• This section focuses on describing the major groups of bacteria that inhabit soil and their distinguishing structural and physiological characteristics.

• These characteristics will be used to categorize organisms according to cell wall/membrane characteristics (structure) or modes of carbon and energy metabolism (physiology).

• An effort is made to review these characteristics from the perspective of the potential roles that they may play in mediating interactions of the microbe with the soil environment.

A. Cell wall structure and the three domains of life.

• The three domains (‰ kingdoms) of life are Bacteria, Ecarya, and Archaea. These divisions are based on analysis of ribosomal RNA (discussed later), which indicates organisms in these groups are distinctly different from an evolutionary (phylogenetic) perspective.

• Differences in the cell wall composition of organisms in these groups also indicate they are distinct from each other (Table 1).

A. Peptidoglycan: the main cell wall polymer in bacteria

• peptidoglycan (also called murein) = alternating resides of N-acetylglucosamine and N-acetyl muramic acid (FIG. 1).

• The peptidoglycan (PG) chains or threads are cross-linked by short peptides to other PG threads to form a strong lattice work (FIG. 2)

• Gram positive (G+) bacteria are characterized by a thick (15-30 nm) layer of PG overlying the cell membrane (FIG. 3,4). The cell wall (PG layer) composes a significant part (15-30%) of the G+ cell's total mass.

• The thickness and other characteristics of the PG layer result in these organisms staining purple (positive) by the Gram procedure. Gram negative (G-) bacteria appear pink.

• The outer layers of all cells are the first point of contact between the organism and the environment. Thus, this is the first line of across which cell nutrients and toxicants must pass against unwanted substances.

• The G+ PG layer has a molecular weight (MW) cutoff of 1200-5000 (i.e., only compounds with an MW ¾1200-5000 will pass). Thus it probably does not effectively screen out many toxicants (like organic soil pollutants, metals, etc.).

However, the PG layer probably does exclude plant polymers (MW in hundreds of thousands) that bacteria use as growth sources. These means that microbes must initiate degradation of these polymers outside of the cell by using extracellular enzymes.

The cell wall of Gram negative (G-) bacteria is composed of the outer membrane, the PG layer, and periplasm (FIG 5).

• Membrane is composed primarily of phospholipid but the outside also contains lipopolysaccharide (LPS). The LPS makes the G- outer layer relatively hydrophobic (FIG 5).

• The membrane is also "tighter" than the G+ PG and is thus more effective at screening out compounds. Channels exist in the membrane called "porins" that allow relatively low MW (<1000) substances to enter (FIG 5,6).

• PG is thin (1-2 nm) and is imbedded between the cell membrane and outer membrane (FIG. 5).

• The MW cutoff for PG in G- likely to be likely to higher than that of G+ d (i.e., >5000 MW).

• Region between the cell membrane and outer membrane, may represent a significant fraction (20-40%) of the total cell volume (FIG. 5).

• Area in which hydrolytic and detoxification enzymes may located.
  

Detoxifying enzymes; beta-lactamase.

Hydrolytic enzymes; such as phosphatases, peptidases.

• Does the periplasm give the G- an advantage over G+ in competing for nutrients/defending against toxicants: G- can concentrate enzymes (like hydrolases) in periplasm, G+ must release enzymes into surrounding environment, and thus may not obtain the benefits of the enzymes activity.

• The cell membrane is similar in both G+ and G- bacteria in being the barrier that permits cells to maintain a physiological environment different from that of the soil (Table 2).

Table 2

• Cells must transport compounds across this hydrophobic layer, and accumulate ions against chemical-electrical gradients. Accomplishing this requires the membrane exert a relatively high degree of selectivity, by using certain transport proteins; permeases and chemoreceptors (FIG. 6).

• Permeases: transport proteins specific for certain inorganic ions, peptides, amino acids and sugars.

• Siderophore receptors: sidero (iron) phore (loving) compounds are chemicals produced by an organism that chelate (chela = "claw") that bind Fe⁺³ thereby enhancing its solubility and uptake by the cell. (FIG. 7A)

• Chemotaxis receptors: membrane proteins that after binding with a nutrient or toxicant compound (the stimulus) activate flagella to move either towards (positive chemotaxis)or away from (negative chemotaxis) the stimulus. (FIG. 7B)

Example: Bacteria grown on benzoate exhibit positive chemotaxis to this chemical as well as a chlorinated analog (3-chlorobenzoate), while glucose-grown cells do not (FIG. 8).

This suggests that the former have produced a chemoreceptor that facilitates the cells' access to the growth substrate.

Top A. Mycelial bacteria.

• Mycelial ("myce" = fungus; "fun" = rope) refers to a growth habit of organisms in which cells remain connected following cell division, resulting in the formation of cell strands or threads (FIG. 9).

As the name implies, this growth habit is also commonly associated with fungi (FIG. 10).

