Documents
Resources
Learning Center
Upload
Plans & pricing Sign in
Sign Out
Get this document free

Biogeochemistry of Winogradsky _and other_ microcosms

VIEWS: 33 PAGES: 28

									Biogeochemistry of Winogradsky
    (and other) microcosms




Martin Johnson, Hywel Williams, Adrian Southern,
Andrzej Tkazc, Tim Lenton, Alastair Grant, Phil Poole
            http://researchpages.net/people/martin-johnson/
          http://www.2collab.com/group:Winogradsky_reading
Closed microcosm 'Smirnoff'
      Created from green pond water July 2004

      Sealed off by cork and wax
          (complete material closure?)



      Seasonal cycle, active photosynthesis
         'Smirnof' is still alive because either:

           I.It meets its C,O,N etc requirements for new growth
           from reservoirs present at creation, which are as yet
           unexhausted
           II. It meets its elemental requirements from gas
           exchange with the outside world, or,
           III. Recycling meets the requirements of the
           photosynthesizers. Stable over what timescale?
Closed microcosm 'Smirnoff'
   I.It meets its C,O,N etc requirements for new growth from
   reservoirs present at creation, which are as yet
   unexhausted?
       Approx 1mmol 'total CO2' in 0.5L of summer pond water

       1mmol C makes 0.03g carbohydrate biomass


   II.It meets its elemental requirements from gas exchange
   with the outside world
       Assume 0.3g biomass C grown -> 10mmol CO must
                                                          2
         have passed through seal in 4.5 years. If pCO2 inside
         microcosm = 0 (giving max gradient from atmospheric
         pCO2) then transfer velocity across seal = ~ 7 cm/hr –
         equivalent to sea surface transfer velocity at under a
         moderate breeze!

   DEFINITELY Carbon cycling occurring! Almost certainly N,
   P, S, etc also, as required by microorganisms.
               CO2                                                                                     Organic
                     Oxygenic photosynthesis (Autotrophy)
                                                                    Aerobic respiration (heterotrophy)   C
                                Nitrification (Chemoautotropy)

        NO3-
                                                                             Organic Organic
                                                                                S      N
                     Assimilatory sulfate reduction
SO42-


                                                            S                   SH2        NH3




 +6     +5     +4         +3         +2           +1            0     -1         -2         -3          -4

                                Oxidation State of C / N / S
    Fully oxic systems are a bit boring?
   Add an oxygen gradient to make things more
    fun! -> Winogradsky column




                                                 Sergei Winogradsky
                                                 1856-1953
               CO2                                                                                        Organic
                       Oxygenic photosynthesis (Autotrophy)
                                                                       Aerobic respiration (heterotrophy)   C
                                  Nitrification (Chemoautotropy)

        NO3-




                                                                                                                          methanotrophy
                                                                                Organic Organic
                                                                                   S      N
                       Assimilatory sulfate reduction
SO42-

                      OXIC PROCESSES SH
                                S N                                2                     2    NH3            CH4
                     ANOXIC PROCESSES
                             NO                     2
                           NO2-




                                                                                                        methanogenesis
                                                                   ANNAMOX


               SO32-
                          Anaerobic sulfate oxidation


                                                                                                        Organic
               CO2                                                                                        C
                                                                                   Anaerobic respiration

 +6     +5      +4          +3         +2           +1         0         -1         -2         -3                        -4
                    Ammonium observations
Rapidly cycled component of the nitrogen cycle, both an N source for organisms and waste
product. Rapidly turned-over in natural systems and highly variable in concentration, thus a
good target to asses convergence of microcosms.

