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BIOL 241 - Pre-Midterm Notes

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University of Waterloo
BIOL 241
Barbara Butler

BIOL  241  –  Introduction  to  Applied  Microbiology     Lecture  1:  Introduction   − Microbes  possess  extraordinary  genetic  and  physiological  diversity   o Adapted  to  survive  in  an  exploit  a  wide  range  of  animate  and  inanimate   environments   − Anoxic  environments  arise  as  a  result  of  aerobic  microbial  metabolism   − Without  nitrogen  fixers,  biology  sto ps   o Hover  method  of  nitrogen  fixation  is  energy  intensive   o Nitrogen  fixers  cycle  energy  and  recycle  materials  from  oxygen  devoid  habitats  back   into  oxic  environments   − Prokaryotic  domains  are  unicellular  and  not  very  complex  entities,  but  have  evolved  to   exploit  energy  sources  like  inorganic  compounds  (Fe,  S,  etc.)  instead  of  just  sunlight  and   organic  compounds     Subdisciplines  of  Microbiology :   − Medical   o Infectious  disease  and  pathogenesis   o Immunology   − Agriculture   − Environmental   − Industry   − Genetics,  genomics,  biotechno logy     Lecture  2:  Microbial  Ecology     Microbial  Ecology :  the  study  of  relationships  between  organisms  and  their  surroundings   (physical/chemical  environment)     Ecosystem:  a  community  of  organisms  and  their  natural  environment   − Almost  never  see  an  individual  mic robe   − If  nutrients  are  available,  microbes  will  divide  to  make  a  population  of  identical  individuals   − Community:  populations  of  multiple  organisms  interacting   − Guild:  a  group  of  organisms  that  carry  out  similar  metabolic  processes   − Ecosystems  need  an  energy  so urce  to  drive  metabolic  activity   o Often  light   o Maintains  organisms,  creates  new  biomass   o Materials  cycled  through  decomposers ,  releasing  minerals  from  dead  organic  matter     Acid  Mine  Drainage:  mines  with  a  lot  of  pyritic  ore  (sulfides,  iron  available  in  aerobi c   environments)  can  support  microbial  growth   − H 2O 4  produced,  leaches  metal  (Fe,  Cu,  Zn)  into  water,  polluting  rivers   − Can  also  be  used  to  mine  copper  in  controlled  ways  in  parts  of  the  US  and  South  America     Microbial  Inhabitants  of  Freshwater  Lake  Ecosystem s   − Sunlight  is  the  main  energy  source;  its  availability  decreases  as  you  go  down  the  water   column   − Photic  zone:  community  1  is  composed  of  oxygen -­‐forming  phototrophs  that  use   photosynthesis  to  make  energy   o Convert  CO2  to  organic  matter  (glucose) 2  and  O   o Ex.  diatoms,  green  algae,  cyanobacteria   − Oxic  zone:  community  2  is  composed  of  aerobes  and  facultative  aerobes  that  consume   organic  matter  made  by  community  1  and  mineralize  it  back  to  carbon  and  water   − Interactions  between  communities  1  and  2  is  the  carbon  cycle   − Anoxic  sediments:  community  3  decomposes  dead  organisms  from  communities  1  and  2,   cycling  minerals   o Guild  3:  fermentation  bacteria;  excrete  simple  organic  compounds  (lactic  acid,   ethanol)  that  guilds  1,  2,  4  use  as  substrates   o Guild  2:  sulfidogenic  bacteria;  reduce4  SO  a2d  S  to  H S   o Guild  4:  use  CO  as  terminal  electron  acceptor;  methanogens,  acetogens   2 3+ o Guld  1:  denitrifying  and  Fe  reducers;  use  nitrite  as  terminal  electron  acceptor     Energy  and  Carbon  Flow  in  Microbial  Metabolism   − Heterotrophy:  organic  compounds  burned  for  energy,  giving  of2  CO ;  electrons  go  into  ETC,   PMF  generated  to  drive  ATPase  activity,  electrons  go  to  terminal  electr2),  give    (O off  2O  an2  H O,  some  carbon  used  for  biosynthesis   o Ex.  Pseudomonas  fluorescens  –  if  no  oxygen,  denitrifies  instead   − Autotrophy:  light  as  energy  source,  ATP  produced,  CO  as  carbon  source   2 o Ex.  plants,  cyanobacteria   − Anoxygenic  phototrophs  use  light  for  energy,  organic  compounds  for  carbon  source   o Ex.  purple  sulfur  bacteria,  purple  non -­‐sulfur  bacteria   − Lithotrophs  (rock  eaters)  oxidize  inorganic  energy  sourc2s  (H S,  Fe ,  etc.)  to  gain  energy,   use  C2  as  carbon  source     Objectives  in  Microbial  Ecology   − Explore  and  understand  biodiversity  of  microorganisms  in  nature  and  interactions  in   communities   − Measure  microbial   activities  in  nature  and  monitor  the  effects  of  microbes  on  ecosystems   o Human  microbiome  project   − Primary  production:  take  energy  and  produce  organic  matter  that  consumers  can  utilize   o Phototrophic,  chemolithotrophic  activity   o CO 2  + 2  H O  +  energy  à  new  biomass   − Decomposition:  breaks  down  organic  matter  into  mineral  components,  cycles  carbon  atoms   o Chemoorganotrophic,  heterotrophic  activity   o Dead  biomass  à 2CO 2 +  H O  +  energy   − Biogeochemical  cycling  of  the  elements  (C,  N,  P,  S,  Fe)     Microorganisms  in  Nature   − Live  in  “common”  or  “extreme”  environments   − Require  the  same  necessities  of  life;  difference  is  flexibility  in  what  is  considered  a  resource,   suitable  physiochemical  condition,  energy  source,  or  electron  acceptor     Niche:  combined  description  of  physical  habitat,  func tional  role,  and  interactions  of  the   microorganism  occurring  at  a  given  location   − Every  organism  has  a  prime  niche  where  it  functions  optimally   − Can’t  have  two  organisms  occupying  the  exact  same  niche     Microenvironment:   where  a  microbe  lives  and  metabolizes   within  its  habitat   − Small  physiochemical  gradients  are  both  spatially  and  temporally  available   − Affected  by  time  and  differing  daily  conditions  (ex.  amount  of  sunlight,  rain)     Microbial  life  in  nature  often  differs  from  microbial  life  in  a  lab  culture.   − Intermittent  entry  of  nutrients  into  an  ecosystem  leads  to  a  feast  or  famine  existence,  so   microbes  have  adaptations  to  allow  them  to  do  this   o Inclusion  bodies   o High  growth  rates  when  nutrients  are  present   o Suspended  animation  (endospore  formation  or  quiescent  pha se)  when  limited   nutrients  or  poor  conditions   o Exponential  growth  is  rare  in  nature  but  often  occurs  in  the  lab   − Non-­‐uniform  distribution  of  resources  in  nature   − Resource  competition  in  nature   o Labs  often  have  pure  microbial  monocultures,  but  that  isn’t  the  ca se  in  the  real   world     Biofilm:  a  community  of  microbes  attached  to  some  surface  that  is  embedded  in   extracellular   polymeric  substances  (EPS)   − If  the  surface  is  suitable,  there  is  irreversible  adhesion  to  the  surf ace   o Microbes  use  the  nutrients  there,  divide,  and  form  a  microcolony   − EPS:  often  polysaccharide,  some  polypeptides;  also  known  as  a  capsule,  slime  layer,  or   gylcocalyx   − Physiochemical  gradients  within  a  mature  biofilm  result  in  a  number  of  potential   microenvironments  in  a  small  area   o Steep  gradients  in  physical  and  chemical  parameters  (pH,  oxygen  level,  substrate   availability)   o Microbes  at  the  surface  have  access  to  all  available  nutrients   o Those  in  the  interior  might  be  living  off  of  metabolic  end  products  excreted  by   others  or  are  in  suspended  animation   − Biofilm  can  be  degraded  by  external  conditions  or  by  organisms  who  recolonize  elsewhere  in   poor  conditions   − Advantages:   o Protection  from  toxicants,  predators,  immune  system  cells   o Ability  to  remain  within  a  favourable  niche   o Nutrient  trapping   o Cooperative  interactions  with  other  microbes   − Disadvantages:   o Highly  competitive   o Primary  colonizer  may  be  forced  out  because  of  competition   o Localized  biomass  can  be  efficiently  preyed  upon  by  larger  organisms   o Easily  infected  by  viruses  due  to  small  distances  between  bacteria   − Problems  resulting  from  biofilm  formation:   o Pipe  clogging   o Corrosion  of  structural  steel  framework   o Increased  drag  on  ship’s  hull   o Periodontal  disease   − Exploitation   o Slow  sand  filtration,  which  relies  in  microbes  in  sand  filters  to  use  organic  material   present  in  drinking  water  to  clean  it   o Vinegar  production   o Leaching  copper  out  of  low -­‐grade  ores  to  recover  metal  values   − Removal   o Abrasions  /  scraping  off  visible  part  of  biofilm   o Antimicrobials   o Hypochlorination     Microbial  Mat:  extremely  thick,  layered,  specialized  mi crobial  community  composed  mainly  of   photosynthetic  or  chemolithotrophic  bacteria   − Macroscopic  (visible  to  the  naked  eye)   − Found  in  hot  springs,  marine  intertidal  zones,  other  extreme  environments   o Ex.  whitish-­‐yellow  mat  along  seafloor  off  of  the  coast  of  Afr ica  where  water  coming   up  from  the  seabed  is2  rich  in  H S,  which  is  a  substrate  to  sulfur  oxidizing   chemolithotrophs   − Cyanobacterial  mats  are  complete  microbial  ecosystems  and  consist  of  populations  of   photosynthetic  primary  producers  and  consumers   o Cyanobacteria  are  aerobic/oxygenic  phototrophs  that  produce  2   o Anoxygenic  phototrophic  bacteria  (ex.  purple  sulfur  bacteria)  live  at  the  bottom,  use   sulfate  from  seawater  as  the  terminal  electron  acceptor, 2provide  H S  to  other  who   split  it  to  make  more  sulfur     Interactions  Between  Microbial  Populations   − Competition  for  similar  resources  or  energy  sources   o Hard  on  both  populations   o Outcome  depends  on  innate  capabilities  of  both  populations  (metabolic  rates,   nutrient  uptake  rates)   − Competitive  exclusion:  competing  for  everything   o Can’t  coexist  and  occupy  the  same  niche  so  one  dies  out  and  inhabits  locations   where  it  will  be  somewhat  successful   o Contributes  to  speciation  since  mutants  evolve  under  selective  pressure  to  become  a   different  species   − Antagonism:  a  specific  inhibitor  of  metabolic  end  products  produced  by  one  microbe  may   impede  the  growth  or  metabolism  of  others   o Lactic  acid  bacteria  produce  organic  acids  that  lower  the  pH  and  affect  neutrophilic   growth   o Bacteriocins  are  inhibitory  to  close  relatives  (separate  strains)  of  the  microbe  that   made  them   o Antibiotics  are  inhibitory  or  lethal  to  other  microbes   − Cooperative  interactions:  interacting  microbes  must  share  a  nearby  (or  the  same)   microenvironment   − Syntrophy:  together,  microorganisms  carry  out  a  transformation  that  neit her  can  conduct   alone   − Consortia:  groups  of  microbes  working  together  in  aerobic  decomposition  of  compounds   within  a  biofilm   − Complementary  metabolic  interactions   -­‐ o Nitrification:  NH 3  à 2NO  (ammonifiers)   NO 2  à  N3  (nitrifiers)   o Buildup  of  nitrite  is  inhibito ry;  nitrifiers  get  rid  of  high  levels  for  ammonifiers   − Symbiosis:  long-­‐standing,  intimate  relationship  between  two  or  more  organisms  that  share   a  particular  ecosystem   o Mutualism:  both  species  benefit   o Parasitism:  one  species  benefits,  the  other  species  is  har med   o Commensalism:  one  species  benefits,  the  other  is  unaffected   o Different  symbiotic  relationships  shift  back  and  forth  along  this  continuum  at   different  times  in  their  relationship     Lecture  3:  Bacteria-­‐Bacteriophage  Interactions     Virus:  a  genetic  element  containing  either  RNA  or  DNA  that  replicates  in  cells  but  is  characterized  by   having  an  extracellular  state  where  it  cannot  replicate  (inert  particles)   − Cannot  replicate  on  its  own;  needs  host  for  that   − There  is  the  odd  virus  that  violates  the  central  dogma   o Instead  of  DNA  à  RNA  à  protein,  a  retrovirus  like  HIV  has  a  single -­‐stranded  RNA   genome  that  is  converted  to  DNA  when  it  infects  the  host  and  then  carries  out   transcription  and  translation     Importance  of  the  Interaction:   − Potential  controller  of  microbial  pop ulation  sizes   − Phage  infection  may  influence  phenotype  of  the  host  prokaryote     Virion:  a  single  virus  particle   − Metabolically  inert   − Infects  host,  takes  