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  1. Aquatic Environments and Microorganisms
    1. Gases and aquatic environments
      1. Oxygen
        1. Aquatic environments are low oxygen diffusion environments (in contrast to the high oxygen diffusion environments provided thin films of water coating soil particles in terrestrial environments)
        2. At higher temperatures and with lower pressure the solubility of oxygen in water is decreased; this can lead to the formation of hypoxic or anoxic zones, which are inhabited by anaerobic microbes
      2. Carbon dioxide-important in many chemical and biological processes; the carbon dioxide-bicarbonate-carbonate equilibrium impacts the pH of water; this equilibrium is impacted by the activity of aquatic microorganisms
      3. Other gases such as nitrogen, hydrogen, and methane are important; they vary in terms of their solubility in water
    2. Nutrients in aquatic environments
      1. Can vary from extremely low to levels approaching those in laboratory media; changes in nutrient levels can cause shifts between low-nutrient responsive and high-nutrient responsive microorganisms; nutrient turnover rates can vary from hundreds to thousands of years (marine environments) to very rapid turnover (marsh and estuarine environments)
      2. Although most aquatic ecosystems are based on the activity of photosynthetic microorganisms, some are based on the activity of chemolithotrophic microorganisms (e.g., deep black smoker areas, subsurface cave systems, and methane seep areas)
      3. Winogradsky columns illustrate the interactions and gradients that occur in aquatic environments
        1. Made by mixing together mud, water, and sources of nutrients (e.g., cellulose and other materials), then incubating the column in light; as column matures, specific members of the microbial community develop in specific microenvironments in response to chemical gradients
        2. In the bottom, anaerobic conditions lead to the accumulation of fermentation products made during the degradation of cellulose
        3. Other anaerobic microorganisms use the fermentation products to carry out anaerobic respiration using sulfate as the electron acceptor and producing sulfide
        4. Sulfide diffuses upwards creating an anaerobic, sulfide-rich zone, where anoxygenic photosynthetic bacteria reside
        5. Further up in the column, chemolithotrophic and mixotrophic organisms may use hydrogen sulfide as an energy source and oxygen as the electron acceptor
        6. At the top are oxygenic photosynthetic organism such as diatoms and cyanobacteria
    3. Nutrient cycles in aquatic environments
      1. Major source of organic matter in illuminated water is phytoplankton, which acquire needed nitrogen and phosphorous from surrounding water
      2. Redfield ratio-ratio of carbon-nitrogen-phosphorus (C:N:P) in phytoplankton; is important for following nutrient dynamics and for studying factors that limit microbial growth
      3. Microbial loop recycles much of the organic matter produced by phytoplankton; the chemoheterotrophic bacteria that function in the microbial loop are consumed by a series of larger predators (protozoa and metazoan zooplankters); microbial loop decreases the amount of organic matter available to higher consumers (e.g., fish); the decrease is thought to be more pronounced in oligotrophic environments
        1. The microbial loop operates best in aerobic environments where both photosynthetic microorganisms are active and the top consumers are able to function; if too much organic matter is added to a water, an anaerobic water is created that will not support top consumers
        2. Confined-animal agriculture can result in massive inputs of organic matter to waters; this can impact oxygen levels and the functioning of the microbial loop
  2. The Microbial Community
    1. A wide variety of microorganisms are found in waters (Table 29.2); most have been discussed in previous chapters; this section focuses on specific adaptations of microorganisms to particular aquatic environments
    2. Ultramicrobacteria or nanobacteria-very small bacteria (volume < 0.08 mm3); dominant bacteria in marine environments; small size protects them from being eaten by nanoflagellates
    3. Thiomargarita namibiensis-very large bacterium (100 to 300 mm in diameter); contains a huge vacuole that is used to store nitrate; also stores sulfur granules; this ability allows it to survive during times when nitrate and sulfur are not readily available
    4. Thioplaca spp.-individual cells, which can be many centimeters long, live in filamentous sheathed structures containing numerous cells; individual cells move up and down within the sheath, moving from oxygen-poor, nitrate-rich waters into sulfide-rich sediments; by doing so it fulfills its nutrient needs
