• Interactions between microbes and their physical, chemical, biological environment.
  
• The latter includes microorganisms as well as plants (roots).
  
• Focus here will be on concepts on strategies used by heterotrophic microbes to survive.
  
  

• Premise is that organisms in soil compete for limited resources, one of the most important of which is energy.

• Most organisms are heterotrophs and so competition is greatest for organic compounds.

• Examine the issue of competition and how this affects microbial growth strategies by considering how organisms' energy needs of microorganisms coincide with energy availability.
  
  

• Organisms needs for energy are reflected in growth curves and can be divided into two general categories; growth and maintenance.

• During these phases, the cell energy need varies over a continuum.

• In the growth phase, metabolic activity levels are at a maximum supporting synthesis of new cells and require relatively large amounts of energy are needed

• lower amount of energy are required for cell maintenance functions,

• At some point a cell's energy need is zero, and the organism is either dormant ordead.

• Note: the dividing line between live vs. dead is not easily defined

• To gain energy, heterotrophs metabolize organic materials from plants, the relative abundance of which varies widely in time and space.

• Spatially, energy availability will be highest near the plants as these release
• exudates from roots and deposit debris on the surface.

• Temporally, energy availability is greatest when the residue first enters the soil: readily decomposable materials (sugars, proteins, etc.) are rapidly depleted, leaving compounds that are more difficult to metabolize.

  
  

• Because organisms do not have access to unlimited energy, their growth rates/patterns may be much different from those studied in the laboratory.

• Growth rates of organisms in soil are not well-established, but are undoubtedly much lower than those measured in laboratory cultures.

Example: Doubling times for many heterotrophic bacteria may be <1 h; thus it takes less than 1 h for formation of a new generation (Table 1).

In soil, double times are more difficult to measure but are estimated to range from 200 h (‰10 d) to 8700 h (‰1 yr).

Thus soil microbes may corresponding to 36 -1 generation per year!

• This indicates that as a whole soil microbes are generally not in states of rapid growth, but rather are operating more in a maintenance or dormancy.

• "Activity" measures also suggest that the majority of the population is inactive or dormant (Table 2).

• The physiological status of the majority component of apparently inactive cells is unknown. Are these organisms dormant? dead ? Active but somehow not responsive to the activity measure?

• The unknown physiological status characteristics has contributes to one of the central enigmas of soil microbiology, that of the "missing bacteria"

• Enumeration of soil bacteria achieved by culture and/or microscopy.

Culture depends on ability of organisms (heterotrophs) to form macrocolonies (visible to the unaided eye) on synthetic media.

Microscopy depends on ability of cells to take-up or react with a stain; most commonly used is acridine orange (= direct count (AODC), or total count.

• Plate count (growth count) is commonly 0.1 to 10% of microscopy count (direct count); difference = "missing" bacteria (FIG 1).

• The missing bacteria (90 to 99.9%, of the total soil bacterial cells) are not recovered by culturing. Presumed to be "viable but non-culturable"

• Implication of VBNC; essentially all cells are functional entities, but the nature/identity of these is unknown because standard heterotrophic plate count techniques are inadequate for their recovery/study.

• Reasons for that cells may not culturable by standard plate count procedures:

1) Viable but are

1. fastidious aerobic heterotrophs
   
2. obligate anaerobes, phototrophs or autotrophs
   
3. injured and require special treatment
   
4. terminally incapacitated and nonrevivable (moribund)

2) Not viable (dead) but detected by microscopy because of nonspecific staining.

• VBNC is often equated by default with all categories; Ideally would like to avoid this because:

Categories 1 c,d and 2 could conceivably represent a large portion of the missing bacteria but be relatively unimportant from an ecosystem perspective.

The potential significance of truly novel organisms is obscured

• Theories, on how organisms/populations separate from each other to minimize competition.

• All are conceptual classifications that lack that strict physiological or taxonomic grounding.

• The lack or rigorous adherence to these concepts is probably to be expected and undoubtedly reflects the fact that boiling down to two category system of classification is an over simplification.
  
  

• zymogenous: ["ferment-producers"] attack readily available carbon sources, and grow rapidly.

Population densities fluctuate widely increasing during episodes of sporadically high nutrient availability and then dropping off as these are depleted.

