

Microbiology an Introduction Twelfth Edition Chapter 27 Environmental Microbiology Copyright © 2016 Pearson Education, Inc. All Rights Reserved Welcom...

Microbiology an Introduction Twelfth Edition Chapter 27 Environmental Microbiology Copyright © 2016 Pearson Education, Inc. All Rights Reserved Welcome to Micro II !! Today’s topics: - Introductions: the prof, the course, the expectations - Dissection of a Journal Article - Lecture Topic: Environmental Microbiology - Pop quiz! 2 Referencing dos and don’ts Referencing. – let’s just go to where the action is! NCBI !! How to reference What to reference 3  Dissection of a scientific paper How to tell a good paper from a bad paper. Points for a good paper: 1. It should be well organized and well written. 2. Introduction set up the importance of the work and define the hypothesis. 3. Methods should be in comprehendible terms and detailed enough to be repeated by another scientist. 4. Results require controls, statistics and reproducibility (no discussion! – results are “cut and dried”) 5. Discussion integrates the results (new data) with the current literature. It is in this section that things get juicy! 6. Conclusion indicates the validity of the hypothesis and typically indicates future work. * Of special note – not all journals are formatted the same way. Most start with an intro followed by methods, results, discussion and conclusion in that order. Others keep the methods at the end of the article and some blend the results and discussion into one unit. As the formatting is usually not controlled by the author the format in which the article is presented is not likely to be a valid critique point. 4 Microbial Diversity and Habitats Learning Objectives 27-1 Define extremophile, and identify two "extreme" habitats. 27-2 Define symbiosis. 27-3 Define mycorrhiza, differentiate endomycorrhizae from ectomycorrhizae, and give an example of each. 5 Microbial Diversity and Habitats Microbial populations are diverse Take advantage of any niches in their environment Compete with other organisms Extremophiles live in extreme conditions (pH, temperature, salinity) Most are members of the Archaea Have extremozymes that make growth possible 6  Symbiosis Close association between two unlike organisms that is beneficial to one or both of them Symbiosis between animals and microbes Ruminants (such as sheep and cows) and digestive bacteria in the rumen Mycorrhizae: relationship between plant roots and fungi that extend the root surface area through which the plant can absorb nutrients (esp. phosphorus) Endomycorrhizae Ectomycorrhizae 7 Symbiosis Not all symbiotic relationships are equivalent!! Commensalism – one of the organisms benefits from the association, the other is unaffected. Many of the organisms that make up our microbiota are commensals (S. epidermidis on our skin). Mutualism – both of the organisms benefit (E. coli synthesizing vitamin K and some B vitamins). Parasitism – one of the organisms benefits by deriving nutrients at the expense of the other (disease causing microbes). 8 Mycorrhizae and Their Considerable Commercial Value 9 Check Your Understanding-1 Check Your Understanding Identify two habitats for extremophile organisms. 27-1 What is the definition of symbiosis? 27-2 Is a truffle an endomycorrhiza or an ectomycorrhiza? 27-3 10 Soil Microbiology and Biogeochemical Cycles Millions of bacteria per gram of soil Most cannot be cultured Largest populations in the top few centimeters Metagenomics is a tool using rRNA genes in to analyze microbiomes in an attempt to detail the microbial population Biogeochemical cycles Elements are oxidized and reduced by microorganisms to meet their metabolic needs; the elements are thus recycled Think of soil as a “biological fire” – a leaf will be consumed by the microbes as they metabolize its organic matter. 11 The Carbon Cycle Photoautotrophs fix CO2 into organic matter using energy from sunlight (examples???; where did the tree come from?) Chemoheterotrophs use organic matter for energy Energy and CO2 are released via respiration; cycle repeats Decomposers oxidize organic compounds from dead plants and animals Excessive CO2 and other greenhouse gasses has unbalanced the carbon cycle and has led to Global warming. 