Environmental

 Microbiology  (BI  304):  Lecture  4  

Biogeochemical  Cycling  
Instructor:  Dr.  Nalina  Nadarajah  
Email:  nnadarajah@centennialcollege.ca  
Biogeochemical  Cycles  (Chapter  16)  
ObjecEve:  To  demonstrate  and  understand  the  carbon  and  
nitrogen  cycles,  including  their  significance  in  terms  of  the  
environment,  and  the  roles  of  microbes  in  each  cycle  

Agenda:  
–  IntroducEon  to  Biogeochemical  Cycles  
–  The  Carbon  Cycle  
–  The  Nitrogen  Cycle  

2  
Introduc:on  to  Biogeochemical  Cycles  
•  Biogeochemical  Cycle:  a  circuit  or  pathway  by  which  a  
chemical  element  or  molecule  moves  through  both  bioEc  
("bio-­‐")  and  abioEc  ("geo-­‐")  compartments  of  an  
ecosystem    

•  All  major  elements  found  in  biological  organisms  are  

cycled  

•  Understanding  these  cycles  allows  us  to  understand  and  

predict  the  development  of  microbial  communiEes  in  the  
environment  

 
3  
Chemical  Composi:on  of  an  E.  coli  Cell  
Elemental   %  dry  mass  of  an   E.g.  Func:on  
Breakdown   E.coli  cell  
Major  Elements  
Carbon   50   Building   blocks   of  
Oxygen   20   all  macromolecules  
Hydrogen   8  
Nitrogen   14   Proteins,  nucleic  acids  
Sulfur   1   Amino  acids,  vitamins  
Phosphorus   3   Nucleic  acids,  ATP  
Minor  Elements  
Potassium   2   OsmoEc  control  
Calcium   0.05   Cell  wall  stability  
Magnesium   0.05   Enzyme  cofactor  
Sodium   1   OsmoEc  control  
4  
 The  Gaia  Hypothesis  
•  Originated  by  James  Lovelock  in  1970’s  (co-­‐developed  by  
the  microbiologist  Lynn  Margulis)  

•  The  earth  is  a  super-­‐organism  and  can  respond  to  drasEc  

environmental  changes  

•  “Living  organisms  and  their  material  environment  are  

Eghtly  coupled.  The  coupled  system  is  a  super-­‐organism,  
and  as  it  evolves  there  emerges  a  new  property,  the  
ability  to  self-­‐regulate  climate  and  chemistry”  

5  
 Comparing  Planetary  Atmospheres  
Current  
Earth  w/o  
Gas   Venus   Mars   Earth  with  
life  
Life  
CO2   96.5%   95%   98%   0.03%  
N2   3.5%   2.7%   1.9%   78%  
O2   trace   0.13%   0.0%   21%  
Ar   70  ppm   1.6%   0.1%   1%  
CH4   0.0   0.0   0.0   1.7  ppm  
Surface  
459   -­‐53   290   14.8  
Temp.  (°C)  

•  According  to  the  Gaia  hypothesis,  development  and  

conEnued  presence  of  life  on  earth  is  responsible  for  the  
drasEc  changes  in  our  atmosphere  
6  
 How  Did  This  Change  Happen?  
•  Microbial  and  plant  acEvity  changed  the  heat-­‐trapping  CO2-­‐
rich  atmosphere  to  the  present:  O2  rich,  CO2  poor  one  

•  Allowed  the  earth’s  average  surface  temperature  to  

decrease  from  290oC  to  14.8oC    

7  
 Development  of  the  Carbon  Cycle  
•  ~  3.8  billion  years  ago,  organic  carbon  was  formed  by  large  
amounts  of  UV  light  reacEon  with  the  CO2  rich  atmosphere  
•  Organic  maeer  used  by  early  heterotrophs  
•  Followed  by  the  ability  of  microbes  to  fix  CO2  
photosyntheEcally  (~3.5  billion  years  ago)  
–  evidence  from  Stromatolites  
–  provided  a  mechanism  for  carbon  recycling  
•  ~  2.8  billion  years  ago  photosyntheEc  microbes  developed  
ability  to  produce  O2  
–  led  to  the  change  in  atmosphere  (accumulaEon  of  O2)  
–  the  development  of  the  ozone  layer    
–  the  development  of  higher  forms  of  life   8  
How  Do  Biogeochemical  Cycles  Relate  To  
The  Gaia  Hypothesis?  
•  Consider  the  basic  Carbon  cycle:  

Autotrophs

Organic
CO2
Carbon

Heterotrophs 9  
 If  Earth  is  a  Superorganism  
•  it  should  be  able  to  respond  to  the  environmental  
changes  
•  why  do  we  see  increasing  environmental  disasters  all  
over  the  world?  

