SOIL ORGANISMS - Soil Ecology - page 205

The species concept is difficult to apply to bacteria because of their genetic
plasticity (Tiedje, 1995). Recent methodological advances have allowed the estab-
lishment of a molecular basis for the definition of genera and species of bacteria.
Characterisation of bacterial 16S rRNA, allows the separation of bacteria at the genus
level; DNA/DNA and DNA/rRNA hybridisation techniques separate species and,
finally, RFLP (Restriction Fragment Length Polymorphism) techniques allow an
evaluation of genetic polymorphism among strains within a single species (Murray
et al., 1990). The concept of bacterial species has been recently redefined on the basis
of experimental results obtained using these techniques. Two bacterial strains belong
to the same species if the percentage of DNA reassociating at 60 °C, using the S1
nuclease technique, is greater than 70 % (Grimont et al., 1980; Wayne et al., 1987).
These authors suggest that higher levels of classification such as classes and families,
which cannot be defined by experimental criterion, should be abandoned (Heulin
and Berge, 1992).
The classification of bacteria has conventionally been based on phenotypic characters
including e.g., cell morphology (rods, cocci, bacilli, ...), cell wall structure (separation
into Gram-positive and Gram-negative through specific staining), the presence of
endospores, the mobility of cells and the shape and position of flagella, where present.
Physiological characteristics usually complemented such descriptions as recognisable
morphological and anatomical characters are often few and variable in bacteria.
Physiological or “functional” classifications are often preferred as they are more informative.
Four categories are first defined depending on the energy source that they use (light or
energy from redox reactions) and the nature of the electron donor (organic or mineral):
(i) photolithotrophic bacteria which acquire energy from light and use oxidisable
mineral substrates (essentially sulphides) as electron donors;
(ii) photo-organotrophic bacteria are photosynthetic organisms that use oxidisable
organic substrates ( e.g., organic acids) as electron donors;
(iii) chemo-lithotrophic bacteria use the energy produced by redox reactions and
four kinds of mineral substrates as electron donors ( i.e., reduced nitrogen, sulphur or iron
compounds and hydrogen);
(iv) chemo-organotrophic bacteria are typical heterotrophic organisms which take their
energy from redox reactions and use organic compounds as electron donors.
Finally, “functional categories” are defined by the chemical transformations bacteria
perform as geochemical agents in laboratory cultures. Some of the most common examples
are the bacteria that mediate the reactions of the carbon cycle ( e.g., aerobic or anaerobic
cellulolytic, chitinolytic...) or the nitrogen cycle ( e.g., nitrifiers, N-fixers, denitrifiers, ...).

2.1.3 ACTINOBACTERIA

The Actinobacteria (formerly the Actinomycetes) are filamentous bacteria. They are
Grampositive, except for members of the family Sphaerophoraceae. They possess a
ramified pseudomycelium whose diameter (0.5 to 1 is much smaller than that of fungi.
They are generally poorly tolerant of acid pH environments and most are unable to
grow in media more acid than pH 5 (see e.g., Waksmann, 1952; Dommergues and
Mangenot, 1970). Their classification is based on the structure of the vegetative