12 Figure 27.2 The Carbon Cycle 13 Check Your Understanding-2 Check Your Understanding What biogeochemical cycle is much publicized as contributing to global warming? 27-4 What is the main source of the carbon in the cellulose forming the mass of a forest? 27-5 14 The Nitrogen Cycle (1 of 6) Nitrogen is required to make proteins and nucleic acids N2 makes up 80% of the atmosphere We are literally at the bottom of a nitrogen ocean. Must be fixed into organic compounds by microorganisms 15 The Nitrogen Cycle 1. Microbial decomposition breaks down proteins into amino acids 2. Deamination: amino groups removed and converted to ammonia (NH3) 3. Ammonification: release of ammonia by bacteria and fungi Ammonia becomes ammonium ions (NH4+ ) in water Microbial decomposition Proteins form dead cells and waste products         Amino acids Microbial decomposition Amino acids         Ammonia (NH3 ) 16 The Nitrogen Cycle Nitrogen fixation: bacterial process that converts nitrogen gas to ammonia Uses nitrogenase enzyme (a very valuable enzyme!!) Note – we are “fixing” nitrogen into the soil not into plants. Free-living nitrogen-fixing bacteria Found in rhizosphere (2mm from the plant root) Azotobacter Beijerinckia Clostridium pasteurianum Cyanobacteria: contain heterocysts that provide anaerobic conditions for fixation 17 The Nitrogen Cycle (3 of 6) Nitrification: oxidation of ammonium ions to produce nitrate Nitrate is needed by plants for protein synthesis (not NH4+) Converting ammonium ions to nitrate is conducted by chemoautotrophic nitrifying bacteria through the Calvin- Benson cycle (Nitrosomonas and Nitrobacter) Nitrosomonas NH4+     NO 2  Ammonium ion Nitrate Nitrite ion Nitrobacter NO2     NO 3  Nitrite ion Nitrate ion 18 The Nitrogen Cycle (4 of 6) Denitrification: nitrate used as an electron acceptor by microbes in the absence of oxygen Microbes like Pseudomonas and Bacillus can thus use nitrate in anaerobic respiration Produces nitrogen gas (lost to the atmosphere) Typically happens in waterlogged soil NO3    NO 2    N2O   N2 Nitrate ion Nitrate Nitriteion Nitrous oxide Nitrous gas 19 The Nitrogen Cycle (6 of 6) Symbiotic nitrogen-fixing bacteria Adapted to leguminous plants (soybeans, peanuts, alfalfa, clover) Form root nodules Rhizobium Bradyrhizobium Frankia (aldur trees) Plant offers anaerobic growth conditions and the bacteria fix nitrogen which can be used by the plant. Lichens Combination of fungus and algae or cyanobacteria. If a member of the group is a cyanobacterium which fixes nitrogen it aids in fixing nitrogen for other plants in the forest. 20 Figure 27.5 The Azolla–Cyanobacteria Symbiosis 21 Figure 27.4 The Formation of a Root Nodule 22 Check Your Understanding-3 Check Your Understanding What is the common name for the group of microbes that oxidize soil nitrogen into a form that is mobile in soil and likely to be used by plants for nutrition? 27-6 Bacteria of the genus Pseudomonas, in the absence of oxygen, will use fully oxidized nitrogen as an electron acceptor, a process in the nitrogen cycle that is given what name? 27-7 23 The Sulfur Cycle The sulfur cycle is much like the nitrogen cycle in that soil microorganisms oxidize the sulfur molecules in preparation for their uptake by plants and animals. Dissimilation: protein decomposition releases H2S into the sulfur cycle. H2S is a reduced form of sulfur and it generally forms under anaerobic conditions Like with the N2 cycle, the reduced form of H2S can be oxidized by microbes and used for energy Some chemoautotrophic bacteria (Beggiatoa, Acidithiobacillus) oxidize H2S to produce NADH which feeds into the ETC Others like the green and purple sulfur bacteria use H 2S in place of water as a source of electrons in photosynthesis. These bacteria thus do not contribute O2 but rather elemental sulfur as a byproduct 24 Figure 27.6 The Sulfur Cycle 25 The sulfur cycle Assimilation: Plants uptake sulfur in an oxidized form (sulfates) to be used for amino acid and protein synthesis. Anaerobic respiration: Some microbes (Desulfovibrio) use the oxidized forms of