• The focus of this section is on physical chemical properties of soil that affect itssuitability as a habitat for microorganisms.

I. Soil Constituents Top

• Conceptually, soil can be divided into mineral and organic constituents, which can be further fractionated according to size (FIG. 1).

• Of the mineral constituents the main size fractions are sand (2 mm-50 um), silt (50 um-2 um), and clay (<2 um).

• The amounts of these three components determine the soil texture (FIG. 2)
  

• Two basic physical parameters are particle density (PD), which is the mass of particles (organic or mineral) per unit volume and bulk density (BD), which is the mass of soil per unit volume soil (FIG. 3)

  mineral PD ranges from 2.60 to 2.75 g cm³ (2.65 "typical")
  organic PD range from1.20 to 1.50 g cm³
  BD ranges from 1.00 to 1.80 g cm³
  
  

• The volume of soil not occupied by solids is the pore space or porosity (PS) and is defined as:
  

  PS = (1- (BD/PD))100

• example: assuming BD = 1.38, PD = 2.65;
  

  PS = (1- (1.38/2.65))100 = 48%

• Increasing clay or organic matter content will decrease BD and increase PS; pore space in soils range from roughly 32 - 62%.

• The total porosity is distributed across a continuum of macropores (>75 um diam) tomicropores (<75 um diam).
  
  macropores allow rapid gas and water movement; micropores retain water more effectively.

• Sandy soils contain mainly macropores, these drain rapidly and do not retain much water. Because water is not retained sandy soils have good gas exchange properties (i.e., oxygen replenishment).

• Clay soils have higher total pore space than sands, but this is mainly micropore space. Thus, clays retain water well but have poor gas exchange characteristics.
  
  

• Microbes "experience" soil environment at the level of the pore or aggregate, the "local" distances may be range from 10 - 100 um. FIG. 4 shows a hypothetical range of physical arrangement at these scales.

• Soil aggregates thus are a sort of basic microbe habitat-forming unit. A soil aggregate may be defined as a clump or granule of mineral; particles (sand, silt, clay) and organic matter held together by biological glues (plant or microbial exudates), compaction, or other forces.

• FIG 5 shows an example of a how fungi might be involved in aggregate formation by releasing glues and entangling particles. The fungus would thus be existing in the pore space as would bacteria colonizing the aggregate surface. However, its also possible that bacteria could be entrapped and live within the aggregate.

  
  

• The amount of water in soil is one of the most important modulators of microbial activity in soil and has major quantitative and qualitative influences biological activity. Some effects of soil water on soil microbial activity are summarized below.

• Thin water films around soil aggregates provide a medium through which some organisms move. Examples of mobile organisms are nematodes, protozoa, fungal spores, and some bacteria. If soils dry and these films shrink, and movement is restricted or stopped.

• Water is essential in aiding solute diffusion, the process on which most are dependent for acquiring at least some of their nutrients. Thus, low amounts of water limit microbial activity via "moisture stress" that may to some degree reflect nutrient deprivation.

• Increasing soil moisture content is counterbalanced by decreased availability of another essential element: oxygen.

• As soils become progressively wetter, the fraction of the pore space filled with water increases, and the air-filled pore space decreases. Thus the availability of oxygen decreases because there is less of it and because water greatly restricts its diffusion into the fluid-filled portions.

• Water-saturated soils are an extreme case in which air is effectively eliminated from soil pore spaces; a condition that, if persistent, can be detrimental to the majority of soil organisms that are "aerobic" and require oxygen for respiration.

• Thus, high levels of soil water may result in a qualitative shift in the type character of predominant active organisms from aerobic to "anaerobic."

• The sufficiency or availability of water in soil is measured in terms of its potential energy, or "potential" for short.

• Water potential (assigned the symbol "Y") has a number of components but the most important in soil is the force that arises from the attraction of water molecules to soil solid surfaces, called the matric potential (Ym).
  
  Based on the energy level, water may be identified as either available or nonavailable. These terms usually refer to whether a plant may take up the water, it's assumed that the same holds true for microbes.

• Available water is held between Y = -0.01 (low energy) to -1.5 MPa (high energy); nonavailable water is held at Y > -1.5 MPa (FIG. 7).

• Because of the high percentage of micropores, clay soils hold the greatest amount of water over the range of Y(FIG. 8). However, half of the water in clay may be unavailable because its held at high Y (FIG. 9).

• Organisms vary in sensitivity to "moisture stress" (Table 1).
  
  
• In general, fungi tolerate water deprivation better than bacteria.

• Bacterial growth may proceed to Y = -2.5 to - 6.5 MPa
  Fungi may grow under drier conditions; Y = -6.5 to -10.5 MPa

  
  

• At low water contents, organisms suffer from moisture stress,while at high water levels there may be negative effects from oxygen depletion. In between, there is a happy median occurring at the point where about 60% of the pore space is water-filled (FIG. 10).
  

Percent water-filled pore space (%WFP) is calculated as:

%WFP = (qv/TP)100

where:

qv = vol water content = (% qm)(P_B)

TP = % total soil porosity = (1- P_B/P_P)(100)

(% qm) = gravimetric water content (g/g)

P_B = soil bulk density (Mg/m³)

P_P = particle density (2.65 Mg/m³)

• The composition of soil atmospheres usually differs from ambient earth in having less O₂ and more CO₂
  

          gas            soil            earth
          O2             20 to <1%       21%
          CO2            0.3 to >5%      0.03%

• The soil atmosphere composition is dynamic and changes with time reflecting biological activity of plant roots and microbes; the major change being enrichment of CO₂ (FIG. 11), and reduction of O₂.

• For soils to remain aerobic, oxygen must be replenished. Oxygen replenishment becomes a problem in wet soils because water greatly reduces oxygen diffusion rates.

          medium            oxygen diffusion rate

          air               1.9 x 10-1 cm2 sec-1,

          water             2.5 x 10-5 cm2 sec-1, (10,000X decrease relative to air)

• Thus, high microbial activity levels in saturated soils may result in anaerobic conditions as oxygen is depleted.
  

• There is also the possibility for the interiors of soil aggregates to become anaerobic as oxygen diffusion through these is even slower than it is through water (oxygen diffusion in soil aggregate = 8.5 x 10^-6 cm² sec^-1; 100,000X decrease relative to air).

• Researchers using microprobes (FIG. 12) have provided evidence that interiors of some aggregates may be devoid of oxygen (FIG. 13), and thus possibly provide a microhabitat (microsite) suitable for an anaerobic microbe within what is otherwise an aerobic environment.

• One last point: In unsaturated, subsurface soils pollution with hydrocarbons (e.g., gasoline) can greatly stimulate microbial activity, and because of the separation from the surface, oxygen replenishment does not keep pace with consumption and the soils may verge on becoming anaerobic (FIGs 14,15).
  
  

• To increase temperature by 1°C requires 0.8 joules (J) of heat energy per g soil, but 4.18 J per g water. Thus, wet soils are generally cooler, and the lower temperatures may slow microbial activity.