over  host  metabolic  machinery,  replicates  to  make  more  virus  particles,   suppresses/destroys  host  genome   − Contains  nucleic  acid  surrounded  by  protein  capsid  and  sometimes  an  envelope   − Naked  virus:  genome  and  capsid  made  of  capsomer  proteins   − Enveloped  virus:  genome  +  capsid  +  envelope   o Envelope  is  often  a  lipid  bilayer  that  the  virus  has  stolen  from  the  host  cell   membrane  and  embedded  with  proteins   o Common  in  animal  viruses   − Very  small  genome  (nm)   o Phage  G,  which  commonly  affects   Bacillus  subtilis  and  Bacillus  megaterium,  has  a  6-­‐7   mB  genome   o Most  genomes  are  1 -­‐5  mB     Quantification  of  Bacteriophages  by  Plaque  Assay   − Add  a  small  amount  of  susceptible  bacterial  host  cells  to  the  phage  sample   − Mix  with  molten  agar,  pour  onto  a  nutrient  agar  base,  and  allow  the  top  to  solidify   − If  incubated  appropriately,  the  bacteria  grow  across  the  plate  forming  a  bacterial  lawn   − Plaques:  clearings  in  the  lawn  that  represent  the  places  where  viral  particles  infected  and   killed  host  cells   o Allow  you  to  quantify  viral  particles     Lytic  Cycle   − Virus  recognizes  and  attaches  to  a  specific  receptor  on  the  host’s  cell  surface;  often  a   glycoprotein  that  the  virus  hijacks  for  its  own  purposes   o TI  bacteria  affects  E.  coli  by  attaching  to  a  protein  involved  in  iron  uptake  system   − With  phages,  entry  and  uncoating  of  genome  (loss  of  capsid)  takes  over  host  cell  machinery   to  create  viral  structural  proteins  and  en zymes   − If  a  cell  allows  viral  replication  to  occur,  it  is  permissive   − Non-­‐permissive  host  cells  result  from  mutations  that  change  the  surface  receptor  of  host   endonucleases  and  destroy  infected  phage  DNA   o Restriction  endonuclease  paired  with  methylase,  which   methylates  DNA  so  that  the   host  recognizes  it  as  its  own;  without  this,  DNA  is  destroyed   − Viral  components  self-­‐assemble  and  lyse  the  cell  to  release  mature  phage  particles  that  move   on  to  the  next  host   − Burst  size:  number  of  viral  particles  released  at  the   end  of  the  cycle;  system  dependent   − Takes  25  minutes  to  1  hour  in  phage  bacterial  system   o Slower  in  animal  cells  (8  hours  to  a  couple  of  days)     Entry  Mechanisms  of  Bacteriophages   − Tail  fibers  attach  to  receptors   − Conformational  change  brings  base  of  tail  in  co ntact  with  host  cell  surface   − Rearrangement  of  tail  proteins  allows  inner  core  tube  proteins  to  extend  into  cell  wall   o Involves  lysozyme  to  break  through  peptidoglycan  layer   − Transfer  of  DNA  through  a  pore  formed  in  lipid  bilayer   − Simpler  to  get  into  animal  ce lls  since  there  is  no  cell  wall;  simply  fuse,  melt  in,  uncoat     Lysogenic  Cycle   − Integrates  genome  into  host  cell  genome,  forming  a   prophage   o Host  cell  =  lysogen   − Cell  division,  offspring  carry  viral  DNA   − Viral  repressor  protein  represses  genes  in  prophage  geno me   − Prophage  can  affect  phenotype  of  host   − If  induced  by  stress,  turns  to  lytic  pathway   − Double-­‐stranded  lambda/temperate  phage  with  single -­‐stranded  cohesive  sites  (sticky  ends)   can  exist  linearly  or  as  a  circular  piece  of  DNA  when   cos  sites  come  together   o att  sites  involved  in  attachment   o Interaction  between  att  site  and  particular  site  on  E.  coli’s  genome  between  gal  and   bio  genes   o Site-­‐specific  viral  nuclease  cuts  both,  forming  a  prophage  that  is  integrated  into  the   host’s  genome   o Lytic  cycle  cuts  out  prophage   DNA;  no  longer  suppresses  viral  genome,  so  it  lyses   the  cell     Transduction:  transfer  of  host  genes  from  one  cell  to  another  by  a  virus   − Generalized  transduction   o DNA  is  packaged  into  a  virus  by  size   o If  host  genome  is  approximately  the  same  size,  it  can  accid entally  be  packaged  into  a   lytic  phase  capsid  and  then  transferred  to  a  new  host  bacterial  cell   − Specialized  /  specific  transduction   o When  prophage  is  cut  out  to  enter  the  lytic  cycle,  sometimes  the  host  DNA  adjacent   to  this  is  cut  out  as  well  and  packed  int o  a  capsid   o Creates  a  defective  phage  with  some  bacterial  DNA  that  is  transferred  to  a  new  host   bacterial  cell   o Involves  only  lysogenic  phages   − Recombination  could  occur  and  change  the  host  cell’s  genotype  or  phenotype   − Occurs  naturally   − Important  way  of  horizontal  gene  transfer   − Exploited  in  biochemical  applications   − Many  natural  bacteria  harbor  lysogens   o Some  are  part  of  genome   o Others  can  go  through  the  lytic  pathway   o Ex.  Diptheria  is  dependent  on  toxin  that  bacteria  produces  from  lysogenic  viral  cells     Viruses  are  consistently  the  most  abundant  biological  entities  present  in  any  ecosystem   − 10  viruses  /  L   9 − 10  bacteria  /  L     Lecture  4:  Terrestrial  and  Aquatic  Environments     Soils  are  rarely  organic  and  commonly  inorganic   − Organic  soils  can  be  anywhere  from  20 -­‐80%  organic   − Develop  in  bogs/marshes  over  long  periods  of  time   − Microbes  are  often  the  first  to  colonize  a  bare  rock  face   o Produce  waste  materials  that  contribute  to  soil  organic  matter  collection  before   other  organisms  can  move  in     Mature  Soil  Profile   − Accumulation  of  layer  on  top  of  bedrock   − O  Horizon:  undecomposed  plant  material  and  exposed  organic  matter  on  soil  surface   − A  Horizon:  top  soil;  rich  in  organic  matter,  lots  of  microbes,  root  zone   − B  Horizon:  subsoil;  less  readily  available  substrate  for  microbes,  rainfall  leaches  minerals   and  nutrients  into  it   − C  Horizon:  mostly  inorganic  matter;  sparse  microbe  populations   − Bedrock:  some  microbes  present   − Soil  microbiologists  typically  look  at  only  the  A  horizon  due  to  agricultural  use  and  plant   activity     What  determines  micr obial  activity  in  the  soil?   − Water  availability   o Microbes  are  essentially  aquatic  organisms  and  require  dissolved  substances   o Lots  of  sand  =  large  pores,  water  readily  drains  out   o Clay  has  small  pores  so  water  can’t  readily  drain  out  and  remains  for  too  long   o Mix  of  sand,  silt,  and  clay  is  ideal   o Competition  for  water  with  plant  roots   o Aboveground  plants  shade  soil,  decrease  evaporation   − Oxygen  availability   o Affected  by  water  availability   o ~21%  O 2  in  the  atmosphere,  10-­‐15  ppm  in  water   o Quickly  used  up  and  difficult  to  replenish  in  waterlogged  soil,  leading  to  an  anoxic   environment   − Nutrient  status   o Microbial  activity  is  often  limited  by  N  and  P,  which  is  why  we  fertilize  agricultural   soils   o C  can  also  be  limiting;  less  likely  though   − Microbial  cells  tend  to  accumulate  near  soil  pores  since  that’s  where  the  resources  are     Plants  greatly  influence  soil  habitats   − Rhizosphere:  the  soil  that  surrounds  plant  roots   o Rhizosphere  effect:  the  environment  and  microbial  communities  present  at  the   rhizosphere  are  different  in  terms  of  num bers,  makeup,  activity,  etc.  than  those  in   the  bulk  soil   o Plant  roots  release  exudates  (nutrients,  vitamins,  hormones,  organic  material)  into   the  soil  for  microbes  to  take  advantage  of   o Apparent  in  extremely  nutrient  poor  soils  (ex.  desert  soils  near  a  cactu s)   − Rhizoplane:  actual  root  surface   o Source  of  root  exudates   − Phyllosphere:  surface  of  plant  leaf   − Epiphytic  microbes  live  on  plant  in  either  advantageous  or  mutualistic  relationships   o Ex.  in  tropical  rainforests,  the  soil  is  nutrient  poor  so  communities  of  nit rogen  fixers   living  on  leaves  fix  nitrogen  for  both  the  rainforest  plants  and  themselves     Deep  Terrestrial  Surfaces  As  Microbial  Habitats   − Subsurface  environment  extending  ~10  km  below  the  ground  surface   − Sometimes  groundwater  flows  through  it   − Subsurface  inhabitants  are  often  prokaryotes  (bacteria,  archaea)  sometimes  yeast,   filamentous  fungi,  grazing  protozoa   o Exception:  in  underground  rivers  in  caves,  larger  animals  grow,  such  as  fish  that   have  evolved  not  to  need  eyes  due  to  isolation   − When  it  rains,  material  seeps  through  surface  layers  to  the  aquitard,  contributing  to   groundwater  that  eventually  connects  with  surface  rivers   − Aquifers  have  low  metabolic  activity  and  limited  nutrients   − Practical  interest:  remedial  potential  of  deep  surface  microbiota  in  event  of  pollutant  reflux   (fertilizers,  nitrate,  chlorinated  solvents)     More  than  50%  of  the  Earth’s  biomass  is  microbial   − Majority  in  sparsely  populated,  large  subsurface  habitats     Aquatic  Environments  As  Microbial  Habitats   − Springs:  groundwater  bubbling  to  surface   − Saline  habitats:  salt  marshes,  estuaries,  oceans   − Niches  based  o2  O ,  sunlight,  salinity   − Lakes   o Photic  zone  near  surface  allows  for  primary  photosynthetic  production,  producing   O 2   o May  be  depleted  at  depth  (below  thermocline)  due  to  low  solubility,  consumpti on   o Anaerobic  molecules  in  deeper  regions   − Temperate  lakes  are  often  stratified   o Water  is  most  dense  around  4   o Upper  regions  warm  up  as  sunlight  hits  lake  in  summer  resulting  in  warm,  light   water  at  the  top  and  cold,  dense  water  at  the  bottom;   thermocline  is  the  area   between  these   o In  fall,  top  water  cools  down  and  the  density  becomes  the  same  as  the  bottom   o Turnover:  two  layers  mix,  reoxygenate  lake,  disperse  organic  nutrients  between   layers   − If  lakes  are  wide  and  not  too  shallow,  turbulence  will  mix  them  up  so   there  is  no   stratification   − Rivers:  flow  and  turbulence  entrain  oxygen  back  into  the  water,  reoxygenating  it   − Dumping  in  organic  material  leads  to  algal  blooms  and  macrophytic  plant  growth   o Eventually  material  dies,  sinks  to  bottom  of  river,  decomposed  by   chemoorganotrophs   o These  microbes  deplete  oxygen  levels  by  doing  this,  creating  an  anoxic  environment   that  kills  the  inhabitants     Biochemical  Oxygen  Demand  (BOD):  a  measure  of  degradable  organic  matter  present  in  water   − Sample  incubated  in  the  dark  for  5  days  a t  20 C   − Difference  between  initial  and  final  amounts  of  dissolved  oxygen  reflects  the  amount  of   degradable  organic  matter  present   o Large  BOD  =  large  difference,  d2pleted  O     Marine  Environment   − Open  ocean:  oligotrophic  due  to  runoff   o Often  oxygenated  the  entir e  way  down   o Low  photosynthetic  activity  because  P,  Fe,  N  restrict  cyanobacteria  and   phytoplankton  activity   − Photic  zone  is  ~200  m  down   o Further  than  in  lake  because  of  low  primary  production   − Dark,  cold  (2-­‐3 C),  high  hydrostatic  pressure  below  the  photic  zone   o Nutrient  poor   o Relies  on  “marine  snow”  where  decomposers  try  to  decompose  algae  and   zooplankton  from  the  photic  zone  before  they  reach  the  bottom   o Psychrotolerant/psychrophilic  and  barotolerant/barophilic  inhabitants   − Inshore  areas  are  nutrient  rich  and  have  greater  productivity   o Microbial  and  invertebrate,  fish,  etc.  occupants   − As  you  go  deeper,  more  archaea  are  present  than  bacteria     Hydrothermal  Vent  Communities   − Driven  by  geothermal  energy   − Found  in  areas  between  tectonic  plates   − Analogous  to  an  oasis   − Hydrothermal  spring:  sea  water  intrudes  into  the  ocean  floor,  mixes  with  molten  magma  in   fractures,  spurted  into  overlying  water  column   − Basalt:  molten  magma  material  bubbles  up  from  the  center  of  the  earth,  spreads  out  as  new   ocean  floor   − Warm  vent:  hot  material  laden  2ith  H S  mixes  with  sea  water,  leading  to  warm  water   o − Hot  vent/black  smoker:  hot  water  (270-­‐380 C)  laden  with  mineral  sulfides  hits  cold   oxygenated  