Chapter 18 Ecology

Chapter 18: Ecology Overview 1. Ecology is the study of interaction between organism and their environment—how the chemical, physical, and biological environments affect particular kinds of organisms and how the organisms affect their environments. 2. Microbial ecology rest on three characteristics of microbes, 1. Their ubiquity, present about everywhere that liquid water exists including extreme conditions; 2. Their abundance, occur in large numbers, about 10^30 prokaryotes on earth and 3. Their metabolic power—they are extremely active in diverse ways. 3. If the components of a thermodynamically feasible reaction are present in a particular environment, a microbe will be there to exploit it in order to grow and reproduce. 4. Prokaryotes are proficient at growing at the expense of low energy yield reaction in two ways, 1. by elicit the help of neighboring microbes by exploiting their ability to scavenge products rendering the reaction equilibrium to support growth and 2. Collection of small bits of energy of each reaction and save until enough to make ATP. (H+ gradient) 5. Microbes have role in setting the concentration of major gases in the atmosphere (CO2, N2, O2), role in degrading plants and animals, secret metabolic end products and chelating agents, modify the mineral composition of rivers, lakes, and oceans, catalyze redox reaction of variety of metal slats contribute to Earth ore deposit, cause rocks to weather, and alter the weather. 6. Well-aerated layer encounter chemoheterotrophs that utilize organic compounds by aerobic respiration, anaerobic pockets have heterotrophs that ferment carbohydrates, deeper will find anaerobic respiration that use a variety of terminal acceptors (nitrate, ferric, sulfate), oxide products of fermentation or pollutants and autrotrophs that derive energy from H2S. 7. Deepest regions are where the hyperthermophiles are, which live at the epense of hydrogen-dependent metabolism (H gas come from earth magma for by geochemical reduction of water in high temperature and pressure), coupling its oxidation to the reduction of metal ion or CO2. 8. Reduction of CO2 produces methane, where it is oxidized by methan-metabolizing microbial specialists called methylotrophs. Methods of Microbial Ecology 1. Aim of all ecology is to determine which organisms are present in a particular environment and what they are doing there, easier for organism that can be seen, not microbes because their activities are largely chemical and cannot be seen. I. Enrichment Culture 1. Enrichment culture means selectively favoring the growth of the desired microbes by adjusting the conditions of the culture. (nitrogen-fixing bacteria are those that fixed nitrogen from atmosphere, so these can grow in a culture where the medium lack nitrogen because they use nitrogen from the air) 2. Power tool for studying microbial ecology, if suspects a microbe is carrying out a particular transformation in a particular environment, then that microbe is inoculate with appropriate medium with that material from the environment. 3. Relying in method is risky because it rest on many unprovable, incorrect assumption, which is it is always possible to culture the microbes that exert a particular ecological impact and that microbes act in nature the same way in culture. II. Studying Microbes in the Laboratory and in Their Natural Environment 1. Most prokaryotes in nature cannot be cultivated, where the number of live microbial cells in environment determines by counting under a microscope exceeds by several orders of magnitude the number that can be cultivated, but ingenious method decrease the gap by mimicking natural environment. 2. Important to obtain pure culture of microbes for determining genome sequence, physiological, or genetic experiments, but drawback is bacteria do not act in pure cultures as they do in nature, where some lose their virulence, replace antigens, alter metabolic activities and in nature microbes function as communities.

