Lecture 6 Environmental microbiology and Aqueous Geochemistry of Natural Waters Please read these Manahan chapters: Ch 5 (aquatic microbial biochemistry) Ch 21 (environmental biochemistry) (Aquatic) Microbial Biochemistry Almost all geochemical processes that occur within the exogenic cycle are influenced by biological activity Some examples include: production/ consumption of organic matter oxidation-reduction dissolution/ precipitation of inorganic materials. Many polluted/contaminated environments are also rife with microbial life and associated chemical transformations. 1
All organisms can be classified as either producers - those that utilize light or other energy sources to create complex organic molecules (autotrophs) or reducers - those that re-extract energy by breaking down those organic molecules (heterotrophs) producers reducers Microorganisms can also be classified based on where they derive their energy and carbon: Respiration Energy sources Carbon sources Organic matter Inorganic carbon (CO 2, HCO 3- ) Chemical Chemoheterotrophs All fungi and protozoans, most bacteria. Chemoheterotrophs use organic sources for both energy and carbon. Chemoautotrophs Use CO 2, for biomass and oxidize substances such as H 2 (Pseudomonas), NH 4+, (Nitrosomonas), S (Thiobacillus) for energy Photochemical (light) Photoheterotrophs A few specialized bacteria that use photoenergy, but are dependent on organic matter for a carbon source Photoautotrophs Algae, cyanobacteria ("bluegreen algae"), photosynthetic bacteria that use light energy to convert CO 2 (HCO 3- ) to biomass by photosynthesis Figure 6.2. (Manahan) Classification of microorganisms among chemoheterotrophs, chemoautotrophs, photo- heterotrophs, and photoautotrophs. harvest solar energy, but can t synthesize organic matter from inorganic carbon - rare. Carbon fixation (synthesize organic matter from inorganic carbon) w/o energy from sun light: use chemical energy not solar energy. Photosynthesis 2
Photoautotrophs and Photosynthesis Algae are one important class of producer, Photoautotroph, aquatic microorganism that conduct photosynthesis. Photosynthesis can be crudely abbreviated as [A]. nco 2 + nh 2 O [CH 2 O] n + no 2 where [CH 2 O] n is generic carbohydrate. photosynthetic production of organic matter actually requires other nutrients, particularly N and P. Our text gives a somewhat more accurate equation for photosynthesis by aquatic organisms: the Fogg formula Wikimedia Commons [B]. 5.7CO 2 + 3.4H 2 O +NH 3 C 5.7 H 9.8 O 2.3 N + 6.25O 2 [C]. We use a still better depiction: the Redfield equation 106CO 2 +16NO 3- + HPO 4 2- + 122H 2 O +18H + C 106 H 263 O 110 N 16 P + 138O 2 or (CH 2 O) 106 (NH 3 ) 16 (H 3 PO 4 ) + 138O 2 Green algae The Redfield ratio C:O:N:P=106:110:16:1 is an important relationship to remember. The Redfield Ratio is a mean value for aquatic autotrophs that holds to within a percent for marine phytoplankton and maybe a few percent for most freshwater organisms. In all three versions of the photosynthesis reaction, Respiration is the reverse reaction. 3
notice important stoichiometric relationships N and P "move" in these ratios in much of the hydrosphere O 2 (+)/ CO 2 (-) = 138/106 = 1.3 N (+)/ P (+) = 16/1 = 16 CO 2 (+)/ N (+) = 106/16 = 6.6 CO 2 (+)/ P (+) = 106/1 =106 O 2 (+)/ N(-) = 138/16 = 8.6 & O 2 (+)/ P(-) = 138/1 = 138 also... Photosynthesis consumes hydrogen ions. Respiration liberates hydrogen ions N (+)/ H + (+) = 16/18 = 0.9 (about equal) CO 2 (+)/ H + (+) = 106/18 = 5.9 Notice the signs of all of these changes. e.g., as O 2 diminishes, CO 2, NO 3- and PO 4 3- all increase. This is occurs at excess respiration over photosynthesis. The opposite is true during photosynthesis ("free" N, P and C are consumed and O 2 is liberated) (Aquatic) Microbial Biochemistry Your book divides microorganisms into 2 categories Eukaryotes: (having well-defined cell nuclei enclosed in a membrane). These include Plants, Fungi, Animals, etc. Only some eukaryotes are microorganisms Prokaryotes: (lacking in nuclei and having genetic material more dispersed through out the cell). These include "True bacteria" and possibly precursor organisms to cellular organelles such as mitochondria or chloroplasts. All prokaryotes are microorganisms. cyanobacteria (previously known as bluegreen algae) are an ancient bacteria group that are photosynthetic prokaryotes. www.ucmp.berkeley.edu/bacteria/cyanointro.html 4