Example: organisms that degrade simple sugars in fresh plant residues.

• autochthonous: ["self-feeders of the earth"] attack more resistent materials present more or less continuously at relative constant levels.

Population densities are relatively stable.

Example: organisms that degrade soil organic matter.

• copiotrohic = "abundant [resource] feeders". Function optimally in the presence of abundant, readily-available carbon sources.

• oligotrophic ="scant [resource] feeders". Function optimally with carbon sources that are present in low amounts and/or not easily decomposed.

  
  

• Organisms maximize survival in crowded (K-selection) or uncrowded (r-selection) environments.
  
  

• K-selected: optimized to function at high population sizes (high K), but low growth rate (low r).

• r-selected: optimized to function at low population sizes (low K), but high growth rates (high r)

• r-organisms are favored where/when resources are high relative to the size of the r-organism population, and vice versa for the K-organisms.

Microbial biomass in soil appears to be largely "inactive"

A. Formation of specialized dormant stages

• Some organisms can transform themselves from a growing "vegetative" cell to a dormant structure.

• There are a variety of these resting structures, that are formed by a diverse collection of organisms and which go by several names. For the sake of simplicity, these will just be collectively referred to as "spores".

• Spores are like plant seeds, structures that can lie dormant for long periods, tolerate adverse environmental conditions, and "sprout" when the environment is favorable.

• In the Bacteria,spores are formed by Actinomycetes (mycelial bacteria) and some other Gram-positive organisms. In the Ecarya, fungi are prolific spore formers. As yet, there are as yet no reports of spore-formation by Archaea (FIG 2).

• Spore-formation is a complex process, the details of which differ depending on organism. However, in general it is a response initiated by starvation or nutrient depletion (FIG 3).

• Gram negative bacteria are unable to differentiate into spores.

• Thus, when starved, vegetative cells must alter their physiology to conserve energy. Whether these organisms can assume a spore-like state of metabolic arrest and still remain viable is unclear. At a minimum, they must reduce their level of metabolic activity dramatically.

• Organisms entering such states make the lines between live/dormant/ dead difficult to discern.
  

• There are two general ways in which plant roots create a habitat for microbes that is distinct from that of the "bulk" soil.

• These are the 1.) associative stimulation mediated through the "rhizosphere effect", and 2.) the direct interactions that occur when the plants allow microbes to enter root cells and establish a "symbiotic" relationship, or suffer invasion from less friendly, "pathogenic" organisms.

• The term "rhizosphere" arises from the observation that plant roots exert a sphere of influence over the immediately adjacent soil (FIG 3).

• A major component of this influence is the relatively large amount of organic material that roots exude (FIG. 4).

• The composition of these exudates varies, but they typically may compounds ranging from simple sugars, to proteins (enzymes), to growth factors such as vitamins (TABLE 3).

• The effect of the exudates is two-fold. First, the high level of readily degradable materials (i.e., sugars) would likely benefit almost any organism. Second, the presence of growth factors may benefit organisms that are unable to produce these by themselves.
  
  
• The stimulatory "rhizosphere effect" is commonly assessed by the R/S ratio, which is defined as:

number of organisms in the rhizosphere soil

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number of organisms in the bulk soil

For a population of organo(hetero)trophic bacteria, a typical R/S might be in the range of 10-50 (TABLE 4)

• Plant roots provide a niche for microbes that have evolved to colonize the interior of the root, sometimes called the "endorhizosphere." For these microbes, the soil may be simply a carrier or temporary residence until plants arrive and provide their real home.

• Examples of endorhizosphere organisms that form symbiotic associations with plants are rhizobia and mychorrhizae.

• Rhizobia are bacteria that infect the roots of legumes (beans, peas, alfalfa, clover); symbiosis = rhizobia provide the plant with nitrogen, plant provides bacteria with carbon (FIG. 5).

• Mychorrhizae are fungi that enter the roots of a wide variety of plants. There are two types: ectomychorrhizae (ECM) and vesicular-arbuscular mychorrhizae (VAM).

symbiosis = fungi help plant gain nutrients from soil (particularly phosphorus), plant provides fungi with carbon (FIG. 5).