MarBiolBacteria, Protozoa & Viruses

MarBiolBacteria, Protozoa & Viruses - Bacteria,...

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Unformatted text preview: Bacteria, Protozoa & Bacteria, Protozoa & Viruses Small World How many bacteria in the ocean? How many bacteria in the ocean? ► About 1029! ► How many stars in the sky? Only about 10 21! ► How about the mass of bacteria in the ocean? ► The entire microbial food web (bacteria & protozoa) have a biomass typically 5­10X the mass of all the multicellular organisms in the sea. ► Since their metabolic rates are faster than the multicellular, they dominate metabolically. Bacteria swim in water on a scale (low Reynolds Bacteria swim in water on a scale (low Reynolds number) where physics is different that the physics experienced by a larger organism ► For the microbes it is like swimming in a thick liquid like honey ► If a bacterium stops swimming, it will coast for the distance of a hydrogen bond and stop. ► Like driving a Formula I Grand Prix car into a wall of granite Marine Bacteria Marine Bacteria ► ► ► Once thought (up to 1970s) by marine scientists that bacteria were not abundant in the ocean and only important as decomposers. Today it is recognized that bacteria are very abundant and play active roles in cycling of nutrients and energy in the ocean. It was also once thought that all life on earth could be divided into two basic groups (prokaryotes & eukaryotes) on the basis of cell structure. Some Abbreviations Some Abbreviations ► Particulate Organic Matter = POM ► Dissolved Organic Matter = DOM ► Particulate Organic Carbon = POC ► Dissolved Organic Carbon = DOC Marine bacteria important in many Marine bacteria important in many ways ► Degradation of particulate POM to DOM ► Nutrient transformations i.e. nitrification (i.e. NH3 to NO2 to NO3) ► Some photosynthesis (photosynthetic bacteria) ► Toxins ► Microbial loop (DOM to POM) ► Pathogens ► Symbionts (in hydrothermal vent organisms, bioluminescent fish etc) All life on earth can be divided into three major groups on All life the basis of sequences of genetic information in ribosomes (make proteins in cells). These are the eubacteria, archaea & eukaryotes. Review: We can also divide all life Review: We can also divide all life into two groups based on cell structure: Prokaryotes & Eukaryotes Prokaryotes have no ► ► ► ► membrane bound organelles such as a nucleus or a chloroplast. They are morphologically simple, about 1­ 2 µm in diameter. The eubacteria and archaea are prokaryotes, and there is tremendous diversity in their taxonomy and metabolism. Archaea tend to occupy extreme environments such as those which are either very hot or cold or salty etc. Higher organisms are eukaryotes and have membrane bound organelles. Archaea Archaea ► ► Archaea are very abundant in cold polar seas, thermal pools, in areas of high salinity (such as the salt evaporation ponds in South San Francisco Bay) , and in cold deep waters in all the world’s oceans. Archaea are also important in anaerobic (no oxygen) areas. Archaea are found in extreme Archaea are found in extreme environments The salt evaporation ponds in South SF Bay The salt evaporation ponds in South SF Bay are colored because of high Archaea concentrations Bacterial Rhodopsin Bacterial Rhodopsin ► This is a purple colored pigment which is used by many bacteria to generate energy. ► This pigment colors the South Bay salt evaporation ponds. ► It is a totally different system than photosynthesis (using chlorophyll) Rhodopsin Rhodopsin ► An important ingredient in the eyes of mammals, rhodopsin is present in the rods of our eyes. When light shines on mammalian rhodopsin, it binds to a molecule called retinal to induce the vision process. Archaea also have a rhodopsin molecule, but with an added twist. Its protein both binds retinal and works to pump protons (the positively charged components of an atom’s nucleus) out of the cell to generate energy. Review: Modes of nutrition Review: Modes of nutrition ► All organisms require a source of energy. ► Can divide all organisms into Autotrophs (those that either get energy from reduced inorganic compounds or sunlight and make their own organic compounds) and Heterotrophs (like us) who obtain their energy only from preformed organic