There are two taxonomic types of Prokaryote in this classification scheme: Bacteria and Archaea (or Archaebacteria). Archaea were first discovered in the 1970s. Archaea exist in some of the most extreme environments on Earth (high temperature, low temperature, high pressure, etc..), as well as more normal settings. Together with some bacterial groups, they are likely candidates organisms for extra-terrestrial environments. Archaea include very ancient types of organisms that are "tuned" to survive in special environments; some are chemosynthetic; i.e., producers that use chemical energy sources to synthesize biomolecules (e.g., Methanogens, Halophiles, Sulfolobus, and their relatives). Methanococcus janaschii www.ucmp.berkeley.edu/archaea/archaeamm.html Microorganisms are widely dispersed in the environment. Many exploit specific ecological niches at chemical or physical interfaces where food sources tend to accumulate. For example: The air-sea interface Biofilms coating rocks or water A microbial mat www.personal.psu.edu/faculty/j/e/jel6/biofilms/ The sediment-water interface oxidized-reduced interface in soils, sediments, etc. 5
No organisms have a greater effect on more environments than microorganisms Another key aspect of bacteria & archaea are their small size: 0.5 µm to several µm. This size and their broad ranges of shapes gives bacteria surface area to volume ratios that are 100-1000 times larger than eukaryotic cells. This means that a relatively small bacterial biomass can have a very large impact on natural waters, compared to a similar mass of Eukaryotic cells. Lifestyles of the small and not so famous bacteria are small and widely dispersed in the environment. Bacteria have relatively simple life cycles, which may last only hours to years. Nevertheless, bacteria can effect very rapid chemical transformations in aquatic environments. Fecal coliform bacteria from a polluted stream. a typical view of a marine microbial community stained with SYBR Gold 2X http://www.virusecology.org/ Marine bacteria, St. Petersburg, FL, USA http://gallery.usgs.gov/photos/06_14_2010_jn1qht6ggb_06_14_2010_0 6
Bacterial population dynamics After "getting used to" a new environment (the lag phase), growth progresses in exponential fashion (the log phase). Exponential growth continues until some resource (space, food, etc..) is used up or some other byproduct of metabolism accumulates to toxic concentration (stationary phase). The death phase begins some time after this. From Manahan, Environmental Chemistry Temperature, substrate concentration, and variables like ph also control bacterial growth and activity rates. The effects of substrate concentration, temperature and ph on bacterial metabolism are shown below. Many bacteria are adapted to live and flourish in semi restricted ranges of ph and temperature. Bacterial metabolism rates are measured by enzymatic activity, the enzyme being used in some way to catalyze a reaction that occurs during growth. Under favorable conditions bacterial growth can be extremely rapid. From Manahan, Environmental Chemistry 7
Classification of microorganism types 2 approaches to the tree of life classification of organisms: the traditional 5 kingdoms approach using physiological differences (Linnaean Phylogeny) 16S rrna using genetic differences (molecular phylogeny) 5 kingdoms approach 16S rrna Uses size, structure and behavior uses genetic differences Stick length reflects extent of difference in genetic make-up Microorganisms emphasized in the lecture are highlighted in red. Figure from Nealson, Ann. Rev Earth Planet. Sci. 8
Physical differences amongst eukaryotes, e.g., animals, are much greater than amongst the procaryotes, leading to the large animal branch and the small procharea branches in the classical phylogeny Figure from Nealson, Ann. Rev Earth Planet. Sci. Metabolic differences: big rrna differences between bacteria (compared to for instance all animals), largely reflects the wide range of bacterial (and archaeal) metabolisms vs. the limited variation in animals. The current view of Life s Major Domains www.ucmp.berkeley.edu/exhibits/historyoflife.php 9