10  
Global  Warming  and  Greenhouse  Gases  
•  The  troposphere  (Earth’s  lower  atmosphere,  up  to  15  km  
thick)  consists  of  a  blanket-­‐like  layer  of  gases  keeping  Earth  
warm  
•  TradiEonally  major  gases  contribuEng  to  heat  storage  were  
H2O  (67%)  and  CO2  (33%)  
•  But  during  last  century,  several  natural  and  syntheEc  gases  
in  troposphere  have  increased  –  resulEng  in  increased  heat  
trapping  
–  natural:  CO2,  methane  (CH4),  nitrous  oxide  (N2O)  
–  syntheEc:  chlorofluorocarbon  (CFC),  trichlorofluoromethane  
(CFC-­‐11;  freon;  CCl3F)  
11  
 Greenhouse  Effect  

Animation 12  
www.combatclimatechange.ie
Why  Biogeochemical  Cycles  Go  Wild?  
•  Remained  stable  for  millions  of  years  
•  Growing  need  for  food  and  energy  has  interfered  
–  formaEon  of  GH  gases    

•  Global  Warming  à  Climate  change  

13  
Why  Biogeochemical  Cycles  Go  Wild?  
•  Remained  stable  for  millions  of  years  
•  Growing  need  for  food  and  energy  has  interfered  
–  formaEon  of  GH  gases    
•  Major  greenhouse  gases  are  the  subject  to  the  Kyoto  Protocol  
–  CO2,  CH4,  N2O  and  three  groups  of  fluorinated  gases    
•  sulfur  hexafluoride  (SF6),  Hydrofluorocarbons  (HFC)  and  
perfluorocarbons  (PFC)  

30  
 Canada  and  the  Kyoto  Protocol  
•  Kyoto  Protocol  established  in  1997  
•  Canada’s  target:  6%  reducEon  in  GHG  by  2012  (compared  to  1990  
levels)  
•  between  1990  and  2008  –  Canada’s  GHG  emission  increased  by  24%  
•  change  of  government  a  factor  (Liberal  Govt.  in  1997;  ConservaEve  
Govt.  from  2006  -­‐  2015)  
•  dramaEc  rise  in  GHG  in  2007  

•  2011  UN  Climate  Change  Conference  in  Durban,  S.A.  –  Canada  

announced  its  formal  withdrawal  from  Kyoto  Accord  as  of  2012  
•  Minister  of  Environment  –  Peter  Kent  (2011):  "The  Kyoto  Protocol  
does  not  cover  the  world's  largest  two  emieers,  United  States  
and  China,  and  therefore  cannot  work"    
 Canada  and  the  Kyoto  Protocol  
•  Canada  has  the  world's  third-­‐largest  oil  reserves  
–  ConservaEve  government  is  reluctant  to  hurt  Canada's  
booming  oil  sands  sector  
•  Canada's  overall  greenhouse  gas  (GHG)  emissions  
–   oil  &  gas  and  transportaEon  
•  Canada  is  one  of  the  largest  per  capita  greenhouse  gas  polluter  
 Latest:  Paris  Agreement  
•  December  2015  in  Paris,  France  
•  195  countries  signed  –  including  USA,  China,  Canada  &  India  
(13  countries  (incl.  Russia,  Iran,  Iraq,  Turkey  remain  yet  to  
raEfy)  
•  Former  US  President  Donald  Trump  announced  U.S.  would  
cease  all  parEcipaEon  in  the  Paris  Agreement  
•  Current  US  President  Joe  Biden  has  requested  UN  on  
rejoining  the  Paris  Agreement  
 Latest:  Paris  Accord  
•  December  2015  in  Paris,  France  
•  195  countries  signed  –  including  USA,  China,  Canada  &  India  
–  On  June  1,  2017,  USA  announced  its  withdrawal  by  2020  