    5. Microorganisms associated with surfaces include prosthecate bacteria and gliding bacteria; they use organic matter on surfaces
    6. Zoosporic fungi, including oomycetes and chytrids, have motile reproductive spores; chytrids are important decomposers, prey on algae, and live in cells of amphibians
    7. Filamentous fungi can sporulate under water; play an important role in processing organic matter
    8. Archaea are important members of oceanic picoplankton (cells < 2 mm); can also be found in freshwater and deep in the ocean
    9. Viruses-present in 10-fold higher concentration than bacteria; the virioplankton may influence microbial loop, may be involved in horizontal gene transfer, and may control microbial community diversity
    10. Microorganisms are constantly mixing and being added to water
      1. Aquatic microorganisms are released into atmosphere then moved to other aquatic locations
      2. Movement of water (e.g., river flow into oceans) moves microorganisms to other locations
      3. Deposition of detritus and animal carcasses bring new microorganisms into aquatic environments
      4. Dust and sediment from terrestrial environment falls into water
  3. Marine Environments
    1. Represents major portion of biosphere; contains 97% of the Earth’s water
      1. The ocean has been called a “high pressure refrigerator” with most of its volume below 100 meters at temperatures near 3°C
      2. Pressure in marine environments increases 1atm/10 meters and can reach 1,000 atm at its greatest depths
        1. Barotolerant-grow at 0 to 400 atm; best growth is at atmospheric pressures
        2. Moderate barophiles-grow best at 400 atm, but will grow at 1 atm
        3. Extreme barophiles-grow only at higher pressures
    2. Most of the nutrient cycling occurs in the upper 300 meters, which is where light penetrates
      1. Phytoplankton grows and then falls
      2. Only 1% of the photosynthetically derived materials from the phytoplankton reach the deep-sea floor (the rest is decomposed); conditions there are oligotrophic (low nutrient concentration)
      3. Carbon cycle in marine environments is poorly understood, but microorganisms are known to play an important role
        1. There is a large amount of dissolved organic material (DOC) and it has a long residence time
        2. Massive deposits of methane hydrate are found at the ocean floor below 500 meters; some marine bacteria consume methane hydrates and serve as food for ice worms; some archaea metabolize methane in conjunction with sulfate, in a process called reverse methanogenesis
      4. Nitrogen and sulfur cycles function at an “ocean scale” and impact global-level processes
        1. Low oxygen levels promote denitrification, which in turn favors nitrogen fixation
        2. Dimethyl sulfoxide (DMS) released from algae can influence atmospheric acidity, Earth’s temperature, and cloud formulation
    3. Much of the marine environment is covered by sea ice; microorganisms grow and reproduce at interface between ice and seawater and in the ice near this interface
    4. Because of increasing human population and urban development in coastal areas, nutrient enrichment and microbial pollution are increasing and taxing the ocean’s seemingly inexhaustible ability to absorb and process pollutants; this is causing detrimental changes in numerous marine environments; some examples are given below
      1. Contamination of shellfish beds resulting in delays in harvesting and causing economic impact
      2. Dead zones (hypoxic and anoxic regions) in the Gulf of Mexico
      3. Algal blooms and red tides
      4. Outbreaks of fish disease caused by the protozoan parasite Pfeisteria piscicida
      5. Global movement of air that has been altered by human activity also impacts marine environments
  4. Freshwater Environments
    1. Lakes
      1. Lakes vary in nutrient status
        1. Oligotrophic lakes are nutrient-poor
        2. Eutrophic lakes are nutrient-rich
      2. Lakes can be thermally stratified; stratified waters undergo seasonal turnovers because of temperature and specific gravity changes
        1. Epilimnion-warm, aerobic, upper layer
        2. Thermocline-region of rapid temperature decrease
        3. Hypolimnion-cold, often anaerobic (particularly in nutrient rich lakes) lower layer
      3. Eutrophication-stimulation of growth of plants, algae, and bacteria by addition of nutrients (enrichment) to a body of water; cyanobacteria and algae contribute to massive algal blooms in strongly eutrophied lakes
    2. Streams and rivers
      1. Horizontal movement minimizes vertical stratification; most of the functional biomass is attached to surfaces
