202 General Microbiology II

Biogeochemical Cycles

Biogeochemical cycles are "pathways" through which organic compounds and elements in inorganic compounds are changed from one chemical state to another (redox cycles involve changes in oxidation level) while they are being transferred from one organism to another (transport cycles involve changes in the locations of compounds or elements)

Carbon cycle

• carbon reservoir amounts and turnover rates:
  • sediments and rocks ~7x10^22 g (~3x10^8 yr)
  • aquatic inorganics ~4x10^19 g (10^5 yr)
  • terrestrial organics ~2x10^18 g (16-40 yr)
  • aquatic organics ~8x10^17 g (1 mo to 20 yr)
  • atmosphere ~5x10^15 g (~4 yr)
• carbon reduction (carbon dioxide fixation) is carried out by phototrophic or lithotrophic bacteria, which reduce carbon dioxide (via Calvin cycle or reductive TCA cycle) to form glucose polymerized to form cellulose (methanogens reduce carbon dioxide or acetate to form methane)
  • phototrophs
    • aerobic - cyanobacteria, algae, green plants
    • anaerobic - purple and green phototrophic bacteria
  • lithotrophs
    • bacteria that oxidize or reduce inorganic substrates - hydrogen bacteria, etc.
    • methanogenic archaea (anaerobic) reduce carbon dioxide or acetate to form methane
• carbon oxidation
  • organic substrate utilization is affected by:
    • several features of the organic substrate:
      • elemental composition
      • arrangement of elements and subunits
      • types of linkages employed
    • other nutrients present
    • physical and other chemical factors
    • variety of microbes present (cooperation vs. competition)
  • organotrophs use three modes of catabolism
    • aerobic respiration - aerobic bacteria, archaea, fungi, plants, animals
    • anaerobic respiration - anaerobic bacteria and archaea
    • fermentation - anaerobic and facultative aerobic bacteria
  • cooperation
    • catabolism of complex carbohydrates involves cooperative activities of groups of different microbes, as described in the following example of anaerobic degradation of cellulose
      • cellulolytic microbes hydrolyze cellulose into glucose, then fermentative bacteria oxidize it to form acetate, carbon dioxide and hydrogen
      • because not all of the catabolic reactions involved are energetically favorable on their own, syntrophy (a process in which two or more different microorganisms cooperate to degrade a substance that neither can degrade alone) is common
        • an example of syntrophy is the case in which an ethanol fermenter and a methanogen living in close approximation carry out two fermentations, one of which is energetically nonfavorable (positive free energy change)

        2 CH3CH2OH + 2 H2O 4 H2 + 2 CH3COOH + 2 H+ (+19 kJ)

        • and the other of which is energetically favorable (negative free energy change)

        4 H2 + CO2 CH4 + 2 H2O (-131 kJ)

        • when coupled with hydrogen utilization, fermentative oxidation of ethanol to acetate becomes feasible because rapid removal of hydrogen makes the overall reaction more favorable (negative free energy change)

        2 CH3CH2OH + CO2 CH4 + 2 CH3COOH + 2 H+ (-111 kJ)

        • so both reactions can proceed
          • these hydrogen-producers (Syntrophomonas, Syntrophobacter, etc.) probably generate their ATP when they convert acetyl-CoA to acetate at the "end" of beta-oxidation of fatty acids (note that mathanogens can also reduce acetate to methane)
          • the rate-limiting step in methanogenesis (Methanobacterium, etc.) is frequently generation of hydrogen and acetate by the slow-growing syntrophic bacteria
        • syntrophic interspecies transfer of hydrogen also occurs with sulfate reducers, homoacetogens, as well as methanogens
        • in terrestrial habitats, methane production in arctic tundra increases when melting occurs, due to increased water content generating the anaerobic conditions these bacteria need to function in their syntrophic associations
    • another example of cooperation is the fact that microbial biomass becomes the predominant substrate in many cases (e.g., sewage treatment) where degradation of complex organic substances is occurring
    • an example of a product resulting from the lack of microbial cooperation in degradation of complex organic substances is coal formation, which is based on the inability of aerobic filamentous fungi to degrade lignin (major carbohydrate in plant material) under anaerobic conditions such as are generated in peat bogs by accumulation of thick layers of dead plant material; over time, the pressure generated by sedimentation compacts this material to form coal
  • competition
    • microbial portions of the carbon cycle are also frequently competitive
    • although it is a cooperative mechanism, syntrophic competition for hydrogen is important in succession and in determining relative proportions of microbes in various habitats
      • in marine waters, sulfate reducers predominate because the sulfate concentration is high and they compete more effectively for hydrogen (especially at very low pH) and catabolize acetate more efficiently than methanogens (Methanococcus, Methanosarcina) which can utilize substrates like trimethyl ammonium (TMA)
      • in freshwater, methanogens predominate because the sulfate concentration is so low that sulfate reduction occurs slowly, mostly at interfaces between water and anaerobic sediments (mud), so the methanogens located here can compete more effectively for hydrogen and they use it to reduce carbon dioxide to generate methane (and energy)