•  Canada  commieed  to  emissions  targets  of  17%  reducEon  

from  2005  levels  by  2020  and  30%  by  2030  
•  How  do  we  achieve  this  goal?  
–  carbon  tax  
•  Canada  will  impose  a  tax  on  carbon  emissions  starEng  in  2018    

–  cap-­‐and-­‐trade  
Why  Biogeochemical  Cycles  Go  Wild?  
•  Remained  stable  for  millions  of  years  
•  Growing  need  for  food  and  energy  has  interfered  
–  formaEon  of  GH  gases    
•  Major  greenhouse  gases  are  the  subject  to  the  Kyoto  Protocol  
–  CO2,  CH4,  N2O  and  three  groups  of  fluorinated  gases    
•  sulfur  hexafluoride  (SF6),  Hydrofluorocarbons  (HFC)  and  
perfluorocarbons  (PFC)  
•  AcEviEes  releasing  greenhouse  gasses:  
–  burning  of  fossil  fuels  and  deforestaEon  –  CO2    
–  manure  management,  paddy  rice  farming,  wetland  changes,  and  
covered  vented  landfill  emissions  –  CH4  
–  over  use  of  ferElizers  –  N2O   39  
Global  Atmospheric  Concentra:on  of  
Selected  GH  gasses  
Microbially  mediated  &  Anthropogenic  
Anthropogenic  Only    (ppt)  
(ppm)  

Sulfur  
CO2   CH4   N2O   CFC  
hexaflouride  (SF6)  

Pre-­‐industrial   278   0.700   0.275   0   0  

2004   377   1.789   0.319   5.22   794  

Atmospheric  
Life  Time     50-­‐200   12   114   3200   45-­‐100  
(in  years)  
40  
Source: Table 31.1 from Text
 Comparison  of  Various  Gases  on  

Source: Environmental Microbiology By Masden, E. Box 7.1, p.291

Greenhouse  Effect  
Type  of  Gas   Contribu:on  Rela:ve  to  CO2  to  GH  Effect  

CO2   1  

CH4   25  

N2O   200  

Ozone   2  000  

CFC-­‐11  (freon)   12  000  

CFC-­‐12   15  000  

41  
 Carbon  Cycle  
•  Reservoir:  sink  or  source  of  an  element  
•  Global  carbon  reservoirs  include    
–  carbonate  rock  in  the  earth’s  crust  (1.2  x  1017  metric  tons)  
–  DOM  &  POM  in  oceans  (2.1  x  1012  metric  tons)  
–  CO2  in  the  atmosphere  (6.7  x  1011  metric  tons)  
•  The  atmospheric  reservoir  is  most  accessible  and  most  
ac:vely  cycled  
•  This  cycle  is  parEcularly  sensiEve  to  human  acEvity;  the  
last  100  years  has  seen  a  28%  increase  in  atmospheric  CO2  
•  This  increase  is  responsible,  in  part,  for  the  Greenhouse  
Effect  and  global  warming  
43  
 •  Global  Carbon  Cycle  
Carbon  Cycle  AnimaEon  

44  

Photo Source: Windows to the Universe; Animation: Environmental Science, Toward a Sustainable Future, 9th ed. by Richard T. Wright
 Carbon  RespiraEon  
•  CO2  fixed  into  organic  compounds  is  consumed  by  
animals  &  heterotrophic  microbes    
–  end  products  of  respiraEon  are  CO2  and  new  cell  mass  
•  More  complex  carbon  cycle  includes  anaerobic  acEvity  
–  fermentaEon  &  methanogenesis  
Aerobic Anaerobic
Fossil fuels
Photosynthesis Fermentation

CO2 + H2O O2 + CH2O CH2O Alcohols, acids,

H2 + CO2

Respiration Methanogenesis

CH4 45  
Source: Figure 14.3 from text
 Organic  Polymers  
•  Most  common  organic  carbon  in  the  environment  are  
plant  polymers,  polymers  used  in  bacterial  and  fungal  
cell  walls,  arthropod  exoskeletons  
•  Form  the  basic  food  supply  that  supports  heterotrophs  
•  3  most  abundant  are  cellulose,  hemicellulose  and  lignin  