seawater,  precipitating  out  insoluble  metal  hydroxides  and  oxides   o Forms  temporal,  sedimentary  chimney  stru cture   − Thriving  animal  and  microbial  communities   − Chemolithotrophs  act  as  primary  producers   o S  oxidizing  (Thiotrix,  Beggiatoa,  Thiobacillus )   o H 2  Fe ,  Mn  oxidizers   o Nitrifiers,  methanotrophs   − Both  freeliving  and  symbiotic  microbes   − Tube  worms  live  in  symbiosis  with  chemolithotrophs   o Trophosome:  spongy  tissue  packed  with  sulfur  granules  and  sulfur  oxidizing   bacteria  in  place  of  a  digestive  tract   o Lack  mouth,  gut,  anus   o Plume:  highly  vascularized,  contains  lots  of  blood  vessels   o O 2 2H S  dissolve  into  bloodstream,  bou nd  by  hemoglobin  and  delivered  to   trophosome  where  bacteria  grow  on  it   o CO  dissolved  in  bloodstream  provides  autotrophs  with  O  that  is  used  to  produce   2 2 organic  materials  that  support  the  worm’s  metabolic  growth   − Mussels  have  symbiotic  relationships  with  mic robes  living  in  their  guts   o Sulfur  oxidizing  bacteria  live  in  gills,  metabolize  sulfur  and  supply  nutrition  to  the   microbe   o Yellow  colour  because  of  sulfur  buildup   − Microbial  communities  that  live  under  warm  vents  are  called   snow  blowers  because  they   blow  tufts  of  bacterial  biomass  into  the  water   − Alvinella  pompejana  (Pompeii  worm)  forms  a  cooperative  relationship  with  the  bacteria  that   grow  as  long  threads  on  its  surface   o Worm  uses  bacteria  for  food,  bacteria  use  worm  as  a  useful  substrate  to  form   biofilms  on   o Found  in  tunnels  near  black  smoker -­‐heated  water  vents     Lecture  5:  The  Carbon  Cycle     Biogeochemical  Cycling   − All  biomass  consists  of  the  following  essential,  biogenic  elements:  C,  P,  H,  O,  N,  S,  K,  Ca,  Mg,  Cl,   Fe   − Elemental  cycling  often  involves  changes  in  th e  oxidation  state  of  an  element,  its  physical   characteristics,  and  metabolic  availability   o Living  organisms  contribute  to  this  through  redox  reactions     Carbon  Cycle   − Primary  production,  consumption,  decomposition:  carbon  cycle  in  a  nutshell   o Also  connected  to  oxygen  cycle;  lots  of  consumption  of  organic  material  in  restricted   area,  O2  is  depleted  and  turned  into  water,  need  oxygenic  photosynthesis  to  convert   it  back  into  O2   o Connected  with  nitrogen  cycling   − 99.5%  of  carbon  in  the  planet  is  locked  into  earth’s  cr ust,  rocks,  etc.     o Mostly  ignored  by  biologists  (although  it  does  turnover  over  long  periods  of  time)   but  geochemists  are  concerned  with  it   − Different  compartments  can  be  reservoirs   o Atmosphere:  carbon  in  the  form  of  CO2,  cycles  rapidly  in  that  reservoir,  gre enhouse   gas   o Land:  major  site  o2  CO  fixation;  soil  humus  (bulk  of  land  C)  very  slowly  biodegraded   o Oceans  (and  other  waters):  site 2of  CO  fixation,  organic  matter  decomposition;  less   influence  than  land  reservoir     o Sediments,  rock:  largest  reservoir  (99.5%),  extremely  long  turnover  time   o Source:  atmosphere,  usually   o Sink:  where  can 2CO  go  so  that  it  isn’t  in  atmosphere?  Put  it  safely  somewhere  else   so  it  doesn’t  contribute  to  global  warming;  typically  plant  biomass   − Fluxes:  the  rate  at  which  an  element  moves  fro m  one  compartment  to  another   o Usually  expressed  per  volume/amount  of  area/time  ( rates  of  movement)   − Soil  organic  matter  traps  carbon   o Humus:  organic  material  in  the  soil  derived  from  decomposing  plants  and   animals/waste  materials/soil  microbes   o Some  of  this  is  very  slow  degrading   − Restricted  amount  of  biota  due  to  limiting  factor s  (nitrogen,  phosphorous,  etc)   o Same  cycling  goes  on  there  –  lose  materials  by  sinking  down  into  sediment,   eventually  form  new  rock  over  time   − We  influence  this  as  well  by  taking  material   out  of  the  deep  subsurface   –  oil,  gas  –  and   burning  it  in  cars/furnaces   o Naturally  recycled  slowly   o Recycled  quickly  to  atmosphere  by  us   which  is  why  we  get  elevated  CO  levels  in  the   2 atmosphere  –  same  with  cutting  down  plants  so  that  they  can  no2  longer  fix  CO   levels     CO 2  Fixation   − Via  photosynthesis  (mostly)  and  chemosynthesis  (minor)   − Primary  production   o Oxygenic  photosynthesis:  higher  plants,  eukaryotic  microalgae,  cyanobacteria                  light   CO 2  + 2 H O  à2  [CH O2  +  O   − Anoxygenic  photosynthesis:  purple  and  green  sulphur  bacteria        light   CO 2  + 2  H S  à2  [CH O]  +  S   − Rate  at  which  primary  production  occurs  has  to  be  faster  than  respiration  rate   o If  this  wasn’t  the  case,  large  amounts  of  biomass  would  not  exist   o Needs  to  be  net  positive  balance  of  photosynthesis  rate  vs.   respiration  rate,  if  you   consider  the  planet  as  a  whole   o Balance  between  these  two  parts  of  the  carbon  cycle  is  critical  to  lif e     Respiration   − Occurs  in  dark  and  light  (by  organotrophs,  phototrophs,  lithotrophs)   − Takes  organic  material  and  consume  it  for  meta bolic  processes  (electron  acceptors)   − Converts  carbon  back  to  CO2   [CH O2  + 2 O  (or  alternate  electron  acceptor2  2  CO  +  H O     Decomposition   − Catabolic,  energy-­‐yielding  reactions  carried  out  by  organotrophs   − As  a  result,  photosynthetically  fixed  C  is  eventually  reminera2i, 4CH   CO   Methanotrophs:  specialize  in  metabolism  of  1-­‐C  compounds: 4  →  →2  CO  +  cells   − Can  metabolize  methane     o Oxidize  it  gradually  to  CO2   endproduct     o Get  energy  out  of  doing  that,  some  of  the  C  from  methane  is  ta ken  up  as   formaldehyde  and  used  in  biosynthesis   − Aerobes,  often  microaerophilic     o Require  oxygen,  but  prefer  to  have  lower  oxygen  tension  th an  normal  atmospheric   levels     o Gradient  organisms  because  they  often  live  at  oxic/anoxic  interface  where  the   gradients  of  available  oxygen  and  available  methane  overlap  sufficiently   o May  change  diurnally  –  methanotrophs  move  up  and  down  to  find  the  concentration   in  the  substrate  that  they    need   − methane  monooxygenase  (MMO)  catalyses  methane  →  methanol  step     Overall  Process  of  A noxic  Decomposition:   − In  the  absence  of  oxygen,  the  consortium  (whole  microbial  community)  must  function   together  to  convert  something  (like  a  tree,  for  example)  to  simple  end  products  that  can  be   recycled   − Hydrolysis  of  polymers  to  make  monomers   o Polymers  take  a  long  time  to  break  down,  but  it  does   happen   o Organic  material  does  decompose  whether  or  not  there  is  oxygen  present   − Primary  fermentation:  monomers  fermented  by  microbes  that  use  them  as  substrates  to   produce  various  end  produc ts   o  ex.  