sulfur in anaerobic respiration converting it back into H2S 26 The Phosphorous Cycle Phosphorus changes from soluble to insoluble forms and organic to inorganic forms (as opposed to changes in its oxidative state) Exists primarily as phosphate ions Related to pH Acidithiobacillus: produces acid that solubilizes phosphate in rocks, freeing it to move through the cycle There is no volatile phosphorus containing product to return phosphorus to the atmosphere – as a result it tends to accumulate in the sea. 27 Check Your Understanding-4 Check Your Understanding Certain nonphotosynthetic bacteria accumulate granules of sulfur within the cell; are the bacteria using hydrogen sulfide or sulfates as an energy source? 27-8 What chemical usually serves as an energy source for organisms that survive in darkness? 27-9 Why does phosphorus tend to accumulate in the seas? 27-10 28  The Degradation of Synthetic Chemicals in Soil and Water (1 of 2) Natural organic matter is easily degraded by microbes Xenobiotics are resistant to degradation Made of chemicals that do not naturally occur in nature (plastics, some pesticides (DDT)) Bioremediation of an Oil Spill in Alaska 29 The Degradation of Synthetic Chemicals in Soil and Water (2 of 2) Bioremediation Use of microbes to detoxify or degrade pollutants Enhanced by nitrogen and phosphorus fertilizer Bioaugmentation Addition of specific microbes to degrade a pollutant. Potentially microbes genetically modified and specifically targeted to the chemical Composting Arranging organic waste to promote microbial degradation by thermophiles Convert plant remains into the equivalent of natural humus 30 Figure 27.8 Composting Municipal Wastes 31 Check Your Understanding-5 Check Your Understanding Why are petroleum products naturally resistant to metabolism by most bacteria? 27-11 What is the definition of the term bioremediation? 27-12 32  Aquatic Microbiology and Sewage Treatment (3 of 3) Aquatic microbiology: study of microorganisms and activities in natural waters Large numbers of microorganisms in water indicate high nutrient levels Many bacteria have appendages and holdfasts to attach to aquatic surfaces 33  Freshwater Microbiota Littoral zone Along the shore; rooted vegetation Limnetic zone Surface of open water away from the shore Photosynthetic algae Profundal zone Deeper water under the limnetic zone; low oxygen Anaerobic purple and green photosynthetic bacteria Benthic zone Bottom sediment; no light or oxygen Desulfovibrio (anaerobic respiration producing H2S) and methane-producing bacteria (Clostridia) may be active in this zone and may thereby offer up the pleasant aroma of the swamp! 34 Seawater Microbiota (1 of 2) Phytoplankton abundant in the top 100 meters Photosynthetic cyanobacteria fix carbon and nitrogen Prochlorococcus Synechococcus Trichodesmium Archaea dominate below 100 meters Crenarchaeota Large populations of Archaea in seafloor sediments 35 Seawater Microbiota (2 of 2) Bioluminescence Luminescent bacteria form symbiotic relationships with benthic- dwelling fish  Aids in attracting and capturing prey – Luciferase enzyme works in the electron transport chain to help emit electron energy as a photon of light 36 Check Your Understanding-6 Check Your Understanding Purple and green sulfur bacteria are photosynthetic organisms, but they are generally found deep in freshwater rather than at the surface. Why? 27-13 37 The Role of Microorganisms in Water Quality (1 of 2) The transmission of infectious diseases (biological pollution) Microbes are filtered from water that percolates into groundwater Some pathogens are transmitted to humans in drinking and recreational water from feces (2 million deaths/yr) Typhoid fever Cholera (Earthquake brings cholera to Haiti, 2010) 38  The Role of Microorganisms in Water Quality (2 of 2) Chemical pollution Water is the universal solvent! Chemicals that enter water are often resistant to biodegradation Eutrophication: overabundance of nutrients in lakes and streams Excessive nitrogen and phosphorus cause algal blooms Dead algae and cyanobacteria are degraded by bacteria, thereby resulting in the net depletion of soluble oxygen Additionally, blooms of toxin- producing Phytoplankton can affect human health. 