Sulfur cycle

• sulfur reservoir amounts (turnover rates not available):
  • sediments and rocks ~10²² g
  • aquatic inorganics ~10²¹ g
  • terrestrial organics - 6-10x10¹⁵ g
  • atmospheric ~3x10¹² g
  • aquatic organics ~4x10⁷ g
  • terrestrial inorganics - unknown
• sulfur oxidation
  • both aerobes (Beggiatoa, Sulfolobus, Thiobacillus, Thiothrix) and anaerobes (Thiospirillum, Thiocapsa, Chromatium, Chlorobium, Prosthecocloris) oxidize sulfide to sulfur and then oxidize it to sulfate, usually in cooperative sequences
  • because sulfide oxidizes spontaneously in the presence of oxygen at neutral pH, microbes that use it as an energy source are generally anaerobic (Thiomicrospira) or acidophilic (Thiobacillus ferrooxidans, Thermothrix); both Thiomicrospira and Thermothrix use nitrate as their terminal electron acceptor
• sulfur reduction
  • facultative anaerobes (Campylobacter, Proteus, Pseudomonas, Salmonella) reduce sulfate to sulfur, then anaerobes (Desulfovibrio, Desulfomonas, Archaeglobus, Desulfobacter, Desulfococcus, Desulfuromonas, Desulfosarcina) reduce sulfur to form sulfide
  • sulfate cannot be reduced unless it is first activated by reacting with ATP to form adenosine phosphosulfate (APS); after that, it can be reduced either dissimilatively or assimilatively
    • dissimilative sulfate reduction - requires reducing power (NADPH) and transfer of electrons from an energy source (via electron transport system)
      • activated sulfate moiety of APS is first reduced to sulfite
      • sulfite is then released from APS
      • sulfite is then reduced to form successively more reduced sulfur compounds, eventually reaching the sulfide level
      • once this level is reached, the sulfide is released (excreted) into the environment
    • assimilative sulfate reduction
      • requires a second activation step at the expense of ATP, formation of phosphoadenosine phosphosulfate (PAPS)
      • it then requires reducing power (NADPH) and transfer of electrons from an energy source (via electron transport system) to the sulfate moiety of PAPS
      • activated sulfate moiety of PAPS is first reduced to sulfite
      • sulfite is then released from PAPS
      • sulfite is then reduced to successively more reduced sulfur compounds, eventually reaching the sulfide level
      • once this level is reached, sulfide can be assimilated (incorporated) into organic compounds such as amino acids
  • rates of sulfate reduction are carbon-limited in nature, because most sulfate isdissimilative and thus requires a source of electrons, which are primarily provided by organotrophic metabolism