      2. Nutrients available in streams and rivers can be from in-stream production or from out-stream sources (leaves, and run-off from riparian areas); under most conditions, such added organic material does not exceed the oxidative capacity of the stream and it remains productive and aesthetically pleasing
      3. Ability to process organic matter is limited
        1. If the amount of organic material is excessive, oxygen is used faster than it can be replenished, which causes the water to become anaerobic
          1. Point sources of pollution include inadequately treated municipal wastes and other materials from specific locations
          2. Nonpoint sources of pollution include field and feedlot run-offs
        2. If the amount of organic material is not excessive, algae will grow, which leads to oxygen production in the daytime and respiration at night (diurnal oxygen shifts)
      4. Dams, which cause the loss of silicon, also impact streams and rivers; this loss reduces the diatom population and increases in the activity of toxic nitrate-utilizing algae
    3. Microorganisms in freshwater ice-(e.g., glaciers and ice sheets) microorganisms in these environments are of interest because they may provide information about when microorganisms were deposited in these environments and about the biogeographic distribution of microorganisms
  5. Water and Disease Transmission
    1. Waterborne pathogens and water purification
      1. Many human pathogens are transmitted by water (e.g., Vibrio spp., Giardia, Cryptosporidium, and Naegleria
      2. Water purification is critical for public health and safety; common steps in water purification are described below
        1. Aeration precipitates iron and manganese, which must then be removed
        2. Sedimentation in a sedimentation basin removes sand and large particles
        3. Coagulation with alum, lime, and/or organic polymers is followed by clarification in a settling basin; removes many of the microorganisms (including many of the viruses), organic matter, toxic contaminants, and suspended particles
        4. Filtration
          1. Rapid sand filtration-physically traps particles (not efficient for removal of Giardia cysts, Cryptosporidium oocysts, Cyclospora and viruses)
          2. Slow sand filtration-biologically removes Giardia, which adheres to microbial layer on the sand particles; recently Cryptosporidium has become of even greater concern than Giardia, because it can be serious, even fatal, in immunocompromised individuals; its small size prevents it from being readily removed by sand filters
        5. Disinfection with chlorine or ozone; can lead to formation of disinfection by-products (DBPs) that may be carcinogens
      3. Because of increasing concern about water safety due to the transmission of Cryptosporidium, viruses, and other waterborne pathogens, the Information Collection Rule (ICR) has been initiated to assess the threat of waterborne pathogens to the waters of cities with populations over 100,000
    2. Sanitary analysis of water
      1. Presence and amount of indicator organisms are monitored; ideal indicator organisms have the following characteristics:
        1. Should be suitable for the analysis of all types of water
        2. Should be present whenever enteric pathogens are present
        3. Should survive longer than the hardiest enteric pathogen
        4. Should not reproduce in the contaminated water
        5. Should be detected by a highly specific assay
        6. Should be detected by a test that is easy to perform and sensitive
        7. Should be harmless to humans (ensuring safety for laboratory personnel)
        8. Concentration of indicator should directly reflect the degree of fecal pollution
      2. Coliforms-the most commonly used indicator organisms
        1. All are facultative anaerobic, gram-negative, nonsporing, rod-shaped bacteria that ferment lactose with gas formation within 48 hours at 35°C (e.g., Escherichia coli, Enterobacter aerogenes, and Klebsiella pneumoniae)
        2. Detected by the following tests
          1. Most probable number (MPN)-statistical estimation; does not distinguish coliforms from fecal coliforms (those derived from intestines of homeothermic animals; can grow at 4
          2. 5°C)
          3. Membrane filtration technique-water is filtered, filter is placed on an absorptive pad containing liquid medium; this is incubated; and colonies are counted; detects total coliforms, fecal coliforms, and fecal streptococci
          4. Presence-absence (P-A) test-detects both coliforms and fecal coliforms
          5. Defined substrate tests (e.g., Colilert) involve the production of a colored product (for total coliforms) or a fluorescent product (for E. coli) from a specific growth substrate
          6. Molecular techniques are now being routinely used to detect E. coli