3. To study microbes in natural environment use of recombinant DNA technology, genomics, modern immunological methods, and radiochemical techniques, are methods that do not depend on culture. 4. Fluorescence in situ hybridization (FISH) uses synthetic fluorescently labeled DNA probes that hybridize to complementary sequences on the genomes of organisms in a sample, which reveals microbes that are present in a particular environment or used to diagnosed larger group of organism. [Might see dependant-organisms] 5. Florescent antibody probes method is high specific and is used to identify particular species or strains but not classes like FISH can. 6. Another useful approach is to sequence certain stretches of DNA from a mixture of organisms in a particular environment, which can answer a broad range of question of the highly specific to the completely general, and the technique has been expanded to the complete complement of microbial DNA. 7. Phylotypes are species identified solely by sequence similarity. 8. Data from DNA extraction only offer marginal information about what various microbes are doing in the environment, but guesses can be made of newly discovered microbe by determined it kinship to known, wellstudied microbes and assume it is similar. 8. Microscope evaluation of practicability uses dyes, adding radioactive compounds (tritium-labeled thymidine) then covering the cell with photographic emultion, technique called microradioautography, which can determine whether a particular microbial cell in a sample can utilize those radioactive substrate. Biogeochemical Cycles 1. Through microbial ecology we have learned that microbes exist in all parts of the biosphere, are sole inhabitants of some ecosystems, interconvert matter, where these interconversion are in approximate balance where these matter are continually being used and from or in a biogeochemical cycle. 2. Generalization of all cycles is their component step are oxidation or reduction reactions, where in most cases the oxidation state of the bioelement changes throughout the cycle. (ie organic matter is oxidized to CO2 and then reduced to organic matter). I. Carbon and Oxygen Cycles 1. Essence of the carbon cycle is a cycling between atmospheric CO2 and fixed carbon, in either organic or inorganic form. 2. Other than pollution, human have added another complexity, where we have created compounds that are resistance to microbial attack, which is a dead-end sum in the carbon cycle, whereas most naturally occurring organic molecules are attack by microbes either slowly in humus. (microbial infallibility) 3. Route by which degradable organic compounds trapped in anaerobic environments are returned to aerobic environment through the action of methanogenic Archaea, which produce abnormal quantities of methane, which is gaseous and soluble in water so it can escape the anaerobic environment. (CH4 also buried in ocean). 4. Methane, other than being burned by human, is oxidize by aerobic bacteria called methylotrophs or escape into the atmosphere where it acts as powerful greenhouse gas. 5. Route of anaerobic methane utilization proved to be biological, mediated by a two-member microbial grouping consisting of an archaeon and a bacterium that together anoxially oxidize methane to carbon dioxide while reducing sulfate to hydrogen sulfide. 6. Sequence of 16S rRNA of archaeal cells showed that they constitute a clade, related branches, of the methanogenic group of the Archaea, which mediate a metabolism similar to methanogenesis but in reverse where methane and water is converted to carbon dioxide and hydrogen. 7. To pull the above reaction the right hydrogen removal is accomplished by surrounding layer consisting of Desulfosarcine, which catalyzes oxidation of hydrogen at the expense of reducting sulfur. 8. Secondary ion mass spectrometry with FISH showed organism grown in the expense methan had a lower concentration of C13 in their grouping and other Archaea have been found with sulfate reducing bacteria mats located over methane vents, stabilized by calcium carbonate form CO2 is release and reacts with seawater. II. The Nitrogen Cycle 1. Insufficient nitrogen limits plant growth, where “Green Revolution” improved agriculture by providing more nitrogen to crops, principally in the form of ammonia or nitrate.

2. All the nitrogen comes from the atmosphere, where it is returned. 3. Dinitrogen is a stable compound due to the high activation energy required to break its nitrogen-nitrogen triple bond and prokaryotes (lighting and volcanic activity) are the only organism that break this bond there by fixing nitrogen, but recently human convert nitrogen to ammonia in chemical method called Haber process. 4. Other step of nitrogen cycle are also exclusive for prokaryotes like the two steps of nitrification by which ammonia is successively converted via nitrate to nitrate ion and the routes—called denitrification and anammox —which fixed nitrogen is returned to gaseous form. [Obligate anaerobes] 5. Nitrification is mediated by autotrophs, in first step by Nitrosomonas, which oxidize ammonia to nitrite while reducing O2 and in second step by Nitrobacter, which oxidizes nitrite to nitrate, also reducing O2 in the process. [No bacteria oxidize ammonia all the way to nitrate and no NH4 and nitrite in top layer soil]. 6. All organism uses nitrogen as a nutrient that they incorporate into cellular constituents and some prokaryotes use it as a substrate for two types of ATP-generating process. 7. The process of reducing nitrate to ammonia to serve as a nutrient is called assimilatory nitrate reduction and reduction and reduction of nitrate as a consequence of serving as a terminal electron acceptor in an anaerobic respiration is called dissimilatory nitrate reduction. 8. Some autotrophic bacteria derived energy by oxidizing ammonia or nitrate and other heterotroph derived energy by anaerobic respiration, with nitrate, nitrite, NO, or N2O serving as terminal electron acceptor. 9. Denitrification is the cascade of anaerobic respiration through which nitrate is successively reduced to N2, where a wide variety of prokaryotes using a broad spectrum of carbon sources can mediate this process. 10. Anammox [Planctomycetes] mediate anaerobic ammonia oxidation, in which fixed nitrogen is recycle by to N2 gas, in which ammonia was oxidized by nitrite yield N2. [proven by use of isotopes in which N2 were from different compounds and biological cause it was stopped by heat, radiation, decouplers] III. The Sulfur Cycle 1. For all organisms, sulfur is an essential nutrient and for some it enters into both oxidative and reductive pathways that generate ATP that process high amounts of sulfur. 2. Massive deposit of elemental sulfur in form of gypsum, from bottom of lakes, were formed by the combination of two steps of the sulfur cycle, both anaerobic: sulfate-reducing bacteria converted sulfate to hydrogen sulfide, and phototrophic bacteria oxidized it to elemental sulfur. 3. Hydrogen sulfide is also oxidized by a variety of autotrophic bacteria mostly through aerobic respiration but in a few cases anaerobic and occurs in any place hydrogen sulfide is produced by sulfate-reducing bacteria in an underlying anaerobic region, but chemoautotrophic sulfur oxidizer locate where rise H2S is with O2. 4. Hydrogen sulfide is spewed out of hydrothermal vents, a complex community of eukaryotes and prokaryotes thrives there due to the fact chemoautotrophic bacteria oxidizing hydrogen sulfide at the expense of oxygen. [no sunlight and affect othe3r organism where tube worms trophosome with these bacteria to give it nutrients]. IV. The Phosphorus Cycle 1. Simplest of the geochemical conversions because the phosphorous stays in the same oxidation state (+5) as phosphate, and in cycling is extremely slow because the cycle had no gasous intermediates. 2. Phosphate being soluble is leached from soil into the ocean, return to land by bird eating sea food and dropping feces on land, or by geological uplift of the ocean floors, where products are phosphate rocks which are mine for use in fertilizers. 3. Phosphine [H3P], gaseous form of phosphate spontaneously ignite in air, but not clear of biological origin, whereas phosphites [PO3-3] and hypophosphites [PO2-3] are oxidize by bacteria for use as a source of phosphate. 4. Phosphonates are made by prokaryotes and eukaryotes, where certain bacteria can break the C-P bond to be use as a source of phosphate. Solid Substrates 1. Only dissolved nutrients can enter the cells of prokaryotes [eukaryotes ingest by phagocytosis], but they can utilize a variety of insoluble nutrients including starch, cellulose, and even agar, by secreting enzymes that break doen these insoluble polymers into soluble units, which enter cell. [digestion occur in ex. environment]