Clostridium  (strict  anaerobe,  endospore  former)  can  g row  on  cellulose  –   cellulitic     o Others  grow  on  carbohydrates,  proteins   –  produce  extracellular  enzymes  to  break   polymers  into  monomers  and  ferment  them  to  end  products   − Secondary  fermentation  (H -­2producing  fatty  acid-­‐oxidizing  syntrophs)   o Lactic  acid  bacteria  (streptococcus,  lactobacillus)  don’t  have  hydrolytic  enzymes;   rely  on  clostridium  to  produce  monomers,  then  ferment  them  to  make  lactic  acid   o Sugar  (glucose)  à  lactic  acid  –  done  by  lactic  acid  bacteria   o Yeast  à  alcohol  can  also  occur  at  this  point,  produces  ethanol  as  an  end  produc ts   o some  volatile  organic  acids  can  be  produced  as  end  products  (acetic  acid)   − H 2  mption  by  methanogenesis  and  acetogenesis   o Methanogens  have  a  narrow  range  of  substrates,  can  use  methanol,  methyl  sulfate,   formate,  alcohol,  ethanol  –  no  more  than  12-­‐15  compounds  long   o To  live,  they  rely  on  other  organisms  to  process  this  material  into  substrates  that   they  can  use  (secondary  fermenters  /  syntr ophs)   − With  all  four  of  these  groups  working  together,  the  organic  molecules  (tree)  can  be   converted  to  simple  inorganic  molecules  (CO2,  H2S,  methane)  and  microbial  biomass   o Sugar,  amino  acid,  FA  fermentation  provides  substrate  for  syntrophs     o Syntrophs  can  only  operate  i2  H  level  is  low;  rely  on  methanogenic  activity  to   maintain  low  partial  pressure   o Syntroph  activity  is  critical  to  provide  substrate  for  methanogens,  homoacetogens     Interspecies  H 2  Transfer:  a  Syntrophic  Reaction   − Syntrophy:  two  organisms  working  together  can  accomplish  something  that  neither  can   alone   − Ethanol  fermentation:     2  C3 CH 2H  +  22  H O  2  4 3H  +  2  CH COO  +  2  H                  ∆G  =  +  19.4  kJ/reaction   − Methanogenesis:   0 4 2H  +2  CO 4 à  2H  +  2   O                     ∆G  =  -­‐  130.7  kJ/reaction   − Coupled  reaction:     -­‐ +   0 2  C3 CH 2H  +  2    4    2 3  CH COO  +  2            ∆G  =  -­‐  111.3  kJ/reaction   −  ∆G  values  are  Gibbs  Free  Energy  values  under  standard  c onditions  (1M  /  1  atm)   o When  number  is  negative,  it  is  an  energy  generating  reaction  so  the  organism  can   grow  there  (use  that  energy  to  make  ATP)   o When  energy  is  positive,  their  habitat  is  not  under  standard  conditions   0 o Concentration  of  hydrogen  is  typically   10-­‐4  atm  or  lower  (not  1  atm),  so  the  real  ∆G   is  negative;  it  is  an  energy  generating  reaction  as  long  as  there  is  something  there  to   take  away  hydrogen  like  a  methanogen   o Quickly  removing  hydrogen:  pulling  reaction  to  the  right,  shifting  equilibrium   –   energy  producing  reaction  as  long  as  methanoge ns  are  there  to  use  up  hydrogen     Example  of  other  reactions  that  occur  during  anoxic  decomposition  reactions :   − Fermentation  of  glucose:   glucose  +  42 O  →  2  acetate  +3  2HCO  + 2      +  4H − Glucose  can  be  fermented  to  produce  acetate  +  bicarbonate  +  H ,  not  just  alcohol  +  CO  or   2 2 ethanol  +  C2   − Interspecies  hydrogen  transfer  (as  seen  in  the  syntrophic  example)   − Methanogenesis  by  acetotrophic  methanogens   acetate +  H 2  →  C4  + 3HCO        − Acetogenesis  from  homoacetogens   4 2H  +  23  HCO  +  H  →  a2etate    4H O     The  Rumen:  A  Methanogenic  Ecosystem   − Cows,  sheep  are  called  ruminant  animals  and  have  a   different  digestive  system  than  we  do     − Eat  vegetable  matter  but  do  not  have  the  enzymes  required  to  break  them  down     o Require  their  rumen,  which  is  filled  with  methanogens,  to  pr ocess  their  food  into   materials  that  the  cow/sheep  can  actually  use     − Rumen  is  essentially  a  very  large  (100-­‐150L  in  volume),  highly  anaerobic  microbial   community  that  undergo  primary  and  secondary  fermentation  to  produce  volatile  f atty   acids,  alcohols,  etc.   o Methanogenesis  occurs,  producing  methane     o Supplies  the  cow  with  endproducts  that  it  can  metabolize   − Cow  chews  cud,  mixes  with  saliva  –  reswallow  it,  goes  into  rumen  of  slurry  of  saliva  and   particulate  matter,  forms  ruminal  content   o Ton  of  microbes  (protozoa,  bacteria,  archaea,  yeast,  microfungi)     o Can  have  10^10  /  10^11  microbes/g  of  ruminal  content     o Some  grazing  protozoa  keep  the  size  of  this  community  under  control   –  when  it  gets   too  big,  some  spill  over  into  the  rest  of  the  cow’s  digestive  system     o Omasum  equivalent  to  stomach,  digests  microbial  biomass  to  release  peptides,   amino  acids,  provides  N  to  cow   − Volatile  fatty  acids  are  pulled  off  into  the  cow’s  bloodstream ,  absorbed  by  vascularization,   shipped  to  cow  cells,  oxidized  to  produce  energy  and  carbon  (from  propionate)   − Nonvolatile  are  worked  on  by  syntrophs,  which  aren’t  as  important  her e  as  in  other  anoxic   habitats   o Still  need  to  process  other  materials  though  (like  grass)   − Makeup  of  microbial  community  changes  as  diet  changes     o Gas  buildup  causes  farmyard  bloat,  rumen  expands  and  the  cow  can’t  burp  it  out   –   can  sometimes  crush  important  organs  