      3. In United States, general guidelines for microbiological quality of drinking water have been set, including standards for coliforms, viruses, and Giardia
      4. Other indicator microorganisms used to test water safety include fecal enterococci; they are being used as indicators for brackish and marine waters because they survive longer than coliforms under these conditions
  6. Wastewater Treatment
    1. Wastewater can contain high levels of organic matter and human pathogens; these can be removed (or their amount decreased) by wastewater treatment; such treatment is one of the most important factors in maintaining public health
    2. Measuring water quality
      1. Total organic carbon (TOC)-quantifies carbon concentration by oxidizing organic matter at high temperatures and measuring the amount of carbon dioxide produced
      2. Chemical oxygen demand (COD)-quantifies the amount of organic matter present (except lignin) by reacting organic material with a strong acid
      3. Biochemical oxygen demand (BOD)-amount of oxygen needed to utilize organic material as growth substrates; indirectly measures the amount of organic material in a sample; can be affected by presence of ammonia, so nitrification (nitrogen oxygen demand-NOD) is inhibited by addition of nitrapyrin to the sample
    3. Water treatment processes
      1. A controlled self-purification; can involve the use of large basins (conventional sewage treatment) where mixing and gas exchange are carefully controlled; can also involve constructed wetlands where reed and aquatic plant communities and their associated microbes facilitate the processing of dissolved nutrients
      2. Primary (physical) treatment-removal of particulates (20 to 30% of the BOD); resulting solid material is called sludge
      3. Secondary (biological) treatment-removal of dissolved carbonaceous materials (90 to 95% of the BOD) and many bacterial pathogens; produces a sludge, which must be further processed or disposed of
        1. Aerated activated sludge systems-involves horizontal flow of materials and the addition of sludge, (which acts as a source of microorganisms the sludge microorganisms oxidize the organic matter; the resulting biomass is later removed)
        2. Trickling filters-vertical flow over gravel on which microorganisms have developed in surface films; the microorganisms degrade the organic matter
        3. Extended aeration systems-reduce the amount of sludge produced by the process of biological self-consumption (endogenous respiration)
        4. All of the above secondary treatment processes as well as the primary treatment produce sludge; anaerobic sludge digestion reduces the amount of sludge that must be disposed of in landfills or by other means; also produces methane, which can be used as a fuel for generation of electrical power; involves three steps
          1. Fermentation of sludge components to form organic acids
          2. Production of methanogenic substrates (acetate, carbon dioxide, and hydrogen)
          3. Methanogenesis
      4. Tertiary treatment (physical/chemical and/or biological)-removes inorganic nitrogen, phosphorus, recalcitrant organics, viruses, etc.
      5. Constructed wetlands use floating emergent and/or submerged plants to provide nutrients for microbial growth in their root zone; they help remove organic matter, inorganic matter and metals from waters
      6. Surface flow soil treatment is also being used to allow aerobic microbial processing of waste
  7. Groundwater Quality and Home Treatment Systems
    1. Groundwater-water in gravel beds and fractured rocks below the surface soil
    2. Microbiology and microbiological processes in groundwater are not well understood; disease-causing organisms and organic matter are removed by adsorption and trapping as they move through the subsurface; microbial predators use trapped pathogens as food
    3. Home treatment mimics the natural adsorption-biological predation process
      1. Anaerobic liquefaction and digestion in a septic tank
      2. Aerobic digestion, adsorption, and filtration of organic material are accomplished by drainage through suitable soil in a leach (drain) field
      3. If drainage is too rapid, there is little adsorption and filtration, with subsequent contamination of well waters and groundwaters, which can lead to nutrient enrichment of ponds, lakes, and rivers
    4. Groundwater can also be contaminated by land disposal of sewage sludges, illegal dumping of septic tank pumpage, improper toxic waste disposal, agricultural runoff, and deep-well injection of industrial wastes
    5. In situ treatment procedures for groundwater are under investigation; microorganisms are critical in many of these remediation efforts

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