compounds. ► Chemoautotrophs obtain their energy from reduced inorganic compounds (such as H2S), and Photoautotrophs (such as photosynthetic organisms) obtain their energy from sunlight. ► Know these terms and what they mean Bacterial Types of nutrition Bacterial Types of nutrition ► There are heterotrophic bacteria that get their energy from DOC (sugars, etc.) Other heterotrophic bacteria can break down POC ► Chemoautotrophic bacteria get their energy from chemically reduced inorganic compounds. For example, in converting H2S to SO2, energy is given off for the bacterium to use for growth. ► Some bacteria are aerobes and live in environments with O2, and others are anaerobes in live in sediments and waters where no O2 is present. How fast can heterotrophic bacteria How fast can heterotrophic bacteria divide? ► Marine bacterium Beneckea (Pseudomonas) can under optimal conditions divide every 10 min. ► Because it has a high surface to volume ratio, it can take up energy and nutrients fast. ► Usually environmental conditions are sub optimal and growth is slower Methanogens Methanogens ► Bacteria that produce methane (a greenhouse gas, CH4) are members of the archaea group. ► In landfills and in marine sediments where there is no oxygen, and there is an abundant supply of organic matter, these bacteria produce methane through the breakdown of organic matter. ► The methane from landfills and sewage treatment plants should not be released to the atmosphere because it increases global warming. It can be captured and used to heat homes or buildings. Methane producing archaea live in the stomach of cows (and many other Methane producing archaea live in the stomach of cows (and many other organisms….humans too). These are anaerobes and live where there is no O2. They also live in the sediments of the ocean and produce methane. If you are a meat eater, you are If you are a meat eater, you are contributing to global warming ► Cows produce methane ► To be fair, rice paddies do also. Her T shirt says “one Less meat eater” These are the sources of methane to These are the sources of methane to our atmosphere ► Rice fields do contribute a lot, so we can’t just blame the cows. ► Maybe we should eat potatoes ► ► ► Methane produced by bacteria in landfills can be used as an energy source It should not be allowed to escape to the atmosphere because it is a gas that increases global warming One molecule of methane us equal to over 20 CO2 molecules as a global warming gas What you should know What you should know ► Bacteria break down particles of organic matter into dissolved chemicals (DOM) such as ammonium (NH4) ► These chemicals can then be used as nutrients for growth of bacteria (and other microbes). ► Know that there are three main domains of life on earth and what they are. ► Do know what a chemoautotroph, photoautotroph, and heterotroph is. ► The following are examples of what the bacteria do in regard to nutrient cycling in the ocean. The genetic diversity of bacteria in The genetic diversity of bacteria in the ocean is extremely high ► Craig Venter (mapped human genome) has sailed ► ► Sorcerer around the world and looks at the genetic diversity of bacteria every 200 miles At each sample place gene sequences are 90% different Why? "It takes all the running you can do, "It takes all the running you can do, to keep in the same place." ► Red Queen & Alice Bacteria (and other microbes) have to evolve to stay Bacteria (and other microbes) have to evolve to stay ahead of viruses which attack them ► Thus genetic diversity changes daily as the bacteria evolve different cell walls, etc. The viruses evolve along with them and try to have better attack devices ► for an evolutionary system, continuing development is needed just in order to maintain its fitness relative to the systems it is co­evolving with ► So the “Red Queen Hypothesis” is that bacteria have evolve as fast as they can just to stay in one place. Bacteria are strongly involved in the global nitrogen (N) cycle Bacteria are strongly involved in the global nitrogen (N) cycle in terms of decomposing N in organic matter and converting N compounds from one state (such as N2 to NH3 ) to another. The marine N cycle. Bacteria very important in N The marine N cycle. Bacteria very important in N transformations such as