Agriculture Reference
In-Depth Information
based methods, and these can facilitate research on pathogen biology, e.g. for
detection of the pathogen in soil, on seeds or as an epiphyte on weeds and other
crop species.
The techniques used to identify bacteria include:
1.
Examining their appearance, including size, shape, colour of pigments
produced, motility and flagellae.
2.
Identifying the substrates on which they can grow. Commercially available
microplate systems are available to detect which of a large array of carbo-
hydrates a bacterium can assimilate.
3.
Other biochemical and physiological traits are used, including: (i) charac-
teristic exudates; (ii) the capacity for nitrate reduction; (iii) the acidification of
a glucose medium; (iv) whether the bacterium can grow aerobically and/or
anaerobically; and (v) the optimum temperature and pH for metabolic
activities.
The resulting 'metabolic fingerprint' from the biochemical tests of (
2
) and
(
3
) serves to identify the species.
4.
The fatty acids of bacteria, which can be determined by gas-liquid chroma-
tography, are used in their identification. They can be characterized both by the
presence of particular fatty acids and the ratios of different fatty acids to each
other.
5.
The DNA sequence of the genes coding for ribosomal RNA (rRNA) are
species specific and can be determined by DNA sequencing (e.g. Roumagnac
et
al.
, 2004a). From such information oligonucleotide primers for initiating PCR
(polymerase chain reaction) amplification of rRNA genes have been designed.
PCR amplification of DNA extracts from bacteria using such specific primers can
be used rapidly and accurately to identify bacterial species (Mark
et al.
, 2002).
6.
The DNA sequence of the spacer region between the 16S and 23S regions of
the genes coding for ribosomal RNA is more variable than the sequences
coding for the 16S and 23S regions themselves. Differences in this labile
region, which can be picked up as differences of length or sequence, can be
useful for identifying between different strains of a bacterial species.
7.
As with higher plants, differences in fragment lengths following treatment
of extracted DNA with different endonuclease enzymes (AFLP) can be used to
identify bacteria (e.g. Roumagnac
et al.
, 2004a).
Epidemiology
Some details of how the various bacterial diseases persist and spread are given
in Table 5.4. Infected crop debris is an important source of infection for most of
these diseases. Bacteria generally persist longer on surface debris than on that
which is ploughed under the soil. For example, the number of culture-forming
units of
Xanthomonas axonopodis
pv.
allii
on onion leaves decreased 10
4
-10
6
times after 9 months of burial 25 cm deep in soil compared to being left on the
soil surface (Gent
et al.
, 2005). Infected volunteers of the allium crops are
another potential source of inoculum.