Plant  component   %  dry  mass  of  plant  

Cellulose   15-­‐60  
Hemicellulose   10-­‐30  
Lignin   5-­‐30  
Protein  and  nucleic  acids   2-­‐16  
46  
Table 16.6 from Text
 Cellulose  
•  Most  abundant  polymer  found  on  Earth  
–  make  up  the  woody  structures  of  plants  
•  Consists  of  linear,  β-­‐1,4  linked  glucose  subunits  (1000  –  
10,000;  MW:  1.8  x  106  g/mol)  
•  Large  and  insoluble  molecule,  must  be  par:ally  degraded  by  
extracellular  microbial  enzymes  (β-­‐1,4-­‐endoglucanase  and  
β-­‐1,4  –exoglucanase  aka  cellulases)  before  it  can  be  taken  
up  and  used  by  bacteria  

47  
 Hemicellulose  
•  Second  most  common  plant  polymer  
•  Branched  and  more  heterogeneous  
–  made  from  a  mixture  of  several  monosaccharides  including  
various  hexoses,  pentoses  (~  200  monomers)  &  uronic  acids  
–  E.g.  pecEn  
•  DegradaEon  similar  to  cellulose;  more  enzymes  involved  
 

Fig. 16.6 from Text 48  

 Lignin  
•  Third  most  common  plant  polymer  
•  Building  blocks  are  randomly  polymerized  tyrosine  &  phenylalanine  
•  Strengthens  cell  wall  and  improves  pathogen  resistance  
•  BiodegradaEon  is  slower  and  less  complete  than  for  other  polymers  
•  Extreme  heterogeneity  makes  evoluEon  of  specific  degradaEve  
enzymes  difficult  
–  broken  down  somewhat  
into  smaller  subunits  by  
H2O2-­‐dependent  lignin  
peroxidase  
–  free-­‐radicals  generated  
help  break-­‐down  
–  subunits  taken  up  by  
microbes  (white  rot  fungi)  
and  degraded  
49  
 Methane  
•  Formed  mostly  by  microbes  in  an  anaerobic  process  called  
methanogenesis    
–  By  methanogens  (obligatory  anaerobic  archae)  
–  e.g.  Methanobacterium,  Methanobrevibacter,  Methanococcus  
4H2  +  CO2                    CH4  +  2H2O        auto  or  heterotrophic?  
•  Occurs  in  specialized  environments  like  wetlands  and  paddy  
fields,  landfills  and  in  the  rumen  gut  
•  ContribuEon  to  global  carbon  cycle,  though  emission  is  of  
environmental  concern  
–  Greenhouse  gas;  25  Emes  more  effecEve  than  CO2  at  trapping  heat  
–  Explosive;  generaEon  in  landfill  sites  must  be  managed  (i.e.  vented)  
50  
Estimates of methane released into the atmosphere
Source Methane emission
(106 metric tons/year)
Biogenic
Ruminants 80 - 100 ü 
Termites 25 - 150
Paddy fields 70 - 120 ü 
Natural wetlands 120 - 200
Landfills 5 - 70 ü 
Oceans and lakes 1 - 20
Tundra 1-5

Abiogenic
Coal mining 10 - 35 ü 
Natural gas flaring and venting 10 - 35
ü 
Industrial and pipeline losses 15 - 45 ü 
Biomass burning 10 - 40
Methane hydrates 2-4
Volcanoes 0.5
Automobiles 0.5 ü 

Total 349 - 820

Total biogenic 302 - 665 81 - 86% of total
Total abiogenic 48 - 155 13 - 19% of total
Anthropogenic 190 – 405 54 - 49% of total
 Methane  Oxida:on  
•  Methanotrophs  (a.k.a  methanophiles)  are  a  group  of  bacteria  
that  have  developed  the  ability  to  use  methane  as  a  source  of  
carbon  and  energy  
•  Chemoheterotrophic  and  aerobic  
–  Methylococcaceae  and  Methylocystaceae  
methane
monooxygenase
CH4 + O2 CH3OH HCHO HCOOH CO2 + H2O
methanol formaldehyde formic
  acid