like  lungs,  killing  the  cow   –  fix  this  by   stabbing  through  to  rumen  to  release  gas   o Acid  buildup  decreases  the  pH  and  causes  the  microbial  community  to  stop  working     Vertebrate  Digestive  Systems   − In  cattle,  sheep  rumen  comes  before  rest  of  digestive  tract   − Other  herbivores  (rabbit,  mice)  have  hindgut  fermentation     o Happens  after  stomach  and  small  intestine  in  cecum,  which  has  microbial   community  to  process  material   − Omnivores  are  colonic  fermenters   o Large  intestine  has  microbial  community  that  contributes  to  digestion     o Technically  could  live  without  them  but  don’t     o Contribute  ~10%  of  nutrition     Paddy  field:  where  rice  is  grown   − There  is  a  nice  anoxic  community  down  by  the  roots   − Over  time,  water  used  as  rice  grows  to  support   growth,  eventually  disappears   o Until  that  happens,  a  lot  of  methane  is  produced  and  released  into  the  atmosphere     Lecture  6:  Nitrogen  and  Sulfur  Cycling     Nitrogen  Cycle   C 106 263O 110N 16  –  an  empirical  formula  for  biomass  (marine  algal  cells)   − N  is  a  key  component  of  biomass   − The  atmosphere  is  the  major  reservoir  of  2  (75 -­‐80%  N ),  but  this  form  of  nitrogen  cannot  be   used  by  most  organisms   − The 2N  fixation  (nitrification)  conducted  by  relatively  few  prokaryotes  is   critical  to  other   organisms   o Done  by  a  few  bacteria,  a  few  Archaea   o ex.  Rhizobium  in  leguminous  plants   − Within  terrestrial  and  aquatic  environments  there  is  much  recycling  of  the  more  easily   available  forms  of  N  (ammonia,  nitrate)     o Released  through  decomposition,  taken  back  up  through  assimilation,   reincorporated  into  biomass  again  and  again   o Eventually  denitrification  occurs  and  cycles  N  back  into  atmosphere   (anammox   process)   − N  is  lost  back  to  the  atmosphere  via  d3nitrif2cation  (NO  →  N )   o Denitrification  is  carried  out  by  a  number  of  microorganisms,  most   of  which  are   facultative  aerobes   − Many  microorganisms  can  ammonify     Nitrogen  Fixation   + -­‐ − Overall  reaction:  8  H  2  8  e3  2  N  à  2  NH  +  H   − Nitrogenase  enzyme  is  made  up  of  two  proteins:  dinitrogenas e  reductase  and  dinitrogenase   − Overall  reaction  takes  N2  and  convert s  it  to  N3  (ammonia  molecules)   o All  of  this  happens  on  this  enzyme  complex   o Intermediates  are  never  free,  just  associated  with  the  protein   − Hydrogen  also  produced,  no  one  really  understands  why   –  requires  electrons  (theoretically   6,  but  in  reality  8  because  2  go  to  make  H2),  also  requires  protons,  lots  of  energy  (16 -­‐24   ATP)  to  carry  out  reaction   − Genes  to  code  for  this:  Nif  genes  (nitrogen  fixation)   − Electron  shuttle  proteins  takes  reduced  electrons,  passes  them  off  to  reductases     o shuttle  proteins  reoxidized   o reductase  is  reduced,  eleectrons  passed  onto  dinitrogenase   o reductase  reoxidized     o series  of  redox  reactions   − Needs  a  lot  of  ATP   o Conformation  change  in  dinitrogenase  reductase   lowers  its  redox  potential  so  that  it   is  capable  of  passing  electrons  on  to  dinitrogenase   − Electrons  come  down  the  chain  one  at  a  time,  used  to  reduce  m olecular  nitrogen  to  ammonia   o Intermediates  are  not  free,  found  up  in  enzyme   − Very  highly  regulated  protein   o If  the  cell  doesn’t  need  to  fix  nitrogen  because  it’s  available,  it  doesn’t     o Process  is  quite  sensitive  to  the  presence  of  O2   o Can  inactivate  the  protein,  shut  down  transcri ption  of  nitrogenase  complex   o Same  with  presence  of  combined  nitrogen  (nitrate,  certain  amino  acids)   − Some  post-­‐translational  control   o Ammonia  switch  off  effect:   ammonia  combines  to  the  reductase,  shuts  down  activity   of  the  nitrogenase   o When  concentrations  of  ammonia  deplete,   it  binds  in  a  reversible  way   o Comes  off,  complex  turns  back  on   o Cell  does  this  to  conserve  energy     Examples  of  nitrogen-­‐fixing  microorganisms:   − Symbiotic   o Legume-­‐rhizobia  symbioses:  soybeans,  clover,  alfalfa,  etc.  with  a  bacterium  of   genera  Rhizobium,  Bradyrhizobium,  Sinorhizobium,  Azorhizobium   o nonleguminous  plants:  Alnus  (alder)  and  others  with  members  of  the   genus  Frankia   (Actinobacteria)   − Free-­‐living  aerobes   o chemoorganotrophs  including  Azotobacter,  Klebsiella,  Methylococcus  and  others   o phototrophs:  many  Cyanobacteria   o chemolithotrophs:  Alcaligenes,  some  Thiobacillus  and  others   − Free-­‐living  anaerobes   o chemoorganotrophs  including  Clostridium,  Desulfovibrio   o phototrophs  including  Chromacium,  Thiocapsa,  Chlorobium,  Rhodospirillum   o chemolithotrophs:  Methanosarcina,  Methanococcus  and  other  methanogens   (Archaea)   − Anaerobes  don’t  have  to  worry  about  protecting  nitrogenase  fro m  O2  inactivation   –  there  is   no  oxygen  present  in  these  environments   − Means  of  protecting  nitrogenase  from  inactivation  by   oxygen:     o Azotobacter  is  a  freeliving  aerobe  that  makes  a  lot  of  slime   to  help  control  the   diffusion  of  O2  into  the  cell  itself,  uses  O 2  very  quickly,  stabilizing  protein  wrapped   around  nitrogenase  complex  prevents  inactivation   o Filamentous  cyanobacteria  photosynthesize  in  daylight,  use  O2  in  dark   –  N2  fixation   then  (temporal  separation);  have  specialized  cells  to  fix  N2  (heterocysts)   o Leghemoglobin  within  bacteroids  of  N -­‐fixing  nodules  (rhizobia-­‐legume  symbiosis)   2 functions  the  same  way  as  ours  –  binds  O2,  used  to  deliver  O2  to  rhizobia  in  a   controlled  way  to  protect  nitrogenase     Heterocysts:  modified  cells  found  in  certain  filamentous  cyan obacteria  (e.g.,  Anabaena)   − Lack  photosystem  II  (&  thus  do  no2  produce  O ),  but  possess  nitroge2ase  &  can  conduct  N   fixation     − Thick-­‐walled  cells   − Proteins  responsible  for  running  photosystem  II  degrade,  a ren’t  there,  no  O2  production   − Run  