mineralization (decomposition), and the transformation of nitrogen from one compound to another Marine N cycle Marine N cycle Chemoautotrophs: examples are those that Chemoautotrophs: examples are those that get energy from certain reduced compounds like H2S, NH3, or H+ ► ► ► ► ► These are reduced compounds and are a potential source of energy. (reduced compounds release energy when they are oxidized). Methanogens are anaerobes and convert the reduced chemicals H+ & H2 to methane (natural gas) Nitrifyers are aerobes, and in deep waters of the ocean convert NH3 to NO3 (this is why there is so much NO3 in the ocean) Sulfur oxidizing bacteria (anaerobes) convert H2S (rotten egg smell in marshes), to SO4 All of these processes release energy to the organisms as they do these conversions Bacteria are also involved in the Bacteria are also involved in the global cycling of sulfur You should know the following You should know the following ► Many bacteria form symbioses with higher organisms and provide energy for them ► Bacteria and cyanobacteria can convert gaseous N2 to ammonia and then into proteins which can then be used by other higher organisms. This is N2 fixation. ► Bacteria are the basis for energy transformations in hydrothermal vent communities Hydrothermal vents Hydrothermal vents At seafloor spreading zones (i.e. mid Atlantic Ridge) or where tectonic plates collide, seawater passes through cracks in the oceans basalt. It is heated by hot magma, and reduced sulfur compounds form (such as H2S..rotten egg smell). Bacteria then use these compounds as an energy source for growth. Many benthic organisms at these hydrothermal vent areas live symbiotically (the bacteria live in specialized organs within the host animal) with the bacteria and use them as a source of energy. Symbiotic bacteria and reduced Symbiotic bacteria and reduced sulfur compounds are the basis of life in hydrothermal vents Hydrothermal vents are located Hydrothermal vents are located along mid ocean ridges Vent organisms depend on bacteria Vent organisms depend on bacteria to convert reduced chemicals to organic matter We will talk more about the We will talk more about the organisms in the vent communities in the lecture on benthos Saga of Alvin’s Lunch Saga of Alvin’s Lunch ► In 1968 sub Alvin from WHOI sank to 1540 m depth and remained there 11 months ► When brought to surface, apples, bologna sandwich and soup still fresh. Holger Jannasch investigated why Holger Jannasch investigated why the lunch was preserved ► ► ► ► ► Water temp was 2­3oC. Jannasch did bacterial incubations at that temperature with and w/o pressure (150 atm). Decomposition was 10­100X slower under pressure Incubation of starch & gelatin at 1830 m for 12 months showed only 0.8­0.9% decomposition Apparently, high pressure & cold temperature retards bacterial decomposition Marine Snow Marine Snow ► Mary Silver (UCSB) pioneered in the study of marine snow ► The snow originates as larvacean houses, feeding nets from jellies etc. Bacteria Colonize Marine snow and Bacteria Colonize Marine snow and help to break it down to dissolved organic carbon (DOC) ► Shown are divers collecting marine snow Bacteria flagella operate like little motors. Bacteria flagella operate like little motors. They use the flagella to swim to marine snow and other particles Marine snow particle 4 mm in dia Marine snow particle 4 mm in dia ► Colonized by bacteria, phytoplankton & zooplankton. Like a little oasis of life. Bacteria “smell” the snow and swim to it. Sediment traps are moored in the ocean to Sediment traps are moored in the ocean to collect marine snow and other POM falling from surface waters ► The particles are an important source of food for the benthos, and particles sink several hundred meters/day How many bacteria in seawater? How many bacteria in seawater? ► Bacteria concentrations quite uniform in the world’s oceans….rarely less than 200,000 or more than 5 million cells per ml. ► Cells divide about every 4­5 days. ► If the population is so stable, and they are reproducing fairly rapidly, this implies that something must be consuming the bacteria. Partially this is done by protozoa in the “microbial loop” (will explain “microbial loop” shortly). ► Another big loss term is from viruses Viruses are VERY abundant in seawater