•  A  new  bacterium  Methylomirabilis  oxifera  was  idenEfied  that  

can  couple  anaerobic  oxida:on  of  methane  to  nitrite  reducEon  
 
Nature. 2006 Apr 13;440:918-21. A microbial consortium couples anaerobic methane oxidation to denitrification.
Raghoebarsing AA, Pol A, van de Pas-Schoonen KT, Smolders AJ, Ettwig KF, Rijpstra WI, Schouten S, Damsté JS, Op den Camp HJ, Jetten MS, Strous M.
Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, Netherlands.
52  
 Methane  Monooxygenase  
•  First  enzyme  idenEfied  as  able  to  
cometabolize  highly  chlorinate  
solvents  like  trichloroethylene  (TCE)  

•  Nonspecific  enzyme  able  to  oxidize  

both  methane  and  TCE  

•  Subsequent  steps  in  degradaEon  are  

either  spontaneous  or  catalyzed  by  
other  bacteria  

•  Working  on  strategy  to  use  

methanotrophs  in  bioremediaEon  of  
contaminated  groundwater   53  
 The  Nitrogen  Cycle  
•  Best  studied  and  most  complex  of  the  mineral  cycles  
•  Nitrogen  is  the  mineral  nutrient  in  most  demand  by  
microbes  and  plants    
•  4th  most  common  element  in  cells  (12-­‐14%  of  dry  weight)  
•  Stable  valences  from  -­‐3  (NH3+)  to  +5  (NO3-­‐)  
–  occurs  in  numerous  oxidaEon  states  

•  Cycle  includes  microbially-­‐catalyzed  processes  of  

nitrogen  fixaEon,  ammonificaEon,  nitrificaEon  and  
denitrificaEon  

57  
Development  of  the  Nitrogen  Cycle  
•  Nitrogen  cycle  emerged  because  nitrogen  was  a  limiEng  
element  for  microbial  growth  

•  N2  was  abundant  in  the  atmosphere,  but  inaccessible  

–  cells  need  organic  N  or  reduced  inorganic  N  

•  Some  microbes  developed  the  ability  to  fix  N2  into  

organic  nitrogen  needed  for  growth  of  other  microbes  

–  using  the  enzyme  nitrogenase  

–  using  the  reducing  atmosphere  found  in  early  Earth  

56  
 •  Nitrogen  Cycle  
Nitrogen  Cycle  

58  

Photo: http://en.wikipedia.org/wiki/File:Nitrogen_Cycle.svg; Animation: Environmental Science, Toward a Sustainable Future, 9th ed. by R. T. Wright
 Nitrogen  Reservoirs  
•  Large  Reservoirs    
–  largely  inaccessible  and  not  acEvely  cycled  
•  N2(g)  in  atmosphere  (78%)  
–  conEnually  released  from  volcanic  and  hydrothermal  erupEons  
•  bound  ammonium  in  the  Earth’s  crust  
 

•  Small  Reservoirs  
–  acEvely  cycled  
•  organic  nitrogen  found  in  living  biomass  and  dead  maeer  
•  inorganic  N  ions  (ammonium,  nitrite  and  nitrate)  are  highly  
water  soluble  and  are  distributed  throughout  the  ecosphere  
1.  Nitrogen  FixaEon  
2.  Ammonium  AssimilaEon/  AmmonificaEon  
3.  NitrificaEon  
4.  Nitrate  ReducEon  
–  assimilatory/  dissimilatory  nitrate  reducEon,  denitrificaEon,  anamox   59  
THE NITROGEN CYCLE
 Nitrogen  Fixa:on  
•  Plants,  animals  &  most  microbes  require  combined  forms  
of  nitrogen  for  growth  
–  ability  to  fix  nitrogen  is  limited  to  a  small  number  of  
bacteria,  archae  and  symbioEc  associaEons  

–  energy  intensive  process  

•  N  fixaEon  –  67%  by  microbial  fixaEon;  30%  by  ferElizer  

producEon  –  Haber-­‐Bosch  Process;  3%  by  atmospheric  
fixaEon  -­‐  lightening    