photosystem  I  to  ge t  electrons  to  drive  nitrogenase  –  end  up  with  induction  of   nitrogenase  genes   − N2  fixation,  produces  ammonia  which  is  quickly  bound  up  into  nitrogen -­‐rich  compounds  like   amino  acids  (glutamine,  asparagine,  ureides);   other  cells  are  producing  photosynthates  like   O2   − N2  from  heterocysts  shipped  to  other  cells  so  that  they  can  run  their  metabolism     Symbiotic  N2  fixation   − Steps  in  the  formation  of  a  root  nodule  in  a  legume  infected  by   Rhizobium   − Important  in  industrial/agricultural  sense   o Plants  are  legumes,  can  have  this  relationship   o Farmers  don’t  have  to  fertilize  those  fields  (plant/microbe  association  fixes  its  own   nitrogen)   o Crop  rotation  trick  used  to  replenish  soil   − Ecological  sense:  pioneering  trees   o Legumes  and  alder  trees  can  exploit  and  grow  successfully  in  N2  poor  soil  if  they   have  a  Rhizobium  bacteria   − Legume:  a  plant  that  produces  its  seeds  in  pods   –  1000s  to  10000s  of  them   o ex.  Peas,  clover,  alfalfa,  soybeans   − Cross-­‐inoculation  –  particular  bacteria  can  only  inter act  with  a  particular  legume   o Rhizobium  variant  that  interacts  with  pea  plants  won’t  interact  with  clover  plants,   etc.   − Roots  in  soil  release  flavonoids   that  attract  Rhizobia  to  the  plant  root  hair   o receptors  on  the  bacterium  and  plant  root  hair  recognize  one  another,  att achment,   signaling  all  occur   o Flavonoids  induce  nod  genes  (for  nodulation)  that  bacteria  produces,  produce s   enzymes  to  make  nod  factors   o Signaling  molecules  that  tell  the  plant  what  to  do:  root  hair  curls  around  bacteria   forming  a  shepherd’s  crook,  bacteria  start  to  colonize  it,  plant  will  start  to  form   infection  thread  (plant  material,  made  on  demand  by  bacterium)   o Bacteria  start  to  grow  up  infection  thread,  expands  to  root  cortex  amongst  plant   cells,  bacteria  invade  plant  cells   o nod  factors  tell  plant  cells  to  grow  and  divide  to  form  a  root  n odule  of  plant  material   containing  rhizobial  cells     o Rhizobia  will  then  begin  to  differentiate:  lose  cell  wall,  become  swollen  into  weird   shapes,  become  “bacteriods”  that  can’t  replicate  (terminal  differentiation)   o Induction  of  nitrogenase  occurs,  N2  fixation     Major  metabolic  reactions  and  nutrient  exchanges  occurring  in  bacteroids   − Bacteroids:  rhizobial  cells  transformed  into  swollen,  misshapen,  branched  shapes  within   the  plant  cell;  possess  nitrogenase  activity;  incapable  of  cell  division   − Symbiosome:  bacteroids  (singly  or  small  groups)  surrounded  by  portions  of  plant  cell   membrane   o N2-­‐fixation  begins  after  symbiosome  formation   o Plant  provides  bacterium  carbon  sources  so  that  it  can  metabolize,  run  nitrogena se   (C4  dicarboxylic  acids  delivered   –  ex.  Fumarate,  succinate,  malate  –  TCA  cycle   components)   o Shipped  involving  transport  systems  (one  plant  derived,  o ne  bacterial  derived)   enabling  bacteroid  to  produce  ATP  and  electrons  to  run  nitrogenase,  metabolism,   etc.     o N2  fixed  to  ammonia,  which  is  then  shipped  out  to  th e  plant  and  incorporated  into   organic  nitrogen  forms  (glutamine,  aspartate,  etc.)   − Leghemoglobin:  O -­2binding  protein;  supplies 2  O  to  the  bacteroid  cell  membrane  where  the   electron  transport  chain  is  and  protects  nitrogena2e  from  O -­‐inactivation   o Synthesis  requires  input  from  the  plant  and  the  bacterium     Ammonification:  production  of  ammonia  during  the   decomposition  of  organic  nitrogen   compounds   − conducted  by  wide  range  of  aerobes,  anaerobes   o R-­‐NH2  à 3  NH 4  (NH )   o e.g.,  proteolysis  →  amino  acid3  →  NH  release   − NH 3  (ammonia)  is  a  water-­‐soluble  gas  that  picks  up  a  proto4  and  becomes  NH  when  it  is   dissolved   o Equilibrium  between  those  matters  in  oxic  conditions  and  animal  feed  lots  (manure)   o In  alkaline  conditions,  shifts3  to  NH   − Oxic  conditions:     o Some  NH3  volatilization  to  atmosphere  (favoured  by  dry,  alkaline  soil)   o Assimilation  by  plants,  microorganisms;  production  of  new  biomass   o NH 4  subject  to  nitrification     − Anoxic  conditions:     + o NH 4  tends  to  be  stable  and  persist  (builds  up)   o Exception:  “anammox”  –  anoxic  ammonia  oxidation;  occurs  in  some  ammonia-­‐rich   habitats  such  as  sewage     Nitrification:  conducted  in  well-­‐drained,  neutral  pH  soils,  aquatic  environments   −  Aerobic,  chemolithotrophic  energy  metabolism   −  Two  groups  of  microorganisms  acting  in  sequence  (two-­‐step  process)   −  Addition  of  high-­‐protein  materials  to  soil  (manure,  sewage)  tends  to  encourage  nitrification   o Ammonification  occurs  first   + -­‐   − NH 4  à  2O (ammonium  oxidizers  or  nitrosofiers)   o Ammonium  ion  à  nitrite   o Nitrosomonas   o Need  2  as  terminal  electron  acceptor     − NO 2  à  3O­‐ (nitrite  oxidizers)   o Nitrite  à  nitrate   o Nitrospira   − Ammonium  oxidizing  Archaea   have  been  discovered  recently ,  but  not  nitrite  oxidizers     Anammox:  (anoxic  ammonia  oxidation)   − Relatively  recent  discovery;  we’re  still  learning  about  it   − First  seen  in  wastewater  treatment  plants  with  high  ammonia  waste,  but  it  also   occurs  in   oceanic  water  column,  marine  sediments   − Ecologically  important  because  it  retur2s  N  back  to  atmosphere   − Anammox  reaction  likely  controlled  b2  O  concentration,  which  affects  nitrite  availability     − Nitrite  comes  from  nitrification  in  a  lot  of  cases   o O 2  gradient  /  oxic-­‐anoxic  interface   o Nitrite  supplied  to  allow  anammox  location  to  occur  nearby   o Potentially  comes  from  denitrification  in  marine  environments   − Brocadia  anammoxidans  (Planctomycetes):  anaerobe  able  to  oxidize  ammonia,  using  nitrite   as  electron  acceptor,  producing  dinitrogen  gas:   + -­‐     NH 4  +  2O
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