1. Microbes, Minerals, and Soil

2. Objective
Pull together information from previous lectures in terms of microbial activities (start discussing how microbes interact with minerals)
Discuss the formation of mineral soils, especially the role of microorganisms.

3. Minerals Primary minerals – made during the cooling of magma
Feldspars
Micas
Silicates
Secondary Minerals – formed from chemical alteration of primary minerals
Clays
Hydrated iron and aluminum oxides
Carbonates

4. Why are minerals important to the study of microbiology?
Major source of elements for Biogeochemical cycling
Fe, Mn, Mg, K, Ca, C, S, …

5. What’s in a cell? Macronutrients Micronutrients
C, H, O, N, S, P, Mg, Na, Ca, Fe
Micronutrients
Cr, Co, Ca, Mn, Mo, Ni, Se, W, V, Zn
C4H7O1.5NP0.08S0.03 …
Where do cells get these nutrients – OM, metabolism minerals Ca SO4 – gypsum, K KFeldspar, Fe FeS Fe Silicates…

6. Soil Mineral Soil – derived from rock (minerals)
Weathering – breakdown to core minerals and often chemical modification
Physical – freeze-thaw, sand-blasting, water, seismic,…
Chemical – non-biological mineral or gas interaction with water to form acids H2CO3, H2SO4, HNO3
Biological – Plant roots, fungi, lichens, bacteria, insects, snails
Microbes may produce reactive metabolites that dissolve rocks
NH3,HNO3, H2SO4, H2CO3, oxalic, citric, gluconic acids…
Gasses (i.e. CO2 or O2) can change one mineral into another

7. How does weathering work?
Acids protonate surfaces and dislodge elements like Si and Al
Acids or other compounds complex with elements like Si and Al allowing them to dissolve

8. Bacterial isolates from weathered rock On Ca-silicate media
Zones of clearing indicate dissolution of Si
Ehrlich, Geomicro, Fig9.4

9. Soil Structure Depends on Parent material
Amount/type of organic matter
Moisture
Particle size
Stones = >2 mm
Sand = mm
Silt = mm
Clay = <0.002 mm
Where would microbes like to live?
Particle sizes will impact the diffusion of water and gasses.
Animals and plants play a role in keeping the structure of soil – loosen by burroning and breaking down particles
Microorganisms – mineralize OM (what does this mean?  break down to CO2, and basic elements NH3,…). Which can then further create acids and break down minerals more.

10. Minerals are changed into different minerals as elements (Si, Al, Fe, Mg) are removed
Soil Evolution
Vermiculite becomes montmorillonite when it loses Si, Al, Fe, Mg due to microbial activity

11. Soil Profiles O – organic material
A – biologicaly active, but often leached
B – enriched with the nutrients leached out of A
C – parent material

12. O/A A
B (note lack of FeOOH)
Fe layer C
New Haven, CT

13. A Maryland Soil

14. Humic Material Complex soil substance created by microorganisms
Humic and fulvic acids, amino acids, lignin, amino sugars,
Complex
Important to soil texture, availability of minerals, detoxification of minerals by binding, increased water holding capacity

15. Humic Acid

16. Humic acids partly responsible for soil color

17. Soil and Water Water dissolves and precipitates minerals
Precipitation of inorganic compounds helps soil clump (phosphates, Ca)
Dissolving minerals may make them more available for microorganisms
Water may displace soil gasses
Create anaerobic conditions, prevent N2 fixation…

18. Soil = 50% solid material and 50% pore spaces where water and gasses can go
Limited interaction with the atmosphere above the soil
Soil has higher CO2 and lower O2 than the atmosphere (gas diffusion is slowed by particles and water)

19. Soil Water Hygroscopic – 3x10-2 um thick Does not freeze
Does not move as a liquid
Difficult to remove
Not available for plants or microbes

20. Soil Water Pellicular Water saturated atmosphere around particles
Moves by inter molecular attraction, but not gravity
Freezes at ~-1.5*C
May be available for microbes

21. Soil Water Gravitational water
When moisture > what the soil atmosphere can hold
Moves by gravity
Responds to hydrostatic pressure
Available for plants and microbes

22. Water Activity and Water Potential
Activity – (aw) – amount of water available for hydration (in terms of relative humidity)
1.0 = pure water
0 = no water
<1.0 – water with solutes
Most bacteria require aw = 0.85
Most fungi require aw = 0.60
What would an obligate halophile require?
As aw decreases more difficult to get water away from solutes

23. Water Activity and Water potential
Water potential – ( ) chemical potential of water and is a measure of the energy available for reaction or movement
Measures the ability of water to move (osmosis)
Pure water = 0
More negative = less available
Adsorption to surfaces of solutes will lower water potential
Microbes (or plants) need a specific range of water potential to survive

24. Nutrient availability
Adsorption – non-ionizable nutrients
Ion exchange – ionizable, bind with surface charges, pH dependant

25. Clay Particles (Negatively charged) Ionic binding of cations
Ion exchange depends on type of crystals
May hold onto solutes and keep out of solution
Good for microbes – microhabitats
Bad for microbes – difficult to remove

26. Clay Particles Extremely reactive surfaces because of charge
Surface charge depends on type of minerals and pH
pHzpc – pH where surface charge is balanced
Above pHzpc = negative charge (not enough H+)
Below pHzpc = positive charge (excess H+)

27. pHzpc Kaolinite: Al2Si2O5(OH)4 = 4.7-5.1 Hematite Fe2O3 = 8.3-8.5
Quartz SiO2 =
Muscovite =
What will the charge be at pH = 7?

28. Soil Types
Different types of minerals and nutrients depending a lot on climate
Tundra
Forest
Agricultural
Desert
Tropical

29. Desert Soils
Lots of soluble salts, gypsum, little subsurface development
May lack N, Zn, Fe, Cu, Mo, Mn…
Plants, microorganisms – specially adapted to the environment
Actinomycetes
Algae
Cyanobacteria

30. Types of Microbes in Soils
108 – 1010 prokaryotic cells per gram
Also fungi
Protozoa
Algae
Viruses

31. Soil Bacteria Physiology Photosynthetic (cyanobacteria) Cellulolytic
Pectinolytic
Saccharolytic
Proteolytic
Ammonifying
Nitrifying
Denitrifying
Fe, Mn, S, oxidizing and reducing…

32. Soil Bacteria – Role in Soil
Degrade OM
Fix N2 – and other steps of N cycle
Organisms involved with vital functions may be in lower abundance
Organisms present will depend on many factors
Nutrients, O2, moisture, pH, Eh, microhabitats..

33. Fungi
propagules/g
Attach lignin and cellulose better than bacteria

34. Protozoa 7x 103 – 4 x 105 /g Saprozoic (degraders)
Holozoic (predators)- eat bacteria