•  FerElizer  producEon  is  expensive;  alternaEves  such  as  

rotaEon  of  crops  between  nitrogen-­‐fixers  (soybeans)  &  
non-­‐fixers  (corn)  are  becoming  popular  
61  
 Nitrogen  Fixa:on:  methods  
•  Atmospheric  fixa:on  by  lightning  (3%)  
–  high  energy  of  lightning  breaks  nitrogen  molecules;  combine  
with  oxygen  in  the  air  forming  nitrogen  oxides;  dissolve  in  
rain,  forming  nitrates    
•  Biological  fixa:on  by  certain  microbes  (67%)  
–  alone  or  in  a  symbioEc  relaEonship  with  some  plants  and  
animals    
–  e.g.  Cyanobacteria  (Anabaena,  Nostoc),  Azotobacteraceae,  
Rhizobia,  Frankia  
•  Industrial  fixa:on  (Haber-­‐Bosch  process)  (30%)  
–  atmospheric  N2  and  H2  (usually  from  natural  gas  or  petroleum)  
can  be  combined  to  form  NH3  under  high  P,  high  T  and  catalyst   62  
 Nitrogen  Fixa:on:  the  chemistry  
•  ReacEon  is  catalyzed  by  the  nitrogenase  enzyme  complex;  
requires  ATP  and  cytochromes  
N2  +  8  H+  +  6  e−  →  2  NH3  +  H2                          ΔG  =  +150  kcal/mol  
•  Ammonia  is  incorporated  into  amino  acids,  nucleic  acids  etc.    
•  ReacEon  is  under  strict  regulaEon;  expression  of  required  
genes  (nif  )  is  inhibited  by  NH3  -­‐-­‐>  Feedback  Inhibi:on  
•  Enzyme  is  extremely  oxygen  sensi:ve  (requires  low  O2  
tensions  to  funcEon)  

63  
 Nitrogen  Fixa:on:  who?  
•  Free-­‐living  soil  bacteria  
–  Azotobacter  (aerobic),  Beijerinckia  (aerobic),  Clostridium  
(anaerobic)  
–  Azotobacter  and  Beijerinckia  can  fix  at  normal  O2  tension  –  
mechanism  to  protect  nitrogenase  enzyme  
•  Rhizobia-­‐legume  symbioEc  relaEonship  
–  rate  of  fixaEon  is  2-­‐3  orders  of  magnitude  higher  than  free-­‐living  
•  Cyanobacteria  
–  predominant  in  aquaEc  environments  
–  fixaEon  rate  1-­‐2  orders  of  magnitude  higher  than  free-­‐living  
terrestrial  microbes  because  they  are  photosyntheEc  
–  have  specialized  heterocysts  with  thick  walls  impermeable  to  O2  
64  
–  e.g.  Anabaena,  Nostoc  
 Rates  of  Nitrogen  Fixa:on  
N2-­‐fixing  system   Nitrogen  fixa:on    
(kg  N/hectare/year)  

Rhizobium-­‐legume   200-­‐300  

Anabaena-­‐Azolla   100-­‐120  

Cyanobacteria-­‐moss   30-­‐40  

Rhizosphere  associaEons   2-­‐25  

Free-­‐living   1-­‐2  

Source: Table 16.13 from Text

Summary for Nitrogen Fixation:

energy intensive

end-product is ammonia

inhibited by ammonia à feed back regulation

occurs in aerobic and anaerobic environments

nitrogenase is O2 sensitive
Ammonium  Assimila:on  (Immobiliza:on)  
•  IncorporaEon  of  NH4+  into  amino  acids  (proteins),  purines  &  
pyrimidines  (nucleic  acids)  and  N-­‐acetylmuramic  acid  (cell  wall)  

 
Ammonifica:on  (Mineraliza:on)  
•  SequenEal  degradaEon  of  nitrogenous  organic  compounds  with  
the  release  of  ammonia  
           Proteins        à            Amino  acid        à        Organic  acid    +    Ammonia  
 