•Used well-documented and established fluorimetric (OPA) method, using sulfite to
make reaction specific to ammonium (e.g. Holmes et al 1999) – or so we thought!
•Changing reagent batch led to significant changes in measured concentrations.
•Intercalibration of different reagent batches with ammonium demonstrated that
there must be another species causing interference, to which different reagent
batches had different sensitivity
•Amino acids tested – all reagent batches showed low sensitivity to a mixed amino
acid standard
•Other likely candidate species (further investigation pending): cyanide ion, mono-
di- and tri-methylamines, hydroxylamine?, hydrazine?.
•It isn’t clear whether this interference is likely to be limited to microcosms (due to
elevated concentrations of interfering species) or whether it has been overlooked in
environmental studies using the fluorimetric method.
•In spite of these problems, ammonium data can be interpreted. Following graphs
have reagent change marked by a vertical line
Ammonia concentration for Mk I columns
Ammonium concentration in Mk I
         columns
Ammonium concentration in Mk II
         columns
Ammonia concentration in Mk III columns


               3.5                     1
                                       2
                3                      3
                                       4
               2.5                     5
                                       6
   micro mol




                2                      7
                                       8
               1.5                     9
                                       10
                1                      14
                                       pond water
               0.5

                0
                     1   11   21 day
Evidence of complex N cycling
                      Nitrate

           0.3
          0.25                        1a
                                      2a
           0.2
                                      3a
   mg/l


          0.15
                                      4a
           0.1
                                      5a
          0.05                        Mean
            0
                 38    66       110
                      Days


                      Nitrite

          0.14
          0.12                        1a
           0.1                        2a
          0.08                        3a
   mg/l




          0.06                        4a
          0.04                        5a
          0.02                        Mean
            0
                 38    66       110
                      Days
                  Potential difference
   Measured the
    potential between
    pairs of carbon rod
    electrodes using a
    standard voltmeter
   Electrodes numbered
    1-4 from top to bottom
   Positioned to give
    gradient across water,
    water-sediment
    interface, sediment
   Not absolute values
    (yet) but at least they
    add up…
Potential difference in Mk II columns
                                         1--4

         900

         800

         700

         600
                                                                          b5
         500
                                                                          b6
    mV




         400                                                              b7
                                                                          b8
         300
                                                                          mean
         200

         100

           0

         -100
                1   11   21   31   41    51     61   71   81   91   101
                                        Days
Potential difference in Mk II columns
                                      Summary

       800

       700

       600

       500

       400                                                                1--2
                                                                          2--3
  mV




       300
                                                                          3--4
       200                                                                1--4

       100

         0

       -100

       -200
              1   11   21   31   41    51       61   71   81   91   101
                                      Days


          (1-2) water, (2-3) water-sediment, (3-4) sediment, (1-4) overall
Potential difference in MkIII columns
                                                Summary


        700

        600

        500

        400

        300                                                                                       1--2
                                                                                                  2--3
   mV




        200
                                                                                                  3--4
        100                                                                                       1--4


          0

        -100

        -200
               3   4   5   6   7   8   9   10   11   12   13   14   15   16   17   18   19   20
        -300
                                                 Days




        (1-2) water, (2-3) water-sediment, (3-4) sediment, (1-4) overall
Eh values in Mk I columns
  Eh values in Mk I columns




Columns 3b,4b,5b turned black around day 53. This
indicates ferrous sulphide in the water column,
suggesting anoxia, which is supported by the Eh levels
for these columns.
             Future improvements
   Better control of ambient
    conditions
   Containers that don’t leak
    (stainless steel electrodes in
    Mk IV)
   Continuous monitoring of
    potential differences
   Combined measurements
   Characterise the biota
    (microscopy or 16S
    analysis?)
    Future Measurement Possibilities
   Materially closed ecosystems are desirable for
    i) closure of mass budget for modelling and ii)
    ensuring any apparent stable recycling
    community is really that. However, there are
    certain obvious difficulties in measuring them!
   Stability / reproducibility looks reasonable so
    breaking one occasionally and fully quantifying
    its contents is a realistic option for quantifying
    the group.
   With an unlimited budget one might envisage
    non-materially intrusive approaches to routine
    monitoring
        Measurement Possibilities for
             closed systems
   Optical methods
       Headspace gas phase analysis
       Coulter counter
       PAM / FRRF fluorescence
   Potentiometric methods
       eH / potential difference
       pH
       Dissolved O2
       Nitrate…
                 Long-term aims
   Materially constrain microcosms to facilitate
    explicit biogeochemical modelling.
   Conduct experiments in parrallel in vitro and in
    silico to test hypotheses (stability, everything is
    everywhere etc).
   Use artificial ecosystem selection to select for
    ecosystems which e.g. favour difficult to isolate
    functional groups (e.g. annamox) or which
    produce valuable natural products e.g. biofuels.
               Discussion points
   Do we need sediments and a complex sulfur
    cycle for Gaian / biogeochemical experimental
    microcosms?
   Is simpler better? Is it possible for them to be
    too simple?
   Pros and cons of materially-closed systems
   I think that the N cycle is where it’s at!
               Thank you