Bacterial metabolism Heterotrophic metabolism is based on the oxidation of organic chemicals, such as sugars, proteins, etc.., to yield ATP and simpler organic compounds. These chemicals are in turn used by bacterial cells for biosynthethesis or for transformative and assimilatory reactions. Bacterial metabolism 2 related activities Bacterial anabolism: the physiological and biochemical activities for acquisition, synthesis, and organization of the chemical constituents of a bacterial cell. Bacterial catabolism: the biochemical activities for the net breakdown of complex substances to simpler substances by living cells. Substances with a high energy level are converted to substances of low energy content, and the organism utilizes a portion of the released energy for cellular processes. 10
Bacterial metabolism anabolism Raw materials Complex bio molecules http://www.bact.wisc.edu/ ATP cycle catabolism Usable energy Bacteria and Archaea As mentioned earlier, these prokaryotes include both heterotrophs and autotrophs. Together, these microscopic organisms are responsible for many of the important transformations of organic and inorganic matter in the environment, such as oxidation and reduction processes in aquatic environments. Recall from last time Aerobic Respiration Recall, respiring organisms utilize O 2 H 2 O to oxidize organic matter. Anaerobic Respiration Once O 2 is used up, various bacteria continue to oxidize available organic matter to derive energy for their metabolism, leading to the redox-ladder. They play a vital role in poising pe and thus governing the geochemistry of many metals in the hydrosphere. 11
Redox Ladder transformations of Fe by Chemoautotrophs in polluted Environments: Examples from acid mine drainage Ground or surface waters issuing from metal ore mines are often acidic because of the oxidation of pyrite associated with the ore body. 4FeS 2 (s) + 14O 2 (g) + 4H 2 O(l) 4Fe 2+ (aq) + 8SO 4 2- (aq) + 8H+(aq) Abiotic pyrite oxidation to produce ferric ions and hydrogen ions is slow. 30,000X magnification But Thiobacillus ferrooxidans (left) catalyzes the oxidation of FeS 2, producing ferric ions and hydrogen ions. It is responsible for iron and inorganic sulfur oxidation of in mine tailings and coal deposits where these compounds are abundant. Subsequent Fe 2+ oxidation by organisms like Gallionella produces Fe 3+ in these environments (next 2 slides) http://www.mines.edu/fs_home/jhoran/ch126/index.htm Gallionella is a microbe that catalyzes Fe oxidation to get energy. 4Fe 2+ (aq) + O 2 (g) + 4H + (aq) 4Fe 3+ (aq) + 2H 2 O(l) http://www.buckman.com/eng/micro101/2266.htm 12
This organism probably produces Fe-hydroxide strands as a means of eliminating waste Fe(III) 4Fe 3+ (aq) + 12 H 2 O(l) 4Fe(OH) 3 (s) + 12H + (aq) http://www.buckman.com/eng/micro101/2266.htm Fe(OH) 3 precipitates cause a rusty color in acid mine drainage waters. Low ph makes these waters quite corrosive in the environment, an attribute that remediation needs to eliminate. http://www.science.uwaterloo.ca/research/ggr/minewastegeochemi stry/acidminedrainage.html see also a related site for a great description of Cr(VI) remediation: http://www.science.uwaterloo.ca/research/ggr/permeablereactiveba rriers/cr-tce_treatment/cr-tce_treatment.html 13
Artificial wetland as passive treatment of acid mine drainage. Abundant plant organic matter provides reducing capacity required to drive waters anoxic, allowing microbial sulfate reduction to kick-in. What are the beneficial consequences of this? http://www.mines.edu/fs_home/jhoran/ch126/amd.htm Microbes and Material Transformation in Exogenic Cycles and Ecosystems Microbes play numerous important roles in chemical transformations in Earth s surface reservoirs. 14
Microbes are responsible for: a. fixation of the nutrient element N to biologically usable forms b. regeneration of nutrient elements from decaying organic matter (cycling nutrients through an ecosystem multiple times) c. releasing inorganic nutrients from minerals. Microbes and organic matter cycling Microbes play an essential role in the cycling of organic matter in various subreservoirs of a healthy ecosystem via the reaction types we have just discussed (and many others) 15