•  Under  N  limi:ng  condi:ons:  immobiliza:on  predominant  
•  Under  N  non-­‐limi:ng  condi:ons:  mineraliza:on  predominant  
•  Fate  of  ammonium  released  into  the  environment:  
-  taken  up  by  plants/  microbes  (incorporated  into  biomass)  
-  bound  to  soil/  humus  
-  adds  to  caEon  exchange  capacity  (CEC),  trapped  in  clay,  escape  to  
67  
atmosphere,  nitrificaEon    
Summary for ammonia assimilation and ammonification
Assimilation and ammonification cycles ammonia between its organic and
inorganic forms

Assimilation predominates at C:N ratios > 20

Ammonification predominates at C:N ratios < 20

68  
 Nitrifica:on  
•  Biological  oxidaEon  of  ammonia  to  nitrite  followed  by  the  
oxidaEon  of  nitrites  to  nitrates  
•  Carried  out  by  a  limited  number  of  autotrophic  bacteria;  2  
steps  carried  out  by  different  populaEons  of  bacteria  
–  closely  coupled,  hence  build-­‐up  of  nitrite  does  not  occur  
–  pH  sensi:ve:  op:mal  6.6  –  8;  completely  inhibited  <  4.5  
•  OxidaEon  of  ammonia  to  nitrite  carried  out  by  
Nitrosomonas;  nitrite  to  nitrate  by  Nitrobacter  or  Nitrospira  
•  Both  reacEons  are  energy-­‐yielding;  nitrifying  bacteria  use  
the  energy  derived  from  nitrificaEon  to  assimilate  CO2  
ammonium monooxygenase
NH3  +  CO2  +  1.5  O2  +  Nitrosomonas  -­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐→  NO2-­‐  +  H2O  +  H+    
NO2-­‐  +  CO2  +  0.5  O2  +  Nitrobacter          -­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐→  NO3-­‐   69  
 Importance  of  Nitrifica:on  to  Soil  
Chemistry  
•  TransformaEon  of  ammonium  ions  to  nitrite  and  nitrate  ions  
results  in  a  change  in  charge  from  ‘+’  to  ‘–’  

•  PosiEvely  charged  ions  are  generally  bound  by  negaEvely  

charged  clay  parEcles  in  soil  

•  NegaEvely  charged  ions  migrate  freely  in  soil  

•  NitrificaEon  is  therefore  ‘nitrogen  mobilizaEon’  

•  Ammonia  in  soil  is  rapidly  oxidized  

–  nitrate  is  taken  up  by  plants  but  can  also  be  leached  from  the  soil  
into  the  groundwater;  eutrophicaEon  in  lakes  
–  health  concerns:  methemoglobinemia,  nitrosamine  (carcinogen)  
70  
Summary for nitrification

Nitrification is an chemoautotrophic, aerobic process

Nitrification is sensitive to a variety of chemical inhibitors and is inhibited at

low pH. (There are a variety of nitrification inhibitors on the market)

Nitrification in managed systems can result in nitrate leaching and

groundwater contamination

71  
 Denitrifica:on  
•  Biologically  mediated,  more  complete  reducEon  of  
nitrate  to  nitrogen  gas  
•  Primary  denitrifying  genera  in  soil  are  Pseudomonas  and  
Alcaligenes  
NO3−  →  NO2−  →  NO  +  N2O  →  N2  (g)  
•  Usually  produce  a  mixture  of  nitrous  oxide  and  nitrogen  
•  Most  oyen  occurs  under  strictly  anaerobic  condi:ons    
–  more  common  in  standing  waters  than  in  running  streams  
•  Problems:  
–  removal  of  limiEng  nutrient,  N2O  causes  depleEon  of  
ozone,  greenhouse  gas  (N2O)  
72  
Summary for Denitrification

Anaerobic respiration using nitrate as TEA

Inhibited by oxygen

Produces a mix of N2 and N2O

Many heterotrophs denitrify

ANaerobic  AMMonium  Oxida:on  
(Anammox)  
•  A  biological  process,  where  ammonium  oxida:on  occurs  
under  anaerobic  condi:ons  using  nitrite  as  TEA  