• Mycelial bacteria may lack cross-walls between vegetative (growing) cells, and so in some ways may behave as multicellular organisms. An example of this behavior is differentiation of some cells from the vegetative form to resting structures (spores), which may involve intercellular communication (FIG. 9, 11)

Mycelial organisms could reach indefinite lengths, and if fragmented, new individuals could arise from either vegetative cells or spores. This makes counting of these organisms by culture techniques complicated.

Mycelial bacteria are also called actinomycetes (literally "ray fungi"), there are a wide variety of actinomycetes all are G+ bacteria. The most common genus in soil is Streptomyces, which is the producer of the antibiotic streptomycin (FIG. 11, Table 3A,B).

• Organisms with this growth habit remain connected following cell division, thus cells separate as individuals (FIG. 12).

• There are a wide variety of non-mycelial cell forms, this group is comprised of organisms that may be either G+ or G-.
  

A. Carbon and energy source
Overviews are given in FIGs. 13 and 14.

1. Carbon source:

• Two possible sources from which organisms obtain carbon needed for synthesizing new cells are atmospheric CO₂ (autotrophs) and organic or "fixed " carbon (heterotrophs).

• Autotrophs (literally "self-feeding") are not directly dependent on others organisms for carbon, but ultimately relay on the activity of heterotrophs to replenish the pool of CO₂.

• Two possible energy sources, light (phototrophs) and chemicals (chemotroph). The focus of this course will be primarily on chemotrophs.

• Two types of chemicals from which energy may be obtained are organic (chemo-organo troph) or inorganic (chemo-litho-troph).
  

• Energy is released from chemical substrates and transformed into a biologically useful form (ATP) through reduction/oxidation (redox) reactions.

     Dreduced + Aoxidized ------electrons ------> Doxidized + Areduced

                    ADP + Pi          ATP + H2O

• D and A = electron donors and acceptors present in either reduced or oxidized forms.

• A_ox = terminal electron acceptor (TEA)

Organism                 Dred               Aox                    

____________________________________________________

eukaryotes               CH2O               O2

prokaryotes              CH2O               O2, NO3-, NO2-, Fe+3, Mn+4, SO4-2, CO2

                         NH4+, NO2-         O2,

                         H2S                O2, NO3-, NO2-

                         Fe+2, Mn+2         O2

                         H2                 O2, NO3-, NO2-, SO4-2, CO2

• Aerobic respiration = use of O₂ as TEA

• Anaerobic respiration = O₂ replaced as TEA (A_ox) by inorganic ions (NO₃^-, SO₄^-2, CO₂); Compound that serves as the designation for the group: nitrate-reducers (denitrifiers), sulfate-reducers. The exception is CO₂ = methanogens (CH₄ is end product)

• TEA utilization in sequence with energy released: O₂ > NO₃^- > Fe⁺³ > SO₄ > CO₂ (FIG. 15).

• The preferentially use of TEAs is reflected in the environment in redox zonation, either vertical in environments like lake sediments (FIG. 16), or horizontal in subsurface environments lake polluted groundwater (FIG. 17).
  
  
• In anaerobic environments non-natural ("xenobiotic") compounds that occur as pollutants may be used essentially as TEAs. These xenobiotics are chlorinated organic compounds like polychlorinated biphenyls, and use as TEA may results in their conversion to less toxic compounds.

a) energy source:

• Some bacteria grow using many compounds as energy sources but can couple them to only one or two TEAs
  
• Example:Pseudomonas
  

D_red = sugars, organic acids, hydrocarbons, halogenated compounds

A_ox = O₂, NO₃^-

• Some bacteria grow using relatively few compounds as energy sources but can couple them to many TEAs
  
• Example: Shewenella
  

D_red = organic acids, hydrocarbons,

A_ox = O₂, NO₃^-, Fe⁺³, SO₄^-2, halogenated compounds

• can switch between modes of energy generation with respect to:
  

electron donor (organic v. inorganic)

electron acceptor (aerobic v. anaerobic)

• Use of H₂ or CO as energy source in place of organics = facultative lithotroph

• Example: Regular activity (aerobic heterotroph)
  

               Dred = organics;      Aox = O2; C = organics

• Facultative activity (facultative lithotroph)
  

               Dred = H2, CO;           Aox = O2; C = CO2

Example: Regular activity (aerobic heterotroph).

          Dred = organics; Aox = O2; C = organics

          Dred = organics; Aox = NO3, Mn+3, Fe+3, organics;  C = organics;

• organic cmpds serve as both e- donor and e- acceptor
  
• no external e- transport
  
• ATP generated by "substrate level phosphorylation"
  
• organic end products: organic acids: formate, acetate, butyrate, proprionate
  
• incomplete energy release; products serve as substrates for other anaerobes.
  
• important in anaerobic foodwebs