Microbes and Elemental Cycling The nitrogen cycle stands out as being particular dependent upon microbial activity because of the wide number of oxidation states and forms of Nitrogen, whose transformations are microbialy-mediated. Microbes and Elemental Cycling Nitrogen is very important in metabolic pathways and is an abundant element in Earth's exogenic environment (e.g., it is the most abundant element in the atmosphere). But... the most common form of nitrogen (N 2 ) is not utilizable by most organisms. For instance, we breath N 2 in and out thousands of time each day without changing it. It is largely through the action of microorganism that "fix" N 2 molecules to either oxidized or reduced forms, that N is made usable to the rest of the biosphere for biomolecule synthesis. 16
Microbes and Elemental Cycling Most biomolecules are based on Nitrogen Nitrogen in the -3 oxidation state (e.g., amines and amino acids). N +5 in NO 3- is the form of N that is easiest for plants to absorb from the environment. Oxidized forms such as this can be absorbed by organisms but must then be enzymatically reduced to N -3 be used in OM synthesis. Biological nitrogen fixation The primary Nitrogen fixation mechanism is by reduction to ammonia via the enzyme nitrogenase, which contains Fe S - Mo cluster complexes as electron transfer centers. Redox! MoFe protein-fe protein complex from involved in nitrogen conversion to ammonia. http://www.chem.cmu.edu/groups/achim/research/magneto.html 17
Biological nitrogen fixation Energy Intensive: It takes a great deal of energy to break the N N triple bond in N 2. Energy Source: Microbial nitrogen reduction ( fixation ) by nitrogenase uses energy from soil organic matter or from sunlight stored in ATP. When microbes have a symbiotic relationship with a the host plant the plant often provides the energy source as fixed OM. Locally Reducing Conditions: Nitrogenase is very sensitive to oxygen, therefore the organism or its host adopts strategies to exclude oxygen from the sites of nitrogenase activity. Biological nitrogen fixation N 2 is converted into plant-utilizable oxidation states by a few genera of microorganisms, providing an important source of this nutrient to natural and agricultural ecosystems. Nitrogen fixing bacteria take two main forms: free-iiving in soil symbiosis with plants. 18
Nitrogen-fixing bacteria form symbiotic associations with the roots of legumes (e.g., clover and lupine) and trees (e.g., alder and locust). Visible nodules are created where bacteria infect a growing root hair. Nodules formed where Rhizobium bacteria infected soybean roots. http://soils.usda.gov/sqi/concepts/soil_biology/bacteria.html The plant supplies simple carbon compounds to the bacteria, and the bacteria convert N 2 into a form the plant host can use. When leaves or roots from the host plant decompose, soil nitrogen increases in the surrounding area. Phosphorous cycling is less dependent on microbial transformations that convert oxidation state, but microorganisms in soil and water do control transformations between organic and inorganic forms. hydrosphere Anthrosphere biosphere geosphere 19
Fungal Microorganism and Phosphorous Cycling Arbuscular mycorrhizas are an important type of fungus found on the vast majority of wild and crop plants, with an important role in mineral nutrient uptake (especially Phosphorous) and sometimes in protecting against drought or pathogenic attack. The fungus obtains sugars from the plant, and the plant obtains mineral nutrients that the fungus absorbs from the soil. Root hairs arbuscules Vesicles http://helios.bto.ed.ac.uk/bto/microbes/mycorrh.htm Part of a clover root infected by an AM fungus. The site of penetration is shown at top right, where the fungus produced a pre-penetration swelling, (then it grew between the root cells and formed finely branched arbuscules (thought to be sites of nutrient exchange) and swollen vesicles (thought to be used for storage). 20