and Viruses are VERY abundant in seawater and constantly attack bacteria Virus abundance and attack modes Virus abundance and attack modes ► ► ► ► In seawater, there are about 5 to 15 million viruses per ml Viruses tend to specialize on specific species of bacteria, cyanobacteria or phytoplankton. There are two main types of virus attack: lysogenic (virus genome becomes part of the hosts DNA and is passed on through many generations until a stress event causes the production of viruses and the rupture of the cell). Lytic infection in which the virus enters the cell, immediately makes the cell produce more viruses, then the cell bursts, thus spreading the viruses. Review: Heterotrophic bacteria are important in the “ microbial loop” Review: Heterotrophic bacteria are important in the “ Dissolved organic matter (DOM) is excreted by marine organisms and is taken up by bacteria (for useas an energy source). The bacteria are then grazed by protozoa which then release more DOM. Some of this bacterial primary productivity is eaten by larger organisms such as zooplankton About 30­50% of all the carbon About 30­50% of all the carbon cycled from DOM to POM is by bacteria in the “Microbial Loop” ► The remainder is by primary production by phytoplankton, macroalgae and seagrasses Like bacteria, populations of coccoid cyanobacteria such as Like bacteria, populations of coccoid cyanobacteria such as Synechococcus (Syn) rise and fall daily as they divide in daytime. Overall population doesn’t increase because of losses from viruses and grazing by protozoa. Cyanobacteria and bacteria are Cyanobacteria and bacteria are grazed (eaten) by protozoa ► Protozoa are unicellular eukaryotic organisms such as ciliates and non photosynthetic flagellates. ► These are the main grazers in the microbial loop. ► Protozoa are very diverse and consist of ciliates, colorless flagellates and amoeboid organisms. Foraminifera (Forams) are protozoan amoebas (eukaryotes) Foraminifera (Forams) are protozoan amoebas (eukaryotes) with a shell that they live inside of. Many have pseudopodia which radiate out and are used in feeding. Some forams are planktonic and some are benthic. The empty shells from forams pile up on the bottom The empty shells from forams pile up on the bottom of the ocean, and about one third of the world’s oceans are thick with these shells. These later become sedimentary rock. Ciliates are also important as Ciliates are also important as grazers on marine bacteria and other microbes. Remember Paramecium? Flagellates are also important Flagellates are also important grazers in the microbial loop In summary, bacteria are very abundant in the ocean. They grow rapidly, and they are In summary, actively eaten by protozoa and attacked by viruses. Thus they are involved in energy transformations. They are also important in cycling of elements such as N, P, S. Some act as essential symbionts in hydrothermal vent communities and as chemoautotrophs convert reduced chemicals from hydrothermal vent waters to organic matter which is then used by benthic animals. Study Guide Study Guide ► ► ► ► ► ► ► ► ► What is biomass of bacteria in ocean relative to that of all other organisms? What are the three major domains of life on earth? What are 7 ways that bacteria are important in the ocean (things that they do) What kind of environments do Archaea typically live in? What is bacterial Rhodopsin and how does that relate to the Human eye What is autotroph, heterotroph, chemoautotroph, photoautotroph? What are methanogens, why is methane important in regard to global warming. What are global sources of methane? Why is bacterial diversity so high and different from one place in the ocean to another? What is the “Red Queen Hypothesis” More Study Guide More Study Guide ► ► ► ► ► ► ► Where do chemoautrophs get their energy. What kinds of chemicals….give an example…reduced or oxidized? Why is there so much nitrate (NO3) in deep waters of the oceans? Where does it come from? What is “Nitrogen Fixation”? Why does POC break down so slowly in the deep sea (Alvin’s Lunch)? What is main source of “Marine Snow” Difference between Lytic and Lysogenic virus life cycles Be able to describe the “Microbial Loop” Why is it important in the ocean? ...
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