  http://researchpages.net/people/martin-johnson/
http://www.2collab.com/group:Winogradsky_reading
Microbes and Processes in Winogradsky column.
 Aerobic Environment
   • Algae and cyanobacteria (photoautotrophy using PS II)
   • Bacteria and eukaryotes respiring (chemoorganoheterotrophy).
   • Sulfide oxidizers (or sulfur bacteria): H2S + O2  S or SO42-
       • Some use CO2 (chemolithoautotrophs), others use organic compounds
          (chemolithoheterotrophs)
       • Examples, Thiobacillus sp. And Beggiatoa sp.
   • Methanotrophs: CH4 + O2  CO2 + 2H2O (chemoorganoheterotrophs)
       • Example, Ralstonia sp., Pseudomonas sp.

 Anaerobic Environment
   Fermentors (chemoorganoheterotrophs)
      • Break down cellulose, etc. and ferment sugars into:
           • alcohols               acetate
           • organic acids          hydrogen
      • Many bacterial groups can conduct fermentation, but not all of these have
        the ability to decompose polymeric compounds such as cellulose.
      • Example, Clostridium species
Anaerobic Environments, Continued

   Sulfur Compounds
       • Sulfate reducers: use sulfate, SO42- + e-  S or H2S, to oxidize organic
         compounds produced by fermentors. (chemoorganoheterotrophs).
            • Many genera of bacteria. Example, Desulfovibrio sp.

      • Phototrophic bacteria: Use light and H2S as electron donor (PS I)
        (photoautotrophs).
           • Examples, purple and green sulfur bacteria.

    Methanogens and Acetogens
       • Methanogens: CO2 + 4H2  CH4 + 2H2O (chemolithoautotrophs)
                       Acetate- + H2O  CH4 + HCO3-
 (chemoorganoheterotrophs)
           • Example: Methanobacterium (Archaea)

      • Acetogens: 2CO2 + 4H2  CH3COOH + 2H2O (chemolithoautotrophs)
          • Example: Homoacetogens
Other possible microbes
 Aerobic Environments
   Hydrogen
        • Hydrogen oxidizers: H2 + ½O2  H2O (both chemolithoheterotrophs and
          chemolithoautotrophs). However, it is unlikely that H2 will make it to the
          aerobic interface (it will be used in the anaerobic environment first)
             • Example, Ralstonia eutrophus
   Iron
        • Iron oxidizers: Fe2+ + H+ + ¼O2  Fe3+ + ½H2O (chemolithoautotrophs)
                         Occurs only at low pH (~2)
             • Example: Thiobacillus ferrooxidans
   Ammonium
        • Nitrifiers:    NH3 + 1½ O2  NO2- + H+ + H2O
                         NO2- + ½ O2  NO3-
             • Example: Nitrosomonas and Nitrobacter, respectively. Both
                chemolithoautotrophs.

 Anaerobic Environments
   Nitrate
        • Denitrifiers: NO3- + 6H+ + 5e-  ½N2 + 3H2O
             • Reaction combined with oxidation of organic matter.
   Iron
        • Iron reducers: Many organisms can utilize Fe3+ as electron acceptor.
Chemical Potential Exploitation
H2S oxidation by NO3-           Anammox               CH4 oxidation by SO42-
                          NH4+ + NO2- = N2 + 2H2O
                                                      Boetius et al. 2000:
  Schulz et al. 1999:        Strous et al. 1999:
    Thiomargarita             Planctomycete
     namibiensis




                   1 mm




  CH4 oxidation by NO3- (Raghoebarsing et al. 2006)
      5CH4 + 8NO3- + 8H+  5CO2 + 4N2 + 14H2O

								
To top