NH4+  +  NO2−  →  N2  +  2H2O  

•  Responsible  for  50%  of  the  N2  gas  produced  in  the  oceans  

•  e.g.  Brocadia,  Kuenenia,  Anammoxoglobus  

–  produces  hydrazine  (rocket  fuel;  highly  toxic)  as  an  intermediate  

•  Used  in  the  removal  of  ammonium  from  wastewater  

treatment  (full-­‐scale  plants  in  the  Netherlands)  
74  
Interrup:on  of  N  Cycle  –  Release  of  N2O  
•  Agricultural  pracEces  responsible  for  large  proporEon  of  
N2O  released  by  human  acEvity:  
–  ammonia  is  primary  source  of  nitrogen  in  ferElizers  
–  only  50%  of  applied  nitrogen  is  assimilated  by  crops  
–  rest  is  lost  through  leaching,  erosion  &  gaseous  emission  and  
may  ulEmately  be  released  as  N2O  
 
•  Other  sources  of  N2O  include    
–  burning  of  biomass  
–  combusEon  of  fossil  fuel  
–  chemical  manufacturing  of  nylon  
75  
Nitrous  Oxide  &  Earth’s  Atmosphere  

•  N2O  is  released  to  the  atmosphere  from  industrial  and  

biological  sources  

•  Contributes  to  global  warming  (Greenhouse  Effect)  &  ozone  

depleEon  

–  long  residence  Eme  (114  years)  &  efficient  at  radiaEon  

absorpEon  (200  X  more  than  CO2)  

–  solar  radiaEon  convert  N2O  to  NO;  factor  in  O3  depleEon  

76  
Photo-­‐dissocia:on  of  N2O  and  
Deple:on  of  Ozone  
N2O  +  hν                              N2  +  O*    
N2O  +  O*                        2  NO  
 
NO  +  O3                          NO2  +  O2  
O3  +  hν                                  O  +  O2  
NO2  +  O                            NO  +  O2  
2O3  +  hν                                            3  O2  

77  
Nitrous  Oxide  &  Earth’s  Atmosphere  
Cont.  
•  N2O  is  produced  by  mulEple  phases  of  the  N  cycle  
–  intermediate  in  denitrificaEon    (wet  soil  with  restricted  O2)  
 

               NO3-­‐                  NO2-­‐                    NO  +  N2O                    N2  (g)  

 
–  by-­‐product  of  nitrificaEon  (aerated,  moist  soils  with  low  O2)  
 

     NH3  +  O2                        NO2-­‐                        N2O                

78  
Nitrate  Contamina:on  of  Groundwater  
•  Use  of  ferElizers  and  large  amounts  of  animal  waste  
cause  excess  ammonia  in  soil  &  groundwater  
•  Nitrifying  bacteria  convert  NH4  to  NO3-­‐;  accumulaEon  in  
soil  
•  Nitrate  is  mobile  in  soil;  transported  to  groundwater  
•  Excess  nitrate  causes  methemoglobinemia  in  infants  
–  nitrate  is  transformed  to  nitrite  in  the  digesEve  system;  nitrite  
oxidizes  iron  in  the  hemoglobin  to  form  methemoglobin,  which  lacks  
the  oxygen-­‐carrying  ability.  This  creates  the  condiEon  known  as  
methemoglobinemia  ("blue  baby  syndrome”)  

•  FormaEon  of  highly  carcinogenic  nitrosamines  in  adults  

79  
Preven:on  of  Nitrate  Contamina:on  

•  Best  Management  PracEces  (BMPs)  for  amount  and  

Eme  of  ferElizer  applicaEon  and  irrigaEon  of  crops  
–  region-­‐specific  since  climate  and  soil  types  vary  by  region  

•  Use  of  slow-­‐release  ferElizers  

–  more  controlled  release  of  ammonia  into  environment  

•  ApplicaEon  of  nitrificaEon  inhibitors  

80  
 Summary  
•  GH  gases  à  global  warming  à  climate  change  
•  UN  acEviEes  to  combat  climate  change  –  Kyoto  Protocol  
&  Paris  Agreement  -­‐  what  is  your  contribuEon?  
•  Carbon  cycle  
–  carbon  respiraEon  
–  organic  carbon  polymers  
–  methane  generaEon  &  oxidaEon  
•  Nitrogen  cycle  
–  Nitrogen  FixaEon  
–  Ammonium  AssimilaEon/  AmmonificaEon  
–  NitrificaEon  
–  DenitrificaEon  
–  Anamox   81