Nitrogen cycle

• nitrogen reservoir amounts and turnover rates:
  • sediments and rocks ~2x10²³ g (~4x10⁸ yr)
  • atmosphere (mostly nitrogen) ~4x10²¹ g (~4x10⁷ yr)
  • aquatic inorganics (mostly nitrogen) ~2x10¹⁹ g (~2x10⁵ yr)
  • terrestrial organics ~3x10¹⁷ g (1-40 yr)
  • aquatic organics ~3x10¹⁶ g (~1 mo)
  • terrestrial inorganics (soil) ~2x10¹⁶ g (less than 1 yr)
• assimilative nitrogen metabolism
  • nitrogen fixation
    • because the nitrogen triple bond is very stable, it requires a great deal of energy as well as reducing power for one dinitrogen molecule to be reduced to form two ammonia molecules (requires 8 protons, 8 electrons and 18-24 ATP)
    • the nitrogen fixation pathway can be divided into two stages:
      • dinitrogenase reduction:
        • flavodoxin is reduced by pyruvate flavodoxin oxidoreductase (in a reaction that requires formation of acetyl-CoA and carbon dioxide from pyruvate and CoA)
        • dinitrogenase reductase (an iron-containing enzyme that reduces dinitrogenase) is then reduced (coupled with oxidation of flavodoxin)
        • dinitrogenase is then reduced (coupled with oxidation of dinitrogenase reductase and cleavage of ATP)
      • dinitrogen reduction occurs in three successive steps (with intermediates bound to the enzyme complex throughout the steps)
        • dinitrogen is reduced by reduced dinitrogenase (which uses a coenzyme containing iron and molybdnym to carry out its reducing activity) to form dinitrogen dihydride (requires reduced dinitrogenase, 4 protons and 4 electrons)
        • dinitrogen dihydride is reduced by dinitrogenase to form dinitrogen tetrahydride (requires reduced dinitrogenase, 2 protons and 2 electrons)
        • dinitrogen tetrahydride is reduced by dinitrogenase to form 2 ammonia molecules (requires reduced dinitrogenase, 2 protons and 2 electrons)
    • nitrogen fixation is an anaerobic process because dinitrogenase reductase is irreversibly inactivated by oxygen
      • Clostridium fixes nitrogen in anaerobic environments
      • Azotobacter uses very fast aerobic respiration (oxygen uptake and reduction) to do it in aerobic environments
      • Anabena uses heterocysts to restrict oxygen access to dinitrogenase reductase
      • Rhizobium forms nodules in plant roots and oxygen access is restricted by leghemoglobin and other molecules such as glutathione
      • Frankia also forms nodules in plant roots and oxygen access must be restricted (but I don't know how)
  • nitrate reduction
    • bacteria, fungi (and plants) reduce nitrate to nitrite, then to hydroxylamine, then to ammonia, then incorporate it into organic compounds
    • aerobic or anaerobic process, but occurs only when ammonia levels are low, because ammonia represses assimilative nitrate reductase, the first enzyme in this nitrate reduction pathway
• dissimilative nitrogen metabolism
  • nitrate reduction
    • bacteria (only) reduce nitrate to nitrite, then some bacteria reduce nitrite to ammonia, whereas others reduce it to nitric oxide gas, then reduce it to nitrous oxide gas, which is reduced further to dinitrogen gas, which is released to the atmosphere (as can occur with any of the gaseous compounds generated in this pathway)
    • anaerobic process, because dissimilative nitrate reductase, the first enzyme in this nitrate reduction pathway, is derepressed only in the absence of oxygen
  • nitrification - sequential oxidation of ammonium ions to nitrate
    • lithotrophic bacteria
      • ammonium bacteria (Nitrosomonas, Nitrosococcus) oxidize ammonia to nitrite, then
      • nitrite bacteria (Nitrobacter) further oxidize nitrite to nitrate
    • organotrophic bacteria and fungi oxidize organic nitrogen (amine groups) to nitrate, especially in acidic environments using a pathway that is essentially the same as for lithotrophic bacteria (above)
  • denitrification
    • Pseudomonas denitrificans and other bacteria reduce nitrate to nitrite, then reduce it to nitric oxide gas, which is reduced to nitrous oxide gas, which is reduced to dinitrogen gas, which is released to the atmosphere (as can occur with any of the gaseous compounds generated in this pathway)
    • anaerobic process, because oxygen represses nitrate reductase

Iron cycle

• iron oxidizing bacteria (Thiobacillus ferrooxidans, Gallionella)
  • oxidation of ferrous iron to ferric iron does not provide sufficient electrochemical potential to allow ATP generation or NADPH formation by normal mechanisms
  • therefore, many iron bacteria also derive electrons from oxidation of hydrogen sulfide, sulfur, thiosulfate
  • because ferrous iron is spontaneously oxidized by oxygen at neutral pH, but not at low pH, these bacteria are typically acidophilic
  • Thiobacillus ferrooxidans uses the natural proton gradient in its low pH environment to generate ATP via ATP synthase, then eliminates excess cytoplasmic protons by coupling oxygen reduction to ferrous iron oxidation using rusticyanin, cytochrome c and cytochrome a1 (all in the cytoplasmic membrane)
• iron reducing bacteria (Pseudomonas, others) reduce ferric iron to ferrous iron via an anaerobic process in which the ferric iron is being used as an "electron sink" (terminal electron acceptor)