39 Water Purity Tests (1 of 2) Indicator organisms Used to detect fecal contamination of water They are ubiquitous and easy to culture Coliforms Aerobic or facultatively anaerobic, gram-negative, non–endospore-forming rods Ferment lactose with acid and gas within 48 hours, at 35°C Predominantly Escherichia coli 40  Water Purity Tests (2 of 2) Presence of coliforms determined by: Most probable number (MPN) method Membrane filtration method Media containing ONPG and MUG Limitations to using coliforms as indicator organisms Growth in biofilms thus inaccurately measurements of the indicator organisms in the water. Viruses and protozoans resistant to chemical disinfection Giardia intestinalis Cryptosporidium 41 Check Your Understanding-7 Check Your Understanding  Which disease is more likely to be transmitted by polluted water, cholera or influenza? 27-14  Name a microorganism that will grow in water even if there is no source of organic matter for energy or a nitrogen source—but does require small inputs of phosphorus. 27-15  Coliforms are the most common bacterial indicator of health-threatening water pollution in the United States. Why is it usually necessary to specify the term fecal coliform? 27-16 42  Water Treatment Coagulation and filtration Particulates in raw water settle out Flocculation: removal of colloidal materials, bacteria, and viruses by adding alum (aluminum potassium sulfate) Filtration: passing water through fine sand or coal; microorganisms adsorb to sand particles Cities are especially concerned about toxic chemicals use activated charcoal in place of sand. Disinfection Chlorination Ozone treatment UV light 43 Figure 27.11 The Steps Involved in Water Treatment in a Typical Municipal Water Purification Plant 44 Check Your Understanding-8 Check Your Understanding How do flocculants such as alum remove colloidal impurities, including microorganisms, from water? 27-17 45  Sewage (Wastewater) Treatment (1 of 5) Primary sewage treatment Removal of solids Sludge collects in sedimentation tanks Biochemical oxygen demand (BOD) Measure of the biodegradable organic matter in water Primary treatment removes 25–35% of BOD Determined by the amount of oxygen required by bacteria to metabolize organic matter 46 Sewage (Wastewater) Treatment (2 of 5) Secondary sewage treatment Activated sludge system Air passes through the effluent from primary treatment Contains aerobic sewage-metabolizing microbes (Zoogloea) Removes 75–95% of BOD Trickling filters Sewage sprayed over rocks or plastic, forming biofilm of aerobic microbes Removes 80–85% of BOD Rotating biological contactor Rotation of disks aerates wastewater 47 Figure 27.12 The Stages in Typical Sewage Treatment 48 Figure 27.13 An Activated Sludge System of Secondary Sewage Treatment 49 Figure 27.14 A Trickling Filter of Secondary Sewage Treatment 50 Sewage (Wastewater) Treatment (3 of 5) Disinfection and release Sewage is disinfected by chlorination before release Sludge digestion Additional treatment of sludge from primary sedimentation tanks Occurs in anaerobic sludge digesters Anaerobic bacteria degrade organic solids into methane and carbon dioxide 51  Sewage (Wastewater) Treatment (4 of 5) Septic tank Device used for primary treatment of sewage from areas with low population density Effluent from the holding tank is piped into a drainage field Decomposed by soil microorganisms Oxidation ponds First stage: settles sludge Second stage: effluent pumped into a system of shallow ponds Grows algae that produce oxygen for aerobic decomposition 52 Sewage (Wastewater) Treatment (5 of 5) Tertiary sewage treatment Removal of remaining BOD, nitrogen, and phosphorus Physical and chemical treatment Chlorination Water is drinkable after treatment 53  Check Your Understanding-9 Check Your Understanding Which type of sewage treatment is designed to remove almost all phosphorus from sewage? 27-18 What metabolic group of anaerobic bacteria is especially encouraged by operation of a sludge digestion system? 27-19 What is the relationship between BOD and the welfare of fish? 27-20 54 Gameshow QUIZ!!! 55