6-Biogeochemical cycling 1


Groundwater

  • Deep subsurface - never exposed to light 

  • Major drinking water source 

  • Anaerobic - fermentation occurring - acids produced: H2, CO2

  • Community dominated by hydrogen consuming methanogens (use CH4) - utilise methyl coenzyme reductase 

  • Plumes - enter into groundwater - eg. hydrocarbons - microbes are able to use the hydrocarbons = attenuation (make less dangerous over time) 

  • Alternative sources of oxidising power (SO4 and NO3) - sulphate reducers and nitrifying bacteria (taking ammonia, nitrate and nitrate as their source of oxygen) 


  • Carbon, hydrogen, oxygen, nitrogen, phosphorous, sulphur (C>N>P>S)

  • Macronutrients - needed in mM concentrations (Ca, Mg, Fe) 

  • Micronutrients - needed on microM scale (Cu) 

  • Cycling due to oxidation and reduction of different molecules 




 

Freshwater environment 

Eg. 

  • Thick plastic curtain on thin part of the eutrophic lake 

  • C and N added to both sides

  • Only phosphate added to one of the basins - it now supports cyanobacterial bloom (photosynthetic bacteria) - standard microbial ratios have significantly changes 

  • Cyanobacteria use light, CO2 - photosynthetic plants below die - nutrients release - hypereutrophication 

  • Showed that the levels of phosphate is more important than the levels of nitrogen 




Bacterial metabolism: phosphite oxidation by sulphate reduction

  • Biological phosphorus almost exclusively in the state of phosphate in redox state of V+ 

  • Lithoautotrophic bacterium from marine sediment in Venice can grow by anaerobic oxidation of phosphite (+|||) to phosphate (V+) - simultaneously reducing sulphate to hydrogen sulphide 

  • First description of a redox reaction involving phosphorus in microbial energy metabolism 

  • May have operated on early Earth and represent an ancient evolutionary trait







Sulphur cycle

  • Elemental and organic sulphur (acquired in organic state and broken down) 

  • Healthy microbiome = this cycle can continue as all the components are present

  • Nitrate and sulphate provide oxygen to anaerobes 


Iron 

  • Microbes can’t survive without iron 

  • When pathogens enter the body, the body sequesters bodily iron (eg. haemoglobin, myoglobin) so less is available to microbes 


  • Orange stream water indicates very unhealthy water (high level of iron utilising microbes) and very acidic 




Nitrogen cycle 


  • Ammonia excreted by animals NH3 → NH4 

  • Nitrifying bacteria takes nitrites to nitrates 

  • Sunlight and nitrogen from fertilisers combine to create rapid plant growth 


Crenarcheaeota

  • Bacteria-like Archeaea 

  • Thrive in the cold 

  • Dominant bacterioplankton in world's oceans 

  • Major role in global biogeochemicals 

  • Discovered over a decade ago 

  • Physiology not understood because its not been possible to grow them in lab cultures 

  • Nitrifiers - obtains energy from the oxidation of ammonia to nitrite 


Nitrification and denitrification 

  • Nitrification - occurs in oxygenated environment 

  • Denitrification - anaerobic environment - way that they source oxygen 


SAR11 bacteria linked to ocean anoxia and nitrogen loss

  • More than a half of all the microbial cells in the oxygen rich surface ocean 

  • Abundant in oxygen minimum zones - where oxygen falls below detection 

  • Microbes have vital role in converting bioavailable nitrogen into N2 gas 

  • Anaerobic metabolism has not been seen in SAR11

  • Unknown how these bacteria contribute to OMZ biogeochemical cycling

  • Genomic analysis of single cells from world largest OMZ - uncharacterised lineages and adaptations for life without oxygen

  • Included genes for respiratory nitrate reductases

  • SARS nar genes verified to encode proteins catalysing the nitrite-producing first step of dentrification


Carbon cycling

  • Land plants fix CO2 (converted into other forms eg, carbohydrates)