Microbes, Minerals, and Soil

• 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.

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

Why are minerals important to the study of microbiology?

• Major source of elements for Biogeochemical cycling– Fe, Mn, Mg, K, Ca, C, S, …

What’s in a cell?

• Macronutrients– 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 …

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

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

Bacterial isolates from weathered rockOn Ca-silicate mediaZones of clearing indicate dissolution of Si

Ehrlich, Geomicro, Fig9.4

Soil Structure

• Depends on – Parent material– Amount/type of organic matter– Moisture– Particle size

• Stones = >2 mm • Sand = 0.05-2 mm• Silt = 0.002-0.005 mm• Clay = <0.002 mm

• 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

Soil Profiles

O – organic materialA – biologicaly active, but often leachedB – enriched with the nutrients leached out of AC – parent material

O/A

A

B (note lack of FeOOH)

Fe layer

C

New Haven, CT

• A Maryland Soil

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

Humic Acid

Humic acids partly responsible for soil color

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…

• 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)

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

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

Soil Water

• Gravitational water– When moisture >

what the soil atmosphere can hold

– Moves by gravity– Responds to

hydrostatic pressure

– Available for plants and microbes

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?

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

Nutrient availability

• Adsorption – non-ionizable nutrients

• Ion exchange – ionizable, bind with surface charges, pH dependant

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

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+)

pHzpc

• Kaolinite: Al2Si2O5(OH)4 = 4.7-5.1

• Hematite Fe2O3 = 8.3-8.5

• Quartz SiO2 = 2.9-3.0

• Muscovite = 6.3-6.6

Soil Types

Different types of minerals and nutrients depending a lot on climate

• Tundra

• Forest

• Agricultural

• Desert

• Tropical

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

Types of Microbes in Soils

• 108 – 1010 prokaryotic cells per gram

• Also fungi

• Protozoa

• Algae

• Viruses

Soil Bacteria

• Physiology– Photosynthetic (cyanobacteria)– Cellulolytic– Pectinolytic– Saccharolytic– Proteolytic– Ammonifying– Nitrifying– Denitrifying– Fe, Mn, S, oxidizing and reducing…

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..

Fungi

• 104 -106 propagules/g

• Attach lignin and cellulose better than bacteria

Protozoa

• 7x 103 – 4 x 105 /g

• Saprozoic (degraders)

• Holozoic (predators)- eat bacteria