2. Insoluble material such as iron, magnesium, and uranium oxide that cannot broken down into soluble subunits can be metabolized by certain bacteria, where Geobacter anaerobically use one of these solid oxide as terminal electron acceptor without taking it into the cell. 3. Geobacters have unusual morphology, where they are common shaped and bear flagella largely on one side in the presence of ferrous ion to let the cell know that ferric oxide is nearly depleted and prominent short pili on the other, which attaches cell firmly and is a conductor of electrons, where they bear cytochromes. [ETC in pili] 4. Geobacter’s nonspecific ability to donate electrons to a solid surface is it capacity to generate a usable electric current because it can donate electron to a piece of metal. [Shewanella has the same abitlty] Microbial Ecosystem 1. Microbes-mediated transformation occur about every where, but the are place on the planet too hot, too cold, too acid, too alkaline, too salty, or too high a hydrostatic pressure for microbes to thrive. I. Soil 1. Upper layers are an active microbial ecosystem in which mant steps of the biogeochemical cycles occur and the number of microbes decreases in lower layers, down to 5 to 6 km below the surface of the earth. II. Oceans 1. Upper regions of ocean is another globally important microbial ecosystem, where half of the photosynthesis (CO2 fixing and oxygen producing of the carbon cycle) occurs on planet is carried out by phytoplankton, which is also the beginning of the food chain for sea life. 2. Eukaryotic phytoplankton are larger, but cyanobacterial phytoplankton [Synechococcus and Prochlorococcus] are more abundant and metabolically active that exert a greater ecological impact. 3. Microbes have proliferated all the way down to the regions of darkness, cold, and crushing hydrostatic pressure that exist at the bottom of the sea, like sulfure-oxidizing bacteria near thermal vent. [water column are mixed so different environment at different depth are not necessarily so] 4. In open seas the concentration of available organic material low but measurable and there is enough organic material to sustain a considerable population of heterotrophic microbes, where the organic material is known as marine snow in which living it dead it dying animal are embedded. [pelagic microbes] 5. Zone where phytoplankton flourish is narrow due to light being able to penetrate 100 m into the ocean, oxygen on the other hand extend all the way to bottom of ocean floor, and phosphorus is scarce at surface but more abundant at 1km, 6. Sea floor is steadily being deposited by organic nutrients, where benthic microbe uses in which oxygen is quickly being depleted, where beneath the sea floor are those that use nitrate[use in oxidation of sulfide to sulfur], sulfate, ot ferric ion as terminal electron acceptor. 7. Thioploca is encases in a long mucous sheath, which serves as a transport route between underlying sediment to get sulfides and overlying water to get the nitrate. 8. Thiomargarita cells remain stationary in strands of cells that is separated by a mucous sheath that sit and wait for H2S to pass by while accumulating nitrate in large vacuoles, and also store elemental sulfur. III. Microbes, Climate, and Weather 1. Microbes play role in the turnover of major gases in the atmosphere, so it affects local weather by causing atmospheric changes that take place over a period of days. 2. Clouds form when certain compounds in the air act as nuclei for water vapor to condense on forming fine droplets, where some of these compounds are sulfur from volcanic emission, burning fuel, high sulfur petroleum, which produces SO2 that is oxidize in air SO3 when hydrated in clouds it is sulfuric acid. 3. Cloudless day sun intense UV radiation beam down on phytoplankton and other causing them to make a protective compound called dimethylsulfoniopropionate (DMSP), which is broken down to dimethylsulfide [DMS] by variety of bacteria that evaporates in air reacting with oxygen to act as nuclei if H2O droplet. (cloud).

Notes take from Schaechter, M., Ingtaham, J., & Neidhardt, F. C. (2006). Microbe. Washington, D.C.: ASM Press.